aboutsummaryrefslogtreecommitdiff
path: root/wqflask/base
AgeCommit message (Expand)Author
2020-02-06Fixed encoding issuezsloan
2020-01-22Fixed issue that caused submitting temp traits to not workzsloan
2020-01-08Made change that I think should fix the unicode stuff once and for allzsloan
2019-12-17Added RGD link to trait page and removed Genotation link since it isn't workingzsloan
2019-12-04Added M to the possible non-number 'chromosome' nameszsloan
2019-12-04Fixed error that sometimes occurs if there's no mean expression and changed i...zsloan
2019-11-21Use updated phenotype display IDs for all phenotypes with codes now, not just...zsloan
2019-11-21Added 3-letter codes to unpublished phenotype traits and fixed issue with ord...zsloan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
2019-10-04Fixed issue where there was an error if the REST API used for aliases was down...Added option to download as JPEG in addition to SVG for basic stats figures zsloan
2019-08-22Changed header drop-down menu layout...Added a couple new third party links Added link to GN1 trait page in trait pages Fixed gene global search table appearance zsloan
2019-08-01Updated aliases to get all species aliases and remove duplicateszsloan
2019-08-01Added wikidata aliases...Fixed year to not be a hyperlink when no pubmed id Fixed first column width so it doesn't go onto two lines for trait details zsloan
2019-08-01Made some more aesthetic changes to various pages and charts/figures...Added some information to the mapping loading page 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
2019-07-18Made change that should fix encoding issue, fingers crossedzsloan
2019-07-03Fixed bug for creating one of the third party links on the trait page...Changed text in several pages (submit trait, mapping error) Changed header menu structure some 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
2019-06-04Added GeneMANIA link...Fixed issue that caused error when creating UCSC RefSeq link Fixed issue that sometimes caused an error for phenotype searches Changed some text on collections page zsloan
2019-05-24Replaced qtlreaper Dataset object with python objectzsloan
2019-05-14Added all of the third party links from GN1...Fixed issue with the script that generates the drop-down menus where phenotype/genotype datasets wouldn't show up for species without any mRNA assay datasets Added icon for smartphones/tablets Made error more informative for main search Added gene symbol column to collections (need to add something that removes the column if it's all empty) zsloan
2019-05-06Removed some unused imports of htmlgen...Fixed a bug that sometimes occurred in search results Changed order of items on index page zsloan
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
2019-03-07Changed the way covariates are displayed when selected for mapping...Made the outlier notification appear for all mapping methods Removed some misleading text saying "Block samples" from the Transform and Filter Data section zsloan
2019-02-22Fixed some appearance issues with several tables...Fixed issue where cofactor selection screens were broken Changed case attributes to be applied across groups, though need to discuss this with Rob since it shouldn't always be done this way Added new inversion transformation zsloan
2019-02-15Fixed error caused by change to N values in database (now takes strings inste......Fixed error that caused N to show up as "null" in the trait sample table instead of "x" zsloan
2019-02-13Removed pylmm references and related functionsPjotr Prins
2019-02-12Added GeneWeaver linkout...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 zsloan
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
2018-10-24- SNP Browser is mostly complete; just need to test more and add SNP density ......- 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" zsloan
2018-10-11- Added fix for GEMMA LOCO...- 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 zsloan
2018-10-01- Can now remove cofactors from correlation scatterplot and select them by ju......- 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") zsloan
2018-08-14Added cofactors to correlation scatterplot and changed it to use Plotly...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 zsloan
2018-05-17Added script to quantile normalize a data set and enter its normalized sample......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) 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
2018-04-16Resolved conflicts after pulling changeszsloan
2018-04-11Added tissue correlation p value to correlation page results, since it was mi......Removed a bunch of unused coded from all correlation-related files and the ctl analysis code zsloan
2018-04-09Removed svg.py, which I know isn't used, and webqtlFormData, which I'm pretty......Also removed some other unused code from the files listed zsloan
2018-04-09Removed unused code from webqtlFormData.pyzsloan
2018-04-09Removed some unused code in webqtlConfig; some might need to be added back in...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
2018-03-22Fix 'def' statement...* End the 'def' statement with a colon (:) * Add an empty line between lines at different indentation levels for clarity. Muriithi Frederick Muriuki
2018-02-10Check for bimbam path and bail out if it is missingPjotr Prins