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2020-03-09I think this should complete consolidating all the collections code.zsloan
2020-03-03Forgot to replace code referring to hmac function user_managerzsloan
2020-02-07Users can now add and do mapping on genotype files that only include a ↵zsloan
subset of samples/strains 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
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 ↵zsloan
index page header style a little
2019-11-21Use updated phenotype display IDs for all phenotypes with codes now, not ↵zsloan
just unpublished ones
2019-11-21Added 3-letter codes to unpublished phenotype traits and fixed issue with ↵zsloan
ordering phenotype results from searches
2019-11-14Changed code to rebuild dataset list each time you view the trait page to ↵zsloan
avoid having to restart each time a new dataset is added. Will need to keep an eye out for any issues, but doesn't seem to affect speed much Fixed logic for UniProt link to use UniProtId instead of protein ID
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 ↵zsloan
Phenotypes name when there's no accession ID
2019-10-18Added UniProt link and fixed issue that caused sample lists to not be formed ↵zsloan
correctly in certain situations
2019-10-04Fixed issue where there was an error if the REST API used for aliases was downzsloan
Added option to download as JPEG in addition to SVG for basic stats figures
2019-08-22Changed header drop-down menu layoutzsloan
Added a couple new third party links Added link to GN1 trait page in trait pages Fixed gene global search table appearance
2019-08-01Updated aliases to get all species aliases and remove duplicateszsloan
2019-08-01Added wikidata aliaseszsloan
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
2019-08-01Made some more aesthetic changes to various pages and charts/figureszsloan
Added some information to the mapping loading page
2019-07-23Added change to automatically update datasets list using rest api instead of ↵zsloan
json file Removed option to edit certain html pages, like news, policies, etc
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 pagezsloan
Changed text in several pages (submit trait, mapping error) Changed header menu structure some
2019-06-24Got non-LOCO GEMMA mapping working with gemma-wrapper (so caching should ↵zsloan
work for that now) Fixed position digits and row highlighting on interval analyst table Updated default MAF to 0.05 Updated footer text
2019-06-18Fixed issue with sorting involving 0's on trait pagezsloan
Fixed links to dataset info pages in search results and correlation results pages
2019-06-05Fixed issue that caused interval mapping to not work because the python ↵zsloan
implementation of the reaper Dataset object doesn't include the addinterval method (so for those situations I still use reaper) 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)
2019-06-04Added GeneMANIA linkzsloan
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
2019-05-24Replaced qtlreaper Dataset object with python objectzsloan
2019-05-14Added all of the third party links from GN1zsloan
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)
2019-05-06Removed some unused imports of htmlgenzsloan
Fixed a bug that sometimes occurred in search results Changed order of items on index page
2019-03-18- Added PCA traits to correlation matrix. You can't change their names yet ↵zsloan
or add them to a collection from the corr matrix page, 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
2019-03-07Changed the way covariates are displayed when selected for mappingzsloan
Made the outlier notification appear for all mapping methods Removed some misleading text saying "Block samples" from the Transform and Filter Data section
2019-02-22Fixed some appearance issues with several tableszsloan
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
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
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