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Use the sys.executable to get the correct python binary to run the
external processes, and setup the environment to point to the correct
PYTHONPATH.
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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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* 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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Ease the selection of a radio button by allowing the user to click on
any of the table cells that are in the same row as the radio button of
concern.
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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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Use the generic worker script as the interface for launching external
processes.
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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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Provide user with a confirmation stage where they can verify all the
data before inserting into the database.
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Enable the user to create a new dataset should the need arise.
A few extra fixes were done, such as:
- Provide list of average methods to choose from
- Provide input elements for some expected fields
- Add a new confirmation step before doing the actual data update
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Rather than using the redirect, that led to exposing the study id as a
get parameter, this commit adds an auxilliary step that allows the
user to choose whether to continue with the new study or go back and
select an existing study.
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- Implement UI enabling selection from existing datasets
- Start implementation of UI that enables creation of new dataset
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Enable the creation of the new study, and redirect appropriately with
the new study id.
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- Build code to populate the "Group" and "Tissue" dropdown lists
- Enable redirect with POST data (code 307) in case there is input
error to enable the user fix their errors
- Move hidden fields to macro to reduce repetition
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Implement the select study UI
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The filetype determines the queries to be run to update the database,
therefore, this commit adds filetype information.
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The GeneChipId value is required for the data being inserted, so this
commit provides the UI to enable selection of the chip.
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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 errors respond with status code 400
- Ensure error messages are displayed for any invalid zip file that is
uploaded.
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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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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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- 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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Add template(s) for the index page and some basic styling to get
started with.
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