…the mp_heatmap_config method once as it's expensive.
* Bump the server version no so the css takes effect on next release.
…ing down the graphs
* master: (21 commits) Added in a rake task for refreshing/populating the OLS cache Update the deployment to remove the ols_database stuff and include the new ols_cache code. Test fix - the data has changed Add a test or two in for the new eurexpress route. Fix for the GO test. Bump ols to v0.3.2 - bugfixes ahoy! Refactor the Eurexpress EMAP tree data gathering to be a touch easier to understand and work with. bugfix - no need to focus the EMAP graphs. When working with the GO graphs, we're only interested in the parentage from the annotated terms. Focus the EMAP graphs so we're working with smaller datasets. no need to ignore the ols_database.yml file anymore - get rid of it small code clean Completley remove the old ontology handling code. * Update the ensembl-mouse-go dataset to use the OLS gem * Update the gene-details dataview to follow these changes Remove the old prepare ontology cache script Remove rubytree and comment out sequel from the Gemfile - sequel is only needed for a short while longer... Update OLS to 0.2.1 (fixes a bunch of warnings) Clean up the Eurexpress DataSet/DataView and switch it to using the new OLS gem. Remove the use of the in memory @ontology_cache from index_builder - the new OLS gem is fast enough to no longer need this. Switch out the old MartSearch::OntologyCache to use the new OLS gem in the index building processes. ... Conflicts: Gemfile.lock
…e new ols_cache code.
… to understand and work with.
* master: (21 commits) change the test name munging to ensure a match with the internal name of the biomart attributes removed the order link for all mirKO vectors Remove the use of NewRelic RPM. Roll back the mongo and bson gems... Key the MGP heatmap indexing by marker symbol - this should stop colonies going missing if the data hasn't found its way into iMits for some reason. Update the dependent gems to latest releases (bundle update). Switch the wtsi-phenotyping datasource to the production wtsi mart. Rename the last two .erubis templates to .erb Update sinatra to 1.3.1 * the erubis function is depricated, so switched to use erb (recommended action) * renamed all .erbuis templates to .erb Yet more debug output... Add in a lot more debugging statements. update rack to 1.3.5 Remove the code to redirect MS::Controller.logger to a file - un-needed. Allow the MS::Controller logger to redirect to a file. Put the logger stuff back in - it wasn't the issue Comment out logger stuff - see if this is the cause of the respawn problems... Remove a now invalid test for the biomart data_origin_url length. * Added in a Logger object to the MartSearch::Controller class * Added a ****-tonne of debug messages throughout the system * Removed a potential infinite loop when constructing the data_origin_url on biomart backed data sources. closes #4789 Change the GO Ontology test to a better example. Correct the colony_prefix attribute name ... Conflicts: Gemfile.lock config/datasources.json lib/martsearch/server/views/dataviews/wtsi-phenotyping/_test_details_protocol_graphs.erb
… of the biomart attributes
…ge from the annotated terms.
* Update the gene-details dataview to follow these changes
…ew OLS gem.