Created by: mkszuba
Have BaseParser::get_source_id_by_source_name() throw an exception rather than return -1 in the event of being unable to find a matching source ID. Backport from ensembl-xref.
I have yet to see a parser which continues happily if it cannot get the ID of a source, therefore each and every one of the parsers I have seen implemented some variant of "if -1, abort". Moreover, the warning message produced before returning -1 has not exactly been helpful.
More consistent behaviour of xref parsers, simpler backporting from ensembl-xref.
Xref parsers currently being backported which have not been merged into feature/xref_sprint yet and use BaseParser::get_source_id_by_source_name() will have to be adapted back to ensembl-xref-like behaviour, especially if their respective unit tests check what exception is thrown upon failure to retrieve a source ID.
Have you added/modified unit tests to test the changes?
I have updated the expected exception message in omim.t and mim2gene.t, which at present are the only two files affected.
If so, do the tests pass/fail?
Have you run the entire test suite and no regression was detected?
Yes, no regression detected.