| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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. | |||
| 2024-02-05 | Fix linting and type errors. | Frederick Muriuki Muriithi | |
| 2024-02-05 | Do general bundle validation and show errors | Frederick Muriuki Muriithi | |
| * Display any and all errors on the UI * Move `validate_bundle` to QC module and refactor to use `missing_files` | |||
| 2024-02-05 | Retrieve list of all files, and list of missing files | Frederick Muriuki Muriithi | |
| Add QC a function to list all files listed in the control file, and another to list only the files missing from the bundle. | |||
| 2024-02-05 | Update UI documentation | Frederick Muriuki Muriithi | |
| Improve the UI documentation by making it more explicit what each section deals with to help aleviate confusion of what the different features do. | |||
| 2024-02-02 | List file types in a single place for easier reuse | Frederick Muriuki Muriithi | |
| 2024-02-02 | Ensure control file defaults are set up in code. | Frederick Muriuki Muriithi | |
| 2024-02-02 | Bug: Specify DictCursor class to return dict-like result | Frederick Muriuki Muriithi | |
| Without specifying the `cursorclass`, the result is a tuple of the form: ((query_col01_val, query_col02_val, ...), ...) where the ellipsis specify the possibility of more than one of the previous form. We specify the DictCursor class instead so that the form changes to: ({query_col01_name: query_col01_val, ...}, ...) which allows us to pick the value we want with a string index. | |||
| 2024-01-24 | Checks: Update code and tests to ensure all checks pass. | Frederick Muriuki Muriithi | |
| 2024-01-24 | redis-prefix: update "upload samples" path | Frederick Muriuki Muriithi | |
| 2024-01-24 | redis-prefix: Update "insert data" path. | Frederick Muriuki Muriithi | |
| 2024-01-24 | redis-prefix: Update file validation code | Frederick Muriuki Muriithi | |
| Update the file validation script and routes to use the redis prefix for jobs. | |||
| 2024-01-23 | Update scripts to use redis prefix. | Frederick Muriuki Muriithi | |
| 2024-01-23 | Add prefix to redis keys | Frederick Muriuki Muriithi | |
| Since the GNQC application might find itself sharing the same redis server and/or database with other applications, add a prefix to its keys. | |||
| 2024-01-23 | Tests: Use prefixes in tests rather than starting redis server | Frederick Muriuki Muriithi | |
| It's easier, and more robust to put the data under a prefix within a redis database rather than try to run a redis server, especially within the test environment. This commit updates the tests to use a redis prefix instead. | |||
| 2024-01-22 | UI: Fix some UI bugs. | Frederick Muriuki Muriithi | |
| 2024-01-22 | scripts: Pass in logger to get detailed updates. | Frederick Muriuki Muriithi | |
| 2024-01-22 | UI: Show progress of R/qtl2 bundle processing. | Frederick Muriuki Muriithi | |
| 2024-01-20 | Fetch sample/case names from database | Frederick Muriuki Muriithi | |
| Fetch the sample/case names from the database rather than from a static file in the repository. Issue: https://issues.genenetwork.org/issues/quality-control/read-samples-from-database-by-species | |||
 |
index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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