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Created with Raphaël 2.2.015Sep141312987652131Aug302625242322191817161512111098542129Jul28272625222120141312118654130Jun282724232221201716141310986532126May252423191817161312111098654328Apr262019181514131187131Mar30292824232221181615141110987432128Feb252423222118171615141098743131Jan2827262018Remove getting source_id or species_id from filename if they are not set. As these have to be set or it dies before that bit is reached.dbi now in Database.pm, so changes madeRemoved the database connection, database creation and process control from the module as this is different to the actual parsing of the data files. See Database.pm and ProcessData.pm So now module should only deal with the parsing of data and release filesremoved local sub new. Should be taken from BaseParserControls the overall process of the parsing. Makes calls for the creation of the database and then subsequent calls to fetch and parse the data files.Database dbi connection etc object. Also controls the population and creation of the xref database.removed local sub new. Should be taken from BaseParser to get the dbi connections etcmy was missingSyntax error with use baseReverting a change in slice retrieval to avoid PAR related issues on the websiteRolling back the code to 1.20 because of issues with re-binning the human Y chromsome density values resulting in a -ve value.Removed unused variableAdding a code for asserting if a reference is a filehandle or notCommit moved to HEAD from branch-64. Moved the slice fetch into the knowngenedensity/genedensity loop so we can continue to use shift to iterate through themdoes not need a release file to work, this is optional nowMoved the slice fetch into the knowngenedensity/genedensity loop so we can continue to use shift to iterate through themCorrected mis-spelling and removed a hanging q which made its way into the codeAssert ref was missing from the importsAccording 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 for