wrote method to recurse through datamodel

Author: frehburg

src/phenopacket_mapper/data_standards/data_model.py

@@ -10,7 +10,7 @@
 
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import Union, List, Literal, Dict, Optional, Any, Callable, Tuple
+from typing import Union, List, Literal, Dict, Optional, Any, Callable, Tuple, Iterable
 import warnings
 
 import pandas as pd
@@ -522,3 +522,28 @@ def __getattr__(self, var_name: str) -> Union[DataField, DataSection, 'OrGroup']
             if f.id == var_name:
                 return f
         raise AttributeError(f"'OrGroup' object has no attribute '{var_name}'")
+
+
+def recursive_collect_all_members_data_model(
+        data_model: Union[DataModel, DataSection, OrGroup, DataField]
+) -> Iterable[Union[DataSection, OrGroup, DataField]]:
+    """Recursively collect all members of a DataModel, DataSection, OrGroup, or DataField
+
+    :param data_model: DataModel, DataSection, OrGroup, or DataField to collect all members from
+    :return: Iterable of DataSection, OrGroup, and DataField members
+    """
+    if isinstance(data_model, DataModel):
+        for f in data_model.fields:
+            yield from recursive_collect_all_members_data_model(f)
+    elif isinstance(data_model, DataSection):
+        yield data_model
+        for f in data_model.fields:
+            yield from recursive_collect_all_members_data_model(f)
+    elif isinstance(data_model, OrGroup):
+        yield data_model
+        for f in data_model.fields:
+            yield from recursive_collect_all_members_data_model(f)
+    elif isinstance(data_model, DataField):
+        yield data_model
+    else:
+        raise ValueError(f"Unsupported data_model type: {type(data_model)}")

tests/utils/test_recursive_collect_all_members_data_model.py

@@ -0,0 +1,62 @@
+import pytest
+
+from phenopacket_mapper import DataModel
+from phenopacket_mapper.data_standards import DataField, DataSection, OrGroup
+from phenopacket_mapper.data_standards.data_model import recursive_collect_all_members_data_model
+
+df1 = DataField(
+    name="test_field_1",
+    specification=str,
+)
+
+df2 = DataField(
+    name="test_field_2",
+    specification=int,
+)
+
+df3 = DataField(
+    name="test_field_3",
+    specification=bool,
+)
+
+ds1 = DataSection(
+    name="test_section_1",
+    fields=(df1, df2)
+)
+
+og1 = OrGroup(
+    name="test_or_group_1",
+    fields=(df1, df2)
+)
+
+
+@pytest.mark.parametrize(
+    "data_model, members",
+    [
+        (
+                DataModel(
+                    name="test",
+                    fields=(df1, df2)
+                ),
+                [df1, df2]
+        ),  # tabular data model
+
+        (
+                DataModel(
+                    name="test",
+                    fields=(ds1, df3)
+                ),
+                [df1, df2, ds1, df3]
+        ),  # hierarchical with section data model
+
+        (
+                DataModel(
+                    name="test",
+                    fields=(og1, df3)
+                ),
+                [df1, df2, og1, df3]
+        ),  # hierarchical with or group data model
+    ]
+)
+def test_recursive_collect_all_members_data_model(data_model, members):
+    assert set(recursive_collect_all_members_data_model(data_model)) == set(members)