Dynamic materialized/drupal view

[abretaud]

As promises in #23, here's a first PR with the changes I made on the drupal view displaying the number of gene per species. There were some hardcoded species name, now it's dynamic.

To do this, in the materialized view, for each tree I store a json listing of per species count, and then I parse it when displaying the drupal view. I have not seen performance problem with ~20000 trees.

I'm not sure if it's really mergeable as is because:

• but there is no more aggregation of gene number by genus as there was before. I don't see a good way to decide which species should be grouped together (maybe on the genus organism column?). If you have a suggestion don't hesitate
• I couldn't find a way to add the filters for each organism, I have some chunks of code on my HDD, but it's not working, and it's lower priority for me right now.

Anyway, feel free to test and make suggestions!

(Sorry for the delay, I had to work on python-chado to speed up the loading process. Loading gff using tripal was just too long when loading several genomes.)

[adf-ncgr]

Hi, sorry for my slow response and thanks a lot for sharing your code. I'm really eager to have a look soon, but am coming up on a few key project deadlines and need to defer it for a few weeks until I have those behind me. But that will be a good time to make changes as we're going to be adding in several new species and rebuilding the families our site uses, and it will give me a good chance to focus on the trees for a while.

[adf-ncgr]

Hi- just FYI, I've finally started looking at this and I think I understand your approach (more or less); with respect to the filtering I think this is something that I'd like to try to address- our current approach is not only too hard-coded and specific to our site but also as the number of species continues to increase, our simple approach is just not sustainable. I've asked the Tripal Help Desk if this might be an appropriate topic for them to discuss with me this Friday- it's short notice for you, so I am not really expecting you'd be able to attend (and it's short notice for them, so not sure whether they might want to defer it to get some more info before trying to advise). In any case, just wanted to let you know this wasn't continuing to languish without any attention from our end... thanks again for initiating this! I am hopeful we'll find a solution that will strike a good balance between having the capabilities of the current module but not being so tied to the data in our site.

[abretaud]

Hi, Thanks for having a look at it! I won't be able to join the tripal help desk call, but let me know the progress or if there's anything I can do to help