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Improve curate metadata parser #1110

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Dec 12, 2022
Merged

Improve curate metadata parser #1110

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da845f4
tests: Failing test for comma separated data in curate metadata TSV
joverlee521 Dec 10, 2022
04f1e4c
read_table_to_dict: only sample the first line
joverlee521 Dec 10, 2022
0f740f3
Update changelog
joverlee521 Dec 10, 2022
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2 changes: 2 additions & 0 deletions CHANGES.md
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Expand Up @@ -7,10 +7,12 @@
* docs: Update the API documentation to reflect the latest state of things in the codebase. [#1087][] (@victorlin)
* Fix support for Biopython version 1.80 which deprecated `Bio.Seq.Seq.ungap()`. [#1102][] (@victorlin)
* export v2: Fixed a bug where colorings for zero values via `--colors` would not get applied to the exported Auspice JSON. [#1100][] (@joverlee521)
* curate: Fixed a bug where metadata TSVs failed to parse if data within a column included comma separated values [#1110][] (@joverlee521)

[#1087]: https://github.com/nextstrain/augur/pull/1087
[#1100]: https://github.com/nextstrain/augur/pull/1100
[#1102]: https://github.com/nextstrain/augur/pull/1102
[#1110]: https://github.com/nextstrain/augur/pull/1110

## 18.2.0 (15 November 2022)

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2 changes: 1 addition & 1 deletion augur/io/metadata.py
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Expand Up @@ -138,7 +138,7 @@ def read_table_to_dict(table, duplicate_reporting=DataErrorMethod.ERROR_FIRST, i
duplicate_ids = set()
with open_file(table) as handle:
# Get sample to determine delimiter
table_sample = handle.read(1024)
table_sample = handle.readline()
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Oh and also, I don't think it's necessary since we don't limit reads later in this function, but we could preserve the 1KiB read limit with:

… = handle.readline(1024)

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Yeah, I didn't think it would be necessary to add a size limit here since we read full records later anyways.


if handle.seekable():
handle.seek(0)
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20 changes: 10 additions & 10 deletions tests/functional/curate/cram/metadata-input.t
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Expand Up @@ -9,28 +9,28 @@ Running the `passthru` subcommand since it does not do any data transformations.
Create metadata TSV file for testing.

$ cat >$TMP/metadata.tsv <<~~
> strain country date
> sequence_A USA 2020-10-01
> sequence_B USA 2020-10-02
> sequence_C USA 2020-10-03
> strain country date authors
> sequence_A USA 2020-10-01 A,B,C,D,E,F,G,H,I,J,K
> sequence_B USA 2020-10-02 A,B,C,D,E,F,G,H,I,J,K
> sequence_C USA 2020-10-03 A,B,C,D,E,F,G,H,I,J,K
> ~~

Test TSV metadata input

$ ${AUGUR} curate passthru \
> --metadata $TMP/metadata.tsv
{"strain": "sequence_A", "country": "USA", "date": "2020-10-01"}
{"strain": "sequence_B", "country": "USA", "date": "2020-10-02"}
{"strain": "sequence_C", "country": "USA", "date": "2020-10-03"}
{"strain": "sequence_A", "country": "USA", "date": "2020-10-01", "authors": "A,B,C,D,E,F,G,H,I,J,K"}
{"strain": "sequence_B", "country": "USA", "date": "2020-10-02", "authors": "A,B,C,D,E,F,G,H,I,J,K"}
{"strain": "sequence_C", "country": "USA", "date": "2020-10-03", "authors": "A,B,C,D,E,F,G,H,I,J,K"}

Test TSV metadata input from stdin

$ cat $TMP/metadata.tsv \
> | ${AUGUR} curate normalize-strings \
> --metadata -
{"strain": "sequence_A", "country": "USA", "date": "2020-10-01"}
{"strain": "sequence_B", "country": "USA", "date": "2020-10-02"}
{"strain": "sequence_C", "country": "USA", "date": "2020-10-03"}
{"strain": "sequence_A", "country": "USA", "date": "2020-10-01", "authors": "A,B,C,D,E,F,G,H,I,J,K"}
{"strain": "sequence_B", "country": "USA", "date": "2020-10-02", "authors": "A,B,C,D,E,F,G,H,I,J,K"}
{"strain": "sequence_C", "country": "USA", "date": "2020-10-03", "authors": "A,B,C,D,E,F,G,H,I,J,K"}

Create metadata CSV file for testing.

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