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tests.py
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from collections import OrderedDict
from mock.mock import patch, Mock
from rest_framework.test import APIClient
from core.common.tests import OCLTestCase
from core.concept_maps.serializers import ConceptMapDetailSerializer
from core.concepts.tests.factories import ConceptFactory, ConceptNameFactory
from core.mappings.tests.factories import MappingFactory
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 ConceptMapTest(OCLTestCase):
maxDiff = None
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, mnemonic='concept_1',
names=[ConceptNameFactory.build(name="concept_1_name")])
self.concept_2 = ConceptFactory(parent=self.org_source, mnemonic='concept_2')
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.org_source_B = OrganizationSourceFactory(organization=self.org, canonical_url='/some/url/B',
full_name='source name B')
self.concept_B_1 = ConceptFactory(parent=self.org_source_B, mnemonic='concept_B_1',
names=[ConceptNameFactory.build(name="concept_B_1_name")])
self.concept_B_2 = ConceptFactory(parent=self.org_source_B, mnemonic='concept_B_2')
self.org_source_B_v1 = OrganizationSourceFactory.build(
version='v1', mnemonic=self.org_source_B.mnemonic, organization=self.org_source_B.parent)
Source.persist_new_version(self.org_source_B_v1, self.org_source_B.created_by)
self.mapping_1 = MappingFactory(parent=self.org_source, to_concept=self.concept_1,
from_concept=self.concept_B_1)
self.mapping_1.populate_fields_from_relations({})
self.mapping_1.save()
self.mapping_2 = MappingFactory(parent=self.org_source, to_concept=self.concept_2,
from_concept=self.concept_B_2)
self.mapping_2.populate_fields_from_relations({})
self.mapping_2.save()
self.mapping_3 = MappingFactory(parent=self.org_source, to_concept=self.concept_1,
from_concept=self.concept_B_2)
self.mapping_3.populate_fields_from_relations({})
self.mapping_3.save()
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)
for mapping in self.org_source_v2.get_mappings_queryset().all():
mapping.populate_fields_from_relations({})
mapping.save()
self.client = APIClient()
def test_public_can_view(self):
response = self.client.get('/fhir/ConceptMap/?url=/some/url')
self.assertEqual(len(response.data['entry']), 1)
resource = response.data['entry'][0]['resource']
self.assertEqual(
resource['identifier'][0]['value'],
'/orgs/' + self.org.mnemonic + '/ConceptMap/' + self.org_source.mnemonic + '/'
)
self.assertEqual(resource['version'], 'v2')
self.assertEqual(len(resource['group']), 1)
self.assertEqual(resource['group'], [{'source': self.org_source_B_v1.canonical_url,
'target': self.org_source.canonical_url,
'element': [
{'code': 'concept_B_1',
'target': [{'code': 'concept_1', 'relationship': 'equivalent'}]},
{'code': 'concept_B_2',
'target': [{'code': 'concept_2', 'relationship': 'equivalent'}]},
{'code': 'concept_B_2',
'target': [{'code': 'concept_1', 'relationship': 'equivalent'}]}]}])
def test_private_can_view(self):
response = self.client.get('/fhir/ConceptMap/?url=/some/url', 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'],
'/orgs/' + self.org.mnemonic + '/ConceptMap/' + self.org_source.mnemonic + '/'
)
self.assertEqual(resource['version'], 'v2')
resource2 = response.data['entry'][1]['resource']
self.assertEqual(
resource2['identifier'][0]['value'],
'/users/' + self.user.mnemonic + '/ConceptMap/' + self.user_source.mnemonic + '/'
)
self.assertEqual(resource2['version'], 'v1')
def test_public_can_list(self):
response = self.client.get('/fhir/ConceptMap/')
self.assertEqual(len(response.data['entry']), 2)
resource = response.data['entry'][0]['resource']
self.assertEqual(
resource['identifier'][0]['value'],
'/orgs/' + self.org.mnemonic + '/ConceptMap/' + self.org_source.mnemonic + '/'
)
self.assertEqual(resource['version'], 'v2')
resource2 = response.data['entry'][1]['resource']
self.assertEqual(
resource2['identifier'][0]['value'],
'/orgs/' + self.org.mnemonic + '/ConceptMap/' + self.org_source_B.mnemonic + '/'
)
self.assertEqual(resource2['version'], 'v1')
def test_find_by_title(self):
response = self.client.get('/fhir/ConceptMap/?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 + '/ConceptMap/' + self.org_source.mnemonic + '/'
)
self.assertEqual(resource['version'], 'v2')
def test_private_can_list(self):
response = self.client.get('/fhir/ConceptMap/', HTTP_AUTHORIZATION='Token ' + self.user_token)
self.assertEqual(len(response.data['entry']), 3)
def test_get_concept_map(self):
response = self.client.get(f'/orgs/{self.org.mnemonic}/ConceptMap/{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')
@patch('core.sources.models.index_source_mappings', Mock())
@patch('core.sources.models.index_source_concepts', Mock())
def test_post_concept_map_without_mappings(self):
response = self.client.post(
f'/users/{self.user.mnemonic}/ConceptMap/',
HTTP_AUTHORIZATION='Token ' + self.user_token,
data={
'url': 'http://localhost/url',
'title': 'test',
'language': 'en',
'identifier': [{
'value': f'/users/{self.user.mnemonic}/ConceptMap/test',
'type': {
'coding': [{
'code': 'ACSN',
'system': 'http://hl7.org/fhir/v2/0203'
}]
}
}],
'version': '1.0',
'name': 'test',
'id': 'test',
'status': 'active'
},
format='json'
)
self.assertEqual(response.status_code, 201)
self.assertEqual(response.data['id'], 'test')
self.assertEqual(response.data['version'], '1.0')
self.assertEqual(response.data['group'], [])
# 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.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.name, 'test')
def test_put_concept_map_without_mappings(self):
response = self.client.put(
f'/users/{self.user.mnemonic}/ConceptMap/{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}/ConceptMap/{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'
},
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')
def test_post_concept_map_with_mappings(self):
response = self.client.post(
f'/users/{self.user.mnemonic}/ConceptMap/',
HTTP_AUTHORIZATION='Token ' + self.user_token,
data={
'url': 'http://localhost/url',
'title': 'test',
'language': 'en',
'identifier': [{
'value': f'/users/{self.user.mnemonic}/ConceptMap/test',
'type': {
'coding': [{
'code': 'ACSN',
'system': 'http://hl7.org/fhir/v2/0203'
}]
}
}],
'version': '1.0',
'name': 'test',
'id': 'test',
'status': 'retired',
'group': [{'source': self.org_source_B_v1.canonical_url,
'target': self.org_source.canonical_url,
'element': [
{'code': 'concept_B_1',
'target': [{'code': 'concept_1', 'relationship': 'equivalent'}]},
{'code': 'concept_B_2',
'target': [{'code': 'concept_2', 'relationship': 'equivalent'}]},
{'code': 'concept_B_2',
'target': [{'code': 'concept_1', 'relationship': 'equivalent'}]}]}]
},
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_mappings_queryset().all()), 3)
# 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.get_mappings_queryset().all()), 3)
def test_post_concept_map_with_mappings_without_canonicals(self):
response = self.client.post(
f'/users/{self.user.mnemonic}/ConceptMap/',
HTTP_AUTHORIZATION='Token ' + self.user_token,
data={
'url': 'http://localhost/url',
'title': 'test',
'language': 'en',
'identifier': [{
'value': f'/users/{self.user.mnemonic}/ConceptMap/test',
'type': {
'coding': [{
'code': 'ACSN',
'system': 'http://hl7.org/fhir/v2/0203'
}]
}
}],
'version': '1.0',
'name': 'test',
'id': 'test',
'status': 'retired',
'group': [{'source': self.org_source_B_v1.url,
'target': self.org_source.url,
'element': [
{'code': 'concept_B_1',
'target': [{'code': 'concept_1', 'relationship': 'equivalent'}]},
{'code': 'concept_B_2',
'target': [{'code': 'concept_2', 'relationship': 'equivalent'}]},
{'code': 'concept_B_2',
'target': [{'code': 'concept_1', 'relationship': 'equivalent'}]}]}]
},
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_mappings_queryset().all()), 3)
# 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.get_mappings_queryset().all()), 3)
def test_put_concept_map_with_all_new_concepts(self):
response = self.putConceptMap()
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_mappings_queryset().all()), 1)
mapping = source.get_mappings_queryset().first()
self.assertEqual(mapping.is_head, True)
self.assertEqual(mapping.from_source_url, self.org_source_B_v1.canonical_url)
self.assertEqual(mapping.to_source_url, self.org_source.canonical_url)
self.assertEqual(mapping.from_concept_code, 'concept_B_1')
self.assertEqual(mapping.to_concept_code, 'concept_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.get_mappings_queryset().all()), 1)
mapping = source.get_mappings_queryset().first()
self.assertEqual(mapping.is_head, False)
self.assertEqual(mapping.from_source_url, self.org_source_B_v1.canonical_url)
self.assertEqual(mapping.to_source_url, self.org_source.canonical_url)
self.assertEqual(mapping.from_concept_code, 'concept_B_1')
self.assertEqual(mapping.to_concept_code, 'concept_1')
def test_translate_positive(self):
self.putConceptMap()
response = self.client.get(
f'/users/{self.user.mnemonic}/ConceptMap/$translate?'
f'system={self.org_source_B_v1.canonical_url}&code=concept_B_1',
HTTP_AUTHORIZATION='Token ' + self.user_token)
self.assertEqual(response.status_code, 200)
self.assertDictEqual(
response.data,
{
'resourceType': 'Parameters',
'parameter': [
OrderedDict([
('name', 'result'),
('valueBoolean', True)
]),
OrderedDict([
('name', 'match'),
(
'part',
[
OrderedDict([
('name', 'equivalence'),
('valueCode', 'equivalent')
]),
OrderedDict([
('name', 'concept'),
('valueCoding', OrderedDict([('system', '/some/url'), ('code', 'concept_1')]))
])
]
)
]),
OrderedDict([
('name', 'match'),
(
'part',
[
OrderedDict([
('name', 'equivalence'),
('valueCode', 'equivalent')
]),
OrderedDict([
('name', 'concept'),
('valueCoding', OrderedDict([('system', '/some/url'), ('code', 'concept_1')]))
])
]
)
])
]
})
def test_public_translate_negative(self):
self.putConceptMap()
response = self.client.get(
f'/users/{self.user.mnemonic}/ConceptMap/$translate?'
f'system={self.org_source_B_v1.canonical_url}&code=concept_1')
self.assertEqual(response.status_code, 200)
self.assertDictEqual(response.data, {
'resourceType': 'Parameters',
'parameter': [OrderedDict(
[('name', 'result'), ('valueBoolean', False)])]})
def putConceptMap(self):
response = self.client.put(
f'/users/{self.user.mnemonic}/ConceptMap/{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}/ConceptMap/{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',
'group': [{'source': self.org_source_B_v1.canonical_url,
'target': self.org_source.canonical_url,
'element': [
{'code': 'concept_B_1',
'target': [{'code': 'concept_1', 'relationship': 'equivalent'}]}]
}]
},
format='json'
)
self.assertEqual(response.status_code, 200)
return response
def test_translate_negative(self):
self.putConceptMap()
response = self.client.get(
f'/users/{self.user.mnemonic}/ConceptMap/$translate?'
f'system={self.org_source_B_v1.canonical_url}&code=concept_1',
HTTP_AUTHORIZATION='Token ' + self.user_token)
self.assertEqual(response.status_code, 200)
self.assertDictEqual(response.data, {
'resourceType': 'Parameters',
'parameter': [OrderedDict(
[('name', 'result'), ('valueBoolean', False)]
)]})
def test_translate_with_target(self):
self.putConceptMap()
response = self.client.get(
f'/users/{self.user.mnemonic}/ConceptMap/$translate?'
f'system={self.org_source_B_v1.canonical_url}&code=concept_B_1'
f'&targetsystem={self.org_source.canonical_url}', HTTP_AUTHORIZATION='Token ' + self.user_token)
self.assertEqual(response.status_code, 200)
self.assertDictEqual(
response.data,
{
'resourceType': 'Parameters',
'parameter': [
OrderedDict([
('name', 'result'),
('valueBoolean', True)
]),
OrderedDict([
('name', 'match'),
(
'part',
[
OrderedDict([
('name', 'equivalence'),
('valueCode', 'equivalent')
]),
OrderedDict([
('name', 'concept'),
('valueCoding', OrderedDict([('system', '/some/url'), ('code', 'concept_1')]))
])
]
)
]),
OrderedDict([
('name', 'match'),
(
'part',
[
OrderedDict([
('name', 'equivalence'),
('valueCode', 'equivalent')
]),
OrderedDict([
('name', 'concept'),
('valueCoding', OrderedDict([('system', '/some/url'), ('code', 'concept_1')]))
])
]
)
])
]
}
)
def test_translate_with_target_negative(self):
self.putConceptMap()
response = self.client.get(
f'/users/{self.user.mnemonic}/ConceptMap/$translate?'
f'system={self.org_source_B_v1.canonical_url}&code=concept_B_1'
f'&targetsystem={self.org_source_B_v1.canonical_url}',
HTTP_AUTHORIZATION='Token ' + self.user_token)
self.assertEqual(response.status_code, 200)
self.assertDictEqual(response.data, {
'resourceType': 'Parameters',
'parameter': [OrderedDict(
[('name', 'result'), ('valueBoolean', False)])]})
def test_unable_to_represent_as_fhir(self):
instance = Source(id='1', uri='/invalid/uri')
serialized = ConceptMapDetailSerializer(instance=instance).data
self.assertDictEqual(serialized, {
'resourceType': 'OperationOutcome',
'issue': [{'severity': 'error', 'details': 'Failed to represent "/invalid/uri" as ConceptMap'}]})