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2022-06-02Add an error display to the progress status reportFrederick Muriuki Muriithi
Enable the progress status page to show all the errors found at any point during the processing of the file.
2022-05-27Remove unnecessary print statementFrederick Muriuki Muriithi
2022-05-20Use standard-error rather than standard_error for consistencyFrederick Muriuki Muriithi
The CLI scripts use "standard-error" so update the web version to fit in with that.
2022-05-20Fix minor bugsFrederick Muriuki Muriithi
2022-05-20Handle errorsFrederick Muriuki Muriithi
Implement code to handle errors in the processing of files.
2022-05-19Update Web-UI: use new error collection paradigmFrederick Muriuki Muriithi
- README.org: document how to run scripts manually - manifest.scm: remove python-rq as a dependency - qc_app/jobs.py: rework job launching and processing - qc_app/parse.py: use reworked job processing - qc_app/templates/job_progress.html: display progress correctly - qc_app/templates/parse_results.html: display final results - scripts/worker.py: new worker script
2022-05-02Optimise strain names parsingFrederick Muriuki Muriithi
- Use a way faster way of parsing the strains file
2022-04-28Use sqlite3 to save the jobs metadataFrederick Muriuki Muriithi
* Use sqlite to save the jobs metadata and enable UI update of the progress for large files
2022-04-28Update queuing and display results of file parsingFrederick Muriuki Muriithi
* Make the 'worker' functions free from needing the application context by passing all the details they need as arguments. * Enable the display of parsing results.
2022-04-26Fix issues caught processing the jobsFrederick Muriuki Muriithi
* Create and push the application context for the worker functions * Fix the update of meta fields
2022-04-26Queue file parsing jobsFrederick Muriuki Muriithi
Enable the queuing of file parsing jobs, since the files could be really large and take a long time to parse and present results. * etc/default_config.py: Add default config for redis server * manifest.scm: Add redis, and rq as dependencies * qc_app/__init__.py * qc_app/jobs.py: module to hold utilities for management of the jobs * qc_app/parse.py: Enqueue the job - extract file-parsing code to callable function * qc_app/templates/base.html: Enable addition of extra meta tags * qc_app/templates/job_progress.html: template to display job progress * qc_app/templates/no_such_job.html: template to indicate when a job id is invalid * quality_control/parsing.py: Add the total size parsed so far
2022-04-25Call parsing function. Fix a few issues.Frederick Muriuki Muriithi
* qc_app/entry.py: Pass filetype onward to parsing endpoint * qc_app/parse.py: Call the function(s) necessary to parse a file * quality_control/errors.py: Fix argument passing to super class
2022-04-25Implement file uploadFrederick Muriuki Muriithi
2022-04-25UI: Add index page and basic stylingFrederick Muriuki Muriithi
Add template(s) for the index page and some basic styling to get started with.
2022-04-20Add scaffolding for web appFrederick Muriuki Muriithi
Add a basic scaffolding for the web interface to the quality-control application.