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2023-10-10Remove authentication from GN3Frederick Muriuki Muriithi
Authentication should be handled by the auth server (gn-auth) and thus, this commit removes code handling user authentication from the GN3 system.
2023-10-06pylint: fix variable name.Frederick Muriuki Muriithi
2023-10-06Make argument mandatoryFrederick Muriuki Muriithi
Make the `base_dir` argument mandatory to force it to be passed in from the point the function is called.
2023-10-06Get `CORRELATION_COMMAND` from current_app not `gn3.settings`Frederick Muriuki Muriithi
The default settings in `gn3.settings` are meant to be overridden thus the code should not be importing the setting from there, rather, the code should get its configurations settings from `flask.current_app.config`.
2023-10-06Provide keyword argument.Frederick Muriuki Muriithi
2023-10-06Pass in configs/settings as function argumentsFrederick Muriuki Muriithi
To avoid reliance of `flask.current_app.config` or on `gn3.settings` modules globally, this commit passes in the appropriate configurations as arguments to the relevant functions.
2023-10-06Settings: Add note to discourage importing directly from defaultsFrederick Muriuki Muriithi
2023-09-21Fix query in update_cross_referencezsloan
2023-09-05Trigger CI buildMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Trigger CI buildMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Update instructions on how to run pylintMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Add pylint: disable=W0402Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove unused importMunyoki Kilyungi
* setup_commands/run_tests.py: Delete sys. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Ignore linting version control files and migrations folderMunyoki Kilyungi
* .pylintrc: Add VCS and migrations to ignore and ignore-paths respectively. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Delete un-used importMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Fix C3001: Lambda expression assigned to a variableMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove un-necessary ellipsisMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove un-necessary string concatenationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove pylint skipMunyoki 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>
2023-09-05Remove unused importMunyoki Kilyungi
* tests/unit/test_file_utils.py: Delete gn3.cache_ipfs_file Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Replace "escape_string" with safe-query parametersMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Delete IPFS testsMunyoki 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>
2023-09-05Remove type annotations for "none_case_attrs" variablesMunyoki 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>
2023-08-24Change get_pheno_csv_sample_data to use group ID instead of phenotype IDzsloan
2023-08-18Commit on success, rollback on error.Frederick Muriuki Muriithi
2023-08-17Fix query for fetching DataId when inserting ProbeSet datazsloan
2023-08-17Fix a couple remaining issues with function parameterszsloan
2023-08-17Fix tests to work with changeszsloan
2023-08-17Combine pheno/mrna update functions + some other fixeszsloan
2023-08-17Fix queries for fetching group nameszsloan
2023-08-17Fix fetch_trait query for phenotypeszsloan
2023-08-17Fix a few misnamed tables in mrna delete/insert functionszsloan
2023-08-17Implement ProbeSet sample data editingzsloan
Currently there's a lot of duplicated code, so I need to ask how best to simplify it later
2023-08-17Fix probeset sample data and CSV sample data functionszsloan
2023-08-17Fix query for retrieving mrna dataset group namezsloan
2023-08-17Fix get_mrna_sample_data queryzsloan
2023-08-17Fix mrna group name queryzsloan
2023-08-17Remove Id select from probeset metadata query, since it's included in colszsloan
2023-08-17Add function for retrieving mRNA Assay group namezsloan
2023-08-17Make several sample_data fetching functions specific to phenotype or mrna ↵zsloan
assay resources, and change their naming accordingly
2023-08-14auth: Remove documentationFrederick 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.
2023-08-04Remove unused importFrederick Muriuki Muriithi
2023-08-04Remove tests for deleted function.Frederick Muriuki Muriithi
2023-08-04Remove the ORM-dependent `update` function.Frederick Muriuki Muriithi
2023-08-02Add deprecation notice to ORM-dependent `update` functionFrederick Muriuki Muriithi
Add a deprecation notice to discourage other devs from using the deprecated `update` function.
2023-08-02Remove ORM-dependent `insert` functionFrederick Muriuki Muriithi
Remove the object-relation-mapping dependent `insert` function to prevent it being used in the code down the line.
2023-08-02Remove ORM-dependent `fetchall` and `fetchone` functionsFrederick Muriuki Muriithi
Remove Object-Relational Mapping dependent function, `fetchall` and `fetchone` so as to prevent theirs use in the code moving forward.
2023-08-02Integrate Temp traits to AuthFrederick 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.
2023-08-02Use correct variableFrederick 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.
2023-08-02Fix module name.Frederick Muriuki Muriithi
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-30 10:49:54 +0000