def test_entity_creation():
props = {
"id": "syn123456",
"concreteType": "org.sagebionetworks.repo.model.Folder",
"parentId": "syn445566",
"name": "Testing123"
}
annos = {'testing': 123}
folder = Entity.create(props, annos)
assert folder.concreteType == 'org.sagebionetworks.repo.model.Folder'
assert folder.__class__ == Folder
assert folder.name == 'Testing123'
assert folder.testing == 123
# In case of unknown concreteType, fall back on generic Entity object
props = {
"id": "syn123456",
"concreteType": "org.sagebionetworks.repo.model.DoesntExist",
"parentId": "syn445566",
"name": "Whatsits"
}
whatsits = Entity.create(props)
assert whatsits.concreteType == 'org.sagebionetworks.repo.model.DoesntExist'
assert whatsits.__class__ == Entity
def test_entityViewSchema__add_scope():
entity_view = EntityViewSchema(parent="idk")
entity_view.add_scope(Entity(parent="also idk", id=123))
entity_view.add_scope(456)
entity_view.add_scope("789")
assert_equals([str(x) for x in ["123", "456", "789"]],
entity_view.scopeIds)
def test_EntityViewSchema__ignore_column_names_set_info_preserved():
"""
tests that ignoredAnnotationColumnNames will be preserved after creating a new EntityViewSchema from properties,
local_state, and annotations
"""
ignored_names = {'a', 'b', 'c'}
entity_view = EntityViewSchema("someName", parent="syn123", ignoredAnnotationColumnNames={'a', 'b', 'c'})
properties, annotations, local_state = split_entity_namespaces(entity_view)
entity_view_copy = Entity.create(properties, annotations, local_state)
assert_equals(ignored_names, entity_view.ignoredAnnotationColumnNames)
assert_equals(ignored_names, entity_view_copy.ignoredAnnotationColumnNames)
def test_EntityViewSchema__ignore_column_names_set_info_preserved():
"""
tests that ignoredAnnotationColumnNames will be preserved after creating a new EntityViewSchema from properties,
local_state, and annotations
"""
ignored_names = {'a', 'b', 'c'}
entity_view = EntityViewSchema("someName", parent="syn123", ignoredAnnotationColumnNames={'a', 'b', 'c'})
properties, annotations, local_state = split_entity_namespaces(entity_view)
entity_view_copy = Entity.create(properties, annotations, local_state)
assert ignored_names == entity_view.ignoredAnnotationColumnNames
assert ignored_names == entity_view_copy.ignoredAnnotationColumnNames
def test_split_entity_namespaces():
"""Test split_entity_namespaces"""
e = {
'concreteType': 'org.sagebionetworks.repo.model.Folder',
'name': 'Henry',
'color': 'blue',
'foo': 1234,
'parentId': 'syn1234'
}
(properties, annotations, local_state) = split_entity_namespaces(e)
assert set(properties.keys()) == {'concreteType', 'name', 'parentId'}
assert properties['name'] == 'Henry'
assert set(annotations.keys()) == {'color', 'foo'}
assert annotations['foo'] == 1234
assert len(local_state) == 0
e = {
'concreteType': 'org.sagebionetworks.repo.model.FileEntity',
'name': 'Henry',
'color': 'blue',
'foo': 1234,
'parentId': 'syn1234',
'dataFileHandleId': 54321,
'cacheDir': '/foo/bar/bat',
'files': ['foo.xyz'],
'path': '/foo/bar/bat/foo.xyz'
}
(properties, annotations, local_state) = split_entity_namespaces(e)
assert set(properties.keys()) == {
'concreteType', 'name', 'parentId', 'dataFileHandleId'
}
assert properties['name'] == 'Henry'
assert properties['dataFileHandleId'] == 54321
assert set(annotations.keys()) == {'color', 'foo'}
assert annotations['foo'] == 1234
assert set(local_state.keys()) == {'cacheDir', 'files', 'path'}
assert local_state['cacheDir'] == '/foo/bar/bat'
f = Entity.create(properties, annotations, local_state)
assert f.properties.dataFileHandleId == 54321
assert f.properties.name == 'Henry'
assert f.annotations.foo == 1234
assert f.__dict__['cacheDir'] == '/foo/bar/bat'
assert f.__dict__['path'] == '/foo/bar/bat/foo.xyz'
def test_Entity():
# Test the basics of creating and accessing properties on an entity
for i in range(2):
e = Entity(name='Test object',
description='I hope this works',
annotations=dict(foo=123,
nerds=['chris', 'jen', 'janey'],
annotations='How confusing!'),
properties=dict(
annotations='/repo/v1/entity/syn1234/annotations',
md5='cdef636522577fc8fb2de4d95875b27c',
parentId='syn1234'),
concreteType='org.sagebionetworks.repo.model.Data')
# Should be able to create an Entity from an Entity
if i == 1:
e = Entity.create(e)
assert e.parentId == 'syn1234'
assert e['parentId'] == 'syn1234'
assert e.properties['parentId'] == 'syn1234'
assert e.properties.parentId == 'syn1234'
assert e.foo == 123
assert e['foo'] == 123
assert e.annotations['foo'] == 123
assert e.annotations.foo == 123
assert hasattr(e, 'parentId')
assert hasattr(e, 'foo')
assert not hasattr(e, 'qwerqwer')
# Annotations is a bit funny, because there is a property call
# 'annotations', which will be masked by a member of the object
# called 'annotations'. Because annotations are open-ended, we
# might even have an annotations called 'annotations', which gets
# really confusing.
assert isinstance(e.annotations, collections.abc.Mapping)
assert isinstance(e['annotations'], collections.abc.Mapping)
assert e.properties[
'annotations'] == '/repo/v1/entity/syn1234/annotations'
assert e.properties.annotations == '/repo/v1/entity/syn1234/annotations'
assert e.annotations.annotations == 'How confusing!'
assert e.annotations['annotations'] == 'How confusing!'
assert e.nerds == ['chris', 'jen', 'janey']
assert all([
k in e for k in [
'name', 'description', 'foo', 'nerds', 'annotations', 'md5',
'parentId'
]
])
# Test modifying properties
e.description = 'Working, so far'
assert e['description'] == 'Working, so far'
e['description'] = 'Wiz-bang flapdoodle'
assert e.description == 'Wiz-bang flapdoodle'
# Test modifying annotations
e.foo = 999
assert e.annotations['foo'] == 999
e['foo'] = 12345
assert e.annotations.foo == 12345
# Test creating a new annotation
e['bar'] = 888
assert e.annotations['bar'] == 888
e['bat'] = 7788
assert e.annotations['bat'] == 7788
# Test replacing annotations object
e.annotations = {
'splat': 'a totally new set of annotations',
'foo': 456
}
assert e.foo == 456
assert e['foo'] == 456
assert isinstance(e.annotations, collections.abc.Mapping)
assert isinstance(e['annotations'], collections.abc.Mapping)
assert e.annotations.foo == 456
assert e.properties[
'annotations'] == '/repo/v1/entity/syn1234/annotations'
assert e.properties.annotations == '/repo/v1/entity/syn1234/annotations'
# test unicode properties
e.train = '時刻表には記載されない 月への列車が来ると聞いて'
e.band = "Motörhead"
e.lunch = "すし"