initial structure for sqlmodel

nwb_linkml/adapters/namespaces.py

@@ -51,7 +51,10 @@ class NamespacesAdapter(Adapter):
                 id = ns.name,
                 description = ns.doc,
                 version = ns.version,
-                imports=[sch.name for sch in ns_schemas]
+                imports=[sch.name for sch in ns_schemas],
+                default_prefix=ns.name,
+                prefixes={ns.name: f'https://example.com/{ns.name}/'},
+
             )
             sch_result.schemas.append(ns_schema)
 

nwb_linkml/adapters/schema.py

@@ -87,6 +87,8 @@ class SchemaAdapter(Adapter):
             sch = SchemaDefinition(
                 name = self.name,
                 id = self.name,
+                default_prefix=self.name,
+                prefixes={self.name:f'https://example.com/{self.name}/'},
                 imports = [i.name for i in self.imports],
                 classes=res.classes,
                 slots=res.slots,
@@ -128,7 +130,10 @@ class SchemaAdapter(Adapter):
             imports=main_imports,
             classes=main_classes,
             slots=classes.slots,
-            types=classes.types
+            types=classes.types,
+            default_prefix=self.name,
+            prefixes={self.name: f'https://example.com/{self.name}/'},
+
         )
 
         split_sch = SchemaDefinition(
@@ -137,7 +142,10 @@ class SchemaAdapter(Adapter):
             imports=imports,
             classes=split_classes,
             slots=classes.slots,
-            types=classes.types
+            types=classes.types,
+            default_prefix=self.name,
+            prefixes={self.name: f'https://example.com/{self.name}/'},
+
         )
         if len(split_classes) > 0:
             res = BuildResult(

nwb_linkml/generators/pydantic.py

@@ -17,7 +17,7 @@ The `serialize` method
 
 """
 import pdb
-from typing import List, Dict, Set
+from typing import List, Dict, Set, Optional
 from copy import deepcopy
 import warnings
 
@@ -384,7 +384,7 @@ class NWBPydanticGenerator(PydanticGenerator):
                 parents[camelcase(class_def.name)] = class_parents
         return parents
 
-    def serialize(self) -> str:
+    def serialize(self, schemaview:Optional[SchemaView]=None) -> str:
         if self.template_file is not None:
             with open(self.template_file) as template_file:
                 template_obj = Template(template_file.read())
@@ -392,7 +392,10 @@ class NWBPydanticGenerator(PydanticGenerator):
             template_obj = Template(default_template(self.pydantic_version))
 
         sv: SchemaView
-        sv = self.schemaview
+        if schemaview:
+            sv = schemaview
+        else:
+            sv = self.schemaview
         schema = sv.schema
         pyschema = SchemaDefinition(
             id=schema.id,

nwb_linkml/generators/sqlmodel.py

@@ -0,0 +1,207 @@
+import pdb
+from collections import defaultdict
+
+from linkml.generators.sqltablegen import SQLTableGenerator
+from linkml.transformers.relmodel_transformer import ForeignKeyPolicy, RelationalModelTransformer
+from linkml.utils.generator import Generator, shared_arguments
+from linkml_runtime.utils.schemaview import SchemaView
+from linkml_runtime.linkml_model import (
+    Annotation,
+    ClassDefinition,
+    ClassDefinitionName,
+    SchemaDefinition,
+)
+
+from nwb_linkml.generators.pydantic import NWBPydanticGenerator
+
+def default_template(pydantic_ver: str = "2") -> str:
+    """Constructs a default template for pydantic classes based on the version of pydantic"""
+    ### HEADER ###
+    template = """
+{#-
+
+  Jinja2 Template for a pydantic classes
+-#}
+from __future__ import annotations
+from datetime import datetime, date
+from enum import Enum
+from typing import List, Dict, Optional, Any, Union
+from sqlmodel import SQLModel, Field
+from nptyping import NDArray, Shape, Float, Float32, Double, Float64, LongLong, Int64, Int, Int32, Int16, Short, Int8, UInt, UInt32, UInt16, UInt8, UInt64, Number, String, Unicode, Unicode, Unicode, String, Bool, Datetime64
+import sys
+if sys.version_info >= (3, 8):
+    from typing import Literal
+else:
+    from typing_extensions import Literal
+
+{% for import_module, import_classes in imports.items() %}
+from {{ import_module }} import (
+    {{ import_classes | join(',\n    ') }}
+)
+{% endfor %}
+
+metamodel_version = "{{metamodel_version}}"
+version = "{{version if version else None}}"
+"""
+    ### BASE MODEL ###
+    if pydantic_ver == "1":
+        template += """
+class WeakRefShimBaseModel(BaseModel):
+   __slots__ = '__weakref__'
+
+class ConfiguredBaseModel(WeakRefShimBaseModel,
+                validate_assignment = True,
+                validate_all = True,
+                underscore_attrs_are_private = True,
+                extra = {% if allow_extra %}'allow'{% else %}'forbid'{% endif %},
+                arbitrary_types_allowed = True,
+                use_enum_values = True):
+    pass
+"""
+    else:
+        template += """
+class ConfiguredBaseModel(BaseModel,
+                validate_assignment = True,
+                validate_default = True,
+                extra = {% if allow_extra %}'allow'{% else %}'forbid'{% endif %},
+                arbitrary_types_allowed = True,
+                use_enum_values = True):
+    pass
+"""
+    ### ENUMS ###
+    template += """
+{% for e in enums.values() %}
+class {{ e.name }}(str, Enum):
+    {% if e.description -%}
+    \"\"\"
+    {{ e.description }}
+    \"\"\"
+    {%- endif %}
+    {% for _, pv in e['values'].items() -%}
+    {% if pv.description -%}
+    # {{pv.description}}
+    {%- endif %}
+    {{pv.label}} = "{{pv.value}}"
+    {% endfor %}
+    {% if not e['values'] -%}
+    dummy = "dummy"
+    {% endif %}
+{% endfor %}
+"""
+    ### CLASSES ###
+    template += """
+{%- for c in schema.classes.values() %}
+class {{ c.name }}
+    {%- if class_isa_plus_mixins[c.name] -%}
+        ({{class_isa_plus_mixins[c.name]|join(', ')}}, table=True)
+    {%- else -%}
+        (ConfiguredBaseModel, table=True)
+    {%- endif -%}
+                  :
+    {% if c.description -%}
+    \"\"\"
+    {{ c.description }}
+    \"\"\"
+    {%- endif %}
+    {% for attr in c.attributes.values() if c.attributes -%}
+    {{attr.name}}: {{ attr.annotations['python_range'].value }} = Field(
+    {%- if predefined_slot_values[c.name][attr.name] -%}
+        {{ predefined_slot_values[c.name][attr.name] }}
+        {%- if attr.equals_string -%}
+        , const=True
+        {%- endif -%} 
+    {%- elif attr.required -%}
+        ...
+    {%- else -%}
+        None
+    {%- endif -%}
+    {%- if attr.title != None %}, title="{{attr.title}}"{% endif -%}
+    {%- if attr.description %}, description=\"\"\"{{attr.description}}\"\"\"{% endif -%}
+    {%- if attr.minimum_value != None %}, ge={{attr.minimum_value}}{% endif -%}
+    {%- if attr.maximum_value != None %}, le={{attr.maximum_value}}{% endif -%}
+    {%- if 'foreign_key' in s.annotations -%}, foreign_key='{{ s.annotations['foreign_key'].value }}' {%- endif -%}
+    {%- if 'primary_key' in s.annotations -%}, primary_key=True {%- endif -%}
+    )
+    {% else -%}
+    None
+    {% endfor %}
+{% endfor %}
+"""
+    ### FWD REFS / REBUILD MODEL ###
+    if pydantic_ver == "1":
+        template += """
+# Update forward refs
+# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/
+{% for c in schema.classes.values() -%}
+{{ c.name }}.update_forward_refs()
+{% endfor %}
+"""
+    else:
+        template += """
+# Model rebuild
+# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
+{% for c in schema.classes.values() -%}
+{{ c.name }}.model_rebuild()
+{% endfor %}    
+"""
+    return template
+
+
+class SQLModelGenerator(NWBPydanticGenerator):
+    """
+    Generate an SQLModels-compatible model
+    """
+
+    def generate_sqla(
+            self,
+            foreign_key_policy: ForeignKeyPolicy = None,
+            **kwargs
+    ):
+        """
+        Adapted from :meth:`linkml.generators.sqlalchemygen.SQLAlchemyGenerator.generate_sqla`
+
+        Need to add SQL annotations to pydantic before passing to
+        the template, but original classes don't return generated values
+
+        - Accept as arguments:
+            -
+
+        Returns:
+            - mappings=tr_result.mappings
+            - backrefs=backrefs
+            - is_join_table
+
+        """
+        sqltr = RelationalModelTransformer(self.schemaview)
+        tr_result = sqltr.transform(**kwargs)
+        tgen = SQLTableGenerator(self.schemaview.schema)
+        tr_schema = tr_result.schema
+        pdb.set_trace()
+        for c in tr_schema.classes.values():
+            for a in c.attributes.values():
+                sql_range = tgen.get_sql_range(a, tr_schema)
+                sql_type = sql_range.__repr__()
+                ann = Annotation("sql_type", sql_type)
+                a.annotations[ann.tag] = ann
+
+        backrefs = defaultdict(list)
+        for m in tr_result.mappings:
+            backrefs[m.source_class].append(m)
+        tr_sv = SchemaView(tr_schema)
+
+        rel_schema_classes_ordered = [
+            tr_sv.get_class(cn, strict=True) for cn in tr_sv.all_classes()
+        ]
+        for c in rel_schema_classes_ordered:
+            # For SQLA there needs to be a primary key for each class;
+            # autogenerate this as a compound key if none declared
+            has_pk = any(a for a in c.attributes.values() if "primary_key" in a.annotations)
+            if not has_pk:
+                for a in c.attributes.values():
+                    ann = Annotation("primary_key", "true")
+                    a.annotations[ann.tag] = ann
+        return tr_sv, backrefs
+
+
+
+

nwb_linkml/lang_elements.py

@@ -12,7 +12,7 @@ from linkml_runtime.linkml_model import \
     TypeDefinition,\
     Prefix,\
     PermissibleValue
-from nwb_linkml.maps.dtype import flat_to_linkml
+from nwb_linkml.maps.dtype import flat_to_linkml, flat_to_python
 
 
 FlatDType = EnumDefinition(
@@ -57,7 +57,8 @@ for nwbtype, linkmltype in flat_to_linkml.items():
     atype = TypeDefinition(
         name=nwbtype,
         minimum_value=amin,
-        typeof=linkmltype
+        typeof=linkmltype,
+        base=flat_to_python[nwbtype]
     )
     DTypeTypes.append(atype)
 
@@ -89,6 +90,10 @@ NwbLangSchema = SchemaDefinition(
     classes=[Arraylike, AnyType],
     types=DTypeTypes,
     imports=['linkml:types'],
-    prefixes={'linkml': Prefix('linkml','https://w3id.org/linkml')}
+    prefixes={
+        'linkml': Prefix('linkml','https://w3id.org/linkml'),
+        'nwb.language': f'https://example.com/nwb.language/'},
+    default_prefix='nwb.language',
+
 )
 

nwb_linkml/maps/dtype.py

@@ -56,4 +56,31 @@ flat_to_npytyping = {
     "bool": "Bool",
     "isodatetime": "Datetime64",
     'AnyType': 'Any'
+}
+
+flat_to_python = {
+    "float" : "float",
+    "float32" : "float",
+    "double" : "double",
+    "float64" : "double",
+    "long" : "int",
+    "int64" : "int",
+    "int" : "int",
+    "int32" : "int",
+    "int16" : "int",
+    "short" : "int",
+    "int8" : "int",
+    "uint" : "int",
+    "uint32" : "int",
+    "uint16" : "int",
+    "uint8" : "int",
+    "uint64" : "int",
+    "numeric" : "float",
+    "text" : "string",
+    "utf" : "string",
+    "utf8" : "string",
+    "utf_8" : "string",
+    "ascii" : "string",
+    "bool" : "boolean",
+    "isodatetime" : "datetime"
 }

nwb_linkml/models/pydantic/core_nwb_base.py

@@ -11,9 +11,13 @@ else:
     from typing_extensions import Literal
 
 
-from .hdmf_common_table import (
+from .core_nwb_base_include import (
-    DynamicTable,
+    ImageArray,
-    VectorData
+    TimeSeriesStartingTime,
+    ImageReferencesArray,
+    ImagesOrderOfImages,
+    TimeSeriesData,
+    TimeSeriesSync
 )
 
 from .hdmf_common_base import (
@@ -21,13 +25,9 @@ from .hdmf_common_base import (
     Container
 )
 
-from .core_nwb_base_include import (
+from .hdmf_common_table import (
-    TimeSeriesStartingTime,
+    VectorData,
-    ImageArray,
+    DynamicTable
-    ImageReferencesArray,
-    TimeSeriesSync,
-    ImagesOrderOfImages,
-    TimeSeriesData
 )
 
 

nwb_linkml/models/pydantic/core_nwb_behavior.py

@@ -11,6 +11,10 @@ else:
     from typing_extensions import Literal
 
 
+from .core_nwb_misc import (
+    IntervalSeries
+)
+
 from .core_nwb_base import (
     TimeSeries,
     NWBDataInterface
@@ -20,10 +24,6 @@ from .core_nwb_behavior_include import (
     SpatialSeriesData
 )
 
-from .core_nwb_misc import (
-    IntervalSeries
-)
-
 
 metamodel_version = "None"
 version = "None"
@@ -43,13 +43,13 @@ class SpatialSeries(TimeSeries):
     """
     name: str = Field(...)
     data: SpatialSeriesData = Field(..., description="""1-D or 2-D array storing position or direction relative to some reference frame.""")
-    reference_frame: Optional[str] = Field(None, description="""Description defining what exactly 'straight-ahead' means.""")
+    reference_frame: Optional[string] = Field(None, description="""Description defining what exactly 'straight-ahead' means.""")
-    description: Optional[str] = Field(None, description="""Description of the time series.""")
+    description: Optional[string] = Field(None, description="""Description of the time series.""")
-    comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
+    comments: Optional[string] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
     starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""")
-    timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
+    timestamps: Optional[List[double]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
-    control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
+    control: Optional[List[integer]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
-    control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
+    control_description: Optional[List[string]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
     sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""")
     
 

nwb_linkml/models/pydantic/core_nwb_ecephys.py

@@ -11,20 +11,20 @@ else:
     from typing_extensions import Literal
 
 
-from .core_nwb_base import (
+from .core_nwb_ecephys_include import (
-    TimeSeries,
+    FeatureExtractionFeatures,
-    NWBContainer,
+    SpikeEventSeriesData,
-    NWBDataInterface
+    FeatureExtractionElectrodes,
+    ClusterWaveformsWaveformMean,
+    ClusterWaveformsWaveformSd,
+    ElectricalSeriesElectrodes,
+    ElectricalSeriesData
 )
 
-from .core_nwb_ecephys_include import (
+from .core_nwb_base import (
-    FeatureExtractionElectrodes,
+    NWBDataInterface,
-    ClusterWaveformsWaveformSd,
+    NWBContainer,
-    ClusterWaveformsWaveformMean,
+    TimeSeries
-    SpikeEventSeriesData,
-    ElectricalSeriesElectrodes,
-    ElectricalSeriesData,
-    FeatureExtractionFeatures
 )
 
 

nwb_linkml/models/pydantic/core_nwb_ecephys_include.py

@@ -11,14 +11,14 @@ else:
     from typing_extensions import Literal
 
 
-from .hdmf_common_table import (
-    DynamicTableRegion
-)
-
 from .nwb_language import (
     Arraylike
 )
 
+from .hdmf_common_table import (
+    DynamicTableRegion
+)
+
 
 metamodel_version = "None"
 version = "None"

nwb_linkml/models/pydantic/core_nwb_epoch.py

@@ -16,9 +16,9 @@ from .hdmf_common_table import (
 )
 
 from .core_nwb_epoch_include import (
-    TimeIntervalsTimeseriesIndex,
+    TimeIntervalsTagsIndex,
     TimeIntervalsTimeseries,
-    TimeIntervalsTagsIndex
+    TimeIntervalsTimeseriesIndex
 )
 
 

nwb_linkml/models/pydantic/core_nwb_epoch_include.py

@@ -11,14 +11,14 @@ else:
     from typing_extensions import Literal
 
 
-from .hdmf_common_table import (
-    VectorIndex
-)
-
 from .core_nwb_base import (
     TimeSeriesReferenceVectorData
 )
 
+from .hdmf_common_table import (
+    VectorIndex
+)
+
 
 metamodel_version = "None"
 version = "None"

nwb_linkml/models/pydantic/core_nwb_file.py

@@ -11,21 +11,10 @@ else:
     from typing_extensions import Literal
 
 
-from .hdmf_common_table import (
-    DynamicTable
-)
-
-from .core_nwb_base import (
-    NWBData,
-    ProcessingModule,
-    NWBDataInterface,
-    NWBContainer
-)
-
 from .core_nwb_file_include import (
     NWBFileGeneral,
-    SubjectAge,
     NWBFileIntervals,
+    SubjectAge,
     NWBFileStimulus
 )
 
@@ -33,6 +22,17 @@ from .core_nwb_misc import (
     Units
 )
 
+from .core_nwb_base import (
+    NWBDataInterface,
+    ProcessingModule,
+    NWBContainer,
+    NWBData
+)
+
+from .hdmf_common_table import (
+    DynamicTable
+)
+
 
 metamodel_version = "None"
 version = "None"

nwb_linkml/models/pydantic/core_nwb_file_include.py

@@ -11,36 +11,40 @@ else:
     from typing_extensions import Literal
 
 
-from .core_nwb_base import (
-    TimeSeries,
-    Images
-)
-
 from .core_nwb_icephys import (
-    ExperimentalConditionsTable,
-    SweepTable,
-    IntracellularElectrode,
-    SequentialRecordingsTable,
-    RepetitionsTable,
     SimultaneousRecordingsTable,
-    IntracellularRecordingsTable
+    SequentialRecordingsTable,
+    SweepTable,
+    RepetitionsTable,
+    IntracellularElectrode,
+    IntracellularRecordingsTable,
+    ExperimentalConditionsTable
 )
 
-from .core_nwb_ogen import (
+from .core_nwb_file import (
-    OptogeneticStimulusSite
+    Subject,
+    LabMetaData
+)
+
+from .hdmf_common_table import (
+    DynamicTable
 )
 
 from .core_nwb_epoch import (
     TimeIntervals
 )
 
-from .core_nwb_file import (
+from .core_nwb_ogen import (
-    LabMetaData,
+    OptogeneticStimulusSite
-    Subject
 )
 
-from .hdmf_common_table import (
+from .core_nwb_ophys import (
-    DynamicTable
+    ImagingPlane
+)
+
+from .core_nwb_base import (
+    Images,
+    TimeSeries
 )
 
 from .core_nwb_device import (
@@ -51,10 +55,6 @@ from .core_nwb_ecephys import (
     ElectrodeGroup
 )
 
-from .core_nwb_ophys import (
-    ImagingPlane
-)
-
 
 metamodel_version = "None"
 version = "None"

nwb_linkml/models/pydantic/core_nwb_icephys.py

@@ -11,39 +11,39 @@ else:
     from typing_extensions import Literal
 
 
-from .core_nwb_base import (
-    TimeSeries,
-    NWBContainer
-)
-
 from .core_nwb_icephys_include import (
-    VoltageClampSeriesCapacitanceSlow,
+    IntracellularResponsesTableResponse,
-    ExperimentalConditionsTableRepetitions,
-    VoltageClampStimulusSeriesData,
     ExperimentalConditionsTableRepetitionsIndex,
-    VoltageClampSeriesResistanceCompPrediction,
+    SimultaneousRecordingsTableRecordingsIndex,
+    CurrentClampStimulusSeriesData,
     VoltageClampSeriesWholeCellSeriesResistanceComp,
+    VoltageClampStimulusSeriesData,
+    VoltageClampSeriesCapacitanceSlow,
+    SimultaneousRecordingsTableRecordings,
+    VoltageClampSeriesResistanceCompPrediction,
     SequentialRecordingsTableSimultaneousRecordings,
     VoltageClampSeriesCapacitanceFast,
-    RepetitionsTableSequentialRecordingsIndex,
     IntracellularStimuliTableStimulus,
-    VoltageClampSeriesResistanceCompCorrection,
+    RepetitionsTableSequentialRecordingsIndex,
-    SequentialRecordingsTableSimultaneousRecordingsIndex,
-    SimultaneousRecordingsTableRecordings,
-    IntracellularResponsesTableResponse,
     VoltageClampSeriesResistanceCompBandwidth,
-    CurrentClampSeriesData,
-    SimultaneousRecordingsTableRecordingsIndex,
     VoltageClampSeriesData,
+    SequentialRecordingsTableSimultaneousRecordingsIndex,
+    ExperimentalConditionsTableRepetitions,
     RepetitionsTableSequentialRecordings,
     VoltageClampSeriesWholeCellCapacitanceComp,
-    CurrentClampStimulusSeriesData,
+    CurrentClampSeriesData,
+    VoltageClampSeriesResistanceCompCorrection,
     SweepTableSeriesIndex
 )
 
+from .core_nwb_base import (
+    NWBContainer,
+    TimeSeries
+)
+
 from .hdmf_common_table import (
-    DynamicTable,
+    AlignedDynamicTable,
-    AlignedDynamicTable
+    DynamicTable
 )
 
 
@@ -64,16 +64,16 @@ class PatchClampSeries(TimeSeries):
     An abstract base class for patch-clamp data - stimulus or response, current or voltage.
     """
     name: str = Field(...)
-    stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""")
+    stimulus_description: Optional[string] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""")
-    sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
+    sweep_number: Optional[integer] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
     data: List[float] = Field(default_factory=list, description="""Recorded voltage or current.""")
     gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""")
-    description: Optional[str] = Field(None, description="""Description of the time series.""")
+    description: Optional[string] = Field(None, description="""Description of the time series.""")
-    comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
+    comments: Optional[string] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
     starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""")
-    timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
+    timestamps: Optional[List[double]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
-    control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
+    control: Optional[List[integer]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
-    control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
+    control_description: Optional[List[string]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
     sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""")
     
 
@@ -86,15 +86,15 @@ class CurrentClampSeries(PatchClampSeries):
     bias_current: Optional[float] = Field(None, description="""Bias current, in amps.""")
     bridge_balance: Optional[float] = Field(None, description="""Bridge balance, in ohms.""")
     capacitance_compensation: Optional[float] = Field(None, description="""Capacitance compensation, in farads.""")
-    stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""")
+    stimulus_description: Optional[string] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""")
-    sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
+    sweep_number: Optional[integer] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
     gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""")
-    description: Optional[str] = Field(None, description="""Description of the time series.""")
+    description: Optional[string] = Field(None, description="""Description of the time series.""")
-    comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
+    comments: Optional[string] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
     starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""")
-    timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
+    timestamps: Optional[List[double]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
-    control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
+    control: Optional[List[integer]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
-    control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
+    control_description: Optional[List[string]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
     sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""")
     
 
@@ -103,19 +103,19 @@ class IZeroClampSeries(CurrentClampSeries):
     Voltage data from an intracellular recording when all current and amplifier settings are off (i.e., CurrentClampSeries fields will be zero). There is no CurrentClampStimulusSeries associated with an IZero series because the amplifier is disconnected and no stimulus can reach the cell.
     """
     name: str = Field(...)
-    stimulus_description: Optional[str] = Field(None, description="""An IZeroClampSeries has no stimulus, so this attribute is automatically set to \"N/A\"""")
+    stimulus_description: Optional[string] = Field(None, description="""An IZeroClampSeries has no stimulus, so this attribute is automatically set to \"N/A\"""")
     bias_current: float = Field(..., description="""Bias current, in amps, fixed to 0.0.""")
     bridge_balance: float = Field(..., description="""Bridge balance, in ohms, fixed to 0.0.""")
     capacitance_compensation: float = Field(..., description="""Capacitance compensation, in farads, fixed to 0.0.""")
     data: CurrentClampSeriesData = Field(..., description="""Recorded voltage.""")
-    sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
+    sweep_number: Optional[integer] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
     gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""")
-    description: Optional[str] = Field(None, description="""Description of the time series.""")
+    description: Optional[string] = Field(None, description="""Description of the time series.""")
-    comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
+    comments: Optional[string] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
     starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""")
-    timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
+    timestamps: Optional[List[double]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
-    control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
+    control: Optional[List[integer]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
-    control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
+    control_description: Optional[List[string]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
     sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""")
     
 
@@ -125,15 +125,15 @@ class CurrentClampStimulusSeries(PatchClampSeries):
     """
     name: str = Field(...)
     data: CurrentClampStimulusSeriesData = Field(..., description="""Stimulus current applied.""")
-    stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""")
+    stimulus_description: Optional[string] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""")
-    sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
+    sweep_number: Optional[integer] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
     gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""")
-    description: Optional[str] = Field(None, description="""Description of the time series.""")
+    description: Optional[string] = Field(None, description="""Description of the time series.""")
-    comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
+    comments: Optional[string] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
     starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""")
-    timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
+    timestamps: Optional[List[double]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
-    control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
+    control: Optional[List[integer]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
-    control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
+    control_description: Optional[List[string]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
     sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""")
     
 
@@ -150,15 +150,15 @@ class VoltageClampSeries(PatchClampSeries):
     resistance_comp_prediction: Optional[VoltageClampSeriesResistanceCompPrediction] = Field(None, description="""Resistance compensation prediction, in percent.""")
     whole_cell_capacitance_comp: Optional[VoltageClampSeriesWholeCellCapacitanceComp] = Field(None, description="""Whole cell capacitance compensation, in farads.""")
     whole_cell_series_resistance_comp: Optional[VoltageClampSeriesWholeCellSeriesResistanceComp] = Field(None, description="""Whole cell series resistance compensation, in ohms.""")
-    stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""")
+    stimulus_description: Optional[string] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""")
-    sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
+    sweep_number: Optional[integer] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
     gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""")
-    description: Optional[str] = Field(None, description="""Description of the time series.""")
+    description: Optional[string] = Field(None, description="""Description of the time series.""")
-    comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
+    comments: Optional[string] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
     starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""")
-    timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
+    timestamps: Optional[List[double]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
-    control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
+    control: Optional[List[integer]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
-    control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
+    control_description: Optional[List[string]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
     sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""")
     
 
@@ -168,15 +168,15 @@ class VoltageClampStimulusSeries(PatchClampSeries):
     """
     name: str = Field(...)
     data: VoltageClampStimulusSeriesData = Field(..., description="""Stimulus voltage applied.""")
-    stimulus_description: Optional[str] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""")
+    stimulus_description: Optional[string] = Field(None, description="""Protocol/stimulus name for this patch-clamp dataset.""")
-    sweep_number: Optional[int] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
+    sweep_number: Optional[integer] = Field(None, description="""Sweep number, allows to group different PatchClampSeries together.""")
     gain: Optional[float] = Field(None, description="""Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp).""")
-    description: Optional[str] = Field(None, description="""Description of the time series.""")
+    description: Optional[string] = Field(None, description="""Description of the time series.""")
-    comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
+    comments: Optional[string] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
     starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""")
-    timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
+    timestamps: Optional[List[double]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
-    control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
+    control: Optional[List[integer]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
-    control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
+    control_description: Optional[List[string]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
     sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""")
     
 
@@ -185,14 +185,14 @@ class IntracellularElectrode(NWBContainer):
     An intracellular electrode and its metadata.
     """
     name: str = Field(...)
-    cell_id: Optional[str] = Field(None, description="""unique ID of the cell""")
+    cell_id: Optional[string] = Field(None, description="""unique ID of the cell""")
-    description: str = Field(..., description="""Description of electrode (e.g.,  whole-cell, sharp, etc.).""")
+    description: string = Field(..., description="""Description of electrode (e.g.,  whole-cell, sharp, etc.).""")
-    filtering: Optional[str] = Field(None, description="""Electrode specific filtering.""")
+    filtering: Optional[string] = Field(None, description="""Electrode specific filtering.""")
-    initial_access_resistance: Optional[str] = Field(None, description="""Initial access resistance.""")
+    initial_access_resistance: Optional[string] = Field(None, description="""Initial access resistance.""")
-    location: Optional[str] = Field(None, description="""Location of the electrode. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""")
+    location: Optional[string] = Field(None, description="""Location of the electrode. Specify the area, layer, comments on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas names for anatomical regions when possible.""")
-    resistance: Optional[str] = Field(None, description="""Electrode resistance, in ohms.""")
+    resistance: Optional[string] = Field(None, description="""Electrode resistance, in ohms.""")
-    seal: Optional[str] = Field(None, description="""Information about seal used for recording.""")
+    seal: Optional[string] = Field(None, description="""Information about seal used for recording.""")
-    slice: Optional[str] = Field(None, description="""Information about slice used for recording.""")
+    slice: Optional[string] = Field(None, description="""Information about slice used for recording.""")
     
 
 class SweepTable(DynamicTable):
@@ -200,12 +200,12 @@ class SweepTable(DynamicTable):
     [DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable, and ExperimentalConditions tables provide enhanced support for experiment metadata.
     """
     name: str = Field(...)
-    sweep_number: Optional[List[int]] = Field(default_factory=list, description="""Sweep number of the PatchClampSeries in that row.""")
+    sweep_number: Optional[List[integer]] = Field(default_factory=list, description="""Sweep number of the PatchClampSeries in that row.""")
     series: Optional[List[PatchClampSeries]] = Field(default_factory=list, description="""The PatchClampSeries with the sweep number in that row.""")
     series_index: SweepTableSeriesIndex = Field(..., description="""Index for series.""")
-    colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
+    colnames: Optional[string] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
-    description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""")
+    description: Optional[string] = Field(None, description="""Description of what is in this dynamic table.""")
-    id: List[int] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
+    id: List[integer] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
     VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""")
     
 
@@ -214,10 +214,10 @@ class IntracellularElectrodesTable(DynamicTable):
     Table for storing intracellular electrode related metadata.
     """
     name: str = Field(...)
-    description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""")
+    description: Optional[string] = Field(None, description="""Description of what is in this dynamic table.""")
     electrode: Optional[List[IntracellularElectrode]] = Field(default_factory=list, description="""Column for storing the reference to the intracellular electrode.""")
-    colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
+    colnames: Optional[string] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
-    id: List[int] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
+    id: List[integer] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
     VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""")
     
 
@@ -226,10 +226,10 @@ class IntracellularStimuliTable(DynamicTable):
     Table for storing intracellular stimulus related metadata.
     """
     name: str = Field(...)
-    description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""")
+    description: Optional[string] = Field(None, description="""Description of what is in this dynamic table.""")
     stimulus: IntracellularStimuliTableStimulus = Field(..., description="""Column storing the reference to the recorded stimulus for the recording (rows).""")
-    colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
+    colnames: Optional[string] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
-    id: List[int] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
+    id: List[integer] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
     VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""")
     
 
@@ -238,10 +238,10 @@ class IntracellularResponsesTable(DynamicTable):
     Table for storing intracellular response related metadata.
     """
     name: str = Field(...)
-    description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""")
+    description: Optional[string] = Field(None, description="""Description of what is in this dynamic table.""")
     response: IntracellularResponsesTableResponse = Field(..., description="""Column storing the reference to the recorded response for the recording (rows)""")
-    colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
+    colnames: Optional[string] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
-    id: List[int] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
+    id: List[integer] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
     VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""")
     
 
@@ -250,14 +250,14 @@ class IntracellularRecordingsTable(AlignedDynamicTable):
     A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response is recorded as part of an experiment. In this case, both the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used.
     """
     name: str = Field("intracellular_recordings", const=True)
-    description: Optional[str] = Field(None, description="""Description of the contents of this table. Inherited from AlignedDynamicTable and overwritten here to fix the value of the attribute.""")
+    description: Optional[string] = Field(None, description="""Description of the contents of this table. Inherited from AlignedDynamicTable and overwritten here to fix the value of the attribute.""")
     electrodes: IntracellularElectrodesTable = Field(..., description="""Table for storing intracellular electrode related metadata.""")
     stimuli: IntracellularStimuliTable = Field(..., description="""Table for storing intracellular stimulus related metadata.""")
     responses: IntracellularResponsesTable = Field(..., description="""Table for storing intracellular response related metadata.""")
-    categories: Optional[str] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""")
+    categories: Optional[string] = Field(None, description="""The names of the categories in this AlignedDynamicTable. Each category is represented by one DynamicTable stored in the parent group. This attribute should be used to specify an order of categories and the category names must match the names of the corresponding DynamicTable in the group.""")
     dynamic_table: Optional[List[DynamicTable]] = Field(default_factory=list, description="""A DynamicTable representing a particular category for columns in the AlignedDynamicTable parent container. The table MUST be aligned with (i.e., have the same number of rows) as all other DynamicTables stored in the AlignedDynamicTable parent container. The name of the category is given by the name of the DynamicTable and its description by the description attribute of the DynamicTable.""")
-    colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
+    colnames: Optional[string] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
-    id: List[int] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
+    id: List[integer] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
     VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""")
     
 
@@ -268,9 +268,9 @@ class SimultaneousRecordingsTable(DynamicTable):
     name: str = Field("simultaneous_recordings", const=True)
     recordings: SimultaneousRecordingsTableRecordings = Field(..., description="""A reference to one or more rows in the IntracellularRecordingsTable table.""")
     recordings_index: SimultaneousRecordingsTableRecordingsIndex = Field(..., description="""Index dataset for the recordings column.""")
-    colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
+    colnames: Optional[string] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
-    description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""")
+    description: Optional[string] = Field(None, description="""Description of what is in this dynamic table.""")
-    id: List[int] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
+    id: List[integer] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
     VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""")
     
 
@@ -281,10 +281,10 @@ class SequentialRecordingsTable(DynamicTable):
     name: str = Field("sequential_recordings", const=True)
     simultaneous_recordings: SequentialRecordingsTableSimultaneousRecordings = Field(..., description="""A reference to one or more rows in the SimultaneousRecordingsTable table.""")
     simultaneous_recordings_index: SequentialRecordingsTableSimultaneousRecordingsIndex = Field(..., description="""Index dataset for the simultaneous_recordings column.""")
-    stimulus_type: Optional[List[str]] = Field(default_factory=list, description="""The type of stimulus used for the sequential recording.""")
+    stimulus_type: Optional[List[string]] = Field(default_factory=list, description="""The type of stimulus used for the sequential recording.""")
-    colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
+    colnames: Optional[string] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
-    description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""")
+    description: Optional[string] = Field(None, description="""Description of what is in this dynamic table.""")
-    id: List[int] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
+    id: List[integer] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
     VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""")
     
 
@@ -295,9 +295,9 @@ class RepetitionsTable(DynamicTable):
     name: str = Field("repetitions", const=True)
     sequential_recordings: RepetitionsTableSequentialRecordings = Field(..., description="""A reference to one or more rows in the SequentialRecordingsTable table.""")
     sequential_recordings_index: RepetitionsTableSequentialRecordingsIndex = Field(..., description="""Index dataset for the sequential_recordings column.""")
-    colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
+    colnames: Optional[string] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
-    description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""")
+    description: Optional[string] = Field(None, description="""Description of what is in this dynamic table.""")
-    id: List[int] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
+    id: List[integer] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
     VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""")
     
 
@@ -308,9 +308,9 @@ class ExperimentalConditionsTable(DynamicTable):
     name: str = Field("experimental_conditions", const=True)
     repetitions: ExperimentalConditionsTableRepetitions = Field(..., description="""A reference to one or more rows in the RepetitionsTable table.""")
     repetitions_index: ExperimentalConditionsTableRepetitionsIndex = Field(..., description="""Index dataset for the repetitions column.""")
-    colnames: Optional[str] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
+    colnames: Optional[string] = Field(None, description="""The names of the columns in this table. This should be used to specify an order to the columns.""")
-    description: Optional[str] = Field(None, description="""Description of what is in this dynamic table.""")
+    description: Optional[string] = Field(None, description="""Description of what is in this dynamic table.""")
-    id: List[int] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
+    id: List[integer] = Field(default_factory=list, description="""Array of unique identifiers for the rows of this dynamic table.""")
     VectorData: Optional[List[VectorData]] = Field(default_factory=list, description="""Vector columns, including index columns, of this dynamic table.""")
     
 

nwb_linkml/models/pydantic/core_nwb_icephys_include.py

@@ -11,16 +11,16 @@ else:
     from typing_extensions import Literal
 
 
-from .hdmf_common_table import (
-    DynamicTableRegion,
-    VectorIndex
-)
-
 from .core_nwb_icephys import (
+    IntracellularRecordingsTable,
     SequentialRecordingsTable,
     RepetitionsTable,
-    SimultaneousRecordingsTable,
+    SimultaneousRecordingsTable
-    IntracellularRecordingsTable
+)
+
+from .hdmf_common_table import (
+    VectorIndex,
+    DynamicTableRegion
 )
 
 from .core_nwb_base import (
@@ -45,7 +45,7 @@ class CurrentClampSeriesData(ConfiguredBaseModel):
     Recorded voltage.
     """
     name: str = Field("data", const=True)
-    unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""")
+    unit: Optional[string] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""")
     
 
 class CurrentClampStimulusSeriesData(ConfiguredBaseModel):
@@ -53,7 +53,7 @@ class CurrentClampStimulusSeriesData(ConfiguredBaseModel):
     Stimulus current applied.
     """
     name: str = Field("data", const=True)
-    unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""")
+    unit: Optional[string] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""")
     
 
 class VoltageClampSeriesData(ConfiguredBaseModel):
@@ -61,7 +61,7 @@ class VoltageClampSeriesData(ConfiguredBaseModel):
     Recorded current.
     """
     name: str = Field("data", const=True)
-    unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""")
+    unit: Optional[string] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""")
     
 
 class VoltageClampSeriesCapacitanceFast(ConfiguredBaseModel):
@@ -69,7 +69,7 @@ class VoltageClampSeriesCapacitanceFast(ConfiguredBaseModel):
     Fast capacitance, in farads.
     """
     name: str = Field("capacitance_fast", const=True)
-    unit: Optional[str] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""")
+    unit: Optional[string] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""")
     
 
 class VoltageClampSeriesCapacitanceSlow(ConfiguredBaseModel):
@@ -77,7 +77,7 @@ class VoltageClampSeriesCapacitanceSlow(ConfiguredBaseModel):
     Slow capacitance, in farads.
     """
     name: str = Field("capacitance_slow", const=True)
-    unit: Optional[str] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""")
+    unit: Optional[string] = Field(None, description="""Unit of measurement for capacitance_fast, which is fixed to 'farads'.""")
     
 
 class VoltageClampSeriesResistanceCompBandwidth(ConfiguredBaseModel):
@@ -85,7 +85,7 @@ class VoltageClampSeriesResistanceCompBandwidth(ConfiguredBaseModel):
     Resistance compensation bandwidth, in hertz.
     """
     name: str = Field("resistance_comp_bandwidth", const=True)
-    unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_bandwidth, which is fixed to 'hertz'.""")
+    unit: Optional[string] = Field(None, description="""Unit of measurement for resistance_comp_bandwidth, which is fixed to 'hertz'.""")
     
 
 class VoltageClampSeriesResistanceCompCorrection(ConfiguredBaseModel):
@@ -93,7 +93,7 @@ class VoltageClampSeriesResistanceCompCorrection(ConfiguredBaseModel):
     Resistance compensation correction, in percent.
     """
     name: str = Field("resistance_comp_correction", const=True)
-    unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_correction, which is fixed to 'percent'.""")
+    unit: Optional[string] = Field(None, description="""Unit of measurement for resistance_comp_correction, which is fixed to 'percent'.""")
     
 
 class VoltageClampSeriesResistanceCompPrediction(ConfiguredBaseModel):
@@ -101,7 +101,7 @@ class VoltageClampSeriesResistanceCompPrediction(ConfiguredBaseModel):
     Resistance compensation prediction, in percent.
     """
     name: str = Field("resistance_comp_prediction", const=True)
-    unit: Optional[str] = Field(None, description="""Unit of measurement for resistance_comp_prediction, which is fixed to 'percent'.""")
+    unit: Optional[string] = Field(None, description="""Unit of measurement for resistance_comp_prediction, which is fixed to 'percent'.""")
     
 
 class VoltageClampSeriesWholeCellCapacitanceComp(ConfiguredBaseModel):
@@ -109,7 +109,7 @@ class VoltageClampSeriesWholeCellCapacitanceComp(ConfiguredBaseModel):
     Whole cell capacitance compensation, in farads.
     """
     name: str = Field("whole_cell_capacitance_comp", const=True)
-    unit: Optional[str] = Field(None, description="""Unit of measurement for whole_cell_capacitance_comp, which is fixed to 'farads'.""")
+    unit: Optional[string] = Field(None, description="""Unit of measurement for whole_cell_capacitance_comp, which is fixed to 'farads'.""")
     
 
 class VoltageClampSeriesWholeCellSeriesResistanceComp(ConfiguredBaseModel):
@@ -117,7 +117,7 @@ class VoltageClampSeriesWholeCellSeriesResistanceComp(ConfiguredBaseModel):
     Whole cell series resistance compensation, in ohms.
     """
     name: str = Field("whole_cell_series_resistance_comp", const=True)
-    unit: Optional[str] = Field(None, description="""Unit of measurement for whole_cell_series_resistance_comp, which is fixed to 'ohms'.""")
+    unit: Optional[string] = Field(None, description="""Unit of measurement for whole_cell_series_resistance_comp, which is fixed to 'ohms'.""")
     
 
 class VoltageClampStimulusSeriesData(ConfiguredBaseModel):
@@ -125,7 +125,7 @@ class VoltageClampStimulusSeriesData(ConfiguredBaseModel):
     Stimulus voltage applied.
     """
     name: str = Field("data", const=True)
-    unit: Optional[str] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""")
+    unit: Optional[string] = Field(None, description="""Base unit of measurement for working with the data. which is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'.""")
     
 
 class SweepTableSeriesIndex(VectorIndex):
@@ -134,7 +134,7 @@ class SweepTableSeriesIndex(VectorIndex):
     """
     name: str = Field("series_index", const=True)
     target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""")
-    description: Optional[str] = Field(None, description="""Description of what these vectors represent.""")
+    description: Optional[string] = Field(None, description="""Description of what these vectors represent.""")
     array: Optional[Union[
         NDArray[Shape["* dim0"], Any],
         NDArray[Shape["* dim0, * dim1"], Any],
@@ -148,7 +148,7 @@ class IntracellularStimuliTableStimulus(TimeSeriesReferenceVectorData):
     Column storing the reference to the recorded stimulus for the recording (rows).
     """
     name: str = Field("stimulus", const=True)
-    description: Optional[str] = Field(None, description="""Description of what these vectors represent.""")
+    description: Optional[string] = Field(None, description="""Description of what these vectors represent.""")
     array: Optional[Union[
         NDArray[Shape["* dim0"], Any],
         NDArray[Shape["* dim0, * dim1"], Any],
@@ -162,7 +162,7 @@ class IntracellularResponsesTableResponse(TimeSeriesReferenceVectorData):
     Column storing the reference to the recorded response for the recording (rows)
     """
     name: str = Field("response", const=True)
-    description: Optional[str] = Field(None, description="""Description of what these vectors represent.""")
+    description: Optional[string] = Field(None, description="""Description of what these vectors represent.""")
     array: Optional[Union[
         NDArray[Shape["* dim0"], Any],
         NDArray[Shape["* dim0, * dim1"], Any],
@@ -177,7 +177,7 @@ class SimultaneousRecordingsTableRecordings(DynamicTableRegion):
     """
     name: str = Field("recordings", const=True)
     table: Optional[IntracellularRecordingsTable] = Field(None, description="""Reference to the IntracellularRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""")
-    description: Optional[str] = Field(None, description="""Description of what this table region points to.""")
+    description: Optional[string] = Field(None, description="""Description of what this table region points to.""")
     array: Optional[Union[
         NDArray[Shape["* dim0"], Any],
         NDArray[Shape["* dim0, * dim1"], Any],
@@ -192,7 +192,7 @@ class SimultaneousRecordingsTableRecordingsIndex(VectorIndex):
     """
     name: str = Field("recordings_index", const=True)
     target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""")
-    description: Optional[str] = Field(None, description="""Description of what these vectors represent.""")
+    description: Optional[string] = Field(None, description="""Description of what these vectors represent.""")
     array: Optional[Union[
         NDArray[Shape["* dim0"], Any],
         NDArray[Shape["* dim0, * dim1"], Any],
@@ -207,7 +207,7 @@ class SequentialRecordingsTableSimultaneousRecordings(DynamicTableRegion):
     """
     name: str = Field("simultaneous_recordings", const=True)
     table: Optional[SimultaneousRecordingsTable] = Field(None, description="""Reference to the SimultaneousRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""")
-    description: Optional[str] = Field(None, description="""Description of what this table region points to.""")
+    description: Optional[string] = Field(None, description="""Description of what this table region points to.""")
     array: Optional[Union[
         NDArray[Shape["* dim0"], Any],
         NDArray[Shape["* dim0, * dim1"], Any],
@@ -222,7 +222,7 @@ class SequentialRecordingsTableSimultaneousRecordingsIndex(VectorIndex):
     """
     name: str = Field("simultaneous_recordings_index", const=True)
     target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""")
-    description: Optional[str] = Field(None, description="""Description of what these vectors represent.""")
+    description: Optional[string] = Field(None, description="""Description of what these vectors represent.""")
     array: Optional[Union[
         NDArray[Shape["* dim0"], Any],
         NDArray[Shape["* dim0, * dim1"], Any],
@@ -237,7 +237,7 @@ class RepetitionsTableSequentialRecordings(DynamicTableRegion):
     """
     name: str = Field("sequential_recordings", const=True)
     table: Optional[SequentialRecordingsTable] = Field(None, description="""Reference to the SequentialRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""")
-    description: Optional[str] = Field(None, description="""Description of what this table region points to.""")
+    description: Optional[string] = Field(None, description="""Description of what this table region points to.""")
     array: Optional[Union[
         NDArray[Shape["* dim0"], Any],
         NDArray[Shape["* dim0, * dim1"], Any],
@@ -252,7 +252,7 @@ class RepetitionsTableSequentialRecordingsIndex(VectorIndex):
     """
     name: str = Field("sequential_recordings_index", const=True)
     target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""")
-    description: Optional[str] = Field(None, description="""Description of what these vectors represent.""")
+    description: Optional[string] = Field(None, description="""Description of what these vectors represent.""")
     array: Optional[Union[
         NDArray[Shape["* dim0"], Any],
         NDArray[Shape["* dim0, * dim1"], Any],
@@ -267,7 +267,7 @@ class ExperimentalConditionsTableRepetitions(DynamicTableRegion):
     """
     name: str = Field("repetitions", const=True)
     table: Optional[RepetitionsTable] = Field(None, description="""Reference to the RepetitionsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here.""")
-    description: Optional[str] = Field(None, description="""Description of what this table region points to.""")
+    description: Optional[string] = Field(None, description="""Description of what this table region points to.""")
     array: Optional[Union[
         NDArray[Shape["* dim0"], Any],
         NDArray[Shape["* dim0, * dim1"], Any],
@@ -282,7 +282,7 @@ class ExperimentalConditionsTableRepetitionsIndex(VectorIndex):
     """
     name: str = Field("repetitions_index", const=True)
     target: Optional[VectorData] = Field(None, description="""Reference to the target dataset that this index applies to.""")
-    description: Optional[str] = Field(None, description="""Description of what these vectors represent.""")
+    description: Optional[string] = Field(None, description="""Description of what these vectors represent.""")
     array: Optional[Union[
         NDArray[Shape["* dim0"], Any],
         NDArray[Shape["* dim0, * dim1"], Any],

nwb_linkml/models/pydantic/core_nwb_image.py

@@ -11,20 +11,20 @@ else:
     from typing_extensions import Literal
 
 
-from .core_nwb_base import (
-    TimeSeries,
-    Image
-)
-
 from .core_nwb_image_include import (
-    ImageSeriesData,
-    RGBAImageArray,
     GrayscaleImageArray,
     RGBImageArray,
+    ImageSeriesData,
     OpticalSeriesFieldOfView,
+    RGBAImageArray,
     OpticalSeriesData
 )
 
+from .core_nwb_base import (
+    Image,
+    TimeSeries
+)
+
 
 metamodel_version = "None"
 version = "None"
@@ -45,7 +45,7 @@ class GrayscaleImage(Image):
     name: str = Field(...)
     array: Optional[NDArray[Shape["* x, * y"], Number]] = Field(None)
     resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""")
-    description: Optional[str] = Field(None, description="""Description of the image.""")
+    description: Optional[string] = Field(None, description="""Description of the image.""")
     
 
 class RGBImage(Image):
@@ -55,7 +55,7 @@ class RGBImage(Image):
     name: str = Field(...)
     array: Optional[NDArray[Shape["* x, * y, 3 r_g_b"], Number]] = Field(None)
     resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""")
-    description: Optional[str] = Field(None, description="""Description of the image.""")
+    description: Optional[string] = Field(None, description="""Description of the image.""")
     
 
 class RGBAImage(Image):
@@ -65,7 +65,7 @@ class RGBAImage(Image):
     name: str = Field(...)
     array: Optional[NDArray[Shape["* x, * y, 4 r_g_b_a"], Number]] = Field(None)
     resolution: Optional[float] = Field(None, description="""Pixel resolution of the image, in pixels per centimeter.""")
-    description: Optional[str] = Field(None, description="""Description of the image.""")
+    description: Optional[string] = Field(None, description="""Description of the image.""")
     
 
 class ImageSeries(TimeSeries):
@@ -74,15 +74,15 @@ class ImageSeries(TimeSeries):
     """
     name: str = Field(...)
     data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""")
-    dimension: Optional[List[int]] = Field(default_factory=list, description="""Number of pixels on x, y, (and z) axes.""")
+    dimension: Optional[List[integer]] = Field(default_factory=list, description="""Number of pixels on x, y, (and z) axes.""")
-    external_file: Optional[List[str]] = Field(default_factory=list, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""")
+    external_file: Optional[List[string]] = Field(default_factory=list, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""")
-    format: Optional[str] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""")
+    format: Optional[string] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""")
-    description: Optional[str] = Field(None, description="""Description of the time series.""")
+    description: Optional[string] = Field(None, description="""Description of the time series.""")
-    comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
+    comments: Optional[string] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
     starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""")
-    timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
+    timestamps: Optional[List[double]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
-    control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
+    control: Optional[List[integer]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
-    control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
+    control_description: Optional[List[string]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
     sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""")
     
 
@@ -92,15 +92,15 @@ class ImageMaskSeries(ImageSeries):
     """
     name: str = Field(...)
     data: ImageSeriesData = Field(..., description="""Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array.""")
-    dimension: Optional[List[int]] = Field(default_factory=list, description="""Number of pixels on x, y, (and z) axes.""")
+    dimension: Optional[List[integer]] = Field(default_factory=list, description="""Number of pixels on x, y, (and z) axes.""")
-    external_file: Optional[List[str]] = Field(default_factory=list, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""")
+    external_file: Optional[List[string]] = Field(default_factory=list, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""")
-    format: Optional[str] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""")
+    format: Optional[string] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""")
-    description: Optional[str] = Field(None, description="""Description of the time series.""")
+    description: Optional[string] = Field(None, description="""Description of the time series.""")
-    comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
+    comments: Optional[string] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
     starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""")
-    timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
+    timestamps: Optional[List[double]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
-    control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
+    control: Optional[List[integer]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
-    control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
+    control_description: Optional[List[string]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
     sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""")
     
 
@@ -112,16 +112,16 @@ class OpticalSeries(ImageSeries):
     distance: Optional[float] = Field(None, description="""Distance from camera/monitor to target/eye.""")
     field_of_view: Optional[OpticalSeriesFieldOfView] = Field(None, description="""Width, height and depth of image, or imaged area, in meters.""")
     data: OpticalSeriesData = Field(..., description="""Images presented to subject, either grayscale or RGB""")
-    orientation: Optional[str] = Field(None, description="""Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference.""")
+    orientation: Optional[string] = Field(None, description="""Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference.""")
-    dimension: Optional[List[int]] = Field(default_factory=list, description="""Number of pixels on x, y, (and z) axes.""")
+    dimension: Optional[List[integer]] = Field(default_factory=list, description="""Number of pixels on x, y, (and z) axes.""")
-    external_file: Optional[List[str]] = Field(default_factory=list, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""")
+    external_file: Optional[List[string]] = Field(default_factory=list, description="""Paths to one or more external file(s). The field is only present if format='external'. This is only relevant if the image series is stored in the file system as one or more image file(s). This field should NOT be used if the image is stored in another NWB file and that file is linked to this file.""")
-    format: Optional[str] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""")
+    format: Optional[string] = Field(None, description="""Format of image. If this is 'external', then the attribute 'external_file' contains the path information to the image files. If this is 'raw', then the raw (single-channel) binary data is stored in the 'data' dataset. If this attribute is not present, then the default format='raw' case is assumed.""")
-    description: Optional[str] = Field(None, description="""Description of the time series.""")
+    description: Optional[string] = Field(None, description="""Description of the time series.""")
-    comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
+    comments: Optional[string] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
     starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""")
-    timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
+    timestamps: Optional[List[double]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
-    control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
+    control: Optional[List[integer]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
-    control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
+    control_description: Optional[List[string]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
     sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""")
     
 
@@ -130,13 +130,13 @@ class IndexSeries(TimeSeries):
     Stores indices to image frames stored in an ImageSeries. The purpose of the IndexSeries is to allow a static image stack to be stored in an Images object, and the images in the stack to be referenced out-of-order. This can be for the display of individual images, or of movie segments (as a movie is simply a series of images). The data field stores the index of the frame in the referenced Images object, and the timestamps array indicates when that image was displayed.
     """
     name: str = Field(...)
-    data: List[int] = Field(default_factory=list, description="""Index of the image (using zero-indexing) in the linked Images object.""")
+    data: List[integer] = Field(default_factory=list, description="""Index of the image (using zero-indexing) in the linked Images object.""")
-    description: Optional[str] = Field(None, description="""Description of the time series.""")
+    description: Optional[string] = Field(None, description="""Description of the time series.""")
-    comments: Optional[str] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
+    comments: Optional[string] = Field(None, description="""Human-readable comments about the TimeSeries. This second descriptive field can be used to store additional information, or descriptive information if the primary description field is populated with a computer-readable string.""")
     starting_time: Optional[TimeSeriesStartingTime] = Field(None, description="""Timestamp of the first sample in seconds. When timestamps are uniformly spaced, the timestamp of the first sample can be specified and all subsequent ones calculated from the sampling rate attribute.""")
-    timestamps: Optional[List[float]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
+    timestamps: Optional[List[double]] = Field(default_factory=list, description="""Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time.""")
-    control: Optional[List[int]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
+    control: Optional[List[integer]] = Field(default_factory=list, description="""Numerical labels that apply to each time point in data for the purpose of querying and slicing data by these values. If present, the length of this array should be the same size as the first dimension of data.""")
-    control_description: Optional[List[str]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
+    control_description: Optional[List[string]] = Field(default_factory=list, description="""Description of each control value. Must be present if control is present. If present, control_description[0] should describe time points where control == 0.""")
     sync: Optional[TimeSeriesSync] = Field(None, description="""Lab-specific time and sync information as provided directly from hardware devices and that is necessary for aligning all acquired time information to a common timebase. The timestamp array stores time in the common timebase. This group will usually only be populated in TimeSeries that are stored external to the NWB file, in files storing raw data. Once timestamp data is calculated, the contents of 'sync' are mostly for archival purposes.""")
     
 

nwb_linkml/models/pydantic/core_nwb_misc.py

@@ -11,35 +11,35 @@ else:
     from typing_extensions import Literal
 
 
+from .core_nwb_misc_include import (
+    DecompositionSeriesSourceChannels,
+    UnitsWaveformSd,
+    AbstractFeatureSeriesData,
+    UnitsObsIntervalsIndex,
+    DecompositionSeriesData,
+    UnitsWaveformsIndexIndex,
+    UnitsElectrodes,
+    UnitsSpikeTimesIndex,
+    UnitsSpikeTimes,
+    UnitsObsIntervals,
+    UnitsElectrodesIndex,
+    UnitsWaveformMean,
+    UnitsWaveformsIndex,
+    UnitsWaveforms
+)
+
 from .hdmf_common_table import (
     DynamicTable
 )
 
-from .core_nwb_misc_include import (
+from .core_nwb_ecephys import (
-    UnitsElectrodes,
+    ElectrodeGroup
-    UnitsElectrodesIndex,
-    UnitsObsIntervalsIndex,
-    UnitsSpikeTimes,
-    UnitsSpikeTimesIndex,
-    UnitsWaveformSd,
-    UnitsWaveformMean,
-    UnitsWaveforms,
-    AbstractFeatureSeriesData,
-    UnitsWaveformsIndexIndex,
-    UnitsObsIntervals,
-    UnitsWaveformsIndex,
-    DecompositionSeriesData,
-    DecompositionSeriesSourceChannels
 )
 
 from .core_nwb_base import (
     TimeSeries
 )
 
-from .core_nwb_ecephys import (
-    ElectrodeGroup
-)
-
 
 metamodel_version = "None"
 version = "None"

nwb_linkml/models/pydantic/core_nwb_misc_include.py

@@ -12,9 +12,9 @@ else:
 
 
 from .hdmf_common_table import (
-    DynamicTableRegion,
     VectorData,
-    VectorIndex
+    VectorIndex,
+    DynamicTableRegion
 )
 
 from .nwb_language import (

nwb_linkml/models/pydantic/core_nwb_ophys.py

@@ -11,22 +11,16 @@ else:
     from typing_extensions import Literal
 
 
-from .core_nwb_base import (
-    TimeSeries,
-    NWBDataInterface,
-    NWBContainer
-)
-
 from .core_nwb_ophys_include import (
-    RoiResponseSeriesRois,
+    PlaneSegmentationImageMask,
     TwoPhotonSeriesFieldOfView,
     ImagingPlaneOriginCoords,
-    RoiResponseSeriesData,
+    RoiResponseSeriesRois,
-    PlaneSegmentationPixelMaskIndex,
-    PlaneSegmentationImageMask,
-    ImagingPlaneGridSpacing,
     PlaneSegmentationVoxelMaskIndex,
-    ImagingPlaneManifold
+    RoiResponseSeriesData,
+    ImagingPlaneManifold,
+    ImagingPlaneGridSpacing,
+    PlaneSegmentationPixelMaskIndex
 )
 
 from .hdmf_common_table import (
@@ -37,6 +31,12 @@ from .core_nwb_image import (
     ImageSeries
 )
 
+from .core_nwb_base import (
+    NWBDataInterface,
+    NWBContainer,
+    TimeSeries
+)
+
 
 metamodel_version = "None"
 version = "None"

nwb_linkml/models/pydantic/core_nwb_ophys_include.py

@@ -12,9 +12,9 @@ else:
 
 
 from .hdmf_common_table import (
-    DynamicTableRegion,
     VectorData,
-    VectorIndex
+    VectorIndex,
+    DynamicTableRegion
 )
 
 from .nwb_language import (

nwb_linkml/models/pydantic/core_nwb_retinotopy.py

@@ -12,13 +12,13 @@ else:
 
 
 from .core_nwb_retinotopy_include import (
-    ImagingRetinotopyAxis1PowerMap,
-    ImagingRetinotopyAxis1PhaseMap,
-    ImagingRetinotopyVasculatureImage,
     ImagingRetinotopySignMap,
+    ImagingRetinotopyFocalDepthImage,
     ImagingRetinotopyAxis2PowerMap,
+    ImagingRetinotopyVasculatureImage,
     ImagingRetinotopyAxis2PhaseMap,
-    ImagingRetinotopyFocalDepthImage
+    ImagingRetinotopyAxis1PowerMap,
+    ImagingRetinotopyAxis1PhaseMap
 )
 
 from .core_nwb_base import (

nwb_linkml/models/pydantic/core_nwb_retinotopy_include.py

@@ -33,9 +33,9 @@ class ImagingRetinotopyAxis1PhaseMap(ConfiguredBaseModel):
     Phase response to stimulus on the first measured axis.
     """
     name: str = Field("axis_1_phase_map", const=True)
-    dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
+    dimension: Optional[integer] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
     field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""")
-    unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""")
+    unit: Optional[string] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""")
     array: Optional[NDArray[Shape["* num_rows, * num_cols"], Float32]] = Field(None)
     
 
@@ -50,9 +50,9 @@ class ImagingRetinotopyAxis1PowerMap(ConfiguredBaseModel):
     Power response on the first measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.
     """
     name: str = Field("axis_1_power_map", const=True)
-    dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
+    dimension: Optional[integer] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
     field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""")
-    unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""")
+    unit: Optional[string] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""")
     array: Optional[NDArray[Shape["* num_rows, * num_cols"], Float32]] = Field(None)
     
 
@@ -67,9 +67,9 @@ class ImagingRetinotopyAxis2PhaseMap(ConfiguredBaseModel):
     Phase response to stimulus on the second measured axis.
     """
     name: str = Field("axis_2_phase_map", const=True)
-    dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
+    dimension: Optional[integer] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
     field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""")
-    unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""")
+    unit: Optional[string] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""")
     array: Optional[NDArray[Shape["* num_rows, * num_cols"], Float32]] = Field(None)
     
 
@@ -84,9 +84,9 @@ class ImagingRetinotopyAxis2PowerMap(ConfiguredBaseModel):
     Power response on the second measured axis. Response is scaled so 0.0 is no power in the response and 1.0 is maximum relative power.
     """
     name: str = Field("axis_2_power_map", const=True)
-    dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
+    dimension: Optional[integer] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
     field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""")
-    unit: Optional[str] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""")
+    unit: Optional[string] = Field(None, description="""Unit that axis data is stored in (e.g., degrees).""")
     array: Optional[NDArray[Shape["* num_rows, * num_cols"], Float32]] = Field(None)
     
 
@@ -101,18 +101,18 @@ class ImagingRetinotopyFocalDepthImage(ConfiguredBaseModel):
     Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format: [rows][columns].
     """
     name: str = Field("focal_depth_image", const=True)
-    bits_per_pixel: Optional[int] = Field(None, description="""Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value.""")
+    bits_per_pixel: Optional[integer] = Field(None, description="""Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value.""")
-    dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
+    dimension: Optional[integer] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
     field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""")
     focal_depth: Optional[float] = Field(None, description="""Focal depth offset, in meters.""")
-    format: Optional[str] = Field(None, description="""Format of image. Right now only 'raw' is supported.""")
+    format: Optional[string] = Field(None, description="""Format of image. Right now only 'raw' is supported.""")
     array: Optional[NDArray[Shape["* num_rows, * num_cols"], UInt16]] = Field(None)
     
 
 class ImagingRetinotopyFocalDepthImageArray(Arraylike):
     
-    num_rows: int = Field(...)
+    num_rows: integer = Field(...)
-    num_cols: int = Field(...)
+    num_cols: integer = Field(...)
     
 
 class ImagingRetinotopySignMap(ConfiguredBaseModel):
@@ -120,7 +120,7 @@ class ImagingRetinotopySignMap(ConfiguredBaseModel):
     Sine of the angle between the direction of the gradient in axis_1 and axis_2.
     """
     name: str = Field("sign_map", const=True)
-    dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
+    dimension: Optional[integer] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
     field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""")
     array: Optional[NDArray[Shape["* num_rows, * num_cols"], Float32]] = Field(None)
     
@@ -136,17 +136,17 @@ class ImagingRetinotopyVasculatureImage(ConfiguredBaseModel):
     Gray-scale anatomical image of cortical surface. Array structure: [rows][columns]
     """
     name: str = Field("vasculature_image", const=True)
-    bits_per_pixel: Optional[int] = Field(None, description="""Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value""")
+    bits_per_pixel: Optional[integer] = Field(None, description="""Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value""")
-    dimension: Optional[int] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
+    dimension: Optional[integer] = Field(None, description="""Number of rows and columns in the image. NOTE: row, column representation is equivalent to height, width.""")
     field_of_view: Optional[float] = Field(None, description="""Size of viewing area, in meters.""")
-    format: Optional[str] = Field(None, description="""Format of image. Right now only 'raw' is supported.""")
+    format: Optional[string] = Field(None, description="""Format of image. Right now only 'raw' is supported.""")
     array: Optional[NDArray[Shape["* num_rows, * num_cols"], UInt16]] = Field(None)
     
 
 class ImagingRetinotopyVasculatureImageArray(Arraylike):
     
-    num_rows: int = Field(...)
+    num_rows: integer = Field(...)
-    num_cols: int = Field(...)
+    num_cols: integer = Field(...)
     
 
 

nwb_linkml/models/pydantic/hdmf_common_sparse.py

@@ -33,9 +33,9 @@ class CSRMatrix(Container):
     A compressed sparse row matrix. Data are stored in the standard CSR format, where column indices for row i are stored in indices[indptr[i]:indptr[i+1]] and their corresponding values are stored in data[indptr[i]:indptr[i+1]].
     """
     name: str = Field(...)
-    shape: Optional[int] = Field(None, description="""The shape (number of rows, number of columns) of this sparse matrix.""")
+    shape: Optional[integer] = Field(None, description="""The shape (number of rows, number of columns) of this sparse matrix.""")
-    indices: List[int] = Field(default_factory=list, description="""The column indices.""")
+    indices: List[integer] = Field(default_factory=list, description="""The column indices.""")
-    indptr: List[int] = Field(default_factory=list, description="""The row index pointer.""")
+    indptr: List[integer] = Field(default_factory=list, description="""The row index pointer.""")
     data: List[Any] = Field(default_factory=list, description="""The non-zero values in the matrix.""")
     
 

nwb_linkml/models/pydantic/hdmf_common_table.py

@@ -17,8 +17,8 @@ from .hdmf_common_base import (
 )
 
 from .hdmf_common_table_include import (
-    VectorDataArray,
+    ElementIdentifiersArray,
-    ElementIdentifiersArray
+    VectorDataArray
 )
 
 

nwb_linkml/namespaces.py

@@ -120,7 +120,7 @@ class GitRepo:
             return False
 
         # Check that the remote matches
-        if self.remote.strip('.git') != self.namespace.repository:
+        if self.remote.strip('.git') != str(self.namespace.repository):
             warnings.warn(f'Repository exists, but has the wrong remote URL.\nExpected: {self.namespace.repository}\nGot:{self.remote.strip(".git")}')
             return False
 

nwb_linkml/schema/core.nwb.base.include.yaml

@@ -6,7 +6,11 @@ imports:
 - nwb.language
 - core.nwb.base.include
 - core.nwb.base
-default_prefix: core.nwb.base.include/
+prefixes:
+  core.nwb.base:
+    prefix_prefix: core.nwb.base
+    prefix_reference: https://example.com/core.nwb.base/
+default_prefix: core.nwb.base
 classes:
   Image__Array:
     name: Image__Array

nwb_linkml/schema/core.nwb.base.yaml

@@ -6,7 +6,11 @@ imports:
 - nwb.language
 - core.nwb.base.include
 - core.nwb.base
-default_prefix: core.nwb.base/
+prefixes:
+  core.nwb.base:
+    prefix_prefix: core.nwb.base
+    prefix_reference: https://example.com/core.nwb.base/
+default_prefix: core.nwb.base
 classes:
   NWBData:
     name: NWBData

nwb_linkml/schema/core.nwb.behavior.include.yaml

@@ -6,7 +6,11 @@ imports:
 - nwb.language
 - core.nwb.behavior.include
 - core.nwb.behavior
-default_prefix: core.nwb.behavior.include/
+prefixes:
+  core.nwb.behavior:
+    prefix_prefix: core.nwb.behavior
+    prefix_reference: https://example.com/core.nwb.behavior/
+default_prefix: core.nwb.behavior
 classes:
   SpatialSeries__data:
     name: SpatialSeries__data

nwb_linkml/schema/core.nwb.behavior.yaml

@@ -6,7 +6,11 @@ imports:
 - nwb.language
 - core.nwb.behavior.include
 - core.nwb.behavior
-default_prefix: core.nwb.behavior/
+prefixes:
+  core.nwb.behavior:
+    prefix_prefix: core.nwb.behavior
+    prefix_reference: https://example.com/core.nwb.behavior/
+default_prefix: core.nwb.behavior
 classes:
   SpatialSeries:
     name: SpatialSeries

nwb_linkml/schema/core.nwb.device.yaml

@@ -4,7 +4,11 @@ imports:
 - core.nwb.base
 - nwb.language
 - core.nwb.device
-default_prefix: core.nwb.device/
+prefixes:
+  core.nwb.device:
+    prefix_prefix: core.nwb.device
+    prefix_reference: https://example.com/core.nwb.device/
+default_prefix: core.nwb.device
 classes:
   Device:
     name: Device

nwb_linkml/schema/core.nwb.ecephys.include.yaml

@@ -7,7 +7,11 @@ imports:
 - nwb.language
 - core.nwb.ecephys.include
 - core.nwb.ecephys
-default_prefix: core.nwb.ecephys.include/
+prefixes:
+  core.nwb.ecephys:
+    prefix_prefix: core.nwb.ecephys
+    prefix_reference: https://example.com/core.nwb.ecephys/
+default_prefix: core.nwb.ecephys
 classes:
   ElectricalSeries__data:
     name: ElectricalSeries__data

nwb_linkml/schema/core.nwb.ecephys.yaml

@@ -7,7 +7,11 @@ imports:
 - nwb.language
 - core.nwb.ecephys.include
 - core.nwb.ecephys
-default_prefix: core.nwb.ecephys/
+prefixes:
+  core.nwb.ecephys:
+    prefix_prefix: core.nwb.ecephys
+    prefix_reference: https://example.com/core.nwb.ecephys/
+default_prefix: core.nwb.ecephys
 classes:
   ElectricalSeries:
     name: ElectricalSeries

nwb_linkml/schema/core.nwb.epoch.include.yaml

@@ -6,7 +6,11 @@ imports:
 - nwb.language
 - core.nwb.epoch.include
 - core.nwb.epoch
-default_prefix: core.nwb.epoch.include/
+prefixes:
+  core.nwb.epoch:
+    prefix_prefix: core.nwb.epoch
+    prefix_reference: https://example.com/core.nwb.epoch/
+default_prefix: core.nwb.epoch
 classes:
   TimeIntervals__tags_index:
     name: TimeIntervals__tags_index

nwb_linkml/schema/core.nwb.epoch.yaml

@@ -6,7 +6,11 @@ imports:
 - nwb.language
 - core.nwb.epoch.include
 - core.nwb.epoch
-default_prefix: core.nwb.epoch/
+prefixes:
+  core.nwb.epoch:
+    prefix_prefix: core.nwb.epoch
+    prefix_reference: https://example.com/core.nwb.epoch/
+default_prefix: core.nwb.epoch
 classes:
   TimeIntervals:
     name: TimeIntervals

nwb_linkml/schema/core.nwb.file.include.yaml

@@ -13,7 +13,11 @@ imports:
 - nwb.language
 - core.nwb.file.include
 - core.nwb.file
-default_prefix: core.nwb.file.include/
+prefixes:
+  core.nwb.file:
+    prefix_prefix: core.nwb.file
+    prefix_reference: https://example.com/core.nwb.file/
+default_prefix: core.nwb.file
 classes:
   NWBFile__stimulus:
     name: NWBFile__stimulus

nwb_linkml/schema/core.nwb.file.yaml

@@ -13,7 +13,11 @@ imports:
 - nwb.language
 - core.nwb.file.include
 - core.nwb.file
-default_prefix: core.nwb.file/
+prefixes:
+  core.nwb.file:
+    prefix_prefix: core.nwb.file
+    prefix_reference: https://example.com/core.nwb.file/
+default_prefix: core.nwb.file
 classes:
   ScratchData:
     name: ScratchData

nwb_linkml/schema/core.nwb.icephys.include.yaml

@@ -7,7 +7,11 @@ imports:
 - nwb.language
 - core.nwb.icephys.include
 - core.nwb.icephys
-default_prefix: core.nwb.icephys.include/
+prefixes:
+  core.nwb.icephys:
+    prefix_prefix: core.nwb.icephys
+    prefix_reference: https://example.com/core.nwb.icephys/
+default_prefix: core.nwb.icephys
 classes:
   CurrentClampSeries__data:
     name: CurrentClampSeries__data

nwb_linkml/schema/core.nwb.icephys.yaml

@@ -7,7 +7,11 @@ imports:
 - nwb.language
 - core.nwb.icephys.include
 - core.nwb.icephys
-default_prefix: core.nwb.icephys/
+prefixes:
+  core.nwb.icephys:
+    prefix_prefix: core.nwb.icephys
+    prefix_reference: https://example.com/core.nwb.icephys/
+default_prefix: core.nwb.icephys
 classes:
   PatchClampSeries:
     name: PatchClampSeries

nwb_linkml/schema/core.nwb.image.include.yaml

@@ -6,7 +6,11 @@ imports:
 - nwb.language
 - core.nwb.image.include
 - core.nwb.image
-default_prefix: core.nwb.image.include/
+prefixes:
+  core.nwb.image:
+    prefix_prefix: core.nwb.image
+    prefix_reference: https://example.com/core.nwb.image/
+default_prefix: core.nwb.image
 classes:
   GrayscaleImage__Array:
     name: GrayscaleImage__Array

nwb_linkml/schema/core.nwb.image.yaml

@@ -6,7 +6,11 @@ imports:
 - nwb.language
 - core.nwb.image.include
 - core.nwb.image
-default_prefix: core.nwb.image/
+prefixes:
+  core.nwb.image:
+    prefix_prefix: core.nwb.image
+    prefix_reference: https://example.com/core.nwb.image/
+default_prefix: core.nwb.image
 classes:
   GrayscaleImage:
     name: GrayscaleImage

nwb_linkml/schema/core.nwb.misc.include.yaml

@@ -7,7 +7,11 @@ imports:
 - nwb.language
 - core.nwb.misc.include
 - core.nwb.misc
-default_prefix: core.nwb.misc.include/
+prefixes:
+  core.nwb.misc:
+    prefix_prefix: core.nwb.misc
+    prefix_reference: https://example.com/core.nwb.misc/
+default_prefix: core.nwb.misc
 classes:
   AbstractFeatureSeries__data:
     name: AbstractFeatureSeries__data

nwb_linkml/schema/core.nwb.misc.yaml

@@ -7,7 +7,11 @@ imports:
 - nwb.language
 - core.nwb.misc.include
 - core.nwb.misc
-default_prefix: core.nwb.misc/
+prefixes:
+  core.nwb.misc:
+    prefix_prefix: core.nwb.misc
+    prefix_reference: https://example.com/core.nwb.misc/
+default_prefix: core.nwb.misc
 classes:
   AbstractFeatureSeries:
     name: AbstractFeatureSeries

nwb_linkml/schema/core.nwb.ogen.yaml

@@ -5,7 +5,11 @@ imports:
 - core.nwb.device
 - nwb.language
 - core.nwb.ogen
-default_prefix: core.nwb.ogen/
+prefixes:
+  core.nwb.ogen:
+    prefix_prefix: core.nwb.ogen
+    prefix_reference: https://example.com/core.nwb.ogen/
+default_prefix: core.nwb.ogen
 classes:
   OptogeneticSeries:
     name: OptogeneticSeries

nwb_linkml/schema/core.nwb.ophys.include.yaml

@@ -8,7 +8,11 @@ imports:
 - nwb.language
 - core.nwb.ophys.include
 - core.nwb.ophys
-default_prefix: core.nwb.ophys.include/
+prefixes:
+  core.nwb.ophys:
+    prefix_prefix: core.nwb.ophys
+    prefix_reference: https://example.com/core.nwb.ophys/
+default_prefix: core.nwb.ophys
 classes:
   TwoPhotonSeries__field_of_view:
     name: TwoPhotonSeries__field_of_view

nwb_linkml/schema/core.nwb.ophys.yaml

@@ -8,7 +8,11 @@ imports:
 - nwb.language
 - core.nwb.ophys.include
 - core.nwb.ophys
-default_prefix: core.nwb.ophys/
+prefixes:
+  core.nwb.ophys:
+    prefix_prefix: core.nwb.ophys
+    prefix_reference: https://example.com/core.nwb.ophys/
+default_prefix: core.nwb.ophys
 classes:
   OnePhotonSeries:
     name: OnePhotonSeries

nwb_linkml/schema/core.nwb.retinotopy.include.yaml

@@ -5,7 +5,11 @@ imports:
 - nwb.language
 - core.nwb.retinotopy.include
 - core.nwb.retinotopy
-default_prefix: core.nwb.retinotopy.include/
+prefixes:
+  core.nwb.retinotopy:
+    prefix_prefix: core.nwb.retinotopy
+    prefix_reference: https://example.com/core.nwb.retinotopy/
+default_prefix: core.nwb.retinotopy
 classes:
   ImagingRetinotopy__axis_1_phase_map:
     name: ImagingRetinotopy__axis_1_phase_map

nwb_linkml/schema/core.nwb.retinotopy.yaml

@@ -5,7 +5,11 @@ imports:
 - nwb.language
 - core.nwb.retinotopy.include
 - core.nwb.retinotopy
-default_prefix: core.nwb.retinotopy/
+prefixes:
+  core.nwb.retinotopy:
+    prefix_prefix: core.nwb.retinotopy
+    prefix_reference: https://example.com/core.nwb.retinotopy/
+default_prefix: core.nwb.retinotopy
 classes:
   ImagingRetinotopy:
     name: ImagingRetinotopy

nwb_linkml/schema/core.yaml

@@ -15,4 +15,8 @@ imports:
 - core.nwb.ogen
 - core.nwb.ophys
 - core.nwb.retinotopy
-default_prefix: core/
+prefixes:
+  core:
+    prefix_prefix: core
+    prefix_reference: https://example.com/core/
+default_prefix: core

nwb_linkml/schema/hdmf-common.base.yaml

@@ -3,7 +3,11 @@ id: hdmf-common.base
 imports:
 - nwb.language
 - hdmf-common.base
-default_prefix: hdmf-common.base/
+prefixes:
+  hdmf-common.base:
+    prefix_prefix: hdmf-common.base
+    prefix_reference: https://example.com/hdmf-common.base/
+default_prefix: hdmf-common.base
 classes:
   Data:
     name: Data

nwb_linkml/schema/hdmf-common.sparse.yaml

@@ -4,7 +4,11 @@ imports:
 - hdmf-common.base
 - nwb.language
 - hdmf-common.sparse
-default_prefix: hdmf-common.sparse/
+prefixes:
+  hdmf-common.sparse:
+    prefix_prefix: hdmf-common.sparse
+    prefix_reference: https://example.com/hdmf-common.sparse/
+default_prefix: hdmf-common.sparse
 classes:
   CSRMatrix:
     name: CSRMatrix

nwb_linkml/schema/hdmf-common.table.include.yaml

@@ -5,7 +5,11 @@ imports:
 - nwb.language
 - hdmf-common.table.include
 - hdmf-common.table
-default_prefix: hdmf-common.table.include/
+prefixes:
+  hdmf-common.table:
+    prefix_prefix: hdmf-common.table
+    prefix_reference: https://example.com/hdmf-common.table/
+default_prefix: hdmf-common.table
 classes:
   VectorData__Array:
     name: VectorData__Array

nwb_linkml/schema/hdmf-common.table.yaml

@@ -5,7 +5,11 @@ imports:
 - nwb.language
 - hdmf-common.table.include
 - hdmf-common.table
-default_prefix: hdmf-common.table/
+prefixes:
+  hdmf-common.table:
+    prefix_prefix: hdmf-common.table
+    prefix_reference: https://example.com/hdmf-common.table/
+default_prefix: hdmf-common.table
 classes:
   VectorData:
     name: VectorData

nwb_linkml/schema/hdmf-common.yaml

@@ -6,4 +6,8 @@ imports:
 - hdmf-common.base
 - hdmf-common.table
 - hdmf-common.sparse
-default_prefix: hdmf-common/
+prefixes:
+  hdmf-common:
+    prefix_prefix: hdmf-common
+    prefix_reference: https://example.com/hdmf-common/
+default_prefix: hdmf-common

nwb_linkml/schema/hdmf-experimental.experimental.yaml

@@ -4,7 +4,11 @@ imports:
 - hdmf-common.table
 - nwb.language
 - hdmf-experimental.experimental
-default_prefix: hdmf-experimental.experimental/
+prefixes:
+  hdmf-experimental.experimental:
+    prefix_prefix: hdmf-experimental.experimental
+    prefix_reference: https://example.com/hdmf-experimental.experimental/
+default_prefix: hdmf-experimental.experimental
 classes:
   EnumData:
     name: EnumData

nwb_linkml/schema/hdmf-experimental.resources.yaml

@@ -4,7 +4,11 @@ imports:
 - hdmf-common.base
 - nwb.language
 - hdmf-experimental.resources
-default_prefix: hdmf-experimental.resources/
+prefixes:
+  hdmf-experimental.resources:
+    prefix_prefix: hdmf-experimental.resources
+    prefix_reference: https://example.com/hdmf-experimental.resources/
+default_prefix: hdmf-experimental.resources
 classes:
   HERD:
     name: HERD

nwb_linkml/schema/hdmf-experimental.yaml

@@ -6,4 +6,8 @@ version: 0.5.0
 imports:
 - hdmf-experimental.experimental
 - hdmf-experimental.resources
-default_prefix: hdmf-experimental/
+prefixes:
+  hdmf-experimental:
+    prefix_prefix: hdmf-experimental
+    prefix_reference: https://example.com/hdmf-experimental/
+default_prefix: hdmf-experimental

nwb_linkml/schema/nwb.language.yaml

@@ -7,85 +7,112 @@ prefixes:
   linkml:
     prefix_prefix: linkml
     prefix_reference: https://w3id.org/linkml
-default_prefix: nwb.language/
+  nwb.language:
+    prefix_prefix: nwb.language
+    prefix_reference: https://example.com/nwb.language/
+default_prefix: nwb.language
 types:
   float:
     name: float
     typeof: float
+    base: float
   float32:
     name: float32
     typeof: float
+    base: float
   double:
     name: double
     typeof: double
+    base: double
   float64:
     name: float64
     typeof: double
+    base: double
   long:
     name: long
     typeof: integer
+    base: int
   int64:
     name: int64
     typeof: integer
+    base: int
   int:
     name: int
     typeof: integer
+    base: int
   int32:
     name: int32
     typeof: integer
+    base: int
   int16:
     name: int16
     typeof: integer
+    base: int
   short:
     name: short
     typeof: integer
+    base: int
   int8:
     name: int8
     typeof: integer
+    base: int
   uint:
     name: uint
     typeof: integer
+    base: int
     minimum_value: 0
   uint32:
     name: uint32
     typeof: integer
+    base: int
     minimum_value: 0
   uint16:
     name: uint16
     typeof: integer
+    base: int
     minimum_value: 0
   uint8:
     name: uint8
     typeof: integer
+    base: int
     minimum_value: 0
   uint64:
     name: uint64
     typeof: integer
+    base: int
     minimum_value: 0
   numeric:
     name: numeric
     typeof: float
+    base: float
   text:
     name: text
     typeof: string
+    base: string
   utf:
     name: utf
     typeof: string
+    base: string
   utf8:
     name: utf8
     typeof: string
+    base: string
   utf_8:
     name: utf_8
     typeof: string
+    base: string
   ascii:
     name: ascii
     typeof: string
+    base: string
   bool:
     name: bool
     typeof: boolean
+    base: boolean
   isodatetime:
     name: isodatetime
     typeof: datetime
+    base: datetime
 enums:
   FlatDType:
     name: FlatDType

poetry.lock

@@ -238,13 +238,13 @@ tests = ["coverage", "pytest"]
 
 [[package]]
 name = "dash"
-version = "2.12.1"
+version = "2.13.0"
 description = "A Python framework for building reactive web-apps. Developed by Plotly."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "dash-2.12.1-py3-none-any.whl", hash = "sha256:23fcde95e59e353c34712c8fa3e90e784a7247a9e5f6ef47e467add10b7e91ab"},
+    {file = "dash-2.13.0-py3-none-any.whl", hash = "sha256:ca21f01f720652c7e2d16d04d4e27803c2b60c4c2a382e750c3d8d778c06e209"},
-    {file = "dash-2.12.1.tar.gz", hash = "sha256:c7d3dccafff2d041a371dcf5bbb2a1701a38ca178c12dce93e64207e3aecbaeb"},
+    {file = "dash-2.13.0.tar.gz", hash = "sha256:07c192db694b9bb4c87d57b6da877413f2695bfcb1d5c51f08995de7dcdd1e92"},
 ]
 
 [package.dependencies]
@@ -1035,13 +1035,13 @@ tenacity = ">=6.2.0"
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pluggy-1.2.0-py3-none-any.whl", hash = "sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849"},
+    {file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"},
-    {file = "pluggy-1.2.0.tar.gz", hash = "sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3"},
+    {file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"},
 ]
 
 [package.extras]
@@ -1590,108 +1590,108 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
 name = "rpds-py"
-version = "0.9.2"
+version = "0.10.0"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "rpds_py-0.9.2-cp310-cp310-macosx_10_7_x86_64.whl", hash = "sha256:ab6919a09c055c9b092798ce18c6c4adf49d24d4d9e43a92b257e3f2548231e7"},
+    {file = "rpds_py-0.10.0-cp310-cp310-macosx_10_7_x86_64.whl", hash = "sha256:c1e0e9916301e3b3d970814b1439ca59487f0616d30f36a44cead66ee1748c31"},
-    {file = "rpds_py-0.9.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:d55777a80f78dd09410bd84ff8c95ee05519f41113b2df90a69622f5540c4f8b"},
+    {file = "rpds_py-0.10.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8ce8caa29ebbdcde67e5fd652c811d34bc01f249dbc0d61e5cc4db05ae79a83b"},
-    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a216b26e5af0a8e265d4efd65d3bcec5fba6b26909014effe20cd302fd1138fa"},
+    {file = "rpds_py-0.10.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ad277f74b1c164f7248afa968700e410651eb858d7c160d109fb451dc45a2f09"},
-    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:29cd8bfb2d716366a035913ced99188a79b623a3512292963d84d3e06e63b496"},
+    {file = "rpds_py-0.10.0-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:8e1c68303ccf7fceb50fbab79064a2636119fd9aca121f28453709283dbca727"},
-    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:44659b1f326214950a8204a248ca6199535e73a694be8d3e0e869f820767f12f"},
+    {file = "rpds_py-0.10.0-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:780fcb855be29153901c67fc9c5633d48aebef21b90aa72812fa181d731c6b00"},
-    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:745f5a43fdd7d6d25a53ab1a99979e7f8ea419dfefebcab0a5a1e9095490ee5e"},
+    {file = "rpds_py-0.10.0-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:bbd7b24d108509a1b9b6679fcc1166a7dd031dbef1f3c2c73788f42e3ebb3beb"},
-    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a987578ac5214f18b99d1f2a3851cba5b09f4a689818a106c23dbad0dfeb760f"},
+    {file = "rpds_py-0.10.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0700c2133ba203c4068aaecd6a59bda22e06a5e46255c9da23cbf68c6942215d"},
-    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:bf4151acb541b6e895354f6ff9ac06995ad9e4175cbc6d30aaed08856558201f"},
+    {file = "rpds_py-0.10.0-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:576da63eae7809f375932bfcbca2cf20620a1915bf2fedce4b9cc8491eceefe3"},
-    {file = "rpds_py-0.9.2-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:03421628f0dc10a4119d714a17f646e2837126a25ac7a256bdf7c3943400f67f"},
+    {file = "rpds_py-0.10.0-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:23750a9b8a329844ba1fe267ca456bb3184984da2880ed17ae641c5af8de3fef"},
-    {file = "rpds_py-0.9.2-cp310-cp310-musllinux_1_2_i686.whl", hash = "sha256:13b602dc3e8dff3063734f02dcf05111e887f301fdda74151a93dbbc249930fe"},
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 [[package]]
@@ -1848,52 +1848,52 @@ pandas = ["pandas (>=1.3.5)"]
 
 [[package]]
 name = "sqlalchemy"
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+version = "2.0.11"
 description = "Database Abstraction Library"
 optional = false
 python-versions = ">=3.7"
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-    {file = "SQLAlchemy-2.0.20.tar.gz", hash = "sha256:ca8a5ff2aa7f3ade6c498aaafce25b1eaeabe4e42b73e25519183e4566a16fc6"},
+    {file = "SQLAlchemy-2.0.11.tar.gz", hash = "sha256:c3cbff7cced3c42dbe71448ce6bf4202b4a2d305e78dd77e3f280ba6cd245138"},
 ]
 
 [package.dependencies]
@@ -1901,7 +1901,7 @@ greenlet = {version = "!=0.4.17", markers = "platform_machine == \"win32\" or pl
 typing-extensions = ">=4.2.0"
 
 [package.extras]
-aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
+aiomysql = ["aiomysql", "greenlet (!=0.4.17)"]
 aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
 asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
@@ -1920,10 +1920,28 @@ postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
 postgresql-psycopg = ["psycopg (>=3.0.7)"]
 postgresql-psycopg2binary = ["psycopg2-binary"]
 postgresql-psycopg2cffi = ["psycopg2cffi"]
-postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
 pymysql = ["pymysql"]
 sqlcipher = ["sqlcipher3-binary"]
 
+[[package]]
+name = "sqlmodel"
+version = "0"
+description = "SQLModel, SQL databases in Python, designed for simplicity, compatibility, and robustness."
+optional = false
+python-versions = "^3.7"
+files = []
+develop = false
+
+[package.dependencies]
+pydantic = "^2.1.1"
+SQLAlchemy = ">=2.0.0,<=2.0.11"
+
+[package.source]
+type = "git"
+url = "https://github.com/honglei/sqlmodel.git"
+reference = "main"
+resolved_reference = "4213c978fc17b6f57337c43295adffd75eb554e4"
+
 [[package]]
 name = "tenacity"
 version = "8.2.3"
@@ -2158,4 +2176,4 @@ tests = ["pytest", "pytest-depends"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "b552d70308f5b757a624b3d0046e54af4297bfba994a8019f4b366cce2fbe06f"
+content-hash = "b2c008f0aadb604723b4e4387f59bf189691c2e2552cd86ed77990f08a3e626c"

pyproject.toml

@@ -23,6 +23,7 @@ dash = {version="^2.12.1", optional=true}
 dash-cytoscape = {version="^0.3.0", optional=true}
 nptyping = "^2.5.0"
 pydantic = "^2.3.0"
+sqlmodel = { git = "https://github.com/honglei/sqlmodel.git", branch = "main" }
 
 [tool.poetry.extras]
 dev = ["nwb_schema_language"]

scripts/generate_core.py

@@ -2,7 +2,7 @@ from argparse import ArgumentParser
 from pathlib import Path
 from linkml_runtime.dumpers import yaml_dumper
 from nwb_linkml.generators.pydantic import NWBPydanticGenerator
-
+from linkml.generators.sqlalchemygen import SQLAlchemyGenerator, TemplateEnum
 from nwb_linkml import io
 
 def generate_core_yaml(output_path:Path):
@@ -28,6 +28,18 @@ def generate_core_pydantic(yaml_path:Path, output_path:Path):
         with open(pydantic_file, 'w') as pfile:
             pfile.write(gen_pydantic)
 
+def generate_core_sqlalchemy(yaml_path:Path, output_path:Path):
+    for schema in yaml_path.glob('*.yaml'):
+        python_name = schema.stem.replace('.', '_').replace('-', '_')
+        pydantic_file = (output_path / python_name).with_suffix('.py')
+
+        generator =SQLAlchemyGenerator(
+            str(schema)
+        )
+        gen_pydantic = generator.generate_sqla(template=TemplateEnum.DECLARATIVE)
+        with open(pydantic_file, 'w') as pfile:
+            pfile.write(gen_pydantic)
+
 def parser() -> ArgumentParser:
     parser = ArgumentParser('Generate NWB core schema')
     parser.add_argument(
@@ -40,7 +52,13 @@ def parser() -> ArgumentParser:
         '--pydantic',
         help="directory to export pydantic models",
         type=Path,
-        default=Path(__file__).parent.parent / 'nwb_linkml' / 'models'
+        default=Path(__file__).parent.parent / 'nwb_linkml' / 'models' / 'pydantic'
+    )
+    parser.add_argument(
+        '--sqlalchemy',
+        help="directory to export sqlalchemy models",
+        type=Path,
+        default=Path(__file__).parent.parent / 'nwb_linkml' / 'models' / 'sqlalchemy'
     )
     return parser
 
@@ -49,8 +67,10 @@ def main():
     args = parser().parse_args()
     args.yaml.mkdir(exist_ok=True)
     args.pydantic.mkdir(exist_ok=True)
+    args.sqlalchemy.mkdir(exist_ok=True)
     generate_core_yaml(args.yaml)
-    generate_core_pydantic(args.yaml, args.pydantic)
+    #generate_core_pydantic(args.yaml, args.pydantic)
+    generate_core_sqlalchemy(args.yaml, args.sqlalchemy)
 
 if __name__ == "__main__":
     main()

tests/test_generate.py

@@ -7,6 +7,7 @@ from .fixtures import nwb_core_fixture, tmp_output_dir
 from linkml_runtime.dumpers import yaml_dumper
 from linkml.generators import PydanticGenerator
 from nwb_linkml.generators.pydantic import NWBPydanticGenerator
+from nwb_linkml.generators.sqlmodel import SQLModelGenerator
 
 from nwb_linkml.lang_elements import NwbLangSchema
 
@@ -30,7 +31,7 @@ def test_generate_pydantic(tmp_output_dir):
     # core_file = tmp_output_dir / 'core.yaml'
     # pydantic_file = tmp_output_dir / 'core.py'
 
-    (tmp_output_dir / 'models').mkdir(exist_ok=True)
+    (tmp_output_dir / 'models' / 'pydantic').mkdir(exist_ok=True, parents=True)
 
     for schema in (tmp_output_dir / 'schema').glob('*.yaml'):
         if not schema.exists():
@@ -38,7 +39,7 @@ def test_generate_pydantic(tmp_output_dir):
         # python friendly name
         python_name = schema.stem.replace('.', '_').replace('-','_')
 
-        pydantic_file = (schema.parent.parent / 'models' / python_name).with_suffix('.py')
+        pydantic_file = (schema.parent.parent / 'models' / 'pydantic' / python_name).with_suffix('.py')
 
         generator = NWBPydanticGenerator(
             str(schema),
@@ -52,3 +53,30 @@ def test_generate_pydantic(tmp_output_dir):
 
         with open(pydantic_file, 'w') as pfile:
             pfile.write(gen_pydantic)
+
+@pytest.mark.depends(on=['test_generate_core'])
+def test_generate_sqlmodel(tmp_output_dir):
+
+    (tmp_output_dir / 'models' / 'sqlmodel').mkdir(exist_ok=True, parents=True)
+
+    for schema in (tmp_output_dir / 'schema').glob('*.yaml'):
+        if not schema.exists():
+            continue
+        # python friendly name
+        python_name = schema.stem.replace('.', '_').replace('-','_')
+
+        sqlmodel_file = (schema.parent.parent / 'models' / 'sqlmodel' / python_name).with_suffix('.py')
+
+        generator = SQLModelGenerator(
+            str(schema),
+            pydantic_version='2',
+            emit_metadata=True,
+            gen_classvars=True,
+            gen_slots=True
+        )
+        gen_sqlmodel = generator.generate_sqla()
+
+
+        with open(sqlmodel_file, 'w') as pfile:
+            pfile.write(gen_sqlmodel)
+