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2018-03-20FixPjotr Prins
2018-03-20Authentication: some mods around defaultsPjotr Prins
2018-03-19- Disabled PYTHONPATH injection - fix Guix instead, see ↵Pjotr Prins
https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d - Renamed WQFLASK_SETTINGS to GN2_SETTINGS
2018-03-18Check that key exists before using itMuriithi Frederick Muriuki
* Ensure the key exists in the json object/dictionary, before trying to use it to retrieve a value.
2018-02-23Provide connections to elasticsearchMuriithi Frederick Muriuki
* Provide connections to elasticsearch at various points in the code. These oversight was caught while running tests.
2018-02-21Fix assumption of existing collectionMuriithi Frederick Muriuki
* 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.
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 ↵Pjotr Prins
PYTHONPATH needed as it is now in the Guix build.
2018-02-15Fix conflictPjotr Prins
2018-02-13Add tests for Registration process.Muriithi Frederick Muriuki
2018-02-13Update module to make it more testableMuriithi Frederick Muriuki
* Update functions to make them more testable. * Update code using updated functions.
2018-02-13@zsloan: we should introduce full parameter checking and sensible defaults ↵Pjotr Prins
for every page we work on. It will help bug tracking. Probably fixes #279
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 useMuriithi Frederick Muriuki
* 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.
2018-02-09Add check for elasticsearchMuriithi Frederick Muriuki
* Add some extra checks to ensure that elasticsearch is running before presenting the UI to the user.
2018-02-05Add code to allow user to change passwordMuriithi Frederick Muriuki
* 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.
2018-02-05Refactor common items to more generic methods.Muriithi Frederick Muriuki
* Refactor code that can be used in more than one place to a more generic method/function that's called by other methods
2018-02-05Send emails for forgotten passwordsMuriithi Frederick Muriuki
* Update the code so that it sends out emails for the "forgot password" feature.
2018-02-05Add SMTP configuration variablesMuriithi Frederick Muriuki
* Add configuration variables to enable the system connect to the configured SMTP server to send out emails.
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 unconfiguredMuriithi Frederick Muriuki
* 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.
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.
2018-01-29Gunicorn 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 DBzsloan
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
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.
2018-01-12Add 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
2017-12-20tools: 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
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