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Test module for xref parsers, test WormbaseDirectParser

Marek Szuba requested to merge github/fork/wbazant/master into master

Created by: wbazant


Add a way to test xref parsers, and a first test, for WormbaseDirectParser.

Use case

I will work on WormbaseDirectParser soon, aiming to develop a more correct way to handle UniProt xrefs for c. elegans. I'll add some tests to the code I touch, probably.

Developers of xref parsers could add their tests to this module and get benefits like I expect - see the section, "Benefits"


Other people can edit WormbaseDirectParser and see if it still works. The test documents a possible bug in WormbaseDirectParser (some duplicate direct_xrefs).

Possible Drawbacks

The repo will take slightly longer to download, and the test suite will run longer.


The test runs fine with prove, although a module issuing mysql commands through the shell is warning me about how using password on the command line can be insecure. I think the Travis setup will be fine with how I changed it.

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