remove MineManager tool. It has its own repo now.
Log a warning message instead of SQL ERROR if precomputed table index creation fails.
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.
tidy up config
Changes to address the concerns raised in #712
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
removed flybase development ontology temporarily, until they release their fixed copy
Merge branch 'beta' of github.com:intermine/intermine into beta
Merge remote-tracking branch 'upstream/beta' into beta
Handle config correctly. Refs #810
variable scope is important! Refs #810