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Make flask use the gunicorn loggers when run under gunicorn,
otherwise, use our custom logging.
Putting the logging setup inside `create_app(…)` would cause each
worker to override the gunicorn loggers, meaning we were not receiving
the logs, especially for `debug(…)` calls.
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The assumption has been that the application will be started in the
root of the repository, and uses that to source the default
settings. It is, however, possible that the application is started in
a totally different working directory, which leads to an error during
startup.
This commit sources the default settings relative to a know file, in
this case the module __init__.py file for qc_app module.
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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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