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2017-08-29Mostly changes related to getting gemma working with covariates and BIMBAM fi......Other changes include: - Fixing links in the network graph - Changing button colors on show trait page - Changing color scheme for heatmap - Making rows highlight in yellow when clicked on - Some changes to table appearance (like giving gene global search a horizontal scroll) zsloan
2017-06-12Fixed issue where 0.0 values would be converted into X's on the trait pagezsloan
2017-06-09- Changed the way the genofile is set so different genofiles can be selected ......- Now shows error page for Correlation Matrix if traits aren't all from the same group (later need to make it check for shared samples, since different groups may contain some of the same samples - Mapping results page now displays the genofile in the information section - Only show Interval Analyst if species is mouse or rat (previously it would show a blank table for other species) - Network Graph now only shows links in a node's info if the relevant information (for example geneid) exists, and the label changes depending on the type of data set - Other minor changes to the appearance of the Network Graph menu (less white space, plus clickable descriptions for a couple options) - Improved Correlations Results page to shorten Description and Authors cell content for Phenotype traits (to keep table width manageable) - Changed the glossary links for LRS and Additive Effect columns for Gene Global Search - Improved appearance for Phenotype Global Search results - Temporarily removed Mapping options/features that don't work from the trait page zsloan
2017-05-31Added various tool options to correlation results page and improved table app......Fixed minor logic issue in trait.py zsloan
2017-05-21Merge from the diet branch.... * refactored ./bin/genenetwork2 and /etc/default_settings - better detection of Guix - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS - removing some default settings, such as PYLMM_COMMAND - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY - added GUIX_JS_PATH for JS modules * Added documentation on installing binary GN2 * Updated Twitter board to latest version in Guix - it had broken * Updated many tools in the latest Guix profile Pjotr Prins
2017-04-17Added option to remove collections from collection list page...Improved appearance of search result and collection tables zsloan
2017-04-05- Temporary traits can be created, viewed, and added to collections...- Correct PCA trait data is created but can't be saved yet - Added inner margins by increasing xDomain and yDomain of probability plot on trait page - Increased X/Y-axis label font size - Turned "processes" to 0 on runserver.py for PROD setting, since it doesn't work with threading - Improved appearance of correlation page table - Added links to github to index page - Removed js_data from GEMMA/PLINK mapping results, since it isn't used for those - Removed "Tissue" from trait page for phenotype traits zsloan
2017-02-09Fixed issue where I forgot to add GeneticType to the query_for_group query fo......Increased digits of some Basic Statistics values from 2 to 3 zsloan
2017-02-09Added genetic_type to DatasetGroup object to differentiate between which grou......Minor changes/improvements for trait page Updated dataset_menu_structure.json zsloan
2017-02-06Merge branch 'master' of github.com:zsloan/genenetwork2zsloan
2017-02-06Fixed appearance of several tables (search, mapping results, sample data)...Temporarily removed second sample table for CFW traits Fixed location of global search bar to work with wider screens zsloan
2017-01-26Merge pull request #1 from genenetwork/testing...Various changes/fixeszsloan
2017-01-26GEMMA now works with CFW data (had to update where it looks for the input fil......Y-axis for GEMMA now says -log(p) Updated the style of the trait sample data table in the trait page Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs) Updated dataset menu json file Added option to show and hide columns to regular search page using colVis Changed regular and global search result table styles/column widths Began work on user trait submission code (not working yet though) Began work on static loading page for mapping results zsloan
2016-12-15Merge pull request #234 from zsloan/master...Various changeszsloan
2016-12-13Fixed a problem related to the last commit that caused a problem when loading...zsloan
2016-12-12Moved a bunch of functions out of the GeneralTrait class that didn't need to ......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 zsloan
2016-11-18Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalError) (1054...Lei Yan
2016-11-15Fixed issue where sample values of 0 would sometimes be displayed as 'x', whi......Fixed issue where the mean would sometimes be displayed into of the additive effect zsloan
2016-11-11Fixed problem that caused checkboxes to not work with Scroller search results......Improved the way the table width is set for search results page zsloan
2016-11-02Added toggleable short and long labels to correlation matrix...Fixed issue where I forgot to remove a parameter from jsonable_table_row in trait.py zsloan
2016-11-02Merge branch 'testing' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-11-02Added Scroller functionality to regular (but not global) search, which increa......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 zsloan
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 th......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) zsloan
2016-10-07Saner handling of TMPDIR and TEMPDIR...Throw error when TMPDIRs are not writable Pjotr Prins
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 M...Lei Yan
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 set......Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py Pjotr 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
2016-08-24Replaced 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
2016-08-16Users 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
2016-08-05Fixed 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
2016-07-27Problem 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 fetch...Pjotr Prins
2016-06-26Resolve conflictsPjotr Prins
2016-06-24Removed function 'get_info' in trait.py that was never used and reomved 'get_...zsloan
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