Chromosome feature loading time

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Chromosome feature loading time

Anestis Gkanogiannis
Hello,

I am very new to the Drupal/Tripal/Chado.
I am developing a site for the cassava genome.

I have loaded the chromosome sequences from a fasta file and several hundred thousands of features from a gff3 file (genes, mRNA, polypeptide, CDS, etc).

In the feature browser, or when I do a feature search, pages for short features (like genes for example) open very rapidly.

On the other hand the pages of chromosomes takes half an hour to load.

I understand that there is a chado operation running that gets the relationships and all the aligned features on the chromosomes.
I tried to disable this operation (by altering the tripal php templates), but still no change; half an hour.

I would appreciate if someone could give me a hint on how to make the chromosome pages load faster (even without the information of the alignments and relationships).


Thank you,

Anestis
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Re: Chromosome feature loading time

Stephen Ficklin-2
Hi Anestis,

Apologies for the slow reply.

Typically we do not create pages for chromosomes as there is too much
associated with them and you are correct that the relationship template
is causing the problem as well as the sequence template. Unfortunately,
the issue cannot be fixed by editing the templates. When designing the
templates we specifically tried to avoid using SQL and so we designed  
API functions to handle the common queries. But because of the way
relationships are stored in Chado it's easier to use an SQL statement
than the API functions to retrieve them.  So that SQL is handled in a
preprocess function inside of the Tripal code.  We would need to adjust
that to fix the problem.

This is the first time I'm aware of that a chromosome page are wanted.  
The quick short-term solution is to not sync chromosome pages.  Long
term, if you need chromosome pages we can look into fixing this
problem.  I have created an issue for this in our issue queue:

https://www.drupal.org/node/2666326

Stephen



On 2/4/2016 3:58 AM, Anestis Gkanogiannis wrote:

> Hello,
>
> I am very new to the Drupal/Tripal/Chado.
> I am developing a site for the cassava genome.
>
> I have loaded the chromosome sequences from a fasta file and several hundred thousands of features from a gff3 file (genes, mRNA, polypeptide, CDS, etc).
>
> In the feature browser, or when I do a feature search, pages for short features (like genes for example) open very rapidly.
>
> On the other hand the pages of chromosomes takes half an hour to load.
>
> I understand that there is a chado operation running that gets the relationships and all the aligned features on the chromosomes.
> I tried to disable this operation (by altering the tripal php templates), but still no change; half an hour.
>
> I would appreciate if someone could give me a hint on how to make the chromosome pages load faster (even without the information of the alignments and relationships).
>
>
> Thank you,
>
> Anestis
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


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