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HadleyKingHadleyKing
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Add additional schema files and reorganize
Changes to be committed: modified: biocompute/services.py new file: config/schemas/1.1.0/dataset_extension.json new file: config/schemas/1.1.0/fhir_extension.json new file: config/schemas/1.1.0/galaxy_extension.json new file: config/schemas/1.1.0/license_extension.json new file: config/schemas/1.1.0/scm_extension.json renamed: config/schemas/dataset_extension.json -> config/schemas/1.2.0/dataset_extension.json renamed: config/schemas/fhir_extension.json -> config/schemas/1.2.0/fhir_extension.json renamed: config/schemas/galaxy_extension.json -> config/schemas/1.2.0/galaxy_extension.json renamed: config/schemas/license_extension.json -> config/schemas/1.2.0/license_extension.json renamed: config/schemas/scm_extension.json -> config/schemas/1.2.0/scm_extension.json renamed: config/schemas/2791object.json -> config/schemas/2791/2791object.json renamed: config/schemas/description_domain.json -> config/schemas/2791/description_domain.json renamed: config/schemas/error_domain.json -> config/schemas/2791/error_domain.json renamed: config/schemas/execution_domain.json -> config/schemas/2791/execution_domain.json renamed: config/schemas/io_domain.json -> config/schemas/2791/io_domain.json renamed: config/schemas/parametric_domain.json -> config/schemas/2791/parametric_domain.json renamed: config/schemas/provenance_domain.json -> config/schemas/2791/provenance_domain.json renamed: config/schemas/usability_domain.json -> config/schemas/2791/usability_domain.json modified: config/settings.py modified: requirements.txt
1 parent 588156e commit f54925b

21 files changed

+321
-8
lines changed

‎biocompute/services.py‎

Lines changed: 15 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -51,15 +51,24 @@ def load_schema(schema_uri):
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- dict: The loaded JSON schema.
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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",
59-
"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/scm_extension.json": f"{BASE_DIR}/config/schemas/scm_extension.json"
54+
"https://w3id.org/ieee/ieee-2791-schema/2791object.json": f"{BASE_DIR}/config/schemas/2791/2791object.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/dataset/dataset_extension.json": f"{BASE_DIR}/config/schemas/1.1.0/dataset_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/fhir/fhir_extension.json": f"{BASE_DIR}/config/schemas/1.1.0/fhir_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/galaxy/galaxy_extension.json": f"{BASE_DIR}/config/schemas/1.1.0/galaxy_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/license/license_extension.json": f"{BASE_DIR}/config/schemas/1.1.0/license_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/scm/scm_extension.json": f"{BASE_DIR}/config/schemas/1.1.0/scm_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.2.0/dataset/dataset_extension.json": f"{BASE_DIR}/config/schemas/1.2.0/dataset_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.2.0/fhir/fhir_extension.json": f"{BASE_DIR}/config/schemas/1.2.0/fhir_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.2.0/galaxy/galaxy_extension.json": f"{BASE_DIR}/config/schemas/1.2.0/galaxy_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.2.0/license/license_extension.json": f"{BASE_DIR}/config/schemas/1.2.0/license_extension.json",
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"https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.2.0/scm/scm_extension.json": f"{BASE_DIR}/config/schemas/1.2.0/scm_extension.json"
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}
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if schema_uri in schema_mapping:
68+
print(schema_uri in schema_mapping, schema_uri)
6269
return jsonref.load_uri(f"file://{schema_mapping[schema_uri]}")
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else:
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print(schema_uri in schema_mapping, schema_uri)
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try:
6473
return jsonref.load_uri(schema_uri)
6574
except (JSONDecodeError, TypeError, RequestsConnectionError) as e:

‎config/schemas/1.1.0/dataset_extension.json‎

Lines changed: 86 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,86 @@
1+
{
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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": {
10+
"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": {
16+
"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": {
21+
"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": [
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"https://creativecommons.org/licenses/by/4.0/"
26+
]
27+
},
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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": [
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"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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},
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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": [
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"category_value",
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"category_name"
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],
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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": [
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"Homo sapiens"
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]
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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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"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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]
83+
84+
}
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}
86+
}

‎config/schemas/1.1.0/fhir_extension.json‎

Lines changed: 67 additions & 0 deletions
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@@ -0,0 +1,67 @@
1+
{
2+
"$schema": "http://json-schema.org/draft-07/schema#",
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"$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",
7+
"required": ["fhir_extension", "extension_schema"],
8+
"additionalProperties": false,
9+
"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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]
18+
19+
},
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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": [
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"fhir_endpoint",
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"fhir_version",
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"fhir_resources"
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],
30+
"properties": {
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"fhir_endpoint": {
32+
"type": "string",
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"description": "Base URI of FHIR server where the resources are stored",
34+
"examples": [
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"http://fhirtest.uhn.ca/baseDstu3"
36+
],
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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": [
48+
"fhir_resource",
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"fhir_id"
50+
],
51+
"properties": {
52+
"fhir_resource": {
53+
"type": "string",
54+
"description": "Type of FHIR resource used"
55+
},
56+
"fhir_id": {
57+
"type": "string",
58+
"description": "Server-specific identifier string"
59+
}
60+
}
61+
}
62+
}
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}
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}
65+
}
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}
67+
}

‎config/schemas/1.1.0/galaxy_extension.json‎

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@@ -0,0 +1,44 @@
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{
2+
"$schema": "http://json-schema.org/draft-07/schema#",
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"$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,
9+
"properties": {
10+
"extension_schema": {
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"type": "string",
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"format": "uri",
13+
"description": "The schema applied to the extension object",
14+
"examples": [
15+
"http://www.w3id.org/biocompute/extension_domain/example.json"
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]
17+
18+
},
19+
"galaxy_extension": {
20+
"type": "object",
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"required": [
22+
"galaxy_url",
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"galaxy_version"
24+
],
25+
"properties": {
26+
"galaxy_url": {
27+
"type": "string",
28+
"description": "The base url for the galaxy instance used to create the BioCompute Object.",
29+
"examples": [
30+
"https://galaxy.aws.biochemistry.gwu.edu/"
31+
],
32+
"format": "uri"
33+
},
34+
"galaxy_version": {
35+
"type": "string",
36+
"description": "The specific version of the Galaxy software used to generate the BioCompute Object.",
37+
"examples": [
38+
"20.01"
39+
]
40+
}
41+
}
42+
}
43+
}
44+
}

‎config/schemas/1.1.0/license_extension.json‎

Lines changed: 41 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,41 @@
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{
2+
"$schema": "http://json-schema.org/draft-07/schema#",
3+
"$id": "http://www.w3id.org/biocompute/extension_domain/1.1.0/license/license_extension.json",
4+
"type": "object",
5+
"description": "The extension to add additional licenses.",
6+
"required": ["licence_extension", "extension_schema"],
7+
"additionalProperties": false,
8+
"properties":{
9+
"extension_schema": {
10+
"title": "extension_schema",
11+
"type": "string",
12+
"format": "uri",
13+
"description": "The schema applied to the extension object",
14+
"examples": [
15+
"http://www.w3id.org/biocompute/extension_domain/example.json"
16+
]
17+
},
18+
"licence_extension":{
19+
"required": [
20+
"data_license",
21+
"scripts_license"
22+
],
23+
"properties": {
24+
"data_license": {
25+
"type": "string",
26+
"examples": [
27+
"https://github.com/example/repo1"
28+
],
29+
"format": "uri"
30+
},
31+
"scripts_license": {
32+
"type": "string",
33+
"examples": [
34+
"https://github.com/example/repo1"
35+
],
36+
"format": "uri"
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}
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}
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}
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}
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}

‎config/schemas/1.1.0/scm_extension.json‎

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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/scm/scm_extension.json",
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"title": "scm_extension",
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"type": "object",
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"description": "The external references extension to a SCM repository",
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"required": ["scm_extension", "extension_schema"],
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"additionalProperties": false,
9+
"properties":{
10+
"extension_schema": {
11+
"title": "extension_schema",
12+
"type": "string",
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"format": "uri",
14+
"description": "The schema applied to the extension object",
15+
"examples": [
16+
"http://www.w3id.org/biocompute/extension_domain/example.json"
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]
18+
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},
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"scm_extension":{
21+
"required": [
22+
"scm_repository",
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"scm_type",
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"scm_commit",
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"scm_path"
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],
27+
"properties": {
28+
"scm_repository": {
29+
"type": "string",
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"examples": [
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"https://github.com/example/repo1"
32+
],
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"format": "uri"
34+
},
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"scm_type": {
36+
"type": "string",
37+
"enum": [
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"git",
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"svn",
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"hg",
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"other"
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]
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},
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"scm_commit": {
45+
"type": "string",
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"examples": [
47+
"c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21"
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]
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},
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"scm_path": {
51+
"type": "string",
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"examples": [
53+
"workflow/hive-viral-mutation-detection.cwl"
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],
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"format": "string"
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},
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"scm_preview": {
58+
"type": "string",
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"examples": [
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"https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl"
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],
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"format": "uri"
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}
64+
}
65+
}
66+
}
67+
}

config/schemas/dataset_extension.json renamed to config/schemas/1.2.0/dataset_extension.json

File renamed without changes.

config/schemas/fhir_extension.json renamed to config/schemas/1.2.0/fhir_extension.json

File renamed without changes.

config/schemas/galaxy_extension.json renamed to config/schemas/1.2.0/galaxy_extension.json

File renamed without changes.

config/schemas/license_extension.json renamed to config/schemas/1.2.0/license_extension.json

File renamed without changes.

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