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2019-02-15Fixed error caused by change to N values in database (now takes strings ↵zsloan
instead of integers) Fixed error that caused N to show up as "null" in the trait sample table instead of "x"
2019-02-13Removed pylmm references and related functionsPjotr Prins
2019-02-12Added GeneWeaver linkoutzsloan
Fixed some issues with sorting in various tables Changed header appearance for some pages Fixed bug where basic stats table would sometimes be duplicated or show up with empty fields
2019-02-05Fixed issue with getting marker info that affected heatmap and possibly ↵zsloan
other functions Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages
2019-01-11Got InDel working for Variant Browserzsloan
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
2018-12-21Fixed collections so they can be very large (1000+ traits)zsloan
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
2018-10-24- SNP Browser is mostly complete; just need to test more and add SNP density ↵zsloan
chart if results exceed some number (5000 on GN1) - Removed unnecessary options from the mode bar for the trait page Plotly figures and changed the default to highlight points the mouse is hovering over - Changed some file/function names related to mapping, which previously were erroneously named "marker_regression"
2018-10-11- Added fix for GEMMA LOCOzsloan
- Added all current SNP browser code (not complete yet) - Added change to convert_geno_to_bimbam that makes it ignore .geno files marked as "filler" (so ones where the .geno file is fake and we sometimes directly receive the genotypes as BIMBAM) - Changes TheSpecies object in species.py to accept species name as well as dataset name
2018-10-01- Can now remove cofactors from correlation scatterplot and select them by ↵zsloan
just clicking their row in collection - Cofactor color picker now works in Safari/Macs - Displays N for relevant samples in trait page sample table - Don't show bar chart when N>256 - Mapping loading page contents better centered - Anonymous collections timeout correctly listed as 30 days now - Minor allele frequency can actually be changed for GEMMA now (previously didn't work) - Fixed transcript position marker location for mapping results - Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password - Users can now map with submitted traits - Histogram width changes depending upon number of bins (need to improve this still) - Improved Q-q plot (previously called "probability plot")
2018-08-14Added cofactors to correlation scatterplot and changed it to use Plotlyzsloan
Added Phenogen track to mapping results Added comparison bar chart figure Simplified global search to not build trait/dataset objects, which speeds thing up considerably Fixed correlation matrix to correctly deal with 0 values Fixed issue where anonymous collections couldn't be created if none already existed
2018-05-17Added script to quantile normalize a data set and enter its normalized ↵zsloan
sample data into ElasticSearch Added option to replace trait page sample/strain values with normalized ones Began editing Lei's scatterplot code Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)
2018-04-19Changed width of top bar and a couple other html objects to 100% instead of ↵zsloan
set width Changed to using BIMBAM files to build Marker objects in dataset.py
2018-04-16Resolved conflicts after pulling changeszsloan
2018-04-11Added tissue correlation p value to correlation page results, since it was ↵zsloan
missing before Removed a bunch of unused coded from all correlation-related files and the ctl analysis code
2018-04-09Removed svg.py, which I know isn't used, and webqtlFormData, which I'm ↵zsloan
pretty sure also isn't used any more. Also removed some other unused code from the files listed
2018-04-09Removed unused code from webqtlFormData.pyzsloan
2018-04-09Removed some unused code in webqtlConfig; some might need to be added back ↵zsloan
in later when other third party links are implemented on the trait/collection pages
2018-04-06Mapping figure output now gives more accurate informationzsloan
Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
2018-03-22Fix 'def' statementMuriithi Frederick Muriuki
* End the 'def' statement with a colon (:) * Add an empty line between lines at different indentation levels for clarity.
2018-02-10Check for bimbam path and bail out if it is missingPjotr Prins
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 ↵zsloan
with Plotly 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
2017-08-29Mostly changes related to getting gemma working with covariates and BIMBAM ↵zsloan
file format 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)
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 ↵zsloan
for mapping - 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
2017-05-31Added various tool options to correlation results page and improved table ↵zsloan
appearance for mRNA assay data sets (still need to improve it for others) Fixed minor logic issue in trait.py
2017-05-21Merge from the diet branch.Pjotr Prins
* 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
2017-04-17Added option to remove collections from collection list pagezsloan
Improved appearance of search result and collection tables
2017-04-05- Temporary traits can be created, viewed, and added to collectionszsloan
- 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
2017-02-09Fixed issue where I forgot to add GeneticType to the query_for_group query ↵zsloan
for non-mRNA Assay datasets Increased digits of some Basic Statistics values from 2 to 3
2017-02-09Added genetic_type to DatasetGroup object to differentiate between which ↵zsloan
groups should show dominance effect Minor changes/improvements for trait page Updated dataset_menu_structure.json
2017-02-06Merge branch 'master' of github.com:zsloan/genenetwork2zsloan
2017-02-06Fixed appearance of several tables (search, mapping results, sample data)zsloan
Temporarily removed second sample table for CFW traits Fixed location of global search bar to work with wider screens
2017-01-26Merge pull request #1 from genenetwork/testingzsloan
Various changes/fixes
2017-01-26GEMMA now works with CFW data (had to update where it looks for the input ↵zsloan
files and how it writes the phenotype file) 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
2016-12-15Merge pull request #234 from zsloan/masterzsloan
Various changes
2016-12-13Fixed a problem related to the last commit that caused a problem when ↵zsloan
loading a collection or doing ctl analysis
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
2016-11-18Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalError) ↵Lei Yan
(1054, "Unknown column 'mouse' in 'where clause'") [SQL: '\n select Geno)
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