Checking the age of subject for anomalies (openMetadataInitiative#33)

* creating a function for age

* create_openminds_age

* checking for nan

* test for create_openminds_age

bids2openminds/main.py

@@ -102,6 +102,30 @@ def create_approaches(layout_df):
     return list(approaches) or None
 
 
+def create_openminds_age(data_subject):
+
+    try:
+        age = pd_table_value(data_subject, "age")
+    except:
+        return None
+
+    if age is None or pd.isna(age):
+        return None
+    elif isinstance(age, float) or isinstance(age, int) or age.isnumeric():
+        return omcore.QuantitativeValue(
+            value=age,
+            unit=controlled_terms.UnitOfMeasurement.year
+        )
+    elif age == "89+":
+        return omcore.QuantitativeValueRange(
+            max_value=None,
+            min_value=89,
+            min_value_unit=controlled_terms.UnitOfMeasurement.year
+        )
+    else:
+        return None
+
+
 def create_dataset_version(bids_layout, dataset_description, layout_df, studied_specimens, file_repository, collection):
 
     # Fetch the dataset type from dataset description file
@@ -246,10 +270,7 @@ def create_subjects(subject_id, layout_df, layout, collection):
         state_cache = []
         if not sessions:
             state = omcore.SubjectState(
-                age=omcore.QuantitativeValue(
-                    value=pd_table_value(data_subject, "age"),
-                    unit=controlled_terms.UnitOfMeasurement.year
-                ),
+                age=create_openminds_age(data_subject),
                 handedness=bids2openminds_instance(pd_table_value(
                     data_subject, "handedness"), "MAP_2_HANDEDNESS", is_list=False),
                 internal_identifier=f"Studied state {subject_name}".strip(),
@@ -262,10 +283,7 @@ def create_subjects(subject_id, layout_df, layout, collection):
             for session in sessions:
                 if not (table_filter(table_filter(layout_df, session, "session"), subject, "subject").empty):
                     state = omcore.SubjectState(
-                        age=omcore.QuantitativeValue(
-                            value=pd_table_value(data_subject, "age"),
-                            unit=controlled_terms.UnitOfMeasurement.year
-                        ),
+                        age=create_openminds_age(data_subject),
                         handedness=bids2openminds_instance(pd_table_value(
                             data_subject, "handedness"), "MAP_2_HANDEDNESS", is_list=False),
                         internal_identifier=f"Studied state {subject_name} {session}".strip(

test/test_subject_age.py

@@ -0,0 +1,22 @@
+import pandas as pd
+import pytest
+from bids2openminds.main import create_openminds_age
+
+example_ages = [("89+", "QuantitativeValueRange"),
+                (45, "QuantitativeValue"), ("XX", None)]
+
+
+@ pytest.mark.parametrize("age,type", example_ages)
+def test_subject_age(age, type):
+    data_subject_table = pd.DataFrame(data={'age': [age]})
+    openminds_age = create_openminds_age(data_subject_table)
+    match type:
+        case "QuantitativeValueRange":
+            assert openminds_age.type_ == 'https://openminds.ebrains.eu/core/QuantitativeValueRange'
+            assert openminds_age.max_value is None
+            assert openminds_age.min_value == 89
+        case "QuantitativeValue":
+            assert openminds_age.type_ == 'https://openminds.ebrains.eu/core/QuantitativeValue'
+            assert openminds_age.value == age
+        case None:
+            assert openminds_age is None