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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.
2018-03-16Just undoing tabulator changes so I can push other changeszsloan
2018-03-15Changed appearance of mapping and correlation options on trait pagezsloan
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
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.
2018-03-02Added option to display selected covariates for GEMMA mappingzsloan
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
2018-02-26Merge /home/lei/gene into testingzsloan
2018-02-26Committing some in-progress changes related to loading correlation page from ↵zsloan
JSON
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.
2018-02-23update corr scatterplot interfaceLei Yan
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
2018-02-14Added 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 ↵zsloan
changes
2018-02-13Merge pull request #285 from pjotrp/testingzsloan
@zsloan: we should introduce full parameter checking and sensible defaults
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
2018-02-12Changed code parsing GEMMA output to fix issue where it wasn't getting the ↵zsloan
correct p-values
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 ↵zsloan
suddenly decided to start running it when it wasn't in the past. Switched correlation table to tabulator
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
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