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.
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rodeos_ingest.common.
KEY_FIRST_SEEN
= 'rodeos::ingest::first_seen'¶ AVU key to use for
first_seen
attribute.
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rodeos_ingest.common.
KEY_LAST_UPDATE
= 'rodeos::ingest::last_update'¶ AVU key to use for
last_update
attribute.
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rodeos_ingest.common.
KEY_MANIFEST_MESSAGE
= 'rodeos::ingest::manifest_message'¶ AVU key with manifest detailed message
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rodeos_ingest.common.
KEY_MANIFEST_STATUS
= 'rodeos::ingest::manifest_status'¶ AVU key for manifest status
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rodeos_ingest.common.
KEY_STATUS
= 'rodeos::ingest::status'¶ AVU key to use destionation run folder ingestion status.
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rodeos_ingest.common.
compute_irods_manifest
(dst_collection, logger, src_folder)¶ Compute manifest from irods checksums.
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rodeos_ingest.common.
compute_local_manifest
(logger, src_folder)¶ Compute local hashdeep manifest.
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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.
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rodeos_ingest.common.
pre_job
(hdlr_mod, logger, meta)¶ Set the
first_seen
meta data value.
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rodeos_ingest.common.
refresh_last_update_metadata
(logger, session, meta)¶ Update the
last_update
andstatus
meta data value.
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rodeos_ingest.common.
run_ichksum
(irods_path: str, recurse: bool = False) → None¶ Run
ichksum $irods_path
.
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rodeos_ingest.common.
to_ingested_path
(orig_path: Union[str, pathlib.Path]) → pathlib.Path¶ Convert a run folder path to an “ingested” path.