Common

This section contains the API documentation fo the rodeos_ingest.common module and sub modules. The intended reader are developers interested in the source code of RODEOS Ingest. Readers that only want to install and/or use the software are probably not interested in it.

Common code for the omics ingest.

rodeos_ingest.common.KEY_FIRST_SEEN = 'rodeos::ingest::first_seen'

AVU key to use for first_seen attribute.

rodeos_ingest.common.KEY_LAST_UPDATE = 'rodeos::ingest::last_update'

AVU key to use for last_update attribute.

rodeos_ingest.common.KEY_MANIFEST_MESSAGE = 'rodeos::ingest::manifest_message'

AVU key with manifest detailed message

rodeos_ingest.common.KEY_MANIFEST_STATUS = 'rodeos::ingest::manifest_status'

AVU key for manifest status

rodeos_ingest.common.KEY_STATUS = 'rodeos::ingest::status'

AVU key to use destionation run folder ingestion status.

rodeos_ingest.common.compute_irods_manifest(dst_collection, logger, src_folder)

Compute manifest from irods checksums.

rodeos_ingest.common.compute_local_manifest(logger, src_folder)

Compute local hashdeep manifest.

rodeos_ingest.common.post_job(hdlr_mod, logger, meta, is_folder_done: Callable[[Union[pathlib.Path, str]], bool], delay_until_at_rest)

Move completed run folders into the “ingested” area.

rodeos_ingest.common.pre_job(hdlr_mod, logger, meta)

Set the first_seen meta data value.

rodeos_ingest.common.refresh_last_update_metadata(logger, session, meta)

Update the last_update and status meta data value.

rodeos_ingest.common.run_ichksum(irods_path: str, recurse: bool = False) → None

Run ichksum $irods_path.

rodeos_ingest.common.to_ingested_path(orig_path: Union[str, pathlib.Path]) → pathlib.Path

Convert a run folder path to an “ingested” path.