[InterMine Dev] Populating Organism name list?

Colton McEntee cjmcentee at gmail.com
Fri May 15 23:10:47 BST 2015

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 <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.


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