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path: root/wqflask/base/data_set.py
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2017-11-06Replaced Histogram and Bar Chart with Plotly version and added new Box Plot w......GEMMA now has option to select genotypes Updated dataset select dropdowns to be ordered correctly Fixed dataset select dropdowns for correlations to not show confidential datasets Added Skewness and Kurtosis to Basic Statistics table Fixed Verify and RNA-seq buttons on trait page Temporarily hardcoded Reference page until we get it to link with database zsloan
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
2017-04-17Added 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
2016-11-18Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalError) (1054...Lei Yan
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
2016-10-29For those case that we have multiple genotypes we would like to add a selector.Lei Yan
2016-10-06Logger: add more granular debug messagesPjotr Prins
2016-10-05Show datasets only on debugPjotr 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
2016-07-27Problem 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
2016-06-24Log: and document SQL callsPjotr 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
2016-06-18Logger: replacing print statementsPjotr Prins
2016-05-23Reaper mapping results are now correct and account for samples with two names......R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues. zsloan
2016-04-29MergePjotr Prins
2016-04-28Added option to export permutation results for mapping page...Added data_scale to dataset objects and basic stats table will now check data scale when calculating range Made interval analyst results table work with datatables Changed the appearance of the basic stats table some by giving it a border zsloan
2016-04-20-a...[PATCH 039/100] Removing commented code Pjotr Prins
2016-04-20-a...[PATCH 038/100] Fix compile errors Pjotr Prins
2016-04-20[PATCH 037/100] WebQtlConfig: sanitizing naming and used varsPjotr Prins
2016-04-20[PATCH 033/100] Refactored file searchingPjotr Prins
2016-04-20[PATCH 032/100] file locating: error checking is built-inPjotr Prins
2016-04-20[PATCH 024/100] Sanitizing file handlingPjotr Prins
2016-04-20[PATCH 023/100] WIP fixing all pathsPjotr Prins
2016-03-18Replaced header with other information in qtl map...Began adding menu to qtl map Fixed global search to not retrieve samples (to increase speed) Got the vector plot working again so it can be displayed alongside the gn1-style plot Only display the vector plot when doing GEMMA to speed up (this might not be necessary) zsloan
2016-03-15Fixed the mapping figure track that lets you zoom into a smaller range...Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1) zsloan
2016-03-02Increased gsearch speed by removing unnecessary query for sample data...Still slower than preferable due to having to query the gn1 database for every trait in the search results zsloan
2016-02-04Most importantly, this commit fixes an issue that caused the trait page to no......An Intro section is also added to the header, though for the time being its contents aren't populated and the edit option isn't working zsloan
2015-11-09Fixed issue that caused mapping to not work; for some reason the path to pylm...zsloan
2015-10-12Changed the location filter for correlation pagezsloan
2015-09-11Comment out some excessive stdout spamDannyArends
2015-09-10Fixed "TypeError: float argument required, not NoneType" about mean....Committer: Lei Yan <lei@penguin.uthsc.edu> On branch master Lei Yan
2015-08-26Fixed issue with colums for the gene global search (still need to change for ......Fixed issue where LRS and LOD are sometimes labeled incorrectly Changed the header of the trait page Added link to GN1 in header Fixxed an issue that made permutations not work with pylmm Fixed "sign in" button when creating a collection while not logged in zsloan