This commit is contained in:
sneakers-the-rat 2024-08-12 22:59:15 -07:00
parent 6c07b87ba0
commit 0a93195726
Signed by untrusted user who does not match committer: jonny
GPG key ID: 6DCB96EF1E4D232D
5 changed files with 13 additions and 8 deletions

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@ -5,8 +5,8 @@ Base class for adapters
import sys import sys
from abc import abstractmethod from abc import abstractmethod
from dataclasses import dataclass, field from dataclasses import dataclass, field
from typing import Any, Generator, List, Literal, Optional, Tuple, Type, TypeVar, Union, overload
from logging import Logger from logging import Logger
from typing import Any, Generator, List, Literal, Optional, Tuple, Type, TypeVar, Union, overload
from linkml_runtime.dumpers import yaml_dumper from linkml_runtime.dumpers import yaml_dumper
from linkml_runtime.linkml_model import ( from linkml_runtime.linkml_model import (
@ -104,6 +104,7 @@ class Adapter(BaseModel):
@property @property
def logger(self) -> Logger: def logger(self) -> Logger:
"""A logger with the name of the adapter class! See :class:`.config`"""
if self._logger is None: if self._logger is None:
self._logger = init_logger(self.__class__.__name__) self._logger = init_logger(self.__class__.__name__)
return self._logger return self._logger

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@ -2,9 +2,9 @@
Manage the operation of nwb_linkml from environmental variables Manage the operation of nwb_linkml from environmental variables
""" """
from typing import Optional, Literal
import tempfile import tempfile
from pathlib import Path from pathlib import Path
from typing import Literal, Optional
from pydantic import ( from pydantic import (
BaseModel, BaseModel,

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@ -577,6 +577,9 @@ class TimeSeriesReferenceVectorDataMixin(VectorDataMixin):
@model_validator(mode="after") @model_validator(mode="after")
def ensure_equal_length(self) -> "TimeSeriesReferenceVectorDataMixin": def ensure_equal_length(self) -> "TimeSeriesReferenceVectorDataMixin":
"""
Each of the three indexing columns must be the same length to work!
"""
assert len(self.idx_start) == len(self.timeseries) == len(self.count), ( assert len(self.idx_start) == len(self.timeseries) == len(self.count), (
f"Columns have differing lengths: idx: {len(self.idx_start)}, count: {len(self.count)}," f"Columns have differing lengths: idx: {len(self.idx_start)}, count: {len(self.count)},"
f" timeseries: {len(self.timeseries)}" f" timeseries: {len(self.timeseries)}"

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@ -4,22 +4,22 @@ import numpy as np
import pytest import pytest
from nwb_linkml.models import ( from nwb_linkml.models import (
ElectricalSeries,
ExtracellularEphysElectrodes,
Device, Device,
ElectrodeGroup,
DynamicTableRegion, DynamicTableRegion,
Units, ElectricalSeries,
ElectrodeGroup,
ExtracellularEphysElectrodes,
IntracellularElectrode, IntracellularElectrode,
IntracellularElectrodesTable, IntracellularElectrodesTable,
IntracellularRecordingsTable,
IntracellularResponsesTable, IntracellularResponsesTable,
IntracellularStimuliTable, IntracellularStimuliTable,
IntracellularRecordingsTable, TimeSeriesReferenceVectorData,
Units,
VoltageClampSeries, VoltageClampSeries,
VoltageClampSeriesData, VoltageClampSeriesData,
VoltageClampStimulusSeries, VoltageClampStimulusSeries,
VoltageClampStimulusSeriesData, VoltageClampStimulusSeriesData,
TimeSeriesReferenceVectorData,
) )

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@ -9,6 +9,7 @@ from nwb_linkml.models.pydantic.core.v2_7_0.namespace import (
VectorIndex, VectorIndex,
VoltageClampStimulusSeries, VoltageClampStimulusSeries,
) )
from .conftest import _ragged_array from .conftest import _ragged_array