Merge branch 'bfabric12' of github.com:fgcz/bfabricPy into bfabric12

fgcz · Nov 3, 2023 · 116bfe8 · 116bfe8
2 parents 961b9e7 + ca4b8ae
commit 116bfe8
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Showing 5 changed files with 68 additions and 35 deletions.
diff --git a/bfabric/__init__.py b/bfabric/__init__.py
@@ -3,7 +3,7 @@
 name = "bfabricPy"
 alias = "suds-py3"
 
-msg = "\033[93m{} version {} (2023-03-31) -- \"{}\"\
+msg = "\033[93m{} version {} (2023-10-11) -- \"{}\"\
     \nCopyright (C) 2014-2023 Functional Genomics Center Zurich\033[0m\n\n"\
     .format(name, __version__, alias)
 

diff --git a/bfabric/_version.py b/bfabric/_version.py
@@ -1 +1 @@
-__version__ = "0.13.5"
+__version__ = "0.13.6"
diff --git a/bfabric/scripts/bfabric_feeder_mascot.py b/bfabric/scripts/bfabric_feeder_mascot.py
@@ -12,6 +12,7 @@
 2012-10-10 Christian Panse <cp@fgcz.ethz.ch>
 2012-10-11 Christian Panse <cp@fgcz.ethz.ch>
 2021-01-06 Christian Panse <cp@fgcz.ethz.ch> - replace multiprocess by caching strategy
+2023-10-20 Christian Panse <cp@fgcz.ethz.ch> - add timestamp
 
 # Usage
 
@@ -31,6 +32,7 @@
 import hashlib
 import getopt
 from suds.client import Client
+from datetime import datetime
 import json
 import itertools
 import http.client
@@ -48,7 +50,11 @@
 
 try:
     DB = json.load(open(DBfilename))
+    print("Read {len} data items from {name} using {size:.1f} GBytes.".format(len=len(DB),
+        name=DBfilename,
+        size=sum(map(lambda x: int(x['resource']['size']), DB.values())) / (1024 * 1024 * 1024)))
 except:
+    print("loading '{}' failed".format(DBfilename))
     pass
 
 
@@ -69,7 +75,7 @@ def query_mascot_result(f):
     regex2 = re.compile(".*.+/(data/.+\.dat)$")
     regex2Result = regex2.match(f)
     if True:
-        print("input>")
+        print("{} input>".format(datetime.now()))
         print("\t{}".format(f))
         if f in DB:
             print("\thit")
@@ -110,7 +116,7 @@ def query_mascot_result(f):
                 print("Exception {}".format(ValueError))
                 raise
 
-            print("output>")
+            print("{} output>".format(datetime.now()))
             if 'errorreport' in rv:
                 print("\tfound errorreport '{}'.".format(rv['errorreport']))
 
@@ -180,7 +186,10 @@ def query_mascot_result(f):
 
 
 def parse_mascot_result_file(f):
-    print("DEBUG parse_mascot_result_file")
+
+    # Getting the current date and time
+    print("{} DEBUG parse_mascot_result_file".format(datetime.now()))
+
     regex0 = re.compile("^title=.*(p([0-9]+).+Proteomics.*(raw|RAW|wiff)).*")
     regex3 = re.compile("^(FILE|COM|release|USERNAME|USERID|TOL|TOLU|ITOL|ITOLU|MODS|IT_MODS|CHARGE|INSTRUMENT|QUANTITATION|DECOY)=(.+)$")
 
@@ -239,7 +248,8 @@ def parse_mascot_result_file(f):
         )
     )
     #TODO
-    print("DEBUG")
+
+    print("{}".format(datetime.now()))
     print(rv)
     print("DEBUG END")
 
@@ -255,17 +265,17 @@ def printFrequency(S):
             count[x] = 1
 
     for key in sorted(count.keys(), key=lambda key: int(key)):
-        print(key, count[key])
+        print("p{}\t{}".format(key, count[key]))
 
 
 def statistics():
-    print(len(DB))
+    print("Statistics ...")
+    print("len(DB)\t=\t{}".format(len(DB)))
     printFrequency(map(lambda x: x['containerid'], DB.values()))
-    print("{} GBytes".format(sum(map(lambda x: int(x['resource']['size']), DB.values())) / (1024 * 1024 * 1024)))
+    print("file size\t=\t{} GBytes".format(sum(map(lambda x: int(x['resource']['size']), DB.values())) / (1024 * 1024 * 1024)))
 
     # printFrequency(map(lambda x: x['description'].split(";"), DB.values()))
-
-    print(json.dumps(list(DB.values())[100], indent=4))
+    # print(json.dumps(list(DB.values())[100], indent=4))
 
 
 if __name__ == "__main__":
@@ -281,10 +291,10 @@ def statistics():
             print("reading file names from stdin ...")
             for f in sys.stdin.readlines():
                 query_mascot_result(f.strip())
-        elif o == "--file" or o == 'f':
+        elif o == "--file" or o == '-f':
             print("processesing", value, "...")
             query_mascot_result(value)
-        elif o == "--statistics" or o == 's':
+        elif o == "--statistics" or o == '-s':
             statistics()
             sys.exit(0)
 

diff --git a/bfabric/scripts/bfabric_save_link_to_workunit.py b/bfabric/scripts/bfabric_save_link_to_workunit.py
@@ -0,0 +1,32 @@
+#!/usr/bin/env python3
+# -*- coding: latin1 -*-
+
+"""
+Copyright (C) 2023 Functional Genomics Center Zurich ETHZ|UZH. All rights reserved.
+
+Christian Panse <cp@fgcz.ethz.ch> 20231011
+"""
+
+import sys
+import os
+from bfabric import Bfabric
+
+def save_link(wuid=294156, link="", name=""):
+    B = Bfabric()
+
+    rv = B.save_object('link',
+        obj={'name': name,
+            'parentclassname': 'workunit',
+            'parentid': wuid,
+            'url': link})
+    B.print_json(rv)
+
+if __name__ == "__main__":
+    if len(sys.argv) == 4:
+        save_link(wuid=sys.argv[1], link=sys.argv[2], name=sys.argv[3])
+    else:
+        print ("Usage:")
+        print ("{} <workunit id> <link> <name>".format(sys.argv[0]))
+        print ("Example:")
+        print ("{} 294156 'https://fgcz-shiny.uzh.ch/exploreDE_prot/?data=p3000/bfabric/Proteomics/SummarizedExperiment/2023/2023-09/2023-09-29/workunit_294156/2363303.rds' 'demo1 link'".format(sys.argv[0]))
+
diff --git a/setup.py b/setup.py
@@ -45,37 +45,28 @@
       python_requires = ">=3.7",
       install_requires = INSTALL_REQUIRES,
       scripts = [
-        'bfabric/scripts/bfabric_delete.py',
-        'bfabric/scripts/bfabric_read.py',
         'bfabric/scripts/bfabric_flask.py',
-        'bfabric/scripts/bfabric_save_importresource_sample.py',
-        'bfabric/scripts/bfabric_save_resource.py',
         'bfabric/scripts/bfabric_feeder_resource_autoQC.py',
-        'bfabric/scripts/bfabric_setResourceStatus_available.py',
         'bfabric/scripts/bfabric_list_not_existing_storage_directories.py',
+        'bfabric/scripts/bfabric_list_not_available_proteomics_workunits.py',
+        'bfabric/scripts/bfabric_upload_resource.py',
+        'bfabric/scripts/bfabric_logthis.py',
+        'bfabric/scripts/bfabric_setResourceStatus_available.py',
         'bfabric/scripts/bfabric_setExternalJobStatus_done.py',
         'bfabric/scripts/bfabric_setWorkunitStatus_available.py',
         'bfabric/scripts/bfabric_setWorkunitStatus_processing.py',
         'bfabric/scripts/bfabric_setWorkunitStatus_failed.py',
-        'bfabric/scripts/bfabric_upload_resource.py',
-        'bfabric/scripts/bfabric_save_fasta.py',
-        'bfabric/scripts/bfabric_save_workunit_attribute.py',
-        'bfabric/scripts/bfabric_save_csv2dataset.py',
-        'bfabric/scripts/bfabric_save_dataset2csv.py',
-        'bfabric/scripts/bfabric_logthis.py',
+        'bfabric/scripts/bfabric_delete.py',
+        'bfabric/scripts/bfabric_read.py',
         'bfabric/scripts/bfabric_read_samples_of_workunit.py',
         'bfabric/scripts/bfabric_read_samples_from_dataset.py',
-        'bfabric/scripts/bfabric_list_not_available_proteomics_workunits.py',
+        'bfabric/scripts/bfabric_save_csv2dataset.py',
+        'bfabric/scripts/bfabric_save_dataset2csv.py',
+        'bfabric/scripts/bfabric_save_fasta.py',
+        'bfabric/scripts/bfabric_save_importresource_sample.py',
+        'bfabric/scripts/bfabric_save_link_to_workunit.py',
+        'bfabric/scripts/bfabric_save_resource.py',
+        'bfabric/scripts/bfabric_save_workunit_attribute.py',
         'bfabric/scripts/bfabric_save_workflowstep.py'
-        #'bfabric/scripts/bfabric_list_executables.py',
-        #'bfabric/scripts/bfabric_list_proteomics_projects.py',
-        #'bfabric/scripts/bfabric_upload_wrapper_creator_executable.py',
-        #'bfabric/scripts/bfabric_upload_submitter_executable.py',
-        #'bfabric/scripts/bfabric_create_bfabricrc.py',
-        #'bfabric/scripts/bfabric_save_importresource.py',
-        ##'bfabric/scripts/bfabric_save_importresource_mascot.py',
-        #'bfabric/scripts/bfabric_wrapper_creator_yaml.py',
-        #'bfabric/scripts/bfabric_submitter_yaml.py',
-        #'bfabric/scripts/fgcz_maxquant_wrapper.py'
         ],
       zip_safe=True)