| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | Rename argument and add documentation to functions. | 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. | |||
| 2024-01-03 | Refactor: Extract potentially reusable functions | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | Frederick Muriuki Muriithi | |
| 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. | |||
| 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. | 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 | |
| 2023-12-25 | 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 | Frederick Muriuki Muriithi | |
| * Set up error objects. * Read the control data. | |||
| 2023-12-20 | Add `pyyaml` as a dependency. | Frederick Muriuki Muriithi | |
| Needed when reading/parsing the R/qtl2 control files. | |||
| 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. | |||
| 2023-12-20 | Reduce table columns | Frederick Muriuki Muriithi | |
| Reduce the table columns displayed by javascript for the platforms. | |||
| 2023-12-20 | Fix ID column key | Frederick Muriuki Muriithi | |
| 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. | |||
| 2023-12-20 | Add favicon | Frederick Muriuki Muriithi | |
| Add a favicon to reduce noise in the logs due to failed requests. | |||
| 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. | Frederick Muriuki Muriithi | |
| 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. | |||
| 2023-12-11 | samples: Fix bugs in code saving samples to db | Frederick Muriuki Muriithi | |
| * Check whether first row in file is for headings * Break infinite loop: check batch has content * Update saving of uploaded files | |||
| 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 | Frederick Muriuki Muriithi | |
| Implements the code enabling the upload of the samples/cases to the database. | |||
| 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 | Frederick Muriuki Muriithi | |
| Fix a bug that was causing the data insertion to fail. | |||
| 2023-11-30 | Handle duplicate dataset creation error | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | Frederick Muriuki Muriithi | |
| 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. | |||
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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