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2016-06-17Removed trailing spaces in .py and .js filesPjotr Prins
2016-06-03Changed appearance of tables to more easily differentiate them from the rest ↵zsloan
of the page (still not totally pleased with them though) Fixed issue where some N/A lrs scores and additive effects were being changed to 0's, which was misleading and kept them from always being sorted at the bottom. They now appear as N/A.
2016-05-31Fixed error when MrnaAssay search results didn't have a geneidzsloan
2016-05-31Allow the json dir to be in the old location.Pjotr Prins
2016-05-26Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-05-26Issue with certain samples (like BXD65a, ones were there are multiple for a ↵zsloan
single BXD or whatever) should be fixed for different mapping methods and data set types Renamed directories with genotypes so tools.py didn't need to be changed (which might mess up other deployments) Fixed error when searching genotype data sets
2016-05-23Reaper mapping results are now correct and account for samples with two ↵zsloan
names (like BXD65a) R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.
2016-05-18Merge branch 'staging' of https://github.com/genenetwork/genenetwork2zsloan
2016-05-18Updated dataset selection dropdown menus and fixed error caused by traits ↵zsloan
with no description
2016-05-17Merge branch 'staging' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-05-13Removing ref. to HTMLPATHPjotr Prins
2016-05-13WebqtlConfig.py: Constant handlingPjotr Prins
2016-05-13Fix paths for imagesPjotr Prins
2016-04-29MergePjotr Prins
2016-04-28Added option to export permutation results for mapping pagezsloan
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
2016-04-20Add filePjotr Prins
2016-04-20-aPjotr Prins
[PATCH 039/100] Removing commented code
2016-04-20-aPjotr Prins
[PATCH 038/100] Fix compile errors
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
2016-04-19Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
Conflicts: wqflask/base/trait.py
2016-04-13Moved the code getting the description/location because it was throwing an ↵zsloan
error for phenotype traits
2016-04-13Global search should be able to return description and location columns nowzsloan
2016-04-11Figured out how to load results into dataTable using AJAX, but still need to ↵zsloan
get it working with Scroller correctly Added code getting the description, etc to trait.py since it was missed from last commit
2016-04-11Changed the way trait data is retrieved for the global search page (it now ↵zsloan
gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py) This change increases the speed by a bit (85 seconds to 66 seconds for example) Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
2016-03-29Forgot to add GeneralObject file needed for haplotype analyst in last commitzsloan
2016-03-18Replaced header with other information in qtl mapzsloan
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)
2016-03-15Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-03-15Fixed the mapping figure track that lets you zoom into a smaller rangezsloan
Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1)
2016-03-14Changed the way headers look across all pageszsloan
Changed the way details are displayed in show trait page Changed search query so that it orders results by symbol
2016-03-03Merge branch 'master' of https://github.com/genenetwork/genenetwork2zsloan
2016-03-02Increased gsearch speed by removing unnecessary query for sample datazsloan
Still slower than preferable due to having to query the gn1 database for every trait in the search results
2016-02-25fixed untracked fileszsloan
2016-02-04Most importantly, this commit fixes an issue that caused the trait page to ↵zsloan
not work because of the new dataset_menu_structure.json file 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
2015-12-14GN1 mapping full genome figure now correct for pylmm and output to web pagezsloan
2015-12-12Changed loop drawing qtl curve to fix some issues; still need to make it ↵zsloan
draw to different chr areas though
2015-11-18Fixed issue where literature and tissue correlation didn't workzsloan
Scatterplot matrix feature only appears if user is logged in now Committing current progress on mapping page (it can at least import the file now, but there are still errors)
2015-11-09Fixed issue that caused mapping to not work; for some reason the path to ↵zsloan
pylmm was wrong
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.Lei Yan
Committer: Lei Yan <lei@penguin.uthsc.edu> On branch master
2015-08-26Fixed issue with colums for the gene global search (still need to change for ↵zsloan
phenotype) 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
2015-07-20Fixed the code that generates the dataset selection drop-down for correlationszsloan
Made changes to the tables of correlation results, collections, and search results: - Added resizeable columns to correlation results and collections, but not to search results because it seems that it requires Y scrolling to be set (I'll check if it makes sense to add scrolling to the search results) - Correlation results and collections are now in scrolling tables - The style is the same across all of these tables now Remaining issues: - It doesn't seem like I can set the column width when initializing dataTables in correlation results. I don't know why this is; it might be due to the table already being the size of a full page. I want to be able to default to some good widths, even if the user can resize them - I tried adding hoverForMore, but it doesn't seem to cooperate with datatable cells; I think this is due to having to put the text in a div.
2015-07-10Fixed the genofile_parser.py script since some .geno files had been ↵zsloan
incorrectly converted to json Fixed GO search to work with combined searches
2015-07-09Mapping methods now check for existing genotype files.zsloan
Currently we still usually get our samplelists from the genofile. This is dumb because it results in us having a bunch of "dummy" genofiles for certain data sets (seems to be mostly human ones). This means that checking for the genofile alone isn't enough to determine if a mapping method should exist for a given group I wrote some code that will instead get the samplelist from the plink .fam file for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy .geno files, but we can't yet do so because it's currently the only place we seem to be storing the sample list for some groups. I also moved gemma into the plink directory to get it out of the git tree. Since it uses the same files as plink, it doesn't make sense for it to be in its own separate directory
2015-07-09Some phenotype searches were throwing an error due to an assert statement in ↵zsloan
trait.py. Since I couldn't find the purpose of the assert statement I removed it.
2015-07-07Added index column and changed the way location is displayed for search resultszsloan