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Update to BcoValidator.load_schema (#341)
Updated the function to check locally for the most used schemas. Improves testing and speed in BCO validation. Changes to be committed: modified: biocompute/services.py renamed: config/IEEE/2791object.json -> config/schemas/2791object.json new file: config/schemas/dataset_extension.json renamed: config/IEEE/description_domain.json -> config/schemas/description_domain.json renamed: config/IEEE/error_domain.json -> config/schemas/error_domain.json renamed: config/IEEE/execution_domain.json -> config/schemas/execution_domain.json new file: config/schemas/fhir_extension.json new file: config/schemas/galaxy_extension.json renamed: config/IEEE/io_domain.json -> config/schemas/io_domain.json new file: config/schemas/license_extension.json renamed: config/IEEE/parametric_domain.json -> config/schemas/parametric_domain.json renamed: config/IEEE/provenance_domain.json -> config/schemas/provenance_domain.json new file: config/schemas/scm_extension.json renamed: config/IEEE/usability_domain.json -> config/schemas/usability_domain.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "$id": "http://www.w3id.org/biocompute/extension_domain/1.1.0/dataset/dataset_extension.json", | ||
| "title": "dataset_extension", | ||
| "type": "object", | ||
| "description": "The external references extension to list additional licenses and dataset catagories for a dataset BCO (dsBCO).", | ||
| "required": ["dataset_extension", "extension_schema"], | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "dataset_extension": { | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "required": ["dataset_categories"], | ||
| "properties": { | ||
| "additional_license": { | ||
| "type": "object", | ||
| "description": "The additional license property contains the details about the licenses applied to the dataset and the script or tool/software used to process the given dataset.", | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "data_license": { | ||
| "title": "data_license", | ||
| "type": "string", | ||
| "description": "The license applied to the data or the dataset by the author", | ||
| "examples": ["https://creativecommons.org/licenses/by/4.0/"] | ||
| }, | ||
| "script_license": { | ||
| "title": "script_license", | ||
| "type": "string", | ||
| "description": "The license applied to the computational script or the tool/software developed to process (parse, QC, align) the input dataset for a final output dataset.", | ||
| "examples": ["https://www.gnu.org/licenses/gpl-3.0.en.html"] | ||
| } | ||
| } | ||
| }, | ||
| "dataset_categories": { | ||
| "title": "dataset_categories", | ||
| "type": "array", | ||
| "description": "Dataset categories describe and provide more information about the dataset which can be used to classify, group, sort and filter datasets.", | ||
| "items": { | ||
| "required": ["category_value", "category_name"], | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "category_value": { | ||
| "type": "string", | ||
| "title": "category_value", | ||
| "description": "An explanation about the purpose of this instance.", | ||
| "examples": ["Homo sapiens"] | ||
| }, | ||
| "category_name": { | ||
| "type": "string", | ||
| "title": "category_name", | ||
| "description": "An explanation about the purpose of this instance.", | ||
| "enum": [ | ||
| "species", | ||
| "molecule", | ||
| "tag", | ||
| "tags", | ||
| "priority", | ||
| "file_type", | ||
| "status", | ||
| "scope" | ||
| ] | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "extension_schema": { | ||
| "title": "extension_schema", | ||
| "type": "string", | ||
| "format": "uri", | ||
| "description": "The schema applied to the extension object", | ||
| "examples": [ | ||
| "http://www.w3id.org/biocompute/extension_domain/example.json" | ||
| ] | ||
| } | ||
| } | ||
| } |
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|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "$id": "https://w3id.org/biocompute/extension_domain/1.1.0/fhir/fhir_extension.json", | ||
| "title": "fhir_extension", | ||
| "type": "object", | ||
| "description": "The external references extension to FHIR resource", | ||
| "required": ["fhir_extension", "extension_schema"], | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "extension_schema": { | ||
| "title": "extension_schema", | ||
| "type": "string", | ||
| "format": "uri", | ||
| "description": "The schema applied to the extension object", | ||
| "examples": [ | ||
| "http://www.w3id.org/biocompute/extension_domain/example.json" | ||
| ] | ||
| }, | ||
| "fhir_extension": { | ||
| "title": "", | ||
| "type": "array", | ||
| "decription": "", | ||
| "items": { | ||
| "required": ["fhir_endpoint", "fhir_version", "fhir_resources"], | ||
| "properties": { | ||
| "fhir_endpoint": { | ||
| "type": "string", | ||
| "description": "Base URI of FHIR server where the resources are stored", | ||
| "examples": ["http://fhirtest.uhn.ca/baseDstu3"], | ||
| "format": "uri" | ||
| }, | ||
| "fhir_version": { | ||
| "type": "string", | ||
| "description": "FHIR version of the server endpoint" | ||
| }, | ||
| "fhir_resources": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "required": ["fhir_resource", "fhir_id"], | ||
| "properties": { | ||
| "fhir_resource": { | ||
| "type": "string", | ||
| "description": "Type of FHIR resource used" | ||
| }, | ||
| "fhir_id": { | ||
| "type": "string", | ||
| "description": "Server-specific identifier string" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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|---|---|---|
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| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "$id": "http://www.w3id.org/biocompute/extension_domain/1.1.0/galaxy/galaxy_extension.json", | ||
| "title": "galaxy_extension", | ||
| "type": "object", | ||
| "description": "The external references **example** extension for a Galaxy BCO.", | ||
| "required": ["galaxy_extension", "extension_schema"], | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "extension_schema": { | ||
| "type": "string", | ||
| "format": "uri", | ||
| "description": "The schema applied to the extension object", | ||
| "examples": [ | ||
| "http://www.w3id.org/biocompute/extension_domain/example.json" | ||
| ] | ||
| }, | ||
| "galaxy_extension": { | ||
| "type": "object", | ||
| "required": ["galaxy_url", "galaxy_version"], | ||
| "properties": { | ||
| "galaxy_url": { | ||
| "type": "string", | ||
| "description": "The base url for the galaxy instance used to create the BioCompute Object.", | ||
| "examples": ["https://galaxy.aws.biochemistry.gwu.edu/"], | ||
| "format": "uri" | ||
| }, | ||
| "galaxy_version": { | ||
| "type": "string", | ||
| "description": "The specific version of the Galaxy software used to generate the BioCompute Object.", | ||
| "examples": ["20.01"] | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "$id": "http://www.w3id.org/biocompute/extension_domain/1.1.0/license/license_extension.json", | ||
| "type": "object", | ||
| "description": "The extension to add additional licenses.", | ||
| "required": ["licence_extension", "extension_schema"], | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "extension_schema": { | ||
| "title": "extension_schema", | ||
| "type": "string", | ||
| "format": "uri", | ||
| "description": "The schema applied to the extension object", | ||
| "examples": [ | ||
| "http://www.w3id.org/biocompute/extension_domain/example.json" | ||
| ] | ||
| }, | ||
| "licence_extension": { | ||
| "required": ["data_license", "scripts_license"], | ||
| "properties": { | ||
| "data_license": { | ||
| "type": "string", | ||
| "examples": ["https://github.com/example/repo1"], | ||
| "format": "uri" | ||
| }, | ||
| "scripts_license": { | ||
| "type": "string", | ||
| "examples": ["https://github.com/example/repo1"], | ||
| "format": "uri" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "$id": "https://w3id.org/biocompute/extension_domain/1.1.0/scm/scm_extension.json", | ||
| "title": "scm_extension", | ||
| "type": "object", | ||
| "description": "The external references extension to a SCM repository", | ||
| "required": ["scm_extension", "extension_schema"], | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "extension_schema": { | ||
| "title": "extension_schema", | ||
| "type": "string", | ||
| "format": "uri", | ||
| "description": "The schema applied to the extension object", | ||
| "examples": [ | ||
| "http://www.w3id.org/biocompute/extension_domain/example.json" | ||
| ] | ||
| }, | ||
| "scm_extension": { | ||
| "required": ["scm_repository", "scm_type", "scm_commit", "scm_path"], | ||
| "properties": { | ||
| "scm_repository": { | ||
| "type": "string", | ||
| "examples": ["https://github.com/example/repo1"], | ||
| "format": "uri" | ||
| }, | ||
| "scm_type": { | ||
| "type": "string", | ||
| "enum": ["git", "svn", "hg", "other"] | ||
| }, | ||
| "scm_commit": { | ||
| "type": "string", | ||
| "examples": ["c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21"] | ||
| }, | ||
| "scm_path": { | ||
| "type": "string", | ||
| "examples": ["workflow/hive-viral-mutation-detection.cwl"], | ||
| "format": "string" | ||
| }, | ||
| "scm_preview": { | ||
| "type": "string", | ||
| "examples": [ | ||
| "https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl" | ||
| ], | ||
| "format": "uri" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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