I installed the modules biosoftware_bench, gmod_dbsf, gmod_dbsf_chado, genes4all, and genes4all_download. Between gmod_dbsf and genes4all I noticed that the organismprop table was being used in SQL for some reason I couldn't figure out. But as a result, there was no data within the "Phylogeny" section of genes4all_download.

I don't know if this issue is better placed with gmod_dbsf or genes4all, but I put it with gmod_dbsf since that module creates tables "gmod_dbsf_organismprop" which has some database constraints to cvterm and organism tables.

For organismprop (in Chado) and gmod_dbsf_organismprop (in Drupal), how do I populate data to make things work?

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alpapan’s picture

alpapan commented
Status: Active » Postponed

Hello

Right, that's a good question. I assumed people had a pre-populated Chado database (let's assume you're most interested about genes4all_download). I'll try to write some support pages in during the conference (the sleepy bits) and post them sometime next week. That would solve the gmod_dbsf part.

For making use of gmod_dbsf (.e.g to write your own modules) that makes use of materialized views, I'll write some docos for it too

sorry for not replying earlier but I haven't found out how to get Drupal to email me every time there is an issue...

a

jmw86069’s picture

jmw86069 commented

Ha ha me neither, regarding Emailing me when there's a post!

I have a Chado database with about 5 million features, but not a single row of data in the organismprop table. Our primary usage to date has been storing genome coordinate features.

What process populates the organismprop table?

(No worries on the timelines, hope the conference went well!)

--James

alpapan’s picture

alpapan commented

Hi

Considering the age of the post, I was wondering if you still need help? I really should write a more extensive manual at some point but no-one else has asked so far...

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