Age | Commit message (Expand) | Author |
---|---|---|
2024-02-28 | Fix bug: fetch from cursor, not return from cursor.execute(…)load-raw-data-no-parsing | Frederick Muriuki Muriithi |
2024-02-21 | Check 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 |
2024-02-21 | Pass 'filename' value to error checker function. | Frederick Muriuki Muriithi |
2024-02-20 | Track 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 |
2024-02-15 | Filter out NULL values | Frederick Muriuki Muriithi |
2024-02-15 | Only log out information if the check is actually run. | Frederick Muriuki Muriithi |
2024-02-13 | Add some parallelism to the QC Checks | Frederick Muriuki Muriithi |
2024-02-13 | Provide nice UI progress indicators. | Frederick Muriuki Muriithi |
2024-02-12 | Check for errors in the 'phenose' file. | Frederick Muriuki Muriithi |
2024-02-12 | Check for errors in the 'pheno' file. | Frederick Muriuki Muriithi |
2024-02-12 | Collect and display errors on 'geno' files in the bundle. | Frederick Muriuki Muriithi |
2024-02-12 | Add scaffolding for running individual files' QC checks | Frederick Muriuki Muriithi |
2024-02-12 | Extract missing files check to external function | Frederick Muriuki Muriithi |
2024-02-12 | Retrive 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 |
2024-02-12 | R/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 |
2024-02-12 | Provide 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 |
2024-02-05 | Run QC on the 'geno' file in R/qtl2 bundle. | Frederick Muriuki Muriithi |
2024-02-05 | Add 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 |
2024-02-05 | Fix linting and type errors. | Frederick Muriuki Muriithi |
2024-01-24 | Checks: Update code and tests to ensure all checks pass. | Frederick Muriuki Muriithi |
2024-01-24 | redis-prefix: Update file validation code...Update the file validation script and routes to use the redis prefix for jobs. | Frederick Muriuki Muriithi |
2024-01-23 | Update scripts to use redis prefix. | Frederick Muriuki Muriithi |
2024-01-22 | scripts: Pass in logger to get detailed updates. | Frederick Muriuki Muriithi |
2024-01-22 | UI: Show progress of R/qtl2 bundle processing. | Frederick Muriuki Muriithi |
2024-01-20 | Fetch 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 |
2024-01-19 | scripts: Process R/qtl2 bundle...Build script to start the processing of the R/qtl2 bundle. | Frederick Muriuki Muriithi |
2024-01-16 | Filter 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 |
2024-01-15 | Update imports: `take` was moved to different package. | Frederick Muriuki Muriithi |
2024-01-15 | Process the `pheno` files....Process the data in the pheno files and insert it into the database. | Frederick Muriuki Muriithi |
2024-01-15 | Initialise `install_phenos` script. | Frederick Muriuki Muriithi |
2024-01-15 | Extract common structure into separate modules. | Frederick Muriuki Muriithi |
2024-01-11 | Update pmap data in the database. | Frederick Muriuki Muriithi |
2024-01-11 | Update gmap data in the database...Update the genetic positions (in centiMorgans) in the database. | Frederick Muriuki Muriithi |
2024-01-11 | Cleanup linting and typing errors. | Frederick Muriuki Muriithi |
2024-01-11 | CLI: Require datasetid as an argument. | Frederick Muriuki Muriithi |
2024-01-10 | Provide convenience functions to avoid subtle call errors | Frederick Muriuki Muriithi |
2024-01-10 | Cross-reference genotype data to the dataset. | Frederick Muriuki Muriithi |
2024-01-10 | Insert genotype data. | Frederick Muriuki Muriithi |
2024-01-10 | Cross-reference individuals to populations. | Frederick Muriuki Muriithi |
2024-01-10 | Insert any new individuals/samples into the database. | Frederick Muriuki Muriithi |
2024-01-10 | Insert any new markers...Insert any new markers found into the database. | Frederick Muriuki Muriithi |
2024-01-09 | WIP: Install genotypes from R/qtl2 bundle...Load the genotype information from the R/qtl2 bundle and insert it into the database. | Frederick Muriuki Muriithi |
2024-01-09 | Fix linting errors | Frederick Muriuki Muriithi |
2024-01-09 | scripts: 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 |
2024-01-08 | Use extracted functions and fix bugs | Frederick Muriuki Muriithi |
2023-12-20 | Fix 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 |
2023-12-18 | Samples: Hook-up external async script to upload the samples. | Frederick Muriuki Muriithi |
2023-12-14 | samples: Create external script and fix some bugs. | Frederick Muriuki Muriithi |
2023-11-30 | Bug: Fix insertion error...Fix a bug that was causing the data insertion to fail. | Frederick Muriuki Muriithi |
2023-11-30 | Fix errors caught by pylint and mypy. | Frederick Muriuki Muriithi |