remove MineManager tool. It has its own repo now.
Log a warning message instead of SQL ERROR if precomputed table index creation fails.
Use correct path to do attribute check. Refs #777
Merge remote-tracking branch 'upstream/beta' into beta
Convert item attributes, refererences and collections to simple objects.

Signed-off-by: Richard Smith <rnsmith100@gmail.com>
Test fix.
update copyright date
tidy up config
update Reactome download script. Apparently if you have an invalid organism, the script fails.
add ant
Changes to address the concerns raised in #712
Merge pull request #805 from intermine/i777

Use correct path to do attribute check. Refs #777
add missing integration key
temporarily remove thalemine until restricted access issue is resolved. Refs #772
correct name of OBO file
don't throw exception when encountering an ontology term without a name. give it the name UNKNOWN and log the error. Refs #830
accept spaces and underscores in filenames. Refs #829
update all keys. Refs #832
Merge pull request #833 from intermine/i830

don't throw exception when encountering an ontology term without a name....
throw an exception if a bad ontology term is encountered. this is a fatal error. Refs #830