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Napa compliance #1246
Napa compliance #1246
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…nce mongo db instance and update study and biosample records for gold:Gs0114663
…s for gold:Gs0114663
…do not have upstream omics records
…rds from legacy to NMDC napa style identifiers
…nch-format-source-code-using-black Format Python source code (PR target: `napa_compliance` branch)
…n omics function for re-iding
…dc_schemainsert_many_pymongopy-more-robust Convert `insert_many_pymongo.py` into `click` CLI command
…mdc-schema into napa_compliance
…refactor to clean up some messy functions.
…to-output-deleted-document-identifier Update `connect_napa_mongo.py` to output tsv with deleted record identifiers
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…n code was used instead of this protoype code
I recommend moving these scripts into a subdirectory (e.g. |
@turbomam to suggest a different directory to put these scripts. |
Ideally it would be something more generic, I've had to make other ad hoc scripts (ie https://github.com/microbiomedata/nmdc-schema/blob/main/nmdc_schema/identify_workflow_duplicates_emp500.py) for data clean up and I'd like this to be co-located. |
@aclum I made a commit in this branch that moves the Python files and adds a few lines to the top of the README. If that's OK with you, then you can merge as far as I'm concerned. |
Sorry, because I did a filesystem move and edited the README, no useful diff shows up here's what I added:
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oops, I missed your "more generic" comment too |
@aclum @eecavanna @mbthornton-lbl I moved the scripts once again to Please let me know if this is acceptable to you We can move identify_workflow_duplicates_emp500.py into |
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I'm OK with the new folder name. I requested a change to some example commands, since they use the old folder name.
Out sick this afternoon. Once the above is resolved, I'm OK with this being merged in without my involvement/review.
Updates paths in the README.md file for code in /src/scripts/task_specific_code
This is acceptable to me, I've addressed Eric's comments about the paths in the README.md file and have requested a re-review. |
This PR merges in python code used during re-iding. There are no changes to the schema or example data. No migrations required, just trying to get old branches merged.