publication url fix


Former-commit-id: daf154e36910f883ada5f31e74b6c0b59d190cdf
changes the worm expression scores from gene to mRNA


Former-commit-id: 93153f920c3e52f91dd8018af1f30ba6d7e16636
Merge branch 'dev' of github.com:intermine/intermine into dev


Former-commit-id: a4cd8a43812c74885f591aa5f48fc5f34bad155e
update homology source to work with new data file content


Former-commit-id: d61eaf37326852ae0e97bfc3e6eb3a949eedf1c1
change project XML config to accept true/false instead of summary/fullRecord. just to be consistent with the rest of the project XML attributes


Former-commit-id: 6264c053029ea7094027c65b38b0cf1aea73cdc3
merge dev into branch


Former-commit-id: 8712f82234ecc72580c2eb9eb803c76ebdb7e8c0
Widget - Applied lower function to the constraint (except list and
filter)



Former-commit-id: e0e972ec5e121801d2347b8324d55b3334eff7fc
Merge branch 'release-intermine-1.2-beta' of github.com:intermine/intermine into release-intermine-1.2-beta


Former-commit-id: 7da33e359b6a17b72e524cf354db54b202aca464
Clone list - fixed bug

Former-commit-id: 9b58fa34edc499d5f3354d4f8641ca0eeaa2c1bc
fixed publiction retriever


Former-commit-id: 31043a709a8a519681afb02a7a332f930dbb6887
Merge branch 'dev' of github.com:intermine/intermine into dev


Former-commit-id: 645c6a86250cfe672367a941307327c6eddb6aad
Complain about malformed queries appropriately.


Former-commit-id: ecb3cbd98483c36312e123e061a9607fa020b8a0
Allow queries to be submitted in compressed form.

This seems totally insane, and indeed it kind of is, but it does mean
we can open up a mechanism for allowing GET requests for otherwise
impossibly long queries.


Former-commit-id: 919b43b7d0bd69917ab5007100baf03ba17a0b50
Added scripts for automating the comparison of enrichment.

These should be cleaned up and used as part of the release procedure.


Former-commit-id: 39c19098ad39376b306edca823ccddba3e29b879
Added a query xml shortening facility.

InterMine suffers from xml-itis. This badly affects GET requests with
long queries in them. This is another method for dealing with this issue
by allowing access to a minimal query storage service on the server,
which means we can refer to queries by id. At present these queries do
not live beyond the life-time of a session, as they live in memory. They
should be treated as very short-lived entities.


Former-commit-id: 4d8c0c9bebcd7e714a955f1b2a0d3e3a2a9c0282
Added the facilities for efficient bi-directional lookup.

At the expense of some extra storage of course. But this should be
more than compensated by avoiding storing duplicate queries.


Former-commit-id: 642b3a1d21dc5b141f4bffd20a256ee79e8f6acc
Added RELEASE_NOTES file describing Intermine 1.1.2 release


Former-commit-id: 4f4e850ec09e2576d0de6c47b6dd17340493e8c7
Updated RELEASE_NOTE. To complete


Former-commit-id: be76c23ee190f40c7d1239dd1ed3e6c903d239b0
Moved Query store into the API package. Future-proofing.

This moved the query-storage out of the webservice package and into the
api where it belongs. It also future proofs the system by allowing for
multiple different implementations of the protocol. Currently the only
existing one is an in-memory store, but this can be expanded with a
persistant store in the future. The QueryStore implementation itself has
a set of defined exceptional states, and returns strings as ids rather
than integers, so that alternate implementations can do what they like.
The current implementation has also been made life-cycle aware.


Former-commit-id: cd87eaccf73020c676410f8a98f2336a3cf6bb1d
Broke the law of Demeter - may she forgive me.

Don't fiddle with objects you don't control. In this case a method
added a value to a map it didn't create; and as we all know, maps
don't always support adding values, do they...


Former-commit-id: 74d3d52f404d354a11dc7db7b157cfa87ddcb3db