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nictiz_webtools

This repository contains several online tools made available by Nictiz (nictiz.nl).

  • Simple ATC/g-standaard medication lookup: requires proprietary source files from z-index.nl.
  • Snomed list generators (build_tree & build_tree_excel): two tools to create user-friendly Snomed lists from Snowstorm. Requires a Snowstorm server.
  • Mapping tool
    This is a crude start to a very flexible mapping tool. The tool is at proof-of-concept level, but functional. The tool is under heavy development. Every component runs in a docker container, with volumes for persistance. Access to the production environment is controlled by a reverse proxy Nginx with letsencrypt companion container, which needs access to ports 80 and 443.
    At this point it supports 1-n mappings from any codesystem to any codesystem. The admin tools are still limited, but the user workflow is very usable at this point.

Getting started

  • Clone repo
  • Setup your .env file (template in .env-template)
  • Start dev environment with docker-compose up
  • Run python manage.py makemigrations and python manage.py migrate in the python container
  • Run python manage.py createsuperuser in python container
  • Run python manage.py collectstatic, confirm 'yes', in python container
  • In /admin/, create groups mentioned below under 'With a fresh DB'
  • In /admin/mapping/, create codesystems, mapping, statuses for each project.
  • For mapping Snomed (snomed.nl), open /mapping/update_snomed/ to import Snomed into a chosen codesystem. Each Snomed concept is imported as a 'component' (work in progress, functional)
  • For mapping NHG (nhg.nl), open /mapping/update_nhg/ to import NHG Excel tables into a chosen codesystem. These NHG tables are proprietary, and need to be obtained. They can be placed in /mapping/resources/nhg/. Each table requires custom code, an example for 'Verrichtingen' is present in the repository. Each line is imported as a 'component' (work in progress, functional).
  • After loading at least two terminology systems, mapping tasks can be created from /mapping/task_create/. You can either supply a list of unique ID's in the text field (one row per ID), or create tasks for each component from the chosen codesystem. If a task already exists for a component, it will be left as is.
  • Users with group membership 'mapping | create tasks', will have a link to the task manager on the project home page.
  • Start production environment with docker-compose -f prod.yml up
  • the shell script 'update' in the root directory will pull the latest changes from the current Git branch and restart the production environment.

With a fresh DB:

Create codesystems

  • 1: Snomed
  • 2: Verrichtingen NHG
  • 3: Labcodeset
  • 4: Diagnostische bepalingen NHG

Create groups: (without ')

  • 'ATC lookup' # Access to the medication ATC/g-standaard lookup module
  • 'HTML tree' # Access to the Snomed list generators
  • 'mapping | access' # Access to the mapping tool - not in use
  • 'mapping | edit mapping' # Edit mappings, this enables changing and adding mappings
  • 'mapping | view tasks' # View tasks in projects
  • 'mapping | create tasks' # Create tasks through CSV entry
  • 'mapping | change task status'
  • 'mapping | place comments'
  • 'mapping | admin codesystems' # Creating codesystems, loading data into codesystems
  • 'mapping | audit' # Create audit reports on mapping rules
  • 'mapping | project statistics' # Show in-depth project statistics on project page

Permission check in template:

{% if 'mapping | edit mapping' in permissions %}

Permission check in class-based view:

class AjaxTargetSearch(UserPassesTestMixin,TemplateView): # UserPassesTestMixin needs to be first! def handle_no_permission(self): return redirect('login') def test_func(self): # return self.request.user.has_perm('Build_Tree.make_taskRecord') # Check for permission return self.request.user.groups.filter(name='AJAX lookup').exists() # Check for group membership

Render an error page

except Exception as e: return render(request, 'mapping/error.html', { 'page_title': 'Error', 'error_text': 'Mogelijk probeer je een taak te openen die niet bestaat.', 'exception' : e, })

.env file

Template can be found in .env-example