[apollo] Delay when displaying Information Editor Panel

[Loraine Guéguen]

Hi Nathan,

I have forgotten to talk with you about one performance problem we have
for displaying the "Information Editor" panel with "Edit Information".
There is always a 10 to 20 seconds delay before the "Information Editor"
panel appears once we have clicked on "Edit Information". Apparently, it
depends on the gene : the longest is the gene, the most time it takes.
That is not very comfortable.
We have Apollo 2.0.2 release with a postgres database. And the gff3 is
directly loaded into the User-Annotation track (can this be one of the
reason for the delay ?).
It seems that the delay is due to 2 SQL requests in the database that
are very long.

Do you have any clue on how to reduce this time ?

Thanks

Loraine Guéguen

PS : Unfortunately, I leave the conference soon, so I will not be able
to discuss about that directly with you or to show you.

[Nathan Dunn]

Thank you for reporting.

If you have timing data for the SQL requests, you can add them here (it will save me time).

https://github.com/GMOD/Apollo/issues/1147

Also, if you can take a picture or give an estimate for how long these genes are that would be great. I think that this will be an easy fix, but you may need to upgrade to see the improvement (once fixed).

Thanks,

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory

Post by Loraine Guéguen
Hi Nathan,
I have forgotten to talk with you about one performance problem we have for displaying the "Information Editor" panel with "Edit Information".
There is always a 10 to 20 seconds delay before the "Information Editor" panel appears once we have clicked on "Edit Information". Apparently, it depends on the gene : the longest is the gene, the most time it takes. That is not very comfortable.
We have Apollo 2.0.2 release with a postgres database. And the gff3 is directly loaded into the User-Annotation track (can this be one of the reason for the delay ?).
It seems that the delay is due to 2 SQL requests in the database that are very long.
Do you have any clue on how to reduce this time ?
Thanks
Loraine Guéguen
PS : Unfortunately, I leave the conference soon, so I will not be able to discuss about that directly with you or to show you.

[Nathan Dunn]

I have a PR for it under review that takes it down to about 50 ms or less, regardless of the feature length.

https://github.com/GMOD/Apollo/pull/1148 <https://github.com/GMOD/Apollo/pull/1148>

Its against mainline, though it might work for 2.0.2. We’ll probably pull it into mainline shortly.

Nathan

Post by Nathan Dunn
Thank you for reporting.
If you have timing data for the SQL requests, you can add them here (it will save me time).
https://github.com/GMOD/Apollo/issues/1147 <https://github.com/GMOD/Apollo/issues/1147>
Also, if you can take a picture or give an estimate for how long these genes are that would be great. I think that this will be an easy fix, but you may need to upgrade to see the improvement (once fixed).
Thanks,
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory

Post by Loraine Guéguen
Hi Nathan,
I have forgotten to talk with you about one performance problem we have for displaying the "Information Editor" panel with "Edit Information".
There is always a 10 to 20 seconds delay before the "Information Editor" panel appears once we have clicked on "Edit Information". Apparently, it depends on the gene : the longest is the gene, the most time it takes. That is not very comfortable.
We have Apollo 2.0.2 release with a postgres database. And the gff3 is directly loaded into the User-Annotation track (can this be one of the reason for the delay ?).
It seems that the delay is due to 2 SQL requests in the database that are very long.
Do you have any clue on how to reduce this time ?
Thanks
Loraine Guéguen
PS : Unfortunately, I leave the conference soon, so I will not be able to discuss about that directly with you or to show you.