Add output_path option to assembly_plan_RDF_to_JSON and update build compiler

src/buildcompiler/buildcompiler.py

@@ -1,5 +1,5 @@
 import sbol2
-from typing import Union, List
+from typing import Union
 import zipfile
 from .abstract_translator import translate_abstract_to_plasmids
 from .sbol2build import golden_gate_assembly_plan
@@ -38,7 +38,10 @@ def assembly_compiler(abstract_design: Union[sbol2.Component, sbol2.Combinatoria
                                               document= document)
 
     # Generate build specifications JSON
-    build_specs_JSON = assembly_plan_RDF_to_JSON(assembly_plan)
+    assembly_plan_RDF_to_JSON(
+        assembly_plan,
+        output_path=f"{files_path}/assemblyplan_output.json",
+    )
 
     # Create zip file with required files
     zip_file = run_opentrons_script_with_json_to_zip(opentrons_script_path= files_path + "/run_sbol2assembly_libre.py",

src/buildcompiler/robotutils.py

@@ -7,8 +7,8 @@
 import zipfile
 from pathlib import Path
 
-def assembly_plan_RDF_to_JSON(file):
-    if type(file)==sbol2.Document:
+def assembly_plan_RDF_to_JSON(file, output_path: str | Path | None = None):
+    if isinstance(file, sbol2.Document):
         doc = file
     else:
         sbol2.Config.setOption('sbol_typed_uris', False)
@@ -77,7 +77,8 @@ def assembly_plan_RDF_to_JSON(file):
     for entry in product_dicts:
         entry['Restriction Enzyme'] = globalEnzyme
 
-    with open('output.json', 'w') as json_file:
+    json_output_path = Path(output_path) if output_path is not None else Path("output.json")
+    with json_output_path.open('w', encoding='utf-8') as json_file:
         json.dump(product_dicts, json_file, indent=4)
 
     return product_dicts
@@ -148,4 +149,4 @@ def run_opentrons_script_with_json_to_zip(
                 if p.is_file():
                     z.write(p, arcname=p.relative_to(tmpdir))
 
-    return out_zip
+    return out_zip

src/sbol2build/robotutils.py

@@ -2,7 +2,7 @@
 import json
 
 def assembly_plan_RDF_to_JSON(file):
-    if type(file)==sbol2.Document:
+    if isinstance(file, sbol2.Document):
         doc = file
     else:
         sbol2.Config.setOption('sbol_typed_uris', False)