eradicate our confounding of release and submission

Co-authored-by: Cornelius Roemer <[email protected]>

ingest/config/config.yaml

@@ -10,14 +10,14 @@ 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', 'released=date_released', '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
@@ -63,7 +63,7 @@ transform:
     'division',
     'location',
     'host',
-    'date_submitted',
+    'date_released',
     'sra_accession',
     'abbr_authors',
     'authors',

ingest/source-data/ncbi-dataset-field-map.tsv

@@ -5,7 +5,7 @@ Isolate Lineage	strain
 Geographic Region	region
 Geographic Location	location
 Isolate Collection date	collected
-Release date	submitted
+Release date	released
 Update date	updated
 Length	length
 Host Name	host