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ga4gh-beacon · Dec 12, 2024 · 724b65c · 724b65c
2 parents 09143f2 + e7ca12a
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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 * NOTE: on 2022-06-20 the previous development repositories have been archived: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/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, $data ) = @_;
     my %url = (
         'SequenceExpression' =>
-'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/$defs/',
+'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/',
         'CopyNumber' =>
-'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/$defs/'
+'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 $UNITYPATH/framework/json
diff --git a/docs/schemas-md/obj/CopyNumber.md b/docs/schemas-md/obj/CopyNumber.md
@@ -1,3 +1,3 @@
 |Term | Description | Type | Properties | Example | Enum|
 | ---| ---| ---| ---| ---| --- |
-| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/CopyNumber) | NA | NA|
+| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber) | NA | NA|
diff --git a/framework/json/common/beaconCommonComponents.json b/framework/json/common/beaconCommonComponents.json
@@ -1,5 +1,4 @@
 {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$defs": {
         "$schema": {
             "$comment": "TO REVIEW: adding a `format` or `regex` attribute that validates correctly against a file path (relative).",
@@ -143,10 +142,6 @@
             ],
             "type": "string"
         },
-        "Info": {
-            "description": "Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification.",
-            "type": "object"
-        },
         "Limit": {
             "default": 10,
             "description": "Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.",
@@ -243,6 +238,7 @@
             "type": "boolean"
         }
     },
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "description": "Definition of relatively simple components used in different points of the Beacon specification, both in requests and responses, therefore not associated exclusively with one or the other. Separate schema documents are provided for complex components.",
     "title": "Beacon Common Components",
     "type": "object"

diff --git a/framework/json/common/info.json b/framework/json/common/info.json
@@ -0,0 +1,6 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "description": "Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification.",
+    "title": "Info",
+    "type": "object"
+}
diff --git a/framework/json/configuration/beaconConfigurationSchema.json b/framework/json/configuration/beaconConfigurationSchema.json
@@ -1,6 +1,4 @@
 {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "additionalProperties": true,
     "$defs": {
         "EntryTypes": {
             "additionalProperties": {
@@ -12,7 +10,9 @@
             "type": "object"
         }
     },
-    "description": "Files complaint with this schema are the configuration ones. The details returned in `service-info` are mirroring the ones in this configuration file.",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "additionalProperties": true,
+    "description": "The Beacon configuration reports several attributes of the beacon instance related to security, maturity and available entry types. Where appropriate the details returned in `service-info` should mirror the ones in this configuration.",
     "properties": {
         "$schema": {
             "$ref": "../common/beaconCommonComponents.json#/$defs/$schema"
@@ -24,7 +24,7 @@
             "description": "Declares the level of maturity of the Beacon instance.",
             "properties": {
                 "productionStatus": {
-                    "description": "`DEV`= 'Service potentially unstable, not real data', which availability and data should not be used in production setups. `TEST`= 'Service stable, not real data'. 'PROD'= 'Service stable, actual data'.",
+                    "description": "* `DEV`: Service potentially unstable, _i.e._ potentially not real data,\n  inconsistent availability; data should not be used in production setups   \n* `TEST`: Service is stable but data should be considered synthetic   * `PROD`: Service stable with real world data  ",
                     "enum": [
                         "DEV",
                         "TEST",
@@ -43,11 +43,11 @@
                     "description": "Default granularity. Some responses could return higher detail, but this would be the granularity by default."
                 },
                 "securityLevels": {
+                    "default": [
+                        "CONTROLLED"
+                    ],
                     "description": "All access levels supported by the Beacon. Any combination is valid, as every option would apply to different parts of the Beacon.",
                     "items": {
-                        "default": [
-                            "CONTROLLED"
-                        ],
                         "enum": [
                             "PUBLIC",
                             "REGISTERED",

diff --git a/framework/json/configuration/beaconMapSchema.json b/framework/json/configuration/beaconMapSchema.json
@@ -1,6 +1,4 @@
 {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "additionalProperties": true,
     "$defs": {
         "Endpoint": {
             "properties": {
@@ -56,6 +54,8 @@
             "type": "object"
         }
     },
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "additionalProperties": true,
     "description": "Map of a Beacon, its entry types and endpoints. It isconceptually similar to a website sitemap.",
     "properties": {
         "$schema": {

diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json
@@ -7,10 +7,10 @@
             "$ref": "../common/beaconCommonComponents.json#/$defs/$schema"
         },
         "aCollectionOf": {
-            "description": "If the entry type is a collection of other entities, (e.g. a Dataset is a collection of Records), then this attribute must list the entities that can be included. One _collection_ can include more than one entry type  (e.g. a Dataset in teh Beacon cdefault model could include Individuals, Biosamples, GenomicVariations, Analyses amnd Runs). In such cases in each individual response (e.g. `resultSetsResponse` of collections of type \"dataset\") will contain entries of a single entry type (e.g. biosamples) even if a dataset may contain records of multiple types.",
-            "includedConcepts": {
-                "$ref": "../common/basicElement.json",
-                "type": "array"
+            "description": "If the entry type is a collection of other entry types, (e.g. a Dataset is a collection of Records), then this attribute must list the entry types that could be included. One collection type could be defined as included more than one entry type (e.g. a Dataset could include Individuals or Genomic Variants), in such cases the entries are alternative, meaning that a given instance of this entry type could be of only one of the types (e.g. a given Dataset contains Individuals, while another Dataset could contain Genomic Variants, but not both at once).",
+            "type": "array",
+            "items": {
+                "$ref": "../common/basicElement.json"
             }
         },
         "additionallySupportedSchemas": {
@@ -71,4 +71,4 @@
     ],
     "title": "",
     "type": "object"
-}
+}