add custom html field generation method for TimeSeries (#1831)

* add custom html field generation method for timeseries

* update CHANGELOG.md

* modify html representation of linked timestamps and data

* add test for html representation of linked data

* update html representation of linked objects

* update html representation test

* Use HDMF 3.12.2

---------

Co-authored-by: Ryan Ly <[email protected]>

CHANGELOG.md

@@ -18,6 +18,7 @@
 - Fix bug where namespaces were loaded in "w-" mode. @h-mayorquin [#1795](https://github.com/NeurodataWithoutBorders/pynwb/pull/1795)
 - Fix bug where pynwb version was reported as "unknown" to readthedocs @stephprince [#1810](https://github.com/NeurodataWithoutBorders/pynwb/pull/1810)
 - Fixed bug to allow linking of `TimeSeries.data` by setting the `data` constructor argument to another `TimeSeries`. @oruebel [#1766](https://github.com/NeurodataWithoutBorders/pynwb/pull/1766)
+- Fix recursion error in html representation generation in jupyter notebooks. @stephprince [#1831](https://github.com/NeurodataWithoutBorders/pynwb/pull/1831)
 
 ### Documentation and tutorial enhancements
 - Add RemFile to streaming tutorial. @bendichter [#1761](https://github.com/NeurodataWithoutBorders/pynwb/pull/1761)

environment-ros3.yml

@@ -6,7 +6,7 @@ channels:
 dependencies:
   - python==3.11
   - h5py==3.8.0
-  - hdmf==3.12.1
+  - hdmf==3.12.2
   - matplotlib==3.7.1
   - numpy==1.24.2
   - pandas==2.0.0

requirements-min.txt

@@ -1,6 +1,6 @@
 # minimum versions of package dependencies for installing PyNWB
 h5py==2.10  # support for selection of datasets with list of indices added in 2.10
-hdmf==3.12.1
+hdmf==3.12.2
 numpy==1.18
 pandas==1.1.5
 python-dateutil==2.7.3

requirements.txt

@@ -1,6 +1,6 @@
 # pinned dependencies to reproduce an entire development environment to use PyNWB
 h5py==3.10.0
-hdmf==3.12.1
+hdmf==3.12.2
 numpy==1.26.1
 pandas==2.1.2
 python-dateutil==2.8.2

setup.py

@@ -20,7 +20,7 @@
 
 reqs = [
     'h5py>=2.10',
-    'hdmf>=3.12.1',
+    'hdmf>=3.12.2',
     'numpy>=1.16',
     'pandas>=1.1.5',
     'python-dateutil>=2.7.3',

src/pynwb/base.py

@@ -287,6 +287,42 @@ def __get_links(self, links):
     def __add_link(self, links_key, link):
         self.fields.setdefault(links_key, list()).append(link)
 
+    def _generate_field_html(self, key, value, level, access_code):
+        def find_location_in_memory_nwbfile(current_location: str, neurodata_object) -> str:
+            """
+            Method for determining the location of a neurodata object within an in-memory NWBFile object. Adapted from
+            neuroconv package.
+            """
+            parent = neurodata_object.parent
+            if parent is None:
+                return neurodata_object.name + "/" + current_location
+            elif parent.name == 'root':
+                # Items in defined top-level places like acquisition, intervals, etc. do not act as 'containers'
+                # in that they do not set the `.parent` attribute; ask if object is in their in-memory dictionaries
+                # instead
+                for parent_field_name, parent_field_value in parent.fields.items():
+                    if isinstance(parent_field_value, dict) and neurodata_object.name in parent_field_value:
+                        return parent_field_name + "/" + neurodata_object.name + "/" + current_location
+                return neurodata_object.name + "/" + current_location
+            return find_location_in_memory_nwbfile(
+                current_location=neurodata_object.name + "/" + current_location, neurodata_object=parent
+            )
+
+        # reassign value if linked timestamp or linked data to avoid recursion error
+        if key in ['timestamps', 'data'] and isinstance(value, TimeSeries):
+            path_to_linked_object = find_location_in_memory_nwbfile(key, value)
+            if key == 'timestamps':
+                value = value.timestamps
+            elif key == 'data':
+                value = value.data
+            key = f'{key} (link to {path_to_linked_object})'
+
+        if key in ['timestamp_link', 'data_link']:
+            linked_key = 'timestamps' if key == 'timestamp_link' else 'data'
+            value = [find_location_in_memory_nwbfile(linked_key, v) for v in value]
+
+        return super()._generate_field_html(key, value, level, access_code)
+
     @property
     def time_unit(self):
         return self.__time_unit

tests/unit/test_base.py

@@ -464,6 +464,20 @@ def test_file_with_starting_time_and_timestamps_in_construct_mode(self):
                 timestamps=[1, 2, 3, 4, 5]
             )
 
+    def test_repr_html(self):
+        """ Test that html representation of linked timestamp data will occur as expected and will not cause a
+        RecursionError
+        """
+        data1 = [0, 1, 2, 3]
+        data2 = [4, 5, 6, 7]
+        timestamps = [0.0, 0.1, 0.2, 0.3]
+        ts1 = TimeSeries(name="test_ts1", data=data1, unit="grams", timestamps=timestamps)
+        ts2 = TimeSeries(name="test_ts2", data=data2, unit="grams", timestamps=ts1)
+        pm = ProcessingModule(name="processing", description="a test processing module")
+        pm.add(ts1)
+        pm.add(ts2)
+        self.assertIn('(link to processing/test_ts1/timestamps)', pm._repr_html_())
+
 
 class TestImage(TestCase):
     def test_init(self):