BLAST tool - improve user interface to find what they need

[mestato]

BLAST tool interface is not very good. Problems:

When selecting a nucleotide database, we offer a number of types of databases:

• mRNA nucleotides
• gene nucleotides
• whole genome contigs, scaffolds or chromosomes

None of these are labeled very well. You have to click on the drop down and then look at the information in parentheses to get an idea of what you are searching. Let's fix this, we can get ideas from other genome databases about how this should look.

We should also link to the BLAST form from genome and transcriptome analysis pages and from organism pages.

[mestato]

Update on loading the above link: "Secure Connection Failed"

[almasaeed2010]

@mestato is this is the link you mean? https://www.hardwoodgenomics.org/blast/report/fPjVoPsAjVo

I tried accessing the URL from 3 different browsers (including FF) and it worked fine for me. an SSL trace shows that our certificate is still valid. (see here for trace: https://www.ssllabs.com/ssltest/analyze.html?d=hardwoodgenomics.org)

I wonder if it's a specific browser version?

[mestato]

No, it was a BLAST result with a query named lcl_contig0000566.

https://www.hardwoodgenomics.org/blast/report/fPjVoPPyt

I got the secure connection error twice. Maybe the results had a already been deleted but the links back were still available.

[almasaeed2010]

Ok I get a 500 error on this page:

and here is the issue:

Fatal error: Maximum execution time of 30+2 seconds exceeded (terminated) in /var/www/html/sites/all/modules/tripal_blast/api/blast_ui.api.inc on line 714

mmap() failed: [12] Cannot allocate memory

mmap() failed: [12] Cannot allocate memory

mmap() failed: [12] Cannot allocate memory

mmap() failed: [12] Cannot allocate memory

[almasaeed2010]

The issue with this is that the generated XML is more than 300MB

333M    2019Mar01_154121.blast.xml

I am not sure if there is a way to tweak the blast program to limit the results to a manageable size.

[almasaeed2010]

Try using XML Stream Reader to limit mem usage

[mestato]

Front page when selecting a blastn program, update text (on page one time): "Search a nucleotide database " to "Search a nucleotide database (genome or transcripts) "

After selecting blastn: Make it clear that there are scaffolds in addition to nucleotides. (They are too far down in list!) Make two lists???

[almasaeed2010]

@mestato would this work?

They are now separated by a title in the dropdown

[mestato]

Yes, wonderful!

[almasaeed2010]

ok this is now live!

Thanks