| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-10-29 | Refactor: refactor code to find lod peaks. | Alexander_Kabui | |
| 2024-10-29 | Refactor: refactoring for code to perform permutation tests. | Alexander_Kabui | |
| 2024-10-29 | Refactor: refactor function to generate plots from scan1 function. | Alexander_Kabui | |
| 2024-10-29 | Refactor: refactor method to compute scan 1. | Alexander_Kabui | |
| 2024-10-29 | Refactor: refactor function to calculate error LOD scores. | Alexander_Kabui | |
| 2024-10-29 | Refactor: refactor functions to compute genetic probabilities: | Alexander_Kabui | |
| 2024-10-29 | Refactor: cleanup comments. | Alexander_Kabui | |
| 2024-10-29 | Refactor: use FALSE for better defaults. | Alexander_Kabui | |
| 2024-10-29 | feat: add defaults for creating cross objects. | Alexander_Kabui | |
| 2024-10-28 | fix: remove dangerous default configs and have a detailed error with how to ↵ | John Nduli | |
| configure | |||
| 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 | |
 |
index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
| about summary refs log tree commit diff |