From 9392121163b07829af07f7dd113c35a676deaca9 Mon Sep 17 00:00:00 2001
From: Ryan Greer <ryanrgreer@outlook.com>
Date: Sat, 29 Nov 2025 13:47:47 -0700
Subject: [PATCH 1/3] draft for transformation helper function

---
 sbs_server/app/utils.py | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/sbs_server/app/utils.py b/sbs_server/app/utils.py
index 54a1556..ffaed4e 100644
--- a/sbs_server/app/utils.py
+++ b/sbs_server/app/utils.py
@@ -1,6 +1,7 @@
 import sbol2
 import sbol2build as s2b
 from sbol2build import abstract_translator as at
+from sbol2build import bacterial_transformation
 
 from typing import List, Tuple
 
@@ -54,4 +55,25 @@ def sbol2build_moclo(part_documents: List[sbol2.Document], backbone_doc: sbol2.D
 
     composite_list = assembly_obj.run()
 
-    return assembly_doc
\ No newline at end of file
+    return assembly_doc
+
+def generate_transformation_metadata(plasmid_uris: List[str], chassis_uri: str, transformation_machine: str, protocol: str, params: str, sbh: sbol2.PartShop) -> sbol2.Document:
+    plasmid_docs = []
+
+    for uri in plasmid_uris:
+        temp_doc = sbol2.Document()
+        sbh.pull(
+            uri,
+            temp_doc
+        )
+        plasmid_docs.append(temp_doc)
+
+    chassis_doc = sbol2.Document()
+    sbh.pull(
+        chassis_uri,
+        chassis_doc
+    )
+
+    return bacterial_transformation(sbol2.Document(), chassis_doc, plasmid_docs)
+
+    
\ No newline at end of file

From 8babc697f9cdc4599e530150121b36adb93f7826 Mon Sep 17 00:00:00 2001
From: Ryan Greer <ryanrgreer@outlook.com>
Date: Fri, 5 Dec 2025 02:07:17 -0700
Subject: [PATCH 2/3] upload transformation endpoint draft

---
 .../app/__pycache__/__init__.cpython-311.pyc  | Bin 0 -> 633 bytes
 .../app/__pycache__/__init__.cpython-313.pyc  | Bin 0 -> 531 bytes
 .../app/__pycache__/main.cpython-311.pyc      | Bin 0 -> 991 bytes
 .../app/__pycache__/main.cpython-313.pyc      | Bin 0 -> 823 bytes
 .../app/__pycache__/views.cpython-311.pyc     | Bin 0 -> 13403 bytes
 .../app/__pycache__/views.cpython-313.pyc     | Bin 0 -> 12011 bytes
 sbs_server/app/utils.py                       |   2 +-
 sbs_server/app/views.py                       |  51 +++++++++++++++++-
 8 files changed, 51 insertions(+), 2 deletions(-)
 create mode 100644 sbs_server/app/__pycache__/__init__.cpython-311.pyc
 create mode 100644 sbs_server/app/__pycache__/__init__.cpython-313.pyc
 create mode 100644 sbs_server/app/__pycache__/main.cpython-311.pyc
 create mode 100644 sbs_server/app/__pycache__/main.cpython-313.pyc
 create mode 100644 sbs_server/app/__pycache__/views.cpython-311.pyc
 create mode 100644 sbs_server/app/__pycache__/views.cpython-313.pyc

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diff --git a/sbs_server/app/utils.py b/sbs_server/app/utils.py
index ffaed4e..8a7533f 100644
--- a/sbs_server/app/utils.py
+++ b/sbs_server/app/utils.py
@@ -74,6 +74,6 @@ def generate_transformation_metadata(plasmid_uris: List[str], chassis_uri: str,
         chassis_doc
     )
 
-    return bacterial_transformation(sbol2.Document(), chassis_doc, plasmid_docs)
+    return bacterial_transformation(sbol2.Document(), chassis_doc, plasmid_docs, transformation_machine, protocol, params)
 
     
\ No newline at end of file
diff --git a/sbs_server/app/views.py b/sbs_server/app/views.py
index 7906ce4..5821330 100644
--- a/sbs_server/app/views.py
+++ b/sbs_server/app/views.py
@@ -2,7 +2,7 @@
 from flask import Flask, render_template, request, jsonify
 from flask_cors import CORS
 from .main import app
-from .utils import abstract_design_2_plasmids, sbol2build_moclo
+from .utils import abstract_design_2_plasmids, sbol2build_moclo, generate_transformation_metadata
 import sys
 import os
 import json
@@ -180,6 +180,55 @@ def upload_assembly():
 
     except Exception as e:
         return jsonify({"error": f"Unexpected server error: {str(e)}"}), 500
+    
+@app.route('/upload_transformation', methods=['POST'])    
+def upload_transformation():
+    if 'auth_token' not in request.form:
+        return jsonify({"error": "Missing SynBioHub Authentication Token"}), 400
+    if 'registry_url' not in request.form:
+        return jsonify({"error": "Missing SynBioHub Registry URL"}), 400
+    if 'collection_uri' not in request.form:
+        return jsonify({"error": "Missing recipient SynBioHub collection URI"}), 400
+
+    if 'plasmid_uris' not in request.form:
+        return jsonify({"error": "Missing plasmid URIs"}), 400
+    if 'chassis_uri' not in request.form:
+        return jsonify({"error": "Missing chassis URI"}), 400
+    if 'machine' not in request.form:
+        return jsonify({"error": "Missing machine"}), 400
+    if 'protocol' not in request.form:
+        return jsonify({"error": "Missing protocol"}), 400
+    if 'params' not in request.form:
+        return jsonify({"error": "Missing trasnformation parameters"}), 400
+
+    auth_token = request.form.get("auth_token")
+    sbh_registry = request.form.get("registry_url")
+    recipient_collection_uri = request.form.get("collection_uri")
+
+    plasmid_uris = request.form.get("plasmid_uris")
+    chassis_uri = request.form.get("chassis_uri")
+    machine_name = request.form.get("machine")
+    protocol = request.form.get("protocol")
+    parameters = request.form.get("params")
+
+    sbh = sbol2.PartShop(sbh_registry)
+    sbh.key = auth_token
+    
+    try:
+        transformation_doc = generate_transformation_metadata(plasmid_uris, chassis_uri, machine_name, protocol, parameters, sbh)
+
+        sbh_response = sbh.submit(
+            doc=transformation_doc,
+            collection=recipient_collection_uri,
+            overwrite=2
+        )
+        return sbh_response.text, sbh_response.status_code
+
+    except ValueError as e:
+        return jsonify({"error": str(e)}), 400
+
+    except Exception as e:
+        return jsonify({"error": f"Unexpected server error: {str(e)}"}), 500
 
 @app.route('/build_pudu', methods=['POST'])
 def build_pudu():

From 00747a3edf4a9800ebe757d92da276176c501dbf Mon Sep 17 00:00:00 2001
From: Ryan Greer <ryanrgreer@outlook.com>
Date: Fri, 5 Dec 2025 02:09:02 -0700
Subject: [PATCH 3/3] remove pycache

---
 .../app/__pycache__/__init__.cpython-311.pyc    | Bin 633 -> 0 bytes
 .../app/__pycache__/__init__.cpython-313.pyc    | Bin 531 -> 0 bytes
 sbs_server/app/__pycache__/main.cpython-311.pyc | Bin 991 -> 0 bytes
 sbs_server/app/__pycache__/main.cpython-313.pyc | Bin 823 -> 0 bytes
 .../app/__pycache__/views.cpython-311.pyc       | Bin 13403 -> 0 bytes
 .../app/__pycache__/views.cpython-313.pyc       | Bin 12011 -> 0 bytes
 6 files changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 sbs_server/app/__pycache__/__init__.cpython-311.pyc
 delete mode 100644 sbs_server/app/__pycache__/__init__.cpython-313.pyc
 delete mode 100644 sbs_server/app/__pycache__/main.cpython-311.pyc
 delete mode 100644 sbs_server/app/__pycache__/main.cpython-313.pyc
 delete mode 100644 sbs_server/app/__pycache__/views.cpython-311.pyc
 delete mode 100644 sbs_server/app/__pycache__/views.cpython-313.pyc

diff --git a/sbs_server/app/__pycache__/__init__.cpython-311.pyc b/sbs_server/app/__pycache__/__init__.cpython-311.pyc
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diff --git a/sbs_server/app/__pycache__/__init__.cpython-313.pyc b/sbs_server/app/__pycache__/__init__.cpython-313.pyc
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