| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 5 days | Use specialised template renderer for phenotypes. | Frederick Muriuki Muriithi | |
| Use the specialised template renderer to keep the rendering consistent. | |||
| 5 days | UI: Remove extraneous text in "View*" pages. | Frederick Muriuki Muriithi | |
| 5 days | Improve breadcrumbs | Frederick Muriuki Muriithi | |
| Update the breadcrumb links such that each will lead back the parent section rather than to generic section pages. This is updated for the relevant parts of the UI. | |||
| 6 days | Prevent user from continuing on error. | Frederick Muriuki Muriithi | |
| 6 days | Prevent errors' table header from scrolling away. | Frederick Muriuki Muriithi | |
| 6 days | Handle common typo likely to exist in control files. | Frederick Muriuki Muriithi | |
| 12 days | Display the files metadata in progress section. | Frederick Muriuki Muriithi | |
| 12 days | Retrieve job files metadata. | Frederick Muriuki Muriithi | |
| 12 days | Fix some linting and mypy issues. | Frederick Muriuki Muriithi | |
| 12 days | UI Styling: make table body text slightly smaller. | Frederick Muriuki Muriithi | |
| 12 days | UI: Clip text that is too long. | Frederick Muriuki Muriithi | |
| 12 days | Improve error text | Frederick Muriuki Muriithi | |
| Move the list to the end of the text to make it easier to clip text in the UI. | |||
| 12 days | Update file metadata using a mapping | Frederick Muriuki Muriithi | |
| Update the metadata using a mapping rather than updating a field at a time to make it easier to ensure everything is updated in one go. | |||
| 12 days | Provide consistent way to build file-specific fully-qualified keys | Frederick Muriuki Muriithi | |
| 12 days | Improve UI: stdout/stderr output | Frederick Muriuki Muriithi | |
| Add styling to section and limit the height of the content. | |||
| 12 days | Display cell value | Frederick Muriuki Muriithi | |
| Display the cell value to enable the user compare the error message to the actual value, in order to figure out how to fix the error(s). | |||
| 12 days | Improve UI: Move if check out of table | Frederick Muriuki Muriithi | |
| Create a new section for the errors display, and only display the table if there is at least one error. | |||
| 12 days | Enable limiting of number of errors to fetch. | Frederick Muriuki Muriithi | |
| 12 days | Save 'pheno' errors in redis as they are found. | Frederick Muriuki Muriithi | |
| 12 days | Add some phenocovar metadata. | Frederick Muriuki Muriithi | |
| 12 days | Fetch a jobs errors from its errors lists. | Frederick Muriuki Muriithi | |
| 12 days | Save phenocovar errors in redis as they are found. | Frederick Muriuki Muriithi | |
| 12 days | Pass the redis connection and fully qualified job id | Frederick Muriuki Muriithi | |
| Pass the redis connection on to the function used to build main since it might need to use a connection to redis. Also pass the computed fully qualified job id rather than recomputing it every time. Update dependent functions to take the new arguments. | |||
| 12 days | Cleanup linting and type (mypy) errors. | Frederick Muriuki Muriithi | |
| 12 days | Wrap everything in try-catch to handle errors gracefully. | Frederick Muriuki Muriithi | |
| Put everything in the build_main function within a try-catch block to ensure we capture all exceptions that might occur in different scripts and log them out. This helps with debugging errors in the asynchronous scripts. | |||
| 13 days | Add emphasis to important point. | Frederick Muriuki Muriithi | |
| 13 days | Fix typo. | Frederick Muriuki Muriithi | |
| 13 days | Send logs to STDOUT too. | Frederick Muriuki Muriithi | |
| 13 days | Launch job and redirect to job status page. | Frederick Muriuki Muriithi | |
| 13 days | Add UI to view status of the job as it runs. | Frederick Muriuki Muriithi | |
| 13 days | Return 0 on completion of QC processing. | Frederick Muriuki Muriithi | |
| 13 days | Change from 'pending' to 'started' on entry to script. | Frederick Muriuki Muriithi | |
| Update the status of the job from 'pending' to 'started' at the entry-point of the script. | |||
| 2024-11-22 | Remove local code that does db connection. | Frederick Muriuki Muriithi | |
| Reuse the code in gn-libs for connecting to the database, rather than using the replicated local code. | |||
| 2024-11-22 | Use gn-libs code for db connection. | Frederick Muriuki Muriithi | |
| Use the code in gn-libs to connect to the database, rather than a local module. | |||
| 2024-11-22 | Add gn-libs as a dependency. | Frederick Muriuki Muriithi | |
| 2024-10-24 | Reduce number of local variables created in function. | Frederick Muriuki Muriithi | |
| Use the values in the argparse.Namespace object directly to avoid creating many local variables. | |||
| 2024-10-24 | Add `jobid` to extraction directory | Frederick Muriuki Muriithi | |
| Add the job id to help "group" files that belong to the same job. | |||
| 2024-10-24 | Check pheno, phenose, and phenonum files with logging | Frederick Muriuki Muriithi | |
| Add logging to the `qc_pheno_file` function so that we get the messages pushed to redis for every file that is being checked for errors. | |||
| 2024-10-24 | Check phenocovar files with logging | Frederick Muriuki Muriithi | |
| Build a function-scope logger using the new `scripts.redis_logger.RedisMessageListHandler` log handler to log-out the messages for each phenocovar file being processed in a more thread-safe way. | |||
| 2024-10-24 | Fix linting and typing errors. | Frederick Muriuki Muriithi | |
| 2024-10-24 | Add a `--loglevel` argument to select loglevel in scripts | Frederick Muriuki Muriithi | |
| To enable selection of log levels within scripts, this commit adds the `--loglevel` argument to the list of arguments that can be passed to scripts. | |||
| 2024-10-24 | Parse entire namespace object rather than individual values. | Frederick Muriuki Muriithi | |
| 2024-10-24 | Move logger creation to `build_main` function | Frederick Muriuki Muriithi | |
| Since the module-level loggers are built mostly the same, move the creation of the logger to the more general function to reduce repetition. | |||
| 2024-10-24 | Add handler to send log messages to specific Redis list | Frederick Muriuki Muriithi | |
| Class `RedisMessageListHandler` builds a log handler that pushes any messages logged out to the redis list specified by its `fullyqualifiedkey` argument. | |||
| 2024-10-24 | Update Redis prefix settings. | Frederick Muriuki Muriithi | |
| 2024-10-24 | Don't compute settings in configuration file. | Frederick Muriuki Muriithi | |
| 2024-10-23 | Add documentation on background jobs. | Frederick Muriuki Muriithi | |
| 2024-10-22 | Document emergent general QC structure for CSV files. | Frederick Muriuki Muriithi | |
| 2024-10-22 | Refactor `qc_pheno_file` and reuse it for different file types. | Frederick Muriuki Muriithi | |
| The QC/QA steps taken by the `qc_pheno_file` function are very similar across the "pheno", "phenose" and "phenonum" files. This commit makes the `qc_pheno_file` function a higher-order function and we pass the file-type specific check(s) as a callable (function) to be used for the QC/QA process. | |||
| 2024-10-22 | Check for errors in `pheno` files. | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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