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path: root/wqflask/base/data_set.py
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2020-04-27Added timeout for when/if it does the REST API query, so it doesn't hang inde...zsloan
2020-04-27Made change that should allow dataset structure to be loaded from Redis inste...zsloan
2020-04-26Removed the code that was still writing the database menu JSONzsloan
2020-04-24Replaced hard-coded instances of GN2 urls with ones pulled from settings filezsloan
2020-04-24Made a fix that should prevent the issue where new datasets cause an error wh...zsloan
2020-04-06Added Mean column for phenotype traits in search and global search result tableszsloan
2020-03-27Fixed issue where GEMMA wasn't showing up for certain groupszsloan
2020-03-27Added integration for using RData files with R/qtl, plus some other changes t...zsloan
2020-02-07Users can now add and do mapping on genotype files that only include a subset......Also filtered the results used by Christian's genome browser, so now it should have an easier time loading when dealing with larger numbers of markers zsloan
2019-12-04Added M to the possible non-number 'chromosome' nameszsloan
2019-11-21Added 3-letter codes to unpublished phenotype traits and fixed issue with ord...zsloan
2019-11-14Changed code to rebuild dataset list each time you view the trait page to avo......Fixed logic for UniProt link to use UniProtId instead of protein ID zsloan
2019-11-05Fixed issue with ordering items in correlation dataset select dropdownzsloan
2019-10-24Changed logic for generating drop-downs such that it shows the correct Phenot...zsloan
2019-10-18Added UniProt link and fixed issue that caused sample lists to not be formed ...zsloan
2019-07-23Added change to automatically update datasets list using rest api instead of ......Removed option to edit certain html pages, like news, policies, etc zsloan
2019-06-24Got non-LOCO GEMMA mapping working with gemma-wrapper (so caching should work......Fixed position digits and row highlighting on interval analyst table Updated default MAF to 0.05 Updated footer text zsloan
2019-06-18Fixed issue with sorting involving 0's on trait page...Fixed links to dataset info pages in search results and correlation results pages zsloan
2019-06-05Fixed issue that caused interval mapping to not work because the python imple......Fixed issue where the last chromosome wasn't displayed for mapping results (though still need to fix issue where points are drawn too far to the right when a specific range is viewed) zsloan
2019-05-24Replaced qtlreaper Dataset object with python objectzsloan
2019-03-18- Added PCA traits to correlation matrix. You can't change their names yet or......but you can click them and access them from the trait page. I'll add the option to access them from the corr matrix page as well, but adding the option to change their names might be trickier since they're currently used as their Redis keys. I need some better way of passing the Redis key around so it can be stored in collections, but this is tricky without changing the structure in ElasticSearch - Fixed the way temp traits work so you can use them with various functions, like mapping, correlations, network graph, etc - Fixed some appearance issue where the network graph options were too wide if a trait name was too long zsloan
2019-02-13Removed pylmm references and related functionsPjotr Prins
2019-02-05Fixed issue with getting marker info that affected heatmap and possibly other......Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages zsloan
2019-01-11Got InDel working for Variant Browser...Changed Variant Browser to display gene name under "Domain" when the user searches a gene term and rows are mislabeled "Intergenic" Fixed Chr option to display correct chromosomes for different species Fixed order for correlation drop-down on trait page Fixed some appearance issues with the mapping results table Improved appearance of correlation scatterplot page zsloan
2018-12-21Fixed collections so they can be very large (1000+ traits)...Added option to submit traits in collection to BNW Fixed issue with "x" values for user-submitted traits Fixed issue where post-publications descriptions were wrongly appearing in global search results zsloan
2018-04-19Changed width of top bar and a couple other html objects to 100% instead of s......Changed to using BIMBAM files to build Marker objects in dataset.py zsloan
2018-04-06Mapping figure output now gives more accurate information...Committing partway through removing a bunch of unused code/files just in case something necessary gets removed zsloan
2017-12-20Bring in some earlier work - mostly documentation and startup handlingPjotr Prins
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