Merge branch 'schema-urgent-fixes' into aCollectionOf-property-fix

ga4gh-beacon · Dec 12, 2024 · 8d9715b · 8d9715b
2 parents a729ef4 + d02c6bf
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -34,7 +34,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
  * Fixed `POST`queries for `g_variant` (w/ examples)
- * Removed 'json' references inside the yaml version (PR [#43] (https://github.com/ga4gh-beacon/beacon-v2/pull/43))
+ * Removed 'json' references inside the yaml version (PR [#43](https://github.com/ga4gh-beacon/beacon-v2/pull/43))
+ * added missing `type: object` to `ResultsetInstance` (PR [#82](https://github.com/ga4gh-beacon/beacon-v2/pull/82))
 
 ### Deprecated
 

diff --git a/README.md b/README.md
@@ -28,7 +28,40 @@ As with other schema projects, here we separate between the schema source files
 
 There is a set of tools in [`/bin`](./bin/) to facilitate the conversion. ATM, after editing `...yaml` schema files somewhere in the `/src` tree, a (local) run of `bin/yamlerRunner.sh` - which re-generates the `....json` files in the `/json` tree) has to be performed before pushing changes.
 
-### Changes
+### 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
+* Filtering terms scopes changed from string to array of strings
+
+## 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
+* Created filtering terms entity
+* Removed validation directories
+* Several fixes to entity types, typos and other non-breaking changes
+
+## 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/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.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.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.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.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.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:

diff --git a/bin/deref_schemas/obj/measurements.yaml b/bin/deref_schemas/obj/measurements.yaml
@@ -168,7 +168,7 @@ measurements:
           title: Value
           type: object
         - $schema: https://json-schema.org/draft/2020-12/schema
-          definitions:
+          $defs:
             TypedQuantity:
               properties:
                 quantity:

diff --git a/bin/deref_schemas/obj/measures.yaml b/bin/deref_schemas/obj/measures.yaml
@@ -166,7 +166,7 @@ measures:
           title: Value
           type: object
         - $schema: https://json-schema.org/draft/2020-12/schema
-          definitions:
+          $defs:
             TypedQuantity:
               properties:
                 quantity:

diff --git a/bin/deref_schemas/obj/pedigrees.yaml b/bin/deref_schemas/obj/pedigrees.yaml
@@ -3,7 +3,7 @@ pedigrees:
   items:
     $schema: https://json-schema.org/draft/2020-12/schema
     additionalProperties: 1
-    definitions:
+    $defs:
       pedigreeMember:
         examples:
         - membersInProband:

diff --git a/bin/deref_schemas/obj/phenotypicConditions.yaml b/bin/deref_schemas/obj/phenotypicConditions.yaml
@@ -3,7 +3,7 @@ phenotypicConditions:
   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/obj/phenotypicFeatures.yaml b/bin/deref_schemas/obj/phenotypicFeatures.yaml
@@ -2,7 +2,7 @@
 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/yamlerRunner.sh b/bin/yamlerRunner.sh
@@ -1,28 +1,13 @@
 BASEDIR=$(dirname $0)
 UNITYPATH=$BASEDIR/..
-
-# initial conversion from separate schemas
-# DEPRECATED
-# BEACONMODELPATH=$BASEDIR/../../beacon-v2-Models/BEACON-V2-Model
-# BEACONFRAMEWORKPATH=$BASEDIR/../../beacon-framework-v2
-
 BEACONMODELNAME=beacon-v2-default-model
 
-# for UPSTREAM in $BEACONMODELPATH $BEACONFRAMEWORKPATH
-# do
-# 	echo "pulling $UPSTREAM"
-# 	git -C $UPSTREAM pull
-# done
-
 for KIND in src json
 do
 	mkdir -p $UNITYPATH/models/$KIND/$BEACONMODELNAME
 	mkdir -p $UNITYPATH/framework/$KIND	
 done
 
-# $BASEDIR/beaconYamler.py -i $BEACONMODELPATH -t json -x yaml -o $UNITYPATH/models/src/$BEACONMODELNAME
-# $BASEDIR/beaconYamler.py -i $BEACONFRAMEWORKPATH -t json -x yaml -o $UNITYPATH/framework/src
-
 # recurring conversion from the source files to the exported versions
 $BASEDIR/beaconYamler.py -i $UNITYPATH/models/src/$BEACONMODELNAME -t yaml -x json -o $UNITYPATH/models/json/$BEACONMODELNAME
 $BASEDIR/beaconYamler.py -i $UNITYPATH/framework/src -t yaml -x json -o $UNITYPATH/framework/json
diff --git a/docs/schemas-md/obj/CopyNumber.md b/docs/schemas-md/obj/CopyNumber.md
@@ -1,3 +1,3 @@
 |Term | Description | Type | Properties | Example | Enum|
 | ---| ---| ---| ---| ---| --- |
-| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/CopyNumber) | NA | NA|
+| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber) | NA | NA|