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tests.py
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tests.py
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import datetime
import os
import uuid
from collections import OrderedDict
from unittest.mock import patch, Mock, ANY
import django
import factory
from colour_runner.django_runner import ColourRunnerMixin
from django.conf import settings
from django.core.files.base import File
from django.core.management import call_command
from django.test import TestCase
from django.test.runner import DiscoverRunner
from mock.mock import call
from requests.auth import HTTPBasicAuth
from rest_framework.exceptions import ValidationError
from rest_framework.test import APITestCase, APITransactionTestCase
from core.collections.models import CollectionReference
from core.common.constants import HEAD
from core.common.tasks import delete_s3_objects, bulk_import_parallel_inline, resources_report, calculate_checksums
from core.common.utils import (
compact_dict_by_values, to_snake_case, flower_get,
to_camel_case,
drop_version, is_versioned_uri, separate_version, to_parent_uri, jsonify_safe, es_get,
get_resource_class_from_resource_name, flatten_dict, is_csv_file, is_url_encoded_string, to_parent_uri_from_kwargs,
set_current_user, get_current_user, set_request_url, get_request_url, nested_dict_values, chunks, api_get,
split_list_by_condition, is_zip_file, get_date_range_label, get_prev_month, from_string_to_date, get_end_of_month,
get_start_of_month, es_id_in, web_url)
from core.concepts.models import Concept
from core.orgs.models import Organization
from core.sources.models import Source
from core.users.models import UserProfile
from core.users.tests.factories import UserProfileFactory
from .backends import OCLOIDCAuthenticationBackend
from .checksums import Checksum
from .fhir_helpers import translate_fhir_query
from .serializers import IdentifierSerializer
from .validators import URIValidator
from ..code_systems.serializers import CodeSystemDetailSerializer
from ..concepts.tests.factories import ConceptFactory, ConceptNameFactory
from ..sources.tests.factories import OrganizationSourceFactory
class CustomTestRunner(ColourRunnerMixin, DiscoverRunner):
pass
class SetupTestEnvironment:
settings.TEST_MODE = True
settings.ELASTICSEARCH_DSL_AUTOSYNC = True
settings.ES_SYNC = True
class BaseTestCase(SetupTestEnvironment):
@staticmethod
def create_lookup_concept_classes(user=None, org=None):
org = org or Organization.objects.get(mnemonic='OCL')
user = user or UserProfile.objects.get(username='ocladmin')
classes_source = OrganizationSourceFactory(updated_by=user, organization=org, mnemonic="Classes", version=HEAD)
datatypes_source = OrganizationSourceFactory(
updated_by=user, organization=org, mnemonic="Datatypes", version=HEAD
)
nametypes_source = OrganizationSourceFactory(
updated_by=user, organization=org, mnemonic="NameTypes", version=HEAD
)
descriptiontypes_source = OrganizationSourceFactory(
updated_by=user, organization=org, mnemonic="DescriptionTypes", version=HEAD
)
maptypes_source = OrganizationSourceFactory(
updated_by=user, organization=org, mnemonic="MapTypes", version=HEAD
)
locales_source = OrganizationSourceFactory(updated_by=user, organization=org, mnemonic="Locales", version=HEAD)
ConceptFactory(
version=HEAD, updated_by=user, parent=classes_source, concept_class="Concept Class",
names=[ConceptNameFactory.build(name="Diagnosis")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=classes_source, concept_class="Concept Class",
names=[ConceptNameFactory.build(name="Drug")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=classes_source, concept_class="Concept Class",
names=[ConceptNameFactory.build(name="Test")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=classes_source, concept_class="Concept Class",
names=[ConceptNameFactory.build(name="Procedure")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=datatypes_source, concept_class="Datatype",
names=[ConceptNameFactory.build(name="None"), ConceptNameFactory.build(name="N/A")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=datatypes_source, concept_class="Datatype",
names=[ConceptNameFactory.build(name="Numeric")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=datatypes_source, concept_class="Datatype",
names=[ConceptNameFactory.build(name="Coded")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=datatypes_source, concept_class="Datatype",
names=[ConceptNameFactory.build(name="Text")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=nametypes_source, concept_class="NameType",
names=[ConceptNameFactory.build(name="FULLY_SPECIFIED"), ConceptNameFactory.build(name="Fully Specified")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=nametypes_source, concept_class="NameType",
names=[ConceptNameFactory.build(name="Short"), ConceptNameFactory.build(name="SHORT")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=nametypes_source, concept_class="NameType",
names=[ConceptNameFactory.build(name="INDEX_TERM"), ConceptNameFactory.build(name="Index Term")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=nametypes_source, concept_class="NameType",
names=[ConceptNameFactory.build(name="None")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=descriptiontypes_source, concept_class="DescriptionType",
names=[ConceptNameFactory.build(name="None")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=descriptiontypes_source, concept_class="DescriptionType",
names=[ConceptNameFactory.build(name="FULLY_SPECIFIED")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=descriptiontypes_source, concept_class="DescriptionType",
names=[ConceptNameFactory.build(name="Definition")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=maptypes_source, concept_class="MapType",
names=[ConceptNameFactory.build(name="SAME-AS"), ConceptNameFactory.build(name="Same As")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=maptypes_source, concept_class="MapType",
names=[ConceptNameFactory.build(name="Is Subset of")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=maptypes_source, concept_class="MapType",
names=[ConceptNameFactory.build(name="Different")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=maptypes_source, concept_class="MapType",
names=[
ConceptNameFactory.build(name="BROADER-THAN"), ConceptNameFactory.build(name="Broader Than"),
ConceptNameFactory.build(name="BROADER_THAN")
]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=maptypes_source, concept_class="MapType",
names=[
ConceptNameFactory.build(name="NARROWER-THAN"), ConceptNameFactory.build(name="Narrower Than"),
ConceptNameFactory.build(name="NARROWER_THAN")
]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=maptypes_source, concept_class="MapType",
names=[ConceptNameFactory.build(name="Q-AND-A")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=maptypes_source, concept_class="MapType",
names=[ConceptNameFactory.build(name="More specific than")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=maptypes_source, concept_class="MapType",
names=[ConceptNameFactory.build(name="Less specific than")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=maptypes_source, concept_class="MapType",
names=[ConceptNameFactory.build(name="Something Else")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=locales_source, concept_class="Locale",
names=[ConceptNameFactory.build(name="en")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=locales_source, concept_class="Locale",
names=[ConceptNameFactory.build(name="es")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=locales_source, concept_class="Locale",
names=[ConceptNameFactory.build(name="fr")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=locales_source, concept_class="Locale",
names=[ConceptNameFactory.build(name="tr")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=locales_source, concept_class="Locale",
names=[ConceptNameFactory.build(name="Abkhazian")]
)
ConceptFactory(
version=HEAD, updated_by=user, parent=locales_source, concept_class="Locale",
names=[ConceptNameFactory.build(name="English")]
)
class OCLAPITransactionTestCase(APITransactionTestCase, BaseTestCase):
@classmethod
def setUpClass(cls):
super().setUpClass()
call_command("loaddata", "core/fixtures/base_entities.yaml")
call_command("loaddata", "core/fixtures/toggles.json")
org = Organization.objects.get(id=1)
org.members.add(1)
class OCLAPITestCase(APITestCase, BaseTestCase):
@classmethod
def setUpClass(cls):
super().setUpClass()
call_command("loaddata", "core/fixtures/base_entities.yaml")
call_command("loaddata", "core/fixtures/toggles.json")
org = Organization.objects.get(id=1)
org.members.add(1)
class OCLTestCase(TestCase, BaseTestCase):
@classmethod
def setUpClass(cls):
super().setUpClass()
call_command("loaddata", "core/fixtures/base_entities.yaml")
call_command("loaddata", "core/fixtures/auth_groups.yaml")
call_command("loaddata", "core/fixtures/toggles.json")
@staticmethod
def factory_to_params(factory_klass, **kwargs):
return {
**factory.build(dict, FACTORY_CLASS=factory_klass),
**kwargs
}
class FhirHelpersTest(OCLTestCase):
def test_language_to_default_locale(self):
query_fields = list(CodeSystemDetailSerializer.Meta.fields)
query_params = {'language': 'eng'}
query_set = Source.objects.all()
query_set = translate_fhir_query(query_fields, query_params, query_set)
self.assertTrue('"sources"."default_locale" = eng' in str(query_set.query))
def test_status_retired(self):
query_fields = list(CodeSystemDetailSerializer.Meta.fields)
query_params = {'status': 'retired'}
query_set = Source.objects.all()
query_set = translate_fhir_query(query_fields, query_params, query_set)
self.assertTrue('WHERE "sources"."retired"' in str(query_set.query))
def test_status_active(self):
query_fields = list(CodeSystemDetailSerializer.Meta.fields)
query_params = {'status': 'active'}
query_set = Source.objects.all()
query_set = translate_fhir_query(query_fields, query_params, query_set)
self.assertTrue('WHERE "sources"."released"' in str(query_set.query))
def test_status_draft(self):
query_fields = list(CodeSystemDetailSerializer.Meta.fields)
query_params = {'status': 'draft'}
query_set = Source.objects.all()
query_set = translate_fhir_query(query_fields, query_params, query_set)
self.assertTrue('WHERE NOT "sources"."released"' in str(query_set.query))
def test_title_to_full_name(self):
query_fields = list(CodeSystemDetailSerializer.Meta.fields)
query_params = {'title': 'some title'}
query_set = Source.objects.all()
query_set = translate_fhir_query(query_fields, query_params, query_set)
self.assertTrue('WHERE "sources"."full_name" = some title' in str(query_set.query))
def test_other_fields(self):
query_fields = list(CodeSystemDetailSerializer.Meta.fields)
query_params = {'version': 'v1', 'id': '2'}
query_set = Source.objects.all()
query_set = translate_fhir_query(query_fields, query_params, query_set)
self.assertTrue('"sources"."version" = v1' in str(query_set.query))
self.assertTrue('"sources"."id" = 2' in str(query_set.query))
class IdentifierSerializerTest(OCLTestCase):
def test_deserialize(self):
data = {'system': '/org/OCL/test',
'value': '1',
'type': {
'text': 'Accession ID',
'coding': [{
'system': 'http://hl7.org/fhir/v2/0203',
'code': 'ACSN',
'display': 'ACSN'
}]
}}
serializer = IdentifierSerializer(data=data)
valid = serializer.is_valid()
self.assertTrue(valid, serializer.errors)
self.assertDictEqual(serializer.validated_data, OrderedDict([
('system', '/org/OCL/test'),
('value', '1'),
('type', OrderedDict([
('text', 'Accession ID'),
('coding', [OrderedDict([
('system', 'http://hl7.org/fhir/v2/0203'),
('code', 'ACSN'),
('display', 'ACSN')])])]))]))
def test_include_ocl_identifier(self):
rep = {}
IdentifierSerializer.include_ocl_identifier('/orgs/OCL/test/1', 'org', rep)
self.assertDictEqual(rep, {'identifier': [
{'system': 'http://localhost:8000',
'type': {
'coding': [{
'code': 'ACSN',
'display': 'Accession ID',
'system': 'http://hl7.org/fhir/v2/0203'}],
'text': 'Accession ID'},
'value': '/orgs/OCL/test/1/'}]})
def test_validate_identifier(self):
IdentifierSerializer.validate_identifier([
{'system': 'http://localhost:8000',
'type': {
'coding': [{
'code': 'ACSN',
'display': 'Accession ID',
'system': 'http://hl7.org/fhir/v2/0203'}],
'text': 'Accession ID'},
'value': '/orgs/OCL/CodeSystem/1/'}])
def test_validate_identifier_with_wrong_owner(self):
with self.assertRaisesRegex(ValidationError, "Owner type='org' is invalid. It must be 'users' or 'orgs'"):
IdentifierSerializer.validate_identifier([
{'system': 'http://localhost:8000',
'type': {
'coding': [{
'code': 'ACSN',
'display': 'Accession ID',
'system': 'http://hl7.org/fhir/v2/0203'}],
'text': 'Accession ID'},
'value': '/org/OCL/CodeSystem/1/'}])
def test_validate_identifier_with_wrong_type(self):
with self.assertRaisesRegex(ValidationError, "Resource type='Code' is invalid. "
"It must be 'CodeSystem' or 'ValueSet' or 'ConceptMap'"):
IdentifierSerializer.validate_identifier([
{'system': 'http://localhost:8000',
'type': {
'coding': [{
'code': 'ACSN',
'display': 'Accession ID',
'system': 'http://hl7.org/fhir/v2/0203'}],
'text': 'Accession ID'},
'value': '/orgs/OCL/Code/1/'}])
class UtilsTest(OCLTestCase):
def test_set_and_get_current_user(self):
set_current_user(lambda self: 'foo')
self.assertEqual(get_current_user(), 'foo')
def test_set_and_get_request_url(self):
set_request_url(lambda self: 'https://foobar.org/foo')
self.assertEqual(get_request_url(), 'https://foobar.org/foo')
def test_compact_dict_by_values(self):
self.assertEqual(compact_dict_by_values({}), {})
self.assertEqual(compact_dict_by_values({'foo': None}), {})
self.assertEqual(compact_dict_by_values({'foo': None, 'bar': None}), {})
self.assertEqual(compact_dict_by_values({'foo': None, 'bar': 1}), {'bar': 1})
self.assertEqual(compact_dict_by_values({'foo': 2, 'bar': 1}), {'foo': 2, 'bar': 1})
self.assertEqual(compact_dict_by_values({'foo': 2, 'bar': ''}), {'foo': 2})
def test_to_snake_case(self):
self.assertEqual(to_snake_case(""), "")
self.assertEqual(to_snake_case("foobar"), "foobar")
self.assertEqual(to_snake_case("foo_bar"), "foo_bar")
self.assertEqual(to_snake_case("fooBar"), "foo_bar")
def test_to_camel_case(self):
self.assertEqual(to_camel_case(""), "")
self.assertEqual(to_camel_case("foobar"), "foobar")
self.assertEqual(to_camel_case("foo_bar"), "fooBar")
self.assertEqual(to_camel_case("fooBar"), "fooBar")
@patch('core.common.utils.requests.get')
def test_flower_get(self, http_get_mock):
http_get_mock.return_value = 'foo-task-response'
self.assertEqual(flower_get('some-url'), 'foo-task-response')
http_get_mock.assert_called_once_with(
'http://flower:5555/some-url',
auth=HTTPBasicAuth(settings.FLOWER_USER, settings.FLOWER_PASSWORD)
)
@patch('core.common.utils.requests.get')
def test_api_get(self, http_get_mock):
user = UserProfileFactory()
http_get_mock.return_value = Mock(json=Mock(return_value='api-response'))
self.assertEqual(api_get('/some-url', user), 'api-response')
http_get_mock.assert_called_once_with(
'http://localhost:8000/some-url',
headers={'Authorization': f'Token {user.get_token()}'}
)
@patch('core.common.utils.settings')
@patch('core.common.utils.requests.get')
def test_es_get(self, http_get_mock, settings_mock):
settings_mock.ES_USER = 'es-user'
settings_mock.ES_PASSWORD = 'es-password'
settings_mock.ES_HOSTS = 'es:9200'
settings_mock.ES_SCHEME = 'http'
http_get_mock.return_value = 'dummy-response'
self.assertEqual(es_get('some-url', timeout=1), 'dummy-response')
http_get_mock.assert_called_with(
'http://es:9200/some-url',
auth=HTTPBasicAuth('es-user', 'es-password'),
timeout=1
)
settings_mock.ES_HOSTS = None
settings_mock.ES_HOST = 'es'
settings_mock.ES_PORT = '9201'
self.assertEqual(es_get('some-url', timeout=1), 'dummy-response')
http_get_mock.assert_called_with(
'http://es:9201/some-url',
auth=HTTPBasicAuth('es-user', 'es-password'),
timeout=1
)
def test_drop_version(self):
self.assertEqual(drop_version(None), None)
self.assertEqual(drop_version(''), '')
self.assertEqual(drop_version('/foo/bar'), '/foo/bar')
self.assertEqual(drop_version('/users/username/'), '/users/username/')
# user-source-concept
self.assertEqual(
drop_version("/users/user/sources/source/concepts/concept/"),
"/users/user/sources/source/concepts/concept/"
)
self.assertEqual(
drop_version("/users/user/sources/source/concepts/concept/version/"),
"/users/user/sources/source/concepts/concept/"
)
self.assertEqual(
drop_version("/users/user/sources/source/concepts/concept/1.23/"),
"/users/user/sources/source/concepts/concept/"
)
self.assertEqual(
drop_version("/users/user/sources/source/source-version/concepts/concept/1.23/"),
"/users/user/sources/source/source-version/concepts/concept/"
)
# org-source-concept
self.assertEqual(
drop_version("/orgs/org/sources/source/concepts/concept/"),
"/orgs/org/sources/source/concepts/concept/"
)
self.assertEqual(
drop_version("/orgs/org/sources/source/concepts/concept/version/"),
"/orgs/org/sources/source/concepts/concept/"
)
self.assertEqual(
drop_version("/orgs/org/sources/source/concepts/concept/1.24/"),
"/orgs/org/sources/source/concepts/concept/"
)
self.assertEqual(
drop_version("/orgs/org/sources/source/source-version/concepts/concept/1.24/"),
"/orgs/org/sources/source/source-version/concepts/concept/"
)
# user-collection-concept
self.assertEqual(
drop_version("/users/user/collections/coll/concepts/concept/"),
"/users/user/collections/coll/concepts/concept/"
)
self.assertEqual(
drop_version("/users/user/collections/coll/concepts/concept/version/"),
"/users/user/collections/coll/concepts/concept/"
)
self.assertEqual(
drop_version("/users/user/collections/coll/concepts/concept/1.23/"),
"/users/user/collections/coll/concepts/concept/"
)
self.assertEqual(
drop_version("/users/user/collections/coll/coll-version/concepts/concept/1.23/"),
"/users/user/collections/coll/coll-version/concepts/concept/"
)
# org-collection-concept
self.assertEqual(
drop_version("/orgs/org/collections/coll/concepts/concept/"),
"/orgs/org/collections/coll/concepts/concept/"
)
self.assertEqual(
drop_version("/orgs/org/collections/coll/concepts/concept/version/"),
"/orgs/org/collections/coll/concepts/concept/"
)
self.assertEqual(
drop_version("/orgs/org/collections/coll/concepts/concept/1.24/"),
"/orgs/org/collections/coll/concepts/concept/"
)
self.assertEqual(
drop_version("/orgs/org/collections/coll/coll-version/concepts/concept/1.24/"),
"/orgs/org/collections/coll/coll-version/concepts/concept/"
)
# user-source
self.assertEqual(drop_version("/users/user/sources/source/"), "/users/user/sources/source/")
self.assertEqual(drop_version("/users/user/sources/source/1.2/"), "/users/user/sources/source/")
# org-source
self.assertEqual(drop_version("/orgs/org/sources/source/"), "/orgs/org/sources/source/")
self.assertEqual(drop_version("/orgs/org/sources/source/version/"), "/orgs/org/sources/source/")
def test_is_versioned_uri(self):
self.assertFalse(is_versioned_uri("/users/user/sources/source/"))
self.assertFalse(is_versioned_uri("/orgs/org/sources/source/"))
self.assertFalse(is_versioned_uri("/orgs/org/collections/coll/concepts/concept/"))
self.assertTrue(is_versioned_uri("/orgs/org/sources/source/version/"))
self.assertTrue(is_versioned_uri("/users/user/sources/source/1.2/"))
self.assertTrue(is_versioned_uri("/orgs/org/sources/source/concepts/concept/1.24/"))
self.assertTrue(is_versioned_uri("/orgs/org/sources/source/source-version/concepts/concept/1.24/"))
self.assertTrue(is_versioned_uri("/orgs/org/collections/coll/concepts/concept/1.24/"))
self.assertTrue(is_versioned_uri("/orgs/org/collections/coll/concepts/concept/version/"))
self.assertTrue(is_versioned_uri("/orgs/org/collections/coll/coll-version/concepts/concept/1.24/"))
self.assertTrue(is_versioned_uri("/users/user/collections/coll/coll-version/concepts/concept/1.23/"))
self.assertTrue(is_versioned_uri("/users/user/collections/coll/concepts/concept/1.23/"))
def test_separate_version(self):
self.assertEqual(
separate_version("/orgs/org/collections/coll/coll-version/concepts/concept/1.24/"),
("1.24", "/orgs/org/collections/coll/coll-version/concepts/concept/")
)
self.assertEqual(
separate_version("/orgs/org/collections/coll/concepts/concept/1.24/"),
("1.24", "/orgs/org/collections/coll/concepts/concept/")
)
self.assertEqual(
separate_version("/orgs/org/collections/coll/concepts/concept/"),
(None, "/orgs/org/collections/coll/concepts/concept/")
)
self.assertEqual(
separate_version("/orgs/org/collections/coll/123/"),
("123", "/orgs/org/collections/coll/")
)
self.assertEqual(
separate_version("/orgs/org/sources/source/HEAD/"),
("HEAD", "/orgs/org/sources/source/")
)
self.assertEqual(
separate_version("/orgs/org/sources/source/"),
(None, "/orgs/org/sources/source/")
)
def test_to_parent_uri(self):
self.assertEqual(
to_parent_uri("/orgs/org/collections/coll/coll-version/concepts/concept/1.24/"),
"/orgs/org/collections/coll/coll-version/"
)
self.assertEqual(
to_parent_uri("/users/user/collections/coll/coll-version/mappings/M1234/1.24/"),
"/users/user/collections/coll/coll-version/"
)
self.assertEqual(
to_parent_uri("/orgs/org/collections/coll/coll-version/concepts/concept"),
"/orgs/org/collections/coll/coll-version/"
)
self.assertEqual(
to_parent_uri("/users/user/collections/coll/coll-version/"),
"/users/user/collections/coll/coll-version/"
)
self.assertEqual(
to_parent_uri("/users/user/collections/coll/"),
"/users/user/collections/coll/"
)
self.assertEqual(
to_parent_uri("/users/user/"),
"/users/user/"
)
self.assertEqual(
to_parent_uri("https://foobar.com/users/user/"),
"https://foobar.com/users/user/"
)
self.assertEqual(
to_parent_uri("https://foobar.com/users/user/sources/source/"),
"https://foobar.com/users/user/sources/source/"
)
self.assertEqual(
to_parent_uri("https://foobar.com/users/user/sources/source/mappings/mapping1/v1/"),
"https://foobar.com/users/user/sources/source/"
)
self.assertEqual(
to_parent_uri("/concepts/"),
"/"
)
def test_jsonify_safe(self):
self.assertEqual(jsonify_safe(None), None)
self.assertEqual(jsonify_safe({}), {})
self.assertEqual(jsonify_safe({'a': 1}), {'a': 1})
self.assertEqual(jsonify_safe('foobar'), 'foobar')
self.assertEqual(jsonify_safe('{"foo": "bar"}'), {'foo': 'bar'})
def test_get_resource_class_from_resource_name(self):
self.assertEqual(get_resource_class_from_resource_name(None), None)
self.assertEqual(get_resource_class_from_resource_name('mappings').__name__, 'Mapping')
self.assertEqual(get_resource_class_from_resource_name('sources').__name__, 'Source')
self.assertEqual(get_resource_class_from_resource_name('source').__name__, 'Source')
self.assertEqual(get_resource_class_from_resource_name('collections').__name__, 'Collection')
self.assertEqual(get_resource_class_from_resource_name('collection').__name__, 'Collection')
self.assertEqual(get_resource_class_from_resource_name('expansion').__name__, 'Expansion')
self.assertEqual(get_resource_class_from_resource_name('reference').__name__, 'CollectionReference')
for name in ['orgs', 'organizations', 'org', 'ORG']:
self.assertEqual(get_resource_class_from_resource_name(name).__name__, 'Organization')
for name in ['user', 'USer', 'user_profile', 'USERS']:
self.assertEqual(get_resource_class_from_resource_name(name).__name__, 'UserProfile')
def test_flatten_dict(self):
self.assertEqual(flatten_dict({'foo': 'bar'}), {'foo': 'bar'})
self.assertEqual(flatten_dict({'foo': 1}), {'foo': '1'})
self.assertEqual(flatten_dict({'foo': 1.1}), {'foo': '1.1'})
self.assertEqual(flatten_dict({'foo': True}), {'foo': 'True'})
self.assertEqual(
flatten_dict({'foo': True, 'bar': {'tao': {'te': 'ching'}}}),
{'foo': 'True', 'bar__tao__te': 'ching'})
self.assertEqual(
flatten_dict({'foo': True, 'bar': {'tao': {'te': 'tao-te-ching'}}}),
{'foo': 'True', 'bar__tao__te': 'tao_te_ching'}
)
# self.assertEqual(
# flatten_dict(
# {
# 'path': [
# {'text': 'MedicationStatement', 'linkid': '/MedicationStatement'},
# {'text': 'Family Planning Modern Method', 'linkid': '/MedicationStatement/method'}
# ],
# 'header_concept_id': 'ModernMethod',
# 'questionnaire_choice_value': 'LA27919-2'
# }
# ),
# dict(
# path__0__text='MedicationStatement', path__0__linkid='/MedicationStatement',
# path__1__text='Family Planning Modern Method', path__1__linkid='/MedicationStatement/method',
# header_concept_id='ModernMethod', questionnaire_choice_value='LA27919-2'
# )
# )
#
# self.assertEqual(
# flatten_dict(
# {
# 'path': [
# {'text': 'MedicationStatement', 'linkid': '/MedicationStatement'},
# {'text': 'Family Planning Modern Method', 'linkid': '/MedicationStatement/method'}
# ],
# 'Applicable Periods': ['FY19', 'FY18'],
# 'foobar': [1],
# 'bar': [],
# 'header_concept_id': 'ModernMethod',
# 'questionnaire_choice_value': 'LA27919-2'
# }
# ),
# {
# 'path__0__text': 'MedicationStatement',
# 'path__0__linkid': '/MedicationStatement',
# 'path__1__text': 'Family Planning Modern Method',
# 'path__1__linkid': '/MedicationStatement/method',
# 'Applicable Periods__0': 'FY19',
# 'Applicable Periods__1': 'FY18',
# 'foobar__0': '1',
# 'header_concept_id': 'ModernMethod',
# 'questionnaire_choice_value': 'LA27919-2',
# }
# )
def test_is_csv_file(self):
self.assertFalse(is_csv_file(name='foo/bar'))
self.assertTrue(is_csv_file(name='foo/bar.csv'))
self.assertFalse(is_csv_file(name='foo.zip'))
file_mock = Mock(spec=File)
file_mock.name = 'unknown_file'
self.assertFalse(is_csv_file(file=file_mock))
file_mock.name = 'unknown_file.json'
self.assertFalse(is_csv_file(file=file_mock))
file_mock.name = 'unknown_file.csv'
self.assertTrue(is_csv_file(file=file_mock))
def test_is_zip_file(self):
self.assertFalse(is_zip_file(name='foo/bar'))
self.assertFalse(is_zip_file(name='foo/bar.csv'))
self.assertTrue(is_zip_file(name='foo.zip'))
self.assertTrue(is_zip_file(name='foo.csv.zip'))
self.assertTrue(is_zip_file(name='foo.json.zip'))
file_mock = Mock(spec=File)
file_mock.name = 'unknown_file'
self.assertFalse(is_zip_file(file=file_mock))
file_mock.name = 'unknown_file.json'
self.assertFalse(is_zip_file(file=file_mock))
file_mock.name = 'unknown_file.csv'
self.assertFalse(is_zip_file(file=file_mock))
file_mock.name = 'unknown_file.csv.zip'
self.assertTrue(is_zip_file(file=file_mock))
file_mock.name = 'unknown_file.json.zip'
self.assertTrue(is_zip_file(file=file_mock))
def test_is_url_encoded_string(self):
self.assertTrue(is_url_encoded_string('foo'))
self.assertFalse(is_url_encoded_string('foo/bar'))
self.assertTrue(is_url_encoded_string('foo%2Fbar'))
self.assertTrue(is_url_encoded_string('foo%2Fbar', False))
def test_to_parent_uri_from_kwargs(self):
self.assertEqual(
to_parent_uri_from_kwargs({'org': 'OCL', 'collection': 'c1'}),
'/orgs/OCL/collections/c1/'
)
self.assertEqual(
to_parent_uri_from_kwargs({'org': 'OCL', 'collection': 'c1', 'version': 'v1'}),
'/orgs/OCL/collections/c1/v1/'
)
self.assertEqual(
to_parent_uri_from_kwargs({'user': 'admin', 'collection': 'c1', 'version': 'v1'}),
'/users/admin/collections/c1/v1/'
)
self.assertEqual(
to_parent_uri_from_kwargs({'user': 'admin', 'source': 's1', 'version': 'v1'}),
'/users/admin/sources/s1/v1/'
)
self.assertEqual(
to_parent_uri_from_kwargs({'org': 'OCL', 'source': 's1'}),
'/orgs/OCL/sources/s1/'
)
self.assertEqual(
to_parent_uri_from_kwargs({'org': 'OCL', 'source': 's1', 'concept': 'c1', 'concept_version': 'v1'}),
'/orgs/OCL/sources/s1/'
)
self.assertEqual(
to_parent_uri_from_kwargs(
{'org': 'OCL', 'source': 's1', 'version': 'v1', 'concept': 'c1', 'concept_version': 'v1'}),
'/orgs/OCL/sources/s1/v1/'
)
self.assertEqual(to_parent_uri_from_kwargs({'org': 'OCL'}), '/orgs/OCL/')
self.assertEqual(to_parent_uri_from_kwargs({'user': 'admin'}), '/users/admin/')
self.assertIsNone(to_parent_uri_from_kwargs({}))
self.assertIsNone(to_parent_uri_from_kwargs(None))
def test_nested_dict_values(self):
self.assertEqual(list(nested_dict_values({})), [])
self.assertEqual(list(nested_dict_values({'a': 1})), [1])
self.assertEqual(list(nested_dict_values({'a': 1, 'b': 'foobar'})), [1, 'foobar'])
self.assertEqual(
list(nested_dict_values({'a': 1, 'b': 'foobar', 'c': {'a': 1, 'b': 'foobar'}})),
[1, 'foobar', 1, 'foobar']
)
self.assertEqual(
list(
nested_dict_values(
{'a': 1, 'b': 'foobar', 'c': {'a': 1, 'b': 'foobar', 'c': {'d': [{'a': 1}, {'b': 'foobar'}]}}}
)
),
[1, 'foobar', 1, 'foobar', [{'a': 1}, {'b': 'foobar'}]]
)
def test_chunks(self):
self.assertEqual(list(chunks([], 1000)), [])
self.assertEqual(list(chunks([1, 2, 3, 4], 3)), [[1, 2, 3], [4]])
self.assertEqual(list(chunks([1, 2, 3, 4], 2)), [[1, 2], [3, 4]])
self.assertEqual(list(chunks([1, 2, 3, 4], 7)), [[1, 2, 3, 4]])
self.assertEqual(list(chunks([1, 2, 3, 4], 4)), [[1, 2, 3, 4]])
def test_split_list_by_condition(self):
even, odd = split_list_by_condition([2, 3, 4, 5, 6, 7], lambda x: x % 2 == 0)
self.assertEqual(even, [2, 4, 6])
self.assertEqual(odd, [3, 5, 7])
even, odd = split_list_by_condition([3, 5, 7], lambda num: num % 2 == 0)
self.assertEqual(even, [])
self.assertEqual(odd, [3, 5, 7])
ref1 = CollectionReference(id=1, include=True)
ref2 = CollectionReference(id=2, include=False)
ref3 = CollectionReference(id=3, include=False)
ref4 = CollectionReference(id=3, include=True)
include, exclude = split_list_by_condition([ref1, ref2, ref3, ref4], lambda ref: ref.include)
self.assertEqual(include, [ref1, ref4])
self.assertEqual(exclude, [ref2, ref3])
def test_get_date_range_label(self):
self.assertEqual(
get_date_range_label('2019-01-01', '2019-01-31'),
'01 - 31 January 2019'
)
self.assertEqual(
get_date_range_label('2019-01-01 10:00:00', '2019-01-01 11:00:00'),
'01 - 01 January 2019'
)
self.assertEqual(
get_date_range_label('2019-01-02 10:10:00', '2019-01-01'),
'02 - 01 January 2019'
)
self.assertEqual(
get_date_range_label('2019-02-01 10:10:00', '2019-01-01'),
'01 February - 01 January 2019'
)
self.assertEqual(
get_date_range_label('2019-01-01', '2020-01-01'),
'01 January 2019 - 01 January 2020'
)
def test_get_prev_month(self):
self.assertEqual(get_prev_month(from_string_to_date('2023-01-01')), from_string_to_date('2022-12-31'))
self.assertEqual(get_prev_month(from_string_to_date('2024-12-01')), from_string_to_date('2024-11-30'))
self.assertEqual(get_prev_month(from_string_to_date('2024-12-05')), from_string_to_date('2024-11-30'))
def test_get_end_of_month(self):
self.assertEqual(get_end_of_month(from_string_to_date('2023-01-01')), from_string_to_date('2023-01-31'))
self.assertEqual(get_end_of_month(from_string_to_date('2024-12-01')), from_string_to_date('2024-12-31'))
self.assertEqual(get_end_of_month(from_string_to_date('2024-12-05')), from_string_to_date('2024-12-31'))
self.assertEqual(get_end_of_month(from_string_to_date('2024-11-05')), from_string_to_date('2024-11-30'))
self.assertEqual(get_end_of_month(from_string_to_date('2024-02-05')), from_string_to_date('2024-02-29'))
self.assertEqual(
get_end_of_month(from_string_to_date('2024-11-30 11:00')), from_string_to_date('2024-11-30 11:00'))
self.assertEqual(
get_end_of_month(from_string_to_date('2024-11-15 11:00')), from_string_to_date('2024-11-30 11:00'))
def test_get_start_of_month(self):
self.assertEqual(get_start_of_month(from_string_to_date('2023-01-01')), from_string_to_date('2023-01-01'))
self.assertEqual(get_start_of_month(from_string_to_date('2024-12-31')), from_string_to_date('2024-12-01'))
self.assertEqual(get_start_of_month(from_string_to_date('2024-02-05')), from_string_to_date('2024-02-01'))
self.assertEqual(get_start_of_month(from_string_to_date('2023-02-28')), from_string_to_date('2023-02-01'))
def test_es_id_in(self):
search = Mock(query=Mock(return_value='search'))
self.assertEqual(es_id_in(search, []), search)
self.assertEqual(es_id_in(search, [1, 2, 3]), 'search')
search.query.assert_called_once_with("terms", _id=[1, 2, 3])
@patch('core.common.utils.settings')
def test_web_url(self, settings_mock):
settings_mock.WEB_URL = 'https://ocl.org'
self.assertEqual(web_url(), 'https://ocl.org')
settings_mock.WEB_URL = None
for env in [None, 'development', 'ci']:
settings_mock.ENV = env
self.assertEqual(web_url(), 'http://localhost:4000')
settings_mock.ENV = 'production'
self.assertEqual(web_url(), 'https://app.openconceptlab.org')
settings_mock.ENV = 'staging'
self.assertEqual(web_url(), 'https://app.staging.openconceptlab.org')
settings_mock.ENV = 'foo'
self.assertEqual(web_url(), 'https://app.foo.openconceptlab.org')
def test_from_string_to_date(self):
self.assertEqual(
from_string_to_date('2023-02-28'), datetime.datetime(2023, 2, 28))
self.assertEqual(
from_string_to_date('2023-02-28 10:00:00'), datetime.datetime(2023, 2, 28, 10))
self.assertEqual(
from_string_to_date('2023-02-29'), None)
class BaseModelTest(OCLTestCase):
def test_model_name(self):
self.assertEqual(Concept().model_name, 'Concept')
self.assertEqual(Source().model_name, 'Source')
def test_app_name(self):
self.assertEqual(Concept().app_name, 'concepts')
self.assertEqual(Source().app_name, 'sources')
class TaskTest(OCLTestCase):
@patch('core.common.tasks.get_export_service')
def test_delete_s3_objects(self, export_service_mock):
s3_mock = Mock(delete_objects=Mock())
export_service_mock.return_value = s3_mock
delete_s3_objects('/some/path')
s3_mock.delete_objects.assert_called_once_with('/some/path')
@patch('core.importers.models.BulkImportParallelRunner.run')
def test_bulk_import_parallel_inline_invalid_json(self, import_run_mock):
content = open(os.path.join(os.path.dirname(__file__), '..', 'samples/invalid_import_json.json'), 'r').read()
result = bulk_import_parallel_inline(to_import=content, username='ocladmin', update_if_exists=False) # pylint: disable=no-value-for-parameter
self.assertEqual(result, {
'error': 'Invalid JSON (Expecting property name enclosed in double quotes)'
})
import_run_mock.assert_not_called()
@patch('core.importers.models.BulkImportParallelRunner.run')
def test_bulk_import_parallel_inline_invalid_without_resource_type(self, import_run_mock):
content = open(
os.path.join(os.path.dirname(__file__), '..', 'samples/invalid_import_without_type.json'), 'r').read()
result = bulk_import_parallel_inline(to_import=content, username='ocladmin', update_if_exists=False) # pylint: disable=no-value-for-parameter
self.assertEqual(result, {
'error': 'Invalid Input ("type" should be present in each line)'
})
import_run_mock.assert_not_called()
@patch('core.importers.models.BulkImportParallelRunner.run')
def test_bulk_import_parallel_inline_valid_json(self, import_run_mock):
import_run_mock.return_value = 'Import Result'
content = open(os.path.join(os.path.dirname(__file__), '..', 'samples/sample_ocldev.json'), 'r').read()
result = bulk_import_parallel_inline(to_import=content, username='ocladmin', update_if_exists=False) # pylint: disable=no-value-for-parameter
self.assertEqual(result, 'Import Result')
import_run_mock.assert_called_once()
@patch('core.common.tasks.EmailMessage')
def test_resources_report(self, email_message_mock):
email_message_instance_mock = Mock(send=Mock(return_value=1))
email_message_mock.return_value = email_message_instance_mock
res = resources_report()
email_message_mock.assert_called_once()
email_message_instance_mock.send.assert_called_once()
email_message_instance_mock.attach.assert_called_once_with(ANY, ANY, 'text/csv')
self.assertTrue('_resource_report_' in email_message_instance_mock.attach.call_args[0][0])
self.assertTrue('.csv' in email_message_instance_mock.attach.call_args[0][0])
self.assertTrue(b'OCL Usage Report' in email_message_instance_mock.attach.call_args[0][1])
self.assertEqual(res, 1)
call_args = email_message_mock.call_args[1]
self.assertTrue("Monthly Resources Report" in call_args['subject'])
self.assertEqual(call_args['to'], ['reports@openconceptlab.org'])
self.assertTrue('Please find attached resources report of' in call_args['body'])
self.assertTrue('for the period of' in call_args['body'])
def test_calculate_checksums(self):
concept = ConceptFactory()
concept_prev_latest = concept.get_latest_version()
Concept.create_new_version_for(
instance=concept.clone(),
data={
'names': [{'locale': 'en', 'name': 'English', 'locale_preferred': True}]
},
user=concept.created_by,
create_parent_version=False
)
concept_latest = concept.get_latest_version()
Concept.objects.filter(id__in=[concept.id, concept_latest.id, concept_prev_latest.id]).update(checksums={})
concept.refresh_from_db()
concept_prev_latest.refresh_from_db()
concept_latest.refresh_from_db()
self.assertEqual(concept.checksums, {})
self.assertEqual(concept_prev_latest.checksums, {})
self.assertEqual(concept_latest.checksums, {})
calculate_checksums('concepts', concept_prev_latest.id)
concept.refresh_from_db()
concept_prev_latest.refresh_from_db()
concept_latest.refresh_from_db()
self.assertEqual(concept_prev_latest.checksums, {'smart': ANY, 'standard': ANY})
self.assertEqual(concept_latest.checksums, {'smart': ANY, 'standard': ANY})
self.assertEqual(concept.checksums, {'smart': ANY, 'standard': ANY})
class URIValidatorTest(OCLTestCase):