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62 fix omim #63

Merged
merged 4 commits into from
Jan 9, 2024
Merged

62 fix omim #63

merged 4 commits into from
Jan 9, 2024

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amc-corey-cox
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@amc-corey-cox amc-corey-cox commented Jan 9, 2024

Quick fix to the load_multi_context function that appears to fix the issue with OMIM being dropped.

Added a context for Monarch KG in the etl_runner so Monarch can keep ownership of the file merged.monarch.csv to watch out for changes that might be breaking.

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amc-corey-cox commented Jan 9, 2024

I had written this longer summary earlier but decided this is better in the comments section.
This provides a quick fix to the load_multi_context function that appears to fix the issue with OMIM being dropped. I'm still unclear why this is happening.

Separately, I've added a context for Monarch KG in the etl_runner similar to merged.oak that is an exact copy of merged and merged.oak. These can now diverge if necessary and Monarch can keep ownership of the file merged.monarch.csv to watch out for changes that might be breaking.

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amc-corey-cox commented Jan 9, 2024

I have elected not to run etl_runner for this PR so we don't add complexity. If you want me to do etl_runner and resubmit, I'm happy to. I suppose I don't know if GitHub runs etl_runner automatically... if so we may need to reconsider that for center cases, i.e. merged.oak and merged.monarch.

@amc-corey-cox amc-corey-cox merged commit 0bc0d5f into main Jan 9, 2024
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@amc-corey-cox amc-corey-cox deleted the 62_fix_OMIM branch January 9, 2024 21:45
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Repair prefixmaps merged output (tracking ticket) Release 2.0 can no longer expand OMIM IDs
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