aboutsummaryrefslogtreecommitdiff
AgeCommit message (Expand)Author
2023-10-27Update RDF prefixes.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-26Fix errors caught by mypy.Frederick Muriuki Muriithi
2023-10-26case-attribute: Fix linting errors.Frederick Muriuki Muriithi
2023-10-25Update __pk__Frederick Muriuki Muriithi
2023-10-25case-attribute: Implement __apply_diff__•••Enable the "apply diff" feature which actually makes changes to the database by applying the given diff. Frederick Muriuki Muriithi
2023-10-25case-attribute: Bug: List ALL case-attribute values•••Fix bug where only one case-attribute value was returned. Frederick Muriuki Muriithi
2023-10-24case-attribute: use isoformat() for datetime objects.Frederick Muriuki Muriithi
2023-10-23case-attribute: View case attribute diffFrederick Muriuki Muriithi
2023-10-19CaseAttribute: change URL, Create diff dir, fix diff•••* Change the URL for listing an inbredset group's case-attribute diffs * Create the diff directory if it does not exist * Add `filename` to the output sent to the browser Frederick Muriuki Muriithi
2023-10-19Handle 404 error(s) at top level.Frederick Muriuki Muriithi
2023-10-12CaseAttributes: List diffs under review•••List diffs under review for a given InbredSet. Regenerate any diff files that might be deleted while still under review. Frederick Muriuki Muriithi
2023-10-12CaseAttribute: Bug: Fix bugs with rejecting diffs.Frederick Muriuki Muriithi
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 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
2023-09-05Trigger CI build•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Trigger CI build•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Update instructions on how to run pylint•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Add pylint: disable=W0402•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
generated by cgit v1.2.3 (git 2.47.1) at 2025-02-28 04:24:10 +0000