def test_EntityViewSchema__ignore_annotation_column_names():
syn = synapseclient.client.Synapse(debug=True, skip_checks=True)
scopeIds = ['123']
entity_view = EntityViewSchema("someName",
scopes=scopeIds,
parent="syn123",
ignoredAnnotationColumnNames={'long1'},
addDefaultViewColumns=False,
addAnnotationColumns=True)
mocked_annotation_result1 = [
Column(name='long1', columnType='INTEGER'),
Column(name='long2', columnType='INTEGER')
]
with patch.object(syn, '_get_annotation_entity_view_columns', return_value=mocked_annotation_result1) as mocked_get_annotations,\
patch.object(syn, 'getColumns') as mocked_get_columns,\
patch.object(SchemaBase, "_before_synapse_store"):
entity_view._before_synapse_store(syn)
mocked_get_columns.assert_called_once_with([])
mocked_get_annotations.assert_called_once_with(scopeIds, 'file')
assert_equals([Column(name='long2', columnType='INTEGER')],
entity_view.columns_to_store)
def test_update_existing_view_type_mask():
properties = {
'id': 'syn123',
'parentId': 'syn456',
'viewTypeMask': 2
}
view = EntityViewSchema(properties=properties)
assert_equals(view['viewTypeMask'], 2)
view.set_entity_types([EntityViewType.FILE])
assert_equals(view['viewTypeMask'], 1)
def test_update_existing_view_type_mask():
properties = {
'id': 'syn123',
'parentId': 'syn456',
'viewTypeMask': 2
}
view = EntityViewSchema(properties=properties)
assert view['viewTypeMask'] == 2
view.set_entity_types([EntityViewType.FILE])
assert view['viewTypeMask'] == 1
def test_EntityViewSchema__repeated_columnName_same_type():
syn = synapseclient.client.Synapse(debug=True, skip_checks=True)
entity_view = EntityViewSchema("someName", parent="syn123")
columns = [Column(name='annoName', columnType='INTEGER'),
Column(name='annoName', columnType='INTEGER')]
with patch.object(syn, 'getColumns') as mocked_get_columns:
filtered_results = entity_view._filter_duplicate_columns(syn, columns)
mocked_get_columns.assert_called_once_with([])
assert_equals(1, len(filtered_results))
assert_equals(Column(name='annoName', columnType='INTEGER'), filtered_results[0])
def test_EntityViewSchema__repeated_columnName_same_type(syn):
syn = Synapse(debug=True, skip_checks=True)
entity_view = EntityViewSchema("someName", parent="syn123")
columns = [Column(name='annoName', columnType='INTEGER'),
Column(name='annoName', columnType='INTEGER')]
with patch.object(syn, 'getColumns') as mocked_get_columns:
filtered_results = entity_view._filter_duplicate_columns(syn, columns)
mocked_get_columns.assert_called_once_with([])
assert 1 == len(filtered_results)
assert Column(name='annoName', columnType='INTEGER') == filtered_results[0]
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__before_synapse_store(syn):
syn = Synapse(debug=True, skip_checks=True)
with patch.object(syn, '_get_default_view_columns') as mocked_get_default,\
patch.object(syn, '_get_annotation_view_columns') as mocked_get_annotations,\
patch.object(SchemaBase, "_before_synapse_store"):
submission_view = EntityViewSchema(scopes=['syn123'], parent="idk")
submission_view._before_synapse_store(syn)
mocked_get_default.assert_called_once_with("entityview",
view_type_mask=1)
mocked_get_annotations.assert_called_once_with(['syn123'],
"entityview",
view_type_mask=1)
def test_set_view_types_invalid_input():
properties = {
'id': 'syn123',
'parentId': 'syn456'
}
view = EntityViewSchema(type='project', properties=properties)
assert view['viewTypeMask'] == 2
pytest.raises(ValueError, view.set_entity_types, None)
def test_input_is_SchemaBase(self):
get_table_colums_results = [Column(name='A'), Column(name='B')]
with patch.object(syn, "getTableColumns", return_value=iter(get_table_colums_results))\
as mock_get_table_coulmns:
schema = EntityViewSchema(parentId="syn123")
results = list(syn.getColumns(schema))
assert_equal(get_table_colums_results, results)
mock_get_table_coulmns.assert_called_with(schema)
def test_entityViewSchema__add_default_columns_when_from_Synapse():
properties = {
u'concreteType': u'org.sagebionetworks.repo.model.table.EntityView'
}
entity_view = EntityViewSchema(parent="idk",
addDefaultViewColumns=True,
properties=properties)
assert_false(entity_view.addDefaultViewColumns)
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_EntityViewSchema__repeated_columnName_different_type():
syn = synapseclient.client.Synapse(debug=True, skip_checks=True)
scopeIds = ['123']
entity_view = EntityViewSchema("someName",
scopes=scopeIds,
parent="syn123")
columns = [
Column(name='annoName', columnType='INTEGER'),
Column(name='annoName', columnType='DOUBLE')
]
with patch.object(syn, 'getColumns') as mocked_get_columns:
filtered_results = entity_view._filter_duplicate_columns(syn, columns)
mocked_get_columns.assert_called_once_with([])
assert_equals(2, len(filtered_results))
assert_equals(columns, filtered_results)
def test_EntityViewSchema__ignore_annotation_column_names():
syn = synapseclient.client.Synapse(debug=True, skip_checks=True)
scopeIds = ['123']
entity_view = EntityViewSchema("someName", scopes=scopeIds, parent="syn123", ignoredAnnotationColumnNames={'long1'},
addDefaultViewColumns=False, addAnnotationColumns=True)
mocked_annotation_result1 = [Column(name='long1', columnType='INTEGER'), Column(name='long2',
columnType='INTEGER')]
with patch.object(syn, '_get_annotation_entity_view_columns', return_value=mocked_annotation_result1)\
as mocked_get_annotations,\
patch.object(syn, 'getColumns') as mocked_get_columns,\
patch.object(SchemaBase, "_before_synapse_store"):
entity_view._before_synapse_store(syn)
mocked_get_columns.assert_called_once_with([])
mocked_get_annotations.assert_called_once_with(scopeIds, EntityViewType.FILE.value)
assert_equals([Column(name='long2', columnType='INTEGER')], entity_view.columns_to_store)
def test_EntityViewSchema__repeated_columnName():
syn = synapseclient.client.Synapse(debug=True, skip_checks=True)
scopeIds = ['123']
entity_view = EntityViewSchema("someName",
scopes=scopeIds,
parent="syn123")
mocked_annotation_result1 = [
Column(name='annoName', columnType='INTEGER'),
Column(name='annoName', columnType='DOUBLE')
]
with patch.object(syn, '_get_annotation_entity_view_columns', return_value=mocked_annotation_result1) as mocked_get_annotations,\
patch.object(syn, 'getColumns') as mocked_get_columns:
assert_raises(ValueError, entity_view._add_annotations_as_columns, syn)
mocked_get_columns.assert_called_once_with([])
mocked_get_annotations.assert_called_once_with(scopeIds, 'file')
def test_entityViewSchema__specified_deprecated_type():
view_type = 'project'
entity_view = EntityViewSchema(parent="idk", type=view_type)
assert EntityViewType.PROJECT.value == entity_view.viewTypeMask
assert entity_view.get('type') is None
def test_entityViewSchema__specified_deprecated_type_in_properties():
view_type = 'project'
properties = {'type': view_type}
entity_view = EntityViewSchema(parent="idk", properties=properties)
assert EntityViewType.PROJECT.value == entity_view.viewTypeMask
assert entity_view.get('type') is None
def test_entityViewSchema__sepcified_add_default_columns():
entity_view = EntityViewSchema(parent="idk", addDefaultViewColumns=False)
assert_false(entity_view.addDefaultViewColumns)
def test_entityViewSchema__sepcified_scopeId():
scopeId = ["123"]
entity_view = EntityViewSchema(parent="idk", scopeId=scopeId)
assert_equals(scopeId, entity_view.scopeId)
def test_entityViewSchema__specified_type():
view_type = 'project'
entity_view = EntityViewSchema(parent="idk", type=view_type)
assert_equals(view_type, entity_view.type)
def test_EntityViewSchema__default_params():
entity_view = EntityViewSchema(parent="idk")
assert_equals('file', entity_view.type)
assert_equals([], entity_view.scopeIds)
assert_equals(True, entity_view.addDefaultViewColumns)
def test_entityViewSchema__specified_both_type_and_viewTypeMask():
entity_view = EntityViewSchema(parent="idk",
type='folder',
includeEntityTypes=[EntityViewType.PROJECT])
assert_equals(EntityViewType.PROJECT.value, entity_view.viewTypeMask)
assert_is_none(entity_view.get('type'))
def test_entityViewSchema__specified_both_type_and_viewTypeMask():
entity_view = EntityViewSchema(parent="idk", type='folder', includeEntityTypes=[EntityViewType.PROJECT])
assert_equals(EntityViewType.PROJECT.value, entity_view.viewTypeMask)
assert_is_none(entity_view.get('type'))
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__specified_deprecated_type_in_properties():
view_type = 'project'
properties = {'type': view_type}
entity_view = EntityViewSchema(parent="idk", properties=properties)
assert_equals(EntityViewType.PROJECT.value, entity_view.viewTypeMask)
assert_is_none(entity_view.get('type'))
def test_EntityViewSchema__default_params():
entity_view = EntityViewSchema(parent="idk")
assert_equals(EntityViewType.FILE.value, entity_view.viewTypeMask)
assert_equals([], entity_view.scopeIds)
assert_equals(True, entity_view.addDefaultViewColumns)
def test_entityViewSchema__specified_deprecated_type():
view_type = 'project'
entity_view = EntityViewSchema(parent="idk", type=view_type)
assert_equals(EntityViewType.PROJECT.value, entity_view.viewTypeMask)
assert_is_none(entity_view.get('type'))
def test_EntityViewSchema__default_params():
entity_view = EntityViewSchema(parent="idk")
assert EntityViewType.FILE.value == entity_view.viewTypeMask
assert [] == entity_view.scopeIds
assert entity_view.addDefaultViewColumns is True
def test_entityViewSchema__specified_both_type_and_viewTypeMask():
entity_view = EntityViewSchema(parent="idk", type='folder', includeEntityTypes=[EntityViewType.PROJECT])
assert EntityViewType.PROJECT.value == entity_view.viewTypeMask
assert entity_view.get('type') is None
def test_entityViewSchema__specified_deprecated_type():
view_type = 'project'
entity_view = EntityViewSchema(parent="idk", type=view_type)
assert_equals(EntityViewType.PROJECT.value, entity_view.viewTypeMask)
assert_is_none(entity_view.get('type'))
def test_entityViewSchema__specified_deprecated_type_in_properties():
view_type = 'project'
properties = {'type': view_type}
entity_view = EntityViewSchema(parent="idk", properties=properties)
assert_equals(EntityViewType.PROJECT.value, entity_view.viewTypeMask)
assert_is_none(entity_view.get('type'))