From 5b47a87236b304317ad1964d7a81c0a1f48f7a5a Mon Sep 17 00:00:00 2001 From: Michael Baudis <675030+mbaudis@users.noreply.github.com> Date: Sat, 17 Jun 2023 17:42:10 -0700 Subject: [PATCH 01/29] Update entryTypeDefinition.yaml The parameter descriptions in the EntryTypeDefinitions schema seem somewhat hard to parse and potentially misleading - this is a go at cleaning them up a bit. --- .../configuration/entryTypeDefinition.yaml | 51 +++++++++---------- 1 file changed, 25 insertions(+), 26 deletions(-) diff --git a/framework/src/configuration/entryTypeDefinition.yaml b/framework/src/configuration/entryTypeDefinition.yaml index 99f3ef974..4ca04013f 100644 --- a/framework/src/configuration/entryTypeDefinition.yaml +++ b/framework/src/configuration/entryTypeDefinition.yaml @@ -1,23 +1,22 @@ $schema: https://json-schema.org/draft/2020-12/schema title: '' -description: "Definition of an element or entry type including the Beacon v2 required\ - \ and suggested attributes. This schema purpose is to describe each type of entities\ - \ included in a Beacon, hence Beacon clients could have some metadata about such\ - \ entities.\n\nThe `id` attribute is the key that should be used in other parts\ - \ of the Beacon Model to allow Beacon clients to identify the different parts (e.g.\ - \ endpoints, filteringTerms, request parameters, etc.) that fully describe an entry\ - \ type." +description: >- + Definition of an element or entity, to describe each type of entity included in + a beacon. + The `id` attribute is the key that should be used in other parts of the data model + to allow Beacon clients to identify the different parts (e.g. endpoints, filteringTerms, + request parameters, etc.) that relvant for an entity. type: object -$comment: 'TO DO: The tagged parts should reference to `common/ontologizedElement.json`. - But that configuration fails to validate. Further investigation is required, but - should not affect the resulting schema.' properties: $schema: $ref: ../common/beaconCommonComponents.yaml#/definitions/$schema id: - $comments: ++++++ THIS IS THE START OF THE ontologized element ++++++ type: string description: A (unique) identifier of the element. + examples: + - biosample + - individual + - dataset name: type: string description: A distinctive name for the element. @@ -26,7 +25,6 @@ properties: description: A textual description for the element. ontologyTermForThisType: $ref: ../common/ontologyTerm.yaml - $comments: ++++++ THIS IS THE END OF THE ontologized element ++++++ partOfSpecification: description: This is label to group together entry types that are part of the same specification. @@ -42,25 +40,26 @@ properties: items: $ref: ../common/referenceToAnSchema.yaml 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). + 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 entity + (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 entity type (e.g. biosamples) even if a dataset + may contain records of multiple types. includedConcepts: type: array $ref: ../common/basicElement.yaml filteringTerms: - description: Reference to the file with the list of filtering terms that could - be used to filter this concept in this instance of Beacon. The referenced file - could be used to populate the `filteringTerms`endpoint. Having it independently - should allow for updating the list of accepted filtering terms when it is necessary. + description: >- + Reference to the list of filtering terms that could be used to filter records + of this entity in this beacon. type: string - $comment: "TO DO: Double-check the proper way of referencing a path or relative\ - \ path. 'format: uri' is throwing validation errors for relative file paths" + $comment: >- + TO DO: Evaluate switch this to `url` or a more specific way for allowing + URLs and local file paths (is this necessary?). nonFilteredQueriesAllowed: $ref: ../common/beaconCommonComponents.yaml#/definitions/NonFilteredQueriesAllowed required: From 6aeb06ffebea6284c7b57f569b981bd08d4a081c Mon Sep 17 00:00:00 2001 From: Michael Baudis <675030+mbaudis@users.noreply.github.com> Date: Mon, 19 Jun 2023 13:11:35 +0200 Subject: [PATCH 02/29] Update entryTypeDefinition.json --- .../json/configuration/entryTypeDefinition.json | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json index 434bebcf6..13c094cc1 100644 --- a/framework/json/configuration/entryTypeDefinition.json +++ b/framework/json/configuration/entryTypeDefinition.json @@ -1,14 +1,13 @@ { - "$comment": "TO DO: The tagged parts should reference to `common/ontologizedElement.json`. But that configuration fails to validate. Further investigation is required, but should not affect the resulting schema.", "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Definition of an element or entry type including the Beacon v2 required and suggested attributes. This schema purpose is to describe each type of entities included in a Beacon, hence Beacon clients could have some metadata about such entities.\n\nThe `id` attribute is the key that should be used in other parts of the Beacon Model to allow Beacon clients to identify the different parts (e.g. endpoints, filteringTerms, request parameters, etc.) that fully describe an entry type.", + "description": "Definition of an element or entity, to describe each type of entity included in a beacon. The `id` attribute is the key that should be used in other parts of the data model to allow Beacon clients to identify the different parts (e.g. endpoints, filteringTerms, request parameters, etc.) that relvant for an entity.", "properties": { "$schema": { "$ref": "../common/beaconCommonComponents.json#/definitions/$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).", + "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 entity (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 entity type (e.g. biosamples) even if a dataset may contain records of multiple types.", "includedConcepts": { "$ref": "../common/basicElement.json", "type": "array" @@ -30,13 +29,17 @@ "type": "string" }, "filteringTerms": { - "$comment": "TO DO: Double-check the proper way of referencing a path or relative path. 'format: uri' is throwing validation errors for relative file paths", - "description": "Reference to the file with the list of filtering terms that could be used to filter this concept in this instance of Beacon. The referenced file could be used to populate the `filteringTerms`endpoint. Having it independently should allow for updating the list of accepted filtering terms when it is necessary.", + "$comment": "TO DO: Evaluate switch this to `url` or a more specific way for allowing URLs and local file paths (is this necessary?).", + "description": "Reference to the list of filtering terms that could be used to filter records of this entity in this beacon.", "type": "string" }, "id": { - "$comments": "++++++ THIS IS THE START OF THE ontologized element ++++++", "description": "A (unique) identifier of the element.", + "examples": [ + "biosample", + "individual", + "dataset" + ], "type": "string" }, "name": { @@ -47,7 +50,6 @@ "$ref": "../common/beaconCommonComponents.json#/definitions/NonFilteredQueriesAllowed" }, "ontologyTermForThisType": { - "$comments": "++++++ THIS IS THE END OF THE ontologized element ++++++", "$ref": "../common/ontologyTerm.json" }, "partOfSpecification": { From d3f7a9262e0b93d1e562f6fd2979d04cca1b941d Mon Sep 17 00:00:00 2001 From: Michael Baudis <675030+mbaudis@users.noreply.github.com> Date: Mon, 19 Jun 2023 13:26:37 +0200 Subject: [PATCH 03/29] removed ontologyTermForThisType requirement It is not clear how to use ontologyTermForThisType w/o examples (i.e. terms for biosample, individual... - added some but incomplete...) and there is also a logical duplication having a "unique" id and an ontology term. Overall this should be clarified but the current modification seems (a) sensible (step). --- .../json/configuration/entryTypeDefinition.json | 17 +++++++++++++---- .../src/configuration/entryTypeDefinition.yaml | 12 ++++++++---- 2 files changed, 21 insertions(+), 8 deletions(-) diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json index 13c094cc1..400fdb004 100644 --- a/framework/json/configuration/entryTypeDefinition.json +++ b/framework/json/configuration/entryTypeDefinition.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Definition of an element or entity, to describe each type of entity included in a beacon. The `id` attribute is the key that should be used in other parts of the data model to allow Beacon clients to identify the different parts (e.g. endpoints, filteringTerms, request parameters, etc.) that relvant for an entity.", + "description": "Definition of an element or entity, to describe each type of entity included in a beacon. The `id` attribute is the key that should be used in other parts of the data model to allow Beacon clients to identify the different parts (e.g. endpoints, filtering terms, request parameters, etc.) that are relvant for an entity.", "properties": { "$schema": { "$ref": "../common/beaconCommonComponents.json#/definitions/$schema" @@ -34,7 +34,7 @@ "type": "string" }, "id": { - "description": "A (unique) identifier of the element.", + "description": "A unique identifier of the element.", "examples": [ "biosample", "individual", @@ -50,7 +50,17 @@ "$ref": "../common/beaconCommonComponents.json#/definitions/NonFilteredQueriesAllowed" }, "ontologyTermForThisType": { - "$ref": "../common/ontologyTerm.json" + "$ref": "../common/ontologyTerm.json", + "examples": [ + { + "id": "EFO:0000542", + "label": "individual" + }, + { + "id": "OBI:0000747", + "label": "material sample" + } + ] }, "partOfSpecification": { "description": "This is label to group together entry types that are part of the same specification.", @@ -61,7 +71,6 @@ "required": [ "id", "name", - "ontologyTermForThisType", "partOfSpecification", "defaultSchema" ], diff --git a/framework/src/configuration/entryTypeDefinition.yaml b/framework/src/configuration/entryTypeDefinition.yaml index 4ca04013f..a101afe75 100644 --- a/framework/src/configuration/entryTypeDefinition.yaml +++ b/framework/src/configuration/entryTypeDefinition.yaml @@ -4,15 +4,15 @@ description: >- Definition of an element or entity, to describe each type of entity included in a beacon. The `id` attribute is the key that should be used in other parts of the data model - to allow Beacon clients to identify the different parts (e.g. endpoints, filteringTerms, - request parameters, etc.) that relvant for an entity. + to allow Beacon clients to identify the different parts (e.g. endpoints, filtering + terms, request parameters, etc.) that are relvant for an entity. type: object properties: $schema: $ref: ../common/beaconCommonComponents.yaml#/definitions/$schema id: type: string - description: A (unique) identifier of the element. + description: A unique identifier of the element. examples: - biosample - individual @@ -25,6 +25,11 @@ properties: description: A textual description for the element. ontologyTermForThisType: $ref: ../common/ontologyTerm.yaml + examples: + - id: EFO:0000542 + label: individual + - id: OBI:0000747 + label: material sample partOfSpecification: description: This is label to group together entry types that are part of the same specification. @@ -65,7 +70,6 @@ properties: required: - id - name - - ontologyTermForThisType - partOfSpecification - defaultSchema additionalProperties: true From dd943aece56a0f814cc1af4272da306e39344c8d Mon Sep 17 00:00:00 2001 From: Michael Baudis <675030+mbaudis@users.noreply.github.com> Date: Mon, 19 Jun 2023 14:43:28 +0200 Subject: [PATCH 04/29] entry type as default instead entity --- .../json/configuration/entryTypeDefinition.json | 6 +++--- framework/src/configuration/entryTypeDefinition.yaml | 12 ++++++------ 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json index 400fdb004..b20352764 100644 --- a/framework/json/configuration/entryTypeDefinition.json +++ b/framework/json/configuration/entryTypeDefinition.json @@ -1,13 +1,13 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Definition of an element or entity, to describe each type of entity included in a beacon. The `id` attribute is the key that should be used in other parts of the data model to allow Beacon clients to identify the different parts (e.g. endpoints, filtering terms, request parameters, etc.) that are relvant for an entity.", + "description": "Definition of an element or entry type, to describe each type of entry type included in a beacon. The `id` attribute is the key that should be used in other parts of the data model to allow Beacon clients to identify the different parts (e.g. endpoints, filtering terms, request parameters, etc.) that are relvant for an entry type.", "properties": { "$schema": { "$ref": "../common/beaconCommonComponents.json#/definitions/$schema" }, "aCollectionOf": { - "description": "If the entry type is a collection of other entities, (e.g. a Dataset is a collection of Records), then this attribute must list the entities that can be included. One _collection_ can include more than one entity (e.g. a Dataset in teh Beacon cdefault model could include Individuals, Biosamples, GenomicVariations, Analyses amnd Runs). In such cases in each individual response (e.g. `resultSetsResponse` of collections of type \"dataset\") will contain entries of a single entity type (e.g. biosamples) even if a dataset may contain records of multiple types.", + "description": "If the entry type is a collection of other entities, (e.g. a Dataset is a collection of Records), then this attribute must list the entities that can be included. One _collection_ can include more than one entry type (e.g. a Dataset in teh Beacon cdefault model could include Individuals, Biosamples, GenomicVariations, Analyses amnd Runs). In such cases in each individual response (e.g. `resultSetsResponse` of collections of type \"dataset\") will contain entries of a single entry type (e.g. biosamples) even if a dataset may contain records of multiple types.", "includedConcepts": { "$ref": "../common/basicElement.json", "type": "array" @@ -30,7 +30,7 @@ }, "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 entity in this beacon.", + "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": { diff --git a/framework/src/configuration/entryTypeDefinition.yaml b/framework/src/configuration/entryTypeDefinition.yaml index a101afe75..136c2980a 100644 --- a/framework/src/configuration/entryTypeDefinition.yaml +++ b/framework/src/configuration/entryTypeDefinition.yaml @@ -1,11 +1,11 @@ $schema: https://json-schema.org/draft/2020-12/schema title: '' description: >- - Definition of an element or entity, to describe each type of entity included in - a beacon. + Definition of an element or entry type, to describe each type of entry type included + in a beacon. The `id` attribute is the key that should be used in other parts of the data model to allow Beacon clients to identify the different parts (e.g. endpoints, filtering - terms, request parameters, etc.) that are relvant for an entity. + terms, request parameters, etc.) that are relvant for an entry type. type: object properties: $schema: @@ -48,11 +48,11 @@ properties: 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 entity + 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 entity type (e.g. biosamples) even if a dataset + contain entries of a single entry type (e.g. biosamples) even if a dataset may contain records of multiple types. includedConcepts: type: array @@ -60,7 +60,7 @@ properties: filteringTerms: description: >- Reference to the list of filtering terms that could be used to filter records - of this entity in this beacon. + of this entry type in this beacon. type: string $comment: >- TO DO: Evaluate switch this to `url` or a more specific way for allowing From 94b789198ec296830c67877097c0c828eef77e30 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oriol=20L=C3=B3pez-Doriga?= Date: Tue, 20 Jun 2023 16:46:19 +0200 Subject: [PATCH 05/29] update entryType description --- framework/json/configuration/entryTypeDefinition.json | 2 +- framework/src/configuration/entryTypeDefinition.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json index b20352764..27d425770 100644 --- a/framework/json/configuration/entryTypeDefinition.json +++ b/framework/json/configuration/entryTypeDefinition.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Definition of an element or entry type, to describe each type of entry type included in a beacon. The `id` attribute is the key that should be used in other parts of the data model to allow Beacon clients to identify the different parts (e.g. endpoints, filtering terms, request parameters, etc.) that are relvant for an entry type.", + "description": "Definition of an element or scope of the element, to describe each type of entry type included in a beacon. The `id` attribute is the key that should be used in other parts of the data model to allow Beacon clients to identify the different parts (e.g. endpoints, filtering terms, request parameters, etc.) that are relvant for an entry type.", "properties": { "$schema": { "$ref": "../common/beaconCommonComponents.json#/definitions/$schema" diff --git a/framework/src/configuration/entryTypeDefinition.yaml b/framework/src/configuration/entryTypeDefinition.yaml index 136c2980a..61916df7e 100644 --- a/framework/src/configuration/entryTypeDefinition.yaml +++ b/framework/src/configuration/entryTypeDefinition.yaml @@ -1,7 +1,7 @@ $schema: https://json-schema.org/draft/2020-12/schema title: '' description: >- - Definition of an element or entry type, to describe each type of entry type included + Definition of an element or scope of the element, to describe each type of entry type included in a beacon. The `id` attribute is the key that should be used in other parts of the data model to allow Beacon clients to identify the different parts (e.g. endpoints, filtering From cb3b2ff3c80f80a7f012914efe33a7ac306f7cc5 Mon Sep 17 00:00:00 2001 From: redmitry Date: Tue, 5 Sep 2023 15:11:08 +0200 Subject: [PATCH 06/29] for templates the format must be "uri-template". --- framework/json/configuration/beaconMapSchema.json | 6 +++--- framework/src/configuration/beaconMapSchema.yaml | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/framework/json/configuration/beaconMapSchema.json b/framework/json/configuration/beaconMapSchema.json index b5335e28b..47fec6701 100644 --- a/framework/json/configuration/beaconMapSchema.json +++ b/framework/json/configuration/beaconMapSchema.json @@ -18,7 +18,7 @@ }, "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", + "format": "uri-template", "type": "string" }, "openAPIEndpointsDefinition": { @@ -32,7 +32,7 @@ }, "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" } }, @@ -50,7 +50,7 @@ }, "url": { "description": "Endpoint URL", - "format": "uri", + "format": "uri-template", "type": "string" } }, diff --git a/framework/src/configuration/beaconMapSchema.yaml b/framework/src/configuration/beaconMapSchema.yaml index ce1cff2c2..83170dab6 100644 --- a/framework/src/configuration/beaconMapSchema.yaml +++ b/framework/src/configuration/beaconMapSchema.yaml @@ -46,7 +46,7 @@ definitions: be the only one implemented, together with ´rootUrl`, in which case the whole map of endpoints is found in the current Map. type: string - format: uri + 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, @@ -55,7 +55,7 @@ definitions: 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 + 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 @@ -74,7 +74,7 @@ definitions: url: description: Endpoint URL type: string - format: uri + format: uri-template returnedEntryType: description: Which entry type is returned by querying this endpoint. It MUST match one of the entry types defined in the Beacon configuration file (`beaconConfiguration.json`). From 08449969411382ad02fa275796eb82c3ce1b22c6 Mon Sep 17 00:00:00 2001 From: Daniel Tsirulnikov Date: Mon, 15 Jul 2024 21:25:49 -0700 Subject: [PATCH 07/29] Fixed #138 --- framework/json/endpoints.json | 9 ++++++++- framework/src/endpoints.yaml | 6 +++++- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/framework/json/endpoints.json b/framework/json/endpoints.json index e394ad28f..c5d7faf62 100644 --- a/framework/json/endpoints.json +++ b/framework/json/endpoints.json @@ -136,7 +136,14 @@ "operationId": "getFilteringTerms", "responses": { "200": { - "$ref": "./responses/beaconFilteringTermsResponse.json" + "content": { + "application/json": { + "schema": { + "$ref": "./responses/beaconFilteringTermsResponse.json" + } + } + }, + "description": "Successful operation." }, "default": { "$ref": "./responses/beaconErrorResponse.json", diff --git a/framework/src/endpoints.yaml b/framework/src/endpoints.yaml index 9e26e10ec..0df8cc69c 100644 --- a/framework/src/endpoints.yaml +++ b/framework/src/endpoints.yaml @@ -116,7 +116,11 @@ paths: - Informational endpoints responses: '200': - $ref: ./responses/beaconFilteringTermsResponse.yaml + description: Successful operation. + content: + application/json: + schema: + $ref: ./responses/beaconFilteringTermsResponse.yaml default: description: An unsuccessful operation. $ref: ./responses/beaconErrorResponse.yaml From 60da8ac078b9fe7a90ab5b4a7a7427022e04ae73 Mon Sep 17 00:00:00 2001 From: Daniel Tsirulnikov Date: Mon, 15 Jul 2024 21:34:19 -0700 Subject: [PATCH 08/29] Additional location fix --- models/json/beacon-v2-default-model/endpoints.json | 9 ++++++++- models/src/beacon-v2-default-model/endpoints.yaml | 6 +++++- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/models/json/beacon-v2-default-model/endpoints.json b/models/json/beacon-v2-default-model/endpoints.json index 9c72ad0ef..255b80b90 100644 --- a/models/json/beacon-v2-default-model/endpoints.json +++ b/models/json/beacon-v2-default-model/endpoints.json @@ -136,7 +136,14 @@ "operationId": "getFilteringTerms", "responses": { "200": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" + } + } + }, + "description": "Successful operation" }, "default": { "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", diff --git a/models/src/beacon-v2-default-model/endpoints.yaml b/models/src/beacon-v2-default-model/endpoints.yaml index a8b5716f0..7c35d79bd 100644 --- a/models/src/beacon-v2-default-model/endpoints.yaml +++ b/models/src/beacon-v2-default-model/endpoints.yaml @@ -116,7 +116,11 @@ paths: - Informational endpoints responses: '200': - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json + description: Successful operation + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json default: description: An unsuccessful operation $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json From 8a97a68431739d495d97331b82e0314cc834e1c9 Mon Sep 17 00:00:00 2001 From: Daniel Tsirulnikov Date: Mon, 15 Jul 2024 21:53:34 -0700 Subject: [PATCH 09/29] Fixed #136 --- models/json/beacon-v2-default-model/analyses/endpoints.json | 6 +++++- .../json/beacon-v2-default-model/biosamples/endpoints.json | 6 +++++- .../genomicVariations/endpoints.json | 6 +++++- .../json/beacon-v2-default-model/individuals/endpoints.json | 6 +++++- models/json/beacon-v2-default-model/runs/endpoints.json | 6 +++++- models/src/beacon-v2-default-model/analyses/endpoints.yaml | 5 ++++- .../src/beacon-v2-default-model/biosamples/endpoints.yaml | 5 ++++- .../genomicVariations/endpoints.yaml | 5 ++++- .../src/beacon-v2-default-model/individuals/endpoints.yaml | 5 ++++- models/src/beacon-v2-default-model/runs/endpoints.yaml | 5 ++++- 10 files changed, 45 insertions(+), 10 deletions(-) diff --git a/models/json/beacon-v2-default-model/analyses/endpoints.json b/models/json/beacon-v2-default-model/analyses/endpoints.json index 570d7201d..3052fc3c3 100644 --- a/models/json/beacon-v2-default-model/analyses/endpoints.json +++ b/models/json/beacon-v2-default-model/analyses/endpoints.json @@ -25,7 +25,11 @@ } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + "in": "query", + "name": "includeResultsetResponses", + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + } }, "limit": { "in": "query", diff --git a/models/json/beacon-v2-default-model/biosamples/endpoints.json b/models/json/beacon-v2-default-model/biosamples/endpoints.json index 533d5ceda..b6f6154fc 100644 --- a/models/json/beacon-v2-default-model/biosamples/endpoints.json +++ b/models/json/beacon-v2-default-model/biosamples/endpoints.json @@ -29,7 +29,11 @@ } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + "in": "query", + "name": "includeResultsetResponses", + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + } }, "limit": { "in": "query", diff --git a/models/json/beacon-v2-default-model/genomicVariations/endpoints.json b/models/json/beacon-v2-default-model/genomicVariations/endpoints.json index e9101f04f..7339a49ce 100644 --- a/models/json/beacon-v2-default-model/genomicVariations/endpoints.json +++ b/models/json/beacon-v2-default-model/genomicVariations/endpoints.json @@ -81,7 +81,11 @@ } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + "in": "query", + "name": "includeResultsetResponses", + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + } }, "limit": { "in": "query", diff --git a/models/json/beacon-v2-default-model/individuals/endpoints.json b/models/json/beacon-v2-default-model/individuals/endpoints.json index 32898cb17..e2ebeee37 100644 --- a/models/json/beacon-v2-default-model/individuals/endpoints.json +++ b/models/json/beacon-v2-default-model/individuals/endpoints.json @@ -25,7 +25,11 @@ } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + "in": "query", + "name": "includeResultsetResponses", + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + } }, "limit": { "in": "query", diff --git a/models/json/beacon-v2-default-model/runs/endpoints.json b/models/json/beacon-v2-default-model/runs/endpoints.json index b5084bba7..d0c9ada44 100644 --- a/models/json/beacon-v2-default-model/runs/endpoints.json +++ b/models/json/beacon-v2-default-model/runs/endpoints.json @@ -33,7 +33,11 @@ } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + "in": "query", + "name": "includeResultsetResponses", + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + } }, "individualId": { "in": "path", diff --git a/models/src/beacon-v2-default-model/analyses/endpoints.yaml b/models/src/beacon-v2-default-model/analyses/endpoints.yaml index 8f5d5457a..71774a9ba 100644 --- a/models/src/beacon-v2-default-model/analyses/endpoints.yaml +++ b/models/src/beacon-v2-default-model/analyses/endpoints.yaml @@ -150,7 +150,10 @@ components: schema: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit includeResultsetResponses: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses + name: includeResultsetResponses + in: query + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses entryId: name: id in: path diff --git a/models/src/beacon-v2-default-model/biosamples/endpoints.yaml b/models/src/beacon-v2-default-model/biosamples/endpoints.yaml index 50b80d8bb..4a396baac 100644 --- a/models/src/beacon-v2-default-model/biosamples/endpoints.yaml +++ b/models/src/beacon-v2-default-model/biosamples/endpoints.yaml @@ -226,7 +226,10 @@ components: schema: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit includeResultsetResponses: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses + name: includeResultsetResponses + in: query + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses entryId: name: id in: path diff --git a/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml b/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml index 44b59a736..2f7f6794e 100644 --- a/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml +++ b/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml @@ -194,7 +194,10 @@ components: schema: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit includeResultsetResponses: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses + name: includeResultsetResponses + in: query + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses entryId: name: id in: path diff --git a/models/src/beacon-v2-default-model/individuals/endpoints.yaml b/models/src/beacon-v2-default-model/individuals/endpoints.yaml index 7ed5a46fe..388ef3fb8 100644 --- a/models/src/beacon-v2-default-model/individuals/endpoints.yaml +++ b/models/src/beacon-v2-default-model/individuals/endpoints.yaml @@ -221,7 +221,10 @@ components: schema: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit includeResultsetResponses: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses + name: includeResultsetResponses + in: query + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses entryId: name: id in: path diff --git a/models/src/beacon-v2-default-model/runs/endpoints.yaml b/models/src/beacon-v2-default-model/runs/endpoints.yaml index 473bea53c..349f8317c 100644 --- a/models/src/beacon-v2-default-model/runs/endpoints.yaml +++ b/models/src/beacon-v2-default-model/runs/endpoints.yaml @@ -182,7 +182,10 @@ components: schema: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit includeResultsetResponses: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses + name: includeResultsetResponses + in: query + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses entryId: name: id in: path From c58a9c466c25b3a9171a25687105ce1eed615cc9 Mon Sep 17 00:00:00 2001 From: Daniel Tsirulnikov Date: Mon, 15 Jul 2024 23:09:38 -0700 Subject: [PATCH 10/29] Fixed #137 --- framework/json/configuration/beaconConfigurationSchema.json | 6 +++--- framework/src/configuration/beaconConfigurationSchema.yaml | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/framework/json/configuration/beaconConfigurationSchema.json b/framework/json/configuration/beaconConfigurationSchema.json index 02d54a3a0..0bbab2e43 100644 --- a/framework/json/configuration/beaconConfigurationSchema.json +++ b/framework/json/configuration/beaconConfigurationSchema.json @@ -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/src/configuration/beaconConfigurationSchema.yaml b/framework/src/configuration/beaconConfigurationSchema.yaml index f6f013d92..43272f3b7 100644 --- a/framework/src/configuration/beaconConfigurationSchema.yaml +++ b/framework/src/configuration/beaconConfigurationSchema.yaml @@ -41,8 +41,8 @@ properties: - PUBLIC - REGISTERED - CONTROLLED - default: - - CONTROLLED + default: + - CONTROLLED entryTypes: $ref: '#/definitions/EntryTypes' definitions: From dd18509123676de54d8fc6254689e4ead92489fe Mon Sep 17 00:00:00 2001 From: Daniel Tsirulnikov Date: Mon, 15 Jul 2024 23:28:52 -0700 Subject: [PATCH 11/29] Fixed #140 --- .../analyses/endpoints.json | 12 +++++---- .../biosamples/endpoints.json | 26 ++++++++++++------- .../cohorts/endpoints.json | 12 +++++---- .../datasets/endpoints.json | 10 ++++--- .../genomicVariations/endpoints.json | 26 ++++++++++++------- .../individuals/endpoints.json | 12 +++++---- .../runs/endpoints.json | 12 +++++---- .../analyses/endpoints.yaml | 6 +++-- .../biosamples/endpoints.yaml | 14 +++++++--- .../cohorts/endpoints.yaml | 6 +++-- .../datasets/endpoints.yaml | 6 +++-- .../genomicVariations/endpoints.yaml | 14 +++++++--- .../individuals/endpoints.yaml | 6 +++-- .../runs/endpoints.yaml | 6 +++-- 14 files changed, 109 insertions(+), 59 deletions(-) diff --git a/models/json/beacon-v2-default-model/analyses/endpoints.json b/models/json/beacon-v2-default-model/analyses/endpoints.json index 570d7201d..afdfe9795 100644 --- a/models/json/beacon-v2-default-model/analyses/endpoints.json +++ b/models/json/beacon-v2-default-model/analyses/endpoints.json @@ -10,14 +10,16 @@ } }, "filters": { + "examples": { + "example1": { + "value": [ + "variantcaller:GATK4.0" + ] + } + }, "in": "query", "name": "filters", "schema": { - "examples": [ - [ - "variantcaller:GATK4.0" - ] - ], "items": { "type": "string" }, diff --git a/models/json/beacon-v2-default-model/biosamples/endpoints.json b/models/json/beacon-v2-default-model/biosamples/endpoints.json index 533d5ceda..a44028d2a 100644 --- a/models/json/beacon-v2-default-model/biosamples/endpoints.json +++ b/models/json/beacon-v2-default-model/biosamples/endpoints.json @@ -10,18 +10,26 @@ } }, "filters": { - "in": "query", - "name": "filters", - "schema": { - "examples": [ - [ + "examples": { + "example1": { + "value": [ "NCIT:C3222" - ], - [ - "OBI:0100058", + ] + }, + "example2": { + "value": [ "NCIT:C4813" ] - ], + }, + "example3": { + "value": [ + "OBI:0100058" + ] + } + }, + "in": "query", + "name": "filters", + "schema": { "items": { "type": "string" }, diff --git a/models/json/beacon-v2-default-model/cohorts/endpoints.json b/models/json/beacon-v2-default-model/cohorts/endpoints.json index 1e36b7462..d5dc4d2ae 100644 --- a/models/json/beacon-v2-default-model/cohorts/endpoints.json +++ b/models/json/beacon-v2-default-model/cohorts/endpoints.json @@ -10,14 +10,16 @@ } }, "filters": { + "examples": { + "example1": { + "value": [ + "OMIABIS:0001017" + ] + } + }, "in": "query", "name": "filters", "schema": { - "examples": [ - [ - "OMIABIS:0001017" - ] - ], "items": { "type": "string" }, diff --git a/models/json/beacon-v2-default-model/datasets/endpoints.json b/models/json/beacon-v2-default-model/datasets/endpoints.json index 3fdc832a4..daac53cc1 100644 --- a/models/json/beacon-v2-default-model/datasets/endpoints.json +++ b/models/json/beacon-v2-default-model/datasets/endpoints.json @@ -10,12 +10,16 @@ } }, "filters": { + "examples": { + "example1": { + "value": [ + "DUO:0000007" + ] + } + }, "in": "query", "name": "filters", "schema": { - "examples": [ - "DUO:0000007" - ], "items": { "type": "string" }, diff --git a/models/json/beacon-v2-default-model/genomicVariations/endpoints.json b/models/json/beacon-v2-default-model/genomicVariations/endpoints.json index e9101f04f..c97a6addc 100644 --- a/models/json/beacon-v2-default-model/genomicVariations/endpoints.json +++ b/models/json/beacon-v2-default-model/genomicVariations/endpoints.json @@ -46,18 +46,26 @@ } }, "filters": { - "in": "query", - "name": "filters", - "schema": { - "examples": [ - [ + "examples": { + "example1": { + "value": [ "EFO:0009655" - ], - [ - "NCIT:C48725", + ] + }, + "example2": { + "value": [ + "NCIT:C48725" + ] + }, + "example3": { + "value": [ "NCIT:C28080" ] - ], + } + }, + "in": "query", + "name": "filters", + "schema": { "items": { "type": "string" }, diff --git a/models/json/beacon-v2-default-model/individuals/endpoints.json b/models/json/beacon-v2-default-model/individuals/endpoints.json index 32898cb17..b7985ebdf 100644 --- a/models/json/beacon-v2-default-model/individuals/endpoints.json +++ b/models/json/beacon-v2-default-model/individuals/endpoints.json @@ -10,14 +10,16 @@ } }, "filters": { + "examples": { + "example1": { + "value": [ + "NCIT:C20197" + ] + } + }, "in": "query", "name": "filters", "schema": { - "examples": [ - [ - "NCIT:C20197" - ] - ], "items": { "type": "string" }, diff --git a/models/json/beacon-v2-default-model/runs/endpoints.json b/models/json/beacon-v2-default-model/runs/endpoints.json index b5084bba7..20eb29751 100644 --- a/models/json/beacon-v2-default-model/runs/endpoints.json +++ b/models/json/beacon-v2-default-model/runs/endpoints.json @@ -18,14 +18,16 @@ } }, "filters": { + "examples": { + "example1": { + "value": [ + "OBI:0002048" + ] + } + }, "in": "query", "name": "filters", "schema": { - "examples": [ - [ - "OBI:0002048" - ] - ], "items": { "type": "string" }, diff --git a/models/src/beacon-v2-default-model/analyses/endpoints.yaml b/models/src/beacon-v2-default-model/analyses/endpoints.yaml index 8f5d5457a..d9acb8d87 100644 --- a/models/src/beacon-v2-default-model/analyses/endpoints.yaml +++ b/models/src/beacon-v2-default-model/analyses/endpoints.yaml @@ -164,5 +164,7 @@ components: type: array items: type: string - examples: - - - variantcaller:GATK4.0 + examples: + example1: + value: + - variantcaller:GATK4.0 diff --git a/models/src/beacon-v2-default-model/biosamples/endpoints.yaml b/models/src/beacon-v2-default-model/biosamples/endpoints.yaml index 50b80d8bb..6bf2712dd 100644 --- a/models/src/beacon-v2-default-model/biosamples/endpoints.yaml +++ b/models/src/beacon-v2-default-model/biosamples/endpoints.yaml @@ -240,7 +240,13 @@ components: type: array items: type: string - examples: - - - NCIT:C3222 - - - OBI:0100058 - - NCIT:C4813 + examples: + example1: + value: + - NCIT:C3222 + example2: + value: + - NCIT:C4813 + example3: + value: + - OBI:0100058 diff --git a/models/src/beacon-v2-default-model/cohorts/endpoints.yaml b/models/src/beacon-v2-default-model/cohorts/endpoints.yaml index 9fd0e999a..db9580a20 100644 --- a/models/src/beacon-v2-default-model/cohorts/endpoints.yaml +++ b/models/src/beacon-v2-default-model/cohorts/endpoints.yaml @@ -215,5 +215,7 @@ components: type: array items: type: string - examples: - - - OMIABIS:0001017 + examples: + example1: + value: + - OMIABIS:0001017 diff --git a/models/src/beacon-v2-default-model/datasets/endpoints.yaml b/models/src/beacon-v2-default-model/datasets/endpoints.yaml index dc2c34d31..b35a19b27 100644 --- a/models/src/beacon-v2-default-model/datasets/endpoints.yaml +++ b/models/src/beacon-v2-default-model/datasets/endpoints.yaml @@ -289,5 +289,7 @@ components: type: array items: type: string - examples: - - DUO:0000007 + examples: + example1: + value: + - DUO:0000007 diff --git a/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml b/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml index 44b59a736..833702830 100644 --- a/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml +++ b/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml @@ -282,7 +282,13 @@ components: type: array items: type: string - examples: - - - EFO:0009655 - - - NCIT:C48725 - - NCIT:C28080 + examples: + example1: + value: + - EFO:0009655 + example2: + value: + - NCIT:C48725 + example3: + value: + - NCIT:C28080 diff --git a/models/src/beacon-v2-default-model/individuals/endpoints.yaml b/models/src/beacon-v2-default-model/individuals/endpoints.yaml index 7ed5a46fe..e6f671b78 100644 --- a/models/src/beacon-v2-default-model/individuals/endpoints.yaml +++ b/models/src/beacon-v2-default-model/individuals/endpoints.yaml @@ -235,5 +235,7 @@ components: type: array items: type: string - examples: - - - NCIT:C20197 + examples: + example1: + value: + - NCIT:C20197 diff --git a/models/src/beacon-v2-default-model/runs/endpoints.yaml b/models/src/beacon-v2-default-model/runs/endpoints.yaml index 473bea53c..72f32a992 100644 --- a/models/src/beacon-v2-default-model/runs/endpoints.yaml +++ b/models/src/beacon-v2-default-model/runs/endpoints.yaml @@ -208,5 +208,7 @@ components: type: array items: type: string - examples: - - - OBI:0002048 + examples: + example1: + value: + - OBI:0002048 From 44ec3840f9580b6e0a607c628ee4ea4777d3057d Mon Sep 17 00:00:00 2001 From: Michael Baudis Date: Fri, 19 Jul 2024 10:43:33 +0200 Subject: [PATCH 12/29] update of inline descriptions in the analysis schema document * clarifications, rewording, example * no schema changes --- .../sections/beaconFilteringTermsResults.json | 32 +++++++++------ .../analyses/defaultSchema.json | 34 +++++++++------- .../beacon-v2-default-model/common/age.json | 4 +- .../common/ageRange.json | 4 +- .../common/complexValue.json | 4 +- .../genomicVariations/requestParameters.json | 6 +-- .../analyses/defaultSchema.yaml | 39 ++++++++++++------- 7 files changed, 75 insertions(+), 48 deletions(-) diff --git a/framework/json/responses/sections/beaconFilteringTermsResults.json b/framework/json/responses/sections/beaconFilteringTermsResults.json index 1755fb582..556d35993 100644 --- a/framework/json/responses/sections/beaconFilteringTermsResults.json +++ b/framework/json/responses/sections/beaconFilteringTermsResults.json @@ -21,6 +21,25 @@ ], "type": "string" }, + "scopes": { + "description": "Entry types affected by this filter.", + "examples": [ + [ + "individual", + "biosample", + "analysis", + "run", + "genomicVariation" + ], + [ + "biosample" + ] + ], + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "description": "Either \"custom\", \"alphanumeric\" or ontology/terminology full name. TODO: An ontology ... with a registered prefix does not need a full name so one may better use CURIE to indicate that the resource can be retrieved from the id. This also will allow to provide an enum here.", "examples": [ @@ -28,17 +47,6 @@ "alphanumeric" ], "type": "string" - }, - "scopes": { - "description": "Entry types affected by this filter.", - "examples": [ - ["individual", "biosample", "analysis", "run", "genomicVariation"], - ["biosample"] - ], - "type": "array", - "items": { - "type": "string" - } } }, "required": [ @@ -115,4 +123,4 @@ } }, "type": "object" -} +} \ No newline at end of file diff --git a/models/json/beacon-v2-default-model/analyses/defaultSchema.json b/models/json/beacon-v2-default-model/analyses/defaultSchema.json index e2fd84089..ef5646e01 100644 --- a/models/json/beacon-v2-default-model/analyses/defaultSchema.json +++ b/models/json/beacon-v2-default-model/analyses/defaultSchema.json @@ -2,17 +2,17 @@ "$comment": "version: ga4gh-beacon-analysis-v2.0.0", "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Schema for a sequencing bioinformatics analysis.", + "description": "The `analysis` schema represents a information about the data analysis steps leading to (a set of) genomic variation call(s).", "properties": { "aligner": { - "description": "Reference to mapping/alignment software", + "description": "Name or identifier of the mapping/alignment software/pipeline", "examples": [ "bwa-0.7.8" ], "type": "string" }, "analysisDate": { - "description": "Date at which analysis was performed.", + "description": "Date at which analysis was performed.\n", "examples": [ "2021-10-17" ], @@ -20,20 +20,22 @@ "type": "string" }, "biosampleId": { - "description": "Reference to the `id` of the biosample this analysis is reporting on.", + "description": "Local reference to the `id` of the biosample this analysis is reporting on.", "examples": [ - "S0001" + "S0001", + "onekgbs-NA07346" ], "type": "string" }, "id": { - "description": "Analysis reference ID (external accession or internal ID)", + "description": "Analysis id for internal referencing; unique in the dataset.", "type": "string" }, "individualId": { - "description": "Reference to the `id` of the individual this analysis is reporting on.", + "description": "Local reference to the `id` of the individual this analysis is reporting on.", "examples": [ - "P0001" + "P0001", + "onekgind-NA07346" ], "type": "string" }, @@ -41,30 +43,32 @@ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info" }, "pipelineName": { - "description": "Analysis pipeline and version if a standardized pipeline was used", + "description": "Analysis pipeline and version.", "examples": [ "Pipeline-panel-0001-v1" ], "type": "string" }, "pipelineRef": { - "description": "Link to Analysis pipeline resource", + "description": "Link to information about or repository of the analysis pipeline.", "examples": [ - "https://doi.org/10.48511/workflowhub.workflow.111.1" + "https://doi.org/10.48511/workflowhub.workflow.111.1", + "https://doi.org/10.1093/bib/bbad541" ], "type": "string" }, "runId": { - "description": "Run identifier (external accession or internal ID).", + "description": "Local reference to the associated experimental run.", "examples": [ "SRR10903401" ], "type": "string" }, "variantCaller": { - "description": "Reference to variant calling software / pipeline", + "description": "Name or identifier of the variant calling software/pipeline", "examples": [ - "GATK4.0" + "GATK4.0", + "labelSeg" ], "type": "string" } @@ -74,6 +78,6 @@ "analysisDate", "pipelineName" ], - "title": "Sequencing bioinformatics analysis", + "title": "Bioinformatics analysis", "type": "object" } \ No newline at end of file diff --git a/models/json/beacon-v2-default-model/common/age.json b/models/json/beacon-v2-default-model/common/age.json index e7f4a6c66..f6b941fde 100644 --- a/models/json/beacon-v2-default-model/common/age.json +++ b/models/json/beacon-v2-default-model/common/age.json @@ -3,7 +3,7 @@ "description": "Age value definition. Provenance: GA4GH Phenopackets v2 `Age`", "properties": { "iso8601duration": { - "description": "Represents age as a ISO8601 duration (e.g., 'P40Y10M05D').", + "description": "Represents age as a ISO8601 duration (e.g., P40Y10M05D).", "example": "P32Y6M1D", "type": "string" } @@ -13,4 +13,4 @@ ], "title": "Age", "type": "object" -} +} \ No newline at end of file diff --git a/models/json/beacon-v2-default-model/common/ageRange.json b/models/json/beacon-v2-default-model/common/ageRange.json index 31fb79c76..1bb6ff693 100644 --- a/models/json/beacon-v2-default-model/common/ageRange.json +++ b/models/json/beacon-v2-default-model/common/ageRange.json @@ -12,8 +12,8 @@ } }, "required": [ - "end", - "start" + "start", + "end" ], "title": "AgeRange", "type": "object" diff --git a/models/json/beacon-v2-default-model/common/complexValue.json b/models/json/beacon-v2-default-model/common/complexValue.json index fd9993392..e60d69cb8 100644 --- a/models/json/beacon-v2-default-model/common/complexValue.json +++ b/models/json/beacon-v2-default-model/common/complexValue.json @@ -40,7 +40,9 @@ "type": "array" } }, - "required": [ "typedQuantities" ], + "required": [ + "typedQuantities" + ], "title": "Complex Value", "type": "object" } \ No newline at end of file diff --git a/models/json/beacon-v2-default-model/genomicVariations/requestParameters.json b/models/json/beacon-v2-default-model/genomicVariations/requestParameters.json index e469211f4..5831f13cf 100644 --- a/models/json/beacon-v2-default-model/genomicVariations/requestParameters.json +++ b/models/json/beacon-v2-default-model/genomicVariations/requestParameters.json @@ -17,7 +17,7 @@ "$ref": "./requestParametersComponents.json#/definitions/Assembly" }, "end": { - "description": "Precise or bracketing the end of the variants of interest: * (0-based, exclusive) - see `start` * for bracket queries, provide 2 values (e.g. [111,222]).", + "description": "Precise or bracketing the end of the variants of interest: * (0-based, exclusive) - see `start` * for bracket queries, provide 2 values (e.g. [111,222]).\"", "items": { "format": "int64", "minimum": 1, @@ -52,7 +52,7 @@ "$ref": "./requestParametersComponents.json#/definitions/RefSeqId" }, "start": { - "description": "Precise or fuzzy start coordinate position(s), allele locus (0-based, inclusive). * `start` only:\n - for single positions, e.g. the start of a specified sequence\nalteration where the size is given through the specified `alternateBases`\n - typical use are queries for SNV and small InDels\n - the use of `start` without an `end` parameter requires the use of\n`alternateBases`\n* 1 value each in both `start` and `end`:\n - for searching any variant falling fully or partially within the range\n between `start` and `end` (a.k.a. \"range query\")\n - additional use of `variantType` OR `alternateBases` can limit the\n scope of the query\n - by convention, partial overlaps of variants with the indicated genomic\n range are accepted; for specific overlap requirements the 4-parameter\n \"Bracket Queries\" should be employed\n* 2 values in both `start` and `end` for constructing a \"Bracket Query\":\n - can be used to match any contiguous genomic interval, e.g. for querying\n imprecise positions\n - identifies all structural variants starting between `start[0]` and `start[1]`,\n and ending between `end[0]` <-> `end[1]`\n - single or double sided precise matches can be achieved by setting\n `start[1]=start[0]+1` and `end[1]=end[0]+1`", + "description": "Precise or fuzzy start coordinate position(s), allele locus (0-based, inclusive). * `start` only:\n - for single positions, e.g. the start of a specified sequence\n alteration where the size is given through the specified `alternateBases`\n - typical use are queries for SNV and small InDels\n - the use of `start` without an `end` parameter requires the use of\n `alternateBases`\n* 1 value in both `start` and `end`:\n - for searching any variant falling fully or partially within the range\n between `start` and `end` (a.k.a. \"range query\")\n - additional use of `variantType` OR `alternateBases` can limit the\n scope of the query\n - by convention, partial overlaps of variants with the indicated genomic\n range are accepted; for specific overlap requirements the 4-parameter\n \"Bracket Queries\" should be employed\n* 2 values in both `start` and `end` for constructing a \"Bracket Query\":\n - can be used to match any contiguous genomic interval, e.g. for querying\n imprecise positions\n - identifies all structural variants starting between `start[0]` and `start[1]`,\n and ending between `end[0]` <-> `end[1]`\n - single or double sided precise matches can be achieved by setting\n `start[1]=start[0]+1` and `end[1]=end[0]+1`", "items": { "format": "int64", "minimum": 0, @@ -87,4 +87,4 @@ }, "type": "object" } -} +} \ No newline at end of file diff --git a/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml b/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml index 8eb87b5be..118bc5dd6 100644 --- a/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml +++ b/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml @@ -1,55 +1,68 @@ $schema: https://json-schema.org/draft/2020-12/schema -title: Sequencing bioinformatics analysis +title: Bioinformatics analysis $comment: 'version: ga4gh-beacon-analysis-v2.0.0' -description: Schema for a sequencing bioinformatics analysis. +description: >- + The `analysis` schema represents a information about the data analysis steps + leading to (a set of) genomic variation call(s). type: object properties: id: - description: Analysis reference ID (external accession or internal ID) + description: >- + Analysis id for internal referencing; unique in the dataset. type: string runId: - description: Run identifier (external accession or internal ID). + description: >- + Local reference to the associated experimental run. type: string examples: - SRR10903401 biosampleId: - description: Reference to the `id` of the biosample this analysis is reporting - on. + description: >- + Local reference to the `id` of the biosample this analysis is reporting on. type: string examples: - S0001 + - onekgbs-NA07346 individualId: - description: Reference to the `id` of the individual this analysis is reporting - on. + description: >- + Local reference to the `id` of the individual this analysis is reporting on. type: string examples: - P0001 + - onekgind-NA07346 analysisDate: - description: Date at which analysis was performed. + description: > + Date at which analysis was performed. type: string format: date examples: - '2021-10-17' pipelineName: - description: Analysis pipeline and version if a standardized pipeline was used + description: >- + Analysis pipeline and version. type: string examples: - Pipeline-panel-0001-v1 pipelineRef: - description: Link to Analysis pipeline resource + description: >- + Link to information about or repository of the analysis pipeline. type: string examples: - https://doi.org/10.48511/workflowhub.workflow.111.1 + - https://doi.org/10.1093/bib/bbad541 aligner: - description: Reference to mapping/alignment software + description: >- + Name or identifier of the mapping/alignment software/pipeline type: string examples: - bwa-0.7.8 variantCaller: - description: Reference to variant calling software / pipeline + description: >- + Name or identifier of the variant calling software/pipeline type: string examples: - GATK4.0 + - labelSeg info: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info required: From 0dfd4096acdf2c6dc8a8b06b5fad9234fd4c8457 Mon Sep 17 00:00:00 2001 From: Daniel Tsirulnikov Date: Mon, 22 Jul 2024 13:53:18 -0700 Subject: [PATCH 13/29] Fixed #135 --- framework/json/endpoints.json | 48 ++++++++-- framework/src/endpoints.yaml | 30 +++++-- .../analyses/endpoints.json | 40 +++++++-- .../biosamples/endpoints.json | 72 +++++++++++++-- .../cohorts/endpoints.json | 56 ++++++++++-- .../datasets/endpoints.json | 88 ++++++++++++++++--- .../beacon-v2-default-model/endpoints.json | 48 ++++++++-- .../genomicVariations/endpoints.json | 56 ++++++++++-- .../individuals/endpoints.json | 72 +++++++++++++-- .../runs/endpoints.json | 56 ++++++++++-- .../analyses/endpoints.yaml | 25 ++++-- .../biosamples/endpoints.yaml | 45 ++++++++-- .../cohorts/endpoints.yaml | 35 ++++++-- .../datasets/endpoints.yaml | 55 +++++++++--- .../beacon-v2-default-model/endpoints.yaml | 30 +++++-- .../genomicVariations/endpoints.yaml | 35 ++++++-- .../individuals/endpoints.yaml | 45 ++++++++-- .../runs/endpoints.yaml | 35 ++++++-- 18 files changed, 737 insertions(+), 134 deletions(-) diff --git a/framework/json/endpoints.json b/framework/json/endpoints.json index e394ad28f..9834870fb 100644 --- a/framework/json/endpoints.json +++ b/framework/json/endpoints.json @@ -63,7 +63,13 @@ "$ref": "#/components/responses/infoOKResponse" }, "default": { - "$ref": "./responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "./responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation." } }, @@ -94,7 +100,13 @@ "description": "Successful operation." }, "default": { - "$ref": "./responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "./responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation." } }, @@ -121,7 +133,13 @@ "description": "Successful operation." }, "default": { - "$ref": "./responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "./responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation." } }, @@ -139,7 +157,13 @@ "$ref": "./responses/beaconFilteringTermsResponse.json" }, "default": { - "$ref": "./responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "./responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation." } }, @@ -165,7 +189,13 @@ "$ref": "#/components/responses/infoOKResponse" }, "default": { - "$ref": "./responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "./responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation." } }, @@ -197,7 +227,13 @@ "description": "Successful operation." }, "default": { - "$ref": "./responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "./responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation." } }, diff --git a/framework/src/endpoints.yaml b/framework/src/endpoints.yaml index 9e26e10ec..04a79e84f 100644 --- a/framework/src/endpoints.yaml +++ b/framework/src/endpoints.yaml @@ -24,7 +24,10 @@ paths: $ref: '#/components/responses/infoOKResponse' default: description: An unsuccessful operation. - $ref: ./responses/beaconErrorResponse.yaml + content: + application/json: + schema: + $ref: ./responses/beaconErrorResponse.yaml /info: parameters: - $ref: '#/components/parameters/requestedSchema' @@ -38,7 +41,10 @@ paths: $ref: '#/components/responses/infoOKResponse' default: description: An unsuccessful operation. - $ref: ./responses/beaconErrorResponse.yaml + content: + application/json: + schema: + $ref: ./responses/beaconErrorResponse.yaml /service-info: get: description: Get information about the beacon using GA4GH ServiceInfo format @@ -68,7 +74,10 @@ paths: $ref: ./responses/beaconConfigurationResponse.yaml default: description: An unsuccessful operation. - $ref: ./responses/beaconErrorResponse.yaml + content: + application/json: + schema: + $ref: ./responses/beaconErrorResponse.yaml /map: get: description: TBD @@ -86,7 +95,10 @@ paths: $ref: ./responses/beaconMapResponse.yaml default: description: An unsuccessful operation. - $ref: ./responses/beaconErrorResponse.yaml + content: + application/json: + schema: + $ref: ./responses/beaconErrorResponse.yaml /entry_types: get: description: TBD @@ -104,7 +116,10 @@ paths: $ref: ./responses/beaconEntryTypesResponse.yaml default: description: An unsuccessful operation. - $ref: ./responses/beaconErrorResponse.yaml + content: + application/json: + schema: + $ref: ./responses/beaconErrorResponse.yaml /filtering_terms: parameters: - $ref: '#/components/parameters/skip' @@ -119,7 +134,10 @@ paths: $ref: ./responses/beaconFilteringTermsResponse.yaml default: description: An unsuccessful operation. - $ref: ./responses/beaconErrorResponse.yaml + content: + application/json: + schema: + $ref: ./responses/beaconErrorResponse.yaml components: responses: infoOKResponse: diff --git a/models/json/beacon-v2-default-model/analyses/endpoints.json b/models/json/beacon-v2-default-model/analyses/endpoints.json index 570d7201d..080ce7e23 100644 --- a/models/json/beacon-v2-default-model/analyses/endpoints.json +++ b/models/json/beacon-v2-default-model/analyses/endpoints.json @@ -147,7 +147,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -165,7 +171,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -196,7 +208,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -225,7 +243,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -256,7 +280,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, diff --git a/models/json/beacon-v2-default-model/biosamples/endpoints.json b/models/json/beacon-v2-default-model/biosamples/endpoints.json index 533d5ceda..c9132d47e 100644 --- a/models/json/beacon-v2-default-model/biosamples/endpoints.json +++ b/models/json/beacon-v2-default-model/biosamples/endpoints.json @@ -144,7 +144,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -162,7 +168,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -193,7 +205,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -222,7 +240,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -253,7 +277,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -282,7 +312,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -313,7 +349,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -349,7 +391,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -387,7 +435,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, diff --git a/models/json/beacon-v2-default-model/cohorts/endpoints.json b/models/json/beacon-v2-default-model/cohorts/endpoints.json index 1e36b7462..4de456859 100644 --- a/models/json/beacon-v2-default-model/cohorts/endpoints.json +++ b/models/json/beacon-v2-default-model/cohorts/endpoints.json @@ -154,7 +154,13 @@ "$ref": "#/components/responses/CollectionsResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -177,7 +183,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -208,7 +220,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -241,7 +259,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -279,7 +303,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -308,7 +338,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -339,7 +375,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, diff --git a/models/json/beacon-v2-default-model/datasets/endpoints.json b/models/json/beacon-v2-default-model/datasets/endpoints.json index 3fdc832a4..e3c43a842 100644 --- a/models/json/beacon-v2-default-model/datasets/endpoints.json +++ b/models/json/beacon-v2-default-model/datasets/endpoints.json @@ -152,7 +152,13 @@ "$ref": "#/components/responses/CollectionsResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -175,7 +181,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -206,7 +218,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -235,7 +253,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -266,7 +290,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -299,7 +329,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -337,7 +373,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -366,7 +408,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -397,7 +445,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -426,7 +480,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -457,7 +517,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, diff --git a/models/json/beacon-v2-default-model/endpoints.json b/models/json/beacon-v2-default-model/endpoints.json index 9c72ad0ef..67d855eb6 100644 --- a/models/json/beacon-v2-default-model/endpoints.json +++ b/models/json/beacon-v2-default-model/endpoints.json @@ -63,7 +63,13 @@ "$ref": "#/components/responses/infoOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -94,7 +100,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -121,7 +133,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -139,7 +157,13 @@ "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -165,7 +189,13 @@ "$ref": "#/components/responses/infoOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -197,7 +227,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, diff --git a/models/json/beacon-v2-default-model/genomicVariations/endpoints.json b/models/json/beacon-v2-default-model/genomicVariations/endpoints.json index e9101f04f..36149c092 100644 --- a/models/json/beacon-v2-default-model/genomicVariations/endpoints.json +++ b/models/json/beacon-v2-default-model/genomicVariations/endpoints.json @@ -275,7 +275,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -293,7 +299,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -324,7 +336,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -353,7 +371,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -384,7 +408,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -413,7 +443,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -444,7 +480,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, diff --git a/models/json/beacon-v2-default-model/individuals/endpoints.json b/models/json/beacon-v2-default-model/individuals/endpoints.json index 32898cb17..b80299c66 100644 --- a/models/json/beacon-v2-default-model/individuals/endpoints.json +++ b/models/json/beacon-v2-default-model/individuals/endpoints.json @@ -140,7 +140,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -173,7 +179,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -206,7 +218,13 @@ "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -224,7 +242,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -255,7 +279,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -284,7 +314,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -315,7 +351,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -344,7 +386,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -375,7 +423,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, diff --git a/models/json/beacon-v2-default-model/runs/endpoints.json b/models/json/beacon-v2-default-model/runs/endpoints.json index b5084bba7..9ce313972 100644 --- a/models/json/beacon-v2-default-model/runs/endpoints.json +++ b/models/json/beacon-v2-default-model/runs/endpoints.json @@ -156,7 +156,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -174,7 +180,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -205,7 +217,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -234,7 +252,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -265,7 +289,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -294,7 +324,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, @@ -325,7 +361,13 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "content": { + "application/json": { + "schema": { + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + } + } + }, "description": "An unsuccessful operation" } }, diff --git a/models/src/beacon-v2-default-model/analyses/endpoints.yaml b/models/src/beacon-v2-default-model/analyses/endpoints.yaml index 8f5d5457a..1910e1a95 100644 --- a/models/src/beacon-v2-default-model/analyses/endpoints.yaml +++ b/models/src/beacon-v2-default-model/analyses/endpoints.yaml @@ -47,7 +47,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /analyses/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -62,7 +65,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get details about one bioinformatics analysis, identified by its (unique) 'id' @@ -80,7 +86,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /analyses/{id}/g_variants: parameters: - $ref: '#/components/parameters/entryId' @@ -99,7 +108,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id' @@ -117,7 +129,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json components: responses: ResultsOKResponse: diff --git a/models/src/beacon-v2-default-model/biosamples/endpoints.yaml b/models/src/beacon-v2-default-model/biosamples/endpoints.yaml index 50b80d8bb..2c7799187 100644 --- a/models/src/beacon-v2-default-model/biosamples/endpoints.yaml +++ b/models/src/beacon-v2-default-model/biosamples/endpoints.yaml @@ -43,7 +43,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /biosamples/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -57,7 +60,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get details about one Biosample, identified by its (unique) 'id' operationId: postOneBiosample @@ -74,7 +80,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /biosamples/{id}/g_variants: parameters: - $ref: '#/components/parameters/entryId' @@ -93,7 +102,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the genomic variants list from one biosample, identified by its (unique) 'id' @@ -111,7 +123,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /biosamples/{id}/analyses: parameters: - $ref: '#/components/parameters/entryId' @@ -130,7 +145,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the analysis list from one biosample, identified by its (unique) 'id' @@ -148,7 +166,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /biosamples/{id}/runs: parameters: - $ref: '#/components/parameters/entryId' @@ -171,7 +192,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the runs list from one biosample, identified by its (unique) 'id' @@ -193,7 +217,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json components: responses: ResultsOKResponse: diff --git a/models/src/beacon-v2-default-model/cohorts/endpoints.yaml b/models/src/beacon-v2-default-model/cohorts/endpoints.yaml index 9fd0e999a..3c2b28ea2 100644 --- a/models/src/beacon-v2-default-model/cohorts/endpoints.yaml +++ b/models/src/beacon-v2-default-model/cohorts/endpoints.yaml @@ -47,7 +47,10 @@ paths: $ref: '#/components/responses/CollectionsResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /cohorts/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -63,7 +66,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get details about one cohort, identified by its (unique) 'id' operationId: postOneCohort @@ -80,7 +86,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /cohorts/{id}/individuals: parameters: - $ref: '#/components/parameters/entryId' @@ -99,7 +108,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the individuals from one cohort, identified by its (unique) 'id' @@ -117,7 +129,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /cohorts/{id}/filtering_terms: parameters: - $ref: '#/components/parameters/entryId' @@ -139,7 +154,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the list of filtering terms that could be used with a given cohort, identified by its (unique) 'id' @@ -161,7 +179,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json components: responses: ResultsOKResponse: diff --git a/models/src/beacon-v2-default-model/datasets/endpoints.yaml b/models/src/beacon-v2-default-model/datasets/endpoints.yaml index dc2c34d31..114b61f67 100644 --- a/models/src/beacon-v2-default-model/datasets/endpoints.yaml +++ b/models/src/beacon-v2-default-model/datasets/endpoints.yaml @@ -47,7 +47,10 @@ paths: $ref: '#/components/responses/CollectionsResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /datasets/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -63,7 +66,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get details about one dataset, identified by its (unique) 'id' operationId: postOneDataset @@ -80,7 +86,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /datasets/{id}/g_variants: parameters: - $ref: '#/components/parameters/entryId' @@ -99,7 +108,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the genomic variants list from one dataset, identified by its (unique) 'id' @@ -117,7 +129,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /datasets/{id}/biosamples: parameters: - $ref: '#/components/parameters/entryId' @@ -136,7 +151,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the biosamples list from one dataset, identified by its (unique) 'id' @@ -154,7 +172,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /datasets/{id}/individuals: parameters: - $ref: '#/components/parameters/entryId' @@ -173,7 +194,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the biosamples list from one dataset, identified by its (unique) 'id' @@ -191,7 +215,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /datasets/{id}/filtering_terms: parameters: - $ref: '#/components/parameters/entryId' @@ -213,7 +240,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the list of filtering terms that could be used with a given dataset, identified by its (unique) 'id' @@ -235,7 +265,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json components: responses: ResultsOKResponse: diff --git a/models/src/beacon-v2-default-model/endpoints.yaml b/models/src/beacon-v2-default-model/endpoints.yaml index a8b5716f0..03be74329 100644 --- a/models/src/beacon-v2-default-model/endpoints.yaml +++ b/models/src/beacon-v2-default-model/endpoints.yaml @@ -24,7 +24,10 @@ paths: $ref: '#/components/responses/infoOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /info: parameters: - $ref: '#/components/parameters/requestedSchema' @@ -38,7 +41,10 @@ paths: $ref: '#/components/responses/infoOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /service-info: get: description: Get information about the beacon using GA4GH ServiceInfo format @@ -68,7 +74,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconConfigurationResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /entry_types: get: description: TBD @@ -86,7 +95,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconEntryTypesResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /map: get: description: TBD @@ -104,7 +116,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconMapResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /filtering_terms: parameters: - $ref: '#/components/parameters/skip' @@ -119,7 +134,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json components: responses: infoOKResponse: diff --git a/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml b/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml index 44b59a736..856831026 100644 --- a/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml +++ b/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml @@ -54,7 +54,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /g_variants/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -69,7 +72,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get details about one genomic variation, identified by its (unique) 'id' @@ -87,7 +93,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /g_variants/{id}/biosamples: parameters: - $ref: '#/components/parameters/entryId' @@ -106,7 +115,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the biosamples list from one genomic variant, identified by its (unique) 'id' @@ -124,7 +136,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /g_variants/{id}/individuals: parameters: - $ref: '#/components/parameters/entryId' @@ -143,7 +158,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the biosamples list from one genomic variant, identified by its (unique) 'id' @@ -161,7 +179,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json components: responses: ResultsOKResponse: diff --git a/models/src/beacon-v2-default-model/individuals/endpoints.yaml b/models/src/beacon-v2-default-model/individuals/endpoints.yaml index 7ed5a46fe..fc9c7c451 100644 --- a/models/src/beacon-v2-default-model/individuals/endpoints.yaml +++ b/models/src/beacon-v2-default-model/individuals/endpoints.yaml @@ -43,7 +43,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /individuals/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -57,7 +60,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get details about one Individual, identified by its (unique) 'id' operationId: postOneIndividual @@ -74,7 +80,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /individuals/{id}/g_variants: parameters: - $ref: '#/components/parameters/entryId' @@ -93,7 +102,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the genomic variants list from one individual, identified by its (unique) 'id' @@ -111,7 +123,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /individuals/{id}/biosamples: parameters: - $ref: '#/components/parameters/entryId' @@ -130,7 +145,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the biosamples list from one individual, identified by its (unique) 'id' @@ -148,7 +166,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /individuals/filtering_terms: get: parameters: @@ -167,7 +188,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the list of filtering terms that could be used with individuals. operationId: postIndividualsFilteringTerms @@ -188,7 +212,10 @@ paths: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json components: responses: ResultsOKResponse: diff --git a/models/src/beacon-v2-default-model/runs/endpoints.yaml b/models/src/beacon-v2-default-model/runs/endpoints.yaml index 473bea53c..0d20e8964 100644 --- a/models/src/beacon-v2-default-model/runs/endpoints.yaml +++ b/models/src/beacon-v2-default-model/runs/endpoints.yaml @@ -43,7 +43,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /runs/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -58,7 +61,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get details about one Run, identified by its (unique) 'id' operationId: postOneRun @@ -75,7 +81,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /runs/{id}/g_variants: parameters: - $ref: '#/components/parameters/entryId' @@ -94,7 +103,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the genomic variants list from one run, identified by its (unique) 'id' @@ -112,7 +124,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json /runs/{id}/analyses: parameters: - $ref: '#/components/parameters/entryId' @@ -131,7 +146,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: description: Get the analysis list from one sequencing run, identified by its (unique) 'id' @@ -149,7 +167,10 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + content: + application/json: + schema: + $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json components: responses: ResultsOKResponse: From 7f0f518cfbd048a06e228d073e785915d5cc71d8 Mon Sep 17 00:00:00 2001 From: Gordon Krieger Date: Tue, 20 Aug 2024 12:33:09 -0400 Subject: [PATCH 14/29] add optional values field to response filtering terms --- .../sections/beaconFilteringTermsResults.json | 17 +++++++++++++++++ .../sections/beaconFilteringTermsResults.yaml | 13 +++++++++++++ 2 files changed, 30 insertions(+) diff --git a/framework/json/responses/sections/beaconFilteringTermsResults.json b/framework/json/responses/sections/beaconFilteringTermsResults.json index 1755fb582..f263928a2 100644 --- a/framework/json/responses/sections/beaconFilteringTermsResults.json +++ b/framework/json/responses/sections/beaconFilteringTermsResults.json @@ -39,6 +39,23 @@ "items": { "type": "string" } + }, + "values": { + "description": "Optional list of possible values for alphanumeric filters", + "examples": [ + [ + "benign", + "likely benign", + "pathogenic" + ], + [ + "pathogenic" + ] + ], + "items": { + "type": "string" + }, + "type": "array" } }, "required": [ diff --git a/framework/src/responses/sections/beaconFilteringTermsResults.yaml b/framework/src/responses/sections/beaconFilteringTermsResults.yaml index 05748d8cc..63d21c76d 100644 --- a/framework/src/responses/sections/beaconFilteringTermsResults.yaml +++ b/framework/src/responses/sections/beaconFilteringTermsResults.yaml @@ -61,6 +61,19 @@ definitions: type: array items: type: string + values: + description: >- + Optional list of possible values for alphanumeric filters + examples: + - + - benign + - likely benign + - pathogenic + - + - pathogenic + type: array + items: + type: string Resource: type: object description: >- From 27d8a4ddb8a9c57efa33c8e1283de73c32d26c83 Mon Sep 17 00:00:00 2001 From: Dmitry Repchevsky Date: Fri, 13 Sep 2024 15:56:13 +0200 Subject: [PATCH 15/29] fix invalid aCollectionOf property definition #114 --- framework/json/configuration/entryTypeDefinition.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json index 434bebcf6..af25f70b1 100644 --- a/framework/json/configuration/entryTypeDefinition.json +++ b/framework/json/configuration/entryTypeDefinition.json @@ -9,9 +9,9 @@ }, "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).", - "includedConcepts": { - "$ref": "../common/basicElement.json", - "type": "array" + "type": "array", + "items": { + "$ref": "../common/basicElement.json" } }, "additionallySupportedSchemas": { @@ -65,4 +65,4 @@ ], "title": "", "type": "object" -} \ No newline at end of file +} From a729ef4f79a2fe6a8b9bccaba10d75ad43fa4deb Mon Sep 17 00:00:00 2001 From: Dmitry Repchevsky Date: Fri, 13 Sep 2024 15:58:34 +0200 Subject: [PATCH 16/29] update yaml --- framework/src/configuration/entryTypeDefinition.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/framework/src/configuration/entryTypeDefinition.yaml b/framework/src/configuration/entryTypeDefinition.yaml index 99f3ef974..f9d47608b 100644 --- a/framework/src/configuration/entryTypeDefinition.yaml +++ b/framework/src/configuration/entryTypeDefinition.yaml @@ -50,8 +50,8 @@ properties: 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). - includedConcepts: - type: array + type: array + items: $ref: ../common/basicElement.yaml filteringTerms: description: Reference to the file with the list of filtering terms that could From 444d7d25f1778e5a4adc7baa1e469a55c01cb70e Mon Sep 17 00:00:00 2001 From: Jordi Rambla Date: Tue, 8 Oct 2024 06:27:26 +0200 Subject: [PATCH 17/29] Removing unused filteringTerms.yaml & json files --- .../analyses/filteringTerms.json | 4 ---- .../biosamples/filteringTerms.json | 4 ---- .../cohorts/filteringTerms.json | 11 ----------- .../datasets/filteringTerms.json | 11 ----------- .../genomicVariations/filteringTerms.json | 13 ------------- .../individuals/filteringTerms.json | 4 ---- .../runs/filteringTerms.json | 4 ---- .../analyses/filteringTerms.yaml | 2 -- .../biosamples/filteringTerms.yaml | 2 -- .../cohorts/filteringTerms.yaml | 6 ------ .../datasets/filteringTerms.yaml | 6 ------ .../genomicVariations/filteringTerms.yaml | 6 ------ .../individuals/filteringTerms.yaml | 2 -- .../runs/filteringTerms.yaml | 2 -- 14 files changed, 77 deletions(-) delete mode 100644 models/json/beacon-v2-default-model/analyses/filteringTerms.json delete mode 100644 models/json/beacon-v2-default-model/biosamples/filteringTerms.json delete mode 100644 models/json/beacon-v2-default-model/cohorts/filteringTerms.json delete mode 100644 models/json/beacon-v2-default-model/datasets/filteringTerms.json delete mode 100644 models/json/beacon-v2-default-model/genomicVariations/filteringTerms.json delete mode 100644 models/json/beacon-v2-default-model/individuals/filteringTerms.json delete mode 100644 models/json/beacon-v2-default-model/runs/filteringTerms.json delete mode 100644 models/src/beacon-v2-default-model/analyses/filteringTerms.yaml delete mode 100644 models/src/beacon-v2-default-model/biosamples/filteringTerms.yaml delete mode 100644 models/src/beacon-v2-default-model/cohorts/filteringTerms.yaml delete mode 100644 models/src/beacon-v2-default-model/datasets/filteringTerms.yaml delete mode 100644 models/src/beacon-v2-default-model/genomicVariations/filteringTerms.yaml delete mode 100644 models/src/beacon-v2-default-model/individuals/filteringTerms.yaml delete mode 100644 models/src/beacon-v2-default-model/runs/filteringTerms.yaml diff --git a/models/json/beacon-v2-default-model/analyses/filteringTerms.json b/models/json/beacon-v2-default-model/analyses/filteringTerms.json deleted file mode 100644 index 9cd753def..000000000 --- a/models/json/beacon-v2-default-model/analyses/filteringTerms.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "filteringTerms": [] -} \ No newline at end of file diff --git a/models/json/beacon-v2-default-model/biosamples/filteringTerms.json b/models/json/beacon-v2-default-model/biosamples/filteringTerms.json deleted file mode 100644 index 9cd753def..000000000 --- a/models/json/beacon-v2-default-model/biosamples/filteringTerms.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "filteringTerms": [] -} \ No newline at end of file diff --git a/models/json/beacon-v2-default-model/cohorts/filteringTerms.json b/models/json/beacon-v2-default-model/cohorts/filteringTerms.json deleted file mode 100644 index d53359eb0..000000000 --- a/models/json/beacon-v2-default-model/cohorts/filteringTerms.json +++ /dev/null @@ -1,11 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "filteringTerms": [ - { - "ftType": "ontologyTerm", - "id": "DUO:0000006", - "label": "health or medical or biomedical research", - "version": "2021-02-23" - } - ] -} \ No newline at end of file diff --git a/models/json/beacon-v2-default-model/datasets/filteringTerms.json b/models/json/beacon-v2-default-model/datasets/filteringTerms.json deleted file mode 100644 index d53359eb0..000000000 --- a/models/json/beacon-v2-default-model/datasets/filteringTerms.json +++ /dev/null @@ -1,11 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "filteringTerms": [ - { - "ftType": "ontologyTerm", - "id": "DUO:0000006", - "label": "health or medical or biomedical research", - "version": "2021-02-23" - } - ] -} \ No newline at end of file diff --git a/models/json/beacon-v2-default-model/genomicVariations/filteringTerms.json b/models/json/beacon-v2-default-model/genomicVariations/filteringTerms.json deleted file mode 100644 index 3241f2272..000000000 --- a/models/json/beacon-v2-default-model/genomicVariations/filteringTerms.json +++ /dev/null @@ -1,13 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "filteringTerms": [ - { - "ftType": "alphanumeric", - "id": "gene" - }, - { - "ftType": "alphanumeric", - "id": "aminoacidChanges" - } - ] -} \ No newline at end of file diff --git a/models/json/beacon-v2-default-model/individuals/filteringTerms.json b/models/json/beacon-v2-default-model/individuals/filteringTerms.json deleted file mode 100644 index 9cd753def..000000000 --- a/models/json/beacon-v2-default-model/individuals/filteringTerms.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "filteringTerms": [] -} \ No newline at end of file diff --git a/models/json/beacon-v2-default-model/runs/filteringTerms.json b/models/json/beacon-v2-default-model/runs/filteringTerms.json deleted file mode 100644 index 9cd753def..000000000 --- a/models/json/beacon-v2-default-model/runs/filteringTerms.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "filteringTerms": [] -} \ No newline at end of file diff --git a/models/src/beacon-v2-default-model/analyses/filteringTerms.yaml b/models/src/beacon-v2-default-model/analyses/filteringTerms.yaml deleted file mode 100644 index 0701175cf..000000000 --- a/models/src/beacon-v2-default-model/analyses/filteringTerms.yaml +++ /dev/null @@ -1,2 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -filteringTerms: [] diff --git a/models/src/beacon-v2-default-model/biosamples/filteringTerms.yaml b/models/src/beacon-v2-default-model/biosamples/filteringTerms.yaml deleted file mode 100644 index 0701175cf..000000000 --- a/models/src/beacon-v2-default-model/biosamples/filteringTerms.yaml +++ /dev/null @@ -1,2 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -filteringTerms: [] diff --git a/models/src/beacon-v2-default-model/cohorts/filteringTerms.yaml b/models/src/beacon-v2-default-model/cohorts/filteringTerms.yaml deleted file mode 100644 index 92b6ef659..000000000 --- a/models/src/beacon-v2-default-model/cohorts/filteringTerms.yaml +++ /dev/null @@ -1,6 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -filteringTerms: - - ftType: ontologyTerm - id: DUO:0000006 - label: health or medical or biomedical research - version: '2021-02-23' diff --git a/models/src/beacon-v2-default-model/datasets/filteringTerms.yaml b/models/src/beacon-v2-default-model/datasets/filteringTerms.yaml deleted file mode 100644 index 92b6ef659..000000000 --- a/models/src/beacon-v2-default-model/datasets/filteringTerms.yaml +++ /dev/null @@ -1,6 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -filteringTerms: - - ftType: ontologyTerm - id: DUO:0000006 - label: health or medical or biomedical research - version: '2021-02-23' diff --git a/models/src/beacon-v2-default-model/genomicVariations/filteringTerms.yaml b/models/src/beacon-v2-default-model/genomicVariations/filteringTerms.yaml deleted file mode 100644 index ca25a1cd9..000000000 --- a/models/src/beacon-v2-default-model/genomicVariations/filteringTerms.yaml +++ /dev/null @@ -1,6 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -filteringTerms: - - ftType: alphanumeric - id: gene - - ftType: alphanumeric - id: aminoacidChanges diff --git a/models/src/beacon-v2-default-model/individuals/filteringTerms.yaml b/models/src/beacon-v2-default-model/individuals/filteringTerms.yaml deleted file mode 100644 index 0701175cf..000000000 --- a/models/src/beacon-v2-default-model/individuals/filteringTerms.yaml +++ /dev/null @@ -1,2 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -filteringTerms: [] diff --git a/models/src/beacon-v2-default-model/runs/filteringTerms.yaml b/models/src/beacon-v2-default-model/runs/filteringTerms.yaml deleted file mode 100644 index 0701175cf..000000000 --- a/models/src/beacon-v2-default-model/runs/filteringTerms.yaml +++ /dev/null @@ -1,2 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -filteringTerms: [] From a17c7b049db3abe76723da01abab2714691cba77 Mon Sep 17 00:00:00 2001 From: Jordi Rambla Date: Fri, 11 Oct 2024 16:50:31 +0200 Subject: [PATCH 18/29] Removing references to filteringTerms URL both in EntryTypeDefinitions and in Map --- framework/json/configuration/beaconMapSchema.json | 7 +------ framework/json/configuration/entryTypeDefinition.json | 5 ----- framework/src/configuration/beaconMapSchema.yaml | 9 --------- framework/src/configuration/entryTypeDefinition.yaml | 8 -------- 4 files changed, 1 insertion(+), 28 deletions(-) diff --git a/framework/json/configuration/beaconMapSchema.json b/framework/json/configuration/beaconMapSchema.json index 47fec6701..f583bbccc 100644 --- a/framework/json/configuration/beaconMapSchema.json +++ b/framework/json/configuration/beaconMapSchema.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "definitions": { + "$defs": { "Endpoint": { "properties": { "endpoints": { @@ -16,11 +16,6 @@ "description": "", "type": "string" }, - "filteringTermsUrl": { - "description": "Optional. Returns the list of filtering terms that could be applied to this entry type. It is added here for convenience of the Beacon clients, so they don't need to parse the OpenAPI endpoints definition to get that endpoint. Also, in very simple Beacons, that endpoint could be the one of the few implemented, together with \u00b4rootUrl` and \u00b4singleEntryUrl`, in which case the whole map of endpoints is found in the current Map.", - "format": "uri-template", - "type": "string" - }, "openAPIEndpointsDefinition": { "description": "Reference to the file that includes the OpenAPI definition of the endpoints implemented in this Beacon instance. The referenced file MUST BE a valid OpenAPI definition file, as it is expected that the Beacon clients (e.g. a Beacon Network) should be able to parse it to discover additional details on the supported verbs, parameters, etc.", "type": "string" diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json index 27d425770..98d1b714b 100644 --- a/framework/json/configuration/entryTypeDefinition.json +++ b/framework/json/configuration/entryTypeDefinition.json @@ -28,11 +28,6 @@ "description": "A textual description for the element.", "type": "string" }, - "filteringTerms": { - "$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 index 83170dab6..24ea2d366 100644 --- a/framework/src/configuration/beaconMapSchema.yaml +++ b/framework/src/configuration/beaconMapSchema.yaml @@ -47,15 +47,6 @@ definitions: 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 index 61916df7e..1e1e04f5f 100644 --- a/framework/src/configuration/entryTypeDefinition.yaml +++ b/framework/src/configuration/entryTypeDefinition.yaml @@ -57,14 +57,6 @@ properties: includedConcepts: type: array $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: $ref: ../common/beaconCommonComponents.yaml#/definitions/NonFilteredQueriesAllowed required: From 414aae5a085d70b34b06883a842c03a318c6b487 Mon Sep 17 00:00:00 2001 From: Jordi Rambla Date: Fri, 11 Oct 2024 17:22:00 +0200 Subject: [PATCH 19/29] Updating "definitions" to "$defs" to comply with Json Schema 2020-12 #173 --- bin/_jsonref2json.py | 4 +- bin/adhoc/beaconCommonComponents.json | 18 +++--- bin/adhoc/ontologyTerm.json | 2 +- bin/beacon_yaml2md.pl | 4 +- .../biosamples/defaultSchema.json | 4 +- bin/deref_schemas/cohorts/defaultSchema.json | 8 +-- bin/deref_schemas/datasets/defaultSchema.json | 2 +- .../genomicVariations/defaultSchema.json | 2 +- .../individuals/defaultSchema.json | 6 +- bin/transform_json2md.sh | 2 +- .../json/common/beaconCommonComponents.json | 18 +++--- framework/json/common/ontologyTerm.json | 2 +- .../beaconConfigurationSchema.json | 8 +-- .../json/configuration/beaconMapSchema.json | 8 +-- .../configuration/entryTypeDefinition.json | 4 +- .../json/configuration/entryTypesSchema.json | 4 +- .../configuration/filteringTermsSchema.json | 4 +- framework/json/endpoints.json | 4 +- .../json/requests/beaconRequestBody.json | 14 ++--- .../json/requests/beaconRequestMeta.json | 6 +- framework/json/requests/filteringTerms.json | 10 ++-- .../json/responses/beaconBooleanResponse.json | 4 +- .../responses/beaconCollectionsResponse.json | 4 +- .../json/responses/beaconCountResponse.json | 4 +- .../responses/beaconEntryTypesResponse.json | 2 +- .../json/responses/beaconErrorResponse.json | 2 +- .../responses/beaconResultsetsResponse.json | 4 +- .../ga4gh-service-info-1-0-0-schema.json | 4 +- .../beaconBooleanResponseSection.json | 2 +- .../sections/beaconCountResponseSection.json | 4 +- .../sections/beaconFilteringTermsResults.json | 6 +- .../responses/sections/beaconInfoResults.json | 14 ++--- .../beaconInformationalResponseMeta.json | 6 +- .../beaconReceivedRequestSummary.json | 14 ++--- .../sections/beaconResponseMeta.json | 10 ++-- .../responses/sections/beaconResultsets.json | 8 +-- .../beaconSummaryResponseSection.json | 4 +- .../analyses/defaultSchema.json | 2 +- .../analyses/endpoints.json | 6 +- .../biosamples/defaultSchema.json | 2 +- .../biosamples/endpoints.json | 46 +++++++-------- .../cohorts/defaultSchema.json | 30 +++++----- .../cohorts/endpoints.json | 44 +++++++-------- .../common/commonDefinitions.json | 2 +- .../common/complexValue.json | 4 +- .../common/dataUseConditions.json | 4 +- .../common/disease.json | 2 +- .../common/exposure.json | 2 +- .../common/pedigree.json | 4 +- .../common/phenotypicFeature.json | 4 +- .../common/quantity.json | 2 +- .../common/referenceRange.json | 2 +- .../common/timeElement.json | 2 +- .../common/timeInterval.json | 4 +- .../datasets/defaultSchema.json | 6 +- .../datasets/endpoints.json | 56 +++++++++---------- .../beacon-v2-default-model/endpoints.json | 28 +++++----- .../genomicVariations/defaultSchema.json | 34 +++++------ .../genomicVariations/endpoints.json | 37 ++++++------ .../genomicVariations/requestParameters.json | 10 ++-- .../requestParametersComponents.json | 4 +- .../individuals/defaultSchema.json | 10 ++-- .../individuals/endpoints.json | 46 +++++++-------- .../runs/defaultSchema.json | 2 +- .../runs/endpoints.json | 36 ++++++------ 65 files changed, 328 insertions(+), 329 deletions(-) diff --git a/bin/_jsonref2json.py b/bin/_jsonref2json.py index a2b9df228..8b569a9ec 100755 --- 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 index 371d5b058..4f1890224 100644 --- 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": "#/$defs/HandoverType" }, "note": { "description": "An optional text including considerations on the handover link provided.", @@ -148,7 +148,7 @@ "ListOfHandovers": { "description": "Set of handovers to be added in one section the response.", "items": { - "$ref": "#/definitions/Handover", + "$ref": "#/$defs/Handover", "description": "Requested schema to be used for individuals in the response." }, "type": "array" @@ -156,7 +156,7 @@ "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 index 1b94438f2..15746e939 100644 --- 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/beacon_yaml2md.pl b/bin/beacon_yaml2md.pl index 96e59c17f..b4b825d32 100755 --- a/bin/beacon_yaml2md.pl +++ b/bin/beacon_yaml2md.pl @@ -729,9 +729,9 @@ sub add_properties_vrs { my ( $property, $data ) = @_; my %url = ( 'SequenceExpression' => -'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/', +'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/$defs/', 'CopyNumber' => -'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/' +'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/$defs/' ); if ( exists $url{$property} ) { $data->{properties} = diff --git a/bin/deref_schemas/biosamples/defaultSchema.json b/bin/deref_schemas/biosamples/defaultSchema.json index 1b5ffc61b..a00ae0a8c 100644 --- a/bin/deref_schemas/biosamples/defaultSchema.json +++ b/bin/deref_schemas/biosamples/defaultSchema.json @@ -357,7 +357,7 @@ }, { "$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": {}, + "$defs": {}, "description": "Used to describe a phenotype that characterizes the subject or biosample.", "properties": { "evidence": { diff --git a/bin/deref_schemas/cohorts/defaultSchema.json b/bin/deref_schemas/cohorts/defaultSchema.json index f9721426c..96aa2913c 100644 --- a/bin/deref_schemas/cohorts/defaultSchema.json +++ b/bin/deref_schemas/cohorts/defaultSchema.json @@ -2,7 +2,7 @@ "$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 index 75c3ff69c..91b8ed620 100644 --- 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 index 8bb046adb..e6aad1848 100644 --- 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": { + "$defs": { "CaseLevelVariant": { "description": "", "properties": { diff --git a/bin/deref_schemas/individuals/defaultSchema.json b/bin/deref_schemas/individuals/defaultSchema.json index cbe33523a..da94f0d4a 100644 --- a/bin/deref_schemas/individuals/defaultSchema.json +++ b/bin/deref_schemas/individuals/defaultSchema.json @@ -1035,7 +1035,7 @@ }, { "$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 index ce73254fc..f4c782785 100755 --- 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#" $fwk_dir/common/ontologyTerm.json cat< `end[1]`\n - single or double sided precise matches can be achieved by setting\n `start[1]=start[0]+1` and `end[1]=end[0]+1`", diff --git a/models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json b/models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json index 60ff1da6e..4fab6770c 100644 --- a/models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json +++ b/models/json/beacon-v2-default-model/genomicVariations/requestParametersComponents.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "definitions": { + "$defs": { "AlternateBases": { "description": "Alternate bases for this variant (starting from `start`). * Accepted values: `[ACGTN]*` * The current specification supports allelic variants, **not** genotype queries\n (i.e. multiple co-occurring alleles).\n* N is a wildcard, that denotes the position of any base,\n and can be used as a standalone base of any type or within a partially known\n sequence. As example, a query of `ANNT` the Ns can take take any form of [ACGT]\n and will match `ANNT`, `ACNT`, `ACCT`, `ACGT` ... and so forth.\n* an *empty value* is used in the case of deletions with the maximally trimmed,\n deleted sequence being indicated in `ReferenceBases`\n* Categorical variant queries, e.g. such *not* being represented through\n sequence & position, make use of the `variantType` parameter.", "pattern": "^([ACGTUNRYSWKMBDHV\\-\\.]*)$", @@ -30,5 +30,5 @@ "type": "string" } }, - "description": "Component definitions used in `requestParameters`." + "description": "Component $defs used in `requestParameters`." } \ No newline at end of file diff --git a/models/json/beacon-v2-default-model/individuals/defaultSchema.json b/models/json/beacon-v2-default-model/individuals/defaultSchema.json index 69f989a65..e5b6876a6 100644 --- a/models/json/beacon-v2-default-model/individuals/defaultSchema.json +++ b/models/json/beacon-v2-default-model/individuals/defaultSchema.json @@ -12,7 +12,7 @@ "type": "array" }, "ethnicity": { - "$ref": "../common/commonDefinitions.json#/definitions/Ethnicity", + "$ref": "../common/commonDefinitions.json#/$defs/Ethnicity", "description": "Ethnic background of the individual. Value from NCIT Race (NCIT:C17049) ontology term descendants, e.g. NCIT:C126531 (Latin American). A geographic ancestral origin category that is assigned to a population group based mainly on physical characteristics that are thought to be distinct and inherent. [ NCI ] " }, "exposures": { @@ -22,7 +22,7 @@ "type": "array" }, "geographicOrigin": { - "$ref": "../common/commonDefinitions.json#/definitions/GeographicLocation", + "$ref": "../common/commonDefinitions.json#/$defs/GeographicLocation", "description": "Individual's country or region of origin (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448), e.g. GAZ:00002459 (United States of America)." }, "id": { @@ -31,7 +31,7 @@ "type": "string" }, "info": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info" + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info" }, "interventionsOrProcedures": { "items": { @@ -40,7 +40,7 @@ "type": "array" }, "karyotypicSex": { - "$ref": "../common/commonDefinitions.json#/definitions/KaryotypicSex", + "$ref": "../common/commonDefinitions.json#/$defs/KaryotypicSex", "description": "The chromosomal sex of an individual represented from a selection of options." }, "measures": { @@ -62,7 +62,7 @@ "type": "array" }, "sex": { - "$ref": "../common/commonDefinitions.json#/definitions/Sex", + "$ref": "../common/commonDefinitions.json#/$defs/Sex", "description": "Sex of the individual. Value from NCIT General Qualifier (NCIT:C27993): 'unknown' (not assessed or not available) (NCIT:C17998), 'female' (NCIT:C16576), or 'male', (NCIT:C20197)." }, "treatments": { diff --git a/models/json/beacon-v2-default-model/individuals/endpoints.json b/models/json/beacon-v2-default-model/individuals/endpoints.json index 32898cb17..affa76262 100644 --- a/models/json/beacon-v2-default-model/individuals/endpoints.json +++ b/models/json/beacon-v2-default-model/individuals/endpoints.json @@ -25,13 +25,13 @@ } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + "$ref": "../../../../framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" }, "limit": { "in": "query", "name": "limit", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit" + "$ref": "../../../../framework/json/common/beaconCommonComponents.json#/$defs/Limit" } }, "requestedSchema": { @@ -48,7 +48,7 @@ "in": "query", "name": "skip", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip" + "$ref": "../../../../framework/json/common/beaconCommonComponents.json#/$defs/Skip" } } }, @@ -59,13 +59,13 @@ "schema": { "oneOf": [ { - "$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" + "$ref": "../../../../framework/json/responses/beaconResultsetsResponse.json" } ] } @@ -115,7 +115,7 @@ "$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": [ @@ -129,7 +129,7 @@ "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" } } }, @@ -140,7 +140,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "$ref": "../../../../framework/json/responses/beaconErrorResponse.json", "description": "An unsuccessful operation" } }, @@ -166,14 +166,14 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" + "$ref": "../../../../framework/json/responses/beaconFilteringTermsResponse.json" } } }, "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "$ref": "../../../../framework/json/responses/beaconErrorResponse.json", "description": "An unsuccessful operation" } }, @@ -188,7 +188,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "../../../../framework/json/requests/beaconRequestBody.json" } } }, @@ -199,14 +199,14 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" + "$ref": "../../../../framework/json/responses/beaconFilteringTermsResponse.json" } } }, "description": "Successful operation" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "$ref": "../../../../framework/json/responses/beaconErrorResponse.json", "description": "An unsuccessful operation" } }, @@ -224,7 +224,7 @@ "$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", "description": "An unsuccessful operation" } }, @@ -244,7 +244,7 @@ "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" } } }, @@ -255,7 +255,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "$ref": "../../../../framework/json/responses/beaconErrorResponse.json", "description": "An unsuccessful operation" } }, @@ -284,7 +284,7 @@ "$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", "description": "An unsuccessful operation" } }, @@ -304,7 +304,7 @@ "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" } } }, @@ -315,7 +315,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "$ref": "../../../../framework/json/responses/beaconErrorResponse.json", "description": "An unsuccessful operation" } }, @@ -344,7 +344,7 @@ "$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", "description": "An unsuccessful operation" } }, @@ -364,7 +364,7 @@ "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" } } }, @@ -375,7 +375,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "$ref": "../../../../framework/json/responses/beaconErrorResponse.json", "description": "An unsuccessful operation" } }, diff --git a/models/json/beacon-v2-default-model/runs/defaultSchema.json b/models/json/beacon-v2-default-model/runs/defaultSchema.json index 6e49d8dfb..61d090df2 100644 --- a/models/json/beacon-v2-default-model/runs/defaultSchema.json +++ b/models/json/beacon-v2-default-model/runs/defaultSchema.json @@ -26,7 +26,7 @@ "type": "string" }, "info": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info" + "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info" }, "libraryLayout": { "description": "Ontology value for the library layout e.g \"PAIRED\", \"SINGLE\" #todo add Ontology name?", diff --git a/models/json/beacon-v2-default-model/runs/endpoints.json b/models/json/beacon-v2-default-model/runs/endpoints.json index b5084bba7..39f4f728c 100644 --- a/models/json/beacon-v2-default-model/runs/endpoints.json +++ b/models/json/beacon-v2-default-model/runs/endpoints.json @@ -33,7 +33,7 @@ } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/IncludeResultsetResponses" + "$ref": "../../../../framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" }, "individualId": { "in": "path", @@ -47,7 +47,7 @@ "in": "query", "name": "limit", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Limit" + "$ref": "../../../../framework/json/common/beaconCommonComponents.json#/$defs/Limit" } }, "requestedSchema": { @@ -64,7 +64,7 @@ "in": "query", "name": "skip", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Skip" + "$ref": "../../../../framework/json/common/beaconCommonComponents.json#/$defs/Skip" } } }, @@ -75,13 +75,13 @@ "schema": { "oneOf": [ { - "$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" } } }, @@ -156,7 +156,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "$ref": "../../../../framework/json/responses/beaconErrorResponse.json", "description": "An unsuccessful operation" } }, @@ -174,7 +174,7 @@ "$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", "description": "An unsuccessful operation" } }, @@ -194,7 +194,7 @@ "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" } } }, @@ -205,7 +205,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "$ref": "../../../../framework/json/responses/beaconErrorResponse.json", "description": "An unsuccessful operation" } }, @@ -234,7 +234,7 @@ "$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", "description": "An unsuccessful operation" } }, @@ -254,7 +254,7 @@ "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" } } }, @@ -265,7 +265,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "$ref": "../../../../framework/json/responses/beaconErrorResponse.json", "description": "An unsuccessful operation" } }, @@ -294,7 +294,7 @@ "$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", "description": "An unsuccessful operation" } }, @@ -314,7 +314,7 @@ "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" } } }, @@ -325,7 +325,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json", + "$ref": "../../../../framework/json/responses/beaconErrorResponse.json", "description": "An unsuccessful operation" } }, From 98b899c3400d475c020a1adad24d7be122f1afe4 Mon Sep 17 00:00:00 2001 From: Michael Baudis Date: Mon, 11 Nov 2024 12:49:21 +0900 Subject: [PATCH 20/29] re-writing of some inline schema descriptions This commit re-writes some of the root descriptions of the response type schemas (mostly) into slightly more verbose and formatted texts. Besides the "documentation is good" paradigm one reason is the intended use of these for generating documentation pages - see the (under construction) rendering at https://bycon.progenetix.org/generated/beacon-responses/ --- .../beaconConfigurationSchema.yaml | 17 +++++++++++------ .../configuration/entryTypeDefinition.yaml | 19 +++++++++++-------- .../src/responses/beaconBooleanResponse.yaml | 7 +++++-- .../responses/beaconCollectionsResponse.yaml | 6 +++++- .../beaconConfigurationResponse.yaml | 6 ++++-- .../src/responses/beaconCountResponse.yaml | 8 ++++++-- .../responses/beaconEntryTypesResponse.yaml | 4 +++- .../src/responses/beaconErrorResponse.yaml | 3 ++- .../src/responses/beaconInfoResponse.yaml | 10 ++++++++-- .../src/responses/beaconMapResponse.yaml | 6 ++++-- .../responses/beaconResultsetsResponse.yaml | 12 +++++++++++- 11 files changed, 70 insertions(+), 28 deletions(-) diff --git a/framework/src/configuration/beaconConfigurationSchema.yaml b/framework/src/configuration/beaconConfigurationSchema.yaml index bcd6a64e4..6eaef9f28 100644 --- a/framework/src/configuration/beaconConfigurationSchema.yaml +++ b/framework/src/configuration/beaconConfigurationSchema.yaml @@ -1,7 +1,9 @@ $schema: https://json-schema.org/draft/2020-12/schema title: Beacon Configuration -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. type: object properties: $schema: @@ -11,16 +13,19 @@ properties: type: object 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, + inconsistent availability; data should not be used in production setups + * `TEST`: Service is stable but data should be considered synthetic + * `PROD`: Service stable with real world data type: string enum: - DEV - TEST - PROD securityAttributes: - description: Configuration of the security aspects of the Beacon. By default, + 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 diff --git a/framework/src/configuration/entryTypeDefinition.yaml b/framework/src/configuration/entryTypeDefinition.yaml index 8f6fe509f..ae7af9215 100644 --- a/framework/src/configuration/entryTypeDefinition.yaml +++ b/framework/src/configuration/entryTypeDefinition.yaml @@ -1,14 +1,17 @@ $schema: https://json-schema.org/draft/2020-12/schema title: '' -description: "Definition of an element or entry type including the Beacon v2 required\ - \ and suggested attributes. This schema purpose is to describe each type of entities\ - \ included in a Beacon, hence Beacon clients could have some metadata about such\ - \ entities.\n\nThe `id` attribute is the key that should be used in other parts\ - \ of the Beacon Model to allow Beacon clients to identify the different parts (e.g.\ - \ endpoints, filteringTerms, request parameters, etc.) that fully describe an entry\ - \ type." +description: >- + Definition of an element or entry type including the Beacon v2 required + and suggested attributes. This schema purpose is to describe each type of entities + included in a Beacon, hence Beacon clients could have some metadata about such + entities. + + The `id` attribute is the key that should be used in other parts of the Beacon + Model to allow Beacon clients to identify the different parts (e.g. endpoints, + filteringTerms, request parameters, etc.) that fully describe an entry type. type: object -$comment: 'TO DO: The tagged parts should reference to `common/ontologizedElement.json`. +$comment: >- + TODO: The tagged parts should reference to `common/ontologizedElement.json`. But that configuration fails to validate. Further investigation is required, but should not affect the resulting schema.' properties: diff --git a/framework/src/responses/beaconBooleanResponse.yaml b/framework/src/responses/beaconBooleanResponse.yaml index 97811e09c..0cf7ac716 100644 --- a/framework/src/responses/beaconBooleanResponse.yaml +++ b/framework/src/responses/beaconBooleanResponse.yaml @@ -1,7 +1,10 @@ $schema: https://json-schema.org/draft/2020-12/schema description: >- - Complete definition for a minimal response that provides *only* a `Boolean` - exists true|false answer. + Complete definition for a minimal response that provides *only* an aggregate + Boolean `"exists": true` or `"exists": false` answer to the query. + + Additional information - which should not consist of record-level information - + can be provided through `beaconHandovers`. type: object properties: meta: diff --git a/framework/src/responses/beaconCollectionsResponse.yaml b/framework/src/responses/beaconCollectionsResponse.yaml index 8b895ce6f..948fd2931 100644 --- a/framework/src/responses/beaconCollectionsResponse.yaml +++ b/framework/src/responses/beaconCollectionsResponse.yaml @@ -1,5 +1,9 @@ $schema: https://json-schema.org/draft/2020-12/schema -description: Beacon response that includes details about the collections in this Beacon. +description: >- + A type of Beacon response that includes details about the **collections** in a + beacon. The types of collections are defined in each beacon's configuration; + if using the Beacon v2+ default model usually the types `dataset` and `cohort` + are supported. type: object properties: meta: diff --git a/framework/src/responses/beaconConfigurationResponse.yaml b/framework/src/responses/beaconConfigurationResponse.yaml index 28d38626d..f4ee49954 100644 --- a/framework/src/responses/beaconConfigurationResponse.yaml +++ b/framework/src/responses/beaconConfigurationResponse.yaml @@ -1,8 +1,10 @@ $schema: https://json-schema.org/draft/2020-12/schema type: object description: >- - Information about the Beacon. Aimed to Beacon clients like web pages - or Beacon networks. + The `beaconConfigurationResponse` returns information about configuration + parameters of a given beacon instance such as maturity or security attributes + or supported entry types. It is directed towards Beacon clients like web pages + or network aggregators. properties: meta: description: >- diff --git a/framework/src/responses/beaconCountResponse.yaml b/framework/src/responses/beaconCountResponse.yaml index f083849bd..f4c854fc6 100644 --- a/framework/src/responses/beaconCountResponse.yaml +++ b/framework/src/responses/beaconCountResponse.yaml @@ -1,7 +1,11 @@ $schema: https://json-schema.org/draft/2020-12/schema description: >- - Complete definition for a response that does not include record level - details but provides `Boolean` and `count` information. + Complete definition for a minimal response that provides an aggregate Boolean + `"exists": true` or `"exists": false` answer to the query as well as the count + of the matched records. + + Additional information - which should not consist of record-level information - + can be provided through `beaconHandovers`. type: object properties: meta: diff --git a/framework/src/responses/beaconEntryTypesResponse.yaml b/framework/src/responses/beaconEntryTypesResponse.yaml index 16e5aef37..2919bf009 100644 --- a/framework/src/responses/beaconEntryTypesResponse.yaml +++ b/framework/src/responses/beaconEntryTypesResponse.yaml @@ -1,7 +1,9 @@ $schema: https://json-schema.org/draft/2020-12/schema type: object description: >- - Response including a list of Entry types definitions. + The `beaconEntryTypesResponse` provides information about the entry types + served through a beacon, including their definitions and pointers to their + schemas. properties: meta: description: >- diff --git a/framework/src/responses/beaconErrorResponse.yaml b/framework/src/responses/beaconErrorResponse.yaml index e902a32fa..eb1669d3a 100644 --- a/framework/src/responses/beaconErrorResponse.yaml +++ b/framework/src/responses/beaconErrorResponse.yaml @@ -1,7 +1,8 @@ $schema: https://json-schema.org/draft/2020-12/schema type: object description: >- - An unsuccessful operation. + A `beaconErrorResponse` denotes an unsuccessful operation, e.g. due to a missing + parameter or an invalid query. The response contains an error object. properties: meta: $ref: ./sections/beaconResponseMeta.yaml diff --git a/framework/src/responses/beaconInfoResponse.yaml b/framework/src/responses/beaconInfoResponse.yaml index 720015f8f..011610860 100644 --- a/framework/src/responses/beaconInfoResponse.yaml +++ b/framework/src/responses/beaconInfoResponse.yaml @@ -1,8 +1,14 @@ $schema: https://json-schema.org/draft/2020-12/schema type: object description: >- - Information about the Beacon. Aimed at Beacon clients like web pages - or Beacon networks. + The `beaconInfoResponse` provides metadata describing a Beacon instance, such + as its name, the organization responsible for the Beacon, contact information, + site logo and alternative URLs and importantly the beacon's API version. It is + based on the GA4GH `service-info` standard. + + The content of the `beaconInfoResponse` can be used by clients such as web front + ends or beacon aggregators to evaluate potential access patterns and to display + information about the beacon. properties: meta: description: >- diff --git a/framework/src/responses/beaconMapResponse.yaml b/framework/src/responses/beaconMapResponse.yaml index 08a70e0ad..c230024bb 100644 --- a/framework/src/responses/beaconMapResponse.yaml +++ b/framework/src/responses/beaconMapResponse.yaml @@ -1,8 +1,10 @@ $schema: https://json-schema.org/draft/2020-12/schema type: object description: >- - Information about the Beacon. Aimed to Beacon clients like web pages - or Beacon networks. + A `beaconMapResponse` provides information about the beacon instance such as the + different endpoints supported by this implementation of the Beacon API. This response + is aimed to allow Beacon clients such as web front ends and Beacon network aggregators + to evaluate which access patterns can be implemented against individual beacons. properties: meta: description: >- diff --git a/framework/src/responses/beaconResultsetsResponse.yaml b/framework/src/responses/beaconResultsetsResponse.yaml index 11e8b732c..b1c54d52c 100644 --- a/framework/src/responses/beaconResultsetsResponse.yaml +++ b/framework/src/responses/beaconResultsetsResponse.yaml @@ -1,5 +1,15 @@ $schema: https://json-schema.org/draft/2020-12/schema -description: Beacon response that includes record level details, grouped in Resultsets. +description: >- + A `beaconResultsetsResponse` returns the results of a query against a beacon + or beacon aggregator. Beyond the `responseSummary` for overall matches the + response contains details about the matches in individual **collections** in + the beacon or beacon network. This type of response is required when serving + a request with a "record" level `responseGranularity`, and `beaconResultsets` + typically contain a list of records matched by the query. + + The types of `beaconResultsets` objects are defined in the beacon's configuration; + e.g. if using the Beacon v2+ default model the types `dataset` and `cohort` are + supported as result sets. type: object properties: meta: From cd1d46028ed237bc159dc2bf0935da3d73e981e1 Mon Sep 17 00:00:00 2001 From: Michael Baudis Date: Mon, 11 Nov 2024 19:41:40 +0900 Subject: [PATCH 21/29] JSON versions of last commit --- framework/json/configuration/beaconConfigurationSchema.json | 4 ++-- framework/json/configuration/entryTypeDefinition.json | 4 ++-- framework/json/responses/beaconBooleanResponse.json | 2 +- framework/json/responses/beaconCollectionsResponse.json | 2 +- framework/json/responses/beaconConfigurationResponse.json | 2 +- framework/json/responses/beaconCountResponse.json | 2 +- framework/json/responses/beaconEntryTypesResponse.json | 2 +- framework/json/responses/beaconErrorResponse.json | 2 +- framework/json/responses/beaconInfoResponse.json | 2 +- framework/json/responses/beaconMapResponse.json | 2 +- framework/json/responses/beaconResultsetsResponse.json | 2 +- 11 files changed, 13 insertions(+), 13 deletions(-) diff --git a/framework/json/configuration/beaconConfigurationSchema.json b/framework/json/configuration/beaconConfigurationSchema.json index 7b3b448ec..20c2e0556 100644 --- a/framework/json/configuration/beaconConfigurationSchema.json +++ b/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", diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json index ff8824678..cf9013827 100644 --- a/framework/json/configuration/entryTypeDefinition.json +++ b/framework/json/configuration/entryTypeDefinition.json @@ -1,8 +1,8 @@ { - "$comment": "TO DO: The tagged parts should reference to `common/ontologizedElement.json`. But that configuration fails to validate. Further investigation is required, but should not affect the resulting schema.", + "$comment": "TODO: The tagged parts should reference to `common/ontologizedElement.json`. But that configuration fails to validate. Further investigation is required, but should not affect the resulting schema.'", "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Definition of an element or entry type including the Beacon v2 required and suggested attributes. This schema purpose is to describe each type of entities included in a Beacon, hence Beacon clients could have some metadata about such entities.\n\nThe `id` attribute is the key that should be used in other parts of the Beacon Model to allow Beacon clients to identify the different parts (e.g. endpoints, filteringTerms, request parameters, etc.) that fully describe an entry type.", + "description": "Definition of an element or entry type including the Beacon v2 required and suggested attributes. This schema purpose is to describe each type of entities included in a Beacon, hence Beacon clients could have some metadata about such entities. \nThe `id` attribute is the key that should be used in other parts of the Beacon Model to allow Beacon clients to identify the different parts (e.g. endpoints, filteringTerms, request parameters, etc.) that fully describe an entry type.", "properties": { "$schema": { "$ref": "../common/beaconCommonComponents.json#/$defs/$schema" diff --git a/framework/json/responses/beaconBooleanResponse.json b/framework/json/responses/beaconBooleanResponse.json index 8491ca4bd..5f1a24f46 100644 --- a/framework/json/responses/beaconBooleanResponse.json +++ b/framework/json/responses/beaconBooleanResponse.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "description": "Complete definition for a minimal response that provides *only* a `Boolean` exists true|false answer.", + "description": "Complete definition for a minimal response that provides *only* an aggregate Boolean `\"exists\": true` or `\"exists\": false` answer to the query. \nAdditional information - which should not consist of record-level information - can be provided through `beaconHandovers`. ", "properties": { "beaconHandovers": { "$ref": "../common/beaconCommonComponents.json#/$defs/ListOfHandovers", diff --git a/framework/json/responses/beaconCollectionsResponse.json b/framework/json/responses/beaconCollectionsResponse.json index 6728e3342..afc01ea1d 100644 --- a/framework/json/responses/beaconCollectionsResponse.json +++ b/framework/json/responses/beaconCollectionsResponse.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Beacon response that includes details about the collections in this Beacon.", + "description": "A type of Beacon response that includes details about the **collections** in a beacon. The types of collections are defined in each beacon's configuration; if using the Beacon v2+ default model usually the types `dataset` and `cohort` are supported.", "properties": { "beaconHandovers": { "$ref": "../common/beaconCommonComponents.json#/$defs/ListOfHandovers", diff --git a/framework/json/responses/beaconConfigurationResponse.json b/framework/json/responses/beaconConfigurationResponse.json index ccd15687e..3551db860 100644 --- a/framework/json/responses/beaconConfigurationResponse.json +++ b/framework/json/responses/beaconConfigurationResponse.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Information about the Beacon. Aimed to Beacon clients like web pages or Beacon networks.", + "description": "The `beaconConfigurationResponse` returns information about configuration parameters of a given beacon instance such as maturity or security attributes or supported entry types. It is directed towards Beacon clients like web pages or network aggregators.", "properties": { "meta": { "$ref": "./sections/beaconInformationalResponseMeta.json", diff --git a/framework/json/responses/beaconCountResponse.json b/framework/json/responses/beaconCountResponse.json index 9222ae90d..769f90894 100644 --- a/framework/json/responses/beaconCountResponse.json +++ b/framework/json/responses/beaconCountResponse.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "description": "Complete definition for a response that does not include record level details but provides `Boolean` and `count` information.", + "description": "Complete definition for a minimal response that provides an aggregate Boolean `\"exists\": true` or `\"exists\": false` answer to the query as well as the count of the matched records.\nAdditional information - which should not consist of record-level information - can be provided through `beaconHandovers`. ", "properties": { "beaconHandovers": { "$ref": "../common/beaconCommonComponents.json#/$defs/ListOfHandovers", diff --git a/framework/json/responses/beaconEntryTypesResponse.json b/framework/json/responses/beaconEntryTypesResponse.json index 2c2cc5514..d18fa8137 100644 --- a/framework/json/responses/beaconEntryTypesResponse.json +++ b/framework/json/responses/beaconEntryTypesResponse.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Response including a list of Entry types definitions.", + "description": "The `beaconEntryTypesResponse` provides information about the entry types served through a beacon, including their definitions and pointers to their schemas.", "properties": { "meta": { "$ref": "./sections/beaconInformationalResponseMeta.json", diff --git a/framework/json/responses/beaconErrorResponse.json b/framework/json/responses/beaconErrorResponse.json index db7b0c0f0..3f01c1a16 100644 --- a/framework/json/responses/beaconErrorResponse.json +++ b/framework/json/responses/beaconErrorResponse.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "An unsuccessful operation.", + "description": "A `beaconErrorResponse` denotes an unsuccessful operation, e.g. due to a missing parameter or an invalid query. The response contains an error object.", "properties": { "error": { "$ref": "../common/beaconCommonComponents.json#/$defs/BeaconError" diff --git a/framework/json/responses/beaconInfoResponse.json b/framework/json/responses/beaconInfoResponse.json index a221e746c..5ed2651fe 100644 --- a/framework/json/responses/beaconInfoResponse.json +++ b/framework/json/responses/beaconInfoResponse.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Information about the Beacon. Aimed at Beacon clients like web pages or Beacon networks.", + "description": "The `beaconInfoResponse` provides metadata describing a Beacon instance, such as its name, the organization responsible for the Beacon, contact information, site logo and alternative URLs and importantly the beacon's API version. It is based on the GA4GH `service-info` standard.\nThe content of the `beaconInfoResponse` can be used by clients such as web front ends or beacon aggregators to evaluate potential access patterns and to display information about the beacon.", "properties": { "meta": { "$ref": "./sections/beaconInformationalResponseMeta.json", diff --git a/framework/json/responses/beaconMapResponse.json b/framework/json/responses/beaconMapResponse.json index d915b4a29..f2c059151 100644 --- a/framework/json/responses/beaconMapResponse.json +++ b/framework/json/responses/beaconMapResponse.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Information about the Beacon. Aimed to Beacon clients like web pages or Beacon networks.", + "description": "A `beaconMapResponse` provides information about the beacon instance such as the different endpoints supported by this implementation of the Beacon API. This response is aimed to allow Beacon clients such as web front ends and Beacon network aggregators to evaluate which access patterns can be implemented against individual beacons.", "properties": { "meta": { "$ref": "./sections/beaconInformationalResponseMeta.json", diff --git a/framework/json/responses/beaconResultsetsResponse.json b/framework/json/responses/beaconResultsetsResponse.json index 8efe9617a..cf6d1660b 100644 --- a/framework/json/responses/beaconResultsetsResponse.json +++ b/framework/json/responses/beaconResultsetsResponse.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "additionalProperties": true, - "description": "Beacon response that includes record level details, grouped in Resultsets.", + "description": "A `beaconResultsetsResponse` returns the results of a query against a beacon or beacon aggregator. Beyond the `responseSummary` for overall matches the response contains details about the matches in individual **collections** in the beacon or beacon network. This type of response is required when serving a request with a \"record\" level `responseGranularity`, and `beaconResultsets` typically contain a list of records matched by the query.\nThe types of `beaconResultsets` objects are defined in the beacon's configuration; e.g. if using the Beacon v2+ default model the types `dataset` and `cohort` are supported as result sets. ", "properties": { "beaconHandovers": { "$ref": "../common/beaconCommonComponents.json#/$defs/ListOfHandovers", From dce8dffdfd6cc7b8ddd54115688faed263426c40 Mon Sep 17 00:00:00 2001 From: costero-e Date: Tue, 12 Nov 2024 16:07:45 +0100 Subject: [PATCH 22/29] adding links in changelog to point to each of the beacon v2 versions --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index b52bd0b92..0868929e1 100644 --- a/README.md +++ b/README.md @@ -33,6 +33,7 @@ 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 @@ -40,6 +41,7 @@ There is a set of tools in [`/bin`](./bin/) to facilitate the conversion. ATM, a ## 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: From beeb5f90a7a00ee3dc0312bca4eaf4a33a9953e9 Mon Sep 17 00:00:00 2001 From: Michael Baudis Date: Sat, 16 Nov 2024 08:52:41 +0900 Subject: [PATCH 23/29] VRS references fix Fixes the broken `https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json` entries to the now canonical `https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json` --- bin/beacon_yaml2md.pl | 4 ++-- bin/deref_schemas/obj/CopyNumber.yaml | 2 +- docs/schemas-md/obj/CopyNumber.md | 2 +- .../genomicVariations/defaultSchema.json | 6 +++--- .../genomicVariations/defaultSchema.yaml | 6 +++--- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/bin/beacon_yaml2md.pl b/bin/beacon_yaml2md.pl index 96e59c17f..9fc75fe5d 100755 --- 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/1.2/vrs.json#/definitions/', 'CopyNumber' => -'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/' +'https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/' ); if ( exists $url{$property} ) { $data->{properties} = diff --git a/bin/deref_schemas/obj/CopyNumber.yaml b/bin/deref_schemas/obj/CopyNumber.yaml index 0ac7b7d77..37906e038 100644 --- a/bin/deref_schemas/obj/CopyNumber.yaml +++ b/bin/deref_schemas/obj/CopyNumber.yaml @@ -1,4 +1,4 @@ --- CopyNumber: - properties: '[VRS definition for CopyNumber](https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/CopyNumber)' + properties: '[VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber)' type: allOf diff --git a/docs/schemas-md/obj/CopyNumber.md b/docs/schemas-md/obj/CopyNumber.md index f4738d0fb..88e7a5ee7 100644 --- a/docs/schemas-md/obj/CopyNumber.md +++ b/docs/schemas-md/obj/CopyNumber.md @@ -1,3 +1,3 @@ |Term | Description | Type | Properties | Example | Enum| | ---| ---| ---| ---| ---| --- | -| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/CopyNumber) | NA | NA| +| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber) | NA | NA| diff --git a/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json b/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json index 5ec02a7fd..394bef5c4 100644 --- a/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json +++ b/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json @@ -272,7 +272,7 @@ "type": "string" }, "location": { - "$ref": "https://raw.githubusercontent.com/ga4gh/vrs/main/schema/vrs.json#/definitions/Location" + "$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/Location" }, "referenceBases": { "description": "Reference bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used\n as a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of insertions with the maximally\n trimmed, inserted sequence being indicated in `AlternateBases`.", @@ -557,10 +557,10 @@ "variation": { "oneOf": [ { - "$ref": "https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/MolecularVariation" + "$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/MolecularVariation" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/SystemicVariation" + "$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/SystemicVariation" }, { "$ref": "#/$defs/LegacyVariation" diff --git a/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml b/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml index 96c3dbff7..b5e5cc9ec 100644 --- a/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml +++ b/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml @@ -10,8 +10,8 @@ required: properties: variation: oneOf: - - $ref: https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/MolecularVariation - - $ref: https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/SystemicVariation + - $ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/MolecularVariation + - $ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/SystemicVariation - $ref: '#/$defs/LegacyVariation' variantInternalId: description: >- @@ -51,7 +51,7 @@ $defs: - location properties: location: - $ref: https://raw.githubusercontent.com/ga4gh/vrs/main/schema/vrs.json#/definitions/Location + $ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/Location variantType: description: >- The `variantType` declares the nature of the variation in relation From c634b81c6c012c0d2973fcf256df762c5fbb0516 Mon Sep 17 00:00:00 2001 From: Michael Baudis Date: Sat, 16 Nov 2024 09:08:49 +0900 Subject: [PATCH 24/29] VRS references from 1.2 => 1.3 The Beacon schema for genomic allows 3 options: * VRS MolecularVariation * VRS SystemicVariation * Beacon LegacyVariation (which adopts the VRS location object but uses separate definitions otherwise) Unfortunately, during Beacon v2 approval only VRS 1.2. was available and then explicitly referenced in the schema. It fast superseded by 1.3 which allows a *much* better definition of "Systemic Variations" such as CNV. This PR changes all VRS references from 1.2 => 1.3 and should be very welcome to implementers (1.3. has been the longstanding standard now until the future 2.x is out; in fact, the `bycon` based implementations such as progenetix.org have been using it for their Beacons for ~2years). --- bin/beacon_yaml2md.pl | 4 ++-- bin/deref_schemas/obj/CopyNumber.yaml | 2 +- docs/schemas-md/obj/CopyNumber.md | 2 +- .../genomicVariations/defaultSchema.json | 8 ++++---- .../genomicVariations/defaultSchema.yaml | 8 ++++---- 5 files changed, 12 insertions(+), 12 deletions(-) diff --git a/bin/beacon_yaml2md.pl b/bin/beacon_yaml2md.pl index 9fc75fe5d..1285de4de 100755 --- 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://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/', +'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/', 'CopyNumber' => -'https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/' +'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/' ); if ( exists $url{$property} ) { $data->{properties} = diff --git a/bin/deref_schemas/obj/CopyNumber.yaml b/bin/deref_schemas/obj/CopyNumber.yaml index 37906e038..ec96fa12b 100644 --- a/bin/deref_schemas/obj/CopyNumber.yaml +++ b/bin/deref_schemas/obj/CopyNumber.yaml @@ -1,4 +1,4 @@ --- CopyNumber: - properties: '[VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber)' + properties: '[VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber)' type: allOf diff --git a/docs/schemas-md/obj/CopyNumber.md b/docs/schemas-md/obj/CopyNumber.md index 88e7a5ee7..e55d7cca3 100644 --- a/docs/schemas-md/obj/CopyNumber.md +++ b/docs/schemas-md/obj/CopyNumber.md @@ -1,3 +1,3 @@ |Term | Description | Type | Properties | Example | Enum| | ---| ---| ---| ---| ---| --- | -| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber) | NA | NA| +| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber) | NA | NA| diff --git a/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json b/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json index 394bef5c4..19d42db14 100644 --- a/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json +++ b/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json @@ -1,5 +1,5 @@ { - "$comment": "version: ga4gh-beacon-variant-v2.0.0", + "$comment": "version: ga4gh-beacon-variant-v2.1.0", "$defs": { "CaseLevelVariant": { "description": "", @@ -272,7 +272,7 @@ "type": "string" }, "location": { - "$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/Location" + "$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/Location" }, "referenceBases": { "description": "Reference bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used\n as a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of insertions with the maximally\n trimmed, inserted sequence being indicated in `AlternateBases`.", @@ -557,10 +557,10 @@ "variation": { "oneOf": [ { - "$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/MolecularVariation" + "$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/MolecularVariation" }, { - "$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/SystemicVariation" + "$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/SystemicVariation" }, { "$ref": "#/$defs/LegacyVariation" diff --git a/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml b/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml index b5e5cc9ec..df68f4d7d 100644 --- a/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml +++ b/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml @@ -1,6 +1,6 @@ $schema: https://json-schema.org/draft/2020-12/schema title: Genomic Variation -$comment: 'version: ga4gh-beacon-variant-v2.0.0' +$comment: 'version: ga4gh-beacon-variant-v2.1.0' description: >- Schema for a genomic variant entry. type: object @@ -10,8 +10,8 @@ required: properties: variation: oneOf: - - $ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/MolecularVariation - - $ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/SystemicVariation + - $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/MolecularVariation + - $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/SystemicVariation - $ref: '#/$defs/LegacyVariation' variantInternalId: description: >- @@ -51,7 +51,7 @@ $defs: - location properties: location: - $ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/Location + $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/Location variantType: description: >- The `variantType` declares the nature of the variation in relation From b1f81dcf9e280f79e3db5050a623bbb2bbd4addb Mon Sep 17 00:00:00 2001 From: Michael Baudis Date: Sat, 16 Nov 2024 09:22:14 +0900 Subject: [PATCH 25/29] removing the schema deparser changes The `beacon_yaml2md.pl` doc generator contains hard coded definitions to VRS 1.2 `CopyNumber` which doesn't exist in 1.3. This should be fixed separately, possibly w/ revision of the schema documentation method/engine. --- bin/beacon_yaml2md.pl | 4 ++-- bin/deref_schemas/obj/CopyNumber.yaml | 2 +- docs/schemas-md/obj/CopyNumber.md | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bin/beacon_yaml2md.pl b/bin/beacon_yaml2md.pl index 1285de4de..9fc75fe5d 100755 --- 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://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/', +'https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/', 'CopyNumber' => -'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/' +'https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/' ); if ( exists $url{$property} ) { $data->{properties} = diff --git a/bin/deref_schemas/obj/CopyNumber.yaml b/bin/deref_schemas/obj/CopyNumber.yaml index ec96fa12b..37906e038 100644 --- 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://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber)' + properties: '[VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber)' type: allOf diff --git a/docs/schemas-md/obj/CopyNumber.md b/docs/schemas-md/obj/CopyNumber.md index e55d7cca3..88e7a5ee7 100644 --- 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://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber) | NA | NA| +| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber) | NA | NA| From 8381c5c225e984477879d918a7b25e7397c3e80f Mon Sep 17 00:00:00 2001 From: Gordon Krieger Date: Tue, 19 Nov 2024 15:56:31 -0500 Subject: [PATCH 26/29] add minItems to filteringTermsResults values field --- .../json/responses/sections/beaconFilteringTermsResults.json | 1 + .../src/responses/sections/beaconFilteringTermsResults.yaml | 1 + 2 files changed, 2 insertions(+) diff --git a/framework/json/responses/sections/beaconFilteringTermsResults.json b/framework/json/responses/sections/beaconFilteringTermsResults.json index f263928a2..6f1a34801 100644 --- a/framework/json/responses/sections/beaconFilteringTermsResults.json +++ b/framework/json/responses/sections/beaconFilteringTermsResults.json @@ -55,6 +55,7 @@ "items": { "type": "string" }, + "minItems": 1, "type": "array" } }, diff --git a/framework/src/responses/sections/beaconFilteringTermsResults.yaml b/framework/src/responses/sections/beaconFilteringTermsResults.yaml index 63d21c76d..1607ba58b 100644 --- a/framework/src/responses/sections/beaconFilteringTermsResults.yaml +++ b/framework/src/responses/sections/beaconFilteringTermsResults.yaml @@ -74,6 +74,7 @@ definitions: type: array items: type: string + minItems: 1 Resource: type: object description: >- From 07a6f025e99cd30d39016027691e9cfddaafa205 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oriol=20L=C3=B3pez-Doriga?= <79700502+costero-e@users.noreply.github.com> Date: Thu, 12 Dec 2024 16:35:32 +0100 Subject: [PATCH 27/29] Update CopyNumber.md --- docs/schemas-md/obj/CopyNumber.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/schemas-md/obj/CopyNumber.md b/docs/schemas-md/obj/CopyNumber.md index 88e7a5ee7..e55d7cca3 100644 --- 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://w3id.org/ga4gh/schema/vrs/1.2/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| From 7bf20b80cff07b5be5d0b370f3054c3e79c8f4ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oriol=20L=C3=B3pez-Doriga?= <79700502+costero-e@users.noreply.github.com> Date: Thu, 12 Dec 2024 16:36:18 +0100 Subject: [PATCH 28/29] Update beacon_yaml2md.pl --- bin/beacon_yaml2md.pl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/beacon_yaml2md.pl b/bin/beacon_yaml2md.pl index 9fc75fe5d..1285de4de 100755 --- 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://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/', +'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/', 'CopyNumber' => -'https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/' +'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/' ); if ( exists $url{$property} ) { $data->{properties} = From 507da0a579583974bca4dc130a0ac84c0b3adc8b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Oriol=20L=C3=B3pez-Doriga?= <79700502+costero-e@users.noreply.github.com> Date: Thu, 12 Dec 2024 16:37:43 +0100 Subject: [PATCH 29/29] Update CopyNumber.yaml --- bin/deref_schemas/obj/CopyNumber.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/deref_schemas/obj/CopyNumber.yaml b/bin/deref_schemas/obj/CopyNumber.yaml index 37906e038..ec96fa12b 100644 --- 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://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber)' + properties: '[VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber)' type: allOf