MRG: ignore extra columns in gbsketch input CSV #188
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…sketch into ignore_extra_columns merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. make test
ctb
changed the title
|
Ready for review & merge @bluegenes !! |
bluegenes
reviewed
Jan 28, 2025
src/utils/mod.rs
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140
| for h in expected_header.iter() { | ||
| if !header.iter().any(|e| *h == e) { | ||
| return Err(anyhow!( | ||
| "Missing column name '{}' in CSV file. Columns should be: {:?}", | ||
| h, | ||
| expected_header | ||
| )); | ||
| } | ||
| } | ||
|
|
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| for h in header.iter() { | ||
| if !expected_header.iter().any(|e| h == *e) { | ||
| eprintln!("WARNING: extra column '{}' in CSV file. Ignoring.", h); | ||
| } |
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I'm worried this accepts input CSVs that contain all columns, but not in the right order. The input code currently uses column indexes, not column names, to read the CSV. This has been on my long list to improve, will make an issue for it now.
For this PR, we could just check for the full expected header first, then allow extra columns? Lmk if you want me to take this on.
|
oh, I see... hmm. I think I have a fix that will let you merge this and then do an improved column-name-based one in the future... let me try. Check out 5c1946a and let me know what you think! |
bluegenes
approved these changes
Jan 28, 2025
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Fixes #187
TODO: