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Implements the code enabling the upload of the samples/cases to the database.
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Notify the user when they try to create a new dataset that has the
same name as an existing dataset and give them the chance to fix it
before continuing.
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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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Log out any DB errors that occur to help with tracking and debugging
failures.
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Due to possible schema differences between local small db on
development computer and those on CI/CD and Production, explicitly
specify the columns being operated on by the queries.
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* To avoid confusion, only display the "alert-success" green on
completion of the parsing process. While parsing, if there are no
errors, then display the "No errors found so far" message without
the green colour.
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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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