Merge pull request #193 from ga4gh-beacon/main

Updating develop after 2.1.1 version upgrade in main
ga4gh-beacon · Dec 13, 2024 · b3448ad · b3448ad
2 parents 1d804b6 + 47af89c
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diff --git a/README.md b/README.md
@@ -30,9 +30,18 @@ There is a set of tools in [`/bin`](./bin/) to facilitate the conversion. ATM, a
 
 ### Changelog
 
+## 2.1.1
+
+*Released, October, 8, 2024*
+[Beacon-v2.1.1](https://github.com/ga4gh-beacon/beacon-v2/tree/5ea17fbd0d2ba533aa1e85f7271f9a2cc9be6794)
+
+* Changed uri for uri-template in Endpoint.singleEntryUrl
+
+
 ## 2.1.0
 
 *Released, July, 19, 2024*
+[Beacon-v2.1.0](https://github.com/ga4gh-beacon/beacon-v2/tree/16862205c79294fae5473f7fa330bf5929b3b120)
 
 * Relocated TypedQuantity required to proper level of the schema for complexValue
 * Added end and start entities for ageRange and iso8601duration for age
@@ -41,6 +50,7 @@ There is a set of tools in [`/bin`](./bin/) to facilitate the conversion. ATM, a
 ## 2.0.1
 
 *Released July, 16, 2024*
+[Beacon-v2.0.1](https://github.com/ga4gh-beacon/beacon-v2/tree/f6f85c445922831bd398552384593206c86287de)
 
 * Replaced ENSGLOSSARY for SO ontology family in documentation examples
 * Moved CURIE to beaconCommonComponents
@@ -51,6 +61,7 @@ There is a set of tools in [`/bin`](./bin/) to facilitate the conversion. ATM, a
 ## 2.0.0
 
 *Released June, 21, 2022*
+[Beacon-v2.0.0](https://github.com/ga4gh-beacon/beacon-v2/tree/d07ef1626321f7428374a4f68d864dfa5e98370f)
 
 * change notes with respect to the repository & documentation are now in [docs.genomebeacons.org](https://docs.genomebeacons.org/changes-todo/)
 * NOTE: on 2022-06-20 the previous development repositories have been archived:

diff --git a/bin/_jsonref2json.py b/bin/_jsonref2json.py
@@ -14,7 +14,7 @@
 #   "$comment": "version: ga4gh-beacon-cohort-v2.0.0",
 #   "$schema": "https://json-schema.org/draft/2020-12/schema",
 #   "additionalProperties": true,
-#   "definitions": {
+#   "$defs": {
 #     "CohortCriteria": {
 #       "description": "THIS IS NOT OK",
 #       "properties": {
@@ -30,7 +30,7 @@
 #     "inclusionCriteria": {
 #       "description": "THIS IS OK",
 #       "type": "object",
-#       "$ref": "#/definitions/CohortCriteria"
+#       "$ref": "#/$defs/CohortCriteria"
 #     }
 #   }
 # }

diff --git a/bin/adhoc/beaconCommonComponents.json b/bin/adhoc/beaconCommonComponents.json
@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "definitions": {
+    "$defs": {
         "$schema": {
             "$comment": "TO REVIEW: adding a `format` or `regex` attribute that validates correctly against a file path (relative).",
             "description": "Refers to the JSON Schema which describes the set of valid attributes for this particular document type. This attribute is mostly used in schemas that should be tested in Beacon implementations.",
@@ -83,7 +83,7 @@
             "description": "A handover is a typed link for attaching actionable links to results, non purely informational, requests. The goal of the handovers is to list the different actions available, e.g.:\n* a link to a request access page * linking to a file for download, e.g. a VCF file\nAnother common scenario is to provide a fast summary response (e.g. BeconCountResponse) and to provide access to different endpoints for the entities matched by the query using temporary access tokens in the handover URLs.",
             "properties": {
                 "handoverType": {
-                    "$ref": "#/definitions/HandoverType"
+                    "$ref": "#/$defs/HandoverType"
                 },
                 "note": {
                     "description": "An optional text including considerations on the handover link provided.",
@@ -148,15 +148,15 @@
         "ListOfHandovers": {
             "description": "Set of handovers to be added in one section the response.",
             "items": {
-                "$ref": "#/definitions/Handover",
+                "$ref": "#/$defs/Handover",
                 "description": "Requested schema to be used for individuals in the response."
             },
             "type": "array"
         },
         "ListOfSchemas": {
             "description": "Set of schemas to be used in the response to a request.",
             "items": {
-                "$ref": "#/definitions/SchemasPerEntity"
+                "$ref": "#/$defs/SchemasPerEntity"
             },
             "type": "array"
         },
@@ -182,22 +182,22 @@
             "description": "Pagination to apply or that has been applied on the results.",
             "properties": {
                 "currentPage": {
-                    "$ref": "#/definitions/PageToken",
+                    "$ref": "#/$defs/PageToken",
                     "description": "Token of the returned page. To be used only in the response to allow the client to check if the returned page is the one requested."
                 },
                 "limit": {
-                    "$ref": "#/definitions/Limit"
+                    "$ref": "#/$defs/Limit"
                 },
                 "nextPage": {
-                    "$ref": "#/definitions/PageToken",
+                    "$ref": "#/$defs/PageToken",
                     "description": "Token of the next page. Used to navigate forward. If empty, it is assumed that no more pages are available"
                 },
                 "previousPage": {
-                    "$ref": "#/definitions/PageToken",
+                    "$ref": "#/$defs/PageToken",
                     "description": "Token of the previous page. Used to navigate backwards. If empty, it is assumed that the current page is the first one."
                 },
                 "skip": {
-                    "$ref": "#/definitions/Skip"
+                    "$ref": "#/$defs/Skip"
                 }
             },
             "type": "object"

diff --git a/bin/adhoc/ontologyTerm.json b/bin/adhoc/ontologyTerm.json
@@ -3,7 +3,7 @@
     "additionalProperties": true,
     "properties": {
         "id": {
-            "$ref": "./beaconCommonComponents.json#/definitions/CURIE"
+            "$ref": "./beaconCommonComponents.json#/$defs/CURIE"
         },
         "label": {
             "description": "The text that describes the term. By default it could be the preferred text of the term, but is it acceptable to customize it for a clearer description and understanding of the term in an specific context.",

diff --git a/bin/beaconYamler.py b/bin/beaconYamler.py
@@ -1,4 +1,4 @@
-#!/usr/local/bin/python3
+#!/usr/bin/env python3
 
 import sys, re, json
 import pathlib

diff --git a/bin/beacon_yaml2md.pl b/bin/beacon_yaml2md.pl
@@ -729,9 +729,9 @@ sub add_properties_vrs {
     my ( $property, $data ) = @_;
     my %url = (
         'SequenceExpression' =>
-'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/',
+'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/',
         'CopyNumber' =>
-'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/'
+'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/'
     );
     if ( exists $url{$property} ) {
         $data->{properties} =

diff --git a/bin/deref_schemas/biosamples/defaultSchema.json b/bin/deref_schemas/biosamples/defaultSchema.json
@@ -357,7 +357,7 @@
                             },
                             {
                                 "$schema": "https://json-schema.org/draft/2020-12/schema",
-                                "definitions": {
+                                "$defs": {
                                     "TypedQuantity": {
                                         "properties": {
                                             "quantity": {
@@ -1479,7 +1479,7 @@
             "description": "List of phenotypic abnormalities of the sample. RECOMMENDED.",
             "items": {
                 "$schema": "https://json-schema.org/draft/2020-12/schema",
-                "definitions": {},
+                "$defs": {},
                 "description": "Used to describe a phenotype that characterizes the subject or biosample.",
                 "properties": {
                     "evidence": {

diff --git a/bin/deref_schemas/biosamples/defaultSchema.yaml b/bin/deref_schemas/biosamples/defaultSchema.yaml
@@ -260,7 +260,7 @@ properties:
               title: Value
               type: object
             - $schema: https://json-schema.org/draft/2020-12/schema
-              definitions:
+              $defs:
                 TypedQuantity:
                   properties:
                     quantity:
@@ -1064,7 +1064,7 @@ properties:
     description: List of phenotypic abnormalities of the sample. RECOMMENDED.
     items:
       $schema: https://json-schema.org/draft/2020-12/schema
-      definitions: {}
+      $defs: {}
       description: Used to describe a phenotype that characterizes the subject or biosample.
       properties:
         evidence:

diff --git a/bin/deref_schemas/cohorts/defaultSchema.json b/bin/deref_schemas/cohorts/defaultSchema.json
@@ -2,7 +2,7 @@
     "$comment": "version: ga4gh-beacon-cohort-v2.0.0",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "additionalProperties": true,
-    "definitions": {
+    "$defs": {
         "CohortCriteria": {
             "description": "Criteria used for defining the cohort. It is assumed that all cohort participants will match or NOT match such criteria.",
             "properties": {
@@ -525,7 +525,7 @@
                     "description": "Phenotypic condition(s) in cohort inclusion criteria",
                     "items": {
                         "$schema": "https://json-schema.org/draft/2020-12/schema",
-                        "definitions": {},
+                        "$defs": {},
                         "description": "Used to describe a phenotype that characterizes the subject or biosample.",
                         "properties": {
                             "evidence": {
@@ -2369,7 +2369,7 @@
                     "description": "Phenotypic condition(s) in cohort inclusion criteria",
                     "items": {
                         "$schema": "https://json-schema.org/draft/2020-12/schema",
-                        "definitions": {},
+                        "$defs": {},
                         "description": "Used to describe a phenotype that characterizes the subject or biosample.",
                         "properties": {
                             "evidence": {
@@ -3418,7 +3418,7 @@
                     "description": "Phenotypic condition(s) in cohort inclusion criteria",
                     "items": {
                         "$schema": "https://json-schema.org/draft/2020-12/schema",
-                        "definitions": {},
+                        "$defs": {},
                         "description": "Used to describe a phenotype that characterizes the subject or biosample.",
                         "properties": {
                             "evidence": {

diff --git a/bin/deref_schemas/cohorts/defaultSchema.yaml b/bin/deref_schemas/cohorts/defaultSchema.yaml
@@ -2,7 +2,7 @@
 $comment: 'version: ga4gh-beacon-cohort-v2.0.0'
 $schema: https://json-schema.org/draft/2020-12/schema
 additionalProperties: &1 !!perl/scalar:JSON::PP::Boolean 1
-definitions:
+$defs:
   CohortCriteria:
     description: Criteria used for defining the cohort. It is assumed that all cohort participants will match or NOT match such criteria.
     properties:
@@ -366,7 +366,7 @@ definitions:
         description: Phenotypic condition(s) in cohort inclusion criteria
         items:
           $schema: https://json-schema.org/draft/2020-12/schema
-          definitions: {}
+          $defs: {}
           description: Used to describe a phenotype that characterizes the subject or biosample.
           properties:
             evidence:
@@ -1660,7 +1660,7 @@ properties:
         description: Phenotypic condition(s) in cohort inclusion criteria
         items:
           $schema: https://json-schema.org/draft/2020-12/schema
-          definitions: {}
+          $defs: {}
           description: Used to describe a phenotype that characterizes the subject or biosample.
           properties:
             evidence:
@@ -2406,7 +2406,7 @@ properties:
         description: Phenotypic condition(s) in cohort inclusion criteria
         items:
           $schema: https://json-schema.org/draft/2020-12/schema
-          definitions: {}
+          $defs: {}
           description: Used to describe a phenotype that characterizes the subject or biosample.
           properties:
             evidence:

diff --git a/bin/deref_schemas/datasets/defaultSchema.json b/bin/deref_schemas/datasets/defaultSchema.json
@@ -16,7 +16,7 @@
             "description": "Data use conditions applying to this dataset.",
             "$schema": "https://json-schema.org/draft/2020-12/schema",
             "additionalProperties": true,
-            "definitions": {
+            "$defs": {
                 "DUODataUse": {
                     "allOf": [
                         {

diff --git a/bin/deref_schemas/datasets/defaultSchema.yaml b/bin/deref_schemas/datasets/defaultSchema.yaml
@@ -13,7 +13,7 @@ properties:
   dataUseConditions:
     $schema: https://json-schema.org/draft/2020-12/schema
     additionalProperties: 1
-    definitions:
+    $defs:
       DUODataUse:
         allOf:
           - description: 'Data Use Ontology codes and additional information associated with a data object (e.g. sample, dataset).'

diff --git a/bin/deref_schemas/genomicVariations/defaultSchema.json b/bin/deref_schemas/genomicVariations/defaultSchema.json
@@ -2,7 +2,7 @@
     "$comment": "version: ga4gh-beacon-variant-v2.0.0",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "additionalProperties": true,
-    "definitions": {
+    "$defs": {
         "CaseLevelVariant": {
             "description": "",
             "properties": {

diff --git a/bin/deref_schemas/genomicVariations/defaultSchema.yaml b/bin/deref_schemas/genomicVariations/defaultSchema.yaml
@@ -2,7 +2,7 @@
 $comment: 'version: ga4gh-beacon-variant-v2.0.0'
 $schema: https://json-schema.org/draft/2020-12/schema
 additionalProperties: &1 !!perl/scalar:JSON::PP::Boolean 1
-definitions:
+$defs:
   CaseLevelVariant:
     description: ''
     properties:

diff --git a/bin/deref_schemas/individuals/defaultSchema.json b/bin/deref_schemas/individuals/defaultSchema.json
@@ -1035,7 +1035,7 @@
                             },
                             {
                                 "$schema": "https://json-schema.org/draft/2020-12/schema",
-                                "definitions": {
+                                "$defs": {
                                     "TypedQuantity": {
                                         "properties": {
                                             "quantity": {
@@ -1812,7 +1812,7 @@
             "items": {
                 "$schema": "https://json-schema.org/draft/2020-12/schema",
                 "additionalProperties": true,
-                "definitions": {
+                "$defs": {
                     "pedigreeMember": {
                         "examples": [
                             {
@@ -2401,7 +2401,7 @@
         "phenotypicFeatures": {
             "items": {
                 "$schema": "https://json-schema.org/draft/2020-12/schema",
-                "definitions": {},
+                "$defs": {},
                 "description": "Used to describe a phenotype that characterizes the subject or biosample.",
                 "properties": {
                     "evidence": {

diff --git a/bin/deref_schemas/individuals/defaultSchema.yaml b/bin/deref_schemas/individuals/defaultSchema.yaml
@@ -739,7 +739,7 @@ properties:
               title: Value
               type: object
             - $schema: https://json-schema.org/draft/2020-12/schema
-              definitions:
+              $defs:
                 TypedQuantity:
                   properties:
                     quantity:
@@ -1299,7 +1299,7 @@ properties:
     items:
       $schema: https://json-schema.org/draft/2020-12/schema
       additionalProperties: 1
-      definitions:
+      $defs:
         pedigreeMember:
           examples:
             - membersInProband:
@@ -1696,7 +1696,7 @@ properties:
   phenotypicFeatures:
     items:
       $schema: https://json-schema.org/draft/2020-12/schema
-      definitions: {}
+      $defs: {}
       description: Used to describe a phenotype that characterizes the subject or biosample.
       properties:
         evidence:

diff --git a/bin/deref_schemas/obj/Complex Value.yaml b/bin/deref_schemas/obj/Complex Value.yaml
@@ -1,7 +1,7 @@
 ---
 Complex Value:
   $schema: https://json-schema.org/draft/2020-12/schema
-  definitions:
+  $defs:
     TypedQuantity:
       properties:
         quantity:

diff --git a/bin/deref_schemas/obj/CopyNumber.yaml b/bin/deref_schemas/obj/CopyNumber.yaml
@@ -1,4 +1,4 @@
 ---
 CopyNumber:
-  properties: '[VRS definition for CopyNumber](https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/CopyNumber)'
+  properties: '[VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber)'
   type: allOf
diff --git a/bin/deref_schemas/obj/dataUseConditions.yaml b/bin/deref_schemas/obj/dataUseConditions.yaml
@@ -2,7 +2,7 @@
 dataUseConditions:
   $schema: https://json-schema.org/draft/2020-12/schema
   additionalProperties: 1
-  definitions:
+  $defs:
     DUODataUse:
       allOf:
       - description: Data Use Ontology codes and additional information associated

diff --git a/bin/deref_schemas/obj/exclusionCriteria.yaml b/bin/deref_schemas/obj/exclusionCriteria.yaml
@@ -413,7 +413,7 @@ exclusionCriteria:
       description: Phenotypic condition(s) in cohort inclusion criteria
       items:
         $schema: https://json-schema.org/draft/2020-12/schema
-        definitions: {}
+        $defs: {}
         description: Used to describe a phenotype that characterizes the subject or
           biosample.
         properties:

diff --git a/bin/deref_schemas/obj/inclusionCriteria.yaml b/bin/deref_schemas/obj/inclusionCriteria.yaml
@@ -413,7 +413,7 @@ inclusionCriteria:
       description: Phenotypic condition(s) in cohort inclusion criteria
       items:
         $schema: https://json-schema.org/draft/2020-12/schema
-        definitions: {}
+        $defs: {}
         description: Used to describe a phenotype that characterizes the subject or
           biosample.
         properties:

diff --git a/bin/deref_schemas/obj/measurementValue.yaml b/bin/deref_schemas/obj/measurementValue.yaml
@@ -3,7 +3,7 @@ measurementValue:
   properties:
     Complex Value:
       $schema: https://json-schema.org/draft/2020-12/schema
-      definitions:
+      $defs:
         TypedQuantity:
           properties:
             quantity: