| Age | Commit message (Expand) | Author |
|---|---|---|
| 2024-10-24 | Move logger creation to `build_main` function•••Since the module-level loggers are built mostly the same, move the creation of the logger to the more general function to reduce repetition. | Frederick Muriuki Muriithi |
| 2024-10-22 | Refactor `qc_pheno_file` and reuse it for different file types.•••The QC/QA steps taken by the `qc_pheno_file` function are very similar across the "pheno", "phenose" and "phenonum" files. This commit makes the `qc_pheno_file` function a higher-order function and we pass the file-type specific check(s) as a callable (function) to be used for the QC/QA process. | Frederick Muriuki Muriithi |
| 2024-10-22 | Check for errors in `pheno` files. | Frederick Muriuki Muriithi |
| 2024-10-21 | Check `phenocovar` files for errors. | Frederick Muriuki Muriithi |
| 2024-10-17 | Cleanup: Delete all extracted files after processing. | Frederick Muriuki Muriithi |
| 2024-10-17 | Leave TODO notes for what needs to be done. | Frederick Muriuki Muriithi |
| 2024-10-17 | Fetch samples from database•••Fetch the samples from the database. These will be used to verify that the samples in the phenotype files already exist in the database and are valid. | Frederick Muriuki Muriithi |
| 2024-10-17 | Undo transpose for any transposed files•••To reduce the complexity involved in the processing of the files, we undo any transposition of the CSV files for those files that are marked as transposed. | Frederick Muriuki Muriithi |
| 2024-10-17 | Pass new arguments to QC function. | Frederick Muriuki Muriithi |
| 2024-10-17 | Add `speciesid` and `populationid` arguments to the script. | Frederick Muriuki Muriithi |
| 2024-10-17 | Add the working directory argument to the script.•••Add a `--working-dir` argument to allow passing a directory where the script process the files within. If not provided, it defaults to a directory within the systems temporary directory. | Frederick Muriuki Muriithi |
| 2024-10-17 | Extract the R/qtl2 bundle for processing.•••To enable processing of the files individually, this commit will enable the extraction of the files into a known working directory in which all further processing will take place. | Frederick Muriuki Muriithi |
| 2024-10-14 | Initialise background script for running QC on phenotype bundles. | Frederick Muriuki Muriithi |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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