| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-02-28 | Fix bug: fetch from cursor, not return from cursor.execute(…)load-raw-data-no-parsing | Frederick Muriuki Muriithi | |
| 2024-02-27 | Remove use of instance path in configurations. | Frederick Muriuki Muriithi | |
| 2024-02-21 | Check that samples/cases are consistent | Frederick Muriuki Muriithi | |
| Ensure that **ALL** samples/cases/individuals mentioned in any of the pheno files actually exist in at least one of the geno files. | |||
| 2024-02-21 | Pass 'filename' value to error checker function. | Frederick Muriuki Muriithi | |
| 2024-02-20 | Track filename in the errors | Frederick 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. | |||
| 2024-02-20 | Generalise fetching of samples/cases/individuals. | Frederick Muriuki Muriithi | |
| 2024-02-20 | Read samples from geno file. | Frederick Muriuki Muriithi | |
| 2024-02-20 | Read each file separately | Frederick Muriuki Muriithi | |
| Provide the function 'read_file_data' in the 'r_qtl.r_qtl2' module to read each file in the bundle separately. The function 'file_data' in the 'r_qtl.r_qtl2' module reads *ALL* the files of a particular type (e.g. geno files) and returns a single generator object with the data from *ALL* the files. This does not render itself very useful for error checking. We needed a way to check for errors, and report them for each and every file in the bundle, for easier tracking and fixing. | |||
| 2024-02-20 | Stand-alone function to read control file | Frederick Muriuki Muriithi | |
| Add a function that, given the path to the zip file, will read the control data. It creates its own context manager. | |||
| 2024-02-16 | Replace genotype codes with values in control file. | Frederick Muriuki Muriithi | |
| 2024-02-16 | Convert missing value codes to None | Frederick Muriuki Muriithi | |
| 2024-02-16 | Strip comment lines. | Frederick Muriuki Muriithi | |
| 2024-02-16 | Read raw text data from a file in the zip bundle | Frederick Muriuki Muriithi | |
| 2024-02-16 | Documentation: Add section on configurations. | Frederick Muriuki Muriithi | |
| 2024-02-15 | Filter out NULL values | Frederick Muriuki Muriithi | |
| 2024-02-15 | Refactor checking for user input errors. | Frederick Muriuki Muriithi | |
| 2024-02-15 | Only log out information if the check is actually run. | Frederick Muriuki Muriithi | |
| 2024-02-15 | Verify that the file actually exist | Frederick Muriuki Muriithi | |
| In case a filename is provided, verify that the file actually exists in the upload directory. | |||
| 2024-02-15 | Provide only the file name, not full path. | Frederick Muriuki Muriithi | |
| There are 2 reasons to provide only the filename and not the full path: * Security: We do not want to inadvertently expose the paths to the outside world, or allow users to enter file system paths for this system. * The code does not assume a complete path, rather, it builds the path to the upload directory using the filename received from the user. | |||
| 2024-02-15 | Provide the log messages to the status page. | Frederick Muriuki Muriithi | |
| 2024-02-14 | Provide endpoint to send data to. | Frederick Muriuki Muriithi | |
| 2024-02-14 | Extract upload progress indication code | Frederick Muriuki Muriithi | |
| * Extract the UI elements and code for indicating upload progress into separate, reusable "modules". * Fix bugs arising from changes. | |||
| 2024-02-13 | Add some parallelism to the QC Checks | Frederick Muriuki Muriithi | |
| 2024-02-13 | Provide nice UI progress indicators. | Frederick Muriuki Muriithi | |
| 2024-02-13 | Make "FILE_TYPES" part of public interface for module/package. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Refactor: Use new decimal places checker. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Build generic decimal places checker. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Check for errors in the 'phenose' file. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Check for errors in the 'pheno' file. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Improve error display for generic errors | Frederick Muriuki Muriithi | |
| 2024-02-12 | Collect and display errors on 'geno' files in the bundle. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Add scaffolding for running individual files' QC checks | Frederick Muriuki Muriithi | |
| 2024-02-12 | UI: Provide QC successful results page | Frederick Muriuki Muriithi | |
| 2024-02-12 | Extract missing files check to external function | Frederick Muriuki Muriithi | |
| 2024-02-12 | Retrive and display generic bundle errors | Frederick Muriuki Muriithi | |
| Implement the first QC check for generic errors e.g. missing files in bundle, etc. Display retrieved errors on UI. | |||
| 2024-02-12 | Raise error if file is missing rather than returning a Union value. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Provide the key for each file listed in the control file. | Frederick Muriuki Muriithi | |
| 2024-02-12 | R/qtl2 QC: Set up scaffolding for QC UI | Frederick Muriuki Muriithi | |
| Set up the scaffolding for the flows and UI that will be used when running QC against the uploaded R/qtl2 bundle. This will be fleshed out later, and the UI is likely to change somewhat, down the line. | |||
| 2024-02-12 | Provide better error messaging | Frederick Muriuki Muriithi | |
| Provide a better error message that can help the user figure out what they did wrong and fix it for themselves instead of the older, cryptic and extremely unhelpful error message. | |||
| 2024-02-08 | Generalise error retrieval: extract common structure | Frederick Muriuki Muriithi | |
| Extract the common structure into a separate function and pass in checkers that return the errors they find. | |||
| 2024-02-08 | Use error objects rather than plain tuple values. | Frederick Muriuki Muriithi | |
| 2024-02-07 | ShortName is optional, remove check and set default | Frederick Muriuki Muriithi | |
| The ShortName is optional, and can be set to the same value as Name. This commit removes the check that made it mandatory. | |||
| 2024-02-07 | Prevent infinite redirect. | Frederick Muriuki Muriithi | |
| 2024-02-07 | Fix error display: setup correct error class | Frederick Muriuki Muriithi | |
| 2024-02-07 | Set up limits for inputs in UI | Frederick Muriuki Muriithi | |
| 2024-02-06 | Check that pheno values are numerical and at least 3 decimal places | Frederick Muriuki Muriithi | |
| 2024-02-06 | Bug: Fix routing issues | Frederick Muriuki Muriithi | |
| Fix the routing issues that were redirecting the flow to the wrong endpoints. | |||
| 2024-02-05 | Run QC on the 'geno' file in R/qtl2 bundle. | Frederick Muriuki Muriithi | |
| 2024-02-05 | Check that data in geno file is valid | Frederick Muriuki Muriithi | |
| Add a function to ensure the values in the geno files are all listed in the control data under the "genotypes" key. | |||
| 2024-02-05 | Add a QC step: Check all listed files exist | Frederick Muriuki Muriithi | |
| Add a QC step to the R/qtl2 bundle processing - check that all files that are listed in the control file also exist in the bundle. | |||
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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