curate: fix endless additional quotes

Resolves <#1312>

We are expecting the CSV-like double quoting when there are internal
quotes. If the field value is already correctly double quoted, then
there should not be any additional quotes.

augur/io/metadata.py

@@ -273,7 +273,8 @@ def visible_worksheet(s: calamine.SheetMetadata) -> bool:
                 # change in a future Python version.
                 raise InvalidDelimiter from error
 
-            metadata_reader = csv.DictReader(handle, dialect=dialect)
+            # Only use the dialect delimiter and keep all other default format params
+            metadata_reader = csv.DictReader(handle, delimiter=dialect.delimiter, doublequote=False)
 
             columns, records = metadata_reader.fieldnames, iter(metadata_reader)
 

tests/functional/curate/cram/metadata-output-with-internal-quotes.t

@@ -12,18 +12,18 @@ Create NDJSON with internal quotes
   > ~~
 
 Test passthru with output to TSV.
-This should not add any quotes around the field with internal quotes.
+This should add double quotes around the internal quotes to match CSV-like quoting.
 
   $ cat records.ndjson \
   >   | ${AUGUR} curate passthru \
   >     --output-metadata output-metadata.tsv
 
   $ cat output-metadata.tsv
   strain\tsubmitting_lab (esc)
-  sequence_A\tSRC VB "Vector", Molecular Biology of Genomes (esc)
+  sequence_A\t"SRC VB ""Vector"", Molecular Biology of Genomes" (esc)
 
 Run the output TSV through augur curate passthru again.
-The new output should still be identical to the first output.
+The new output should still be identical to the first output because it is already double quoted.
 
   $ ${AUGUR} curate passthru \
   > --metadata output-metadata.tsv \