From cfcc85d34df506f726c89f68c9fb367f945e265f Mon Sep 17 00:00:00 2001 From: Michael Baudis Date: Sat, 6 Jul 2024 15:51:54 +0200 Subject: [PATCH 1/2] Hot Fix to align with json The last fix for the wrong level of `required` was only done in json... Please always add `src` first since (well, both). --- models/src/beacon-v2-default-model/common/complexValue.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/models/src/beacon-v2-default-model/common/complexValue.yaml b/models/src/beacon-v2-default-model/common/complexValue.yaml index 98207b12b..058a91b9f 100644 --- a/models/src/beacon-v2-default-model/common/complexValue.yaml +++ b/models/src/beacon-v2-default-model/common/complexValue.yaml @@ -9,8 +9,8 @@ properties: type: array items: $ref: '#/definitions/TypedQuantity' - required: - - typedQuantities +required: + - typedQuantities definitions: TypedQuantity: @@ -32,4 +32,4 @@ definitions: label: Millimeter of Mercury required: - quantityType - - quantity \ No newline at end of file + - quantity From 9f9c96ab9f6c4f2b5b14ed33db10b26325d9ac14 Mon Sep 17 00:00:00 2001 From: Oriol Lopez-Doriga Date: Wed, 10 Jul 2024 14:59:03 +0200 Subject: [PATCH 2/2] renaming endpoints for beaconMap --- .../beacon-v2-default-model/beaconMap.json | 62 +++++++++---------- .../beacon-v2-default-model/beaconMap.yaml | 62 +++++++++---------- 2 files changed, 62 insertions(+), 62 deletions(-) diff --git a/models/json/beacon-v2-default-model/beaconMap.json b/models/json/beacon-v2-default-model/beaconMap.json index 4c9a12a78..a7681a24f 100644 --- a/models/json/beacon-v2-default-model/beaconMap.json +++ b/models/json/beacon-v2-default-model/beaconMap.json @@ -1,9 +1,9 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "endpointSets": { - "analysis": { + "analysisEndpoints": { "endpoints": { - "genomicVariant": { + "genomicVariantLookup": { "returnedEntryType": "genomicVariant", "url": "https://exampleBeacons.org/analyses/{id}/g_variants" } @@ -13,17 +13,17 @@ "rootUrl": "https://exampleBeacons.org/analyses", "singleEntryUrl": "https://exampleBeacons.org/analyses/{id}" }, - "biosample": { + "biosampleEndpoints": { "endpoints": { - "analysis": { + "analysisLookup": { "returnedEntryType": "analysis", "url": "https://exampleBeacons.org/biosamples/{id}/analyses" }, - "genomicVariant": { + "genomicVariantLookup": { "returnedEntryType": "genomicVariant", "url": "https://exampleBeacons.org/biosamples/{id}/g_variants" }, - "run": { + "runLookup": { "returnedEntryType": "run", "url": "https://exampleBeacons.org/biosamples/{id}/runs" } @@ -33,25 +33,25 @@ "rootUrl": "https://exampleBeacons.org/biosamples", "singleEntryUrl": "https://exampleBeacons.org/biosamples/{id}" }, - "cohort": { + "cohortEndpoints": { "endpoints": { - "analyses": { + "analysisLookup": { "returnedEntryType": "analysis", "url": "https://exampleBeacons.org/cohorts/{id}/analyses" }, - "biosample": { + "biosampleLookup": { "returnedEntryType": "biosample", "url": "https://exampleBeacons.org/cohorts/{id}/biosamples" }, - "genomicVariant": { + "genomicVariantLookup": { "returnedEntryType": "genomicVariant", "url": "https://exampleBeacons.org/cohorts/{id}/g_variants" }, - "individual": { + "individualLookup": { "returnedEntryType": "individual", "url": "https://exampleBeacons.org/cohorts/{id}/individuals" }, - "runs": { + "runLookup": { "returnedEntryType": "run", "url": "https://exampleBeacons.org/cohorts/{id}/runs" } @@ -62,25 +62,25 @@ "rootUrl": "https://exampleBeacons.org/cohorts", "singleEntryUrl": "https://exampleBeacons.org/cohorts/{id}" }, - "dataset": { + "datasetEndpoints": { "endpoints": { - "analyses": { + "analysisLookup": { "returnedEntryType": "analysis", "url": "https://exampleBeacons.org/datasets/{id}/analyses" }, - "biosample": { + "biosampleLookup": { "returnedEntryType": "biosample", "url": "https://exampleBeacons.org/datasets/{id}/biosamples" }, - "genomicVariant": { + "genomicVariantLookup": { "returnedEntryType": "genomicVariant", "url": "https://exampleBeacons.org/datasets/{id}/g_variants" }, - "individual": { + "individualLookup": { "returnedEntryType": "individual", "url": "https://exampleBeacons.org/datasets/{id}/individuals" }, - "runs": { + "runLookup": { "returnedEntryType": "run", "url": "https://exampleBeacons.org/datasets/{id}/runs" } @@ -91,21 +91,21 @@ "rootUrl": "https://exampleBeacons.org/datasets", "singleEntryUrl": "https://exampleBeacons.org/datasets/{id}" }, - "genomicVariant": { + "genomicVariantEndpoints": { "endpoints": { - "analyses": { + "analysisLookup": { "returnedEntryType": "analysis", "url": "https://exampleBeacons.org/g_variants/{id}/analyses" }, - "biosample": { + "biosampleLookup": { "returnedEntryType": "biosample", "url": "https://exampleBeacons.org/g_variants/{id}/biosamples" }, - "individual": { + "individualLookup": { "returnedEntryType": "individual", "url": "https://exampleBeacons.org/g_variants/{id}/individuals" }, - "runs": { + "runLookup": { "returnedEntryType": "run", "url": "https://exampleBeacons.org/g_variants/{id}/runs" } @@ -115,21 +115,21 @@ "rootUrl": "https://exampleBeacons.org/g_variants", "singleEntryUrl": "https://exampleBeacons.org/g_variants/{id}" }, - "individual": { + "individualEndpoints": { "endpoints": { - "analyses": { + "analysisLookup": { "returnedEntryType": "analysis", "url": "https://exampleBeacons.org/individuals/{id}/analyses" }, - "biosample": { + "biosampleLookup": { "returnedEntryType": "biosample", "url": "https://exampleBeacons.org/individuals/{id}/biosamples" }, - "genomicVariant": { + "genomicVariantLookup": { "returnedEntryType": "genomicVariant", "url": "https://exampleBeacons.org/individuals/{id}/g_variants" }, - "runs": { + "runLookup": { "returnedEntryType": "run", "url": "https://exampleBeacons.org/individuals/{id}/runs" } @@ -140,13 +140,13 @@ "rootUrl": "https://exampleBeacons.org/individuals", "singleEntryUrl": "https://exampleBeacons.org/individuals/{id}" }, - "run": { + "runEndpoints": { "endpoints": { - "analysis": { + "analysisLookup": { "returnedEntryType": "analysis", "url": "https://exampleBeacons.org/runs/{id}/analyses" }, - "genomicVariant": { + "genomicVariantLookup": { "returnedEntryType": "genomicVariant", "url": "https://exampleBeacons.org/runs/{id}/g_variants" } diff --git a/models/src/beacon-v2-default-model/beaconMap.yaml b/models/src/beacon-v2-default-model/beaconMap.yaml index 3da0cd2a4..823d60f74 100644 --- a/models/src/beacon-v2-default-model/beaconMap.yaml +++ b/models/src/beacon-v2-default-model/beaconMap.yaml @@ -1,119 +1,119 @@ $schema: https://json-schema.org/draft/2020-12/schema endpointSets: - dataset: + datasetEndpoints: entryType: dataset openAPIEndpointsDefinition: https://exampleBeacons.org/datasets/endpoints.json rootUrl: https://exampleBeacons.org/datasets singleEntryUrl: https://exampleBeacons.org/datasets/{id} filteringTermsUrl: https://exampleBeacons.org/datasets/{id}/filtering_terms endpoints: - genomicVariant: + genomicVariantLookup: returnedEntryType: genomicVariant url: https://exampleBeacons.org/datasets/{id}/g_variants - biosample: + biosampleLookup: returnedEntryType: biosample url: https://exampleBeacons.org/datasets/{id}/biosamples - individual: + individualLookup: returnedEntryType: individual url: https://exampleBeacons.org/datasets/{id}/individuals - runs: + runLookup: returnedEntryType: run url: https://exampleBeacons.org/datasets/{id}/runs - analyses: + analysisLookup: returnedEntryType: analysis url: https://exampleBeacons.org/datasets/{id}/analyses - cohort: + cohortEndpoints: entryType: cohort openAPIEndpointsDefinition: https://exampleBeacons.org/cohorts/endpoints.json rootUrl: https://exampleBeacons.org/cohorts singleEntryUrl: https://exampleBeacons.org/cohorts/{id} filteringTermsUrl: https://exampleBeacons.org/cohorts/{id}/filtering_terms endpoints: - individual: + individualLookup: returnedEntryType: individual url: https://exampleBeacons.org/cohorts/{id}/individuals - genomicVariant: + genomicVariantLookup: returnedEntryType: genomicVariant url: https://exampleBeacons.org/cohorts/{id}/g_variants - biosample: + biosampleLookup: returnedEntryType: biosample url: https://exampleBeacons.org/cohorts/{id}/biosamples - runs: + runLookup: returnedEntryType: run url: https://exampleBeacons.org/cohorts/{id}/runs - analyses: + analysisLookup: returnedEntryType: analysis url: https://exampleBeacons.org/cohorts/{id}/analyses - genomicVariant: + genomicVariantEndpoints: entryType: genomicVariant openAPIEndpointsDefinition: https://exampleBeacons.org/genomicVariations/endpoints.json rootUrl: https://exampleBeacons.org/g_variants singleEntryUrl: https://exampleBeacons.org/g_variants/{id} endpoints: - biosample: + biosampleLookup: returnedEntryType: biosample url: https://exampleBeacons.org/g_variants/{id}/biosamples - individual: + individualLookup: returnedEntryType: individual url: https://exampleBeacons.org/g_variants/{id}/individuals - runs: + runLookup: returnedEntryType: run url: https://exampleBeacons.org/g_variants/{id}/runs - analyses: + analysisLookup: returnedEntryType: analysis url: https://exampleBeacons.org/g_variants/{id}/analyses - individual: + individualEndpoints: entryType: individual openAPIEndpointsDefinition: https://exampleBeacons.org/individuals/endpoints.json rootUrl: https://exampleBeacons.org/individuals singleEntryUrl: https://exampleBeacons.org/individuals/{id} filteringTermsUrl: https://exampleBeacons.org/individuals/{id}/filtering_terms endpoints: - genomicVariant: + genomicVariantLookup: returnedEntryType: genomicVariant url: https://exampleBeacons.org/individuals/{id}/g_variants - biosample: + biosampleLookup: returnedEntryType: biosample url: https://exampleBeacons.org/individuals/{id}/biosamples - runs: + runLookup: returnedEntryType: run url: https://exampleBeacons.org/individuals/{id}/runs - analyses: + analysisLookup: returnedEntryType: analysis url: https://exampleBeacons.org/individuals/{id}/analyses - biosample: + biosampleEndpoints: entryType: biosample openAPIEndpointsDefinition: https://exampleBeacons.org/biosamples/endpoints.json rootUrl: https://exampleBeacons.org/biosamples singleEntryUrl: https://exampleBeacons.org/biosamples/{id} endpoints: - run: + runLookup: returnedEntryType: run url: https://exampleBeacons.org/biosamples/{id}/runs - analysis: + analysisLookup: returnedEntryType: analysis url: https://exampleBeacons.org/biosamples/{id}/analyses - genomicVariant: + genomicVariantLookup: returnedEntryType: genomicVariant url: https://exampleBeacons.org/biosamples/{id}/g_variants - run: + runEndpoints: entryType: run openAPIEndpointsDefinition: https://exampleBeacons.org/runs/endpoints.json rootUrl: https://exampleBeacons.org/runs singleEntryUrl: https://exampleBeacons.org/runs/{id} endpoints: - analysis: + analysisLookup: returnedEntryType: analysis url: https://exampleBeacons.org/runs/{id}/analyses - genomicVariant: + genomicVariantLookup: returnedEntryType: genomicVariant url: https://exampleBeacons.org/runs/{id}/g_variants - analysis: + analysisEndpoints: entryType: analysis openAPIEndpointsDefinition: https://exampleBeacons.org/analyses/endpoints.json rootUrl: https://exampleBeacons.org/analyses singleEntryUrl: https://exampleBeacons.org/analyses/{id} endpoints: - genomicVariant: + genomicVariantLookup: returnedEntryType: genomicVariant url: https://exampleBeacons.org/analyses/{id}/g_variants