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wurmlab / sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
https://sequenceserver.com
GNU Affero General Public License v3.0
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BLAST button not working with sequenceserver 3.1.3 and tree widget enabled #784

Open lukaszsobala opened 3 months ago

lukaszsobala commented 3 months ago

Hello,

The issue is explained in the description. When the tree widget is disabled, the BLAST button does work. I have tested this on 2 separate devices. Also, I have tested in both Firefox and Chromium.

The bug seems to be related to the predefined command line options, which don't seem to be loading at all. They are quite slow to load in 3.1.2 already...

yannickwurm commented 3 months ago

Thanks Lukasz, I'm sorry that sucks. The tree widget is still considered as experimental :/ Have you tried debugging the javascript?

I'm surprised by your comment about the command-line options though. Where do you feel they're not loading correctly?

Kind regards, Yannick

lukaszsobala commented 3 months ago

Hi Yannick,

I am sorry but I have no clue about how to debug javascript!

When you paste a sequence here, for example: https://lukprot.hirszfeld.pl/ the options I predefined take 5-10 seconds to load up on 3.1.2 when you select the databases. This might be because there are so many databases in the tree. On 3.1.3 this does not seem to work at all (even with 1 database selected when the tree widget is active).

Cheers, Łukasz

kuntzagk commented 3 months ago

I have run into the same problem here. When examining the delivered javascript it looks like the "query_stats.js" delivered is much smaller then in 3.1.2. It is identical to the code checked into GH while on 3.1.2 it contains other contain (when loaded in browser, code on disk is identical) So I guess some kind of magic code replacement is not happening.

hth

jasongallant commented 2 months ago

+1 I had a user report in on this issue from https://www.efishgenomics.com/blast_search/ with the same issue. I disabled tree for the time being, but it sure is much messier looking. Any ideas what might be behind this?

Thanks in advance

yannickwurm commented 3 weeks ago

Hi folks - there have been several changes in the underlying code and process.

I'm unsure as to why this broke. A likely contributor is our migrating from using a long deprecated version of bootstrap to using tailwind, and updating a bunch of deprecated javascript libraries. Another possible contributor are the increased cross-sight forgery protections.

We'd be most eager for contributions that look into this. The likely best place to begin any fixes is on what's currently in master. Though a first step is likely here https://github.com/wurmlab/sequenceserver/pull/799