| Age | Commit message (Expand) | Author |
|---|---|---|
| 2024-10-02 | Add rdf-tests after the check phase.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> HEADmain | Munyoki Kilyungi |
| 2024-10-02 | Use pathlib to fetch the directory path for tests.•••* 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> | Munyoki Kilyungi |
| 2024-10-02 | Fix pylint failure.•••* tests/fixtures/rdf.py (rdf_setup): Fix C0301. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-10-02 | feat: cleaner handling of virtuoso process | John Nduli |
| 2024-10-02 | Fix typo in comments.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-10-02 | Move sparql-auth URIs to gn3-conf in documentation.•••We want to strictly keep secrets in the secret file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-10-02 | Add all rdf-tests to GN3 CI.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 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 | Add virtuoso ini file to be used during testing.•••tests/fixtures/virtuoso.py: New file. 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 |
| 2024-09-30 | chore: pylint code fix | John Nduli |
| 2024-09-30 | feat: rollback mysql transaction when rdf insert fails | John Nduli |
| 2024-09-30 | fix: rdf and sql queries for fetching rif data•••SQL queries fail because we get bytes instead of strings which cannot be decoded. We decode results from DictCursor to fix this. For RDF, we cast `?symbol` to a string. | John Nduli |
| 2024-09-28 | Update documentation on how to run tests. | Frederick Muriuki Muriithi |
| 2024-09-28 | Lint: fix some linting errors. | Frederick Muriuki Muriithi |
| 2024-09-27 | Debug command. | Frederick Muriuki Muriithi |
| 2024-09-27 | Skip failing test. | Frederick Muriuki Muriithi |
| 2024-09-27 | Bug: Use absolute paths in place of relative paths.•••Similar issue to commit 11d543eeca08fe0df4bf2be7222234fadb516a51 | Frederick Muriuki Muriithi |
| 2024-09-27 | Fix Pair-Scan output paths•••Related to 4940195460008192b6ca6269e1fb8c172ada4f17c | Frederick Muriuki Muriithi |
| 2024-09-27 | Set `include_package_data=True` to install R files too. | Frederick Muriuki Muriithi |
| 2024-09-27 | Add a MANIFEST.in to include R scripts. | Frederick Muriuki Muriithi |
| 2024-09-27 | Bug: Use absolute path in place of relative path•••Prior to this commit, an assumption is made that the application is invoked with the root of the repository being the current working directory. If this assumption is not met, then the system will not find the appropriate path. This commit forces the use of an absolute path, which should help avoid issues with misplaced relative paths. | Frederick Muriuki Muriithi |
| 2024-09-27 | Use existing fixture to retrieve settings. | Frederick Muriuki Muriithi |
| 2024-09-27 | Fix R/qtl output paths•••The script now takes the --outdir parameter as the output directory, only using TMPDIR if nothing is passed "output" in the output directory was also changed to "gn3" to be consistent with recent changes to GN3's code | zsloan |
| 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 | Handle missing GN3_SECRETS for CI testing.•••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 | Revert "Remove one-line if/else statement."•••This reverts commit 0d15840913c9cc401d1e74295aa5e17e34f2987b. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Add section on setting up virtuoso locally.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Update docs to use default virtuoso ports.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Update docs on how to use SPARQL default ports.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Remove one-line if/else statement.•••* gn3/db/rdf/wiki.py (__sanitize_result): When fetching pubmed_ids and categories, default to [] if the key misses, and remove the subsequent one-line if/else statement. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Load GN3_SECRETS after loading GN3_CONF settings.•••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 | Make sure the the test graph is empty before running rdf tests.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Update docs to highlight sparql conf params in SECRETS file.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Use correct object modifier for a label when inserting a comment.•••* gn3/db/rdf/wiki.py (update_wiki_comment) [query]: Replace "rdf:label" with "rdfs:label". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Update docstring for "update_wiki_comment".•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Use correct object modifier in triple when fetching comment history.•••* gn3/db/rdf/wiki.py (get_comment_history) [query]: Replace ?symbolName with ?symbolName. 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 |
| 2024-09-23 | Use correct modifier when getting species name in SPARQL.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Remove dead variable from RDF query.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Alphabetically sort the categories and pubmed_ids array.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Remove un-necessary triple in comment history RDF query.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-19 | Use correct return type.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-19 | Remove extraneous keyword.•••* gn3/api/metadata_api/wiki.py (edit_wiki): Remove comment_id from args---it's already in the insert_dict. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Pass in insert_dict instead of payload in "get_wiki_entries".•••* gn3/api/metadata_api/wiki.py (edit_wiki) [insert_dict]: Add species, categories fields. [update_wiki_comment]: Pass in insert_dict, and get rid of redundant keys. Directly pass in sparql_auth's conf params instead of a dict. * gn3/db/rdf/wiki.py (get_next_comment_version): Get rid of redundant params. Use fields directly from insert_dict. Directly pass in sparql_auth's conf params instead of a dict. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Pass in the createtime as an arg when inserting into RDF graph.•••* gn3/api/metadata_api/wiki.py (edit_wiki): Pass in the createtime as an arg. * gn3/db/rdf/wiki.py: Remove un-used imports. (update_wiki_comment): Use passed in "created" arg in the createtime field. This makes sure that the SQL/RDF timestamps match. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
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