| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2025-04-14 | Include effect mean/SE for 4-way crosses in R/qtl results | zsloan | |
| 2025-04-08 | Pass application log-level to the worker. | Frederick Muriuki Muriithi | |
| 2025-04-08 | Use computed job queue to avoid collisions. | Frederick Muriuki Muriithi | |
| 2025-04-08 | Add a function to compute the job queue from the settings. | Frederick Muriuki Muriithi | |
| 2025-04-08 | APPLICATION_ENVIRONMENT: New configuration variable | Frederick Muriuki Muriithi | |
| Add a new application configuration variable, "APPLICATION_ENVIRONMENT" that will be useful to distinguish resources for different instances of the application that might run on the same host. The default value is an empty string in order to allow backwards compatibility with existing code. An example of where this finds utility: If you run multiple instances of the application, but they all share the same redis instance, then key-collisions from the different running applications will happen, leading to subtle, difficult to troubleshoot bugs. | |||
| 2025-04-08 | Add logging to worker. | Frederick Muriuki Muriithi | |
| 2025-04-08 | sheepdog.worker: Pass in the queue name on the CLI | Frederick Muriuki Muriithi | |
| Pass in the name of the queue where the jobs are queued to the worker. | |||
| 2025-04-08 | BUG: Provide a tuple, of tuple of floats | Frederick Muriuki Muriithi | |
| The downstream functions seem to expect a tuple of tuples of floats. | |||
| 2025-04-08 | Use correct key. | Frederick Muriuki Muriithi | |
| 2025-04-08 | Indent code properly. | Frederick Muriuki Muriithi | |
| 2025-04-08 | feat: Append GN3 computation completion marker to log file. | Alexander_Kabui | |
| 2025-04-08 | fix: Pylint fix for unused variable. | Alexander_Kabui | |
| 2025-04-07 | Remove debug logging: current_app.logger requires app context. | Frederick Muriuki Muriithi | |
| 2025-04-07 | Log out debug messages separate from active statements. | Frederick Muriuki Muriithi | |
| 2025-04-07 | Split the command if its a single, non-json-parseable string. | Frederick Muriuki Muriithi | |
| 2025-03-27 | feat: Check for founder and covar file in rqtl2 metadata. | Alexander_Kabui | |
| 2025-03-21 | Use HTTPS for LLM endpoint. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-03-18 | Order species by species id. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-03-07 | Merge pull request #218 from genenetwork/chores/refactor-qtl2-script | Alexander Kabui | |
| refactor rqtl2 script. | |||
| 2025-03-07 | refactor function to process scan1 results. | Alexander_Kabui | |
| 2025-03-07 | Convert wikiId and versionId to ints. | Munyoki Kilyungi | |
| This fixes failing tests. * gn3/db/rdf/wiki.py (__sanitize_result): Convert versionId and wiki Id to ints. (get_wiki_entries_by_symbol): Get string representation of VersionId and the wikiId instead of the the URI. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-03-07 | Revert "fix: Replace file path fetching code in rqtl2.py with ↵ | Munyoki Kilyungi | |
| current_app.root_path" This reverts commit e7baf1a4cf05a4e7794a6531c92d367fcd8f1651. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-03-04 | Use self-holsted LLM API end-point. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-03-04 | fix: Replace file path fetching code in rqtl2.py with current_app.root_path | Munyoki Kilyungi (aider) | |
| 2025-02-28 | Eliminate carriage-return and newline characters. | Frederick Muriuki Muriithi | |
| 2025-02-28 | Print out the stack trace to help debug failures. | Frederick Muriuki Muriithi | |
| 2025-02-28 | Fix issues caught by mypy. | Frederick Muriuki Muriithi | |
| 2025-02-28 | Fix linting errors. | Frederick Muriuki Muriithi | |
| 2025-02-26 | feat: Add utility function for reading files and improve logging | Alexander_Kabui | |
| * Add `read_file(file_path)` utility function to streamline file reading. * Updated `run_process()` to return log contents instead of just the log file path. | |||
| 2025-02-25 | fix: handle extra columns in permutations CSV reader to prevent unpacking error. | Alexander_Kabui | |
| 2025-02-24 | Fetch rscript from os env if it isn't set in the app's config. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-02-21 | Fix versioning of WIKI entries. | Munyoki Kilyungi | |
| * gn3/api/metadata_api/wiki.py (edit_wiki)[next_version]: Set to the latest+1 if a comment id exists. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-02-20 | refactor: Skip permutation test when NO_OF_PERMUTATION less than 0. | Alexander_Kabui | |
| 2025-02-19 | fix: Read and parse correct permutation file from R/qtl2. | Alexander_Kabui | |
| 2025-02-19 | fix: Read and parse correct permutation file from R/qtl1 | Alexander_Kabui | |
| 2025-02-10 | feat: Add LMDB sample data retrieval API endpoint with tests | Munyoki Kilyungi (aider) | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-02-07 | refactor: Add rqtl2 default method and update unittests. | Alexander_Kabui | |
| 2025-02-07 | feat: Add the qtl to method to be used. | Alexander_Kabui | |
| 2025-02-07 | feat: Enable streaming functionality for rqtl2. | Alexander_Kabui | |
| 2025-02-07 | fix: fix for fetching significance results. | Alexander_Kabui | |
| 2025-02-06 | refactor: code refactoring. | Alexander_Kabui | |
| 2025-02-06 | feat: Include the physical map position in results. | Alexander_Kabui | |
| 2025-02-06 | refactor: Rename pheno_map to physical_map . | Alexander_Kabui | |
| 2025-02-06 | mypy fixes. | Alexander_Kabui | |
| 2025-02-06 | feat: Add functionality to process output to compute endpoint. | Alexander_Kabui | |
| 2025-02-06 | refactor process qtl2 results function to include output reading. | Alexander_Kabui | |
| 2025-02-06 | feat: Add function to process qtl2 output results. | Alexander_Kabui | |
| 2025-02-06 | feat: Add function to process qtl scan results. | Alexander_Kabui | |
| 2025-02-06 | feat: Add function to process permutation results. | Alexander_Kabui | |
| 2025-02-06 | feat: Add function to fetch significance results. | Alexander_Kabui | |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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