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2024-01-09WIP: Install genotypes from R/qtl2 bundle...Load the genotype information from the R/qtl2 bundle and insert it into the database. Frederick Muriuki Muriithi
2024-01-09Raise 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
2024-01-09Fix linting errorsFrederick Muriuki Muriithi
2024-01-09scripts: Log to redis...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. Frederick Muriuki Muriithi
2024-01-08Add channel authorization.Frederick Muriuki Muriithi
2024-01-08Fix errors with types.Frederick Muriuki Muriithi
2024-01-08Upload R/qtl2 zip bundle and check for errors.Frederick Muriuki Muriithi
2024-01-08Implement "create-population" route.Frederick Muriuki Muriithi
2024-01-08Implement "POST" path for "select-population" route.Frederick Muriuki Muriithi
2024-01-08Use extracted functions and fix bugsFrederick Muriuki Muriithi
2024-01-08Extract common database functions into a separate package.Frederick Muriuki Muriithi
2024-01-05Improve styling.Frederick Muriuki Muriithi
2024-01-05UI to select the population under which the data falls.Frederick Muriuki Muriithi
2024-01-05Initialise R/qtl2 bundle upload path...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. Frederick Muriuki Muriithi
2024-01-05Add missing import.Frederick Muriuki Muriithi
2024-01-05Revert "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
2024-01-04Parse 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 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
2024-01-04Parse 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....* 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
2024-01-03Add tests for `founder_geno` parsing.Frederick Muriuki Muriithi
2024-01-03Parse the phenotype data from the R/qtl2 bundle.Frederick Muriuki Muriithi
2024-01-03Rename argument and add documentation to functions.Frederick Muriuki Muriithi
2024-01-03Extract 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
2024-01-03Refactor: Extract potentially reusable functions...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. Frederick Muriuki Muriithi
2024-01-02Inherit from `gnqc-py` in `guix-bioinformatics`.Frederick Muriuki Muriithi
2024-01-02Cleanup guix definitions in preparation for deployment.Frederick Muriuki Muriithi
2024-01-02Mark tests as unit tests.Frederick Muriuki Muriithi
2024-01-02Abstract away non-transposed file processing...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. Frederick Muriuki Muriithi
2024-01-02Cleanup: Fix linting and typing errors and update docs.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....Check that the parsing of non-transposed geno files. Leave in failing test for transposed geno files. Frederick Muriuki Muriithi
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
2023-12-25Generalise to read both genetic and physical maps.Frederick Muriuki Muriithi
2023-12-25Read genetic map filesFrederick Muriuki Muriithi
2023-12-20Read genotype filesFrederick Muriuki Muriithi
2023-12-20Read R/qtl2 format files...* Set up error objects. * Read the control data. Frederick Muriuki Muriithi
2023-12-20Add `pyyaml` as a dependency....Needed when reading/parsing the R/qtl2 control files. Frederick Muriuki Muriithi
2023-12-20Provide instance_path at client creation.Frederick Muriuki Muriithi
2023-12-20Stop 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
2023-12-20Reduce table columns...Reduce the table columns displayed by javascript for the platforms. Frederick Muriuki Muriithi