| Age | Commit message (Expand) | Author |
|---|
| 2024-10-02 | Spin up a local virtuoso instance to run RDF tests against....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-10-02 | Set a default password for sparql....* 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>
| Munyoki Kilyungi |
| 2024-09-28 | Lint: fix some linting errors. | Frederick Muriuki Muriithi |
| 2024-09-27 | Skip failing test. | Frederick Muriuki Muriithi |
| 2024-09-27 | Use existing fixture to retrieve settings. | Frederick Muriuki Muriithi |
| 2024-09-23 | Revert "Add pytest.mark.unit_test for all rdf test-cases."...This reverts commit f6d9b0cfb842b53e8777e9918549f1ed1ee5892e. Failing
tests because of how we run tests using guix.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Add pytest.mark.unit_test for all rdf test-cases....This makes sure that all the test correctly run in CD.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Fix or ignore pylint errors....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Remove dead comment....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Use test fixtures to set-up a test named graph....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Add RDF test cases....* 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>
| Munyoki Kilyungi |
| 2024-09-12 | Fix failing tests after merging in Pjotr's pull request. | Frederick Muriuki Muriithi |
| 2024-09-12 | rqtl_wrapper: minor fixes | Pjotr Prins |
| 2024-09-12 | Fix Rqtl test | Pjotr Prins |
| 2024-09-11 | Add test cases for wiki.__sanitize_result....* tests/unit/db/rdf/test_wiki.py (test_sanitize_result): New file.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-03 | Make pylint fixes. | Alexander_Kabui |
| 2024-09-03 | Add tests for fetching and populating references. | Alexander_Kabui |
| 2024-09-03 | Add unittests for formatting bib info. | Alexander_Kabui |
| 2024-05-27 | Pylint fixes. | Alexander_Kabui |
| 2024-05-27 | Delete llm obsolete unittests | Alexander_Kabui |
| 2024-01-17 | fix pylint errors | Alexander_Kabui |
| 2024-01-17 | temp fix:disable pylint check | Alexander_Kabui |
| 2024-01-17 | Feature/gn llm refactoring (#147)...* refactor code for processing response from fahamu client
* Add tests for gn-llm | Alexander Kabui |
| 2023-10-10 | Remove 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 |
| 2023-09-05 | Fix C3001: Lambda expression assigned to a variable...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove un-necessary string concatenation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove 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 |
| 2023-09-05 | Remove unused import...* tests/unit/test_file_utils.py: Delete gn3.cache_ipfs_file
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Replace "escape_string" with safe-query parameters...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Delete IPFS tests...* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit,
test_cache_ipfs_file_cache_miss): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-08-17 | Fix tests to work with changes | zsloan |
| 2023-08-04 | Remove unused import | Frederick Muriuki Muriithi |
| 2023-08-04 | Remove tests for deleted function. | Frederick Muriuki Muriithi |
| 2023-08-02 | Remove ORM-dependent `insert` function...Remove the object-relation-mapping dependent `insert` function to prevent it
being used in the code down the line.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Remove ORM-dependent `fetchall` and `fetchone` functions...Remove Object-Relational Mapping dependent function, `fetchall` and `fetchone`
so as to prevent theirs use in the code moving forward.
| Frederick Muriuki Muriithi |
| 2023-07-19 | Extract code dealing with ProbeSets to their own module. | Frederick Muriuki Muriithi |
| 2023-07-11 | Revert "Skip tests broken by Python-3.10 temporarily"...This reverts commit f52247c15f3694f3dd5fd0fd79c3e15376137e07.
| Frederick Muriuki Muriithi |
| 2023-07-05 | Skip tests broken by Python-3.10 temporarily...Skip the tests that have been broken by the migrations to Python-3.10
temporarily, until we can fix them.
| Frederick Muriuki Muriithi |
| 2023-07-05 | Update test: create throw-away variable...* Commit `b529c700` changes the return value to a tuple of values rather than
a single string value. Handle that in the test.
| Frederick Muriuki Muriithi |
| 2023-05-30 | Fix linting errors and failing tests...* scripts/register_sys_admin.py: fix linting error
* tests/unit/auth/fixtures/oauth2_client_fixtures.py: hash client secret in
database. The code expects it hashed in the database.
| Frederick Muriuki Muriithi |
| 2023-05-25 | Set whether resource is publicly viewable on creation | Frederick Muriuki Muriithi |
| 2023-04-25 | auth: Roles: Check for editability...Some roles should not be user-editable, and as such, we need to check before
allowing any edits on such roles. This commit makes that possible.
| Frederick Muriuki Muriithi |
| 2023-04-10 | Migrations for linking genotype files. | Frederick Muriuki Muriithi |
| 2023-04-06 | Fix linting issues | Frederick Muriuki Muriithi |
| 2023-04-06 | Remove deprecated `gn3.db_utils.database_connector` function...Remove the deprecated function and fix a myriad of bugs that arise from
removing the function.
Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
| Frederick Muriuki Muriithi |
| 2023-04-04 | Add tables to link genotype data | Frederick Muriuki Muriithi |
| 2023-03-23 | tests: Set up fixture and mock out config variable | Frederick Muriuki Muriithi |
| 2023-03-22 | auth: Remove the tables used for linking data to resources...The way data is linked to the resources needs to be reworked. This commit
removes all the existing migration scripts that created the tables formerly
used for linking data in preparation for reworking the system.
| Frederick Muriuki Muriithi |
| 2023-03-20 | Fix get_all_species test | zsloan |
| 2023-03-09 | auth: redis data: migrate data in redis...Implement the code to migrate the data from redis to SQLite.
| Frederick Muriuki Muriithi |
