[InterMine Dev] Populating Organism name list?

Julie Sullivan julie at flymine.org
Mon May 18 09:43:52 BST 2015


Hi Colton,

Here's the organism section in the tutorial:

http://intermine.readthedocs.org/en/latest/get-started/tutorial/#updating-organism-and-publication-information

You'll want to run the "entrez-organism" data source and redeploy your 
webapp.

Let me know if that doesn't fix your problem!

Julie

On 15/05/15 23:10, Colton McEntee wrote:
> To anyone willing or able to help,
>
> I was trying to make a list (from the List tab) in my intermine web app,
> but the "For Organisms:" field only has the options "Any" and an empty
> option. Upon comparison with the MalariaMine tutorial, it appears that
> the tutorial also doesn't populate this list. I can't find any
> information in the documentation describing how to populate this list.
>
> On the other hand, I know it's not supposed to be blank because FlyMine
> has a dozen or so options in it. See:
> http://www.flymine.org/release-40.0/bag.do
>
> Tracing the field back through bagBuild.jsp, BagBuildController.java,
> BagQueryConfig.java, and TagManager.java I don't feel any closer to
> figuring out where or how flymine populates the organisms option list.
> All the classes are there, but it's not clear how exactly it's getting
> data from the database and it's even less clear how to load that data
> into the database.
>
> And I can't find access to the flymine raw data to construct my own
> local copy to look through its database for anything that might be relevant.
>
> Is there any meaningful documentation for the actual core API for
> intermine? The closest I can get are some JavaDocs that helpfully
> describe the TagManager as "Manager class for tags", without going into
> more detail as to how it's actually used or how it interfaces with the
> database.
>
> Is there higher level documentation that actually describes program
> control flow in intermine? Reading through JSPs and Java in order to
> reverse engineer the actual functionality is fruitless and mind
> bogglingly tedious.
>
> Thanks,
>
> Colton
>
>
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