add error on new pass on construct method

src/pynwb/core.py

@@ -47,6 +47,19 @@ def _error_on_new_warn_on_construct(self, error_msg: str):
             raise ValueError(error_msg)
         warn(error_msg)
 
+    def _error_on_new_pass_on_construct(self, error_msg: str):
+        """
+        Raise an error when a check is violated on instance creation.
+        When reading from a file, do nothing, ensuring that files with
+        invalid data or deprecated neurodata types can be read.
+        If error_msg is set to None the function will simply return
+        without further action.
+        """
+        if error_msg is None:
+            return
+        if not self._in_construct_mode:
+            raise ValueError(error_msg)
+
     def _get_type_map(self):
         return get_type_map()
 
@@ -128,7 +141,7 @@ def __init__(self, **kwargs):
         notes, description = popargs('notes', 'description', kwargs)
         super().__init__(**kwargs)
         if notes != '':
-            self._error_on_new_warn_on_construct(
+            self._error_on_new_pass_on_construct(
                     error_msg=("The `notes` argument of ScratchData.__init__ has been deprecated and will be removed in PyNWB 4.0. "
                                "Use description instead.")
                     )
@@ -137,7 +150,7 @@ def __init__(self, **kwargs):
                                  'argument is recommended.')
             description = notes
         if not description:
-            self._error_on_new_warn_on_construct(error_msg='ScratchData.description is required.')
+            self._error_on_new_pass_on_construct(error_msg='ScratchData.description is required.')
         self.description = description
 
     @property
@@ -147,7 +160,7 @@ def notes(self):
 
     @notes.setter
     def notes(self, value):
-        self._error_on_new_warn_on_construct(
+        self._error_on_new_pass_on_construct(
                     error_msg='Use of ScratchData.notes has been deprecated and will be removed in PyNWB 4.0. Use ScratchData.description instead.')
         self.description = value
 

src/pynwb/ecephys.py

@@ -227,7 +227,7 @@ class Clustering(NWBDataInterface):
              'shape': (None,)},
             {'name': 'name', 'type': str, 'doc': 'the name of this container', 'default': 'Clustering'})
     def __init__(self, **kwargs):
-        self._error_on_new_warn_on_construct(
+        self._error_on_new_pass_on_construct(
             error_msg='The Clustering neurodata type is deprecated. Use pynwb.misc.Units or NWBFile.units instead'
         )
         args_to_set = popargs_to_dict(('description', 'num', 'peak_over_rms', 'times'), kwargs)
@@ -263,7 +263,7 @@ class ClusterWaveforms(NWBDataInterface):
              'doc': 'the standard deviations of waveforms for each cluster'},
             {'name': 'name', 'type': str, 'doc': 'the name of this container', 'default': 'ClusterWaveforms'})
     def __init__(self, **kwargs):
-        self._error_on_new_warn_on_construct(
+        self._error_on_new_pass_on_construct(
             error_msg='The ClusterWaveforms neurodata type is deprecated. Use pynwb.misc.Units or NWBFile.units instead'
         )
         args_to_set = popargs_to_dict(('clustering_interface', 'waveform_filtering',

src/pynwb/file.py

@@ -492,14 +492,14 @@ def __init__(self, **kwargs):
         icephys_electrodes = args_to_set['icephys_electrodes']
         ic_electrodes = args_to_set['ic_electrodes']
         if icephys_electrodes is None and ic_electrodes is not None:
-            self._error_on_new_warn_on_construct(error_msg=("Use of the ic_electrodes parameter is deprecated. "
+            self._error_on_new_pass_on_construct(error_msg=("Use of the ic_electrodes parameter is deprecated. "
                                                             "Use the icephys_electrodes parameter instead"))
             args_to_set['icephys_electrodes'] = ic_electrodes
         args_to_set.pop('ic_electrodes')  # do not set this arg
 
         # backwards-compatibility for sweep table
         if args_to_set['sweep_table'] is not None:
-            self._error_on_new_warn_on_construct(error_msg=("SweepTable is deprecated. Use the "
+            self._error_on_new_pass_on_construct(error_msg=("SweepTable is deprecated. Use the "
                                                             "IntracellularRecordingsTable instead. See also the "
                                                             "NWBFile.add_intracellular_recordings function."))
 
@@ -783,8 +783,10 @@ def _check_sweep_table(self):
         """
         if self.sweep_table is None:
             if self._in_construct_mode:
+                # Construct the SweepTable without triggering errors in construct mode because SweepTable has been deprecated
                 sweep_table = SweepTable.__new__(SweepTable, parent=self, in_construct_mode=True)
                 sweep_table.__init__(name='sweep_table')
+                sweep_table._in_construct_mode = False
             else:
                 sweep_table = SweepTable(name='sweep_table')
             self.sweep_table = sweep_table

src/pynwb/icephys.py

@@ -342,7 +342,6 @@ def __init__(self, **kwargs):
                    'See also the NWBFile.add_intracellular_recordings function.')
         if not self._in_construct_mode:
             raise ValueError(error_msg)
-        warnings.warn(error_msg)
 
         super().__init__(**kwargs)
 

src/pynwb/image.py

@@ -96,7 +96,8 @@ def __init__(self, **kwargs):
         if self._change_external_file_format():
             self._error_on_new_warn_on_construct(error_msg=f"{self.__class__.__name__} '{self.name}': "
                                                 "The value for 'format' has been changed to 'external'. "
-                                                "Setting a default value for 'format' is deprecated.")
+                                                "If an external file is detected, setting a value for "
+                                                "'format' other than 'external' is deprecated.")
 
         if not self._check_image_series_dimension():
             warnings.warn(
@@ -194,7 +195,7 @@ def bits_per_pixel(self):
     @bits_per_pixel.setter
     def bits_per_pixel(self, val):
         if val is not None:
-            self._error_on_new_warn_on_construct(error_msg="bits_per_pixel is deprecated")
+            self._error_on_new_pass_on_construct(error_msg="bits_per_pixel is deprecated")
             self.fields['bits_per_pixel'] = val
 
 
@@ -251,13 +252,13 @@ class IndexSeries(TimeSeries):
     def __init__(self, **kwargs):
         indexed_timeseries, indexed_images = popargs('indexed_timeseries', 'indexed_images', kwargs)
         if kwargs['unit'] and kwargs['unit'] != 'N/A':
-            self._error_on_new_warn_on_construct(error_msg=("The 'unit' field of IndexSeries is "
+            self._error_on_new_pass_on_construct(error_msg=("The 'unit' field of IndexSeries is "
                                                             "fixed to the value 'N/A'."))
         if not indexed_timeseries and not indexed_images:
             msg = "Either indexed_timeseries or indexed_images must be provided when creating an IndexSeries."
             raise ValueError(msg)
         if indexed_timeseries:
-            self._error_on_new_warn_on_construct("The indexed_timeseries field of IndexSeries is deprecated. "
+            self._error_on_new_pass_on_construct("The indexed_timeseries field of IndexSeries is deprecated. "
                                                  "Use the indexed_images field instead.")
         kwargs['unit'] = 'N/A'  # fixed value starting in NWB 2.5
         super().__init__(**kwargs)

src/pynwb/ophys.py

@@ -114,13 +114,13 @@ def __init__(self, **kwargs):
             args_to_set['optical_channel'] = [args_to_set['optical_channel']]
         if args_to_set['manifold'] is not None:
             error_msg = "The 'manifold' argument is deprecated in favor of 'origin_coords' and 'grid_spacing'."
-            self._error_on_new_warn_on_construct(error_msg=error_msg)
+            self._error_on_new_pass_on_construct(error_msg=error_msg)
         if args_to_set['conversion'] != 1.0:
             error_msg = "The 'conversion' argument is deprecated in favor of 'origin_coords' and 'grid_spacing'."
-            self._error_on_new_warn_on_construct(error_msg=error_msg)
+            self._error_on_new_pass_on_construct(error_msg=error_msg)
         if args_to_set['unit'] != 'meters':
             error_msg = "The 'unit' argument is deprecated in favor of 'origin_coords_unit' and 'grid_spacing_unit'."
-            self._error_on_new_warn_on_construct(error_msg=error_msg)
+            self._error_on_new_pass_on_construct(error_msg=error_msg)
         for key, val in args_to_set.items():
             setattr(self, key, val)