Merge pull request #38 from nextstrain/update-transform-field-names

`transform-field-names`: Skip field if `old_field_name` == `new_field_name`

tests/transform-field-names/transform-field-names.t

@@ -0,0 +1,26 @@
+Verify behavior of `transform-field-names`
+
+If the `--field-map` includes a old field name that is the same as the new field
+name, this should be no-op.
+
+  $ echo '{"strain": "A"}' \
+  >  | $TESTDIR/../../transform-field-names \
+  >      --field-map "strain=strain"
+  {"strain":"A"}
+
+If the `--field-map` overwrites an existing field, then skip renaming and
+print a loud warning.
+
+  $ echo '{"strain": "A", "isolate": "B"}' \
+  >  | $TESTDIR/../../transform-field-names \
+  >      --field-map "isolate=strain"
+  WARNING: skipping rename of isolate because record already has a field named strain.
+  {"strain":"A","isolate":"B"}
+
+The `--field-map` may overwrite an existing field if using `--force` flag.
+
+  $ echo '{"strain": "A", "isolate": "B"}' \
+  >  | $TESTDIR/../../transform-field-names \
+  >      --field-map "isolate=strain" \
+  >      --force
+  {"strain":"B"}

transform-field-names

@@ -16,8 +16,9 @@ if __name__ == '__main__':
     parser.add_argument("--field-map", nargs="+",
         help="Fields names in the NDJSON record mapped to new field names, " +
              "formatted as '{old_field_name}={new_field_name}'. " +
-             "If the old field does not exist in record, the new field will be added with an empty string value." +
-             "If the new field already exists in record, then the renaming of the old field will be skipped.")
+             "If the old field does not exist in record, the new field will be added with an empty string value. " +
+             "If the new field already exists in record, then the renaming of the old field will be skipped. " +
+             "Skips the field if the old field name is the same as the new field name (case-sensitive).")
     parser.add_argument("--force", action="store_true",
         help="Force renaming of old field even if the new field already exists. " +
              "Please keep in mind this will overwrite the value of the new field.")
@@ -27,6 +28,10 @@ if __name__ == '__main__':
     field_map = {}
     for field in args.field_map:
         old_name, new_name = field.split('=')
+
+        if old_name == new_name:
+            continue
+
         field_map[old_name] = new_name
 
     for record in stdin: