Skip annotations for fields that do not exist in record

I don't think we should support adding new fields with record
annotations because it's hard to ensure that the new field gets added
across all records that are streamed through the command.

This is a deviation from the original nextstrain/ingest script, but I
think a necessary one to avoid bugs in the final output metadata.

augur/curate/apply_record_annotations.py

@@ -45,6 +45,12 @@ def run(args, records):
         if record_id is None:
             raise AugurError(f"ID field {args.id_field!r} does not exist in record")
 
-        record.update(annotations.get(record_id, {}))
+        record_annotations = annotations.get(record_id, {})
+        for field in list(record_annotations.keys()):
+            if field not in record:
+                print_err(f"WARNING: Skipping annotation for field {field!r} that does not exist in record")
+                del record_annotations[field]
+
+        record.update(record_annotations)
 
         yield record

tests/functional/curate/cram/apply-record-annotations/annotating-new-fields.t

@@ -2,7 +2,7 @@ Setup
 
   $ export AUGUR="${AUGUR:-$TESTDIR/../../../../../bin/augur}"
 
-Test that annotations for new fields are added to the record.
+Test that annotations for new fields that are not in the record results in warning message.
 
   $ cat >annotations.tsv <<~~
   > record_2	new_field	annotation_1
@@ -16,16 +16,6 @@ Test that annotations for new fields are added to the record.
   $ cat records.ndjson \
   >   |  ${AUGUR} curate apply-record-annotations \
   >       --annotations annotations.tsv
+  WARNING: Skipping annotation for field 'new_field' that does not exist in record
   {"accession": "record_1", "field_1": "value_1"}
-  {"accession": "record_2", "field_1": "value_1", "new_field": "annotation_1"}
-
-
-  $ cat records.ndjson \
-  >   |  ${AUGUR} curate apply-record-annotations \
-  >       --annotations annotations.tsv \
-  >       --output-metadata metadata.tsv
-
-  $ cat metadata.tsv
-  accession\tfield_1 (esc)
-  record_1\tvalue_1 (esc)
-  record_2\tvalue_1 (esc)
+  {"accession": "record_2", "field_1": "value_1"}