| Age | Commit message (Expand) | Author |
|---|
| 2024-01-10 | Make identifier column name explicit...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.
| Frederick Muriuki Muriithi |
| 2024-01-09 | Raise exception on reading non-existing file...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.
| Frederick Muriuki Muriithi |
| 2024-01-05 | Add missing import. | Frederick Muriuki Muriithi |
| 2024-01-05 | Revert "QC: Check for only one decimal place."...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.
| Frederick Muriuki Muriithi |
| 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...While 'covar' files can contain cross information, they do not have
to, and therefore, we need to test for cross information separately.
| Frederick Muriuki Muriithi |
| 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....* 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
| Frederick Muriuki Muriithi |
| 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....The processing of transposed files is similar across files. This
commit extracts the common parts into a separate function.
| Frederick Muriuki Muriithi |
| 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....Check that the parsing of non-transposed geno files.
Leave in failing test for transposed geno files.
| Frederick Muriuki Muriithi |
| 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...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.
| Frederick Muriuki Muriithi |
| 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...The number columns in each contents line should be equal to the nember
of columns in the header line.
| Frederick Muriuki Muriithi |
| 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...- Ensure errors respond with status code 400
- Ensure error messages are displayed for any invalid zip file that is
uploaded.
| Frederick Muriuki Muriithi |
| 2022-06-17 | Test endpoint '/parse/parse'...* Ensure error messages are displayed if a request is made to the
'/parse/parse' endpoint with invalid, or missing data.
| Frederick Muriuki Muriithi |
| 2022-06-16 | Add more UI tests...- Test upload with missing or invalid data
- Test triggering the parsing of the file
| Frederick Muriuki Muriithi |
| 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....Remove the old code that relied on exceptions to parse errors in the
uploaded files.
| Frederick Muriuki Muriithi |
| 2022-05-18 | Parse files with new non-exception functions...Parse the files with the new functions that return error objects
instead of raising exceptions
| Frederick Muriuki Muriithi |
| 2022-05-18 | Return errors when found or None otherwise...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.
| Frederick Muriuki Muriithi |
| 2022-05-02 | Optimise strain names parsing...- Use a way faster way of parsing the strains file
| Frederick Muriuki Muriithi |
| 2022-04-25 | Advance seek_position on error...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.
| Frederick Muriuki Muriithi |
| 2022-04-25 | `take`: function to select a few items from an iterable...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.
| Frederick Muriuki Muriithi |
