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Created with Raphaël 2.2.018Dec1716125229Nov272120181312118765131Oct28211816151410927Sep262524232018171612114330Aug292827232221128226Jul252419181225Jun2421201918171413117529May24151483229Apr2625171512111085432121Mar201918DBASSParser: Do not create unmapped xrefsDBASSParser: Slightly restructure synonym extractionDBASSParser: check for unexpected columns in input dataDBASSParser: add some commentsDBASSParser: fix error messageDBASSParser: remove dead codeDBASSParser: add /x to all regular expressionsDBASSParser: Store descriptions and linkage types as NULLs, not empty stringsDBASSParser: Remove unused package variablesDBASSParser: apply perltidyDBASSParser: use 'use parent' instead of 'use base'DBASSParser: enable warningsRemove dud testing prototype.Sample test for RGD parser. Add a shortcut for the database handle into the DB class. All tests will need access to this feature.Adjustments to schema to tolerate InnoDB constraints, adjust deployment process to work with MySQL generally, and split test and production DB classes apart. The TestDB class injects a test DB name and triggers cleanup at the end.Break out DB schema from Test DB schema, so that one auto-cleans and the other does not.Generated a DBIC schema from the xref schema, hacked it about to have primary keys and relations where needed, and built a crude harness to auto-instantiate a DB for unit testing.BaseParser: add_direct_xref() can now update info_typeBaseParser: add protection against inserting duplicates to add_direct_xref()BaseParser: get_direct_xref() can now return all matching IDsBaseParser: have get_direct_xref() handle null values of linkage_xref correctlyBaseParser: have add_to_direct_xref() actually use linkageBaseParser: add_dependent_xref_maponly() can now update info_typeBaseParser: factor dependent-xref creation out of add_dependent_xref()BaseParser: implement _update_xref_info_type()MIMParser: default info_type for new xrefs is now UNMAPPEDremoved all MGI related codeupdated croak messagescolumn cleanupENSCORESW-2835: check for required_columnscleanup and refactoringReplaced custom sql insert with BaseParser method call, other post-review updates and applied perltidyremoved auto_diagReset the MGI_Desc_Parser to master as the updates for it is in a seperate xref_parser_mgi_desc branchUsed Text:CSV and removed mgi_description dependencyPost-review changes and tidy upcorrected the indentation and updated the verbose if blockupdated to use Text::CSVremoved unused position variable, moved synonyms split inside if condition, removed desc intialisation inside if blockremoved ccds and uniprot source entries for MGI for species mus_musculus