Merge branch 'dev' into auto_publish_action

Author: CodyCBakerPhD

nwbinspector/checks/nwbfile_metadata.py

@@ -2,13 +2,15 @@
 import re
 
 from pynwb import NWBFile
-from pynwb.file import Subject
+from pynwb.file import Subject, ProcessingModule
 
 from ..register_checks import register_check, InspectorMessage, Importance
 
 duration_regex = r"^P(?!$)(\d+(?:\.\d+)?Y)?(\d+(?:\.\d+)?M)?(\d+(?:\.\d+)?W)?(\d+(?:\.\d+)?D)?(T(?=\d)(\d+(?:\.\d+)?H)?(\d+(?:\.\d+)?M)?(\d+(?:\.\d+)?S)?)?$"
 species_regex = r"[A-Z][a-z]* [a-z]+"
 
+PROCESSING_MODULE_CONFIG = ["ophys", "ecephys", "icephys", "behavior", "misc", "ogen", "retinotopy"]
+
 
 @register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=NWBFile)
 def check_experimenter(nwbfile: NWBFile):
@@ -42,23 +44,6 @@ def check_subject_age(subject: Subject):
         )
 
 
-# @nwbinspector_check(severity=1, neurodata_type=NWBFile)
-# def check_keywords(nwbfile: NWBFile):
-#     """Check if keywords have been added for the session."""
-#     if not nwbfile.keywords:
-#         return "Metadata /general/keywords is missing!"
-
-
-# @nwbinspector_check(severity=1, neurodata_type=NWBFile)
-# def check_doi_publications(nwbfile: NWBFile):
-#     """Check if related_publications have been added as doi links."""
-#     valid_starts = ["doi:", "http://dx.doi.org/", "https://doi.org/"]
-#     if nwbfile.related_publications:
-#         for publication in nwbfile.related_publications:
-#             if any([publication.startswith(valid_start) for valid_start in valid_starts]):
-#                 return f"Metadata /general/related_publications '{publication}' does not include 'doi'!"
-
-
 @register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=NWBFile)
 def check_subject_exists(nwbfile: NWBFile):
     """Check if subject exists."""
@@ -95,8 +80,27 @@ def check_subject_species(subject: Subject):
         )
 
 
-# @nwbinspector_check(severity=2, neurodata_type=NWBFile)
-# def check_subject_species(nwbfile: NWBFile):
-#     """Check if the subject species has been specified, if one exists."""
-#     if nwbfile.subject and not nwbfile.subject.species:
-#         return "Metadata /general/subject/species is missing!"
+@register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=ProcessingModule)
+def check_processing_module_name(processing_module: ProcessingModule):
+    if processing_module.name not in PROCESSING_MODULE_CONFIG:
+        return InspectorMessage(
+            f"Processing module is named {processing_module.name}. It is recommended to use the "
+            f"schema module names: {', '.join(PROCESSING_MODULE_CONFIG)}"
+        )
+
+
+# @nwbinspector_check(severity=1, neurodata_type=NWBFile)
+# def check_keywords(nwbfile: NWBFile):
+#     """Check if keywords have been added for the session."""
+#     if not nwbfile.keywords:
+#         return "Metadata /general/keywords is missing!"
+
+
+# @nwbinspector_check(severity=1, neurodata_type=NWBFile)
+# def check_doi_publications(nwbfile: NWBFile):
+#     """Check if related_publications have been added as doi links."""
+#     valid_starts = ["doi:", "http://dx.doi.org/", "https://doi.org/"]
+#     if nwbfile.related_publications:
+#         for publication in nwbfile.related_publications:
+#             if any([publication.startswith(valid_start) for valid_start in valid_starts]):
+#                 return f"Metadata /general/related_publications '{publication}' does not include 'doi'!"

tests/unit_tests/test_nwbfile_metadata.py

@@ -2,7 +2,7 @@
 from datetime import datetime
 
 from pynwb import NWBFile
-from pynwb.file import Subject
+from pynwb.file import Subject, ProcessingModule
 import pytest
 
 from nwbinspector import InspectorMessage, Importance
@@ -15,6 +15,8 @@
     check_subject_species,
     check_subject_exists,
     check_subject_id_exists,
+    check_processing_module_name,
+    PROCESSING_MODULE_CONFIG,
 )
 from nwbinspector.register_checks import Severity
 from nwbinspector.tools import make_minimal_nwbfile
@@ -199,9 +201,23 @@ def test_pass_check_subject_id_exist():
     assert check_subject_id_exists(subject) is None
 
 
-@pytest.mark.skip(reason="TODO")
-def test_check_subject_id():
-    pass
+def test_check_processing_module_name():
+    processing_module = ProcessingModule("test", "desc")
+    assert check_processing_module_name(processing_module) == InspectorMessage(
+        severity=Severity.NO_SEVERITY,
+        message=f"Processing module is named test. It is recommended to use the schema "
+        f"module names: {', '.join(PROCESSING_MODULE_CONFIG)}",
+        importance=Importance.BEST_PRACTICE_SUGGESTION,
+        check_function_name="check_processing_module_name",
+        object_type="ProcessingModule",
+        object_name="test",
+        location="/",
+    )
+
+
+def test_pass_check_processing_module_name():
+    processing_module = ProcessingModule("ecephys", "desc")
+    assert check_processing_module_name(processing_module) is None
 
 
 @pytest.mark.skip(reason="TODO")