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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 functions...Add a `required_access(...)` function to be used to check that the user has the appropriate privileges to act on the case attributes. Frederick Muriuki Muriithi
2023-10-10Update imports...Update imports after removing the authentication from GN3 Frederick Muriuki Muriithi
2023-10-10Implement some queuing logic for diffs...Queue the diffs into files - this might change somewhat once we verify whether case-attribute editing needs an approval step. Frederick Muriuki Muriithi
2023-10-10Check whether there's changes before queuing the diff.Frederick Muriuki Muriithi
2023-10-10Process Edit data. Fix bugs and typos....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 Frederick Muriuki Muriithi
2023-10-10Retrieve InbredSet Group's samples/strains...Retrieve the samples/strains that relate to a particular InbredSet group. Frederick Muriuki Muriithi
2023-10-10Retrieve InbredSet group details.Frederick Muriuki Muriithi
2023-10-10Clean-up original data, and case-attribute names...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. Frederick Muriuki Muriithi
2023-10-10Implement computing of diffsFrederick Muriuki Muriithi
2023-10-10Extract fetching of case-attribute names...Extract the fetching of case-attribute names into a separate function that can be used elsewhere. Frederick Muriuki Muriithi
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 GN3...Authentication should be handled by the auth server (gn-auth) and thus, this commit removes code handling user authentication from the GN3 system. Frederick Muriuki Muriithi
2023-10-06pylint: fix variable name.Frederick Muriuki Muriithi
2023-10-06Make argument mandatory...Make the `base_dir` argument mandatory to force it to be passed in from the point the function is called. Frederick Muriuki Muriithi
2023-10-06Get `CORRELATION_COMMAND` from current_app not `gn3.settings`...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`. Frederick Muriuki Muriithi
2023-10-06Provide keyword argument.Frederick Muriuki Muriithi
2023-10-06Pass in configs/settings as function arguments...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. Frederick Muriuki Muriithi
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 import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Fix C3001: Lambda expression assigned to a variable...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Remove un-necessary ellipsis...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Remove un-necessary string concatenation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Remove pylint skip...* 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> Munyoki Kilyungi
2023-09-05Replace "escape_string" with safe-query parameters...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Remove type annotations for "none_case_attrs" variables...* 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> Munyoki Kilyungi
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 editing...Currently there's a lot of duplicated code, so I need to ask how best to simplify it later zsloan
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
generated by cgit v1.2.3 (git 2.46.2) at 2024-12-04 19:12:19 +0000