| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | |
| 2022-06-22 | Test the results pages | Frederick Muriuki Muriithi | |
| 2022-06-21 | Test the progress indication feature | Frederick Muriuki Muriithi | |
| 2022-06-21 | Rename fixture: fixture gives back the redis url, not a server | Frederick Muriuki Muriithi | |
| 2022-06-21 | Update tests: Ensure errors return status code 400 | Frederick Muriuki Muriithi | |
| 2022-06-21 | Test the upload of zip files works as expected | Frederick Muriuki Muriithi | |
| - Ensure errors respond with status code 400 - Ensure error messages are displayed for any invalid zip file that is uploaded. | |||
| 2022-06-17 | Test endpoint '/parse/parse' | Frederick Muriuki Muriithi | |
| * Ensure error messages are displayed if a request is made to the '/parse/parse' endpoint with invalid, or missing data. | |||
| 2022-06-16 | Add more UI tests | Frederick Muriuki Muriithi | |
| - Test upload with missing or invalid data - Test triggering the parsing of the file | |||
| 2022-06-15 | Setup test fixtures and initial tests for web-UI | Frederick Muriuki Muriithi | |
| 2022-06-10 | Update tests: Accept zeroes as valid values | Frederick Muriuki Muriithi | |
| 2022-05-18 | Remove obsoleted code. Fix linting errors. | Frederick Muriuki Muriithi | |
| Remove the old code that relied on exceptions to parse errors in the uploaded files. | |||
| 2022-05-18 | Parse files with new non-exception functions | Frederick Muriuki Muriithi | |
| Parse the files with the new functions that return error objects instead of raising exceptions | |||
| 2022-05-18 | Return errors when found or None otherwise | Frederick Muriuki Muriithi | |
| This commit adds a number of functions that return the error object when an error is found, or `None` otherwise. It avoids the use of exceptions as control flow constructs. | |||
| 2022-05-02 | Optimise strain names parsing | Frederick Muriuki Muriithi | |
| - Use a way faster way of parsing the strains file | |||
| 2022-04-25 | Advance seek_position on error | Frederick Muriuki Muriithi | |
| Advance the seek position, once we have yielded up an error to causing an infinite loop in certain conditions, where the `parse_errors` function ends up resuming the gile in the same position once it experiences an error. | |||
| 2022-04-25 | `take`: function to select a few items from an iterable | Frederick Muriuki Muriithi | |
| To avoid processing all the items in an iterable, the `take` function is added in this commit. It realised a limited number (specified at call time) of items from the iterable given. | |||
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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