SynBioHub PartShop client, collection pulls, and stricter Golden Gate digest handling

README.md

@@ -163,6 +163,27 @@ plan = compiler.plan(abstract_designs)
 result = compiler.execute(plan)
 ```
 
+
+Authenticated and anonymous repository access are both supported:
+
+```python
+compiler = BuildCompiler.from_synbiohub(
+    collections=["https://synbiohub.org/public/igem/igem_collection/1"],
+    repository_url="https://synbiohub.org",
+    auth_token="<token>",
+)
+
+compiler = BuildCompiler.from_synbiohub(
+    repository_url="https://synbiohub.org",
+    email="user@example.org",
+    password="<password>",
+)
+
+compiler = BuildCompiler.from_synbiohub(
+    repository_url="https://synbiohub.org",
+)
+```
+
 A convenience wrapper may exist:
 
 ```python

notebooks/buildcompiler_synbiohub_authenticated_tutorial.ipynb

@@ -0,0 +1,210 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# BuildCompiler SynBioHub Authenticated Tutorial"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This tutorial shows how to authenticate to SynBioHub with email/password, load inventory collections into BuildCompiler's internal SBOL document, and prepare an assembly workflow from an abstract design URI."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from getpass import getpass\n",
+    "import sbol2\n",
+    "\n",
+    "from buildcompiler.api import BuildCompiler"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "repository_url = 'https://synbiohub.org'\n",
+    "email = input('SynBioHub user/email: ').strip()\n",
+    "password = getpass('SynBioHub password: ')\n",
+    "\n",
+    "abstract_design_uri = 'https://synbiohub.org/user/Gon/abstract_design/standard_GFP/1'\n",
+    "collections = [\n",
+    "    'https://synbiohub.org/user/Gon/impl_test/impl_test_collection/1',\n",
+    "    'https://synbiohub.org/user/Gon/Enzyme_Implementations/Enzyme_Implementations_collection/1',\n",
+    "]\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "doc = sbol2.Document()\n",
+    "compiler = BuildCompiler.from_synbiohub(\n",
+    "    collections=collections,\n",
+    "    repository_url=repository_url,\n",
+    "    email=email,\n",
+    "    password=password,\n",
+    "    sbol_doc=doc,\n",
+    ")\n",
+    "\n",
+    "print(f'Loaded objects: {len(doc.componentDefinitions)} component definitions, {len(doc.implementations)} implementations')\n",
+    "print('Repository client:', type(compiler.repository_client).__name__)\n",
+    "print('In-memory auth token available:', compiler.repository_client.auth_token is not None)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## What BuildCompiler does with this setup\n",
+    "\n",
+    "- Pulls each collection URI using authenticated `sbol2.PartShop` into `sbol_doc`.\n",
+    "- Reuses the same authenticated pull client for identity-based resolver misses in planning/execution.\n",
+    "- Uses inventory indexing to find compatible plasmids containing abstract-design parts and compatible backbones/reagents."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Assembly simulation behavior\n",
+    "\n",
+    "Legacy Golden Gate simulation now enforces strict digest validation:\n",
+    "\n",
+    "- Restriction digest must yield exactly **2 fragments**.\n",
+    "- For part plasmids, the smaller fragment is selected as the insert.\n",
+    "- For the backbone plasmid, the larger fragment is selected as the backbone.\n",
+    "- If digest count is unexpected, simulation fails with a clear error message naming the reactant.\n",
+    "- Successful assembly encodes reagent usage and links generated product implementations with `wasGeneratedBy` to one assembly activity per assembled design product."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Pull the abstract design into the same in-memory document\n",
+    "if doc.find(abstract_design_uri) is None:\n",
+    "    compiler.repository_client.pull_identity(abstract_design_uri)\n",
+    "\n",
+    "abstract_design = doc.find(abstract_design_uri)\n",
+    "print('Abstract design found:', abstract_design is not None, type(abstract_design).__name__)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Run full build using the abstract design object\n",
+    "# Note: this assumes your pulled inventory contains compatible lvl1 part plasmids, backbone, and reagents.\n",
+    "result = compiler.full_build([abstract_design])\n",
+    "print('Build status:', result.status)\n",
+    "print('Stage results:', [(s.stage.value, s.status.value) for s in result.stage_results])\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Check whether lvl1 assembly was selected\n",
+    "lvl1 = [s for s in result.stage_results if s.stage.value == 'assembly_lvl1']\n",
+    "print('Lvl1 stage entries:', len(lvl1))\n",
+    "if lvl1:\n",
+    "    print('Lvl1 status:', lvl1[0].status.value)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Access the best-practice SBOL build document\n",
+    "build_doc = result.build_document\n",
+    "print('Build document objects:', len(build_doc.componentDefinitions), 'CDs,', len(build_doc.implementations), 'implementations,', len(build_doc.activities), 'activities')\n",
+    "# build_doc.write('build_result.xml')\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Enable detailed reporting and inspect full diagnostic report when builds fail\n",
+    "from buildcompiler.api import BuildOptions\n",
+    "\n",
+    "debug_options = BuildOptions()\n",
+    "debug_options.reporting.include_detailed_report = True\n",
+    "debug_result = compiler.full_build([abstract_design], options=debug_options)\n",
+    "print('Debug status:', debug_result.status)\n",
+    "print('Missing inputs:', [m.missing_identity for m in debug_result.missing_inputs])\n",
+    "print('Warnings:', [w.message if hasattr(w, 'message') else str(w) for w in debug_result.warnings])\n",
+    "debug_result.report\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Validate full build document\n",
+    "build_doc.validate()\n",
+    "print('Full build document validation completed.')\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Build a focused assembly-only document and validate\n",
+    "assembly_doc = sbol2.Document()\n",
+    "for activity in build_doc.activities:\n",
+    "    if 'assembly' in activity.displayId.lower():\n",
+    "        activity.copy(assembly_doc)\n",
+    "\n",
+    "for impl in build_doc.implementations:\n",
+    "    if getattr(impl, 'wasGeneratedBy', None):\n",
+    "        impl.copy(assembly_doc)\n",
+    "        built_obj = build_doc.find(impl.built)\n",
+    "        if built_obj is not None:\n",
+    "            built_obj.copy(assembly_doc)\n",
+    "\n",
+    "assembly_doc.validate()\n",
+    "print('Assembly-only document validation completed.')\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}