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2025-08-06Change order of query parameters.Frederick Muriuki Muriithi
2025-07-07Rename dict key.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add unit tests for get_changes.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Fix mypy errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Fix pylint errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Fix pylint errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete "update_case_attribute"Munyoki Kilyungi
To update an attribute, you can use the "apply_change" function instead. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add function for adding a change.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add function for viewing a single diff change.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add test cases for "update_case_attributes."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Store edit status in enum class.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Return the case_attr id after queuing.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete "approve_case_attribute."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete "reject_case_attribute."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete "insert_case_attribute_audit."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete "get_unreviewed_diffs."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Delete "get_case_attributes."Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-07Add test case for queue_edit.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-22Fix pylint errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-22Add test case for deleting wiki data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-28Fix linting errors.Frederick Muriuki Muriithi
2024-10-14Replace CONSTRUCT with SELECT for fetching RIF NCBI entries.Munyoki Kilyungi
* gn3/db/rdf/wiki.py: Delete datetime import. Import sparql_query. [RIF_CONTEXT]: Delete. (get_rif_entries_by_symbol): Replace CONSTRUCT with SELECT. * tests/unit/db/rdf/test_wiki.py (test_get_rif_entries_by_symbol): Update tests. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Replace species' shortName with it's full name in NCBI test data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Remove "@id" from NCBI test data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Update the NCBI expected test data context.Munyoki Kilyungi
* tests/unit/db/rdf/data.py: [LPL_RIF_ENTRIES]: Update "@context". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Add function for fetching NCBI data.Munyoki Kilyungi
* gn3/db/rdf/wiki.py: Import datetime. [RIF_CONTEXT]: New global variable defining the json-ld context for NCBI rif data. (get_rif_entries_by_symbol): New function. * tests/unit/db/rdf/data.py: New file containing expected NCBI test data. * tests/unit/db/rdf/test_wiki.py (test_update_wiki_comment): New test case. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Spin up a local virtuoso instance to run RDF tests against.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Set a default password for sparql.Munyoki Kilyungi
* tests/fixtures/rdf.py: Import config. (get_sparql_auth_conf): Load GN3 config from GN3_SECRETS and GN3_CONF if the respective envs are set. Set sane defaults for sparql_conf. (rdf_setup): Remove "fxtr_app_config". * tests/unit/db/rdf/test_wiki.py (test_get_wiki_entries_by_symbol): Ditto. (test_get_comment_history): Ditto. (test_update_wiki_comment): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-28Lint: fix some linting errors.Frederick Muriuki Muriithi
2024-09-27Use existing fixture to retrieve settings.Frederick Muriuki Muriithi
2024-09-23Revert "Add pytest.mark.unit_test for all rdf test-cases."Munyoki Kilyungi
This reverts commit f6d9b0cfb842b53e8777e9918549f1ed1ee5892e. Failing tests because of how we run tests using guix. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Add pytest.mark.unit_test for all rdf test-cases.Munyoki Kilyungi
This makes sure that all the test correctly run in CD. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Fix or ignore pylint errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Remove dead comment.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Use test fixtures to set-up a test named graph.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Add RDF test cases.Munyoki Kilyungi
* pytest.ini: Add rdf pytest marker. * tests/test_data/ttl-files/test-data.ttl: New file with turtle test data for RIF editing. * tests/unit/db/rdf/test_wiki.py (test_sanitize_result): New test case. (test_get_comment_history): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-11Add test cases for wiki.__sanitize_result.Munyoki Kilyungi
* tests/unit/db/rdf/test_wiki.py (test_sanitize_result): New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove un-necessary string concatenationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Replace "escape_string" with safe-query parametersMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-17Fix tests to work with changeszsloan
2023-08-04Remove unused importFrederick Muriuki Muriithi
2023-08-04Remove tests for deleted function.Frederick Muriuki Muriithi
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.
2023-07-19Extract code dealing with ProbeSets to their own module.Frederick Muriuki Muriithi
2023-07-11Revert "Skip tests broken by Python-3.10 temporarily"Frederick Muriuki Muriithi
This reverts commit f52247c15f3694f3dd5fd0fd79c3e15376137e07.
2023-07-05Skip tests broken by Python-3.10 temporarilyFrederick Muriuki Muriithi
Skip the tests that have been broken by the migrations to Python-3.10 temporarily, until we can fix them.
2023-03-20Fix get_all_species testzsloan
2022-05-27Move sql for CRUD operations on case-attrs from gn2 to gn3BonfaceKilz
2022-05-27Move sql for modifying case-attributes from gn2 to gn3BonfaceKilz
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-11-25 12:34:17 +0000