The blast_sequence table is big and only getting bigger

[childers]

I've been getting warnings about the blast.sequence table growing large, and on looking at the table definitions, it seems like this is because records are never deleted when the blast database the record refers to is also deleted.

Right now this one table id around 935 MB. I did some basic tests and it looks like queries on this table may take a significant amount of time to return results.

I think the only reason we have this is for displaying the subject sequence in the results page. This functionality should be reproducible either using the included BLAST+ tools.

[deming7h777]

I try to use postgres schema to access blast_sequence table but encounter the permission issue

[deming7h777]

I try to use postgres schema to access blast_sequence table but encounter the permission issue

ERROR: permission denied for relation blast_sequence
and then I try : GRANT ALL PRIVILEGES ON TABLE blast_sequence TO django;
GRANT ALL PRIVILEGES ON TABLES IN SCHEMA public TO django;
but still get the same error

[deming7h777]

I went through three script yesterday to figure out the procedure for replacing current fasta-view by blast+ application.

1. setup.py ( check if it need more installation for blast+)
2. blast.result.js ( there are further more package need to figure out eg. codemirror)
3. result.html

[deming7h777]

1.Encounter the issue No alias or index file found for nucleotide database
2.After figuring out, I try to use blastdbcmd -list /home/vagrant/genomics-workspace/media/blast/db -recursive but fail
3.Then I try to replace full path by ./ then somehow it works
4. There are several argument for blastdbcmd such like blastdbcmd [-h] [-help] [-db dbname] [-dbtype molecule_type]
[-entry sequence_identifier] [-entry_batch input_file] [-pig PIG] [-info]
[-range numbers] [-strand strand] [-mask_sequence_with mask_algo_id]
[-out output_file] [-outfmt format] [-target_only] [-get_dups]
[-line_length number] [-ctrl_a] [-show_blastdb_search_path]
[-list directory] [-remove_redundant_dbs] [-recursive]
[-list_outfmt format] [-exact_length] [-long_seqids] [-logfile File_Name]
[-version]
I pick " - entry " as the argument to extract sequence from BLAST database but it seems like I still choose the wrong value to search

[deming7h777]

There are three python package that can use for CLI:

1. Click ( include: django-click)
2. Docopt
3. Fire (develop by google)

The way than can used by javascript:

1. fixed package.json bin
2. commander.js

[deming7h777]

Get Javascript and Python get communicate using Json

1. Ajax include JQuery and Js

[deming7h777]

Alright, so for sending data from the client (JavaScript) to the backend (your Django app) you need to employ something called Ajax, it stands for Asynchronous JavaScript and XML. Basically what it does is allowing you to communicate with your backend services without the need of having to reload the page, which, you would have to do using a normal POST or PUT form submission.

The easiest implementation is using jQuery. jQuery is first and foremost a DOM manipulation library but since its inception has grown to encompass much more than that.

example code :
'''
$(document).ready(function() {
$.ajax({
method: 'POST',
url: '/path/to/your/view/',
data: {'yourJavaScriptArrayKey': yourJavaScriptArray},
success: function (data) {
//this gets called when server returns an OK response
alert("it worked!");
},
error: function (data) {
alert("it didnt work");
}
});
});
'''

[deming7h777]

so far we need three steps to achieve the goal

1. build the folder /blast/templatetags
2. put the function script under /blast/templatetags e.g. blastdbcmd.py
3. add some more AJAX line in result.html or blast-result.js

[childers]

For future reference. This is in branch "blastdbcmd"

[deming7h777]

different path between blast/views.py and media/blast/db (where the BLAST DATABASE is)
the only problem right now is that we need to change the default path set by " blastdbcmd"