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tests.py
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tests.py
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from django.core.exceptions import ValidationError
from mock import patch, Mock, PropertyMock
from mock.mock import ANY
from core.collections.documents import CollectionDocument
from core.collections.models import CollectionReference, Collection, Expansion
from core.collections.models import ExpansionParameters
from core.collections.parsers import CollectionReferenceExpressionStringParser, \
CollectionReferenceSourceAllExpressionParser, CollectionReferenceOldStyleToExpandedStructureParser, \
CollectionReferenceParser
from core.collections.tests.factories import OrganizationCollectionFactory, ExpansionFactory, UserCollectionFactory
from core.collections.utils import is_mapping, is_concept, is_version_specified, \
get_concept_by_expression
from core.common.constants import OPENMRS_VALIDATION_SCHEMA
from core.common.tasks import add_references, seed_children_to_new_version
from core.common.tasks import update_collection_active_concepts_count
from core.common.tasks import update_collection_active_mappings_count
from core.common.tests import OCLTestCase, OCLAPITestCase
from core.concepts.documents import ConceptDocument
from core.concepts.models import Concept
from core.concepts.tests.factories import ConceptFactory, ConceptNameFactory
from core.mappings.documents import MappingDocument
from core.mappings.tests.factories import MappingFactory
from core.orgs.tests.factories import OrganizationFactory
from core.sources.tests.factories import OrganizationSourceFactory
from core.users.models import UserProfile
class CollectionTest(OCLTestCase):
def test_canonical_url_field(self):
collection = OrganizationCollectionFactory.build()
for uri in [
'https://coll.com', 'http://coll.com', 'ws:coll.com', 'mailto:foo@bar.com', 'tox:skyzohkey@ricin.im',
'tox:DFB4958A86122ACF81BB852DBC767DB8A3A7281A8EDBC83121B30C294E295869121B298FEEA2',
'urn:oid:2.16.840.1.113883.6.238', 'telnet://192.0.2.16:80/', 'localhost:9000',
'news:comp.infosystems.www.servers.unix', 'ldap://[2001:db8::7]/c=GB?objectClass?on',
'ftp://ftp.is.co.za/rfc/rfc1808.txt', 'urn:oasis:names:specification:docbook:dtd:xml:4.1.2',
'123.432.12.19:9000'
]:
collection.canonical_url = uri
collection.full_clean()
for uri in [
'foobar', 'foobar.com', '123.432.12.19'
]:
collection.canonical_url = uri
with self.assertRaises(ValidationError) as ex:
collection.full_clean()
self.assertEqual(ex.exception.message_dict, {'canonical_url': ['Enter a valid URI.']})
def test_resource_version_type(self):
self.assertEqual(Collection().resource_version_type, 'Collection Version')
def test_resource_type(self):
self.assertEqual(Collection().resource_type, 'Collection')
def test_get_search_document(self):
self.assertEqual(Collection.get_search_document(), CollectionDocument)
def test_collection(self):
self.assertEqual(Collection(mnemonic='coll').collection, 'coll')
self.assertEqual(Collection().collection, '')
def test_is_versioned(self):
self.assertTrue(Collection().is_versioned)
def test_add_expressions(self):
collection = OrganizationCollectionFactory()
expansion = ExpansionFactory(collection_version=collection)
collection.expansion_uri = expansion.uri
collection.save()
self.assertEqual(collection.expansion.concepts.count(), 0)
self.assertEqual(collection.references.count(), 0)
self.assertEqual(collection.active_concepts, None)
source = OrganizationSourceFactory()
concept = ConceptFactory(parent=source, sources=[source])
concept_expression = concept.uri
collection.add_expressions({'expressions': [concept_expression]}, collection.created_by)
collection.refresh_from_db()
self.assertEqual(collection.expansion.concepts.count(), 1)
self.assertEqual(collection.references.count(), 1)
self.assertEqual(collection.references.first().expression, concept.uri)
self.assertEqual(collection.expansion.concepts.first().id, concept.id)
self.assertEqual(collection.active_concepts, 1)
_, errors = collection.add_expressions({'concepts': [concept_expression]}, collection.created_by)
self.assertEqual(
errors, {concept_expression: ['Concept or Mapping reference name must be unique in a collection.']}
)
collection.refresh_from_db()
self.assertEqual(collection.expansion.concepts.count(), 1)
self.assertEqual(collection.references.count(), 1)
self.assertEqual(collection.active_concepts, 1)
def test_add_expressions_openmrs_schema(self):
collection = OrganizationCollectionFactory(custom_validation_schema=OPENMRS_VALIDATION_SCHEMA)
expansion = ExpansionFactory(collection_version=collection)
collection.expansion_uri = expansion.uri
collection.save()
self.assertEqual(collection.expansion.concepts.count(), 0)
self.assertEqual(collection.references.count(), 0)
source = OrganizationSourceFactory()
concept = ConceptFactory(parent=source, sources=[source])
concept_expression = concept.uri
collection.add_expressions({'expressions': [concept_expression]}, collection.created_by)
self.assertEqual(collection.references.count(), 1)
self.assertEqual(collection.references.first().expression, concept.uri)
self.assertEqual(collection.expansion.concepts.count(), 1)
self.assertEqual(collection.expansion.concepts.first(), concept)
concept2 = ConceptFactory(parent=source, sources=[source])
collection.add_expressions({'expressions': [concept2.uri]}, collection.created_by)
self.assertEqual(collection.expansion.concepts.count(), 2)
self.assertEqual(collection.references.count(), 2)
@patch('core.collections.models.batch_index_resources')
def test_delete_references(self, batch_index_resources_mock):
batch_index_resources_mock.apply_async = Mock()
collection = OrganizationCollectionFactory()
expansion = ExpansionFactory(collection_version=collection)
collection.expansion_uri = expansion.uri
collection.save()
source = OrganizationSourceFactory()
concept1 = ConceptFactory(parent=source)
concept2 = ConceptFactory(parent=source)
mapping = MappingFactory(from_concept=concept1, to_concept=concept2, parent=source)
collection.add_expressions({'expressions': [concept1.uri, concept2.uri, mapping.uri]}, collection.created_by)
self.assertEqual(collection.expansion.concepts.count(), 2)
self.assertEqual(collection.expansion.mappings.count(), 1)
self.assertEqual(collection.references.count(), 3)
collection.delete_references(
[concept2.get_latest_version().uri, concept2.uri, mapping.get_latest_version().uri, mapping.uri])
self.assertEqual(collection.expansion.concepts.count(), 1)
self.assertEqual(collection.expansion.mappings.count(), 0)
self.assertEqual(collection.references.count(), 1)
self.assertEqual(collection.expansion.concepts.first().uri, concept1.uri)
self.assertEqual(collection.references.first().expression, concept1.uri)
batch_index_resources_mock.apply_async.assert_called()
def test_seed_references(self):
collection1 = OrganizationCollectionFactory()
expansion1 = ExpansionFactory(collection_version=collection1)
collection1.expansion_uri = expansion1.uri
collection1.save()
collection2 = OrganizationCollectionFactory(
version='v1', mnemonic=collection1.mnemonic, organization=collection1.organization
)
expansion2 = ExpansionFactory(collection_version=collection2)
collection2.expansion_uri = expansion2.uri
collection2.save()
self.assertTrue(collection1.is_head)
self.assertFalse(collection2.is_head)
source = OrganizationSourceFactory()
concept = ConceptFactory(parent=source, sources=[source])
concept_expression = concept.uri
collection1.add_expressions({'expressions': [concept_expression]}, collection1.created_by)
self.assertEqual(collection1.references.count(), 1)
self.assertEqual(collection2.references.count(), 0)
collection2.seed_references()
self.assertEqual(collection1.references.count(), 1)
self.assertEqual(collection2.references.count(), 1)
self.assertEqual(collection1.references.first().expression, collection2.references.first().expression)
self.assertNotEqual(collection1.references.first().id, collection2.references.first().id)
def test_validate_reference_already_exists(self):
collection = OrganizationCollectionFactory()
expansion = ExpansionFactory(collection_version=collection)
collection.expansion_uri = expansion.uri
collection.save()
ch_locale = ConceptNameFactory.build(locale_preferred=True, locale='ch')
en_locale = ConceptNameFactory.build(locale_preferred=True, locale='en')
concept = ConceptFactory(names=[ch_locale, en_locale])
reference = CollectionReference(expression=concept.uri, collection=collection)
reference.save()
self.assertEqual(collection.references.count(), 1)
with self.assertRaises(ValidationError) as ex:
collection.validate(reference)
self.assertEqual(
ex.exception.message_dict,
{
concept.uri: [
'Concept or Mapping reference name must be unique in a collection.'
]
}
)
def test_validate_openmrs_schema_duplicate_locale_type(self):
ch_locale = ConceptNameFactory.build(locale_preferred=True, locale='ch')
en_locale = ConceptNameFactory.build(locale_preferred=True, locale='en')
concept1 = ConceptFactory(names=[ch_locale, en_locale])
collection = OrganizationCollectionFactory(custom_validation_schema=OPENMRS_VALIDATION_SCHEMA)
expansion = ExpansionFactory(collection_version=collection)
collection.expansion_uri = expansion.uri
collection.save()
expansion.concepts.add(concept1)
concept1_reference = CollectionReference(
expression=concept1.uri, collection=collection, system=concept1.parent.uri, version='HEAD')
concept1_reference.save()
ch_locale = ConceptNameFactory.build(name=ch_locale.name, locale_preferred=True, locale='ch')
en_locale = ConceptNameFactory.build(name=en_locale.name, locale_preferred=True, locale='en')
concept2 = ConceptFactory(names=[ch_locale, en_locale])
concept2_reference = CollectionReference(
expression=concept2.uri, collection=collection, system=concept2.parent.uri, version='HEAD')
with self.assertRaises(ValidationError) as ex:
collection.validate(concept2_reference)
self.assertEqual(
ex.exception.message_dict,
{'names': ['Concept fully specified name must be unique for same collection and locale.']}
)
def test_validate_openmrs_schema_matching_name_locale(self):
ch_locale = ConceptNameFactory.build(locale_preferred=False, locale='ch')
concept1 = ConceptFactory(names=[ch_locale])
collection = OrganizationCollectionFactory(custom_validation_schema=OPENMRS_VALIDATION_SCHEMA)
expansion = ExpansionFactory(collection_version=collection)
collection.expansion_uri = expansion.uri
collection.save()
collection.expansion.concepts.add(concept1)
concept1_reference = CollectionReference(
expression=concept1.uri, collection=collection, system=concept1.parent.uri, version='HEAD')
concept1_reference.save()
en_locale1 = ConceptNameFactory.build(locale='en', locale_preferred=False, name='name')
en_locale2 = ConceptNameFactory.build(locale='en', locale_preferred=True, name='name')
concept2 = ConceptFactory(names=[en_locale1, en_locale2])
concept2_reference = CollectionReference(
expression=concept2.uri, collection=collection, system=concept2.parent.uri, version='HEAD')
with self.assertRaises(ValidationError) as ex:
collection.validate(concept2_reference)
self.assertEqual(
ex.exception.message_dict,
{'names': ['Concept fully specified name must be unique for same collection and locale.']}
)
def test_parent_id(self):
self.assertIsNone(Collection().parent_id)
self.assertEqual(Collection(user_id=1).parent_id, 1)
self.assertEqual(Collection(organization_id=1).parent_id, 1)
def test_last_concept_update(self):
collection = OrganizationCollectionFactory()
expansion = ExpansionFactory(collection_version=collection)
collection.expansion_uri = expansion.uri
collection.save()
self.assertIsNone(collection.last_concept_update)
concept = ConceptFactory()
collection.expansion.concepts.add(concept)
self.assertEqual(collection.last_concept_update, concept.updated_at)
def test_last_mapping_update(self):
collection = OrganizationCollectionFactory()
expansion = ExpansionFactory(collection_version=collection)
collection.expansion_uri = expansion.uri
collection.save()
self.assertIsNone(collection.last_mapping_update)
mapping = MappingFactory()
collection.expansion.mappings.add(mapping)
self.assertEqual(collection.last_mapping_update, mapping.updated_at)
def test_last_child_update(self):
collection = OrganizationCollectionFactory()
self.assertEqual(collection.last_child_update, collection.updated_at)
expansion = ExpansionFactory(collection_version=collection)
collection.expansion_uri = expansion.uri
collection.save()
self.assertEqual(collection.last_child_update, collection.updated_at)
mapping = MappingFactory()
collection.expansion.mappings.add(mapping)
self.assertEqual(collection.last_child_update, mapping.updated_at)
concept = ConceptFactory()
collection.expansion.concepts.add(concept)
self.assertEqual(collection.last_child_update, concept.updated_at)
@patch('core.collections.models.Collection.expansion', new_callable=PropertyMock)
@patch('core.collections.models.Collection.batch_index')
def test_index_children(self, batch_index_mock, expansion_mock):
expansion_mock.return_value = Mock(concepts='concepts-qs', mappings='mappings-qs')
collection = Collection(expansion_uri='foobar')
collection.index_children()
self.assertEqual(batch_index_mock.call_count, 2)
self.assertEqual(batch_index_mock.mock_calls[0].args, ('concepts-qs', ConceptDocument))
self.assertEqual(batch_index_mock.mock_calls[1].args, ('mappings-qs', MappingDocument))
def test_get_cascaded_mapping_uris_from_concept_expressions(self):
concept1 = ConceptFactory()
concept2 = ConceptFactory(parent=concept1.parent)
mapping1 = MappingFactory(
from_concept=concept1, to_concept=concept2, parent=concept1.parent)
mapping2 = MappingFactory(from_concept=concept1)
mapping3 = MappingFactory(to_concept=concept2, parent=concept1.parent)
collection = OrganizationCollectionFactory()
expansion = ExpansionFactory(collection_version=collection)
expansion.mappings.set([mapping1, mapping2, mapping3])
expressions = [concept1.get_latest_version().url, concept2.get_latest_version().url]
self.assertEqual(collection.get_cascaded_mapping_uris_from_concept_expressions(expressions), [])
collection.expansion_uri = expansion.url
collection.save()
self.assertEqual(
sorted(collection.get_cascaded_mapping_uris_from_concept_expressions(expressions)),
sorted([mapping1.url, mapping2.url])
)
def test_references_distribution(self):
collection = OrganizationCollectionFactory()
reference1 = CollectionReference(expression='/foo/concepts/', collection=collection, reference_type='concepts')
reference2 = CollectionReference(expression='/foo/mappings', collection=collection, reference_type='mappings')
reference3 = CollectionReference(
expression='/bar/concepts', collection=collection, reference_type='mappings', include=False)
reference1.save()
reference2.save()
reference3.save()
self.assertEqual(collection.references.count(), 3)
distribution = collection.references_distribution
self.assertEqual(distribution, {'concepts': 1, 'mappings': 2, 'include': 2, 'exclude': 1, 'total': 3})
def test_referenced_sources_distribution(self):
self.maxDiff = None
collection = OrganizationCollectionFactory()
source1 = OrganizationSourceFactory()
source2 = OrganizationSourceFactory()
source2_v1 = OrganizationSourceFactory(mnemonic=source2.mnemonic, version='v1', organization=source2.parent)
concept1 = ConceptFactory(parent=source1)
concept2 = ConceptFactory(parent=source2)
concept3 = ConceptFactory(parent=source2)
mapping = MappingFactory(parent=source2)
concept2_latest_version = concept2.get_latest_version()
concept2_latest_version.sources.add(source2_v1)
reference1 = CollectionReference(
expression=concept1.uri, collection=collection, system=source1.uri, code=concept1.mnemonic
)
reference2 = CollectionReference(
expression=concept2_latest_version.uri, collection=collection, system=source2_v1.uri,
code=concept2.mnemonic, resource_version=concept2_latest_version.version
)
reference3 = CollectionReference(
expression=concept3.uri, collection=collection, system=source2.uri,
code=concept3.mnemonic
)
reference4 = CollectionReference(
expression=mapping.uri, collection=collection, system=source2.uri, reference_type='mappings'
)
reference1.clean()
reference1.save()
reference2.clean()
reference2.save()
reference3.clean()
reference3.save()
reference4.clean()
reference4.save()
distribution = collection.referenced_sources_distribution
self.assertCountEqual(
distribution,
[{
'id': 'HEAD',
'version_url': source1.uri,
'type': 'Source Version',
'short_code': source1.mnemonic,
'released': False,
'distribution': {
'include_reference': True,
'concepts': 1,
'mappings': 0,
'references': 1
}
}, {
'id': 'v1',
'version_url': source2_v1.uri,
'type': 'Source Version',
'short_code': source2.mnemonic,
'released': False,
'distribution': {
'include_reference': True,
'concepts': 1,
'mappings': 0,
'references': 1
}
}, {
'id': 'HEAD',
'version_url': source2.uri,
'type': 'Source Version',
'short_code': source2.mnemonic,
'released': False,
'distribution': {
'include_reference': True,
'concepts': 1,
'mappings': 1,
'references': 2
}
}]
)
def test_referenced_collections_distribution(self): # pylint: disable=too-many-locals
self.maxDiff = None
collection = OrganizationCollectionFactory()
collection2 = OrganizationCollectionFactory()
source1 = OrganizationSourceFactory()
source2 = OrganizationSourceFactory()
source2_v1 = OrganizationSourceFactory(mnemonic=source2.mnemonic, version='v1', organization=source2.parent)
concept1 = ConceptFactory(parent=source1)
concept2 = ConceptFactory(parent=source2)
concept3 = ConceptFactory(parent=source2)
mapping = MappingFactory(parent=source2)
concept2_latest_version = concept2.get_latest_version()
concept2_latest_version.sources.add(source2_v1)
reference1 = CollectionReference(
expression=concept1.uri, collection=collection, system=source1.uri, code=concept1.mnemonic
)
reference2 = CollectionReference(
expression=concept2_latest_version.uri, collection=collection, system=source2_v1.uri,
code=concept2.mnemonic, resource_version=concept2_latest_version.version
)
reference3 = CollectionReference(
expression=concept3.uri, collection=collection, system=source2.uri,
code=concept3.mnemonic
)
reference4 = CollectionReference(
expression=mapping.uri, collection=collection, system=source2.uri, reference_type='mappings'
)
reference1.clean()
reference1.save()
reference2.clean()
reference2.save()
reference3.clean()
reference3.save()
reference4.clean()
reference4.save()
reference5 = CollectionReference(
expression=collection.uri, collection=collection2, valueset=[collection.uri], reference_type='concepts'
)
reference6 = CollectionReference(
expression=collection.uri, collection=collection2, valueset=[collection.uri], reference_type='mappings'
)
reference5.clean()
reference5.save()
reference6.clean()
reference6.save()
distribution = collection2.referenced_collections_distribution
self.assertCountEqual(
distribution,
[{
'id': 'HEAD',
'version_url': collection.uri,
'type': 'Collection Version',
'short_code': collection.mnemonic,
'released': False,
'autoexpand': True,
'distribution': {
'include_reference': True,
'concepts': 0, # no expansion
'mappings': 0,
'references': 2
}
}]
)
class CollectionReferenceTest(OCLTestCase):
def test_uri(self):
org = OrganizationFactory(mnemonic='MyOrg')
collection = OrganizationCollectionFactory(organization=org, mnemonic='MyCollection', version='HEAD')
reference = CollectionReference(expression='/foo/bar', collection=collection)
reference.save()
self.assertEqual(reference.uri, f'/orgs/MyOrg/collections/MyCollection/references/{reference.id}/')
collection_v1 = OrganizationCollectionFactory(organization=org, mnemonic='MyCollection', version='v1')
reference = CollectionReference(expression='/foo/bar', collection=collection_v1)
reference.save()
self.assertEqual(reference.uri, f'/orgs/MyOrg/collections/MyCollection/v1/references/{reference.id}/')
def test_invalid_expression(self):
reference = CollectionReference(expression='', collection=OrganizationCollectionFactory())
with self.assertRaises(ValidationError) as ex:
reference.full_clean()
self.assertEqual(
ex.exception.message_dict,
{'expression': ['This field cannot be blank.']}
)
def test_reference_type(self):
reference = CollectionReference(expression='')
self.assertEqual(reference.reference_type, 'concepts')
reference = CollectionReference(expression=None)
self.assertEqual(reference.reference_type, 'concepts')
reference = CollectionReference(
expression='/parent/parent-mnemonic/sources/source-mnemonic/concepts/concept-mnemonic/',
reference_type=None
)
reference.clean()
self.assertEqual(reference.reference_type, 'concepts')
reference = CollectionReference(
expression='/parent/parent-mnemonic/sources/source-mnemonic/concepts/concept-mnemonic/',
reference_type='mappings' # if you set wrong it stays as is
)
reference.clean()
self.assertEqual(reference.reference_type, 'mappings')
reference = CollectionReference(
expression='/parent/parent-mnemonic/sources/source-mnemonic/mappings/mapping-mnemonic/',
reference_type=None
)
reference.clean()
self.assertEqual(reference.reference_type, 'mappings')
reference = CollectionReference(
expression='/parent/parent-mnemonic/sources/source-mnemonic/mappings/mapping-mnemonic/',
reference_type='mappings'
)
reference.clean()
self.assertEqual(reference.reference_type, 'mappings')
def test_reference_as_concept_version(self):
collection = OrganizationCollectionFactory()
concept = ConceptFactory()
expression = concept.uri
reference = CollectionReference(
expression=expression, collection=collection, system=concept.parent.uri, version='HEAD')
reference.full_clean()
self.assertEqual(len(reference._concepts), 1) # pylint: disable=protected-access
self.assertTrue(isinstance(reference._concepts[0], Concept)) # pylint: disable=protected-access
self.assertEqual(reference._concepts[0].id, concept.id) # pylint: disable=protected-access
def test_concept_filter_schema(self):
ref = CollectionReference(expression='/concepts/', filter=None)
ref.clean()
ref = CollectionReference(expression='/concepts/', filter='')
ref.clean()
ref = CollectionReference(expression='/concepts/', filter=[])
ref.clean()
with self.assertRaises(ValidationError):
ref = CollectionReference(expression='/concepts/', filter=[{}, {}])
ref.clean()
with self.assertRaises(ValidationError):
ref = CollectionReference(expression='/concepts/', filter=[{'foo': 'bar'}])
ref.clean()
with self.assertRaises(ValidationError):
ref = CollectionReference(expression='/concepts/', filter=[{'property': 'bar'}])
ref.clean()
with self.assertRaises(ValidationError) as ex:
ref = CollectionReference(
expression='/concepts/', filter=[{'property': 'map_type', 'value': 'foobar', 'op': '='}])
ref.clean()
self.assertEqual(ex.exception.message_dict, {'filter': ['Invalid filter schema.']})
ref = CollectionReference(
expression='/concepts/', filter=[{'property': 'concept_class', 'value': 'foobar', 'op': '='}])
ref.clean()
ref = CollectionReference(
expression='/concepts/', filter=[{'property': 'external_id', 'value': 'foobar', 'op': 'in'}])
ref.clean()
def test_mapping_filter_schema(self):
mapping = MappingFactory()
MappingDocument().update([mapping]) # to create mappings index in ES
ref = CollectionReference(expression='/mappings/', filter=None, reference_type='mappings')
ref.clean()
ref = CollectionReference(expression='/mappings/', filter='', reference_type='mappings')
ref.clean()
ref = CollectionReference(expression='/mappings/', filter=[], reference_type='mappings')
ref.clean()
with self.assertRaises(ValidationError):
ref = CollectionReference(expression='/mappings/', filter=[{}, {}], reference_type='mappings')
ref.clean()
with self.assertRaises(ValidationError):
ref = CollectionReference(expression='/mappings/', filter=[{'foo': 'bar'}], reference_type='mappings')
ref.clean()
with self.assertRaises(ValidationError):
ref = CollectionReference(expression='/mappings/', filter=[{'property': 'bar'}], reference_type='mappings')
ref.clean()
with self.assertRaises(ValidationError) as ex:
ref = CollectionReference(
expression='/mappings/',
reference_type='mappings',
filter=[{'property': 'concept_class', 'value': 'foobar', 'op': '='}])
ref.clean()
self.assertEqual(ex.exception.message_dict, {'filter': ['Invalid filter schema.']})
ref = CollectionReference(
expression='/mappings/',
reference_type='mappings',
filter=[{'property': 'map_type', 'value': 'foobar', 'op': '='}])
ref.clean()
ref = CollectionReference(
expression='/mappings/',
reference_type='mappings',
filter=[{'property': 'external_id', 'value': 'foobar', 'op': 'in'}])
ref.clean()
def test_get_concepts(self): # pylint: disable=too-many-locals,too-many-statements
source = OrganizationSourceFactory()
source_v1 = OrganizationSourceFactory(organization=source.organization, mnemonic=source.mnemonic, version='v1')
coll1 = OrganizationCollectionFactory()
coll1_v1 = OrganizationCollectionFactory(organization=coll1.organization, mnemonic=coll1.mnemonic, version='v1')
coll2 = OrganizationCollectionFactory()
coll2_v1 = OrganizationCollectionFactory(organization=coll2.organization, mnemonic=coll2.mnemonic, version='v1')
concept1 = ConceptFactory(parent=source)
prev_latest_version = concept1.get_latest_version()
prev_latest_version.is_latest_version = True
prev_latest_version.save()
Concept.create_new_version_for(concept1.clone(), {}, concept1.created_by)
concept1_latest = concept1.get_latest_version()
concept1.sources.add(source)
concept1_latest.sources.add(source)
prev_latest_version.sources.add(source_v1)
expansion_coll1 = ExpansionFactory(collection_version=coll1)
coll1.expansion_uri = expansion_coll1.uri
coll1.save()
expansion_coll1_v1 = ExpansionFactory(collection_version=coll1_v1)
coll1_v1.expansion_uri = expansion_coll1_v1.uri
coll1_v1.save()
concept2 = ConceptFactory(parent=source)
expansion_coll1_v1.concepts.add(concept1_latest)
mapping1 = MappingFactory(from_concept=concept1, to_concept=concept2, parent=source)
reference = CollectionReference(system=source.uri, created_by=source.created_by)
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 2)
self.assertEqual(
sorted(list(concepts.values_list('id', flat=True))), sorted([concept1.id, concept2.id])
)
self.assertEqual(mappings.count(), 0)
reference = CollectionReference(
system=source.uri, created_by=source.created_by, cascade={'method': 'sourcemappings'}
)
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 2)
self.assertEqual(
sorted(list(concepts.values_list('id', flat=True))), sorted([concept1.id, concept2.id])
)
self.assertEqual(mappings.count(), 1)
self.assertEqual(mappings.first().id, mapping1.id)
reference = CollectionReference(
system=source.uri,
code=concept1.mnemonic,
created_by=source.created_by,
cascade={'method': 'sourcemappings'}
)
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 1)
self.assertEqual(
sorted(list(concepts.values_list('id', flat=True))), sorted([concept1.id])
)
self.assertEqual(mappings.count(), 1)
self.assertEqual(mappings.first().id, mapping1.id)
reference = CollectionReference(
system=source.uri,
code=concept1.mnemonic,
created_by=source.created_by,
cascade={'method': 'sourcetoconcepts'}
)
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 2)
self.assertEqual(
sorted(list(concepts.values_list('id', flat=True))), sorted([concept1.id, concept2.id])
)
self.assertEqual(mappings.count(), 1)
self.assertEqual(mappings.first().id, mapping1.id)
reference = CollectionReference(
system=source.uri,
code=concept1.mnemonic,
created_by=source.created_by,
cascade={'method': 'sourcetoconcepts'},
transform='resourceVersions'
)
concepts, mappings = reference.get_concepts()
concepts = concepts.distinct('id')
self.assertEqual(concepts.count(), 2)
self.assertEqual(
sorted(list(concepts.values_list('id', flat=True))),
sorted([concept1_latest.id, concept2.get_latest_version().id])
)
self.assertEqual(mappings.count(), 1)
self.assertEqual(mappings.first().id, mapping1.get_latest_version().id)
reference = CollectionReference(
system=source.uri,
code=concept1.mnemonic,
created_by=source.created_by,
cascade={'method': 'sourcetoconcepts'},
transform='extensional'
)
concepts, mappings = reference.get_concepts()
concepts = concepts.distinct('id')
self.assertEqual(concepts.count(), 2)
self.assertEqual(
sorted(list(concepts.values_list('id', flat=True))),
sorted([concept1_latest.versioned_object_id, concept2.versioned_object_id])
)
self.assertEqual(mappings.count(), 1)
self.assertEqual(mappings.first().versioned_object_id, mapping1.versioned_object_id)
reference = CollectionReference(
system=source.uri,
valueset=[coll1_v1.uri, coll2_v1.uri],
created_by=source.created_by
)
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 0)
self.assertEqual(mappings.count(), 0)
reference = CollectionReference(
system=source.uri,
valueset=[coll1_v1.uri],
created_by=source.created_by,
transform='resourceversions'
)
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 1)
self.assertEqual(
sorted(list(concepts.values_list('id', flat=True))), sorted([concept1_latest.id])
)
self.assertEqual(mappings.count(), 0)
reference = CollectionReference(
system=source.uri,
valueset=[coll1_v1.uri],
created_by=source.created_by,
transform='extensional'
)
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 0) # coll_v1 has latest version of concept1
self.assertEqual(mappings.count(), 0)
reference = CollectionReference(
system=source.uri,
created_by=source.created_by,
code=concept1.mnemonic,
transform='resourceversions'
)
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 1)
self.assertEqual(
sorted(list(concepts.values_list('id', flat=True))), sorted([concept1_latest.id])
)
self.assertEqual(mappings.count(), 0)
reference = CollectionReference(
system=source.uri,
created_by=source.created_by,
code=concept1.mnemonic,
transform='extensional'
)
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 1)
self.assertEqual(
sorted(list(concepts.values_list('id', flat=True))), sorted([concept1_latest.versioned_object_id])
)
self.assertEqual(mappings.count(), 0)
reference = CollectionReference(
system=source.uri,
created_by=source.created_by,
code=concept1.mnemonic,
)
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 1)
self.assertEqual(
sorted(list(concepts.values_list('id', flat=True))), sorted([concept1.id])
)
self.assertEqual(mappings.count(), 0)
reference = CollectionReference(
system=f"{source.uri}|v1",
created_by=source.created_by,
code=concept1.mnemonic,
resource_version=prev_latest_version.version
)
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 1)
self.assertEqual(
sorted(list(concepts.values_list('id', flat=True))), sorted([prev_latest_version.id])
)
self.assertEqual(mappings.count(), 0)
parser = CollectionReferenceParser({'expression': '/concepts/'})
parser.parse()
parser.to_reference_structure()
references = parser.to_objects()
reference = references[0]
self.assertEqual(reference.expression, '/concepts/')
concepts, mappings = reference.get_concepts()
self.assertEqual(concepts.count(), 0)
self.assertEqual(mappings.count(), 0)
def test_build_expression(self):
self.assertEqual(
CollectionReference(expression='/foobar/').build_expression(), '/foobar/')
self.assertEqual(
CollectionReference(expression='/foobar/', system='http://foo.com').build_expression(), '/foobar/')
reference = CollectionReference(
system='http://source.com',
version='v1',
valueset=['http//coll.com', 'https://coll-global.com'],
namespace='/orgs/MyOrg/',
code='c1',
reference_type='concepts',
resource_version='123'
)
self.assertEqual(reference.build_expression(), 'http://source.com|v1/concepts/c1/123/')
reference = CollectionReference(
system='http://source.com',
version='v1',
namespace='/orgs/MyOrg/',
code='c1',
reference_type='concepts',
resource_version='123'
)
self.assertEqual(reference.build_expression(), 'http://source.com|v1/concepts/c1/123/')
reference = CollectionReference(
system='http://source.com',
namespace='/orgs/MyOrg/',
version='v1',
)
self.assertEqual(reference.build_expression(), 'http://source.com|v1')
reference = CollectionReference(
system='http://source.com',
namespace='/orgs/MyOrg/',
)
self.assertEqual(reference.build_expression(), 'http://source.com')
reference = CollectionReference(
system='/orgs/MyOrg/sources/MySource/',
version='v1',
valueset=['http//coll.com', 'https://coll-global.com'],
namespace='/orgs/MyOrg/',
code='c1',
reference_type='concepts',
resource_version='123'
)
self.assertEqual(reference.build_expression(), '/orgs/MyOrg/sources/MySource/v1/concepts/c1/123/')
reference = CollectionReference(
system='/orgs/MyOrg/sources/MySource/',
reference_type='concepts',
)
self.assertEqual(reference.build_expression(), '/orgs/MyOrg/sources/MySource/concepts/')
reference = CollectionReference(
reference_type='concepts',
)
self.assertEqual(reference.build_expression(), '/concepts/')
reference = CollectionReference(
reference_type='mappings',
)
self.assertEqual(reference.build_expression(), '/mappings/')
reference = CollectionReference(
system='/orgs/MyOrg/sources/MySource/',
reference_type='concepts',
filter=[{'property': 'q', 'value': 'foo', 'op': '='}, {'property': 'name', 'value': 'foobar', 'op': '='}]
)
self.assertEqual(
reference.build_expression(), '/orgs/MyOrg/sources/MySource/concepts/?q=foo&name=foobar'
)
reference = CollectionReference(
valueset=['/orgs/MyOrg/collections/Coll/'],
reference_type='concepts',
filter=[{'property': 'q', 'value': 'foo', 'op': '='}, {'property': 'name', 'value': 'foobar', 'op': '='}]
)
self.assertEqual(
reference.build_expression(), '/orgs/MyOrg/collections/Coll/concepts/?q=foo&name=foobar'
)
reference = CollectionReference(
valueset=['/orgs/MyOrg/collections/Coll/', '/orgs/MyOrg/collections/Coll1/'],
reference_type='concepts',
filter=[{'property': 'q', 'value': 'foo', 'op': '='}, {'property': 'name', 'value': 'foobar', 'op': '='}]
)
self.assertEqual(
reference.build_expression(), '/orgs/MyOrg/collections/Coll/concepts/?q=foo&name=foobar'
)
class CollectionUtilsTest(OCLTestCase):
def test_is_mapping(self):
self.assertFalse(is_mapping(None))
self.assertFalse(is_mapping(''))
self.assertFalse(is_mapping('orgs/org-1/sources/source-1/mapping/'))
self.assertTrue(is_mapping('orgs/org-1/sources/source-1/mappings/'))
self.assertTrue(is_mapping('users/user-1/sources/source-1/mappings/'))
self.assertTrue(is_mapping('users/user-1/collections/coll-1/mappings/'))
self.assertTrue(is_mapping('/mappings/'))
def test_is_concept(self):
self.assertFalse(is_concept(None))
self.assertFalse(is_concept(''))
self.assertFalse(is_concept('orgs/org-1/sources/source-1/concept/'))
self.assertTrue(is_concept('orgs/org-1/sources/source-1/concepts/'))
self.assertTrue(is_concept('users/user-1/sources/source-1/concepts/'))
self.assertTrue(is_concept('users/user-1/collections/coll-1/concepts/'))
self.assertTrue(is_concept('/concepts/'))
def test_is_version_specified(self):
concept_head = ConceptFactory()
concept_v1 = ConceptFactory(
parent=concept_head.parent, version='v1', mnemonic=concept_head.mnemonic, versioned_object=concept_head
)
self.assertTrue(is_version_specified(concept_v1.uri))
self.assertFalse(is_version_specified(concept_head.uri))
def test_get_concept_by_expression(self):
concept_head = ConceptFactory()
concept_v1 = ConceptFactory(
parent=concept_head.parent, version='v1', mnemonic=concept_head.mnemonic, versioned_object=concept_head
)
self.assertEqual(get_concept_by_expression(concept_head.uri), concept_head)
self.assertEqual(get_concept_by_expression(concept_v1.uri), concept_v1)
self.assertIsNone(get_concept_by_expression('/foobar/'))
class TasksTest(OCLTestCase):
def test_add_references_task(self):
collection = OrganizationCollectionFactory()
expansion = ExpansionFactory(collection_version=collection)
collection.expansion_uri = expansion.uri