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2023-01-09Add Show/Hide Columns to collections/viewzsloan
2023-01-09Add back option to search on trait page table...This was mistakenly removed when the table code was refactored a while back zsloan
2023-01-05Turn on homology track by defaultzsloan
2023-01-04auth: Add `/user-profile` endpoint...Display some details for the currently logged in user at the `/user-profile` endpoint. Frederick Muriuki Muriithi
2022-12-29auth: Redirect on login and cleanup...* wqflask/wqflask/oauth2/routes.py: remove unused imports. Add placeholder endpoint "/register-client" * wqflask/wqflask/templates/oauth2/login.html: enable redirect to specific endpoints Frederick Muriuki Muriithi
2022-12-29auth: Provide decorator to limit access to routes...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 Frederick Muriuki Muriithi
2022-12-29Implement "login" via OAuth2Frederick Muriuki Muriithi
2022-12-23Remove try/except around mapping, because it makes it hard to see proper erro...zsloan
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 path...Fix syntax error in multiline if statement zsloan
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 the...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 zsloan
2022-12-21Replace hard-coded homology source file...Remove limitation on when to show homology track zsloan
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 range...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. zsloan
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
2022-12-15Change if blocks in template to allow changing owner when an owner isn't curr...zsloan
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 ProbeSet_Dat...zsloan
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 50...zsloan
2022-12-06Use a dataset's name to fetch it's metadata...* wqflask/wqflask/views.py (show_trait_page): Use a dataset's name - from the query parameters - to fetch metadata. Munyoki Kilyungi
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 script...* 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 Frederick Muriuki Muriithi
2022-12-03jobs: Add debug UI...* 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 Frederick Muriuki Muriithi
2022-12-02correlations: display "--" whenever "lit_corr" is None...* wqflask/wqflask/correlation/show_corr_results.py: Check for `None` and display "--" in its place. Frederick Muriuki Muriithi
2022-12-02correlations: Fix description...* wqflask/wqflask/correlation/rust_correlation.py: Add `Probe_Target_Description` to the description field for "ProbeSet" traits. Frederick Muriuki Muriithi
2022-12-02correlations: Format `sample_r` value correctly....* wqflask/wqflask/correlation/show_corr_results.py: Use scientific notation with 2 decimal places Frederick Muriuki Muriithi
2022-12-02correlation: Remove unused argument...* 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. Frederick Muriuki Muriithi
2022-12-01Return Chr and Mb separately for phenotype /traits API requestzsloan
2022-12-01Fix Exception that's raised when query_sql returns None...* wqflask/base/data_set/dataset.py: Delete itertools, DictCursor. (DataSet.get_accession_id): Handle a case where query_sql returns a None value. Munyoki Kilyungi
2022-12-01Reproduce ValueError when query_sql returns None...* wqflask/tests/unit/base/test_data_set.py (TestDatasetAccessionId): New test cases. Munyoki Kilyungi
2022-12-01Delete complicated unmaintainable test-cases marked for skipping...* wqflask/tests/unit/base/test_data_set.py (TestDataSetTypes) [test_set_dataset_key_mrna, test_set_dataset_key_pheno, test_set_dataset_geno]: Delete. Munyoki Kilyungi
2022-12-01Change API Phenotype query to get other fields, including Locus positionzsloan
2022-12-01Variety of changes to basic stats figures...- Left-aligned bar-chart title - Changed y-axis label for Violin Plot to 'Density' - Always display modebar options - Increase font size for y axis label for Violin Plot zsloan
2022-12-01Prevent error when user account doesn't have an email address (which is curre...zsloan
2022-12-01Fix group-management URLzsloan
2022-12-01Remove min-width for trait page main divzsloan
2022-12-01Increase width of email/password inputs on login page + change some textzsloan
2022-12-01Add line-break below probability plotzsloan
2022-11-30Remove box plot (violin plot is enough)zsloan
2022-11-30Remove check for shortnames/fullnames in probeset metadata query...Some rows in InfoFiles have NULL values thereby causing an exception to be raised. All InfoFiles.DB_Name are unique. * wqflask/base/data_set/dataset.py (DataSet.get_accession_id): Remove shortname/fullname check in query. Munyoki Kilyungi