Merge pull request #198 from ga4gh-beacon/schema-urgent-fixes

Schema urgent fixes

README.md

@@ -33,13 +33,15 @@ There is a set of tools in [`/bin`](./bin/) to facilitate the conversion. ATM, a
 ## 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
@@ -48,6 +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
@@ -58,6 +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 * NOTE: on 2022-06-20 the previous development repositories have been archived:

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"
 #     }
 #   }
 # }

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"

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.",

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} =

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": {

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": {

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": [
                         {

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": {

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": {

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

bin/transform_json2md.sh

@@ -43,7 +43,7 @@ Fixing errors in JSON
 EOT
 
 # For mysteriorous reasons ontologyTerm.json (within CURIE) only works (jsonref2json.js) with $ref: url
-sed -i "s#\./beaconCommonComponents.json\#/definitions/CURIE#$adhoc_url/beaconCommonComponents.json\#/definitions/CURIE#" $fwk_dir/common/ontologyTerm.json
+sed -i "s#\./beaconCommonComponents.json\#/$defs/CURIE#$adhoc_url/beaconCommonComponents.json\#/$defs/CURIE#" $fwk_dir/common/ontologyTerm.json
 
 cat<<EOT
 ====================================

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|

framework/json/configuration/beaconConfigurationSchema.json

@@ -12,7 +12,7 @@
     },
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "additionalProperties": true,
-    "description": "Files complaint with this schema are the configuration ones. The details returned in `service-info` are mirroring the ones in this configuration file.",
+    "description": "The Beacon configuration reports several attributes of the beacon instance related to security, maturity and available entry types. Where appropriate the details returned in `service-info` should mirror the ones in this configuration.",
     "properties": {
         "$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",

framework/json/configuration/beaconMapSchema.json

@@ -14,11 +14,6 @@
                     "description": "",
                     "type": "string"
                 },
-                "filteringTermsUrl": {
-                    "description": "Optional. Returns the list of filtering terms that could be applied to this entry type. It is added here for convenience of the Beacon clients, so they don't need to parse the OpenAPI endpoints definition to get that endpoint. Also, in very simple Beacons, that endpoint could be the one of the few implemented, together with \u00b4rootUrl` and \u00b4singleEntryUrl`, in which case the whole map of endpoints is found in the current Map.",
-                    "format": "uri",
-                    "type": "string"
-                },
                 "openAPIEndpointsDefinition": {
                     "description": "Reference to the file that includes the OpenAPI definition of the endpoints implemented in this Beacon instance. The referenced file MUST BE a valid OpenAPI definition file, as it is expected that the Beacon clients (e.g. a Beacon Network) should be able to parse it to discover additional details on the supported verbs, parameters, etc.",
                     "type": "string"
@@ -30,7 +25,7 @@
                 },
                 "singleEntryUrl": {
                     "description": "Optional, but recommended. Returns only one instance of this entry, identified by an `id`. It is added here for convenience of the Beacon clients, so they don't need to parse the OpenAPI endpoints definition to get that base endpoint. Also, in very simple Beacons, that endpoint could be the only one implemented, together with \u00b4rootUrl`, in which case the whole map of endpoints is found in the current Map.",
-                    "format": "uri",
+                    "format": "uri-template",
                     "type": "string"
                 }
             },
@@ -48,7 +43,7 @@
                 },
                 "url": {
                     "description": "Endpoint URL",
-                    "format": "uri",
+                    "format": "uri-template",
                     "type": "string"
                 }
             },