Extension-domain

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Extension Domain (extension_domain)

The extension_domain is a space for a user to add additional structured information that is not defined in the BioCompute schema. It is optional. While the extension domain is not defined by IEEE-2791-2020, each extension in this domain must provide a reference to the schema that defines it in order to validate. The extension domain allows a user to define additional fields and is the place to add any additional structured information.

Condensed example:

"extension_domain":{
},

Components of the Extension Domain

Field	Required
extension_schema	OPTIONAL

Domain Components

Extensions

A valid JSON schema for each extension used in this domain is expected to be specified. The schema should be namespaced, and it is recommended that resolving the namespaced URI will provide the extension’s JSON Schema. The URL must be provided in the extension_schema field.

Extension Domain Examples

• FHIR extension
• SCM extension

We provide an example here that is neither exclusive nor exhaustive. The following example is taken from Extension to External References: Software Configuration Management (SCM) v1.1.0

   "extension_domain":[
       {
           "extension_schema": "https://w3id.org/biocompute/extension_domain/1.1.0/scm/scm_extension.json",
           "scm_extension": {
               "scm_repository": "https://github.com/example/repo1",
               "scm_type": "git",
               "scm_commit": "c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21",
               "scm_path": "workflow/hive-viral-mutation-detection.cwl",
               "scm_preview": "https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl"
           }
       }
   ]

SCM Repository (scm_repository)

The base url for the SCM repository.

SCM Type (scm_type)

A classifier for the type of SCM database. This field is a list of predefined values. Third-party scm types can be used, and if so the other value MUST be used. The options for this field include git (Git, including GitHub/GitLab), svn (Subversion), hg (mercurial) and others.

SCM Commit (scm_commit)

This field is a reference to a revision within the scm repository. This SHOULD be a repository-wide commit identifier (e.g. afba51a222e199f5b58f9d19450f189055e93c44 or name of a tag (e.g. v1.0.0), but MAY be a name of a branch (e.g. master).

SCM Path (scm_path)

This is the path from the repository to the source code referenced. scm_path should NOT start with /.

SCM Preview (scm_preview)

The full URI for the source code is referenced by the BioCompute Object.