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Automated GenBank ingest failing #475

Closed

4 of 5 tasks

joverlee521 opened this issue Sep 12, 2024 · 0 comments · Fixed by #476

Closed

4 of 5 tasks

Automated GenBank ingest failing #475

joverlee521 opened this issue Sep 12, 2024 · 0 comments · Fixed by #476

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joverlee521 commented Sep 12, 2024 •

edited by j23414

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Automated GenBank ingest failures

Both workflows failed during transform-rki-data-to-ndjson. This is due to upstream changes in the RKI data. RKI announced in robert-koch-institut/SARS-CoV-2-Sequenzdaten_aus_Deutschland#59 that some variables have been renamed. This particular error comes from SEQUENCE.ID being renamed to igs_id, but we use other columns as well.

The available variables are listed in the top level README

TODOs

update RKI_INDEX_COL in bin/transform-rki-data-to-ndjson
update COLUMN_MAP in bin/transform-rki
add new date format %Y-%m-%dT%H:%M:%S to expected date_formats
parse new JSON blob for pango_lineage
diff with old version on S3 (s3://nextstrain-data/files/ncov/rki/metadata.tsv.zst)

The text was updated successfully, but these errors were encountered:

joverlee521 assigned joverlee521 and j23414 and unassigned joverlee521

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Update RKI data processing #476

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j23414 mentioned this issue

Update RKI data processing #476

Merged

1 task

j23414 closed this as completed in #476

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