Assembly helper functions

sbs_server/app/utils.py

@@ -0,0 +1,57 @@
+import sbol2
+import sbol2build as s2b
+from sbol2build import abstract_translator as at
+
+from typing import List, Tuple
+
+def abstract_design_2_plasmids(abstract_design_uri: str, plasmid_collection_uri: str, plasmid_vector_uri: str, sbh: sbol2.PartShop) -> Tuple[List[sbol2.Document], sbol2.Document, str]:
+    abstract_design_doc = sbol2.Document()
+    sbh.pull(
+        abstract_design_uri,
+        abstract_design_doc
+    )
+
+    abstract_design_id = at.extract_toplevel_definition(abstract_design_doc).displayId
+
+    plasmid_collection_doc = sbol2.Document()
+    sbh.pull(
+        plasmid_collection_uri,
+        plasmid_collection_doc
+    )
+
+    backbone_doc = sbol2.Document()
+    sbh.pull(
+        plasmid_vector_uri,
+        backbone_doc,
+    )
+
+    mocloplasmid_list = at.translate_abstract_to_plasmids(
+        abstract_design_doc, plasmid_collection_doc, backbone_doc
+    )
+
+    part_documents = []
+    for mocloPlasmid in mocloplasmid_list:
+        temp_doc = sbol2.Document()
+        mocloPlasmid.definition.copy(temp_doc)
+        at.copy_sequences(
+            mocloPlasmid.definition,
+            temp_doc,
+            plasmid_collection_doc
+        )
+        part_documents.append(temp_doc)
+
+    return part_documents, backbone_doc, abstract_design_id
+
+def sbol2build_moclo(part_documents: List[sbol2.Document], backbone_doc: sbol2.Document, abstract_design_id: str) -> sbol2.Document:
+    assembly_doc = sbol2.Document()
+    assembly_obj = s2b.golden_gate_assembly_plan(
+        f"{abstract_design_id}_assembly_plan",
+        part_documents,
+        backbone_doc,
+        "BsaI",
+        assembly_doc
+    )
+
+    composite_list = assembly_obj.run()
+
+    return assembly_doc

sbs_server/app/views.py

@@ -2,12 +2,12 @@
 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
 import sys
 import os
 import json
 import xml.etree.ElementTree as ET
 
-import sbol2build
 import tricahue
 import sbol2 as sb2
 import pudu
@@ -132,24 +132,6 @@ def upload_file_from_sbs_post_up():
         "status": "success"
     }
     return jsonify(sbs_upload_response_dict)
-
-
-
-@app.route('/sbol_2_build_golden_gate', methods=['POST'])
-def sbol_2_build_golden_gate():
-    # Error checking in the request
-    print("request", request.files)
-
-    if 'plasmid_backbone' not in request.files:
-        return jsonify({"error": "Missing plasmid backbone"}), 400
-    if 'insert_parts' not in request.files:
-        return jsonify({"error": "Missing insert parts"}), 400
-    if 'wizard_selections' not in request.form:
-        return jsonify({"error": "Missing wizard selections"}), 400
-
-    wizard_selection = request.form.get('wizard_selections')
-    plasmid_backbone = request.files.get('plasmid_backbone')
-    insert_parts = request.files.getlist('insert_parts')
 
     # Parse the json
 
@@ -177,16 +159,24 @@ def sbol_2_build_golden_gate():
     assembly_obj = sbol2build.golden_gate_assembly_plan('testassem', part_docs, bb_doc, restriction_enzyme, assembly_doc)
 
     try:
-        composites = assembly_obj.run()
+        # Run abstract translator to get plasmids
+        plasmid_documents, vector_doc, design_id = abstract_design_2_plasmids(abstract_design_uri, plasmid_collection_uri, plasmid_vector_uri, sbh)
+
+        # Run plasmids through sbol2build to generate assembly plan
+        assembly_plan_doc = sbol2build_moclo(plasmid_documents, vector_doc, design_id)
+        assembly_plan_doc.displayId = f"{design_id}_assembly"
 
-        return_string = assembly_doc.writeString()
-
-        # Return the file as a response
-        return return_string
+
+        sbh_response = sbh.submit(
+            doc=assembly_plan_doc,
+            collection=recipient_collection_uri,
+            overwrite=2
+        )
+        return sbh_response.text, sbh_response.status_code
 
     except ValueError as e:
-        # catch sbol2build errors and return to frontend
         return jsonify({"error": str(e)}), 400
+
     except Exception as e:
         return jsonify({"error": f"Unexpected server error: {str(e)}"}), 500