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Created with Raphaël 2.2.05Dec43230Nov2928272623222120191817161413129876532131Oct3029262524232218171615121098543128Sep2725242118171413121110654330Aug2924232221201716151413109876432131Jul3027262524232019181613119543229Jun2827262523222120191815141312warn which non_patch chromosomes might have been excluded[ENSCORESW-315]. Fixing a bug where the bind params need to be reused on subsequent queries. MySQL/DBI/DBD::mysql is really bad at warning us when we submit a query with a single ? and no bind parameters (it compensates). Wish it didn'tRegression testingRegression tests are namespaced accordingly[ENSCORESW-314]. Synonym lookup bug fixed. Passed coord system id into the lookup rather than the actual coord system name. Bad bad bad[ENSCORESW-313]. Adding support for external db id lookup and filtering by them on synonymsMouse is upgraded to mm10 from UCSCDefault user addedPermissions comes through as normal octal notation so no need to do lots of individual onesSplitting the permissions checks out morebetter globbingNo verboseFirst pass script used to check the sanity of the data files directoryRemoved code authorship statementsUpdating docs.Inlining this statement causes issues with perl 5.16. reported by mm14efficiency improvement - retrieve attrib type details at start and reusesupport for multispecies dbsadded a quick_check to enable quick heuristic check to allow rapid processing of genomes where there are no alternative transcriptsminor improvement to how code handles arraysWe modify seq_region_attrib so that needs to be doneCopy across any codon attributesOrdering only by the session's created date failed to realise we could have more than one entry for the same stable id. Ordering now by the score as a way of getting rid of this ambiguity. Issue was picked up by Rhoda running the code on an older MySQL version which consistently exhibited different behaviour to later MySQL versionsImproving debuggingallow for column configurationSwitching to using the alter table command after Kieron's suggestion. Seems niceOver-ride transcript_names_from_gene (we don't want that behaviour for worms)Use transcript display xrefs provided by FlyBaseNew biotype added for PC genes (IG_LV_gene)Simple code for sumamrising the exon/trasncript statisticsPass back no transcripts if we lacked a source IDget_alt_attrib_codes was added as a fresh dependency. This module missed it. We return nothing for this a we don't have alt_attrib codes for variationsAdded explicit call to use the $ENV proxy settings. LWP Simple did not do this by default.Added a sleep for web service retries.Missing sql alias added.Fixed an omission in taking hash keys on a reference.merging changes from branch-ensembl-69JGI version 2 should not be used, removed every reference to itcvs/release/ens…cvs/release/ensembl/64= does not work. We just assigned $type to 'cisred'. eq is what was wantedFinal changes to ensure the code works as expected