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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.zsloan
Later we will want to run all mapping methods outside of the web server, though
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/masterPjotr Prins
Fix global search "il6" for "Internal Server Error". Add single quote…
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 ↵Lei Yan
MySQL query.
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, doesPjotr Prins
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'
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 ↵zsloan
and uncommented simplejson import Added "Reset" option to network graph that returns all the nodes/edges Made the visualization options area in the network graph a little wider
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 ↵Pjotr Prins
settings Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
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 ↵zsloan
correlation slider. The first only displays the edges for the specified trait/node, the second changes layout, and the third hides nodes/edges with abs(correlation) less than the slider's value 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)
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 ↵zsloan
GN2 and third party links when clicking a node, view scatterplot when clicking an edge, and edges appearance varies based upon correlation Fixed issue that caused error with correlation page
2016-08-26Fixed appearance (border width mostly) of basic stats table on trait pagezsloan
Removed unnecessary datatables javascript code that referred to basic stats table
2016-08-24Fixed issue causing bootstrap results to not plot correctly.zsloan
2016-08-24Replaced post-publication description with pre-publication description for ↵zsloan
confidential phenotype traits in search results and trait pages 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
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
global search results
2016-08-16Users can now select specific traits from collection when using collection ↵zsloan
tools (correlation matrix, wgcna, etc) To do the above, changed the way form submission worked for those features; previously each feature had its own form, but that was dumb so instead I wrote a javascript function that just changed a single form's target url Duplicate traits can no longer by added to collections Fixed the digits for a few table columns in collection (additive effect, etc).
2016-08-15Removed text recommending winsoring when mapping since that feature isn't ↵zsloan
implemented yet Added padding to header text of Basic Statistics table
2016-08-12Changed pop-up asking to import collections to less obtrusive checkboxzsloan
Decreased collections/list table width
2016-08-11Added prompt when user logs in that lets them choose to import existing ↵zsloan
anonymous collections as user collections
2016-08-08Fixed bug where Interval Analyst result wouldn't appear for chromosome X in ↵zsloan
mice/rats Fixed broken image link in Interval Analyst table for rats Small change to column width of gene global search
2016-08-05Fixed issue that caused some interval mapping results to be wrong; the cause ↵zsloan
seems to be related to some strains being renamed in the genofiles Added a message to the Add to Collection page warning users that anonymous collections will only be stored for 5 days Updated genofiles
2016-08-03Fixed issue with certain sample names (for example BXD48a, BXD72a, etc) that ↵zsloan
caused single chromosome mapping to not work Disabled bootstrap for mapping unil issue causing wrong results is fixed Added header to first column of basic statistics table and increased width to avoid rows spilling over to second line
2016-07-29Fixed issue where you couldn't delete collections when logged inzsloan
2016-07-29Merge branch 'cookie_sessions' of github.com:zsloan/genenetwork2 into ↵zsloan
development Conflicts: wqflask/base/data_set.py
2016-07-29Fixed a couple issues where you couldn't remove or add traits to user ↵zsloan
collections
2016-07-27Problem with phenotype traits should be fixed nowzsloan
2016-07-27Fixed problem with phenotype traits causing errorzsloan
Can now remove traits from collections and add to existing collections Fixed a few other minor collection bugs
2016-07-26Docs: genotypePjotr Prins
2016-07-20Changed anonymous collections to list of dictionaries instead of a ↵zsloan
dictionary of dictionaries Can now add collections, view list of collections, and view collections from the collection list with anonymous collections
2016-07-19Now correctly displays number of collections in top menu bar for non-logged ↵zsloan
in users
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