Switch to using the BioVeL configuration of SEEK.
Changed ruby version back to 1.9.3
Migrated
Fixed references to Project#name and Institution#name
Fix the version number code to use the commit hash.

Now with added git and reduced levels of hg.
Merge remote-tracking branch 'origin/master'

* origin/master:
  Fixed references to Project#name and Institution#name
  Migrated
  Changed ruby version back to 1.9.3
Fixed another reference to Project#name
Merge branch 'master' of github.com:BioVeL/seek
Fixed yet another reference to Project#name
Tests should run with programmes enabled by default.
swapped to use biovel config
Merge remote-tracking branch 'seek/biovel-config'

* seek/biovel-config: (29 commits)
  swapped to use biovel config
  fixed conflict
  remove coverage files
  added a couple of tests specific to the biovel sharing form, and fixed the .name problem
  cherry-pick and fixed 5da4de60a765f884cc83e7296f565cd13e7e5c1a
  update tags
  added coveralls
  fix to error (invalid route) when providing an incorrect or expired password code - SYSMO-1568
  dont start soffice for now
  update tags
  try again at starting soffice for tests
  fixed gemset name
  fixed get_all_as_json for Presentation, which was being caused by mismatch of the Presentation class with  ActsAsTree::Presentation following upgrade of acts_as_tree
  removed the delayed_job_admin gem, since it is know to have potential security issues
  updated pothoven-attachment_fu and uuidtools gem
  updated the mysql2 gem
  updated the jquery-rails gem
  updated feedjira gem
  updated colorize and docsplit gems
  try updating acts_as_tree to the latest version
  ...

Conflicts:
	config/initializers/seek_configuration.rb-sysmo
	config/locales/en.yml-sysmo
Merge remote-tracking branch 'seek/master'

* seek/master:
  tell travis to build nokogiri using system libraries
Add Coveralls integration back into test_helper.

Looks like it got lost in a merge somewhere.
Merge remote-tracking branch 'seek/master'

* seek/master:
  run all tests together for coverall
  skip jws tests when running with travis
  Add Coveralls integration back into test_helper.
Merge remote-tracking branch 'seek/master'

* seek/master: (21 commits)
  update tags
  added a 15 minute time limit for reindexing jobs - SYSMO-1571
  fixed type in strain search terms
  update tags
  some tidying up of associate organism and strain  with assay
  updated Exception notification initialisation code for newer gem, and updated reindexing job to send notification email - SYSMO-1571 SYSMO-1570
  updated exception nofication to the latest version
  temporarily don't put the reindexing job back on the queye when it fails - SYSMO-1571
  Backed out changeset ae7a71aecfc4 Didn't solve problem. Will put back to latest version and rebuild index entirely with the newer gem. SYSMO-1570
  reverted sunspot gem back to 2.1.0 - SYSMO-1570
  fix to page title for Programmes
  moved get_all_as_json up to acts_as_asset since the method is the same across all assets
  consolidated and simplified genotype and phenotype handling into its own module, reducing some duplication
  cleaned up the model extraction code a little
  run full suite of tests, but just with ruby 2.1.2 (we will have another branch for comprehensive testing)
  started tying things together ready to be inserted into the db
  resolve projects, assays, datafiles, contributors, sops to activerecord items, and replace in the hash
  reading and parsing the biosamples treatment info from the raw template
  skip jws tests when running with travis
  no need for the project_institutions list to have a max-height and scroll overflow - SYSMO-1561
  ...
Merge remote-tracking branch 'seek/master'

* seek/master:
  update tags
  code tidy up
  enhancemts to handle the moses biosample data - to recognise data that already exists from the key, and include substances and units for the treatments
  updated to expect additional treatment columns, and updated spreadsheets to match
  tidying up and refactoring code
  updated biosample parsing code to conform with ruby style guidelines
  allow age at sampling unit to be a string, and now include them in sample info inserted
  apply access policy to biosample details according to the first datafile they are linked to
  handling treatments
  added reek and rubocop gems
  inserting samples (with the exception of the age which is incompatible, need to discuss with Olga)
  background reindex samples
  inserting specimens
  background reindex specimen
  inserting strains and genotypes
  background reindex strains
  making organisms concrete and validating against the ncbi id
  tying the biosamples together
  updated the restart background tasks button to call seek:workers and start up the workers for different queues correctly. Seperated the code for starting and stopping out of the rake task and into a module, and added a restart action
  run the authorization jobs from their own seperate queue and associated worker
Clean up models_controller.rb before real changes.

Lots of bad whitespace.
Update rubyzip version with new API.

Taverna Player is the only dependency that uses rubyzip so use the version of
that which uses the latest rubyzip API too.
Merge branch 'new-zip'

* new-zip:
  Update rubyzip version with new API.
  Clean up models_controller.rb before real changes.