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ingest: Switch to full_authors and authors fields
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Switch `authors` to `full_authors` and `abbr_authors` to `authors` so
that the abbreviated author field is used by `augur export` in the
phylogenetic workflow.

Resolves <#290>
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joverlee521 committed Nov 19, 2024
1 parent af33cf2 commit 7008947
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Showing 2 changed files with 4 additions and 4 deletions.
6 changes: 3 additions & 3 deletions ingest/defaults/config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -40,11 +40,11 @@ curate:
# List of string fields to titlecase
fields: ['region', 'country', 'division', 'location']
# Authors field name
authors_field: 'authors'
authors_field: 'full_authors'
# Authors default value if authors value is empty
authors_default_value: '?'
# Field name for the generated abbreviated authors
abbr_authors_field: 'abbr_authors'
abbr_authors_field: 'authors'
# General geolocation rules to apply to geolocation fields
geolocation_rules_url: 'https://raw.githubusercontent.com/nextstrain/ncov-ingest/master/source-data/gisaid_geoLocationRules.tsv'
# Local geolocation rules that are only applicable to mpox data
Expand All @@ -71,8 +71,8 @@ curate:
'host',
'date_submitted',
'sra_accession',
'abbr_authors',
'authors',
'full_authors',
'institution'
]

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2 changes: 1 addition & 1 deletion ingest/defaults/ncbi-dataset-field-map.tsv
Original file line number Diff line number Diff line change
Expand Up @@ -13,5 +13,5 @@ Isolate Lineage source isolation_source
BioProjects bioproject_accession
BioSample accession biosample_accession
SRA Accessions sra_accession
Submitter Names authors
Submitter Names full_authors
Submitter Affiliation submitting_organization

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