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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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obnoxious behavior if > 500 results #25

Open bradfordcondon opened 6 years ago

bradfordcondon commented 6 years ago

A user was confused because their blast results had over 500 results, and therefore no results were displayed.

https://github.com/statonlab/hardwoods_site/issues/199

After some fiddling I discovered that you can set the max target sequences in the advanced options to return 500 or fewer sequences (see below).

Rather than return no results, why not return the first 500 results and display a warning that there are more results?

default blast parameters: error, 500+ sequences

screen shot 2018-02-27 at 11 58 01 am

max target = 50

screen shot 2018-02-27 at 12 00 07 pm

edit: Also, the error message reads

We have provided the result files for Download at the top of this page; however, we suggest you re-submit your query using a more stringent e-value (i.e. a smaller number).

However, no download link is provided. Note that the link is provided if < 500 entries

ekcannon commented 6 years ago

It's great to have more people using this module so that annoyances like this can be identified and addressed. As I wrote the code to bail if >500 results (a quick solution to a problem that was holding up a website release), I'll tackle improved handling of large results sets.

bradfordcondon commented 6 years ago

As I wrote the code to bail if >500 results (a quick solution to a problem that was holding up a website release), I'll tackle improved handling of large results sets.

Great and thank you! IMO This module works great and is easy to administer so I'm a big fan. I'd be happy to contribute as well.

Cheers

bradfordcondon commented 6 years ago

Oh i forgot the second part of this issue:

The error reads

We have provided the result files for Download at the top of this page; however, we suggest you re-submit your query using a more stringent e-value (i.e. a smaller number).

However, on my site at least, no download link is provided.

laceysanderson commented 6 years ago

Part of the issue with >500 results is the XML reader this module is using. It reads the entire file into memory resulting in a WSOD for large files. The solution is to switch to a stream-based XML reader as suggested in Issue #12.

The lack of download files is a simple bug however that should be easy to fix :-)

bradfordcondon commented 6 years ago

woops sorry for creating an issue largely duplicate with #12

embarrassing considering theres only 2 other issues lol