| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-09-05 | Update instructions on how to run pylint | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Add pylint: disable=W0402 | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Remove unused import | Munyoki Kilyungi | |
| * setup_commands/run_tests.py: Delete sys. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Ignore linting version control files and migrations folder | Munyoki Kilyungi | |
| * .pylintrc: Add VCS and migrations to ignore and ignore-paths respectively. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Delete un-used import | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Fix C3001: Lambda expression assigned to a variable | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Remove un-necessary ellipsis | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Remove un-necessary string concatenation | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Remove pylint skip | Munyoki Kilyungi | |
| * gn3/auth/authentication/oauth2/models/oauth2token.py (introspect_token, check_permission): Delete "pylint: disable=[no-self-use]". R0022: Useless option value for 'disable', 'no-self-use' was moved to an optional extension, see https://pylint.pycqa.org/en/latest/whatsnew/2/2.14/summary.html#removed-checkers. * gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py (delete_authorization_code): Ditto. * tests/unit/test_heatmaps.py (test_cluster_traits): Delete "pylint: disable=R0201". R0022: Useless option value for 'disable', 'no-self-use' was moved to an optional extension, see https://pylint.pycqa.org/en/latest/whatsnew/2/2.14/summary.html#removed-checkers. * tests/unit/computations/test_partial_correlations.py (test_tissue_correlation): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Remove unused import | Munyoki Kilyungi | |
| * tests/unit/test_file_utils.py: Delete gn3.cache_ipfs_file Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Replace "escape_string" with safe-query parameters | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Delete IPFS tests | Munyoki Kilyungi | |
| * tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit, test_cache_ipfs_file_cache_miss): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Remove type annotations for "none_case_attrs" variables | Munyoki Kilyungi | |
| * gn3/db/sample_data.py (update_sample_data, delete_sample_data, insert_sample_data): Remove type hints for "none_case_attrs". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-08-24 | Change get_pheno_csv_sample_data to use group ID instead of phenotype ID | zsloan | |
| 2023-08-18 | Commit on success, rollback on error. | Frederick Muriuki Muriithi | |
| 2023-08-17 | Fix query for fetching DataId when inserting ProbeSet data | zsloan | |
| 2023-08-17 | Fix a couple remaining issues with function parameters | zsloan | |
| 2023-08-17 | Fix tests to work with changes | zsloan | |
| 2023-08-17 | Combine pheno/mrna update functions + some other fixes | zsloan | |
| 2023-08-17 | Fix queries for fetching group names | zsloan | |
| 2023-08-17 | Fix fetch_trait query for phenotypes | zsloan | |
| 2023-08-17 | Fix a few misnamed tables in mrna delete/insert functions | zsloan | |
| 2023-08-17 | Implement ProbeSet sample data editing | zsloan | |
| Currently there's a lot of duplicated code, so I need to ask how best to simplify it later | |||
| 2023-08-17 | Fix probeset sample data and CSV sample data functions | zsloan | |
| 2023-08-17 | Fix query for retrieving mrna dataset group name | zsloan | |
| 2023-08-17 | Fix get_mrna_sample_data query | zsloan | |
| 2023-08-17 | Fix mrna group name query | zsloan | |
| 2023-08-17 | Remove Id select from probeset metadata query, since it's included in cols | zsloan | |
| 2023-08-17 | Add function for retrieving mRNA Assay group name | zsloan | |
| 2023-08-17 | Make several sample_data fetching functions specific to phenotype or mrna ↵ | zsloan | |
| assay resources, and change their naming accordingly | |||
| 2023-08-14 | auth: Remove documentation | Frederick Muriuki Muriithi | |
| The authentication/authorisation stuff is being moved to a separate repository. This commit removes the documentation for how to run migrations from this repository since it has been moved over to the new repository. | |||
| 2023-08-04 | Remove unused import | Frederick Muriuki Muriithi | |
| 2023-08-04 | Remove tests for deleted function. | Frederick Muriuki Muriithi | |
| 2023-08-04 | Remove the ORM-dependent `update` function. | Frederick Muriuki Muriithi | |
| 2023-08-02 | Add deprecation notice to ORM-dependent `update` function | Frederick Muriuki Muriithi | |
| Add a deprecation notice to discourage other devs from using the deprecated `update` function. | |||
| 2023-08-02 | Remove ORM-dependent `insert` function | Frederick Muriuki Muriithi | |
| Remove the object-relation-mapping dependent `insert` function to prevent it being used in the code down the line. | |||
| 2023-08-02 | Remove ORM-dependent `fetchall` and `fetchone` functions | Frederick Muriuki Muriithi | |
| Remove Object-Relational Mapping dependent function, `fetchall` and `fetchone` so as to prevent theirs use in the code moving forward. | |||
| 2023-08-02 | Integrate Temp traits to Auth | Frederick Muriuki Muriithi | |
| Temporary traits are not saved to the database, and have no attached resource (at this time). As such, make them all simply public-read to enable access for users. This might change after more information on usage of temporary traits is collected and considered. | |||
| 2023-08-02 | Use correct variable | Frederick Muriuki Muriithi | |
| After copying the calls to assign appropriate roles to the admin in the script, I forgot to update the variable name. This commit fixes that. | |||
| 2023-08-02 | Fix module name. | Frederick Muriuki Muriithi | |
| 2023-08-02 | Assign `group-leader` role to the admin for automatic group. | Frederick Muriuki Muriithi | |
| 2023-07-31 | Fix typing issue | Frederick Muriuki Muriithi | |
| 2023-07-31 | Fix linting and typing issues. | Frederick Muriuki Muriithi | |
| 2023-07-31 | Fix bugs. Return resource without data items. | Frederick Muriuki Muriithi | |
| * Fix bugs introduced while attempting pagination. * Return resource object without attached data items. | |||
| 2023-07-31 | Paginate the resource data items. | Frederick Muriuki Muriithi | |
| 2023-07-26 | Fix variable name. | Frederick Muriuki Muriithi | |
| 2023-07-26 | Remove debug statement. | Frederick Muriuki Muriithi | |
| 2023-07-26 | Fetch `metadata_audit` trail with direct query functions. | Frederick Muriuki Muriithi | |
| 2023-07-26 | Function to create a metadata audit trail. | Frederick Muriuki Muriithi | |
| 2023-07-26 | Merge pull request #126 from BonfaceKilz/fix/pin-python-3.9 | BonfaceKilz | |
| Roll back to python 3.9 in .guix-channel | |||
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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