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2020-08-19Replace `izip` with python's built-in equivalentBonfaceKilz
Run `2to3-3.8 -f itertools -w . && 2to3-3.8 -f itertools_imports -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools_imports> and <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools>
2020-08-19Fix dictionary iteration methodsBonfaceKilz
Run `2to3-3.8 -f dict -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-dict> and <https://stackoverflow.com/questions/17695456/why-does-python-3-need-dict-items-to-be-wrapped-with-list>
2020-07-06Fixed some of the logic with how traits are authenticated to avoid situation ↵zsloan
where a trait is authenticated twice
2020-06-20Added some admin functionality and fixed issue with temp traitszsloan
2020-06-17A user's id is now set as a parameter if it doesn't already existauthentication_testzsloan
2020-06-17Adding all the authentication stuffzsloan
2020-06-05Commiting other current group/resource management code, plus the new fileszsloan
2020-03-10Added back macaque monkey to dropdown generation, not sure why it was ↵zsloan
removed; need to ask Rob
2019-12-09Fixed minor issue that caused the sample list to be fetched incorrectly for ↵zsloan
a group groups
2019-10-18Added UniProt link and fixed issue that caused sample lists to not be formed ↵zsloan
correctly in certain situations
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)
2019-04-04Fixed issue where dataset_menu_structure.json included some groups with no ↵zsloan
visible datasets
2019-04-03Fixed an issue that caused global phenotype search to often not work and ↵zsloan
certain phenotype datasets to not show up in drop-downs
2019-03-27Changed gen_select_dataset.py to be able to show multiple datasets under the ↵zsloan
Phenotype type (for example the GI Tract Metabolome data) Fixed issue where full description was given for some unpublished traits Fixed code related to editing certain pages (like news) with CKEditor, but it still won't work until the CKEditor library is included in GUIX or something
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
2018-12-05Fixed issue where SNP track for mapping did not appear correctlyzsloan
Updated style for a variety of tables Moved transform/blocking tools for trait sample table into its own tab Added some new customization options to network graph Started work on implementing third party link-outs Updated drop-down generation script to order datasets according to CreateTime
2018-11-20Added option to select chromosome from trait page when mappingzsloan
Put transform/blocking tools into their own tab (still need to change formatting of tab's contents) Improved appearance of search result page table (still need to change a few other tables) Fixed issue that caused parent/f1 strains to not be blocked correctly when using "block by index" tool Basic Stats figures now load when the user clicks the tab, to improve initial page load time
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")
2018-05-25Fixed issue causing anonymous collections to not work on my branch and ↵zsloan
staging, though still not sure why it's working on production without that change Added script to convert the dryad format genotype files to BIMBAM removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable
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)
2018-04-23Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter ↵zsloan
instead of -lmm 1 (Wald test) Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)
2018-04-16Resolved conflicts after pulling changeszsloan
2018-04-12README and docsPjotr Prins
2018-04-09Removed unused code from get_select_dataset.py and get_group_samplelists.py ↵zsloan
scripts
2018-04-09Removed unused code from convert_geno_to_bimbam.py and corestats.pyzsloan
2017-12-06Fixed drop-down group orderzsloan
2017-12-04Fixed drop-down scripts to more appropriately deal with BXD300 groups ↵zsloan
(though there's still a minor issue with a few datasets) Added some header data to mapping output file Fixed links in Network Group nodes/edges
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
2017-09-07Added the script to convert bimbam to kinship matriceszsloan
2017-09-05Added file converting genofiles to bimbamzsloan
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
2017-02-08Changed the way .fam files are written/read, which fixes the issue with ↵zsloan
GEMMA mapping accuracy.
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
2016-09-30Add missing __init__.pyPjotr Prins
2016-09-13Fixed the path for the json file in gen_select_dataset.py since it was wrong ↵zsloan
and uncommented simplejson import Added "Reset" option to network graph that returns all the nodes/edges Made the visualization options area in the network graph a little wider
2016-09-13Run scripts from ./wqflask - just like the webserverPjotr Prins
2016-09-10CommentPjotr 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
2016-07-16README: added infoPjotr Prins
2016-06-19Renamed settings so they are grouped togetherPjotr Prins
2016-06-18Changed file permssions to non-executablePjotr Prins
2016-06-18Disable setting sys.pathsPjotr Prins
2016-06-17ConflictPjotr Prins
2016-06-17Removed trailing spaces in .py and .js filesPjotr Prins
2016-06-16Generating the menu is now obsoletePjotr Prins
2016-04-20More hard-codedpjotrp
2016-04-20[PATCH 037/100] WebQtlConfig: sanitizing naming and used varsPjotr Prins
2016-02-18Edited gen_select_dataset to remove confidential datasetszsloan
Also hard-coded the removal of Macaque Monkey since I couldn't think of a good way to retroactively check if every dataset in a species is confidential
2016-01-29Info button should now work for phenotype and genotype datasetszsloan
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