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[wip] Attempt to eradicate confounding of release and submission #216

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[wip] Attempt to eradicate confounding of release and submission #216

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6 changes: 3 additions & 3 deletions ingest/config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,14 @@ transform:
# Fields to rename.
# This is the first step in the pipeline, so any references to field names
# in the configs below should use the new field names
field_map: ['collected=date', 'submitted=date_submitted', 'genbank_accession=accession', 'submitting_organization=institution']
field_map: ['collected=date', 'genbank_accession=accession', 'submitting_organization=institution']
# Standardized strain name regex
# Currently accepts any characters because we do not have a clear standard for strain names
strain_regex: '^.+$'
# Back up strain name field if 'strain' doesn't match regex above
strain_backup_fields: ['accession']
# List of date fields to standardize
date_fields: ['date', 'date_submitted']
date_fields: ['date', 'date_released']
# Expected date formats present in date fields
# These date formats should use directives expected by datetime
# See https://docs.python.org/3.9/library/datetime.html#strftime-and-strptime-format-codes
Expand Down Expand Up @@ -59,7 +59,7 @@ transform:
'division',
'location',
'host',
'date_submitted',
'date_released',
'sra_accession',
'abbr_authors',
'reverse',
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2 changes: 1 addition & 1 deletion ingest/source-data/ncbi-dataset-field-map.tsv
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Expand Up @@ -5,7 +5,7 @@ Isolate Lineage strain
Geographic Region region
Geographic Location location
Isolate Collection date collected
Release date submitted
Release date date_released
Update date updated
Length length
Host Name host
Expand Down