| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-02-20 | Generalise fetching of samples/cases/individuals. | Frederick Muriuki Muriithi | |
| 2024-02-20 | Read samples from geno file. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Build generic decimal places checker. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Provide the key for each file listed in the control file. | Frederick Muriuki Muriithi | |
| 2024-02-08 | Use error objects rather than plain tuple values. | Frederick Muriuki Muriithi | |
| 2024-02-06 | Check that pheno values are numerical and at least 3 decimal places | Frederick Muriuki Muriithi | |
| 2024-02-05 | Check that data in geno file is valid | Frederick Muriuki Muriithi | |
| Add a function to ensure the values in the geno files are all listed in the control data under the "genotypes" key. | |||
| 2024-02-05 | Fix linting and type errors. | Frederick Muriuki Muriithi | |
| 2024-02-05 | Retrieve list of all files, and list of missing files | Frederick Muriuki Muriithi | |
| Add QC a function to list all files listed in the control file, and another to list only the files missing from the bundle. | |||
| 2024-02-02 | Ensure control file defaults are set up in code. | Frederick Muriuki Muriithi | |
| 2024-01-24 | Checks: Update code and tests to ensure all checks pass. | Frederick Muriuki Muriithi | |
| 2024-01-23 | Tests: Use prefixes in tests rather than starting redis server | Frederick Muriuki Muriithi | |
| It's easier, and more robust to put the data under a prefix within a redis database rather than try to run a redis server, especially within the test environment. This commit updates the tests to use a redis prefix instead. | |||
| 2024-01-20 | Fetch sample/case names from database | Frederick Muriuki Muriithi | |
| 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 | |||
| 2024-01-15 | Update imports: `take` was moved to different package. | Frederick Muriuki Muriithi | |
| 2024-01-15 | Process `na.strings` even for default cases | Frederick Muriuki Muriithi | |
| There was a bug where the `na.strings` were not processed correctly if the user called the `r_qtl.r_qtl2.file_data(...)` function without explicitly providing the `process_*` arguments. This commit fixes that. | |||
| 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 | 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. | |||
| 2024-01-05 | 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 | 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. | |||
| 2024-01-02 | Mark tests as unit tests. | Frederick Muriuki Muriithi | |
| 2023-12-28 | Rework parsing of transposed geno files. | Frederick Muriuki Muriithi | |
| 2023-12-28 | Handle transposed geno files. | Frederick Muriuki Muriithi | |
| 2023-12-27 | Tests: Test parsing of non-transposed geno files. | Frederick Muriuki Muriithi | |
| Check that the parsing of non-transposed geno files. Leave in failing test for transposed geno files. | |||
| 2023-12-27 | Tests: Test parsing of pmap files. Merge testing of map files. | Frederick Muriuki Muriithi | |
| 2023-12-27 | Tests: Add tests for parsing gmap files. | Frederick Muriuki Muriithi | |
| 2023-12-20 | Provide instance_path at client creation. | Frederick Muriuki Muriithi | |
| 2023-12-20 | Stop relying on "GUIX_ENVIRONMENT" envvar | Frederick Muriuki Muriithi | |
| While we run the service under GNU Guix, there is no telling where anyone else with access to the code (which is open-source) will run the application. This means we need a more dynamic way to get the paths for any commands we choose to run. | |||
| 2023-11-24 | QC: Check for only one decimal place. | Frederick Muriuki Muriithi | |
| 2023-11-15 | Linting: Fix linting errors. | Frederick Muriuki Muriithi | |
| 2022-11-16 | tests: Fix some failing tests | Frederick Muriuki Muriithi | |
| 2022-11-16 | qc: Allow whole numbers or numbers where the decimals are all zeroes | Frederick Muriuki Muriithi | |
| 2022-08-31 | Commit missing files. | Frederick Muriuki Muriithi | |
| 2022-08-31 | Update test: use new script name. | Frederick Muriuki Muriithi | |
| 2022-07-07 | Fix test | Frederick Muriuki Muriithi | |
| 2022-06-28 | Check for inconsistent columns | Frederick Muriuki Muriithi | |
| The number columns in each contents line should be equal to the nember of columns in the header line. | |||
| 2022-06-22 | Test zipfiles uploads: commit forgotten tests | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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