| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2025-01-09 | feat: Init add streaming module for genenetwork3. | Alexander_Kabui | |
| 2025-01-08 | refactor: Modify error message for run_process function. | Alexander_Kabui | |
| 2025-01-08 | refactor: Return results as dict with correct metadata for subprocess. | Alexander_Kabui | |
| 2025-01-08 | refactor: Pass arg commands to subprocess as a list. | Alexander_Kabui | |
| * Use with open context for subprocess. * Correctly handle subprocess error. | |||
| 2025-01-07 | feat: Revert commit 688d6a4. | Alexander_Kabui | |
| 2025-01-07 | feat: remove shell True to for debug. | Alexander_Kabui | |
| 2024-12-20 | Add todo note for writing rqtl file. | Alexander_Kabui | |
| 2024-12-20 | fix: Pylint fixes. | Alexander_Kabui | |
| 2024-12-20 | feat: Enable streaming for output. | Alexander_Kabui | |
| 2024-12-17 | feat: Init integrate streaming functionality to rqtl1. | Alexander_Kabui | |
| 2024-12-13 | fix: Fix unused variables pylint. | Alexander_Kabui | |
| 2024-12-13 | Fix pylint error line too long. | Alexander_Kabui | |
| 2024-12-13 | fix: Fetch the correct value from rqtl output file for permutation. | Alexander_Kabui | |
| 2024-12-12 | Remove quote marks for qtl output. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-12-12 | Fetch RSCRIPT command from global environment variable. | Munyoki Kilyungi | |
| * gn3/commands.py (compose_rqtl_cmd): Fetch RSCRIPT from global environment. Otherwise default to "Rscript". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-12-07 | Check whether genofile/phenofile exist separately. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-12-04 | Temp disable with for test Popen processes. | Alexander_Kabui | |
| 2024-12-04 | refactor: make pylint fixes. | Alexander_Kabui | |
| 2024-12-04 | Merge pull request #203 from genenetwork/feature/rqtl2-endpoints-with-files | Alexander Kabui | |
| Feature/rqtl2 endpoints with files | |||
| 2024-12-02 | Fix probeset metadata query to include dataset name | zsloan | |
| Previously this attempted to fetch probeset metadata using only the probeset name, but this is wrong. The dataset name is also needed. | |||
| 2024-11-28 | feat: define general endpoint for streaming stdout using unique identifier. | Alexander_Kabui | |
| 2024-11-27 | feat: return run id for compute and streaming api's. | Alexander_Kabui | |
| 2024-11-26 | feat: Implement reading from file functionality | Alexander_Kabui | |
| Implement read from the last position for a file. | |||
| 2024-11-22 | feat: return pointer position from where the file was last read. | Alexander_Kabui | |
| 2024-11-22 | feat: Add new endpoint to read stdout given a file identifier. | Alexander_Kabui | |
| 2024-11-22 | feat: register rqtl2 blueprint to app. | Alexander_Kabui | |
| 2024-11-22 | feat: implement ednpoint for computing qtl using rqtl2. | Alexander_Kabui | |
| Capture stdout results to a file. | |||
| 2024-11-15 | Fix bug where case attribute editing didn't work if a case attribute was | zsloan | |
| called 'Strain' This is because the code was also using 'Strain' for the strain name. At least for the time being, I addressed this by changing those instances to 'Sample' instead (which I don't believe is ever a case attribute name). | |||
| 2024-11-14 | Fix auth endpoint for case attribute editing | zsloan | |
| 2024-11-14 | Fix case attribute query | zsloan | |
| 2024-11-12 | Remove unused setting. | Frederick Muriuki Muriithi | |
| The BCRYPT_SALT setting is not used anywhere in GN3 or GN2 | |||
| 2024-11-12 | Remove unused import. | Frederick Muriuki Muriithi | |
| 2024-11-12 | mypy: Rename and annotate variables to silence mypy | Frederick Muriuki Muriithi | |
| 2024-11-12 | Pure aesthetics: No functional change. | Frederick Muriuki Muriithi | |
| This commit has no functional change it implements. It is purely a aesthetics change to please Frederick. | |||
| 2024-11-11 | Allow extra database connection options on URI | Frederick Muriuki Muriithi | |
| Update the database URI parsing to allow setting of extra connection option on the URI string. | |||
| 2024-10-28 | fix: remove dangerous default configs and have a detailed error with how to ↵ | John Nduli | |
| configure | |||
| 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 | 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> | |||
| 2024-09-30 | 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. | |||
| 2024-09-27 | Debug command. | Frederick Muriuki Muriithi | |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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