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Fix/rki tsv csv #409

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merged 9 commits into from
Jul 11, 2023
Merged

Fix/rki tsv csv #409

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9a7b597
fix: RKI ingest
rneher Jul 4, 2023
bac89af
fix: missing line continuation
rneher Jul 4, 2023
facbd11
Remove RKI lineage downloads
joverlee521 Jul 5, 2023
faf0ff1
Fix typo in RKI metadata file
joverlee521 Jul 5, 2023
35d4311
transform-rki-data-to-ndjson: update index column
joverlee521 Jul 5, 2023
486cdbd
transform-rki-data-to-ndjson: convert NA to empty strings
joverlee521 Jul 5, 2023
fa9bf37
transform-rki: update `COLUMN_MAP`
joverlee521 Jul 5, 2023
3a7f3d4
StandardizeDataRki: add new expected date format
joverlee521 Jul 6, 2023
5ec9651
Use correct default branch `main` for RKI
corneliusroemer Jul 11, 2023
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14 changes: 6 additions & 8 deletions bin/transform-rki
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Original file line number Diff line number Diff line change
Expand Up @@ -29,14 +29,12 @@ from lib.utils.transformpipeline.transforms import (AddHardcodedMetadataRki,
UserProvidedAnnotations)

COLUMN_MAP = {
"DATE_DRAW": "date",
"RECEIVE_DATE": "date_submitted",
"PROCESSING_DATE": "date_released",
"SENDING_LAB_PC": "originating_lab",
"SEQUENCING_LAB_PC": "submitting_lab",
"GISAID_ACCESSION": "strain_gisaid",
"lineage": "pango_lineage",
"SEQ_REASON": "sampling_strategy",
"SEQUENCE.DATE_OF_SAMPLING": "date",
"SEQUENCE.PUSHED_TO_DWH": "date_submitted",
"DL.ID": "originating_lab",
"SL.ID": "submitting_lab",
"PANGOLIN.LINEAGE_LATEST": "pango_lineage",
"SEQUENCE.SEQUENCING_REASON": "sampling_strategy",
Comment on lines +32 to +37
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Full disclosure: I made these column changes using Google Translate to translate the RKI docs of the metadata fields.

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They are correct :)

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Thank you for checking 🙏

}


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