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Created with Raphaël 2.2.05Dec4328Nov26252322181514121187531Oct302925242321181715121110987432130Sep27262523191817131211109653230Aug29272322201916151298765231Jul302926252423221918171615111043228Jun27262421201918171312111065331May302928232221171514131098732130Apr2927262423221918171615121110953227Mar26252221201918151211654128Feb2726252221201918[ENSCORESW-777]. Added TranscriptAdaptor support for fetching by source(s).[ENSCORESW-777]. Tests TranscriptAdaptor support for fetching by source(s).fetch_all_by_biotype as in GeneAdaptor, which implies the inclusion of method biotype_contraintuse parent does inheritence, too. (ds23).Patches applied to human empty test DBPatches applied to circular slice core DBPatches applied to human core test DBBumping the versionMerge from HEAD. Deprecating the fetch_nearest_Gene_by_Feature() method. It is unreliable and a replacement is being developedcvs/release/ens…cvs/release/ensembl/74Deprecating the fetch_nearest_Gene_by_Feature() method. It is unreliable and a replacement is being developedrevisions to CliHelper to support dbs where no production name is set, and to improve default behaviour where single_species mode not specified. Also expanded test coverage to support this, adding the nameless and test_collection test dbs for this purposetransfer method called on an Exon will return an Exon, not a GeneUpdated version to 75[ENSCORESW-752]. Updated _columns, store, update and _objs_from_sth methods to take into accountAdd column source in a specific order so the table definition comparison between a patched db and current one succeedsAdded licenceStart of Ensembl 75 core table definitions: first two patchesPatch for the addition of transcript source columnSchema version patch for 74->75Adding aliases in for user, hostname and pass because this drives me crazy once a month.The Ensembl license has been changed from Apache-like to Apache 2.0[ENSCORESW-767]. Made the number in ens-staging optional so we will pick up on the ens-staging aliasadded extra pathway sources for 7 plants speciescleanup of the ncRNA sources for plants genomesRemoved PGSC from the list of sources for gene and transcript namesupdated the uri asociated with source Gramene_Pathway::arabidopsis_thalianaAdded in UniGene::solanum_tuberosum source to potato speciesupdated READMEreverting change. XS module will be changed to not modify stack contentsswitch to using the local as default. otherwise we cannot have a test passing until we have committed to version controlswitch to using ENV variables. Otherwise we run the risk of not being able to run the tests in any kind of test harness toolDo not use deprecaated calls. add_gene() has become add_Gene()adding internal tests to ensure the logic of fetch by ids works post modificationA number of params are missing their - flag. That means the new XS rearrange does not work (it is a bug not a feature)Record the tables we have just modified. Otherwise subsequent tests failTake a copy of @args. Ensures the new XS code will work properlyupdated goslim_goa::EG to point to ensemblgenomes_ontology_21_74added bread wheat species, triticum_aestivumReplaced Uniprot_gn by Uniprot_gn_trans_name in transcript_display_xref_sourcesRemoved since new release cycle not yet started.