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import os
import random
import string
from datetime import datetime
from dateutil.tz import tzlocal
from tempfile import gettempdir
from hdmf.spec import RefSpec
from hdmf.utils import get_docval, docval, popargs
from pynwb import get_type_map, TimeSeries, NWBFile, register_class, load_namespaces, get_class
from pynwb.spec import NWBNamespaceBuilder, NWBGroupSpec, NWBAttributeSpec, NWBDatasetSpec
from pynwb.file import LabMetaData
from pynwb.testing import TestCase, remove_test_file
def id_generator(N=10):
"""
Generator a random string of characters.
"""
return ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(N))
class TestExtension(TestCase):
def setUp(self):
self.tempdir = gettempdir()
self.prefix = id_generator()
self.ext_source = '%s_extension.yaml' % self.prefix
self.ns_path = '%s_namespace.yaml' % self.prefix
def tearDown(self):
for f in (self.ext_source, self.ns_path):
path = os.path.join(self.tempdir, f)
remove_test_file(path)
def test_export(self):
ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', self.prefix, version='0.1.0')
ext1 = NWBGroupSpec('A custom ElectricalSeries for my lab',
attributes=[NWBAttributeSpec(name='trode_id', doc='the tetrode id', dtype='int')],
neurodata_type_inc='ElectricalSeries',
neurodata_type_def='TetrodeSeries')
ns_builder.add_spec(self.ext_source, ext1)
ns_builder.export(self.ns_path, outdir=self.tempdir)
def test_load_namespace(self):
self.test_export()
get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
def test_get_class(self):
self.test_export()
type_map = get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
type_map.get_dt_container_cls('TetrodeSeries', self.prefix)
def test_load_namespace_with_reftype_attribute(self):
ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', self.prefix, version='0.1.0')
test_ds_ext = NWBDatasetSpec(doc='test dataset to add an attr',
name='test_data', shape=(None,),
attributes=[NWBAttributeSpec(name='target_ds',
doc='the target the dataset applies to',
dtype=RefSpec('TimeSeries', 'object'))],
neurodata_type_def='my_new_type')
ns_builder.add_spec(self.ext_source, test_ds_ext)
ns_builder.export(self.ns_path, outdir=self.tempdir)
get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
def test_load_namespace_with_reftype_attribute_check_autoclass_const(self):
ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', self.prefix, version='0.1.0')
test_ds_ext = NWBDatasetSpec(doc='test dataset to add an attr',
name='test_data', shape=(None,),
attributes=[NWBAttributeSpec(name='target_ds',
doc='the target the dataset applies to',
dtype=RefSpec('TimeSeries', 'object'))],
neurodata_type_def='my_new_type')
ns_builder.add_spec(self.ext_source, test_ds_ext)
ns_builder.export(self.ns_path, outdir=self.tempdir)
type_map = get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
my_new_type = type_map.get_dt_container_cls('my_new_type', self.prefix)
docval = None
for tmp in get_docval(my_new_type.__init__):
if tmp['name'] == 'target_ds':
docval = tmp
break
self.assertIsNotNone(docval)
self.assertEqual(docval['type'], TimeSeries)
def test_lab_meta(self):
ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', self.prefix, version='0.1.0')
test_meta_ext = NWBGroupSpec(
neurodata_type_def='MyTestMetaData',
neurodata_type_inc='LabMetaData',
doc='my test meta data',
attributes=[
NWBAttributeSpec(name='test_attr', dtype='float', doc='test_dtype')])
ns_builder.add_spec(self.ext_source, test_meta_ext)
ns_builder.export(self.ns_path, outdir=self.tempdir)
ns_abs_path = os.path.join(self.tempdir, self.ns_path)
load_namespaces(ns_abs_path)
@register_class('MyTestMetaData', self.prefix)
class MyTestMetaData(LabMetaData):
__nwbfields__ = ('test_attr',)
@docval({'name': 'name', 'type': str, 'doc': 'name'},
{'name': 'test_attr', 'type': float, 'doc': 'test attribute'})
def __init__(self, **kwargs):
test_attr = popargs('test_attr', kwargs)
super().__init__(**kwargs)
self.test_attr = test_attr
nwbfile = NWBFile("a file with header data", "NB123A", datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal()))
nwbfile.add_lab_meta_data(MyTestMetaData(name='test_name', test_attr=5.))
def test_lab_meta_auto(self):
ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', self.prefix, version='0.1.0')
test_meta_ext = NWBGroupSpec(
neurodata_type_def='MyTestMetaData',
neurodata_type_inc='LabMetaData',
doc='my test meta data',
attributes=[
NWBAttributeSpec(name='test_attr', dtype='float', doc='test_dtype')])
ns_builder.add_spec(self.ext_source, test_meta_ext)
ns_builder.export(self.ns_path, outdir=self.tempdir)
ns_abs_path = os.path.join(self.tempdir, self.ns_path)
load_namespaces(ns_abs_path)
MyTestMetaData = get_class('MyTestMetaData', self.prefix)
nwbfile = NWBFile("a file with header data", "NB123A", datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal()))
nwbfile.add_lab_meta_data(MyTestMetaData(name='test_name', test_attr=5.))
class TestCatchDupNS(TestCase):
def setUp(self):
self.tempdir = gettempdir()
self.prefix = id_generator()
self.ext_source1 = '%s_extension1.yaml' % self.prefix
self.ns_path1 = '%s_namespace1.yaml' % self.prefix
self.ext_source2 = '%s_extension2.yaml' % self.prefix
self.ns_path2 = '%s_namespace2.yaml' % self.prefix
def tearDown(self):
files = (self.ext_source1,
self.ns_path1,
self.ext_source2,
self.ns_path2)
for f in files:
path = os.path.join(self.tempdir, f)
remove_test_file(path)
def test_catch_dup_name(self):
ns_builder1 = NWBNamespaceBuilder('Extension for us in my Lab', "pynwb_test_extension1", version='0.1.0')
ext1 = NWBGroupSpec('A custom ElectricalSeries for my lab',
attributes=[NWBAttributeSpec(name='trode_id', doc='the tetrode id', dtype='int')],
neurodata_type_inc='ElectricalSeries',
neurodata_type_def='TetrodeSeries')
ns_builder1.add_spec(self.ext_source1, ext1)
ns_builder1.export(self.ns_path1, outdir=self.tempdir)
ns_builder2 = NWBNamespaceBuilder('Extension for us in my Lab', "pynwb_test_extension1", version='0.1.0')
ext2 = NWBGroupSpec('A custom ElectricalSeries for my lab',
attributes=[NWBAttributeSpec(name='trode_id', doc='the tetrode id', dtype='int')],
neurodata_type_inc='ElectricalSeries',
neurodata_type_def='TetrodeSeries')
ns_builder2.add_spec(self.ext_source2, ext2)
ns_builder2.export(self.ns_path2, outdir=self.tempdir)
type_map = get_type_map(extensions=os.path.join(self.tempdir, self.ns_path1))
type_map.load_namespaces(os.path.join(self.tempdir, self.ns_path2))
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