Remove the die statement since Eddie has indicated these should exist in
the future and the tool worked alright for data-transfer.
updated ur submodule to 0324309
updated workflow submodule to 071908d
Add data sources for the LIMS oracle databases
Add new class CommonRDBMS for logging and DB pausing

Logging functions moved to CommonRDBMS and also used from GMSchema via Exporter

Pausing functionality is only used in Dwrac and Oltp, but left a note for
the switchover in GMSchema
Refactor to inherit from Genome::DataSource::CommonRDBMS
Limit disconnections to only Genome RDBMS datasources, not all UR RDBMS data sources
Step 1 of removing dblinks from raw SQL queries

These are the simple cases
Another simple case of switching data sources
Remove support for --subject-names option

This required the subject_name column in the genome_model table, which
hasn't existed in a while.  If it's still needed, then support for joining
to genome_subject will have to get added.
make the test quiet
Refactor to pass an iterator that does the query rather than just the query
Refactor to get work_order_id info from separate database

We won't be able to join to OLTP anymore, so when filtering by work_order_id,
first do a query to find out which models go with that work_order,
then do a query to get the relevent info for those models
Switch to use the Dwrac data source

This also nukes the union that pulls in Sanger rows.  It was technically
a problem because of the join on misc_attribute in the main Genome database
with joins to Oltp and Dwrac on either side.

The conclusion was that this class is only used by the data importer that
migrates data from the LIMS database to Genome's, and Sanger data is
handled via a completely different process - getting rows from the
sequence_read table, making allocations for them and inserting them
as imported instrument data.
whitespace
More simple cases of moving to the Oltp or Dwrac data source
Merge branch containing Postgres transition prep work
sort as UR would instead of assuming a hard-coded order
order by entry_date

With IDs changing to UUIDs we cannot (and should never have) depended on
the IDs representing temporal progression.
Merge remote-tracking branch: upstream/master