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Created with Raphaël 2.2.03Dec2130Nov292524232219181615121110985432129Oct2726252221191815141312118654130Sep292724212017161513109872131Aug2726252423201918171613121195429Jul27262322212019161413128762129Jun282524222118171615141110987432128May272421201917141211765423Apr222120191615141312876131Mar3029252322191817161512109853125FebGet MGI mapping to ensembl from MGI sitefirst attempt at new parsers for zebrafishMake this script able to notice databases that has disappeared.Make te db_current view sane.Also look at the rnaseq databases.Also update is_current in the db table.Modified viewsVarious fixes and additions.Add code to cope with the cases where an analysis does not have aUpdate get_all_DBEntries() and get_all_DBLinks().Bad PODchanges to get it to do what I think it should do - 1) staging and staging2, 2) add an initial mapping_set entry if this is new species 3) warn if there is no mapping_set entry but this is not a new species - in this case I the genebuilders should be adding the old one since this is the scenario we want to catch! (need to check the assembly hasn't changed), 4) dry_run, ie preview modeCreate even more beautiful SQL.Guard against a couple of undefs.Allow for using 'regulation' as a group name alias for 'funcgen'.Update schema for the analysis_description table to reflect the currentAdded options to specify details for connecting to a DNA DB. If your sourcemapping problem fixRestore this script to original shape.*** empty log message ***use newer version of myisamchk (/software one is ver 4)Remove old files and add a README that explains why.Add README describing that the attrib_type master table lives in theFix SQL syntax error.Patch patch_60_61_b.sql was already applied to schema, so insert it'sApply patch_60_61_a.sql to schema.Apply patch_60_61_c.sql to schema.# patch_60_61_c.sqlRemove some debug statements.Fix missing bound parameter (!)Remove references to dead Collection code.Add usage info.Add space.Add text to the --about switch.Update --about text.Much more helpful output!Also get the Experimental Factor Ontology (EFO).merge in of new CDS remark checking code (ie copes with phases)more resilientchanges to do checks per chromosome