monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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ClinVar #1005

Closed TomConlin closed 3 years ago

TomConlin commented 3 years ago

Noticed a couple of monarch associations lacked predicates and isolated it to a case where the XML includes a stanza stating "not provided" instead of just not providing the stanza as the rest do. Also noticed an empty literal which are not emitted any more.

Required some upkeep to to get the subsetter back in working order added a new translation for likely patho call

Put a warning in the original subsetter that it no longer scales.

Started moving data transfer commands to rsync as it seems more robust (found instance where scp had truncated a file just moving between monarch 4 and 5) .