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AgeCommit message (Expand)Author
2018-03-26Update configurations...* Have the authorisation URLs build up from the client id and client secret values. Muriithi Frederick Muriuki
2018-03-26Add code to enable OAuth2 login...* Add some code to handle the login if the user chooses to login via GitHub or ORCID. Muriithi Frederick Muriuki
2018-03-26Delay after save for indexing...* Elasticsearch need a short delay after adding document for it to index the document for subsequent access. Muriithi Frederick Muriuki
2018-03-26Add more configuration variables....* Add configurations for elasticsearch and github. Muriithi Frederick Muriuki
2018-03-26Add save_user() function...* On successful login via OAuth2, save the details of the user in elasticsearch store, to avoid hitting the external provider for the basic details. Muriithi Frederick Muriuki
2018-03-26Add functions to help handle github login...* Add functions to help with the github OAuth2 login process Muriithi Frederick Muriuki
2018-03-26Add elasticsearch_tools module...* Collect variables and functions for using the elasticsearch system in a separate module. Muriithi Frederick Muriuki
2018-03-26Add client_id and client_secret configurations...* Provide the OAuth2 client_id and client_secret values in configuration variables. Muriithi Frederick Muriuki
2018-03-26Add template elements for OAuth login...* Add html elements that will be used to prompt users to login with either GitHub or ORCID. Muriithi Frederick Muriuki
2018-03-26Add configuration variables for external services...* Add configuration variables for GitHub and ORCID which will be used by the system to allow users to login. Muriithi Frederick Muriuki
2018-03-16Just undoing tabulator changes so I can push other changeszsloan
2018-03-15Changed appearance of mapping and correlation options on trait page...Fixed issue where changed sample values were not passed to qtlreaper mapping ("Interval Mapping") Loading factors and their plot are hidden in situations where there's some error with calculating principal components Added GEMMA description and changed order of descriptions for mapping options on trait page zsloan
2018-03-02Added option to display selected covariates for GEMMA mapping...Changed layout/appearance of mapping options Partially fixed issue with deleting collections Changes to correlation table still in progress; having trouble getting tabulator to load JSON zsloan
2018-02-26Merge /home/lei/gene into testingzsloan
2018-02-26Committing some in-progress changes related to loading correlation page from ...zsloan
2018-02-23update corr scatterplot interfaceLei Yan
2018-02-14Added empty collection error page to git, since it wasn't on productionzsloan
2018-02-13Resolved conflictzsloan
2018-02-13Just committing very minor change to correlation table so I can pull other ch...zsloan
2018-02-13@zsloan: we should introduce full parameter checking and sensible defaults fo......work on. It will help bug tracking. Probably fixes #279 Pjotr Prins
2018-02-12Changed code parsing GEMMA output to fix issue where it wasn't getting the co...zsloan
2018-02-12Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2018-02-12Quick parallel correlation should work, though I'm not sure why the code sudd......Switched correlation table to tabulator zsloan
2018-02-10Fixing GEMMA LOCOPjotr Prins
2018-02-10Fixed finding PATHs - one return statement!Pjotr Prins
2018-02-10Check for bimbam path and bail out if it is missingPjotr Prins
2018-01-30gunicorn dev and prod modes addedPjotr Prins
2018-01-29Gunicorn worksPjotr Prins
2018-01-29startup script: adapting for gunicornPjotr Prins
2018-01-24Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2018-01-24Added links for markers in mapping results table when genotypes exist in DB...Added more info to trait details for phenotype traits Changed order of mapping methods Fixed layout of mapping loading screen to hopefully be centered on different screen sizes Improved layout of some elements in mapping results page zsloan
2018-01-04Merge pull request #270 from pjotrp/testing...Merge some older commitszsloan
2017-12-20Added submit_bnw even though it isn't working yet, just so views.py doesn't t...zsloan
2017-12-20Fixed issue that caused Mb ticks to get out of alignment for mapping figurezsloan
2017-12-20Fixed the way PLINK outputs phenotype files (though there's still some proble......Added some code related to new plotly probability plot, though it's commented out until it looks how I want it to Added some code for adding the BNW link to GN2, though it's not working yet Updated dataset menu structure JSON file zsloan
2017-12-20tools: find path for JS and gemma_wrapperPjotr Prins
2017-12-20Bring in some earlier work - mostly documentation and startup handlingPjotr Prins
2017-12-06Fixed drop-down group orderzsloan
2017-12-04Fixed drop-down scripts to more appropriately deal with BXD300 groups (though......Added some header data to mapping output file Fixed links in Network Group nodes/edges zsloan
2017-11-22Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2017-11-22Added option to export csv of full mapping resultszsloan
2017-11-21Merge pull request #258 from lyan6/master...improved scatter plotszsloan
2017-11-17Fixed issue that caused GEMMA LOCO to not work on productionzsloan
2017-11-06Replaced Histogram and Bar Chart with Plotly version and added new Box Plot w......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 zsloan
2017-10-02Merge branch 'testing' of github.com:genenetwork/genenetwork2Lei Yan
2017-10-02save as svg button workLei Yan
2017-09-22Fixed issue that caused covariates to not work for certain data set groupszsloan
2017-09-22Fixed issue that caused LOCO to not work when remapping or using single chrom...zsloan
2017-09-21LOCO should work with GEMMA (when BIMBAM available), though I still need to d...zsloan
2017-09-14Committing current progress towards implementing LOCO for GEMMA, not done yetzsloan
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