Merge branch 'schema-urgent-fixes' into remove-conflicting-filteringT…

…erms-definitions
ga4gh-beacon · Sep 27, 2024 · 7275c3f · 7275c3f
2 parents 7489882 + ba16137
commit 7275c3f
Show file tree

Hide file tree

Showing 126 changed files with 420 additions and 410 deletions.
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/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/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/framework/json/common/beaconCommonComponents.json b/framework/json/common/beaconCommonComponents.json
@@ -1,6 +1,5 @@
 {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "definitions": {
+    "$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.",
@@ -88,7 +87,7 @@
             "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": "#/$defs/HandoverType"
                 },
                 "note": {
                     "description": "An optional text including considerations on the handover link provided.",
@@ -157,15 +156,15 @@
         "ListOfHandovers": {
             "description": "Set of handovers to be added in one section the response.",
             "items": {
-                "$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": "#/$defs/SchemasPerEntity"
             },
             "type": "array"
         },
@@ -191,22 +190,22 @@
             "description": "Pagination to apply or that has been applied on the results.",
             "properties": {
                 "currentPage": {
-                    "$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"
@@ -243,6 +242,7 @@
             "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/ontologyTerm.json b/framework/json/common/ontologyTerm.json
@@ -4,7 +4,7 @@
     "description": "Definition of an ontology term.",
     "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/framework/json/configuration/beaconConfigurationSchema.json b/framework/json/configuration/beaconConfigurationSchema.json
@@ -1,7 +1,5 @@
 {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "additionalProperties": true,
-    "definitions": {
+    "$defs": {
         "EntryTypes": {
             "additionalProperties": {
                 "$ref": "./entryTypeDefinition.json",
@@ -12,13 +10,15 @@
             "type": "object"
         }
     },
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "additionalProperties": true,
     "description": "Files complaint with this schema are the configuration ones. The details returned in `service-info` are mirroring the ones in this configuration file.",
     "properties": {
         "$schema": {
-            "$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
+            "$ref": "../common/beaconCommonComponents.json#/$defs/$schema"
         },
         "entryTypes": {
-            "$ref": "#/definitions/EntryTypes"
+            "$ref": "#/$defs/EntryTypes"
         },
         "maturityAttributes": {
             "description": "Declares the level of maturity of the Beacon instance.",
@@ -39,7 +39,7 @@
             "description": "Configuration of the security aspects of the Beacon. By default, a Beacon that does not declare the configuration settings would return `boolean` (true/false) responses, and only if the user is authenticated and explicitly authorized to access the Beacon resources. Although this is the safest set of settings, it is not recommended unless the Beacon shares very sensitive information. Non sensitive Beacons should preferably opt for a `record` and `PUBLIC` combination.",
             "properties": {
                 "defaultGranularity": {
-                    "$ref": "../common/beaconCommonComponents.json#/definitions/Granularity",
+                    "$ref": "../common/beaconCommonComponents.json#/$defs/Granularity",
                     "description": "Default granularity. Some responses could return higher detail, but this would be the granularity by default."
                 },
                 "securityLevels": {

diff --git a/framework/json/configuration/beaconMapSchema.json b/framework/json/configuration/beaconMapSchema.json
@@ -1,12 +1,10 @@
 {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "additionalProperties": true,
-    "definitions": {
+    "$defs": {
         "Endpoint": {
             "properties": {
                 "endpoints": {
                     "additionalProperties": {
-                        "$ref": "#/definitions/RelatedEndpoint"
+                        "$ref": "#/$defs/RelatedEndpoint"
                     },
                     "description": "Optional. A list describing additional endpoints implemented by this Beacon instance for that entry type. Additional details on the endpoint parameters, supported HTTP verbs, etc. could be obtained by parsing the OpenAPI definition referenced in the `openAPIEndpointsDefinition` attribute.",
                     "minProperties": 0,
@@ -61,14 +59,16 @@
             "type": "object"
         }
     },
+    "$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": {
         "$schema": {
-            "$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
+            "$ref": "../common/beaconCommonComponents.json#/$defs/$schema"
         },
         "endpointSets": {
             "additionalProperties": {
-                "$ref": "#/definitions/Endpoint"
+                "$ref": "#/$defs/Endpoint"
             },
             "description": "List of enpoints included in this Beacon instance. This is list is meant to inform Beacon clients, e.g. a Beacon Network, about the available endpoints, it is not used to generate any automatic list, but could be used for Beacon validation purposes.",
             "minProperties": 1,

diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json
@@ -5,7 +5,7 @@
     "description": "Definition of an element or entry type including the Beacon v2 required and suggested attributes. This schema purpose is to  describe each type of entities included in a Beacon, hence Beacon clients could have some metadata about such entities.\n\nThe `id` attribute is the key that should be used in other parts of the Beacon Model to allow Beacon clients to identify the different parts (e.g. endpoints, filteringTerms, request parameters, etc.) that fully describe an entry type.",
     "properties": {
         "$schema": {
-            "$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
+            "$ref": "../common/beaconCommonComponents.json#/$defs/$schema"
         },
         "aCollectionOf": {
             "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).",
@@ -44,7 +44,7 @@
             "type": "string"
         },
         "nonFilteredQueriesAllowed": {
-            "$ref": "../common/beaconCommonComponents.json#/definitions/NonFilteredQueriesAllowed"
+            "$ref": "../common/beaconCommonComponents.json#/$defs/NonFilteredQueriesAllowed"
         },
         "ontologyTermForThisType": {
             "$comments": "++++++ THIS IS THE END OF THE ontologized element ++++++",

diff --git a/framework/json/configuration/entryTypesSchema.json b/framework/json/configuration/entryTypesSchema.json
@@ -1,7 +1,5 @@
 {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "additionalProperties": true,
-    "definitions": {
+    "$defs": {
         "EntryTypes": {
             "additionalProperties": {
                 "$ref": "./entryTypeDefinition.json",
@@ -11,10 +9,12 @@
             "minProperties": 1
         }
     },
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "additionalProperties": true,
     "description": "Schema for the Enrty Types list.",
     "properties": {
         "entryTypes": {
-            "$ref": "#/definitions/EntryTypes",
+            "$ref": "#/$defs/EntryTypes",
             "description": "List of entry types."
         }
     },