aboutsummaryrefslogtreecommitdiff
path: root/wqflask
AgeCommit message (Expand)Author
2018-03-18Check that key exists before using it...* Ensure the key exists in the json object/dictionary, before trying to use it to retrieve a value. 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
2018-02-23Provide connections to elasticsearch...* Provide connections to elasticsearch at various points in the code. These oversight was caught while running tests. Muriithi Frederick Muriuki
2018-02-23update corr scatterplot interfaceLei Yan
2018-02-21Fix assumption of existing collection...* When logging in, if a user selects "Import existing collections", the system would throw an exception, since Redis would return a NoneType, which would then be accessed by json.loads(), which doesn't seem to know how to process that. This fixes that, by providing a string representing an empty json array ("[]"), in place of the NoneType. Muriithi Frederick Muriuki
2018-02-19Add more login tests.Muriithi Frederick Muriuki
2018-02-15Added unittest examplePjotr Prins
2018-02-15Fixing authentication stuff so it uses parameters properly. Also no PYTHONPAT......it is now in the Guix build. Pjotr Prins
2018-02-15Fix conflictPjotr Prins
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
2018-02-13Add tests for Registration process.Muriithi Frederick Muriuki
2018-02-13Update module to make it more testable...* Update functions to make them more testable. * Update code using updated functions. Muriithi Frederick Muriuki
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
2018-02-09Check elasticsearch at point of use...* Instead of checking for the state of elasticsearch at startup, check the state at the moment the user requests a feature that depends on elasticsearch. This reduces the chances that the user is dropped onto an exception page when elasticsearch server goes down. Muriithi Frederick Muriuki
2018-02-09Add check for elasticsearch...* Add some extra checks to ensure that elasticsearch is running before presenting the UI to the user. Muriithi Frederick Muriuki
2018-02-05Add code to allow user to change password...* After the email is sent to the user, there is need to provide a way for the user to actually change their password, and have the results saved. Muriithi Frederick Muriuki
2018-02-05Refactor common items to more generic methods....* Refactor code that can be used in more than one place to a more generic method/function that's called by other methods Muriithi Frederick Muriuki
2018-02-05Send emails for forgotten passwords...* Update the code so that it sends out emails for the "forgot password" feature. Muriithi Frederick Muriuki
2018-02-05Add SMTP configuration variables...* Add configuration variables to enable the system connect to the configured SMTP server to send out emails. Muriithi Frederick Muriuki
2018-02-05Merge remote-tracking branch 'origin/testing' into testingMuriithi Frederick Muriuki
2018-01-30gunicorn dev and prod modes addedPjotr Prins
2018-01-30Fail safely if elasticsearch is down or unconfigured...* If elasticsearch server is down, or the configuration variables are not provided at startup or in a configuration file, then do not allow the system to simply crash, but instead, inform the user that they cannot use the services that depend on elasticsearch to be running. Muriithi Frederick Muriuki
2018-01-30Set to None if no value provided...* 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. Muriithi Frederick Muriuki
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
2018-01-19Use 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
2018-01-19Add OAuth2 login code for ORCID...* Add code to handle the login via ORCID Muriithi Frederick Muriuki
2018-01-19Update configurations...* Have the authorisation URLs build up from the client id and client secret values. Muriithi Frederick Muriuki
2018-01-19Add 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
2018-01-19Delay after save for indexing...* Elasticsearch need a short delay after adding document for it to index the document for subsequent access. Muriithi Frederick Muriuki
2018-01-19Add more configuration variables....* Add configurations for elasticsearch and github. Muriithi Frederick Muriuki
2018-01-19Add 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
2018-01-12Add functions to help handle github login...* Add functions to help with the github OAuth2 login process Muriithi Frederick Muriuki
2018-01-12Add elasticsearch_tools module...* Collect variables and functions for using the elasticsearch system in a separate module. Muriithi Frederick Muriuki
2018-01-12Add client_id and client_secret configurations...* Provide the OAuth2 client_id and client_secret values in configuration variables. Muriithi Frederick Muriuki
2018-01-10Add 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