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AgeCommit message (Expand)Author
2024-02-28Fix bug: fetch from cursor, not return from cursor.execute(…)load-raw-data-no-parsingFrederick Muriuki Muriithi
2024-02-21Check that samples/cases are consistent...Ensure that **ALL** samples/cases/individuals mentioned in any of the pheno files actually exist in at least one of the geno files. Frederick Muriuki Muriithi
2024-02-21Pass 'filename' value to error checker function.Frederick Muriuki Muriithi
2024-02-20Track filename in the errors...R/qtl2 bundles can contain more than one file, of the same type. When errors are encountered in any of the files, we need to be able to inform the user which file it is, in addition to the line and column number. Frederick Muriuki Muriithi
2024-02-15Filter out NULL valuesFrederick Muriuki Muriithi
2024-02-15Only log out information if the check is actually run.Frederick Muriuki Muriithi
2024-02-13Add some parallelism to the QC ChecksFrederick Muriuki Muriithi
2024-02-13Provide nice UI progress indicators.Frederick Muriuki Muriithi
2024-02-12Check for errors in the 'phenose' file.Frederick Muriuki Muriithi
2024-02-12Check for errors in the 'pheno' file.Frederick Muriuki Muriithi
2024-02-12Collect and display errors on 'geno' files in the bundle.Frederick Muriuki Muriithi
2024-02-12Add scaffolding for running individual files' QC checksFrederick Muriuki Muriithi
2024-02-12Extract missing files check to external functionFrederick Muriuki Muriithi
2024-02-12Retrive and display generic bundle errors...Implement the first QC check for generic errors e.g. missing files in bundle, etc. Display retrieved errors on UI. Frederick Muriuki Muriithi
2024-02-12R/qtl2 QC: Set up scaffolding for QC UI...Set up the scaffolding for the flows and UI that will be used when running QC against the uploaded R/qtl2 bundle. This will be fleshed out later, and the UI is likely to change somewhat, down the line. Frederick Muriuki Muriithi
2024-02-12Provide better error messaging...Provide a better error message that can help the user figure out what they did wrong and fix it for themselves instead of the older, cryptic and extremely unhelpful error message. Frederick Muriuki Muriithi
2024-02-05Run QC on the 'geno' file in R/qtl2 bundle.Frederick Muriuki Muriithi
2024-02-05Add a QC step: Check all listed files exist...Add a QC step to the R/qtl2 bundle processing - check that all files that are listed in the control file also exist in the bundle. Frederick Muriuki Muriithi
2024-02-05Fix linting and type errors.Frederick Muriuki Muriithi
2024-01-24Checks: Update code and tests to ensure all checks pass.Frederick Muriuki Muriithi
2024-01-24redis-prefix: Update file validation code...Update the file validation script and routes to use the redis prefix for jobs. Frederick Muriuki Muriithi
2024-01-23Update scripts to use redis prefix.Frederick Muriuki Muriithi
2024-01-22scripts: Pass in logger to get detailed updates.Frederick Muriuki Muriithi
2024-01-22UI: Show progress of R/qtl2 bundle processing.Frederick Muriuki Muriithi
2024-01-20Fetch sample/case names from database...Fetch the sample/case names from the database rather than from a static file in the repository. Issue: https://issues.genenetwork.org/issues/quality-control/read-samples-from-database-by-species Frederick Muriuki Muriithi
2024-01-19scripts: Process R/qtl2 bundle...Build script to start the processing of the R/qtl2 bundle. Frederick Muriuki Muriithi
2024-01-16Filter out items with values of `None`....The ProbeSetData table does not allow `NULL` for the `value` column for good reason - if there is no value, just don't have a record for that particular sample. Frederick Muriuki Muriithi
2024-01-15Update imports: `take` was moved to different package.Frederick Muriuki Muriithi
2024-01-15Process the `pheno` files....Process the data in the pheno files and insert it into the database. Frederick Muriuki Muriithi
2024-01-15Initialise `install_phenos` script.Frederick Muriuki Muriithi
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 database...Update the genetic positions (in centiMorgans) in the database. Frederick Muriuki Muriithi
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 markers...Insert any new markers found into the database. Frederick Muriuki Muriithi
2024-01-09WIP: Install genotypes from R/qtl2 bundle...Load the genotype information from the R/qtl2 bundle and insert it into the database. Frederick Muriuki Muriithi
2024-01-09Fix linting errorsFrederick Muriuki Muriithi
2024-01-09scripts: Log to redis...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. Frederick Muriuki Muriithi
2024-01-08Use extracted functions and fix bugsFrederick Muriuki Muriithi
2023-12-20Fix ID column key...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. Frederick Muriuki Muriithi
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 error...Fix a bug that was causing the data insertion to fail. Frederick Muriuki Muriithi
2023-11-30Fix errors caught by pylint and mypy.Frederick Muriuki Muriithi