Add Composite Check Functionality to SBOL Utilities

sbol_utilities/helper_functions.py

@@ -363,4 +363,31 @@ def is_circular(obj: Union[sbol3.Component, sbol3.LocalSubComponent, sbol3.Exter
     :param obj: design to be checked
     :return: true if circular
     """    
-    return any(n==sbol3.SO_CIRCULAR for n in obj.types)
+    return any(n==sbol3.SO_CIRCULAR for n in obj.types)
+
+def is_composite(obj):
+    """Check if an SBOL Component is a composite.
+
+    A composite component is defined as:
+    1. Having a DNA type.
+    2. Being generated by an assembly plan activity.
+
+    :param obj: SBOL Component to be checked.
+    :return: True if the component is composite, otherwise False.
+    """
+
+    def has_dna_type(o):
+        """Check if the component has a DNA type."""
+        return any(tyto.SO.DNA == tyto.SO.get_uri_by_term(t) for t in o.types)
+
+    def has_assembly_plan(o):
+        """Check if the component was generated by an assembly plan."""
+        for activity_ref in o.generated_by:
+            activity = activity_ref.lookup()
+            if activity and 'http://sbols.org/v3#assemblyPlan' in activity.types and sbol3.SBOL_DESIGN in activity.types:
+                return True
+        return False
+
+    if isinstance(obj, sbol3.Component):
+        return has_dna_type(obj) and has_assembly_plan(obj)
+    return False

test/test_helpers.py

@@ -1,6 +1,8 @@
 import unittest
 import os
 from pathlib import Path
+import sbol3
+import tyto
 
 from sbol_utilities import component
 
@@ -31,6 +33,36 @@ def test_url_sanitization(self):
         self.assertEqual(strip_filetype_suffix('http://foo/bar/baz.gb'), 'http://foo/bar/baz')
         self.assertEqual(strip_filetype_suffix('http://foo/bar/baz.qux'), 'http://foo/bar/baz.qux')
 
+    def test_is_composite(self):
+        """Test the is_composite function."""
+        # Set up a test SBOL document and namespace
+        doc = sbol3.Document()
+        sbol3.set_namespace('http://sbolstandard.org/test')
+        # Case 1: Valid composite component (Has DNA type + Assembly Plan)
+        comp1 = sbol3.Component('comp1', types=[tyto.SO.DNA])
+        assembly_activity = sbol3.Activity('activity1')
+        assembly_activity.types.append("http://sbols.org/v3#assemblyPlan")
+        assembly_activity.types.append(sbol3.SBOL_DESIGN)
+        # Add activity to the document
+        doc.add(assembly_activity)
+        comp1.generated_by.append(sbol3.ReferencedObject(assembly_activity.identity))  
+        doc.add(comp1)
+        self.assertTrue(is_composite(comp1), "Expected comp1 to be composite")
+        # Case 2: Not composite (No DNA type, but has Assembly Plan)
+        comp2 = sbol3.Component('comp2', types=[tyto.SO.RNA])  # RNA type instead of DNA
+        comp2.generated_by.append(sbol3.ReferencedObject(assembly_activity.identity))
+        doc.add(comp2)
+        self.assertFalse(is_composite(comp2), "Expected comp2 to NOT be composite")
+        # Case 3: Not composite (Has DNA type, but no Assembly Plan)
+        comp3 = sbol3.Component('comp3', types=[tyto.SO.DNA])
+        doc.add(comp3)
+        self.assertFalse(is_composite(comp3), "Expected comp3 to NOT be composite")
+        # Case 4: Not composite (No DNA type, No Assembly Plan)
+        comp4 = sbol3.Component('comp4', types=[tyto.SO.RNA])
+        doc.add(comp4)
+        self.assertFalse(is_composite(comp4), "Expected comp4 to NOT be composite")
+
+
     def test_filtering_top_level_objects(self):
         """Check filtering Top Level Objects by a condition"""
         test_dir = os.path.dirname(os.path.realpath(__file__))