diff --git a/bin/yamlerRunner.sh b/bin/yamlerRunner.sh index a7821edf..f6c16395 100755 --- a/bin/yamlerRunner.sh +++ b/bin/yamlerRunner.sh @@ -1,28 +1,13 @@ BASEDIR=$(dirname $0) UNITYPATH=$BASEDIR/.. - -# initial conversion from separate schemas -# DEPRECATED -# BEACONMODELPATH=$BASEDIR/../../beacon-v2-Models/BEACON-V2-Model -# BEACONFRAMEWORKPATH=$BASEDIR/../../beacon-framework-v2 - BEACONMODELNAME=beacon-v2-default-model -# for UPSTREAM in $BEACONMODELPATH $BEACONFRAMEWORKPATH -# do -# echo "pulling $UPSTREAM" -# git -C $UPSTREAM pull -# done - for KIND in src json do mkdir -p $UNITYPATH/models/$KIND/$BEACONMODELNAME mkdir -p $UNITYPATH/framework/$KIND done -# $BASEDIR/beaconYamler.py -i $BEACONMODELPATH -t json -x yaml -o $UNITYPATH/models/src/$BEACONMODELNAME -# $BASEDIR/beaconYamler.py -i $BEACONFRAMEWORKPATH -t json -x yaml -o $UNITYPATH/framework/src - # recurring conversion from the source files to the exported versions $BASEDIR/beaconYamler.py -i $UNITYPATH/models/src/$BEACONMODELNAME -t yaml -x json -o $UNITYPATH/models/json/$BEACONMODELNAME $BASEDIR/beaconYamler.py -i $UNITYPATH/framework/src -t yaml -x json -o $UNITYPATH/framework/json diff --git a/models/json/beacon-v2-default-model/analyses/endpoints.json b/models/json/beacon-v2-default-model/analyses/endpoints.json index 165a5e9b..ec8fe9d8 100644 --- a/models/json/beacon-v2-default-model/analyses/endpoints.json +++ b/models/json/beacon-v2-default-model/analyses/endpoints.json @@ -91,7 +91,7 @@ "paths": { "/analyses": { "get": { - "description": "Get a list of bioinformatics analysis", + "description": "Get a Beacon response for bioinformatics analyses", "operationId": "getAnalyses", "parameters": [ { @@ -123,7 +123,7 @@ ] }, "post": { - "description": "Get a list of bioinformatics analysis", + "description": "Get a Beacon response for bioinformatics analyses", "operationId": "postAnalysesRequest", "requestBody": { "content": { @@ -207,8 +207,8 @@ }, "/analyses/{id}/g_variants": { "get": { - "description": "Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id'", - "operationId": "getOneAnalysisVariants", + "description": "Get a *genomic variations* response for one bioinformatics analysis, identified by its (unique) 'id'", + "operationId": "getOneAnalysisVariationsRequest", "parameters": [ { "$ref": "#/components/parameters/requestedSchema" @@ -239,8 +239,8 @@ } ], "post": { - "description": "Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id'", - "operationId": "postOneAnalysisVariantsRequest", + "description": "Get a *genomic variations* response for one bioinformatics analysis, identified by its (unique) 'id'", + "operationId": "postOneAnalysisVariationsRequest", "requestBody": { "content": { "application/json": { diff --git a/models/json/beacon-v2-default-model/biosamples/endpoints.json b/models/json/beacon-v2-default-model/biosamples/endpoints.json index 20f297fe..56968b13 100644 --- a/models/json/beacon-v2-default-model/biosamples/endpoints.json +++ b/models/json/beacon-v2-default-model/biosamples/endpoints.json @@ -95,7 +95,7 @@ "paths": { "/biosamples": { "get": { - "description": "Get a list of biosamples", + "description": "Get a Beacon response for biosamples", "operationId": "getBiosamples", "parameters": [ { @@ -127,7 +127,7 @@ ] }, "post": { - "description": "Get a list of biosamples", + "description": "Get a Beacon response for biosamples", "operationId": "postBiosamplesRequest", "requestBody": { "content": { @@ -204,8 +204,8 @@ }, "/biosamples/{id}/analyses": { "get": { - "description": "Get the analysis list from one biosample, identified by its (unique) 'id'", - "operationId": "getOneBiosampleAnalysis", + "description": "Get an *analyses* response from one biosample, identified by its (unique) 'id'", + "operationId": "getOneBiosampleAnalyses", "parameters": [ { "$ref": "#/components/parameters/requestedSchema" @@ -236,8 +236,8 @@ } ], "post": { - "description": "Get the analysis list from one biosample, identified by its (unique) 'id'", - "operationId": "postOneBiosampleAnalysis", + "description": "Get an *analyses* response from one biosample, identified by its (unique) 'id'", + "operationId": "postOneBiosampleAnalyses", "requestBody": { "content": { "application/json": { @@ -264,8 +264,8 @@ }, "/biosamples/{id}/g_variants": { "get": { - "description": "Get the genomic variants list from one biosample, identified by its (unique) 'id'", - "operationId": "getOneBiosampleGenomicVariants", + "description": "Get a *genomic variations* response from one biosample, identified by its (unique) 'id'", + "operationId": "getOneBiosampleGenomicVariations", "parameters": [ { "$ref": "#/components/parameters/requestedSchema" @@ -296,8 +296,8 @@ } ], "post": { - "description": "Get the genomic variants list from one biosample, identified by its (unique) 'id'", - "operationId": "postOneBiosampleGenomicVariants", + "description": "Get a *genomic variations* response from one biosample, identified by its (unique) 'id'", + "operationId": "postOneBiosampleGenomicVariations", "requestBody": { "content": { "application/json": { @@ -324,7 +324,7 @@ }, "/biosamples/{id}/runs": { "get": { - "description": "Get the runs list from one biosample, identified by its (unique) 'id'", + "description": "Get a *runs* response from one biosample, identified by its (unique) 'id'", "operationId": "getOneBiosampleRuns", "parameters": [ { @@ -363,7 +363,7 @@ } ], "post": { - "description": "Get the runs list from one biosample, identified by its (unique) 'id'", + "description": "Get a *runs* response from one biosample, identified by its (unique) 'id'", "operationId": "postOneBiosampleRuns", "requestBody": { "content": { diff --git a/models/json/beacon-v2-default-model/cohorts/endpoints.json b/models/json/beacon-v2-default-model/cohorts/endpoints.json index b56550bc..7908ea74 100644 --- a/models/json/beacon-v2-default-model/cohorts/endpoints.json +++ b/models/json/beacon-v2-default-model/cohorts/endpoints.json @@ -108,7 +108,7 @@ "paths": { "/cohorts": { "get": { - "description": "Get a list of cohorts", + "description": "Get a Beacon *cohorts* response", "operationId": "getCohorts", "parameters": [ { @@ -137,7 +137,7 @@ ] }, "post": { - "description": "Get a list of cohorts", + "description": "Get a Beacon *cohorts* response", "operationId": "postCohortsRequest", "requestBody": { "content": { @@ -219,7 +219,7 @@ }, "/cohorts/{id}/filtering_terms": { "get": { - "description": "Get the list of filtering terms that could be used with a given cohort, identified by its (unique) 'id'", + "description": "Get a response about the *filtering terms* that could be used with a given cohort, identified by its (unique) 'id'", "operationId": "getOneCohortFilteringTerms", "parameters": [ { @@ -255,7 +255,7 @@ } ], "post": { - "description": "Get the list of filtering terms that could be used with a given cohort, identified by its (unique) 'id'", + "description": "Get a response about the *filtering terms* that could be used with a given cohort, identified by its (unique) 'id'", "operationId": "postOneCohortFilteringTerms", "requestBody": { "content": { @@ -290,7 +290,7 @@ }, "/cohorts/{id}/individuals": { "get": { - "description": "Get the individuals from one cohort, identified by its (unique) 'id'", + "description": "Get an *individuals* response for one cohort, identified by its (unique) 'id'", "operationId": "getOneCohortIndividuals", "parameters": [ { @@ -322,7 +322,7 @@ } ], "post": { - "description": "Get the individuals from one cohort, identified by its (unique) 'id'", + "description": "Get an *individuals* response for one cohort, identified by its (unique) 'id'", "operationId": "postOneCohortEntries", "requestBody": { "content": { diff --git a/models/json/beacon-v2-default-model/datasets/endpoints.json b/models/json/beacon-v2-default-model/datasets/endpoints.json index 53831fff..29994ad6 100644 --- a/models/json/beacon-v2-default-model/datasets/endpoints.json +++ b/models/json/beacon-v2-default-model/datasets/endpoints.json @@ -135,7 +135,7 @@ ] }, "post": { - "description": "Get a list of datasets", + "description": "Get a Beacon *datasets* response", "operationId": "postDatasetsRequest", "requestBody": { "content": { @@ -217,7 +217,7 @@ }, "/datasets/{id}/biosamples": { "get": { - "description": "Get the biosamples list from one dataset, identified by its (unique) 'id'", + "description": "Get a *biosamples* response for one dataset, identified by its (unique) 'id'", "operationId": "getOneDatasetBiosamples", "parameters": [ { @@ -249,7 +249,7 @@ } ], "post": { - "description": "Get the biosamples list from one dataset, identified by its (unique) 'id'", + "description": "Get a *biosamples* response for one dataset, identified by its (unique) 'id'", "operationId": "postOneDatasetBiosamples", "requestBody": { "content": { @@ -277,7 +277,7 @@ }, "/datasets/{id}/filtering_terms": { "get": { - "description": "Get the list of filtering terms that could be used with a given dataset, identified by its (unique) 'id'", + "description": "Get a response about the *filtering terms* that could be used with a given dataset, identified by its (unique) 'id'", "operationId": "getOneDatasetFilteringTerms", "parameters": [ { @@ -313,7 +313,7 @@ } ], "post": { - "description": "Get the list of filtering terms that could be used with a given dataset, identified by its (unique) 'id'", + "description": "Get a response about the *filtering terms* that could be used with a given dataset, identified by its (unique) 'id'", "operationId": "postOneDatasetFilteringTerms", "requestBody": { "content": { @@ -348,7 +348,7 @@ }, "/datasets/{id}/g_variants": { "get": { - "description": "Get the genomic variants list from one dataset, identified by its (unique) 'id'", + "description": "Get a *genomic variations* response for one dataset, identified by its (unique) 'id'", "operationId": "getOneDatasetEntries", "parameters": [ { @@ -380,7 +380,7 @@ } ], "post": { - "description": "Get the genomic variants list from one dataset, identified by its (unique) 'id'", + "description": "Get a *genomic variations* response for one dataset, identified by its (unique) 'id'", "operationId": "postOneDatasetEntries", "requestBody": { "content": { @@ -408,7 +408,7 @@ }, "/datasets/{id}/individuals": { "get": { - "description": "Get the individuals list from one dataset, identified by its (unique) 'id'", + "description": "Get an *individuals* response for one dataset, identified by its (unique) 'id'", "operationId": "getOneDatasetIndividuals", "parameters": [ { @@ -440,7 +440,7 @@ } ], "post": { - "description": "Get the biosamples list from one dataset, identified by its (unique) 'id'", + "description": "Get an *individuals* response for one dataset, identified by its (unique) 'id'", "operationId": "postOneDatasetIndividuals", "requestBody": { "content": { diff --git a/models/json/beacon-v2-default-model/genomicVariations/endpoints.json b/models/json/beacon-v2-default-model/genomicVariations/endpoints.json index 2d29ed7b..362d4a44 100644 --- a/models/json/beacon-v2-default-model/genomicVariations/endpoints.json +++ b/models/json/beacon-v2-default-model/genomicVariations/endpoints.json @@ -193,8 +193,8 @@ "paths": { "/g_variants": { "get": { - "description": "Get a list of example entries", - "operationId": "getExampleEntries", + "description": "Get a Beacon response for genomic variations", + "operationId": "getGenomicVariations", "parameters": [ { "$ref": "#/components/parameters/requestedSchema" @@ -258,8 +258,8 @@ ] }, "post": { - "description": "Get a list of example entries", - "operationId": "postExampleEntriesRequest", + "description": "Get a Beacon response for genomic variations", + "operationId": "postGenomicVariationsRequest", "requestBody": { "content": { "application/json": { @@ -335,8 +335,8 @@ }, "/g_variants/{id}/biosamples": { "get": { - "description": "Get the biosamples list from one genomic variant, identified by its (unique) 'id'", - "operationId": "getOneGenomicVariantBiosamples", + "description": "Get a *biosamples* response from one genomic variant, identified by its (unique) 'id'", + "operationId": "getOneGenomicVariationBiosamples", "parameters": [ { "$ref": "#/components/parameters/requestedSchema" @@ -367,8 +367,8 @@ } ], "post": { - "description": "Get the biosamples list from one genomic variant, identified by its (unique) 'id'", - "operationId": "postOneGenomicVariantBiosamples", + "description": "Get a *biosamples* response from one genomic variant, identified by its (unique) 'id'", + "operationId": "postOneGenomicVariationBiosamples", "requestBody": { "content": { "application/json": { @@ -395,8 +395,8 @@ }, "/g_variants/{id}/individuals": { "get": { - "description": "Get the individuals list from one genomic variant, identified by its (unique) 'id'", - "operationId": "getOneGenomicVariantIndividuals", + "description": "Get an *individuals* response from one genomic variant, identified by its (unique) 'id'", + "operationId": "getOneGenomicVariationIndividuals", "parameters": [ { "$ref": "#/components/parameters/requestedSchema" @@ -427,8 +427,8 @@ } ], "post": { - "description": "Get the biosamples list from one genomic variant, identified by its (unique) 'id'", - "operationId": "postOneGenomicVariantIndividuals", + "description": "Get an *individuals* response from one genomic variant, identified by its (unique) 'id'", + "operationId": "postOneGenomicVariationIndividuals", "requestBody": { "content": { "application/json": { diff --git a/models/json/beacon-v2-default-model/individuals/endpoints.json b/models/json/beacon-v2-default-model/individuals/endpoints.json index 81970991..cd7d307c 100644 --- a/models/json/beacon-v2-default-model/individuals/endpoints.json +++ b/models/json/beacon-v2-default-model/individuals/endpoints.json @@ -123,7 +123,7 @@ ] }, "post": { - "description": "Get a list of example entries", + "description": "Get a Beacon response for individuals", "operationId": "postIndividualsRequest", "requestBody": { "content": { @@ -238,7 +238,7 @@ } ], "post": { - "description": "Get details about one Individual, identified by its (unique) 'id'", + "description": "Get details about one individual, identified by its (unique) 'id'", "operationId": "postOneIndividual", "requestBody": { "content": { @@ -266,7 +266,7 @@ }, "/individuals/{id}/biosamples": { "get": { - "description": "Get the biosamples list from one individual, identified by its (unique) 'id'", + "description": "Get a *biosamples* response for one individual, identified by its (unique) 'id'", "operationId": "getOneIndividualBiosamples", "parameters": [ { @@ -298,7 +298,7 @@ } ], "post": { - "description": "Get the biosamples list from one individual, identified by its (unique) 'id'", + "description": "Get a *biosamples* response for one individual, identified by its (unique) 'id'", "operationId": "postOneIndividualBiosamples", "requestBody": { "content": { @@ -326,7 +326,7 @@ }, "/individuals/{id}/g_variants": { "get": { - "description": "Get the genomic variants list from one individual, identified by its (unique) 'id'", + "description": "Get a *genomic variations* response for one individual, identified by its (unique) 'id'", "operationId": "getOneIndividualGenomicVariants", "parameters": [ { @@ -358,7 +358,7 @@ } ], "post": { - "description": "Get the genomic variants list from one individual, identified by its (unique) 'id'", + "description": "Get a *genomic variations* response for one individual, identified by its (unique) 'id'", "operationId": "potOneIndividualGenomicVariants", "requestBody": { "content": { diff --git a/models/json/beacon-v2-default-model/runs/endpoints.json b/models/json/beacon-v2-default-model/runs/endpoints.json index c76e63cd..70ade3bc 100644 --- a/models/json/beacon-v2-default-model/runs/endpoints.json +++ b/models/json/beacon-v2-default-model/runs/endpoints.json @@ -107,7 +107,7 @@ "paths": { "/runs": { "get": { - "description": "Get a list of sequencing runs", + "description": "Get a Beacon response for experimental runs", "operationId": "getRuns", "parameters": [ { @@ -139,7 +139,7 @@ ] }, "post": { - "description": "Get a list of sequencing runs", + "description": "Get a Beacon response for experimental runs", "operationId": "postRunsRequest", "requestBody": { "content": { @@ -167,7 +167,7 @@ }, "/runs/{id}": { "get": { - "description": "Get details about one sequencing run, identified by its (unique) 'id'", + "description": "Get details about one experimental run, identified by its (unique) 'id'", "operationId": "getOneRun", "responses": { "200": { @@ -188,7 +188,7 @@ } ], "post": { - "description": "Get details about one Run, identified by its (unique) 'id'", + "description": "Get details about one experimental run, identified by its (unique) 'id'", "operationId": "postOneRun", "requestBody": { "content": { @@ -216,7 +216,7 @@ }, "/runs/{id}/analyses": { "get": { - "description": "Get the analysis list from one sequencing run, identified by its (unique) 'id'", + "description": "Get a *analyses* response for one experimental run, identified by its (unique) 'id'", "operationId": "getOneRunAnalysis", "parameters": [ { @@ -248,7 +248,7 @@ } ], "post": { - "description": "Get the analysis list from one sequencing run, identified by its (unique) 'id'", + "description": "Get a *analyses* response for one experimental run, identified by its (unique) 'id'", "operationId": "postOneRunAnalysis", "requestBody": { "content": { @@ -276,8 +276,8 @@ }, "/runs/{id}/g_variants": { "get": { - "description": "Get the genomic variants list from one run, identified by its (unique) 'id'", - "operationId": "getOneRunGenomicVariants", + "description": "Get a *genomic variations* response for one experimental run, identified by its (unique) 'id'", + "operationId": "getOneRunGenomicVariations", "parameters": [ { "$ref": "#/components/parameters/requestedSchema" @@ -308,8 +308,8 @@ } ], "post": { - "description": "Get the genomic variants list from one run, identified by its (unique) 'id'", - "operationId": "potOneRunGenomicVariants", + "description": "Get a *genomic variations* response for one experimental run, identified by its (unique) 'id'", + "operationId": "potOneRunGenomicVariations", "requestBody": { "content": { "application/json": { diff --git a/models/src/beacon-v2-default-model/analyses/endpoints.yaml b/models/src/beacon-v2-default-model/analyses/endpoints.yaml index 25199079..fed2b166 100644 --- a/models/src/beacon-v2-default-model/analyses/endpoints.yaml +++ b/models/src/beacon-v2-default-model/analyses/endpoints.yaml @@ -18,7 +18,7 @@ paths: - $ref: '#/components/parameters/limit' - $ref: '#/components/parameters/includeResultsetResponses' - $ref: '#/components/parameters/filters' - description: Get a list of bioinformatics analysis + description: Get a Beacon response for bioinformatics analyses operationId: getAnalyses tags: - GET Endpoints @@ -28,7 +28,7 @@ paths: default: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: - description: Get a list of bioinformatics analysis + description: Get a Beacon response for bioinformatics analyses operationId: postAnalysesRequest tags: - POST Endpoints @@ -52,7 +52,8 @@ paths: parameters: - $ref: '#/components/parameters/entryId' get: - description: Get details about one bioinformatics analysis, identified by its + description: >- + Get details about one bioinformatics analysis, identified by its (unique) 'id' operationId: getOneAnalysis tags: @@ -64,7 +65,8 @@ paths: description: An unsuccessful operation $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 + description: >- + Get details about one bioinformatics analysis, identified by its (unique) 'id' operationId: postOneAnalysisRequest tags: @@ -89,9 +91,10 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the list of variants instances for one bioinformatics analysis, + description: >- + Get a *genomic variations* response for one bioinformatics analysis, identified by its (unique) 'id' - operationId: getOneAnalysisVariants + operationId: getOneAnalysisVariationsRequest tags: - GET Endpoints responses: @@ -101,9 +104,10 @@ paths: description: An unsuccessful operation $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, + description: >- + Get a *genomic variations* response for one bioinformatics analysis, identified by its (unique) 'id' - operationId: postOneAnalysisVariantsRequest + operationId: postOneAnalysisVariationsRequest tags: - POST Endpoints requestBody: diff --git a/models/src/beacon-v2-default-model/biosamples/endpoints.yaml b/models/src/beacon-v2-default-model/biosamples/endpoints.yaml index 8959192a..8595c173 100644 --- a/models/src/beacon-v2-default-model/biosamples/endpoints.yaml +++ b/models/src/beacon-v2-default-model/biosamples/endpoints.yaml @@ -18,7 +18,7 @@ paths: - $ref: '#/components/parameters/limit' - $ref: '#/components/parameters/includeResultsetResponses' - $ref: '#/components/parameters/filters' - description: Get a list of biosamples + description: Get a Beacon response for biosamples operationId: getBiosamples tags: - GET Endpoints @@ -28,7 +28,7 @@ paths: default: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: - description: Get a list of biosamples + description: Get a Beacon response for biosamples operationId: postBiosamplesRequest tags: - POST Endpoints @@ -48,7 +48,8 @@ paths: parameters: - $ref: '#/components/parameters/entryId' get: - description: Get details about one biosample, identified by its (unique) 'id' + description: >- + Get details about one biosample, identified by its (unique) 'id' operationId: getOneBiosample tags: - GET Endpoints @@ -59,7 +60,8 @@ paths: description: An unsuccessful operation $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' + description: >- + Get details about one Biosample, identified by its (unique) 'id' operationId: postOneBiosample tags: - POST Endpoints @@ -83,9 +85,10 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the genomic variants list from one biosample, identified by + description: >- + Get a *genomic variations* response from one biosample, identified by its (unique) 'id' - operationId: getOneBiosampleGenomicVariants + operationId: getOneBiosampleGenomicVariations tags: - GET Endpoints responses: @@ -95,9 +98,10 @@ paths: description: An unsuccessful operation $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 + description: >- + Get a *genomic variations* response from one biosample, identified by its (unique) 'id' - operationId: postOneBiosampleGenomicVariants + operationId: postOneBiosampleGenomicVariations tags: - POST Endpoints requestBody: @@ -120,9 +124,10 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the analysis list from one biosample, identified by its (unique) - 'id' - operationId: getOneBiosampleAnalysis + description: >- + Get an *analyses* response from one biosample, identified by its + (unique) 'id' + operationId: getOneBiosampleAnalyses tags: - GET Endpoints responses: @@ -132,9 +137,10 @@ paths: description: An unsuccessful operation $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' - operationId: postOneBiosampleAnalysis + description: >- + Get an *analyses* response from one biosample, identified by its + (unique) 'id' + operationId: postOneBiosampleAnalyses tags: - POST Endpoints requestBody: @@ -157,8 +163,8 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the runs list from one biosample, identified by its (unique) - 'id' + description: >- + Get a *runs* response from one biosample, identified by its (unique) 'id' operationId: getOneBiosampleRuns tags: - GET Endpoints @@ -173,8 +179,8 @@ paths: description: An unsuccessful operation $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' + description: >- + Get a *runs* response from one biosample, identified by its (unique) 'id' operationId: postOneBiosampleRuns tags: - POST Endpoints diff --git a/models/src/beacon-v2-default-model/cohorts/endpoints.yaml b/models/src/beacon-v2-default-model/cohorts/endpoints.yaml index ec525f0a..b9585b70 100644 --- a/models/src/beacon-v2-default-model/cohorts/endpoints.yaml +++ b/models/src/beacon-v2-default-model/cohorts/endpoints.yaml @@ -22,7 +22,7 @@ paths: - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - $ref: '#/components/parameters/filters' - description: Get a list of cohorts + description: Get a Beacon *cohorts* response operationId: getCohorts tags: - GET Endpoints @@ -32,7 +32,7 @@ paths: default: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: - description: Get a list of cohorts + description: Get a Beacon *cohorts* response operationId: postCohortsRequest tags: - POST Endpoints @@ -89,7 +89,8 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the individuals from one cohort, identified by its (unique) + description: >- + Get an *individuals* response for one cohort, identified by its (unique) 'id' operationId: getOneCohortIndividuals tags: @@ -101,7 +102,8 @@ paths: description: An unsuccessful operation $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) + description: >- + Get an *individuals* response for one cohort, identified by its (unique) 'id' operationId: postOneCohortEntries tags: @@ -125,8 +127,9 @@ paths: parameters: - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the list of filtering terms that could be used with a given - cohort, identified by its (unique) 'id' + description: >- + Get a response about the *filtering terms* that could be used with a + given cohort, identified by its (unique) 'id' operationId: getOneCohortFilteringTerms tags: - GET Endpoints @@ -141,8 +144,9 @@ paths: description: An unsuccessful operation $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' + description: >- + Get a response about the *filtering terms* that could be used with a + given cohort, identified by its (unique) 'id' operationId: postOneCohortFilteringTerms tags: - POST Endpoints diff --git a/models/src/beacon-v2-default-model/datasets/endpoints.yaml b/models/src/beacon-v2-default-model/datasets/endpoints.yaml index cf1d47fd..320f0cd6 100644 --- a/models/src/beacon-v2-default-model/datasets/endpoints.yaml +++ b/models/src/beacon-v2-default-model/datasets/endpoints.yaml @@ -32,7 +32,7 @@ paths: default: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: - description: Get a list of datasets + description: Get a Beacon *datasets* response operationId: postDatasetsRequest tags: - POST Endpoints @@ -89,7 +89,8 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the genomic variants list from one dataset, identified by its + description: >- + Get a *genomic variations* response for one dataset, identified by its (unique) 'id' operationId: getOneDatasetEntries tags: @@ -101,7 +102,8 @@ paths: description: An unsuccessful operation $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 + description: >- + Get a *genomic variations* response for one dataset, identified by its (unique) 'id' operationId: postOneDatasetEntries tags: @@ -126,7 +128,8 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the biosamples list from one dataset, identified by its (unique) + description: >- + Get a *biosamples* response for one dataset, identified by its (unique) 'id' operationId: getOneDatasetBiosamples tags: @@ -138,7 +141,8 @@ paths: description: An unsuccessful operation $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) + description: >- + Get a *biosamples* response for one dataset, identified by its (unique) 'id' operationId: postOneDatasetBiosamples tags: @@ -163,7 +167,8 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the individuals list from one dataset, identified by its (unique) + description: >- + Get an *individuals* response for one dataset, identified by its (unique) 'id' operationId: getOneDatasetIndividuals tags: @@ -175,7 +180,8 @@ paths: description: An unsuccessful operation $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) + description: >- + Get an *individuals* response for one dataset, identified by its (unique) 'id' operationId: postOneDatasetIndividuals tags: @@ -199,8 +205,9 @@ paths: parameters: - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the list of filtering terms that could be used with a given - dataset, identified by its (unique) 'id' + description: >- + Get a response about the *filtering terms* that could be used with a + given dataset, identified by its (unique) 'id' operationId: getOneDatasetFilteringTerms tags: - GET Endpoints @@ -215,8 +222,9 @@ paths: description: An unsuccessful operation $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' + description: >- + Get a response about the *filtering terms* that could be used with a + given dataset, identified by its (unique) 'id' operationId: postOneDatasetFilteringTerms tags: - POST Endpoints diff --git a/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml b/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml index 4c9bbdae..3f4397d3 100644 --- a/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml +++ b/models/src/beacon-v2-default-model/genomicVariations/endpoints.yaml @@ -29,8 +29,8 @@ paths: - $ref: '#/components/parameters/geneId' - $ref: '#/components/parameters/aminoacidChange' - $ref: '#/components/parameters/filters' - description: Get a list of example entries - operationId: getExampleEntries + description: Get a Beacon response for genomic variations + operationId: getGenomicVariations tags: - GET Endpoints responses: @@ -39,8 +39,8 @@ paths: default: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: - description: Get a list of example entries - operationId: postExampleEntriesRequest + description: Get a Beacon response for genomic variations + operationId: postGenomicVariationsRequest tags: - POST Endpoints requestBody: @@ -59,8 +59,8 @@ paths: parameters: - $ref: '#/components/parameters/entryId' get: - description: Get details about one genomic variation, identified by its (unique) - 'id' + description: >- + Get details about one genomic variation, identified by its (unique) 'id' operationId: getOneGenomicVariation tags: - GET Endpoints @@ -71,8 +71,8 @@ paths: description: An unsuccessful operation $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' + description: >- + Get details about one genomic variation, identified by its (unique) 'id' operationId: postOneGenomicVariation tags: - POST Endpoints @@ -96,9 +96,10 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the biosamples list from one genomic variant, identified by - its (unique) 'id' - operationId: getOneGenomicVariantBiosamples + description: >- + Get a *biosamples* response from one genomic variant, identified by its + (unique) 'id' + operationId: getOneGenomicVariationBiosamples tags: - GET Endpoints responses: @@ -108,9 +109,10 @@ paths: description: An unsuccessful operation $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' - operationId: postOneGenomicVariantBiosamples + description: >- + Get a *biosamples* response from one genomic variant, identified by its + (unique) 'id' + operationId: postOneGenomicVariationBiosamples tags: - POST Endpoints requestBody: @@ -133,9 +135,10 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the individuals list from one genomic variant, identified by + description: >- + Get an *individuals* response from one genomic variant, identified by its (unique) 'id' - operationId: getOneGenomicVariantIndividuals + operationId: getOneGenomicVariationIndividuals tags: - GET Endpoints responses: @@ -145,9 +148,10 @@ paths: description: An unsuccessful operation $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 + description: >- + Get an *individuals* response from one genomic variant, identified by its (unique) 'id' - operationId: postOneGenomicVariantIndividuals + operationId: postOneGenomicVariationIndividuals tags: - POST Endpoints requestBody: diff --git a/models/src/beacon-v2-default-model/individuals/endpoints.yaml b/models/src/beacon-v2-default-model/individuals/endpoints.yaml index b220dd86..8adfaa77 100644 --- a/models/src/beacon-v2-default-model/individuals/endpoints.yaml +++ b/models/src/beacon-v2-default-model/individuals/endpoints.yaml @@ -28,7 +28,7 @@ paths: default: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: - description: Get a list of example entries + description: Get a Beacon response for individuals operationId: postIndividualsRequest tags: - POST Endpoints @@ -48,7 +48,8 @@ paths: parameters: - $ref: '#/components/parameters/entryId' get: - description: Get details about one individual, identified by its (unique) 'id' + description: >- + Get details about one individual, identified by its (unique) 'id' operationId: getOneIndividual tags: - GET Endpoints @@ -59,7 +60,8 @@ paths: description: An unsuccessful operation $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' + description: >- + Get details about one individual, identified by its (unique) 'id' operationId: postOneIndividual tags: - POST Endpoints @@ -83,7 +85,8 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the genomic variants list from one individual, identified by + description: >- + Get a *genomic variations* response for one individual, identified by its (unique) 'id' operationId: getOneIndividualGenomicVariants tags: @@ -95,7 +98,8 @@ paths: description: An unsuccessful operation $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 + description: >- + Get a *genomic variations* response for one individual, identified by its (unique) 'id' operationId: potOneIndividualGenomicVariants tags: @@ -120,7 +124,8 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the biosamples list from one individual, identified by its + description: >- + Get a *biosamples* response for one individual, identified by its (unique) 'id' operationId: getOneIndividualBiosamples tags: @@ -132,7 +137,8 @@ paths: description: An unsuccessful operation $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 + description: >- + Get a *biosamples* response for one individual, identified by its (unique) 'id' operationId: postOneIndividualBiosamples tags: diff --git a/models/src/beacon-v2-default-model/runs/endpoints.yaml b/models/src/beacon-v2-default-model/runs/endpoints.yaml index 1b360641..773f7bdd 100644 --- a/models/src/beacon-v2-default-model/runs/endpoints.yaml +++ b/models/src/beacon-v2-default-model/runs/endpoints.yaml @@ -18,7 +18,7 @@ paths: - $ref: '#/components/parameters/limit' - $ref: '#/components/parameters/includeResultsetResponses' - $ref: '#/components/parameters/filters' - description: Get a list of sequencing runs + description: Get a Beacon response for experimental runs operationId: getRuns tags: - GET Endpoints @@ -28,7 +28,7 @@ paths: default: $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json post: - description: Get a list of sequencing runs + description: Get a Beacon response for experimental runs operationId: postRunsRequest tags: - POST Endpoints @@ -48,8 +48,8 @@ paths: parameters: - $ref: '#/components/parameters/entryId' get: - description: Get details about one sequencing run, identified by its (unique) - 'id' + description: >- + Get details about one experimental run, identified by its (unique) 'id' operationId: getOneRun tags: - GET Endpoints @@ -60,7 +60,8 @@ paths: description: An unsuccessful operation $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' + description: >- + Get details about one experimental run, identified by its (unique) 'id' operationId: postOneRun tags: - POST Endpoints @@ -84,9 +85,10 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the genomic variants list from one run, identified by its (unique) - 'id' - operationId: getOneRunGenomicVariants + description: >- + Get a *genomic variations* response for one experimental run, identified + by its (unique) 'id' + operationId: getOneRunGenomicVariations tags: - GET Endpoints responses: @@ -96,9 +98,10 @@ paths: description: An unsuccessful operation $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' - operationId: potOneRunGenomicVariants + description: >- + Get a *genomic variations* response for one experimental run, identified + by its (unique) 'id' + operationId: potOneRunGenomicVariations tags: - POST Endpoints requestBody: @@ -121,7 +124,8 @@ paths: - $ref: '#/components/parameters/requestedSchema' - $ref: '#/components/parameters/skip' - $ref: '#/components/parameters/limit' - description: Get the analysis list from one sequencing run, identified by its + description: >- + Get a *analyses* response for one experimental run, identified by its (unique) 'id' operationId: getOneRunAnalysis tags: @@ -133,7 +137,8 @@ paths: description: An unsuccessful operation $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 + description: >- + Get a *analyses* response for one experimental run, identified by its (unique) 'id' operationId: postOneRunAnalysis tags: