ingest: add url curation

Author: rneher

ingest/bin/curate-urls.py

@@ -0,0 +1,43 @@
+"""custom curate script to add URLs"""
+import sys
+import argparse
+from typing import Iterable
+
+from augur.curate import validate_records
+from augur.io.json import dump_ndjson, load_ndjson
+
+def run(args: argparse.Namespace, records: Iterable[dict]) -> Iterable[dict]:
+
+    for index, record in enumerate(records):
+        record = record.copy()
+
+        ppx_accession = record.get('PPX_accession', None) # versioned
+        insdc_accession = record.get('INSDC_accession', None) # versioned
+
+        # Add INSDC_accession__url and PPX_accession__url fields to NDJSON records
+        record['PPX_accession__url'] = f"https://pathoplexus.org/seq/{ppx_accession}" \
+            if ppx_accession \
+            else ""
+        record['INSDC_accession__url'] = f"https://www.ncbi.nlm.nih.gov/nuccore/{insdc_accession}" \
+            if insdc_accession \
+            else ""
+
+        yield record
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description=__doc__)
+    args = parser.parse_args()
+
+    records = load_ndjson(sys.stdin)
+
+    # Validate records have the same input fields
+    validated_input_records = validate_records(records, __doc__, True)
+
+    # Run this custom curate command to get modified records
+    modified_records = run(args, validated_input_records)
+
+    # Validate modified records have the same output fields
+    validated_output_records = validate_records(modified_records, __doc__, False)
+
+    dump_ndjson(validated_output_records)

ingest/defaults/config.yaml

@@ -147,7 +147,9 @@ curate:
     'date',
     'accession', # unversioned PPX accession
     'PPX_accession',
+    'PPX_accession__url',
     'INSDC_accession',
+    'INSDC_accession__url',
     'region',
     'country',
     'division',

ingest/rules/curate.smk

@@ -82,6 +82,7 @@ rule curate:
                 --abbr-authors-field {params.abbr_authors_field:q} \
             | augur curate apply-geolocation-rules \
                 --geolocation-rules {input.geolocation_rules:q} \
+            | python ./bin/curate-urls.py \
             | augur curate apply-record-annotations \
                 --annotations {input.annotations:q} \
                 --id-field {params.annotations_id:q} \