| Age | Commit message (Expand) | Author |
|---|---|---|
| 2024-12-03 | Fix some linting and mypy issues. | Frederick Muriuki Muriithi |
| 2024-12-03 | Improve error text...Move the list to the end of the text to make it easier to clip text in the UI. | Frederick Muriuki Muriithi |
| 2024-12-03 | Update file metadata using a mapping...Update the metadata using a mapping rather than updating a field at a time to make it easier to ensure everything is updated in one go. | Frederick Muriuki Muriithi |
| 2024-12-03 | Provide consistent way to build file-specific fully-qualified keys | Frederick Muriuki Muriithi |
| 2024-12-03 | Save 'pheno' errors in redis as they are found. | Frederick Muriuki Muriithi |
| 2024-12-03 | Add some phenocovar metadata. | Frederick Muriuki Muriithi |
| 2024-12-03 | Save phenocovar errors in redis as they are found. | Frederick Muriuki Muriithi |
| 2024-12-03 | Pass the redis connection and fully qualified job id...Pass the redis connection on to the function used to build main since it might need to use a connection to redis. Also pass the computed fully qualified job id rather than recomputing it every time. Update dependent functions to take the new arguments. | Frederick Muriuki Muriithi |
| 2024-12-02 | Fix typo. | Frederick Muriuki Muriithi |
| 2024-12-02 | Return 0 on completion of QC processing. | Frederick Muriuki Muriithi |
| 2024-10-24 | Reduce number of local variables created in function....Use the values in the argparse.Namespace object directly to avoid creating many local variables. | Frederick Muriuki Muriithi |
| 2024-10-24 | Add `jobid` to extraction directory...Add the job id to help "group" files that belong to the same job. | Frederick Muriuki Muriithi |
| 2024-10-24 | Check pheno, phenose, and phenonum files with logging...Add logging to the `qc_pheno_file` function so that we get the messages pushed to redis for every file that is being checked for errors. | Frederick Muriuki Muriithi |
| 2024-10-24 | Check phenocovar files with logging...Build a function-scope logger using the new `scripts.redis_logger.RedisMessageListHandler` log handler to log-out the messages for each phenocovar file being processed in a more thread-safe way. | Frederick Muriuki Muriithi |
| 2024-10-24 | Fix linting and typing errors. | Frederick Muriuki Muriithi |
| 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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