| Age | Commit message (Expand) | Author |
|---|---|---|
| 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 | Rename argument and add documentation to functions. | 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 |
| 2024-01-03 | Refactor: 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 |
| 2024-01-02 | Inherit from `gnqc-py` in `guix-bioinformatics`. | Frederick Muriuki Muriithi |
| 2024-01-02 | Cleanup guix definitions in preparation for deployment. | Frederick Muriuki Muriithi |
| 2024-01-02 | Mark tests as unit tests. | Frederick Muriuki Muriithi |
| 2024-01-02 | Abstract 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 |
| 2024-01-02 | Cleanup: Fix linting and typing errors and update docs. | 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 |
| 2023-12-25 | Generalise to read both genetic and physical maps. | Frederick Muriuki Muriithi |
| 2023-12-25 | Read genetic map files | Frederick Muriuki Muriithi |
| 2023-12-20 | Read genotype files | Frederick Muriuki Muriithi |
| 2023-12-20 | Read R/qtl2 format files...* Set up error objects. * Read the control data. | Frederick Muriuki Muriithi |
| 2023-12-20 | Add `pyyaml` as a dependency....Needed when reading/parsing the R/qtl2 control 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 |
| 2023-12-20 | Reduce table columns...Reduce the table columns displayed by javascript for the platforms. | Frederick Muriuki Muriithi |
| 2023-12-20 | Fix ID column key...Fix the wrong assumption that the ID key will always be "ProbeSetID". The key for the ID column could change from study to study or dataset to dataset. | Frederick Muriuki Muriithi |
| 2023-12-20 | Add favicon...Add a favicon to reduce noise in the logs due to failed requests. | Frederick Muriuki Muriithi |
| 2023-12-19 | Commit missing templates. | Frederick Muriuki Muriithi |
| 2023-12-19 | Bug: Commit population before trying to upload data. | Frederick Muriuki Muriithi |
| 2023-12-18 | Samples: Hook-up external async script to upload the samples. | Frederick Muriuki Muriithi |
| 2023-12-14 | samples: Create external script and fix some bugs. | Frederick Muriuki Muriithi |
| 2023-12-14 | Pass connection to `species_by_id` function....To make `species_by_id` function reusable even outside of the application context, pass in the database connection instead of creating the connection inside the function. | Frederick Muriuki Muriithi |
| 2023-12-11 | samples: Fix bugs in code saving samples to db...* Check whether first row in file is for headings * Break infinite loop: check batch has content * Update saving of uploaded files | Frederick Muriuki Muriithi |
| 2023-12-07 | Samples: Read an save data to db. | Frederick Muriuki Muriithi |
| 2023-12-07 | Samples: Provide preview feature. | Frederick Muriuki Muriithi |
| 2023-12-06 | Feature: Upload Samples/Cases...Implements the code enabling the upload of the samples/cases to the database. | Frederick Muriuki Muriithi |
| 2023-11-30 | Remove link to non-existent file. | Frederick Muriuki Muriithi |
| 2023-11-30 | Error logging: Add more details to help with debugging. | Frederick Muriuki Muriithi |
| 2023-11-30 | Bug: Fix insertion error...Fix a bug that was causing the data insertion to fail. | Frederick Muriuki Muriithi |
| 2023-11-30 | Handle duplicate dataset creation error...Notify the user when they try to create a new dataset that has the same name as an existing dataset and give them the chance to fix it before continuing. | Frederick Muriuki Muriithi |
| 2023-11-30 | Fix errors caught by pylint and mypy. | Frederick Muriuki Muriithi |
| 2023-11-28 | Handle generic MySQL errors at the top-level. | Frederick Muriuki Muriithi |
| 2023-11-28 | Capture, log and handle generic exceptions...Handle any and all unforeseen error conditions gracefully by capturing the exceptions, logging out for debug purposes and providing the user with a generic error page. | Frederick Muriuki Muriithi |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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