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2018-03-26Use elasticsearch rather than mysql for local accounts...* Register local accounts onto elasticsearch rather than mysql. * Login from the accounts on elasticsearch * Harmonise local and oauth2 logins to use the same code. Muriithi Frederick Muriuki
2018-03-26Add OAuth2 login code for ORCID...* Add code to handle the login via ORCID Muriithi Frederick Muriuki
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 elasticsearch module to the path...* Add some code to set up the path for the python-elasticsearch module. 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
2018-02-13Merge pull request #285 from pjotrp/testing...@zsloan: we should introduce full parameter checking and sensible defaultszsloan
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
2018-02-12Merge pull request #277 from pjotrp/gn-production...Gn productionzsloan
2018-02-11Added gunicorn pid so we can not run twicePjotr Prins
2018-02-11Using eventlet workerszsloan
2018-02-10Fix env variable $GEMMA_WRAPPER_COMMANDPjotr Prins
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
2018-01-31Merge pull request #275 from pjotrp/pjotr...Added cli swith and set timeout to 3 minutes for gunicorn-dev modezsloan
2018-01-31Startup: longer timeout for gunicorn-dev modePjotr Prins
2018-01-31Startup: added -cli optionPjotr Prins
2018-01-30Merge pull request #274 from pjotrp/pjotr...Add gunicorn supportzsloan
2018-01-30gunicorn dev and prod modes addedPjotr Prins
2018-01-29Fixed gunicorn examplePjotr Prins
2018-01-29Gunicorn worksPjotr Prins
2018-01-29startup script: adapting for gunicornPjotr Prins
2018-01-29Added checks in startup script, removed r-auwerx pathPjotr Prins
2018-01-29Bumped versionPjotr 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
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