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tests.py
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import json
from fhir.resources.codesystem import CodeSystem
from mock.mock import patch, Mock
from rest_framework.test import APIClient
from core.code_systems.converter import CodeSystemConverter
from core.code_systems.serializers import CodeSystemDetailSerializer
from core.code_systems.views import CodeSystemLookupNotFoundError
from core.common.tests import OCLTestCase
from core.concepts.models import Concept
from core.concepts.tests.factories import ConceptFactory
from core.orgs.tests.factories import OrganizationFactory
from core.sources.models import Source
from core.sources.tests.factories import OrganizationSourceFactory, UserSourceFactory
from core.users.tests.factories import UserProfileFactory
class CodeSystemTest(OCLTestCase):
@patch('core.sources.models.index_source_concepts', Mock(__name__='index_source_concepts'))
@patch('core.sources.models.index_source_mappings', Mock(__name__='index_source_mappings'))
def setUp(self):
super().setUp()
self.org = OrganizationFactory()
self.org_source = OrganizationSourceFactory(organization=self.org, canonical_url='/some/url',
full_name='source name')
self.org_source_v1 = OrganizationSourceFactory.build(
version='v1', mnemonic=self.org_source.mnemonic, organization=self.org_source.parent)
Source.persist_new_version(self.org_source_v1, self.org_source.created_by)
self.concept_1 = ConceptFactory(parent=self.org_source, names=1, names__name="concept_1_name")
self.concept_2 = ConceptFactory(parent=self.org_source)
self.org_source_v2 = OrganizationSourceFactory.build(
version='v2', mnemonic=self.org_source.mnemonic, organization=self.org_source.parent)
Source.persist_new_version(self.org_source_v2, self.org_source.created_by)
self.user = UserProfileFactory()
self.user_token = self.user.get_token()
self.user_source = UserSourceFactory(user=self.user, public_access='None', canonical_url='/some/url')
self.user_source_v1 = UserSourceFactory.build(
version='v1', mnemonic=self.user_source.mnemonic, user=self.user_source.parent)
Source.persist_new_version(self.user_source_v1, self.user_source.created_by)
self.client = APIClient()
def test_public_can_view(self):
response = self.client.get('/fhir/CodeSystem/?url=/some/url')
self.assertEqual(len(response.data['entry']), 1)
self.assertEqual(response.data['total'], 1)
resource = response.data['entry'][0]['resource']
self.assertEqual(
resource['identifier'][0]['value'],
'/orgs/' + self.org.mnemonic + '/CodeSystem/' + self.org_source.mnemonic + '/'
)
self.assertEqual(resource['version'], 'v2')
self.assertEqual(len(resource['concept']), 2)
self.assertEqual(resource['concept'][0]['code'], self.concept_1.mnemonic)
self.assertEqual(resource['concept'][1]['code'], self.concept_2.mnemonic)
def test_private_can_view(self):
response = self.client.get('/fhir/CodeSystem/?url=/some/url', HTTP_AUTHORIZATION='Token ' + self.user_token)
self.assertEqual(len(response.data['entry']), 2)
self.assertEqual(response.data['total'], 2)
resource = response.data['entry'][0]['resource']
self.assertEqual(
resource['identifier'][0]['value'],
'/users/' + self.user.mnemonic + '/CodeSystem/' + self.user_source.mnemonic + '/'
)
self.assertEqual(resource['version'], 'v1')
resource_2 = response.data['entry'][1]['resource']
self.assertEqual(
resource_2['identifier'][0]['value'],
'/orgs/' + self.org.mnemonic + '/CodeSystem/' + self.org_source.mnemonic + '/'
)
self.assertEqual(resource_2['version'], 'v2')
def test_public_can_list(self):
response = self.client.get('/fhir/CodeSystem/')
self.assertEqual(len(response.data['entry']), 1)
resource = response.data['entry'][0]['resource']
self.assertEqual(
resource['identifier'][0]['value'],
'/orgs/' + self.org.mnemonic + '/CodeSystem/' + self.org_source.mnemonic + '/'
)
self.assertEqual(resource['version'], 'v2')
def test_find_by_title(self):
response = self.client.get('/fhir/CodeSystem/?title=source name')
self.assertEqual(len(response.data['entry']), 1)
resource = response.data['entry'][0]['resource']
self.assertEqual(
resource['identifier'][0]['value'],
'/orgs/' + self.org.mnemonic + '/CodeSystem/' + self.org_source.mnemonic + '/'
)
self.assertEqual(resource['version'], 'v2')
def test_find_by_code(self):
response = self.client.get('/fhir/CodeSystem/?code=' + self.concept_1.mnemonic)
self.assertEqual(len(response.data['entry']), 1)
resource = response.data['entry'][0]['resource']
self.assertEqual(
resource['identifier'][0]['value'],
'/orgs/' + self.org.mnemonic + '/CodeSystem/' + self.org_source.mnemonic + '/'
)
self.assertEqual(resource['version'], 'v2')
def test_find_by_non_supported_param(self):
response = self.client.get('/fhir/CodeSystem/?non_supported_param=' + self.concept_1.mnemonic)
self.assertEqual(response.status_code, 400)
def test_private_can_list(self):
response = self.client.get('/fhir/CodeSystem/', HTTP_AUTHORIZATION='Token ' + self.user_token)
self.assertEqual(len(response.data['entry']), 2)
resource = response.data['entry'][0]['resource']
self.assertEqual(
resource['identifier'][0]['value'],
'/users/' + self.user.mnemonic + '/CodeSystem/' + self.user_source.mnemonic + '/'
)
self.assertEqual(resource['version'], 'v1')
resource_2 = response.data['entry'][1]['resource']
self.assertEqual(
resource_2['identifier'][0]['value'],
'/orgs/' + self.org.mnemonic + '/CodeSystem/' + self.org_source.mnemonic + '/'
)
self.assertEqual(resource_2['version'], 'v2')
def test_get_code_system(self):
response = self.client.get(f'/orgs/{self.org.mnemonic}/CodeSystem/{self.org_source.mnemonic}/')
self.assertEqual(response.status_code, 200)
self.assertEqual(response.data['id'], self.org_source.mnemonic)
self.assertEqual(response.data['version'], 'v2')
def test_validate_code_for_code_system(self):
response = self.client.get(f'/fhir/CodeSystem/$validate-code/'
f'?url={self.org_source.canonical_url}&code={self.concept_1.mnemonic}')
self.assertEqual(response.status_code, 200)
self.assertJSONEqual(json.dumps(response.data), json.dumps(
{'resourceType': 'Parameters', 'parameter': [{'name': 'result', 'valueBoolean': True}]}))
def test_validate_code_for_code_system_via_post(self):
response = self.client.post(
'/fhir/CodeSystem/$validate-code/',
data={
'resourceType': 'Parameters',
'parameter': [
{'name': 'url', 'valueUri': self.org_source.canonical_url},
{'name': 'code', 'valueCode': self.concept_1.mnemonic}
]
},
format='json'
)
self.assertEqual(response.status_code, 200)
self.assertJSONEqual(json.dumps(response.data), json.dumps(
{'resourceType': 'Parameters', 'parameter': [{'name': 'result', 'valueBoolean': True}]}))
def test_validate_code_for_code_system_negative(self):
response = self.client.get(f'/fhir/CodeSystem/$validate-code/'
f'?url={self.org_source.canonical_url}&code=non_existing_code')
self.assertEqual(response.status_code, 200)
self.assertJSONEqual(json.dumps(response.data), json.dumps(
{'resourceType': 'Parameters', 'parameter': [
{'name': 'result', 'valueBoolean': False}
]}))
def test_validate_code_for_code_system_with_invalid_url_negative(self):
response = self.client.get(f'/fhir/CodeSystem/$validate-code/'
f'?url=non_existing_url&code=${self.concept_1.mnemonic}')
self.assertEqual(response.status_code, 200)
self.assertJSONEqual(json.dumps(response.data), json.dumps(
{'resourceType': 'Parameters', 'parameter': [
{'name': 'result', 'valueBoolean': False}
]}))
def test_validate_code_with_display_for_code_system(self):
response = self.client.get(f'/fhir/CodeSystem/$validate-code/'
f'?url={self.org_source.canonical_url}'
f'&code={self.concept_1.mnemonic}'
f'&display={self.concept_1.display_name}')
self.assertEqual(response.status_code, 200)
self.assertJSONEqual(json.dumps(response.data), json.dumps(
{'resourceType': 'Parameters', 'parameter': [{'name': 'result', 'valueBoolean': True}]}))
def test_validate_code_with_display_for_code_system_negative(self):
response = self.client.get(f'/fhir/CodeSystem/$validate-code/'
f'?url={self.org_source.canonical_url}'
f'&code={self.concept_1.mnemonic}'
f'&display=wrong_display')
self.assertEqual(response.status_code, 200)
self.assertJSONEqual(json.dumps(response.data), json.dumps(
{'resourceType': 'Parameters', 'parameter': [
{'name': 'result', 'valueBoolean': False}
]}))
def test_lookup_for_code_system(self):
response = self.client.get(f'/fhir/CodeSystem/$lookup/'
f'?system={self.org_source.canonical_url}'
f'&code={self.concept_1.mnemonic}')
self.assertEqual(response.status_code, 200)
self.assertJSONEqual(json.dumps(response.data), json.dumps(
{'resourceType': 'Parameters', 'parameter': [
{'name': 'name', 'valueString': self.org_source.mnemonic},
{'name': 'version', 'valueString': self.org_source_v2.version},
{'name': 'display', 'valueString': self.concept_1.display_name}]}))
def test_lookup_for_empty_code_system(self):
response = self.client.get('/fhir/CodeSystem/$lookup/?system=&code=')
self.assertEqual(response.status_code, 400)
self.assertJSONEqual(json.dumps(response.data), json.dumps(CodeSystemLookupNotFoundError().detail))
def test_lookup_for_code_system_with_new_canonical(self):
self.org_source.canonical_url = '/new/url'
Source.save(self.org_source)
response = self.client.get(f'/fhir/CodeSystem/$lookup/'
f'?system={self.org_source.canonical_url}'
f'&code={self.concept_1.mnemonic}')
self.assertEqual(response.status_code, 400)
self.assertJSONEqual(json.dumps(response.data), json.dumps(CodeSystemLookupNotFoundError().detail))
response = self.client.get(f'/fhir/CodeSystem/$lookup/'
f'?system={self.org_source_v1.canonical_url}'
f'&code={self.concept_1.mnemonic}')
self.assertEqual(response.status_code, 200)
self.assertJSONEqual(json.dumps(response.data), json.dumps(
{'resourceType': 'Parameters', 'parameter': [
{'name': 'name', 'valueString': self.org_source.mnemonic},
{'name': 'version', 'valueString': self.org_source_v2.version},
{'name': 'display', 'valueString': self.concept_1.display_name}]}))
@patch('core.sources.models.index_source_concepts', Mock(__name__='index_source_concepts'))
@patch('core.sources.models.index_source_mappings', Mock(__name__='index_source_mappings'))
def test_post_code_system_without_concepts(self):
response = self.client.post(
f'/users/{self.user.mnemonic}/CodeSystem/',
HTTP_AUTHORIZATION='Token ' + self.user_token,
data={
'url': 'http://localhost/url',
'title': 'test',
'language': 'en',
'identifier': [{
'value': f'/users/{self.user.mnemonic}/CodeSystem/test',
'type': {
'coding': [{
'code': 'ACSN',
'system': 'http://hl7.org/fhir/v2/0203'
}]
}
}],
'version': '1.0',
'name': 'test',
'id': 'test',
'status': 'retired',
'content': 'fragment'
},
format='json'
)
self.assertEqual(response.status_code, 201)
self.assertEqual(response.data['id'], 'test')
self.assertEqual(response.data['version'], '1.0')
# check if HEAD persisted
sources = Source.objects.filter(mnemonic='test', version='HEAD', user=self.user)
self.assertEqual(len(sources), 1)
source = sources.first()
self.assertEqual(source.canonical_url, 'http://localhost/url')
self.assertEqual(source.retired, True)
self.assertEqual(source.name, 'test')
# check if version persisted
sources = Source.objects.filter(mnemonic='test', version='1.0', user=self.user)
self.assertEqual(len(sources), 1)
source = sources.first()
self.assertEqual(source.canonical_url, 'http://localhost/url')
self.assertEqual(source.retired, True)
self.assertEqual(source.name, 'test')
@patch('core.sources.models.index_source_concepts', Mock(__name__='index_source_concepts'))
@patch('core.sources.models.index_source_mappings', Mock(__name__='index_source_mappings'))
def test_put_code_system_without_concepts(self):
response = self.client.put(
f'/users/{self.user.mnemonic}/CodeSystem/{self.user_source.mnemonic}/',
HTTP_AUTHORIZATION='Token ' + self.user_token,
data={
'url': 'http://localhost/url',
'title': 'test',
'language': 'en',
'identifier': [{
'value': f'/users/{self.user.mnemonic}/CodeSystem/{self.user_source.mnemonic}/',
'type': {
'coding': [{
'code': 'ACSN',
'system': 'http://hl7.org/fhir/v2/0203'
}]
}
}],
'version': '1.0',
'name': 'test',
'id': self.user_source.mnemonic,
'status': 'draft',
'content': 'fragment'
},
format='json'
)
self.assertEqual(response.status_code, 200)
self.assertEqual(response.data['id'], self.user_source.mnemonic)
self.assertEqual(response.data['version'], '1.0')
self.assertEqual(response.data['status'], 'draft')
# check if HEAD persisted
sources = Source.objects.filter(mnemonic=self.user_source.mnemonic, version='HEAD', user=self.user)
self.assertEqual(len(sources), 1)
source = sources.first()
self.assertEqual(source.canonical_url, 'http://localhost/url')
self.assertEqual(source.retired, False)
self.assertEqual(source.name, 'test')
# check if version persisted
sources = Source.objects.filter(mnemonic=self.user_source.mnemonic, version='1.0', user=self.user)
self.assertEqual(len(sources), 1)
source = sources.first()
self.assertEqual(source.canonical_url, 'http://localhost/url')
self.assertEqual(source.retired, False)
self.assertEqual(source.name, 'test')
@patch('core.sources.models.index_source_concepts', Mock(__name__='index_source_concepts'))
@patch('core.sources.models.index_source_mappings', Mock(__name__='index_source_mappings'))
def test_post_code_system_with_concepts(self):
response = self.client.post(
f'/users/{self.user.mnemonic}/CodeSystem/',
HTTP_AUTHORIZATION='Token ' + self.user_token,
data={
'url': 'http://localhost/url',
'title': 'test',
'language': 'en',
'identifier': [{
'value': f'/users/{self.user.mnemonic}/CodeSystem/test',
'type': {
'coding': [{
'code': 'ACSN',
'system': 'http://hl7.org/fhir/v2/0203'
}]
}
}],
'version': '1.0',
'name': 'test',
'id': 'test',
'status': 'retired',
'content': 'fragment',
'concept': [{
'code': 'test',
'display': 'Test',
'property': [{
'code': 'conceptclass',
'valueString': 'Locale'
}, {
'code': 'datatype',
'valueString': 'N/A'
}],
'designation': [{
'value': 'Testing',
'language': 'en',
'use': {
'code': 'fully qualified'
}
}]
}]
},
format='json'
)
self.assertEqual(response.status_code, 201)
self.assertEqual(response.data['id'], 'test')
self.assertEqual(response.data['version'], '1.0')
# check if HEAD persisted
sources = Source.objects.filter(mnemonic='test', version='HEAD', user=self.user)
self.assertEqual(len(sources), 1)
source = sources.first()
self.assertEqual(source.canonical_url, 'http://localhost/url')
self.assertEqual(source.retired, True)
self.assertEqual(source.name, 'test')
self.assertEqual(len(source.get_concepts_queryset().all()), 1)
concept = source.get_concepts_queryset().first()
self.assertEqual(concept.is_head, True)
self.assertEqual(concept.mnemonic, 'test')
self.assertEqual(concept.display_name, 'Test')
self.assertEqual(len(concept.names.all()), 2)
# check if version persisted
sources = Source.objects.filter(mnemonic='test', version='1.0', user=self.user)
self.assertEqual(len(sources), 1)
source = sources.first()
self.assertEqual(source.canonical_url, 'http://localhost/url')
self.assertEqual(source.retired, True)
self.assertEqual(source.name, 'test')
self.assertEqual(len(source.concepts.all()), 1)
concept = source.concepts.first()
self.assertEqual(concept.mnemonic, 'test')
self.assertEqual(concept.display_name, 'Test')
self.assertEqual(concept.is_head, False)
self.assertEqual(len(concept.names.all()), 2)
@patch('core.sources.models.index_source_concepts', Mock(__name__='index_source_concepts'))
@patch('core.sources.models.index_source_mappings', Mock(__name__='index_source_mappings'))
def test_put_code_system_with_all_new_concepts(self):
response = self.client.put(
f'/users/{self.user.mnemonic}/CodeSystem/{self.user_source.mnemonic}/',
HTTP_AUTHORIZATION='Token ' + self.user_token,
data={
'url': 'http://localhost/url',
'title': 'test',
'language': 'en',
'identifier': [{
'value': f'/users/{self.user.mnemonic}/CodeSystem/{self.user_source.mnemonic}/',
'type': {
'coding': [{
'code': 'ACSN',
'system': 'http://hl7.org/fhir/v2/0203'
}]
}
}],
'version': '1.0',
'name': 'test',
'id': self.user_source.mnemonic,
'status': 'draft',
'content': 'fragment',
'concept': [{
'code': 'test',
'display': 'Test',
'property': [{
'code': 'conceptclass',
'valueString': 'Locale'
}, {
'code': 'datatype',
'valueString': 'N/A'
}]
}]
},
format='json'
)
self.assertEqual(response.status_code, 200)
self.assertEqual(response.data['id'], self.user_source.mnemonic)
self.assertEqual(response.data['version'], '1.0')
self.assertEqual(response.data['status'], 'draft')
# check if HEAD persisted
sources = Source.objects.filter(mnemonic=self.user_source.mnemonic, version='HEAD', user=self.user)
self.assertEqual(len(sources), 1)
source = sources.first()
self.assertEqual(source.canonical_url, 'http://localhost/url')
self.assertEqual(source.retired, False)
self.assertEqual(source.name, 'test')
self.assertEqual(len(source.get_concepts_queryset().all()), 1)
concept = source.get_concepts_queryset().first()
self.assertEqual(concept.is_head, True)
self.assertEqual(concept.mnemonic, 'test')
self.assertEqual(concept.display_name, 'Test')
self.assertEqual(len(concept.names.all()), 1)
# check if version persisted
sources = Source.objects.filter(mnemonic=self.user_source.mnemonic, version='1.0', user=self.user)
self.assertEqual(len(sources), 1)
source = sources.first()
self.assertEqual(source.canonical_url, 'http://localhost/url')
self.assertEqual(source.retired, False)
self.assertEqual(source.name, 'test')
self.assertEqual(len(source.concepts.all()), 1)
concept = source.concepts.first()
self.assertEqual(concept.mnemonic, 'test')
self.assertEqual(concept.display_name, 'Test')
self.assertEqual(concept.is_head, False)
self.assertEqual(len(concept.names.all()), 1)
@patch('core.sources.models.index_source_concepts', Mock(__name__='index_source_concepts'))
@patch('core.sources.models.index_source_mappings', Mock(__name__='index_source_mappings'))
def test_put_code_system_with_existing_concepts(self):
response = self.client.put(
f'/users/{self.user.mnemonic}/CodeSystem/{self.user_source.mnemonic}/',
HTTP_AUTHORIZATION='Token ' + self.user_token,
data={
'url': 'http://localhost/url',
'title': 'test',
'language': 'en',
'identifier': [{
'value': f'/users/{self.user.mnemonic}/CodeSystem/{self.user_source.mnemonic}/',
'type': {
'coding': [{
'code': 'ACSN',
'system': 'http://hl7.org/fhir/v2/0203'
}]
}
}],
'version': '1.0',
'name': 'test',
'id': self.user_source.mnemonic,
'status': 'draft',
'content': 'fragment',
'concept': [{
'code': 'test',
'display': 'Test',
'property': [
{
'code': 'conceptclass',
'valueString': 'Locale'
},
{
'code': 'datatype',
'valueString': 'N/A'
}]
}]
},
format='json'
)
self.assertEqual(response.status_code, 200)
response = self.client.put(
f'/users/{self.user.mnemonic}/CodeSystem/{self.user_source.mnemonic}/',
HTTP_AUTHORIZATION='Token ' + self.user_token,
data={
'url': 'http://localhost/url',
'title': 'test',
'language': 'en',
'identifier': [{
'value': f'/users/{self.user.mnemonic}/CodeSystem/{self.user_source.mnemonic}/',
'type': {
'coding': [{
'code': 'ACSN',
'system': 'http://hl7.org/fhir/v2/0203'
}]
}
}],
'version': '2.0',
'name': 'test',
'id': self.user_source.mnemonic,
'status': 'draft',
'content': 'fragment',
'concept': [{
'code': 'test',
'display': 'Test',
'property': [{
'code': 'conceptclass',
'valueString': 'Locale'
}, {
'code': 'datatype',
'valueString': 'N/A'
}]
}, {
'code': 'test2',
'display': 'Test2',
'property': [{
'code': 'conceptclass',
'valueString': 'Locale'
}, {
'code': 'datatype',
'valueString': 'N/A'
}]
}]
},
format='json'
)
self.assertEqual(response.status_code, 200)
self.assertEqual(response.data['id'], self.user_source.mnemonic)
self.assertEqual(response.data['version'], '2.0')
# check if HEAD persisted
sources = Source.objects.filter(mnemonic=self.user_source.mnemonic, version='HEAD', user=self.user)
self.assertEqual(len(sources), 1)
source = sources.first()
self.assertEqual(source.canonical_url, 'http://localhost/url')
self.assertEqual(source.retired, False)
self.assertEqual(source.name, 'test')
self.assertEqual(len(source.get_concepts_queryset().all()), 2)
concepts = source.get_concepts_queryset().order_by('mnemonic').all()
self.assertEqual(concepts[0].is_head, True)
self.assertEqual(concepts[0].mnemonic, 'test')
self.assertEqual(concepts[0].display_name, 'Test')
self.assertEqual(len(concepts[0].names.all()), 1)
self.assertEqual(concepts[1].is_head, True)
self.assertEqual(concepts[1].mnemonic, 'test2')
self.assertEqual(concepts[1].display_name, 'Test2')
self.assertEqual(len(concepts[1].names.all()), 1)
# check if version persisted
sources = Source.objects.filter(mnemonic=self.user_source.mnemonic, version='2.0', user=self.user)
self.assertEqual(len(sources), 1)
source = sources.first()
self.assertEqual(source.canonical_url, 'http://localhost/url')
self.assertEqual(source.retired, False)
self.assertEqual(source.name, 'test')
concepts = Concept.objects.filter(sources__id=source.id).order_by('mnemonic').all()
self.assertEqual(len(concepts), 2)
self.assertEqual(concepts[0].mnemonic, 'test')
self.assertEqual(concepts[0].display_name, 'Test')
self.assertEqual(concepts[0].is_head, False)
self.assertEqual(len(concepts[0].names.all()), 1)
self.assertEqual(concepts[1].mnemonic, 'test2')
self.assertEqual(concepts[1].display_name, 'Test2')
self.assertEqual(concepts[1].is_head, False)
self.assertEqual(len(concepts[1].names.all()), 1)
def test_unable_to_represent_as_fhir(self):
instance = Source(id='1', uri='/invalid/uri')
serialized = CodeSystemDetailSerializer(instance=instance).data
self.assertDictEqual(serialized, {
'resourceType': 'OperationOutcome',
'issue': [{'severity': 'error', 'details': 'Failed to represent "/invalid/uri" as CodeSystem'}]})
def test_conversion_from_fhir(self):
code_system = CodeSystem(**{
'resourceType': 'CodeSystem',
'id': 'test',
'content': 'complete',
'status': 'draft'
})
can_convert = CodeSystemConverter.can_convert_from_fhir(code_system)
self.assertTrue(can_convert)
source = CodeSystemConverter.from_fhir(code_system)
self.assertEqual(source['mnemonic'], 'test')
def test_conversion_to_fhir(self):
source = OrganizationSourceFactory.build(mnemonic='test')
can_convert = CodeSystemConverter.can_convert_to_fhir(source)
self.assertTrue(can_convert)
code_system = CodeSystemConverter.to_fhir(source)
self.assertEqual(code_system['id'], 'test')