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Load the genotype information from the R/qtl2 bundle and insert it
into the database.
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Add a logger that will log output to a redis list. This will be useful
to retrieve the output(s) of the running script to help display some
form of progress to the user.
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Fix the wrong assumption that the ID key will always be
"ProbeSetID". The key for the ID column could change from study to
study or dataset to dataset.
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Fix a bug that was causing the data insertion to fail.
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Log out any DB errors that occur to help with tracking and debugging
failures.
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Insert the ProbeSets first before inserting the average data and
cross-referencing it.
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* Avoid overwriting existing data by adding a random string to the
name of the ProbeSet
* Read ProbeSet names separately from the means for the strains, to
avoid entering the same ProbeSet record over and over with varying
names.
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The "ProbeSetId" value in the file is actually stored in the database
in the `ProbeSet.Name` field, whereas the `ProbeSetXRef` table
actually uses the `ProbeSet.Id` value to define the
relationships. This commit fixes that issue.
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* Display the status of the job, as it is running
* Display STDERR output if an error occurs
* Display STDOUT output as job is running and on successful completion
of the job
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- Hook up external data insertion script to webserver code
- Provide rudimentary status indication
- Generalise some job creation details
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* Fix bug where stderr was not being updated on redis appropriately
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* quality_control/file_utils.py (new file): extract common file
utilities.
* quality_control/parsing.py (refactor): extract common file
utilities.
* scripts/insert_data.py: Implement data insertion for averages/means
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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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Add a generic worker script, whose purpose is:
- to launch the specific worker script
- to capture both stdin and stderr streams and put them on redis
In this way, we can launch redis-aware and redis-unaware workers and
capture their outputs or errors for later processing.
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As preparation for building a new generic worker script, this commit
renames the file validation script from 'worker.py' to
'validate_file.py' so as to ensure the name conforms better to what
the script does.
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Use the builtin mimetypes which gives better results
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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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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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- 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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Since progress indication is not part of the parsing, this commit
extracts the progress indication into functions with well defined
input arguments that hide the progress indication logic from the
parsing function.
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Use the new code that collects the errors in the CLI client.
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- Use a way faster way of parsing the strains file
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While the application is developed with GNU Guix, the end user might
not be using it, and therefore, this commit provides a way for the
user to install the application with the usual python package
management systems.
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