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Remove use of ncov-ingest geolocation rules #17

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joverlee521 opened this issue Feb 7, 2025 · 2 comments
Open
8 of 17 tasks

Remove use of ncov-ingest geolocation rules #17

joverlee521 opened this issue Feb 7, 2025 · 2 comments
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@joverlee521
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joverlee521 commented Feb 7, 2025 •
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Once augur curate apply-geolocation-rules uses built-in default rules (nextstrain/augur#1744 + nextstrain/augur#1745), we can remove the use of ncov-ingest geolocation rules from pathogen ingest workflows.

TODOs

Based on GitHub search

We can prioritize updating the pathogen-repo-guide, docs, zika, and mpox

Other pathogens can be updated later as needed
@jameshadfield
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Other pathogens can be updated later as needed

Once the new version of Augur is out, will these at least need to use --no-default-rules, or will they be OK because their custom rules will essentially include the default rules as they fetch (a similar version of) the defaults and use them as custom rules?

@joverlee521
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Other pathogens can be updated later as needed

Once the new version of Augur is out, will these at least need to use --no-default-rules, or will they be OK because their custom rules will essentially include the default rules as they fetch (a similar version of) the defaults and use them as custom rules?

They should be okay because their custom rules still include the ncov-ingest rules that will override the default Augur rules.

@joverlee521 joverlee521 self-assigned this Feb 12, 2025
This was referenced Feb 13, 2025
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j23414 added a commit to nextstrain/dengue that referenced this issue Mar 4, 2025
@j23414
ingest: Remove use of ncov-ingest geolocation rules
436e947 
Remove the use of the ncov-ingest geolocation rules since Augur
now uses the built-in geolocation rules by default.

Depends on the release of
<nextstrain/augur#1745>

Part of larger migration
nextstrain/public#17
@j23414 j23414 mentioned this issue Mar 4, 2025
Merged
1 task
j23414 added a commit to nextstrain/WNV that referenced this issue Mar 5, 2025
@j23414
ingest: Remove use of ncov-ingest geolocation rules
204809f 
Remove the use of the ncov-ingest geolocation rules since Augur
now uses the built-in geolocation rules by default.

Depends on the release of
<nextstrain/augur#1745>

Part of larger migration
nextstrain/public#17
@j23414 j23414 mentioned this issue Mar 5, 2025
Merged
1 task
j23414 added a commit to nextstrain/lassa that referenced this issue Mar 5, 2025
@j23414
ingest: Remove use of ncov-ingest geolocation rules
56a43e1 
Remove the use of the ncov-ingest geolocation rules since Augur
now uses the built-in geolocation rules by default.

Depends on the release of
<nextstrain/augur#1745>

Part of larger migration
nextstrain/public#17
@j23414 j23414 mentioned this issue Mar 5, 2025
Merged
1 task
j23414 added a commit to nextstrain/norovirus that referenced this issue Mar 5, 2025
@j23414
ingest: Remove use of ncov-ingest geolocation rules
3d1c23c 
Remove the use of the ncov-ingest geolocation rules since Augur
now uses the built-in geolocation rules by default.

Depends on the release of
<nextstrain/augur#1745>

Part of larger migration
nextstrain/public#17
@j23414 j23414 mentioned this issue Mar 5, 2025
Merged
1 task
DOH-LMT2303 pushed a commit to nextstrain/WNV that referenced this issue Mar 5, 2025
@j23414
ingest: Remove use of ncov-ingest geolocation rules (#75)
188cda2 
Remove the use of the ncov-ingest geolocation rules since Augur
now uses the built-in geolocation rules by default.

Depends on the release of
<nextstrain/augur#1745>

Part of larger migration
nextstrain/public#17
j23414 added a commit to nextstrain/lassa that referenced this issue Mar 5, 2025
@j23414
ingest: Remove use of ncov-ingest geolocation rules (#56)
976a18a 
Remove the use of the ncov-ingest geolocation rules since Augur
now uses the built-in geolocation rules by default.

Depends on the release of
<nextstrain/augur#1745>

Part of larger migration
nextstrain/public#17
j23414 added a commit to nextstrain/norovirus that referenced this issue Mar 5, 2025
@j23414
ingest: Remove use of ncov-ingest geolocation rules (#8)
514d06d 
Remove the use of the ncov-ingest geolocation rules since Augur
now uses the built-in geolocation rules by default.

Depends on the release of
<nextstrain/augur#1745>

Part of larger migration
nextstrain/public#17
j23414 added a commit to nextstrain/dengue that referenced this issue Mar 5, 2025
@j23414
ingest: Remove use of ncov-ingest geolocation rules (#100)
bbc5fa4 
Remove the use of the ncov-ingest geolocation rules since Augur
now uses the built-in geolocation rules by default.

Depends on the release of
<nextstrain/augur#1745>

Part of larger migration
nextstrain/public#17
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