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2023-10-12CaseAttributes: Bug: Fix privileges checkFrederick Muriuki Muriithi
2023-10-12CaseAttribute: Bug: Fix query - include time_stamp.Frederick Muriuki Muriithi
2023-10-12CaseAttribute: Encode/Decode to/from JSON appropriately.Frederick Muriuki Muriithi
2023-10-12Remove unnecessary clutter.Frederick Muriuki Muriithi
2023-10-12CaseAttribute: Bug: enumerate the privileges correctly.Frederick Muriuki Muriithi
2023-10-11CaseAttribute: Reject a diff (delete file).Frederick Muriuki Muriithi
2023-10-11CaseAttribute: Load diff from file.Frederick Muriuki Muriithi
2023-10-11CaseAttribute: Save diff to db at queue time.Frederick Muriuki Muriithi
2023-10-11CaseAttribute: Save the diff to the database.Frederick Muriuki Muriithi
2023-10-10Do authorisation checks for relevant functionsFrederick Muriuki Muriithi
Add a `required_access(...)` function to be used to check that the user has the appropriate privileges to act on the case attributes.
2023-10-10Update importsFrederick Muriuki Muriithi
Update imports after removing the authentication from GN3
2023-10-10Implement some queuing logic for diffsFrederick Muriuki Muriithi
Queue the diffs into files - this might change somewhat once we verify whether case-attribute editing needs an approval step.
2023-10-10Check whether there's changes before queuing the diff.Frederick Muriuki Muriithi
2023-10-10Process Edit data. Fix bugs and typos.Frederick Muriuki Muriithi
Process the edit data into a CSV form for diff generation. Fix bug in: * processing of original data into a CSV * variable passed to DictWriter * arguments to functions
2023-10-10Retrieve InbredSet Group's samples/strainsFrederick Muriuki Muriithi
Retrieve the samples/strains that relate to a particular InbredSet group.
2023-10-10Retrieve InbredSet group details.Frederick Muriuki Muriithi
2023-10-10Clean-up original data, and case-attribute namesFrederick Muriuki Muriithi
For diff-generation purposes, this commit processes the data into a form that is useful for generation of the CSV files to be used for the diffs.
2023-10-10Implement computing of diffsFrederick Muriuki Muriithi
2023-10-10Extract fetching of case-attribute namesFrederick Muriuki Muriithi
Extract the fetching of case-attribute names into a separate function that can be used elsewhere.
2023-10-10Rename function: Make it clearer what function does.Frederick Muriuki Muriithi
2023-10-10Bug: Fix missing cursor object.Frederick Muriuki Muriithi
2023-10-10Add scaffolding for add/delete endpoints.Frederick Muriuki Muriithi
2023-10-10Add scaffolding for case-attribute editing logic.Frederick Muriuki Muriithi
2023-10-10Extract fetching of case-attributes by InbredSetIdFrederick Muriuki Muriithi
2023-10-10Editing: Retrieve case-attribute values for an InbredSet group.Frederick Muriuki Muriithi
2023-10-10Editing: Retrieve case attributes by the related InbredSetFrederick Muriuki Muriithi
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
2023-09-05Delete 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>
2023-09-05Replace "escape_string" with safe-query parametersMunyoki Kilyungi
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
2023-08-17Combine 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
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 13:39:44 +0000