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Created with Raphaël 2.2.021Jan1716151410987421Dec201917141312111076543230Nov2928272623222120191817161413129876532131Oct3029262524232218171615121098543128Sep2725242118171413121110654330Aug2924232221201716151413109876432131Jul3027262524232019181613119543229Jun28272625Adding patch from Dan Staines, see issue: ENSCORESW-340Ok, so it needed some text to pad it out...Added a trivial test for single-threaded cases.proteinFeatureAdaptor now cleans up after itselfupdating the figure on how long it takes to run. The original estimate only took CPU time into account. This code does a lot in the DB so CPU usage is low[ENSCORESW-335]. Allowed the input param force_species to populate species. Does using a hash. Higher up the levels we use a hash map plus decoding aliases so no need to worry about clashes between common and scientific names[ENSCORESW-334]. EnsemblGenomes can also hand over species. Fixed the query to use an IN and bring EG in as wellSwitching to a more informaive outputRemoved commas that shouldn't be before "rusage" in mem reqs. It used to work with thosefixed stable_id method call; stable(), should be called stable_id()fixed stable_id method call; stable(), should be called stable_id()Filter terms out which span more than 1 ontology. This is not the right way to do it but is the best for the momentFoxed Type, sTDERR => STDERRFoxed Type, sTDERR => STDERRfetch_all_failed_jobs method replaced by fetch_all_by_analysis_id_status(undef,'FAILED')ENSCORESW-318: method fetch_all should not be used in attribute contextRemoved DBI and the bad bits of error checkingAllow for multiple dirs to be givenadded tests for method fethc_alladded method fetch_alladding test cases for gene_attribadded test cases for undefined objectsfetch_all_by_ method expanded to work even if no object is called onpatch submitted by ak4. --dumppath flag is not needed unless -dropbaks is onOnly use the coordinates with the smaller seq_region_id (usually 1-22,X,Y) to avoid mapping the LRG to the patch regionOnly use the coordinates with the smaller seq_region_id (usually 1-22,X,Y) to avoid mapping the LRG to the patch regionUses the new Net moduleKaryotype assigner. Don't like it being here but it's got to go in.Adding net based modulesAdded UniGene::* plants specific sources, and IPI::arabidopsis_thaliana sourceAdded UniGene::* plants specific sources, and IPI::arabidopsis_thaliana sourceInitial commit. Written by Mikkel. Mikkel is doing something kinky with source ids.Improved variable names. Mikkel is doing something kinky with source ids.Added gene_display_xref_sources subroutine.Add synonym sources for vectorbase species.Never allow someone to commit a MultiTestDB fileHave added all plants missing species, plus all gramene plants speciesHave added all plants missing species, plus all gramene plants speciesHave replaced the deprecated "fetch_all_failed_jobs" by "fetch_all_by_analysis_id_status".check if source is HGNC or MGI