Commit 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 them

According 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 @_

db_name in external_db. Clean up a few bugs while I'm at it.

Bugs corrected:

  A list (rather than a list reference) was returned if the
  external_db_id for the given db_name could not be found.

  The list returned from list_gene_ids_by_external_db_id() (in
  DBEntryAdaptor) was used as a hash.

Storing 'intersection_of' lines for terms, storing relationships between terms not defined in the current ontology.

dependent_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 simpler

The 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 checking

get_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 changed

get_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)

Ignoring terms referenced in intersection_of lines, until we redesign the db/ parsing script to be able to store them.

any whitespace.


Some reformatting.

-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 done

dependencys 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 :-)

The display Xref for Gene should come from FlyBase and not choosen from
the transcript display xrefs sources.
Moreover, since we run the pipeline in fullmode, the method called is
from the drosophila module and not the generic method from the DisplayXrefs
module.

mode (like FlyBase ftp server).