hexylena
commented
5 months ago Please let me know if I should split this into three issues, one for preview, one for peek, and one for MSA or so.
Open hexylena opened 5 months ago
hexylena
commented
5 months ago Please let me know if I should split this into three issues, one for preview, one for peek, and one for MSA or so.
This took a while to track down, big thanks to @wm75 for noticing the issue (https://github.com/usegalaxy-eu/issues/issues/522)
When a fasta file is uploaded to Galaxy that includes a blank first line it is correctly detected as a fasta file, however certain tools will break (namely the MSA visualisation). Many tools will process this file happily, but not the MSA visualisation.
It is not easy to detect this issue as Galaxy does not make it obvious there's a blank line:
[as a user] In the preview is that a suspicious amount of whitespace? or do the UI devs just want more whitespace because that's the current design trend? Did they just want to line it up with the upload button? (folks love lining stuff up), or is that just space that would be occupied by a column header if it was there? I don't know. But selecting the text doesn't make it obvious there's a line there, I don't know how I'd know where the text was supposed to start.
Perhaps line numbers in the preview would be a good solution here? Additionally retaining whitespace in the peek would be helpful and make it very clear (due to the very small padding around the element, a whole blank line would be very obvious.)
Perhaps also the MSA visualisation should be updated to
.strip()or similar to enable it to handle what other tools consider as valid fasta files. Also which github should I contact them on? From that error message I have no idea and no way to find out.I'm filling this as a feature, but I guess if I was thinking about this as a user I think this is a bug, that it's not obvious to me as a user why tools fail.