diff --git a/bycon/config/entity_defaults.yaml b/bycon/config/entity_defaults.yaml index e40dbb630..552bb4901 100644 --- a/bycon/config/entity_defaults.yaml +++ b/bycon/config/entity_defaults.yaml @@ -1,76 +1,59 @@ -info: - description: >- - The `info` endpoint provides information about the Beacon, such as its name, - the organization responsible for the Beacon, a contact email, - and the API version. It is based on the GA4GH `service-info` standard. - request_entity_path_id: info - request_entity_path_aliases: - - "/" - - "service-info" - - "service_info" - response_entity_id: info - response_schema: beaconInfoResponse - bycon_response_class: BeaconInfoResponse - beacon_schema: - entity_type: configuration - schema: https://progenetix.org/services/schemas/beaconInfoResults/ - is_beacon_entity: true - content: {} - -################################################################################ - -beaconMap: - description: >- - The `beaconMap` object provides a map of the Beacon's REST endpoints. - request_entity_path_id: map - response_entity_id: beaconMap - collection: Null - response_schema: beaconMapResponse - bycon_response_class: BeaconInfoResponse - beacon_schema: - entity_type: map - schema: https://progenetix.org/services/schemas/beaconMapSchema/ - is_beacon_entity: true - -################################################################################ - -configuration: - request_entity_path_id: configuration - response_entity_id: configuration +dataset: + request_entity_path_id: datasets + response_entity_id: dataset collection: Null - response_schema: beaconConfigurationResponse - bycon_response_class: BeaconInfoResponse + response_schema: beaconCollectionsResponse + bycon_response_class: BeaconDataResponse beacon_schema: - entity_type: configuration - schema: https://progenetix.org/services/schemas/beaconConfigurationSchema/ + entity_type: dataset + schema: https://progenetix.org/services/schemas/dataset/ + pagination: + skip: 0 + limit: 10 is_beacon_entity: true + path_id_value_bycon_parameter: dataset_ids + examples: + - /progenetix -################################################################################ +############################################################################## -entryType: - request_entity_path_id: entry_types - response_entity_id: entryType - collection: Null - response_schema: beaconEntryTypesResponse - bycon_response_class: BeaconInfoResponse +cohort: + request_entity_path_id: cohorts + response_entity_id: cohort + collection: collations + response_schema: beaconCollectionsResponse + bycon_response_class: BeaconDataResponse beacon_schema: - entity_type: entryType - schema: https://progenetix.org/services/schemas/entryTypesSchema/ + entity_type: cohort + schema: https://progenetix.org/services/schemas/cohort/ + pagination: + skip: 0 + limit: 10 is_beacon_entity: true + path_id_value_bycon_parameter: filters ################################################################################ -filteringTerm: - request_entity_path_id: filtering_terms - response_entity_id: filteringTerm - collection: collations - response_schema: beaconFilteringTermsResponse +genomicVariant: + request_entity_path_id: g_variants + request_entity_path_aliases: + - genomicVariations + - variants + response_entity_id: genomicVariant + collection: variants + response_schema: beaconResultsetsResponse bycon_response_class: BeaconDataResponse beacon_schema: - entity_type: filteringTerm - schema: https://progenetix.org/services/schemas/filteringTermsSchema/ + entity_type: genomicVariant + schema: https://progenetix.org/services/schemas/genomicVariant/ + h->o_access_key: variants.id is_beacon_entity: true - path_id_value_bycon_parameter: filters + path_id_value_bycon_parameter: variant_ids + examples: + - /pgxvar-5bab576a727983b2e00b8d32 + - /pgxvar-5bab576a727983b2e00b8d32/individuals + - ?geneId=CDKN2A&variantMaxSize=100000&limit=5 + - ?referenceName=NC_000017.11&start=7577120&referenceBases=G&alternateBases=A ################################################################################ @@ -87,6 +70,21 @@ analysis: is_beacon_entity: true path_id_value_bycon_parameter: analysis_ids +############################################################################## + +run: + request_entity_path_id: runs + response_entity_id: run + collection: analyses + response_schema: beaconResultsetsResponse + bycon_response_class: BeaconDataResponse + beacon_schema: + entity_type: run + schema: https://progenetix.org/services/schemas/run/ + h->o_access_key: analyses.id + is_beacon_entity: true + path_id_value_bycon_parameter: run_ids + ################################################################################ biosample: @@ -103,28 +101,10 @@ biosample: h->o_access_key: biosamples.id is_beacon_entity: true path_id_value_bycon_parameter: biosample_ids - tests: + examples: - ?filters=NCIT:C4017&limit=3 + - ?referenceName=refseq:NC_000009.12&variantType=EFO:0030067&start=21000000,21975098&end=21967753,23000000&filters=NCIT:C3058&limit=10 -############################################################################## - -genomicVariant: - request_entity_path_id: g_variants - request_entity_path_aliases: - - genomicVariations - - variants - response_entity_id: genomicVariant - collection: variants - response_schema: beaconResultsetsResponse - bycon_response_class: BeaconDataResponse - beacon_schema: - entity_type: genomicVariant - schema: https://progenetix.org/services/schemas/genomicVariant/ - h->o_access_key: variants.id - is_beacon_entity: true - path_id_value_bycon_parameter: variant_ids - tests: - - ?geneId=CDKN2A&variantMaxSize=100000&limit=5 ############################################################################## @@ -140,55 +120,84 @@ individual: h->o_access_key: individuals.id is_beacon_entity: true path_id_value_bycon_parameter: individual_ids - tests: + examples: - ?filters=EFO:0030049&limit=5 -############################################################################## -run: - request_entity_path_id: runs - response_entity_id: run - collection: analyses - response_schema: beaconResultsetsResponse +################################################################################ + +filteringTerm: + request_entity_path_id: filtering_terms + response_entity_id: filteringTerm + collection: collations + response_schema: beaconFilteringTermsResponse bycon_response_class: BeaconDataResponse beacon_schema: - entity_type: run - schema: https://progenetix.org/services/schemas/run/ - h->o_access_key: analyses.id + entity_type: filteringTerm + schema: https://progenetix.org/services/schemas/filteringTermsSchema/ is_beacon_entity: true - path_id_value_bycon_parameter: run_ids + path_id_value_bycon_parameter: filters + ################################################################################ -cohort: - request_entity_path_id: cohorts - response_entity_id: cohort - collection: collations - response_schema: beaconCollectionsResponse - bycon_response_class: BeaconDataResponse +info: + description: >- + The `info` endpoint provides information about the Beacon, such as its name, + the organization responsible for the Beacon, a contact email, + and the API version. It is based on the GA4GH `service-info` standard. + request_entity_path_id: info + request_entity_path_aliases: + - "/" + - "service-info" + - "service_info" + response_entity_id: info + response_schema: beaconInfoResponse + bycon_response_class: BeaconInfoResponse beacon_schema: - entity_type: cohort - schema: https://progenetix.org/services/schemas/cohort/ - pagination: - skip: 0 - limit: 10 + entity_type: configuration + schema: https://progenetix.org/services/schemas/beaconInfoResults/ is_beacon_entity: true - path_id_value_bycon_parameter: filters + content: {} -############################################################################## +################################################################################ -dataset: - request_entity_path_id: datasets - response_entity_id: dataset +beaconMap: + description: >- + The `beaconMap` object provides a map of the Beacon's REST endpoints. + request_entity_path_id: map + response_entity_id: beaconMap collection: Null - response_schema: beaconCollectionsResponse - bycon_response_class: BeaconDataResponse + response_schema: beaconMapResponse + bycon_response_class: BeaconInfoResponse beacon_schema: - entity_type: dataset - schema: https://progenetix.org/services/schemas/dataset/ - pagination: - skip: 0 - limit: 10 + entity_type: map + schema: https://progenetix.org/services/schemas/beaconMapSchema/ + is_beacon_entity: true + +################################################################################ + +configuration: + request_entity_path_id: configuration + response_entity_id: configuration + collection: Null + response_schema: beaconConfigurationResponse + bycon_response_class: BeaconInfoResponse + beacon_schema: + entity_type: configuration + schema: https://progenetix.org/services/schemas/beaconConfigurationSchema/ + is_beacon_entity: true + +################################################################################ + +entryType: + request_entity_path_id: entry_types + response_entity_id: entryType + collection: Null + response_schema: beaconEntryTypesResponse + bycon_response_class: BeaconInfoResponse + beacon_schema: + entity_type: entryType + schema: https://progenetix.org/services/schemas/entryTypesSchema/ is_beacon_entity: true - path_id_value_bycon_parameter: dataset_ids diff --git a/bycon/lib/schema_parsing.py b/bycon/lib/schema_parsing.py index 826a7fb8c..f04ca8501 100644 --- a/bycon/lib/schema_parsing.py +++ b/bycon/lib/schema_parsing.py @@ -20,6 +20,7 @@ def read_schema_file(schema_name, item, ext="json"): schema_name = r_p_id s_f_p = get_default_schema_file_path(schema_name, "defaultSchema", ext) + # prdbug(f'...read_schema_file {schema_name}: {s_f_p}') if s_f_p is False: # in case the name had been used as request_entity_path_id s_f_p = get_schema_file_path(schema_name, ext) diff --git a/bycon/schemas/framework/json/common/examples/basicElement-example.json b/bycon/schemas/framework/json/common/examples/basicElement-example.json deleted file mode 100644 index 6038a82a2..000000000 --- a/bycon/schemas/framework/json/common/examples/basicElement-example.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "id": "BEex1", - "name": "Basic Element example one" -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/common/examples/beaconCommonComponents-example.json b/bycon/schemas/framework/json/common/examples/beaconCommonComponents-example.json deleted file mode 100644 index 5970fa772..000000000 --- a/bycon/schemas/framework/json/common/examples/beaconCommonComponents-example.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "beaconId": "org.example.beacon.v2", - "apiVersion": "v2.0", - "beaconError": { - "errorCode": 404, - "errorMessage": "the provided parameters are incomplete. 'xyz' is missing." - }, - "listOfSchemas": [ - { - "entityType": "EntryTypeA", - "schema": "entry-typeA-schema-v0.1" - }, - { - "entityType": "EntryTypeB", - "schema": "entry-typeB-schema-v1.0" - } - ], - "schemasPerEntity": { - "entityType": "Individual", - "schema": "ga4gh-phenopacket-individual-v0.1" - }, - "pagination": { - "skip": 0, - "limit": 10 - }, - "includeResultsetResponses": "HIT", - "filters": [ - "BTO:0000199", - "PATO:0000383" - ], - "exists": true, - "numTotalResults": 123, - "info": {}, - "handover": { - "handoverType": { - "id": "EFO:0004157", - "label": "BAM format" - }, - "url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0", - "note": "This handover link provides access to a summarized VCF." - }, - "handoverType": { - "id": "EFO:0004157", - "label": "BAM format" - }, - "listOfHandovers": [ - { - "handoverType": { - "id": "EFO:0004157", - "label": "BAM format" - }, - "url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0", - "note": "This handover link provides access to a summarized VCF." - }, - { - "handoverType": { - "id": "EFO:0004157", - "label": "BAM format" - }, - "url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0", - "note": "This handover link provides access to a summarized VCF." - } - ] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/common/examples/elementWithDescription-example.json b/bycon/schemas/framework/json/common/examples/elementWithDescription-example.json deleted file mode 100644 index ae117c321..000000000 --- a/bycon/schemas/framework/json/common/examples/elementWithDescription-example.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "id": "EWDex1", - "name": "Element with description one", - "description": "A longer textual description for the element." -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/common/examples/ontologizedElement-example.json b/bycon/schemas/framework/json/common/examples/ontologizedElement-example.json deleted file mode 100644 index 631d7dc56..000000000 --- a/bycon/schemas/framework/json/common/examples/ontologizedElement-example.json +++ /dev/null @@ -1,10 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "id": "OEex1", - "name": "Element with a description and associated ontology term.", - "description": "Non-mandatory, longer textual description for the element.", - "ontologyTermForThisType": { - "id": "DUO:0000004", - "label": "General Research Use" - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/common/examples/ontologyTerm-example.json b/bycon/schemas/framework/json/common/examples/ontologyTerm-example.json deleted file mode 100644 index a23ea909b..000000000 --- a/bycon/schemas/framework/json/common/examples/ontologyTerm-example.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "id": "DUO:0000004", - "label": "General Research Use" -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/common/examples/referenceToAnSchema-MAX-example.json b/bycon/schemas/framework/json/common/examples/referenceToAnSchema-MAX-example.json deleted file mode 100644 index acbc4640c..000000000 --- a/bycon/schemas/framework/json/common/examples/referenceToAnSchema-MAX-example.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "id": "RTAEex1", - "name": "Reference to schema one with all its properties.", - "description": "A longer textual description for the element.", - "referenceToSchemaDefinition": "https://example-schemas.org/an-schema-address.json", - "schemaVersion": "v1.0" -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/common/examples/referenceToAnSchema-MIN-example.json b/bycon/schemas/framework/json/common/examples/referenceToAnSchema-MIN-example.json deleted file mode 100644 index 9d63a4176..000000000 --- a/bycon/schemas/framework/json/common/examples/referenceToAnSchema-MIN-example.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "id": "RTAEex1", - "name": "Reference to schema one with all its properties.", - "referenceToSchemaDefinition": "https://example-schemas.org/an-schema-address.json" -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/common/validation/beaconCommonComponents.json b/bycon/schemas/framework/json/common/validation/beaconCommonComponents.json deleted file mode 100644 index 1625e3c90..000000000 --- a/bycon/schemas/framework/json/common/validation/beaconCommonComponents.json +++ /dev/null @@ -1,54 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "title": "Schema for validating Beacon Common Components examples", - "type": "object", - "properties": { - "$schema": { - "type": "string", - "description": "Added here to allow the example to comply with the 'additionalProperties:true' restriction." - }, - "beaconId": { - "$ref": "../beaconCommonComponents.json#/$defs/BeaconId" - }, - "apiVersion": { - "$ref": "../beaconCommonComponents.json#/$defs/ApiVersion" - }, - "beaconError": { - "$ref": "../beaconCommonComponents.json#/$defs/BeaconError" - }, - "listOfSchemas": { - "$ref": "../beaconCommonComponents.json#/$defs/ListOfSchemas" - }, - "schemasPerEntity": { - "$ref": "../beaconCommonComponents.json#/$defs/SchemasPerEntity" - }, - "pagination": { - "$ref": "../beaconCommonComponents.json#/$defs/Pagination" - }, - "includeResultsetResponses": { - "$ref": "../beaconCommonComponents.json#/$defs/IncludeResultsetResponses" - }, - "filters": { - "$ref": "../beaconCommonComponents.json#/$defs/Filters" - }, - "exists": { - "$ref": "../beaconCommonComponents.json#/$defs/Exists" - }, - "numTotalResults": { - "$ref": "../beaconCommonComponents.json#/$defs/NumTotalResults" - }, - "info": { - "$ref": "../beaconCommonComponents.json#/$defs/Info" - }, - "handover": { - "$ref": "../beaconCommonComponents.json#/$defs/Handover" - }, - "handoverType": { - "$ref": "../beaconCommonComponents.json#/$defs/HandoverType" - }, - "listOfHandovers": { - "$ref": "../beaconCommonComponents.json#/$defs/ListOfHandovers" - } - }, - "additionalProperties": false -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/configuration/examples/beaconConfiguration-example.json b/bycon/schemas/framework/json/configuration/examples/beaconConfiguration-example.json deleted file mode 100644 index c30fbff51..000000000 --- a/bycon/schemas/framework/json/configuration/examples/beaconConfiguration-example.json +++ /dev/null @@ -1,62 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "maturityAttributes": { - "productionStatus": "DEV" - }, - "securityAttributes": { - "defaultGranularity": "boolean", - "securityLevels": [ - "PUBLIC", - "REGISTERED", - "CONTROLLED" - ] - }, - "entryTypes": { - "dataset": { - "id": "dataset", - "name": "Dataset", - "ontologyTermForThisType": { - "id": "NCIT:C47824", - "label": "Data set" - }, - "partOfSpecification": "Beacon v2.0", - "description": "A Dataset is a collection of records, like rows in a database or cards in a cardholder.", - "defaultSchema": { - "id": "datasetDefaultSchema", - "name": "Default schema for datasets", - "referenceToSchemaDefinition": "./datasets/defaultSchema.json", - "schemaVersion": "v.2" - }, - "aCollectionOf": [ - { - "id": "exampleEntry", - "name": "Example entries" - } - ], - "endpoint": "/datasets", - "filteringTermsReference": "./datasets/filteringTerms.json", - "additionallySupportedSchemas": [], - "nonFilteredQueriesAllowed": true - }, - "exampleEntry": { - "id": "exampleEntry", - "name": "Example Entry", - "ontologyTermForThisType": { - "id": "NCIT:C20181", - "label": "Conceptual Entity" - }, - "partOfSpecification": "Beacon v2.0", - "description": "A generic entry type to allow testing and playing with the specification.", - "defaultSchema": { - "id": "ExampleEntryTypeDefaultschema", - "name": "Default schema for an example entries", - "referenceToSchemaDefinition": "./exampleEntry/defaultSchema.json", - "schemaVersion": "v.2" - }, - "endpoint": "./exampleEntries", - "filteringTermsReference": "./exampleEntry/filteringTerms.json", - "additionallySupportedSchemas": [], - "nonFilteredQueriesAllowed": false - } - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/configuration/examples/beaconConfigurationFilteringTerms-example.json b/bycon/schemas/framework/json/configuration/examples/beaconConfigurationFilteringTerms-example.json deleted file mode 100644 index 7613a69f1..000000000 --- a/bycon/schemas/framework/json/configuration/examples/beaconConfigurationFilteringTerms-example.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "filteringTerms": [ - { - "ftType": "alphanumeric", - "id": "age", - "scope": "individual" - }, - { - "ftType": "ontologyTerm", - "id": "HP:0002664", - "label": "Neoplasm", - "scope": "biosample" - }, - { - "ftType": "alphanumeric", - "id": "NCIT:C100094", - "label": "HGNC gene name", - "scope": "genomicVariant" - } - ] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/configuration/examples/beaconMap-MIN-example.json b/bycon/schemas/framework/json/configuration/examples/beaconMap-MIN-example.json deleted file mode 100644 index 00a34d73d..000000000 --- a/bycon/schemas/framework/json/configuration/examples/beaconMap-MIN-example.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "endpointSets": { - "datasets": { - "entryType": "dataset", - "rootUrl": "https://exampleBeacons.org/datasets" - } - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/configuration/examples/beaconMap-example.json b/bycon/schemas/framework/json/configuration/examples/beaconMap-example.json deleted file mode 100644 index 546d61626..000000000 --- a/bycon/schemas/framework/json/configuration/examples/beaconMap-example.json +++ /dev/null @@ -1,25 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "endpointSets": { - "dataset": { - "entryType": "dataset", - "openAPIEndpointsDefinition": "./datasets/endpoints.json", - "rootUrl": "https://exampleBeacons.org/datasets", - "singleEntryUrl": "https://exampleBeacons.org/datasets/{id}", - "filteringTermsUrl": "https://exampleBeacons.org/datasets/{id}/filteringTerms", - "endpoints": { - "exampleEntries": { - "returnedEntryType": "exampleEntry", - "url": "https://exampleBeacons.org/datasets/{id}/exampleEntries" - } - } - }, - "exampleEntry": { - "entryType": "exampleEntry", - "openAPIEndpointsDefinition": "./exampleEntries/endpoints.json", - "rootUrl": "https://exampleBeacons.org/exampleEntries", - "singleEntryUrl": "https://exampleBeacons.org/exampleEntries/{id}", - "filteringTermsUrl": "https://exampleBeacons.org/exampleEntries/{id}/filteringTerms" - } - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/configuration/examples/entriesCollectionDefinition_MIN_example.json b/bycon/schemas/framework/json/configuration/examples/entriesCollectionDefinition_MIN_example.json deleted file mode 100644 index c8d0a2ad3..000000000 --- a/bycon/schemas/framework/json/configuration/examples/entriesCollectionDefinition_MIN_example.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "id": "dataset", - "name": "Dataset", - "ontologyTermForThisType": { - "id": "NCIT:C47824", - "label": "Data set" - }, - "partOfSpecification": "Beacon v2.0", - "defaultSchema": { - "id": "datasetDefaultSchema", - "name": "Default schema for datasets", - "referenceToSchemaDefinition": "./datasets/defaultSchema.json", - "schemaVersion": "v.2" - }, - "aCollectionOf": [ - { - "id": "exampleEntry", - "name": "Example entries" - } - ] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/configuration/examples/entriesCollectionDefinition_example.json b/bycon/schemas/framework/json/configuration/examples/entriesCollectionDefinition_example.json deleted file mode 100644 index 335790cdb..000000000 --- a/bycon/schemas/framework/json/configuration/examples/entriesCollectionDefinition_example.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "id": "dataset", - "name": "Dataset", - "ontologyTermForThisType": { - "id": "NCIT:C47824", - "label": "Data set" - }, - "partOfSpecification": "Beacon v2.0", - "description": "A Dataset is a collection of records, like rows in a database or cards in a cardholder.", - "defaultSchema": { - "id": "datasetDefaultSchema", - "name": "Default schema for datasets", - "referenceToSchemaDefinition": "./datasets/defaultSchema.json", - "schemaVersion": "v.2" - }, - "aCollectionOf": [ - { - "id": "exampleEntry", - "name": "Example entries" - } - ], - "endpoint": "/datasets", - "filteringTermsReference": "./datasets/filteringTerms.json", - "additionallySupportedSchemas": [ - { - "id": "ohdsi-atlas-cohort", - "name": "OHDSI ATLAS Cohort", - "description": "ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data converted to the OMOP Common Data Model V5.", - "referenceToSchemaDefinition": "https://raw.githubusercontent.com/OHDSIBr/ATLAS-JSON-Schema/2.7.4/single/atlas_cohort_definition.json", - "schemaVersion": "2.7.4" - } - ] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/configuration/examples/entryTypeDefinition-MIN-example.json b/bycon/schemas/framework/json/configuration/examples/entryTypeDefinition-MIN-example.json deleted file mode 100644 index e58098c1b..000000000 --- a/bycon/schemas/framework/json/configuration/examples/entryTypeDefinition-MIN-example.json +++ /dev/null @@ -1,15 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "id": "individual", - "name": "Individual entry", - "ontologyTermForThisType": { - "id": "DUO:0000004", - "label": "General Research Use" - }, - "partOfSpecification": "Beacon v2", - "defaultSchema": { - "id": "bdfGenericEntryType-v2", - "name": "Beacon v2 default schema for a basic element.", - "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/master/default_dataset_schema.json" - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/requests/examples-fullDocuments/beaconRequestBody-MAX-example.json b/bycon/schemas/framework/json/requests/examples-fullDocuments/beaconRequestBody-MAX-example.json deleted file mode 100644 index a41b87fd5..000000000 --- a/bycon/schemas/framework/json/requests/examples-fullDocuments/beaconRequestBody-MAX-example.json +++ /dev/null @@ -1,35 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "apiVersion": "2.0", - "requestedSchemas": [ - { - "entityType": "EntryTypeA", - "schema": "entry-typeA-schema-v0.1" - } - ] - }, - "query": { - "requestParameters": { - "datasets": { - "datasetIds": [ - "DatasetXYZ", - "Dataset123" - ] - } - }, - "filters": [ - { - "id": "EFO:0001212", - "scope": "biosamples" - } - ], - "includeResultsetResponses": "HIT", - "pagination": { - "skip": 0, - "limit": 10 - }, - "testMode": false, - "requestedGranularity": "boolean" - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/requests/examples-fullDocuments/beaconRequestBody-MIN-example.json b/bycon/schemas/framework/json/requests/examples-fullDocuments/beaconRequestBody-MIN-example.json deleted file mode 100644 index 3916d4984..000000000 --- a/bycon/schemas/framework/json/requests/examples-fullDocuments/beaconRequestBody-MIN-example.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "apiVersion": "2.0" - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/requests/examples-sections/beaconRequestMeta-example.json b/bycon/schemas/framework/json/requests/examples-sections/beaconRequestMeta-example.json deleted file mode 100644 index b28f42e7e..000000000 --- a/bycon/schemas/framework/json/requests/examples-sections/beaconRequestMeta-example.json +++ /dev/null @@ -1,10 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "apiVersion": "2.0", - "requestedSchemas": [ - { - "entityType": "EntryTypeA", - "schema": "entry-typeA-schema-v0.1" - } - ] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/requests/examples-sections/filteringTerms-example.json b/bycon/schemas/framework/json/requests/examples-sections/filteringTerms-example.json deleted file mode 100644 index 2c49300d0..000000000 --- a/bycon/schemas/framework/json/requests/examples-sections/filteringTerms-example.json +++ /dev/null @@ -1,21 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "filters": [ - { - "id": "HP:0002664", - "includeDescendantTerms": true, - "similarity": "exact", - "scope": "biosamples" - }, - { - "id": "age", - "operator": ">=", - "value": "P70Y", - "scope": "individuals" - }, - { - "id": "demographic.ethnicity:asian", - "scope": "cohorts" - } - ] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/requests/examples-sections/requestParameters-example.json b/bycon/schemas/framework/json/requests/examples-sections/requestParameters-example.json deleted file mode 100644 index c7f65cb91..000000000 --- a/bycon/schemas/framework/json/requests/examples-sections/requestParameters-example.json +++ /dev/null @@ -1,13 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "exampleEntry": { - "description": "All the required fields to query any kind of variant (e.g. SNP, DUP,\netc.).", - "type": "object", - "properties": { - "id": { - "description": "Id of the entry to display.", - "type": "string" - } - } - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/requests/validation/filteringTerms.json b/bycon/schemas/framework/json/requests/validation/filteringTerms.json deleted file mode 100644 index 350845bd9..000000000 --- a/bycon/schemas/framework/json/requests/validation/filteringTerms.json +++ /dev/null @@ -1,109 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "title": "Filtering Term Element", - "description": "Rules for selecting records based upon the field values those records contain. Filters are seperated by the logical AND operator.", - "properties": { - "$schema": { - "type": "string", - "description": "Added here to allow the example to comply with the 'additionalProperties:true' restriction." - }, - "filters": { - "type": "array", - "items": { - "anyOf": [ - { - "$ref": "#/$defs/OntologyFilter" - }, - { - "$ref": "#/$defs/AlphanumericFilter" - }, - { - "$ref": "#/$defs/CustomFilter" - } - ] - } - } - }, - "$defs": { - "OntologyFilter": { - "type": "object", - "description": "Filter results to include records that contain a specific ontology term.", - "required": [ - "id" - ], - "properties": { - "id": { - "type": "string", - "description": "Term ID to be queried, using CURIE syntax where possible.", - "example": "HP:0002664" - }, - "includeDescendantTerms": { - "type": "boolean", - "default": true, - "description": "Define if the Beacon should implement the ontology hierarchy, thus query the descendant terms of `id`." - }, - "similarity": { - "type": "string", - "enum": [ - "exact", - "high", - "medium", - "low" - ], - "default": "exact", - "description": "Allow the Beacon to return results which do not match the filter exactly, but do match to a certain degree of similarity. The Beacon defines the semantic similarity model implemented and how to apply the thresholds of 'high', 'medium' and 'low' similarity." - } - } - }, - "AlphanumericFilter": { - "description": "Filter results based on operators and values applied to alphanumeric fields.", - "type": "object", - "required": [ - "id", - "operator", - "value" - ], - "properties": { - "id": { - "type": "string", - "description": "Field identfier to be queried.", - "example": "age" - }, - "operator": { - "type": "string", - "enum": [ - "=", - "<", - ">", - "!", - ">=", - "<=" - ], - "description": "Defines how the value relates to the field `id`.", - "default": "=", - "example": ">" - }, - "value": { - "type": "string", - "description": "Alphanumeric search term to be used within the query which can contain wildcard characters (%) to denote any number of unknown characters. Values can be assocatied with units if applicable.", - "example": "P70Y" - } - } - }, - "CustomFilter": { - "type": "object", - "description": "Filter results to include records that contain a custom term defined by this Beacon.", - "required": [ - "id" - ], - "properties": { - "id": { - "type": "string", - "description": "Custom filter terms should contain a unique identifier.", - "example": "demographic.ethnicity:asian" - } - } - } - }, - "additionalProperties": false -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/beaconCollectionsResponse.json b/bycon/schemas/framework/json/responses/beaconCollectionsResponse.json index f67c6f843..e6a9e9f67 100644 --- a/bycon/schemas/framework/json/responses/beaconCollectionsResponse.json +++ b/bycon/schemas/framework/json/responses/beaconCollectionsResponse.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "description": "Beacon response that includes details about the collections in this Beacon.", + "description": "A type of Beacon response that includes details about the **collections** in a beacon. The types of collections are defined in each beacon's configuration; if using the Beacon v2+ default model usually the types `dataset` and `cohort` are supported.", "type": "object", "properties": { "meta": { diff --git a/bycon/schemas/framework/json/responses/beaconResultsetsResponse.json b/bycon/schemas/framework/json/responses/beaconResultsetsResponse.json index 5f8d78ba6..fe67014b7 100644 --- a/bycon/schemas/framework/json/responses/beaconResultsetsResponse.json +++ b/bycon/schemas/framework/json/responses/beaconResultsetsResponse.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "description": "Beacon response that includes record level details, grouped in Resultsets.", + "description": "A `beaconResultsetsResponse` returns the results of a query against a beacon, which - beyond the summary count response for overall matches - contains details about the matches in individual **collections** in the beacon or beacon network. The types of `beaconResultsets` objects are defined in the beacon's configuration; if using the Beacon v2+ default model the types `dataset` and `cohort` are supported. `beaconResultsets` typically contain a list of records matched by the query.", "type": "object", "properties": { "meta": { diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconBooleanResponse-example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconBooleanResponse-example.json deleted file mode 100644 index 3f4b5844d..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconBooleanResponse-example.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "org.example.beacon.v2", - "apiVersion": "v2.0", - "returnedSchemas": [ - { - "entityType": "EntryTypeB", - "schema": "entry-typeB-schema-v1.0" - } - ], - "receivedRequestSummary": { - "apiVersion": "2.0", - "requestedSchemas": [ - { - "entityType": "EntryTypeB", - "schema": "entry-typeB-schema-v1.0" - } - ], - "pagination": { - "skip": 0, - "limit": 10 - } - } - }, - "responseSummary": { - "exists": true - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MID-example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MID-example.json deleted file mode 100644 index 08e38485e..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MID-example.json +++ /dev/null @@ -1,74 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "org.example.beacon.v2", - "apiVersion": "v2.0", - "returnedSchemas": [ - { - "entityType": "dataset", - "schema": "dataset-schema-v1.0" - } - ], - "receivedRequestSummary": { - "apiVersion": "2.0", - "requestedSchemas": [ - { - "entityType": "dataset", - "schema": "dataset-schema-v1.0" - } - ], - "pagination": { - "skip": 0, - "limit": 10 - } - } - }, - "responseSummary": { - "exists": true - }, - "response": { - "collections": [ - { - "$schema": "https://schemas-fake-depot.org/beaconv2/datasetSchema.json", - "id": "Dataset1", - "name": "Dataset One", - "description": "This is the first dataset", - "createDateTime": "2011-01-11T11:11:11Z", - "updateDateTime": "2011-01-11T11:11:11Z", - "version": "v1", - "dataUseConditions": { - "duoDataUse": [ - { - "id": "DUO:0000007", - "label": "disease specific research", - "modifiers": [ - { - "id": "HP:0001631" - } - ], - "version": "2021-02-23" - } - ] - } - }, - { - "$schema": "https://schemas-fake-depot.org/beaconv2/datasetSchema.json", - "id": "Dataset2", - "name": "Dataset Two", - "description": "This is the second dataset", - "createDateTime": "2012-02-22T22:22:22Z", - "updateDateTime": "2012-02-22T22:22:22Z", - "version": "v2", - "dataUseConditions": { - "duoDataUse": [ - { - "id": "DUO:0000042", - "label": "general research use", - "version": "2021-02-23" - } - ] - } - } - ] - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MIN-example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MIN-example.json deleted file mode 100644 index 24b737ddd..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconCollectionsResponse-MIN-example.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "org.example.beacon.v2", - "apiVersion": "v2.0", - "returnedSchemas": [ - { - "entityType": "dataset", - "schema": "dataset-schema-v1.0" - } - ], - "receivedRequestSummary": { - "apiVersion": "2.0", - "requestedSchemas": [ - { - "entityType": "dataset", - "schema": "dataset-schema-v1.0" - } - ], - "pagination": { - "skip": 0, - "limit": 10 - } - } - }, - "responseSummary": { - "exists": true - }, - "response": { - "collections": [] - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconConfigurationResponse-example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconConfigurationResponse-example.json deleted file mode 100644 index 8b30842ed..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconConfigurationResponse-example.json +++ /dev/null @@ -1,74 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "string", - "apiVersion": "string", - "returnedSchemas": [ - { - "entityType": "info", - "schema": "beacon-map-v2.0.0" - } - ] - }, - "response": { - "$schema": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/configuration/beaconConfigurationSchema.json", - "maturityAttributes": { - "productionStatus": "DEV" - }, - "securityAttributes": { - "defaultGranularity": "boolean", - "securityLevels": [ - "PUBLIC", - "REGISTERED", - "CONTROLLED" - ] - }, - "entryTypes": { - "dataset": { - "id": "dataset", - "name": "Dataset", - "ontologyTermForThisType": { - "id": "NCIT:C47824", - "label": "Data set" - }, - "partOfSpecification": "Beacon v2.0", - "description": "A Dataset is a collection of records, like rows in a database or cards in a cardholder.", - "defaultSchema": { - "id": "datasetDefaultSchema", - "name": "Default schema for datasets", - "referenceToSchemaDefinition": "./datasets/defaultSchema.json", - "schemaVersion": "v.2" - }, - "aCollectionOf": [ - { - "id": "exampleEntry", - "name": "Example entries" - } - ], - "endpoint": "/datasets", - "filteringTermsReference": "./datasets/filteringTerms.json", - "additionallySupportedSchemas": [] - }, - "exampleEntry": { - "id": "exampleEntry", - "name": "Example Entry", - "ontologyTermForThisType": { - "id": "NCIT:C20181", - "label": "Conceptual Entity" - }, - "partOfSpecification": "Beacon v2.0", - "description": "A generic entry type to allow testing and playing with the specification.", - "defaultSchema": { - "id": "ExampleEntryTypeDefaultschema", - "name": "Default schema for an example entries", - "referenceToSchemaDefinition": "./exampleEntry/defaultSchema.json", - "schemaVersion": "v.2" - }, - "endpoint": "./exampleEntries", - "filteringTermsReference": "./exampleEntry/filteringTerms.json", - "additionallySupportedSchemas": [] - } - } - }, - "info": {} -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconCountResponse-example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconCountResponse-example.json deleted file mode 100644 index 08a2f0d9c..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconCountResponse-example.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "org.example.beacon.v2", - "apiVersion": "v2.0", - "returnedSchemas": [ - { - "entityType": "EntryTypeB", - "schema": "entry-typeB-schema-v1.0" - } - ], - "receivedRequestSummary": { - "apiVersion": "2.0", - "requestedSchemas": [ - { - "entityType": "EntryTypeB", - "schema": "entry-typeB-schema-v1.0" - } - ], - "pagination": { - "skip": 0, - "limit": 10 - } - } - }, - "responseSummary": { - "exists": true, - "numTotalResults": 25355 - }, - "info": { - "someInterestingStuff": "this is the interesting stuff" - }, - "beaconHandovers": [ - { - "handoverType": { - "id": "EFO:0004157", - "label": "BAM format" - }, - "url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0", - "note": "This handover link provides access to a summarized VCF." - }, - { - "handoverType": { - "id": "EFO:0004157", - "label": "BAM format" - }, - "url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0", - "note": "This handover link provides access to a summarized VCF." - } - ] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconEntryTypesResponse-example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconEntryTypesResponse-example.json deleted file mode 100644 index c59f54eba..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconEntryTypesResponse-example.json +++ /dev/null @@ -1,63 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "string", - "apiVersion": "string", - "returnedSchemas": [ - { - "entityType": "info", - "schema": "beacon-map-v2.0.0" - } - ] - }, - "response": { - "$schema": "../../configuration/entryTypesSchema.json", - "entryTypes": { - "dataset": { - "id": "dataset", - "name": "Dataset", - "ontologyTermForThisType": { - "id": "NCIT:C47824", - "label": "Data set" - }, - "partOfSpecification": "Beacon v2.0", - "description": "A Dataset is a collection of records, like rows in a database or cards in a cardholder.", - "defaultSchema": { - "id": "datasetDefaultSchema", - "name": "Default schema for datasets", - "referenceToSchemaDefinition": "./datasets/defaultSchema.json", - "schemaVersion": "v.2" - }, - "aCollectionOf": [ - { - "id": "exampleEntry", - "name": "Example entries" - } - ], - "endpoint": "/datasets", - "filteringTermsReference": "./datasets/filteringTerms.json", - "additionallySupportedSchemas": [] - }, - "exampleEntry": { - "id": "exampleEntry", - "name": "Example Entry", - "ontologyTermForThisType": { - "id": "NCIT:C20181", - "label": "Conceptual Entity" - }, - "partOfSpecification": "Beacon v2.0", - "description": "A generic entry type to allow testing and playing with the specification.", - "defaultSchema": { - "id": "ExampleEntryTypeDefaultschema", - "name": "Default schema for an example entries", - "referenceToSchemaDefinition": "./exampleEntry/defaultSchema.json", - "schemaVersion": "v.2" - }, - "endpoint": "./exampleEntries", - "filteringTermsReference": "./exampleEntry/filteringTerms.json", - "additionallySupportedSchemas": [] - } - } - }, - "info": {} -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconErrorResponse_example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconErrorResponse_example.json deleted file mode 100644 index 392fed166..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconErrorResponse_example.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "org.example.beacon.v2", - "apiVersion": "v2.0", - "receivedRequestSummary": { - "apiVersion": "v2.0", - "requestedSchemas": [ - { - "entityType": "Individual", - "schema": "ga4gh-phenopacket-individual-v0.1" - } - ], - "requestParameters": [ - { - "entity": "individual", - "parameters": [ - { - "id": "123" - }, - { - "position": "1234556" - } - ] - } - ], - "filters": [ - "BTO:0000199", - "PATO:0000383" - ], - "pagination": { - "skip": 1, - "limit": 10 - } - }, - "returnedSchemas": [] - }, - "error": { - "errorCode": 400, - "errorMessage": "Bad request. Missing parameter 'id'." - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconFilteringTermsResponse-example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconFilteringTermsResponse-example.json deleted file mode 100644 index 541b8d762..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconFilteringTermsResponse-example.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "string", - "apiVersion": "string", - "returnedSchemas": [ - { - "map": "beacon-map-v2.0.0" - } - ] - }, - "response": { - "resources": [ - { - "id": "hp", - "name": "Human Phenotype Ontology", - "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "27-03-2020", - "namespacePrefix": "HP", - "iriPrefix": "http://purl.obolibrary.org/obo/HP_" - } - ], - "filteringTerms": [ - { - "type": "numeric", - "id": "PATO:0000011", - "label": "age" - }, - { - "type": "Human Phenotype Ontology", - "id": "HP:0008773", - "label": "Aplasia/Hypoplasia of the middle ear" - }, - { - "type": "custom", - "id": "ownsIPhone", - "label": "Individuals associated with this term owns an IPhone" - } - ] - }, - "info": {} -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconInfo-MAX-example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconInfo-MAX-example.json deleted file mode 100644 index a5a60f007..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconInfo-MAX-example.json +++ /dev/null @@ -1,43 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "string", - "apiVersion": "string", - "returnedSchemas": [ - { - "entityType": "info", - "schema": "beacon-info-v2.0.0" - } - ] - }, - "response": { - "id": "org.ga4gh.beacon", - "name": "string", - "apiVersion": "v0.3", - "environment": "dev", - "organization": { - "id": "string", - "name": "string", - "description": "string", - "address": "string", - "welcomeUrl": "string", - "contactUrl": "string", - "logoUrl": "string", - "info": {} - }, - "description": "string", - "version": "v0.1", - "welcomeUrl": "http://example.org/wiki/Main_Page", - "alternativeUrl": "http://example.org/wiki/Main_Page", - "createDateTime": "2012-07-19 or 2017-01-17T20:33:40Z", - "updateDateTime": "2012-07-19 or 2017-01-17T20:33:40Z", - "info": { - "additionalInfoKey1": "additionalInfoValue1", - "additionalInfoKey2": [ - "additionalInfoValue2", - "additionalInfoValue3" - ] - } - }, - "info": {} -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconInfo-MIN-example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconInfo-MIN-example.json deleted file mode 100644 index 9a6166258..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconInfo-MIN-example.json +++ /dev/null @@ -1,23 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "string", - "apiVersion": "string", - "returnedSchemas": [ - { - "entityType": "info", - "schema": "beacon-info-v2.0.0" - } - ] - }, - "response": { - "id": "org.ga4gh.beacon", - "name": "string", - "apiVersion": "v0.3", - "environment": "dev", - "organization": { - "id": "string", - "name": "string" - } - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconMapResponse-example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconMapResponse-example.json deleted file mode 100644 index be3a5f570..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconMapResponse-example.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "string", - "apiVersion": "string", - "returnedSchemas": [ - { - "entityType": "info", - "schema": "beacon-map-v2.0.0" - } - ] - }, - "response": { - "$schema": "../../configuration/beaconMapSchema.json", - "endpointSets": { - "dataset": { - "entryType": "dataset", - "openAPIEndpointsDefinition": "./datasets/endpoints.json", - "rootUrl": "https://exampleBeacons.org/datasets", - "singleEntryUrl": "https://exampleBeacons.org/datasets/{id}", - "filteringTermsUrl": "https://exampleBeacons.org/datasets/{id}/filteringTerms", - "endpoints": { - "exampleEntries": { - "returnedEntryType": "exampleEntry", - "url": "https://exampleBeacons.org/datasets/{id}/exampleEntries" - } - } - }, - "exampleEntry": { - "entryType": "exampleEntry", - "openAPIEndpointsDefinition": "./exampleEntries/endpoints.json", - "rootUrl": "https://exampleBeacons.org/exampleEntries", - "singleEntryUrl": "https://exampleBeacons.org/exampleEntries/{id}", - "filteringTermsUrl": "https://exampleBeacons.org/exampleEntries/{id}/filteringTerms" - } - } - }, - "info": {} -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconResultsetResponse-MIN-example.json b/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconResultsetResponse-MIN-example.json deleted file mode 100644 index 6b5546ac1..000000000 --- a/bycon/schemas/framework/json/responses/examples-fullDocuments/beaconResultsetResponse-MIN-example.json +++ /dev/null @@ -1,30 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "meta": { - "beaconId": "org.example.beacon.v2", - "apiVersion": "v2.0", - "returnedSchemas": [ - { - "entityType": "EntryTypeB", - "schema": "entry-typeB-schema-v1.0" - } - ], - "receivedRequestSummary": { - "apiVersion": "2.0", - "requestedSchemas": [ - { - "entityType": "EntryTypeB", - "schema": "entry-typeB-schema-v1.0" - } - ], - "pagination": { - "skip": 0, - "limit": 10 - } - } - }, - "responseSummary": { - "exists": true - }, - "resultSets": [] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-sections/beaconBooleanResponseSection-example.json b/bycon/schemas/framework/json/responses/examples-sections/beaconBooleanResponseSection-example.json deleted file mode 100644 index 864453272..000000000 --- a/bycon/schemas/framework/json/responses/examples-sections/beaconBooleanResponseSection-example.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "exists": true -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-sections/beaconCountResponseSection-example.json b/bycon/schemas/framework/json/responses/examples-sections/beaconCountResponseSection-example.json deleted file mode 100644 index 2d37e996c..000000000 --- a/bycon/schemas/framework/json/responses/examples-sections/beaconCountResponseSection-example.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "exists": true, - "numTotalResults": 45363 -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-sections/beaconInformationalResponseMeta-example.json b/bycon/schemas/framework/json/responses/examples-sections/beaconInformationalResponseMeta-example.json deleted file mode 100644 index 6cf1511ac..000000000 --- a/bycon/schemas/framework/json/responses/examples-sections/beaconInformationalResponseMeta-example.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "beaconId": "org.examplebeacons.beacon-v2", - "apiVersion": "v2.0", - "returnedSchemas": [] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-sections/beaconReceivedRequestSummary-MAX-example.json b/bycon/schemas/framework/json/responses/examples-sections/beaconReceivedRequestSummary-MAX-example.json deleted file mode 100644 index 48576c07e..000000000 --- a/bycon/schemas/framework/json/responses/examples-sections/beaconReceivedRequestSummary-MAX-example.json +++ /dev/null @@ -1,30 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "apiVersion": "v2.0", - "requestedSchemas": [ - { - "entityType": "Individual", - "schema": "ga4gh-phenopacket-individual-v0.1" - } - ], - "requestParameters": { - "individual": { - "parameters": [ - { - "id": "123" - } - ] - } - }, - "IncludeResultsetResponses": "HIT", - "filters": [ - "BTO:0000199", - "PATO:0000383" - ], - "pagination": { - "skip": 1, - "limit": 10 - }, - "testMode": false, - "requestedGranularity": "count" -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-sections/beaconReceivedRequestSummary-MIN-example.json b/bycon/schemas/framework/json/responses/examples-sections/beaconReceivedRequestSummary-MIN-example.json deleted file mode 100644 index f88151035..000000000 --- a/bycon/schemas/framework/json/responses/examples-sections/beaconReceivedRequestSummary-MIN-example.json +++ /dev/null @@ -1,7 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "apiVersion": "v2.0", - "requestedSchemas": [], - "pagination": {}, - "requestedGranularity": "boolean" -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-sections/beaconResponseMeta-example.json b/bycon/schemas/framework/json/responses/examples-sections/beaconResponseMeta-example.json deleted file mode 100644 index 702dfca82..000000000 --- a/bycon/schemas/framework/json/responses/examples-sections/beaconResponseMeta-example.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "beaconId": "org.example.beacon.v2", - "apiVersion": "v2.0", - "returnedSchemas": [ - { - "entityType": "EntryTypeB", - "schema": "entry-typeB-schema-v1.0" - } - ], - "returnedGranularity": "count", - "receivedRequestSummary": { - "apiVersion": "2.0", - "requestedSchemas": [ - { - "entityType": "EntryTypeB", - "schema": "entry-typeB-schema-v1.0" - } - ], - "pagination": { - "skip": 0, - "limit": 10 - }, - "testMode": true, - "requestedGranularity": "count" - } -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-sections/beaconResultsetEmpty-example.json b/bycon/schemas/framework/json/responses/examples-sections/beaconResultsetEmpty-example.json deleted file mode 100644 index 65decb75e..000000000 --- a/bycon/schemas/framework/json/responses/examples-sections/beaconResultsetEmpty-example.json +++ /dev/null @@ -1,10 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "resultSets": [ - { - "id": "correctEmptyResultSet", - "type": "dataset", - "exists": false - } - ] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-sections/beaconResultsets-MAX-example.json b/bycon/schemas/framework/json/responses/examples-sections/beaconResultsets-MAX-example.json deleted file mode 100644 index 3f84bedc9..000000000 --- a/bycon/schemas/framework/json/responses/examples-sections/beaconResultsets-MAX-example.json +++ /dev/null @@ -1,36 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "resultSets": [ - { - "id": "datasetA", - "type": "dataset", - "exists": false - }, - { - "id": "datasetB", - "type": "dataset", - "exists": true, - "resultsCount": 2, - "resultsHandovers": [ - { - "handoverType": { - "id": "EFO:0004157", - "label": "BAM format" - }, - "url": "https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0", - "note": "This handover link provides access to a summarized VCF." - } - ], - "results": [ - { - "id": "BEex3", - "name": "Basic Element example three" - }, - { - "id": "BEex4", - "name": "Basic Element example four" - } - ] - } - ] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-sections/beaconResultsets-MID-example.json b/bycon/schemas/framework/json/responses/examples-sections/beaconResultsets-MID-example.json deleted file mode 100644 index 4d131b7d5..000000000 --- a/bycon/schemas/framework/json/responses/examples-sections/beaconResultsets-MID-example.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "resultSets": [ - { - "id": "correctWithResults", - "type": "dataset", - "exists": true, - "resultsCount": 1, - "results": [ - { - "id": "BEex1", - "name": "Basic Element example one" - } - ] - }, - { - "id": "correctWOresults", - "type": "dataset", - "exists": false - } - ] -} \ No newline at end of file diff --git a/bycon/schemas/framework/json/responses/examples-sections/beaconResultsets-MIN-example.json b/bycon/schemas/framework/json/responses/examples-sections/beaconResultsets-MIN-example.json deleted file mode 100644 index 4a05c045c..000000000 --- a/bycon/schemas/framework/json/responses/examples-sections/beaconResultsets-MIN-example.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "resultSets": [] -} \ No newline at end of file diff --git a/bycon/schemas/framework/src/common/examples/basicElement-example.yaml b/bycon/schemas/framework/src/common/examples/basicElement-example.yaml deleted file mode 100644 index eb95fb2dd..000000000 --- a/bycon/schemas/framework/src/common/examples/basicElement-example.yaml +++ /dev/null @@ -1,3 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -id: BEex1 -name: Basic Element example one diff --git a/bycon/schemas/framework/src/common/examples/beaconCommonComponents-example.yaml b/bycon/schemas/framework/src/common/examples/beaconCommonComponents-example.yaml deleted file mode 100644 index 8183f01ce..000000000 --- a/bycon/schemas/framework/src/common/examples/beaconCommonComponents-example.yaml +++ /dev/null @@ -1,44 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -beaconId: org.example.beacon.v2 -apiVersion: v2.0 -beaconError: - errorCode: 404 - errorMessage: the provided parameters are incomplete. 'xyz' is missing. -listOfSchemas: - - entityType: EntryTypeA - schema: entry-typeA-schema-v0.1 - - entityType: EntryTypeB - schema: entry-typeB-schema-v1.0 -schemasPerEntity: - entityType: Individual - schema: ga4gh-phenopacket-individual-v0.1 -pagination: - skip: 0 - limit: 10 -includeResultsetResponses: HIT -filters: - - BTO:0000199 - - PATO:0000383 -exists: true -numTotalResults: 123 -info: {} -handover: - handoverType: - id: EFO:0004157 - label: BAM format - url: https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0 - note: This handover link provides access to a summarized VCF. -handoverType: - id: EFO:0004157 - label: BAM format -listOfHandovers: - - handoverType: - id: EFO:0004157 - label: BAM format - url: https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0 - note: This handover link provides access to a summarized VCF. - - handoverType: - id: EFO:0004157 - label: BAM format - url: https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0 - note: This handover link provides access to a summarized VCF. diff --git a/bycon/schemas/framework/src/common/examples/elementWithDescription-example.yaml b/bycon/schemas/framework/src/common/examples/elementWithDescription-example.yaml deleted file mode 100644 index fd3516e7c..000000000 --- a/bycon/schemas/framework/src/common/examples/elementWithDescription-example.yaml +++ /dev/null @@ -1,4 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -id: EWDex1 -name: Element with description one -description: A longer textual description for the element. diff --git a/bycon/schemas/framework/src/common/examples/ontologizedElement-example.yaml b/bycon/schemas/framework/src/common/examples/ontologizedElement-example.yaml deleted file mode 100644 index 80ac707e6..000000000 --- a/bycon/schemas/framework/src/common/examples/ontologizedElement-example.yaml +++ /dev/null @@ -1,7 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -id: OEex1 -name: Element with a description and associated ontology term. -description: Non-mandatory, longer textual description for the element. -ontologyTermForThisType: - id: DUO:0000004 - label: General Research Use diff --git a/bycon/schemas/framework/src/common/examples/ontologyTerm-example.yaml b/bycon/schemas/framework/src/common/examples/ontologyTerm-example.yaml deleted file mode 100644 index e891e465a..000000000 --- a/bycon/schemas/framework/src/common/examples/ontologyTerm-example.yaml +++ /dev/null @@ -1,3 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -id: DUO:0000004 -label: General Research Use diff --git a/bycon/schemas/framework/src/common/examples/referenceToAnSchema-MAX-example.yaml b/bycon/schemas/framework/src/common/examples/referenceToAnSchema-MAX-example.yaml deleted file mode 100644 index b8b11ca91..000000000 --- a/bycon/schemas/framework/src/common/examples/referenceToAnSchema-MAX-example.yaml +++ /dev/null @@ -1,6 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -id: RTAEex1 -name: Reference to schema one with all its properties. -description: A longer textual description for the element. -referenceToSchemaDefinition: https://example-schemas.org/an-schema-address.json -schemaVersion: v1.0 diff --git a/bycon/schemas/framework/src/common/examples/referenceToAnSchema-MIN-example.yaml b/bycon/schemas/framework/src/common/examples/referenceToAnSchema-MIN-example.yaml deleted file mode 100644 index 003f6d312..000000000 --- a/bycon/schemas/framework/src/common/examples/referenceToAnSchema-MIN-example.yaml +++ /dev/null @@ -1,4 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -id: RTAEex1 -name: Reference to schema one with all its properties. -referenceToSchemaDefinition: https://example-schemas.org/an-schema-address.json diff --git a/bycon/schemas/framework/src/common/validation/beaconCommonComponents.yaml b/bycon/schemas/framework/src/common/validation/beaconCommonComponents.yaml deleted file mode 100644 index 83d74e56f..000000000 --- a/bycon/schemas/framework/src/common/validation/beaconCommonComponents.yaml +++ /dev/null @@ -1,37 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -title: Schema for validating Beacon Common Components examples -type: object -properties: - $schema: - type: string - description: Added here to allow the example to comply with the 'additionalProperties:true' - restriction. - beaconId: - $ref: ../beaconCommonComponents.yaml#/$defs/BeaconId - apiVersion: - $ref: ../beaconCommonComponents.yaml#/$defs/ApiVersion - beaconError: - $ref: ../beaconCommonComponents.yaml#/$defs/BeaconError - listOfSchemas: - $ref: ../beaconCommonComponents.yaml#/$defs/ListOfSchemas - schemasPerEntity: - $ref: ../beaconCommonComponents.yaml#/$defs/SchemasPerEntity - pagination: - $ref: ../beaconCommonComponents.yaml#/$defs/Pagination - includeResultsetResponses: - $ref: ../beaconCommonComponents.yaml#/$defs/IncludeResultsetResponses - filters: - $ref: ../beaconCommonComponents.yaml#/$defs/Filters - exists: - $ref: ../beaconCommonComponents.yaml#/$defs/Exists - numTotalResults: - $ref: ../beaconCommonComponents.yaml#/$defs/NumTotalResults - info: - $ref: ../beaconCommonComponents.yaml#/$defs/Info - handover: - $ref: ../beaconCommonComponents.yaml#/$defs/Handover - handoverType: - $ref: ../beaconCommonComponents.yaml#/$defs/HandoverType - listOfHandovers: - $ref: ../beaconCommonComponents.yaml#/$defs/ListOfHandovers -additionalProperties: false diff --git a/bycon/schemas/framework/src/configuration/examples/beaconConfiguration-example.yaml b/bycon/schemas/framework/src/configuration/examples/beaconConfiguration-example.yaml deleted file mode 100644 index fbd34966b..000000000 --- a/bycon/schemas/framework/src/configuration/examples/beaconConfiguration-example.yaml +++ /dev/null @@ -1,48 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -maturityAttributes: - productionStatus: DEV -securityAttributes: - defaultGranularity: boolean - securityLevels: - - PUBLIC - - REGISTERED - - CONTROLLED -entryTypes: - dataset: - id: dataset - name: Dataset - ontologyTermForThisType: - id: NCIT:C47824 - label: Data set - partOfSpecification: Beacon v2.0 - description: A Dataset is a collection of records, like rows in a database or - cards in a cardholder. - defaultSchema: - id: datasetDefaultSchema - name: Default schema for datasets - referenceToSchemaDefinition: ./datasets/defaultSchema.json - schemaVersion: v.2 - aCollectionOf: - - id: exampleEntry - name: Example entries - endpoint: /datasets - filteringTermsReference: ./datasets/filteringTerms.json - additionallySupportedSchemas: [] - nonFilteredQueriesAllowed: true - exampleEntry: - id: exampleEntry - name: Example Entry - ontologyTermForThisType: - id: NCIT:C20181 - label: Conceptual Entity - partOfSpecification: Beacon v2.0 - description: A generic entry type to allow testing and playing with the specification. - defaultSchema: - id: ExampleEntryTypeDefaultschema - name: Default schema for an example entries - referenceToSchemaDefinition: ./exampleEntry/defaultSchema.json - schemaVersion: v.2 - endpoint: ./exampleEntries - filteringTermsReference: ./exampleEntry/filteringTerms.json - additionallySupportedSchemas: [] - nonFilteredQueriesAllowed: false diff --git a/bycon/schemas/framework/src/configuration/examples/beaconConfigurationFilteringTerms-example.yaml b/bycon/schemas/framework/src/configuration/examples/beaconConfigurationFilteringTerms-example.yaml deleted file mode 100644 index 6218e18cc..000000000 --- a/bycon/schemas/framework/src/configuration/examples/beaconConfigurationFilteringTerms-example.yaml +++ /dev/null @@ -1,13 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -filteringTerms: - - ftType: alphanumeric - id: age - scope: individual - - ftType: ontologyTerm - id: HP:0002664 - label: Neoplasm - scope: biosample - - ftType: alphanumeric - id: NCIT:C100094 - label: HGNC gene name - scope: genomicVariant diff --git a/bycon/schemas/framework/src/configuration/examples/beaconMap-MIN-example.yaml b/bycon/schemas/framework/src/configuration/examples/beaconMap-MIN-example.yaml deleted file mode 100644 index be65cc24d..000000000 --- a/bycon/schemas/framework/src/configuration/examples/beaconMap-MIN-example.yaml +++ /dev/null @@ -1,5 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -endpointSets: - datasets: - entryType: dataset - rootUrl: https://exampleBeacons.org/datasets diff --git a/bycon/schemas/framework/src/configuration/examples/beaconMap-example.yaml b/bycon/schemas/framework/src/configuration/examples/beaconMap-example.yaml deleted file mode 100644 index f6e2d1567..000000000 --- a/bycon/schemas/framework/src/configuration/examples/beaconMap-example.yaml +++ /dev/null @@ -1,18 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -endpointSets: - dataset: - entryType: dataset - openAPIEndpointsDefinition: ./datasets/endpoints.json - rootUrl: https://exampleBeacons.org/datasets - singleEntryUrl: https://exampleBeacons.org/datasets/{id} - filteringTermsUrl: https://exampleBeacons.org/datasets/{id}/filteringTerms - endpoints: - exampleEntries: - returnedEntryType: exampleEntry - url: https://exampleBeacons.org/datasets/{id}/exampleEntries - exampleEntry: - entryType: exampleEntry - openAPIEndpointsDefinition: ./exampleEntries/endpoints.json - rootUrl: https://exampleBeacons.org/exampleEntries - singleEntryUrl: https://exampleBeacons.org/exampleEntries/{id} - filteringTermsUrl: https://exampleBeacons.org/exampleEntries/{id}/filteringTerms diff --git a/bycon/schemas/framework/src/configuration/examples/entriesCollectionDefinition_MIN_example.yaml b/bycon/schemas/framework/src/configuration/examples/entriesCollectionDefinition_MIN_example.yaml deleted file mode 100644 index d9200f7ee..000000000 --- a/bycon/schemas/framework/src/configuration/examples/entriesCollectionDefinition_MIN_example.yaml +++ /dev/null @@ -1,15 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -id: dataset -name: Dataset -ontologyTermForThisType: - id: NCIT:C47824 - label: Data set -partOfSpecification: Beacon v2.0 -defaultSchema: - id: datasetDefaultSchema - name: Default schema for datasets - referenceToSchemaDefinition: ./datasets/defaultSchema.json - schemaVersion: v.2 -aCollectionOf: - - id: exampleEntry - name: Example entries diff --git a/bycon/schemas/framework/src/configuration/examples/entriesCollectionDefinition_example.yaml b/bycon/schemas/framework/src/configuration/examples/entriesCollectionDefinition_example.yaml deleted file mode 100644 index e2e800528..000000000 --- a/bycon/schemas/framework/src/configuration/examples/entriesCollectionDefinition_example.yaml +++ /dev/null @@ -1,27 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -id: dataset -name: Dataset -ontologyTermForThisType: - id: NCIT:C47824 - label: Data set -partOfSpecification: Beacon v2.0 -description: A Dataset is a collection of records, like rows in a database or cards - in a cardholder. -defaultSchema: - id: datasetDefaultSchema - name: Default schema for datasets - referenceToSchemaDefinition: ./datasets/defaultSchema.json - schemaVersion: v.2 -aCollectionOf: - - id: exampleEntry - name: Example entries -endpoint: /datasets -filteringTermsReference: ./datasets/filteringTerms.json -additionallySupportedSchemas: - - id: ohdsi-atlas-cohort - name: OHDSI ATLAS Cohort - description: ATLAS is an open source software tool for researchers to conduct - scientific analyses on standardized observational data converted to the OMOP - Common Data Model V5. - referenceToSchemaDefinition: https://raw.githubusercontent.com/OHDSIBr/ATLAS-JSON-Schema/2.7.4/single/atlas_cohort_definition.json - schemaVersion: 2.7.4 diff --git a/bycon/schemas/framework/src/configuration/examples/entryTypeDefinition-MIN-example.yaml b/bycon/schemas/framework/src/configuration/examples/entryTypeDefinition-MIN-example.yaml deleted file mode 100644 index 3d402ba7b..000000000 --- a/bycon/schemas/framework/src/configuration/examples/entryTypeDefinition-MIN-example.yaml +++ /dev/null @@ -1,11 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -id: individual -name: Individual entry -ontologyTermForThisType: - id: DUO:0000004 - label: General Research Use -partOfSpecification: Beacon v2 -defaultSchema: - id: bdfGenericEntryType-v2 - name: Beacon v2 default schema for a basic element. - referenceToSchemaDefinition: https://raw.githubusercontent.com/ga4gh-beacon/specification-v2-default-schemas/master/default_dataset_schema.yaml diff --git a/bycon/schemas/framework/src/requests/examples-fullDocuments/beaconRequestBody-MAX-example.yaml b/bycon/schemas/framework/src/requests/examples-fullDocuments/beaconRequestBody-MAX-example.yaml deleted file mode 100644 index 0d6fc8f10..000000000 --- a/bycon/schemas/framework/src/requests/examples-fullDocuments/beaconRequestBody-MAX-example.yaml +++ /dev/null @@ -1,21 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - apiVersion: '2.0' - requestedSchemas: - - entityType: EntryTypeA - schema: entry-typeA-schema-v0.1 -query: - requestParameters: - datasets: - datasetIds: - - DatasetXYZ - - Dataset123 - filters: - - id: EFO:0001212 - scope: biosamples - includeResultsetResponses: HIT - pagination: - skip: 0 - limit: 10 - testMode: false - requestedGranularity: boolean diff --git a/bycon/schemas/framework/src/requests/examples-fullDocuments/beaconRequestBody-MIN-example.yaml b/bycon/schemas/framework/src/requests/examples-fullDocuments/beaconRequestBody-MIN-example.yaml deleted file mode 100644 index a9898a8ce..000000000 --- a/bycon/schemas/framework/src/requests/examples-fullDocuments/beaconRequestBody-MIN-example.yaml +++ /dev/null @@ -1,3 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - apiVersion: '2.0' diff --git a/bycon/schemas/framework/src/requests/examples-sections/beaconRequestMeta-example.yaml b/bycon/schemas/framework/src/requests/examples-sections/beaconRequestMeta-example.yaml deleted file mode 100644 index a8a84a866..000000000 --- a/bycon/schemas/framework/src/requests/examples-sections/beaconRequestMeta-example.yaml +++ /dev/null @@ -1,5 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -apiVersion: '2.0' -requestedSchemas: - - entityType: EntryTypeA - schema: entry-typeA-schema-v0.1 diff --git a/bycon/schemas/framework/src/requests/examples-sections/filteringTerms-example.yaml b/bycon/schemas/framework/src/requests/examples-sections/filteringTerms-example.yaml deleted file mode 100644 index 9f518eb09..000000000 --- a/bycon/schemas/framework/src/requests/examples-sections/filteringTerms-example.yaml +++ /dev/null @@ -1,12 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -filters: - - id: HP:0002664 - includeDescendantTerms: true - similarity: exact - scope: biosamples - - id: age - operator: '>=' - value: P70Y - scope: individuals - - id: demographic.ethnicity:asian - scope: cohorts diff --git a/bycon/schemas/framework/src/requests/examples-sections/requestParameters-example.yaml b/bycon/schemas/framework/src/requests/examples-sections/requestParameters-example.yaml deleted file mode 100644 index de757452a..000000000 --- a/bycon/schemas/framework/src/requests/examples-sections/requestParameters-example.yaml +++ /dev/null @@ -1,9 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -exampleEntry: - description: "All the required fields to query any kind of variant (e.g. SNP, DUP,\n\ - etc.)." - type: object - properties: - id: - description: Id of the entry to display. - type: string diff --git a/bycon/schemas/framework/src/requests/validation/filteringTerms.yaml b/bycon/schemas/framework/src/requests/validation/filteringTerms.yaml deleted file mode 100644 index 181d03559..000000000 --- a/bycon/schemas/framework/src/requests/validation/filteringTerms.yaml +++ /dev/null @@ -1,88 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -title: Filtering Term Element -description: Rules for selecting records based upon the field values those records - contain. Filters are seperated by the logical AND operator. -properties: - $schema: - type: string - description: Added here to allow the example to comply with the 'additionalProperties:true' - restriction. - filters: - type: array - items: - anyOf: - - $ref: '#/$defs/OntologyFilter' - - $ref: '#/$defs/AlphanumericFilter' - - $ref: '#/$defs/CustomFilter' -$defs: - OntologyFilter: - type: object - description: Filter results to include records that contain a specific ontology - term. - required: - - id - properties: - id: - type: string - description: Term ID to be queried, using CURIE syntax where possible. - example: HP:0002664 - includeDescendantTerms: - type: boolean - default: true - description: Define if the Beacon should implement the ontology hierarchy, - thus query the descendant terms of `id`. - similarity: - type: string - enum: - - exact - - high - - medium - - low - default: exact - description: Allow the Beacon to return results which do not match the filter - exactly, but do match to a certain degree of similarity. The Beacon defines - the semantic similarity model implemented and how to apply the thresholds - of 'high', 'medium' and 'low' similarity. - AlphanumericFilter: - description: Filter results based on operators and values applied to alphanumeric - fields. - type: object - required: - - id - - operator - - value - properties: - id: - type: string - description: Field identfier to be queried. - example: age - operator: - type: string - enum: - - '=' - - < - - '>' - - '!' - - '>=' - - <= - description: Defines how the value relates to the field `id`. - default: '=' - example: '>' - value: - type: string - description: Alphanumeric search term to be used within the query which can - contain wildcard characters (%) to denote any number of unknown characters. Values - can be assocatied with units if applicable. - example: P70Y - CustomFilter: - type: object - description: Filter results to include records that contain a custom term defined - by this Beacon. - required: - - id - properties: - id: - type: string - description: Custom filter terms should contain a unique identifier. - example: demographic.ethnicity:asian -additionalProperties: false diff --git a/bycon/schemas/framework/src/responses/beaconCollectionsResponse.yaml b/bycon/schemas/framework/src/responses/beaconCollectionsResponse.yaml index 8b895ce6f..948fd2931 100644 --- a/bycon/schemas/framework/src/responses/beaconCollectionsResponse.yaml +++ b/bycon/schemas/framework/src/responses/beaconCollectionsResponse.yaml @@ -1,5 +1,9 @@ $schema: https://json-schema.org/draft/2020-12/schema -description: Beacon response that includes details about the collections in this Beacon. +description: >- + A type of Beacon response that includes details about the **collections** in a + beacon. The types of collections are defined in each beacon's configuration; + if using the Beacon v2+ default model usually the types `dataset` and `cohort` + are supported. type: object properties: meta: diff --git a/bycon/schemas/framework/src/responses/beaconResultsetsResponse.yaml b/bycon/schemas/framework/src/responses/beaconResultsetsResponse.yaml index 11e8b732c..b83128fc5 100644 --- a/bycon/schemas/framework/src/responses/beaconResultsetsResponse.yaml +++ b/bycon/schemas/framework/src/responses/beaconResultsetsResponse.yaml @@ -1,5 +1,11 @@ $schema: https://json-schema.org/draft/2020-12/schema -description: Beacon response that includes record level details, grouped in Resultsets. +description: >- + A `beaconResultsetsResponse` returns the results of a query against a beacon, + which - beyond the summary count response for overall matches - contains details + about the matches in individual **collections** in the beacon or beacon network. + The types of `beaconResultsets` objects are defined in the beacon's configuration; + if using the Beacon v2+ default model the types `dataset` and `cohort` are supported. + `beaconResultsets` typically contain a list of records matched by the query. type: object properties: meta: diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconBooleanResponse-example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconBooleanResponse-example.yaml deleted file mode 100644 index b07490ac4..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconBooleanResponse-example.yaml +++ /dev/null @@ -1,17 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: org.example.beacon.v2 - apiVersion: v2.0 - returnedSchemas: - - entityType: EntryTypeB - schema: entry-typeB-schema-v1.0 - receivedRequestSummary: - apiVersion: '2.0' - requestedSchemas: - - entityType: EntryTypeB - schema: entry-typeB-schema-v1.0 - pagination: - skip: 0 - limit: 10 -responseSummary: - exists: true diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconCollectionsResponse-MID-example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconCollectionsResponse-MID-example.yaml deleted file mode 100644 index 5b83a5441..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconCollectionsResponse-MID-example.yaml +++ /dev/null @@ -1,45 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: org.example.beacon.v2 - apiVersion: v2.0 - returnedSchemas: - - entityType: dataset - schema: dataset-schema-v1.0 - receivedRequestSummary: - apiVersion: '2.0' - requestedSchemas: - - entityType: dataset - schema: dataset-schema-v1.0 - pagination: - skip: 0 - limit: 10 -responseSummary: - exists: true -response: - collections: - - $schema: https://schemas-fake-depot.org/beaconv2/datasetSchema.json - id: Dataset1 - name: Dataset One - description: This is the first dataset - createDateTime: '2011-01-11T11:11:11Z' - updateDateTime: '2011-01-11T11:11:11Z' - version: v1 - dataUseConditions: - duoDataUse: - - id: DUO:0000007 - label: disease specific research - modifiers: - - id: HP:0001631 - version: '2021-02-23' - - $schema: https://schemas-fake-depot.org/beaconv2/datasetSchema.json - id: Dataset2 - name: Dataset Two - description: This is the second dataset - createDateTime: '2012-02-22T22:22:22Z' - updateDateTime: '2012-02-22T22:22:22Z' - version: v2 - dataUseConditions: - duoDataUse: - - id: DUO:0000042 - label: general research use - version: '2021-02-23' diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconCollectionsResponse-MIN-example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconCollectionsResponse-MIN-example.yaml deleted file mode 100644 index 0b54963c0..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconCollectionsResponse-MIN-example.yaml +++ /dev/null @@ -1,19 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: org.example.beacon.v2 - apiVersion: v2.0 - returnedSchemas: - - entityType: dataset - schema: dataset-schema-v1.0 - receivedRequestSummary: - apiVersion: '2.0' - requestedSchemas: - - entityType: dataset - schema: dataset-schema-v1.0 - pagination: - skip: 0 - limit: 10 -responseSummary: - exists: true -response: - collections: [] diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconConfigurationResponse-example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconConfigurationResponse-example.yaml deleted file mode 100644 index a1d5d8eed..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconConfigurationResponse-example.yaml +++ /dev/null @@ -1,55 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: string - apiVersion: string - returnedSchemas: - - entityType: info - schema: beacon-map-v2.0.0 -response: - $schema: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/configuration/beaconConfigurationSchema.json - maturityAttributes: - productionStatus: DEV - securityAttributes: - defaultGranularity: boolean - securityLevels: - - PUBLIC - - REGISTERED - - CONTROLLED - entryTypes: - dataset: - id: dataset - name: Dataset - ontologyTermForThisType: - id: NCIT:C47824 - label: Data set - partOfSpecification: Beacon v2.0 - description: A Dataset is a collection of records, like rows in a database or - cards in a cardholder. - defaultSchema: - id: datasetDefaultSchema - name: Default schema for datasets - referenceToSchemaDefinition: ./datasets/defaultSchema.json - schemaVersion: v.2 - aCollectionOf: - - id: exampleEntry - name: Example entries - endpoint: /datasets - filteringTermsReference: ./datasets/filteringTerms.json - additionallySupportedSchemas: [] - exampleEntry: - id: exampleEntry - name: Example Entry - ontologyTermForThisType: - id: NCIT:C20181 - label: Conceptual Entity - partOfSpecification: Beacon v2.0 - description: A generic entry type to allow testing and playing with the specification. - defaultSchema: - id: ExampleEntryTypeDefaultschema - name: Default schema for an example entries - referenceToSchemaDefinition: ./exampleEntry/defaultSchema.json - schemaVersion: v.2 - endpoint: ./exampleEntries - filteringTermsReference: ./exampleEntry/filteringTerms.json - additionallySupportedSchemas: [] -info: {} diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconCountResponse-example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconCountResponse-example.yaml deleted file mode 100644 index 516a777f8..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconCountResponse-example.yaml +++ /dev/null @@ -1,31 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: org.example.beacon.v2 - apiVersion: v2.0 - returnedSchemas: - - entityType: EntryTypeB - schema: entry-typeB-schema-v1.0 - receivedRequestSummary: - apiVersion: '2.0' - requestedSchemas: - - entityType: EntryTypeB - schema: entry-typeB-schema-v1.0 - pagination: - skip: 0 - limit: 10 -responseSummary: - exists: true - numTotalResults: 25355 -info: - someInterestingStuff: this is the interesting stuff -beaconHandovers: - - handoverType: - id: EFO:0004157 - label: BAM format - url: https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0 - note: This handover link provides access to a summarized VCF. - - handoverType: - id: EFO:0004157 - label: BAM format - url: https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0 - note: This handover link provides access to a summarized VCF. diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconEntryTypesResponse-example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconEntryTypesResponse-example.yaml deleted file mode 100644 index 635bc54fa..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconEntryTypesResponse-example.yaml +++ /dev/null @@ -1,47 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: string - apiVersion: string - returnedSchemas: - - entityType: info - schema: beacon-map-v2.0.0 -response: - $schema: ../../configuration/entryTypesSchema.json - entryTypes: - dataset: - id: dataset - name: Dataset - ontologyTermForThisType: - id: NCIT:C47824 - label: Data set - partOfSpecification: Beacon v2.0 - description: A Dataset is a collection of records, like rows in a database or - cards in a cardholder. - defaultSchema: - id: datasetDefaultSchema - name: Default schema for datasets - referenceToSchemaDefinition: ./datasets/defaultSchema.json - schemaVersion: v.2 - aCollectionOf: - - id: exampleEntry - name: Example entries - endpoint: /datasets - filteringTermsReference: ./datasets/filteringTerms.json - additionallySupportedSchemas: [] - exampleEntry: - id: exampleEntry - name: Example Entry - ontologyTermForThisType: - id: NCIT:C20181 - label: Conceptual Entity - partOfSpecification: Beacon v2.0 - description: A generic entry type to allow testing and playing with the specification. - defaultSchema: - id: ExampleEntryTypeDefaultschema - name: Default schema for an example entries - referenceToSchemaDefinition: ./exampleEntry/defaultSchema.json - schemaVersion: v.2 - endpoint: ./exampleEntries - filteringTermsReference: ./exampleEntry/filteringTerms.json - additionallySupportedSchemas: [] -info: {} diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconErrorResponse_example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconErrorResponse_example.yaml deleted file mode 100644 index dd8b6cf2c..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconErrorResponse_example.yaml +++ /dev/null @@ -1,24 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: org.example.beacon.v2 - apiVersion: v2.0 - receivedRequestSummary: - apiVersion: v2.0 - requestedSchemas: - - entityType: Individual - schema: ga4gh-phenopacket-individual-v0.1 - requestParameters: - - entity: individual - parameters: - - id: '123' - - position: '1234556' - filters: - - BTO:0000199 - - PATO:0000383 - pagination: - skip: 1 - limit: 10 - returnedSchemas: [] -error: - errorCode: 400 - errorMessage: Bad request. Missing parameter 'id'. diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconFilteringTermsResponse-example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconFilteringTermsResponse-example.yaml deleted file mode 100644 index 8af3f8d58..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconFilteringTermsResponse-example.yaml +++ /dev/null @@ -1,25 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: string - apiVersion: string - returnedSchemas: - - map: beacon-map-v2.0.0 -response: - resources: - - id: hp - name: Human Phenotype Ontology - url: http://purl.obolibrary.org/obo/hp.owl - version: 27-03-2020 - namespacePrefix: HP - iriPrefix: http://purl.obolibrary.org/obo/HP_ - filteringTerms: - - type: numeric - id: PATO:0000011 - label: age - - type: Human Phenotype Ontology - id: HP:0008773 - label: Aplasia/Hypoplasia of the middle ear - - type: custom - id: ownsIPhone - label: Individuals associated with this term owns an IPhone -info: {} diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconInfo-MAX-example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconInfo-MAX-example.yaml deleted file mode 100644 index 5d5e1b5d4..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconInfo-MAX-example.yaml +++ /dev/null @@ -1,33 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: string - apiVersion: string - returnedSchemas: - - entityType: info - schema: beacon-info-v2.0.0 -response: - id: org.ga4gh.beacon - name: string - apiVersion: v0.3 - environment: dev - organization: - id: string - name: string - description: string - address: string - welcomeUrl: string - contactUrl: string - logoUrl: string - info: {} - description: string - version: v0.1 - welcomeUrl: http://example.org/wiki/Main_Page - alternativeUrl: http://example.org/wiki/Main_Page - createDateTime: 2012-07-19 or 2017-01-17T20:33:40Z - updateDateTime: 2012-07-19 or 2017-01-17T20:33:40Z - info: - additionalInfoKey1: additionalInfoValue1 - additionalInfoKey2: - - additionalInfoValue2 - - additionalInfoValue3 -info: {} diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconInfo-MIN-example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconInfo-MIN-example.yaml deleted file mode 100644 index 2f8a5821f..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconInfo-MIN-example.yaml +++ /dev/null @@ -1,15 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: string - apiVersion: string - returnedSchemas: - - entityType: info - schema: beacon-info-v2.0.0 -response: - id: org.ga4gh.beacon - name: string - apiVersion: v0.3 - environment: dev - organization: - id: string - name: string diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconMapResponse-example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconMapResponse-example.yaml deleted file mode 100644 index 9fd9f339d..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconMapResponse-example.yaml +++ /dev/null @@ -1,27 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: string - apiVersion: string - returnedSchemas: - - entityType: info - schema: beacon-map-v2.0.0 -response: - $schema: ../../configuration/beaconMapSchema.json - endpointSets: - dataset: - entryType: dataset - openAPIEndpointsDefinition: ./datasets/endpoints.json - rootUrl: https://exampleBeacons.org/datasets - singleEntryUrl: https://exampleBeacons.org/datasets/{id} - filteringTermsUrl: https://exampleBeacons.org/datasets/{id}/filteringTerms - endpoints: - exampleEntries: - returnedEntryType: exampleEntry - url: https://exampleBeacons.org/datasets/{id}/exampleEntries - exampleEntry: - entryType: exampleEntry - openAPIEndpointsDefinition: ./exampleEntries/endpoints.json - rootUrl: https://exampleBeacons.org/exampleEntries - singleEntryUrl: https://exampleBeacons.org/exampleEntries/{id} - filteringTermsUrl: https://exampleBeacons.org/exampleEntries/{id}/filteringTerms -info: {} diff --git a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconResultsetResponse-MIN-example.yaml b/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconResultsetResponse-MIN-example.yaml deleted file mode 100644 index be8ac429b..000000000 --- a/bycon/schemas/framework/src/responses/examples-fullDocuments/beaconResultsetResponse-MIN-example.yaml +++ /dev/null @@ -1,18 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -meta: - beaconId: org.example.beacon.v2 - apiVersion: v2.0 - returnedSchemas: - - entityType: EntryTypeB - schema: entry-typeB-schema-v1.0 - receivedRequestSummary: - apiVersion: '2.0' - requestedSchemas: - - entityType: EntryTypeB - schema: entry-typeB-schema-v1.0 - pagination: - skip: 0 - limit: 10 -responseSummary: - exists: true -resultSets: [] diff --git a/bycon/schemas/framework/src/responses/examples-sections/beaconBooleanResponseSection-example.yaml b/bycon/schemas/framework/src/responses/examples-sections/beaconBooleanResponseSection-example.yaml deleted file mode 100644 index 5ac473e17..000000000 --- a/bycon/schemas/framework/src/responses/examples-sections/beaconBooleanResponseSection-example.yaml +++ /dev/null @@ -1,2 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -exists: true diff --git a/bycon/schemas/framework/src/responses/examples-sections/beaconCountResponseSection-example.yaml b/bycon/schemas/framework/src/responses/examples-sections/beaconCountResponseSection-example.yaml deleted file mode 100644 index d7816bb57..000000000 --- a/bycon/schemas/framework/src/responses/examples-sections/beaconCountResponseSection-example.yaml +++ /dev/null @@ -1,3 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -exists: true -numTotalResults: 45363 diff --git a/bycon/schemas/framework/src/responses/examples-sections/beaconInformationalResponseMeta-example.yaml b/bycon/schemas/framework/src/responses/examples-sections/beaconInformationalResponseMeta-example.yaml deleted file mode 100644 index 5cc5d4601..000000000 --- a/bycon/schemas/framework/src/responses/examples-sections/beaconInformationalResponseMeta-example.yaml +++ /dev/null @@ -1,4 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -beaconId: org.examplebeacons.beacon-v2 -apiVersion: v2.0 -returnedSchemas: [] diff --git a/bycon/schemas/framework/src/responses/examples-sections/beaconReceivedRequestSummary-MAX-example.yaml b/bycon/schemas/framework/src/responses/examples-sections/beaconReceivedRequestSummary-MAX-example.yaml deleted file mode 100644 index 13f962342..000000000 --- a/bycon/schemas/framework/src/responses/examples-sections/beaconReceivedRequestSummary-MAX-example.yaml +++ /dev/null @@ -1,18 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -apiVersion: v2.0 -requestedSchemas: - - entityType: Individual - schema: ga4gh-phenopacket-individual-v0.1 -requestParameters: - individual: - parameters: - - id: '123' -IncludeResultsetResponses: HIT -filters: - - BTO:0000199 - - PATO:0000383 -pagination: - skip: 1 - limit: 10 -testMode: false -requestedGranularity: count diff --git a/bycon/schemas/framework/src/responses/examples-sections/beaconReceivedRequestSummary-MIN-example.yaml b/bycon/schemas/framework/src/responses/examples-sections/beaconReceivedRequestSummary-MIN-example.yaml deleted file mode 100644 index 738787d90..000000000 --- a/bycon/schemas/framework/src/responses/examples-sections/beaconReceivedRequestSummary-MIN-example.yaml +++ /dev/null @@ -1,5 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -apiVersion: v2.0 -requestedSchemas: [] -pagination: {} -requestedGranularity: boolean diff --git a/bycon/schemas/framework/src/responses/examples-sections/beaconResponseMeta-example.yaml b/bycon/schemas/framework/src/responses/examples-sections/beaconResponseMeta-example.yaml deleted file mode 100644 index c0ac31f9a..000000000 --- a/bycon/schemas/framework/src/responses/examples-sections/beaconResponseMeta-example.yaml +++ /dev/null @@ -1,17 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -beaconId: org.example.beacon.v2 -apiVersion: v2.0 -returnedSchemas: - - entityType: EntryTypeB - schema: entry-typeB-schema-v1.0 -returnedGranularity: count -receivedRequestSummary: - apiVersion: '2.0' - requestedSchemas: - - entityType: EntryTypeB - schema: entry-typeB-schema-v1.0 - pagination: - skip: 0 - limit: 10 - testMode: true - requestedGranularity: count diff --git a/bycon/schemas/framework/src/responses/examples-sections/beaconResultsetEmpty-example.yaml b/bycon/schemas/framework/src/responses/examples-sections/beaconResultsetEmpty-example.yaml deleted file mode 100644 index 6168d412b..000000000 --- a/bycon/schemas/framework/src/responses/examples-sections/beaconResultsetEmpty-example.yaml +++ /dev/null @@ -1,5 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -resultSets: - - id: correctEmptyResultSet - type: dataset - exists: false diff --git a/bycon/schemas/framework/src/responses/examples-sections/beaconResultsets-MAX-example.yaml b/bycon/schemas/framework/src/responses/examples-sections/beaconResultsets-MAX-example.yaml deleted file mode 100644 index f2ae4015b..000000000 --- a/bycon/schemas/framework/src/responses/examples-sections/beaconResultsets-MAX-example.yaml +++ /dev/null @@ -1,20 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -resultSets: - - id: datasetA - type: dataset - exists: false - - id: datasetB - type: dataset - exists: true - resultsCount: 2 - resultsHandovers: - - handoverType: - id: EFO:0004157 - label: BAM format - url: https://api.mygenomeservice.org/Handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0 - note: This handover link provides access to a summarized VCF. - results: - - id: BEex3 - name: Basic Element example three - - id: BEex4 - name: Basic Element example four diff --git a/bycon/schemas/framework/src/responses/examples-sections/beaconResultsets-MID-example.yaml b/bycon/schemas/framework/src/responses/examples-sections/beaconResultsets-MID-example.yaml deleted file mode 100644 index ee552789c..000000000 --- a/bycon/schemas/framework/src/responses/examples-sections/beaconResultsets-MID-example.yaml +++ /dev/null @@ -1,12 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -resultSets: - - id: correctWithResults - type: dataset - exists: true - resultsCount: 1 - results: - - id: BEex1 - name: Basic Element example one - - id: correctWOresults - type: dataset - exists: false diff --git a/bycon/schemas/framework/src/responses/examples-sections/beaconResultsets-MIN-example.yaml b/bycon/schemas/framework/src/responses/examples-sections/beaconResultsets-MIN-example.yaml deleted file mode 100644 index 98a5a52ca..000000000 --- a/bycon/schemas/framework/src/responses/examples-sections/beaconResultsets-MIN-example.yaml +++ /dev/null @@ -1,2 +0,0 @@ -$schema: https://json-schema.org/draft/2020-12/schema -resultSets: [] diff --git a/bycon/schemas/models/json/bycon-model/analyses/defaultSchema.json b/bycon/schemas/models/json/bycon-model/analyses/defaultSchema.json index feab380a1..34276b2b0 100644 --- a/bycon/schemas/models/json/bycon-model/analyses/defaultSchema.json +++ b/bycon/schemas/models/json/bycon-model/analyses/defaultSchema.json @@ -70,9 +70,6 @@ "GATK4.0", "labelSeg" ] - }, - "info": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info" } }, "required": [ diff --git a/bycon/schemas/models/json/bycon-model/analyses/endpoints.json b/bycon/schemas/models/json/bycon-model/analyses/endpoints.json index 861b9c559..ce0e4987c 100644 --- a/bycon/schemas/models/json/bycon-model/analyses/endpoints.json +++ b/bycon/schemas/models/json/bycon-model/analyses/endpoints.json @@ -43,7 +43,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -57,7 +57,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -69,14 +69,14 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconResultsetsResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -99,7 +99,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -113,7 +113,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -125,7 +125,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -159,7 +159,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -173,7 +173,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -185,7 +185,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -200,13 +200,13 @@ "schema": { "oneOf": [ { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconBooleanResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconCountResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconResultsetsResponse.json" } ] } @@ -229,18 +229,18 @@ "name": "skip", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip" } }, "limit": { "name": "limit", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit" } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" }, "entryId": { "name": "id", diff --git a/bycon/schemas/models/json/bycon-model/biosamples/endpoints.json b/bycon/schemas/models/json/bycon-model/biosamples/endpoints.json index ab263951c..f7ad29a36 100644 --- a/bycon/schemas/models/json/bycon-model/biosamples/endpoints.json +++ b/bycon/schemas/models/json/bycon-model/biosamples/endpoints.json @@ -43,7 +43,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -57,7 +57,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -69,7 +69,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -92,7 +92,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -106,7 +106,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -118,7 +118,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -152,7 +152,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -166,7 +166,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -178,7 +178,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -212,7 +212,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -226,7 +226,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -238,7 +238,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -272,14 +272,14 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconResultsetsResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -293,7 +293,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -305,14 +305,14 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconResultsetsResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -327,13 +327,13 @@ "schema": { "oneOf": [ { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconBooleanResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconCountResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconResultsetsResponse.json" } ] } @@ -356,18 +356,18 @@ "name": "skip", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip" } }, "limit": { "name": "limit", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit" } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" }, "entryId": { "name": "id", diff --git a/bycon/schemas/models/json/bycon-model/biosamples/filteringTerms.json b/bycon/schemas/models/json/bycon-model/biosamples/filteringTerms.json index 864839b9c..fe599fec9 100644 --- a/bycon/schemas/models/json/bycon-model/biosamples/filteringTerms.json +++ b/bycon/schemas/models/json/bycon-model/biosamples/filteringTerms.json @@ -2,6 +2,6 @@ "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "array", "items": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/$defs/FilteringTerm" + "$ref": "https://progenetix.org/services/schemas/sections/beaconFilteringTermsResults.json#/$defs/FilteringTerm" } } \ No newline at end of file diff --git a/bycon/schemas/models/json/bycon-model/cohorts/endpoints.json b/bycon/schemas/models/json/bycon-model/cohorts/endpoints.json index 55189de30..accce16d2 100644 --- a/bycon/schemas/models/json/bycon-model/cohorts/endpoints.json +++ b/bycon/schemas/models/json/bycon-model/cohorts/endpoints.json @@ -50,7 +50,7 @@ "$ref": "#/components/responses/CollectionsResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -64,7 +64,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -76,7 +76,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -104,7 +104,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -118,7 +118,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -130,7 +130,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -164,7 +164,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -178,7 +178,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -190,7 +190,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -221,14 +221,14 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -242,7 +242,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -254,14 +254,14 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -274,7 +274,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconCollectionsResponse.json" } } } @@ -284,7 +284,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconCollectionsResponse.json" } } } @@ -305,14 +305,14 @@ "name": "skip", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip" } }, "limit": { "name": "limit", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit" } }, "entryId": { diff --git a/bycon/schemas/models/json/bycon-model/datasets/defaultSchema.json b/bycon/schemas/models/json/bycon-model/datasets/defaultSchema.json index c395e1554..2fb0a5a99 100644 --- a/bycon/schemas/models/json/bycon-model/datasets/defaultSchema.json +++ b/bycon/schemas/models/json/bycon-model/datasets/defaultSchema.json @@ -52,9 +52,6 @@ "http://example.org/wiki/Main_Page" ] }, - "info": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info" - }, "dataUseConditions": { "description": "Data use conditions applying to this dataset.", "$ref": "../common/dataUseConditions.json" diff --git a/bycon/schemas/models/json/bycon-model/datasets/endpoints.json b/bycon/schemas/models/json/bycon-model/datasets/endpoints.json index 2beb927dd..a80c0928f 100644 --- a/bycon/schemas/models/json/bycon-model/datasets/endpoints.json +++ b/bycon/schemas/models/json/bycon-model/datasets/endpoints.json @@ -508,14 +508,14 @@ "name": "skip", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip" } }, "limit": { "name": "limit", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit" } }, "entryId": { diff --git a/bycon/schemas/models/json/bycon-model/endpoints.json b/bycon/schemas/models/json/bycon-model/endpoints.json index 2a2bea5c1..b0abc5d1e 100644 --- a/bycon/schemas/models/json/bycon-model/endpoints.json +++ b/bycon/schemas/models/json/bycon-model/endpoints.json @@ -32,7 +32,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -55,7 +55,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -73,7 +73,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/ga4gh-service-info-1-0-0-schema.json" + "$ref": "https://progenetix.org/services/schemas/ga4gh-service-info-1-0-0-schema.json" } } } @@ -95,14 +95,14 @@ "application/json": { "schema": { "description": "Response of a request for information about a Beacon", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconConfigurationResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconConfigurationResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -122,14 +122,14 @@ "application/json": { "schema": { "description": "Response of a request for information about a Beacon", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconEntryTypesResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconEntryTypesResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -149,14 +149,14 @@ "application/json": { "schema": { "description": "Response of a request for information about a Beacon", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconMapResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconMapResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -178,11 +178,11 @@ ], "responses": { "200": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json" }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -196,7 +196,7 @@ "application/json": { "schema": { "description": "Response of a request for information about a Beacon", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconInfoResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconInfoResponse.json" } } } @@ -217,14 +217,14 @@ "name": "skip", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip" } }, "limit": { "name": "limit", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit" } } } diff --git a/bycon/schemas/models/json/bycon-model/genomicVariations/endpoints.json b/bycon/schemas/models/json/bycon-model/genomicVariations/endpoints.json index 12889e486..9378ec82f 100644 --- a/bycon/schemas/models/json/bycon-model/genomicVariations/endpoints.json +++ b/bycon/schemas/models/json/bycon-model/genomicVariations/endpoints.json @@ -76,7 +76,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -90,7 +90,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -102,7 +102,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -125,7 +125,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -139,7 +139,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -151,7 +151,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -185,7 +185,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -199,7 +199,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -211,7 +211,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -245,7 +245,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -259,7 +259,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -271,7 +271,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -286,13 +286,13 @@ "schema": { "oneOf": [ { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconBooleanResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconCountResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconResultsetsResponse.json" } ] } @@ -315,18 +315,18 @@ "name": "skip", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip" } }, "limit": { "name": "limit", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit" } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" }, "entryId": { "name": "id", diff --git a/bycon/schemas/models/json/bycon-model/individuals/endpoints.json b/bycon/schemas/models/json/bycon-model/individuals/endpoints.json index 8b4b8d0e8..31ddaae63 100644 --- a/bycon/schemas/models/json/bycon-model/individuals/endpoints.json +++ b/bycon/schemas/models/json/bycon-model/individuals/endpoints.json @@ -43,7 +43,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -57,7 +57,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -69,7 +69,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -92,7 +92,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -106,7 +106,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -118,7 +118,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -152,7 +152,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -166,7 +166,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -178,7 +178,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -212,7 +212,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -226,7 +226,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -238,7 +238,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -264,14 +264,14 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -285,7 +285,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -297,14 +297,14 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -319,13 +319,13 @@ "schema": { "oneOf": [ { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconBooleanResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconCountResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconResultsetsResponse.json" } ] } @@ -348,18 +348,18 @@ "name": "skip", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip" } }, "limit": { "name": "limit", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit" } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" }, "entryId": { "name": "id", diff --git a/bycon/schemas/models/json/bycon-model/phenopackets/endpoints.json b/bycon/schemas/models/json/bycon-model/phenopackets/endpoints.json index 0780b7c17..a56ef7037 100644 --- a/bycon/schemas/models/json/bycon-model/phenopackets/endpoints.json +++ b/bycon/schemas/models/json/bycon-model/phenopackets/endpoints.json @@ -43,7 +43,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -57,7 +57,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -69,7 +69,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -92,7 +92,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -106,7 +106,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -118,7 +118,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -152,7 +152,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -166,7 +166,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -178,7 +178,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -212,7 +212,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -226,7 +226,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -238,7 +238,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -264,14 +264,14 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -285,7 +285,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -297,14 +297,14 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json" } } } }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -319,13 +319,13 @@ "schema": { "oneOf": [ { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconBooleanResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconCountResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconResultsetsResponse.json" } ] } @@ -348,18 +348,18 @@ "name": "skip", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip" } }, "limit": { "name": "limit", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit" } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" }, "entryId": { "name": "id", diff --git a/bycon/schemas/models/json/bycon-model/runs/endpoints.json b/bycon/schemas/models/json/bycon-model/runs/endpoints.json index 7616ec112..ffe8c9eb0 100644 --- a/bycon/schemas/models/json/bycon-model/runs/endpoints.json +++ b/bycon/schemas/models/json/bycon-model/runs/endpoints.json @@ -43,7 +43,7 @@ "$ref": "#/components/responses/ResultsOKResponse" }, "default": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -57,7 +57,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -69,7 +69,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -92,7 +92,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -106,7 +106,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -118,7 +118,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -152,7 +152,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -166,7 +166,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -178,7 +178,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -212,7 +212,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } }, @@ -226,7 +226,7 @@ "content": { "application/json": { "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json" + "$ref": "https://progenetix.org/services/schemas/beaconRequestBody.json" } } }, @@ -238,7 +238,7 @@ }, "default": { "description": "An unsuccessful operation", - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconErrorResponse.json" } } } @@ -253,13 +253,13 @@ "schema": { "oneOf": [ { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconBooleanResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconCountResponse.json" }, { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json" + "$ref": "https://progenetix.org/services/schemas/beaconResultsetsResponse.json" } ] } @@ -282,18 +282,18 @@ "name": "skip", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip" } }, "limit": { "name": "limit", "in": "query", "schema": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit" } }, "includeResultsetResponses": { - "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" + "$ref": "https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses" }, "entryId": { "name": "id", diff --git a/bycon/schemas/models/src/bycon-model/analyses/defaultSchema.yaml b/bycon/schemas/models/src/bycon-model/analyses/defaultSchema.yaml index fd8aadef0..7c88e3ad5 100644 --- a/bycon/schemas/models/src/bycon-model/analyses/defaultSchema.yaml +++ b/bycon/schemas/models/src/bycon-model/analyses/defaultSchema.yaml @@ -65,8 +65,6 @@ properties: examples: - GATK4.0 - labelSeg - info: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info required: - id - analysisDate diff --git a/bycon/schemas/models/src/bycon-model/analyses/endpoints.yaml b/bycon/schemas/models/src/bycon-model/analyses/endpoints.yaml index 422b5c712..cc17b316a 100644 --- a/bycon/schemas/models/src/bycon-model/analyses/endpoints.yaml +++ b/bycon/schemas/models/src/bycon-model/analyses/endpoints.yaml @@ -26,7 +26,7 @@ paths: '200': $ref: '#/components/responses/ResultsOKResponse' default: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get a list of bioinformatics analysis operationId: postAnalysesRequest @@ -36,7 +36,7 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': @@ -44,10 +44,10 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json + $ref: https://progenetix.org/services/schemas/beaconResultsetsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /analyses/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -62,7 +62,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get details about one bioinformatics analysis, identified by its (unique) 'id' @@ -73,14 +73,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /analyses/{id}/g_variants: parameters: - $ref: '#/components/parameters/entryId' @@ -99,7 +99,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id' @@ -110,14 +110,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json components: responses: ResultsOKResponse: @@ -126,9 +126,9 @@ components: application/json: schema: oneOf: - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json + - $ref: https://progenetix.org/services/schemas/beaconBooleanResponse.json + - $ref: https://progenetix.org/services/schemas/beaconCountResponse.json + - $ref: https://progenetix.org/services/schemas/beaconResultsetsResponse.json parameters: requestedSchema: name: requestedSchema @@ -143,14 +143,14 @@ components: name: skip in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip limit: name: limit in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit includeResultsetResponses: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses entryId: name: id in: path diff --git a/bycon/schemas/models/src/bycon-model/biosamples/endpoints.yaml b/bycon/schemas/models/src/bycon-model/biosamples/endpoints.yaml index cac16a53e..02e64577b 100644 --- a/bycon/schemas/models/src/bycon-model/biosamples/endpoints.yaml +++ b/bycon/schemas/models/src/bycon-model/biosamples/endpoints.yaml @@ -26,7 +26,7 @@ paths: '200': $ref: '#/components/responses/ResultsOKResponse' default: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get a list of biosamples operationId: postBiosamplesRequest @@ -36,14 +36,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /biosamples/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -57,7 +57,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get details about one Biosample, identified by its (unique) 'id' operationId: postOneBiosample @@ -67,14 +67,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /biosamples/{id}/g_variants: parameters: - $ref: '#/components/parameters/entryId' @@ -93,7 +93,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the genomic variants list from one biosample, identified by its (unique) 'id' @@ -104,14 +104,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /biosamples/{id}/analyses: parameters: - $ref: '#/components/parameters/entryId' @@ -130,7 +130,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the analysis list from one biosample, identified by its (unique) 'id' @@ -141,14 +141,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /biosamples/{id}/runs: parameters: - $ref: '#/components/parameters/entryId' @@ -168,10 +168,10 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json + $ref: https://progenetix.org/services/schemas/beaconResultsetsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the runs list from one biosample, identified by its (unique) 'id' @@ -182,7 +182,7 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': @@ -190,10 +190,10 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json + $ref: https://progenetix.org/services/schemas/beaconResultsetsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json components: responses: ResultsOKResponse: @@ -202,9 +202,9 @@ components: application/json: schema: oneOf: - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json + - $ref: https://progenetix.org/services/schemas/beaconBooleanResponse.json + - $ref: https://progenetix.org/services/schemas/beaconCountResponse.json + - $ref: https://progenetix.org/services/schemas/beaconResultsetsResponse.json parameters: requestedSchema: name: requestedSchema @@ -219,14 +219,14 @@ components: name: skip in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip limit: name: limit in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit includeResultsetResponses: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses entryId: name: id in: path diff --git a/bycon/schemas/models/src/bycon-model/biosamples/filteringTerms.yaml b/bycon/schemas/models/src/bycon-model/biosamples/filteringTerms.yaml index c111a466c..4b80745f3 100644 --- a/bycon/schemas/models/src/bycon-model/biosamples/filteringTerms.yaml +++ b/bycon/schemas/models/src/bycon-model/biosamples/filteringTerms.yaml @@ -1,4 +1,4 @@ $schema: https://json-schema.org/draft/2020-12/schema type: array items: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/sections/beaconFilteringTermsResults.json#/$defs/FilteringTerm \ No newline at end of file + $ref: https://progenetix.org/services/schemas/sections/beaconFilteringTermsResults.json#/$defs/FilteringTerm \ No newline at end of file diff --git a/bycon/schemas/models/src/bycon-model/cohorts/endpoints.yaml b/bycon/schemas/models/src/bycon-model/cohorts/endpoints.yaml index 957c722d2..6deb1ec73 100644 --- a/bycon/schemas/models/src/bycon-model/cohorts/endpoints.yaml +++ b/bycon/schemas/models/src/bycon-model/cohorts/endpoints.yaml @@ -30,7 +30,7 @@ paths: '200': $ref: '#/components/responses/CollectionsResponse' default: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get a list of cohorts operationId: postCohortsRequest @@ -40,14 +40,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/CollectionsResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /cohorts/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -63,7 +63,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get details about one cohort, identified by its (unique) 'id' operationId: postOneCohort @@ -73,14 +73,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /cohorts/{id}/individuals: parameters: - $ref: '#/components/parameters/entryId' @@ -99,7 +99,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the individuals from one cohort, identified by its (unique) 'id' @@ -110,14 +110,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /cohorts/{id}/filtering_terms: parameters: - $ref: '#/components/parameters/entryId' @@ -136,10 +136,10 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json + $ref: https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the list of filtering terms that could be used with a given cohort, identified by its (unique) 'id' @@ -150,7 +150,7 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': @@ -158,10 +158,10 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json + $ref: https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json components: responses: ResultsOKResponse: @@ -169,13 +169,13 @@ components: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json + $ref: https://progenetix.org/services/schemas/beaconCollectionsResponse.json CollectionsResponse: description: Successful collection list operation. content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCollectionsResponse.json + $ref: https://progenetix.org/services/schemas/beaconCollectionsResponse.json parameters: requestedSchema: name: requestedSchema @@ -190,12 +190,12 @@ components: name: skip in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip limit: name: limit in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit entryId: name: id in: path diff --git a/bycon/schemas/models/src/bycon-model/datasets/defaultSchema.yaml b/bycon/schemas/models/src/bycon-model/datasets/defaultSchema.yaml index c933ae795..030f0ad1b 100644 --- a/bycon/schemas/models/src/bycon-model/datasets/defaultSchema.yaml +++ b/bycon/schemas/models/src/bycon-model/datasets/defaultSchema.yaml @@ -38,8 +38,6 @@ properties: 3986 format). examples: - http://example.org/wiki/Main_Page - info: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Info dataUseConditions: description: Data use conditions applying to this dataset. $ref: ../common/dataUseConditions.yaml diff --git a/bycon/schemas/models/src/bycon-model/datasets/endpoints.yaml b/bycon/schemas/models/src/bycon-model/datasets/endpoints.yaml index e66f602de..8b0fe3538 100644 --- a/bycon/schemas/models/src/bycon-model/datasets/endpoints.yaml +++ b/bycon/schemas/models/src/bycon-model/datasets/endpoints.yaml @@ -308,12 +308,12 @@ components: name: skip in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip limit: name: limit in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit entryId: name: id in: path diff --git a/bycon/schemas/models/src/bycon-model/endpoints.yaml b/bycon/schemas/models/src/bycon-model/endpoints.yaml index ea7bfd4a0..1fe736774 100644 --- a/bycon/schemas/models/src/bycon-model/endpoints.yaml +++ b/bycon/schemas/models/src/bycon-model/endpoints.yaml @@ -24,7 +24,7 @@ paths: $ref: '#/components/responses/infoOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /info: parameters: - $ref: '#/components/parameters/requestedSchema' @@ -38,7 +38,7 @@ paths: $ref: '#/components/responses/infoOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /service-info: get: description: Get information about the beacon using GA4GH ServiceInfo format @@ -51,7 +51,7 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/ga4gh-service-info-1-0-0-schema.json + $ref: https://progenetix.org/services/schemas/ga4gh-service-info-1-0-0-schema.json /configuration: get: description: TBD @@ -65,10 +65,10 @@ paths: application/json: schema: description: Response of a request for information about a Beacon - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconConfigurationResponse.json + $ref: https://progenetix.org/services/schemas/beaconConfigurationResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /entry_types: get: description: TBD @@ -83,10 +83,10 @@ paths: application/json: schema: description: Response of a request for information about a Beacon - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconEntryTypesResponse.json + $ref: https://progenetix.org/services/schemas/beaconEntryTypesResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /map: get: description: TBD @@ -101,10 +101,10 @@ paths: application/json: schema: description: Response of a request for information about a Beacon - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconMapResponse.json + $ref: https://progenetix.org/services/schemas/beaconMapResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /filtering_terms: parameters: - $ref: '#/components/parameters/skip' @@ -116,10 +116,10 @@ paths: - Informational endpoints responses: '200': - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json + $ref: https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json components: responses: infoOKResponse: @@ -128,7 +128,7 @@ components: application/json: schema: description: Response of a request for information about a Beacon - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconInfoResponse.json + $ref: https://progenetix.org/services/schemas/beaconInfoResponse.json parameters: requestedSchema: name: requestedSchema @@ -143,9 +143,9 @@ components: name: skip in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip limit: name: limit in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit diff --git a/bycon/schemas/models/src/bycon-model/genomicVariations/endpoints.yaml b/bycon/schemas/models/src/bycon-model/genomicVariations/endpoints.yaml index b2d13a177..bde5ad986 100644 --- a/bycon/schemas/models/src/bycon-model/genomicVariations/endpoints.yaml +++ b/bycon/schemas/models/src/bycon-model/genomicVariations/endpoints.yaml @@ -37,7 +37,7 @@ paths: '200': $ref: '#/components/responses/ResultsOKResponse' default: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get a list of example entries operationId: postExampleEntriesRequest @@ -47,14 +47,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /g_variants/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -69,7 +69,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get details about one genomic variation, identified by its (unique) 'id' @@ -80,14 +80,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /g_variants/{id}/biosamples: parameters: - $ref: '#/components/parameters/entryId' @@ -106,7 +106,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the biosamples list from one genomic variant, identified by its (unique) 'id' @@ -117,14 +117,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /g_variants/{id}/individuals: parameters: - $ref: '#/components/parameters/entryId' @@ -143,7 +143,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the biosamples list from one genomic variant, identified by its (unique) 'id' @@ -154,14 +154,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json components: responses: ResultsOKResponse: @@ -170,9 +170,9 @@ components: application/json: schema: oneOf: - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json + - $ref: https://progenetix.org/services/schemas/beaconBooleanResponse.json + - $ref: https://progenetix.org/services/schemas/beaconCountResponse.json + - $ref: https://progenetix.org/services/schemas/beaconResultsetsResponse.json parameters: requestedSchema: name: requestedSchema @@ -187,14 +187,14 @@ components: name: skip in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip limit: name: limit in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit includeResultsetResponses: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses entryId: name: id in: path diff --git a/bycon/schemas/models/src/bycon-model/individuals/endpoints.yaml b/bycon/schemas/models/src/bycon-model/individuals/endpoints.yaml index b6311ecba..d52b671f7 100644 --- a/bycon/schemas/models/src/bycon-model/individuals/endpoints.yaml +++ b/bycon/schemas/models/src/bycon-model/individuals/endpoints.yaml @@ -26,7 +26,7 @@ paths: '200': $ref: '#/components/responses/ResultsOKResponse' default: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get a list of example entries operationId: postIndividualsRequest @@ -36,14 +36,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /individuals/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -57,7 +57,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get details about one Individual, identified by its (unique) 'id' operationId: postOneIndividual @@ -67,14 +67,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /individuals/{id}/g_variants: parameters: - $ref: '#/components/parameters/entryId' @@ -93,7 +93,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the genomic variants list from one individual, identified by its (unique) 'id' @@ -104,14 +104,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /individuals/{id}/biosamples: parameters: - $ref: '#/components/parameters/entryId' @@ -130,7 +130,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the biosamples list from one individual, identified by its (unique) 'id' @@ -141,14 +141,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /individuals/filtering_terms: get: parameters: @@ -164,10 +164,10 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json + $ref: https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the list of filtering terms that could be used with individuals. operationId: postIndividualsFilteringTerms @@ -177,7 +177,7 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': @@ -185,10 +185,10 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json + $ref: https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json components: responses: ResultsOKResponse: @@ -197,9 +197,9 @@ components: application/json: schema: oneOf: - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json + - $ref: https://progenetix.org/services/schemas/beaconBooleanResponse.json + - $ref: https://progenetix.org/services/schemas/beaconCountResponse.json + - $ref: https://progenetix.org/services/schemas/beaconResultsetsResponse.json parameters: requestedSchema: name: requestedSchema @@ -214,14 +214,14 @@ components: name: skip in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip limit: name: limit in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit includeResultsetResponses: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses entryId: name: id in: path diff --git a/bycon/schemas/models/src/bycon-model/phenopackets/endpoints.yaml b/bycon/schemas/models/src/bycon-model/phenopackets/endpoints.yaml index 59a86873b..5b3f6529b 100644 --- a/bycon/schemas/models/src/bycon-model/phenopackets/endpoints.yaml +++ b/bycon/schemas/models/src/bycon-model/phenopackets/endpoints.yaml @@ -26,7 +26,7 @@ paths: '200': $ref: '#/components/responses/ResultsOKResponse' default: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get a list of example entries operationId: postIndividualsRequest @@ -36,14 +36,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /phenopackets/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -57,7 +57,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get details about one Individual, identified by its (unique) 'id' operationId: postOneIndividual @@ -67,14 +67,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /phenopackets/{id}/g_variants: parameters: - $ref: '#/components/parameters/entryId' @@ -93,7 +93,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the genomic variants list from one individual, identified by its (unique) 'id' @@ -104,14 +104,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /phenopackets/{id}/biosamples: parameters: - $ref: '#/components/parameters/entryId' @@ -130,7 +130,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the biosamples list from one individual, identified by its (unique) 'id' @@ -141,14 +141,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /phenopackets/filtering_terms: get: parameters: @@ -164,10 +164,10 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json + $ref: https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the list of filtering terms that could be used with phenopackets. operationId: postIndividualsFilteringTerms @@ -177,7 +177,7 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': @@ -185,10 +185,10 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconFilteringTermsResponse.json + $ref: https://progenetix.org/services/schemas/beaconFilteringTermsResponse.json default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json components: responses: ResultsOKResponse: @@ -197,9 +197,9 @@ components: application/json: schema: oneOf: - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json + - $ref: https://progenetix.org/services/schemas/beaconBooleanResponse.json + - $ref: https://progenetix.org/services/schemas/beaconCountResponse.json + - $ref: https://progenetix.org/services/schemas/beaconResultsetsResponse.json parameters: requestedSchema: name: requestedSchema @@ -214,14 +214,14 @@ components: name: skip in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip limit: name: limit in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit includeResultsetResponses: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses entryId: name: id in: path diff --git a/bycon/schemas/models/src/bycon-model/runs/endpoints.yaml b/bycon/schemas/models/src/bycon-model/runs/endpoints.yaml index 0e0bd5ba6..108421bb4 100644 --- a/bycon/schemas/models/src/bycon-model/runs/endpoints.yaml +++ b/bycon/schemas/models/src/bycon-model/runs/endpoints.yaml @@ -26,7 +26,7 @@ paths: '200': $ref: '#/components/responses/ResultsOKResponse' default: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get a list of sequencing runs operationId: postRunsRequest @@ -36,14 +36,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /runs/{id}: parameters: - $ref: '#/components/parameters/entryId' @@ -58,7 +58,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get details about one Run, identified by its (unique) 'id' operationId: postOneRun @@ -68,14 +68,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /runs/{id}/g_variants: parameters: - $ref: '#/components/parameters/entryId' @@ -94,7 +94,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the genomic variants list from one run, identified by its (unique) 'id' @@ -105,14 +105,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json /runs/{id}/analyses: parameters: - $ref: '#/components/parameters/entryId' @@ -131,7 +131,7 @@ paths: $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json post: description: Get the analysis list from one sequencing run, identified by its (unique) 'id' @@ -142,14 +142,14 @@ paths: content: application/json: schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/requests/beaconRequestBody.json + $ref: https://progenetix.org/services/schemas/beaconRequestBody.json required: true responses: '200': $ref: '#/components/responses/ResultsOKResponse' default: description: An unsuccessful operation - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconErrorResponse.json + $ref: https://progenetix.org/services/schemas/beaconErrorResponse.json components: responses: ResultsOKResponse: @@ -158,9 +158,9 @@ components: application/json: schema: oneOf: - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconBooleanResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconCountResponse.json - - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/responses/beaconResultsetsResponse.json + - $ref: https://progenetix.org/services/schemas/beaconBooleanResponse.json + - $ref: https://progenetix.org/services/schemas/beaconCountResponse.json + - $ref: https://progenetix.org/services/schemas/beaconResultsetsResponse.json parameters: requestedSchema: name: requestedSchema @@ -175,14 +175,14 @@ components: name: skip in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Skip + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Skip limit: name: limit in: query schema: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/Limit + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/Limit includeResultsetResponses: - $ref: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/$defs/IncludeResultsetResponses + $ref: https://progenetix.org/services/schemas/beaconCommonComponents.json#/$defs/IncludeResultsetResponses entryId: name: id in: path diff --git a/docs/changes.md b/docs/changes.md index 6884aacf2..7d9197c6c 100644 --- a/docs/changes.md +++ b/docs/changes.md @@ -6,6 +6,13 @@ While changes are documented for individual point versions we actually do not push releases out for all of them; they serve more as internal development milestones. +### 2024-11-10 (v2.0.9) + +* switching schema model internal references to own server instead of the hardcoded + Github repo from the standard schema; e.g. + - from + - to + ### 2024-11-09 (v2.0.8) * some library re-shuffling/condensation diff --git a/docs/generated/argument_definitions.md b/docs/generated/argument_definitions.md index 526a12f18..9baa8c69c 100644 --- a/docs/generated/argument_definitions.md +++ b/docs/generated/argument_definitions.md @@ -1,5 +1,8 @@ # `bycon` Arguments and Parameters -The following is a list of arguments and parameters used in the `bycon` package as well as the `byconaut` tools. +The following is a list of arguments and parameters used in the `bycon` package +as well as the `byconaut` tools. +Parameters are listed in `snake_case` format although for command line arguments +(and also optionally web requests) `camelCase` versions are required (see the `cmdFlags`). ## Definitions ### `user_name` **type:** string diff --git a/docs/generated/beacon-responses.md b/docs/generated/beacon-responses.md index da51086a2..2b8c84ba6 100644 --- a/docs/generated/beacon-responses.md +++ b/docs/generated/beacon-responses.md @@ -4,180 +4,218 @@ The following is a list of standard Beacon responses supported by the `bycon` pa Responses for individual entities or endpoints are grouped by their Beacon framework response classes (e.g. `beaconResultsetsResponse` for `biosamples`, `g_variants` etc.). + + Please be reminded about the general syntax used in Beacon: A **path element** such as `/biosamples` corresponds to an entity (here `biosample`). Below these relations are indicated by the `@` symbol. -## beaconInfoResponse -### info @ `/info` +#### Schemas **{S}**, Tests **{T}** and Examples **{E}** +Tests, examples and schemas are run from the server defined in this site's build instructions +(see the `reference_server_url` entry in `mkdocs.yaml` file in the repository's root). -#### Description -The `info` endpoint provides information about the Beacon, such as its name, the organization responsible for the Beacon, a contact email, and the API version. It is based on the GA4GH `service-info` standard. +## beaconCollectionsResponse -#### Schema for _configuration_ +A type of Beacon response that includes details about the **collections** in a beacon. The types of collections are defined in each beacon's configuration; if using the Beacon v2+ default model usually the types `dataset` and `cohort` are supported. -* +* **{S}** <{{config.reference_server_url}}/services/schemas/beaconCollectionsResponse> -#### Tests +### dataset @ `/datasets` -* <{{config.reference_server_url}}/beacon/info> +A dataset available in the beacon. -## beaconMapResponse +* **{S}** <{{config.reference_server_url}}/services/schemas/dataset> -### beaconMap @ `/map` +* **{T}** <{{config.reference_server_url}}/beacon/datasets?testMode=true> -#### Description +* **{E}** <{{config.reference_server_url}}/beacon/datasets/progenetix> -The `beaconMap` object provides a map of the Beacon's REST endpoints. -#### Schema for _map_ -* +### cohort @ `/cohorts` -#### Tests +A cohort available in the beacon. -* <{{config.reference_server_url}}/beacon/map> +* **{S}** <{{config.reference_server_url}}/services/schemas/cohort> -## beaconConfigurationResponse +* **{T}** <{{config.reference_server_url}}/beacon/cohorts?testMode=true> -### configuration @ `/configuration` -#### Schema for _configuration_ -* - -#### Tests +## beaconResultsetsResponse -* <{{config.reference_server_url}}/beacon/configuration> +A `beaconResultsetsResponse` returns the results of a query against a beacon, which - beyond the summary count response for overall matches - contains details about the matches in individual **collections** in the beacon or beacon network. The types of `beaconResultsets` objects are defined in the beacon's configuration; if using the Beacon v2+ default model the types `dataset` and `cohort` are supported. `beaconResultsets` typically contain a list of records matched by the query. +* **{S}** <{{config.reference_server_url}}/services/schemas/beaconResultsetsResponse> +### genomicVariant @ `/g_variants` -## beaconEntryTypesResponse +* **{S}** <{{config.reference_server_url}}/services/schemas/genomicVariant> -### entryType @ `/entry_types` +* **{T}** <{{config.reference_server_url}}/beacon/g_variants?testMode=true> -#### Schema for _entryType_ +* **{E}** <{{config.reference_server_url}}/beacon/g_variants/pgxvar-5bab576a727983b2e00b8d32> -* +* **{E}** <{{config.reference_server_url}}/beacon/g_variants/pgxvar-5bab576a727983b2e00b8d32/individuals> -#### Tests +* **{E}** <{{config.reference_server_url}}/beacon/g_variants?geneId=CDKN2A&variantMaxSize=100000&limit=5> -* <{{config.reference_server_url}}/beacon/entry_types> +* **{E}** <{{config.reference_server_url}}/beacon/g_variants?referenceName=NC_000017.11&start=7577120&referenceBases=G&alternateBases=A> -## beaconFilteringTermsResponse +### analysis @ `/analyses` -### filteringTerm @ `/filtering_terms` +The `analysis` schema represents a information about the data analysis steps leading to (a set of) genomic variation call(s). -#### Schema for _filteringTerm_ -* -#### Tests +* **{S}** <{{config.reference_server_url}}/services/schemas/analysis> -* <{{config.reference_server_url}}/beacon/filtering_terms?testMode=true> +* **{T}** <{{config.reference_server_url}}/beacon/analyses?testMode=true> -## beaconResultsetsResponse +### run @ `/runs` -### analysis @ `/analyses` +Schema for the experimental run (e.g. sequencing run, array processing...) leading to the raw data for the (computational) analysis. NOTE: In the bycon environment run parameters are stored in the analysis documents and rewritten into this schema at export time. -#### Schema for _analysis_ -* -#### Tests +* **{S}** <{{config.reference_server_url}}/services/schemas/run> -* <{{config.reference_server_url}}/beacon/analyses?testMode=true> +* **{T}** <{{config.reference_server_url}}/beacon/runs?testMode=true> ### biosample @ `/biosamples` -#### Schema for _biosample_ +A Biosample refers to a unit of biological material from which the substrate molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g. sequencing, array hybridisation, mass-spectrometry) are extracted. Examples would be a tissue biopsy, a single cell from a culture for single cell genome sequencing or a protein fraction from a gradient centrifugation. Several instances (e.g. technical replicates) or types of experiments (e.g. genomic array as well as RNA-seq experiments) may refer to the same Biosample. -* -#### Tests -* <{{config.reference_server_url}}/beacon/biosamples?testMode=true> +* **{S}** <{{config.reference_server_url}}/services/schemas/biosample> -* <{{config.reference_server_url}}/beacon/biosamples?filters=NCIT:C4017&limit=3> +* **{T}** <{{config.reference_server_url}}/beacon/biosamples?testMode=true> +* **{E}** <{{config.reference_server_url}}/beacon/biosamples?filters=NCIT:C4017&limit=3> + +* **{E}** <{{config.reference_server_url}}/beacon/biosamples?referenceName=refseq:NC_000009.12&variantType=EFO:0030067&start=21000000,21975098&end=21967753,23000000&filters=NCIT:C3058&limit=10> -### genomicVariant @ `/g_variants` -#### Schema for _genomicVariant_ +### individual @ `/individuals` -* +None -#### Tests -* <{{config.reference_server_url}}/beacon/g_variants?testMode=true> -* <{{config.reference_server_url}}/beacon/g_variants?geneId=CDKN2A&variantMaxSize=100000&limit=5> +* **{S}** <{{config.reference_server_url}}/services/schemas/individual> +* **{T}** <{{config.reference_server_url}}/beacon/individuals?testMode=true> +* **{E}** <{{config.reference_server_url}}/beacon/individuals?filters=EFO:0030049&limit=5> -### individual @ `/individuals` -#### Schema for _individual_ -* +## beaconFilteringTermsResponse -#### Tests +The filtering terms response provides information about available individual filters for a beacon's entry types as well as optional information about the ontologies the filters belong to. -* <{{config.reference_server_url}}/beacon/individuals?testMode=true> +* **{S}** <{{config.reference_server_url}}/services/schemas/beaconFilteringTermsResponse> -* <{{config.reference_server_url}}/beacon/individuals?filters=EFO:0030049&limit=5> +### filteringTerm @ `/filtering_terms` +Schema for the Filtering Terms list related to the hosting entry type. It is kept separated to allow updating it independently. -### run @ `/runs` -#### Schema for _run_ +* **{S}** <{{config.reference_server_url}}/services/schemas/filteringTermsSchema> -* +* **{T}** <{{config.reference_server_url}}/beacon/filtering_terms?testMode=true> -#### Tests -* <{{config.reference_server_url}}/beacon/runs?testMode=true> +## beaconInfoResponse +Information about the Beacon. Aimed at Beacon clients like web pages or Beacon networks. -## beaconCollectionsResponse +* **{S}** <{{config.reference_server_url}}/services/schemas/beaconInfoResponse> -### cohort @ `/cohorts` +### info @ `/info` -#### Schema for _cohort_ +Metadata describing a Beacon instance. -* +The `info` endpoint provides information about the Beacon, such as its name, the organization responsible for the Beacon, a contact email, and the API version. It is based on the GA4GH `service-info` standard. -#### Tests -* <{{config.reference_server_url}}/beacon/cohorts?testMode=true> +* **{S}** <{{config.reference_server_url}}/services/schemas/beaconInfoResults> +* **{T}** <{{config.reference_server_url}}/beacon/info> -### dataset @ `/datasets` -#### Schema for _dataset_ -* +## beaconMapResponse + +Information about the Beacon. Aimed to Beacon clients like web pages or Beacon networks. + +* **{S}** <{{config.reference_server_url}}/services/schemas/beaconMapResponse> + +### beaconMap @ `/map` + +Map of a Beacon, its entry types and endpoints. It isconceptually similar to a website sitemap. + +The `beaconMap` object provides a map of the Beacon's REST endpoints. + + + +* **{S}** <{{config.reference_server_url}}/services/schemas/beaconMapSchema> + +* **{T}** <{{config.reference_server_url}}/beacon/map> + + + +## beaconConfigurationResponse + +Information about the Beacon. Aimed to Beacon clients like web pages or Beacon networks. + +* **{S}** <{{config.reference_server_url}}/services/schemas/beaconConfigurationResponse> + +### configuration @ `/configuration` + +Files complaint with this schema are the configuration ones. The details returned in `service-info` are mirroring the ones in this configuration file. + + + +* **{S}** <{{config.reference_server_url}}/services/schemas/beaconConfigurationSchema> + +* **{T}** <{{config.reference_server_url}}/beacon/configuration> + + + +## beaconEntryTypesResponse + +Response including a list of Entry types definitions. + +* **{S}** <{{config.reference_server_url}}/services/schemas/beaconEntryTypesResponse> + +### entryType @ `/entry_types` + +Schema for the entry types list. + + -#### Tests +* **{S}** <{{config.reference_server_url}}/services/schemas/entryTypesSchema> -* <{{config.reference_server_url}}/beacon/datasets?testMode=true> +* **{T}** <{{config.reference_server_url}}/beacon/entry_types> diff --git a/markdowner.py b/markdowner.py index 877fa5072..e8fa0a8a1 100755 --- a/markdowner.py +++ b/markdowner.py @@ -3,10 +3,11 @@ import inspect, sys, re, yaml from os import getlogin, makedirs, path, system from pathlib import Path +from json_ref_dict import RefDict, materialize dir_path = path.dirname( path.abspath(__file__) ) -from bycon import BYC +from bycon import * #BYC, read_schema_file import byconServices ################################################################################ @@ -41,6 +42,12 @@ def main(): #>------------------------------------------------------------------------<# + """ + The block below parses the `entity_defaults.yaml` file and extracts some + definitions, examples and links for creating a Markdown page (for processing + with the mkdocs engine). + Very scripty single use code... + """ pp_f = path.join(generated_docs_path, f"beacon-responses.md") pp_fh = open(pp_f, "w") @@ -51,10 +58,14 @@ def main(): The following is a list of standard Beacon responses supported by the `bycon` package. Responses for individual entities or endpoints are grouped by their Beacon framework response classes (e.g. `beaconResultsetsResponse` for `biosamples`, `g_variants` etc.). - +\n\n Please be reminded about the general syntax used in Beacon: A **path element** such as `/biosamples` corresponds to an entity (here `biosample`). Below these relations are indicated by the `@` symbol. +\n\n +#### Schemas **{S}**, Tests **{T}** and Examples **{E}** +Tests, examples and schemas are run from the server defined in this site's build instructions +(see the `reference_server_url` entry in `mkdocs.yaml` file in the repository's root). \n\n""") for e, e_d in BYC["entity_defaults"].items(): @@ -67,20 +78,36 @@ def main(): for r_s in beacon_ets: pp_fh.write(f'## {r_s}\n\n') + if (schema := read_schema_file(r_s, "")): + if len((s_desc := schema.get("description"), "")) > 1: + pp_fh.write(f'{s_desc}\n\n') + e_url = '{{config.reference_server_url}}/services/schemas' + f'/{r_s}' + pp_fh.write(f'* **{{S}}** <{e_url}>\n\n') for e_d in beacon_ets[r_s]: pp_fh.write(f'### {e_d["response_entity_id"]} @ `/{e_d["request_entity_path_id"]}`\n\n') + b_s = e_d.get("beacon_schema", {}) + b_s_s = b_s.get("schema", "") + b_s_n = b_s_s.rstrip("/").split('/')[-1] + + description = "" + # TODO: Doesn't work if schema has reference to external file ... + if (schema := read_schema_file(b_s_n, "")): + if len((s_desc := schema.get("description"), "")) > 1: + description += f'{s_desc}\n\n' if (d := e_d.get("description")): - pp_fh.write(f'#### Description\n\n{e_d["description"]}\n\n') - if (s := e_d.get("beacon_schema")): - pp_fh.write(f'#### Schema for _{s.get("entity_type")}_\n\n') - pp_fh.write(f'* <{s.get("schema", "")}>\n\n') + description += f'{d}\n\n' + if len(description) > 2: + pp_fh.write(f'{description}\n\n') + s_url = '{{config.reference_server_url}}/services/schemas' + f'/{b_s_n}' + pp_fh.write(f'* **{{S}}** <{s_url}>\n\n') test_url = '{{config.reference_server_url}}/beacon' + f'/{e_d["request_entity_path_id"]}' if "BeaconDataResponse" in e_d.get("bycon_response_class", ""): test_url += "?testMode=true" - pp_fh.write(f'#### Tests\n\n* <{test_url}>\n\n') - for e in e_d.get("tests", []): - e_url = '{{config.reference_server_url}}/beacon' + f'/{e_d["request_entity_path_id"]}' - pp_fh.write(f'* <{e_url}{e}>\n\n') + pp_fh.write(f'* **{{T}}** <{test_url}>\n\n') + if len(e_s := e_d.get("examples", [])) > 0: + for e in e_s: + e_url = '{{config.reference_server_url}}/beacon' + f'/{e_d["request_entity_path_id"]}' + pp_fh.write(f'* **{{E}}** <{e_url}{e}>\n\n') pp_fh.write('\n\n') pp_fh.close() @@ -97,7 +124,14 @@ def main(): }, "argument_definitions": { "title": "`bycon` Arguments and Parameters", - "preamble": "The following is a list of arguments and parameters used in the `bycon` package as well as the `byconaut` tools." + "preamble": """ +The following is a list of arguments and parameters used in the `bycon` package +as well as the `byconaut` tools. + + +Parameters are listed in `snake_case` format although for command line arguments +(and also optionally web requests) `camelCase` versions are required (see the `cmdFlags`). +""" } } diff --git a/mkdocs.yaml b/mkdocs.yaml index d288e66d9..c4294a50e 100644 --- a/mkdocs.yaml +++ b/mkdocs.yaml @@ -4,7 +4,7 @@ site_author: Michael Baudis repo_name: bycon repo_url: https://github.com/progenetix/bycon -reference_server_url: https://beaconplus.progenetix.org +reference_server_url: https://progenetix.org ############################################################################### diff --git a/setup.py b/setup.py index 740aae41f..4ad277151 100755 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ setup( name="bycon", - version="2.0.8", + version="2.0.9", description="A Python-based environment for the Beacon v2 genomics API", long_description=long_description, long_description_content_type="text/markdown",