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.
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
all identifier sources only ever store SO terms, so use more specific key. Refs #832
Merge pull request #785 from rnsmith/beta

Log a warning message instead of SQL ERROR if precomputed table index cr...
address some ontology term merging issues. Refs #832
checkstyle fix
key fix Refs #832
for LOOKUP queries with wildcards, return when there is a match. Refs #676
Added enrichment identifiers to download function.
raise batch size
Merge pull request #808 from rnsmith/simple-items

Item attributes, references and referencelists are simple objects
checktyle Refs #808
Merge branch 'beta' into i676