From a14a35007cf50e8c0a932cbe0d5cc1691ba289c1 Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Wed, 13 Sep 2023 13:55:23 -0700
Subject: [PATCH 1/2] Copy transform-strain-names from monkeypox

Copied from: https://github.com/nextstrain/monkeypox/blob/5969604dfe426745b789746427b580c69d484790/ingest/bin/transform-strain-names
---
 README.md                                     |  1 +
 .../transform-strain-names.t                  | 17 +++++++
 transform-strain-names                        | 50 +++++++++++++++++++
 3 files changed, 68 insertions(+)
 create mode 100644 tests/transform-strain-names/transform-strain-names.t
 create mode 100755 transform-strain-names

diff --git a/README.md b/README.md
index 0fbe706..008ec43 100644
--- a/README.md
+++ b/README.md
@@ -114,6 +114,7 @@ Potential augur curate scripts
 - [transform-authors](transform-authors) - Abbreviates full author lists to '<first author> et al.'
 - [transform-field-names](transform-field-names) - Rename fields of NDJSON records
 - [transform-genbank-location](transform-genbank-location) - Parses `location` field with the expected pattern `"<country_value>[:<region>][, <locality>]"` based on [GenBank's country field](https://www.ncbi.nlm.nih.gov/genbank/collab/country/)
+- [transform-strain-names](transform-strain-names) - Ordered search for strain names across several fields.
 
 ## Software requirements
 
diff --git a/tests/transform-strain-names/transform-strain-names.t b/tests/transform-strain-names/transform-strain-names.t
new file mode 100644
index 0000000..1c05df7
--- /dev/null
+++ b/tests/transform-strain-names/transform-strain-names.t
@@ -0,0 +1,17 @@
+Look for strain name in "strain" or a list of backup fields.
+
+If strain entry exists, do not do anything.
+
+  $ echo '{"strain": "i/am/a/strain", "strain_s": "other"}' \
+  >   | $TESTDIR/../../transform-strain-names \
+  >       --strain-regex '^.+$' \
+  >       --backup-fields strain_s accession
+  {"strain":"i/am/a/strain","strain_s":"other"}
+
+If strain entry does not exists, search the backup fields
+
+  $ echo '{"strain_s": "other"}' \
+  >   | $TESTDIR/../../transform-strain-names \
+  >       --strain-regex '^.+$' \
+  >       --backup-fields accession strain_s 
+  {"strain_s":"other","strain":"other"}
\ No newline at end of file
diff --git a/transform-strain-names b/transform-strain-names
new file mode 100755
index 0000000..d86c0e4
--- /dev/null
+++ b/transform-strain-names
@@ -0,0 +1,50 @@
+#!/usr/bin/env python3
+"""
+Verifies strain name pattern in the 'strain' field of the NDJSON record from
+stdin. Adds a 'strain' field to the record if it does not already exist.
+
+Outputs the modified records to stdout.
+"""
+import argparse
+import json
+import re
+from sys import stderr, stdin, stdout
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(
+        description=__doc__,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
+    parser.add_argument("--strain-regex", default="^.+$",
+        help="Regex pattern for strain names. " +
+             "Strain names that do not match the pattern will be dropped.")
+    parser.add_argument("--backup-fields", nargs="*",
+        help="List of backup fields to use as strain name if the value in 'strain' " +
+             "does not match the strain regex pattern. " +
+             "If multiple fields are provided, will use the first field that has a non-empty string.")
+
+    args = parser.parse_args()
+
+    strain_name_pattern = re.compile(args.strain_regex)
+
+    for index, record in enumerate(stdin):
+        record = json.loads(record)
+
+        # Verify strain name matches the strain regex pattern
+        if strain_name_pattern.match(record.get('strain', '')) is None:
+            # Default to empty string if not matching pattern
+            record['strain'] = ''
+            # Use non-empty value of backup fields if provided
+            if args.backup_fields:
+                for field in args.backup_fields:
+                    if record.get(field):
+                        record['strain'] = str(record[field])
+                        break
+
+        if record['strain'] == '':
+            print(f"WARNING: Record number {index} has an empty string as the strain name.", file=stderr)
+
+
+        json.dump(record, stdout, allow_nan=False, indent=None, separators=',:')
+        print()

From 6f196f77968ccab63d895fbadb11b87f72e8404d Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Fri, 15 Sep 2023 16:40:17 -0700
Subject: [PATCH 2/2] Add Cram tests

---
 .github/workflows/ci.yaml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 610bbe0..c6a218a 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -13,3 +13,11 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - uses: nextstrain/.github/actions/shellcheck@master
+
+  cram:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+      - run: pip install cram
+      - run: cram tests/
\ No newline at end of file