Merge pull request #191 from ga4gh-beacon/clean-up

Clean up
ga4gh-beacon · Dec 12, 2024 · 1d3eeb3 · 1d3eeb3
2 parents 8e0c390 + 724b65c
commit 1d3eeb3
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Showing 28 changed files with 95 additions and 146 deletions.
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/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/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/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/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/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/transform_json2md.sh b/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
 ====================================

diff --git a/framework/json/configuration/beaconMapSchema.json b/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-template",
-                    "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"

diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json
@@ -28,11 +28,6 @@
             "description": "A textual description for the element.",
             "type": "string"
         },
-        "filteringTerms": {
-            "$comment": "TO DO: Evaluate switch this to `url` or a more specific way for allowing URLs and local file paths (is this necessary?).",
-            "description": "Reference to the list of filtering terms that could be used to filter records of this entry type in this beacon.",
-            "type": "string"
-        },
         "id": {
             "description": "A unique identifier of the element.",
             "examples": [

diff --git a/framework/src/configuration/beaconMapSchema.yaml b/framework/src/configuration/beaconMapSchema.yaml
@@ -47,15 +47,6 @@ $defs:
           whole map of endpoints is found in the current Map.
         type: string
         format: uri-template
-      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 ´rootUrl` and ´singleEntryUrl`, in which
-          case the whole map of endpoints is found in the current Map.
-        type: string
-        format: uri-template
       endpoints:
         description: Optional. A list describing additional endpoints implemented
           by this Beacon instance for that entry type. Additional details on the endpoint

diff --git a/framework/src/configuration/entryTypeDefinition.yaml b/framework/src/configuration/entryTypeDefinition.yaml
@@ -56,14 +56,6 @@ properties:
     type: array
     items:
       $ref: ../common/basicElement.yaml
-  filteringTerms:
-    description: >-
-      Reference to the list of filtering terms that could be used to filter records
-      of this entry type in this beacon.
-    type: string
-    $comment: >-
-      TO DO: Evaluate switch this to `url` or a more specific way for allowing
-      URLs and local file paths (is this necessary?).
   nonFilteredQueriesAllowed:
     $ref: ../common/beaconCommonComponents.yaml#/$defs/NonFilteredQueriesAllowed
 required:

diff --git a/models/json/beacon-v2-default-model/analyses/filteringTerms.json b/models/json/beacon-v2-default-model/analyses/filteringTerms.json
diff --git a/models/json/beacon-v2-default-model/biosamples/endpoints.json b/models/json/beacon-v2-default-model/biosamples/endpoints.json
@@ -75,13 +75,13 @@
                         "schema": {
                             "oneOf": [
                                 {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json"
+                                    "$ref": "../../../../framework/json/responses/beaconBooleanResponse.json"
                                 },
                                 {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json"
+                                    "$ref": "../../../../framework/json/responses/beaconCountResponse.json"
                                 },
                                 {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json"
+                                    "$ref": "../../../../framework/json/responses/beaconResultsetsResponse.json"
                                 }
                             ]
                         }
@@ -131,7 +131,7 @@
                         "$ref": "#/components/responses/ResultsOKResponse"
                     },
                     "default": {
-                        "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json"
+                        "$ref": "../../../../framework/json/responses/beaconErrorResponse.json"
                     }
                 },
                 "tags": [
@@ -145,7 +145,7 @@
                     "content": {
                         "application/json": {
                             "schema": {
-                                "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json"
+                                "$ref": "../../../../framework/json/requests/beaconRequestBody.json"
                             }
                         }
                     },
@@ -206,7 +206,7 @@
                     "content": {
                         "application/json": {
                             "schema": {
-                                "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json"
+                                "$ref": "../../../../framework/json/requests/beaconRequestBody.json"
                             }
                         }
                     },
@@ -278,7 +278,7 @@
                     "content": {
                         "application/json": {
                             "schema": {
-                                "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json"
+                                "$ref": "../../../../framework/json/requests/beaconRequestBody.json"
                             }
                         }
                     },
@@ -350,7 +350,7 @@
                     "content": {
                         "application/json": {
                             "schema": {
-                                "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json"
+                                "$ref": "../../../../framework/json/requests/beaconRequestBody.json"
                             }
                         }
                     },
@@ -396,7 +396,7 @@
                         "content": {
                             "application/json": {
                                 "schema": {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json"
+                                    "$ref": "../../../../framework/json/responses/beaconResultsetsResponse.json"
                                 }
                             }
                         },
@@ -429,7 +429,7 @@
                     "content": {
                         "application/json": {
                             "schema": {
-                                "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json"
+                                "$ref": "../../../../framework/json/requests/beaconRequestBody.json"
                             }
                         }
                     },
@@ -440,7 +440,7 @@
                         "content": {
                             "application/json": {
                                 "schema": {
-                                    "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json"
+                                    "$ref": "../../../../framework/json/responses/beaconResultsetsResponse.json"
                                 }
                             }
                         },

diff --git a/models/json/beacon-v2-default-model/biosamples/filteringTerms.json b/models/json/beacon-v2-default-model/biosamples/filteringTerms.json