Add extensions.py to showcase issue hdmf-dev/hdmf#354

extensions.py

@@ -0,0 +1,60 @@
+import pynwb
+from pynwb import NWBHDF5IO, NWBFile, ProcessingModule
+from pynwb import register_class, load_namespaces
+from pynwb.ecephys import ElectricalSeries
+from pynwb import NWBData
+from hdmf.utils import docval, call_docval_func, getargs, get_docval
+
+ns_path = "spec/ndx-mies.namespace.yaml"
+ext_source = "spec/ndx-mies.extensions.yaml"
+
+from pynwb import get_class, load_namespaces
+
+load_namespaces(ns_path)
+
+from datetime import datetime
+from dateutil.tz import tzlocal
+from pynwb import NWBFile
+
+start_time = datetime(2017, 4, 3, 11, tzinfo=tzlocal())
+create_date = datetime(2017, 4, 15, 12, tzinfo=tzlocal())
+
+@register_class('GeneratedBy', 'ndx-mies')
+class GeneratedBy(NWBData):
+
+    __nwbfields__ = ('data',)
+
+    @docval(*get_docval(NWBData.__init__))
+    def __init__(self, **kwargs):
+        call_docval_func(super(NWBData, self).__init__, kwargs)
+        self.data = getargs('data', kwargs)
+
+
+nwbfile = NWBFile('demonstrate caching', 'NWB456', start_time,
+        file_create_date=create_date, lab_meta_data=[GeneratedBy(name="GeneratedBy", data=[1, 2, [1, 2]])])
+
+device = nwbfile.create_device(name='device_ITC18USB_Dev_0')
+
+io = NWBHDF5IO('cache_spec_example.nwb', mode='w')
+io.write(nwbfile)
+io.close()
+
+####################
+# By default, PyNWB does not use the namespaces cached in a file--you must
+# explicitly specify this. This behavior is enabled by the *load_namespaces*
+# argument to the :py:class:`~pynwb.NWBHDF5IO` constructor.
+
+with NWBHDF5IO('cache_spec_example.nwb', mode='r+', load_namespaces=True) as nwb_io:
+    nwb = nwb_io.read()
+
+    spike_module = ProcessingModule(name='spikes', description='detected spikes')
+    nwb.add_processing_module(spike_module)
+
+    # This is the container which is causing the problem
+    dev = nwb.devices["device_ITC18USB_Dev_0"]
+    print(type(dev))
+    print(dev)
+    print(type(dev.parent))
+    print(dev.parent)
+
+    nwb_io.write(nwb)