Add check subject weight

docs/best_practices/nwbfile_metadata.rst

@@ -238,6 +238,16 @@ Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_subject_a
 
 
 
+.. _best_practice_subject_weight:
+
+Subject Weight
+~~~~~~~~~~~~~
+
+The ``weight`` of a :ref:`nwb-schema:sec-Subject` should have the form '[numeric] [string]', where the numeric part is the weight value and the string part is the unit. For example, "70 kg" or "250 g". This format ensures that both the weight value and its unit are clearly specified and can be easily parsed.
+
+Check function: :py:meth:`~nwbinspector.checks._nwbfile_metadata.check_subject_weight_format`
+
+
 .. _best_practice_subject_dob:
 
 Date of Birth

src/nwbinspector/checks/__init__.py

@@ -49,6 +49,7 @@
     check_subject_sex,
     check_subject_species_exists,
     check_subject_species_form,
+    check_subject_weight_format,
 )
 from ._ogen import (
     check_optogenetic_stimulus_site_has_optogenetic_series,
@@ -75,6 +76,7 @@
 from ._time_series import (
     check_data_orientation,
     check_missing_unit,
+    check_rate_is_not_negative,
     check_rate_is_not_zero,
     check_regular_timestamps,
     check_resolution,
@@ -146,4 +148,6 @@
     "check_spatial_series_radians_magnitude",
     "check_spatial_series_dims",
     "check_spatial_series_degrees_magnitude",
+    "check_rate_is_not_negative",
+    "check_subject_weight_format",
 ]

src/nwbinspector/checks/_nwbfile_metadata.py

@@ -300,6 +300,19 @@ def check_subject_species_form(subject: Subject) -> Optional[InspectorMessage]:
     return None
 
 
+@register_check(importance=Importance.CRITICAL, neurodata_type=Subject)
+def check_subject_weight_format(subject: Subject) -> Optional[InspectorMessage]:
+    """Check if the subject weight has the form '[numeric] [string]'."""
+    if subject.weight is None:
+        return None
+
+    weight_str = str(subject.weight)
+    if not re.match(r"^\d+(\.\d+)?\s?\w+$", weight_str):
+        return InspectorMessage(
+            message="Subject weight should have the form '[numeric] [string]'."
+        )
+    return None
+
 @register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=ProcessingModule)
 def check_processing_module_name(processing_module: ProcessingModule) -> Optional[InspectorMessage]:
     """Check if the name of a processing module is of a valid modality."""

src/nwbinspector/checks/_time_series.py

@@ -182,3 +182,16 @@ def check_rate_is_not_zero(time_series: TimeSeries) -> Optional[InspectorMessage
         )
 
     return None
+
+
+@register_check(importance=Importance.CRITICAL, neurodata_type=TimeSeries)
+def check_rate_is_not_negative(time_series: TimeSeries) -> Optional[InspectorMessage]:
+    if time_series.data is None:
+        return None
+
+    if time_series.rate < 0.0:
+        return InspectorMessage(
+            f"{time_series.name} has a negative sampling rate value of {time_series.rate}Hz.The sampling rate should have a positive value."
+        )
+
+    return None

tests/unit_tests/test_nwbfile_metadata.py

@@ -22,6 +22,7 @@
     check_subject_sex,
     check_subject_species_exists,
     check_subject_species_form,
+    check_subject_weight_format,
 )
 from nwbinspector.checks._nwbfile_metadata import PROCESSING_MODULE_CONFIG
 from nwbinspector.testing import make_minimal_nwbfile
@@ -409,6 +410,52 @@ def test_check_subject_age_iso8601_range_fail_2():
     )
 
 
+def test_check_subject_weight_format_pass():
+    subject = Subject(weight="70 kg")
+    assert check_subject_weight_format(subject) is None
+
+
+def test_check_subject_weight_format_invalid_no_unit():
+    subject = Subject(weight="70")
+    assert check_subject_weight_format(subject) == InspectorMessage(
+        message="Subject weight should have the form '[numeric] [string]'.",
+        importance=Importance.CRITICAL,
+        check_function_name="check_subject_weight_format",
+        object_type="Subject",
+        object_name=subject.name,
+        location="/",
+    )
+
+
+def test_check_subject_weight_format_no_space():
+    subject = Subject(weight="70kg")
+    assert check_subject_weight_format(subject) == InspectorMessage(
+        message="Subject weight should have the form '[numeric] [string]'.",
+        importance=Importance.CRITICAL,
+        check_function_name="check_subject_weight_format",
+        object_type="Subject",
+        object_name=subject.name,
+        location="/",
+    )
+
+
+def test_check_subject_weight_format_invalid_non_numeric():
+    subject = Subject(weight="seventy kg")
+    assert check_subject_weight_format(subject) == InspectorMessage(
+        message="Subject weight should have the form '[numeric] [string]'.",
+        importance=Importance.CRITICAL,
+        check_function_name="check_subject_weight_format",
+        object_type="Subject",
+        object_name=subject.name,
+        location="/",
+    )
+
+
+def test_check_subject_weight_format_none():
+    subject = Subject(weight=None)
+    assert check_subject_weight_format(subject) is None
+
+
 def test_check_subject_proper_age_range_pass():
     subject = Subject(subject_id="001", age="P1D/P3D")
     assert check_subject_proper_age_range(subject) is None

tests/unit_tests/test_time_series.py

@@ -1,11 +1,14 @@
 import h5py
 import numpy as np
 import pynwb
+import pytest
+from packaging import version
 
 from nwbinspector import Importance, InspectorMessage
 from nwbinspector.checks import (
     check_data_orientation,
     check_missing_unit,
+    check_rate_is_not_negative,
     check_rate_is_not_zero,
     check_regular_timestamps,
     check_resolution,
@@ -235,6 +238,29 @@ def test_check_rate_is_not_zero_fail():
     )
 
 
+def test_check_rate_is_not_negative_pass():
+    time_series = pynwb.TimeSeries(name="test", unit="test_units", data=[1, 2, 3], rate=4.0)
+    assert check_rate_is_not_negative(time_series) is None
+
+
+def test_check_rate_is_not_negative_fail():
+    # TODO: Install pynwb < 2.5.0 to test this
+    # Check pynwb version and skip this test if pynwb >= 2.5.0
+    if version.parse(pynwb.__version__) >= version.parse("2.5.0"):
+        pytest.skip("This test is not applicable for pynwb >= 2.5.0")
+
+    time_series = pynwb.TimeSeries(name="TimeSeriesTest", unit="n.a.", data=[1, 2, 3], rate=-4.0)
+
+    assert check_rate_is_not_negative(time_series) == InspectorMessage(
+        message=f"{time_series.name} has a negative sampling rate value of {time_series.rate}Hz.The sampling rate should have a positive value.",
+        importance=Importance.CRITICAL,
+        check_function_name="check_rate_is_not_negative",
+        object_type="TimeSeries",
+        object_name="TimeSeriesTest",
+        location="/",
+    )
+
+
 def test_pass_check_timestamps_ascending_pass():
     time_series = pynwb.TimeSeries(name="test_time_series", unit="test_units", data=[1, 2, 3], timestamps=[1, 2, 3])
     assert check_timestamps_ascending(time_series) is None