Fix curate internal quotes take 2 #1565
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1565 +/- ##
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Coverage 72.29% 72.29%
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Files 79 79
Lines 8276 8276
Branches 1691 1691
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Hits 5983 5983
Misses 2008 2008
Partials 285 285 ☔ View full report in Codecov by Sentry. |
genehack
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Aug 2, 2024
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Let's discuss this topic more first. I'll open an issue for it. |
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Saving this here for later… |
tsibley
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This construction reads a bit clearer and cleaner. It's also a good example of how to use `augur merge`. The limitation on non-seekable streams means the rule now uses additional transient disk space, but it typically shouldn't be an issue. The way Augur's slow start up time impacts `augur merge` also contributes to a longer rule execution time, but it should be negligible in the context of the larger workflow and presumably we'll fix the slow start up eventually.¹ The output is semantically identical but has some syntactic changes re: quoting. It's worth noting that the pre-existing TSV format was _not_ IANA TSV, despite it (still) being treated as such in a few places, but was (and remains) a CSV-like TSV with some quoted fields (and some mangled quotes², e.g. the "institution" column for accession KJ556895). We really need to sort out our TSV formats³, but that's for a larger project. ¹ <nextstrain/augur#1628> ² <nextstrain/augur#1565> ³ <nextstrain/augur#1566>
tsibley
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This construction reads a bit clearer and cleaner. It's also a good example of how to use `augur merge`. The limitation on non-seekable streams means the workflow now uses additional transient disk space, but it typically shouldn't be an issue. The way Augur's slow start up time impacts `augur merge` also contributes to a longer rule execution time, but it should be negligible in the context of the larger workflow and presumably we'll fix the slow start up eventually.¹ The output is semantically identical but has some syntactic changes re: quoting. It's worth noting that the pre-existing TSV format was _not_ IANA TSV, despite it (still) being treated as such in a few places, but was (and remains) a CSV-like TSV with some quoted fields (and some mangled quotes², e.g. the "institution" column for accession KJ556895). We really need to sort out our TSV formats³, but that's for a larger project. ¹ <nextstrain/augur#1628> ² <nextstrain/augur#1565> ³ <nextstrain/augur#1566>
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I think this PR should be ready for review based on #1566 (comment). |
tsibley
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Oct 3, 2024
tsibley
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This construction reads a bit clearer and cleaner. It's also a good example of how to use `augur merge`. The limitation on non-seekable streams means the workflow now uses additional transient disk space, but it typically shouldn't be an issue. The way Augur's slow start up time impacts `augur merge` also contributes to a longer rule execution time, but it should be negligible in the context of the larger workflow and presumably we'll fix the slow start up eventually.¹ The output is semantically identical but has some syntactic changes re: quoting. It's worth noting that the pre-existing TSV format was _not_ IANA TSV, despite it (still) being treated as such in a few places, but was (and remains) a CSV-like TSV with some quoted fields. We really need to sort out our TSV formats³, but that's for a larger project. ¹ <nextstrain/augur#1628> ² <nextstrain/augur#1565> ³ <nextstrain/augur#1566> Ported-from: <nextstrain/measles@4d73b7f> Related-to: <nextstrain/measles#52> Related-to: <#65>
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genehack
approved these changes
Oct 7, 2024
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Reminder that this is approved and apparently just waiting for changelog and merge :) |
This reverts commit 915672e. Per discussion in <#1563 (comment)>, keep CSV-like TSV where quotes may be added or removed, but parsed values should be equivalent.
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.
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Thanks for the ping @corneliusroemer! I've rebased onto master and added a Changelog entry. I'll merge once all the tests pass again. |
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Description of proposed changes
Follow the general pattern of creating CSV-like TSVs as discussed in #1563 (comment).
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.
Related issue(s)
Resolves #1312
Checklist