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HadleyKingHadleyKing
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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
1 parent 5c5c1f7 commit 588156e

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-6
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‎biocompute/services.py‎

Lines changed: 10 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -50,12 +50,16 @@ def load_schema(schema_uri):
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Returns:
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- dict: The loaded JSON schema.
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"""
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if schema_uri == \
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"https://w3id.org/ieee/ieee-2791-schema/2791object.json":
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return jsonref.load_uri(
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f"file://{BASE_DIR}/config/IEEE/2791object.json"
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)
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schema_mapping = {
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"https://w3id.org/ieee/ieee-2791-schema/2791object.json": f"{BASE_DIR}/config/schemas/2791object.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/dataset_extension.json": f"{BASE_DIR}/config/schemas/dataset_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/fhir_extension.json": f"{BASE_DIR}/config/schemas/fhir_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/galaxy_extension.json": f"{BASE_DIR}/config/schemas/galaxy_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/license_extension.json": f"{BASE_DIR}/config/schemas/license_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/scm_extension.json": f"{BASE_DIR}/config/schemas/scm_extension.json"
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}
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if schema_uri in schema_mapping:
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return jsonref.load_uri(f"file://{schema_mapping[schema_uri]}")
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try:
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return jsonref.load_uri(schema_uri)
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except (JSONDecodeError, TypeError, RequestsConnectionError) as e:

config/IEEE/2791object.json renamed to config/schemas/2791object.json

File renamed without changes.

‎config/schemas/dataset_extension.json‎

Lines changed: 78 additions & 0 deletions
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@@ -0,0 +1,78 @@
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{
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"$schema": "http://json-schema.org/draft-07/schema#",
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"$id": "http://www.w3id.org/biocompute/extension_domain/1.1.0/dataset/dataset_extension.json",
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"title": "dataset_extension",
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"type": "object",
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"description": "The external references extension to list additional licenses and dataset catagories for a dataset BCO (dsBCO).",
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"required": ["dataset_extension", "extension_schema"],
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"additionalProperties": false,
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"properties": {
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"dataset_extension": {
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"type": "object",
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"additionalProperties": false,
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"required": ["dataset_categories"],
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"properties": {
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"additional_license": {
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"type": "object",
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"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.",
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"additionalProperties": false,
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"properties": {
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"data_license": {
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"title": "data_license",
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"type": "string",
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"description": "The license applied to the data or the dataset by the author",
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"examples": ["https://creativecommons.org/licenses/by/4.0/"]
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},
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"script_license": {
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"title": "script_license",
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"type": "string",
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"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.",
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"examples": ["https://www.gnu.org/licenses/gpl-3.0.en.html"]
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}
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}
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},
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"dataset_categories": {
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"title": "dataset_categories",
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"type": "array",
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"description": "Dataset categories describe and provide more information about the dataset which can be used to classify, group, sort and filter datasets.",
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"items": {
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"required": ["category_value", "category_name"],
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"additionalProperties": false,
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"properties": {
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"category_value": {
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"type": "string",
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"title": "category_value",
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"description": "An explanation about the purpose of this instance.",
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"examples": ["Homo sapiens"]
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},
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"category_name": {
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"type": "string",
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"title": "category_name",
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"description": "An explanation about the purpose of this instance.",
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"enum": [
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"species",
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"molecule",
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"tag",
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"tags",
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"priority",
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"file_type",
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"status",
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"scope"
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]
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}
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}
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}
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}
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}
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},
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"extension_schema": {
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"title": "extension_schema",
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"type": "string",
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"format": "uri",
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"description": "The schema applied to the extension object",
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"examples": [
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"http://www.w3id.org/biocompute/extension_domain/example.json"
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]
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}
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}
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}

config/IEEE/description_domain.json renamed to config/schemas/description_domain.json

File renamed without changes.

config/IEEE/error_domain.json renamed to config/schemas/error_domain.json

File renamed without changes.

config/IEEE/execution_domain.json renamed to config/schemas/execution_domain.json

File renamed without changes.

‎config/schemas/fhir_extension.json‎

Lines changed: 57 additions & 0 deletions
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{
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"$schema": "http://json-schema.org/draft-07/schema#",
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"$id": "https://w3id.org/biocompute/extension_domain/1.1.0/fhir/fhir_extension.json",
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"title": "fhir_extension",
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"type": "object",
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"description": "The external references extension to FHIR resource",
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"required": ["fhir_extension", "extension_schema"],
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"additionalProperties": false,
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"properties": {
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"extension_schema": {
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"title": "extension_schema",
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"type": "string",
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"format": "uri",
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"description": "The schema applied to the extension object",
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"examples": [
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"http://www.w3id.org/biocompute/extension_domain/example.json"
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]
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},
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"fhir_extension": {
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"title": "",
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"type": "array",
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"decription": "",
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"items": {
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"required": ["fhir_endpoint", "fhir_version", "fhir_resources"],
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"properties": {
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"fhir_endpoint": {
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"type": "string",
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"description": "Base URI of FHIR server where the resources are stored",
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"examples": ["http://fhirtest.uhn.ca/baseDstu3"],
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"format": "uri"
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},
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"fhir_version": {
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"type": "string",
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"description": "FHIR version of the server endpoint"
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},
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"fhir_resources": {
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"type": "array",
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"items": {
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"type": "object",
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"required": ["fhir_resource", "fhir_id"],
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"properties": {
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"fhir_resource": {
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"type": "string",
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"description": "Type of FHIR resource used"
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},
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"fhir_id": {
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"type": "string",
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"description": "Server-specific identifier string"
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}
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}
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}
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}
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}
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}
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}
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}
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}

‎config/schemas/galaxy_extension.json‎

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{
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"$schema": "http://json-schema.org/draft-07/schema#",
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"$id": "http://www.w3id.org/biocompute/extension_domain/1.1.0/galaxy/galaxy_extension.json",
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"title": "galaxy_extension",
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"type": "object",
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"description": "The external references **example** extension for a Galaxy BCO.",
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"required": ["galaxy_extension", "extension_schema"],
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"additionalProperties": false,
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"properties": {
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"extension_schema": {
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"type": "string",
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"format": "uri",
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"description": "The schema applied to the extension object",
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"examples": [
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"http://www.w3id.org/biocompute/extension_domain/example.json"
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]
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},
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"galaxy_extension": {
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"type": "object",
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"required": ["galaxy_url", "galaxy_version"],
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"properties": {
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"galaxy_url": {
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"type": "string",
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"description": "The base url for the galaxy instance used to create the BioCompute Object.",
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"examples": ["https://galaxy.aws.biochemistry.gwu.edu/"],
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"format": "uri"
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},
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"galaxy_version": {
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"type": "string",
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"description": "The specific version of the Galaxy software used to generate the BioCompute Object.",
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"examples": ["20.01"]
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}
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}
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}
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}
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}

config/IEEE/io_domain.json renamed to config/schemas/io_domain.json

File renamed without changes.

‎config/schemas/license_extension.json‎

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@@ -0,0 +1,34 @@
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{
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"$schema": "http://json-schema.org/draft-07/schema#",
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"$id": "http://www.w3id.org/biocompute/extension_domain/1.1.0/license/license_extension.json",
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"type": "object",
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"description": "The extension to add additional licenses.",
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"required": ["licence_extension", "extension_schema"],
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"additionalProperties": false,
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"properties": {
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"extension_schema": {
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"title": "extension_schema",
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"type": "string",
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"format": "uri",
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"description": "The schema applied to the extension object",
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"examples": [
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"http://www.w3id.org/biocompute/extension_domain/example.json"
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]
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},
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"licence_extension": {
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"required": ["data_license", "scripts_license"],
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"properties": {
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"data_license": {
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"type": "string",
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"examples": ["https://github.com/example/repo1"],
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"format": "uri"
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},
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"scripts_license": {
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"type": "string",
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"examples": ["https://github.com/example/repo1"],
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"format": "uri"
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}
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}
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}
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}
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}

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