robinandeer / puzzle

Variant caller GUI + genetic disease analysis
https://robinandeer.gitbooks.io/puzzle/content/
MIT License
22 stars 7 forks source link

Incompatible usage of GeminiPlugin #231

Open DamianSkrzypczak opened 6 years ago

DamianSkrzypczak commented 6 years ago

Hello,

issue is during execution of command gemini browser my.db --use puzzle there is problem with compatibility of interfaces:

In line 267 of file gemini_browser.py there is usage of GeminiPlugin which class which comes from line 22 (init is most important in this case, that's why line 22) of file plugin.py from puzzle module.

As You can see in comparison, GeminiPlugin has big issue with attribute "db", it's not used in init()

In my opinion this is issue with puzzle module because there is no access to db attribute other than x = GeminiPlugin( vtype="sv") x.db = args.db which is wrong because such thing like database parameter is pretty much required for this class to create object. I've done some local change (like code above) to run, browser is running without problem but there should be some unittest for it (don't trust my manual testing hah).

Please put proper argument into initialize method of class GeminiPlugin.