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import os
import numpy as np
from hdmf import Container
from hdmf.term_set import TermSet, TermSetWrapper, TypeConfigurator
from hdmf.testing import TestCase, remove_test_file
from hdmf.common import (VectorData, unload_type_config,
get_loaded_type_config, load_type_config)
from hdmf.utils import popargs
CUR_DIR = os.path.dirname(os.path.realpath(__file__))
try:
from linkml_runtime.utils.schemaview import SchemaView # noqa: F401
import schemasheets # noqa: F401
import oaklib # noqa: F401
import yaml # noqa: F401
REQUIREMENTS_INSTALLED = True
except ImportError:
REQUIREMENTS_INSTALLED = False
class TestTermSet(TestCase):
"""Tests for TermSet"""
def setUp(self):
if not REQUIREMENTS_INSTALLED:
self.skipTest("optional LinkML module is not installed")
def test_termset_setup(self):
termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
self.assertEqual(termset.name, 'Species')
self.assertEqual(list(termset.sources), ['NCBI_TAXON'])
def test_repr_short(self):
termset = TermSet(term_schema_path='tests/unit/example_test_term_set2.yaml')
output = ('Schema Path: tests/unit/example_test_term_set2.yaml\nSources: NCBI_TAXON\nTerms: \n'
' - Homo sapiens\n - Mus musculus\n - Ursus arctos horribilis\nNumber of terms: 3')
self.assertEqual(repr(termset), output)
def test_repr_html_short(self):
termset = TermSet(term_schema_path='tests/unit/example_test_term_set2.yaml')
output = ('<b>Schema Path: </b>tests/unit/example_test_term_set2.yaml<br><b>Sources:'
' </b>NCBI_TAXON<br><b> Terms: </b><li> Homo sapiens </li><li> Mus musculus'
' </li><li> Ursus arctos horribilis </li><i> Number of terms:</i> 3')
self.assertEqual(termset._repr_html_(), output)
def test_repr_long(self):
termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
output = ('Schema Path: tests/unit/example_test_term_set.yaml\nSources: NCBI_TAXON\nTerms: \n'
' - Homo sapiens\n - Mus musculus\n - Ursus arctos horribilis\n ... ... \n'
' - Ailuropoda melanoleuca\nNumber of terms: 5')
self.assertEqual(repr(termset), output)
def test_repr_html_long(self):
termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
output = ('<b>Schema Path: </b>tests/unit/example_test_term_set.yaml<br><b>Sources:'
' </b>NCBI_TAXON<br><b> Terms: </b><li> Homo sapiens </li><li> Mus musculus'
' </li><li> Ursus arctos horribilis </li>... ...<li> Ailuropoda melanoleuca'
' </li><i> Number of terms:</i> 5')
self.assertEqual(termset._repr_html_(), output)
def test_view_set(self):
termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
expected = ['Homo sapiens', 'Mus musculus', 'Ursus arctos horribilis', 'Myrmecophaga tridactyla',
'Ailuropoda melanoleuca']
self.assertEqual(list(termset.view_set), expected)
self.assertIsInstance(termset.view, SchemaView)
def test_termset_validate(self):
termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
self.assertEqual(termset.validate('Homo sapiens'), True)
def test_termset_validate_false(self):
termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
self.assertEqual(termset.validate('missing_term'), False)
def test_get_item(self):
termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
self.assertEqual(termset['Homo sapiens'].id, 'NCBI_TAXON:9606')
self.assertEqual(termset['Homo sapiens'].description, 'the species is human')
self.assertEqual(
termset['Homo sapiens'].meaning,
'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606'
)
def test_get_item_key_error(self):
termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
with self.assertRaises(ValueError):
termset['Homo Ssapiens']
def test_schema_sheets_and_path_provided_error(self):
folder = os.path.join(CUR_DIR, "test_term_set_input", "schemasheets")
with self.assertRaises(ValueError):
TermSet(term_schema_path='tests/unit/example_test_term_set.yaml', schemasheets_folder=folder)
def test_view_set_sheets(self):
folder = os.path.join(CUR_DIR, "test_term_set_input", "schemasheets")
termset = TermSet(schemasheets_folder=folder)
expected = ['ASTROCYTE', 'INTERNEURON', 'MICROGLIAL_CELL', 'MOTOR_NEURON',
'OLIGODENDROCYTE', 'PYRAMIDAL_NEURON']
self.assertEqual(list(termset.view_set), expected)
self.assertIsInstance(termset.view, SchemaView)
def test_enum_expander(self):
schema_path = 'tests/unit/example_dynamic_term_set.yaml'
termset = TermSet(term_schema_path=schema_path, dynamic=True)
# check that interneuron term is in materialized schema
self.assertIn("CL:0000099", termset.view_set)
# check that motor neuron term is in materialized schema
self.assertIn("CL:0000100", termset.view_set)
# check that pyramidal neuron is in materialized schema
self.assertIn("CL:0000598", termset.view_set)
self.assertIsInstance(termset.view, SchemaView)
expected_path = os.path.join("tests", "unit", "expanded_example_dynamic_term_set.yaml")
expected_path = os.path.normpath(expected_path)
actual_path = os.path.normpath(termset.expanded_termset_path)
self.assertEqual(actual_path, expected_path)
filename = os.path.splitext(os.path.basename(schema_path))[0]
remove_test_file(f"tests/unit/expanded_{filename}.yaml")
def test_enum_expander_output(self):
schema_path = 'tests/unit/example_dynamic_term_set.yaml'
termset = TermSet(term_schema_path=schema_path, dynamic=True)
convert_path = termset._TermSet__enum_expander()
convert_path = os.path.normpath(convert_path)
expected_path = os.path.join("tests", "unit", "expanded_example_dynamic_term_set.yaml")
expected_path = os.path.normpath(expected_path)
self.assertEqual(convert_path, expected_path)
filename = os.path.splitext(os.path.basename(schema_path))[0]
remove_test_file(f"tests/unit/expanded_{filename}.yaml")
def test_folder_output(self):
folder = os.path.join(CUR_DIR, "test_term_set_input", "schemasheets")
termset = TermSet(schemasheets_folder=folder)
actual_path = termset._TermSet__schemasheets_convert()
expected_path = os.path.normpath(os.path.join(os.path.dirname(folder), "schemasheets/nwb_static_enums.yaml"))
self.assertEqual(actual_path, expected_path)
class TestTermSetWrapper(TestCase):
"""Tests for the TermSetWrapper"""
def setUp(self):
if not REQUIREMENTS_INSTALLED:
self.skipTest("optional LinkML module is not installed")
self.termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
self.wrapped_array = TermSetWrapper(value=np.array(['Homo sapiens']), termset=self.termset)
self.wrapped_list = TermSetWrapper(value=['Homo sapiens'], termset=self.termset)
c_data = np.array([('Homo sapiens', 24)], dtype=[('species', 'U50'), ('age', 'i4')])
self.wrapped_comp_array = TermSetWrapper(value=c_data,
termset=self.termset,
field='species')
self.np_data = VectorData(
name='Species_1',
description='...',
data=self.wrapped_array
)
def test_properties(self):
self.assertEqual(self.wrapped_array.value, ['Homo sapiens'])
self.assertEqual(self.wrapped_array.termset.view_set, self.termset.view_set)
self.assertEqual(self.wrapped_array.dtype, 'U12') # this covers __getattr__
self.assertEqual(self.wrapped_comp_array.field, 'species')
def test_get_item(self):
self.assertEqual(self.np_data.data[0], 'Homo sapiens')
def test_validate_error(self):
with self.assertRaises(ValueError):
VectorData(name='Species_1',
description='...',
data=TermSetWrapper(value=['Missing Term'],
termset=self.termset))
def test_wrapper_validate_attribute(self):
col1 = VectorData(
name='Species_1',
description=TermSetWrapper(value='Homo sapiens',
termset=self.termset),
data=['Human']
)
self.assertTrue(isinstance(col1.description, TermSetWrapper))
def test_wrapper_validate_dataset(self):
col1 = VectorData(
name='Species_1',
description='...',
data=TermSetWrapper(value=['Homo sapiens'],
termset=self.termset)
)
self.assertTrue(isinstance(col1.data, TermSetWrapper))
def test_wrapper_append(self):
data_obj = VectorData(name='species', description='...', data=self.wrapped_list)
data_obj.append('Mus musculus')
self.assertEqual(data_obj.data.value, ['Homo sapiens', 'Mus musculus'])
def test_wrapper_append_error(self):
data_obj = VectorData(name='species', description='...', data=self.wrapped_list)
with self.assertRaises(ValueError):
data_obj.append('bad_data')
def test_wrapper_extend(self):
data_obj = VectorData(name='species', description='...', data=self.wrapped_list)
data_obj.extend(['Mus musculus'])
self.assertEqual(data_obj.data.value, ['Homo sapiens', 'Mus musculus'])
def test_wrapper_extend_error(self):
data_obj = VectorData(name='species', description='...', data=self.wrapped_list)
with self.assertRaises(ValueError):
data_obj.extend(['bad_data'])
class TestTypeConfig(TestCase):
def setUp(self):
if not REQUIREMENTS_INSTALLED:
self.skipTest("optional LinkML module is not installed")
def tearDown(self):
unload_type_config()
def test_get_loaded_type_config_error(self):
with self.assertRaises(ValueError):
get_loaded_type_config()
def test_config_path(self):
path = 'tests/unit/hdmf_config.yaml'
tc = TypeConfigurator(path=path)
self.assertEqual(tc.path, [path])
def test_get_config(self):
path = 'tests/unit/hdmf_config.yaml'
tc = TypeConfigurator(path=path)
self.assertEqual(tc.get_config('VectorData', 'hdmf-common'),
{'description': {'termset': 'example_test_term_set.yaml'}})
def test_get_config_namespace_error(self):
path = 'tests/unit/hdmf_config.yaml'
tc = TypeConfigurator(path=path)
with self.assertRaises(ValueError):
tc.get_config('VectorData', 'hdmf-common11')
def test_get_config_container_error(self):
path = 'tests/unit/hdmf_config.yaml'
tc = TypeConfigurator(path=path)
with self.assertRaises(ValueError):
tc.get_config('VectorData11', 'hdmf-common')
def test_already_loaded_path_error(self):
path = 'tests/unit/hdmf_config.yaml'
tc = TypeConfigurator(path=path)
with self.assertRaises(ValueError):
tc.load_type_config(config_path=path)
def test_load_two_unique_configs(self):
path = 'tests/unit/hdmf_config.yaml'
path2 = 'tests/unit/hdmf_config2.yaml'
tc = TypeConfigurator(path=path)
tc.load_type_config(config_path=path2)
config = {'namespaces': {'hdmf-common': {'version': '3.12.2',
'data_types': {'VectorData': {'name': None},
'VectorIndex': {'data': '...'},
'Data': {'description': {'termset': 'example_test_term_set.yaml'}},
'EnumData': {'description': {'termset': 'example_test_term_set.yaml'}}}},
'foo_namespace': {'version': '...',
'data_types': {'ExtensionContainer': {'description': None}}},
'namespace2': {'version': 0, 'data_types':
{'MythicData': {'description':
{'termset': 'example_test_term_set.yaml'}}}}}}
self.assertEqual(tc.path, [path, path2])
self.assertEqual(tc.config, config)
class ExtensionContainer(Container):
__fields__ = ("description",)
def __init__(self, **kwargs):
description, namespace = popargs('description', 'namespace', kwargs)
self.namespace = namespace
super().__init__(**kwargs)
self.description = description
@property
def data_type(self):
"""
Return the spec data type associated with this container.
"""
return "ExtensionContainer"
class TestGlobalTypeConfig(TestCase):
def setUp(self):
if not REQUIREMENTS_INSTALLED:
self.skipTest("optional LinkML module is not installed")
load_type_config(config_path='tests/unit/hdmf_config.yaml')
def tearDown(self):
unload_type_config()
def test_load_config(self):
config = get_loaded_type_config()
self.assertEqual(config,
{'namespaces': {'hdmf-common': {'version': '3.12.2',
'data_types': {'VectorData':
{'description': {'termset': 'example_test_term_set.yaml'}},
'VectorIndex': {'data': '...'}}}, 'foo_namespace':
{'version': '...', 'data_types':
{'ExtensionContainer': {'description': None}}}}}
)
def test_validate_with_config(self):
data = VectorData(name='foo', data=[0], description='Homo sapiens')
self.assertEqual(data.description.value, 'Homo sapiens')
def test_namespace_warn(self):
with self.assertWarns(Warning):
ExtensionContainer(name='foo',
namespace='foo',
description='Homo sapiens')
def test_container_type_warn(self):
with self.assertWarns(Warning):
ExtensionContainer(name='foo',
namespace='hdmf-common',
description='Homo sapiens')
def test_already_wrapped_warn(self):
terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
with self.assertWarns(Warning):
VectorData(name='foo',
data=[0],
description=TermSetWrapper(value='Homo sapiens', termset=terms))
def test_field_not_in_config(self):
unload_type_config()
load_type_config(config_path='tests/unit/hdmf_config2.yaml')
VectorData(name='foo', data=[0], description='Homo sapiens')
def test_spec_none(self):
with self.assertWarns(Warning):
ExtensionContainer(name='foo',
namespace='foo_namespace',
description='Homo sapiens')
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