diff --git a/.gitignore b/.gitignore
index df4b189..0bbc78a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@ doc/_build/
doc/output/
api_test.py
log/*
+synthea_output/
diff --git a/requirements.txt b/requirements.txt
index 044be4c..f199714 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,4 +4,6 @@ django_js_reverse
python-decouple
django-cryptography
djangorestframework
+drf_yasg2
pandas
+
diff --git a/webservice/apps/api/apps.py b/webservice/apps/api/apps.py
index 8a12abb..591460c 100644
--- a/webservice/apps/api/apps.py
+++ b/webservice/apps/api/apps.py
@@ -9,58 +9,58 @@ class ApiConfig(AppConfig):
verbose_name = _('API')
verbose_name_plural = _('APIs')
- try:
- assert settings.SWAGGER_SETTINGS
- except AttributeError:
- # We only load this setting, if it is not available in the overall settings.py file
- settings.SWAGGER_SETTINGS = {
- 'SECURITY_DEFINITIONS': {
- 'Hawk': {
- 'type': 'apiKey',
- 'description': 'HTTP Holder-Of-Key Authentication Scheme, https://github.com/hapijs/hawk, https://hawkrest.readthedocs.io/en/latest/
Ex header:
\'Authorization\': \'Hawk mac="F4+S9cu7yZiZEgdtqzMpOOdudvqcV2V2Yzk2WcphECc=", hash="+7fKUX+djeQolvnLTxr0X47e//UHKbkRlajwMw3tx3w=", id="7FI5JET4", ts="1592905433", nonce="DlV-fL"\'',
- 'name': 'Authorization',
- 'in': 'header'
- }
- }
- }
+ # try:
+ # assert settings.SWAGGER_SETTINGS
+ # except AttributeError:
+ # # We only load this setting, if it is not available in the overall settings.py file
+ # settings.SWAGGER_SETTINGS = {
+ # 'SECURITY_DEFINITIONS': {
+ # 'Hawk': {
+ # 'type': 'apiKey',
+ # 'description': 'HTTP Holder-Of-Key Authentication Scheme, https://github.com/hapijs/hawk, https://hawkrest.readthedocs.io/en/latest/
Ex header:
\'Authorization\': \'Hawk mac="F4+S9cu7yZiZEgdtqzMpOOdudvqcV2V2Yzk2WcphECc=", hash="+7fKUX+djeQolvnLTxr0X47e//UHKbkRlajwMw3tx3w=", id="7FI5JET4", ts="1592905433", nonce="DlV-fL"\'',
+ # 'name': 'Authorization',
+ # 'in': 'header'
+ # }
+ # }
+ # }
- try:
- assert settings.REST_FRAMEWORK
- except AttributeError:
- # We only load this setting, if it is not available in the overall settings.py file
- # To protect all API views with Hawk by default, put this in your settings:
- # https://hawkrest.readthedocs.io/en/latest/usage.html#protecting-api-views-with-hawk
- settings.REST_FRAMEWORK = {
+ # try:
+ # assert settings.REST_FRAMEWORK
+ # except AttributeError:
+ # # We only load this setting, if it is not available in the overall settings.py file
+ # # To protect all API views with Hawk by default, put this in your settings:
+ # # https://hawkrest.readthedocs.io/en/latest/usage.html#protecting-api-views-with-hawk
+ # settings.REST_FRAMEWORK = {
- 'DEFAULT_AUTHENTICATION_CLASSES': (
- 'apps.api.authentication.APIHawk',
- ),
+ # 'DEFAULT_AUTHENTICATION_CLASSES': (
+ # 'apps.api.authentication.APIHawk',
+ # ),
- 'DEFAULT_PERMISSION_CLASSES': (
- 'rest_framework.permissions.IsAuthenticated',
- ),
+ # 'DEFAULT_PERMISSION_CLASSES': (
+ # 'rest_framework.permissions.IsAuthenticated',
+ # ),
- # 'DEFAULT_AUTHENTICATION_CLASSES': (
- # 'rest_framework.authentication.TokenAuthentication',
- # ),
+ # # 'DEFAULT_AUTHENTICATION_CLASSES': (
+ # # 'rest_framework.authentication.TokenAuthentication',
+ # # ),
- # 'DEFAULT_PERMISSION_CLASSES': (
- # 'rest_framework.permissions.IsAuthenticated', ),
+ # # 'DEFAULT_PERMISSION_CLASSES': (
+ # # 'rest_framework.permissions.IsAuthenticated', ),
- # Use Django's standard `django.contrib.auth` permissions,
- # or allow read-only access for unauthenticated users.
- #'DEFAULT_PERMISSION_CLASSES': [
- # 'rest_framework.permissions.DjangoModelPermissionsOrAnonReadOnly'
- #],
- 'DEFAULT_PAGINATION_CLASS': 'rest_framework.pagination.PageNumberPagination',
- 'PAGE_SIZE': 10
- }
+ # # Use Django's standard `django.contrib.auth` permissions,
+ # # or allow read-only access for unauthenticated users.
+ # #'DEFAULT_PERMISSION_CLASSES': [
+ # # 'rest_framework.permissions.DjangoModelPermissionsOrAnonReadOnly'
+ # #],
+ # 'DEFAULT_PAGINATION_CLASS': 'rest_framework.pagination.PageNumberPagination',
+ # 'PAGE_SIZE': 10
+ # }
- try:
- assert settings.HAWK_MESSAGE_EXPIRATION
- except AttributeError:
- # We only load this setting, if it is not available in the overall settings.py file
- settings.HAWK_MESSAGE_EXPIRATION = 60
+ # try:
+ # assert settings.HAWK_MESSAGE_EXPIRATION
+ # except AttributeError:
+ # # We only load this setting, if it is not available in the overall settings.py file
+ # settings.HAWK_MESSAGE_EXPIRATION = 60
def ready(self):
from . import signals
\ No newline at end of file
diff --git a/webservice/apps/api/urls.py b/webservice/apps/api/urls.py
index 0a40e1e..9138647 100644
--- a/webservice/apps/api/urls.py
+++ b/webservice/apps/api/urls.py
@@ -7,24 +7,24 @@ from drf_yasg2 import openapi
from . import views
-from apps.dropoff.api.views import DatadropViewSet
-from apps.invitation.api.views import InvitationViewSet
-from apps.researcher.api.views import ResearcherViewSet
-from apps.storage.api.views import StorageEngineViewSet, StorageLocationViewSet
-from apps.study.api.views import StudyViewSet
-from apps.virtual_machine.api.views import (VirtualMachineViewSet,
- VirtualMachineOperatingSystemViewSet,
- VirtualMachineProfileViewSet,
- VirtualMachineMemoryViewSet,
- VirtualMachineNetworkViewSet,
- VirtualMachineStorageViewSet,
- VirtualMachineGPUViewSet)
+# from apps.dropoff.api.views import DatadropViewSet
+# from apps.invitation.api.views import InvitationViewSet
+# from apps.researcher.api.views import ResearcherViewSet
+# from apps.storage.api.views import StorageEngineViewSet, StorageLocationViewSet
+# from apps.study.api.views import StudyViewSet
+# from apps.virtual_machine.api.views import (VirtualMachineViewSet,
+# VirtualMachineOperatingSystemViewSet,
+# VirtualMachineProfileViewSet,
+# VirtualMachineMemoryViewSet,
+# VirtualMachineNetworkViewSet,
+# VirtualMachineStorageViewSet,
+# VirtualMachineGPUViewSet)
schema_view = get_schema_view(
openapi.Info(
- title="Virtual Research Environment API",
+ title="Synthea WebService API",
default_version='v1',
- description="Here you can see a list of API endpoints and actions that are available to communicate with the VRE API",
+ description="Info about Synthea WebServer API",
terms_of_service="https://www.rug.nl",
contact=openapi.Contact(email="vre_team@rug.nl"),
license=openapi.License(name="MIT License"),
@@ -33,27 +33,27 @@ schema_view = get_schema_view(
permission_classes=(permissions.AllowAny,),
)
-api_router_v1 = routers.DefaultRouter()
+#api_router_v1 = routers.DefaultRouter()
-api_router_v1.register(r'researchers', ResearcherViewSet)
+# api_router_v1.register(r'researchers', ResearcherViewSet)
-api_router_v1.register(r'studies', StudyViewSet)
+# api_router_v1.register(r'studies', StudyViewSet)
-api_router_v1.register(r'dropoffs', DatadropViewSet)
+# api_router_v1.register(r'dropoffs', DatadropViewSet)
-api_router_v1.register(r'invitations', InvitationViewSet)
+# api_router_v1.register(r'invitations', InvitationViewSet)
-api_router_v1.register(r'storageengines', StorageEngineViewSet)
-api_router_v1.register(r'storagelocations', StorageLocationViewSet)
+# api_router_v1.register(r'storageengines', StorageEngineViewSet)
+# api_router_v1.register(r'storagelocations', StorageLocationViewSet)
-# Order is important for virtual machines. Longest match first
-api_router_v1.register(r'virtualmachines/profiles', VirtualMachineProfileViewSet)
-api_router_v1.register(r'virtualmachines/storage', VirtualMachineStorageViewSet)
-api_router_v1.register(r'virtualmachines/memory', VirtualMachineMemoryViewSet)
-api_router_v1.register(r'virtualmachines/network', VirtualMachineNetworkViewSet)
-api_router_v1.register(r'virtualmachines/gpu', VirtualMachineGPUViewSet)
-api_router_v1.register(r'virtualmachines/os', VirtualMachineOperatingSystemViewSet)
-api_router_v1.register(r'virtualmachines', VirtualMachineViewSet)
+# # Order is important for virtual machines. Longest match first
+# api_router_v1.register(r'virtualmachines/profiles', VirtualMachineProfileViewSet)
+# api_router_v1.register(r'virtualmachines/storage', VirtualMachineStorageViewSet)
+# api_router_v1.register(r'virtualmachines/memory', VirtualMachineMemoryViewSet)
+# api_router_v1.register(r'virtualmachines/network', VirtualMachineNetworkViewSet)
+# api_router_v1.register(r'virtualmachines/gpu', VirtualMachineGPUViewSet)
+# api_router_v1.register(r'virtualmachines/os', VirtualMachineOperatingSystemViewSet)
+# api_router_v1.register(r'virtualmachines', VirtualMachineViewSet)
# Main namespace for the API urls
app_name = 'api'
@@ -66,6 +66,10 @@ urlpatterns = [
# Also this will give the full url to the OpenAPI documentation
path('info/', views.Info.as_view(), name='info'),
+ path('states/', views.States.as_view(), name='states'),
+ path('modules/', views.Modules.as_view(), name='modules'),
+ path('generate/', views.Generate.as_view(), name='generate'),
+
# Add extra namespace for versioning the API
- path('v1/', include((api_router_v1.urls,'api'),namespace='v1')),
+ #path('v1/', include((api_router_v1.urls,'api'),namespace='v1')),
]
\ No newline at end of file
diff --git a/webservice/apps/api/views.py b/webservice/apps/api/views.py
index 0049650..9c1491a 100644
--- a/webservice/apps/api/views.py
+++ b/webservice/apps/api/views.py
@@ -1,11 +1,23 @@
from rest_framework.views import APIView
from rest_framework.response import Response
+from django.http import FileResponse
+
+from django.views.decorators.csrf import csrf_exempt
+
from rest_framework.decorators import schema
+from rest_framework import status
from django.urls import reverse
from lib.utils.general import get_ip_address
+from apps.synthea.api.serializers import SyntheaSerializer
+
+from apps.synthea.lib.utils import available_states, available_modules,run_synthea
+
+import mimetypes
+
+
@schema(None)
class Info(APIView):
"""
@@ -49,4 +61,37 @@ class Info(APIView):
except AttributeError:
pass
- return Response(data)
\ No newline at end of file
+ return Response(data)
+
+
+#@schema(None)
+class States(APIView):
+
+ def get(self, request, format=None):
+ return Response(available_states())
+
+
+class Modules(APIView):
+
+ def get(self, request, format=None):
+ return Response(available_modules())
+
+class Generate(APIView):
+
+ def post(self, request, format=None):
+ print('Post data')
+ print(request.data)
+
+ serializer = SyntheaSerializer(data=request.data)
+ if serializer.is_valid():
+ synthea = serializer.save()
+ zipfile = synthea.generate()
+ print(zipfile)
+ response = FileResponse(zipfile.open('rb'), content_type='application/zip')
+ response['Content-Disposition'] = f'attachment; filename={zipfile.name}'
+
+ return response
+
+
+ #return Response(serializer.data, status=status.HTTP_201_CREATED)
+ return Response(serializer.errors, status=status.HTTP_400_BAD_REQUEST)
\ No newline at end of file
diff --git a/webservice/apps/synthea/api/serializers.py b/webservice/apps/synthea/api/serializers.py
new file mode 100644
index 0000000..460c287
--- /dev/null
+++ b/webservice/apps/synthea/api/serializers.py
@@ -0,0 +1,8 @@
+from rest_framework import serializers
+
+from apps.synthea.models import Synthea
+
+class SyntheaSerializer(serializers.ModelSerializer):
+ class Meta:
+ model = Synthea
+ fields = ['state', 'population', 'gender', 'age', 'module']
\ No newline at end of file
diff --git a/webservice/apps/synthea/apps.py b/webservice/apps/synthea/apps.py
index 4ea0616..bfe5f91 100644
--- a/webservice/apps/synthea/apps.py
+++ b/webservice/apps/synthea/apps.py
@@ -7,4 +7,43 @@ class SyntheaConfig(AppConfig):
name = 'apps.synthea'
label = 'synthea'
verbose_name = _('Synthea')
- verbose_name_plural = _('Synthea')
\ No newline at end of file
+ verbose_name_plural = _('Synthea')
+
+ try:
+ assert settings.SYNTHEA_BASE_DIR
+ except AttributeError:
+ # We only load this setting, if it is not available in the overall settings.py file
+ settings.SYNTHEA_BASE_DIR = settings.BASE_DIR / '../synthea'
+
+ try:
+ assert settings.SYNTHEA_OUTPUT_DIR
+ except AttributeError:
+ # We only load this setting, if it is not available in the overall settings.py file
+ settings.SYNTHEA_OUTPUT_DIR = settings.BASE_DIR / '../synthea_output'
+
+ try:
+ assert settings.SYNTHEA_MODULE_DIR
+ except AttributeError:
+ # We only load this setting, if it is not available in the overall settings.py file
+ settings.SYNTHEA_MODULE_DIR = settings.SYNTHEA_BASE_DIR / 'src/main/resources/modules/'
+
+
+ try:
+ assert settings.SYNTHEA_RESOURCE_DIR
+ except AttributeError:
+ # We only load this setting, if it is not available in the overall settings.py file
+ settings.SYNTHEA_RESOURCE_DIR = settings.SYNTHEA_BASE_DIR / 'src/main/resources/'
+
+ try:
+ assert settings.SYNTHEA_STATES_DIR
+ except AttributeError:
+ # We only load this setting, if it is not available in the overall settings.py file
+ settings.SYNTHEA_STATES_DIR = settings.SYNTHEA_BASE_DIR / 'src/main/resources/geography/'
+
+
+
+ try:
+ assert settings.SYNTHEA_EXPORT_TYPE
+ except AttributeError:
+ # We only load this setting, if it is not available in the overall settings.py file
+ settings.SYNTHEA_EXPORT_TYPE = 'fhir_stu3'
\ No newline at end of file
diff --git a/webservice/apps/synthea/forms.py b/webservice/apps/synthea/forms.py
index 01fbc7c..78d7ec6 100644
--- a/webservice/apps/synthea/forms.py
+++ b/webservice/apps/synthea/forms.py
@@ -1,3 +1,5 @@
+from django.utils.translation import gettext_lazy as _
+
from django.forms import ModelForm
from django import forms
@@ -12,16 +14,16 @@ class SyntheaForm(ModelForm):
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')]
+ state_options = [('',_('Select'))]
for item in available_states():
- state_options.append((item,item))
+ state_options.append((item['id'],item['name']))
- module_options = [('','Any')]
+ module_options = [('',_('Any'))]
for item in available_modules():
- module_options.append((item['module'],item['name']))
+ module_options.append((item['id'],item['name']))
widgets = {
'state': forms.Select(choices=state_options),
- 'gender': forms.Select(choices=[('','Any'),('m','Male'),('f','Female')]),
+ 'gender': forms.Select(choices=[('',_('Any')),('m',_('Male')),('f',_('Female'))]),
'module': forms.Select(choices=module_options)
}
\ No newline at end of file
diff --git a/webservice/apps/synthea/lib/utils.py b/webservice/apps/synthea/lib/utils.py
index ab0d59e..73a1044 100644
--- a/webservice/apps/synthea/lib/utils.py
+++ b/webservice/apps/synthea/lib/utils.py
@@ -5,36 +5,41 @@ 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/')
+from django.conf import settings
+from uuid import uuid4
- 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()
+
+def available_states():
+ states = []
+ # Read the timezones.csv file from the Synthea resources. This should give us all the 'state' on the first column
+ df = pd.read_csv(settings.SYNTHEA_STATES_DIR / 'timezones.csv', index_col=False)
+ for state in df[df.columns[0]].to_list():
+ states.append({'id' : state , 'name' : state})
+
+ #states = df[df.columns[0]].to_list()
+ # Sort on name
+ states = sorted(states, key=lambda k: k['name'].lower())
+ #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.
+ # Assumption here: Only .json files in the main folder are modules. The rest are submodules...
modules = []
- for module in location.iterdir():
+ for module in settings.SYNTHEA_MODULE_DIR.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.append({'id' : 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']
+ # Add a unique dir to the output, so multiple Synthea processes can run parallel
+ temp_id = uuid4().hex
+ output_folder = settings.SYNTHEA_OUTPUT_DIR / temp_id
+
+ synthea_cmd = [settings.SYNTHEA_BASE_DIR / 'run_synthea','--exporter.baseDirectory',output_folder]
zip_file = 'Synthea_'
- zip_export = location
if population:
synthea_cmd.append('-p')
@@ -62,7 +67,7 @@ def run_synthea(state = None, population = None, gender = None, age = None, modu
process_ok = False
log = ''
- with subprocess.Popen(synthea_cmd,cwd=location, stdout=subprocess.PIPE,stderr=subprocess.PIPE) as process:
+ with subprocess.Popen(synthea_cmd,cwd=settings.SYNTHEA_BASE_DIR, stdout=subprocess.PIPE,stderr=subprocess.PIPE) as process:
for line in process.stdout:
line = line.decode('utf8')
log += line
@@ -70,14 +75,10 @@ def run_synthea(state = None, population = None, gender = None, age = None, modu
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():
+ with ZipFile(f'{output_folder}/{zip_file}_{temp_id}.zip', 'w') as export:
+ for file in (output_folder / settings.SYNTHEA_EXPORT_TYPE).iterdir():
export.write(file,file.name)
- return Path(f'{zip_export}/{zip_file}.zip')
+ return (log,Path(f'{output_folder}/{zip_file}_{temp_id}.zip'))
else:
- raise Exception(log)
-
-
-
-
+ raise Exception(log)
\ No newline at end of file
diff --git a/webservice/apps/synthea/migrations/0002_auto_20201116_1457.py b/webservice/apps/synthea/migrations/0002_auto_20201116_1457.py
new file mode 100644
index 0000000..09bc913
--- /dev/null
+++ b/webservice/apps/synthea/migrations/0002_auto_20201116_1457.py
@@ -0,0 +1,38 @@
+# Generated by Django 3.1.3 on 2020-11-16 13:57
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('synthea', '0001_initial'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='synthea',
+ name='log',
+ field=models.TextField(blank=True, help_text='Synthea logfile output', verbose_name='Log'),
+ ),
+ migrations.AlterField(
+ model_name='synthea',
+ name='age',
+ field=models.CharField(blank=True, default='18-100', help_text='Select the age range. Enter [min age]-[max age]', max_length=10, verbose_name='Age range'),
+ ),
+ migrations.AlterField(
+ model_name='synthea',
+ name='gender',
+ field=models.CharField(blank=True, help_text='Select the gender type', max_length=1, verbose_name='Gender'),
+ ),
+ migrations.AlterField(
+ model_name='synthea',
+ name='module',
+ field=models.CharField(blank=True, help_text='Select the module', max_length=50, verbose_name='Module'),
+ ),
+ migrations.AlterField(
+ model_name='synthea',
+ name='state',
+ field=models.CharField(help_text='The state for which synthea generate data.', max_length=200, verbose_name='State'),
+ ),
+ ]
diff --git a/webservice/apps/synthea/models.py b/webservice/apps/synthea/models.py
index 8892f2d..755f071 100644
--- a/webservice/apps/synthea/models.py
+++ b/webservice/apps/synthea/models.py
@@ -7,6 +7,8 @@ from django_cryptography.fields import encrypt
from lib.utils.general import get_random_string
from lib.models.base import MetaDataModel
+from .lib.utils import run_synthea
+
import uuid
# Create your models here.
@@ -18,7 +20,25 @@ class Synthea(MetaDataModel):
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'))
+ population = models.PositiveSmallIntegerField(_('Population'), 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'))
+ age = models.CharField(_('Age range'), blank=True,default='18-100', max_length=10, help_text=_('Select the age range. Enter [min age]-[max age]'))
module = models.CharField(_('Module'),blank=True, max_length=50, help_text=_('Select the module'))
+ log = models.TextField(_('Log'),blank=True, help_text=_('Synthea logfile output'))
+
+
+ def generate(self):
+ log,zip_file = run_synthea(
+ self.state,
+ self.population,
+ self.gender,
+ self.age,
+ self.module
+ )
+
+ self.log = log
+
+ self.save()
+
+ return zip_file
+
diff --git a/webservice/apps/synthea/templates/synthea/generator_form.html b/webservice/apps/synthea/templates/synthea/generator_form.html
index 3aafae7..965505a 100644
--- a/webservice/apps/synthea/templates/synthea/generator_form.html
+++ b/webservice/apps/synthea/templates/synthea/generator_form.html
@@ -9,7 +9,7 @@
{% endblock %}
{% block content %}
-Synthea generartor
+Synthea Generator
Enter the form fields and press submit. U vraagt, wij draaien ;)