From afcac54560d74538f1513905674c6b92c2bcbcf5 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Thu, 1 Aug 2024 16:38:21 -0700 Subject: [PATCH] curate: fix endless additional quotes Resolves 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 | 3 ++- .../curate/cram/metadata-output-with-internal-quotes.t | 6 +++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/augur/io/metadata.py b/augur/io/metadata.py index 95ae7b84b..041829cd8 100644 --- a/augur/io/metadata.py +++ b/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) columns, records = metadata_reader.fieldnames, iter(metadata_reader) diff --git a/tests/functional/curate/cram/metadata-output-with-internal-quotes.t b/tests/functional/curate/cram/metadata-output-with-internal-quotes.t index 0c8541798..1e3725f7e 100644 --- a/tests/functional/curate/cram/metadata-output-with-internal-quotes.t +++ b/tests/functional/curate/cram/metadata-output-with-internal-quotes.t @@ -12,7 +12,7 @@ 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 \ @@ -20,10 +20,10 @@ This should not add any quotes around the field with internal quotes. $ 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 \