From da37553008276d90f89ed3a0d1f3f7bbc1dd3449 Mon Sep 17 00:00:00 2001
From: Gonzalo Vidal <35148159+Gonza10V@users.noreply.github.com>
Date: Fri, 3 Oct 2025 14:38:25 -0600
Subject: [PATCH 1/3] Create robotutils.py

---
 src/sbol2build/robotutils.py | 71 ++++++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 src/sbol2build/robotutils.py

diff --git a/src/sbol2build/robotutils.py b/src/sbol2build/robotutils.py
new file mode 100644
index 0000000..04470ac
--- /dev/null
+++ b/src/sbol2build/robotutils.py
@@ -0,0 +1,71 @@
+def assembly_plan_RDF_to_JSON(file):
+    sbol2.Config.setOption('sbol_typed_uris', False)
+    doc = sbol2.Document()
+    doc.read(file)
+
+    # Known SO roles
+    PRODUCT_ROLE = 'http://identifiers.org/so/SO:0000804'
+    BackBone_ROLE = 'http://identifiers.org/so/SO:0000755'
+    ENZYME_ROLE = 'http://identifiers.org/obi/OBI:0000732'
+
+    PARTS_ROLE_LIST = [
+        'http://identifiers.org/so/SO:0000031', 'http://identifiers.org/so/SO:0000316',
+        'http://identifiers.org/so/SO:0001977', 'http://identifiers.org/so/SO:0001956',
+        'http://identifiers.org/so/SO:0000188', 'http://identifiers.org/so/SO:0000839',
+        'http://identifiers.org/so/SO:0000167', 'http://identifiers.org/so/SO:0000139',
+        'http://identifiers.org/so/SO:0001979', 'http://identifiers.org/so/SO:0001955',
+        'http://identifiers.org/so/SO:0001546', 'http://identifiers.org/so/SO:0001263',
+        'http://identifiers.org/SO:0000141', 'http://identifiers.org/so/SO:0000141'
+    ]
+
+    product_dicts = []
+    globalEnzyme = None
+
+    for cd in doc.componentDefinitions:
+        print(f"\n🔍 Checking Component: {cd.displayId}")
+        print(f"  Types: {cd.types}")
+        print(f"  Roles: {cd.roles}")
+
+        if ENZYME_ROLE in cd.roles:
+            globalEnzyme = cd.identity
+            print(f"✅ Found enzyme definition: {globalEnzyme}")
+
+        if PRODUCT_ROLE in cd.roles:
+            result = {
+                'Product': cd.identity,
+                'Backbone': None,
+                'PartsList': [],
+                'Restriction Enzyme': None
+            }
+
+            for comp in cd.components:
+                sub_cd = doc.componentDefinitions.get(comp.definition)
+                if sub_cd is None:
+                    print(f"⚠️ Component definition for {comp.displayId} not found.")
+                    continue
+
+                print(f"  → Subcomponent: {sub_cd.displayId}")
+                print(f"    Roles: {sub_cd.roles}")
+
+                if BackBone_ROLE in sub_cd.roles:
+                    result['Backbone'] = sub_cd.identity
+                    print(f"    🧬 Assigned Backbone: {sub_cd.identity}")
+
+                if any(role in PARTS_ROLE_LIST for role in sub_cd.roles):
+                    result['PartsList'].append(sub_cd.identity)
+                    print(f"    🧩 Added Part: {sub_cd.identity}")
+
+            if not result['Backbone']:
+                print(f"⚠️ No backbone found for product {cd.displayId}")
+            if not result['PartsList']:
+                print(f"⚠️ No parts found for product {cd.displayId}")
+
+            product_dicts.append(result)
+
+    for entry in product_dicts:
+        entry['Restriction Enzyme'] = globalEnzyme
+
+    with open('output.json', 'w') as json_file:
+        json.dump(product_dicts, json_file, indent=4)
+
+    return product_dicts

From 1fc8614f8ae4ea436fe07223be4b31c94caf745b Mon Sep 17 00:00:00 2001
From: Gonzalo Vidal <35148159+Gonza10V@users.noreply.github.com>
Date: Fri, 3 Oct 2025 14:45:42 -0600
Subject: [PATCH 2/3] Update robotutils.py

---
 src/sbol2build/robotutils.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/sbol2build/robotutils.py b/src/sbol2build/robotutils.py
index 04470ac..6e48303 100644
--- a/src/sbol2build/robotutils.py
+++ b/src/sbol2build/robotutils.py
@@ -1,3 +1,6 @@
+import sbol2
+import JSON
+
 def assembly_plan_RDF_to_JSON(file):
     sbol2.Config.setOption('sbol_typed_uris', False)
     doc = sbol2.Document()

From 038476a4308966f43ff197860d94511a6978d845 Mon Sep 17 00:00:00 2001
From: Gonzalo Vidal <35148159+Gonza10V@users.noreply.github.com>
Date: Fri, 17 Oct 2025 14:00:24 -0600
Subject: [PATCH 3/3] Fix import statement for JSON module

---
 src/sbol2build/robotutils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sbol2build/robotutils.py b/src/sbol2build/robotutils.py
index 6e48303..0d451b0 100644
--- a/src/sbol2build/robotutils.py
+++ b/src/sbol2build/robotutils.py
@@ -1,5 +1,5 @@
 import sbol2
-import JSON
+import json
 
 def assembly_plan_RDF_to_JSON(file):
     sbol2.Config.setOption('sbol_typed_uris', False)