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2025-03-18Order species by species id.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-07Merge pull request #218 from genenetwork/chores/refactor-qtl2-scriptAlexander Kabui
refactor rqtl2 script.
2025-03-07refactor function to process scan1 results.Alexander_Kabui
2025-03-07Convert 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>
2025-03-07Revert "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>
2025-03-04Use self-holsted LLM API end-point.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-04fix: Replace file path fetching code in rqtl2.py with current_app.root_pathMunyoki Kilyungi (aider)
2025-02-28Eliminate carriage-return and newline characters.Frederick Muriuki Muriithi
2025-02-28Print out the stack trace to help debug failures.Frederick Muriuki Muriithi
2025-02-28Fix issues caught by mypy.Frederick Muriuki Muriithi
2025-02-28Fix linting errors.Frederick Muriuki Muriithi
2025-02-26feat: Add utility function for reading files and improve loggingAlexander_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.
2025-02-25fix: handle extra columns in permutations CSV reader to prevent unpacking error.Alexander_Kabui
2025-02-24Fetch rscript from os env if it isn't set in the app's config.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-21Fix 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>
2025-02-20refactor: Skip permutation test when NO_OF_PERMUTATION less than 0.Alexander_Kabui
2025-02-19fix: Read and parse correct permutation file from R/qtl2.Alexander_Kabui
2025-02-19fix: Read and parse correct permutation file from R/qtl1Alexander_Kabui
2025-02-10feat: Add LMDB sample data retrieval API endpoint with testsMunyoki Kilyungi (aider)
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-07refactor: Add rqtl2 default method and update unittests.Alexander_Kabui
2025-02-07feat: Add the qtl to method to be used.Alexander_Kabui
2025-02-07feat: Enable streaming functionality for rqtl2.Alexander_Kabui
2025-02-07fix: fix for fetching significance results.Alexander_Kabui
2025-02-06refactor: code refactoring.Alexander_Kabui
2025-02-06feat: Include the physical map position in results.Alexander_Kabui
2025-02-06refactor: Rename pheno_map to physical_map .Alexander_Kabui
2025-02-06mypy fixes.Alexander_Kabui
2025-02-06feat: Add functionality to process output to compute endpoint.Alexander_Kabui
2025-02-06refactor process qtl2 results function to include output reading.Alexander_Kabui
2025-02-06feat: Add function to process qtl2 output results.Alexander_Kabui
2025-02-06feat: Add function to process qtl scan results.Alexander_Kabui
2025-02-06feat: Add function to process permutation results.Alexander_Kabui
2025-02-06feat: Add function to fetch significance results.Alexander_Kabui
2025-02-06Refactor: return the relative file to the workspace directory.Alexander_Kabui
2025-02-06Minor fix.Alexander_Kabui
2025-02-06Refactor workspace directory creation to use pathlib's mkdir method.Alexander_Kabui
2025-02-06refactor: Minor cleanup.Alexander_Kabui
2025-02-06refactor: Refactor run_process function.Alexander_Kabui
2025-02-06refactor: Add file_path to output only if it is created.Alexander_Kabui
2025-02-06refactor: Check if data before attempting write operation.Alexander_Kabui
2025-02-06refactor: return code for Calledprocesserror response.Alexander_Kabui
2025-02-06refactor: Refactor compute endpoint for rqtl2.Alexander_Kabui
2025-02-06feat: Add module docstring for rqtl2 computations.Alexander_Kabui
2025-02-06refactor: remove unused imports.Alexander_Kabui
2025-02-06feat: Add function to write input data to a json file.Alexander_Kabui
2025-02-06feat: Add function to prepare files and workspace directory for computation.Alexander_Kabui
2025-02-06feat: Add utility function to create a file if it does not exist.Alexander_Kabui
2025-02-06feat: Add function to compose an rqtl2 run command.Alexander_Kabui
2025-02-06feat: Add function to validate list of keys in object.Alexander_Kabui
2025-02-06feat: Add function to generate rqtl2 data files.Alexander_Kabui
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-11-27 07:12:24 +0000