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2018-03-20Authentication: some mods around defaultsPjotr Prins
2018-03-19RELEASENOTESPjotr 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
2018-03-19Merge pull request #5 from fredmanglis/testingPjotr Prins
Testing
2018-03-18Initialise mapping testsMuriithi Frederick Muriuki
* Add mapping tests, and build the first of the tests.
2018-03-18Move import to the top of the page.Muriithi Frederick Muriuki
* Mainly to tell the dependencies easily.
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.
2018-03-14Add tests for main web functionalityMuriithi Frederick Muriuki
2018-03-12Add tests to check links.Muriithi Frederick Muriuki
2018-03-09Add link_checker moduleMuriithi Frederick Muriuki
* Add the module that will hold the code to test the links on the system.
2018-03-09Use argparse to handle argumentsMuriithi Frederick Muriuki
* Use argparse to handle commandline arguments. * Create initial layout of how the code might end up - lots of the code is currently commented out.
2018-02-23Add tests to check that the UI is setup correctlyMuriithi Frederick Muriuki
* Check that the links for OAuth2 logins via ORCID and GitHub are setup correctly.
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.
2018-02-23Add new tests for orcid loginsMuriithi Frederick Muriuki
2018-02-23Add new test for github loginsMuriithi Frederick Muriuki
2018-02-23Remove failing codeMuriithi Frederick Muriuki
* With the parameterized module, the testcase cannot be run independently at this time.
2018-02-21Simplify test. Check for content, rather than urlMuriithi Frederick Muriuki
* The test functions were very similar, so this commit refactors out the common test code to a single method, and passes in the data to the test using the parameterized package. * Check that the page content after a login attempt is the expected content, rather than checking the url.
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
2018-02-19Add a runner for all integration tests.Muriithi Frederick Muriuki
2018-02-19Add test for local loginMuriithi Frederick Muriuki
* Add an integration test to test that the login process for users registered locally to genenetwork2 works as expected.
2018-02-19Create parametrized superclass for testsMuriithi Frederick Muriuki
* Since the tests require that some parameters be provided while running the tests, create a class that helps abstract away the details of retrieving and setting the expected parameters.
2018-02-19Rename file and move common codeMuriithi Frederick Muriuki
* Rename the file to make it an importable module * Refactor the test to move common code out to a super class.
2018-02-16Add registration testMuriithi Frederick Muriuki
* Add integration test to check the registration process.
2018-02-16Merge branch 'pjotrp-gn-testing-es' into testingMuriithi Frederick Muriuki
2018-02-15Requests addedPjotr Prins
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
2018-02-12Merge pull request #277 from pjotrp/gn-productionzsloan
Gn production
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
2018-02-09Check 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.
2018-02-05Check each part of the PYTHONPATHMuriithi Frederick Muriuki
* PYTHONPATH may be composed of multiple locations in the filesystem, thus the need to test that each location exists and is a directory.
2018-02-05Merge remote-tracking branch 'origin/testing' into testingMuriithi Frederick Muriuki
2018-01-31Merge pull request #275 from pjotrp/pjotrzsloan
Added cli swith and set timeout to 3 minutes for gunicorn-dev mode
2018-01-31Startup: longer timeout for gunicorn-dev modePjotr Prins
2018-01-31Startup: added -cli optionPjotr Prins
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