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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
2023-01-09Add 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
2022-12-23Remove 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
2022-12-15Fix bug where changing a resource owner throws an error due to users without ↵zsloan
email_addresses (can happen for orcid/github users currently)
2022-12-15Change if blocks in template to allow changing owner when an owner isn't ↵zsloan
currently set
2022-12-14Add description to REST API /traits output for phenotypeszsloan
2022-12-13Change default text_dir to TEXTDIR, since that points to the GN1 ↵zsloan
ProbeSet_DataMatrix files
2022-12-13add check for file in web/ProbeSetFreeze_DataMatrix folder (#758)Alexander Kabui
2022-12-12Change logic in compute_correlation_rust so that it doesn't re-run the top ↵zsloan
500 correlations for sample correlations of non-probeset traits (which it was previously doing and caused many wrong results
2022-12-06Use a dataset's name to fetch it's metadataMunyoki Kilyungi
* wqflask/wqflask/views.py (show_trait_page): Use a dataset's name - from the query parameters - to fetch metadata.
2022-12-05Put metadata fetching for show_trait_page in try/except to get it working againzsloan
2022-12-05scripts: add GN2 results parsing to parser scriptFrederick Muriuki Muriithi
* wqflask/scripts/parse_corr_gn1_results_to_csv.py: Rename script * wqflask/scripts/parse_corr_html_results_to_csv.py: * Use argparse to parse CLI arguments * Add parsing for GN2 results
2022-12-03jobs: Add debug UIFrederick Muriuki Muriithi
* wqflask/scripts/run_external.py: Save the actual return code * wqflask/wqflask/__init__.py: Use new jobs blueprint * wqflask/wqflask/api/jobs.py: Add new jobs debug route * wqflask/wqflask/templates/jobs/debug.html: new template for when job is found * wqflask/wqflask/templates/jobs/no-such-job.html: new template for when the job is not found
2022-12-02correlations: display "--" whenever "lit_corr" is NoneFrederick Muriuki Muriithi
* wqflask/wqflask/correlation/show_corr_results.py: Check for `None` and display "--" in its place.
2022-12-02correlations: Fix descriptionFrederick Muriuki Muriithi
* wqflask/wqflask/correlation/rust_correlation.py: Add `Probe_Target_Description` to the description field for "ProbeSet" traits.
2022-12-02correlations: Format `sample_r` value correctly.Frederick Muriuki Muriithi
* wqflask/wqflask/correlation/show_corr_results.py: Use scientific notation with 2 decimal places
2022-12-02correlation: Remove unused argumentFrederick Muriuki Muriithi
* wqflask/wqflask/correlation/rust_correlation.py: The `get_sample_corr_data` function no longer has the `all_samples` parameter, thus passing the argument leads to a failure. This commit removes the argument from the call.
2022-12-01Return Chr and Mb separately for phenotype /traits API requestzsloan
2022-12-01Fix Exception that's raised when query_sql returns NoneMunyoki Kilyungi
* wqflask/base/data_set/dataset.py: Delete itertools, DictCursor. (DataSet.get_accession_id): Handle a case where query_sql returns a None value.
2022-12-01Reproduce ValueError when query_sql returns NoneMunyoki Kilyungi
* wqflask/tests/unit/base/test_data_set.py (TestDatasetAccessionId): New test cases.
2022-12-01Delete complicated unmaintainable test-cases marked for skippingMunyoki Kilyungi
* wqflask/tests/unit/base/test_data_set.py (TestDataSetTypes) [test_set_dataset_key_mrna, test_set_dataset_key_pheno, test_set_dataset_geno]: Delete.
2022-12-01Change API Phenotype query to get other fields, including Locus positionzsloan