| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | Frederick Muriuki Muriithi | |
| Update the genetic positions (in centiMorgans) in the database. | |||
| 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 | Frederick Muriuki Muriithi | |
| Insert any new markers found into the database. | |||
| 2024-01-10 | Make identifier column name explicit | Frederick Muriuki Muriithi | |
| Since the R/qtl2 bundle generator could name the identifier column anything, this commit converts the incoming identifier column name into something explicit that we know and can use. | |||
| 2024-01-09 | WIP: Install genotypes from R/qtl2 bundle | Frederick Muriuki Muriithi | |
| Load the genotype information from the R/qtl2 bundle and insert it into the database. | |||
| 2024-01-09 | Raise exception on reading non-existing file | Frederick Muriuki Muriithi | |
| The validation checks ensure that whatever files are listed in the control file exist in the zip file bundle. It is still possible, however, that the code tries to read a file that does not exist in the file and is not listed in the control file. In those cases, raise the appropriate exception. | |||
| 2024-01-09 | Fix linting errors | Frederick Muriuki Muriithi | |
| 2024-01-09 | scripts: Log to redis | Frederick Muriuki Muriithi | |
| 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. | |||
| 2024-01-08 | Add channel authorization. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Fix errors with types. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Upload R/qtl2 zip bundle and check for errors. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Implement "create-population" route. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Implement "POST" path for "select-population" route. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Use extracted functions and fix bugs | Frederick Muriuki Muriithi | |
| 2024-01-08 | Extract common database functions into a separate package. | Frederick Muriuki Muriithi | |
| 2024-01-05 | Improve styling. | Frederick Muriuki Muriithi | |
| 2024-01-05 | UI to select the population under which the data falls. | Frederick Muriuki Muriithi | |
| 2024-01-05 | Initialise R/qtl2 bundle upload path | Frederick Muriuki Muriithi | |
| Initialise the upload path for R/qtl2 bundles. This commit adds UI that allows the user to select from existing species, before proceeding to the next stage. | |||
| 2024-01-05 | Add missing import. | Frederick Muriuki Muriithi | |
| 2024-01-05 | Revert "QC: Check for only one decimal place." | Frederick Muriuki Muriithi | |
| This reverts commit c213b0010c3ddc8d3215adab65bd489a9b884e30. After a larger discussion with Arthur, Rob and Pjotr present, it was verified that the strict checks are important. This reverts the commit that allowed for looser checks. | |||
| 2024-01-04 | Parse sex information from R/qtl bundle. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Parse cross information from R/qtl2 bundle. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Process sex and cross information data in "covar" files. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Rename test module | Frederick Muriuki Muriithi | |
| While 'covar' files can contain cross information, they do not have to, and therefore, we need to test for cross information separately. | |||
| 2024-01-04 | Parse multiple files with same file key. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Test parsing of multiple files for single key | Frederick Muriuki Muriithi | |
| 2024-01-04 | Add tests for parsing cross information (covar) files. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Add tests for parsing 'phenocovar' files. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Rename test module. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Use generic parser. Remove obsoleted functions. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Parse founder_geno files. Generalise parsing files. | Frederick Muriuki Muriithi | |
| * Add tests for parsing "founder_geno" files * Extract common file parsing structure out to more general function * Use generic function to parse "founder_geno" file in test | |||
| 2024-01-03 | Add tests for `founder_geno` parsing. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Parse the phenotype data from the R/qtl2 bundle. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Rename argument and add documentation to functions. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Extract processing of transposed files into reusable function. | Frederick Muriuki Muriithi | |
| The processing of transposed files is similar across files. This commit extracts the common parts into a separate function. | |||
| 2024-01-03 | Refactor: Extract potentially reusable functions | Frederick Muriuki Muriithi | |
| The processing of transposed files is probably going to be very similar, thus the need to extract some reusable code from the geno-file-specific function in preparation. | |||
| 2024-01-02 | Inherit from `gnqc-py` in `guix-bioinformatics`. | Frederick Muriuki Muriithi | |
| 2024-01-02 | Cleanup guix definitions in preparation for deployment. | Frederick Muriuki Muriithi | |
| 2024-01-02 | Mark tests as unit tests. | Frederick Muriuki Muriithi | |
| 2024-01-02 | Abstract away non-transposed file processing | Frederick Muriuki Muriithi | |
| Since the processing of non-transposed files is mostly similar, abstract away the common operations into a separate function and use the function instead of repeating the same pattern of code throughout the codebase. | |||
| 2024-01-02 | Cleanup: Fix linting and typing errors and update docs. | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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