minor design change in relevance bar

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@20939 2913f559-6b04-0410-9a09-c530ee9f5186
added option to disable pubmed similarity

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21004 2913f559-6b04-0410-9a09-c530ee9f5186
removed unneeded javascript (used in similarity)

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21006 2913f559-6b04-0410-9a09-c530ee9f5186
- some changes in URL rewriting rules:
  /experiments/E-ACCN-12345/anything.sdrf.html redirects to /experiments/E-ACCN/12345/samples.html
  + some dancing around the bug in urlrewritefilter 4.0.3

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21082 2913f559-6b04-0410-9a09-c530ee9f5186
- disabled relevanceScoring for now as it causes memory leak

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21137 2913f559-6b04-0410-9a09-c530ee9f5186
- added reading bam.prop files when constructing Ensembl links (not complete; Ensembl release -> URL mapping is missing)

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21172 2913f559-6b04-0410-9a09-c530ee9f5186
- slight update to allow for graceful degradation if .prop file is missing for a particular bam file

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21173 2913f559-6b04-0410-9a09-c530ee9f5186
- added close for input stream to make sure we get no issues with leaking open file handles

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21174 2913f559-6b04-0410-9a09-c530ee9f5186
- added R ExpressionSet representation in the interface (pending tooltip hint text)

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21290 2913f559-6b04-0410-9a09-c530ee9f5186
- Send to GenomeSpace activity, step 1

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21297 2913f559-6b04-0410-9a09-c530ee9f5186
- Added GenomeSpace OpenID client (untested!)

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21313 2913f559-6b04-0410-9a09-c530ee9f5186
- GenomeSpace auth works now

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21318 2913f559-6b04-0410-9a09-c530ee9f5186
- rewritten using Java 7 "try with resource" syntax

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21320 2913f559-6b04-0410-9a09-c530ee9f5186
- added dynamic discovery of GenomeSpace OpenID Provider URL

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21321 2913f559-6b04-0410-9a09-c530ee9f5186
- adding more functionality to GenomeSpace integration.. Almost there

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21334 2913f559-6b04-0410-9a09-c530ee9f5186
- explicit typing as it switches to float for values above 1M samples/assays which we're about to reach

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21341 2913f559-6b04-0410-9a09-c530ee9f5186
- explicit typing as it switches to float for values above 1M samples/assays which we're about to reach - now in programmatic access, too

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21343 2913f559-6b04-0410-9a09-c530ee9f5186
- some Java 7 cleanup
- GS uploaded file info retrieval

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21346 2913f559-6b04-0410-9a09-c530ee9f5186
- a little fix for type conversion (y'days commit)

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21364 2913f559-6b04-0410-9a09-c530ee9f5186
- upload a file functionality implemented (pending testing and checking if it works through proxy)

git-svn-id: svn://bar.ebi.ac.uk/trunk/arrayexpress-interface@21365 2913f559-6b04-0410-9a09-c530ee9f5186