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tables in the production database.

corresponding analysis_description.

Add the following proxy methods:

* get_all_object_xrefs()    alias for get_all_DBEntries()
* get_all_xrefs()           alias for get_all_DBLinks()

These have no documentation as of yet.

changes to get it to do what I think it should do - 1) staging and staging2, 2) add an initial mapping_set entry if this is  new species 3) warn if there is no mapping_set entry but this is not a new species - in this case I the genebuilders should be adding the old one since this is the scenario we want to catch! (need to check the assembly hasn't changed), 4) dry_run, ie preview mode

ensembl_production database.

(gene) DB contains no DNA, script will throw because it won't be able to
check the translation of transcripts later.

Also print gene stable IDs only when they are present.

production database.

Remove old files.

patch identifier too.

#
# Title:
#   Modify the indexes of the object_xref tables.
#
# Description:
# The object_xref_id field of the object_xref table was found to for
# some reason not be a primary key.  This field is always unique, so why
# not add it as the primary key?  Also re-jig the other indexes while we
# are at it.