| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | |
| 2024-09-27 | Bug: Use absolute paths in place of relative paths. | Frederick Muriuki Muriithi | |
| Similar issue to commit 11d543eeca08fe0df4bf2be7222234fadb516a51 | |||
| 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. | |||
| 2024-09-23 | Revert "Remove one-line if/else statement." | Munyoki Kilyungi | |
| This reverts commit 0d15840913c9cc401d1e74295aa5e17e34f2987b. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-23 | Remove one-line if/else statement. | Munyoki Kilyungi | |
| * 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> | |||
| 2024-09-23 | Use correct object modifier for a label when inserting a comment. | Munyoki Kilyungi | |
| * gn3/db/rdf/wiki.py (update_wiki_comment) [query]: Replace "rdf:label" with "rdfs:label". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-09-23 | Update docstring for "update_wiki_comment". | Munyoki Kilyungi | |
| 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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