Initial commit

webservice/apps/synthea/__init__.py

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+default_app_config = 'apps.synthea.apps.SyntheaConfig'

webservice/apps/synthea/admin.py

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+from django.contrib import admin
+
+# Register your models here.

webservice/apps/synthea/apps.py

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+from django.apps import AppConfig
+from django.utils.translation import ugettext_lazy as _
+
+from django.conf import settings
+
+class SyntheaConfig(AppConfig):
+    name = 'apps.synthea'
+    label = 'synthea'
+    verbose_name = _('Synthea')
+    verbose_name_plural = _('Synthea')

webservice/apps/synthea/forms.py

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+from django.forms import ModelForm
+from django import forms
+
+from apps.synthea.models import Synthea
+
+from .lib.utils import available_states, available_modules
+
+class SyntheaForm(ModelForm):
+
+    class Meta:
+        model = Synthea
+        fields = ['state', 'population', 'gender', 'age', 'module']
+
+        # This is loaded only once during startup. So changing the state data will not be picked up after a restart
+        state_options = [('','Any')]
+        for item in available_states():
+            state_options.append((item,item))
+
+        module_options = [('','Any')]
+        for item in available_modules():
+            module_options.append((item['module'],item['name']))
+
+        widgets = {
+            'state': forms.Select(choices=state_options),
+            'gender': forms.Select(choices=[('','Any'),('m','Male'),('f','Female')]),
+            'module': forms.Select(choices=module_options)
+        }

webservice/apps/synthea/lib/utils.py

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+from pathlib import Path
+import pandas as pd
+import shlex
+import subprocess
+from zipfile import ZipFile
+import json
+
+def available_states():
+    #TODO: Make a setting for this path
+    location = Path('/opt/development/synthea_webservice/synthea/src/main/resources/geography/')
+
+    df = pd.read_csv(location / 'timezones.csv', index_col=False)
+    # The state information is expected in the first column
+    states = df[df.columns[0]].to_list()
+    states.sort()
+    return states
+
+def available_modules():
+    #TODO: Make a setting for this path
+    location = Path('/opt/development/synthea_webservice/synthea/src/main/resources/modules/')
+
+    # Assumption here: A folder is a single module. And all .json in the main modules folder is a module.
+    modules = []
+    for module in location.iterdir():
+        if module.is_file() and module.suffix == '.json':
+            data = json.loads(module.read_text())
+            modules.append({'module' : module.name.replace('.json',''), 'name' : data['name']})
+
+    modules = sorted(modules, key=lambda k: k['name'].lower())
+    return modules
+
+def run_synthea(state = None, population = None, gender = None, age = None, module = None):
+    # TODO: Make synthea setting(s)
+    location = '/opt/development/synthea_webservice/synthea/'
+    synthea_cmd = ['/opt/development/synthea_webservice/synthea/run_synthea']
+    zip_file = 'Synthea_'
+    zip_export = location
+
+    if population:
+        synthea_cmd.append('-p')
+        synthea_cmd.append(str(population))
+        zip_file += f'population_{population}_'
+
+    if gender:
+        synthea_cmd.append('-g')
+        synthea_cmd.append(gender.upper())
+        zip_file += f'gender_{gender}_'
+
+    if age:
+        synthea_cmd.append('-a')
+        synthea_cmd.append(age)
+        zip_file += f'age_{age}_'
+
+    if module:
+        synthea_cmd.append('-m')
+        synthea_cmd.append(module)
+        zip_file += f'module_{module}_'
+
+    if state:
+        synthea_cmd.append(state)
+        zip_file += f'state_{state}'
+
+    process_ok = False
+    log = ''
+    with subprocess.Popen(synthea_cmd,cwd=location, stdout=subprocess.PIPE,stderr=subprocess.PIPE) as process:
+        for line in process.stdout:
+            line = line.decode('utf8')
+            log += line
+            if not process_ok:
+                process_ok = line.find('BUILD SUCCESSFUL') >= 0
+
+    if process_ok:
+        with ZipFile(f'{zip_export}/{zip_file}.zip', 'w') as export:
+            for file in Path(location + 'output/fhir_stu3').iterdir():
+                export.write(file,file.name)
+
+        return Path(f'{zip_export}/{zip_file}.zip')
+    else:
+        raise Exception(log)
+
+
+
+

webservice/apps/synthea/migrations/0001_initial.py

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+# Generated by Django 3.1.3 on 2020-11-13 09:36
+
+from django.db import migrations, models
+import uuid
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Synthea',
+            fields=[
+                ('created_at', models.DateTimeField(auto_now_add=True, help_text='The date and time this model has been created', verbose_name='Date created')),
+                ('updated_at', models.DateTimeField(auto_now=True, help_text='The date and time this model has been updated', verbose_name='Date updated')),
+                ('id', models.UUIDField(default=uuid.uuid4, editable=False, help_text='A unique id', primary_key=True, serialize=False, unique=True, verbose_name='ID')),
+                ('state', models.CharField(help_text='The state for which synthea generate data.', max_length=200, verbose_name='Stage')),
+                ('population', models.PositiveSmallIntegerField(default=50, help_text='The size of the population', verbose_name='Population')),
+                ('gender', models.CharField(help_text='Select the gender type', max_length=1, verbose_name='Gender')),
+                ('age', models.CharField(help_text='Select the age range', max_length=10, verbose_name='Age range')),
+                ('module', models.CharField(help_text='Select the module', max_length=50, verbose_name='Mopdule')),
+            ],
+            options={
+                'verbose_name': 'token',
+                'verbose_name_plural': 'tokens',
+            },
+        ),
+    ]

webservice/apps/synthea/models.py

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+from django.contrib.auth.models import User
+from django.db import models
+from django.utils.translation import gettext_lazy as _
+
+from django_cryptography.fields import encrypt
+
+from lib.utils.general import get_random_string
+from lib.models.base import MetaDataModel
+
+import uuid
+
+# Create your models here.
+class Synthea(MetaDataModel):
+    
+    class Meta:
+        verbose_name = _('token')
+        verbose_name_plural = _('tokens')
+
+    id         = models.UUIDField(_('ID'), primary_key=True, unique=True,  default=uuid.uuid4, editable=False, help_text=_('A unique id'))
+    state      = models.CharField(_('State'), max_length=200, help_text=_('The state for which synthea generate data.'))
+    population = models.PositiveSmallIntegerField(_('Population'), blank=True, default=50, help_text=_('The size of the population'))
+    gender     = models.CharField(_('Gender'), blank=True,max_length=1, help_text=_('Select the gender type'))
+    age        = models.CharField(_('Age range'), blank=True,max_length=10, help_text=_('Select the age range'))
+    module     = models.CharField(_('Module'),blank=True, max_length=50, help_text=_('Select the module'))

webservice/apps/synthea/templates/synthea/generator_form.html

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+{% extends 'base.html' %} <!-- Add this for inheritance -->
+{% load i18n %}
+
+{% block title %}{% trans "Generate a new Synthea data set" %}{% endblock %}
+{% block pagetitle %}{% trans "Generate a new Synthea data set" %}{% endblock %}
+
+{% block menu %}
+  {% include 'synthea/menu.html' %}
+{% endblock %}
+
+{% block content %}
+<h1>Synthea generartor</h1>
+<p>Enter the form fields and press submit. <small>U vraagt, wij draaien ;)</small></p>
+<form method="POST" class="post-form">  
+    {% csrf_token %}
+    <table>
+    {{ form.as_table }}
+    </table>
+    <button type="submit" class="save btn btn-default">Save</button>  
+</form>  
+{% endblock %}

webservice/apps/synthea/templates/synthea/index.html

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+{% extends 'base.html' %} <!-- Add this for inheritance -->
+{% load i18n %}
+
+{% block title %}{% trans "dHealth Synthea" %}{% endblock %}
+{% block pagetitle %}{% trans "dHealth Synthea" %}{% endblock %}
+
+{% block menu %}
+  {% include 'synthea/menu.html' %}
+{% endblock %}
+
+{% block content %}
+<h1>dHealt Nederland</h1>
+<p>Onder leiding van UMCG</p>
+{% endblock %}

webservice/apps/synthea/templates/synthea/menu.html

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+{% load i18n %}
+<li class="rug-nav--secondary__item">
+    <a class="rug-nav--secondary__link js--togglable-switch" data-toggle-class="rug-nav--secondary__link--selected" data-toggle-group="submenu" data-toggle-id="menu-2427370b-9435-44d9-bca7-b93ec9d03cc0-33.31" data-toggle-mode="togglable">{% trans "Menu" %}</a>
+    <ul class="rug-nav--secondary__sub rug-nav--secondary__sub--hidden js--togglable-item" data-toggle-class="rug-block" data-toggle-group="submenu" data-toggle-id="menu-2427370b-9435-44d9-bca7-b93ec9d03cc0-33.31">
+        <li class="rug-nav--secondary__sub__item" data-menu-id="b512aa55-f0cb-4588-9054-302caa5fa951-33.34">
+            <a class="rug-nav--secondary__sub__link" href="{% url 'index' %}"><span class="rug-nav--secondary__sub__link-text">{% trans "Informatie" %}</span></a>
+          </li>
+        <li class="rug-nav--secondary__sub__item" data-menu-id="b512aa55-f0cb-4588-9054-302caa5fa951-33.35">
+            <a class="rug-nav--secondary__sub__link" href="{% url 'generator_form' %}"><span class="rug-nav--secondary__sub__link-text">{% trans "Generator" %}</span></a>
+        </li>
+
+        <li class="rug-nav--secondary__sub__item" data-menu-id="b512aa55-f0cb-4588-9054-302caa5fa951-33.36">
+            <a class="rug-nav--secondary__sub__link" href="{% url 'api_info' %}"><span class="rug-nav--secondary__sub__link-text">{% trans "API" %}</span></a>
+        </li>
+
+    </ul>
+  </li>  

webservice/apps/synthea/tests.py

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+from django.test import TestCase
+
+# Create your tests here.

webservice/apps/synthea/urls.py

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+from django.urls import path, include
+
+from . import views
+
+urlpatterns = [
+    path('', views.index, name='index'),
+    path('api/', views.index, name='api_info'),
+    path('generate/', views.show_synthea_form, name='generator_form'),
+]

webservice/apps/synthea/views.py

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+from django.shortcuts import render
+from django.http import HttpResponse
+from apps.synthea.forms import SyntheaForm  
+
+from .lib.utils import run_synthea
+
+import mimetypes
+# Create your views here.
+
+def index(request):
+    template_name = 'synthea/index.html'
+    return render(request,template_name,{})
+
+def show_synthea_form(request):
+    template_name = 'synthea/generator_form.html'
+
+    # if this is a POST request we need to process the form data
+    if request.method == 'POST':
+        # create a form instance and populate it with data from the request:
+        form = SyntheaForm(request.POST)
+        # check whether it's valid:
+        if form.is_valid():
+            # process the data in form.cleaned_data as required
+
+            try:
+                zipfile = run_synthea(
+                    form.cleaned_data['state'],
+                    form.cleaned_data['population'],
+                    form.cleaned_data['gender'],
+                    form.cleaned_data['age'],
+                    form.cleaned_data['module']
+                )
+                
+                mime_type, _ = mimetypes.guess_type(zipfile)
+                response = HttpResponse(zipfile.open('rb'), content_type=mime_type)
+                response['Content-Disposition'] = f'attachment; filename={zipfile.name}'
+
+                return response
+
+            except Exception as ex:
+                print(ex)
+
+    # if a GET (or any other method) we'll create a blank form
+    else:
+        form = SyntheaForm()
+
+    return render(request,template_name,{
+        'form':form
+    })