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Xref parser testing framework

Marek Szuba requested to merge feature/parse_test into feature/xref_sprint

Created by: nerdstrike


Adds a single unit test for a parser, and a database test harness to facilitate that. Small opening in BaseParser made to remove tight dependency on XrefParser::Database

Use case

Testing parsers is hard. They require a database handle as argument, and the testable output appears directly in the database.


A test harness without needing to use Bio::EnsEMBL::Test. ORM functionality should make query-based testing easier, and allow schema upgrades to occur without undue suffering by way of DBIC.

Possible Drawbacks

DBIC dependencies, foreign key conflicts in constraint-free xref code, no Travis harness, but we should be adding that to the new repo instead of this one. Generated ORM is now diverged from original schema - there are changes that are required for DBIC to work with the schema.


I wrote the only tests that exist. No Travis yet.

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