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Napa compliance #1246

Merged
merged 50 commits into from
Jul 16, 2024
Merged

Napa compliance #1246

merged 50 commits into from
Jul 16, 2024

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aclum
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@aclum aclum commented Oct 26, 2023

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.

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aclum commented Oct 26, 2023

aclum and others added 17 commits October 26, 2023 17:32
…rds from legacy to NMDC napa style identifiers
…nch-format-source-code-using-black

Format Python source code (PR target: `napa_compliance` branch)
…dc_schemainsert_many_pymongopy-more-robust

Convert `insert_many_pymongo.py` into `click` CLI command
@aclum aclum requested a review from mbthornton-lbl February 22, 2024 22:52
@aclum aclum changed the base branch from main-old to main July 11, 2024 23:02
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github-actions bot commented Jul 11, 2024

PR Preview Action v1.4.7
🚀 Deployed preview to https://microbiomedata.github.io/nmdc-schema/pr-preview/pr-1246/
on branch gh-pages at 2024-07-16 22:16 UTC

@aclum aclum marked this pull request as ready for review July 11, 2024 23:20
@aclum aclum requested a review from turbomam July 11, 2024 23:20
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eecavanna commented Jul 15, 2024

I recommend moving these scripts into a subdirectory (e.g. nmdc_schema/re_id_scripts). I think that will distinguish them from general-purpose schema-related code. Note: Moving them might require updating some import statements.

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aclum commented Jul 15, 2024

@turbomam to suggest a different directory to put these scripts.

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aclum commented Jul 15, 2024

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.

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@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.

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Sorry, because I did a filesystem move and edited the README, no useful diff shows up

here's what I added:

This code has been executed, the results were accepted, and it should not need to be run again. It is being included as
documentation. The Python files have been moved from `nmdc_schema/` to `nmdc_schema/completed_napa_compliance/` and they
shouldn't be expected to work from that location.

One shouldn't assume that the installation notes below are intended for any other nmdc-schema development.

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oops, I missed your "more generic" comment too

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turbomam commented Jul 16, 2024

@aclum @eecavanna @mbthornton-lbl I moved the scripts once again to src/scripts/task_specific_code/ and added a little more to the README.md

Please let me know if this is acceptable to you

We can move identify_workflow_duplicates_emp500.py into src/scripts/task_specific_code/ in a separate PR. That file isn't present in this branch.

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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.

src/scripts/task_specific_code/README.md Outdated Show resolved Hide resolved
Updates paths in the README.md file for code in /src/scripts/task_specific_code
@aclum aclum requested a review from eecavanna July 16, 2024 22:14
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aclum commented Jul 16, 2024

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.

@aclum aclum merged commit 249034d into main Jul 16, 2024
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@aclum aclum deleted the napa_compliance branch July 16, 2024 22:23
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6 participants