| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-10-29 | feat: add defaults for creating cross objects. | Alexander_Kabui | |
| 2024-10-28 | refactor: Minor fixes for file, remove comments | Alexander_Kabui | |
| 2024-10-25 | feat: add function to fetch load peaks for 1 QTL. | Alexander_Kabui | |
| 2024-10-25 | Minor fix. | Alexander_Kabui | |
| 2024-10-25 | Refactor: apply code formatting. | Alexander_Kabui | |
| 2024-10-25 | feat: add code to perform permutation for single Qtl. | Alexander_Kabui | |
| 2024-10-25 | feat: add method to generate LOD curves for the genome scan. | Alexander_Kabui | |
| 2024-10-25 | feat: Add method to perform 1 pair scan. | Alexander_Kabui | |
| 2024-10-25 | feat: add code to perform genetic probabilities. | Alexander_Kabui | |
| 2024-10-24 | feat: create implementation for creating cross object using r-qtl2. | Alexander_Kabui | |
| 2024-10-18 | refactor: replace gn3.auth.db with gn3.sqlite_db_utils and drop all refs to ↵ | John Nduli | |
| gn3.auth | |||
| 2024-10-18 | refactor: move definition of auth errs and remove auth cli utils | John Nduli | |
| 2024-10-18 | refactor: remove unused gn3.auth modules | John Nduli | |
| 2024-10-15 | Lint: Fix linting errors. | Frederick Muriuki Muriithi | |
| 2024-10-15 | Pass in correct file path. | Frederick Muriuki Muriithi | |
| 2024-10-15 | fix: use require_token to validate gn3 apis | John Nduli | |
| 2024-10-14 | Run python black against file. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-14 | Replace 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> | |||
| 2024-10-14 | Replace species' shortName with it's full name in NCBI test data. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-14 | Remove "@id" from NCBI test data. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-14 | Update 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> | |||
| 2024-10-14 | Add end-point for fetching NCBI metadata. | Munyoki Kilyungi | |
| * gn3/api/metadata.py: Register "wiki.rif_blueprint". * gn3/api/metadata_api/wiki.py: Import "get_rif_entries_by_symbol". [rif_blueprint]: New blueprint. (get_ncbi_rif_entries): New endpoint: "metadata/rif/<symbol>". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-14 | Add 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> | |||
| 2024-10-14 | Add NCBI test turtle data. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-02 | Add rdf-tests after the check phase. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-02 | Use 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> | |||
| 2024-10-02 | Fix pylint failure. | Munyoki Kilyungi | |
| * tests/fixtures/rdf.py (rdf_setup): Fix C0301. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-02 | feat: cleaner handling of virtuoso process | John Nduli | |
| 2024-10-02 | Fix typo in comments. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-02 | Move sparql-auth URIs to gn3-conf in documentation. | Munyoki Kilyungi | |
| We want to strictly keep secrets in the secret file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-02 | Add all rdf-tests to GN3 CI. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-02 | Spin up a local virtuoso instance to run RDF tests against. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-02 | Add virtuoso ini file to be used during testing. | Munyoki Kilyungi | |
| tests/fixtures/virtuoso.py: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-10-02 | Set 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> | |||
| 2024-09-30 | 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 | John Nduli | |
| 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. | |||
| 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. | Frederick Muriuki Muriithi | |
| Similar issue to commit 11d543eeca08fe0df4bf2be7222234fadb516a51 | |||
| 2024-09-27 | Fix Pair-Scan output paths | Frederick Muriuki Muriithi | |
| Related to 4940195460008192b6ca6269e1fb8c172ada4f17c | |||
| 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 | Frederick Muriuki Muriithi | |
| 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. | |||
| 2024-09-27 | Use existing fixture to retrieve settings. | Frederick Muriuki Muriithi | |
| 2024-09-27 | Fix R/qtl output paths | zsloan | |
| 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 | |||
| 2024-09-23 | Revert "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> | |||
| 2024-09-23 | Add 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> | |||
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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