diff --git a/generate_docs.py b/generate_docs.py index fa65d81..5f0eafc 100644 --- a/generate_docs.py +++ b/generate_docs.py @@ -59,6 +59,7 @@ def normalize_row(row, max_cols): "ionreporter", #400 "network", #500 "torrentsuite", #500 + "prepopulatedplanningsession", #500 ] API_VERSION = "v1" DEMO_API_BASE_URL = "http://mytorrentserver/rundb/api/v1/" diff --git a/source/auto_api_ref_docs/activeionchefprepkitinfo.rst b/source/auto_api_ref_docs/activeionchefprepkitinfo.rst index c71b3c5..95d6032 100644 --- a/source/auto_api_ref_docs/activeionchefprepkitinfo.rst +++ b/source/auto_api_ref_docs/activeionchefprepkitinfo.rst @@ -12,37 +12,43 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/activeionchefprepkitinfo/schem Fields table ------------ -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -**isActive** Boolean data. Ex: True true false false true false boolean -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**flowCount** Integer data. Ex: 2673 n/a false false false false integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**applicationType** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**uid** Unicode string data. Ex: "Hello World" n/a false false false true string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**categories** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false true string -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +**isActive** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**samplePrep_instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**flowCount** Integer data. Ex: 2673 n/a false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**applicationType** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**uid** Unicode string data. Ex: "Hello World" n/a false false false true string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**categories** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -74,7 +80,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 2, + "total_count": 4, "offset": 0, "limit": 1, "next": "/rundb/api/v1/activeionchefprepkitinfo/?offset=1&limit=1&format=json" @@ -82,38 +88,47 @@ Torrent Server response "objects": [ { "isActive": true, + "templatingSize": "", "kitType": "IonChefPrepKit", - "description": "ION PGM IC 200 KIT", + "description": "Ion PI IC 200 Kit", "nucleotideType": "", - "instrumentType": "pgm", + "instrumentType": "proton", + "samplePrep_instrumentType": "IC", "runMode": "", "parts": [ { - "barcode": "100020579", - "id": 20085, - "resource_uri": "/rundb/api/v1/kitpart/20085/", - "kit": "/rundb/api/v1/kitinfo/20042/" + "barcode": "100022895", + "id": 20124, + "resource_uri": "/rundb/api/v1/kitpart/20124/", + "kit": "/rundb/api/v1/kitinfo/20057/" }, { - "barcode": "100020580", - "id": 20086, - "resource_uri": "/rundb/api/v1/kitpart/20086/", - "kit": "/rundb/api/v1/kitinfo/20042/" + "barcode": "100022894", + "id": 20125, + "resource_uri": "/rundb/api/v1/kitpart/20125/", + "kit": "/rundb/api/v1/kitinfo/20057/" }, { - "barcode": "01", - "id": 20123, - "resource_uri": "/rundb/api/v1/kitpart/20123/", - "kit": "/rundb/api/v1/kitinfo/20042/" + "barcode": "02", + "id": 20126, + "resource_uri": "/rundb/api/v1/kitpart/20126/", + "kit": "/rundb/api/v1/kitinfo/20057/" + }, + { + "barcode": "100023442", + "id": 20130, + "resource_uri": "/rundb/api/v1/kitpart/20130/", + "kit": "/rundb/api/v1/kitinfo/20057/" } ], "flowCount": 0, "applicationType": "", - "uid": "ICPREP0001", - "resource_uri": "/rundb/api/v1/activeionchefprepkitinfo/20042/", - "id": 20042, + "uid": "ICPREP0002", + "libraryReadLength": 0, + "resource_uri": "/rundb/api/v1/activeionchefprepkitinfo/20057/", + "id": 20057, "categories": "", - "name": "ION PGM IC 200 KIT" + "name": "Ion PI IC 200 Kit" } ] } diff --git a/source/auto_api_ref_docs/activelibrarykitinfo.rst b/source/auto_api_ref_docs/activelibrarykitinfo.rst index 2901a7c..e093beb 100644 --- a/source/auto_api_ref_docs/activelibrarykitinfo.rst +++ b/source/auto_api_ref_docs/activelibrarykitinfo.rst @@ -12,37 +12,43 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/activelibrarykitinfo/schema/`` Fields table ------------ -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -**isActive** Boolean data. Ex: True true false false true false boolean -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**flowCount** Integer data. Ex: 2673 n/a false false false false integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**applicationType** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**uid** Unicode string data. Ex: "Hello World" n/a false false false true string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**categories** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false true string -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +**isActive** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**samplePrep_instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**flowCount** Integer data. Ex: 2673 n/a false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**applicationType** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**uid** Unicode string data. Ex: "Hello World" n/a false false false true string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**categories** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -74,7 +80,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 14, + "total_count": 15, "offset": 0, "limit": 1, "next": "/rundb/api/v1/activelibrarykitinfo/?offset=1&limit=1&format=json" @@ -82,26 +88,22 @@ Torrent Server response "objects": [ { "isActive": true, + "templatingSize": "", "kitType": "LibraryKit", - "description": "Ion Fragment Library Kit", + "description": "MuSeek Library Preparation Kit", "nucleotideType": "dna", "instrumentType": "", + "samplePrep_instrumentType": "", "runMode": "", - "parts": [ - { - "barcode": "4466464", - "id": 20014, - "resource_uri": "/rundb/api/v1/kitpart/20014/", - "kit": "/rundb/api/v1/kitinfo/20005/" - } - ], + "parts": [], "flowCount": 0, "applicationType": "", - "uid": "LIB0002", - "resource_uri": "/rundb/api/v1/activelibrarykitinfo/20005/", - "id": 20005, + "uid": "LIB0012", + "libraryReadLength": 0, + "resource_uri": "/rundb/api/v1/activelibrarykitinfo/20025/", + "id": 20025, "categories": "", - "name": "IonFragmentLibKit2" + "name": "MuSeek(tm) Library Preparation Kit" } ] } diff --git a/source/auto_api_ref_docs/activepgmlibrarykitinfo.rst b/source/auto_api_ref_docs/activepgmlibrarykitinfo.rst index bbb99b1..93785c1 100644 --- a/source/auto_api_ref_docs/activepgmlibrarykitinfo.rst +++ b/source/auto_api_ref_docs/activepgmlibrarykitinfo.rst @@ -12,37 +12,43 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/activepgmlibrarykitinfo/schema Fields table ------------ -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -**isActive** Boolean data. Ex: True true false false true false boolean -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**flowCount** Integer data. Ex: 2673 n/a false false false false integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**applicationType** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**uid** Unicode string data. Ex: "Hello World" n/a false false false true string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**categories** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false true string -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +**isActive** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**samplePrep_instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**flowCount** Integer data. Ex: 2673 n/a false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**applicationType** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**uid** Unicode string data. Ex: "Hello World" n/a false false false true string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**categories** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -82,26 +88,22 @@ Torrent Server response "objects": [ { "isActive": true, + "templatingSize": "", "kitType": "LibraryKit", - "description": "Ion Fragment Library Kit", + "description": "MuSeek Library Preparation Kit", "nucleotideType": "dna", "instrumentType": "", + "samplePrep_instrumentType": "", "runMode": "", - "parts": [ - { - "barcode": "4466464", - "id": 20014, - "resource_uri": "/rundb/api/v1/kitpart/20014/", - "kit": "/rundb/api/v1/kitinfo/20005/" - } - ], + "parts": [], "flowCount": 0, "applicationType": "", - "uid": "LIB0002", - "resource_uri": "/rundb/api/v1/activepgmlibrarykitinfo/20005/", - "id": 20005, + "uid": "LIB0012", + "libraryReadLength": 0, + "resource_uri": "/rundb/api/v1/activepgmlibrarykitinfo/20025/", + "id": 20025, "categories": "", - "name": "IonFragmentLibKit2" + "name": "MuSeek(tm) Library Preparation Kit" } ] } diff --git a/source/auto_api_ref_docs/activepgmsequencingkitinfo.rst b/source/auto_api_ref_docs/activepgmsequencingkitinfo.rst index 0489ec9..10c80ff 100644 --- a/source/auto_api_ref_docs/activepgmsequencingkitinfo.rst +++ b/source/auto_api_ref_docs/activepgmsequencingkitinfo.rst @@ -12,37 +12,43 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/activepgmsequencingkitinfo/sch Fields table ------------ -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -**isActive** Boolean data. Ex: True true false false true false boolean -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**flowCount** Integer data. Ex: 2673 n/a false false false false integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**applicationType** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**uid** Unicode string data. Ex: "Hello World" n/a false false false true string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**categories** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false true string -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +**isActive** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**samplePrep_instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**flowCount** Integer data. Ex: 2673 n/a false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**applicationType** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**uid** Unicode string data. Ex: "Hello World" n/a false false false true string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**categories** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -82,44 +88,41 @@ Torrent Server response "objects": [ { "isActive": true, + "templatingSize": "", "kitType": "SequencingKit", - "description": "(200bp) Ion PGM 200 Sequencing Kit", + "description": "Ion PGM Install Kit", "nucleotideType": "", "instrumentType": "pgm", + "samplePrep_instrumentType": "", "runMode": "", "parts": [ { - "barcode": "4474004", - "id": 20009, - "resource_uri": "/rundb/api/v1/kitpart/20009/", - "kit": "/rundb/api/v1/kitinfo/20003/" + "barcode": "4480217", + "id": 20019, + "resource_uri": "/rundb/api/v1/kitpart/20019/", + "kit": "/rundb/api/v1/kitinfo/20020/" }, { - "barcode": "4474005", - "id": 20010, - "resource_uri": "/rundb/api/v1/kitpart/20010/", - "kit": "/rundb/api/v1/kitinfo/20003/" + "barcode": "4480282", + "id": 20020, + "resource_uri": "/rundb/api/v1/kitpart/20020/", + "kit": "/rundb/api/v1/kitinfo/20020/" }, { - "barcode": "4474006", - "id": 20011, - "resource_uri": "/rundb/api/v1/kitpart/20011/", - "kit": "/rundb/api/v1/kitinfo/20003/" - }, - { - "barcode": "4474007", - "id": 20012, - "resource_uri": "/rundb/api/v1/kitpart/20012/", - "kit": "/rundb/api/v1/kitinfo/20003/" + "barcode": "4480284", + "id": 20021, + "resource_uri": "/rundb/api/v1/kitpart/20021/", + "kit": "/rundb/api/v1/kitinfo/20020/" } ], - "flowCount": 500, + "flowCount": 100, "applicationType": "", - "uid": "SEQ0003", - "resource_uri": "/rundb/api/v1/activepgmsequencingkitinfo/20003/", - "id": 20003, - "categories": "", - "name": "IonPGM200Kit" + "uid": "SEQ0006", + "libraryReadLength": 0, + "resource_uri": "/rundb/api/v1/activepgmsequencingkitinfo/20020/", + "id": 20020, + "categories": "readLengthDerivableFromFlows;flowsDerivableFromReadLength;", + "name": "IonPGMInstallKit" } ] } diff --git a/source/auto_api_ref_docs/activeprotonlibrarykitinfo.rst b/source/auto_api_ref_docs/activeprotonlibrarykitinfo.rst index db8e27a..ccb2c16 100644 --- a/source/auto_api_ref_docs/activeprotonlibrarykitinfo.rst +++ b/source/auto_api_ref_docs/activeprotonlibrarykitinfo.rst @@ -12,37 +12,43 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/activeprotonlibrarykitinfo/sch Fields table ------------ -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -**isActive** Boolean data. Ex: True true false false true false boolean -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**flowCount** Integer data. Ex: 2673 n/a false false false false integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**applicationType** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**uid** Unicode string data. Ex: "Hello World" n/a false false false true string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**categories** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false true string -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +**isActive** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**samplePrep_instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**flowCount** Integer data. Ex: 2673 n/a false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**applicationType** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**uid** Unicode string data. Ex: "Hello World" n/a false false false true string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**categories** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -74,7 +80,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 13, + "total_count": 14, "offset": 0, "limit": 1, "next": "/rundb/api/v1/activeprotonlibrarykitinfo/?offset=1&limit=1&format=json" @@ -82,26 +88,22 @@ Torrent Server response "objects": [ { "isActive": true, + "templatingSize": "", "kitType": "LibraryKit", - "description": "Ion Fragment Library Kit", + "description": "MuSeek Library Preparation Kit", "nucleotideType": "dna", "instrumentType": "", + "samplePrep_instrumentType": "", "runMode": "", - "parts": [ - { - "barcode": "4466464", - "id": 20014, - "resource_uri": "/rundb/api/v1/kitpart/20014/", - "kit": "/rundb/api/v1/kitinfo/20005/" - } - ], + "parts": [], "flowCount": 0, "applicationType": "", - "uid": "LIB0002", - "resource_uri": "/rundb/api/v1/activeprotonlibrarykitinfo/20005/", - "id": 20005, + "uid": "LIB0012", + "libraryReadLength": 0, + "resource_uri": "/rundb/api/v1/activeprotonlibrarykitinfo/20025/", + "id": 20025, "categories": "", - "name": "IonFragmentLibKit2" + "name": "MuSeek(tm) Library Preparation Kit" } ] } diff --git a/source/auto_api_ref_docs/activeprotonsequencingkitinfo.rst b/source/auto_api_ref_docs/activeprotonsequencingkitinfo.rst index 3dde7e0..c134b88 100644 --- a/source/auto_api_ref_docs/activeprotonsequencingkitinfo.rst +++ b/source/auto_api_ref_docs/activeprotonsequencingkitinfo.rst @@ -12,37 +12,43 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/activeprotonsequencingkitinfo/ Fields table ------------ -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -**isActive** Boolean data. Ex: True true false false true false boolean -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**flowCount** Integer data. Ex: 2673 n/a false false false false integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**applicationType** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**uid** Unicode string data. Ex: "Hello World" n/a false false false true string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**categories** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false true string -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +**isActive** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**samplePrep_instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**flowCount** Integer data. Ex: 2673 n/a false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**applicationType** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**uid** Unicode string data. Ex: "Hello World" n/a false false false true string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**categories** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -74,7 +80,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 4, + "total_count": 7, "offset": 0, "limit": 1, "next": "/rundb/api/v1/activeprotonsequencingkitinfo/?offset=1&limit=1&format=json" @@ -82,50 +88,22 @@ Torrent Server response "objects": [ { "isActive": true, + "templatingSize": "", "kitType": "SequencingKit", - "description": "Ion PI Sequencing 200 Kit v2", + "description": "Ion PI Hi-Q Sequencing 200 Kit_NoBF", "nucleotideType": "", "instrumentType": "proton", + "samplePrep_instrumentType": "OT_IC", "runMode": "", - "parts": [ - { - "barcode": "4482282", - "id": 20078, - "resource_uri": "/rundb/api/v1/kitpart/20078/", - "kit": "/rundb/api/v1/kitinfo/20044/" - }, - { - "barcode": "4482284", - "id": 20079, - "resource_uri": "/rundb/api/v1/kitpart/20079/", - "kit": "/rundb/api/v1/kitinfo/20044/" - }, - { - "barcode": "4485149", - "id": 20094, - "resource_uri": "/rundb/api/v1/kitpart/20094/", - "kit": "/rundb/api/v1/kitinfo/20044/" - }, - { - "barcode": "4485521", - "id": 20095, - "resource_uri": "/rundb/api/v1/kitpart/20095/", - "kit": "/rundb/api/v1/kitinfo/20044/" - }, - { - "barcode": "4484082", - "id": 20096, - "resource_uri": "/rundb/api/v1/kitpart/20096/", - "kit": "/rundb/api/v1/kitinfo/20044/" - } - ], - "flowCount": 500, + "parts": [], + "flowCount": 520, "applicationType": "", - "uid": "SEQ0012", - "resource_uri": "/rundb/api/v1/activeprotonsequencingkitinfo/20044/", - "id": 20044, - "categories": "", - "name": "ProtonI200Kit-v2" + "uid": "CUSTOM0002", + "libraryReadLength": 0, + "resource_uri": "/rundb/api/v1/activeprotonsequencingkitinfo/20075/", + "id": 20075, + "categories": "readLengthDerivableFromFlows;flowsDerivableFromReadLength;", + "name": "IonProtonIHiQ_NoBF" } ] } diff --git a/source/auto_api_ref_docs/activesequencingkitinfo.rst b/source/auto_api_ref_docs/activesequencingkitinfo.rst index dcaf6cb..8d82899 100644 --- a/source/auto_api_ref_docs/activesequencingkitinfo.rst +++ b/source/auto_api_ref_docs/activesequencingkitinfo.rst @@ -12,37 +12,43 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/activesequencingkitinfo/schema Fields table ------------ -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -**isActive** Boolean data. Ex: True true false false true false boolean -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**flowCount** Integer data. Ex: 2673 n/a false false false false integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**applicationType** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**uid** Unicode string data. Ex: "Hello World" n/a false false false true string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**categories** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false true string -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +**isActive** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**samplePrep_instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**flowCount** Integer data. Ex: 2673 n/a false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**applicationType** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**uid** Unicode string data. Ex: "Hello World" n/a false false false true string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**categories** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -74,7 +80,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 9, + "total_count": 12, "offset": 0, "limit": 1, "next": "/rundb/api/v1/activesequencingkitinfo/?offset=1&limit=1&format=json" @@ -82,44 +88,41 @@ Torrent Server response "objects": [ { "isActive": true, + "templatingSize": "", "kitType": "SequencingKit", - "description": "(200bp) Ion PGM 200 Sequencing Kit", + "description": "Ion PGM Install Kit", "nucleotideType": "", "instrumentType": "pgm", + "samplePrep_instrumentType": "", "runMode": "", "parts": [ { - "barcode": "4474004", - "id": 20009, - "resource_uri": "/rundb/api/v1/kitpart/20009/", - "kit": "/rundb/api/v1/kitinfo/20003/" + "barcode": "4480217", + "id": 20019, + "resource_uri": "/rundb/api/v1/kitpart/20019/", + "kit": "/rundb/api/v1/kitinfo/20020/" }, { - "barcode": "4474005", - "id": 20010, - "resource_uri": "/rundb/api/v1/kitpart/20010/", - "kit": "/rundb/api/v1/kitinfo/20003/" + "barcode": "4480282", + "id": 20020, + "resource_uri": "/rundb/api/v1/kitpart/20020/", + "kit": "/rundb/api/v1/kitinfo/20020/" }, { - "barcode": "4474006", - "id": 20011, - "resource_uri": "/rundb/api/v1/kitpart/20011/", - "kit": "/rundb/api/v1/kitinfo/20003/" - }, - { - "barcode": "4474007", - "id": 20012, - "resource_uri": "/rundb/api/v1/kitpart/20012/", - "kit": "/rundb/api/v1/kitinfo/20003/" + "barcode": "4480284", + "id": 20021, + "resource_uri": "/rundb/api/v1/kitpart/20021/", + "kit": "/rundb/api/v1/kitinfo/20020/" } ], - "flowCount": 500, + "flowCount": 100, "applicationType": "", - "uid": "SEQ0003", - "resource_uri": "/rundb/api/v1/activesequencingkitinfo/20003/", - "id": 20003, - "categories": "", - "name": "IonPGM200Kit" + "uid": "SEQ0006", + "libraryReadLength": 0, + "resource_uri": "/rundb/api/v1/activesequencingkitinfo/20020/", + "id": 20020, + "categories": "readLengthDerivableFromFlows;flowsDerivableFromReadLength;", + "name": "IonPGMInstallKit" } ] } diff --git a/source/auto_api_ref_docs/analysisargs.rst b/source/auto_api_ref_docs/analysisargs.rst index 17c342a..e657307 100644 --- a/source/auto_api_ref_docs/analysisargs.rst +++ b/source/auto_api_ref_docs/analysisargs.rst @@ -90,25 +90,25 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 27, + "total_count": 19, "offset": 0, "limit": 1, "next": "/rundb/api/v1/analysisargs/?offset=1&limit=1&format=json" }, "objects": [ { - "chipType": "314v2", + "chipType": "314", "thumbnailalignmentargs": "", "thumbnailanalysisargs": "", "samplePrepKitName": "", - "id": 5, + "id": 1, "sequenceKitName": "", "analysisargs": "Analysis --from-beadfind --use-alternative-etbR-equation", "thumbnailcalibrateargs": "", "chip_default": true, "beadfindargs": "justBeadFind", "templateKitName": "", - "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 20 --calibration-training=100000 --flow-signals-type scaled-residual", + "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 20", "prethumbnailbasecallerargs": "", "alignmentargs": "stage1 map4", "thumbnailbasecallerargs": "", @@ -116,9 +116,9 @@ Torrent Server response "thumbnailbeadfindargs": "", "calibrateargs": "calibrate --skipDroop", "libraryKitName": "", - "name": "default_314v2", + "name": "default_314", "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 20", - "resource_uri": "/rundb/api/v1/analysisargs/5/" + "resource_uri": "/rundb/api/v1/analysisargs/1/" } ] } diff --git a/source/auto_api_ref_docs/analysismetrics.rst b/source/auto_api_ref_docs/analysismetrics.rst index 4356ddb..025a151 100644 --- a/source/auto_api_ref_docs/analysismetrics.rst +++ b/source/auto_api_ref_docs/analysismetrics.rst @@ -35,7 +35,7 @@ field help text ------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- **libFinal** Integer data. Ex: 2673 n/a false false false false integer ------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**loading** Floating point numeric data. Ex: 26.73 0.0 false false false false float +**loading** Floating point numeric data. Ex: 26.73 0 false false false false float ------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- **lib** Integer data. Ex: 2673 n/a false false false false integer ------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- @@ -118,7 +118,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 38886, + "total_count": 51527, "offset": 0, "limit": 1, "next": "/rundb/api/v1/analysismetrics/?offset=1&limit=1&format=json" @@ -135,7 +135,7 @@ Torrent Server response "washout_live": 0, "id": 1, "libFinal": 0, - "loading": 0.0, + "loading": 0, "lib": 7197, "keypass_all_beads": 0, "dud": 208, diff --git a/source/auto_api_ref_docs/applproduct.rst b/source/auto_api_ref_docs/applproduct.rst index 622bf37..f213013 100644 --- a/source/auto_api_ref_docs/applproduct.rst +++ b/source/auto_api_ref_docs/applproduct.rst @@ -12,73 +12,85 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/applproduct/schema/`` Fields table ------------ -========================================= ============================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -========================================= ============================================================================== ======= ======== ======== ===== ====== ======= -**isDualNucleotideTypeBySampleSupported** Boolean data. Ex: True false false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**defaultHotSpotRegionBedFileName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isTargetRegionBEDFileSupported** Boolean data. Ex: True true false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isSamplePrepKitSupported** Boolean data. Ex: True true false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**defaultPESeqKit** A single related resource. Can be either a URI or set of nested resource data. n/a true false false false related ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**defaultPELibKit** A single related resource. Can be either a URI or set of nested resource data. n/a true false false false related ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**defaultSeqKit** A single related resource. Can be either a URI or set of nested resource data. n/a true false false false related ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**defaultBarcodeKitName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**productCode** Unicode string data. Ex: "Hello World" any false false false true string ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isControlSeqTypeBySampleSupported** Boolean data. Ex: True false false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**defaultChipType** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isPairedEndSupported** Boolean data. Ex: True true false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**appl** A single related resource. Can be either a URI or set of nested resource data. n/a false false false false related ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isDefault** Boolean data. Ex: True false false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isTargetTechniqueSelectionSupported** Boolean data. Ex: True true false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isHotspotRegionBEDFileSuppported** Boolean data. Ex: True true false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**productName** Unicode string data. Ex: "Hello World" n/a false false false false string ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isBarcodeKitSelectionRequired** Boolean data. Ex: True false false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isDefaultBarcoded** Boolean data. Ex: True false false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**defaultTargetRegionBedFileName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isActive** Boolean data. Ex: True true false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isReferenceBySampleSupported** Boolean data. Ex: True false false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**defaultFlowCount** Integer data. Ex: 2673 0 false false false false integer ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**defaultLibKit** A single related resource. Can be either a URI or set of nested resource data. n/a true false false false related ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**barcodeKitSelectableType** Unicode string data. Ex: "Hello World" false false true false string ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**defaultGenomeRefName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isVisible** Boolean data. Ex: True false false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**isDefaultPairedEnd** Boolean data. Ex: True false false false true false boolean ------------------------------------------ ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -========================================= ============================================================================== ======= ======== ======== ===== ====== ======= +========================================================= ============================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +========================================================= ============================================================================== ======= ======== ======== ===== ====== ======= +**isDualNucleotideTypeBySampleSupported** Boolean data. Ex: True false false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultHotSpotRegionBedFileName** Unicode string data. Ex: "Hello World" n/a true false false false string +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isTargetRegionBEDFileSupported** Boolean data. Ex: True true false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isSamplePrepKitSupported** Boolean data. Ex: True true false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultSeqKit** A single related resource. Can be either a URI or set of nested resource data. n/a true false false false related +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultBarcodeKitName** Unicode string data. Ex: "Hello World" n/a true false false false string +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isHotSpotBEDFileBySampleSupported** Boolean data. Ex: True false false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isTargetRegionBEDFileBySampleSupported** Boolean data. Ex: True false false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**productCode** Unicode string data. Ex: "Hello World" any false false false true string +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isControlSeqTypeBySampleSupported** Boolean data. Ex: True false false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultChipType** Unicode string data. Ex: "Hello World" n/a true false false false string +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isPairedEndSupported** Boolean data. Ex: True true false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**appl** A single related resource. Can be either a URI or set of nested resource data. n/a false false false false related +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isTargetRegionBEDFileSelectionRequiredForRefSelection** Boolean data. Ex: True false false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isDefault** Boolean data. Ex: True false false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isTargetTechniqueSelectionSupported** Boolean data. Ex: True true false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isHotspotRegionBEDFileSuppported** Boolean data. Ex: True true false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isVisible** Boolean data. Ex: True false false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**productName** Unicode string data. Ex: "Hello World" n/a false false false false string +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isBarcodeKitSelectionRequired** Boolean data. Ex: True false false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isDefaultBarcoded** Boolean data. Ex: True false false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultTargetRegionBedFileName** Unicode string data. Ex: "Hello World" n/a true false false false string +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isActive** Boolean data. Ex: True true false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isReferenceBySampleSupported** Boolean data. Ex: True false false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultFlowCount** Integer data. Ex: 2673 0 false false false false integer +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultLibKit** A single related resource. Can be either a URI or set of nested resource data. n/a true false false false related +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**barcodeKitSelectableType** Unicode string data. Ex: "Hello World" false false true false string +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultGenomeRefName** Unicode string data. Ex: "Hello World" n/a true false false false string +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultSamplePrepKit** A single related resource. Can be either a URI or set of nested resource data. n/a true false false false related +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultControlSeqKit** A single related resource. Can be either a URI or set of nested resource data. n/a true false false false related +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultIonChefPrepKit** A single related resource. Can be either a URI or set of nested resource data. n/a true false false false related +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultIonChefSequencingKit** A single related resource. Can be either a URI or set of nested resource data. n/a true false false false related +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**isDefaultPairedEnd** Boolean data. Ex: True false false false true false boolean +--------------------------------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ ------- +**defaultTemplateKit** A single related resource. Can be either a URI or set of nested resource data. n/a true false false false related +========================================================= ============================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -110,7 +122,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 12, + "total_count": 14, "offset": 0, "limit": 1, "next": "/rundb/api/v1/applproduct/?offset=1&limit=1&format=json" @@ -121,14 +133,14 @@ Torrent Server response "defaultHotSpotRegionBedFileName": "", "isTargetRegionBEDFileSupported": true, "isSamplePrepKitSupported": true, - "defaultPESeqKit": null, - "defaultPELibKit": null, "defaultSeqKit": { "isActive": true, + "templatingSize": "", "kitType": "SequencingKit", "description": "Ion PGM Sequencing 200 Kit v2", "nucleotideType": "", "instrumentType": "pgm", + "samplePrep_instrumentType": "", "runMode": "", "parts": [ { @@ -159,13 +171,16 @@ Torrent Server response "flowCount": 500, "applicationType": "", "uid": "SEQ0009", + "libraryReadLength": 0, "resource_uri": "/rundb/api/v1/kitinfo/20033/", "id": 20033, - "categories": "", + "categories": "readLengthDerivableFromFlows;flowsDerivableFromReadLength;", "name": "IonPGM200Kit-v2" }, "defaultBarcodeKitName": null, + "isHotSpotBEDFileBySampleSupported": false, "id": 20001, + "isTargetRegionBEDFileBySampleSupported": true, "productCode": "AMPS_0", "isControlSeqTypeBySampleSupported": false, "defaultChipType": null, @@ -183,24 +198,28 @@ Torrent Server response "alternate_name": "AmpliSeq DNA", "resource_uri": "/rundb/api/v1/runtype/2/" }, + "isTargetRegionBEDFileSelectionRequiredForRefSelection": true, "instrumentType": "pgm", "isDefault": true, "isTargetTechniqueSelectionSupported": true, "description": "", "isHotspotRegionBEDFileSuppported": true, + "isVisible": true, "productName": "AMPS_default", "isBarcodeKitSelectionRequired": false, "isDefaultBarcoded": false, "defaultTargetRegionBedFileName": "", "isActive": true, - "isReferenceBySampleSupported": false, + "isReferenceBySampleSupported": true, "defaultFlowCount": 500, "defaultLibKit": { "isActive": true, + "templatingSize": "", "kitType": "LibraryKit", "description": "Ion AmpliSeq 2.0 Library Kit", "nucleotideType": "dna", "instrumentType": "", + "samplePrep_instrumentType": "", "runMode": "", "parts": [ { @@ -213,6 +232,7 @@ Torrent Server response "flowCount": 0, "applicationType": "", "uid": "LIB0008", + "libraryReadLength": 0, "resource_uri": "/rundb/api/v1/kitinfo/20012/", "id": 20012, "categories": "", @@ -220,9 +240,13 @@ Torrent Server response }, "barcodeKitSelectableType": "all", "defaultGenomeRefName": "hg19", - "isVisible": true, + "defaultSamplePrepKit": null, + "defaultControlSeqKit": null, + "defaultIonChefPrepKit": "/rundb/api/v1/kitinfo/20042/", + "resource_uri": "/rundb/api/v1/applproduct/20001/", + "defaultIonChefSequencingKit": "/rundb/api/v1/kitinfo/20033/", "isDefaultPairedEnd": false, - "resource_uri": "/rundb/api/v1/applproduct/20001/" + "defaultTemplateKit": "/rundb/api/v1/kitinfo/20034/" } ] } diff --git a/source/auto_api_ref_docs/availableionchefplannedexperiment.rst b/source/auto_api_ref_docs/availableionchefplannedexperiment.rst index 2a66a7b..f8f1e96 100644 --- a/source/auto_api_ref_docs/availableionchefplannedexperiment.rst +++ b/source/auto_api_ref_docs/availableionchefplannedexperiment.rst @@ -43,6 +43,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sequencekitname** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**base_recalibration_mode** Unicode string data. Ex: "Hello World" true false true false string +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **storageHost** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string @@ -55,7 +57,7 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipType** Unicode string data. Ex: "Hello World" false false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**chefProgress** Floating point numeric data. Ex: 26.73 0 false false true false float --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **library** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -67,7 +69,7 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **barcodeId** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string +**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -93,8 +95,6 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **forward3primeadapter** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ---------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **applicationGroupDisplayedName** Unicode string data. Ex: "Hello World" n/a true true true false string @@ -125,6 +125,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chefMessage** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **childPlans** A list of data. Ex: ['abc', 26.73, 8] [] false false false false list --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -139,6 +141,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePostBeadfind** Boolean data. Ex: True false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planGUID** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -183,8 +187,6 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleGrouping** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**base_recalibrate** Boolean data. Ex: True n/a false false false false boolean ---------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -224,288 +226,12 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 10, + "total_count": 0, "offset": 0, "limit": 1, - "next": "/rundb/api/v1/availableionchefplannedexperiment/?offset=1&limit=1&format=json" + "next": null }, - "objects": [ - { - "planDisplayedName": "C18S2_package1_Thur_psp4", - "autoAnalyze": true, - "templatingKitBarcode": null, - "preAnalysis": true, - "chefStatus": "", - "applicationGroup": "/rundb/api/v1/applicationgroup/1/", - "libkit": null, - "platform": "", - "categories": "", - "planPGM": null, - "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --calibration-training=100000 --flow-signals-type scaled-residual --max-phasing-levels 2", - "alignmentargs": "stage1 map4", - "thumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", - "sampleSet_planTotal": 0, - "projects": [ - "Chef_p1v2_dev_IE" - ], - "notes": "148420", - "sequencekitname": "ProtonIIC200Kit", - "storageHost": null, - "expName": "", - "cycles": null, - "isReverseRun": false, - "storage_options": "A", - "thumbnailalignmentargs": "stage1 map4", - "chipType": "P1.1.17", - "chefProgress": 0.0, - "library": "hg19", - "reverselibrarykey": "", - "sampleTubeLabel": "00049613", - "seqKitBarcode": null, - "barcodeId": "IonXpress", - "chefLogPath": null, - "isPlanGroup": false, - "realign": false, - "sampleGroupingName": "", - "experiment": "/rundb/api/v1/experiment/23817/", - "bedfile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed", - "isReusable": false, - "isDuplicateReads": false, - "thumbnailbeadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=100,100 --beadfind-thumbnail 1", - "librarykitname": "Ion AmpliSeq 2.0 Library Kit", - "adapter": null, - "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1", - "tfKey": "ATCG", - "parentPlan": null, - "forward3primeadapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC", - "planStatus": "pending", - "chefLastUpdate": null, - "samplePrepKitName": "Ion AmpliSeq Exome Kit", - "applicationGroupDisplayedName": "DNA", - "metaData": {}, - "sampleSet_uid": null, - "isFavorite": false, - "sampleSet_planIndex": 0, - "qcValues": [ - { - "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102054/", - "id": 266238, - "qcType": { - "description": "", - "minThreshold": 0, - "maxThreshold": 100, - "defaultThreshold": 30, - "qcName": "Usable Sequence (%)", - "id": 3, - "resource_uri": "/rundb/api/v1/qctype/3/" - }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266238/" - }, - { - "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102054/", - "id": 266237, - "qcType": { - "description": "", - "minThreshold": 1, - "maxThreshold": 100, - "defaultThreshold": 30, - "qcName": "Key Signal (1-100)", - "id": 2, - "resource_uri": "/rundb/api/v1/qctype/2/" - }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266237/" - }, - { - "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102054/", - "id": 266236, - "qcType": { - "description": "", - "minThreshold": 0, - "maxThreshold": 100, - "defaultThreshold": 30, - "qcName": "Bead Loading (%)", - "id": 1, - "resource_uri": "/rundb/api/v1/qctype/1/" - }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266236/" - } - ], - "analysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=216,224 --bkg-bfmask-update false --gpuWorkLoad 1 --total-timeout 600 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json", - "thumbnailcalibrateargs": "calibrate --skipDroop", - "templatingKitName": "Ion PI IC 200 Kit", - "runType": "AMPS_EXOME", - "username": "ionuser", - "planName": "C18S2_package1_Thur_psp4", - "sampleDisplayedName": "", - "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000 --calibration-training=100000 --flow-signals-type scaled-residual", - "controlSequencekitname": "", - "chefMessage": "", - "childPlans": [], - "pairedEndLibraryAdapterName": "", - "runMode": "single", - "irworkflow": "", - "planExecuted": false, - "project": "Chef_p1v2_dev_IE", - "usePostBeadfind": false, - "runname": null, - "planGUID": "994fd167-7d5a-43e5-acca-c8ffa069350e", - "planShortID": "0KXAK", - "sampleSetGroupType": null, - "sample": "", - "planExecutedDate": null, - "reverse_primer": null, - "id": 102054, - "barcodedSamples": { - "1": { - "barcodeSampleInfo": { - "IonXpress_001": { - "description": "", - "reference": "hg19", - "targetRegionBedFile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed", - "hotSpotRegionBedFile": "", - "nucleotideType": "DNA", - "controlSequenceType": "", - "externalId": "" - } - }, - "barcodes": [ - "IonXpress_001" - ] - } - }, - "regionfile": "", - "selectedPlugins": { - "coverageAnalysis": { - "userInput": "", - "version": "4.2-r88700", - "features": [], - "name": "coverageAnalysis", - "id": 827 - }, - "validateVariantCaller": { - "userInput": { - "variant_caller_name": "variantCaller", - "truth_major_snp": "NA12878_NIST_NoChrY_SNP.bed", - "region": "NIST", - "sample": "NA12878", - "truth_minor_snp": "None", - "truth_major_indel": "NA12878_NIST_NoChrY_indel.bed", - "truth_minor_indel": "None" - }, - "version": "0.2.1", - "features": [], - "name": "validateVariantCaller", - "id": 732 - }, - "variantCaller": { - "userInput": { - "torrent_variant_caller": { - "snp_min_allele_freq": "0.10000000000000001", - "snp_strand_bias": "0.97999999999999998", - "hotspot_min_coverage": 6, - "hotspot_min_cov_each_strand": 3, - "hotspot_min_allele_freq": "0.10000000000000001", - "snp_min_variant_score": 15, - "hotspot_strand_bias": "0.94999999999999996", - "hp_max_length": 8, - "filter_insertion_predictions": "0.20000000000000001", - "indel_min_variant_score": 20, - "indel_min_coverage": 10, - "heavy_tailed": 3, - "outlier_probability": "0.01", - "data_quality_stringency": 5, - "snp_min_cov_each_strand": 0, - "hotspot_min_variant_score": 10, - "indel_strand_bias": "0.90000000000000002", - "tvc_parameters_version": "germline_low_stringency_proton-3.6.66827", - "downsample_to_coverage": 400, - "filter_unusual_predictions": "0.25", - "indel_min_allele_freq": "0.14999999999999999", - "do_snp_realignment": 1, - "prediction_precision": 1, - "indel_min_cov_each_strand": 5, - "filter_deletion_predictions": "0.20000000000000001", - "suppress_recalibration": 0, - "snp_min_coverage": 5 - }, - "meta": { - "repository_id": "", - "ts_version": "4.0", - "name": "External file AmpliseqExome.germline_lowstringency_p1.4_0.20130920.parameters.json", - "user_selections": { - "chip": "proton_p1", - "frequency": "germline", - "library": "ampliseq", - "panel": "/rundb/api/v1/contentupload/53/" - }, - "librarytype": "ampliseq", - "trimreads": true, - "tooltip": "Retrieved from external file", - "tvcargs": "tvc", - "built_in": false, - "configuration": "", - "compatibility": {} - }, - "long_indel_assembler": { - "min_indel_size": 4, - "short_suffix_match": 5, - "output_mnv": 0, - "min_var_count": 5, - "min_var_freq": "0.14999999999999999", - "kmer_len": 19, - "max_hp_length": 8, - "relative_strand_bias": "0.80000000000000004" - }, - "freebayes": { - "gen_min_coverage": 5, - "allow_mnps": 1, - "allow_complex": 0, - "read_max_mismatch_fraction": 1, - "read_mismatch_limit": 10, - "allow_indels": 1, - "min_mapping_qv": 4, - "gen_min_alt_allele_freq": "0.10000000000000001", - "allow_snps": 1, - "gen_min_indel_alt_allele_freq": "0.14999999999999999" - } - }, - "version": "4.2-r88446", - "features": [], - "name": "variantCaller", - "id": 826 - }, - "AmpliconStats": { - "userInput": "", - "version": "0.4.5", - "features": [], - "name": "AmpliconStats", - "id": 774 - } - }, - "beadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=216,224 --total-timeout 600", - "sampleSet": null, - "isSystemDefault": false, - "autoName": null, - "libraryKey": "TCAG", - "flows": 520, - "thumbnailanalysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=100,100 --bkg-bfmask-update false --gpuWorkLoad 1 --bkg-debug-param 1 --beadfind-thumbnail 1 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json", - "date": "2014-06-26T04:47:43.000023+00:00", - "isSystem": false, - "variantfrequency": "", - "sampleSetDisplayedName": "", - "calibrateargs": "calibrate --skipDroop", - "flowsInOrder": "", - "sampleGrouping": null, - "base_recalibrate": true, - "chipBarcode": null, - "usePreBeadfind": true, - "resource_uri": "/rundb/api/v1/availableionchefplannedexperiment/102054/", - "reverse3primeadapter": "" - } - ] + "objects": [] } Allowed HTTP methods diff --git a/source/auto_api_ref_docs/availableionchefplannedexperimentsummary.rst b/source/auto_api_ref_docs/availableionchefplannedexperimentsummary.rst index 3aca958..df44382 100644 --- a/source/auto_api_ref_docs/availableionchefplannedexperimentsummary.rst +++ b/source/auto_api_ref_docs/availableionchefplannedexperimentsummary.rst @@ -23,13 +23,11 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **preAnalysis** Boolean data. Ex: True false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**isSystemDefault** Boolean data. Ex: True false false false true false boolean -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planShortID** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planStatus** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime +**runMode** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **templatingKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -37,8 +35,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planExecutedDate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefStatus** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **reverse_primer** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -55,8 +51,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planIndex** Integer data. Ex: 2673 0 false false false false integer ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planTotal** Integer data. Ex: 2673 0 false false false false integer @@ -67,7 +61,7 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planPGM** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**isSystemDefault** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **autoName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -85,12 +79,10 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefMessage** Unicode string data. Ex: "Hello World" false false true false string +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **adapter** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **irworkflow** Unicode string data. Ex: "Hello World" false false true false string @@ -107,6 +99,8 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -148,66 +142,12 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 10, + "total_count": 0, "offset": 0, "limit": 1, - "next": "/rundb/api/v1/availableionchefplannedexperimentsummary/?offset=1&limit=1&format=json" + "next": null }, - "objects": [ - { - "isReverseRun": false, - "planDisplayedName": "C18S2_package1_Thur_psp4", - "storage_options": "A", - "preAnalysis": true, - "isSystemDefault": false, - "planShortID": "0KXAK", - "planStatus": "pending", - "chefLastUpdate": null, - "templatingKitBarcode": null, - "sampleTubeLabel": "00049613", - "planExecutedDate": null, - "chefStatus": "", - "samplePrepKitName": "Ion AmpliSeq Exome Kit", - "reverse_primer": null, - "seqKitBarcode": null, - "id": 102054, - "metaData": {}, - "sampleSet_uid": null, - "isFavorite": false, - "sampleSet_planIndex": 0, - "chefLogPath": null, - "isPlanGroup": false, - "sampleSet_planTotal": 0, - "templatingKitName": "Ion PI IC 200 Kit", - "runType": "AMPS_EXOME", - "planPGM": null, - "chefProgress": 0.0, - "autoName": null, - "isReusable": false, - "controlSequencekitname": "", - "date": "2014-06-26T04:47:43.000023+00:00", - "isSystem": false, - "libkit": null, - "categories": "", - "planName": "C18S2_package1_Thur_psp4", - "chefMessage": "", - "pairedEndLibraryAdapterName": "", - "runMode": "single", - "adapter": null, - "irworkflow": "", - "chipBarcode": null, - "planExecuted": false, - "username": "ionuser", - "usePostBeadfind": false, - "storageHost": null, - "expName": "", - "runname": null, - "usePreBeadfind": true, - "planGUID": "994fd167-7d5a-43e5-acca-c8ffa069350e", - "cycles": null, - "resource_uri": "/rundb/api/v1/availableionchefplannedexperimentsummary/102054/" - } - ] + "objects": [] } Allowed HTTP methods diff --git a/source/auto_api_ref_docs/availableonetouchplannedexperiment.rst b/source/auto_api_ref_docs/availableonetouchplannedexperiment.rst index d93c811..6363fc4 100644 --- a/source/auto_api_ref_docs/availableonetouchplannedexperiment.rst +++ b/source/auto_api_ref_docs/availableonetouchplannedexperiment.rst @@ -43,6 +43,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sequencekitname** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**base_recalibration_mode** Unicode string data. Ex: "Hello World" true false true false string +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **storageHost** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string @@ -55,7 +57,7 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipType** Unicode string data. Ex: "Hello World" false false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**chefProgress** Floating point numeric data. Ex: 26.73 0 false false true false float --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **library** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -67,7 +69,7 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **barcodeId** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string +**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -93,8 +95,6 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **forward3primeadapter** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ---------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **applicationGroupDisplayedName** Unicode string data. Ex: "Hello World" n/a true true true false string @@ -125,6 +125,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chefMessage** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **childPlans** A list of data. Ex: ['abc', 26.73, 8] [] false false false false list --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -139,6 +141,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePostBeadfind** Boolean data. Ex: True false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planGUID** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -183,8 +187,6 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleGrouping** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**base_recalibrate** Boolean data. Ex: True n/a false false false false boolean ---------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -224,14 +226,14 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 119, + "total_count": 85, "offset": 0, "limit": 1, "next": "/rundb/api/v1/availableonetouchplannedexperiment/?offset=1&limit=1&format=json" }, "objects": [ { - "planDisplayedName": "-R65726-pat25_treatment_dbsa", + "planDisplayedName": "-R78595-2X_POU_L040_W3_3", "autoAnalyze": true, "templatingKitBarcode": null, "preAnalysis": true, @@ -241,23 +243,24 @@ Torrent Server response "platform": "", "categories": "", "planPGM": null, - "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --calibration-training=100000 --flow-signals-type scaled-residual --max-phasing-levels 2", - "alignmentargs": "stage1 map4", - "thumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", + "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --max-phasing-levels 2", + "alignmentargs": "-J 25 --end-repair 15 --do-repeat-clip --context stage1 map4", + "thumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", "sampleSet_planTotal": 0, "projects": [ - "auto_chip" + "p1_ie_chem" ], - "notes": "", - "sequencekitname": "ProtonI200Kit-v3", + "notes": "HiQ_val settings", + "sequencekitname": "IonProtonIHiQ", + "base_recalibration_mode": "standard_recal", "storageHost": null, "expName": "", "cycles": null, "isReverseRun": false, "storage_options": "A", - "thumbnailalignmentargs": "stage1 map4", + "thumbnailalignmentargs": "-J 25 --end-repair 15 --do-repeat-clip --context stage1 map4", "chipType": "P1.1.17", - "chefProgress": 0.0, + "chefProgress": 0, "library": "hg19", "reverselibrarykey": "", "sampleTubeLabel": "", @@ -267,30 +270,29 @@ Torrent Server response "isPlanGroup": false, "realign": false, "sampleGroupingName": "", - "experiment": "/rundb/api/v1/experiment/23946/", + "experiment": "/rundb/api/v1/experiment/32970/", "bedfile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed", "isReusable": false, "isDuplicateReads": false, "thumbnailbeadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=100,100 --beadfind-thumbnail 1", "librarykitname": "Ion AmpliSeq 2.0 Library Kit", "adapter": null, - "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1", + "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1", "tfKey": "ATCG", "parentPlan": null, "forward3primeadapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC", "planStatus": "planned", - "chefLastUpdate": null, "samplePrepKitName": "Ion AmpliSeq Exome Kit", "applicationGroupDisplayedName": "DNA", "metaData": {}, "sampleSet_uid": null, - "isFavorite": false, + "isFavorite": true, "sampleSet_planIndex": 0, "qcValues": [ { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102183/", - "id": 266490, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111207/", + "id": 289470, "qcType": { "description": "", "minThreshold": 0, @@ -300,12 +302,12 @@ Torrent Server response "id": 3, "resource_uri": "/rundb/api/v1/qctype/3/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266490/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289470/" }, { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102183/", - "id": 266489, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111207/", + "id": 289469, "qcType": { "description": "", "minThreshold": 1, @@ -315,12 +317,12 @@ Torrent Server response "id": 2, "resource_uri": "/rundb/api/v1/qctype/2/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266489/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289469/" }, { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102183/", - "id": 266488, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111207/", + "id": 289468, "qcType": { "description": "", "minThreshold": 0, @@ -330,162 +332,238 @@ Torrent Server response "id": 1, "resource_uri": "/rundb/api/v1/qctype/1/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266488/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289468/" } ], "analysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=216,224 --bkg-bfmask-update false --gpuWorkLoad 1 --total-timeout 600 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json", "thumbnailcalibrateargs": "calibrate --skipDroop", - "templatingKitName": "Ion PI Template OT2 200 Kit v3", + "templatingKitName": "Ion PI Hi-Q OT2 200 Kit", "runType": "AMPS_EXOME", "username": "ionuser", - "planName": "-R65726-pat25_treatment_dbsa", + "planName": "-R78595-2X_POU_L040_W3_3", "sampleDisplayedName": "", - "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000 --calibration-training=100000 --flow-signals-type scaled-residual", + "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", "controlSequencekitname": "", "chefMessage": "", + "templatingSize": "", "childPlans": [], "pairedEndLibraryAdapterName": "", "runMode": "single", "irworkflow": "", "planExecuted": false, - "project": "auto_chip", + "project": "p1_ie_chem", "usePostBeadfind": false, + "libraryReadLength": 0, "runname": null, - "planGUID": "3e94bf7c-ec86-4474-8884-3ae8c16827b8", - "planShortID": "076B8", + "planGUID": "e6b0a446-7b90-4a9a-aa3b-d59336da12d3", + "planShortID": "FIWLX", "sampleSetGroupType": null, "sample": "", "planExecutedDate": null, "reverse_primer": null, - "id": 102183, + "id": 111207, "barcodedSamples": { - "148541": { + "609463": { "barcodeSampleInfo": { - "IonXpress_002": { + "IonXpress_089": { "description": "", "reference": "hg19", "targetRegionBedFile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed", "hotSpotRegionBedFile": "", - "nucleotideType": "dna", + "nucleotideType": "DNA", "controlSequenceType": "", "externalId": "" }, - "IonXpress_001": { + "IonXpress_078": { "description": "", "reference": "hg19", "targetRegionBedFile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed", "hotSpotRegionBedFile": "", - "nucleotideType": "dna", + "nucleotideType": "DNA", "controlSequenceType": "", "externalId": "" } }, "barcodes": [ - "IonXpress_002", - "IonXpress_001" + "IonXpress_078", + "IonXpress_089" ] } }, "regionfile": "", "selectedPlugins": { - "coverageAnalysis": { + "SystematicErrorAnalysis": { "userInput": "", - "version": "4.3-r88797", + "version": "0.8.5", "features": [], - "name": "coverageAnalysis", - "id": 828 + "name": "SystematicErrorAnalysis", + "id": 734 }, - "validateVariantCaller": { - "userInput": { - "variant_caller_name": "variantCaller", - "truth_major_snp": "NA12878_NIST_NoChrY_SNP.bed", - "region": "NIST", - "sample": "NA12878", - "truth_minor_snp": "None", - "truth_major_indel": "NA12878_NIST_NoChrY_indel.bed", - "truth_minor_indel": "None" - }, - "version": "0.2.1", + "pixelDrift": { + "userInput": "", + "version": "1.1.1", "features": [], - "name": "validateVariantCaller", - "id": 732 + "name": "pixelDrift", + "id": 1000 }, "variantCaller": { "userInput": { "torrent_variant_caller": { - "snp_min_allele_freq": "0.10000000000000001", - "snp_strand_bias": "0.97999999999999998", + "snp_min_allele_freq": "0.1", + "snp_strand_bias": "0.98", "hotspot_min_coverage": 6, "hotspot_min_cov_each_strand": 3, - "hotspot_min_allele_freq": "0.10000000000000001", + "position_bias": "0.75", + "hotspot_min_allele_freq": "0.1", "snp_min_variant_score": 15, - "hotspot_strand_bias": "0.94999999999999996", + "mnp_min_variant_score": 60, + "hotspot_strand_bias": "0.95", "hp_max_length": 8, - "filter_insertion_predictions": "0.20000000000000001", + "filter_insertion_predictions": "0.2", "indel_min_variant_score": 20, "indel_min_coverage": 10, "heavy_tailed": 3, "outlier_probability": "0.01", + "position_bias_ref_fraction": "0.05", + "indel_strand_bias_pval": 1, "data_quality_stringency": 5, "snp_min_cov_each_strand": 0, + "indel_as_hpindel": 1, + "snp_strand_bias_pval": "0.01", + "mnp_strand_bias": "0.98", + "mnp_strand_bias_pval": "0.01", + "hotspot_strand_bias_pval": 1, "hotspot_min_variant_score": 10, - "indel_strand_bias": "0.90000000000000002", - "tvc_parameters_version": "germline_low_stringency_proton-3.6.66827", + "sse_prob_threshold": "0.2", + "do_mnp_realignment": 0, + "indel_strand_bias": "0.9", "downsample_to_coverage": 400, "filter_unusual_predictions": "0.25", - "indel_min_allele_freq": "0.14999999999999999", - "do_snp_realignment": 1, + "indel_min_allele_freq": "0.25", + "mnp_min_allele_freq": "0.1", + "mnp_min_coverage": 5, + "do_snp_realignment": 0, + "mnp_min_cov_each_strand": 0, + "snp_min_coverage": 5, "prediction_precision": 1, "indel_min_cov_each_strand": 5, - "filter_deletion_predictions": "0.20000000000000001", + "filter_deletion_predictions": "0.2", + "realignment_threshold": 0, "suppress_recalibration": 0, - "snp_min_coverage": 5 + "position_bias_pval": "0.05", + "use_position_bias": 1 }, "meta": { - "repository_id": "", - "ts_version": "4.0", - "name": "External file AmpliseqExome.germline_lowstringency_p1.4_0.20130920.parameters.json", + "ts_version": "4.4", + "name": "Generic - Proton - Germ Line - Low Stringency", "user_selections": { "chip": "proton_p1", "frequency": "germline", "library": "ampliseq", - "panel": "/rundb/api/v1/contentupload/53/" + "panel": "" }, "librarytype": "ampliseq", "trimreads": true, - "tooltip": "Retrieved from external file", + "tooltip": "Parameter settings optimized for high frequency variants and minimum false negatives on AmpliSeq libraries and Proton chips", "tvcargs": "tvc", - "built_in": false, - "configuration": "", - "compatibility": {} + "barcode_mode": "match", + "based_on": "ampliseqexome_germline_lowstringency_p1_parameters.json", + "built_in": true, + "configuration": "germline_low_stringency_proton", + "compatibility": { + "chip": [ + "proton_p1" + ], + "frequency": [ + "germline" + ], + "stringency": [ + "low" + ], + "library": [ + "wholegenome", + "ampliseq" + ] + } }, "long_indel_assembler": { "min_indel_size": 4, "short_suffix_match": 5, "output_mnv": 0, "min_var_count": 5, - "min_var_freq": "0.14999999999999999", + "min_var_freq": "0.15", "kmer_len": 19, "max_hp_length": 8, - "relative_strand_bias": "0.80000000000000004" + "relative_strand_bias": "0.8" }, "freebayes": { "gen_min_coverage": 5, "allow_mnps": 1, "allow_complex": 0, + "read_snp_limit": 10, "read_max_mismatch_fraction": 1, - "read_mismatch_limit": 10, "allow_indels": 1, "min_mapping_qv": 4, - "gen_min_alt_allele_freq": "0.10000000000000001", + "gen_min_alt_allele_freq": "0.1", "allow_snps": 1, - "gen_min_indel_alt_allele_freq": "0.14999999999999999" + "gen_min_indel_alt_allele_freq": "0.15" } }, - "version": "4.2-r88446", + "version": "4.4.0.6", "features": [], "name": "variantCaller", - "id": 826 + "id": 994 + }, + "validateVariantCaller": { + "userInput": { + "variant_caller_name": "variantCaller", + "truth_major_snp": "NA12878_NIST_NoChrY_SNP.bed", + "region": "NIST", + "sample": "NA12878", + "truth_minor_snp": "None", + "truth_major_indel": "NA12878_NIST_NoChrY_indel.bed", + "truth_minor_indel": "None" + }, + "version": "0.2.1", + "features": [], + "name": "validateVariantCaller", + "id": 732 + }, + "flowCell": { + "userInput": "", + "version": "0.2.2", + "features": [], + "name": "flowCell", + "id": 195 + }, + "validateVariantCaller-Lite": { + "userInput": { + "variant_caller_name": "recent", + "truth_major": "NA12878_AmpliseqExome_nist_new2.18.vcf", + "region": "NIST-new", + "sample": "NA12878", + "runmode": "Lite", + "truth_minor": "None", + "truth_region": "NIST_AExome.new2.18.bed" + }, + "version": "1.1.6", + "features": [], + "name": "validateVariantCaller-Lite", + "id": 964 + }, + "coverageAnalysis": { + "userInput": "", + "version": "4.4.0.12", + "features": [], + "name": "coverageAnalysis", + "id": 995 + }, + "flowErr": { + "userInput": "", + "version": "0.2", + "features": [], + "name": "flowErr", + "id": 131 } }, "beadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=216,224 --total-timeout 600", @@ -495,17 +573,16 @@ Torrent Server response "libraryKey": "TCAG", "flows": 520, "thumbnailanalysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=100,100 --bkg-bfmask-update false --gpuWorkLoad 1 --bkg-debug-param 1 --beadfind-thumbnail 1 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json", - "date": "2014-06-27T17:51:43.000186+00:00", + "date": "2015-01-29T18:04:59.000418+00:00", "isSystem": false, "variantfrequency": "", "sampleSetDisplayedName": "", "calibrateargs": "calibrate --skipDroop", "flowsInOrder": "", "sampleGrouping": null, - "base_recalibrate": true, "chipBarcode": null, "usePreBeadfind": true, - "resource_uri": "/rundb/api/v1/availableonetouchplannedexperiment/102183/", + "resource_uri": "/rundb/api/v1/availableonetouchplannedexperiment/111207/", "reverse3primeadapter": "" } ] diff --git a/source/auto_api_ref_docs/availableonetouchplannedexperimentsummary.rst b/source/auto_api_ref_docs/availableonetouchplannedexperimentsummary.rst index 7a00723..952d431 100644 --- a/source/auto_api_ref_docs/availableonetouchplannedexperimentsummary.rst +++ b/source/auto_api_ref_docs/availableonetouchplannedexperimentsummary.rst @@ -23,13 +23,11 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **preAnalysis** Boolean data. Ex: True false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**isSystemDefault** Boolean data. Ex: True false false false true false boolean -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planShortID** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planStatus** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime +**runMode** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **templatingKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -37,8 +35,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planExecutedDate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefStatus** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **reverse_primer** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -55,8 +51,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planIndex** Integer data. Ex: 2673 0 false false false false integer ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planTotal** Integer data. Ex: 2673 0 false false false false integer @@ -67,7 +61,7 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planPGM** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**isSystemDefault** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **autoName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -85,12 +79,10 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefMessage** Unicode string data. Ex: "Hello World" false false true false string +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **adapter** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **irworkflow** Unicode string data. Ex: "Hello World" false false true false string @@ -107,6 +99,8 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -148,7 +142,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 119, + "total_count": 85, "offset": 0, "limit": 1, "next": "/rundb/api/v1/availableonetouchplannedexperimentsummary/?offset=1&limit=1&format=json" @@ -156,43 +150,39 @@ Torrent Server response "objects": [ { "isReverseRun": false, - "planDisplayedName": "-R65726-pat25_treatment_dbsa", + "planDisplayedName": "-R78595-2X_POU_L040_W3_3", "storage_options": "A", "preAnalysis": true, - "isSystemDefault": false, - "planShortID": "076B8", + "planShortID": "FIWLX", "planStatus": "planned", - "chefLastUpdate": null, + "runMode": "single", "templatingKitBarcode": null, "sampleTubeLabel": "", "planExecutedDate": null, - "chefStatus": "", "samplePrepKitName": "Ion AmpliSeq Exome Kit", "reverse_primer": null, "seqKitBarcode": null, - "id": 102183, + "id": 111207, "metaData": {}, "sampleSet_uid": null, - "isFavorite": false, + "isFavorite": true, "sampleSet_planIndex": 0, - "chefLogPath": null, "isPlanGroup": false, "sampleSet_planTotal": 0, - "templatingKitName": "Ion PI Template OT2 200 Kit v3", + "templatingKitName": "Ion PI Hi-Q OT2 200 Kit", "runType": "AMPS_EXOME", "planPGM": null, - "chefProgress": 0.0, + "isSystemDefault": false, "autoName": null, "isReusable": false, "controlSequencekitname": "", - "date": "2014-06-27T17:51:43.000186+00:00", + "date": "2015-01-29T18:04:59.000418+00:00", "isSystem": false, "libkit": null, "categories": "", - "planName": "-R65726-pat25_treatment_dbsa", - "chefMessage": "", + "planName": "-R78595-2X_POU_L040_W3_3", + "templatingSize": "", "pairedEndLibraryAdapterName": "", - "runMode": "single", "adapter": null, "irworkflow": "", "chipBarcode": null, @@ -201,11 +191,12 @@ Torrent Server response "usePostBeadfind": false, "storageHost": null, "expName": "", + "libraryReadLength": 0, "runname": null, "usePreBeadfind": true, - "planGUID": "3e94bf7c-ec86-4474-8884-3ae8c16827b8", + "planGUID": "e6b0a446-7b90-4a9a-aa3b-d59336da12d3", "cycles": null, - "resource_uri": "/rundb/api/v1/availableonetouchplannedexperimentsummary/102183/" + "resource_uri": "/rundb/api/v1/availableonetouchplannedexperimentsummary/111207/" } ] } diff --git a/source/auto_api_ref_docs/availableplannedexperimentsummary.rst b/source/auto_api_ref_docs/availableplannedexperimentsummary.rst index e88e805..da90775 100644 --- a/source/auto_api_ref_docs/availableplannedexperimentsummary.rst +++ b/source/auto_api_ref_docs/availableplannedexperimentsummary.rst @@ -23,13 +23,11 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **preAnalysis** Boolean data. Ex: True false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**isSystemDefault** Boolean data. Ex: True false false false true false boolean -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planShortID** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planStatus** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime +**runMode** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **templatingKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -37,8 +35,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planExecutedDate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefStatus** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **reverse_primer** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -55,8 +51,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planIndex** Integer data. Ex: 2673 0 false false false false integer ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planTotal** Integer data. Ex: 2673 0 false false false false integer @@ -67,7 +61,7 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planPGM** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**isSystemDefault** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **autoName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -85,12 +79,10 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefMessage** Unicode string data. Ex: "Hello World" false false true false string +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **adapter** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **irworkflow** Unicode string data. Ex: "Hello World" false false true false string @@ -107,6 +99,8 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -148,7 +142,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 399, + "total_count": 95, "offset": 0, "limit": 1, "next": "/rundb/api/v1/availableplannedexperimentsummary/?offset=1&limit=1&format=json" @@ -156,43 +150,39 @@ Torrent Server response "objects": [ { "isReverseRun": false, - "planDisplayedName": "-R65726-pat25_treatment_dbsa", + "planDisplayedName": "-R78595-2X_POU_L040_W3_3", "storage_options": "A", "preAnalysis": true, - "isSystemDefault": false, - "planShortID": "076B8", + "planShortID": "FIWLX", "planStatus": "planned", - "chefLastUpdate": null, + "runMode": "single", "templatingKitBarcode": null, "sampleTubeLabel": "", "planExecutedDate": null, - "chefStatus": "", "samplePrepKitName": "Ion AmpliSeq Exome Kit", "reverse_primer": null, "seqKitBarcode": null, - "id": 102183, + "id": 111207, "metaData": {}, "sampleSet_uid": null, - "isFavorite": false, + "isFavorite": true, "sampleSet_planIndex": 0, - "chefLogPath": null, "isPlanGroup": false, "sampleSet_planTotal": 0, - "templatingKitName": "Ion PI Template OT2 200 Kit v3", + "templatingKitName": "Ion PI Hi-Q OT2 200 Kit", "runType": "AMPS_EXOME", "planPGM": null, - "chefProgress": 0.0, + "isSystemDefault": false, "autoName": null, "isReusable": false, "controlSequencekitname": "", - "date": "2014-06-27T17:51:43.000186+00:00", + "date": "2015-01-29T18:04:59.000418+00:00", "isSystem": false, "libkit": null, "categories": "", - "planName": "-R65726-pat25_treatment_dbsa", - "chefMessage": "", + "planName": "-R78595-2X_POU_L040_W3_3", + "templatingSize": "", "pairedEndLibraryAdapterName": "", - "runMode": "single", "adapter": null, "irworkflow": "", "chipBarcode": null, @@ -201,11 +191,12 @@ Torrent Server response "usePostBeadfind": false, "storageHost": null, "expName": "", + "libraryReadLength": 0, "runname": null, "usePreBeadfind": true, - "planGUID": "3e94bf7c-ec86-4474-8884-3ae8c16827b8", + "planGUID": "e6b0a446-7b90-4a9a-aa3b-d59336da12d3", "cycles": null, - "resource_uri": "/rundb/api/v1/availableplannedexperimentsummary/102183/" + "resource_uri": "/rundb/api/v1/availableplannedexperimentsummary/111207/" } ] } diff --git a/source/auto_api_ref_docs/chip.rst b/source/auto_api_ref_docs/chip.rst index 2361464..b99582d 100644 --- a/source/auto_api_ref_docs/chip.rst +++ b/source/auto_api_ref_docs/chip.rst @@ -60,7 +60,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 20, + "total_count": 12, "offset": 0, "limit": 1, "next": "/rundb/api/v1/chip/?offset=1&limit=1&format=json" @@ -68,23 +68,24 @@ Torrent Server response "objects": [ { "slots": 1, - "calibrateargs": "calibrate", - "prebasecallerargs": "BaseCaller", - "description": "PIv2", - "prethumbnailbasecallerargs": "BaseCaller", - "alignmentargs": "", - "thumbnailbasecallerargs": "BaseCaller", - "analysisargs": "Analysis", - "basecallerargs": "BaseCaller", - "thumbnailbeadfindargs": "justBeadFind", + "calibrateargs": "calibrate --skipDroop", + "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 20", + "description": "314", + "prethumbnailbasecallerargs": "", + "alignmentargs": "stage1 map4", + "thumbnailbasecallerargs": "", + "analysisargs": "Analysis --from-beadfind --use-alternative-etbR-equation", + "thumbnailcalibrateargs": "", + "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 20", + "thumbnailbeadfindargs": "", "thumbnailalignmentargs": "", - "thumbnailanalysisargs": "Analysis", - "instrumentType": "proton", + "thumbnailanalysisargs": "", + "instrumentType": "pgm", "beadfindargs": "justBeadFind", - "resource_uri": "/rundb/api/v1/chip/16/", - "id": 16, - "isActive": false, - "name": "900AMPS_EXOME" + "resource_uri": "/rundb/api/v1/chip/1/", + "id": 1, + "isActive": true, + "name": "314" } ] } diff --git a/source/auto_api_ref_docs/clusterinfohistory.rst b/source/auto_api_ref_docs/clusterinfohistory.rst new file mode 100644 index 0000000..5af8dc2 --- /dev/null +++ b/source/auto_api_ref_docs/clusterinfohistory.rst @@ -0,0 +1,94 @@ +Clusterinfohistory Resource +========================================================================== + +Resource URL: ``http://mytorrentserver/rundb/api/v1/clusterinfohistory/`` + + +Schema URL: ``http://mytorrentserver/rundb/api/v1/clusterinfohistory/schema/`` + + +.. include:: ../manual_api_ref_docs/clusterinfohistory.rst + +Fields table +------------ + +================ ==================================================== ======= ======== ======== ===== ====== ======== +field help text default nullable readonly blank unique type +================ ==================================================== ======= ======== ======== ===== ====== ======== +**username** Unicode string data. Ex: "Hello World" ION false false true false string +---------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**name** Unicode string data. Ex: "Hello World" n/a true true false false string +---------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**created** A date & time as a string. Ex: "2010-11-10T03:07:43" true false false true false datetime +---------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**text** Unicode string data. Ex: "Hello World" false false false false string +---------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**object_pk** Integer data. Ex: 2673 n/a false false false false integer +---------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**id** Integer data. Ex: 2673 false false true true integer +---------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +================ ==================================================== ======= ======== ======== ===== ====== ======== + +Example request +--------------- + +Request URL: ``http://mytorrentserver/rundb/api/v1/clusterinfohistory/?format=json&limit=1`` + + +Python example +^^^^^^^^^^^^^^ + +.. code-block:: python + + + import requests + + ts_api_request = requests.get("http://mytorrentserver/rundb/api/v1/clusterinfohistory/", params={"format": "json", "limit": 1}) + ts_api_response = ts_api_request.json() + + clusterinfohistorys = ts_api_response["objects"] + + for clusterinfohistory in clusterinfohistorys: + print clusterinfohistory + +Torrent Server response +^^^^^^^^^^^^^^^^^^^^^^^ + +.. code-block:: javascript + + { + "meta": { + "previous": null, + "total_count": 27, + "offset": 0, + "limit": 1, + "next": "/rundb/api/v1/clusterinfohistory/?offset=1&limit=1&format=json" + }, + "objects": [ + { + "username": "system", + "name": null, + "created": "2014-07-28T17:39:23.000473+00:00", + "network_test": "success", + "object_pk": 1, + "state": "Error", + "address_test": "success", + "text": "charm01 state changed from Good to Error
Error: Host key verification failed.\r\nCannot access server charm01 with secure shell\n
address_test: success
network_test: success
access_test: failure
", + "error": "Host key verification failed.\r\nCannot access server charm01 with secure shell\n ", + "access_test": "failure", + "id": 650559, + "resource_uri": "/rundb/api/v1/clusterinfohistory/650559/" + } + ] + } + +Allowed HTTP methods +-------------------- + +- get +- post +- put +- delete +- patch + diff --git a/source/auto_api_ref_docs/compositedatamanagement.rst b/source/auto_api_ref_docs/compositedatamanagement.rst index 395d7f9..bd21f05 100644 --- a/source/auto_api_ref_docs/compositedatamanagement.rst +++ b/source/auto_api_ref_docs/compositedatamanagement.rst @@ -78,23 +78,23 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 43343, + "total_count": 56041, "offset": 0, "limit": 1, "next": "/rundb/api/v1/compositedatamanagement/?offset=1&limit=1&format=json" }, "objects": [ { - "misc_diskspace": 0.0, + "misc_diskspace": 0, "expName": "", - "basecall_state": "Deleting", - "in_process": true, + "basecall_state": "Deleted", + "in_process": false, "misc_state": "Deleted", "timeStamp": "2011-09-08T18:19:32.000098+00:00", "basecall_keep": null, "misc_keep": null, "output_keep": null, - "basecall_diskspace": 0.0, + "basecall_diskspace": 0, "resultsName": "Auto__1", "output_state": "Deleted", "sigproc_state": "Deleted", @@ -104,7 +104,7 @@ Torrent Server response "resource_uri": "/rundb/api/v1/compositedatamanagement/1/", "expDir": "/results1/BBDefault/R_2011_08_25_16_44_20_user_BBD-43", "id": 1, - "output_diskspace": 0.0 + "output_diskspace": 0 } ] } diff --git a/source/auto_api_ref_docs/compositeexperiment.rst b/source/auto_api_ref_docs/compositeexperiment.rst index 37c5c43..15d8ca7 100644 --- a/source/auto_api_ref_docs/compositeexperiment.rst +++ b/source/auto_api_ref_docs/compositeexperiment.rst @@ -78,7 +78,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 20366, + "total_count": 26763, "offset": 0, "limit": 1, "next": "/rundb/api/v1/compositeexperiment/?offset=1&limit=1&format=json" @@ -92,62 +92,62 @@ Torrent Server response "status": "Completed", "processedflows": 0, "analysis_metrics": { - "ignored": 1364892, - "lib": 118063544, + "ignored": 1416707, + "lib": 122792563, "total_wells": 164699136, - "pinned": 463867, - "live": 118074386, + "pinned": 345310, + "live": 122796187, "excluded": 16095180, - "bead": 118525043, + "bead": 123099544, "resource_uri": "", - "id": 41726, - "empty": 28250154, - "libFinal": 85604279 + "id": 54528, + "empty": 23742395, + "libFinal": 85173747 }, - "timeStamp": "2014-06-28T07:11:58.000789+00:00", + "timeStamp": "2015-02-03T02:21:07.000963+00:00", "analysismetrics": { - "ignored": 1364892, - "lib": 118063544, + "ignored": 1416707, + "lib": 122792563, "total_wells": 164699136, - "pinned": 463867, - "live": 118074386, + "pinned": 345310, + "live": 122796187, "excluded": 16095180, - "bead": 118525043, + "bead": 123099544, "resource_uri": "", - "id": 41726, - "empty": 28250154, - "libFinal": 85604279 + "id": 54528, + "empty": 23742395, + "libFinal": 85173747 }, - "reportLink": "/output/Home/Auto_user_Z28-428--r65714-pou4_dbsa_23958_304393/", - "id": 304393, + "reportLink": "/output/Home/Auto_user_F3--909--R78811-mosaic1tru4_1xot2_na12878_1400Mmol_4chips-co_33084_317423/", + "id": 317423, "reportStatus": "Nothing", "quality_metrics": { - "q0_mean_read_length": 178.362197969099, - "q0_reads": 85604279, - "q0_bases": "15268567358", - "q20_reads": 85604279, - "q20_bases": "13060288783", - "q20_mean_read_length": 178, - "id": 39683, + "q0_mean_read_length": 203.07748070541, + "q0_reads": 85173747, + "q0_bases": "17296869963", + "q20_reads": 85173747, + "q20_bases": "15168226464", + "q20_mean_read_length": 203, + "id": 50272, "resource_uri": "" }, - "resultsName": "Auto_user_Z28-428--r65714-pou4_dbsa_23958", + "resultsName": "Auto_user_F3--909--R78811-mosaic1tru4_1xot2_na12878_1400Mmol_4chips-co_33084", "projects": [ { "resource_uri": "", - "id": 1385, - "name": "auto_chip", - "modified": "2014-06-27T21:21:43.000081+00:00" + "id": 1622, + "name": "mosaic_enterprise", + "modified": "2015-02-02T18:26:29.000916+00:00" } ], "qualitymetrics": { - "q0_mean_read_length": 178.362197969099, - "q0_reads": 85604279, - "q0_bases": "15268567358", - "q20_reads": 85604279, - "q20_bases": "13060288783", - "q20_mean_read_length": 178, - "id": 39683, + "q0_mean_read_length": 203.07748070541, + "q0_reads": 85173747, + "q0_bases": "17296869963", + "q20_reads": 85173747, + "q20_bases": "15168226464", + "q20_mean_read_length": 203, + "id": 50272, "resource_uri": "" }, "eas": { @@ -155,13 +155,13 @@ Torrent Server response "reference": "hg19", "barcodeKitName": "IonXpress" }, - "resource_uri": "/rundb/api/v1/compositeresult/304393/", + "resource_uri": "/rundb/api/v1/compositeresult/317423/", "libmetrics": { - "i100Q20_reads": 61016174, - "aveKeyCounts": 89.0, - "id": 41874, + "i100Q20_reads": 63353502, + "aveKeyCounts": 84, + "id": 52457, "resource_uri": "", - "q20_mean_alignment_length": 159 + "q20_mean_alignment_length": 180 }, "autoExempt": false, "representative": false @@ -170,62 +170,62 @@ Torrent Server response "status": "Completed", "processedflows": 520, "analysis_metrics": { - "ignored": 9939, - "lib": 726685, + "ignored": 6676, + "lib": 754498, "total_wells": 960000, - "pinned": 44080, - "live": 726723, + "pinned": 40056, + "live": 754506, "excluded": 0, - "bead": 738396, + "bead": 756432, "resource_uri": "", - "id": 41695, - "empty": 167585, - "libFinal": 517179 + "id": 54510, + "empty": 156836, + "libFinal": 502627 }, - "timeStamp": "2014-06-28T00:18:42.000351+00:00", + "timeStamp": "2015-02-02T21:18:01.000809+00:00", "analysismetrics": { - "ignored": 9939, - "lib": 726685, + "ignored": 6676, + "lib": 754498, "total_wells": 960000, - "pinned": 44080, - "live": 726723, + "pinned": 40056, + "live": 754506, "excluded": 0, - "bead": 738396, + "bead": 756432, "resource_uri": "", - "id": 41695, - "empty": 167585, - "libFinal": 517179 + "id": 54510, + "empty": 156836, + "libFinal": 502627 }, - "reportLink": "/output/Home/Auto_user_Z28-428--r65714-pou4_dbsa_23958_tn_304394/", - "id": 304394, + "reportLink": "/output/Home/Auto_user_F3--909--R78811-mosaic1tru4_1xot2_na12878_1400Mmol_4chips-co_33084_tn_317424/", + "id": 317424, "reportStatus": "Nothing", "quality_metrics": { - "q0_mean_read_length": 176.041268110267, - "q0_reads": 517179, - "q0_bases": "91044847", - "q20_reads": 517179, - "q20_bases": "77321419", - "q20_mean_read_length": 176, - "id": 39658, + "q0_mean_read_length": 202.425096542764, + "q0_reads": 502627, + "q0_bases": "101744319", + "q20_reads": 502627, + "q20_bases": "88430873", + "q20_mean_read_length": 202, + "id": 50259, "resource_uri": "" }, - "resultsName": "Auto_user_Z28-428--r65714-pou4_dbsa_23958_tn", + "resultsName": "Auto_user_F3--909--R78811-mosaic1tru4_1xot2_na12878_1400Mmol_4chips-co_33084_tn", "projects": [ { "resource_uri": "", - "id": 1385, - "name": "auto_chip", - "modified": "2014-06-27T21:21:43.000081+00:00" + "id": 1622, + "name": "mosaic_enterprise", + "modified": "2015-02-02T18:26:29.000916+00:00" } ], "qualitymetrics": { - "q0_mean_read_length": 176.041268110267, - "q0_reads": 517179, - "q0_bases": "91044847", - "q20_reads": 517179, - "q20_bases": "77321419", - "q20_mean_read_length": 176, - "id": 39658, + "q0_mean_read_length": 202.425096542764, + "q0_reads": 502627, + "q0_bases": "101744319", + "q20_reads": 502627, + "q20_bases": "88430873", + "q20_mean_read_length": 202, + "id": 50259, "resource_uri": "" }, "eas": { @@ -233,43 +233,43 @@ Torrent Server response "reference": "hg19", "barcodeKitName": "IonXpress" }, - "resource_uri": "/rundb/api/v1/compositeresult/304394/", + "resource_uri": "/rundb/api/v1/compositeresult/317424/", "libmetrics": { - "i100Q20_reads": 358815, - "aveKeyCounts": 88.0, - "id": 41849, + "i100Q20_reads": 364623, + "aveKeyCounts": 84, + "id": 52444, "resource_uri": "", - "q20_mean_alignment_length": 155 + "q20_mean_alignment_length": 177 }, "autoExempt": false, "representative": false } ], "library": "hg19", - "sample": "148541", + "sample": "609600", "runMode": "single", "storage_options": "D", - "repResult": "/rundb/api/v1/compositeresult/304394/", - "id": 23958, + "repResult": "/rundb/api/v1/compositeresult/317424/", + "id": 33084, "archived": false, "barcodeId": "IonXpress", "sampleSetName": "", "star": false, - "resultDate": "2014-06-28T07:11:58.000789+00:00", + "resultDate": "2015-02-03T02:21:07.000963+00:00", "flows": 520, "plan": { - "runType": "AMPS_EXOME", - "id": 102195, + "runType": "WGNM", + "id": 111321, "resource_uri": "" }, - "date": "2014-06-27T21:19:01+00:00", + "date": "2015-02-02T18:23:59+00:00", "ftpStatus": "Complete", - "notes": "", + "notes": "mosaic 1 ot 4 chips 1400M molecules", "chipDescription": "PI", - "pgmName": "Z28", + "pgmName": "f3", "keep": false, - "expName": "R_2014_06_27_17_13_22_user_Z28-428--r65714-pou4_dbsa", - "resource_uri": "/rundb/api/v1/compositeexperiment/23958/" + "expName": "R_2015_02_02_13_18_20_user_F3--909--R78811-mosaic1tru4_1xot2_na12878_1400Mmol_4chips-co", + "resource_uri": "/rundb/api/v1/compositeexperiment/33084/" } ] } diff --git a/source/auto_api_ref_docs/compositeresult.rst b/source/auto_api_ref_docs/compositeresult.rst index e7b559d..31cbc8d 100644 --- a/source/auto_api_ref_docs/compositeresult.rst +++ b/source/auto_api_ref_docs/compositeresult.rst @@ -76,7 +76,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 43354, + "total_count": 56103, "offset": 0, "limit": 1, "next": "/rundb/api/v1/compositeresult/?offset=1&limit=1&format=json" @@ -116,7 +116,7 @@ Torrent Server response "id": 293943, "reportStatus": "Nothing", "quality_metrics": { - "q0_mean_read_length": 168.0, + "q0_mean_read_length": 168, "q0_reads": 91521301, "q0_bases": "15380233572", "q20_reads": 91521301, @@ -135,7 +135,7 @@ Torrent Server response } ], "qualitymetrics": { - "q0_mean_read_length": 168.0, + "q0_mean_read_length": 168, "q0_reads": 91521301, "q0_bases": "15380233572", "q20_reads": 91521301, @@ -152,7 +152,7 @@ Torrent Server response "resource_uri": "/rundb/api/v1/compositeresult/293943/", "libmetrics": { "i100Q20_reads": 56284561, - "aveKeyCounts": 71.0, + "aveKeyCounts": 71, "id": 32368, "resource_uri": "", "q20_mean_alignment_length": 142 diff --git a/source/auto_api_ref_docs/content.rst b/source/auto_api_ref_docs/content.rst index 5b18ee5..4467a1a 100644 --- a/source/auto_api_ref_docs/content.rst +++ b/source/auto_api_ref_docs/content.rst @@ -60,7 +60,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 72, + "total_count": 140, "offset": 0, "limit": 1, "next": "/rundb/api/v1/content/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/contentupload.rst b/source/auto_api_ref_docs/contentupload.rst index cc58878..632536b 100644 --- a/source/auto_api_ref_docs/contentupload.rst +++ b/source/auto_api_ref_docs/contentupload.rst @@ -56,7 +56,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 25, + "total_count": 53, "offset": 0, "limit": 1, "next": "/rundb/api/v1/contentupload/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/datamanagementhistory.rst b/source/auto_api_ref_docs/datamanagementhistory.rst index d6ed60e..3d199e0 100644 --- a/source/auto_api_ref_docs/datamanagementhistory.rst +++ b/source/auto_api_ref_docs/datamanagementhistory.rst @@ -60,7 +60,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 474229, + "total_count": 610567, "offset": 0, "limit": 1, "next": "/rundb/api/v1/datamanagementhistory/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/dnabarcode.rst b/source/auto_api_ref_docs/dnabarcode.rst index dbf170d..447d289 100644 --- a/source/auto_api_ref_docs/dnabarcode.rst +++ b/source/auto_api_ref_docs/dnabarcode.rst @@ -72,26 +72,26 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 9387, + "total_count": 10186, "offset": 0, "limit": 1, "next": "/rundb/api/v1/dnabarcode/?offset=1&limit=1&format=json" }, "objects": [ { - "index": 9, - "name": "IonXpress", - "score_cutoff": 2.0, - "sequence": "TGAGCGGAAC", + "index": 1, + "name": "ionxpress10K", + "score_cutoff": 0, + "sequence": "CTTACCAACAGCCACTGGCAGTGCGAAGCAACAAC", "floworder": "", - "adapter": "GAT", - "id": 761, - "length": 10, - "id_str": "IonXpress_009", - "score_mode": 1, + "adapter": "GAGCGGCGTCGTGC", + "id": 21838, + "length": 35, + "id_str": "IonFusion_P1_WA1_1a2a", + "score_mode": 0, "type": "", "annotation": "", - "resource_uri": "/rundb/api/v1/dnabarcode/761/" + "resource_uri": "/rundb/api/v1/dnabarcode/21838/" } ] } diff --git a/source/auto_api_ref_docs/eventlog.rst b/source/auto_api_ref_docs/eventlog.rst index c965dfd..406b79f 100644 --- a/source/auto_api_ref_docs/eventlog.rst +++ b/source/auto_api_ref_docs/eventlog.rst @@ -58,7 +58,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 625153, + "total_count": 790125, "offset": 0, "limit": 1, "next": "/rundb/api/v1/eventlog/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/experiment.rst b/source/auto_api_ref_docs/experiment.rst index 3a7fb96..00641cf 100644 --- a/source/auto_api_ref_docs/experiment.rst +++ b/source/auto_api_ref_docs/experiment.rst @@ -12,99 +12,149 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/experiment/schema/`` Fields table ------------ -====================== ================================================================================================== ======= ======== ======== ===== ====== ======== -field help text default nullable readonly blank unique type -====================== ================================================================================================== ======= ======== ======== ===== ====== ======== -**isReverseRun** Boolean data. Ex: True false false false true false boolean ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**storage_options** Unicode string data. Ex: "Hello World" A false false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chipType** Unicode string data. Ex: "Hello World" n/a false false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**user_ack** Unicode string data. Ex: "Hello World" U false false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**results** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**sample** Unicode string data. Ex: "Hello World" n/a false true true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**reverse_primer** Unicode string data. Ex: "Hello World" n/a true false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**seqKitBarcode** Unicode string data. Ex: "Hello World" false false true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**id** Integer data. Ex: 2673 false false true true integer ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**metaData** Unicode string data. Ex: "Hello World" {} false false true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**log** Unicode string data. Ex: "Hello World" {} false false true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**sequencekitbarcode** Unicode string data. Ex: "Hello World" n/a true false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**eas_set** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a true false true false related ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**runtype** Unicode string data. Ex: "Hello World" n/a false false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**platform** Unicode string data. Ex: "Hello World" false false true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**samples** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a true false true false related ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**pinnedRepResult** Boolean data. Ex: True false false false true false boolean ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**reagentBarcode** Unicode string data. Ex: "Hello World" false false true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**star** Boolean data. Ex: True false false false true false boolean ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**isProton** Unicode string data. Ex: "Hello World" n/a false true false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**expCompInfo** Unicode string data. Ex: "Hello World" false false true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**resultDate** A date & time as a string. Ex: "2010-11-10T03:07:43" true true false false false datetime ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**flows** Integer data. Ex: 2673 n/a false false false false integer ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**plan** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**date** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a false false false false datetime ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**diskusage** Integer data. Ex: 2673 n/a true false false false integer ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**unique** Unicode string data. Ex: "Hello World" n/a false false false true string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**expDir** Unicode string data. Ex: "Hello World" n/a false false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**autoAnalyze** Boolean data. Ex: True true false false true false boolean ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**ftpStatus** Unicode string data. Ex: "Hello World" false false true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**flowsInOrder** Unicode string data. Ex: "Hello World" false false true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**baselineRun** Boolean data. Ex: True false false false true false boolean ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**displayName** Unicode string data. Ex: "Hello World" false false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**notes** Unicode string data. Ex: "Hello World" n/a true false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**sequencekitname** Unicode string data. Ex: "Hello World" n/a true false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chipBarcode** Unicode string data. Ex: "Hello World" false false true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**pgmName** Unicode string data. Ex: "Hello World" n/a false false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**storageHost** Unicode string data. Ex: "Hello World" n/a true false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**expName** Unicode string data. Ex: "Hello World" n/a false false false false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**status** Unicode string data. Ex: "Hello World" false false true false string ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**usePreBeadfind** Boolean data. Ex: True true false false true false boolean ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**cycles** Integer data. Ex: 2673 n/a false false false false integer ----------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**rawdatastyle** Unicode string data. Ex: "Hello World" single true false false false string -====================== ================================================================================================== ======= ======== ======== ===== ====== ======== +=========================== ================================================================================================== ======= ======== ======== ===== ====== ======== +field help text default nullable readonly blank unique type +=========================== ================================================================================================== ======= ======== ======== ===== ====== ======== +**isReverseRun** Boolean data. Ex: True false false false true false boolean +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefLotNumber** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chipType** Unicode string data. Ex: "Hello World" n/a false false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**user_ack** Unicode string data. Ex: "Hello World" U false false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**results** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefSolutionsPart** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**runtype** Unicode string data. Ex: "Hello World" n/a false false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**storage_options** Unicode string data. Ex: "Hello World" A false false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefChipExpiration1** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefChipExpiration2** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**diskusage** Integer data. Ex: 2673 n/a true false false false integer +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefStatus** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**reverse_primer** Unicode string data. Ex: "Hello World" n/a true false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**seqKitBarcode** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**id** Integer data. Ex: 2673 false false true true integer +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefReagentsPart** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**metaData** Unicode string data. Ex: "Hello World" {} false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefInstrumentName** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**log** Unicode string data. Ex: "Hello World" {} false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**sequencekitbarcode** Unicode string data. Ex: "Hello World" n/a true false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**eas_set** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a true false true false related +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefReagentID** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**platform** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**sample** Unicode string data. Ex: "Hello World" n/a false true true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**samples** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a true false true false related +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefManufactureDate** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefSamplePos** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**pinnedRepResult** Boolean data. Ex: True false false false true false boolean +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefReagentsExpiration** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefSolutionsLot** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**reagentBarcode** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefProgress** Floating point numeric data. Ex: 26.73 0 false false true false float +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefKitType** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**star** Boolean data. Ex: True false false false true false boolean +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefPackageVer** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**isProton** Unicode string data. Ex: "Hello World" n/a false true false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**expCompInfo** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**flowsInOrder** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**flows** Integer data. Ex: 2673 n/a false false false false integer +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**resultDate** A date & time as a string. Ex: "2010-11-10T03:07:43" true true false false false datetime +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefTipRackBarcode** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**plan** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**date** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a false false false false datetime +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefExtraInfo_1** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefExtraInfo_2** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**unique** Unicode string data. Ex: "Hello World" n/a false false false true string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**expDir** Unicode string data. Ex: "Hello World" n/a false false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**autoAnalyze** Boolean data. Ex: True true false false true false boolean +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**ftpStatus** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefMessage** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**cycles** Integer data. Ex: 2673 n/a false false false false integer +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**displayName** Unicode string data. Ex: "Hello World" false false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**notes** Unicode string data. Ex: "Hello World" n/a true false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**sequencekitname** Unicode string data. Ex: "Hello World" n/a true false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chipBarcode** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**pgmName** Unicode string data. Ex: "Hello World" n/a false false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefSolutionsExpiration** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefReagentsLot** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**storageHost** Unicode string data. Ex: "Hello World" n/a true false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**expName** Unicode string data. Ex: "Hello World" n/a false false false false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**status** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**usePreBeadfind** Boolean data. Ex: True true false false true false boolean +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefChipType2** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**chefChipType1** Unicode string data. Ex: "Hello World" false false true false string +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**baselineRun** Boolean data. Ex: True false false false true false boolean +--------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**rawdatastyle** Unicode string data. Ex: "Hello World" single true false false false string +=========================== ================================================================================================== ======= ======== ======== ===== ====== ======== Example request --------------- @@ -136,7 +186,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 21008, + "total_count": 27197, "offset": 0, "limit": 1, "next": "/rundb/api/v1/experiment/?offset=1&limit=1&format=json" @@ -144,16 +194,25 @@ Torrent Server response "objects": [ { "isReverseRun": false, - "storage_options": "A", + "chefLotNumber": "", "chipType": "", "user_ack": "U", + "chefLogPath": null, "results": [], - "sample": "E115943-lq204-01-L8095", - "runMode": "", + "chefSolutionsPart": "", + "runtype": "GENS", + "chefLastUpdate": null, + "storage_options": "A", + "chefChipExpiration1": "", + "chefChipExpiration2": "", + "diskusage": null, + "chefStatus": "", "reverse_primer": null, "seqKitBarcode": "", "id": 10132, + "chefReagentsPart": "", "metaData": {}, + "chefInstrumentName": "", "log": {}, "sequencekitbarcode": "", "resource_uri": "/rundb/api/v1/experiment/10132/", @@ -162,6 +221,8 @@ Torrent Server response "isEditable": true, "hotSpotRegionBedFile": "", "results": [], + "mixedTypeRNA_reference": null, + "analysisargs": "", "targetRegionBedFile": "/results/uploads/BED/19/hg19/unmerged/detail/Ion-TargetSeq-Exome-50Mb-hg19_revA.bed", "thumbnailalignmentargs": "", "thumbnailanalysisargs": "", @@ -169,7 +230,8 @@ Torrent Server response "barcodedSamples": {}, "reference": "hg19", "isOneTimeOverride": false, - "analysisargs": "", + "mixedTypeRNA_hotSpotRegionBedFile": null, + "mixedTypeRNA_targetRegionBedFile": null, "thumbnailcalibrateargs": "", "realign": false, "selectedPlugins": { @@ -269,13 +331,14 @@ Torrent Server response "calibrateargs": "", "tfKey": "", "libraryKitBarcode": null, - "base_recalibrate": true, "basecallerargs": "", + "base_recalibration_mode": "standard_recal", "resource_uri": "/rundb/api/v1/experimentanalysissettings/10575/" } ], - "runtype": "GENS", + "chefReagentID": "", "platform": "PGM", + "sample": "E115943-lq204-01-L8095", "samples": [ { "status": "run", @@ -293,32 +356,47 @@ Torrent Server response "name": "E115943-lq204-01-L8095" } ], + "chefManufactureDate": "", + "chefSamplePos": "", "pinnedRepResult": false, + "chefReagentsExpiration": "", + "chefSolutionsLot": "", "reagentBarcode": "", + "chefProgress": 0, + "chefKitType": "", "star": false, + "chefPackageVer": "", "isProton": "False", "expCompInfo": "", - "resultDate": "2013-05-15T18:30:24.000171+00:00", + "flowsInOrder": "", "flows": 400, + "resultDate": "2013-05-15T18:30:24.000171+00:00", + "chefTipRackBarcode": "", "plan": "/rundb/api/v1/plannedexperiment/88364/", "date": "2013-05-15T18:30:24.000167+00:00", - "diskusage": null, + "chefExtraInfo_1": "", + "chefExtraInfo_2": "", "unique": "ea5aefc7-e1ec-4c79-9843-b0e299253a9a", "expDir": "", "autoAnalyze": true, "ftpStatus": "Complete", - "flowsInOrder": "", - "baselineRun": false, + "chefMessage": "", + "cycles": 0, "displayName": "ea5aefc7-e1ec-4c79-9843-b0e299253a9a", + "runMode": "", "notes": "OT2 lq204_01 Lib8095 275bp lr2 4B bead 1.2B lib SDS_10mMEDTA break ", "sequencekitname": "", "chipBarcode": "", "pgmName": "", + "chefSolutionsExpiration": "", + "chefReagentsLot": "", "storageHost": null, "expName": "ea5aefc7-e1ec-4c79-9843-b0e299253a9a", "status": "planned", "usePreBeadfind": false, - "cycles": 0, + "chefChipType2": "", + "chefChipType1": "", + "baselineRun": false, "rawdatastyle": "single" } ] diff --git a/source/auto_api_ref_docs/experimentanalysissettings.rst b/source/auto_api_ref_docs/experimentanalysissettings.rst index 25eadb8..e40d3fe 100644 --- a/source/auto_api_ref_docs/experimentanalysissettings.rst +++ b/source/auto_api_ref_docs/experimentanalysissettings.rst @@ -12,77 +12,83 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/experimentanalysissettings/sch Fields table ------------ -============================== ================================================================================================== ======= ======== ======== ===== ====== ======== -field help text default nullable readonly blank unique type -============================== ================================================================================================== ======= ======== ======== ===== ====== ======== -**isEditable** Boolean data. Ex: True false false false true false boolean ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**hotSpotRegionBedFile** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**results** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a true false true false related ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**targetRegionBedFile** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**thumbnailalignmentargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**thumbnailanalysisargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**id** Integer data. Ex: 2673 false false true true integer ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**barcodedSamples** Unicode string data. Ex: "Hello World" {} true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**reference** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**isOneTimeOverride** Boolean data. Ex: True false false false true false boolean ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**analysisargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**thumbnailcalibrateargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**realign** Boolean data. Ex: True false false false true false boolean ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**selectedPlugins** Unicode string data. Ex: "Hello World" {} true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**experiment** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**barcodeKitName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**beadfindargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**threePrimeAdapter** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**thumbnailbasecallerargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**status** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**prebasecallerargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**prethumbnailbasecallerargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**alignmentargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**isDuplicateReads** Boolean data. Ex: True false false false true false boolean ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**libraryKey** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**date** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**libraryKitName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**thumbnailbeadfindargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**calibrateargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**tfKey** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**libraryKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**base_recalibrate** Boolean data. Ex: True true false false true false boolean ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**basecallerargs** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -============================== ================================================================================================== ======= ======== ======== ===== ====== ======== +===================================== ================================================================================================== ============== ======== ======== ===== ====== ======== +field help text default nullable readonly blank unique type +===================================== ================================================================================================== ============== ======== ======== ===== ====== ======== +**isEditable** Boolean data. Ex: True false false false true false boolean +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**hotSpotRegionBedFile** Unicode string data. Ex: "Hello World" n/a true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**results** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a true false true false related +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**mixedTypeRNA_reference** Unicode string data. Ex: "Hello World" n/a true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**analysisargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**targetRegionBedFile** Unicode string data. Ex: "Hello World" n/a true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**thumbnailalignmentargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**thumbnailanalysisargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**id** Integer data. Ex: 2673 false false true true integer +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**barcodedSamples** Unicode string data. Ex: "Hello World" {} true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**reference** Unicode string data. Ex: "Hello World" n/a true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**isOneTimeOverride** Boolean data. Ex: True false false false true false boolean +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**mixedTypeRNA_hotSpotRegionBedFile** Unicode string data. Ex: "Hello World" n/a true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**mixedTypeRNA_targetRegionBedFile** Unicode string data. Ex: "Hello World" n/a true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**thumbnailcalibrateargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**realign** Boolean data. Ex: True false false false true false boolean +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**selectedPlugins** Unicode string data. Ex: "Hello World" {} true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**experiment** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**barcodeKitName** Unicode string data. Ex: "Hello World" n/a true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**beadfindargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**threePrimeAdapter** Unicode string data. Ex: "Hello World" n/a true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**thumbnailbasecallerargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**status** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**prebasecallerargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**prethumbnailbasecallerargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**alignmentargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**isDuplicateReads** Boolean data. Ex: True false false false true false boolean +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**libraryKey** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**date** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**libraryKitName** Unicode string data. Ex: "Hello World" n/a true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**thumbnailbeadfindargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**calibrateargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**tfKey** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**libraryKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**basecallerargs** Unicode string data. Ex: "Hello World" false false true false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**base_recalibration_mode** Unicode string data. Ex: "Hello World" standard_recal false false false false string +------------------------------------- -------------------------------------------------------------------------------------------------- -------------- -------- -------- ----- ------ -------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +===================================== ================================================================================================== ============== ======== ======== ===== ====== ======== Example request --------------- @@ -114,7 +120,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 23666, + "total_count": 31073, "offset": 0, "limit": 1, "next": "/rundb/api/v1/experimentanalysissettings/?offset=1&limit=1&format=json" @@ -124,6 +130,8 @@ Torrent Server response "isEditable": true, "hotSpotRegionBedFile": "", "results": [], + "mixedTypeRNA_reference": null, + "analysisargs": "", "targetRegionBedFile": "/results/uploads/BED/15/hg19/unmerged/detail/Ion-TargetSeq-Exome-50Mb-hg19.bed", "thumbnailalignmentargs": "", "thumbnailanalysisargs": "", @@ -131,7 +139,8 @@ Torrent Server response "barcodedSamples": {}, "reference": "hg19", "isOneTimeOverride": false, - "analysisargs": "", + "mixedTypeRNA_hotSpotRegionBedFile": null, + "mixedTypeRNA_targetRegionBedFile": null, "thumbnailcalibrateargs": "", "realign": false, "selectedPlugins": { @@ -160,8 +169,8 @@ Torrent Server response "calibrateargs": "", "tfKey": "", "libraryKitBarcode": null, - "base_recalibrate": true, "basecallerargs": "", + "base_recalibration_mode": "standard_recal", "resource_uri": "/rundb/api/v1/experimentanalysissettings/138/" } ] diff --git a/source/auto_api_ref_docs/filemonitor.rst b/source/auto_api_ref_docs/filemonitor.rst index 60206bb..4e94b45 100644 --- a/source/auto_api_ref_docs/filemonitor.rst +++ b/source/auto_api_ref_docs/filemonitor.rst @@ -72,7 +72,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 8, + "total_count": 24, "offset": 0, "limit": 1, "next": "/rundb/api/v1/filemonitor/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/fileserver.rst b/source/auto_api_ref_docs/fileserver.rst index b4b66bb..ad7c757 100644 --- a/source/auto_api_ref_docs/fileserver.rst +++ b/source/auto_api_ref_docs/fileserver.rst @@ -15,7 +15,7 @@ Fields table ================ ====================================== ======= ======== ======== ===== ====== ======= field help text default nullable readonly blank unique type ================ ====================================== ======= ======== ======== ===== ====== ======= -**percentfull** Floating point numeric data. Ex: 26.73 0.0 true false false false float +**percentfull** Floating point numeric data. Ex: 26.73 0 true false false false float ---------------- -------------------------------------- ------- -------- -------- ----- ------ ------- **name** Unicode string data. Ex: "Hello World" n/a false false false false string ---------------- -------------------------------------- ------- -------- -------- ----- ------ ------- @@ -58,19 +58,19 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 2, + "total_count": 3, "offset": 0, "limit": 1, "next": "/rundb/api/v1/fileserver/?offset=1&limit=1&format=json" }, "objects": [ { - "percentfull": 82.6372068824745, - "name": "gs1-nfs", - "filesPrefix": "/ion-data/results/", - "comments": "gs1-nfs:/gs1/ion-data", - "id": 5, - "resource_uri": "/rundb/api/v1/fileserver/5/" + "percentfull": 0.0130563724119952, + "name": "ddn2", + "filesPrefix": "/ion-data2/results", + "comments": "1.1 petabytes storage", + "id": 10, + "resource_uri": "/rundb/api/v1/fileserver/10/" } ] } diff --git a/source/auto_api_ref_docs/globalconfig.rst b/source/auto_api_ref_docs/globalconfig.rst index b9e654e..62e7452 100644 --- a/source/auto_api_ref_docs/globalconfig.rst +++ b/source/auto_api_ref_docs/globalconfig.rst @@ -12,71 +12,71 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/globalconfig/schema/`` Fields table ------------ -============================= ====================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -============================= ====================================== ======= ======== ======== ===== ====== ======= -**enable_version_lock** Boolean data. Ex: True false false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**site_name** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**enable_support_upload** Boolean data. Ex: True false false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**plugin_output_folder** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**auto_archive_ack** Boolean data. Ex: True false false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**default_plugin_script** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**default_storage_options** Unicode string data. Ex: "Hello World" D false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**selected** Boolean data. Ex: True false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**check_news_posts** Boolean data. Ex: True true false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**realign** Boolean data. Ex: True false false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**ts_update_status** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**mark_duplicates** Boolean data. Ex: True false false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**plugin_folder** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**auto_archive_enable** Boolean data. Ex: True false false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**reference_path** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**enable_auto_security** Boolean data. Ex: True true false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**fasta_path** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**enable_nightly_email** Boolean data. Ex: True true false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**barcode_args** Unicode string data. Ex: "Hello World" {} false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**sec_update_status** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**default_flow_order** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**records_to_display** Integer data. Ex: 2673 20 false false true false integer ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**base_recalibrate** Boolean data. Ex: True true false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**default_library_key** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**web_root** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**default_test_fragment_key** Unicode string data. Ex: "Hello World" false false true false string ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**enable_auto_pkg_dl** Boolean data. Ex: True true false false true false boolean ------------------------------ -------------------------------------- ------- -------- -------- ----- ------ ------- -**enable_compendia_OCP** Boolean data. Ex: True false false false true false boolean -============================= ====================================== ======= ======== ======== ===== ====== ======= +============================= ====================================== ============== ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ====================================== ============== ======== ======== ===== ====== ======= +**enable_version_lock** Boolean data. Ex: True false false false true false boolean +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**site_name** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**enable_support_upload** Boolean data. Ex: True false false false true false boolean +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**plugin_output_folder** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**auto_archive_ack** Boolean data. Ex: True false false false true false boolean +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**enable_compendia_OCP** Boolean data. Ex: True false false false true false boolean +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**base_recalibration_mode** Unicode string data. Ex: "Hello World" standard_recal false false false false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**default_storage_options** Unicode string data. Ex: "Hello World" D false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**selected** Boolean data. Ex: True false false true false boolean +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**check_news_posts** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**realign** Boolean data. Ex: True false false false true false boolean +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**ts_update_status** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**mark_duplicates** Boolean data. Ex: True false false false true false boolean +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**plugin_folder** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**default_plugin_script** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**reference_path** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**enable_auto_security** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**fasta_path** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**enable_nightly_email** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**barcode_args** Unicode string data. Ex: "Hello World" {} false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**sec_update_status** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**default_flow_order** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**records_to_display** Integer data. Ex: 2673 20 false false true false integer +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**default_library_key** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**web_root** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**default_test_fragment_key** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**auto_archive_enable** Boolean data. Ex: True false false false true false boolean +----------------------------- -------------------------------------- -------------- -------- -------- ----- ------ ------- +**enable_auto_pkg_dl** Boolean data. Ex: True true false false true false boolean +============================= ====================================== ============== ======== ======== ===== ====== ======= Example request --------------- @@ -120,19 +120,20 @@ Torrent Server response "enable_support_upload": false, "plugin_output_folder": "plugin_out", "auto_archive_ack": true, - "default_plugin_script": "launch.sh", + "enable_compendia_OCP": true, "id": 1, + "base_recalibration_mode": "standard_recal", "resource_uri": "/rundb/api/v1/globalconfig/1/", "default_storage_options": "D", "selected": false, "check_news_posts": true, "realign": false, - "ts_update_status": "No updates", + "ts_update_status": "Ready to install", "mark_duplicates": false, "plugin_folder": "plugins", - "auto_archive_enable": true, + "default_plugin_script": "launch.sh", "reference_path": "", - "enable_auto_security": false, + "enable_auto_security": true, "fasta_path": "", "enable_nightly_email": true, "barcode_args": { @@ -142,12 +143,11 @@ Torrent Server response "default_flow_order": "TACG", "name": "Config", "records_to_display": 50, - "base_recalibrate": true, "default_library_key": "TCAG", "web_root": "http://blackbird.ite", "default_test_fragment_key": "ATCG", - "enable_auto_pkg_dl": false, - "enable_compendia_OCP": true + "auto_archive_enable": true, + "enable_auto_pkg_dl": true } ] } diff --git a/source/auto_api_ref_docs/ionchefplantemplate.rst b/source/auto_api_ref_docs/ionchefplantemplate.rst index 803f43d..ef14618 100644 --- a/source/auto_api_ref_docs/ionchefplantemplate.rst +++ b/source/auto_api_ref_docs/ionchefplantemplate.rst @@ -43,6 +43,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sequencekitname** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**base_recalibration_mode** Unicode string data. Ex: "Hello World" true false true false string +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **storageHost** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string @@ -55,7 +57,7 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipType** Unicode string data. Ex: "Hello World" false false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**chefProgress** Floating point numeric data. Ex: 26.73 0 false false true false float --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **library** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -67,7 +69,7 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **barcodeId** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string +**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -93,8 +95,6 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **forward3primeadapter** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ---------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **applicationGroupDisplayedName** Unicode string data. Ex: "Hello World" n/a true true true false string @@ -125,6 +125,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chefMessage** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **childPlans** A list of data. Ex: ['abc', 26.73, 8] [] false false false false list --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -139,6 +141,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePostBeadfind** Boolean data. Ex: True false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planGUID** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -183,8 +187,6 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleGrouping** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**base_recalibrate** Boolean data. Ex: True n/a false false false false boolean ---------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -224,14 +226,14 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 7, + "total_count": 17, "offset": 0, "limit": 1, "next": "/rundb/api/v1/ionchefplantemplate/?offset=1&limit=1&format=json" }, "objects": [ { - "planDisplayedName": "chef_useGUI_Exome Panel_AmpliSeqExome.20131001", + "planDisplayedName": "IC_P1v2_VAL_ccp", "autoAnalyze": true, "templatingKitBarcode": null, "preAnalysis": true, @@ -241,13 +243,16 @@ Torrent Server response "platform": "", "categories": "", "planPGM": null, - "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --calibration-training=100000 --flow-signals-type scaled-residual --max-phasing-levels 2", + "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --max-phasing-levels 2", "alignmentargs": "stage1 map4", - "thumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", + "thumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", "sampleSet_planTotal": 0, - "projects": [], - "notes": "Uploaded from amplseq.com and available at-jira.itw_wiki_x_HAHcAg\r\nReplace _ with slashes for link to Document collection on JIRA\r\nAdded AmpliseqExome.germline_lowstringency_p1.4_0.20130920.parameters.json parameter file.", - "sequencekitname": "ProtonIIC200Kit", + "projects": [ + "IC_P1v2_val" + ], + "notes": "", + "sequencekitname": "IonProtonIHiQ", + "base_recalibration_mode": "no_recal", "storageHost": null, "expName": "", "cycles": null, @@ -255,7 +260,7 @@ Torrent Server response "storage_options": "A", "thumbnailalignmentargs": "stage1 map4", "chipType": "P1.1.17", - "chefProgress": 0.0, + "chefProgress": 0, "library": "hg19", "reverselibrarykey": "", "sampleTubeLabel": "", @@ -265,20 +270,19 @@ Torrent Server response "isPlanGroup": false, "realign": false, "sampleGroupingName": "", - "experiment": "/rundb/api/v1/experiment/21899/", - "bedfile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed", + "experiment": "/rundb/api/v1/experiment/32917/", + "bedfile": "/results/uploads/BED/44/hg19/unmerged/detail/CCP.20131001.designed.bed", "isReusable": true, "isDuplicateReads": false, "thumbnailbeadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=100,100 --beadfind-thumbnail 1", "librarykitname": "Ion AmpliSeq 2.0 Library Kit", "adapter": null, - "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1", + "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1", "tfKey": "ATCG", "parentPlan": null, "forward3primeadapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC", "planStatus": "pending", - "chefLastUpdate": null, - "samplePrepKitName": "Ion AmpliSeq Exome Kit", + "samplePrepKitName": "", "applicationGroupDisplayedName": "DNA", "metaData": {}, "sampleSet_uid": null, @@ -287,8 +291,8 @@ Torrent Server response "qcValues": [ { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/100136/", - "id": 262521, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111154/", + "id": 289314, "qcType": { "description": "", "minThreshold": 0, @@ -298,12 +302,12 @@ Torrent Server response "id": 3, "resource_uri": "/rundb/api/v1/qctype/3/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/262521/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289314/" }, { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/100136/", - "id": 262520, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111154/", + "id": 289313, "qcType": { "description": "", "minThreshold": 1, @@ -313,12 +317,12 @@ Torrent Server response "id": 2, "resource_uri": "/rundb/api/v1/qctype/2/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/262520/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289313/" }, { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/100136/", - "id": 262519, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111154/", + "id": 289312, "qcType": { "description": "", "minThreshold": 0, @@ -328,155 +332,187 @@ Torrent Server response "id": 1, "resource_uri": "/rundb/api/v1/qctype/1/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/262519/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289312/" } ], "analysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=216,224 --bkg-bfmask-update false --gpuWorkLoad 1 --total-timeout 600 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json", "thumbnailcalibrateargs": "calibrate --skipDroop", - "templatingKitName": "Ion PI IC 200 Kit", - "runType": "AMPS_EXOME", + "templatingKitName": "Ion PROTON IC v2 Universal", + "runType": "AMPS", "username": "ionuser", - "planName": "chef_useGUI_Exome_Panel_AmpliSeqExome.20131001", + "planName": "IC_P1v2_VAL_ccp", "sampleDisplayedName": "", - "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000 --calibration-training=100000 --flow-signals-type scaled-residual", + "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", "controlSequencekitname": "", "chefMessage": "", + "templatingSize": "200", "childPlans": [], "pairedEndLibraryAdapterName": "", "runMode": "single", "irworkflow": "", "planExecuted": false, - "project": "", + "project": "IC_P1v2_val", "usePostBeadfind": false, + "libraryReadLength": 200, "runname": null, - "planGUID": "83e69cd8-ca3a-4ff2-b4ac-dd637184e28e", - "planShortID": "YHFWJ", + "planGUID": "b55face2-df5f-434c-89df-210f384170cb", + "planShortID": "IL9TF", "sampleSetGroupType": null, "sample": "", "planExecutedDate": null, "reverse_primer": null, - "id": 100136, + "id": 111154, "barcodedSamples": {}, - "regionfile": "", + "regionfile": "/results/uploads/BED/47/hg19/unmerged/detail/CCP.20131001.hotspots.bed", "selectedPlugins": { + "SystematicErrorAnalysis": { + "userInput": "", + "version": "0.8.5", + "features": [], + "name": "SystematicErrorAnalysis", + "id": 734 + }, "IonReporterUploader": { "userInput": { "accountName": "None", "userInputInfo": "", "accountId": "0" }, - "version": "4.1-r87449", + "version": "4.4.0.2", "features": [ "export" ], "name": "IonReporterUploader", - "id": 804 - }, - "coverageAnalysis": { - "userInput": "", - "version": "4.2-r86949", - "features": [], - "name": "coverageAnalysis", - "id": 800 - }, - "validateVariantCaller": { - "userInput": { - "variant_caller_name": "variantCaller", - "truth_major_snp": "NA12878_NIST_NoChrY_SNP.bed", - "region": "NIST", - "sample": "NA12878", - "truth_minor_snp": "None", - "truth_major_indel": "NA12878_NIST_NoChrY_indel.bed", - "truth_minor_indel": "None" - }, - "version": "0.2.1", - "features": [], - "name": "validateVariantCaller", - "id": 732 + "id": 993 }, "variantCaller": { "userInput": { "torrent_variant_caller": { - "snp_min_allele_freq": "0.10000000000000001", - "snp_strand_bias": "0.97999999999999998", + "snp_min_allele_freq": "0.02", + "snp_strand_bias": "0.95", "hotspot_min_coverage": 6, - "hotspot_min_cov_each_strand": 3, - "hotspot_min_allele_freq": "0.10000000000000001", - "snp_min_variant_score": 15, - "hotspot_strand_bias": "0.94999999999999996", + "hotspot_min_cov_each_strand": 2, + "position_bias": "0.75", + "hotspot_min_allele_freq": "0.01", + "snp_min_variant_score": 6, + "mnp_min_variant_score": 400, + "hotspot_strand_bias": "0.95", "hp_max_length": 8, - "filter_insertion_predictions": "0.20000000000000001", - "indel_min_variant_score": 20, - "indel_min_coverage": 10, + "filter_insertion_predictions": "0.2", + "indel_min_variant_score": 6, + "indel_min_coverage": 15, "heavy_tailed": 3, - "outlier_probability": "0.01", - "data_quality_stringency": 5, + "outlier_probability": "0.005", + "position_bias_ref_fraction": "0.05", + "indel_strand_bias_pval": 1, + "data_quality_stringency": "6.5", "snp_min_cov_each_strand": 0, - "hotspot_min_variant_score": 10, - "indel_strand_bias": "0.90000000000000002", - "tvc_parameters_version": "germline_low_stringency_proton-3.6.66827", - "downsample_to_coverage": 400, - "filter_unusual_predictions": "0.25", - "indel_min_allele_freq": "0.14999999999999999", + "indel_as_hpindel": 0, + "snp_strand_bias_pval": 1, + "mnp_strand_bias": "0.95", + "mnp_strand_bias_pval": 1, + "hotspot_strand_bias_pval": 1, + "hotspot_min_variant_score": 6, + "do_mnp_realignment": 1, + "indel_strand_bias": "0.9", + "downsample_to_coverage": 2000, + "filter_unusual_predictions": "0.3", + "indel_min_allele_freq": "0.05", + "mnp_min_allele_freq": "0.02", + "mnp_min_coverage": 6, "do_snp_realignment": 1, + "mnp_min_cov_each_strand": 0, + "snp_min_coverage": 6, "prediction_precision": 1, - "indel_min_cov_each_strand": 5, - "filter_deletion_predictions": "0.20000000000000001", + "indel_min_cov_each_strand": 2, + "filter_deletion_predictions": "0.2", + "realignment_threshold": 1, "suppress_recalibration": 0, - "snp_min_coverage": 5 + "position_bias_pval": "0.05", + "use_position_bias": 0 }, "meta": { - "repository_id": "", - "ts_version": "4.0", - "name": "External file AmpliseqExome.germline_lowstringency_p1.4_0.20130920.parameters.json", + "ts_version": "4.4", + "name": "Generic - Proton - Somatic - Low Stringency", "user_selections": { "chip": "proton_p1", - "frequency": "germline", + "frequency": "somatic", "library": "ampliseq", - "panel": "/rundb/api/v1/contentupload/53/" + "panel": "/rundb/api/v1/contentupload/48/" }, "librarytype": "ampliseq", "trimreads": true, - "tooltip": "Retrieved from external file", + "tooltip": "Parameter settings optimized for low frequency variants and minimum false negatives on Proton chips", "tvcargs": "tvc", - "built_in": false, - "configuration": "", - "compatibility": {} + "barcode_mode": "match", + "based_on": "ampliseqexome_somatic_lowstringency_p1_parameters.json", + "built_in": true, + "configuration": "somatic_low_stringency_proton", + "compatibility": { + "chip": [ + "proton_p1" + ], + "frequency": [ + "somatic" + ], + "stringency": [ + "low" + ], + "library": [ + "wholegenome", + "ampliseq", + "targetseq" + ] + } }, "long_indel_assembler": { "min_indel_size": 4, "short_suffix_match": 5, "output_mnv": 0, "min_var_count": 5, - "min_var_freq": "0.14999999999999999", + "min_var_freq": "0.15", "kmer_len": 19, "max_hp_length": 8, - "relative_strand_bias": "0.80000000000000004" + "relative_strand_bias": "0.8" }, "freebayes": { - "gen_min_coverage": 5, + "gen_min_coverage": 6, "allow_mnps": 1, "allow_complex": 0, + "read_snp_limit": 10, "read_max_mismatch_fraction": 1, - "read_mismatch_limit": 10, "allow_indels": 1, "min_mapping_qv": 4, - "gen_min_alt_allele_freq": "0.10000000000000001", + "gen_min_alt_allele_freq": "0.035", "allow_snps": 1, - "gen_min_indel_alt_allele_freq": "0.14999999999999999" + "gen_min_indel_alt_allele_freq": "0.1" } }, - "version": "4.1-r74477", + "version": "4.4.0.6", "features": [], "name": "variantCaller", - "id": 698 + "id": 994 }, - "AmpliconStats": { + "validateVariantCaller": { "userInput": "", - "version": "0.4.5", + "version": "0.2.1", "features": [], - "name": "AmpliconStats", - "id": 774 + "name": "validateVariantCaller", + "id": 732 + }, + "validateVariantCaller-Lite": { + "userInput": "", + "version": "1.1.6", + "features": [], + "name": "validateVariantCaller-Lite", + "id": 964 + }, + "coverageAnalysis": { + "userInput": "", + "version": "4.4.0.12", + "features": [], + "name": "coverageAnalysis", + "id": 995 } }, "beadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=216,224 --total-timeout 600", @@ -484,19 +520,18 @@ Torrent Server response "isSystemDefault": false, "autoName": null, "libraryKey": "TCAG", - "flows": 520, + "flows": 400, "thumbnailanalysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=100,100 --bkg-bfmask-update false --gpuWorkLoad 1 --bkg-debug-param 1 --beadfind-thumbnail 1 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json", - "date": "2014-05-20T13:56:24.000114+00:00", + "date": "2015-01-28T19:57:42.000445+00:00", "isSystem": false, "variantfrequency": "", "sampleSetDisplayedName": "", "calibrateargs": "calibrate --skipDroop", "flowsInOrder": "", "sampleGrouping": null, - "base_recalibrate": true, "chipBarcode": null, "usePreBeadfind": true, - "resource_uri": "/rundb/api/v1/ionchefplantemplate/100136/", + "resource_uri": "/rundb/api/v1/ionchefplantemplate/111154/", "reverse3primeadapter": "" } ] diff --git a/source/auto_api_ref_docs/ionchefplantemplatesummary.rst b/source/auto_api_ref_docs/ionchefplantemplatesummary.rst index 184ac84..da405f1 100644 --- a/source/auto_api_ref_docs/ionchefplantemplatesummary.rst +++ b/source/auto_api_ref_docs/ionchefplantemplatesummary.rst @@ -23,13 +23,11 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **preAnalysis** Boolean data. Ex: True false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**isSystemDefault** Boolean data. Ex: True false false false true false boolean -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planShortID** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planStatus** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime +**runMode** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **templatingKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -37,8 +35,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planExecutedDate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefStatus** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **reverse_primer** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -55,8 +51,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planIndex** Integer data. Ex: 2673 0 false false false false integer ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planTotal** Integer data. Ex: 2673 0 false false false false integer @@ -67,7 +61,7 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planPGM** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**isSystemDefault** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **autoName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -85,12 +79,10 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefMessage** Unicode string data. Ex: "Hello World" false false true false string +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **adapter** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **irworkflow** Unicode string data. Ex: "Hello World" false false true false string @@ -107,6 +99,8 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -148,7 +142,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 7, + "total_count": 17, "offset": 0, "limit": 1, "next": "/rundb/api/v1/ionchefplantemplatesummary/?offset=1&limit=1&format=json" @@ -156,43 +150,39 @@ Torrent Server response "objects": [ { "isReverseRun": false, - "planDisplayedName": "chef_useGUI_Exome Panel_AmpliSeqExome.20131001", + "planDisplayedName": "IC_P1v2_VAL_ccp", "storage_options": "A", "preAnalysis": true, - "isSystemDefault": false, - "planShortID": "YHFWJ", + "planShortID": "IL9TF", "planStatus": "pending", - "chefLastUpdate": null, + "runMode": "single", "templatingKitBarcode": null, "sampleTubeLabel": "", "planExecutedDate": null, - "chefStatus": "", - "samplePrepKitName": "Ion AmpliSeq Exome Kit", + "samplePrepKitName": "", "reverse_primer": null, "seqKitBarcode": null, - "id": 100136, + "id": 111154, "metaData": {}, "sampleSet_uid": null, "isFavorite": true, "sampleSet_planIndex": 0, - "chefLogPath": null, "isPlanGroup": false, "sampleSet_planTotal": 0, - "templatingKitName": "Ion PI IC 200 Kit", - "runType": "AMPS_EXOME", + "templatingKitName": "Ion PROTON IC v2 Universal", + "runType": "AMPS", "planPGM": null, - "chefProgress": 0.0, + "isSystemDefault": false, "autoName": null, "isReusable": true, "controlSequencekitname": "", - "date": "2014-05-20T13:56:24.000114+00:00", + "date": "2015-01-28T19:57:42.000445+00:00", "isSystem": false, "libkit": null, "categories": "", - "planName": "chef_useGUI_Exome_Panel_AmpliSeqExome.20131001", - "chefMessage": "", + "planName": "IC_P1v2_VAL_ccp", + "templatingSize": "200", "pairedEndLibraryAdapterName": "", - "runMode": "single", "adapter": null, "irworkflow": "", "chipBarcode": null, @@ -201,11 +191,12 @@ Torrent Server response "usePostBeadfind": false, "storageHost": null, "expName": "", + "libraryReadLength": 200, "runname": null, "usePreBeadfind": true, - "planGUID": "83e69cd8-ca3a-4ff2-b4ac-dd637184e28e", + "planGUID": "b55face2-df5f-434c-89df-210f384170cb", "cycles": null, - "resource_uri": "/rundb/api/v1/ionchefplantemplatesummary/100136/" + "resource_uri": "/rundb/api/v1/ionchefplantemplatesummary/111154/" } ] } diff --git a/source/auto_api_ref_docs/ionchefprepkitinfo.rst b/source/auto_api_ref_docs/ionchefprepkitinfo.rst index c261c9a..83f5dd0 100644 --- a/source/auto_api_ref_docs/ionchefprepkitinfo.rst +++ b/source/auto_api_ref_docs/ionchefprepkitinfo.rst @@ -12,37 +12,43 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/ionchefprepkitinfo/schema/`` Fields table ------------ -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -**isActive** Boolean data. Ex: True true false false true false boolean -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**flowCount** Integer data. Ex: 2673 n/a false false false false integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**applicationType** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**uid** Unicode string data. Ex: "Hello World" n/a false false false true string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**categories** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false true string -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +**isActive** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**samplePrep_instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**flowCount** Integer data. Ex: 2673 n/a false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**applicationType** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**uid** Unicode string data. Ex: "Hello World" n/a false false false true string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**categories** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -74,7 +80,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 2, + "total_count": 4, "offset": 0, "limit": 1, "next": "/rundb/api/v1/ionchefprepkitinfo/?offset=1&limit=1&format=json" @@ -82,38 +88,47 @@ Torrent Server response "objects": [ { "isActive": true, + "templatingSize": "", "kitType": "IonChefPrepKit", - "description": "ION PGM IC 200 KIT", + "description": "Ion PI IC 200 Kit", "nucleotideType": "", - "instrumentType": "pgm", + "instrumentType": "proton", + "samplePrep_instrumentType": "IC", "runMode": "", "parts": [ { - "barcode": "100020579", - "id": 20085, - "resource_uri": "/rundb/api/v1/kitpart/20085/", - "kit": "/rundb/api/v1/kitinfo/20042/" + "barcode": "100022895", + "id": 20124, + "resource_uri": "/rundb/api/v1/kitpart/20124/", + "kit": "/rundb/api/v1/kitinfo/20057/" }, { - "barcode": "100020580", - "id": 20086, - "resource_uri": "/rundb/api/v1/kitpart/20086/", - "kit": "/rundb/api/v1/kitinfo/20042/" + "barcode": "100022894", + "id": 20125, + "resource_uri": "/rundb/api/v1/kitpart/20125/", + "kit": "/rundb/api/v1/kitinfo/20057/" }, { - "barcode": "01", - "id": 20123, - "resource_uri": "/rundb/api/v1/kitpart/20123/", - "kit": "/rundb/api/v1/kitinfo/20042/" + "barcode": "02", + "id": 20126, + "resource_uri": "/rundb/api/v1/kitpart/20126/", + "kit": "/rundb/api/v1/kitinfo/20057/" + }, + { + "barcode": "100023442", + "id": 20130, + "resource_uri": "/rundb/api/v1/kitpart/20130/", + "kit": "/rundb/api/v1/kitinfo/20057/" } ], "flowCount": 0, "applicationType": "", - "uid": "ICPREP0001", - "resource_uri": "/rundb/api/v1/ionchefprepkitinfo/20042/", - "id": 20042, + "uid": "ICPREP0002", + "libraryReadLength": 0, + "resource_uri": "/rundb/api/v1/ionchefprepkitinfo/20057/", + "id": 20057, "categories": "", - "name": "ION PGM IC 200 KIT" + "name": "Ion PI IC 200 Kit" } ] } diff --git a/source/auto_api_ref_docs/kitinfo.rst b/source/auto_api_ref_docs/kitinfo.rst index 834b652..efea0b7 100644 --- a/source/auto_api_ref_docs/kitinfo.rst +++ b/source/auto_api_ref_docs/kitinfo.rst @@ -12,37 +12,43 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/kitinfo/schema/`` Fields table ------------ -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -**isActive** Boolean data. Ex: True true false false true false boolean -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**flowCount** Integer data. Ex: 2673 n/a false false false false integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**applicationType** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**uid** Unicode string data. Ex: "Hello World" n/a false false false true string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**categories** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false true string -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +**isActive** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**samplePrep_instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**flowCount** Integer data. Ex: 2673 n/a false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**applicationType** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**uid** Unicode string data. Ex: "Hello World" n/a false false false true string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**categories** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -74,27 +80,37 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 67, + "total_count": 75, "offset": 0, "limit": 1, "next": "/rundb/api/v1/kitinfo/?offset=1&limit=1&format=json" }, "objects": [ { - "isActive": true, - "kitType": "ControlSequenceKitType", - "description": "ERCC Mix 1", - "nucleotideType": "rna", + "isActive": false, + "templatingSize": "", + "kitType": "TemplatingKit", + "description": "Ion OneTouch 200 Template Kit v2 DL", + "nucleotideType": "", "instrumentType": "", + "samplePrep_instrumentType": "OT", "runMode": "", - "parts": [], + "parts": [ + { + "barcode": "4480285", + "id": 20040, + "resource_uri": "/rundb/api/v1/kitpart/20040/", + "kit": "/rundb/api/v1/kitinfo/20019/" + } + ], "flowCount": 0, - "applicationType": "RNA", - "uid": "CONSEQ0006", - "resource_uri": "/rundb/api/v1/kitinfo/20061/", - "id": 20061, + "applicationType": "", + "uid": "TEMPLT0001", + "libraryReadLength": 0, + "resource_uri": "/rundb/api/v1/kitinfo/20019/", + "id": 20019, "categories": "", - "name": "ERCC Mix 1" + "name": "Ion OneTouch 200 Template Kit v2 DL" } ] } diff --git a/source/auto_api_ref_docs/kitpart.rst b/source/auto_api_ref_docs/kitpart.rst index a5cad81..279fa06 100644 --- a/source/auto_api_ref_docs/kitpart.rst +++ b/source/auto_api_ref_docs/kitpart.rst @@ -54,7 +54,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 139, + "total_count": 166, "offset": 0, "limit": 1, "next": "/rundb/api/v1/kitpart/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/libmetrics.rst b/source/auto_api_ref_docs/libmetrics.rst index cd8d9d8..447066c 100644 --- a/source/auto_api_ref_docs/libmetrics.rst +++ b/source/auto_api_ref_docs/libmetrics.rst @@ -242,7 +242,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 39455, + "total_count": 49960, "offset": 0, "limit": 1, "next": "/rundb/api/v1/libmetrics/?offset=1&limit=1&format=json" @@ -257,7 +257,7 @@ Torrent Server response "i250Q17_reads": 0, "q10_longest_alignment": 137, "i50Q10_reads": 5244, - "aveKeyCounts": 82.0, + "aveKeyCounts": 82, "i50Q17_reads": 5050, "total_mapped_target_bases": "0", "i200Q7_reads": 0, @@ -322,7 +322,7 @@ Torrent Server response "i150Q7_reads": 0, "i400Q10_reads": 0, "q10_mean_alignment_length": 104, - "raw_accuracy": 0.0, + "raw_accuracy": 0, "sysSNR": 17.32, "q17_mapped_bases": "524626", "Index_Version": "tmap-f2", diff --git a/source/auto_api_ref_docs/librarykey.rst b/source/auto_api_ref_docs/librarykey.rst index bc4c963..8213c30 100644 --- a/source/auto_api_ref_docs/librarykey.rst +++ b/source/auto_api_ref_docs/librarykey.rst @@ -70,13 +70,13 @@ Torrent Server response "objects": [ { "direction": "Forward", - "name": "Ion TCAG", - "sequence": "TCAG", - "description": "Default forward library key", + "name": "bc01_seq_primer", + "sequence": "CGAT", + "description": "bc01only", "runMode": "single", - "id": 3, - "isDefault": true, - "resource_uri": "/rundb/api/v1/librarykey/3/" + "id": 6, + "isDefault": false, + "resource_uri": "/rundb/api/v1/librarykey/6/" } ] } diff --git a/source/auto_api_ref_docs/librarykitinfo.rst b/source/auto_api_ref_docs/librarykitinfo.rst index ec99b80..1c2e10e 100644 --- a/source/auto_api_ref_docs/librarykitinfo.rst +++ b/source/auto_api_ref_docs/librarykitinfo.rst @@ -12,37 +12,43 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/librarykitinfo/schema/`` Fields table ------------ -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -**isActive** Boolean data. Ex: True true false false true false boolean -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**flowCount** Integer data. Ex: 2673 n/a false false false false integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**applicationType** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**uid** Unicode string data. Ex: "Hello World" n/a false false false true string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**categories** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false true string -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +**isActive** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**samplePrep_instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**flowCount** Integer data. Ex: 2673 n/a false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**applicationType** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**uid** Unicode string data. Ex: "Hello World" n/a false false false true string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**categories** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -74,7 +80,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 18, + "total_count": 19, "offset": 0, "limit": 1, "next": "/rundb/api/v1/librarykitinfo/?offset=1&limit=1&format=json" @@ -82,26 +88,22 @@ Torrent Server response "objects": [ { "isActive": true, + "templatingSize": "", "kitType": "LibraryKit", - "description": "Ion Fragment Library Kit", + "description": "MuSeek Library Preparation Kit", "nucleotideType": "dna", "instrumentType": "", + "samplePrep_instrumentType": "", "runMode": "", - "parts": [ - { - "barcode": "4466464", - "id": 20014, - "resource_uri": "/rundb/api/v1/kitpart/20014/", - "kit": "/rundb/api/v1/kitinfo/20005/" - } - ], + "parts": [], "flowCount": 0, "applicationType": "", - "uid": "LIB0002", - "resource_uri": "/rundb/api/v1/librarykitinfo/20005/", - "id": 20005, + "uid": "LIB0012", + "libraryReadLength": 0, + "resource_uri": "/rundb/api/v1/librarykitinfo/20025/", + "id": 20025, "categories": "", - "name": "IonFragmentLibKit2" + "name": "MuSeek(tm) Library Preparation Kit" } ] } diff --git a/source/auto_api_ref_docs/librarykitpart.rst b/source/auto_api_ref_docs/librarykitpart.rst index 7c12b3d..be30816 100644 --- a/source/auto_api_ref_docs/librarykitpart.rst +++ b/source/auto_api_ref_docs/librarykitpart.rst @@ -54,17 +54,17 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 17, + "total_count": 21, "offset": 0, "limit": 1, "next": "/rundb/api/v1/librarykitpart/?offset=1&limit=1&format=json" }, "objects": [ { - "barcode": "A25908", - "id": 20140, - "resource_uri": "/rundb/api/v1/librarykitpart/20140/", - "kit": "/rundb/api/v1/kitinfo/20065/" + "barcode": "4462907", + "id": 20013, + "resource_uri": "/rundb/api/v1/librarykitpart/20013/", + "kit": "/rundb/api/v1/kitinfo/20004/" } ] } diff --git a/source/auto_api_ref_docs/location.rst b/source/auto_api_ref_docs/location.rst index d4f0dd5..755beaf 100644 --- a/source/auto_api_ref_docs/location.rst +++ b/source/auto_api_ref_docs/location.rst @@ -63,11 +63,11 @@ Torrent Server response }, "objects": [ { - "name": "Local", - "resource_uri": "/rundb/api/v1/location/3/", - "defaultlocation": false, + "name": "Home", + "resource_uri": "/rundb/api/v1/location/1/", + "defaultlocation": true, "comments": "", - "id": 3 + "id": 1 } ] } diff --git a/source/auto_api_ref_docs/monitorresult.rst b/source/auto_api_ref_docs/monitorresult.rst index 772f418..6346906 100644 --- a/source/auto_api_ref_docs/monitorresult.rst +++ b/source/auto_api_ref_docs/monitorresult.rst @@ -82,7 +82,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 159, + "total_count": 49, "offset": 0, "limit": 1, "next": "/rundb/api/v1/monitorresult/?offset=1&limit=1&format=json" @@ -92,44 +92,44 @@ Torrent Server response "status": "Completed", "processedflows": 0, "libmetrics": { - "i100Q20_reads": 61016174, - "aveKeyCounts": 89.0, - "id": 41874, + "i100Q20_reads": 63353502, + "aveKeyCounts": 84, + "id": 52457, "resource_uri": "", - "q20_mean_alignment_length": 159 + "q20_mean_alignment_length": 180 }, - "timeStamp": "2014-06-28T07:11:58.000789+00:00", + "timeStamp": "2015-02-03T02:21:07.000963+00:00", "analysismetrics": { - "ignored": 1364892, - "lib": 118063544, + "ignored": 1416707, + "lib": 122792563, "total_wells": 164699136, - "pinned": 463867, - "live": 118074386, + "pinned": 345310, + "live": 122796187, "excluded": 16095180, - "bead": 118525043, + "bead": 123099544, "resource_uri": "", - "id": 41726, - "empty": 28250154, - "libFinal": 85604279 + "id": 54528, + "empty": 23742395, + "libFinal": 85173747 }, - "reportLink": "/output/Home/Auto_user_Z28-428--r65714-pou4_dbsa_23958_304393/", + "reportLink": "/output/Home/Auto_user_F3--909--R78811-mosaic1tru4_1xot2_na12878_1400Mmol_4chips-co_33084_317423/", "library": "hg19", - "id": 304393, + "id": 317423, "reportStatus": "Nothing", "experiment": { "ftpStatus": "Complete", "chipInstrumentType": "proton", - "displayName": "user Z28-428--r65714-pou4 dbsa", + "displayName": "user F3--909--R78811-mosaic1tru4 1xot2 na12878 1400Mmol 4chips-co", "chipType": "P1.1.17", - "notes": "", + "notes": "mosaic 1 ot 4 chips 1400M molecules", "chipDescription": "PI", - "resultDate": "2014-06-28T07:11:58.000789+00:00", + "resultDate": "2015-02-03T02:21:07.000963+00:00", "flows": 520, "runMode": "single", - "expName": "R_2014_06_27_17_13_22_user_Z28-428--r65714-pou4_dbsa", + "expName": "R_2015_02_02_13_18_20_user_F3--909--R78811-mosaic1tru4_1xot2_na12878_1400Mmol_4chips-co", "storage_options": "D", - "pgmName": "Z28", - "date": "2014-06-27T21:19:01+00:00", + "pgmName": "f3", + "date": "2015-02-02T18:23:59+00:00", "star": false, "resource_uri": "", "qcThresholds": { @@ -137,30 +137,30 @@ Torrent Server response "Usable Sequence (%)": 30, "Bead Loading (%)": 30 }, - "id": 23958, + "id": 33084, "plan": { - "runType": "AMPS_EXOME", - "id": 102195, + "runType": "WGNM", + "id": 111321, "resource_uri": "" } }, - "resultsName": "Auto_user_Z28-428--r65714-pou4_dbsa_23958", + "resultsName": "Auto_user_F3--909--R78811-mosaic1tru4_1xot2_na12878_1400Mmol_4chips-co_33084", "projects": [ { "resource_uri": "", - "id": 1385, - "name": "auto_chip", - "modified": "2014-06-27T21:21:43.000081+00:00" + "id": 1622, + "name": "mosaic_enterprise", + "modified": "2015-02-02T18:26:29.000916+00:00" } ], "qualitymetrics": { - "q0_mean_read_length": 178.362197969099, - "q0_reads": 85604279, - "q0_bases": "15268567358", - "q20_reads": 85604279, - "q20_bases": "13060288783", - "q20_mean_read_length": 178, - "id": 39683, + "q0_mean_read_length": 203.07748070541, + "q0_reads": 85173747, + "q0_bases": "17296869963", + "q20_reads": 85173747, + "q20_bases": "15168226464", + "q20_mean_read_length": 203, + "id": 50272, "resource_uri": "" }, "eas": { @@ -168,7 +168,7 @@ Torrent Server response "reference": "hg19", "barcodeKitName": "IonXpress" }, - "resource_uri": "/rundb/api/v1/monitorresult/304393/", + "resource_uri": "/rundb/api/v1/monitorresult/317423/", "barcodeId": "IonXpress", "autoExempt": false, "representative": false diff --git a/source/auto_api_ref_docs/obsoletereferencegenome.rst b/source/auto_api_ref_docs/obsoletereferencegenome.rst index 3fb1f97..2e43a32 100644 --- a/source/auto_api_ref_docs/obsoletereferencegenome.rst +++ b/source/auto_api_ref_docs/obsoletereferencegenome.rst @@ -39,7 +39,7 @@ field help text default ------------------ ---------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- **celery_task_id** Unicode string data. Ex: "Hello World" false false true false string ------------------ ---------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- -**date** A date & time as a string. Ex: "2010-11-10T03:07:43" 2014-06-28T14:03:44.000226+00:00 false false false false datetime +**date** A date & time as a string. Ex: "2010-11-10T03:07:43" 2015-02-03T02:29:30.000916+00:00 false false false false datetime ------------------ ---------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- **verbose_error** Unicode string data. Ex: "Hello World" false false true false string ------------------ ---------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- diff --git a/source/auto_api_ref_docs/onetouchplantemplate.rst b/source/auto_api_ref_docs/onetouchplantemplate.rst index 4ae2fd8..0e8ece4 100644 --- a/source/auto_api_ref_docs/onetouchplantemplate.rst +++ b/source/auto_api_ref_docs/onetouchplantemplate.rst @@ -43,6 +43,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sequencekitname** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**base_recalibration_mode** Unicode string data. Ex: "Hello World" true false true false string +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **storageHost** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string @@ -55,7 +57,7 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipType** Unicode string data. Ex: "Hello World" false false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**chefProgress** Floating point numeric data. Ex: 26.73 0 false false true false float --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **library** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -67,7 +69,7 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **barcodeId** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string +**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -93,8 +95,6 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **forward3primeadapter** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ---------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **applicationGroupDisplayedName** Unicode string data. Ex: "Hello World" n/a true true true false string @@ -125,6 +125,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chefMessage** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **childPlans** A list of data. Ex: ['abc', 26.73, 8] [] false false false false list --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -139,6 +141,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePostBeadfind** Boolean data. Ex: True false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planGUID** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -183,8 +187,6 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleGrouping** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**base_recalibrate** Boolean data. Ex: True n/a false false false false boolean ---------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -224,14 +226,14 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 58, + "total_count": 111, "offset": 0, "limit": 1, "next": "/rundb/api/v1/onetouchplantemplate/?offset=1&limit=1&format=json" }, "objects": [ { - "planDisplayedName": "chef_nonGUI_Exome Panel_AmpliSeqExome.20131001", + "planDisplayedName": "Ceph_RnD_IC_PIv2", "autoAnalyze": true, "templatingKitBarcode": null, "preAnalysis": true, @@ -241,13 +243,14 @@ Torrent Server response "platform": "", "categories": "", "planPGM": null, - "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --calibration-training=100000 --flow-signals-type scaled-residual --max-phasing-levels 2", + "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --max-phasing-levels 2", "alignmentargs": "stage1 map4", - "thumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", + "thumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", "sampleSet_planTotal": 0, "projects": [], - "notes": "Uploaded from amplseq.com and available at-jira.itw_wiki_x_HAHcAg\r\nReplace _ with slashes for link to Document collection on JIRA\r\nAdded AmpliseqExome.germline_lowstringency_p1.4_0.20130920.parameters.json parameter file.", - "sequencekitname": "ProtonIIC200Kit", + "notes": "", + "sequencekitname": "IonProtonIHiQ", + "base_recalibration_mode": "standard_recal", "storageHost": null, "expName": "", "cycles": null, @@ -255,40 +258,39 @@ Torrent Server response "storage_options": "A", "thumbnailalignmentargs": "stage1 map4", "chipType": "P1.1.17", - "chefProgress": 0.0, + "chefProgress": 0, "library": "hg19", "reverselibrarykey": "", "sampleTubeLabel": "", "seqKitBarcode": null, - "barcodeId": "IonXpress", + "barcodeId": "", "chefLogPath": null, "isPlanGroup": false, "realign": false, "sampleGroupingName": "", - "experiment": "/rundb/api/v1/experiment/21987/", - "bedfile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed", + "experiment": "/rundb/api/v1/experiment/32900/", + "bedfile": "", "isReusable": true, - "isDuplicateReads": false, + "isDuplicateReads": true, "thumbnailbeadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=100,100 --beadfind-thumbnail 1", - "librarykitname": "Ion AmpliSeq 2.0 Library Kit", + "librarykitname": "Ion Xpress Plus Fragment Library Kit", "adapter": null, - "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1", + "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1", "tfKey": "ATCG", "parentPlan": null, "forward3primeadapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC", "planStatus": "planned", - "chefLastUpdate": null, - "samplePrepKitName": "Ion AmpliSeq Exome Kit", + "samplePrepKitName": "", "applicationGroupDisplayedName": "DNA", "metaData": {}, "sampleSet_uid": null, - "isFavorite": true, + "isFavorite": false, "sampleSet_planIndex": 0, "qcValues": [ { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/100224/", - "id": 262674, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111137/", + "id": 289263, "qcType": { "description": "", "minThreshold": 0, @@ -298,12 +300,12 @@ Torrent Server response "id": 3, "resource_uri": "/rundb/api/v1/qctype/3/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/262674/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289263/" }, { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/100224/", - "id": 262673, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111137/", + "id": 289262, "qcType": { "description": "", "minThreshold": 1, @@ -313,12 +315,12 @@ Torrent Server response "id": 2, "resource_uri": "/rundb/api/v1/qctype/2/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/262673/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289262/" }, { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/100224/", - "id": 262672, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111137/", + "id": 289261, "qcType": { "description": "", "minThreshold": 0, @@ -328,19 +330,20 @@ Torrent Server response "id": 1, "resource_uri": "/rundb/api/v1/qctype/1/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/262672/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289261/" } ], "analysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=216,224 --bkg-bfmask-update false --gpuWorkLoad 1 --total-timeout 600 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json", "thumbnailcalibrateargs": "calibrate --skipDroop", - "templatingKitName": "Ion PI Template OT2 200 Kit v3", - "runType": "AMPS_EXOME", - "username": "ionuser", - "planName": "chef_nonGUI_Exome_Panel_AmpliSeqExome.20131001", + "templatingKitName": "Ion PI Hi-Q OT2 200 Kit", + "runType": "WGNM", + "username": "ionadmin", + "planName": "Ceph_RnD_IC_PIv2", "sampleDisplayedName": "", - "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000 --calibration-training=100000 --flow-signals-type scaled-residual", + "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", "controlSequencekitname": "", "chefMessage": "", + "templatingSize": "", "childPlans": [], "pairedEndLibraryAdapterName": "", "runMode": "single", @@ -348,14 +351,15 @@ Torrent Server response "planExecuted": false, "project": "", "usePostBeadfind": false, + "libraryReadLength": 0, "runname": null, - "planGUID": "a81c02b6-e8f7-411f-aeeb-302fa16baa51", - "planShortID": "2OXYZ", + "planGUID": "f35c5c0d-f01a-405c-9049-8139b2f26a13", + "planShortID": "8SJUE", "sampleSetGroupType": null, "sample": "", "planExecutedDate": null, "reverse_primer": null, - "id": 100224, + "id": 111137, "barcodedSamples": {}, "regionfile": "", "selectedPlugins": { @@ -365,111 +369,19 @@ Torrent Server response "userInputInfo": "", "accountId": "0" }, - "version": "4.1-r87449", + "version": "4.4.0.2", "features": [ "export" ], "name": "IonReporterUploader", - "id": 804 + "id": 993 }, - "coverageAnalysis": { + "duplicateReads_useZC": { "userInput": "", - "version": "4.2-r86949", - "features": [], - "name": "coverageAnalysis", - "id": 800 - }, - "variantCaller": { - "userInput": { - "torrent_variant_caller": { - "snp_min_allele_freq": "0.10000000000000001", - "snp_strand_bias": "0.97999999999999998", - "hotspot_min_coverage": 6, - "hotspot_min_cov_each_strand": 3, - "hotspot_min_allele_freq": "0.10000000000000001", - "snp_min_variant_score": 15, - "hotspot_strand_bias": "0.94999999999999996", - "hp_max_length": 8, - "filter_insertion_predictions": "0.20000000000000001", - "indel_min_variant_score": 20, - "indel_min_coverage": 10, - "heavy_tailed": 3, - "outlier_probability": "0.01", - "data_quality_stringency": 5, - "snp_min_cov_each_strand": 0, - "hotspot_min_variant_score": 10, - "indel_strand_bias": "0.90000000000000002", - "tvc_parameters_version": "germline_low_stringency_proton-3.6.66827", - "downsample_to_coverage": 400, - "filter_unusual_predictions": "0.25", - "indel_min_allele_freq": "0.14999999999999999", - "do_snp_realignment": 1, - "prediction_precision": 1, - "indel_min_cov_each_strand": 5, - "filter_deletion_predictions": "0.20000000000000001", - "suppress_recalibration": 0, - "snp_min_coverage": 5 - }, - "meta": { - "repository_id": "", - "ts_version": "4.0", - "name": "External file AmpliseqExome.germline_lowstringency_p1.4_0.20130920.parameters.json", - "user_selections": { - "chip": "proton_p1", - "frequency": "germline", - "library": "ampliseq", - "panel": "/rundb/api/v1/contentupload/53/" - }, - "librarytype": "ampliseq", - "trimreads": true, - "tooltip": "Retrieved from external file", - "tvcargs": "tvc", - "built_in": false, - "configuration": "", - "compatibility": {} - }, - "long_indel_assembler": { - "min_indel_size": 4, - "short_suffix_match": 5, - "output_mnv": 0, - "min_var_count": 5, - "min_var_freq": "0.14999999999999999", - "kmer_len": 19, - "max_hp_length": 8, - "relative_strand_bias": "0.80000000000000004" - }, - "freebayes": { - "gen_min_coverage": 5, - "allow_mnps": 1, - "allow_complex": 0, - "read_max_mismatch_fraction": 1, - "read_mismatch_limit": 10, - "allow_indels": 1, - "min_mapping_qv": 4, - "gen_min_alt_allele_freq": "0.10000000000000001", - "allow_snps": 1, - "gen_min_indel_alt_allele_freq": "0.14999999999999999" - } - }, - "version": "4.1-r74477", - "features": [], - "name": "variantCaller", - "id": 698 - }, - "validateVariantCaller": { - "userInput": { - "variant_caller_name": "variantCaller", - "truth_major_snp": "NA12878_NIST_NoChrY_SNP.bed", - "region": "NIST", - "sample": "NA12878", - "truth_minor_snp": "None", - "truth_major_indel": "NA12878_NIST_NoChrY_indel.bed", - "truth_minor_indel": "None" - }, - "version": "0.2.1", + "version": "1.0.0", "features": [], - "name": "validateVariantCaller", - "id": 732 + "name": "duplicateReads_useZC", + "id": 429 } }, "beadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=216,224 --total-timeout 600", @@ -479,17 +391,16 @@ Torrent Server response "libraryKey": "TCAG", "flows": 520, "thumbnailanalysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=100,100 --bkg-bfmask-update false --gpuWorkLoad 1 --bkg-debug-param 1 --beadfind-thumbnail 1 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json", - "date": "2014-05-20T13:55:02.000398+00:00", + "date": "2015-01-28T18:37:09.000403+00:00", "isSystem": false, "variantfrequency": "", "sampleSetDisplayedName": "", "calibrateargs": "calibrate --skipDroop", "flowsInOrder": "", "sampleGrouping": null, - "base_recalibrate": true, "chipBarcode": null, "usePreBeadfind": true, - "resource_uri": "/rundb/api/v1/onetouchplantemplate/100224/", + "resource_uri": "/rundb/api/v1/onetouchplantemplate/111137/", "reverse3primeadapter": "" } ] diff --git a/source/auto_api_ref_docs/onetouchplantemplatesummary.rst b/source/auto_api_ref_docs/onetouchplantemplatesummary.rst index 303967c..0b4b770 100644 --- a/source/auto_api_ref_docs/onetouchplantemplatesummary.rst +++ b/source/auto_api_ref_docs/onetouchplantemplatesummary.rst @@ -23,13 +23,11 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **preAnalysis** Boolean data. Ex: True false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**isSystemDefault** Boolean data. Ex: True false false false true false boolean -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planShortID** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planStatus** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime +**runMode** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **templatingKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -37,8 +35,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planExecutedDate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefStatus** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **reverse_primer** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -55,8 +51,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planIndex** Integer data. Ex: 2673 0 false false false false integer ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planTotal** Integer data. Ex: 2673 0 false false false false integer @@ -67,7 +61,7 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planPGM** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**isSystemDefault** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **autoName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -85,12 +79,10 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefMessage** Unicode string data. Ex: "Hello World" false false true false string +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **adapter** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **irworkflow** Unicode string data. Ex: "Hello World" false false true false string @@ -107,6 +99,8 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -148,7 +142,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 58, + "total_count": 111, "offset": 0, "limit": 1, "next": "/rundb/api/v1/onetouchplantemplatesummary/?offset=1&limit=1&format=json" @@ -156,56 +150,53 @@ Torrent Server response "objects": [ { "isReverseRun": false, - "planDisplayedName": "chef_nonGUI_Exome Panel_AmpliSeqExome.20131001", + "planDisplayedName": "Ceph_RnD_IC_PIv2", "storage_options": "A", "preAnalysis": true, - "isSystemDefault": false, - "planShortID": "2OXYZ", + "planShortID": "8SJUE", "planStatus": "planned", - "chefLastUpdate": null, + "runMode": "single", "templatingKitBarcode": null, "sampleTubeLabel": "", "planExecutedDate": null, - "chefStatus": "", - "samplePrepKitName": "Ion AmpliSeq Exome Kit", + "samplePrepKitName": "", "reverse_primer": null, "seqKitBarcode": null, - "id": 100224, + "id": 111137, "metaData": {}, "sampleSet_uid": null, - "isFavorite": true, + "isFavorite": false, "sampleSet_planIndex": 0, - "chefLogPath": null, "isPlanGroup": false, "sampleSet_planTotal": 0, - "templatingKitName": "Ion PI Template OT2 200 Kit v3", - "runType": "AMPS_EXOME", + "templatingKitName": "Ion PI Hi-Q OT2 200 Kit", + "runType": "WGNM", "planPGM": null, - "chefProgress": 0.0, + "isSystemDefault": false, "autoName": null, "isReusable": true, "controlSequencekitname": "", - "date": "2014-05-20T13:55:02.000398+00:00", + "date": "2015-01-28T18:37:09.000403+00:00", "isSystem": false, "libkit": null, "categories": "", - "planName": "chef_nonGUI_Exome_Panel_AmpliSeqExome.20131001", - "chefMessage": "", + "planName": "Ceph_RnD_IC_PIv2", + "templatingSize": "", "pairedEndLibraryAdapterName": "", - "runMode": "single", "adapter": null, "irworkflow": "", "chipBarcode": null, "planExecuted": false, - "username": "ionuser", + "username": "ionadmin", "usePostBeadfind": false, "storageHost": null, "expName": "", + "libraryReadLength": 0, "runname": null, "usePreBeadfind": true, - "planGUID": "a81c02b6-e8f7-411f-aeeb-302fa16baa51", + "planGUID": "f35c5c0d-f01a-405c-9049-8139b2f26a13", "cycles": null, - "resource_uri": "/rundb/api/v1/onetouchplantemplatesummary/100224/" + "resource_uri": "/rundb/api/v1/onetouchplantemplatesummary/111137/" } ] } diff --git a/source/auto_api_ref_docs/plannedexperiment.rst b/source/auto_api_ref_docs/plannedexperiment.rst index 56d07e4..ca2680a 100644 --- a/source/auto_api_ref_docs/plannedexperiment.rst +++ b/source/auto_api_ref_docs/plannedexperiment.rst @@ -43,6 +43,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sequencekitname** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**base_recalibration_mode** Unicode string data. Ex: "Hello World" true false true false string +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **storageHost** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string @@ -55,7 +57,7 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipType** Unicode string data. Ex: "Hello World" false false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**chefProgress** Floating point numeric data. Ex: 26.73 0 false false true false float --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **library** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -67,7 +69,7 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **barcodeId** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string +**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -93,8 +95,6 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **forward3primeadapter** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ---------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **applicationGroupDisplayedName** Unicode string data. Ex: "Hello World" n/a true true true false string @@ -125,6 +125,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chefMessage** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **childPlans** A list of data. Ex: ['abc', 26.73, 8] [] false false false false list --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -139,6 +141,8 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePostBeadfind** Boolean data. Ex: True false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +--------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planGUID** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -183,8 +187,6 @@ field help text --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleGrouping** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**base_recalibrate** Boolean data. Ex: True n/a false false false false boolean ---------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -224,15 +226,15 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 18369, + "total_count": 24558, "offset": 0, "limit": 1, "next": "/rundb/api/v1/plannedexperiment/?offset=1&limit=1&format=json" }, "objects": [ { - "planDisplayedName": "CopyOfSystemDefault_R_2014_06_27_14_19_01_user_P19-606", - "autoAnalyze": true, + "planDisplayedName": "CopyOfSystemDefault_R_2015_02_02_17_43_41_user_GT1-126", + "autoAnalyze": false, "templatingKitBarcode": null, "preAnalysis": true, "chefStatus": "", @@ -241,21 +243,22 @@ Torrent Server response "platform": "PROTON", "categories": "", "planPGM": null, - "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --calibration-training=100000 --flow-signals-type scaled-residual", + "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --disable-all-filters on --phasing-residual-filter=2.0 --num-unfiltered 1000", "alignmentargs": "stage1 map4", - "thumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", + "thumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --barcode-bam-tag --disable-all-filters on --phasing-residual-filter=2.0 --num-unfiltered 100000", "sampleSet_planTotal": 0, "projects": [], "notes": "", "sequencekitname": "ProtonI200Kit-v3", + "base_recalibration_mode": "standard_recal", "storageHost": null, - "expName": "R_2014_06_27_14_19_01_user_P19-606", + "expName": "R_2015_02_02_17_43_41_user_GT1-126", "cycles": null, "isReverseRun": false, "storage_options": "A", "thumbnailalignmentargs": "stage1 map4", - "chipType": "P1.0.20", - "chefProgress": 0.0, + "chipType": "P2.2.1", + "chefProgress": 0, "library": "hg19", "reverselibrarykey": "", "sampleTubeLabel": null, @@ -265,19 +268,18 @@ Torrent Server response "isPlanGroup": false, "realign": false, "sampleGroupingName": "", - "experiment": "/rundb/api/v1/experiment/23975/", + "experiment": "/rundb/api/v1/experiment/33090/", "bedfile": "", "isReusable": false, "isDuplicateReads": false, - "thumbnailbeadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=50,50 --beadfind-thumbnail 1 --bkg-use-proton-well-correction false --bkg-exp-tail-fit false --bkg-pca-dark-matter true", + "thumbnailbeadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=100,100 --beadfind-thumbnail 1 --beadfind-diagnostics 2", "librarykitname": "Ion Xpress Plus Fragment Library Kit", "adapter": null, - "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1", + "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --disable-all-filters on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1 --barcode-bam-tag", "tfKey": "ATCG", "parentPlan": null, "forward3primeadapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC", "planStatus": "run", - "chefLastUpdate": null, "samplePrepKitName": null, "applicationGroupDisplayedName": "DNA", "metaData": {}, @@ -287,8 +289,8 @@ Torrent Server response "qcValues": [ { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102212/", - "id": 266571, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111327/", + "id": 289776, "qcType": { "description": "", "minThreshold": 0, @@ -298,12 +300,12 @@ Torrent Server response "id": 1, "resource_uri": "/rundb/api/v1/qctype/1/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266571/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289776/" }, { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102212/", - "id": 266570, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111327/", + "id": 289775, "qcType": { "description": "", "minThreshold": 1, @@ -313,12 +315,12 @@ Torrent Server response "id": 2, "resource_uri": "/rundb/api/v1/qctype/2/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266570/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289775/" }, { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102212/", - "id": 266569, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111327/", + "id": 289774, "qcType": { "description": "", "minThreshold": 0, @@ -328,19 +330,20 @@ Torrent Server response "id": 3, "resource_uri": "/rundb/api/v1/qctype/3/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266569/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289774/" } ], - "analysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=80,112 --bkg-bfmask-update false --gpuWorkLoad 1 --total-timeout 600 --bkg-use-proton-well-correction false --bkg-exp-tail-fit false --bkg-pca-dark-matter true", + "analysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel false --region-size=216,224 --bkg-bfmask-update false --gpuWorkLoad 1 --total-timeout 600 --bkg-well-xtalk-name /opt/ion/config/xtalk.p2.2.1.settings.20140120.json", "thumbnailcalibrateargs": "calibrate --skipDroop", "templatingKitName": "Ion PI Template OT2 200 Kit v3", "runType": "GENS", "username": null, - "planName": "CopyOfSystemDefault_R_2014_06_27_14_19_01_user_P19-606", + "planName": "CopyOfSystemDefault_R_2015_02_02_17_43_41_user_GT1-126", "sampleDisplayedName": "", - "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000 --calibration-training=100000 --flow-signals-type scaled-residual", + "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --disable-all-filters on --phasing-residual-filter=2.0 --num-unfiltered 100000", "controlSequencekitname": null, "chefMessage": "", + "templatingSize": "", "childPlans": [], "pairedEndLibraryAdapterName": null, "runMode": "single", @@ -348,35 +351,35 @@ Torrent Server response "planExecuted": true, "project": "", "usePostBeadfind": false, + "libraryReadLength": 0, "runname": null, - "planGUID": "80384c15-e0e2-4909-9d4c-950731bf1cf4", - "planShortID": "G5B50", + "planGUID": "8aad7839-ccf2-46c2-9158-4f76b8b6d491", + "planShortID": "G76FR", "sampleSetGroupType": null, "sample": "", "planExecutedDate": null, "reverse_primer": null, - "id": 102212, + "id": 111327, "barcodedSamples": {}, "regionfile": "", "selectedPlugins": {}, - "beadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=80,112 --total-timeout 600 --bkg-use-proton-well-correction false --bkg-exp-tail-fit false --bkg-pca-dark-matter true", + "beadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=216,224 --total-timeout 600", "sampleSet": null, "isSystemDefault": false, "autoName": null, "libraryKey": "TCAG", - "flows": 260, - "thumbnailanalysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=50,50 --bkg-bfmask-update false --gpuWorkLoad 1 --bkg-debug-param 1 --beadfind-thumbnail 1 --bkg-use-proton-well-correction false --bkg-exp-tail-fit false --bkg-pca-dark-matter true", - "date": "2014-06-27T23:36:06.000229+00:00", + "flows": 60, + "thumbnailanalysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel false --region-size=100,100 --bkg-bfmask-update false --gpuWorkLoad 1 --bkg-debug-param 0 --beadfind-thumbnail 1 --bkg-debug-files --bkg-well-xtalk-name /opt/ion/config/xtalk.p2.2.1.settings.20140120.json", + "date": "2015-02-02T22:44:33.000729+00:00", "isSystem": false, "variantfrequency": "", "sampleSetDisplayedName": "", "calibrateargs": "calibrate --skipDroop", "flowsInOrder": "TACGTACGTCTGAGCATCGATCGATGTACAGC", "sampleGrouping": null, - "base_recalibrate": true, "chipBarcode": null, "usePreBeadfind": true, - "resource_uri": "/rundb/api/v1/plannedexperiment/102212/", + "resource_uri": "/rundb/api/v1/plannedexperiment/111327/", "reverse3primeadapter": "" } ] diff --git a/source/auto_api_ref_docs/plannedexperimentdb.rst b/source/auto_api_ref_docs/plannedexperimentdb.rst index 0663209..21f1d06 100644 --- a/source/auto_api_ref_docs/plannedexperimentdb.rst +++ b/source/auto_api_ref_docs/plannedexperimentdb.rst @@ -23,15 +23,13 @@ field help text ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **preAnalysis** Boolean data. Ex: True false false true false boolean ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**isSystemDefault** Boolean data. Ex: True false false false true false boolean +**planShortID** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **username** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**planShortID** Unicode string data. Ex: "Hello World" n/a true false false false string -------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planStatus** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime +**runMode** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **templatingKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -39,8 +37,6 @@ field help text ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planExecutedDate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefStatus** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **reverse_primer** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -61,8 +57,6 @@ field help text ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **qcValues** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a true false true false related ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string -------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planTotal** Integer data. Ex: 2673 0 false false false false integer @@ -77,7 +71,7 @@ field help text ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planPGM** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**isSystemDefault** Boolean data. Ex: True false false false true false boolean ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **autoName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -95,7 +89,7 @@ field help text ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefMessage** Unicode string data. Ex: "Hello World" false false true false string +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **parentPlan** Unicode string data. Ex: "Hello World" None false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -105,12 +99,10 @@ field help text ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string +**sampleGrouping** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **adapter** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**sampleGrouping** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related -------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **irworkflow** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -125,6 +117,8 @@ field help text ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -166,7 +160,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 18369, + "total_count": 24558, "offset": 0, "limit": 1, "next": "/rundb/api/v1/plannedexperimentdb/?offset=1&limit=1&format=json" @@ -174,23 +168,21 @@ Torrent Server response "objects": [ { "isReverseRun": false, - "planDisplayedName": "CopyOfSystemDefault_R_2014_06_27_14_19_01_user_P19-606", + "planDisplayedName": "CopyOfSystemDefault_R_2015_02_02_17_43_41_user_GT1-126", "storage_options": "A", "preAnalysis": true, - "isSystemDefault": false, + "planShortID": "G76FR", "username": null, - "planShortID": "G5B50", "planStatus": "run", - "chefLastUpdate": null, + "runMode": "single", "templatingKitBarcode": null, "sampleTubeLabel": null, "planExecutedDate": null, - "chefStatus": "", "samplePrepKitName": null, "reverse_primer": null, "applicationGroup": "/rundb/api/v1/applicationgroup/1/", "seqKitBarcode": null, - "id": 102212, + "id": 111327, "metaData": {}, "sampleSet_uid": null, "isFavorite": false, @@ -198,8 +190,8 @@ Torrent Server response "qcValues": [ { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102212/", - "id": 266571, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111327/", + "id": 289776, "qcType": { "description": "", "minThreshold": 0, @@ -209,12 +201,12 @@ Torrent Server response "id": 1, "resource_uri": "/rundb/api/v1/qctype/1/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266571/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289776/" }, { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102212/", - "id": 266570, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111327/", + "id": 289775, "qcType": { "description": "", "minThreshold": 1, @@ -224,12 +216,12 @@ Torrent Server response "id": 2, "resource_uri": "/rundb/api/v1/qctype/2/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266570/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289775/" }, { "threshold": 30, - "plannedExperiment": "/rundb/api/v1/plannedexperiment/102212/", - "id": 266569, + "plannedExperiment": "/rundb/api/v1/plannedexperiment/111327/", + "id": 289774, "qcType": { "description": "", "minThreshold": 0, @@ -239,46 +231,45 @@ Torrent Server response "id": 3, "resource_uri": "/rundb/api/v1/qctype/3/" }, - "resource_uri": "/rundb/api/v1/plannedexperimentqc/266569/" + "resource_uri": "/rundb/api/v1/plannedexperimentqc/289774/" } ], - "chefLogPath": null, "isPlanGroup": false, "sampleSet_planTotal": 0, - "experiment": "/rundb/api/v1/experiment/23975/", + "experiment": "/rundb/api/v1/experiment/33090/", "projects": [], "runType": "GENS", "sampleSet": null, "planPGM": null, - "chefProgress": 0.0, + "isSystemDefault": false, "autoName": null, "isReusable": false, "controlSequencekitname": null, - "date": "2014-06-27T23:36:06.000229+00:00", + "date": "2015-02-02T22:44:33.000729+00:00", "isSystem": false, "libkit": null, "categories": "", - "planName": "CopyOfSystemDefault_R_2014_06_27_14_19_01_user_P19-606", - "chefMessage": "", + "planName": "CopyOfSystemDefault_R_2015_02_02_17_43_41_user_GT1-126", + "templatingSize": "", "parentPlan": null, "childPlans": [], "templatingKitName": "Ion PI Template OT2 200 Kit v3", "pairedEndLibraryAdapterName": null, - "runMode": "single", - "adapter": null, "sampleGrouping": null, + "adapter": null, "irworkflow": "", "chipBarcode": null, "planExecuted": true, "project": "", "usePostBeadfind": false, "storageHost": null, - "expName": "R_2014_06_27_14_19_01_user_P19-606", + "expName": "R_2015_02_02_17_43_41_user_GT1-126", + "libraryReadLength": 0, "runname": null, "usePreBeadfind": true, - "planGUID": "80384c15-e0e2-4909-9d4c-950731bf1cf4", + "planGUID": "8aad7839-ccf2-46c2-9158-4f76b8b6d491", "cycles": null, - "resource_uri": "/rundb/api/v1/plannedexperimentdb/102212/" + "resource_uri": "/rundb/api/v1/plannedexperimentdb/111327/" } ] } diff --git a/source/auto_api_ref_docs/plannedexperimentqc.rst b/source/auto_api_ref_docs/plannedexperimentqc.rst index 0cab574..abaaa0b 100644 --- a/source/auto_api_ref_docs/plannedexperimentqc.rst +++ b/source/auto_api_ref_docs/plannedexperimentqc.rst @@ -56,7 +56,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 22524, + "total_count": 41067, "offset": 0, "limit": 1, "next": "/rundb/api/v1/plannedexperimentqc/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/plantemplatebasicinfo.rst b/source/auto_api_ref_docs/plantemplatebasicinfo.rst index d638daa..d7ed529 100644 --- a/source/auto_api_ref_docs/plantemplatebasicinfo.rst +++ b/source/auto_api_ref_docs/plantemplatebasicinfo.rst @@ -15,6 +15,8 @@ Fields table ================================= ============================================================================== ======= ======== ======== ===== ====== ======== field help text default nullable readonly blank unique type ================================= ============================================================================== ======= ======== ======== ===== ====== ======== +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +--------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **isReverseRun** Boolean data. Ex: True false false false true false boolean --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **planDisplayedName** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -25,15 +27,13 @@ field help text --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **reference** Unicode string data. Ex: "Hello World" true true true false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- -**isSystemDefault** Boolean data. Ex: True false false false true false boolean +**planShortID** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **hotSpotRegionBedFile** Unicode string data. Ex: "Hello World" true true true false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- -**planShortID** Unicode string data. Ex: "Hello World" n/a true false false false string ---------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **planStatus** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime +**runMode** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **templatingKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- @@ -41,8 +41,6 @@ field help text --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **planExecutedDate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- -**chefStatus** Unicode string data. Ex: "Hello World" false false true false string ---------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **reverse_primer** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -63,8 +61,6 @@ field help text --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **seqKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string ---------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **sampleGroupName** Unicode string data. Ex: "Hello World" n/a true true true false string @@ -77,7 +73,7 @@ field help text --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **planPGM** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**isSystemDefault** Boolean data. Ex: True false false false true false boolean --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **autoName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- @@ -85,12 +81,8 @@ field help text --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **controlSequencekitname** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- -**irAccountName** Unicode string data. Ex: "Hello World" n/a true true true false string ---------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **sequencingInstrumentType** Unicode string data. Ex: "Hello World" n/a true true true false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- -**targetRegionBedFile** Unicode string data. Ex: "Hello World" true true true false string ---------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **date** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **isSystem** Boolean data. Ex: True false false false true false boolean @@ -101,13 +93,13 @@ field help text --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **planName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- -**chefMessage** Unicode string data. Ex: "Hello World" false false true false string +**irAccountName** Unicode string data. Ex: "Hello World" n/a true true true false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **templatePrepInstrumentType** Unicode string data. Ex: "Hello World" n/a true true true false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string +**targetRegionBedFile** Unicode string data. Ex: "Hello World" true true true false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **adapter** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- @@ -125,6 +117,8 @@ field help text --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +--------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -170,60 +164,56 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 66, + "total_count": 129, "offset": 0, "limit": 1, "next": "/rundb/api/v1/plantemplatebasicinfo/?offset=1&limit=1&format=json" }, "objects": [ { + "templatingSize": "200", "isReverseRun": false, - "planDisplayedName": "chef_nonGUI_Exome Panel_AmpliSeqExome.20131001", + "planDisplayedName": "IC_P1v2_VAL_ccp", "storage_options": "A", "preAnalysis": true, "reference": "hg19", - "isSystemDefault": false, - "hotSpotRegionBedFile": "", - "planShortID": "2OXYZ", - "planStatus": "planned", - "chefLastUpdate": null, + "planShortID": "IL9TF", + "hotSpotRegionBedFile": "/results/uploads/BED/47/hg19/unmerged/detail/CCP.20131001.hotspots.bed", + "planStatus": "pending", + "runMode": "single", "templatingKitBarcode": null, "sampleTubeLabel": "", "planExecutedDate": null, - "chefStatus": "", - "samplePrepKitName": "Ion AmpliSeq Exome Kit", + "samplePrepKitName": "", "reverse_primer": null, "applicationGroup": "/rundb/api/v1/applicationgroup/1/", "applicationGroupDisplayedName": "DNA", - "id": 100224, + "id": 111154, "metaData": {}, "sampleSet_uid": null, "isFavorite": true, "sampleSet_planIndex": 0, "seqKitBarcode": null, - "chefLogPath": null, "isPlanGroup": false, "sampleGroupName": "", - "templatingKitName": "Ion PI Template OT2 200 Kit v3", + "templatingKitName": "Ion PROTON IC v2 Universal", "barcodeKitName": "IonXpress", - "runType": "AMPS_EXOME", + "runType": "AMPS", "planPGM": null, - "chefProgress": 0.0, + "isSystemDefault": false, "autoName": null, "isReusable": true, "controlSequencekitname": "", - "irAccountName": "None", "sequencingInstrumentType": "PROTON", - "targetRegionBedFile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed", - "date": "2014-05-20T13:55:02.000398+00:00", + "date": "2015-01-28T19:57:42.000445+00:00", "isSystem": false, "libkit": null, "categories": "", - "planName": "chef_nonGUI_Exome_Panel_AmpliSeqExome.20131001", - "chefMessage": "", - "templatePrepInstrumentType": "OneTouch", + "planName": "IC_P1v2_VAL_ccp", + "irAccountName": "None", + "templatePrepInstrumentType": "IonChef", "pairedEndLibraryAdapterName": "", - "runMode": "single", + "targetRegionBedFile": "/results/uploads/BED/44/hg19/unmerged/detail/CCP.20131001.designed.bed", "adapter": null, "irworkflow": "", "chipBarcode": null, @@ -232,13 +222,14 @@ Torrent Server response "usePostBeadfind": false, "storageHost": null, "expName": "", + "libraryReadLength": 200, "runname": null, "usePreBeadfind": true, - "planGUID": "a81c02b6-e8f7-411f-aeeb-302fa16baa51", + "planGUID": "b55face2-df5f-434c-89df-210f384170cb", "cycles": null, - "notes": "Uploaded from amplseq.com and available at-jira.itw_wiki_x_HAHcAg\r\nReplace _ with slashes for link to Document collection on JIRA\r\nAdded AmpliseqExome.germline_lowstringency_p1.4_0.20130920.parameters.json parameter file.", + "notes": "", "sampleSet_planTotal": 0, - "resource_uri": "/rundb/api/v1/plantemplatebasicinfo/100224/" + "resource_uri": "/rundb/api/v1/plantemplatebasicinfo/111154/" } ] } diff --git a/source/auto_api_ref_docs/plantemplatesummary.rst b/source/auto_api_ref_docs/plantemplatesummary.rst index 0363d91..0b67114 100644 --- a/source/auto_api_ref_docs/plantemplatesummary.rst +++ b/source/auto_api_ref_docs/plantemplatesummary.rst @@ -23,13 +23,11 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **preAnalysis** Boolean data. Ex: True false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**isSystemDefault** Boolean data. Ex: True false false false true false boolean -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planShortID** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planStatus** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime +**runMode** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **templatingKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -37,8 +35,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planExecutedDate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefStatus** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **reverse_primer** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -55,8 +51,6 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planIndex** Integer data. Ex: 2673 0 false false false false integer ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefLogPath** Unicode string data. Ex: "Hello World" n/a true false false false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planTotal** Integer data. Ex: 2673 0 false false false false integer @@ -67,7 +61,7 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planPGM** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefProgress** Floating point numeric data. Ex: 26.73 0.0 false false true false float +**isSystemDefault** Boolean data. Ex: True false false false true false boolean ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **autoName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- @@ -85,12 +79,10 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **planName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**chefMessage** Unicode string data. Ex: "Hello World" false false true false string +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **adapter** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **irworkflow** Unicode string data. Ex: "Hello World" false false true false string @@ -107,6 +99,8 @@ field help text ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string ------------------------------- ---------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean @@ -148,7 +142,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 66, + "total_count": 129, "offset": 0, "limit": 1, "next": "/rundb/api/v1/plantemplatesummary/?offset=1&limit=1&format=json" @@ -156,43 +150,39 @@ Torrent Server response "objects": [ { "isReverseRun": false, - "planDisplayedName": "chef_nonGUI_Exome Panel_AmpliSeqExome.20131001", + "planDisplayedName": "IC_P1v2_VAL_ccp", "storage_options": "A", "preAnalysis": true, - "isSystemDefault": false, - "planShortID": "2OXYZ", - "planStatus": "planned", - "chefLastUpdate": null, + "planShortID": "IL9TF", + "planStatus": "pending", + "runMode": "single", "templatingKitBarcode": null, "sampleTubeLabel": "", "planExecutedDate": null, - "chefStatus": "", - "samplePrepKitName": "Ion AmpliSeq Exome Kit", + "samplePrepKitName": "", "reverse_primer": null, "seqKitBarcode": null, - "id": 100224, + "id": 111154, "metaData": {}, "sampleSet_uid": null, "isFavorite": true, "sampleSet_planIndex": 0, - "chefLogPath": null, "isPlanGroup": false, "sampleSet_planTotal": 0, - "templatingKitName": "Ion PI Template OT2 200 Kit v3", - "runType": "AMPS_EXOME", + "templatingKitName": "Ion PROTON IC v2 Universal", + "runType": "AMPS", "planPGM": null, - "chefProgress": 0.0, + "isSystemDefault": false, "autoName": null, "isReusable": true, "controlSequencekitname": "", - "date": "2014-05-20T13:55:02.000398+00:00", + "date": "2015-01-28T19:57:42.000445+00:00", "isSystem": false, "libkit": null, "categories": "", - "planName": "chef_nonGUI_Exome_Panel_AmpliSeqExome.20131001", - "chefMessage": "", + "planName": "IC_P1v2_VAL_ccp", + "templatingSize": "200", "pairedEndLibraryAdapterName": "", - "runMode": "single", "adapter": null, "irworkflow": "", "chipBarcode": null, @@ -201,11 +191,12 @@ Torrent Server response "usePostBeadfind": false, "storageHost": null, "expName": "", + "libraryReadLength": 200, "runname": null, "usePreBeadfind": true, - "planGUID": "a81c02b6-e8f7-411f-aeeb-302fa16baa51", + "planGUID": "b55face2-df5f-434c-89df-210f384170cb", "cycles": null, - "resource_uri": "/rundb/api/v1/plantemplatesummary/100224/" + "resource_uri": "/rundb/api/v1/plantemplatesummary/111154/" } ] } diff --git a/source/auto_api_ref_docs/plugin.rst b/source/auto_api_ref_docs/plugin.rst index 4ae7c83..5c77fff 100644 --- a/source/auto_api_ref_docs/plugin.rst +++ b/source/auto_api_ref_docs/plugin.rst @@ -94,7 +94,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 102, + "total_count": 113, "offset": 0, "limit": 1, "next": "/rundb/api/v1/plugin/?offset=1&limit=1&format=json" @@ -102,17 +102,17 @@ Torrent Server response "objects": [ { "active": true, - "id": 493, + "id": 64, "isPlanConfig": false, "autorunMutable": true, "script": "launch.sh", - "selected": true, - "version": "0.2.0", + "selected": false, + "version": "0.2", "hasAbout": false, "input": "False", "majorBlock": false, "status": {}, - "description": "Ion Torrent Plugin - 'BarcodeAlignStats' v0.2.0", + "description": "Ion Torrent Plugin - 'bubbleRun' v0.2", "autorun": false, "pluginsettings": { "runtype": [ @@ -123,16 +123,16 @@ Torrent Server response "features": [], "runlevel": [] }, - "date": "2013-05-30T21:32:15.000437+00:00", - "path": "/results/plugins/BarcodeAlignStats", + "date": "2011-11-30T19:29:06.000945+00:00", + "path": "/results/plugins/bubbleRun", "isConfig": false, - "name": "BarcodeAlignStats", + "name": "bubbleRun", "userinputfields": {}, "url": "", "config": {}, - "versionedName": "BarcodeAlignStats--v0.2.0", + "versionedName": "bubbleRun--v0.2", "isInstance": false, - "resource_uri": "/rundb/api/v1/plugin/493/" + "resource_uri": "/rundb/api/v1/plugin/64/" } ] } diff --git a/source/auto_api_ref_docs/pluginresult.rst b/source/auto_api_ref_docs/pluginresult.rst index 5e6a9ed..78f104d 100644 --- a/source/auto_api_ref_docs/pluginresult.rst +++ b/source/auto_api_ref_docs/pluginresult.rst @@ -86,42 +86,33 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 788680, + "total_count": 1139160, "offset": 0, "limit": 1, "next": "/rundb/api/v1/pluginresult/?offset=1&limit=1&format=json" }, "objects": [ { - "size": "3484344", - "apikey": null, - "plugin": "/rundb/api/v1/plugin/823/", - "resultName": "Auto_user_Z28-428--r65714-pou4_dbsa_23958", - "reportLink": "/output/Home/Auto_user_Z28-428--r65714-pou4_dbsa_23958_304393/", - "pluginVersion": "4.2-r88266", - "jobid": 3145172, - "owner": "/rundb/api/v1/user/1/", - "pluginName": "AssemblerSPAdes", - "state": "Completed", - "result": "/rundb/api/v1/results/304393/", - "starttime": "2014-06-28T13:49:00.000133+00:00", - "duration": "0:01:54.098431", - "path": "/results/analysis/output/Home/Auto_user_Z28-428--r65714-pou4_dbsa_23958_304393/plugin_out/AssemblerSPAdes_out.815369", + "size": "-1", + "apikey": "8181ec3b22ee3629484f708729e6d8ca9ff2a2b2", + "plugin": "/rundb/api/v1/plugin/131/", + "resultName": "Auto_user_F3--909--R78811-mosaic1tru4_1xot2_na12878_1400Mmol_4chips-co_33084", + "reportLink": "/output/Home/Auto_user_F3--909--R78811-mosaic1tru4_1xot2_na12878_1400Mmol_4chips-co_33084_317423/", + "pluginVersion": "0.2", + "jobid": 4654296, + "owner": "/rundb/api/v1/user/2/", + "pluginName": "flowErr", + "state": "Started", + "result": "/rundb/api/v1/results/317423/", + "starttime": "2015-02-03T02:21:15.000116+00:00", + "duration": "0:08:36.532955", + "path": "/results/analysis/output/Home/Auto_user_F3--909--R78811-mosaic1tru4_1xot2_na12878_1400Mmol_4chips-co_33084_317423/plugin_out/flowErr_out.1171946", "store": {}, - "endtime": "2014-06-28T13:50:54.000232+00:00", - "config": { - "only_barcodes": "", - "spadesOptions": "-k 21,33,55,77,99", - "spadesversion": "3.1.0", - "RAM": "32G", - "min_reads": "500", - "bgenome": "None", - "runSpades": "1", - "fraction_of_reads": "1" - }, - "id": 815369, - "inodes": "396", - "resource_uri": "/rundb/api/v1/pluginresult/815369/" + "endtime": null, + "config": {}, + "id": 1171946, + "inodes": "-1", + "resource_uri": "/rundb/api/v1/pluginresult/1171946/" } ] } diff --git a/source/auto_api_ref_docs/project.rst b/source/auto_api_ref_docs/project.rst index 4f36365..5a737d7 100644 --- a/source/auto_api_ref_docs/project.rst +++ b/source/auto_api_ref_docs/project.rst @@ -12,27 +12,25 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/project/schema/`` Fields table ------------ -================ ================================================================================================== ======= ======== ======== ===== ====== ======== -field help text default nullable readonly blank unique type -================ ================================================================================================== ======= ======== ======== ===== ====== ======== -**name** Unicode string data. Ex: "Hello World" n/a false false false true string ----------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**creator** A single related resource. Can be either a URI or set of nested resource data. n/a false false false false related ----------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**created** A date & time as a string. Ex: "2010-11-10T03:07:43" true false false true false datetime ----------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**results** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a true false false false related ----------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**modified** A date & time as a string. Ex: "2010-11-10T03:07:43" true false false true false datetime ----------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**id** Integer data. Ex: 2673 false false true true integer ----------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**resultsCount** Integer data. Ex: 2673 n/a false true false false integer ----------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**public** Boolean data. Ex: True true false false true false boolean ----------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -================ ================================================================================================== ======= ======== ======== ===== ====== ======== +================ ============================================================================== ======= ======== ======== ===== ====== ======== +field help text default nullable readonly blank unique type +================ ============================================================================== ======= ======== ======== ===== ====== ======== +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +---------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- +**creator** A single related resource. Can be either a URI or set of nested resource data. n/a false false false false related +---------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- +**created** A date & time as a string. Ex: "2010-11-10T03:07:43" true false false true false datetime +---------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- +**modified** A date & time as a string. Ex: "2010-11-10T03:07:43" true false false true false datetime +---------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- +**id** Integer data. Ex: 2673 false false true true integer +---------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- +**resultsCount** Integer data. Ex: 2673 n/a false true false false integer +---------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- +**public** Boolean data. Ex: True true false false true false boolean +---------------- ------------------------------------------------------------------------------ ------- -------- -------- ----- ------ -------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +================ ============================================================================== ======= ======== ======== ===== ====== ======== Example request --------------- @@ -64,7 +62,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 1457, + "total_count": 1684, "offset": 0, "limit": 1, "next": "/rundb/api/v1/project/?offset=1&limit=1&format=json" @@ -74,32 +72,6 @@ Torrent Server response "name": "3gb_snapps", "creator": "/rundb/api/v1/user/2/", "created": "2012-07-03T15:14:33.000509+00:00", - "results": [ - "/rundb/api/v1/results/2305/", - "/rundb/api/v1/results/1499/", - "/rundb/api/v1/results/2304/", - "/rundb/api/v1/results/1511/", - "/rundb/api/v1/results/30467/", - "/rundb/api/v1/results/30458/", - "/rundb/api/v1/results/30457/", - "/rundb/api/v1/results/30490/", - "/rundb/api/v1/results/30464/", - "/rundb/api/v1/results/30459/", - "/rundb/api/v1/results/30460/", - "/rundb/api/v1/results/30496/", - "/rundb/api/v1/results/3298/", - "/rundb/api/v1/results/30463/", - "/rundb/api/v1/results/30446/", - "/rundb/api/v1/results/30489/", - "/rundb/api/v1/results/30466/", - "/rundb/api/v1/results/30456/", - "/rundb/api/v1/results/30491/", - "/rundb/api/v1/results/2609/", - "/rundb/api/v1/results/1466/", - "/rundb/api/v1/results/1498/", - "/rundb/api/v1/results/2300/", - "/rundb/api/v1/results/1497/" - ], "modified": "2012-07-03T15:14:33.000509+00:00", "id": 1, "resultsCount": 24, diff --git a/source/auto_api_ref_docs/projectresults.rst b/source/auto_api_ref_docs/projectresults.rst index 298ffbb..f1d1e04 100644 --- a/source/auto_api_ref_docs/projectresults.rst +++ b/source/auto_api_ref_docs/projectresults.rst @@ -98,7 +98,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 43354, + "total_count": 56103, "offset": 0, "limit": 1, "next": "/rundb/api/v1/projectresults/?offset=1&limit=1&format=json" @@ -121,47 +121,7 @@ Torrent Server response "tfSffLink": "/output/Home/Auto_user_D1--632--R54651-p8s2_827b2_20m_man-cf_17446_293943/R_2014_01_22_16_30_23_user_D1--632--R54651-p8s2_827b2_20m_man-cf_Auto_user_D1--632--R54651-p8s2_827b2_20m_man-cf_17446.tf.sff", "diskusage": 151, "projects": [ - { - "name": "chef_827_909_20min_ext", - "creator": "/rundb/api/v1/user/1/", - "created": "2014-01-22T18:50:10.000920+00:00", - "results": [ - "/rundb/api/v1/results/294145/", - "/rundb/api/v1/results/293993/", - "/rundb/api/v1/results/293992/", - "/rundb/api/v1/results/293991/", - "/rundb/api/v1/results/293990/", - "/rundb/api/v1/results/293946/", - "/rundb/api/v1/results/293945/", - "/rundb/api/v1/results/293944/", - "/rundb/api/v1/results/293943/", - "/rundb/api/v1/results/293934/", - "/rundb/api/v1/results/293933/", - "/rundb/api/v1/results/293930/", - "/rundb/api/v1/results/293929/", - "/rundb/api/v1/results/293928/", - "/rundb/api/v1/results/293927/", - "/rundb/api/v1/results/293917/", - "/rundb/api/v1/results/293916/", - "/rundb/api/v1/results/293915/", - "/rundb/api/v1/results/293914/", - "/rundb/api/v1/results/293913/", - "/rundb/api/v1/results/293912/", - "/rundb/api/v1/results/293908/", - "/rundb/api/v1/results/293907/", - "/rundb/api/v1/results/293906/", - "/rundb/api/v1/results/293905/", - "/rundb/api/v1/results/293904/", - "/rundb/api/v1/results/293903/", - "/rundb/api/v1/results/293902/", - "/rundb/api/v1/results/293901/" - ], - "modified": "2014-01-22T18:50:10.000920+00:00", - "id": 1080, - "resultsCount": 29, - "public": true, - "resource_uri": "/rundb/api/v1/project/1080/" - } + "/rundb/api/v1/project/1080/" ], "resultsType": "", "tfFastq": "_", diff --git a/source/auto_api_ref_docs/qualitymetrics.rst b/source/auto_api_ref_docs/qualitymetrics.rst index c4042c5..641a7c8 100644 --- a/source/auto_api_ref_docs/qualitymetrics.rst +++ b/source/auto_api_ref_docs/qualitymetrics.rst @@ -106,7 +106,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 37351, + "total_count": 47862, "offset": 0, "limit": 1, "next": "/rundb/api/v1/qualitymetrics/?offset=1&limit=1&format=json" @@ -118,7 +118,7 @@ Torrent Server response "q20_median_read_length": 0, "q20_reads": 0, "report": "/rundb/api/v1/results/269819/", - "q17_mean_read_length": 0.0, + "q17_mean_read_length": 0, "q17_100bp_reads": 0, "resource_uri": "/rundb/api/v1/qualitymetrics/9943/", "q0_max_read_length": 0, @@ -134,11 +134,11 @@ Torrent Server response "q0_50bp_reads": 0, "q17_150bp_reads": 0, "q0_150bp_reads": 0, - "q0_mean_read_length": 0.0, + "q0_mean_read_length": 0, "q17_bases": "0", "q0_mode_read_length": 0, "q20_mode_read_length": 0, - "q20_max_read_length": 0.0, + "q20_max_read_length": 0, "q20_bases": "0", "q0_median_read_length": 0, "q0_100bp_reads": 0, diff --git a/source/auto_api_ref_docs/referencegenome.rst b/source/auto_api_ref_docs/referencegenome.rst index 48bac43..4b60a01 100644 --- a/source/auto_api_ref_docs/referencegenome.rst +++ b/source/auto_api_ref_docs/referencegenome.rst @@ -39,7 +39,7 @@ field help text default ------------------ ---------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- **celery_task_id** Unicode string data. Ex: "Hello World" false false true false string ------------------ ---------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- -**date** A date & time as a string. Ex: "2010-11-10T03:07:43" 2014-06-28T14:05:04.000158+00:00 false false false false datetime +**date** A date & time as a string. Ex: "2010-11-10T03:07:43" 2015-02-03T02:30:36.000120+00:00 false false false false datetime ------------------ ---------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- **verbose_error** Unicode string data. Ex: "Hello World" false false true false string ------------------ ---------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- @@ -78,7 +78,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 5, + "total_count": 23, "offset": 0, "limit": 1, "next": "/rundb/api/v1/referencegenome/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/results.rst b/source/auto_api_ref_docs/results.rst index cdd0e53..d2d8d88 100644 --- a/source/auto_api_ref_docs/results.rst +++ b/source/auto_api_ref_docs/results.rst @@ -124,7 +124,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 43354, + "total_count": 56103, "offset": 0, "limit": 1, "next": "/rundb/api/v1/results/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/rig.rst b/source/auto_api_ref_docs/rig.rst index 31dfbf0..34d3346 100644 --- a/source/auto_api_ref_docs/rig.rst +++ b/source/auto_api_ref_docs/rig.rst @@ -41,6 +41,8 @@ field help text ------------------- ------------------------------------------------------------------------------ ------------- -------- -------- ----- ------ ------- **last_init_date** Unicode string data. Ex: "Hello World" false false true false string ------------------- ------------------------------------------------------------------------------ ------------- -------- -------- ----- ------ ------- +**updateCommand** Unicode string data. Ex: "Hello World" {} false false true false string +------------------- ------------------------------------------------------------------------------ ------------- -------- -------- ----- ------ ------- **alarms** Unicode string data. Ex: "Hello World" {} false false true false string ------------------- ------------------------------------------------------------------------------ ------------- -------- -------- ----- ------ ------- **serial** Unicode string data. Ex: "Hello World" n/a true false false false string @@ -84,7 +86,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 175, + "total_count": 203, "offset": 0, "limit": 1, "next": "/rundb/api/v1/rig/?offset=1&limit=1&format=json" @@ -110,6 +112,7 @@ Torrent Server response "id": 1 }, "last_init_date": "", + "updateCommand": {}, "alarms": {}, "serial": "", "host_address": "", diff --git a/source/auto_api_ref_docs/sample.rst b/source/auto_api_ref_docs/sample.rst index 894aa22..e6fc98f 100644 --- a/source/auto_api_ref_docs/sample.rst +++ b/source/auto_api_ref_docs/sample.rst @@ -66,7 +66,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 7765, + "total_count": 9668, "offset": 0, "limit": 1, "next": "/rundb/api/v1/sample/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/samplegrouptype_cv.rst b/source/auto_api_ref_docs/samplegrouptype_cv.rst index 86d887b..3594dee 100644 --- a/source/auto_api_ref_docs/samplegrouptype_cv.rst +++ b/source/auto_api_ref_docs/samplegrouptype_cv.rst @@ -68,7 +68,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 5, + "total_count": 6, "offset": 0, "limit": 1, "next": "/rundb/api/v1/samplegrouptype_cv/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/sampleset.rst b/source/auto_api_ref_docs/sampleset.rst index fe812b8..6483118 100644 --- a/source/auto_api_ref_docs/sampleset.rst +++ b/source/auto_api_ref_docs/sampleset.rst @@ -68,29 +68,27 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 1, + "total_count": 2, "offset": 0, "limit": 1, - "next": null + "next": "/rundb/api/v1/sampleset/?offset=1&limit=1&format=json" }, "objects": [ { - "status": "created", + "status": "planned", "description": "", - "sampleCount": 4, - "displayedName": "Set", - "SampleGroupType_CV": "/rundb/api/v1/samplegrouptype_cv/3/", + "sampleCount": 2, + "displayedName": "Test", + "SampleGroupType_CV": null, "samples": [ - "/rundb/api/v1/samplesetitem/14/", - "/rundb/api/v1/samplesetitem/15/", - "/rundb/api/v1/samplesetitem/16/", - "/rundb/api/v1/samplesetitem/17/" + "/rundb/api/v1/samplesetitem/18/", + "/rundb/api/v1/samplesetitem/19/" ], - "lastModifiedDate": "2013-10-07T12:04:51.000432+00:00", - "sampleGroupTypeName": "Tumor_Normal", - "creationDate": "2013-10-07T12:04:51.000432+00:00", - "id": 5, - "resource_uri": "/rundb/api/v1/sampleset/5/" + "lastModifiedDate": "2014-11-14T06:28:07.000121+00:00", + "sampleGroupTypeName": "", + "creationDate": "2014-11-14T01:04:50.000223+00:00", + "id": 7, + "resource_uri": "/rundb/api/v1/sampleset/7/" } ] } diff --git a/source/auto_api_ref_docs/samplesetitem.rst b/source/auto_api_ref_docs/samplesetitem.rst index 11eafca..777f053 100644 --- a/source/auto_api_ref_docs/samplesetitem.rst +++ b/source/auto_api_ref_docs/samplesetitem.rst @@ -70,25 +70,25 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 4, + "total_count": 6, "offset": 0, "limit": 1, "next": "/rundb/api/v1/samplesetitem/?offset=1&limit=1&format=json" }, "objects": [ { - "sample": "/rundb/api/v1/sample/4877/", - "gender": "Female", - "relationshipGroup": 1, + "sample": "/rundb/api/v1/sample/11104/", + "gender": "", + "relationshipGroup": 0, "cellularityPct": null, - "relationshipRole": "Self", - "cancerType": null, - "sampleSet": "/rundb/api/v1/sampleset/5/", - "lastModifiedDate": "2013-10-07T12:04:51.000440+00:00", + "relationshipRole": "", + "cancerType": "", + "sampleSet": "/rundb/api/v1/sampleset/7/", + "lastModifiedDate": "2014-11-14T01:04:50.000314+00:00", "dnabarcode": null, - "creationDate": "2013-10-07T12:04:51.000440+00:00", - "id": 14, - "resource_uri": "/rundb/api/v1/samplesetitem/14/" + "creationDate": "2014-11-14T01:04:50.000314+00:00", + "id": 18, + "resource_uri": "/rundb/api/v1/samplesetitem/18/" } ] } diff --git a/source/auto_api_ref_docs/samplesetiteminfo.rst b/source/auto_api_ref_docs/samplesetiteminfo.rst index e752bd5..b3eb13e 100644 --- a/source/auto_api_ref_docs/samplesetiteminfo.rst +++ b/source/auto_api_ref_docs/samplesetiteminfo.rst @@ -84,7 +84,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 4, + "total_count": 6, "offset": 0, "limit": 1, "next": "/rundb/api/v1/samplesetiteminfo/?offset=1&limit=1&format=json" diff --git a/source/auto_api_ref_docs/sequencingkitinfo.rst b/source/auto_api_ref_docs/sequencingkitinfo.rst index ec264f9..2838c0c 100644 --- a/source/auto_api_ref_docs/sequencingkitinfo.rst +++ b/source/auto_api_ref_docs/sequencingkitinfo.rst @@ -12,37 +12,43 @@ Schema URL: ``http://mytorrentserver/rundb/api/v1/sequencingkitinfo/schema/`` Fields table ------------ -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -field help text default nullable readonly blank unique type -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= -**isActive** Boolean data. Ex: True true false false true false boolean -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**description** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**instrumentType** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**runMode** Unicode string data. Ex: "Hello World" false false true false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**flowCount** Integer data. Ex: 2673 n/a false false false false integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**applicationType** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**uid** Unicode string data. Ex: "Hello World" n/a false false false true string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**id** Integer data. Ex: 2673 false false true true integer -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**categories** Unicode string data. Ex: "Hello World" true false false false string -------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- -**name** Unicode string data. Ex: "Hello World" n/a false false false true string -=================== ================================================================================================== ======= ======== ======== ===== ====== ======= +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +field help text default nullable readonly blank unique type +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= +**isActive** Boolean data. Ex: True true false false true false boolean +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**templatingSize** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**kitType** Unicode string data. Ex: "Hello World" n/a false false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**description** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**nucleotideType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**samplePrep_instrumentType** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**runMode** Unicode string data. Ex: "Hello World" false false true false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**parts** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a false false false false related +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**flowCount** Integer data. Ex: 2673 n/a false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**applicationType** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**uid** Unicode string data. Ex: "Hello World" n/a false false false true string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**libraryReadLength** Integer data. Ex: 2673 0 false false false false integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**id** Integer data. Ex: 2673 false false true true integer +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**categories** Unicode string data. Ex: "Hello World" true false false false string +----------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ ------- +**name** Unicode string data. Ex: "Hello World" n/a false false false true string +============================= ================================================================================================== ======= ======== ======== ===== ====== ======= Example request --------------- @@ -74,52 +80,49 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 18, + "total_count": 21, "offset": 0, "limit": 1, "next": "/rundb/api/v1/sequencingkitinfo/?offset=1&limit=1&format=json" }, "objects": [ { - "isActive": false, + "isActive": true, + "templatingSize": "", "kitType": "SequencingKit", - "description": "(200bp) Ion Sequencing 200 Kit", + "description": "Ion PGM Install Kit", "nucleotideType": "", "instrumentType": "pgm", + "samplePrep_instrumentType": "", "runMode": "", "parts": [ { - "barcode": "4471258", - "id": 20005, - "resource_uri": "/rundb/api/v1/kitpart/20005/", - "kit": "/rundb/api/v1/kitinfo/20002/" + "barcode": "4480217", + "id": 20019, + "resource_uri": "/rundb/api/v1/kitpart/20019/", + "kit": "/rundb/api/v1/kitinfo/20020/" }, { - "barcode": "4471257", - "id": 20006, - "resource_uri": "/rundb/api/v1/kitpart/20006/", - "kit": "/rundb/api/v1/kitinfo/20002/" + "barcode": "4480282", + "id": 20020, + "resource_uri": "/rundb/api/v1/kitpart/20020/", + "kit": "/rundb/api/v1/kitinfo/20020/" }, { - "barcode": "4471259", - "id": 20007, - "resource_uri": "/rundb/api/v1/kitpart/20007/", - "kit": "/rundb/api/v1/kitinfo/20002/" - }, - { - "barcode": "4471260", - "id": 20008, - "resource_uri": "/rundb/api/v1/kitpart/20008/", - "kit": "/rundb/api/v1/kitinfo/20002/" + "barcode": "4480284", + "id": 20021, + "resource_uri": "/rundb/api/v1/kitpart/20021/", + "kit": "/rundb/api/v1/kitinfo/20020/" } ], - "flowCount": 520, + "flowCount": 100, "applicationType": "", - "uid": "SEQ0002", - "resource_uri": "/rundb/api/v1/sequencingkitinfo/20002/", - "id": 20002, - "categories": "", - "name": "IonSeq200Kit" + "uid": "SEQ0006", + "libraryReadLength": 0, + "resource_uri": "/rundb/api/v1/sequencingkitinfo/20020/", + "id": 20020, + "categories": "readLengthDerivableFromFlows;flowsDerivableFromReadLength;", + "name": "IonPGMInstallKit" } ] } diff --git a/source/auto_api_ref_docs/sequencingkitpart.rst b/source/auto_api_ref_docs/sequencingkitpart.rst index f9eec13..938de7a 100644 --- a/source/auto_api_ref_docs/sequencingkitpart.rst +++ b/source/auto_api_ref_docs/sequencingkitpart.rst @@ -54,17 +54,17 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 64, + "total_count": 77, "offset": 0, "limit": 1, "next": "/rundb/api/v1/sequencingkitpart/?offset=1&limit=1&format=json" }, "objects": [ { - "barcode": "A25592", - "id": 20132, - "resource_uri": "/rundb/api/v1/sequencingkitpart/20132/", - "kit": "/rundb/api/v1/kitinfo/20063/" + "barcode": "4468994", + "id": 20004, + "resource_uri": "/rundb/api/v1/sequencingkitpart/20004/", + "kit": "/rundb/api/v1/kitinfo/20001/" } ] } diff --git a/source/auto_api_ref_docs/template.rst b/source/auto_api_ref_docs/template.rst index 3f72204..ac92d7e 100644 --- a/source/auto_api_ref_docs/template.rst +++ b/source/auto_api_ref_docs/template.rst @@ -60,20 +60,20 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 9, + "total_count": 11, "offset": 0, "limit": 1, "next": "/rundb/api/v1/template/?offset=1&limit=1&format=json" }, "objects": [ { - "isofficial": true, - "name": "TF1.2(tA-tB30') Hyb extend", - "sequence": "GTTTTAGGGTCCCCGGGGTTAAAAGGTTTCGAACACGATGTCGGAGACACGCAGGGATGAGATGG", - "comments": "", - "key": "ATCGT", - "id": 7, - "resource_uri": "/rundb/api/v1/template/7/" + "isofficial": false, + "name": "DxTF-1", + "sequence": "GAATAATCCAGCCCGCCAGGCATGGAAGAGCGTCGTAAAGTATTGCAGGTTCAGGCGGCGGAAAGCGTGATTGACTACTGGCAAATAAAGTACGTTCCACCTTTGACACCATTTTCCGTAGTGAACTGACGCTGCCAAACGCCGACCGCG", + "comments": "Disabled J.Sabina, 12/7/2014; Same as TF_1.", + "key": "ATCG", + "id": 10, + "resource_uri": "/rundb/api/v1/template/10/" } ] } diff --git a/source/auto_api_ref_docs/tfmetrics.rst b/source/auto_api_ref_docs/tfmetrics.rst index b6d9f79..03c653c 100644 --- a/source/auto_api_ref_docs/tfmetrics.rst +++ b/source/auto_api_ref_docs/tfmetrics.rst @@ -80,7 +80,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 7320, + "total_count": 16469, "offset": 0, "limit": 1, "next": "/rundb/api/v1/tfmetrics/?offset=1&limit=1&format=json" @@ -91,15 +91,15 @@ Torrent Server response "Q10Mean": 79.7, "SysSNR": 20.19, "HPAccuracy": "0 : 560244/582614, 1 : 356550/377171, 2 : 35115/45374, 3 : 0/0, 4 : 521/4373, 5 : 0/0, 6 : 0/0, 7 : 0/0", - "Q17ReadCount": 3992.0, + "Q17ReadCount": 3992, "sequence": "TTGCGCGCGCTGTGAATGCGCTGCTGTCGAATCGCGCTGCGCTGAACGTCGCGTGCGCGAACGATCTGAGACTGCCAAGGCACACAGGGGATAGG", "Q17Histo": "951 0 0 1 9 5 2 7 6 277 5 0 1 2 3 0 2 1 6 1 7 2 3 3 0 0 10 1 0 26 0 2 0 1 2 3 5 1 1 0 2 6 2 1 9 0 3 5 2 0 7 0 2 5 4 2 6 2 34 4 13 1 15 5 18 7 8 6 12 7 9 12 1 9 1 44 0 67 0 29 2 37 7 3 6 305 356 544 0 35 14 1116 1019 52 150 16 0 0 0 0 0", "name": "TF_D", - "aveKeyCount": 71.0, - "number": 4119.0, + "aveKeyCount": 71, + "number": 4119, "id": 1, - "keypass": 5368.0, - "Q10ReadCount": 4586.0, + "keypass": 5368, + "Q10ReadCount": 4586, "report": "/rundb/api/v1/results/89/", "resource_uri": "/rundb/api/v1/tfmetrics/1/", "Q17Mean": 66.56, diff --git a/source/auto_api_ref_docs/threeprimeadapter.rst b/source/auto_api_ref_docs/threeprimeadapter.rst index 108114b..5dcdecc 100644 --- a/source/auto_api_ref_docs/threeprimeadapter.rst +++ b/source/auto_api_ref_docs/threeprimeadapter.rst @@ -66,7 +66,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 17, + "total_count": 24, "offset": 0, "limit": 1, "next": "/rundb/api/v1/threeprimeadapter/?offset=1&limit=1&format=json" @@ -74,15 +74,15 @@ Torrent Server response "objects": [ { "direction": "Forward", - "name": "Ion P1B", - "sequence": "ATCACCGACTGCCCATAGAGAGGCTGAGAC", + "name": "AV1_ML1", + "sequence": "ATCATGAGAGCTTCACCGACTGCATGATGCTGAGCTGCTGACTCTGAATGTGTGC", "chemistryType": "", "runMode": "single", - "uid": "FWD_0001", - "resource_uri": "/rundb/api/v1/threeprimeadapter/1/", - "id": 1, - "isDefault": true, - "description": "Default forward adapter" + "uid": "AV1_ML1", + "resource_uri": "/rundb/api/v1/threeprimeadapter/18/", + "id": 18, + "isDefault": false, + "description": "mosaic adapter 1" } ] } diff --git a/source/auto_api_ref_docs/user.rst b/source/auto_api_ref_docs/user.rst index fc153db..1da905e 100644 --- a/source/auto_api_ref_docs/user.rst +++ b/source/auto_api_ref_docs/user.rst @@ -27,7 +27,7 @@ field help text ---------------- ----------------------------------------------------------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- **email** Unicode string data. Ex: "Hello World" false false true false string ---------------- ----------------------------------------------------------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- -**last_login** A date & time as a string. Ex: "2010-11-10T03:07:43" 2014-06-28T14:04:05.000090+00:00 false false false false datetime +**last_login** A date & time as a string. Ex: "2010-11-10T03:07:43" 2015-02-03T02:29:47.000645+00:00 false false false false datetime ---------------- ----------------------------------------------------------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- **full_name** Unicode string data. Ex: "Hello World" n/a false false false false string ---------------- ----------------------------------------------------------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- @@ -35,7 +35,7 @@ field help text ---------------- ----------------------------------------------------------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- **id** Integer data. Ex: 2673 false false true true integer ---------------- ----------------------------------------------------------------------------------------------------- -------------------------------- -------- -------- ----- ------ -------- -**date_joined** A date & time as a string. Ex: "2010-11-10T03:07:43" 2014-06-28T14:04:05.000090+00:00 false false false false datetime +**date_joined** A date & time as a string. Ex: "2010-11-10T03:07:43" 2015-02-03T02:29:47.000646+00:00 false false false false datetime ================ ===================================================================================================== ================================ ======== ======== ===== ====== ======== Example request @@ -68,7 +68,7 @@ Torrent Server response { "meta": { "previous": null, - "total_count": 20, + "total_count": 23, "offset": 0, "limit": 1, "next": "/rundb/api/v1/user/?offset=1&limit=1&format=json" @@ -79,21 +79,21 @@ Torrent Server response "phone_number": "", "name": "", "title": "user", - "last_read_news_post": "1984-11-05T05:00:00+00:00", + "last_read_news_post": "2013-09-12T14:03:31.000755+00:00", "note": "", - "id": 6, + "id": 8, "resource_uri": "" }, - "username": "dm_contact", + "username": "bernpuc", "first_name": "", "last_name": "", "is_active": true, - "email": "ts-admin@mailman.itw", - "last_login": "2013-03-13T17:28:05.000596+00:00", + "email": "bernard.puc@lifetech.com", + "last_login": "2013-09-17T13:58:41+00:00", "full_name": "", - "resource_uri": "/rundb/api/v1/user/6/", - "id": 6, - "date_joined": "2013-03-13T17:28:05.000596+00:00" + "resource_uri": "/rundb/api/v1/user/8/", + "id": 8, + "date_joined": "2013-05-13T13:50:03+00:00" } ] } diff --git a/source/auto_api_ref_index.rst b/source/auto_api_ref_index.rst index fba96df..e0a3f33 100644 --- a/source/auto_api_ref_index.rst +++ b/source/auto_api_ref_index.rst @@ -23,6 +23,7 @@ Torrent Server REST API v1 Resources auto_api_ref_docs/availableonetouchplannedexperimentsummary.rst auto_api_ref_docs/availableplannedexperimentsummary.rst auto_api_ref_docs/chip.rst + auto_api_ref_docs/clusterinfohistory.rst auto_api_ref_docs/compositedatamanagement.rst auto_api_ref_docs/compositeexperiment.rst auto_api_ref_docs/compositeresult.rst diff --git a/source/auto_database_ref_docs/rundb_analysisargs.rst b/source/auto_database_ref_docs/rundb_analysisargs.rst index 75f76e4..feba6a4 100644 --- a/source/auto_database_ref_docs/rundb_analysisargs.rst +++ b/source/auto_database_ref_docs/rundb_analysisargs.rst @@ -12,3 +12,49 @@ Postgres table: ``rundb_analysisargs`` Schema ------- ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| Field | Type | Description | ++==============================+==================================+=================================================================+ +| active | Boolean (Either True or False) | active | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| alignmentargs | String (up to 5000) | Default Alignment args | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| analysisargs | String (up to 5000) | Default Analysis args | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| basecallerargs | String (up to 5000) | Default Basecaller args | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| beadfindargs | String (up to 5000) | Default Beadfind args | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| calibrateargs | String (up to 5000) | Default Calibration args, used for recalibration | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| chipType | String (up to 128) | chipType | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| chip\_default | Boolean (Either True or False) | chip default | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| id | Integer | ID | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| libraryKitName | String (up to 512) | libraryKitName | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| name | String (up to 256) | name | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| prebasecallerargs | String (up to 5000) | Default Pre Basecaller args, used for recalibration | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| prethumbnailbasecallerargs | String (up to 5000) | Default Thumbnail Pre Basecaller args, used for recalibration | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| samplePrepKitName | String (up to 512) | samplePrepKitName | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| sequenceKitName | String (up to 512) | sequenceKitName | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| templateKitName | String (up to 512) | templateKitName | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| thumbnailalignmentargs | String (up to 5000) | Default Thumbnail Alignment args | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| thumbnailanalysisargs | String (up to 5000) | Default Thumbnail Analysis args | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| thumbnailbasecallerargs | String (up to 5000) | Default Thumbnail Basecaller args | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| thumbnailbeadfindargs | String (up to 5000) | Default Thumbnail Beadfind args | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ +| thumbnailcalibrateargs | String (up to 5000) | Default Thumbnail Calibration args, used for recalibration | ++------------------------------+----------------------------------+-----------------------------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_analysismetrics.rst b/source/auto_database_ref_docs/rundb_analysismetrics.rst index 714aa60..63af618 100644 --- a/source/auto_database_ref_docs/rundb_analysismetrics.rst +++ b/source/auto_database_ref_docs/rundb_analysismetrics.rst @@ -12,3 +12,77 @@ Postgres table: ``rundb_analysismetrics`` Schema ------- ++---------------------------+-------------------------+---------------------------------+ +| Field | Type | Description | ++===========================+=========================+=================================+ +| adjusted\_addressable | Integer | adjusted addressable | ++---------------------------+-------------------------+---------------------------------+ +| amb | Integer | amb | ++---------------------------+-------------------------+---------------------------------+ +| bead | Integer | bead | ++---------------------------+-------------------------+---------------------------------+ +| dud | Integer | dud | ++---------------------------+-------------------------+---------------------------------+ +| empty | Integer | empty | ++---------------------------+-------------------------+---------------------------------+ +| excluded | Integer | excluded | ++---------------------------+-------------------------+---------------------------------+ +| id | Integer | ID | ++---------------------------+-------------------------+---------------------------------+ +| ignored | Integer | ignored | ++---------------------------+-------------------------+---------------------------------+ +| keypass\_all\_beads | Integer | keypass all beads | ++---------------------------+-------------------------+---------------------------------+ +| lib | Integer | lib | ++---------------------------+-------------------------+---------------------------------+ +| libFinal | Integer | libFinal | ++---------------------------+-------------------------+---------------------------------+ +| libKp | Integer | libKp | ++---------------------------+-------------------------+---------------------------------+ +| libLive | Integer | libLive | ++---------------------------+-------------------------+---------------------------------+ +| libMix | Integer | libMix | ++---------------------------+-------------------------+---------------------------------+ +| lib\_pass\_basecaller | Integer | lib pass basecaller | ++---------------------------+-------------------------+---------------------------------+ +| lib\_pass\_cafie | Integer | lib pass cafie | ++---------------------------+-------------------------+---------------------------------+ +| live | Integer | live | ++---------------------------+-------------------------+---------------------------------+ +| loading | Floating point number | loading | ++---------------------------+-------------------------+---------------------------------+ +| pinned | Integer | pinned | ++---------------------------+-------------------------+---------------------------------+ +| report | Results (ForeignKey) | the related rundb.Results row | ++---------------------------+-------------------------+---------------------------------+ +| sysCF | Floating point number | sysCF | ++---------------------------+-------------------------+---------------------------------+ +| sysDR | Floating point number | sysDR | ++---------------------------+-------------------------+---------------------------------+ +| sysIE | Floating point number | sysIE | ++---------------------------+-------------------------+---------------------------------+ +| tf | Integer | tf | ++---------------------------+-------------------------+---------------------------------+ +| tfFinal | Integer | tfFinal | ++---------------------------+-------------------------+---------------------------------+ +| tfKp | Integer | tfKp | ++---------------------------+-------------------------+---------------------------------+ +| tfLive | Integer | tfLive | ++---------------------------+-------------------------+---------------------------------+ +| tfMix | Integer | tfMix | ++---------------------------+-------------------------+---------------------------------+ +| total | Integer | total | ++---------------------------+-------------------------+---------------------------------+ +| washout | Integer | washout | ++---------------------------+-------------------------+---------------------------------+ +| washout\_ambiguous | Integer | washout ambiguous | ++---------------------------+-------------------------+---------------------------------+ +| washout\_dud | Integer | washout dud | ++---------------------------+-------------------------+---------------------------------+ +| washout\_library | Integer | washout library | ++---------------------------+-------------------------+---------------------------------+ +| washout\_live | Integer | washout live | ++---------------------------+-------------------------+---------------------------------+ +| washout\_test\_fragment | Integer | washout test fragment | ++---------------------------+-------------------------+---------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_applicationgroup.rst b/source/auto_database_ref_docs/rundb_applicationgroup.rst index 42b2098..d9c8b92 100644 --- a/source/auto_database_ref_docs/rundb_applicationgroup.rst +++ b/source/auto_database_ref_docs/rundb_applicationgroup.rst @@ -12,3 +12,17 @@ Postgres table: ``rundb_applicationgroup`` Schema ------- ++---------------+----------------------------------+---------------+ +| Field | Type | Description | ++===============+==================================+===============+ +| description | String (up to 1024) | description | ++---------------+----------------------------------+---------------+ +| id | Integer | ID | ++---------------+----------------------------------+---------------+ +| isActive | Boolean (Either True or False) | isActive | ++---------------+----------------------------------+---------------+ +| name | String (up to 127) | name | ++---------------+----------------------------------+---------------+ +| uid | String (up to 32) | uid | ++---------------+----------------------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_applproduct.rst b/source/auto_database_ref_docs/rundb_applproduct.rst index 2bc8559..e6e83d5 100644 --- a/source/auto_database_ref_docs/rundb_applproduct.rst +++ b/source/auto_database_ref_docs/rundb_applproduct.rst @@ -12,3 +12,91 @@ Postgres table: ``rundb_applproduct`` Schema ------- ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| Field | Type | Description | ++=========================================================+==================================+=========================================================+ +| applType | RunType (ForeignKey) | the related rundb.RunType row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| barcodeKitSelectableType | String (up to 64) | barcodeKitSelectableType | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultAvalancheSequencingKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultAvalancheTemplateKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultBarcodeKitName | String (up to 128) | defaultBarcodeKitName | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultChipType | String (up to 128) | defaultChipType | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultControlSeqKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultFlowCount | Positive integer | defaultFlowCount | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultGenomeRefName | String (up to 1024) | defaultGenomeRefName | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultHotSpotRegionBedFileName | String (up to 1024) | defaultHotSpotRegionBedFileName | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultIonChefPrepKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultIonChefSequencingKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultLibraryKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultPairedEndAdapterKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultPairedEndLibraryKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultPairedEndSequencingKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultSamplePrepKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultSequencingKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultTargetRegionBedFileName | String (up to 1024) | defaultTargetRegionBedFileName | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| defaultTemplateKit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| description | String (up to 1024) | description | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| id | Integer | ID | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| instrumentType | String (up to 64) | instrumentType | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isActive | Boolean (Either True or False) | isActive | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isBarcodeKitSelectionRequired | Boolean (Either True or False) | isBarcodeKitSelectionRequired | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isControlSeqTypeBySampleSupported | Boolean (Either True or False) | isControlSeqTypeBySampleSupported | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isDefault | Boolean (Either True or False) | isDefault | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isDefaultBarcoded | Boolean (Either True or False) | isDefaultBarcoded | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isDefaultPairedEnd | Boolean (Either True or False) | isDefaultPairedEnd | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isDualNucleotideTypeBySampleSupported | Boolean (Either True or False) | isDualNucleotideTypeBySampleSupported | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isHotSpotBEDFileBySampleSupported | Boolean (Either True or False) | isHotSpotBEDFileBySampleSupported | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isHotspotRegionBEDFileSuppported | Boolean (Either True or False) | isHotspotRegionBEDFileSuppported | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isPairedEndSupported | Boolean (Either True or False) | isPairedEndSupported | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isReferenceBySampleSupported | Boolean (Either True or False) | isReferenceBySampleSupported | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isSamplePrepKitSupported | Boolean (Either True or False) | isSamplePrepKitSupported | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isTargetRegionBEDFileBySampleSupported | Boolean (Either True or False) | isTargetRegionBEDFileBySampleSupported | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isTargetRegionBEDFileSelectionRequiredForRefSelection | Boolean (Either True or False) | isTargetRegionBEDFileSelectionRequiredForRefSelection | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isTargetRegionBEDFileSupported | Boolean (Either True or False) | isTargetRegionBEDFileSupported | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isTargetTechniqueSelectionSupported | Boolean (Either True or False) | isTargetTechniqueSelectionSupported | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| isVisible | Boolean (Either True or False) | isVisible | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| productCode | String (up to 64) | productCode | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ +| productName | String (up to 128) | productName | ++---------------------------------------------------------+----------------------------------+---------------------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_backup.rst b/source/auto_database_ref_docs/rundb_backup.rst index c7258cf..87cb2e6 100644 --- a/source/auto_database_ref_docs/rundb_backup.rst +++ b/source/auto_database_ref_docs/rundb_backup.rst @@ -12,3 +12,19 @@ Postgres table: ``rundb_backup`` Schema ------- ++--------------+----------------------------------+------------------------------------+ +| Field | Type | Description | ++==============+==================================+====================================+ +| backupDate | Date (with time) | backupDate | ++--------------+----------------------------------+------------------------------------+ +| backupName | String (up to 256) | backupName | ++--------------+----------------------------------+------------------------------------+ +| backupPath | String (up to 512) | backupPath | ++--------------+----------------------------------+------------------------------------+ +| experiment | Experiment (ForeignKey) | the related rundb.Experiment row | ++--------------+----------------------------------+------------------------------------+ +| id | Integer | ID | ++--------------+----------------------------------+------------------------------------+ +| isBackedUp | Boolean (Either True or False) | isBackedUp | ++--------------+----------------------------------+------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_backupconfig.rst b/source/auto_database_ref_docs/rundb_backupconfig.rst index a1cbb13..9f1d282 100644 --- a/source/auto_database_ref_docs/rundb_backupconfig.rst +++ b/source/auto_database_ref_docs/rundb_backupconfig.rst @@ -12,3 +12,35 @@ Postgres table: ``rundb_backupconfig`` Schema ------- ++----------------------+----------------------------------+----------------------------------+ +| Field | Type | Description | ++======================+==================================+==================================+ +| backup\_directory | String (up to 256) | backup directory | ++----------------------+----------------------------------+----------------------------------+ +| backup\_threshold | Integer | backup threshold | ++----------------------+----------------------------------+----------------------------------+ +| bandwidth\_limit | Integer | bandwidth limit | ++----------------------+----------------------------------+----------------------------------+ +| comments | Text | comments | ++----------------------+----------------------------------+----------------------------------+ +| email | Email address | email | ++----------------------+----------------------------------+----------------------------------+ +| grace\_period | Integer | grace period | ++----------------------+----------------------------------+----------------------------------+ +| id | Integer | ID | ++----------------------+----------------------------------+----------------------------------+ +| keepTN | Boolean (Either True or False) | keepTN | ++----------------------+----------------------------------+----------------------------------+ +| location | Location (ForeignKey) | the related rundb.Location row | ++----------------------+----------------------------------+----------------------------------+ +| name | String (up to 64) | name | ++----------------------+----------------------------------+----------------------------------+ +| number\_to\_backup | Integer | number to backup | ++----------------------+----------------------------------+----------------------------------+ +| online | Boolean (Either True or False) | online | ++----------------------+----------------------------------+----------------------------------+ +| status | String (up to 512) | status | ++----------------------+----------------------------------+----------------------------------+ +| timeout | Integer | timeout | ++----------------------+----------------------------------+----------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_chip.rst b/source/auto_database_ref_docs/rundb_chip.rst index 5558d8f..7b7ae13 100644 --- a/source/auto_database_ref_docs/rundb_chip.rst +++ b/source/auto_database_ref_docs/rundb_chip.rst @@ -12,3 +12,19 @@ Postgres table: ``rundb_chip`` Schema ------- ++------------------+----------------------------------+------------------+ +| Field | Type | Description | ++==================+==================================+==================+ +| description | String (up to 128) | description | ++------------------+----------------------------------+------------------+ +| id | Integer | ID | ++------------------+----------------------------------+------------------+ +| instrumentType | String (up to 64) | instrumentType | ++------------------+----------------------------------+------------------+ +| isActive | Boolean (Either True or False) | isActive | ++------------------+----------------------------------+------------------+ +| name | String (up to 128) | name | ++------------------+----------------------------------+------------------+ +| slots | Integer | slots | ++------------------+----------------------------------+------------------+ + diff --git a/source/auto_database_ref_docs/rundb_content.rst b/source/auto_database_ref_docs/rundb_content.rst index 3d39bb4..8e8b927 100644 --- a/source/auto_database_ref_docs/rundb_content.rst +++ b/source/auto_database_ref_docs/rundb_content.rst @@ -12,3 +12,19 @@ Postgres table: ``rundb_content`` Schema ------- ++-----------------+------------------------------+---------------------------------------+ +| Field | Type | Description | ++=================+==============================+=======================================+ +| contentupload | ContentUpload (ForeignKey) | the related rundb.ContentUpload row | ++-----------------+------------------------------+---------------------------------------+ +| file | String (up to 255) | file | ++-----------------+------------------------------+---------------------------------------+ +| id | Integer | ID | ++-----------------+------------------------------+---------------------------------------+ +| meta | Text | meta | ++-----------------+------------------------------+---------------------------------------+ +| path | String (up to 255) | path | ++-----------------+------------------------------+---------------------------------------+ +| publisher | Publisher (ForeignKey) | the related rundb.Publisher row | ++-----------------+------------------------------+---------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_contentupload.rst b/source/auto_database_ref_docs/rundb_contentupload.rst index c86886c..28230ba 100644 --- a/source/auto_database_ref_docs/rundb_contentupload.rst +++ b/source/auto_database_ref_docs/rundb_contentupload.rst @@ -12,3 +12,17 @@ Postgres table: ``rundb_contentupload`` Schema ------- ++--------------+--------------------------+-----------------------------------+ +| Field | Type | Description | ++==============+==========================+===================================+ +| file\_path | String (up to 255) | file path | ++--------------+--------------------------+-----------------------------------+ +| id | Integer | ID | ++--------------+--------------------------+-----------------------------------+ +| meta | Text | meta | ++--------------+--------------------------+-----------------------------------+ +| publisher | Publisher (ForeignKey) | the related rundb.Publisher row | ++--------------+--------------------------+-----------------------------------+ +| status | String (up to 255) | status | ++--------------+--------------------------+-----------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_cruncher.rst b/source/auto_database_ref_docs/rundb_cruncher.rst index 522d4df..875e414 100644 --- a/source/auto_database_ref_docs/rundb_cruncher.rst +++ b/source/auto_database_ref_docs/rundb_cruncher.rst @@ -12,3 +12,21 @@ Postgres table: ``rundb_cruncher`` Schema ------- ++------------+-------------------------+----------------------------------+ +| Field | Type | Description | ++============+=========================+==================================+ +| comments | Text | comments | ++------------+-------------------------+----------------------------------+ +| date | Date (with time) | date | ++------------+-------------------------+----------------------------------+ +| id | Integer | ID | ++------------+-------------------------+----------------------------------+ +| info | Text | info | ++------------+-------------------------+----------------------------------+ +| location | Location (ForeignKey) | the related rundb.Location row | ++------------+-------------------------+----------------------------------+ +| name | String (up to 200) | name | ++------------+-------------------------+----------------------------------+ +| state | String (up to 8) | state | ++------------+-------------------------+----------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_dm_prune_field.rst b/source/auto_database_ref_docs/rundb_dm_prune_field.rst index a24dc04..734a1f7 100644 --- a/source/auto_database_ref_docs/rundb_dm_prune_field.rst +++ b/source/auto_database_ref_docs/rundb_dm_prune_field.rst @@ -12,3 +12,11 @@ Postgres table: ``rundb_dm_prune_field`` Schema ------- ++---------+---------------------+---------------+ +| Field | Type | Description | ++=========+=====================+===============+ +| id | Integer | ID | ++---------+---------------------+---------------+ +| rule | String (up to 64) | rule | ++---------+---------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_dm_prune_group.rst b/source/auto_database_ref_docs/rundb_dm_prune_group.rst index beddba6..1041696 100644 --- a/source/auto_database_ref_docs/rundb_dm_prune_group.rst +++ b/source/auto_database_ref_docs/rundb_dm_prune_group.rst @@ -12,3 +12,15 @@ Postgres table: ``rundb_dm_prune_group`` Schema ------- ++------------+----------------------------------+---------------+ +| Field | Type | Description | ++============+==================================+===============+ +| editable | Boolean (Either True or False) | editable | ++------------+----------------------------------+---------------+ +| id | Integer | ID | ++------------+----------------------------------+---------------+ +| name | String (up to 128) | name | ++------------+----------------------------------+---------------+ +| ruleNums | Comma-separated integers | ruleNums | ++------------+----------------------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_dm_reports.rst b/source/auto_database_ref_docs/rundb_dm_reports.rst index 6cfaced..8bb0bed 100644 --- a/source/auto_database_ref_docs/rundb_dm_reports.rst +++ b/source/auto_database_ref_docs/rundb_dm_reports.rst @@ -12,3 +12,19 @@ Postgres table: ``rundb_dm_reports`` Schema ------- ++--------------+----------------------------------+---------------+ +| Field | Type | Description | ++==============+==================================+===============+ +| autoAge | Integer | autoAge | ++--------------+----------------------------------+---------------+ +| autoPrune | Boolean (Either True or False) | autoPrune | ++--------------+----------------------------------+---------------+ +| autoType | String (up to 32) | autoType | ++--------------+----------------------------------+---------------+ +| id | Integer | ID | ++--------------+----------------------------------+---------------+ +| location | String (up to 512) | location | ++--------------+----------------------------------+---------------+ +| pruneLevel | String (up to 128) | pruneLevel | ++--------------+----------------------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_dmfileset.rst b/source/auto_database_ref_docs/rundb_dmfileset.rst index a5fa4d6..ef77fe2 100644 --- a/source/auto_database_ref_docs/rundb_dmfileset.rst +++ b/source/auto_database_ref_docs/rundb_dmfileset.rst @@ -12,3 +12,35 @@ Postgres table: ``rundb_dmfileset`` Schema ------- ++------------------------+----------------------------------+----------------------+ +| Field | Type | Description | ++========================+==================================+======================+ +| auto\_action | String (up to 8) | auto action | ++------------------------+----------------------------------+----------------------+ +| auto\_trigger\_age | Integer | auto trigger age | ++------------------------+----------------------------------+----------------------+ +| auto\_trigger\_usage | Integer | auto trigger usage | ++------------------------+----------------------------------+----------------------+ +| backup\_directory | String (up to 256) | backup directory | ++------------------------+----------------------------------+----------------------+ +| bandwidth\_limit | Integer | bandwidth limit | ++------------------------+----------------------------------+----------------------+ +| del\_empty\_dir | Boolean (Either True or False) | del empty dir | ++------------------------+----------------------------------+----------------------+ +| description | String (up to 256) | description | ++------------------------+----------------------------------+----------------------+ +| enabled | Boolean (Either True or False) | enabled | ++------------------------+----------------------------------+----------------------+ +| exclude | Text | exclude | ++------------------------+----------------------------------+----------------------+ +| id | Integer | ID | ++------------------------+----------------------------------+----------------------+ +| include | Text | include | ++------------------------+----------------------------------+----------------------+ +| keepwith | Text | keepwith | ++------------------------+----------------------------------+----------------------+ +| type | String (up to 48) | type | ++------------------------+----------------------------------+----------------------+ +| version | String (up to 8) | version | ++------------------------+----------------------------------+----------------------+ + diff --git a/source/auto_database_ref_docs/rundb_dmfilestat.rst b/source/auto_database_ref_docs/rundb_dmfilestat.rst index 604748b..98fb4a2 100644 --- a/source/auto_database_ref_docs/rundb_dmfilestat.rst +++ b/source/auto_database_ref_docs/rundb_dmfilestat.rst @@ -12,3 +12,27 @@ Postgres table: ``rundb_dmfilestat`` Schema ------- ++------------------+----------------------------------+-----------------------------------+ +| Field | Type | Description | ++==================+==================================+===================================+ +| action\_state | String (up to 8) | action state | ++------------------+----------------------------------+-----------------------------------+ +| archivepath | String (up to 512) | archivepath | ++------------------+----------------------------------+-----------------------------------+ +| created | Date (with time) | created | ++------------------+----------------------------------+-----------------------------------+ +| diskspace | Floating point number | diskspace | ++------------------+----------------------------------+-----------------------------------+ +| dmfileset | DMFileSet (ForeignKey) | the related rundb.DMFileSet row | ++------------------+----------------------------------+-----------------------------------+ +| files\_in\_use | String (up to 512) | files in use | ++------------------+----------------------------------+-----------------------------------+ +| id | Integer | ID | ++------------------+----------------------------------+-----------------------------------+ +| preserve\_data | Boolean (Either True or False) | preserve data | ++------------------+----------------------------------+-----------------------------------+ +| result | Results (ForeignKey) | the related rundb.Results row | ++------------------+----------------------------------+-----------------------------------+ +| user\_comment | Text | user comment | ++------------------+----------------------------------+-----------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_dnabarcode.rst b/source/auto_database_ref_docs/rundb_dnabarcode.rst index efa6514..37fb223 100644 --- a/source/auto_database_ref_docs/rundb_dnabarcode.rst +++ b/source/auto_database_ref_docs/rundb_dnabarcode.rst @@ -12,3 +12,31 @@ Postgres table: ``rundb_dnabarcode`` Schema ------- ++-----------------+-------------------------+----------------+ +| Field | Type | Description | ++=================+=========================+================+ +| adapter | String (up to 128) | adapter | ++-----------------+-------------------------+----------------+ +| annotation | String (up to 512) | annotation | ++-----------------+-------------------------+----------------+ +| floworder | String (up to 128) | floworder | ++-----------------+-------------------------+----------------+ +| id | Integer | ID | ++-----------------+-------------------------+----------------+ +| id\_str | String (up to 128) | id str | ++-----------------+-------------------------+----------------+ +| index | Integer | index | ++-----------------+-------------------------+----------------+ +| length | Integer | length | ++-----------------+-------------------------+----------------+ +| name | String (up to 128) | name | ++-----------------+-------------------------+----------------+ +| score\_cutoff | Floating point number | score cutoff | ++-----------------+-------------------------+----------------+ +| score\_mode | Integer | score mode | ++-----------------+-------------------------+----------------+ +| sequence | String (up to 128) | sequence | ++-----------------+-------------------------+----------------+ +| type | String (up to 64) | type | ++-----------------+-------------------------+----------------+ + diff --git a/source/auto_database_ref_docs/rundb_emailaddress.rst b/source/auto_database_ref_docs/rundb_emailaddress.rst index 2cd8826..debdcf6 100644 --- a/source/auto_database_ref_docs/rundb_emailaddress.rst +++ b/source/auto_database_ref_docs/rundb_emailaddress.rst @@ -12,3 +12,13 @@ Postgres table: ``rundb_emailaddress`` Schema ------- ++------------+----------------------------------+---------------+ +| Field | Type | Description | ++============+==================================+===============+ +| email | Email address | email | ++------------+----------------------------------+---------------+ +| id | Integer | ID | ++------------+----------------------------------+---------------+ +| selected | Boolean (Either True or False) | selected | ++------------+----------------------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_eventlog.rst b/source/auto_database_ref_docs/rundb_eventlog.rst index 58ebdfb..fe9e996 100644 --- a/source/auto_database_ref_docs/rundb_eventlog.rst +++ b/source/auto_database_ref_docs/rundb_eventlog.rst @@ -12,3 +12,19 @@ Postgres table: ``rundb_eventlog`` Schema ------- ++-----------------+---------------------+--------------------------------------------+ +| Field | Type | Description | ++=================+=====================+============================================+ +| content\_type | ContentType | the related contenttypes.ContentType row | ++-----------------+---------------------+--------------------------------------------+ +| created | Date (with time) | created | ++-----------------+---------------------+--------------------------------------------+ +| id | Integer | ID | ++-----------------+---------------------+--------------------------------------------+ +| row\_pk | Positive integer | row pk | ++-----------------+---------------------+--------------------------------------------+ +| text | Text | comment | ++-----------------+---------------------+--------------------------------------------+ +| username | String (up to 32) | username | ++-----------------+---------------------+--------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_experiment.rst b/source/auto_database_ref_docs/rundb_experiment.rst index 006957c..a174b32 100644 --- a/source/auto_database_ref_docs/rundb_experiment.rst +++ b/source/auto_database_ref_docs/rundb_experiment.rst @@ -12,3 +12,135 @@ Postgres table: ``rundb_experiment`` Schema ------- ++---------------------------+----------------------------------+-------------------------------------------+ +| Field | Type | Description | ++===========================+==================================+===========================================+ +| autoAnalyze | Boolean (Either True or False) | autoAnalyze | ++---------------------------+----------------------------------+-------------------------------------------+ +| baselineRun | Boolean (Either True or False) | baselineRun | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefChipExpiration1 | String (up to 64) | chefChipExpiration1 | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefChipExpiration2 | String (up to 64) | chefChipExpiration2 | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefChipType1 | String (up to 64) | chefChipType1 | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefChipType2 | String (up to 64) | chefChipType2 | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefExtraInfo\_1 | String (up to 128) | chefExtraInfo 1 | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefExtraInfo\_2 | String (up to 128) | chefExtraInfo 2 | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefInstrumentName | String (up to 200) | chefInstrumentName | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefKitType | String (up to 64) | chefKitType | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefLastUpdate | Date (with time) | chefLastUpdate | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefLogPath | String (up to 512) | chefLogPath | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefLotNumber | String (up to 64) | chefLotNumber | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefManufactureDate | String (up to 64) | chefManufactureDate | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefMessage | Text | chefMessage | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefPackageVer | String (up to 64) | chefPackageVer | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefProgress | Floating point number | chefProgress | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefReagentID | String (up to 64) | chefReagentID | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefReagentsExpiration | String (up to 64) | chefReagentsExpiration | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefReagentsLot | String (up to 64) | chefReagentsLot | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefReagentsPart | String (up to 64) | chefReagentsPart | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefSamplePos | String (up to 64) | chefSamplePos | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefSolutionsExpiration | String (up to 64) | chefSolutionsExpiration | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefSolutionsLot | String (up to 64) | chefSolutionsLot | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefSolutionsPart | String (up to 64) | chefSolutionsPart | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefStatus | String (up to 256) | chefStatus | ++---------------------------+----------------------------------+-------------------------------------------+ +| chefTipRackBarcode | String (up to 64) | chefTipRackBarcode | ++---------------------------+----------------------------------+-------------------------------------------+ +| chipBarcode | String (up to 64) | chipBarcode | ++---------------------------+----------------------------------+-------------------------------------------+ +| chipType | String (up to 32) | chipType | ++---------------------------+----------------------------------+-------------------------------------------+ +| cycles | Integer | cycles | ++---------------------------+----------------------------------+-------------------------------------------+ +| date | Date (with time) | date | ++---------------------------+----------------------------------+-------------------------------------------+ +| diskusage | Integer | diskusage | ++---------------------------+----------------------------------+-------------------------------------------+ +| displayName | String (up to 128) | displayName | ++---------------------------+----------------------------------+-------------------------------------------+ +| expCompInfo | Text | expCompInfo | ++---------------------------+----------------------------------+-------------------------------------------+ +| expDir | String (up to 512) | expDir | ++---------------------------+----------------------------------+-------------------------------------------+ +| expName | String (up to 128) | expName | ++---------------------------+----------------------------------+-------------------------------------------+ +| flows | Integer | flows | ++---------------------------+----------------------------------+-------------------------------------------+ +| flowsInOrder | Text | flowsInOrder | ++---------------------------+----------------------------------+-------------------------------------------+ +| ftpStatus | String (up to 512) | ftpStatus | ++---------------------------+----------------------------------+-------------------------------------------+ +| id | Integer | ID | ++---------------------------+----------------------------------+-------------------------------------------+ +| isReverseRun | Boolean (Either True or False) | isReverseRun | ++---------------------------+----------------------------------+-------------------------------------------+ +| log | Text | log | ++---------------------------+----------------------------------+-------------------------------------------+ +| metaData | Text | metaData | ++---------------------------+----------------------------------+-------------------------------------------+ +| notes | String (up to 1024) | notes | ++---------------------------+----------------------------------+-------------------------------------------+ +| pgmName | String (up to 64) | pgmName | ++---------------------------+----------------------------------+-------------------------------------------+ +| pinnedRepResult | Boolean (Either True or False) | pinned representative result | ++---------------------------+----------------------------------+-------------------------------------------+ +| plan | PlannedExperiment (ForeignKey) | the related rundb.PlannedExperiment row | ++---------------------------+----------------------------------+-------------------------------------------+ +| platform | String (up to 128) | platform | ++---------------------------+----------------------------------+-------------------------------------------+ +| rawdatastyle | String (up to 24) | rawdatastyle | ++---------------------------+----------------------------------+-------------------------------------------+ +| reagentBarcode | String (up to 64) | reagentBarcode | ++---------------------------+----------------------------------+-------------------------------------------+ +| repResult | Results (ForeignKey) | the related rundb.Results row | ++---------------------------+----------------------------------+-------------------------------------------+ +| resultDate | Date (with time) | resultDate | ++---------------------------+----------------------------------+-------------------------------------------+ +| reverse\_primer | String (up to 128) | reverse primer | ++---------------------------+----------------------------------+-------------------------------------------+ +| runMode | String (up to 64) | runMode | ++---------------------------+----------------------------------+-------------------------------------------+ +| seqKitBarcode | String (up to 64) | seqKitBarcode | ++---------------------------+----------------------------------+-------------------------------------------+ +| sequencekitbarcode | String (up to 512) | sequencekitbarcode | ++---------------------------+----------------------------------+-------------------------------------------+ +| sequencekitname | String (up to 512) | sequencekitname | ++---------------------------+----------------------------------+-------------------------------------------+ +| star | Boolean (Either True or False) | star | ++---------------------------+----------------------------------+-------------------------------------------+ +| status | String (up to 512) | status | ++---------------------------+----------------------------------+-------------------------------------------+ +| storageHost | String (up to 128) | storageHost | ++---------------------------+----------------------------------+-------------------------------------------+ +| storage\_options | String (up to 200) | storage options | ++---------------------------+----------------------------------+-------------------------------------------+ +| unique | String (up to 512) | unique | ++---------------------------+----------------------------------+-------------------------------------------+ +| usePreBeadfind | Boolean (Either True or False) | usePreBeadfind | ++---------------------------+----------------------------------+-------------------------------------------+ +| user\_ack | String (up to 24) | user ack | ++---------------------------+----------------------------------+-------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_experimentanalysissettings.rst b/source/auto_database_ref_docs/rundb_experimentanalysissettings.rst index 3311807..f29b2a7 100644 --- a/source/auto_database_ref_docs/rundb_experimentanalysissettings.rst +++ b/source/auto_database_ref_docs/rundb_experimentanalysissettings.rst @@ -12,3 +12,77 @@ Postgres table: ``rundb_experimentanalysissettings`` Schema ------- ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| Field | Type | Description | ++======================================+==================================+=========================================================+ +| alignmentargs | String (up to 5000) | Alignment args | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| analysisargs | String (up to 5000) | Analysis args | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| barcodeKitName | String (up to 128) | barcodeKitName | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| barcodedSamples | Text | barcodedSamples | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| base\_recalibration\_mode | String (up to 64) | base recalibration mode | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| basecallerargs | String (up to 5000) | Basecaller args | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| beadfindargs | String (up to 5000) | Beadfind args | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| calibrateargs | String (up to 5000) | Calibration args, used for recalibration | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| date | Date (with time) | date | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| experiment | Experiment (ForeignKey) | the related rundb.Experiment row | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| hotSpotRegionBedFile | String (up to 1024) | hotSpotRegionBedFile | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| id | Integer | ID | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| isDuplicateReads | Boolean (Either True or False) | isDuplicateReads | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| isEditable | Boolean (Either True or False) | isEditable | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| isOneTimeOverride | Boolean (Either True or False) | isOneTimeOverride | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| libraryKey | String (up to 64) | libraryKey | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| libraryKitBarcode | String (up to 512) | libraryKitBarcode | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| libraryKitName | String (up to 512) | libraryKitName | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| mixedTypeRNA\_hotSpotRegionBedFile | String (up to 1024) | mixedTypeRNA hotSpotRegionBedFile | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| mixedTypeRNA\_reference | String (up to 512) | mixedTypeRNA reference | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| mixedTypeRNA\_targetRegionBedFile | String (up to 1024) | mixedTypeRNA targetRegionBedFile | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| prebasecallerargs | String (up to 5000) | Pre Basecaller args, used for recalibration | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| prethumbnailbasecallerargs | String (up to 5000) | Thumbnail Pre Basecaller args, used for recalibration | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| realign | Boolean (Either True or False) | realign | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| reference | String (up to 512) | reference | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| selectedPlugins | Text | selectedPlugins | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| status | String (up to 512) | status | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| targetRegionBedFile | String (up to 1024) | targetRegionBedFile | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| tfKey | String (up to 64) | tfKey | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| threePrimeAdapter | String (up to 512) | 3' adapter | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| thumbnailalignmentargs | String (up to 5000) | Thumbnail Alignment args | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| thumbnailanalysisargs | String (up to 5000) | Thumbnail Analysis args | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| thumbnailbasecallerargs | String (up to 5000) | Thumbnail Basecaller args | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| thumbnailbeadfindargs | String (up to 5000) | Thumbnail Beadfind args | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ +| thumbnailcalibrateargs | String (up to 5000) | Thumbnail Calibration args, used for recalibration | ++--------------------------------------+----------------------------------+---------------------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_filemonitor.rst b/source/auto_database_ref_docs/rundb_filemonitor.rst index 96208d6..db0c5c4 100644 --- a/source/auto_database_ref_docs/rundb_filemonitor.rst +++ b/source/auto_database_ref_docs/rundb_filemonitor.rst @@ -12,3 +12,31 @@ Postgres table: ``rundb_filemonitor`` Schema ------- ++--------------------+------------------------+------------------+ +| Field | Type | Description | ++====================+========================+==================+ +| celery\_task\_id | String (up to 60) | celery task id | ++--------------------+------------------------+------------------+ +| created | Date (with time) | created | ++--------------------+------------------------+------------------+ +| id | Integer | ID | ++--------------------+------------------------+------------------+ +| local\_dir | String (up to 512) | local dir | ++--------------------+------------------------+------------------+ +| md5sum | String (up to 32) | md5sum | ++--------------------+------------------------+------------------+ +| name | String (up to 255) | name | ++--------------------+------------------------+------------------+ +| progress | Big (8 byte) integer | progress | ++--------------------+------------------------+------------------+ +| size | Big (8 byte) integer | size | ++--------------------+------------------------+------------------+ +| status | String (up to 60) | status | ++--------------------+------------------------+------------------+ +| tags | String (up to 1024) | tags | ++--------------------+------------------------+------------------+ +| updated | Date (with time) | updated | ++--------------------+------------------------+------------------+ +| url | String (up to 2000) | url | ++--------------------+------------------------+------------------+ + diff --git a/source/auto_database_ref_docs/rundb_fileserver.rst b/source/auto_database_ref_docs/rundb_fileserver.rst index 7fe9998..e11eae1 100644 --- a/source/auto_database_ref_docs/rundb_fileserver.rst +++ b/source/auto_database_ref_docs/rundb_fileserver.rst @@ -12,3 +12,19 @@ Postgres table: ``rundb_fileserver`` Schema ------- ++---------------+-------------------------+----------------------------------+ +| Field | Type | Description | ++===============+=========================+==================================+ +| comments | Text | comments | ++---------------+-------------------------+----------------------------------+ +| filesPrefix | String (up to 200) | filesPrefix | ++---------------+-------------------------+----------------------------------+ +| id | Integer | ID | ++---------------+-------------------------+----------------------------------+ +| location | Location (ForeignKey) | the related rundb.Location row | ++---------------+-------------------------+----------------------------------+ +| name | String (up to 200) | name | ++---------------+-------------------------+----------------------------------+ +| percentfull | Floating point number | percentfull | ++---------------+-------------------------+----------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_globalconfig.rst b/source/auto_database_ref_docs/rundb_globalconfig.rst index 3e126c1..2a19894 100644 --- a/source/auto_database_ref_docs/rundb_globalconfig.rst +++ b/source/auto_database_ref_docs/rundb_globalconfig.rst @@ -12,3 +12,67 @@ Postgres table: ``rundb_globalconfig`` Schema ------- ++--------------------------------+----------------------------------+---------------------------------------+ +| Field | Type | Description | ++================================+==================================+=======================================+ +| auto\_archive\_ack | Boolean (Either True or False) | Auto-Acknowledge Delete? | ++--------------------------------+----------------------------------+---------------------------------------+ +| auto\_archive\_enable | Boolean (Either True or False) | Enable Auto Actions? | ++--------------------------------+----------------------------------+---------------------------------------+ +| barcode\_args | Text | barcode args | ++--------------------------------+----------------------------------+---------------------------------------+ +| base\_recalibration\_mode | String (up to 64) | base recalibration mode | ++--------------------------------+----------------------------------+---------------------------------------+ +| check\_news\_posts | Boolean (Either True or False) | check for news posts | ++--------------------------------+----------------------------------+---------------------------------------+ +| default\_flow\_order | String (up to 100) | default flow order | ++--------------------------------+----------------------------------+---------------------------------------+ +| default\_library\_key | String (up to 50) | default library key | ++--------------------------------+----------------------------------+---------------------------------------+ +| default\_plugin\_script | String (up to 500) | default plugin script | ++--------------------------------+----------------------------------+---------------------------------------+ +| default\_storage\_options | String (up to 500) | default storage options | ++--------------------------------+----------------------------------+---------------------------------------+ +| default\_test\_fragment\_key | String (up to 50) | default test fragment key | ++--------------------------------+----------------------------------+---------------------------------------+ +| enable\_auto\_pkg\_dl | Boolean (Either True or False) | Enable Package Auto Download | ++--------------------------------+----------------------------------+---------------------------------------+ +| enable\_auto\_security | Boolean (Either True or False) | Enable Security Updates | ++--------------------------------+----------------------------------+---------------------------------------+ +| enable\_compendia\_OCP | Boolean (Either True or False) | Enable OCP? | ++--------------------------------+----------------------------------+---------------------------------------+ +| enable\_nightly\_email | Boolean (Either True or False) | Enable Nightly Email Notifications? | ++--------------------------------+----------------------------------+---------------------------------------+ +| enable\_support\_upload | Boolean (Either True or False) | Enable Support Upload? | ++--------------------------------+----------------------------------+---------------------------------------+ +| enable\_version\_lock | Boolean (Either True or False) | Enable TS Version Lock | ++--------------------------------+----------------------------------+---------------------------------------+ +| fasta\_path | String (up to 512) | fasta path | ++--------------------------------+----------------------------------+---------------------------------------+ +| id | Integer | ID | ++--------------------------------+----------------------------------+---------------------------------------+ +| mark\_duplicates | Boolean (Either True or False) | mark duplicates | ++--------------------------------+----------------------------------+---------------------------------------+ +| name | String (up to 512) | name | ++--------------------------------+----------------------------------+---------------------------------------+ +| plugin\_folder | String (up to 512) | plugin folder | ++--------------------------------+----------------------------------+---------------------------------------+ +| plugin\_output\_folder | String (up to 500) | plugin output folder | ++--------------------------------+----------------------------------+---------------------------------------+ +| realign | Boolean (Either True or False) | realign | ++--------------------------------+----------------------------------+---------------------------------------+ +| records\_to\_display | Integer | records to display | ++--------------------------------+----------------------------------+---------------------------------------+ +| reference\_path | String (up to 1000) | reference path | ++--------------------------------+----------------------------------+---------------------------------------+ +| sec\_update\_status | String (up to 128) | sec update status | ++--------------------------------+----------------------------------+---------------------------------------+ +| selected | Boolean (Either True or False) | selected | ++--------------------------------+----------------------------------+---------------------------------------+ +| site\_name | String (up to 500) | site name | ++--------------------------------+----------------------------------+---------------------------------------+ +| ts\_update\_status | String (up to 256) | ts update status | ++--------------------------------+----------------------------------+---------------------------------------+ +| web\_root | String (up to 500) | web root | ++--------------------------------+----------------------------------+---------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_kitinfo.rst b/source/auto_database_ref_docs/rundb_kitinfo.rst index 3535600..20bad84 100644 --- a/source/auto_database_ref_docs/rundb_kitinfo.rst +++ b/source/auto_database_ref_docs/rundb_kitinfo.rst @@ -12,3 +12,37 @@ Postgres table: ``rundb_kitinfo`` Schema ------- ++------------------------------+----------------------------------+-----------------------------+ +| Field | Type | Description | ++==============================+==================================+=============================+ +| applicationType | String (up to 64) | applicationType | ++------------------------------+----------------------------------+-----------------------------+ +| categories | String (up to 256) | categories | ++------------------------------+----------------------------------+-----------------------------+ +| description | String (up to 3024) | description | ++------------------------------+----------------------------------+-----------------------------+ +| flowCount | Positive integer | flowCount | ++------------------------------+----------------------------------+-----------------------------+ +| id | Integer | ID | ++------------------------------+----------------------------------+-----------------------------+ +| instrumentType | String (up to 64) | instrumentType | ++------------------------------+----------------------------------+-----------------------------+ +| isActive | Boolean (Either True or False) | isActive | ++------------------------------+----------------------------------+-----------------------------+ +| kitType | String (up to 64) | kitType | ++------------------------------+----------------------------------+-----------------------------+ +| libraryReadLength | Positive integer | libraryReadLength | ++------------------------------+----------------------------------+-----------------------------+ +| name | String (up to 512) | name | ++------------------------------+----------------------------------+-----------------------------+ +| nucleotideType | String (up to 64) | nucleotideType | ++------------------------------+----------------------------------+-----------------------------+ +| runMode | String (up to 64) | runMode | ++------------------------------+----------------------------------+-----------------------------+ +| samplePrep\_instrumentType | String (up to 64) | samplePrep instrumentType | ++------------------------------+----------------------------------+-----------------------------+ +| templatingSize | String (up to 64) | templatingSize | ++------------------------------+----------------------------------+-----------------------------+ +| uid | String (up to 10) | uid | ++------------------------------+----------------------------------+-----------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_kitpart.rst b/source/auto_database_ref_docs/rundb_kitpart.rst index dc2acb8..779d7f0 100644 --- a/source/auto_database_ref_docs/rundb_kitpart.rst +++ b/source/auto_database_ref_docs/rundb_kitpart.rst @@ -12,3 +12,13 @@ Postgres table: ``rundb_kitpart`` Schema ------- ++-----------+------------------------+---------------------------------+ +| Field | Type | Description | ++===========+========================+=================================+ +| barcode | String (up to 64) | barcode | ++-----------+------------------------+---------------------------------+ +| id | Integer | ID | ++-----------+------------------------+---------------------------------+ +| kit | KitInfo (ForeignKey) | the related rundb.KitInfo row | ++-----------+------------------------+---------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_libmetrics.rst b/source/auto_database_ref_docs/rundb_libmetrics.rst index 4f26640..35b4d34 100644 --- a/source/auto_database_ref_docs/rundb_libmetrics.rst +++ b/source/auto_database_ref_docs/rundb_libmetrics.rst @@ -12,3 +12,201 @@ Postgres table: ``rundb_libmetrics`` Schema ------- ++--------------------------------+-------------------------+---------------------------------+ +| Field | Type | Description | ++================================+=========================+=================================+ +| Genome\_Version | String (up to 512) | Genome Version | ++--------------------------------+-------------------------+---------------------------------+ +| Index\_Version | String (up to 512) | Index Version | ++--------------------------------+-------------------------+---------------------------------+ +| align\_sample | Integer | align sample | ++--------------------------------+-------------------------+---------------------------------+ +| aveKeyCounts | Floating point number | aveKeyCounts | ++--------------------------------+-------------------------+---------------------------------+ +| cf | Floating point number | cf | ++--------------------------------+-------------------------+---------------------------------+ +| dr | Floating point number | dr | ++--------------------------------+-------------------------+---------------------------------+ +| duplicate\_reads | Integer | duplicate reads | ++--------------------------------+-------------------------+---------------------------------+ +| genome | String (up to 512) | genome | ++--------------------------------+-------------------------+---------------------------------+ +| genomesize | Big (8 byte) integer | genomesize | ++--------------------------------+-------------------------+---------------------------------+ +| i100Q10\_reads | Integer | i100Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i100Q17\_reads | Integer | i100Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i100Q20\_reads | Integer | i100Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i100Q47\_reads | Integer | i100Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i100Q7\_reads | Integer | i100Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i150Q10\_reads | Integer | i150Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i150Q17\_reads | Integer | i150Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i150Q20\_reads | Integer | i150Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i150Q47\_reads | Integer | i150Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i150Q7\_reads | Integer | i150Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i200Q10\_reads | Integer | i200Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i200Q17\_reads | Integer | i200Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i200Q20\_reads | Integer | i200Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i200Q47\_reads | Integer | i200Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i200Q7\_reads | Integer | i200Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i250Q10\_reads | Integer | i250Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i250Q17\_reads | Integer | i250Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i250Q20\_reads | Integer | i250Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i250Q47\_reads | Integer | i250Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i250Q7\_reads | Integer | i250Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i300Q10\_reads | Integer | i300Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i300Q17\_reads | Integer | i300Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i300Q20\_reads | Integer | i300Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i300Q47\_reads | Integer | i300Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i300Q7\_reads | Integer | i300Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i350Q10\_reads | Integer | i350Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i350Q17\_reads | Integer | i350Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i350Q20\_reads | Integer | i350Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i350Q47\_reads | Integer | i350Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i350Q7\_reads | Integer | i350Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i400Q10\_reads | Integer | i400Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i400Q17\_reads | Integer | i400Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i400Q20\_reads | Integer | i400Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i400Q47\_reads | Integer | i400Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i400Q7\_reads | Integer | i400Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i450Q10\_reads | Integer | i450Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i450Q17\_reads | Integer | i450Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i450Q20\_reads | Integer | i450Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i450Q47\_reads | Integer | i450Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i450Q7\_reads | Integer | i450Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i500Q10\_reads | Integer | i500Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i500Q17\_reads | Integer | i500Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i500Q20\_reads | Integer | i500Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i500Q47\_reads | Integer | i500Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i500Q7\_reads | Integer | i500Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i50Q10\_reads | Integer | i50Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i50Q17\_reads | Integer | i50Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i50Q20\_reads | Integer | i50Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i50Q47\_reads | Integer | i50Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i50Q7\_reads | Integer | i50Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i550Q10\_reads | Integer | i550Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i550Q17\_reads | Integer | i550Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i550Q20\_reads | Integer | i550Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i550Q47\_reads | Integer | i550Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i550Q7\_reads | Integer | i550Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i600Q10\_reads | Integer | i600Q10 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i600Q17\_reads | Integer | i600Q17 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i600Q20\_reads | Integer | i600Q20 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i600Q47\_reads | Integer | i600Q47 reads | ++--------------------------------+-------------------------+---------------------------------+ +| i600Q7\_reads | Integer | i600Q7 reads | ++--------------------------------+-------------------------+---------------------------------+ +| id | Integer | ID | ++--------------------------------+-------------------------+---------------------------------+ +| ie | Floating point number | ie | ++--------------------------------+-------------------------+---------------------------------+ +| q10\_alignments | Integer | q10 alignments | ++--------------------------------+-------------------------+---------------------------------+ +| q10\_longest\_alignment | Integer | q10 longest alignment | ++--------------------------------+-------------------------+---------------------------------+ +| q10\_mapped\_bases | Big (8 byte) integer | q10 mapped bases | ++--------------------------------+-------------------------+---------------------------------+ +| q10\_mean\_alignment\_length | Integer | q10 mean alignment length | ++--------------------------------+-------------------------+---------------------------------+ +| q17\_alignments | Integer | q17 alignments | ++--------------------------------+-------------------------+---------------------------------+ +| q17\_longest\_alignment | Integer | q17 longest alignment | ++--------------------------------+-------------------------+---------------------------------+ +| q17\_mapped\_bases | Big (8 byte) integer | q17 mapped bases | ++--------------------------------+-------------------------+---------------------------------+ +| q17\_mean\_alignment\_length | Integer | q17 mean alignment length | ++--------------------------------+-------------------------+---------------------------------+ +| q20\_alignments | Integer | q20 alignments | ++--------------------------------+-------------------------+---------------------------------+ +| q20\_longest\_alignment | Integer | q20 longest alignment | ++--------------------------------+-------------------------+---------------------------------+ +| q20\_mapped\_bases | Big (8 byte) integer | q20 mapped bases | ++--------------------------------+-------------------------+---------------------------------+ +| q20\_mean\_alignment\_length | Integer | q20 mean alignment length | ++--------------------------------+-------------------------+---------------------------------+ +| q47\_alignments | Integer | q47 alignments | ++--------------------------------+-------------------------+---------------------------------+ +| q47\_longest\_alignment | Integer | q47 longest alignment | ++--------------------------------+-------------------------+---------------------------------+ +| q47\_mapped\_bases | Big (8 byte) integer | q47 mapped bases | ++--------------------------------+-------------------------+---------------------------------+ +| q47\_mean\_alignment\_length | Integer | q47 mean alignment length | ++--------------------------------+-------------------------+---------------------------------+ +| q7\_alignments | Integer | q7 alignments | ++--------------------------------+-------------------------+---------------------------------+ +| q7\_longest\_alignment | Integer | q7 longest alignment | ++--------------------------------+-------------------------+---------------------------------+ +| q7\_mapped\_bases | Big (8 byte) integer | q7 mapped bases | ++--------------------------------+-------------------------+---------------------------------+ +| q7\_mean\_alignment\_length | Integer | q7 mean alignment length | ++--------------------------------+-------------------------+---------------------------------+ +| raw\_accuracy | Floating point number | raw accuracy | ++--------------------------------+-------------------------+---------------------------------+ +| report | Results (ForeignKey) | the related rundb.Results row | ++--------------------------------+-------------------------+---------------------------------+ +| sysSNR | Floating point number | sysSNR | ++--------------------------------+-------------------------+---------------------------------+ +| totalNumReads | Integer | totalNumReads | ++--------------------------------+-------------------------+---------------------------------+ +| total\_mapped\_reads | Big (8 byte) integer | total mapped reads | ++--------------------------------+-------------------------+---------------------------------+ +| total\_mapped\_target\_bases | Big (8 byte) integer | total mapped target bases | ++--------------------------------+-------------------------+---------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_librarykey.rst b/source/auto_database_ref_docs/rundb_librarykey.rst index 6f32da2..ca4a91b 100644 --- a/source/auto_database_ref_docs/rundb_librarykey.rst +++ b/source/auto_database_ref_docs/rundb_librarykey.rst @@ -12,3 +12,21 @@ Postgres table: ``rundb_librarykey`` Schema ------- ++---------------+----------------------------------+-----------------------+ +| Field | Type | Description | ++===============+==================================+=======================+ +| description | String (up to 1024) | description | ++---------------+----------------------------------+-----------------------+ +| direction | String (up to 20) | direction | ++---------------+----------------------------------+-----------------------+ +| id | Integer | ID | ++---------------+----------------------------------+-----------------------+ +| isDefault | Boolean (Either True or False) | use this by default | ++---------------+----------------------------------+-----------------------+ +| name | String (up to 256) | name | ++---------------+----------------------------------+-----------------------+ +| runMode | String (up to 64) | runMode | ++---------------+----------------------------------+-----------------------+ +| sequence | String (up to 64) | sequence | ++---------------+----------------------------------+-----------------------+ + diff --git a/source/auto_database_ref_docs/rundb_librarykit.rst b/source/auto_database_ref_docs/rundb_librarykit.rst index 948c4bb..f56bafc 100644 --- a/source/auto_database_ref_docs/rundb_librarykit.rst +++ b/source/auto_database_ref_docs/rundb_librarykit.rst @@ -12,3 +12,15 @@ Postgres table: ``rundb_librarykit`` Schema ------- ++---------------+-----------------------+---------------+ +| Field | Type | Description | ++===============+=======================+===============+ +| description | String (up to 3024) | description | ++---------------+-----------------------+---------------+ +| id | Integer | ID | ++---------------+-----------------------+---------------+ +| name | String (up to 512) | name | ++---------------+-----------------------+---------------+ +| sap | String (up to 7) | sap | ++---------------+-----------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_location.rst b/source/auto_database_ref_docs/rundb_location.rst index d00a4af..bed745f 100644 --- a/source/auto_database_ref_docs/rundb_location.rst +++ b/source/auto_database_ref_docs/rundb_location.rst @@ -12,3 +12,15 @@ Postgres table: ``rundb_location`` Schema ------- ++-------------------+----------------------------------+----------------------------------------------------------------------+ +| Field | Type | Description | ++===================+==================================+======================================================================+ +| comments | Text | comments | ++-------------------+----------------------------------+----------------------------------------------------------------------+ +| defaultlocation | Boolean (Either True or False) | Set as the Default Location - Only one location can be the default | ++-------------------+----------------------------------+----------------------------------------------------------------------+ +| id | Integer | ID | ++-------------------+----------------------------------+----------------------------------------------------------------------+ +| name | String (up to 200) | name | ++-------------------+----------------------------------+----------------------------------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_message.rst b/source/auto_database_ref_docs/rundb_message.rst index a5021d6..bd3181c 100644 --- a/source/auto_database_ref_docs/rundb_message.rst +++ b/source/auto_database_ref_docs/rundb_message.rst @@ -12,3 +12,23 @@ Postgres table: ``rundb_message`` Schema ------- ++-----------+--------------------+---------------+ +| Field | Type | Description | ++===========+====================+===============+ +| body | Text | body | ++-----------+--------------------+---------------+ +| expires | Text | expires | ++-----------+--------------------+---------------+ +| id | Integer | ID | ++-----------+--------------------+---------------+ +| level | Integer | level | ++-----------+--------------------+---------------+ +| route | Text | route | ++-----------+--------------------+---------------+ +| status | Text | status | ++-----------+--------------------+---------------+ +| tags | Text | tags | ++-----------+--------------------+---------------+ +| time | Date (with time) | time | ++-----------+--------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_monitordata.rst b/source/auto_database_ref_docs/rundb_monitordata.rst index 6b7690a..0387bc6 100644 --- a/source/auto_database_ref_docs/rundb_monitordata.rst +++ b/source/auto_database_ref_docs/rundb_monitordata.rst @@ -12,3 +12,13 @@ Postgres table: ``rundb_monitordata`` Schema ------- ++-----------+----------------------+---------------+ +| Field | Type | Description | ++===========+======================+===============+ +| id | Integer | ID | ++-----------+----------------------+---------------+ +| name | String (up to 128) | name | ++-----------+----------------------+---------------+ +| treeDat | Text | treeDat | ++-----------+----------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_newspost.rst b/source/auto_database_ref_docs/rundb_newspost.rst index 38f0fd5..da7203a 100644 --- a/source/auto_database_ref_docs/rundb_newspost.rst +++ b/source/auto_database_ref_docs/rundb_newspost.rst @@ -12,3 +12,19 @@ Postgres table: ``rundb_newspost`` Schema ------- ++-----------+-----------------------+---------------+ +| Field | Type | Description | ++===========+=======================+===============+ +| guid | String (up to 64) | guid | ++-----------+-----------------------+---------------+ +| id | Integer | ID | ++-----------+-----------------------+---------------+ +| link | String (up to 2000) | link | ++-----------+-----------------------+---------------+ +| summary | String (up to 300) | summary | ++-----------+-----------------------+---------------+ +| title | String (up to 140) | title | ++-----------+-----------------------+---------------+ +| updated | Date (with time) | updated | ++-----------+-----------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_plannedexperiment.rst b/source/auto_database_ref_docs/rundb_plannedexperiment.rst index 05099f6..0bcc4bc 100644 --- a/source/auto_database_ref_docs/rundb_plannedexperiment.rst +++ b/source/auto_database_ref_docs/rundb_plannedexperiment.rst @@ -12,3 +12,113 @@ Postgres table: ``rundb_plannedexperiment`` Schema ------- ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| Field | Type | Description | ++===============================+===========================================+====================================================+ +| adapter | String (up to 256) | adapter | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| applicationGroup | ApplicationGroup (ForeignKey) | the related rundb.ApplicationGroup row | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| autoName | String (up to 512) | autoName | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| categories | String (up to 64) | categories | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| chipBarcode | String (up to 64) | chipBarcode | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| controlSequencekitname | String (up to 512) | controlSequencekitname | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| cycles | Integer | cycles | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| date | Date (with time) | date | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| expName | String (up to 128) | expName | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| get\_sample\_count | Integer | None | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| id | Integer | ID | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| irworkflow | String (up to 1024) | irworkflow | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| isFavorite | Boolean (Either True or False) | isFavorite | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| isPlanGroup | Boolean (Either True or False) | isPlanGroup | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| isReusable | Boolean (Either True or False) | isReusable | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| isReverseRun | Boolean (Either True or False) | isReverseRun | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| isSystem | Boolean (Either True or False) | isSystem | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| isSystemDefault | Boolean (Either True or False) | isSystemDefault | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| latestEAS | ExperimentAnalysisSettings (ForeignKey) | the related rundb.ExperimentAnalysisSettings row | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| libkit | String (up to 512) | libkit | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| libraryReadLength | Positive integer | libraryReadLength | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| metaData | Text | metaData | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| pairedEndLibraryAdapterName | String (up to 512) | pairedEndLibraryAdapterName | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| parentPlan | PlannedExperiment (ForeignKey) | the related rundb.PlannedExperiment row | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| planDisplayedName | String (up to 512) | planDisplayedName | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| planExecuted | Boolean (Either True or False) | planExecuted | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| planExecutedDate | Date (with time) | planExecutedDate | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| planGUID | String (up to 512) | planGUID | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| planName | String (up to 512) | planName | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| planPGM | String (up to 128) | planPGM | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| planShortID | String (up to 5) | planShortID | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| planStatus | String (up to 512) | planStatus | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| preAnalysis | Boolean (Either True or False) | preAnalysis | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| reverse\_primer | String (up to 128) | reverse primer | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| runMode | String (up to 64) | runMode | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| runType | String (up to 512) | runType | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| runname | String (up to 255) | runname | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| sampleGrouping | SampleGroupType\_CV (ForeignKey) | the related rundb.SampleGroupType\_CV row | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| samplePrepKitName | String (up to 512) | samplePrepKitName | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| sampleSet | SampleSet (ForeignKey) | the related rundb.SampleSet row | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| sampleSet\_planIndex | Positive integer | sampleSet planIndex | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| sampleSet\_planTotal | Positive integer | sampleSet planTotal | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| sampleSet\_uid | String (up to 512) | sampleSet uid | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| sampleTubeLabel | String (up to 512) | sampleTubeLabel | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| seqKitBarcode | String (up to 64) | seqKitBarcode | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| storageHost | String (up to 128) | storageHost | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| storage\_options | String (up to 200) | storage options | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| templatingKitBarcode | String (up to 64) | templatingKitBarcode | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| templatingKitName | String (up to 512) | templatingKitName | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| templatingSize | String (up to 64) | templatingSize | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| usePostBeadfind | Boolean (Either True or False) | usePostBeadfind | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| usePreBeadfind | Boolean (Either True or False) | usePreBeadfind | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ +| username | String (up to 128) | username | ++-------------------------------+-------------------------------------------+----------------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_plannedexperimentqc.rst b/source/auto_database_ref_docs/rundb_plannedexperimentqc.rst index 5e09597..8519484 100644 --- a/source/auto_database_ref_docs/rundb_plannedexperimentqc.rst +++ b/source/auto_database_ref_docs/rundb_plannedexperimentqc.rst @@ -12,3 +12,15 @@ Postgres table: ``rundb_plannedexperimentqc`` Schema ------- ++---------------------+----------------------------------+-------------------------------------------+ +| Field | Type | Description | ++=====================+==================================+===========================================+ +| id | Integer | ID | ++---------------------+----------------------------------+-------------------------------------------+ +| plannedExperiment | PlannedExperiment (ForeignKey) | the related rundb.PlannedExperiment row | ++---------------------+----------------------------------+-------------------------------------------+ +| qcType | QCType (ForeignKey) | the related rundb.QCType row | ++---------------------+----------------------------------+-------------------------------------------+ +| threshold | Positive integer | threshold | ++---------------------+----------------------------------+-------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_plugin.rst b/source/auto_database_ref_docs/rundb_plugin.rst index a7a8719..c1b6b90 100644 --- a/source/auto_database_ref_docs/rundb_plugin.rst +++ b/source/auto_database_ref_docs/rundb_plugin.rst @@ -12,3 +12,41 @@ Postgres table: ``rundb_plugin`` Schema ------- ++-------------------+----------------------------------+-------------------+ +| Field | Type | Description | ++===================+==================================+===================+ +| active | Boolean (Either True or False) | active | ++-------------------+----------------------------------+-------------------+ +| autorun | Boolean (Either True or False) | autorun | ++-------------------+----------------------------------+-------------------+ +| autorunMutable | Boolean (Either True or False) | autorunMutable | ++-------------------+----------------------------------+-------------------+ +| config | Text | config | ++-------------------+----------------------------------+-------------------+ +| date | Date (with time) | date | ++-------------------+----------------------------------+-------------------+ +| description | Text | description | ++-------------------+----------------------------------+-------------------+ +| id | Integer | ID | ++-------------------+----------------------------------+-------------------+ +| majorBlock | Boolean (Either True or False) | majorBlock | ++-------------------+----------------------------------+-------------------+ +| name | String (up to 512) | name | ++-------------------+----------------------------------+-------------------+ +| path | String (up to 512) | path | ++-------------------+----------------------------------+-------------------+ +| pluginsettings | Text | pluginsettings | ++-------------------+----------------------------------+-------------------+ +| script | String (up to 256) | script | ++-------------------+----------------------------------+-------------------+ +| selected | Boolean (Either True or False) | selected | ++-------------------+----------------------------------+-------------------+ +| status | Text | status | ++-------------------+----------------------------------+-------------------+ +| url | URL | url | ++-------------------+----------------------------------+-------------------+ +| userinputfields | Text | userinputfields | ++-------------------+----------------------------------+-------------------+ +| version | String (up to 256) | version | ++-------------------+----------------------------------+-------------------+ + diff --git a/source/auto_database_ref_docs/rundb_pluginresult.rst b/source/auto_database_ref_docs/rundb_pluginresult.rst index 76b90db..7750549 100644 --- a/source/auto_database_ref_docs/rundb_pluginresult.rst +++ b/source/auto_database_ref_docs/rundb_pluginresult.rst @@ -12,3 +12,33 @@ Postgres table: ``rundb_pluginresult`` Schema ------- ++-------------+------------------------+---------------------------------+ +| Field | Type | Description | ++=============+========================+=================================+ +| apikey | String (up to 256) | apikey | ++-------------+------------------------+---------------------------------+ +| config | Text | config | ++-------------+------------------------+---------------------------------+ +| endtime | Date (with time) | endtime | ++-------------+------------------------+---------------------------------+ +| id | Integer | ID | ++-------------+------------------------+---------------------------------+ +| inodes | Big (8 byte) integer | inodes | ++-------------+------------------------+---------------------------------+ +| jobid | Integer | jobid | ++-------------+------------------------+---------------------------------+ +| owner | User (ForeignKey) | the related auth.User row | ++-------------+------------------------+---------------------------------+ +| plugin | Plugin (ForeignKey) | the related rundb.Plugin row | ++-------------+------------------------+---------------------------------+ +| result | Results (ForeignKey) | the related rundb.Results row | ++-------------+------------------------+---------------------------------+ +| size | Big (8 byte) integer | size | ++-------------+------------------------+---------------------------------+ +| starttime | Date (with time) | starttime | ++-------------+------------------------+---------------------------------+ +| state | String (up to 20) | state | ++-------------+------------------------+---------------------------------+ +| store | Text | store | ++-------------+------------------------+---------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_project.rst b/source/auto_database_ref_docs/rundb_project.rst index fa2e8e0..17c5eb5 100644 --- a/source/auto_database_ref_docs/rundb_project.rst +++ b/source/auto_database_ref_docs/rundb_project.rst @@ -12,3 +12,19 @@ Postgres table: ``rundb_project`` Schema ------- ++------------+----------------------------------+-----------------------------+ +| Field | Type | Description | ++============+==================================+=============================+ +| created | Date (with time) | created | ++------------+----------------------------------+-----------------------------+ +| creator | User (ForeignKey) | the related auth.User row | ++------------+----------------------------------+-----------------------------+ +| id | Integer | ID | ++------------+----------------------------------+-----------------------------+ +| modified | Date (with time) | modified | ++------------+----------------------------------+-----------------------------+ +| name | String (up to 64) | name | ++------------+----------------------------------+-----------------------------+ +| public | Boolean (Either True or False) | public | ++------------+----------------------------------+-----------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_publisher.rst b/source/auto_database_ref_docs/rundb_publisher.rst index e0d7b65..dd574a4 100644 --- a/source/auto_database_ref_docs/rundb_publisher.rst +++ b/source/auto_database_ref_docs/rundb_publisher.rst @@ -12,3 +12,19 @@ Postgres table: ``rundb_publisher`` Schema ------- ++----------------+----------------------+---------------+ +| Field | Type | Description | ++================+======================+===============+ +| date | Date (with time) | date | ++----------------+----------------------+---------------+ +| global\_meta | Text | global meta | ++----------------+----------------------+---------------+ +| id | Integer | ID | ++----------------+----------------------+---------------+ +| name | String (up to 200) | name | ++----------------+----------------------+---------------+ +| path | String (up to 512) | path | ++----------------+----------------------+---------------+ +| version | String (up to 256) | version | ++----------------+----------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_qctype.rst b/source/auto_database_ref_docs/rundb_qctype.rst index 943f6ad..d2e409d 100644 --- a/source/auto_database_ref_docs/rundb_qctype.rst +++ b/source/auto_database_ref_docs/rundb_qctype.rst @@ -12,3 +12,19 @@ Postgres table: ``rundb_qctype`` Schema ------- ++--------------------+-----------------------+--------------------+ +| Field | Type | Description | ++====================+=======================+====================+ +| defaultThreshold | Positive integer | defaultThreshold | ++--------------------+-----------------------+--------------------+ +| description | String (up to 1024) | description | ++--------------------+-----------------------+--------------------+ +| id | Integer | ID | ++--------------------+-----------------------+--------------------+ +| maxThreshold | Positive integer | maxThreshold | ++--------------------+-----------------------+--------------------+ +| minThreshold | Positive integer | minThreshold | ++--------------------+-----------------------+--------------------+ +| qcName | String (up to 512) | qcName | ++--------------------+-----------------------+--------------------+ + diff --git a/source/auto_database_ref_docs/rundb_qualitymetrics.rst b/source/auto_database_ref_docs/rundb_qualitymetrics.rst index 9f55e8d..27584d9 100644 --- a/source/auto_database_ref_docs/rundb_qualitymetrics.rst +++ b/source/auto_database_ref_docs/rundb_qualitymetrics.rst @@ -12,3 +12,65 @@ Postgres table: ``rundb_qualitymetrics`` Schema ------- ++-----------------------------+-------------------------+---------------------------------+ +| Field | Type | Description | ++=============================+=========================+=================================+ +| id | Integer | ID | ++-----------------------------+-------------------------+---------------------------------+ +| q0\_100bp\_reads | Integer | q0 100bp reads | ++-----------------------------+-------------------------+---------------------------------+ +| q0\_150bp\_reads | Integer | q0 150bp reads | ++-----------------------------+-------------------------+---------------------------------+ +| q0\_50bp\_reads | Integer | q0 50bp reads | ++-----------------------------+-------------------------+---------------------------------+ +| q0\_bases | Big (8 byte) integer | q0 bases | ++-----------------------------+-------------------------+---------------------------------+ +| q0\_max\_read\_length | Integer | q0 max read length | ++-----------------------------+-------------------------+---------------------------------+ +| q0\_mean\_read\_length | Floating point number | q0 mean read length | ++-----------------------------+-------------------------+---------------------------------+ +| q0\_median\_read\_length | Integer | q0 median read length | ++-----------------------------+-------------------------+---------------------------------+ +| q0\_mode\_read\_length | Integer | q0 mode read length | ++-----------------------------+-------------------------+---------------------------------+ +| q0\_reads | Integer | q0 reads | ++-----------------------------+-------------------------+---------------------------------+ +| q17\_100bp\_reads | Integer | q17 100bp reads | ++-----------------------------+-------------------------+---------------------------------+ +| q17\_150bp\_reads | Integer | q17 150bp reads | ++-----------------------------+-------------------------+---------------------------------+ +| q17\_50bp\_reads | Integer | q17 50bp reads | ++-----------------------------+-------------------------+---------------------------------+ +| q17\_bases | Big (8 byte) integer | q17 bases | ++-----------------------------+-------------------------+---------------------------------+ +| q17\_max\_read\_length | Integer | q17 max read length | ++-----------------------------+-------------------------+---------------------------------+ +| q17\_mean\_read\_length | Floating point number | q17 mean read length | ++-----------------------------+-------------------------+---------------------------------+ +| q17\_median\_read\_length | Integer | q17 median read length | ++-----------------------------+-------------------------+---------------------------------+ +| q17\_mode\_read\_length | Integer | q17 mode read length | ++-----------------------------+-------------------------+---------------------------------+ +| q17\_reads | Integer | q17 reads | ++-----------------------------+-------------------------+---------------------------------+ +| q20\_100bp\_reads | Integer | q20 100bp reads | ++-----------------------------+-------------------------+---------------------------------+ +| q20\_150bp\_reads | Integer | q20 150bp reads | ++-----------------------------+-------------------------+---------------------------------+ +| q20\_50bp\_reads | Integer | q20 50bp reads | ++-----------------------------+-------------------------+---------------------------------+ +| q20\_bases | Big (8 byte) integer | q20 bases | ++-----------------------------+-------------------------+---------------------------------+ +| q20\_max\_read\_length | Floating point number | q20 max read length | ++-----------------------------+-------------------------+---------------------------------+ +| q20\_mean\_read\_length | Integer | q20 mean read length | ++-----------------------------+-------------------------+---------------------------------+ +| q20\_median\_read\_length | Integer | q20 median read length | ++-----------------------------+-------------------------+---------------------------------+ +| q20\_mode\_read\_length | Integer | q20 mode read length | ++-----------------------------+-------------------------+---------------------------------+ +| q20\_reads | Integer | q20 reads | ++-----------------------------+-------------------------+---------------------------------+ +| report | Results (ForeignKey) | the related rundb.Results row | ++-----------------------------+-------------------------+---------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_referencegenome.rst b/source/auto_database_ref_docs/rundb_referencegenome.rst index efaf044..6a46393 100644 --- a/source/auto_database_ref_docs/rundb_referencegenome.rst +++ b/source/auto_database_ref_docs/rundb_referencegenome.rst @@ -12,3 +12,39 @@ Postgres table: ``rundb_referencegenome`` Schema ------- ++--------------------+----------------------------------+-------------------------------------+ +| Field | Type | Description | ++====================+==================================+=====================================+ +| celery\_task\_id | String (up to 60) | celery task id | ++--------------------+----------------------------------+-------------------------------------+ +| date | Date (with time) | date | ++--------------------+----------------------------------+-------------------------------------+ +| enabled | Boolean (Either True or False) | enabled | ++--------------------+----------------------------------+-------------------------------------+ +| file\_monitor | FileMonitor (ForeignKey) | the related rundb.FileMonitor row | ++--------------------+----------------------------------+-------------------------------------+ +| id | Integer | ID | ++--------------------+----------------------------------+-------------------------------------+ +| identity\_hash | String (up to 40) | identity hash | ++--------------------+----------------------------------+-------------------------------------+ +| index\_version | String (up to 512) | index version | ++--------------------+----------------------------------+-------------------------------------+ +| name | String (up to 512) | name | ++--------------------+----------------------------------+-------------------------------------+ +| notes | Text | notes | ++--------------------+----------------------------------+-------------------------------------+ +| reference\_path | String (up to 1024) | reference path | ++--------------------+----------------------------------+-------------------------------------+ +| short\_name | String (up to 512) | short name | ++--------------------+----------------------------------+-------------------------------------+ +| source | String (up to 512) | source | ++--------------------+----------------------------------+-------------------------------------+ +| species | String (up to 512) | species | ++--------------------+----------------------------------+-------------------------------------+ +| status | String (up to 512) | status | ++--------------------+----------------------------------+-------------------------------------+ +| verbose\_error | String (up to 3000) | verbose error | ++--------------------+----------------------------------+-------------------------------------+ +| version | String (up to 100) | version | ++--------------------+----------------------------------+-------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_remoteaccount.rst b/source/auto_database_ref_docs/rundb_remoteaccount.rst index d2fd278..15a11e9 100644 --- a/source/auto_database_ref_docs/rundb_remoteaccount.rst +++ b/source/auto_database_ref_docs/rundb_remoteaccount.rst @@ -12,3 +12,21 @@ Postgres table: ``rundb_remoteaccount`` Schema ------- ++--------------------+-----------------------+-------------------+ +| Field | Type | Description | ++====================+=======================+===================+ +| access\_token | String (up to 2048) | access token | ++--------------------+-----------------------+-------------------+ +| account\_label | String (up to 64) | account label | ++--------------------+-----------------------+-------------------+ +| id | Integer | ID | ++--------------------+-----------------------+-------------------+ +| refresh\_token | String (up to 2048) | refresh token | ++--------------------+-----------------------+-------------------+ +| remote\_resource | String (up to 2048) | remote resource | ++--------------------+-----------------------+-------------------+ +| token\_expires | Date (with time) | token expires | ++--------------------+-----------------------+-------------------+ +| user\_name | String (up to 255) | user name | ++--------------------+-----------------------+-------------------+ + diff --git a/source/auto_database_ref_docs/rundb_reportstorage.rst b/source/auto_database_ref_docs/rundb_reportstorage.rst index 795b87a..0d73755 100644 --- a/source/auto_database_ref_docs/rundb_reportstorage.rst +++ b/source/auto_database_ref_docs/rundb_reportstorage.rst @@ -12,3 +12,17 @@ Postgres table: ``rundb_reportstorage`` Schema ------- ++-----------------+----------------------------------+-----------------+ +| Field | Type | Description | ++=================+==================================+=================+ +| default | Boolean (Either True or False) | default | ++-----------------+----------------------------------+-----------------+ +| dirPath | String (up to 200) | dirPath | ++-----------------+----------------------------------+-----------------+ +| id | Integer | ID | ++-----------------+----------------------------------+-----------------+ +| name | String (up to 200) | name | ++-----------------+----------------------------------+-----------------+ +| webServerPath | String (up to 200) | webServerPath | ++-----------------+----------------------------------+-----------------+ + diff --git a/source/auto_database_ref_docs/rundb_results.rst b/source/auto_database_ref_docs/rundb_results.rst index f28007f..34240fa 100644 --- a/source/auto_database_ref_docs/rundb_results.rst +++ b/source/auto_database_ref_docs/rundb_results.rst @@ -12,3 +12,67 @@ Postgres table: ``rundb_results`` Schema ------- ++-------------------+-------------------------------------------+----------------------------------------------------+ +| Field | Type | Description | ++===================+===========================================+====================================================+ +| analysisVersion | String (up to 256) | analysisVersion | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| analysismetrics | AnalysisMetrics (ForeignKey) | the related rundb.AnalysisMetrics row | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| autoExempt | Boolean (Either True or False) | autoExempt | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| diskusage | Integer | diskusage | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| eas | ExperimentAnalysisSettings (ForeignKey) | the related rundb.ExperimentAnalysisSettings row | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| experiment | Experiment (ForeignKey) | the related rundb.Experiment row | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| fastqLink | String (up to 512) | fastqLink | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| framesProcessed | Integer | framesProcessed | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| id | Integer | ID | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| libmetrics | LibMetrics (ForeignKey) | the related rundb.LibMetrics row | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| log | Text | log | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| metaData | Text | metaData | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| parentIDs | String (up to 512) | parentIDs | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| processedCycles | Integer | processedCycles | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| processedflows | Integer | processedflows | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| qualitymetrics | QualityMetrics (ForeignKey) | the related rundb.QualityMetrics row | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| reference | String (up to 64) | reference | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| reportLink | String (up to 512) | reportLink | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| reportStatus | String (up to 64) | reportStatus | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| reportstorage | ReportStorage (ForeignKey) | the related rundb.ReportStorage row | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| representative | Boolean (Either True or False) | representative | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| resultsName | String (up to 512) | resultsName | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| resultsType | String (up to 512) | resultsType | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| runid | String (up to 10) | runid | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| sffLink | String (up to 512) | sffLink | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| status | String (up to 64) | status | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| tfFastq | String (up to 512) | tfFastq | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| tfSffLink | String (up to 512) | tfSffLink | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| timeStamp | Date (with time) | timeStamp | ++-------------------+-------------------------------------------+----------------------------------------------------+ +| timeToComplete | String (up to 64) | timeToComplete | ++-------------------+-------------------------------------------+----------------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_rig.rst b/source/auto_database_ref_docs/rundb_rig.rst index 0ccd08f..bd149fc 100644 --- a/source/auto_database_ref_docs/rundb_rig.rst +++ b/source/auto_database_ref_docs/rundb_rig.rst @@ -12,3 +12,45 @@ Postgres table: ``rundb_rig`` Schema ------- ++---------------------+----------------------------------+----------------------------------+ +| Field | Type | Description | ++=====================+==================================+==================================+ +| alarms | Text | alarms | ++---------------------+----------------------------------+----------------------------------+ +| comments | Text | comments | ++---------------------+----------------------------------+----------------------------------+ +| ftppassword | String (up to 64) | ftppassword | ++---------------------+----------------------------------+----------------------------------+ +| ftprootdir | String (up to 64) | ftprootdir | ++---------------------+----------------------------------+----------------------------------+ +| ftpserver | String (up to 128) | ftpserver | ++---------------------+----------------------------------+----------------------------------+ +| ftpusername | String (up to 64) | ftpusername | ++---------------------+----------------------------------+----------------------------------+ +| host\_address | String (up to 1024) | host address | ++---------------------+----------------------------------+----------------------------------+ +| last\_clean\_date | String (up to 512) | last clean date | ++---------------------+----------------------------------+----------------------------------+ +| last\_experiment | String (up to 512) | last experiment | ++---------------------+----------------------------------+----------------------------------+ +| last\_init\_date | String (up to 512) | last init date | ++---------------------+----------------------------------+----------------------------------+ +| location | Location (ForeignKey) | the related rundb.Location row | ++---------------------+----------------------------------+----------------------------------+ +| name | String (up to 200) | name | ++---------------------+----------------------------------+----------------------------------+ +| serial | String (up to 24) | serial | ++---------------------+----------------------------------+----------------------------------+ +| state | String (up to 512) | state | ++---------------------+----------------------------------+----------------------------------+ +| type | String (up to 1024) | type | ++---------------------+----------------------------------+----------------------------------+ +| updateCommand | Text | updateCommand | ++---------------------+----------------------------------+----------------------------------+ +| updateflag | Boolean (Either True or False) | updateflag | ++---------------------+----------------------------------+----------------------------------+ +| updatehome | String (up to 256) | updatehome | ++---------------------+----------------------------------+----------------------------------+ +| version | Text | version | ++---------------------+----------------------------------+----------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_runtype.rst b/source/auto_database_ref_docs/rundb_runtype.rst index b9c9a08..767718b 100644 --- a/source/auto_database_ref_docs/rundb_runtype.rst +++ b/source/auto_database_ref_docs/rundb_runtype.rst @@ -12,3 +12,21 @@ Postgres table: ``rundb_runtype`` Schema ------- ++-------------------+----------------------+------------------+ +| Field | Type | Description | ++===================+======================+==================+ +| alternate\_name | String (up to 512) | alternate name | ++-------------------+----------------------+------------------+ +| barcode | String (up to 512) | barcode | ++-------------------+----------------------+------------------+ +| description | Text | description | ++-------------------+----------------------+------------------+ +| id | Integer | ID | ++-------------------+----------------------+------------------+ +| meta | Text | meta | ++-------------------+----------------------+------------------+ +| nucleotideType | String (up to 64) | nucleotideType | ++-------------------+----------------------+------------------+ +| runType | String (up to 512) | runType | ++-------------------+----------------------+------------------+ + diff --git a/source/auto_database_ref_docs/rundb_sample.rst b/source/auto_database_ref_docs/rundb_sample.rst index f3e7ebc..6317330 100644 --- a/source/auto_database_ref_docs/rundb_sample.rst +++ b/source/auto_database_ref_docs/rundb_sample.rst @@ -12,3 +12,21 @@ Postgres table: ``rundb_sample`` Schema ------- ++-----------------+-----------------------+-----------------+ +| Field | Type | Description | ++=================+=======================+=================+ +| date | Date (with time) | date | ++-----------------+-----------------------+-----------------+ +| description | String (up to 1024) | description | ++-----------------+-----------------------+-----------------+ +| displayedName | String (up to 127) | displayedName | ++-----------------+-----------------------+-----------------+ +| externalId | String (up to 127) | externalId | ++-----------------+-----------------------+-----------------+ +| id | Integer | ID | ++-----------------+-----------------------+-----------------+ +| name | String (up to 127) | name | ++-----------------+-----------------------+-----------------+ +| status | String (up to 512) | status | ++-----------------+-----------------------+-----------------+ + diff --git a/source/auto_database_ref_docs/rundb_sampleannotation_cv.rst b/source/auto_database_ref_docs/rundb_sampleannotation_cv.rst index 0230dd1..c09bfc2 100644 --- a/source/auto_database_ref_docs/rundb_sampleannotation_cv.rst +++ b/source/auto_database_ref_docs/rundb_sampleannotation_cv.rst @@ -12,3 +12,25 @@ Postgres table: ``rundb_sampleannotation_cv`` Schema ------- ++-----------------------+------------------------------------+---------------------------------------------+ +| Field | Type | Description | ++=======================+====================================+=============================================+ +| annotationType | String (up to 127) | annotationType | ++-----------------------+------------------------------------+---------------------------------------------+ +| iRAnnotationType | String (up to 127) | iRAnnotationType | ++-----------------------+------------------------------------+---------------------------------------------+ +| iRValue | String (up to 127) | iRValue | ++-----------------------+------------------------------------+---------------------------------------------+ +| id | Integer | ID | ++-----------------------+------------------------------------+---------------------------------------------+ +| isActive | Boolean (Either True or False) | isActive | ++-----------------------+------------------------------------+---------------------------------------------+ +| isIRCompatible | Boolean (Either True or False) | isIRCompatible | ++-----------------------+------------------------------------+---------------------------------------------+ +| sampleGroupType\_CV | SampleGroupType\_CV (ForeignKey) | the related rundb.SampleGroupType\_CV row | ++-----------------------+------------------------------------+---------------------------------------------+ +| uid | String (up to 32) | uid | ++-----------------------+------------------------------------+---------------------------------------------+ +| value | String (up to 127) | value | ++-----------------------+------------------------------------+---------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_sampleattribute.rst b/source/auto_database_ref_docs/rundb_sampleattribute.rst index e2a4cee..e7d94e8 100644 --- a/source/auto_database_ref_docs/rundb_sampleattribute.rst +++ b/source/auto_database_ref_docs/rundb_sampleattribute.rst @@ -12,3 +12,27 @@ Postgres table: ``rundb_sampleattribute`` Schema ------- ++--------------------+----------------------------------------+-------------------------------------------------+ +| Field | Type | Description | ++====================+========================================+=================================================+ +| creationDate | Date (with time) | creationDate | ++--------------------+----------------------------------------+-------------------------------------------------+ +| creator | User (ForeignKey) | the related auth.User row | ++--------------------+----------------------------------------+-------------------------------------------------+ +| dataType | SampleAttributeDataType (ForeignKey) | the related rundb.SampleAttributeDataType row | ++--------------------+----------------------------------------+-------------------------------------------------+ +| description | String (up to 1024) | description | ++--------------------+----------------------------------------+-------------------------------------------------+ +| displayedName | String (up to 127) | displayedName | ++--------------------+----------------------------------------+-------------------------------------------------+ +| id | Integer | ID | ++--------------------+----------------------------------------+-------------------------------------------------+ +| isActive | Boolean (Either True or False) | isActive | ++--------------------+----------------------------------------+-------------------------------------------------+ +| isMandatory | Boolean (Either True or False) | isMandatory | ++--------------------+----------------------------------------+-------------------------------------------------+ +| lastModifiedDate | Date (with time) | lastModifiedDate | ++--------------------+----------------------------------------+-------------------------------------------------+ +| lastModifiedUser | User (ForeignKey) | the related auth.User row | ++--------------------+----------------------------------------+-------------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_sampleattributedatatype.rst b/source/auto_database_ref_docs/rundb_sampleattributedatatype.rst index b9c61ff..22b41a6 100644 --- a/source/auto_database_ref_docs/rundb_sampleattributedatatype.rst +++ b/source/auto_database_ref_docs/rundb_sampleattributedatatype.rst @@ -12,3 +12,15 @@ Postgres table: ``rundb_sampleattributedatatype`` Schema ------- ++---------------+----------------------------------+---------------+ +| Field | Type | Description | ++===============+==================================+===============+ +| dataType | String (up to 64) | dataType | ++---------------+----------------------------------+---------------+ +| description | String (up to 1024) | description | ++---------------+----------------------------------+---------------+ +| id | Integer | ID | ++---------------+----------------------------------+---------------+ +| isActive | Boolean (Either True or False) | isActive | ++---------------+----------------------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_sampleattributevalue.rst b/source/auto_database_ref_docs/rundb_sampleattributevalue.rst index 30587ab..2c9b9a9 100644 --- a/source/auto_database_ref_docs/rundb_sampleattributevalue.rst +++ b/source/auto_database_ref_docs/rundb_sampleattributevalue.rst @@ -12,3 +12,23 @@ Postgres table: ``rundb_sampleattributevalue`` Schema ------- ++--------------------+--------------------------------+-----------------------------------------+ +| Field | Type | Description | ++====================+================================+=========================================+ +| creationDate | Date (with time) | creationDate | ++--------------------+--------------------------------+-----------------------------------------+ +| creator | User (ForeignKey) | the related auth.User row | ++--------------------+--------------------------------+-----------------------------------------+ +| id | Integer | ID | ++--------------------+--------------------------------+-----------------------------------------+ +| lastModifiedDate | Date (with time) | lastModifiedDate | ++--------------------+--------------------------------+-----------------------------------------+ +| lastModifiedUser | User (ForeignKey) | the related auth.User row | ++--------------------+--------------------------------+-----------------------------------------+ +| sample | Sample (ForeignKey) | the related rundb.Sample row | ++--------------------+--------------------------------+-----------------------------------------+ +| sampleAttribute | SampleAttribute (ForeignKey) | the related rundb.SampleAttribute row | ++--------------------+--------------------------------+-----------------------------------------+ +| value | String (up to 1024) | value | ++--------------------+--------------------------------+-----------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_samplegrouptype_cv.rst b/source/auto_database_ref_docs/rundb_samplegrouptype_cv.rst index 599b89e..98701bf 100644 --- a/source/auto_database_ref_docs/rundb_samplegrouptype_cv.rst +++ b/source/auto_database_ref_docs/rundb_samplegrouptype_cv.rst @@ -12,3 +12,23 @@ Postgres table: ``rundb_samplegrouptype_cv`` Schema ------- ++--------------------+----------------------------------+--------------------+ +| Field | Type | Description | ++====================+==================================+====================+ +| description | String (up to 1024) | description | ++--------------------+----------------------------------+--------------------+ +| displayedName | String (up to 127) | displayedName | ++--------------------+----------------------------------+--------------------+ +| iRAnnotationType | String (up to 127) | iRAnnotationType | ++--------------------+----------------------------------+--------------------+ +| iRValue | String (up to 127) | iRValue | ++--------------------+----------------------------------+--------------------+ +| id | Integer | ID | ++--------------------+----------------------------------+--------------------+ +| isActive | Boolean (Either True or False) | isActive | ++--------------------+----------------------------------+--------------------+ +| isIRCompatible | Boolean (Either True or False) | isIRCompatible | ++--------------------+----------------------------------+--------------------+ +| uid | String (up to 32) | uid | ++--------------------+----------------------------------+--------------------+ + diff --git a/source/auto_database_ref_docs/rundb_sampleset.rst b/source/auto_database_ref_docs/rundb_sampleset.rst index 22ae834..b456d0b 100644 --- a/source/auto_database_ref_docs/rundb_sampleset.rst +++ b/source/auto_database_ref_docs/rundb_sampleset.rst @@ -12,3 +12,25 @@ Postgres table: ``rundb_sampleset`` Schema ------- ++-----------------------+------------------------------------+---------------------------------------------+ +| Field | Type | Description | ++=======================+====================================+=============================================+ +| SampleGroupType\_CV | SampleGroupType\_CV (ForeignKey) | the related rundb.SampleGroupType\_CV row | ++-----------------------+------------------------------------+---------------------------------------------+ +| creationDate | Date (with time) | creationDate | ++-----------------------+------------------------------------+---------------------------------------------+ +| creator | User (ForeignKey) | the related auth.User row | ++-----------------------+------------------------------------+---------------------------------------------+ +| description | String (up to 1024) | description | ++-----------------------+------------------------------------+---------------------------------------------+ +| displayedName | String (up to 127) | displayedName | ++-----------------------+------------------------------------+---------------------------------------------+ +| id | Integer | ID | ++-----------------------+------------------------------------+---------------------------------------------+ +| lastModifiedDate | Date (with time) | lastModifiedDate | ++-----------------------+------------------------------------+---------------------------------------------+ +| lastModifiedUser | User (ForeignKey) | the related auth.User row | ++-----------------------+------------------------------------+---------------------------------------------+ +| status | String (up to 512) | status | ++-----------------------+------------------------------------+---------------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_samplesetitem.rst b/source/auto_database_ref_docs/rundb_samplesetitem.rst index aa6783a..b263d1b 100644 --- a/source/auto_database_ref_docs/rundb_samplesetitem.rst +++ b/source/auto_database_ref_docs/rundb_samplesetitem.rst @@ -12,3 +12,33 @@ Postgres table: ``rundb_samplesetitem`` Schema ------- ++---------------------+---------------------------+------------------------------------+ +| Field | Type | Description | ++=====================+===========================+====================================+ +| cancerType | String (up to 127) | cancerType | ++---------------------+---------------------------+------------------------------------+ +| cellularityPct | Integer | cellularityPct | ++---------------------+---------------------------+------------------------------------+ +| creationDate | Date (with time) | creationDate | ++---------------------+---------------------------+------------------------------------+ +| creator | User (ForeignKey) | the related auth.User row | ++---------------------+---------------------------+------------------------------------+ +| dnabarcode | dnaBarcode (ForeignKey) | the related rundb.dnaBarcode row | ++---------------------+---------------------------+------------------------------------+ +| gender | String (up to 127) | gender | ++---------------------+---------------------------+------------------------------------+ +| id | Integer | ID | ++---------------------+---------------------------+------------------------------------+ +| lastModifiedDate | Date (with time) | lastModifiedDate | ++---------------------+---------------------------+------------------------------------+ +| lastModifiedUser | User (ForeignKey) | the related auth.User row | ++---------------------+---------------------------+------------------------------------+ +| relationshipGroup | Integer | relationshipGroup | ++---------------------+---------------------------+------------------------------------+ +| relationshipRole | String (up to 127) | relationshipRole | ++---------------------+---------------------------+------------------------------------+ +| sample | Sample (ForeignKey) | the related rundb.Sample row | ++---------------------+---------------------------+------------------------------------+ +| sampleSet | SampleSet (ForeignKey) | the related rundb.SampleSet row | ++---------------------+---------------------------+------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_sequencingkit.rst b/source/auto_database_ref_docs/rundb_sequencingkit.rst index 57a7c7c..c59d5a7 100644 --- a/source/auto_database_ref_docs/rundb_sequencingkit.rst +++ b/source/auto_database_ref_docs/rundb_sequencingkit.rst @@ -12,3 +12,15 @@ Postgres table: ``rundb_sequencingkit`` Schema ------- ++---------------+-----------------------+---------------+ +| Field | Type | Description | ++===============+=======================+===============+ +| description | String (up to 3024) | description | ++---------------+-----------------------+---------------+ +| id | Integer | ID | ++---------------+-----------------------+---------------+ +| name | String (up to 512) | name | ++---------------+-----------------------+---------------+ +| sap | String (up to 7) | sap | ++---------------+-----------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_sharedserver.rst b/source/auto_database_ref_docs/rundb_sharedserver.rst new file mode 100644 index 0000000..4b509ba --- /dev/null +++ b/source/auto_database_ref_docs/rundb_sharedserver.rst @@ -0,0 +1,32 @@ +Database Table rundb_sharedserver +============================================================================ + +Postgres database: ``iondb`` + + +Postgres table: ``rundb_sharedserver`` + + +.. include:: ../manual_database_ref_docs/rundb_sharedserver.rst + +Schema +------- + ++------------+----------------------------------+---------------+ +| Field | Type | Description | ++============+==================================+===============+ +| active | Boolean (Either True or False) | active | ++------------+----------------------------------+---------------+ +| address | String (up to 128) | address | ++------------+----------------------------------+---------------+ +| comments | Text | comments | ++------------+----------------------------------+---------------+ +| id | Integer | ID | ++------------+----------------------------------+---------------+ +| name | String (up to 128) | name | ++------------+----------------------------------+---------------+ +| password | String (up to 64) | password | ++------------+----------------------------------+---------------+ +| username | String (up to 64) | username | ++------------+----------------------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_supportupload.rst b/source/auto_database_ref_docs/rundb_supportupload.rst index 062fa37..3dba3f6 100644 --- a/source/auto_database_ref_docs/rundb_supportupload.rst +++ b/source/auto_database_ref_docs/rundb_supportupload.rst @@ -12,3 +12,37 @@ Postgres table: ``rundb_supportupload`` Schema ------- ++--------------------+------------------------------+---------------------------------------+ +| Field | Type | Description | ++====================+==============================+=======================================+ +| account | RemoteAccount (ForeignKey) | the related rundb.RemoteAccount row | ++--------------------+------------------------------+---------------------------------------+ +| celery\_task\_id | String (up to 60) | celery task id | ++--------------------+------------------------------+---------------------------------------+ +| contact\_email | Email address | contact email | ++--------------------+------------------------------+---------------------------------------+ +| created | Date (with time) | created | ++--------------------+------------------------------+---------------------------------------+ +| description | Text | description | ++--------------------+------------------------------+---------------------------------------+ +| file | FileMonitor (ForeignKey) | the related rundb.FileMonitor row | ++--------------------+------------------------------+---------------------------------------+ +| id | Integer | ID | ++--------------------+------------------------------+---------------------------------------+ +| local\_message | String (up to 2048) | local message | ++--------------------+------------------------------+---------------------------------------+ +| local\_status | String (up to 255) | local status | ++--------------------+------------------------------+---------------------------------------+ +| result | Results (ForeignKey) | the related rundb.Results row | ++--------------------+------------------------------+---------------------------------------+ +| ticket\_id | String (up to 255) | ticket id | ++--------------------+------------------------------+---------------------------------------+ +| ticket\_message | String (up to 2048) | ticket message | ++--------------------+------------------------------+---------------------------------------+ +| ticket\_status | String (up to 255) | ticket status | ++--------------------+------------------------------+---------------------------------------+ +| updated | Date (with time) | updated | ++--------------------+------------------------------+---------------------------------------+ +| user | User (ForeignKey) | the related auth.User row | ++--------------------+------------------------------+---------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_template.rst b/source/auto_database_ref_docs/rundb_template.rst index 56f6a14..f5c0844 100644 --- a/source/auto_database_ref_docs/rundb_template.rst +++ b/source/auto_database_ref_docs/rundb_template.rst @@ -12,3 +12,19 @@ Postgres table: ``rundb_template`` Schema ------- ++--------------+----------------------------------+---------------+ +| Field | Type | Description | ++==============+==================================+===============+ +| comments | Text | comments | ++--------------+----------------------------------+---------------+ +| id | Integer | ID | ++--------------+----------------------------------+---------------+ +| isofficial | Boolean (Either True or False) | isofficial | ++--------------+----------------------------------+---------------+ +| key | String (up to 64) | key | ++--------------+----------------------------------+---------------+ +| name | String (up to 64) | name | ++--------------+----------------------------------+---------------+ +| sequence | Text | sequence | ++--------------+----------------------------------+---------------+ + diff --git a/source/auto_database_ref_docs/rundb_tfmetrics.rst b/source/auto_database_ref_docs/rundb_tfmetrics.rst index b6d8417..e8a4d7d 100644 --- a/source/auto_database_ref_docs/rundb_tfmetrics.rst +++ b/source/auto_database_ref_docs/rundb_tfmetrics.rst @@ -12,3 +12,39 @@ Postgres table: ``rundb_tfmetrics`` Schema ------- ++----------------+-------------------------+---------------------------------+ +| Field | Type | Description | ++================+=========================+=================================+ +| HPAccuracy | Text | HPAccuracy | ++----------------+-------------------------+---------------------------------+ +| Q10Histo | Text | Q10Histo | ++----------------+-------------------------+---------------------------------+ +| Q10Mean | Floating point number | Q10Mean | ++----------------+-------------------------+---------------------------------+ +| Q10ReadCount | Floating point number | Q10ReadCount | ++----------------+-------------------------+---------------------------------+ +| Q17Histo | Text | Q17Histo | ++----------------+-------------------------+---------------------------------+ +| Q17Mean | Floating point number | Q17Mean | ++----------------+-------------------------+---------------------------------+ +| Q17ReadCount | Floating point number | Q17ReadCount | ++----------------+-------------------------+---------------------------------+ +| SysSNR | Floating point number | SysSNR | ++----------------+-------------------------+---------------------------------+ +| aveKeyCount | Floating point number | aveKeyCount | ++----------------+-------------------------+---------------------------------+ +| corrHPSNR | Text | corrHPSNR | ++----------------+-------------------------+---------------------------------+ +| id | Integer | ID | ++----------------+-------------------------+---------------------------------+ +| keypass | Floating point number | keypass | ++----------------+-------------------------+---------------------------------+ +| name | String (up to 128) | name | ++----------------+-------------------------+---------------------------------+ +| number | Floating point number | number | ++----------------+-------------------------+---------------------------------+ +| report | Results (ForeignKey) | the related rundb.Results row | ++----------------+-------------------------+---------------------------------+ +| sequence | String (up to 512) | sequence | ++----------------+-------------------------+---------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_threeprimeadapter.rst b/source/auto_database_ref_docs/rundb_threeprimeadapter.rst index 7a98b95..8c7ba96 100644 --- a/source/auto_database_ref_docs/rundb_threeprimeadapter.rst +++ b/source/auto_database_ref_docs/rundb_threeprimeadapter.rst @@ -12,3 +12,25 @@ Postgres table: ``rundb_threeprimeadapter`` Schema ------- ++-----------------+----------------------------------+-----------------------+ +| Field | Type | Description | ++=================+==================================+=======================+ +| chemistryType | String (up to 64) | chemistryType | ++-----------------+----------------------------------+-----------------------+ +| description | String (up to 1024) | description | ++-----------------+----------------------------------+-----------------------+ +| direction | String (up to 20) | direction | ++-----------------+----------------------------------+-----------------------+ +| id | Integer | ID | ++-----------------+----------------------------------+-----------------------+ +| isDefault | Boolean (Either True or False) | use this by default | ++-----------------+----------------------------------+-----------------------+ +| name | String (up to 256) | name | ++-----------------+----------------------------------+-----------------------+ +| runMode | String (up to 64) | runMode | ++-----------------+----------------------------------+-----------------------+ +| sequence | String (up to 512) | sequence | ++-----------------+----------------------------------+-----------------------+ +| uid | String (up to 32) | uid | ++-----------------+----------------------------------+-----------------------+ + diff --git a/source/auto_database_ref_docs/rundb_usereventlog.rst b/source/auto_database_ref_docs/rundb_usereventlog.rst index 216d76b..27a9594 100644 --- a/source/auto_database_ref_docs/rundb_usereventlog.rst +++ b/source/auto_database_ref_docs/rundb_usereventlog.rst @@ -12,3 +12,15 @@ Postgres table: ``rundb_usereventlog`` Schema ------- ++-------------+------------------------------+---------------------------------------+ +| Field | Type | Description | ++=============+==============================+=======================================+ +| id | Integer | ID | ++-------------+------------------------------+---------------------------------------+ +| text | Text | text | ++-------------+------------------------------+---------------------------------------+ +| timeStamp | Date (with time) | timeStamp | ++-------------+------------------------------+---------------------------------------+ +| upload | ContentUpload (ForeignKey) | the related rundb.ContentUpload row | ++-------------+------------------------------+---------------------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_userprofile.rst b/source/auto_database_ref_docs/rundb_userprofile.rst index 18de8e6..5b92bce 100644 --- a/source/auto_database_ref_docs/rundb_userprofile.rst +++ b/source/auto_database_ref_docs/rundb_userprofile.rst @@ -12,3 +12,21 @@ Postgres table: ``rundb_userprofile`` Schema ------- ++--------------------------+----------------------+-----------------------------+ +| Field | Type | Description | ++==========================+======================+=============================+ +| id | Integer | ID | ++--------------------------+----------------------+-----------------------------+ +| last\_read\_news\_post | Date (with time) | last read news post | ++--------------------------+----------------------+-----------------------------+ +| name | String (up to 93) | name | ++--------------------------+----------------------+-----------------------------+ +| note | Text | note | ++--------------------------+----------------------+-----------------------------+ +| phone\_number | String (up to 256) | phone number | ++--------------------------+----------------------+-----------------------------+ +| title | String (up to 256) | title | ++--------------------------+----------------------+-----------------------------+ +| user | User (ForeignKey) | the related auth.User row | ++--------------------------+----------------------+-----------------------------+ + diff --git a/source/auto_database_ref_docs/rundb_variantfrequencies.rst b/source/auto_database_ref_docs/rundb_variantfrequencies.rst index f7e1938..e792eca 100644 --- a/source/auto_database_ref_docs/rundb_variantfrequencies.rst +++ b/source/auto_database_ref_docs/rundb_variantfrequencies.rst @@ -12,3 +12,13 @@ Postgres table: ``rundb_variantfrequencies`` Schema ------- ++---------------+-----------------------+---------------+ +| Field | Type | Description | ++===============+=======================+===============+ +| description | String (up to 3024) | description | ++---------------+-----------------------+---------------+ +| id | Integer | ID | ++---------------+-----------------------+---------------+ +| name | String (up to 512) | name | ++---------------+-----------------------+---------------+ + diff --git a/source/auto_database_ref_index.rst b/source/auto_database_ref_index.rst index df037a1..8de6f82 100644 --- a/source/auto_database_ref_index.rst +++ b/source/auto_database_ref_index.rst @@ -51,7 +51,6 @@ Torrent Server Database Tables auto_database_ref_docs/rundb_reportstorage.rst auto_database_ref_docs/rundb_results.rst auto_database_ref_docs/rundb_rig.rst - auto_database_ref_docs/rundb_runscript.rst auto_database_ref_docs/rundb_runtype.rst auto_database_ref_docs/rundb_sample.rst auto_database_ref_docs/rundb_sampleannotation_cv.rst @@ -62,6 +61,7 @@ Torrent Server Database Tables auto_database_ref_docs/rundb_sampleset.rst auto_database_ref_docs/rundb_samplesetitem.rst auto_database_ref_docs/rundb_sequencingkit.rst + auto_database_ref_docs/rundb_sharedserver.rst auto_database_ref_docs/rundb_supportupload.rst auto_database_ref_docs/rundb_template.rst auto_database_ref_docs/rundb_tfmetrics.rst diff --git a/source/templates/layout.html b/source/templates/layout.html index fb8bb36..26f5992 100644 --- a/source/templates/layout.html +++ b/source/templates/layout.html @@ -2,7 +2,7 @@ {% block footer %}
- ©2014 Life Technologies Corporation. All rights reserved.
+ © 2015 Thermo Fisher Scientific Inc. All rights reserved.
The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners.
For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.