| Age | Commit message (Expand) | Author |
|---|
| 2023-01-20 | oauth2: Revoke token on logout...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.
| Frederick Muriuki Muriithi |
| 2023-01-19 | Replace angle brackets in trait descriptions for correlation results, since p... | zsloan |
| 2023-01-19 | oauth2: Implement user registration. | Frederick Muriuki Muriithi |
| 2023-01-19 | Feature/toggle switch caching (#762)...* add optional use cache checkbox
* add check for use_cache | Alexander Kabui |
| 2023-01-12 | Add BXD-NIA-AD to list of BXD_GROUP_EXCEPTIONS (so the correct options show u... | zsloan |
| 2023-01-12 | Revert "bug: use stderr in case of job errors"...This reverts commit 4666392bbc34e693f21895ccb62abb816ff95874.
| Frederick Muriuki Muriithi |
| 2023-01-12 | mechanical-rob: use new file(s) for correlation correctness...* 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.
| Frederick Muriuki Muriithi |
| 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...This was mistakenly removed when the table code was refactored a while back
| zsloan |
| 2023-01-05 | Turn on homology track by default | zsloan |
| 2023-01-04 | auth: Add `/user-profile` endpoint...Display some details for the currently logged in user at the
`/user-profile` endpoint.
| Frederick Muriuki Muriithi |
| 2022-12-29 | auth: 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 |
| 2022-12-29 | auth: 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 |
| 2022-12-29 | Implement "login" via OAuth2 | Frederick Muriuki Muriithi |
| 2022-12-23 | Remove try/except around mapping, because it makes it hard to see proper erro... | zsloan |
| 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...Fix syntax error in multiline if statement
| zsloan |
| 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...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 |
| 2022-12-21 | Replace hard-coded homology source file...Remove limitation on when to show homology track
| zsloan |
| 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...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 |
| 2022-12-21 | 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 |
| 2022-12-15 | Change if blocks in template to allow changing owner when an owner isn't curr... | zsloan |
| 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 ProbeSet_Dat... | zsloan |
| 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 50... | zsloan |
| 2022-12-06 | Use 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 |
| 2022-12-05 | 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...* 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 |
| 2022-12-03 | jobs: 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 |
| 2022-12-02 | correlations: display "--" whenever "lit_corr" is None...* wqflask/wqflask/correlation/show_corr_results.py: Check for `None`
and display "--" in its place.
| Frederick Muriuki Muriithi |
| 2022-12-02 | correlations: Fix description...* wqflask/wqflask/correlation/rust_correlation.py: Add
`Probe_Target_Description` to the description field for "ProbeSet"
traits.
| Frederick Muriuki Muriithi |
| 2022-12-02 | correlations: Format `sample_r` value correctly....* wqflask/wqflask/correlation/show_corr_results.py: Use scientific
notation with 2 decimal places
| Frederick Muriuki Muriithi |
| 2022-12-02 | correlation: 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 |
| 2022-12-01 | Return Chr and Mb separately for phenotype /traits API request | zsloan |
| 2022-12-01 | Fix Exception that's raised when query_sql returns None...* 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 |
| 2022-12-01 | Reproduce ValueError when query_sql returns None...* wqflask/tests/unit/base/test_data_set.py (TestDatasetAccessionId):
New test cases.
| Munyoki Kilyungi |
| 2022-12-01 | Delete 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 |
| 2022-12-01 | Change API Phenotype query to get other fields, including Locus position | zsloan |
