cwltool.cwlprov.ro

Stores class definition of ResearchObject and WritableBagFile.

Module Contents

Classes

ResearchObject

CWLProv Research Object.

class cwltool.cwlprov.ro.ResearchObject(fsaccess, temp_prefix_ro='tmp', orcid='', full_name='')

CWLProv Research Object.

Parameters:

• fsaccess (cwltool.stdfsaccess.StdFsAccess)

• temp_prefix_ro (str)

• orcid (str)

• full_name (str)

self_check()

Raise ValueError if this RO is closed.

Return type:

None

__str__()

Represent this RO as a string.

Return type:

str

user_provenance(document)

Add the user provenance.

Parameters:

document (prov.model.ProvDocument)

Return type:

None

add_tagfile(path, timestamp=None)

Add tag files to our research object.

Parameters:

• path (str)

• timestamp (Optional[datetime.datetime])

Return type:

None

add_uri(uri, timestamp=None)

Parameters:

• uri (str)

• timestamp (Optional[datetime.datetime])

Return type:

cwltool.cwlprov.Aggregate

add_annotation(about, content, motivated_by='oa:describing')

Cheap URI relativize for current directory and /.

Parameters:

• about (str)

• content (List[str])

• motivated_by (str)

Return type:

str

generate_snapshot(prov_dep)

Copy all of the CWL files to the snapshot/ directory.

Parameters:

prov_dep (cwltool.utils.CWLObjectType)

Return type:

None

has_data_file(sha1hash)

Confirm the presence of the given file in the RO.

Parameters:

sha1hash (str)

Return type:

bool

add_data_file(from_fp, timestamp=None, content_type=None)

Copy inputs to data/ folder.

Parameters:

• from_fp (IO[Any])

• timestamp (Optional[datetime.datetime])

• content_type (Optional[str])

Return type:

str

add_to_manifest(rel_path, checksums)

Add files to the research object manifest.

Parameters:

• rel_path (str)

• checksums (Dict[str, str])

Return type:

None