i'm just sorta making a mess here. coming back tomorrow

README.md

@@ -4,3 +4,5 @@ Translating NWB schema language to linkml
 (very WIP dont @ me)
 
 Just submitting to pypi to squat the package name
+
+[![Coverage Status](https://coveralls.io/repos/github/p2p-ld/nwb-linkml/badge.svg)](https://coveralls.io/github/p2p-ld/nwb-linkml)

nwb_linkml/poetry.lock

@@ -2336,11 +2336,10 @@ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.link
 testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [extras]
-dev = ["nwb_schema_language"]
 plot = ["dash", "dash-cytoscape"]
 tests = ["coverage", "coveralls", "pytest", "pytest-cov", "pytest-depends", "pytest-emoji", "pytest-md"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "b04ae68224e5d20ec7f929e29d318f02fcc14fc8ca486cddf567985b45fe5951"
+content-hash = "5427416a9edebc2ab2c4f7f7c9779b2b9c7e4c1c2da5dcc0968ee633110973fa"

nwb_linkml/src/nwb_linkml/io/hdf5.py

@@ -1,13 +1,96 @@
 """
 This is a sandbox file that should be split out to its own pydantic-hdf5 package, but just experimenting here to get our bearings
 """
-from typing import Optional, List, Dict
+from typing import Optional, List, Dict, overload, Literal, Type, Any
 from pathlib import Path
 from types import ModuleType
+from typing import TypeVar, TYPE_CHECKING
+from abc import abstractmethod
 
 import h5py
+from pydantic import BaseModel
+from dataclasses import dataclass, field
 
 from nwb_linkml.translate import generate_from_nwbfile
+#from nwb_linkml.models.core_nwb_file import NWBFile
+if TYPE_CHECKING:
+    from nwb_linkml.models.core_nwb_file import NWBFile
+
+@dataclass
+class HDF5Element():
+
+    cls: h5py.Dataset | h5py.Group
+    models: Dict[str, ModuleType]
+    parent: Type[BaseModel]
+
+    @abstractmethod
+    def read(self) -> BaseModel | List[BaseModel]:
+        """
+        Constructs the pydantic model from the given hdf5 element
+        """
+
+    @abstractmethod
+    def write(self) -> h5py.Dataset | h5py.Group:
+        """
+        Create the h5py object from the in-memory pydantic model
+        """
+
+    @property
+    def name(self) -> str:
+        """Just the terminal group name"""
+        return self.cls.name.split('/')[-1]
+
+    def get_model(self) -> Type[BaseModel | dict]:
+        """
+        Find our model
+        - If we have a neurodata_type in our attrs, use that
+        - Otherwise, use our parent to resolve the type
+        """
+        if 'neurodata_type' in self.cls.attrs.keys():
+            return get_model(self.cls.attrs, self.models)
+        else:
+            parent_model  = get_model(self.cls.parent.attrs, self.models)
+            field = parent_model.model_fields.get(self.name)
+            if issubclass(type(field.annotation), BaseModel):
+                return field.annotation
+            else:
+                return dict
+                #raise NotImplementedError('Need to unpack at least listlike annotations')
+
+@dataclass
+class H5Dataset(HDF5Element):
+    cls: h5py.Dataset
+
+    def read(self) -> Any:
+        if self.cls.shape == ():
+            return self.cls[()]
+        elif len(self.cls.shape) == 1:
+            return self.cls[:].tolist()
+        else:
+            raise NotImplementedError('oop')
+
+@dataclass
+class H5Group(HDF5Element):
+    cls: h5py.Group
+
+    def read(self) -> BaseModel:
+        data = {}
+        model = self.get_model()
+
+        model_attrs = {
+            k:v for k, v in self.cls.attrs.items() if k in model.model_fields.keys()
+        }
+        data.update(model_attrs)
+
+        for k, v in self.cls.items():
+            if isinstance(v, h5py.Group):
+                data[k] = H5Group(cls=v, models=self.models, parent=model).read()
+            elif isinstance(v, h5py.Dataset):
+                data[k] = H5Dataset(cls=v, models=self.models, parent=model).read()
+
+
+        return model(**data)
+
 
 class HDF5IO():
 
@@ -21,6 +104,38 @@ class HDF5IO():
             self._modules = generate_from_nwbfile(self.path)
         return self._modules
 
+    @overload
+    def read(self, path:None) -> 'NWBFile': ...
+
+    @overload
+    def read(self, path:str) -> BaseModel | Dict[str, BaseModel]: ...
+
+    def read(self, path:Optional[str] = None):
+        h5f = h5py.File(str(self.path))
+
+        if path:
+            src = h5f.get(path)
+            parent = get_model(src.attrs, self.modules)
+        else:
+            src = h5f
+            parent = getattr(self.modules['core'], 'NWBFile')
+
+        data = {}
+        for k, v in src.items():
+            if isinstance(v, h5py.Group):
+                data[k] = H5Group(cls=v, models=self.modules, parent=parent).read()
+            elif isinstance(v, h5py.Dataset):
+                data[k] = H5Dataset(cls=v, models=self.modules, parent=parent).read()
+
+        if path is None:
+            return parent(**data)
+        if 'neurodata_type' in src.attrs:
+            raise NotImplementedError('Making a submodel not supported yet')
+        else:
+            return data
+
+
+
     def process_group(self, group:h5py.Group|h5py.File) -> dict | list:
         attrs = dict(group.attrs)
 
@@ -53,9 +168,13 @@ class HDF5IO():
         if len(data.shape) == 1:
             return list(data[:])
 
+def get_model(attrs: h5py.AttributeManager, models: Dict[str, ModuleType]) -> Type[BaseModel]:
+    ns = attrs.get('namespace')
+    model_name = attrs.get('neurodata_type')
+    return getattr(models[ns], model_name)
 
-if __name__ == "__main__":
-    NWBFILE = Path('/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb')
-    h5f = HDF5IO(NWBFILE)
+# if __name__ == "__main__":
+#     NWBFILE = Path('/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb')
+#     h5f = HDF5IO(NWBFILE)
 
 

nwb_linkml/src/nwb_linkml/models/core_nwb_base.py

@@ -172,17 +172,17 @@ class ImagesOrderOfImages(ImageReferences):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-NWBData.model_rebuild()
-TimeSeriesReferenceVectorData.model_rebuild()
-Image.model_rebuild()
-ImageReferences.model_rebuild()
-NWBContainer.model_rebuild()
-NWBDataInterface.model_rebuild()
-TimeSeries.model_rebuild()
-TimeSeriesData.model_rebuild()
-TimeSeriesStartingTime.model_rebuild()
-TimeSeriesSync.model_rebuild()
-ProcessingModule.model_rebuild()
-Images.model_rebuild()
-ImagesOrderOfImages.model_rebuild()
+# NWBData.model_rebuild()
+# TimeSeriesReferenceVectorData.model_rebuild()
+# Image.model_rebuild()
+# ImageReferences.model_rebuild()
+# NWBContainer.model_rebuild()
+# NWBDataInterface.model_rebuild()
+# TimeSeries.model_rebuild()
+# TimeSeriesData.model_rebuild()
+# TimeSeriesStartingTime.model_rebuild()
+# TimeSeriesSync.model_rebuild()
+# ProcessingModule.model_rebuild()
+# Images.model_rebuild()
+# ImagesOrderOfImages.model_rebuild()
     

nwb_linkml/src/nwb_linkml/models/core_nwb_behavior.py

@@ -124,13 +124,13 @@ class Position(NWBDataInterface):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-SpatialSeries.model_rebuild()
-SpatialSeriesData.model_rebuild()
-BehavioralEpochs.model_rebuild()
-BehavioralEvents.model_rebuild()
-BehavioralTimeSeries.model_rebuild()
-PupilTracking.model_rebuild()
-EyeTracking.model_rebuild()
-CompassDirection.model_rebuild()
-Position.model_rebuild()
+# SpatialSeries.model_rebuild()
+# SpatialSeriesData.model_rebuild()
+# BehavioralEpochs.model_rebuild()
+# BehavioralEvents.model_rebuild()
+# BehavioralTimeSeries.model_rebuild()
+# PupilTracking.model_rebuild()
+# EyeTracking.model_rebuild()
+# CompassDirection.model_rebuild()
+# Position.model_rebuild()
     

nwb_linkml/src/nwb_linkml/models/core_nwb_device.py

@@ -40,5 +40,5 @@ class Device(NWBContainer):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-Device.model_rebuild()
+# Device.model_rebuild()
     

nwb_linkml/src/nwb_linkml/models/core_nwb_ecephys.py

@@ -231,21 +231,21 @@ class Clustering(NWBDataInterface):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-ElectricalSeries.model_rebuild()
-ElectricalSeriesData.model_rebuild()
-ElectricalSeriesElectrodes.model_rebuild()
-SpikeEventSeries.model_rebuild()
-SpikeEventSeriesData.model_rebuild()
-FeatureExtraction.model_rebuild()
-FeatureExtractionFeatures.model_rebuild()
-FeatureExtractionElectrodes.model_rebuild()
-EventDetection.model_rebuild()
-EventWaveform.model_rebuild()
-FilteredEphys.model_rebuild()
-LFP.model_rebuild()
-ElectrodeGroup.model_rebuild()
-ClusterWaveforms.model_rebuild()
-ClusterWaveformsWaveformMean.model_rebuild()
-ClusterWaveformsWaveformSd.model_rebuild()
-Clustering.model_rebuild()
+# ElectricalSeries.model_rebuild()
+# ElectricalSeriesData.model_rebuild()
+# ElectricalSeriesElectrodes.model_rebuild()
+# SpikeEventSeries.model_rebuild()
+# SpikeEventSeriesData.model_rebuild()
+# FeatureExtraction.model_rebuild()
+# FeatureExtractionFeatures.model_rebuild()
+# FeatureExtractionElectrodes.model_rebuild()
+# EventDetection.model_rebuild()
+# EventWaveform.model_rebuild()
+# FilteredEphys.model_rebuild()
+# LFP.model_rebuild()
+# ElectrodeGroup.model_rebuild()
+# ClusterWaveforms.model_rebuild()
+# ClusterWaveformsWaveformMean.model_rebuild()
+# ClusterWaveformsWaveformSd.model_rebuild()
+# Clustering.model_rebuild()
     

nwb_linkml/src/nwb_linkml/models/core_nwb_epoch.py

@@ -98,8 +98,8 @@ class TimeIntervalsTimeseriesIndex(VectorIndex):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-TimeIntervals.model_rebuild()
-TimeIntervalsTagsIndex.model_rebuild()
-TimeIntervalsTimeseries.model_rebuild()
-TimeIntervalsTimeseriesIndex.model_rebuild()
+# TimeIntervals.model_rebuild()
+# TimeIntervalsTagsIndex.model_rebuild()
+# TimeIntervalsTimeseries.model_rebuild()
+# TimeIntervalsTimeseriesIndex.model_rebuild()
     

nwb_linkml/src/nwb_linkml/models/core_nwb_file.py

@@ -218,15 +218,15 @@ class SubjectAge(ConfiguredBaseModel):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-ScratchData.model_rebuild()
-NWBFile.model_rebuild()
-NWBFileStimulus.model_rebuild()
-NWBFileGeneral.model_rebuild()
-NWBFileGeneralSourceScript.model_rebuild()
-NWBFileGeneralExtracellularEphys.model_rebuild()
-NWBFileGeneralIntracellularEphys.model_rebuild()
-NWBFileIntervals.model_rebuild()
-LabMetaData.model_rebuild()
-Subject.model_rebuild()
-SubjectAge.model_rebuild()
+# ScratchData.model_rebuild()
+# NWBFile.model_rebuild()
+# NWBFileStimulus.model_rebuild()
+# NWBFileGeneral.model_rebuild()
+# NWBFileGeneralSourceScript.model_rebuild()
+# NWBFileGeneralExtracellularEphys.model_rebuild()
+# NWBFileGeneralIntracellularEphys.model_rebuild()
+# NWBFileIntervals.model_rebuild()
+# LabMetaData.model_rebuild()
+# Subject.model_rebuild()
+# SubjectAge.model_rebuild()
     

nwb_linkml/src/nwb_linkml/models/core_nwb_icephys.py

@@ -560,42 +560,42 @@ class ExperimentalConditionsTableRepetitionsIndex(VectorIndex):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-PatchClampSeries.model_rebuild()
-CurrentClampSeries.model_rebuild()
-CurrentClampSeriesData.model_rebuild()
-IZeroClampSeries.model_rebuild()
-CurrentClampStimulusSeries.model_rebuild()
-CurrentClampStimulusSeriesData.model_rebuild()
-VoltageClampSeries.model_rebuild()
-VoltageClampSeriesData.model_rebuild()
-VoltageClampSeriesCapacitanceFast.model_rebuild()
-VoltageClampSeriesCapacitanceSlow.model_rebuild()
-VoltageClampSeriesResistanceCompBandwidth.model_rebuild()
-VoltageClampSeriesResistanceCompCorrection.model_rebuild()
-VoltageClampSeriesResistanceCompPrediction.model_rebuild()
-VoltageClampSeriesWholeCellCapacitanceComp.model_rebuild()
-VoltageClampSeriesWholeCellSeriesResistanceComp.model_rebuild()
-VoltageClampStimulusSeries.model_rebuild()
-VoltageClampStimulusSeriesData.model_rebuild()
-IntracellularElectrode.model_rebuild()
-SweepTable.model_rebuild()
-SweepTableSeriesIndex.model_rebuild()
-IntracellularElectrodesTable.model_rebuild()
-IntracellularStimuliTable.model_rebuild()
-IntracellularStimuliTableStimulus.model_rebuild()
-IntracellularResponsesTable.model_rebuild()
-IntracellularResponsesTableResponse.model_rebuild()
-IntracellularRecordingsTable.model_rebuild()
-SimultaneousRecordingsTable.model_rebuild()
-SimultaneousRecordingsTableRecordings.model_rebuild()
-SimultaneousRecordingsTableRecordingsIndex.model_rebuild()
-SequentialRecordingsTable.model_rebuild()
-SequentialRecordingsTableSimultaneousRecordings.model_rebuild()
-SequentialRecordingsTableSimultaneousRecordingsIndex.model_rebuild()
-RepetitionsTable.model_rebuild()
-RepetitionsTableSequentialRecordings.model_rebuild()
-RepetitionsTableSequentialRecordingsIndex.model_rebuild()
-ExperimentalConditionsTable.model_rebuild()
-ExperimentalConditionsTableRepetitions.model_rebuild()
-ExperimentalConditionsTableRepetitionsIndex.model_rebuild()
-    
+# PatchClampSeries.model_rebuild()
+# CurrentClampSeries.model_rebuild()
+# CurrentClampSeriesData.model_rebuild()
+# IZeroClampSeries.model_rebuild()
+# CurrentClampStimulusSeries.model_rebuild()
+# CurrentClampStimulusSeriesData.model_rebuild()
+# VoltageClampSeries.model_rebuild()
+# VoltageClampSeriesData.model_rebuild()
+# VoltageClampSeriesCapacitanceFast.model_rebuild()
+# VoltageClampSeriesCapacitanceSlow.model_rebuild()
+# VoltageClampSeriesResistanceCompBandwidth.model_rebuild()
+# VoltageClampSeriesResistanceCompCorrection.model_rebuild()
+# VoltageClampSeriesResistanceCompPrediction.model_rebuild()
+# VoltageClampSeriesWholeCellCapacitanceComp.model_rebuild()
+# VoltageClampSeriesWholeCellSeriesResistanceComp.model_rebuild()
+# VoltageClampStimulusSeries.model_rebuild()
+# VoltageClampStimulusSeriesData.model_rebuild()
+# IntracellularElectrode.model_rebuild()
+# SweepTable.model_rebuild()
+# SweepTableSeriesIndex.model_rebuild()
+# IntracellularElectrodesTable.model_rebuild()
+# IntracellularStimuliTable.model_rebuild()
+# IntracellularStimuliTableStimulus.model_rebuild()
+# IntracellularResponsesTable.model_rebuild()
+# IntracellularResponsesTableResponse.model_rebuild()
+# IntracellularRecordingsTable.model_rebuild()
+# SimultaneousRecordingsTable.model_rebuild()
+# SimultaneousRecordingsTableRecordings.model_rebuild()
+# SimultaneousRecordingsTableRecordingsIndex.model_rebuild()
+# SequentialRecordingsTable.model_rebuild()
+# SequentialRecordingsTableSimultaneousRecordings.model_rebuild()
+# SequentialRecordingsTableSimultaneousRecordingsIndex.model_rebuild()
+# RepetitionsTable.model_rebuild()
+# RepetitionsTableSequentialRecordings.model_rebuild()
+# RepetitionsTableSequentialRecordingsIndex.model_rebuild()
+# ExperimentalConditionsTable.model_rebuild()
+# ExperimentalConditionsTableRepetitions.model_rebuild()
+# ExperimentalConditionsTableRepetitionsIndex.model_rebuild()
+#

nwb_linkml/src/nwb_linkml/models/core_nwb_image.py

@@ -169,14 +169,14 @@ class IndexSeries(TimeSeries):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-GrayscaleImage.model_rebuild()
-RGBImage.model_rebuild()
-RGBAImage.model_rebuild()
-ImageSeries.model_rebuild()
-ImageSeriesData.model_rebuild()
-ImageMaskSeries.model_rebuild()
-OpticalSeries.model_rebuild()
-OpticalSeriesFieldOfView.model_rebuild()
-OpticalSeriesData.model_rebuild()
-IndexSeries.model_rebuild()
+# GrayscaleImage.model_rebuild()
+# RGBImage.model_rebuild()
+# RGBAImage.model_rebuild()
+# ImageSeries.model_rebuild()
+# ImageSeriesData.model_rebuild()
+# ImageMaskSeries.model_rebuild()
+# OpticalSeries.model_rebuild()
+# OpticalSeriesFieldOfView.model_rebuild()
+# OpticalSeriesData.model_rebuild()
+# IndexSeries.model_rebuild()
     

nwb_linkml/src/nwb_linkml/models/core_nwb_misc.py

@@ -335,23 +335,23 @@ class UnitsWaveformsIndexIndex(VectorIndex):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-AbstractFeatureSeries.model_rebuild()
-AbstractFeatureSeriesData.model_rebuild()
-AnnotationSeries.model_rebuild()
-IntervalSeries.model_rebuild()
-DecompositionSeries.model_rebuild()
-DecompositionSeriesData.model_rebuild()
-DecompositionSeriesSourceChannels.model_rebuild()
-Units.model_rebuild()
-UnitsSpikeTimesIndex.model_rebuild()
-UnitsSpikeTimes.model_rebuild()
-UnitsObsIntervalsIndex.model_rebuild()
-UnitsObsIntervals.model_rebuild()
-UnitsElectrodesIndex.model_rebuild()
-UnitsElectrodes.model_rebuild()
-UnitsWaveformMean.model_rebuild()
-UnitsWaveformSd.model_rebuild()
-UnitsWaveforms.model_rebuild()
-UnitsWaveformsIndex.model_rebuild()
-UnitsWaveformsIndexIndex.model_rebuild()
+# AbstractFeatureSeries.model_rebuild()
+# AbstractFeatureSeriesData.model_rebuild()
+# AnnotationSeries.model_rebuild()
+# IntervalSeries.model_rebuild()
+# DecompositionSeries.model_rebuild()
+# DecompositionSeriesData.model_rebuild()
+# DecompositionSeriesSourceChannels.model_rebuild()
+# Units.model_rebuild()
+# UnitsSpikeTimesIndex.model_rebuild()
+# UnitsSpikeTimes.model_rebuild()
+# UnitsObsIntervalsIndex.model_rebuild()
+# UnitsObsIntervals.model_rebuild()
+# UnitsElectrodesIndex.model_rebuild()
+# UnitsElectrodes.model_rebuild()
+# UnitsWaveformMean.model_rebuild()
+# UnitsWaveformSd.model_rebuild()
+# UnitsWaveforms.model_rebuild()
+# UnitsWaveformsIndex.model_rebuild()
+# UnitsWaveformsIndexIndex.model_rebuild()
     

nwb_linkml/src/nwb_linkml/models/core_nwb_ogen.py

@@ -59,6 +59,6 @@ class OptogeneticStimulusSite(NWBContainer):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-OptogeneticSeries.model_rebuild()
-OptogeneticStimulusSite.model_rebuild()
+# OptogeneticSeries.model_rebuild()
+# OptogeneticStimulusSite.model_rebuild()
     

nwb_linkml/src/nwb_linkml/models/core_nwb_ophys.py

@@ -310,24 +310,24 @@ class CorrectedImageStack(NWBDataInterface):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-OnePhotonSeries.model_rebuild()
-TwoPhotonSeries.model_rebuild()
-TwoPhotonSeriesFieldOfView.model_rebuild()
-RoiResponseSeries.model_rebuild()
-RoiResponseSeriesData.model_rebuild()
-RoiResponseSeriesRois.model_rebuild()
-DfOverF.model_rebuild()
-Fluorescence.model_rebuild()
-ImageSegmentation.model_rebuild()
-PlaneSegmentation.model_rebuild()
-PlaneSegmentationImageMask.model_rebuild()
-PlaneSegmentationPixelMaskIndex.model_rebuild()
-PlaneSegmentationVoxelMaskIndex.model_rebuild()
-ImagingPlane.model_rebuild()
-ImagingPlaneManifold.model_rebuild()
-ImagingPlaneOriginCoords.model_rebuild()
-ImagingPlaneGridSpacing.model_rebuild()
-OpticalChannel.model_rebuild()
-MotionCorrection.model_rebuild()
-CorrectedImageStack.model_rebuild()
-    
+# OnePhotonSeries.model_rebuild()
+# TwoPhotonSeries.model_rebuild()
+# TwoPhotonSeriesFieldOfView.model_rebuild()
+# RoiResponseSeries.model_rebuild()
+# RoiResponseSeriesData.model_rebuild()
+# RoiResponseSeriesRois.model_rebuild()
+# DfOverF.model_rebuild()
+# Fluorescence.model_rebuild()
+# ImageSegmentation.model_rebuild()
+# PlaneSegmentation.model_rebuild()
+# PlaneSegmentationImageMask.model_rebuild()
+# PlaneSegmentationPixelMaskIndex.model_rebuild()
+# PlaneSegmentationVoxelMaskIndex.model_rebuild()
+# ImagingPlane.model_rebuild()
+# ImagingPlaneManifold.model_rebuild()
+# ImagingPlaneOriginCoords.model_rebuild()
+# ImagingPlaneGridSpacing.model_rebuild()
+# OpticalChannel.model_rebuild()
+# MotionCorrection.model_rebuild()
+# CorrectedImageStack.model_rebuild()
+#

nwb_linkml/src/nwb_linkml/models/core_nwb_retinotopy.py

@@ -125,12 +125,12 @@ class ImagingRetinotopyVasculatureImage(ConfiguredBaseModel):
 
 # Model rebuild
 # see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
-ImagingRetinotopy.model_rebuild()
-ImagingRetinotopyAxis1PhaseMap.model_rebuild()
-ImagingRetinotopyAxis1PowerMap.model_rebuild()
-ImagingRetinotopyAxis2PhaseMap.model_rebuild()
-ImagingRetinotopyAxis2PowerMap.model_rebuild()
-ImagingRetinotopyFocalDepthImage.model_rebuild()
-ImagingRetinotopySignMap.model_rebuild()
-ImagingRetinotopyVasculatureImage.model_rebuild()
+# ImagingRetinotopy.model_rebuild()
+# ImagingRetinotopyAxis1PhaseMap.model_rebuild()
+# ImagingRetinotopyAxis1PowerMap.model_rebuild()
+# ImagingRetinotopyAxis2PhaseMap.model_rebuild()
+# ImagingRetinotopyAxis2PowerMap.model_rebuild()
+# ImagingRetinotopyFocalDepthImage.model_rebuild()
+# ImagingRetinotopySignMap.model_rebuild()
+# ImagingRetinotopyVasculatureImage.model_rebuild()
     

nwb_linkml/src/nwb_linkml/translate.py

@@ -16,6 +16,7 @@ from nwb_linkml.io.schema import load_schema_file
 from nwb_linkml.generators.pydantic import NWBPydanticGenerator
 from nwb_linkml.map import apply_preload
 from nwb_linkml.adapters import SchemaAdapter, NamespacesAdapter
+#from nwb_linkml.models import core, hdmf_common
 
 def make_namespace_adapter(schema: dict) -> NamespacesAdapter:
     """
@@ -118,6 +119,8 @@ def generate_from_nwbfile(path:Path) -> Dict[str, ModuleType]:
     namespaces = []
     h5f = h5py.File(path, 'r')
     for ns_name, ns in h5f['specifications'].items():
+        #if ns_name in ('core', 'hdmf-common'):
+        #    continue
         ns_schema = {}
         for version in ns.values():
             for schema_name, schema in version.items():
@@ -133,6 +136,7 @@ def generate_from_nwbfile(path:Path) -> Dict[str, ModuleType]:
         adapter.namespaces.namespaces[0].name: generate_pydantic(adapter)
         for adapter in adapters
     }
+    #pydantic_modules.update({'core': core, 'hdmf-common': hdmf_common})
     return pydantic_modules
 
 

nwb_linkml/tests/test_io/test_io_hdf5.py

@@ -0,0 +1,10 @@
+import pytest
+from pathlib import Path
+
+from nwb_linkml.io.hdf5 import HDF5IO
+
+def test_hdf_read():
+    NWBFILE = Path('/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb')
+
+    io = HDF5IO(path=NWBFILE)
+    model = io.read('/general')