Select top-level design for lvl2 TU extraction

Author: Gonza10V

src/buildcompiler/buildcompiler.py

@@ -19,6 +19,7 @@
 from .abstract_translator import (
     enumerate_design_variants,
     extract_combinatorial_design_parts,
+    extract_toplevel_definition,
     get_or_pull,
     get_compatible_plasmids,
 )
@@ -1612,7 +1613,7 @@ def _extract_lvl2_TUs(  # TODO send to misc helper file instead of buildcompiler
     Returns:
         A list of TU component definitions in sequential order.
     """
-    top_design = design_doc.componentDefinitions[0]
+    top_design = extract_toplevel_definition(design_doc)
 
     return [
         design_doc.get(comp.definition) for comp in top_design.getInSequentialOrder()

tests/unit/stages/test_assembly_lvl2.py

@@ -268,3 +268,30 @@ def fail_get_backbone(*args, **kwargs):
 
     assert products
     assert captured["backbone"] is supplied_lvl2_backbone
+
+
+def test_extract_lvl2_tus_uses_top_level_composite_not_document_order():
+    from buildcompiler.buildcompiler import _extract_lvl2_TUs
+
+    doc = sbol2.Document()
+    tu1 = sbol2.ComponentDefinition("tu1", sbol2.BIOPAX_DNA)
+    tu2 = sbol2.ComponentDefinition("tu2", sbol2.BIOPAX_DNA)
+    composite = sbol2.ComponentDefinition("lvl2_design", sbol2.BIOPAX_DNA)
+
+    # Add child TUs before the composite to ensure extraction does not depend on
+    # ComponentDefinition serialization/document order.
+    doc.addComponentDefinition(tu1)
+    doc.addComponentDefinition(tu2)
+    doc.addComponentDefinition(composite)
+
+    tu1_component = composite.components.create("tu1_component")
+    tu1_component.definition = tu1.identity
+    tu2_component = composite.components.create("tu2_component")
+    tu2_component.definition = tu2.identity
+
+    tu_order = composite.sequenceConstraints.create("tu1_before_tu2")
+    tu_order.subject = tu1_component.identity
+    tu_order.object = tu2_component.identity
+    tu_order.restriction = sbol2.SBOL_RESTRICTION_PRECEDES
+
+    assert _extract_lvl2_TUs(doc) == [tu1, tu2]