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2024-01-15Extract common structure into separate modules.Frederick Muriuki Muriithi
2024-01-11Update pmap data in the database.Frederick Muriuki Muriithi
2024-01-11Update gmap data in the databaseFrederick Muriuki Muriithi
Update the genetic positions (in centiMorgans) in the database.
2024-01-11Cleanup linting and typing errors.Frederick Muriuki Muriithi
2024-01-11CLI: Require datasetid as an argument.Frederick Muriuki Muriithi
2024-01-10Provide convenience functions to avoid subtle call errorsFrederick Muriuki Muriithi
2024-01-10Cross-reference genotype data to the dataset.Frederick Muriuki Muriithi
2024-01-10Insert genotype data.Frederick Muriuki Muriithi
2024-01-10Cross-reference individuals to populations.Frederick Muriuki Muriithi
2024-01-10Insert any new individuals/samples into the database.Frederick Muriuki Muriithi
2024-01-10Insert any new markersFrederick Muriuki Muriithi
Insert any new markers found into the database.
2024-01-09WIP: Install genotypes from R/qtl2 bundleFrederick Muriuki Muriithi
Load the genotype information from the R/qtl2 bundle and insert it into the database.
2024-01-09Fix linting errorsFrederick Muriuki Muriithi
2024-01-09scripts: Log to redisFrederick Muriuki Muriithi
Add a logger that will log output to a redis list. This will be useful to retrieve the output(s) of the running script to help display some form of progress to the user.
2024-01-08Use extracted functions and fix bugsFrederick Muriuki Muriithi
2023-12-20Fix ID column keyFrederick Muriuki Muriithi
Fix the wrong assumption that the ID key will always be "ProbeSetID". The key for the ID column could change from study to study or dataset to dataset.
2023-12-18Samples: Hook-up external async script to upload the samples.Frederick Muriuki Muriithi
2023-12-14samples: Create external script and fix some bugs.Frederick Muriuki Muriithi
2023-11-30Bug: Fix insertion errorFrederick Muriuki Muriithi
Fix a bug that was causing the data insertion to fail.
2023-11-30Fix errors caught by pylint and mypy.Frederick Muriuki Muriithi
2023-11-15Log out DB errors even when handledFrederick Muriuki Muriithi
Log out any DB errors that occur to help with tracking and debugging failures.
2023-11-15Remove debugging statement.Frederick Muriuki Muriithi
2023-11-15Bug: Insert ProbeSets before average data and cross-refsFrederick Muriuki Muriithi
Insert the ProbeSets first before inserting the average data and cross-referencing it.
2023-11-15mypy: Fix typing errors.Frederick Muriuki Muriithi
2023-11-15Linting: Fix linting errors.Frederick Muriuki Muriithi
2023-10-30Prevent overwrite. Avoid inserting same probeset multiple times.Frederick Muriuki Muriithi
* Avoid overwriting existing data by adding a random string to the name of the ProbeSet * Read ProbeSet names separately from the means for the strains, to avoid entering the same ProbeSet record over and over with varying names.
2023-10-18Link to `ProbeSet.Id` in XRef TableFrederick Muriuki Muriithi
The "ProbeSetId" value in the file is actually stored in the database in the `ProbeSet.Name` field, whereas the `ProbeSetXRef` table actually uses the `ProbeSet.Id` value to define the relationships. This commit fixes that issue.
2023-10-16Fix bug: Insert ProbeSets if they do not exist.Frederick Muriuki Muriithi
2023-10-16Fix bug: Provide the platform_id to `insert_means`Frederick Muriuki Muriithi
2023-10-16Fix bug: parsing fields from query.Frederick Muriuki Muriithi
2022-08-05Update job status. Display stdout and stderr outputsFrederick Muriuki Muriithi
* Display the status of the job, as it is running * Display STDERR output if an error occurs * Display STDOUT output as job is running and on successful completion of the job
2022-08-04Implement data insertionFrederick Muriuki Muriithi
- Hook up external data insertion script to webserver code - Provide rudimentary status indication - Generalise some job creation details
2022-08-04Handle stderr outputFrederick Muriuki Muriithi
* Fix bug where stderr was not being updated on redis appropriately
2022-08-04Format queries for output. Get rid of extraneous output.Frederick Muriuki Muriithi
2022-07-19Save standard error data. Fix linting and typing errors.Frederick Muriuki Muriithi
2022-07-19Implement data insertion (averages/means)Frederick Muriuki Muriithi
* quality_control/file_utils.py (new file): extract common file utilities. * quality_control/parsing.py (refactor): extract common file utilities. * scripts/insert_data.py: Implement data insertion for averages/means
2022-07-19Check connections before launchingFrederick Muriuki Muriithi
* qc_app/__init__.py (refactor): Check connection before launching the application * qc_app/check_connections.py (new file): Add code to check connections * qc_app/db_utils.py (refactor): enable passing the database uri as an argument to the connection creation function. * scripts/worker.py (refactor): Use new code to check for redis connection.
2022-07-19Add generic worker scriptFrederick Muriuki Muriithi
Add a generic worker script, whose purpose is: - to launch the specific worker script - to capture both stdin and stderr streams and put them on redis In this way, we can launch redis-aware and redis-unaware workers and capture their outputs or errors for later processing.
2022-07-19Rename file validation scriptFrederick Muriuki Muriithi
As preparation for building a new generic worker script, this commit renames the file validation script from 'worker.py' to 'validate_file.py' so as to ensure the name conforms better to what the script does.
2022-07-07Replace 'magic' with builtin 'mimetypes'Frederick Muriuki Muriithi
Use the builtin mimetypes which gives better results
2022-06-28Check for inconsistent columnsFrederick Muriuki Muriithi
The number columns in each contents line should be equal to the nember of columns in the header line.
2022-06-15Fix linting and type errorsFrederick Muriuki Muriithi
2022-06-10Enable upload of zipfilesFrederick Muriuki Muriithi
2022-06-02Enable user abortion of file parsingFrederick Muriuki Muriithi
Enable the user to abort the background parsing of the file.
2022-06-02Add an error display to the progress status reportFrederick Muriuki Muriithi
Enable the progress status page to show all the errors found at any point during the processing of the file.
2022-05-19Update Web-UI: use new error collection paradigmFrederick Muriuki Muriithi
- README.org: document how to run scripts manually - manifest.scm: remove python-rq as a dependency - qc_app/jobs.py: rework job launching and processing - qc_app/parse.py: use reworked job processing - qc_app/templates/job_progress.html: display progress correctly - qc_app/templates/parse_results.html: display final results - scripts/worker.py: new worker script
2022-05-19Extract progress indication from the parsingFrederick Muriuki Muriithi
Since progress indication is not part of the parsing, this commit extracts the progress indication into functions with well defined input arguments that hide the progress indication logic from the parsing function.
2022-05-18Update CLI: use new error collection codeFrederick Muriuki Muriithi
Use the new code that collects the errors in the CLI client.
2022-05-11Tag string as a python f-string to fix error display bugFrederick Muriuki Muriithi
2022-05-02Optimise strain names parsingFrederick Muriuki Muriithi
- Use a way faster way of parsing the strains file
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-05 15:09:24 +0000