| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-01-20 | oauth2: Revoke token on logout | Frederick 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. | |||
| 2023-01-19 | Replace angle brackets in trait descriptions for correlation results, since ↵ | zsloan | |
| previously it wasn't showing some e-mail addresses (in brackets) | |||
| 2023-01-19 | oauth2: Implement user registration. | Frederick Muriuki Muriithi | |
| 2023-01-19 | Feature/toggle switch caching (#762) | Alexander Kabui | |
| * add optional use cache checkbox * add check for use_cache | |||
| 2023-01-12 | Add BXD-NIA-AD to list of BXD_GROUP_EXCEPTIONS (so the correct options show ↵ | zsloan | |
| up in correlation drop-down) | |||
| 2023-01-12 | Revert "bug: use stderr in case of job errors" | Frederick Muriuki Muriithi | |
| This reverts commit 4666392bbc34e693f21895ccb62abb816ff95874. | |||
| 2023-01-12 | mechanical-rob: use new file(s) for correlation correctness | Frederick 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. | |||
| 2023-01-12 | bug: use stderr in case of job errors | Frederick Muriuki Muriithi | |
| 2023-01-09 | Add Show/Hide Columns to collections/view | zsloan | |
| 2023-01-09 | Add back option to search on trait page table | zsloan | |
| This was mistakenly removed when the table code was refactored a while back | |||
| 2023-01-05 | Turn on homology track by default | zsloan | |
| 2023-01-04 | auth: Add `/user-profile` endpoint | Frederick Muriuki Muriithi | |
| Display some details for the currently logged in user at the `/user-profile` endpoint. | |||
| 2022-12-29 | auth: Redirect on login and cleanup | Frederick 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 | |||
| 2022-12-29 | auth: Provide decorator to limit access to routes | Frederick 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 | |||
| 2022-12-29 | Implement "login" via OAuth2 | Frederick Muriuki Muriithi | |
| 2022-12-23 | Remove try/except around mapping, because it makes it hard to see proper ↵ | zsloan | |
| error logs | |||
| 2022-12-23 | No tracking: remove revolvermaps | Pjotr Prins | |
| 2022-12-21 | Remove unnecessary if statement from drawHomologyBand | zsloan | |
| 2022-12-21 | Fix logic for filtering homology data | zsloan | |
| 2022-12-21 | Make homology track display directional arrows based on query strand | zsloan | |
| 2022-12-21 | Fix homology source file path | zsloan | |
| Fix syntax error in multiline if statement | |||
| 2022-12-21 | Replace a couple other instances of hg38 with query | zsloan | |
| 2022-12-21 | Substitute mm10/hg38 with ref/source in display_mapping_results.py | zsloan | |
| 2022-12-21 | Change homology logic to include lines that start/end outside of the | zsloan | |
| 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 | |||
| 2022-12-21 | Replace hard-coded homology source file | zsloan | |
| Remove limitation on when to show homology track | |||
| 2022-12-21 | Add code drawing homology band in mapping figure | zsloan | |
| 2022-12-21 | Add showHomology parameter to mapping endpoint | zsloan | |
| 2022-12-21 | Add code loading contents of homology file for given mb range | zsloan | |
| 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. | |||
| 2022-12-21 | Add homology band option to run_mapping.py | zsloan | |
| 2022-12-21 | Add homology band options to mapping template | zsloan | |
| 2022-12-15 | Add BXD-NIA-AD to list of BXD-equivalent groups in display_mapping_results.py | zsloan | |
| 2022-12-15 | Fix bug where changing a resource owner throws an error due to users without ↵ | zsloan | |
| email_addresses (can happen for orcid/github users currently) | |||
| 2022-12-15 | Change if blocks in template to allow changing owner when an owner isn't ↵ | zsloan | |
| currently set | |||
| 2022-12-14 | Add description to REST API /traits output for phenotypes | zsloan | |
| 2022-12-13 | Change default text_dir to TEXTDIR, since that points to the GN1 ↵ | zsloan | |
| ProbeSet_DataMatrix files | |||
| 2022-12-13 | add check for file in web/ProbeSetFreeze_DataMatrix folder (#758) | Alexander Kabui | |
| 2022-12-12 | Change 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 | |||
| 2022-12-06 | Use a dataset's name to fetch it's metadata | Munyoki Kilyungi | |
| * wqflask/wqflask/views.py (show_trait_page): Use a dataset's name - from the query parameters - to fetch metadata. | |||
| 2022-12-05 | Put metadata fetching for show_trait_page in try/except to get it working again | zsloan | |
| 2022-12-05 | scripts: add GN2 results parsing to parser script | Frederick 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 | |||
| 2022-12-03 | jobs: Add debug UI | Frederick 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 | |||
| 2022-12-02 | correlations: display "--" whenever "lit_corr" is None | Frederick Muriuki Muriithi | |
| * wqflask/wqflask/correlation/show_corr_results.py: Check for `None` and display "--" in its place. | |||
| 2022-12-02 | correlations: Fix description | Frederick Muriuki Muriithi | |
| * wqflask/wqflask/correlation/rust_correlation.py: Add `Probe_Target_Description` to the description field for "ProbeSet" traits. | |||
| 2022-12-02 | correlations: Format `sample_r` value correctly. | Frederick Muriuki Muriithi | |
| * wqflask/wqflask/correlation/show_corr_results.py: Use scientific notation with 2 decimal places | |||
| 2022-12-02 | correlation: Remove unused argument | Frederick 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. | |||
| 2022-12-01 | Return Chr and Mb separately for phenotype /traits API request | zsloan | |
| 2022-12-01 | Fix Exception that's raised when query_sql returns None | Munyoki Kilyungi | |
| * wqflask/base/data_set/dataset.py: Delete itertools, DictCursor. (DataSet.get_accession_id): Handle a case where query_sql returns a None value. | |||
| 2022-12-01 | Reproduce ValueError when query_sql returns None | Munyoki Kilyungi | |
| * wqflask/tests/unit/base/test_data_set.py (TestDatasetAccessionId): New test cases. | |||
| 2022-12-01 | Delete complicated unmaintainable test-cases marked for skipping | Munyoki 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. | |||
| 2022-12-01 | Change API Phenotype query to get other fields, including Locus position | zsloan | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
| aboutsummaryrefslogtreecommitdiff |