epilepsy-cause-workflow

[eatyourpeas]

Fixes #1136

Overview

Largely extends work already done on EpilepsyCause. The main reason for the PR was to add the list of requested causes detailed in issue #1136

In the process the workflow for updating causes and maintaining up to date lists of causes has been improved

Code changes

• general_functions/epilepsy_causes.py: adds two new functions, the first which dumps the active list of epilepsy causes as a file to the root, either as markdown, json or csv. The second accepts a list of python objects with a the structure {'preferredTerm': 'preferredTerm', 'conceptId': 'conceptId', 'term': 'term'} and saves to the database. It logs a list to the console of success and failures. If the conceptId is provided it will look up for the snomed server and persist in that way
• Adds the new causes requested to two lists - the first the list of snomed causes, the second a new list of causes for seeding where smomed concept ids are not known, using the new function.

Documentation changes (done or required as a result of this PR)

The workflow for adding new causes has been clarified and updated in the developer docs. The next step will be to expose these new functions to the Epilepsy12 team, but there needs to be robust clinical oversight of this beforehand.

In addition, there is a new page in the clinician docs with the list of causes and syndromes for users to see.

Related Issues

closes #1136

[mbarton]

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[mbarton]

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