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import datetime
import os
from hdmf.spec.namespace import SpecNamespace, NamespaceCatalog
from hdmf.spec.spec import GroupSpec
from hdmf.spec.write import NamespaceBuilder, YAMLSpecWriter, export_spec
from hdmf.testing import TestCase
class TestSpec(TestCase):
def setUp(self):
# create a builder for the namespace
self.ns_name = "mylab"
self.date = datetime.datetime.now()
self.ns_builder = NamespaceBuilder(doc="mydoc",
name=self.ns_name,
full_name="My Laboratory",
version="0.0.1",
author="foo",
contact="foo@bar.com",
namespace_cls=SpecNamespace,
date=self.date)
# create extensions
ext1 = GroupSpec('A custom DataSeries interface',
attributes=[],
datasets=[],
groups=[],
data_type_inc=None,
data_type_def='MyDataSeries')
ext2 = GroupSpec('An extension of a DataSeries interface',
attributes=[],
datasets=[],
groups=[],
data_type_inc='MyDataSeries',
data_type_def='MyExtendedMyDataSeries')
ext2.add_dataset(doc='test',
dtype='float',
name='testdata')
self.data_types = [ext1, ext2]
# add the extension
self.ext_source_path = 'mylab.extensions.yaml'
self.namespace_path = 'mylab.namespace.yaml'
def _test_extensions_file(self):
with open(self.ext_source_path, 'r') as file:
match_str = """groups:
- data_type_def: MyDataSeries
doc: A custom DataSeries interface
- data_type_def: MyExtendedMyDataSeries
data_type_inc: MyDataSeries
doc: An extension of a DataSeries interface
datasets:
- name: testdata
dtype: float
doc: test
"""
nsstr = file.read()
self.assertEqual(nsstr, match_str)
def _test_namespace_file(self):
with open(self.namespace_path, 'r') as file:
match_str = """namespaces:
- author: foo
contact: foo@bar.com
date: '%s'
doc: mydoc
full_name: My Laboratory
name: mylab
schema:
- doc: Extensions for my lab
source: mylab.extensions.yaml
title: Extensions for my lab
version: 0.0.1
""" % self.date.isoformat() # noqa: E122
nsstr = file.read()
self.assertEqual(nsstr, match_str)
class TestNamespaceBuilder(TestSpec):
NS_NAME = 'test_ns'
def setUp(self):
super().setUp()
for data_type in self.data_types:
self.ns_builder.add_spec(source=self.ext_source_path, spec=data_type)
self.ns_builder.add_source(source=self.ext_source_path,
doc='Extensions for my lab',
title='My lab extensions')
self.ns_builder.export(self.namespace_path)
def tearDown(self):
if os.path.exists(self.ext_source_path):
os.remove(self.ext_source_path)
if os.path.exists(self.namespace_path):
os.remove(self.namespace_path)
def test_export_namespace(self):
self._test_namespace_file()
self._test_extensions_file()
def test_read_namespace(self):
ns_catalog = NamespaceCatalog()
ns_catalog.load_namespaces(self.namespace_path, resolve=True)
loaded_ns = ns_catalog.get_namespace(self.ns_name)
self.assertEqual(loaded_ns.doc, "mydoc")
self.assertEqual(loaded_ns.author, "foo")
self.assertEqual(loaded_ns.contact, "foo@bar.com")
self.assertEqual(loaded_ns.full_name, "My Laboratory")
self.assertEqual(loaded_ns.name, "mylab")
self.assertEqual(loaded_ns.date, self.date.isoformat())
self.assertDictEqual(loaded_ns.schema[0], {'doc': 'Extensions for my lab',
'source': 'mylab.extensions.yaml',
'title': 'Extensions for my lab'})
self.assertEqual(loaded_ns.version, "0.0.1")
def test_get_source_files(self):
ns_catalog = NamespaceCatalog()
ns_catalog.load_namespaces(self.namespace_path, resolve=True)
loaded_ns = ns_catalog.get_namespace(self.ns_name)
self.assertListEqual(loaded_ns.get_source_files(), ['mylab.extensions.yaml'])
def test_get_source_description(self):
ns_catalog = NamespaceCatalog()
ns_catalog.load_namespaces(self.namespace_path, resolve=True)
loaded_ns = ns_catalog.get_namespace(self.ns_name)
descr = loaded_ns.get_source_description('mylab.extensions.yaml')
self.assertDictEqual(descr, {'doc': 'Extensions for my lab',
'source': 'mylab.extensions.yaml',
'title': 'Extensions for my lab'})
def test_missing_version(self):
"""Test that creating a namespace builder without a version raises an error."""
msg = "Namespace '%s' missing key 'version'. Please specify a version for the extension." % self.ns_name
with self.assertRaisesWith(ValueError, msg):
self.ns_builder = NamespaceBuilder(doc="mydoc",
name=self.ns_name,
full_name="My Laboratory",
author="foo",
contact="foo@bar.com",
namespace_cls=SpecNamespace,
date=self.date)
class TestYAMLSpecWrite(TestSpec):
def setUp(self):
super().setUp()
for data_type in self.data_types:
self.ns_builder.add_spec(source=self.ext_source_path, spec=data_type)
self.ns_builder.add_source(source=self.ext_source_path,
doc='Extensions for my lab',
title='My lab extensions')
def tearDown(self):
if os.path.exists(self.ext_source_path):
os.remove(self.ext_source_path)
if os.path.exists(self.namespace_path):
os.remove(self.namespace_path)
def test_init(self):
temp = YAMLSpecWriter('.')
self.assertEqual(temp._YAMLSpecWriter__outdir, '.')
def test_write_namespace(self):
temp = YAMLSpecWriter()
self.ns_builder.export(self.namespace_path, writer=temp)
self._test_namespace_file()
self._test_extensions_file()
def test_get_name(self):
self.assertEqual(self.ns_name, self.ns_builder.name)
class TestExportSpec(TestSpec):
def test_export(self):
"""Test that export_spec writes the correct files."""
export_spec(self.ns_builder, self.data_types, '.')
self._test_namespace_file()
self._test_extensions_file()
def tearDown(self):
if os.path.exists(self.ext_source_path):
os.remove(self.ext_source_path)
if os.path.exists(self.namespace_path):
os.remove(self.namespace_path)
def _test_namespace_file(self):
with open(self.namespace_path, 'r') as file:
match_str = """namespaces:
- author: foo
contact: foo@bar.com
date: '%s'
doc: mydoc
full_name: My Laboratory
name: mylab
schema:
- source: mylab.extensions.yaml
version: 0.0.1
""" % self.date.isoformat() # noqa: E122
nsstr = file.read()
self.assertEqual(nsstr, match_str)
def test_missing_data_types(self):
"""Test that calling export_spec on a namespace builder without data types raises a warning."""
with self.assertWarnsWith(UserWarning, 'No data types specified. Exiting.'):
export_spec(self.ns_builder, [], '.')
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