diff --git a/framework/json/common/beaconCommonComponents.json b/framework/json/common/beaconCommonComponents.json index 10ee8912a..8c73c1074 100644 --- a/framework/json/common/beaconCommonComponents.json +++ b/framework/json/common/beaconCommonComponents.json @@ -142,10 +142,6 @@ ], "type": "string" }, - "Info": { - "description": "Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification.", - "type": "object" - }, "Limit": { "default": 10, "description": "Size of the page. Use `0` to return all the results or the maximum allowed by the Beacon, if there is any.", diff --git a/framework/json/common/info.json b/framework/json/common/info.json new file mode 100644 index 000000000..69826f5ed --- /dev/null +++ b/framework/json/common/info.json @@ -0,0 +1,6 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "description": "Placeholder to allow the Beacon to return any additional information that is necessary or could be of interest in relation to the query or the entry returned. It is recommended to encapsulate additional informations in this attribute instead of directly adding attributes at the same level than the others in order to avoid collision in the names of attributes in future versions of the specification.", + "title": "Info", + "type": "object" +} \ No newline at end of file diff --git a/framework/json/responses/beaconBooleanResponse.json b/framework/json/responses/beaconBooleanResponse.json index 8491ca4bd..dc36a6ddb 100644 --- a/framework/json/responses/beaconBooleanResponse.json +++ b/framework/json/responses/beaconBooleanResponse.json @@ -7,7 +7,7 @@ "description": "List of handovers that apply to the whole response, not to any resultset or result in particular." }, "info": { - "$ref": "../common/beaconCommonComponents.json#/$defs/Info", + "$ref": "../common/info.json", "description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification." }, "meta": { diff --git a/framework/json/responses/beaconCollectionsResponse.json b/framework/json/responses/beaconCollectionsResponse.json index 6728e3342..ca8cdb726 100644 --- a/framework/json/responses/beaconCollectionsResponse.json +++ b/framework/json/responses/beaconCollectionsResponse.json @@ -8,7 +8,7 @@ "description": "List of handovers that apply to the whole response, not to any resultset or result in particular." }, "info": { - "$ref": "../common/beaconCommonComponents.json#/$defs/Info", + "$ref": "../common/info.json", "description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification." }, "meta": { diff --git a/framework/json/responses/beaconCountResponse.json b/framework/json/responses/beaconCountResponse.json index 9222ae90d..acf4ffcc7 100644 --- a/framework/json/responses/beaconCountResponse.json +++ b/framework/json/responses/beaconCountResponse.json @@ -7,7 +7,7 @@ "description": "List of handovers that apply to the whole response, not to any resultset or result in particular." }, "info": { - "$ref": "../common/beaconCommonComponents.json#/$defs/Info", + "$ref": "../common/info.json", "description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification." }, "meta": { diff --git a/framework/json/responses/beaconResultsetsResponse.json b/framework/json/responses/beaconResultsetsResponse.json index 8efe9617a..094ed57a6 100644 --- a/framework/json/responses/beaconResultsetsResponse.json +++ b/framework/json/responses/beaconResultsetsResponse.json @@ -8,7 +8,7 @@ "description": "List of handovers that apply to the whole response, not to any resultset or result in particular." }, "info": { - "$ref": "../common/beaconCommonComponents.json#/$defs/Info", + "$ref": "../common/info.json", "description": "Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification." }, "meta": { diff --git a/framework/json/responses/sections/beaconInfoResults.json b/framework/json/responses/sections/beaconInfoResults.json index f795b2dbe..0773b1dba 100644 --- a/framework/json/responses/sections/beaconInfoResults.json +++ b/framework/json/responses/sections/beaconInfoResults.json @@ -20,7 +20,7 @@ "type": "string" }, "info": { - "$ref": "../../common/beaconCommonComponents.json#/$defs/Info", + "$ref": "../../common/info.json", "description": "Additional unspecified metadata about the host Organization." }, "logoUrl": { @@ -86,7 +86,7 @@ "$ref": "../../common/beaconCommonComponents.json#/$defs/BeaconId" }, "info": { - "$ref": "../../common/beaconCommonComponents.json#/$defs/Info", + "$ref": "../../common/info.json", "description": "Additional unspecified metadata about the Beacon service." }, "name": { diff --git a/framework/src/common/beaconCommonComponents.yaml b/framework/src/common/beaconCommonComponents.yaml index b77fab3ce..8af76d1a9 100644 --- a/framework/src/common/beaconCommonComponents.yaml +++ b/framework/src/common/beaconCommonComponents.yaml @@ -212,16 +212,6 @@ $defs: minimum: 0 examples: - 123 - Info: - description: >- - Placeholder to allow the Beacon to return any additional information that - is necessary or could be of interest in relation to the query or the entry - returned. - It is recommended to encapsulate additional informations in this attribute - instead of directly adding attributes at the same level than the others in - order to avoid collision in the names of attributes in future versions of - the specification. - type: object ListOfHandovers: description: Set of handovers to be added in one section the response. type: array diff --git a/framework/src/common/info.yaml b/framework/src/common/info.yaml new file mode 100644 index 000000000..2b29ef3fd --- /dev/null +++ b/framework/src/common/info.yaml @@ -0,0 +1,11 @@ +$schema: https://json-schema.org/draft/2020-12/schema +title: Info +description: >- + Placeholder to allow the Beacon to return any additional information that + is necessary or could be of interest in relation to the query or the entry + returned. + It is recommended to encapsulate additional informations in this attribute + instead of directly adding attributes at the same level than the others in + order to avoid collision in the names of attributes in future versions of + the specification. +type: object diff --git a/framework/src/responses/beaconBooleanResponse.yaml b/framework/src/responses/beaconBooleanResponse.yaml index 97811e09c..b68dc849d 100644 --- a/framework/src/responses/beaconBooleanResponse.yaml +++ b/framework/src/responses/beaconBooleanResponse.yaml @@ -17,7 +17,7 @@ properties: description: >- Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification. - $ref: ../common/beaconCommonComponents.yaml#/$defs/Info + $ref: ../common/info.yaml beaconHandovers: description: >- List of handovers that apply to the whole response, not to any resultset diff --git a/framework/src/responses/beaconCollectionsResponse.yaml b/framework/src/responses/beaconCollectionsResponse.yaml index 8b895ce6f..93a35702c 100644 --- a/framework/src/responses/beaconCollectionsResponse.yaml +++ b/framework/src/responses/beaconCollectionsResponse.yaml @@ -27,7 +27,7 @@ properties: description: >- Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification. - $ref: ../common/beaconCommonComponents.yaml#/$defs/Info + $ref: ../common/info.yaml beaconHandovers: description: List of handovers that apply to the whole response, not to any resultset or result in particular. diff --git a/framework/src/responses/beaconCountResponse.yaml b/framework/src/responses/beaconCountResponse.yaml index f083849bd..27d1dddbf 100644 --- a/framework/src/responses/beaconCountResponse.yaml +++ b/framework/src/responses/beaconCountResponse.yaml @@ -17,7 +17,7 @@ properties: description: >- Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification. - $ref: ../common/beaconCommonComponents.yaml#/$defs/Info + $ref: ../common/info.yaml beaconHandovers: description: >- List of handovers that apply to the whole response, not to any resultset diff --git a/framework/src/responses/beaconResultsetsResponse.yaml b/framework/src/responses/beaconResultsetsResponse.yaml index 11e8b732c..39601cbda 100644 --- a/framework/src/responses/beaconResultsetsResponse.yaml +++ b/framework/src/responses/beaconResultsetsResponse.yaml @@ -15,7 +15,7 @@ properties: description: >- Additional details that could be of interest. Provided to clearly enclose any attribute that is not part of the Beacon specification. - $ref: ../common/beaconCommonComponents.yaml#/$defs/Info + $ref: ../common/info.yaml beaconHandovers: description: >- List of handovers that apply to the whole response, not to any resultset diff --git a/framework/src/responses/sections/beaconInfoResults.yaml b/framework/src/responses/sections/beaconInfoResults.yaml index 2127e4a1f..3c5cbaebc 100644 --- a/framework/src/responses/sections/beaconInfoResults.yaml +++ b/framework/src/responses/sections/beaconInfoResults.yaml @@ -67,7 +67,7 @@ properties: info: description: >- Additional unspecified metadata about the Beacon service. - $ref: ../../common/beaconCommonComponents.yaml#/$defs/Info + $ref: ../../common/info.yaml $defs: BeaconOrganization: description: >- @@ -109,5 +109,5 @@ $defs: 3986 format). info: description: Additional unspecified metadata about the host Organization. - $ref: ../../common/beaconCommonComponents.yaml#/$defs/Info + $ref: ../../common/info.yaml additionalProperties: true diff --git a/models/json/beacon-v2-default-model/analyses/defaultSchema.json b/models/json/beacon-v2-default-model/analyses/defaultSchema.json index a082caa73..7def347a9 100644 --- a/models/json/beacon-v2-default-model/analyses/defaultSchema.json +++ b/models/json/beacon-v2-default-model/analyses/defaultSchema.json @@ -38,7 +38,7 @@ "type": "string" }, "info": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info" + "$ref": "../common/info.json" }, "pipelineName": { "description": "Analysis pipeline and version if a standardized pipeline was used", diff --git a/models/json/beacon-v2-default-model/biosamples/defaultSchema.json b/models/json/beacon-v2-default-model/biosamples/defaultSchema.json index 392f5988a..e6eca7082 100644 --- a/models/json/beacon-v2-default-model/biosamples/defaultSchema.json +++ b/models/json/beacon-v2-default-model/biosamples/defaultSchema.json @@ -82,7 +82,7 @@ "type": "string" }, "info": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info" + "$ref": "../common/info.json" }, "measurements": { "description": "List of measurements of the sample.", diff --git a/models/json/beacon-v2-default-model/datasets/defaultSchema.json b/models/json/beacon-v2-default-model/datasets/defaultSchema.json index 3efa64e7d..51e28141c 100644 --- a/models/json/beacon-v2-default-model/datasets/defaultSchema.json +++ b/models/json/beacon-v2-default-model/datasets/defaultSchema.json @@ -37,7 +37,7 @@ "type": "string" }, "info": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info" + "$ref": "../common/info.json" }, "name": { "description": "Name of the dataset", diff --git a/models/json/beacon-v2-default-model/individuals/defaultSchema.json b/models/json/beacon-v2-default-model/individuals/defaultSchema.json index e5b6876a6..c916b09bd 100644 --- a/models/json/beacon-v2-default-model/individuals/defaultSchema.json +++ b/models/json/beacon-v2-default-model/individuals/defaultSchema.json @@ -31,7 +31,7 @@ "type": "string" }, "info": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info" + "$ref": "../common/info.json" }, "interventionsOrProcedures": { "items": { @@ -63,7 +63,7 @@ }, "sex": { "$ref": "../common/commonDefinitions.json#/$defs/Sex", - "description": "Sex of the individual. Value from NCIT General Qualifier (NCIT:C27993): 'unknown' (not assessed or not available) (NCIT:C17998), 'female' (NCIT:C16576), or 'male', (NCIT:C20197)." + "description": "Sex of the individual. Value from NCIT General Qualifier `NCIT:C27993`: * `unknown`: not assessed or not availablel `NCIT:C17998` * `female`: `NCIT:C16576` * `male`: `NCIT:C20197`" }, "treatments": { "items": { diff --git a/models/json/beacon-v2-default-model/runs/defaultSchema.json b/models/json/beacon-v2-default-model/runs/defaultSchema.json index 61d090df2..e3f4040d9 100644 --- a/models/json/beacon-v2-default-model/runs/defaultSchema.json +++ b/models/json/beacon-v2-default-model/runs/defaultSchema.json @@ -26,7 +26,7 @@ "type": "string" }, "info": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info" + "$ref": "../common/info.json" }, "libraryLayout": { "description": "Ontology value for the library layout e.g \"PAIRED\", \"SINGLE\" #todo add Ontology name?", diff --git a/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml b/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml index 5c454121a..3022bb09f 100644 --- a/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml +++ b/models/src/beacon-v2-default-model/analyses/defaultSchema.yaml @@ -51,7 +51,7 @@ properties: examples: - GATK4.0 info: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info + $ref: ../common/info.yaml required: - id - analysisDate diff --git a/models/src/beacon-v2-default-model/biosamples/defaultSchema.yaml b/models/src/beacon-v2-default-model/biosamples/defaultSchema.yaml index 008c4575b..c90eda4d0 100644 --- a/models/src/beacon-v2-default-model/biosamples/defaultSchema.yaml +++ b/models/src/beacon-v2-default-model/biosamples/defaultSchema.yaml @@ -160,7 +160,7 @@ properties: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json example: {} info: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info + $ref: ../common/info.yaml required: - id - biosampleStatus diff --git a/models/src/beacon-v2-default-model/datasets/defaultSchema.yaml b/models/src/beacon-v2-default-model/datasets/defaultSchema.yaml index 7741c5707..1747613c6 100644 --- a/models/src/beacon-v2-default-model/datasets/defaultSchema.yaml +++ b/models/src/beacon-v2-default-model/datasets/defaultSchema.yaml @@ -40,7 +40,7 @@ properties: examples: - https://example.org/wiki/Main_Page info: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info + $ref: ../common/info.yaml dataUseConditions: description: Data use conditions applying to this dataset. $ref: ../common/dataUseConditions.yaml diff --git a/models/src/beacon-v2-default-model/individuals/defaultSchema.yaml b/models/src/beacon-v2-default-model/individuals/defaultSchema.yaml index adc28d3e3..ede6165f2 100644 --- a/models/src/beacon-v2-default-model/individuals/defaultSchema.yaml +++ b/models/src/beacon-v2-default-model/individuals/defaultSchema.yaml @@ -9,9 +9,11 @@ properties: type: string example: P0001 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)." + description: >- + Sex of the individual. Value from NCIT General Qualifier `NCIT:C27993`: + * `unknown`: not assessed or not availablel `NCIT:C17998` + * `female`: `NCIT:C16576` + * `male`: `NCIT:C20197` $ref: ../common/commonDefinitions.yaml#/$defs/Sex karyotypicSex: description: The chromosomal sex of an individual represented from a selection @@ -60,7 +62,7 @@ properties: items: $ref: ../common/exposure.yaml info: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info + $ref: ../common/info.yaml required: - id - sex diff --git a/models/src/beacon-v2-default-model/runs/defaultSchema.yaml b/models/src/beacon-v2-default-model/runs/defaultSchema.yaml index 1ba08836f..fc7efff95 100644 --- a/models/src/beacon-v2-default-model/runs/defaultSchema.yaml +++ b/models/src/beacon-v2-default-model/runs/defaultSchema.yaml @@ -74,7 +74,7 @@ properties: - id: EFO:0010938 label: large-insert clone DNA microarray info: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info + $ref: ../common/info.yaml required: - id - biosampleId