wfexs_backend.fetchers.trs_files

wfexs_backend.fetchers.trs_files#

Module Contents#

Classes#

GA4GHTRSFetcher

API#

class wfexs_backend.fetchers.trs_files.GA4GHTRSFetcher(scheme_catalog: wfexs_backend.scheme_catalog.SchemeCatalog, progs: wfexs_backend.common.ProgsMapping = dict(), setup_block: Mapping[str, Any] | None = None)#

Bases: wfexs_backend.fetchers.AbstractSchemeRepoFetcher

INTERNAL_TRS_SCHEME_PREFIX: Final[str] = 'wfexs.trs.files'#
TRS_SCHEME_PREFIX: Final[str] = 'trs'#
TRS_TOOLS_SUFFIX: Final[str] = 'tools/'#
TRS_FILES_SUFFIX: Final[str] = '/files'#
TRS_DESCRIPTOR_INFIX: Final[str] = '/descriptor/'#
classmethod GetSchemeHandlers() → Mapping[str, DocumentedStatefulProtocolFetcher]#
property description: str#
classmethod GetNeededPrograms() → Sequence[SymbolicName]#
classmethod GuessTRSParams(orig_wf_url: URIType | parse.ParseResult, override_version_id: WFVersionId | None = None, logger: logging.Logger | None = None, fail_ok: bool = False, scheme_catalog: SchemeCatalog | None = None, offline: bool = False) → Tuple[RepoURL, str, Sequence[str], WorkflowId, WFVersionId, str, Sequence[URIWithMetadata], Mapping[str, Any] | None] | None#
classmethod GuessRepoParams(orig_wf_url: URIType | parse.ParseResult, logger: logging.Logger | None = None, fail_ok: bool = False, offline: bool = False) → RemoteRepo | None#
classmethod BuildRepoPIDFromTRSParams(trs_endpoint: str, workflow_id: wfexs_backend.workflow.WorkflowId, version_id: WFVersionId | None) → wfexs_backend.common.URIType#
materialize_repo_from_repo(repo: wfexs_backend.fetchers.RemoteRepo, repo_tag_destdir: PathLikePath | None = None, base_repo_destdir: PathLikePath | None = None, doUpdate: bool | None = True) → wfexs_backend.fetchers.MaterializedRepo#
build_pid_from_repo(remote_repo: wfexs_backend.fetchers.RemoteRepo) → str | None#

This method is required to generate a PID which usually represents an element (usually a workflow) in a repository. If the fetcher does not recognize the type of repo, either using repo_url content or the repo type in the worst case, it should return None

fetch(remote_file: wfexs_backend.common.URIType, cachedFilename: wfexs_backend.common.PathLikePath, secContext: SecurityContextConfig | None = None, explicit_redirects: bool = False) → wfexs_backend.fetchers.ProtocolFetcherReturn#

Method to download contents from TRS files related to a tool

Parameters:

  • remote_file

  • cachedFilename – Destination filename for the fetched content

  • secContext – The security context containing the credentials