-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
On branch 1.2.0 Your branch is up to date with 'origin/1.2.0'. Changes to be committed: modified: README.md modified: dataset/README.md modified: dataset/dataset_extension.json modified: fhir/README.md modified: fhir/fhir_extension.json modified: galaxy/README.md modified: galaxy/galaxy_extension.json modified: license/README.md modified: license/license_extension.json modified: scm/README.md modified: scm/scm_extension.json
1 parent
a61ab84
commit 1764153
Showing
11 changed files
with
252 additions
and
318 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,2 +1,3 @@ | ||
# extension_schema | ||
|
||
extension schema for BCO |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,86 +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", | ||
"$schema": "http://json-schema.org/draft-07/schema#", | ||
"$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, | ||
"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", | ||
"file_type", | ||
"status", | ||
"scope" | ||
] | ||
} | ||
} | ||
} | ||
} | ||
"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" | ||
] | ||
|
||
} | ||
} | ||
} | ||
} | ||
}, | ||
"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" | ||
] | ||
} | ||
} | ||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,67 +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", | ||
"$schema": "http://json-schema.org/draft-07/schema#", | ||
"$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", | ||
"format": "uri", | ||
"description": "The schema applied to the extension object", | ||
"examples": [ | ||
"http://www.w3id.org/biocompute/extension_domain/example.json" | ||
] | ||
|
||
}, | ||
"fhir_extension":{ | ||
"title": "", | ||
"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", | ||
"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" | ||
} | ||
} | ||
} | ||
} | ||
"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" | ||
} | ||
} | ||
} | ||
} | ||
} | ||
} | ||
} | ||
} | ||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,44 +1,36 @@ | ||
{ | ||
"$schema": "http://json-schema.org/draft-07/schema#", | ||
"$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" | ||
] | ||
|
||
"$schema": "http://json-schema.org/draft-07/schema#", | ||
"$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_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" | ||
] | ||
} | ||
} | ||
"galaxy_version": { | ||
"type": "string", | ||
"description": "The specific version of the Galaxy software used to generate the BioCompute Object.", | ||
"examples": ["20.01"] | ||
} | ||
} | ||
} | ||
} | ||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,41 +1,34 @@ | ||
{ | ||
"$schema": "http://json-schema.org/draft-07/schema#", | ||
"$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" | ||
] | ||
"$schema": "http://json-schema.org/draft-07/schema#", | ||
"$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" | ||
}, | ||
"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" | ||
} | ||
} | ||
"scripts_license": { | ||
"type": "string", | ||
"examples": ["https://github.com/example/repo1"], | ||
"format": "uri" | ||
} | ||
} | ||
} | ||
} | ||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,67 +1,50 @@ | ||
{ | ||
"$schema": "http://json-schema.org/draft-07/schema#", | ||
"$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" | ||
] | ||
|
||
"$schema": "http://json-schema.org/draft-07/schema#", | ||
"$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_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" | ||
} | ||
} | ||
"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" | ||
} | ||
} | ||
} | ||
} | ||
} |