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2016-10-06CTL requires 2 traits minimally. Also use traits/phenotypes consistentlyPjotr Prins
2016-10-05CTL now displays proper error if fewer than 4 traits are selected. Also, WGCN......I also improved the formatting for the html for both CTl and WGCNA Analysis. zsloan
2016-10-05Show datasets only on debugPjotr Prins
2016-10-05Minor editPjotr Prins
2016-10-05Reverted on genotype selector on page show_trait_mapping_tools.html - pending...Pjotr Prins
2016-10-05print statements should be loggerPjotr Prins
2016-10-05print statements should be loggerPjotr Prins
2016-10-05Merge branch 'zsloan' into jsonPjotr Prins
2016-10-05Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloanPjotr Prins
2016-10-04Fixed issue that caused adding to existing collections when not logged in to ......The problem was that it would get the collection name from the "new_collection" field instead of the "existing_collections" dropdown. zsloan
2016-10-04Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloanPjotr Prins
2016-10-03Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
2016-10-03Fixed problem that caused R/qtl with permutations to not work correctlyzsloan
2016-10-03Moved rqtl mapping code out of marker_regression and into its own file....Later we will want to run all mapping methods outside of the web server, though zsloan
2016-10-03Config: supporting JSON OVERRIDESPjotr Prins
2016-10-03Debug: sanitize some outputPjotr Prins
2016-10-03Config: use server port settingPjotr Prins
2016-10-03Error page: reduce cookie sizePjotr Prins
2016-10-02Error page: trim error messagesPjotr Prins
2016-10-02Errors: added time stamps in UTCPjotr Prins
2016-10-02Error page: also display the URLPjotr Prins
2016-10-02Merge branch 'master' of github.com:genenetwork/genenetwork2Pjotr Prins
2016-10-02Error page: use cookies to fixate the animation for one errorPjotr Prins
2016-10-02Error: remove test errorPjotr Prins
2016-10-02Error screen improvements with animated gifsPjotr Prins
2016-09-30Merge pull request #192 from lyan6/master...Fix global search "il6" for "Internal Server Error". Add single quote…Pjotr Prins
2016-09-30Add missing __init__.pyPjotr Prins
2016-09-30Add logging for qtlreaperPjotr Prins
2016-09-29Fix global search "il6" for "Internal Server Error". Add single quotes into M...Lei Yan
2016-09-27Conflict in wqflask/wqflask/templates/show_trait_mapping_tools.htmlzsloan
2016-09-26Test: mechanical Rob executes scanone testPjotr Prins
2016-09-25Logger: use output for assessing mapping parametersPjotr Prins
2016-09-25Make sure MAPPING_PATH existsPjotr Prins
2016-09-25Settings: enforce MAPPING_PATH only when running plink_gemmaPjotr Prins
2016-09-25I was getting below error with the small database. This commit, at least, does...not assume the item exists. ERROR:wqflask:Exception on /marker_regression [POST] Traceback (most recent call last): File "/home/wrk/.guix-profile/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py", line 1817, in wsgi_app response = self.full_dispatch_request() File "/home/wrk/.guix-profile/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py", line 1477, in full_dispatch_request rv = self.handle_user_exception(e) File "/home/wrk/.guix-profile/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py", line 1381, in handle_user_exception reraise(exc_type, exc_value, tb) File "/home/wrk/.guix-profile/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py", line 1475, in full_dispatch_request rv = self.dispatch_request() File "/home/wrk/.guix-profile/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py", line 1461, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/export2/izip/git/opensource/genenetwork/sumo_gn2/wqflask/wqflask/views.py", line 460, in marker_regression_page template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid) File "/export2/izip/git/opensource/genenetwork/sumo_gn2/wqflask/wqflask/marker_regression/marker_regression.py", line 74, in __init__ value = start_vars['value:' + sample] KeyError: 'value:BXD80' Pjotr Prins
2016-09-25tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2Pjotr Prins
2016-09-13Save Image now works for Network Graph and downloads current graph as a pngzsloan
2016-09-13Fixed the path for the json file in gen_select_dataset.py since it was wrong ......Added "Reset" option to network graph that returns all the nodes/edges Made the visualization options area in the network graph a little wider zsloan
2016-09-13Run scripts from ./wqflask - just like the webserverPjotr Prins
2016-09-10CommentPjotr Prins
2016-09-10Support for running maintenance scripts so they can pick up all webserver set......Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py Pjotr Prins
2016-09-10Merge branch 'development' of github.com:genenetwork/genenetwork2 into zsloanPjotr Prins
2016-09-09Added a couple options for network graph - Focus Trait, Layout, and a correla......Changed/added a couple node/edge attributes for network graph Updated dataset menu structure json file to include the human RETINA data set Added css file for network graph page (specifically to make the appearance of the options resemble the RETINA website's) zsloan
2016-09-09Merge branch 'master' of github.com:genenetwork/genenetwork2Pjotr Prins
2016-09-02Added Network Graph feature that uses cytoscape.js. Currently you can view GN......Fixed issue that caused error with correlation page zsloan
2016-08-26Fixed appearance (border width mostly) of basic stats table on trait page...Removed unnecessary datatables javascript code that referred to basic stats table zsloan
2016-08-24Fixed issue causing bootstrap results to not plot correctly.zsloan
2016-08-24Replaced post-publication description with pre-publication description for co......Fixed table style for mapping results and interval analyst tables and added additive/dominance effect columns to the former Fixed mapping figure X-axis to accurately label Centimorgans vs Megabases (previously it would always say Megabases) Removed the "Sequence Site" marker from mapping result figure when mapping with genetics (centimorgans) scale Removed some unused javascript libary imports from search/global search pages zsloan
2016-08-17Updated dataTables from 1.10.8 to 1.10.12 on search result pagezsloan
2016-08-17Fixed problem where Year column didn't sort properly in phenotype search and ...zsloan
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