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2016-12-12Moved a bunch of functions out of the GeneralTrait class that didn't need to ↵zsloan
be there and changed the code that calls them accordingly Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static) Removed some unused code from show_trait.py changed appearance of table headers some, though needs a little more work Updated dataset_menu_structure.json
2016-11-15Fixed issue where sample values of 0 would sometimes be displayed as 'x', ↵zsloan
which would result in wrong correlation results Fixed issue where the mean would sometimes be displayed into of the additive effect
2016-11-11Fixed problem that caused checkboxes to not work with Scroller search ↵zsloan
results pages Improved the way the table width is set for search results page
2016-11-02Added toggleable short and long labels to correlation matrixzsloan
Fixed issue where I forgot to remove a parameter from jsonable_table_row in trait.py
2016-11-02Merge branch 'testing' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-11-02Added Scroller functionality to regular (but not global) search, which ↵zsloan
increases table load speed In order to implement Scroller (and make table look nicer), all rows are the same height and excess description/authors text is shown in a tooltip Increased table width for non-Geno DBs Fixed issue where Genotype traits did not fetch their location_repr (text for displaying location), causing that column to be blank in searches Fixed issue causing Correlation Matrix cells to not be colored corresponding with their correlation and also increased cell font a little Fixed issue where dataset link in the Correlation Page did not correctly point to corresponding GN1 page
2016-10-31Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingPjotr Prins
2016-10-31Merge branch 'master' of github.com:lyan6/genenetwork2 into lyanPjotr Prins
2016-10-29For those case that we have multiple genotypes we would like to add a selector.Lei Yan
2016-10-25Just removed some extraneous spaces in trait.pyzsloan
2016-10-25Replaced the Download Table button for collection page with python version ↵zsloan
that displays metadata, etc Removed currently unused javascript and css imports related to the DataTables buttons import (since it was replaced with the python export) from regular search, both global searches, and the view_collection page Added a bunch of parameters to the jsonable function for the GeneralTrait object in order to later create a json version of the search results and implement the client-side Scroller feature (which dynamically loads table rows from json when you scroll)
2016-10-07Saner handling of TMPDIR and TEMPDIRPjotr Prins
Throw error when TMPDIRs are not writable
2016-10-06Logger: add more granular debug messagesPjotr Prins
2016-10-05Show datasets only on debugPjotr Prins
2016-10-03Debug: sanitize some outputPjotr Prins
2016-09-29Fix global search "il6" for "Internal Server Error". Add single quotes into ↵Lei Yan
MySQL query.
2016-09-25tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2Pjotr Prins
2016-09-13Run scripts from ./wqflask - just like the webserverPjotr 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
2016-09-02Added 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
2016-08-24Replaced 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
2016-08-16Users 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).
2016-08-05Fixed 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
2016-07-27Problem with phenotype traits should be fixed nowzsloan
2016-06-26gn_server: simplifyPjotr Prins
2016-06-26gn_server: simplifyPjotr Prins
2016-06-26gn_server: introduced one new query to fetch a dataset record and force ↵Pjotr Prins
fetch1 to return a tuple
2016-06-26Resolve conflictsPjotr Prins
2016-06-24Removed function 'get_info' in trait.py that was never used and reomved ↵zsloan
'get_trait_info' call from search_result_page.py because its query was already being run
2016-06-24Log: and document SQL callsPjotr Prins
2016-06-23Logger: SQLPjotr Prins
2016-06-23Logger: SQLPjotr Prins
2016-06-23Log: SQL queriesPjotr Prins
2016-06-23Add fetchall iteratorPjotr Prins
2016-06-23Removed dependency on dataset_menu_structure.jsonPjotr Prins
2016-06-23Backend: moved methods into call modulePjotr Prins
2016-06-23Refactored dir name dbFunction to dbPjotr Prins
2016-06-22Fixed a couple more errors with the correlation page that occurred when you ↵zsloan
selected Tissue correlation with traits from data sets without 'data_ids'
2016-06-21No longer runs query to get symbol_values_dict when no id_list to fix ↵zsloan
occasional error with correlation page
2016-06-18Logging settingsPjotr Prins
2016-06-18LoggerPjotr Prins
2016-06-18Logger: replacing print statementsPjotr Prins
2016-06-18Changed file permssions to non-executablePjotr Prins
2016-06-17Removed trailing spaces in .py and .js filesPjotr Prins
2016-06-03Changed appearance of tables to more easily differentiate them from the rest ↵zsloan
of the page (still not totally pleased with them though) Fixed issue where some N/A lrs scores and additive effects were being changed to 0's, which was misleading and kept them from always being sorted at the bottom. They now appear as N/A.
2016-05-31Fixed error when MrnaAssay search results didn't have a geneidzsloan
2016-05-31Allow the json dir to be in the old location.Pjotr Prins
2016-05-26Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-05-26Issue with certain samples (like BXD65a, ones were there are multiple for a ↵zsloan
single BXD or whatever) should be fixed for different mapping methods and data set types Renamed directories with genotypes so tools.py didn't need to be changed (which might mess up other deployments) Fixed error when searching genotype data sets
2016-05-23Reaper mapping results are now correct and account for samples with two ↵zsloan
names (like BXD65a) R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.
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