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2016-09-27Remove reintroduced geno fileszsloan
2016-09-27Conflict in wqflask/wqflask/templates/show_trait_mapping_tools.htmlzsloan
2016-09-25Make sure MAPPING_PATH existsPjotr Prins
2016-09-25Settings: enforce MAPPING_PATH only when running plink_gemmaPjotr Prins
2016-09-25Removed large genotype_files from repository. The current set was saved...in http://files.genenetwork.org/data_files/ and can be used when unpacked in GENENETWORK_FILES (see ./etc/default_settings.py) Pjotr Prins
2016-09-25Testing: looking for a way to run pylmmPjotr 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
2016-09-25Doc: Section on reproducibility... - fixed SVG URLs Pjotr 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
2016-09-13Merge pull request #181 from pjotrp/zsloan...Run scripts from ./wqflask - just like the webserverzsloan
2016-09-13Run scripts from ./wqflask - just like the webserverPjotr Prins
2016-09-12Merge pull request #180 from pjotrp/zsloan...Support maintenance scriptszsloan
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
2016-09-10Doc: Rpy2 notePjotr 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
2016-09-09Doc: note on guix pathsPjotr 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
2016-08-16Users can now select specific traits from collection when using collection to......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). zsloan
2016-08-15Removed text recommending winsoring when mapping since that feature isn't imp......Added padding to header text of Basic Statistics table zsloan
2016-08-12Changed pop-up asking to import collections to less obtrusive checkbox...Decreased collections/list table width zsloan
2016-08-11Added prompt when user logs in that lets them choose to import existing anony...zsloan
2016-08-08Fixed bug where Interval Analyst result wouldn't appear for chromosome X in m......Fixed broken image link in Interval Analyst table for rats Small change to column width of gene global search zsloan
2016-08-08Doc: gn_execPjotr Prins
2016-08-05Fixed issue that caused some interval mapping results to be wrong; the cause ......Added a message to the Add to Collection page warning users that anonymous collections will only be stored for 5 days Updated genofiles zsloan
2016-08-03Fixed issue with certain sample names (for example BXD48a, BXD72a, etc) that ......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 zsloan
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 develop......Conflicts: wqflask/base/data_set.py zsloan
2016-07-29Fixed a couple issues where you couldn't remove or add traits to user collect...zsloan
2016-07-27Problem with phenotype traits should be fixed nowzsloan
2016-07-27Fixed problem with phenotype traits causing error...Can now remove traits from collections and add to existing collections Fixed a few other minor collection bugs zsloan
2016-07-26Docs: genotypePjotr Prins
2016-07-21Doc: SNP handlingPjotr Prins
2016-07-20Changed anonymous collections to list of dictionaries instead of a dictionary......Can now add collections, view list of collections, and view collections from the collection list with anonymous collections zsloan
2016-07-19Now correctly displays number of collections in top menu bar for non-logged i...zsloan
2016-07-18Merge branch 'cookie_sessions' of github.com:genenetwork/genenetwork2 into co...zsloan
2016-07-18Now correctly displays existing collections in 'add to collection' dropdown menuzsloan
2016-07-18Merge pull request #171 from zsloan/cookie_sessions...Cookie sessionszsloan
2016-07-18Committing latest changes to anon collection stuff, but still need to fix som...zsloan
2016-07-17Doc: genotype dataPjotr Prins
2016-07-16R/qtl: geno formatPjotr Prins
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