Merge branch 'dev' into better_fix_curl

Author: CodyCBakerPhD

docs/best_practices/nwbfile_metadata.rst

@@ -202,13 +202,19 @@ Species
 ~~~~~~~
 
 The ``species`` of a :nwb-schema:ref:`sec-Subject` should be set to the proper
-:wikipedia:`Latin binomial <Binomial_nomenclature>`. *E.g.*, a rat would be "Rattus norvegicus". Specific subspecies
-may be further specified by a dash, *e.g.*, "Rattus norvegicus - Long Evans".
+:wikipedia:`Latin binomial <Binomial_nomenclature>`. *E.g.*, a rat would be "Rattus norvegicus".
 
 Check function: :py:meth:`~nwbinspector.checks.nwbfile_metadata.check_subject_species`
 
 
 
+Strain
+~~~~~~~
+
+The ``strain`` of a :nwb-schema:ref:`sec-Subject` should be set to further indicate the subspecies or breed or common genetic modification. *E.g.*, common strains for species "Rattus norvegicus" might include "Long Evans", "Sprague-Dawley", "Wistar", or "C57BL/6". If no specific strain is used, then simply indicate "Wild Type".
+
+
+
 .. _best_practice_subject_age:
 
 Age

nwbinspector/checks/nwbfile_metadata.py

@@ -6,6 +6,7 @@
 from pynwb.file import Subject
 
 from ..register_checks import register_check, InspectorMessage, Importance
+from ..utils import is_module_installed
 
 duration_regex = (
     r"^P(?!$)(\d+(?:\.\d+)?Y)?(\d+(?:\.\d+)?M)?(\d+(?:\.\d+)?W)?(\d+(?:\.\d+)?D)?(T(?=\d)(\d+(?:\.\d+)?H)?(\d+(?:\.\d+)"
@@ -38,12 +39,31 @@ def check_session_start_time_future_date(nwbfile: NWBFile):
 
 
 @register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=NWBFile)
-def check_experimenter(nwbfile: NWBFile):
+def check_experimenter_exists(nwbfile: NWBFile):
     """Check if an experimenter has been added for the session."""
     if not nwbfile.experimenter:
         return InspectorMessage(message="Experimenter is missing.")
 
 
+@register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=NWBFile)
+def check_experimenter_form(nwbfile: NWBFile):
+    """Check the text form of each experimenter to see if it matches the DANDI regex pattern."""
+    if is_module_installed(module_name="dandi"):
+        from dandischema.models import NAME_PATTERN  # for most up to date version of the regex
+    else:
+        NAME_PATTERN = r"^([\w\s\-\.']+),\s+([\w\s\-\.']+)$"  # copied on 7/12/22
+
+    for experimenter in nwbfile.experimenter:
+        experimenter = experimenter.decode() if isinstance(experimenter, bytes) else experimenter
+        if re.match(string=experimenter, pattern=NAME_PATTERN) is None:
+            yield InspectorMessage(
+                message=(
+                    f"The name of experimenter '{experimenter}' does not match the DANDI form "
+                    "(Last, First Middle or Last, First M.)."
+                )
+            )
+
+
 @register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=NWBFile)
 def check_experiment_description(nwbfile: NWBFile):
     """Check if a description has been added for the session."""

setup.py

@@ -5,7 +5,7 @@
     long_description = f.read()
 setup(
     name="nwbinspector",
-    version="0.4.8",
+    version="0.4.9",
     description="Tool to inspect NWB files for best practices compliance.",
     long_description=long_description,
     long_description_content_type="text/markdown",

tests/unit_tests/test_nwbfile_metadata.py

@@ -7,7 +7,8 @@
 from nwbinspector import (
     InspectorMessage,
     Importance,
-    check_experimenter,
+    check_experimenter_exists,
+    check_experimenter_form,
     check_experiment_description,
     check_institution,
     check_keywords,
@@ -70,37 +71,79 @@ def test_check_session_start_time_future_date_fail():
     )
 
 
-def test_check_experimenter_pass():
+def test_check_experimenter_exists_pass():
     nwbfile = NWBFile(
         session_description="",
         identifier=str(uuid4()),
         session_start_time=datetime.now().astimezone(),
         experimenter=["Last, First"],
     )
-    assert check_experimenter(nwbfile) is None
+    assert check_experimenter_exists(nwbfile) is None
 
 
-def test_check_experimenter_bytestring_pass():
+def test_check_experimenter_exists_bytestring_pass():
     nwbfile = NWBFile(
         session_description="",
         identifier=str(uuid4()),
         session_start_time=datetime.now().astimezone(),
         experimenter=[b"Last, First"],
     )
-    assert check_experimenter(nwbfile) is None
+    assert check_experimenter_exists(nwbfile) is None
 
 
-def test_check_experimenter_fail():
-    assert check_experimenter(minimal_nwbfile) == InspectorMessage(
+def test_check_experimenter_exists_fail():
+    assert check_experimenter_exists(minimal_nwbfile) == InspectorMessage(
         message="Experimenter is missing.",
         importance=Importance.BEST_PRACTICE_SUGGESTION,
-        check_function_name="check_experimenter",
+        check_function_name="check_experimenter_exists",
         object_type="NWBFile",
         object_name="root",
         location="/",
     )
 
 
+def test_check_experimenter_form_pass():
+    nwbfile = NWBFile(
+        session_description="",
+        identifier=str(uuid4()),
+        session_start_time=datetime.now().astimezone(),
+        experimenter=["Last, First"],
+    )
+    assert check_experimenter_form(nwbfile=nwbfile) is None
+
+
+def test_check_experimenter_form_bytestring_pass():
+    nwbfile = NWBFile(
+        session_description="",
+        identifier=str(uuid4()),
+        session_start_time=datetime.now().astimezone(),
+        experimenter=[b"Last, First"],
+    )
+    assert check_experimenter_form(nwbfile=nwbfile) is None
+
+
+def test_check_experimenter_form_fail():
+    nwbfile = NWBFile(
+        session_description="",
+        identifier=str(uuid4()),
+        session_start_time=datetime.now().astimezone(),
+        experimenter=["First Middle Last"],
+    )
+    assert check_experimenter_form(nwbfile=nwbfile) == [
+        InspectorMessage(
+            message=(
+                "The name of experimenter 'First Middle Last' does not match the DANDI form "
+                "(Last, First Middle or Last, First M.)."
+            ),
+            importance=Importance.BEST_PRACTICE_SUGGESTION,
+            check_function_name="check_experimenter_form",
+            object_type="NWBFile",
+            object_name="root",
+            location="/",
+        )
+    ]
+
+
 def test_check_experiment_description():
     assert check_experiment_description(minimal_nwbfile) == InspectorMessage(
         message="Experiment description is missing.",