diff --git a/beacon.yaml b/beacon.yaml index 0ffbb53..02c72e7 100644 --- a/beacon.yaml +++ b/beacon.yaml @@ -139,7 +139,8 @@ paths: /datasets/{id}/variant_interpretations: post: description: | - Get the variants interpretations by datasetId. + Get the variants interpretations (`VariantInterpretationResponse`) by + dataset ID. operationId: getVariantsInterpretationsByDatasetId tags: - Endpoints @@ -157,35 +158,13 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/Forbidden' /filtering_terms: get: description: | @@ -223,11 +202,11 @@ paths: application/json: schema: $ref: '#/components/schemas/FilteringTermsResponse' - /individuals: post: description: | - Get response to a beacon query for individual information. + Get response to a beacon query for individual information + (`IndividualResponse`). operationId: postIndividualResponse tags: - Endpoints @@ -239,39 +218,17 @@ paths: required: false responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but s/he is not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Forbidden' /individuals/{id}: post: description: | - Get an individual by its Id. + Get an individual (`IndividualResponse`) by its Id. operationId: postIndividualById tags: - Endpoints @@ -290,39 +247,17 @@ paths: required: false responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but s/he is not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Forbidden' /individuals/{id}/biosamples: post: description: | - Get biosamples found in this individual. + Get biosamples (`BiosampleResponse`) found in this individual. operationId: postBiosamplesByIndividualId tags: - Endpoints @@ -341,39 +276,18 @@ paths: required: false responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but s/he is not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Forbidden' /individuals/{id}/g_variants: post: description: | - Get variants that have been stored for this individual. + Get variants (`GenomicVariantResponse`) that have been stored for this + individual. operationId: postVariantsByIndividualId tags: - Endpoints @@ -392,39 +306,17 @@ paths: required: false responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but s/he is not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Forbidden' /individuals/{id}/cohorts: post: description: | - Get cohort(s) of this individual. + Get cohort(s) (`CohortResponse`) of this individual. operationId: postCohortsByIndividual tags: - Endpoints @@ -442,39 +334,46 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/Forbidden' + /individuals/{id}/interactors: + post: + description: | + Get interactor(s) (`InteractorResponse`) of this individual. + operationId: postInteractorsByIndividual + tags: + - Endpoints + parameters: + - name: id + in: path + description: Individual ID + required: true + schema: + type: string + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/Request' + responses: + '200': + $ref: '#/components/responses/Success' + '400': + $ref: '#/components/responses/BadRequest' + '401': + $ref: '#/components/responses/Unauthorized' + '403': + $ref: '#/components/responses/Forbidden' /biosamples: post: description: | - Get response to a beacon query for biosample information. + Get response to a beacon query for biosample information + (`BiosampleResponse`). operationId: postSampleResponse tags: - Endpoints @@ -486,39 +385,17 @@ paths: required: false responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Forbidden' /biosamples/{id}: post: description: | - Get a biosample by its Id. + Get a biosample (`BiosampleResponse`) by its Id. operationId: postBiosampleById tags: - Endpoints @@ -537,39 +414,18 @@ paths: required: false responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Forbidden' /biosamples/{id}/individuals: post: description: | - Get the individual to whom this biosample belongs to. + Get the individual information (`IndividualResponse`) to whom this + biosample belongs to. operationId: postInvidigualsByBiosampleId tags: - Endpoints @@ -588,39 +444,18 @@ paths: required: false responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but s/he is not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Forbidden' /biosamples/{id}/g_variants: post: description: | - Get the variants that have been stored for this biosample. + Get the variants (`GenomicVariantResponse`) that have been stored for + this biosample. operationId: postVariantsByBiosampleId tags: - Endpoints @@ -639,39 +474,17 @@ paths: required: false responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but s/he is not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Forbidden' /biosamples/{id}/runs: post: description: | - Get the runs that have been stored for this biosample. + Get the runs (`RunResponse`) that have been stored for this biosample. operationId: postRunsByBiosampleId tags: - Endpoints @@ -689,39 +502,18 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but s/he is not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Forbidden' /biosamples/{id}/variants_in_sample: post: description: | - Get the variants in sample in which this biosample is found. + Get the variants in sample (`VariantInSampleResponse`) in which this + biosample is found. operationId: getVariantsInSampleByBiosampleId tags: - Endpoints @@ -739,39 +531,18 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Forbidden' /g_variants: post: description: | - Any kind of genomic query that wants to query variants. + Any kind of genomic query that wants to query variants + (`GenomicVariantResponse`). operationId: postGenomicVariant tags: - Endpoints @@ -783,39 +554,17 @@ paths: required: false responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but s/he is not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Forbidden' /g_variants/{id}: post: description: | - Get a variant by its Id. + Get a variant (`GenomicVariantResponse`) by its Id. operationId: getGenomicVariantById tags: - Endpoints @@ -833,39 +582,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but s/he is not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/GenomicVariantResponse' + $ref: '#/components/responses/Forbidden' /g_variants/{id}/biosamples: post: description: | - Get the biosamples where this variant is found. + Get the biosamples (`BiosampleResponse`) where this variant is found. operationId: getBiosamplesByVariantId tags: - Endpoints @@ -883,39 +610,18 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but s/he is not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Forbidden' /g_variants/{id}/individuals: post: description: | - Get the individuals in which this variant is found. + Get the individuals (`IndividualResponse`) in which this variant is + found. operationId: getIndividualsByVariantId tags: - Endpoints @@ -933,39 +639,18 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Forbidden' /g_variants/{id}/variants_in_sample: post: description: | - Get the variants in sample in which this variant is found. + Get the variants in sample (`VariantInSampleResponse`) in which this + variant is found. operationId: getVariantsInSampleByVariantId tags: - Endpoints @@ -983,39 +668,18 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Forbidden' /g_variants/{id}/variant_interpretations: post: description: | - Get the variants interpretations by variantId. + Get the variants interpretations (`VariantInterpretationResponse`) by + variant ID. operationId: getVariantsInterpretationsByVariantId tags: - Endpoints @@ -1033,39 +697,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/Forbidden' /runs: post: description: | - Any kind of genomic query that wants to query runs. + Any kind of genomic query that wants to query runs (`RunResponse`). operationId: postRun tags: - Endpoints @@ -1076,39 +718,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Forbidden' /runs/{id}: post: description: | - Get a run by its `id`. + Get a run (`RunResponse`) by its `id`. operationId: postRunById tags: - Endpoints @@ -1126,39 +746,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Forbidden' /runs/{id}/biosamples: post: description: | - Get the biosamples in which this run is found. + Get the biosamples (`BiosampleResponse`) in which this run is found. operationId: postBiosamplesByRunId tags: - Endpoints @@ -1176,39 +774,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/BiosampleResponse' - '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Unauthorized' + '403': + $ref: '#/components/responses/Forbidden' /runs/{id}/analyses: post: description: | - Get the analyses in which this run is found. + Get the analyses (`AnalysisResponse`) in which this run is found. operationId: postAnalysesByRunId tags: - Endpoints @@ -1226,39 +802,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/AnalysisResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/AnalysisResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/AnalysisResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/AnalysisResponse' + $ref: '#/components/responses/Forbidden' /analyses: post: description: | - Any kind of query that wants to query analysis. + Any kind of query that wants to query analysis (`AnalysisResponse`). operationId: postAnalyses tags: - Endpoints @@ -1269,39 +823,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/AnalysisResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/AnalysisResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/AnalysisResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Forbidden' /analyses/{id}: post: description: | - Get an analysis by its `id`. + Get an analysis (`AnalysisResponse`) by its `id`. operationId: postAnalysisById tags: - Endpoints @@ -1319,39 +851,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/AnalysisResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/AnalysisResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/AnalysisResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/AnalysisResponse' + $ref: '#/components/responses/Forbidden' /analyses/{id}/runs: post: description: | - Get the runs in which this analysis is found. + Get the runs (`RunResponse`) in which this analysis is found. operationId: postRunsByAnalysisId tags: - Endpoints @@ -1369,39 +879,18 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/RunResponse' + $ref: '#/components/responses/Forbidden' /analyses/{id}/variants_in_sample: post: description: | - Get the variants in sample in which this analysis is found. + Get the variants in sample (`VariantInSampleResponse`) in which this + analysis is found. operationId: getVariantsInSampleByAnalysisId tags: - Endpoints @@ -1419,39 +908,18 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Forbidden' /variants_in_sample: post: description: | - Any kind of query that wants to query variants in sample. + Any kind of query that wants to query variants in sample + (`VariantInSampleResponse`). operationId: postVariantsInSample tags: - Endpoints @@ -1462,39 +930,18 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInSampleResponse' + $ref: '#/components/responses/Forbidden' /variants_interpretations: post: description: | - Any kind of query that wants to query variant interpretations. + Any kind of query that wants to query variant interpretations + (`VariantInterpretationResponse`). operationId: postVariantInterpretation tags: - Endpoints @@ -1505,39 +952,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/VariantInterpretationResponse' + $ref: '#/components/responses/Forbidden' /interactors: post: description: | - Any kind of query that wants to query interactors. + Any kind of query that wants to query interactors (`InteractorResponse`). operationId: postInteractors tags: - Endpoints @@ -1548,39 +973,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/InteractorResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/InteractorResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/InteractorResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/InteractorResponse' + $ref: '#/components/responses/Forbidden' /interactors/{id}: post: description: | - Get an interactor by its `id`. + Get an interactor (`InteractorResponse`) by its `id`. operationId: postInteractorById tags: - Endpoints @@ -1598,39 +1001,18 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/InteractorResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/InteractorResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/InteractorResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/InteractorResponse' + $ref: '#/components/responses/Forbidden' /interactors/{id}/individuals: post: description: | - Get the individuals in which this interactor is found. + Get the individuals (`IndividualResponse`) in which this interactor is + found. operationId: postIndividualsByInteractorId tags: - Endpoints @@ -1648,39 +1030,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Forbidden' /cohorts: post: description: | - Any kind of query that wants to query cohorts. + Any kind of query that wants to query cohorts (`CohortResponse`). operationId: postCohorts tags: - Endpoints @@ -1691,39 +1051,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/Forbidden' /cohorts/{id}: post: description: | - Get a cohort by its `id`. + Get a cohort (`CohortResponse`) by its `id`. operationId: postCohortById tags: - Endpoints @@ -1741,39 +1079,17 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/CohortResponse' + $ref: '#/components/responses/Forbidden' /cohorts/{id}/individuals: post: description: | - Get the individuals linked to this cohort. + Get the individuals (`IndividualResponse`) linked to this cohort. operationId: postIndividualsByCohortId tags: - Endpoints @@ -1791,36 +1107,81 @@ paths: $ref: '#/components/schemas/Request' responses: '200': - description: | - Successful operation - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Success' '400': - description: | - Bad request (e.g. missing mandatory parameter) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/BadRequest' '401': - description: >- - Unauthorised (e.g. when an unauthenticated user tries to access a - protected resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Unauthorized' '403': - description: >- - Forbidden (e.g. the resource is protected for all users or the user - is authenticated but they are not granted for this resource) - content: - application/json: - schema: - $ref: '#/components/schemas/IndividualResponse' + $ref: '#/components/responses/Forbidden' components: + responses: + Success: + description: | + Successful operation. + content: + application/json: + schema: + oneOf: + - $ref: '#/components/schemas/VariantInterpretationResponse' + - $ref: '#/components/schemas/IndividualResponse' + - $ref: '#/components/schemas/BiosampleResponse' + - $ref: '#/components/schemas/GenomicVariantResponse' + - $ref: '#/components/schemas/CohortResponse' + - $ref: '#/components/schemas/RunResponse' + - $ref: '#/components/schemas/VariantInSampleResponse' + - $ref: '#/components/schemas/AnalysisResponse' + - $ref: '#/components/schemas/InteractorResponse' + BadRequest: + description: | + Bad request (e.g. missing mandatory parameter). + content: + application/json: + schema: + oneOf: + - $ref: '#/components/schemas/VariantInterpretationResponse' + - $ref: '#/components/schemas/IndividualResponse' + - $ref: '#/components/schemas/BiosampleResponse' + - $ref: '#/components/schemas/GenomicVariantResponse' + - $ref: '#/components/schemas/CohortResponse' + - $ref: '#/components/schemas/RunResponse' + - $ref: '#/components/schemas/VariantInSampleResponse' + - $ref: '#/components/schemas/AnalysisResponse' + - $ref: '#/components/schemas/InteractorResponse' + Unauthorized: + description: | + Unauthorised (e.g. when an unauthenticated user tries to access a + protected resource). + content: + application/json: + schema: + oneOf: + - $ref: '#/components/schemas/VariantInterpretationResponse' + - $ref: '#/components/schemas/IndividualResponse' + - $ref: '#/components/schemas/BiosampleResponse' + - $ref: '#/components/schemas/GenomicVariantResponse' + - $ref: '#/components/schemas/CohortResponse' + - $ref: '#/components/schemas/RunResponse' + - $ref: '#/components/schemas/VariantInSampleResponse' + - $ref: '#/components/schemas/AnalysisResponse' + - $ref: '#/components/schemas/InteractorResponse' + Forbidden: + description: | + Forbidden (e.g. the resource is protected for all users or the user + is authenticated but they are not granted for this resource). + content: + application/json: + schema: + oneOf: + - $ref: '#/components/schemas/VariantInterpretationResponse' + - $ref: '#/components/schemas/IndividualResponse' + - $ref: '#/components/schemas/BiosampleResponse' + - $ref: '#/components/schemas/GenomicVariantResponse' + - $ref: '#/components/schemas/CohortResponse' + - $ref: '#/components/schemas/RunResponse' + - $ref: '#/components/schemas/VariantInSampleResponse' + - $ref: '#/components/schemas/AnalysisResponse' + - $ref: '#/components/schemas/InteractorResponse' schemas: Chromosome: description: | @@ -1994,47 +1355,51 @@ components: Format of the response. type: object properties: - Info: + info: type: string example: 'beacon-info-v2.0.0-draft.3' - Dataset: + dataset: type: string example: 'beacon-dataset-v2.0.0-draft.3' + filteringTerm: + type: string + example: + 'beacon-filtering-term-v2.0.0-draft.3' RequestedSchemas: description: | Format of the responses and version of the Beacon handling this request. type: object properties: - VariantIdentification: + variantIdentification: type: string example: ga4gh-variant-representation-v0.1 - VariantAnnotation: + variantAnnotation: type: string example: beacon-variant-annotation-draft-2 - Individual: + individual: type: string example: ga4gh-phenopacket-individual-v0.1 - Biosample: + biosample: type: string example: ga4gh-schemablocks-biosample-v0.1 - Run: + run: type: string example: beacon-run-draft-3 - Analysis: + analysis: type: string example: beacon-analysis-draft-2 - VariantInSample: + variantInSample: type: string example: beacon-variant-in-sample-draft-3 - VariantInterpretation: + variantInterpretation: type: string example: beacon-variant-interpretation-draft-2 - Interactor: + interactor: type: string example: beacon-interactor-draft-2 - Cohort: + cohort: type: string example: beacon-cohort-draft-3 InfoRequestMeta: @@ -2090,19 +1455,19 @@ components: description: | Variant description using either the default or an alternative schema. type: object - oneOf: + anyOf: - $ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/draft.3/default_variant_identification_schema.yaml#/components/schemas/VariantIdentification' - $ref: '#/components/schemas/AlternativeSchema' VariantAnnotation: description: | Default schema for variant annotation type: object - oneOf: + anyOf: - $ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/draft.3/default_variant_annotations_schema.yaml#/components/schemas/VariantAnnotation' - $ref: '#/components/schemas/AlternativeSchema' - VariantReponseResults: + VariantResponseResults: description: | - Description pending + TBD properties: variant: $ref: '#/components/schemas/Variant' @@ -2126,8 +1491,8 @@ components: description: | Number of pages to skip. type: integer - minimum: 1 - default: 1 + minimum: 0 + default: 0 example: 1 limit: description: | @@ -2171,7 +1536,7 @@ components: $ref: '#/components/schemas/RequestQuery' RequestQuery: description: | - Description pending + TBD type: object properties: individual: @@ -2280,6 +1645,28 @@ components: Either `alternateBases` or `variantType` is required, with the exception of range queries (single `start` and `end` parameters). type: string + variantMinLength: + description: > + Minimum length in bases of a genomic variant. This is an optional + parameter without prescribed use. While a length is commonly available + for structural variants such as copy number variations, it is + recommended that length based queries should also be supported for + variants with indicated referenceBases and alternateBases, to enable + length-specific wildcard queries. + type: integer + format: int64 + minimum: 0 + variantMaxLength: + description: > + Maximum length in bases of a genomic variant. This is an optional + parameter without prescribed use. While a length is commonly available + for structural variants such as copy number variations, it is + recommended that length based queries should also be supported for + variants with indicated referenceBases and alternateBases, to enable + length-specific wildcard queries. + type: integer + format: int64 + minimum: 1 mateName: $ref: '#/components/schemas/Chromosome' IndividualFields: @@ -2403,7 +1790,7 @@ components: $ref: '#/components/schemas/RequestedSchemas' InfoResponseMeta: description: | - Meta information about the reponse. + Meta information about the response. type: object properties: beaconId: @@ -2452,7 +1839,7 @@ components: GenomicVariantResponseContent: description: | - Description pending + TBD type: object required: - exists @@ -2472,7 +1859,7 @@ components: results: type: array items: - $ref: '#/components/schemas/VariantReponseResults' + $ref: '#/components/schemas/VariantResponseResults' info: type: object resultsHandover: @@ -2486,7 +1873,7 @@ components: # IndividualRequest: # description: | - # Description pending + # TBD # type: object # required: # - meta @@ -2510,7 +1897,7 @@ components: $ref: '#/components/schemas/IndividualResponseContent' IndividualResponseContent: description: | - Description pending + TBD type: object required: - exists @@ -2542,13 +1929,13 @@ components: description: | Default schema for describing invididuals. type: object - oneOf: + anyOf: - $ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/draft.3/default_individual_schema.yaml#/components/schemas/Individual' - $ref: '#/components/schemas/AlternativeSchema' # BiosampleRequest: # description: | - # Description pending + # TBD # type: object # required: # - meta @@ -2572,7 +1959,7 @@ components: $ref: '#/components/schemas/BiosampleResponseContent' BiosampleResponseContent: description: | - Description pending + TBD type: object required: - exists @@ -2607,7 +1994,7 @@ components: description: | Default schema for describing biosamples. type: object - oneOf: + anyOf: - $ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/draft.3/default_biosample_schema.yaml#/components/schemas/Biosample' - $ref: '#/components/schemas/AlternativeSchema' @@ -2625,7 +2012,7 @@ components: $ref: '#/components/schemas/RunResponseContent' RunResponseContent: description: | - Description pending + TBD type: object required: - exists @@ -2660,7 +2047,7 @@ components: description: | Default schema for describing runs. type: object - oneOf: + anyOf: - $ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/draft.3/default_run_schema.yaml#/components/schemas/Run' - $ref: '#/components/schemas/AlternativeSchema' @@ -2678,7 +2065,7 @@ components: $ref: '#/components/schemas/AnalysisResponseContent' AnalysisResponseContent: description: | - TODO + TBD type: object required: - exists @@ -2713,7 +2100,7 @@ components: description: | Default schema for describing runs. type: object - oneOf: + anyOf: - $ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/draft.3/default_analysis_schema.yaml#/components/schemas/Analysis' - $ref: '#/components/schemas/AlternativeSchema' @@ -2731,7 +2118,7 @@ components: $ref: '#/components/schemas/VariantInSampleResponseContent' VariantInSampleResponseContent: description: | - TODO + TBD type: object required: - exists @@ -2766,7 +2153,7 @@ components: description: | Default schema for describing runs. type: object - oneOf: + anyOf: - $ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/draft.3/default_variant_in_sample_schema.yaml#/components/schemas/VariantInSample' - $ref: '#/components/schemas/AlternativeSchema' @@ -2784,7 +2171,7 @@ components: $ref: '#/components/schemas/VariantInterpretationResponseContent' VariantInterpretationResponseContent: description: | - TODO + TBD type: object required: - exists @@ -2819,7 +2206,7 @@ components: description: | Default schema for describing runs. type: object - oneOf: + anyOf: - $ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/draft.3/default_variant_interpretation_schema.yaml#/components/schemas/VariantInterpretation' - $ref: '#/components/schemas/AlternativeSchema' @@ -2837,7 +2224,7 @@ components: $ref: '#/components/schemas/InteractorResponseContent' InteractorResponseContent: description: | - TODO + TBD type: object required: - exists @@ -2872,7 +2259,7 @@ components: description: | Default schema for describing runs. type: object - oneOf: + anyOf: - $ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/draft.3/default_interactor_schema.yaml#/components/schemas/Interactor' - $ref: '#/components/schemas/AlternativeSchema' @@ -2890,7 +2277,7 @@ components: $ref: '#/components/schemas/CohortResponseContent' CohortResponseContent: description: | - TODO + TBD type: object required: - exists @@ -2925,13 +2312,18 @@ components: description: | Default schema for describing runs. type: object - oneOf: + anyOf: - $ref: 'https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/draft.3/default_cohort_schema.yaml#/components/schemas/Cohort' - $ref: '#/components/schemas/AlternativeSchema' InfoResponse: description: | - Response of a query over Beacon info. Use `InfoResponseContent` when querying the Beacon info endpoints, and `DatasetResponseContent` when querying the datasets endpoint. + Response of a query over Beacon info. + + Use `InfoResponseContent` when querying the Beacon info endpoints, + `DatasetResponseContent` when querying the datasets endpoint, and + `FilteringTermResponseContent` when querying the filtering terms + endpoint. type: object required: - meta @@ -2943,9 +2335,10 @@ components: oneOf: - $ref: '#/components/schemas/InfoResponseContent' - $ref: '#/components/schemas/DatasetResponseContent' + - $ref: '#/components/schemas/FilteringTermResponseContent' InfoResponseContent: description: | - Description pending + TBD type: object required: - results @@ -2962,23 +2355,26 @@ components: description: | Default schema for describing Beacon info. type: object - oneOf: + anyOf: - $ref: '#/components/schemas/BeaconInfo' - $ref: '#/components/schemas/AlternativeSchema' DatasetResponseContent: description: | - Description pending + TBD type: object required: - results properties: error: $ref: '#/components/schemas/BeaconError' + numTotalResults: + type: integer + minimum: 0 results: type: array items: - $ref: '#/components/schemas/BeaconDataset' #'#/components/schemas/DatasetResponseResults' + $ref: '#/components/schemas/BeaconDataset' info: type: object @@ -3197,7 +2593,7 @@ components: datasetId: type: string description: | - not provided + `id` of the dataset. exists: description: >- Indicator of whether the given allele was observed in the dataset. @@ -3270,9 +2666,6 @@ components: type: string DataUseConditions: type: object - required: - - consentCodeDataUse - - adamDataUse description: | Data use conditions ruling this dataset. properties: @@ -3282,6 +2675,10 @@ components: adamDataUse: $ref: >- https://raw.githubusercontent.com/ga4gh/ADA-M/v1.0.1/adam.yaml#/components/schemas/Adam + duoDataUse: + type: array + items: + $ref: '#/components/schemas/DUODataUse' Handover: type: object required: @@ -3349,6 +2746,8 @@ components: type: array items: $ref: '#/components/schemas/FilteringTerm' + info: + type: object FilteringTerm: type: object description: | @@ -3403,3 +2802,28 @@ components: description: The full Internationalized Resource Identifier (IRI) prefix type: string example: http://purl.obolibrary.org/obo/HP_ + DUODataUse: + allOf: + - description: | + TBD + - $ref: '#/components/schemas/OntologyResource' + - type: object + required: + - id + - version + properties: + version: + type: string + example: '17-07-2016' + modifiers: + type: array + items: + allOf: + - $ref: '#/components/schemas/OntologyResource' + - example: + - id: 'EFO:0001645' + - id: 'EFO:0001655' + - example: + - id: 'DUO:0000007' + - label: 'disease specific research' + - version: '17-07-2016'