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Initialise the upload path for R/qtl2 bundles. This commit adds UI
that allows the user to select from existing species, before
proceeding to the next stage.
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Implements the code enabling the upload of the samples/cases to the database.
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Handle any and all unforeseen error conditions gracefully by capturing
the exceptions, logging out for debug purposes and providing the user
with a generic error page.
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Check the connections in the wsgi.py file, outside of the `create_app`
application factory to avoid issues with tests failing due to test app
not initialising because of missing connections in the test
environment.
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* qc_app/__init__.py (refactor): Check connection before launching the
application
* qc_app/check_connections.py (new file): Add code to check
connections
* qc_app/db_utils.py (refactor): enable passing the database uri as an
argument to the connection creation function.
* scripts/worker.py (refactor): Use new code to check for redis
connection.
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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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* 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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Add a basic scaffolding for the web interface to the quality-control
application.
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