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2023-01-30oauth2: split out code into separate modulesFrederick Muriuki Muriithi
To ease development and maintenance, split the code into separate modules, nesting the blueprints for a more modular feel.
2023-01-28mechanical-rob: unescape html entities.Frederick Muriuki Muriithi
2023-01-28oauth2: List the user roles. View a particular role's details.Frederick Muriuki Muriithi
2023-01-26Dump metadata in addition to sample data.Munyoki Kilyungi
* scripts/sampledata: Dump metadata in addition to data.
2023-01-26oauth2: UI: Rework user dashboard UIFrederick Muriuki Muriithi
Separate the roles, resources and group information from the overview page.
2023-01-25mechanical-rob: corrs: Activate tests. Print out whitespaceFrederick Muriuki Muriithi
* Activate the correlation correctness tests * Print out whitespace characters in such a form that allows visual comparison of differences to help with fixing issues caught by tests.
2023-01-25mechanical-rob: move newlineFrederick Muriuki Muriithi
2023-01-25mechanical-rob: Fix bugs with corrs testFrederick Muriuki Muriithi
* Replace CRLF in html output with newline to prevent equality comparisons from failing if that's the only difference. * Only include failures that have actual content: filter out empty failure items * Print out an extra newline on completion of checks
2023-01-24mechanical-rob: update corrs tests and clean up dataFrederick Muriuki Muriithi
2023-01-24scripts: Provide help info for script.Frederick Muriuki Muriithi
2023-01-24correlations: Escape strings for htmlFrederick Muriuki Muriithi
Improves upon commit 63aff5ca22cfb5caaa38ac1d737afa48fc8dbf02
2023-01-24mechanical-rob: eliminate extraneous spaces before comparisonsFrederick Muriuki Muriithi
2023-01-23oauth2: create groupFrederick Muriuki Muriithi
Enable creation of a new group.
2023-01-23oauth2: Retain email input, and "next uri" on errorFrederick Muriuki Muriithi
Retain the "next uri" and the email the user had input in the case of an error, so that the user has the chance to correct their input, and still get to the uri they originally intended to (on success).
2023-01-21oauth2: Cleanup fetching of roles and groups. Update template.Frederick Muriuki Muriithi
2023-01-20Make dump script faster by using concurrency moduleMunyoki Kilyungi
2023-01-20Dump all sample data into a given directoryMunyoki Kilyungi
* scripts/sampledata.py: Import gen_dropdown_json. (main): Dump all the sample data from all the datasets into a given directory.
2023-01-20Return a trait's display name if the name is non-existentMunyoki Kilyungi
* scripts/sampledata.py (fetch_all_traits): Should the name of a trait not exists, e.g. in probeset data, return it's display name.
2023-01-20Update demo to dump entire dataset for BXDPublishMunyoki Kilyungi
* scripts/sampledata.py: Import os and sys. <__name__>: Add demo to dump "BXDPublish" dataset.
2023-01-20Remove hard-coded valuesMunyoki Kilyungi
* scripts/sampledata.py (dump_sample_data): Remove hard-coded values for trait_id and dataset_name.
2023-01-20Fix typoMunyoki Kilyungi
2023-01-20Add example that demos dumping data from an entire datasetMunyoki Kilyungi
2023-01-20Add a function that fetches all the traits given the right paramsMunyoki Kilyungi
* scripts/sampledata.py (fetch_all_traits): New function.
2023-01-20Create script to dumple sample data given the dataset and trait idMunyoki Kilyungi
* scripts/sampledata.py: New file.
2023-01-20oauth2: Add user-profile template and dummy endpointsFrederick Muriuki Muriithi
* wqflask/wqflask/oauth2/routes.py: add some dummy endpoints to be fleshed out * wqflask/wqflask/templates/oauth2/view-user.html: Add missing template for the /user-profile endpoint
2023-01-20oauth2: Revoke token on logoutFrederick Muriuki Muriithi
If a user logs out of the session, and their token is not revoked, if their token were to leak somehow, then an attacker could use it before it expired. Explicit revocation of the token helps avoid that.
2023-01-19Replace angle brackets in trait descriptions for correlation results, since ↵zsloan
previously it wasn't showing some e-mail addresses (in brackets)
2023-01-19oauth2: Implement user registration.Frederick Muriuki Muriithi
2023-01-19Feature/toggle switch caching (#762)Alexander Kabui
* add optional use cache checkbox * add check for use_cache
2023-01-12Add BXD-NIA-AD to list of BXD_GROUP_EXCEPTIONS (so the correct options show ↵zsloan
up in correlation drop-down)
2023-01-12Revert "bug: use stderr in case of job errors"Frederick Muriuki Muriithi
This reverts commit 4666392bbc34e693f21895ccb62abb816ff95874.
2023-01-12mechanical-rob: use new file(s) for correlation correctnessFrederick Muriuki Muriithi
* test/requests/correlation_results_text_files/BXD_10710_vs_BXDPublish.csv new sample file for testing. * test/requests/correlation_tests.py: update test code to use new sample files * wqflask/wqflask/correlation/show_corr_results.py: Fix minor issues exposed by tests.
2023-01-12bug: use stderr in case of job errorsFrederick Muriuki Muriithi
2023-01-12mechanical-rob: deactivate correctness tests for now.Frederick Muriuki Muriithi
2023-01-09Add Show/Hide Columns to collections/viewzsloan
2023-01-09Add back option to search on trait page tablezsloan
This was mistakenly removed when the table code was refactored a while back
2023-01-05Turn on homology track by defaultzsloan
2023-01-04auth: Add `/user-profile` endpointFrederick Muriuki Muriithi
Display some details for the currently logged in user at the `/user-profile` endpoint.
2022-12-29auth: Redirect on login and cleanupFrederick Muriuki Muriithi
* wqflask/wqflask/oauth2/routes.py: remove unused imports. Add placeholder endpoint "/register-client" * wqflask/wqflask/templates/oauth2/login.html: enable redirect to specific endpoints
2022-12-29auth: Provide decorator to limit access to routesFrederick Muriuki Muriithi
Define the new `oauth2_required` decorator that checks for the existence and validity of a token before allowing access to the given endpoint. Move the `user_logged_in` check to the `checks.py` module. * wqflask/wqflask/oauth2/checks.py: new file * wqflask/wqflask/oauth2/routes.py: import new decorator
2022-12-29Implement "login" via OAuth2Frederick Muriuki Muriithi
2022-12-29README: Update invocation command for pytestFrederick Muriuki Muriithi
Invoke pytest via python so as to ensure that all the relevant modules are found when running tests.
2022-12-23Remove try/except around mapping, because it makes it hard to see proper ↵zsloan
error logs
2022-12-23No tracking: remove revolvermapsPjotr Prins
2022-12-21Remove unnecessary if statement from drawHomologyBandzsloan
2022-12-21Fix logic for filtering homology datazsloan
2022-12-21Make homology track display directional arrows based on query strandzsloan
2022-12-21Fix homology source file pathzsloan
Fix syntax error in multiline if statement
2022-12-21Replace a couple other instances of hg38 with queryzsloan
2022-12-21Substitute mm10/hg38 with ref/source in display_mapping_results.pyzsloan