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2024-02-28tests: test with just the message - don't include markupFrederick Muriuki Muriithi
Markup can, and will change as improvements are made, but the error messages will not change that often, plus that is what we want to actually test for, not the markup.
2024-02-28tests: Update unit tests: remove use of obsoleted functions.Frederick Muriuki Muriithi
2024-02-20Track filename in the errorsFrederick Muriuki Muriithi
R/qtl2 bundles can contain more than one file, of the same type. When errors are encountered in any of the files, we need to be able to inform the user which file it is, in addition to the line and column number.
2024-02-20Generalise fetching of samples/cases/individuals.Frederick Muriuki Muriithi
2024-02-20Read samples from geno file.Frederick Muriuki Muriithi
2024-02-12Build generic decimal places checker.Frederick Muriuki Muriithi
2024-02-12Provide the key for each file listed in the control file.Frederick Muriuki Muriithi
2024-02-08Use error objects rather than plain tuple values.Frederick Muriuki Muriithi
2024-02-06Check that pheno values are numerical and at least 3 decimal placesFrederick Muriuki Muriithi
2024-02-05Check that data in geno file is validFrederick Muriuki Muriithi
Add a function to ensure the values in the geno files are all listed in the control data under the "genotypes" key.
2024-02-05Fix linting and type errors.Frederick Muriuki Muriithi
2024-02-05Retrieve list of all files, and list of missing filesFrederick 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.
2024-02-02Ensure control file defaults are set up in code.Frederick Muriuki Muriithi
2024-01-24Checks: Update code and tests to ensure all checks pass.Frederick Muriuki Muriithi
2024-01-23Tests: Use prefixes in tests rather than starting redis serverFrederick 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.
2024-01-20Fetch sample/case names from databaseFrederick 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
2024-01-15Update imports: `take` was moved to different package.Frederick Muriuki Muriithi
2024-01-15Process `na.strings` even for default casesFrederick 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.
2024-01-10Make identifier column name explicitFrederick 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.
2024-01-09Raise exception on reading non-existing fileFrederick 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.
2024-01-05Add missing import.Frederick Muriuki Muriithi
2024-01-05Revert "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.
2024-01-04Parse sex information from R/qtl bundle.Frederick Muriuki Muriithi
2024-01-04Parse cross information from R/qtl2 bundle.Frederick Muriuki Muriithi
2024-01-04Process sex and cross information data in "covar" files.Frederick Muriuki Muriithi
2024-01-04Rename test moduleFrederick Muriuki Muriithi
While 'covar' files can contain cross information, they do not have to, and therefore, we need to test for cross information separately.
2024-01-04Parse multiple files with same file key.Frederick Muriuki Muriithi
2024-01-04Test parsing of multiple files for single keyFrederick Muriuki Muriithi
2024-01-04Add tests for parsing cross information (covar) files.Frederick Muriuki Muriithi
2024-01-04Add tests for parsing 'phenocovar' files.Frederick Muriuki Muriithi
2024-01-04Rename test module.Frederick Muriuki Muriithi
2024-01-03Use generic parser. Remove obsoleted functions.Frederick Muriuki Muriithi
2024-01-03Parse 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
2024-01-03Add tests for `founder_geno` parsing.Frederick Muriuki Muriithi
2024-01-03Parse the phenotype data from the R/qtl2 bundle.Frederick Muriuki Muriithi
2024-01-03Extract 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.
2024-01-02Mark tests as unit tests.Frederick Muriuki Muriithi
2023-12-28Rework parsing of transposed geno files.Frederick Muriuki Muriithi
2023-12-28Handle transposed geno files.Frederick Muriuki Muriithi
2023-12-27Tests: 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.
2023-12-27Tests: Test parsing of pmap files. Merge testing of map files.Frederick Muriuki Muriithi
2023-12-27Tests: Add tests for parsing gmap files.Frederick Muriuki Muriithi
2023-12-20Provide instance_path at client creation.Frederick Muriuki Muriithi
2023-12-20Stop relying on "GUIX_ENVIRONMENT" envvarFrederick 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.
2023-11-24QC: Check for only one decimal place.Frederick Muriuki Muriithi
2023-11-15Linting: Fix linting errors.Frederick Muriuki Muriithi
2022-11-16tests: Fix some failing testsFrederick Muriuki Muriithi
2022-11-16qc: Allow whole numbers or numbers where the decimals are all zeroesFrederick Muriuki Muriithi
2022-08-31Commit missing files.Frederick Muriuki Muriithi
2022-08-31Update test: use new script name.Frederick Muriuki Muriithi