weaver.provenance

Definitions related to Provenance features and the W3C PROV specification.

Module Contents

weaver.provenance.AnyProvenanceFormat

class weaver.provenance.ProvenancePathType

Constants container that provides similar functionalities to ExtendedEnum without explicit Enum membership.

PROV = '/prov'

PROV_INFO = '/prov/info'

PROV_WHO = '/prov/who'

PROV_INPUTS = '/prov/inputs'

PROV_OUTPUTS = '/prov/outputs'

PROV_RUN = '/prov/run'

PROV_RUNS = '/prov/runs'

classmethod types() → List[str]

classmethod as_type(prov: Any) → str | None

classmethod get(prov: weaver.typedefs.AnyKey | weaver.base.EnumType | ProvenancePathType, default: Any | None = None, run_id: str | None = None) → ProvenancePathType | None

class weaver.provenance.ProvenanceFormat

Constants container that provides similar functionalities to ExtendedEnum without explicit Enum membership.

PROV_JSON = 'PROV-JSON'

PROV_JSONLD = 'PROV-JSONLD'

PROV_XML = 'PROV-XML'

PROV_TURTLE = 'PROV-TURTLE'

PROV_N = 'PROV-N'

PROV_NT = 'PROV-NT'

_media_types

_rev_path_types

classmethod get(prov_format: AnyProvenanceFormat | None, default: Any | None = None, allow_media_type: bool = False) → ProvenanceFormat | None

classmethod media_types() → List[weaver.formats.ContentType]

classmethod formats() → List[ProvenanceFormat]

classmethod as_media_type(prov_format: AnyProvenanceFormat | None) → weaver.formats.AnyContentType | None

classmethod resolve_compatible_formats(prov: ProvenancePathType | str | None, prov_format: ProvenanceFormat | str | None, output_format: weaver.formats.OutputFormat | str | None) → Tuple[ProvenanceFormat | None, str | None]

Resolves multiple OutputFormat and ProvenanceFormat combinations for compatible formats.

Compatible formats depend on the PROV endpoint being requested. If output format is not specified, apply the corresponding PROV format that will work transparently. Otherwise, ensure they are aligned against the expected PROV endpoints and supported Media-Types.

Returns:

Tuple of a resolved PROV format if only the output format was specified, and the relevant error detail if they are incompatible.

class weaver.provenance.WeaverResearchObject(job: weaver.datatype.Job, settings: weaver.typedefs.AnySettingsContainer, fs_access: cwltool.stdfsaccess.StdFsAccess, temp_prefix_ro: str = 'tmp', orcid: str = '', full_name: str = '')

Defines extended Provenance details with Weaver operations and referencing the active server instance.

Initialize the ResearchObject.

job

ro_uuid

base_uri = 'arcp://uuid,Uninferable/'

settings

static sha1_uuid(document: prov.model.ProvDocument, identifier: str) → str

Generate a prefixed SHA1 hash from the identifier value.

initialize_provenance(full_name: str, host_provenance: bool, user_provenance: bool, orcid: str, fsaccess: cwltool.stdfsaccess.StdFsAccess, run_uuid: uuid.UUID | None = None) → cwltool.cwlprov.provenance_profile.ProvenanceProfile

Hook Weaver metadata onto user provenance step.

resolve_user() → Tuple[str, str]

Override cwltool default machine user.

resolve_host() → Tuple[str, str]

Override cwltool default machine host.