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2023-01-23init file_storageAlexander_Kabui
2023-01-23init query for last modificationAlexander_Kabui
2023-01-23fetch id for a given probesetAlexander_Kabui
2023-01-23fetch all strains for a given datasetAlexander_Kabui
2023-01-23fetch all strain namesAlexander_Kabui
2023-01-23init fetch all probeset datasetsAlexander_Kabui
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
2022-12-21Change homology logic to include lines that start/end outside of thezsloan
given mb range This is to avoid a situation where a user zooms in and a bar should encompass the whole area but isn't displayed (because its start/end don't both fall within the given Mb range) This commit also renames mm10/hg38 to ref/query to be more generic
2022-12-21Replace hard-coded homology source filezsloan
Remove limitation on when to show homology track
2022-12-21Add code drawing homology band in mapping figurezsloan
2022-12-21Add showHomology parameter to mapping endpointzsloan
2022-12-21Add code loading contents of homology file for given mb rangezsloan
Currently this hard-codes the source file. Not sure how we want to store this data yet so just using a CSV file for now.
2022-12-21Add homology band option to run_mapping.pyzsloan
2022-12-21Add homology band options to mapping templatezsloan
2022-12-15Add BXD-NIA-AD to list of BXD-equivalent groups in display_mapping_results.pyzsloan