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tripal / tripal_blast

Provides an user interface to BLAST on Tripal sites.
https://tripal.github.io/tripal_blast/
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Unable to set regex for linkouts #43

Closed ekcannon closed 5 years ago

ekcannon commented 6 years ago

I don't know how this used to work. It doesn't appear to be possible to turn on the "FASTA header format" section.

When a new BLAST database node is started, the default linkout type is 'none', so the "FASTA header format" section is turned off, since 'none' doesn't require a regex. Changing the linkout type to, for example, 'Generic', does not activate the "FASTA header format" section. Saving the linkout type 'Generic' without setting the FASTA header information results in an invalid blastdb record which then has to be repaired by hand.

This problem is recent. We last built BLAST database nodes about two-three months ago with no problems.

ekcannon commented 6 years ago

This may be a javascript or ajax problem as it works properly on some websites.

laceysanderson commented 5 years ago

This should be fixed now -just added a commit that brought back the ajax trigger on the linkouts form element. Can you test with the most recent dev @ekcannon ?

laceysanderson commented 5 years ago

@ekcannon did you get the chance to test this?

btski commented 5 years ago

@laceysanderson AJAX trigger works fine in the most recent github developer version. I was also able to reproduce the error with the current drush release. Thanks for the fix! I'm trying to add additional linkout options. I'm interested in offering multiple hyperlinks per query name. Basically have some kind of delimited sequence name and use regex to parse specific accessions (Example: Local, GenBank, PubMed, PMC, etc). Also wish to allow unlinked values.

Aside from my particular goals, I'd like to provide a little feedback. In the summary portion, having the sequence names cropped by custom regex seems to limit the utility of hyperlinking in the first place. Instead of cropping the entire sequence name, why not make the whole thing hyperlinked instead? Cropping has the potential advantage of making the link destination more obvious, but if an admin is building a BLAST database using specific sequence names, I would assume they would want to retain the full sequence names post BLAST alignment. Granted, the full names are retained in the different download formats.

Edit - I've decided one hyperlink per sequence name will be adequate. I can redirect to other data sources from my local sequence pages.

ekcannon commented 5 years ago

Ugh. This issue fell off my desk some time last summer. It appears that I fixed it back in August '18, but never submitted a pull request for my fix. This also means that my copy of this module is that far behind the main one. I'll need to get everything sorted out and will probably have a pull request to submit.

laceysanderson commented 5 years ago

Thanks for the feedback @btski! Would you like to add a couple of issues: a) multiple links per hit, b) show full name rather then only captured portion. These are great feature requests and I would welcome PRs for them if you would like guidance towards a general solution :-)

I'm going to close the current issue since the fix to functionality has been confirmed. If you are still encountering problems once you update to the new version @ekcannon then please open another issue!