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2018-01-30Set to None if no value providedMuriithi Frederick Muriuki
* Add a method to set the configuration variables to None if the configuration values are not provided at startup or in the configuration files. The system already checks for these values, and if they are absent, it simply fails to display the OAuth service as available for use to login.
2018-01-19Use elasticsearch rather than mysql for local accountsMuriithi Frederick Muriuki
* Register local accounts onto elasticsearch rather than mysql. * Login from the accounts on elasticsearch * Harmonise local and oauth2 logins to use the same code.
2018-01-19Add OAuth2 login code for ORCIDMuriithi Frederick Muriuki
* Add code to handle the login via ORCID
2018-01-19Update configurationsMuriithi Frederick Muriuki
* Have the authorisation URLs build up from the client id and client secret values.
2018-01-19Add code to enable OAuth2 loginMuriithi Frederick Muriuki
* Add some code to handle the login if the user chooses to login via GitHub or ORCID.
2018-01-19Delay after save for indexingMuriithi Frederick Muriuki
* Elasticsearch need a short delay after adding document for it to index the document for subsequent access.
2018-01-19Add more configuration variables.Muriithi Frederick Muriuki
* Add configurations for elasticsearch and github.
2018-01-19Add save_user() functionMuriithi Frederick Muriuki
* On successful login via OAuth2, save the details of the user in elasticsearch store, to avoid hitting the external provider for the basic details.
2018-01-19Add elasticsearch module to the pathMuriithi Frederick Muriuki
* Add some code to set up the path for the python-elasticsearch module.
2018-01-12Add functions to help handle github loginMuriithi Frederick Muriuki
* Add functions to help with the github OAuth2 login process
2018-01-12Add elasticsearch_tools moduleMuriithi Frederick Muriuki
* Collect variables and functions for using the elasticsearch system in a separate module.
2018-01-12Add client_id and client_secret configurationsMuriithi Frederick Muriuki
* Provide the OAuth2 client_id and client_secret values in configuration variables.
2018-01-10Add template elements for OAuth loginMuriithi Frederick Muriuki
* Add html elements that will be used to prompt users to login with either GitHub or ORCID.
2018-01-10Add configuration variables for external servicesMuriithi Frederick Muriuki
* Add configuration variables for GitHub and ORCID which will be used by the system to allow users to login.
2018-01-04Merge pull request #270 from pjotrp/testingzsloan
Merge some older commits
2017-12-20Added submit_bnw even though it isn't working yet, just so views.py doesn't ↵zsloan
throw an error
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 ↵zsloan
problem preventing it from working) 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
2017-12-20VERSIONPjotr Prins
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 ↵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
2017-11-22Merge 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/masterzsloan
improved scatter plots
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 ↵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
2017-10-02Merge 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 ↵zsloan
chromosome view
2017-09-21LOCO should work with GEMMA (when BIMBAM available), though I still need to ↵zsloan
do more testing
2017-09-14Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2017-09-14Committing current progress towards implementing LOCO for GEMMA, not done yetzsloan
2017-09-14Merge pull request #264 from pjotrp/testingzsloan
./bin/genenetwork2: add GEM_PATH for gemma-wrapper
2017-09-14./bin/genenetwork2: add GEM_PATH for gemma-wrapperPjotr Prins
2017-09-13update Correlation Scatterplot formatLei Yan
2017-09-12Merge branch 'testing' of github.com:genenetwork/genenetwork2Lei Yan
2017-09-12change corr_scatterplot precision formatLei Yan
2017-09-07Updated show trait page to correctly show GEMMA options for certain data setszsloan
2017-09-07Added the script to convert bimbam to kinship matriceszsloan
2017-09-05Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2017-09-05Added file converting genofiles to bimbamzsloan
2017-09-05Merge pull request #259 from pjotrp/testingzsloan
gemma-wrapper: find binary in profile
2017-09-04gemma-wrapper: find binary in profilePjotr Prins
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)
2017-08-23Update corr scatterplotLei Yan
2017-08-03remove bracketsLei Yan
2017-08-02Remove duplicate codesLei Yan
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