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path: root/wqflask/base/webqtlConfig.py
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2023-01-12Add BXD-NIA-AD to list of BXD_GROUP_EXCEPTIONS (so the correct options show ↵zsloan
up in correlation drop-down)
2022-11-02Update Phenogen URL to rn7zsloan
2022-10-14Add BXD_GROUP_EXCEPTIONS to webqtlConfig.py instead of having the groups ↵zsloan
hardcoded into show_trait.build_correlation_tools (+ add BXD-Heart-Metals to that list) I'm not sure why this logic exists, so it might be removed entirely later. I'm asking Rob
2022-08-31add new environment variable:TEXTDIRAlexander_Kabui
2021-04-30autopep8: Run autopep8 100 times with target rulesBonfaceKilz
Rules used are: E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242, E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306, E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121, E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
2021-04-30autopep8: Fix E20-E27BonfaceKilz
Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3
2021-03-17Added the RRID urls for mouse and rat to webqtlConfigzsloan
2021-02-18Changed DEFAULT_PERMISSIONS AND SUPER_PERMISSIONS to not have permissions be ↵zsloan
lists (I think the proxy expects them to not be lists, but then returns them as lists; need to check about this)
2021-02-18Fixed SUPER_PRIVILEGES and DEFAULT_PRIVILEGESzsloan
2020-07-25Removing bimbam check. We'll get rid of bimbam anyway.Pjotr Prins
2020-06-20Added some admin functionality and fixed issue with temp traitszsloan
2020-05-21Made search result table width variable again and fixed row highlighting, ↵zsloan
though later I need to go through and redo a bunch of CSS stuff
2019-12-17Added RGD link to trait page and removed Genotation link since it isn't workingzsloan
2019-10-18Added UniProt link and fixed issue that caused sample lists to not be formed ↵zsloan
correctly in certain situations
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
2019-07-03Fixed 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
2019-06-04Added 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
2019-05-14Added 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)
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"
2018-04-09Removed 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
2018-02-10Check for bimbam path and bail out if it is missingPjotr 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)
2017-05-21Merge 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
2017-04-05- 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
2016-10-07Saner handling of TMPDIR and TEMPDIRPjotr Prins
Throw error when TMPDIRs are not writable
2016-09-25tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2Pjotr Prins
2016-09-10Support for running maintenance scripts so they can pick up all webserver ↵Pjotr Prins
settings Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
2016-06-17Removed trailing spaces in .py and .js filesPjotr Prins
2016-05-31Allow the json dir to be in the old location.Pjotr Prins
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.
2016-05-13Removing ref. to HTMLPATHPjotr Prins
2016-05-13WebqtlConfig.py: Constant handlingPjotr Prins
2016-05-13Fix paths for imagesPjotr Prins
2016-04-20Add filePjotr Prins
2016-02-25fixed untracked fileszsloan
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
2015-07-09Mapping 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
2015-03-27Changed HTMLPATH in webqtlConfig since I forgot to in the last commit (since ↵zsloan
it used to point to the now-renamed 'web' directory). It obviously also needs to be renamed later, but I'll have to find every place that calls webqtlConfig.HTMLPATH first to do so.
2015-03-25Pair scan image now loads properlyzsloan
2015-03-24Change back port location and home directory location; this should be in ↵zsloan
external settings
2015-03-23Updates to make GN2 work on my version of penguin (ports, and paths)DannyArends
2013-08-07Fixed things with the dataset dropdowns and mRNA datasetsZachary Sloan
Improved the templates for a couple pages related to changing user password, etc
2013-07-19Created file gen_group_samplelists that iterates through all genofilesZachary Sloan
and builds each groups' samplelist
2013-07-18Added Amelie's rat data genotypesZachary Sloan
Got human mapping mostly working Fixed dataset dropdown menus
2013-07-18Added to installation notesZachary Sloan
Removed webqtlConfigLocal file containing passwords Updated main page dropdown menus (dataset_menu_structure.json)
2013-06-13Merge /home/sam/gene into flaskZachary Sloan
Conflicts: wqflask/wqflask/templates/index_page.html Merging the code on Sam's branch onto my own
2013-04-17Created file with pickled SNPIterator (from input.py) dataZachary Sloan
for HLC datasets Still need to read in file