| Age | Commit message (Expand) | Author |
|---|---|---|
| 2024-10-24 | Parse entire namespace object rather than individual values. | 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 |
| 2024-10-17 | Extract common functions. | Frederick Muriuki Muriithi |
| 2024-10-14 | Initialise background script for running QC on phenotype bundles. | Frederick Muriuki Muriithi |
| 2024-10-14 | BugFix: Use provided prefix...Use the provided prefix rather than calling `jobs.jobsnamespace()` function that depends of an app context existing. | Frederick Muriuki Muriithi |
| 2024-10-14 | Make addition of arguments independent of each other. | Frederick Muriuki Muriithi |
| 2024-08-16 | Log out correct parameters. | Frederick Muriuki Muriithi |
| 2024-08-13 | Bug: cross reference with NULL cM when "gmap" file is absent...The "gmap" file might not exist in some bundles. In those instances, cross-reference the data without including the genotypes' physical positions (cM). | Frederick Muriuki Muriithi |
| 2024-08-08 | Fix bugs and pass in logger to functions. | Frederick Muriuki Muriithi |
| 2024-08-06 | Pass logger on to inner functions...Pass the logger forward to inner functions to help with debugging things. | Frederick Muriuki Muriithi |
| 2024-07-25 | Rename module: qc_app --> uploader | Frederick Muriuki Muriithi |
| 2024-07-05 | bug: Return a hashable key, not a dict. | Frederick Muriuki Muriithi |
| 2024-07-02 | Call correct method. | Frederick Muriuki Muriithi |
| 2024-07-02 | Ensure no duplicated values for the query. | Frederick Muriuki Muriithi |
| 2024-04-03 | Reduce size of data inserted per query...Reduce the size of data inserted per query since MariDB allows a packet with a maximum size of 1GB. This should hopefully resolve the …OperationalError: (2006, 'Server has gone away') error. | Frederick Muriuki Muriithi |
| 2024-02-15 | Filter out NULL values | Frederick Muriuki Muriithi |
| 2024-02-05 | Fix linting and type errors. | 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 |
| 2024-01-19 | 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 |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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