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ingest: use new augur curate commands #70

Merged
merged 7 commits into from
Jul 18, 2024
Merged

ingest: use new augur curate commands #70

merged 7 commits into from
Jul 18, 2024

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j23414
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@j23414 j23414 commented Jul 17, 2024 •
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Description of proposed changes

Updates the curate rule to use the new augur curate commands.
Updates ingest/vendored to pull in latest changes including nextstrain/ingest#45.

Includes additional changes to rename transform to curate to conform the pathogen-repo-guide
Includes additional change to remove reverse and institution columns since they are blank and seemingly unused.

Related issue(s)

Mirroring changes in nextstrain/pathogen-repo-guide#53
Resolves #67

Checklist

  • Checks pass
  • Confirmed only diff is the added period to <first author> et al. and the removal of the reverse and institution columns.

@j23414 j23414 linked an issue Jul 17, 2024 that may be closed by this pull request
ingest: use new augur curate commands #67
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@j23414 j23414 requested a review from a team July 17, 2024 15:48
genehack
genehack approved these changes Jul 17, 2024
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Tiny nit: if you use git mv to rename files, rather than delete/re-add, I think there's better history and change tracking.

@j23414
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j23414 commented Jul 17, 2024

Ohh interesting, I did use git mv in 5690058 but perhaps the subsequent changes muddied the history.

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tsibley commented Jul 17, 2024

Tiny nit: if you use git mv to rename files, rather than delete/re-add, I think there's better history and change tracking.

git mv is exactly the same operation as rm + add. Tracking of moves/copies is done entirely by content similarity. There are config options to tweak how "hard" git tries to identify moves/copies; they're pretty conservative by default and it's nice to tune them upwards sometimes. I've also noticed that github.com's diff sometimes has worse move/copy detection than what I have configured locally.

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git mv is exactly the same operation as rm + add.

TIL!

joverlee521
joverlee521 approved these changes Jul 17, 2024
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ingest/config/config.yaml
'authors',
'institution'
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non-blocking

FWIW, institution can be populated by adding submitter-affiliation=institution to the field_map config.

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Thanks! Looking around the code configs, I decided to add a functionally populated institution column in 644faa9

@j23414
Replace vendored scripts with augur curate
d5358bc 
Vendored scripts for the curate rule have been ported to `augur curate`
and are available starting from Augur 25.0.0.¹

¹ <https://github.com/nextstrain/augur/releases/tag/25.0.0>
@j23414
Add subset_metadata
4b0eab1 
Separate out selecting metadata columns into a rule to match the pathogen repo guide
@j23414
Drop unused and blank metadata columns
33162d9
@j23414
Rename transform to curate
4d7a99f 
To conform to the pathogen-repo-guide

https://github.com/nextstrain/pathogen-repo-guide/blob/89b3c5dbc9b8f6a009f4a19c3ac56113bc5511ee/ingest/rules/curate.smk#L57
@j23414
git subrepo pull (merge) ingest/vendored
fa412c9 
subrepo:
  subdir:   "ingest/vendored"
  merged:   "258ab8c"
upstream:
  origin:   "https://github.com/nextstrain/ingest"
  branch:   "main"
  commit:   "258ab8c"
git-subrepo:
  version:  "0.4.6"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "110b9eb"
@j23414
Add functional institution column
644faa9
@j23414 j23414 force-pushed the 67-ingest-use-new-augur-curate-commands branch from 9ca3015 to 644faa9 Compare July 18, 2024 15:44
genehack
genehack approved these changes Jul 18, 2024
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ingest/config/config.yaml Outdated
@@ -8,7 +8,7 @@ ncbi_taxon_id:
general: "11250"

# Params for the transform rulegeneral
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probably want to update the comment too?

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lol, good catch, will update

@j23414 j23414 merged commit 211ba44 into master Jul 18, 2024
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@j23414 j23414 deleted the 67-ingest-use-new-augur-curate-commands branch July 18, 2024 20:28
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@joverlee521 joverlee521 joverlee521 approved these changes

@genehack genehack genehack approved these changes

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ingest: use new augur curate commands
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