| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-01-16 | Create intermediate step | Frederick Muriuki Muriithi | |
| We do not have the option to modify the request and then redirect with the modification in place. To go around that, this commit creates an intermediate step that informs the user of their progress, while allowing us to store the filename for future steps. | |||
| 2024-01-16 | Build a sha512 hash from the uploaded file's name and timestamp | Frederick Muriuki Muriithi | |
| Build a sha512 message digest from the file's name and the timestamp of when the file was uploaded. This ensures that the filename is URL-safe, and reduces chances of name conflicts in the upload directory which could lead to data corruption when processing the files and saving the files into the database. | |||
| 2024-01-16 | Filter out items with values of `None`. | Frederick Muriuki Muriithi | |
| The ProbeSetData table does not allow `NULL` for the `value` column for good reason - if there is no value, just don't have a record for that particular sample. | |||
| 2024-01-16 | Provide defaults for various control variables | Frederick Muriuki Muriithi | |
| `na.strings` has a default value of "NA" as stated in https://kbroman.org/qtl2/assets/vignettes/input_files.html#CSV_files quote: > Missing value codes will be specified in the control file (as > na.strings, with default value "NA") and will apply across all > files, so a missing value code for one file cannot be an allowed > value in another file. for `comment.char` > The CSV files can include a header with a set of comment lines > initiated by a value specified in the control file as comment.char > (with default value "#"). for `sep`: The default separator is expected to be the comma, as stated in https://kbroman.org/qtl2/assets/vignettes/input_files.html#field-separator quote: > If the data files use a separator other than a comma ... | |||
| 2024-01-15 | Update imports: `take` was moved to different package. | Frederick Muriuki Muriithi | |
| 2024-01-15 | Process `na.strings` even for default cases | Frederick 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. | |||
| 2024-01-15 | Extract common functional tools to separate package. | Frederick Muriuki Muriithi | |
| 2024-01-15 | Process the `pheno` files. | Frederick Muriuki Muriithi | |
| Process the data in the pheno files and insert it into the database. | |||
| 2024-01-15 | Initialise `install_phenos` script. | Frederick Muriuki Muriithi | |
| 2024-01-15 | Extract common structure into separate modules. | Frederick Muriuki Muriithi | |
| 2024-01-11 | Update pmap data in the database. | Frederick Muriuki Muriithi | |
| 2024-01-11 | Update gmap data in the database | Frederick Muriuki Muriithi | |
| Update the genetic positions (in centiMorgans) in the database. | |||
| 2024-01-11 | Cleanup linting and typing errors. | Frederick Muriuki Muriithi | |
| 2024-01-11 | CLI: Require datasetid as an argument. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Provide convenience functions to avoid subtle call errors | Frederick Muriuki Muriithi | |
| 2024-01-10 | Cross-reference genotype data to the dataset. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Insert genotype data. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Cross-reference individuals to populations. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Insert any new individuals/samples into the database. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Insert any new markers | Frederick Muriuki Muriithi | |
| Insert any new markers found into the database. | |||
| 2024-01-10 | Make identifier column name explicit | Frederick 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. | |||
| 2024-01-09 | WIP: Install genotypes from R/qtl2 bundle | Frederick Muriuki Muriithi | |
| Load the genotype information from the R/qtl2 bundle and insert it into the database. | |||
| 2024-01-09 | Raise exception on reading non-existing file | Frederick 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. | |||
| 2024-01-09 | Fix linting errors | Frederick Muriuki Muriithi | |
| 2024-01-09 | scripts: Log to redis | Frederick Muriuki Muriithi | |
| 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. | |||
| 2024-01-08 | Add channel authorization. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Fix errors with types. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Upload R/qtl2 zip bundle and check for errors. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Implement "create-population" route. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Implement "POST" path for "select-population" route. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Use extracted functions and fix bugs | Frederick Muriuki Muriithi | |
| 2024-01-08 | Extract common database functions into a separate package. | Frederick Muriuki Muriithi | |
| 2024-01-05 | Improve styling. | Frederick Muriuki Muriithi | |
| 2024-01-05 | UI to select the population under which the data falls. | Frederick Muriuki Muriithi | |
| 2024-01-05 | Initialise R/qtl2 bundle upload path | Frederick Muriuki Muriithi | |
| 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. | |||
| 2024-01-05 | Add missing import. | Frederick Muriuki Muriithi | |
| 2024-01-05 | Revert "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. | |||
| 2024-01-04 | 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 | 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 | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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