Fix reading file with linked TimeSeriesReferenceVectorData (#1865)

CHANGELOG.md

@@ -1,8 +1,9 @@
 # PyNWB Changelog
 
-## PyNWB 2.6.1 (Upcoming)
+## PyNWB 2.6.1 (March 25, 2024)
 
 ### Bug fixes
+- Fix bug with reading file with linked `TimeSeriesReferenceVectorData` @rly [#1865](https://github.com/NeurodataWithoutBorders/pynwb/pull/1865)
 - Fix bug where extra keyword arguments could not be passed to `NWBFile.add_{x}_column`` for use in custom `VectorData`` classes. @rly [#1861](https://github.com/NeurodataWithoutBorders/pynwb/pull/1861)
 
 ## PyNWB 2.6.0 (February 21, 2024)

src/pynwb/io/epoch.py

@@ -1,3 +1,4 @@
+from hdmf.build import LinkBuilder
 from hdmf.common.table import VectorData
 from hdmf.common.io.table import DynamicTableMap
 
@@ -8,13 +9,18 @@
 
 @register_map(TimeIntervals)
 class TimeIntervalsMap(DynamicTableMap):
-    pass
 
     @DynamicTableMap.constructor_arg('columns')
     def columns_carg(self, builder, manager):
         # handle the case when a TimeIntervals is read with a non-TimeSeriesReferenceVectorData "timeseries" column
         # this is the case for NWB schema v2.4 and earlier, where the timeseries column was a regular VectorData.
         timeseries_builder = builder.get('timeseries')
+
+        # handle the case when the TimeIntervals has a "timeseries" column that is a link (e.g., it exists in
+        # a different file that was shallow copied to this file).
+        if isinstance(timeseries_builder, LinkBuilder):
+            timeseries_builder = timeseries_builder.builder
+
         # if we have a timeseries column and the type is VectorData instead of TimeSeriesReferenceVectorData
         if (timeseries_builder is not None and
                 timeseries_builder.attributes['neurodata_type'] != 'TimeSeriesReferenceVectorData'):

tests/integration/hdf5/test_file_copy.py

@@ -0,0 +1,44 @@
+import os
+from pynwb.base import TimeSeriesReference
+from pynwb import NWBHDF5IO
+from pynwb.testing import TestCase
+from pynwb.testing.mock.file import mock_NWBFile
+from pynwb.testing.mock.base import mock_TimeSeries
+
+
+class TestFileCopy(TestCase):
+
+    def setUp(self):
+        self.path1 = "test_a.h5"
+        self.path2 = "test_b.h5"
+
+    def tearDown(self):
+        if os.path.exists(self.path1):
+            os.remove(self.path1)
+        if os.path.exists(self.path2):
+            os.remove(self.path2)
+
+    def test_copy_file_link_timeintervals_timeseries(self):
+        """Test copying a file with a TimeSeriesReference in a TimeIntervals object and reading that copy.
+
+        Based on https://github.com/NeurodataWithoutBorders/pynwb/issues/1863
+        """
+        new_nwb = mock_NWBFile()
+        test_ts = mock_TimeSeries(name="test_ts", timestamps=[1.0, 2.0, 3.0], data=[1.0, 2.0, 3.0])
+        new_nwb.add_acquisition(test_ts)
+        new_nwb.add_trial(start_time=1.0, stop_time=2.0, timeseries=[test_ts])
+
+        with NWBHDF5IO(self.path1, 'w') as io:
+            io.write(new_nwb)
+
+        with NWBHDF5IO(self.path1, 'r') as base_io:
+            # the TimeIntervals object is copied but the TimeSeriesReferenceVectorData is linked
+            nwb_add = base_io.read().copy()
+            with NWBHDF5IO(self.path2, 'w', manager=base_io.manager) as out_io:
+                out_io.write(nwb_add)
+
+        with NWBHDF5IO(self.path2, 'r') as io:
+            nwb = io.read()
+            ts_val = nwb.trials["timeseries"][0][0]
+            assert isinstance(ts_val, TimeSeriesReference)
+            assert ts_val.timeseries is nwb.acquisition["test_ts"]