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2025-04-22Implement delete_wiki API endpoint.Munyoki Kilyungi
* gn3/api/metadata_api/wiki.py: Import delete_wiki_entries_by_id. (delete_wiki): New API endpoint. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-22Add function to delete wiki entries by wiki_id.Munyoki Kilyungi
* delete_wiki_entries_by_id: New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-22Add test case for deleting wiki data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-22Correctly ignore broad-expection-raised exceptions.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-22Autopep-8 file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-22sheepdog/worker.py: Fix logging-fstring-interpolation warning.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-22Auto-pep8 files.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-22Reduce arguments in run_async_cmd by using options dictionary.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-14Include effect mean/SE for 4-way crosses in R/qtl resultszsloan
2025-04-09Initialise the sheepdog package to ensure the worker gets installed.Frederick Muriuki Muriithi
2025-04-08Fix failing test.Frederick Muriuki Muriithi
2025-04-08Pass application log-level to the worker.Frederick Muriuki Muriithi
2025-04-08Use computed job queue to avoid collisions.Frederick Muriuki Muriithi
2025-04-08Add a function to compute the job queue from the settings.Frederick Muriuki Muriithi
2025-04-08APPLICATION_ENVIRONMENT: New configuration variableFrederick 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.
2025-04-08Add logging to worker.Frederick Muriuki Muriithi
2025-04-08sheepdog.worker: Pass in the queue name on the CLIFrederick Muriuki Muriithi
Pass in the name of the queue where the jobs are queued to the worker.
2025-04-08BUG: Provide a tuple, of tuple of floatsFrederick Muriuki Muriithi
The downstream functions seem to expect a tuple of tuples of floats.
2025-04-08Use correct key.Frederick Muriuki Muriithi
2025-04-08Indent code properly.Frederick Muriuki Muriithi
2025-04-08refactor: Explicity define no of cores for rqtl2 computation.Alexander_Kabui
2025-04-08feat: Append GN3 computation completion marker to log file.Alexander_Kabui
2025-04-08fix: Pylint fix for unused variable.Alexander_Kabui
2025-04-08refactor: Check for geno_tranposed and founder_geno_transposed.Alexander_Kabui
2025-04-07Remove debug logging: current_app.logger requires app context.Frederick Muriuki Muriithi
2025-04-07Log out debug messages separate from active statements.Frederick Muriuki Muriithi
2025-04-07Split the command if its a single, non-json-parseable string.Frederick Muriuki Muriithi
2025-03-27refactor: Temporary disable checking sex covariates in rqtl2.Alexander_Kabui
2025-03-27feat: Check for founder and covar file in rqtl2 metadata.Alexander_Kabui
2025-03-21Use HTTPS for LLM endpoint.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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.
2025-03-07Demo CI in gn nairobi meet.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-07refactor function to process scan1 results.Alexander_Kabui
2025-03-07refactor: Construct map object from cross with columns (Marker, chr,cM, Mb).Alexander_Kabui
2025-03-07fix: Minor rqtl2 fixes.Alexander_Kabui
2025-03-07refactor rqtl2 script.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>
2025-03-04Revert "test: Add unit tests for fibonacci function in rqtl2 module"Munyoki Kilyungi
This reverts commit 9bad745abd94fd0eeb0b0dc6aba0d6a74db33f81.
2025-03-04Revert "docs: Add module and function docstrings for unit tests of fibonacci ↵Munyoki Kilyungi
function". This reverts commit 6a76e302f11c0a0aa0bc0ac8487ad250f8afb9bb.
2025-03-04Revert "feat: Add Python implementation of Fibonacci number calculation".Munyoki Kilyungi
This reverts commit 280c5e97d21501c03f672ed3576ae3eddfc76420.
2025-03-04Use self-holsted LLM API end-point.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-04docs: Add module and function docstrings for unit tests of fibonacci functionMunyoki Kilyungi (aider)
2025-03-04test: Add unit tests for fibonacci function in rqtl2 moduleMunyoki Kilyungi (aider)
2025-03-04feat: Add Python implementation of Fibonacci number calculationMunyoki Kilyungi (aider)
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
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-11-21 18:18:11 +0000