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Created with Raphaël 2.2.014Sep1312987652131Aug302625242322191817161512111098542129Jul28272625222120141312118654130Jun282724232221201716141310986532126May252423191817161312111098654328Apr262019181514131187131Mar30292824232221181615141110987432128Feb252423222118171615141098743131Jan282726201814131211According to test cases adaptor() should be nullable by passing an undef through to the mutator. Detection of a purposful undef is by checking the length of @_In fetch_all_by_Slice_and_external_dbname_link(): Allow for non-uniqueChange to comment: added new flag to relation table.Added 'intersection_of' flag to 'term' table.Storing 'intersection_of' lines for terms, storing relationships between terms not defined in the current ontology.set to ftp to passive if it fails the first timeparse parameters to run/run_script via has rather than list for easu maintainanceProperly handle both Ensembl and Ensembl Genomes ontology databases.removed some commneted code from reset_DBAdatproCorrectly pick up Ensembl Genomes ontology database.use new parameter passing argsdependent_source table now has a string that is the name of the source for the dependent value rather than the source_id as this could involve too many items in the list and user may not realise what to list. So using a name is simplerThe header of the HGNC file being processed is now used to find the indexes to be used on an array holding the data. This was hard coded earlier. Code is harder to read now maybe but will deal with changes in the data format and has better error checkingget_valid codes now returns an hash that contians an array of values rather than just a single xref_id. Due to more than one xref_id having the same acc for the same source name (priority xrefs). So calls using this needed to be changedget_valid codes now returns an has that contians an array of values rather than just a xref_id. Due to more than one xref_id haing the same acc for the same source name (priority xrefs)Changed db adaptor to ditag adaptor on call to Ditag::new()circular reference fixAllow the ontology database to be called ensemblgenomes_ontology_NN.Allow the ontology database to be called ensemblgenomes_ontology_NN.Do not delete older databases.Ignoring terms referenced in intersection_of lines, until we redesign the db/ parsing script to be able to store them.Regarding dbname_file: don't require tab-delimited file, but allow forremoved commented out code-force command line option added to remove user interaction so that the farm can be utilised. if -force is used then user will not be asked if they want to update or delete data it will just be donedependencys added so that for a source to be loaded then all of its dependecies must be loaded before it. Stored in a table dependent_source.new print_stats method created from code already there, which has been tidied up. -force checked before user requests and if set default actions are taken (for use with farm). Removed old subs that are never called. Plus general tidying :-)FlyBase gff file locations updated.give an error message rather than die if no xrefs foundremoved commented out codeRemove general messages to STDERRNew module to deal with fetching files needed. Removed from BaseParser.pmCorrected inherited parent class.Dump taken after branching of release 64.Change the way display_xrefs are set for Gene and Transcript.Add fullname as the description of the Name (for gene) if it is existing.Construct Net::FTP with Passive => 1 when server's side is not supporting activeFix misspelling in comment.Use new modules OfficialNaming .pm and DirectXrefs.pmuse file handles properlyuse strict before any code is written