[curate rename] allow column duplication

See discussion in PR review for context
<#1506 (comment)>

augur/curate/rename.py

@@ -2,7 +2,7 @@
 Renames fields / columns of the input data
 """
 
-from typing import Iterable, Literal, Union, Dict, List, Tuple
+from typing import Iterable, Literal, Union, List, Tuple
 import argparse
 from augur.io.print import print_err
 from augur.errors import AugurError
@@ -14,9 +14,9 @@ def register_parser(parent_subparsers):
 
     required = parser.add_argument_group(title="REQUIRED")
     required.add_argument("--field-map", nargs="+", required=True,
-        help="Fields names in the NDJSON record mapped to new field names, " +
-             "formatted as '{old_field_name}={new_field_name}'. " +
+        help="Rename fields/columns via '{old_field_name}={new_field_name}'. " +
              "If the new field already exists, then the renaming of the old field will be skipped. " +
+             "Multiple entries with the same '{old_field_name}' will duplicate the field/column. " +
              "Skips the field if the old field name is the same as the new field name (case-sensitive).")
 
     optional = parser.add_argument_group(title="OPTIONAL")
@@ -27,10 +27,10 @@ def register_parser(parent_subparsers):
     return parser
 
 
-def parse_field_map(field_map_arg: List[str]) -> Dict[str,str]:
-    seen_old, seen_new = set(), set()
+def parse_field_map(field_map_arg: List[str]) -> List[Tuple[str,str]]:
+    seen_new = set() # keep track of the new field names
 
-    field_map = {}
+    field_map = []
     for field in field_map_arg:
         fields = [n.strip() for n in field.split('=')]
         if len(fields)!=2:
@@ -42,46 +42,44 @@ def parse_field_map(field_map_arg: List[str]) -> Dict[str,str]:
             raise AugurError(f"The field-map {field!r} doesn't specify a name for the existing field.")
         if not new_name:
             raise AugurError(f"The field-map {field!r} doesn't specify a name for the new field.")
-        if old_name in seen_old:
-            raise AugurError(f"Asked to rename field {old_name!r} multiple times.")
         if new_name in seen_new:
             raise AugurError(f"Asked to rename multiple fields to {new_name!r}.")
-        seen_old.add(old_name)
         seen_new.add(new_name)
 
-        if old_name == new_name:
-            continue
-
-        field_map[old_name] = new_name
+        field_map.append((old_name, new_name))
     return field_map
 
 
-def transform_columns(existing_fields: List[str], field_map: Dict[str,str], force: bool) -> List[Tuple[str,str]]:
+def transform_columns(existing_fields: List[str], field_map: List[Tuple[str,str]], force: bool) -> List[Tuple[str,str]]:
     """
     Calculate the mapping of old column names to new column names
     """
     # check that all columns to be renamed exist
-    for name in list(field_map.keys()):
-        if name not in existing_fields:
-            print_err(f"WARNING: Asked to rename field {name!r} (to {field_map[name]!r}) but it doesn't exist in the input data.")
-            del field_map[name]
+    for idx,names in enumerate(field_map[:]):
+        old_name, new_name = names
+        if old_name not in existing_fields:
+            print_err(f"WARNING: Asked to rename field {old_name!r} (to {new_name!r}) but it doesn't exist in the input data.")
+            field_map.pop(idx)
 
     # iterate through field_map and remove rename requests if they would drop an existing column
     # doing this ahead-of-time allows us to preserve the order of fields using a simpler implementation
     if not force:
-        for old_field, new_field in list(field_map.items()):
-            if new_field in existing_fields:
+        for idx, fields in enumerate(field_map[:]):
+            old_field, new_field = fields
+            if new_field in existing_fields and new_field!=old_field:
                 print_err(
                     f"WARNING: skipping rename of {old_field} because record",
                     f"already has a field named {new_field}."
                 )
-                del field_map[old_field]
+                field_map.pop(idx)
+
+    names_to_change, new_names = set([f[0] for f in field_map]), set([f[1] for f in field_map])
 
     m = []
     for field in existing_fields:
-        if field in field_map:
-            m.append((field, field_map[field]))
-        elif field in field_map.values():
+        if field in names_to_change:
+            m += [(field,new_field) for old_field, new_field in field_map if old_field==field]
+        elif field in new_names:
             pass # another column is renamed to this name, so we drop it
         else:
             m.append((field, field)) # no change to field name

tests/functional/curate/cram/rename/duplicate.t

@@ -0,0 +1,24 @@
+Setup
+
+  $ export AUGUR="${AUGUR:-$TESTDIR/../../../../../bin/augur}"
+
+  $ cat >records.ndjson <<~~
+  > {"accession": "record_1", "country": "country_1"}
+  > {"accession": "record_2", "country": "country_2"}
+  > ~~
+
+
+Asking to rename the same column multiple times results in duplication of the column.
+Additional columns are inserted next to the existing one, and the order of the new columns
+matches the field-map
+
+  $ $AUGUR curate rename --field-map "accession=id" "accession=genbank_accession" < <(cat records.ndjson)
+  {"id": "record_1", "genbank_accession": "record_1", "country": "country_1"}
+  {"id": "record_2", "genbank_accession": "record_2", "country": "country_2"}
+
+
+We can use the same name to keep the original column
+
+  $ $AUGUR curate rename --field-map "accession=id" "accession=accession" < <(cat records.ndjson)
+  {"id": "record_1", "accession": "record_1", "country": "country_1"}
+  {"id": "record_2", "accession": "record_2", "country": "country_2"}