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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>
2025-04-08Fix failing test.Frederick Muriuki Muriithi
2025-03-04Revert "test: Add unit tests for fibonacci function in rqtl2 module"Munyoki Kilyungi
This reverts commit 9bad745abd94fd0eeb0b0dc6aba0d6a74db33f81.
2025-03-04Revert "docs: Add module and function docstrings for unit tests of fibonacci ↵Munyoki Kilyungi
function". This reverts commit 6a76e302f11c0a0aa0bc0ac8487ad250f8afb9bb.
2025-03-04docs: Add module and function docstrings for unit tests of fibonacci functionMunyoki Kilyungi (aider)
2025-03-04test: Add unit tests for fibonacci function in rqtl2 moduleMunyoki Kilyungi (aider)
2025-02-28Fix linting errors.Frederick Muriuki Muriithi
2025-02-10feat: Add LMDB sample data retrieval API endpoint with testsMunyoki Kilyungi (aider)
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-07refactor: Add rqtl2 default method and update unittests.Alexander_Kabui
2025-02-06Add test assertions for writing data to csv.Alexander_Kabui
2025-02-06feat: Add unittests for rqtl2 computations.Alexander_Kabui
2025-01-27Delete un-used database_connection test.Munyoki Kilyungi
* tests/unit/test_db_utils.py (test_database_connection): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-01-26Skip test that checks working of MySQLdb rather than GN3.Frederick Muriuki Muriithi
2024-11-11Allow extra database connection options on URIFrederick Muriuki Muriithi
Update the database URI parsing to allow setting of extra connection option on the URI string.
2024-10-18refactor: replace gn3.auth.db with gn3.sqlite_db_utils and drop all refs to ↵John Nduli
gn3.auth
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>
2024-10-14Add NCBI test turtle data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Use pathlib to fetch the directory path for tests.Munyoki Kilyungi
* tests/fixtures/rdf.py: import pathlib. (rdf_setup): Use pathlib to get the dir name for the tests folder. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Fix pylint failure.Munyoki Kilyungi
* tests/fixtures/rdf.py (rdf_setup): Fix C0301. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02feat: cleaner handling of virtuoso processJohn Nduli
2024-10-02Fix typo in comments.Munyoki Kilyungi
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>
2024-10-02Add virtuoso ini file to be used during testing.Munyoki Kilyungi
tests/fixtures/virtuoso.py: New file. 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
2024-09-27Skip failing test.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>
2024-09-23Handle missing GN3_SECRETS for CI testing.Munyoki Kilyungi
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>
2024-09-23Load GN3_SECRETS after loading GN3_CONF settings.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-11-22 07:23:47 +0000