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Created with Raphaël 2.2.019Oct1817141312111076543230Sep29282726232221201615141312987652131Aug302625242322191817161512111098542129Jul28272625222120141312118654130Jun282724232221201716141310986532126May252423191817161312111098654328Apr262019181514131187131Mar30292824232221Make this upload stable IDs into release 65 databases correctly.Update to deal with schema 65.Bringing in the DataFile infrastructure. First pass implementation can perform CRUD and has associated test cases. Currently lacks a good way of passing the base directory in. Will be addressed.Bringing in a new method which allows us to retrieve the last inserted identifier into the table this adaptor is working with via DBI. Should be called from within an execute block so we do not need to wrap this in a work_with_dbh callBrought in a new method for getting single value meta items from the meta table. This is then used in MetaContainer for just about every call reducing duplicated logic.Meant to use " and not ' in an error messageBringing in a new method allowing us to detect a scheme*** empty log message ***Reformat for readability.Transferring Doxygen filter into EnsEMBL CVS.For release 64: Be specific about what table the created_date andTiny optimization in internal_id_rescore().Remove alt_allele entry if reset_to_parsing_finished is usedremoved fullmode optiontypo fixchanges related to stable_id mergeremove partupdate modechanges related to stable_id mergechanges related to stable_id mergechanges related to stable_id mergechanges related to stable_id mergeadded example of using previous release of core to test new xrefsChange species to database parameterchanges related to stable_id mergechanges related to stable_id mergechanges related to stable_id mergeCheck if $ontology_version is defined before using it. It won't be ifAdd filters to remove Beta characters and to remove backslash from the gene name.Use --skip-opt when dumping the old data to allow for using diff toFinally implement --species and --type correctly.Added SchistoDB and jgi_triad sourcesUpdated SchistoDB source namebug fix to not obtaining results from prepare callremoved partupdate mode, no lonfger feasablechnage 64 -> 65 for mouse and human databasesBarking up the wrong tree...Fix syntax error.Implement --species and --type command line options.Added extra dbs to the listUpdate info on new flags.