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This reverts commit 960c1a5b831d8761a3e1716f86ded4cc5b67eea0.
After meeting with Arthur, it was confirmed that the CSV file should
not have values in the exponential notation.
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The CLI scripts use "standard-error" so update the web version to fit
in with that.
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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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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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Remove the old code that relied on exceptions to parse errors in the
uploaded files.
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- replace `line_number` with `line` and `column_number` with `column`
to save on slot name lengths.
- Fix the type name for the `DuplicateHeading` namedtuple type
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Parse the files with the new functions that return error objects
instead of raising exceptions
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This commit adds a number of functions that return the error object
when an error is found, or `None` otherwise. It avoids the use of
exceptions as control flow constructs.
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Add documentation on how to run the development version of the
GeneNetwork Quality Control application.
Update the license to the agpl3+ license used by genenetwork3
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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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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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* 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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Advance the seek position, once we have yielded up an error to causing
an infinite loop in certain conditions, where the `parse_errors`
function ends up resuming the gile in the same position once it
experiences an error.
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To avoid processing all the items in an iterable, the `take` function
is added in this commit. It realised a limited number (specified at
call time) of items from the iterable given.
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Add template(s) for the index page and some basic styling to get
started with.
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Ignore the flask instance directory if it is present in the
repository. The directory being present in the repository is mostly a
development convenience feature.
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Build a function to collect all the parsing errors into a "sequence"
of dict objects containing the issues found.
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Add a basic scaffolding for the web interface to the quality-control
application.
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Derive a "correct" sample file from an existing sample file with
errors for testing with large files.
Fix issue caught by test.
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* Implement remaining file parsing tests and some helpers functions
needed for ensuring the tests work.
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* Improve tests that ensure parsing fails in case the file has errors
* Add strains.csv file
* Implement minimum viable functionality that passes the implemented tests
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Add dummy failing tests and a stub for the parsing of the files
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Change the exception name to be more descriptive.
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Add some sample files to be used for testing that the parsing works as
expected.
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Without the `tests/__init__.py` file, the tests directory was not
considered a package and therefore, running:
$ pytest
would fail with import error notifications. This fixes that.
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Add a minimum viable implementation that passes the tests for the
function that checks for the validity of the headers
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