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Feature/baseparser synonym columns

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

Created by: mkszuba

Description

BaseParser: All inserts into 'synonym' now explicitly specify target columns.

Use case

Part of the 2018 xref sprint has been devoted to making the xref database schema a bit more self-constrained so that it could in principle work with database engines other than MyISAM. One of the changes made here has been the addition of an internal key column to the table 'synonym'. Make sure inserts into that table do not get confused by the possible presence of a new column.

Benefits

Inserts into 'synonym' will work with both original (as still found in table.sql) and improved (as found in the xref-parser test suite) xref database schema.

Possible Drawbacks

None I can think of.

Testing

Have you added/modified unit tests to test the changes?

Yes and no - there are tests for this but they are not present in the repository yet, they will be added once MIMParser has been backported from ensembl-xref.

If so, do the tests pass/fail?

They failed before the change and pass afterwards.

Have you run the entire test suite and no regression was detected?

Yes, no regressions detected.

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