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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
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Use the generic worker script as the interface for launching external
processes.
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As part of updating the database with the new data, there is a need to
select the appropriate dataset that the data belongs to, and this
commit provides the UI to assist the user do that.
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The number columns in each contents line should be equal to the nember
of columns in the header line.
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* Ensure error messages are displayed if a request is made to the
'/parse/parse' endpoint with invalid, or missing data.
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Enable the user to abort the background parsing of the file.
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Enable the progress status page to show all the errors found at any
point during the processing of the file.
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Implement code to handle errors in the processing of files.
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- 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
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- Use a way faster way of parsing the strains file
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* Use sqlite to save the jobs metadata and enable UI update of the
progress for large files
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* 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.
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* Create and push the application context for the worker functions
* Fix the update of meta fields
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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
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* 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
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