Level 2 assembly, transformation, and test suite

.github/workflows/python-package.yml

@@ -37,5 +37,8 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with unittest
+      env:
+          SBH_USERNAME: ${{ secrets.SBH_USERNAME }}
+          SBH_PASSWORD: ${{ secrets.SBH_PASSWORD }}
       run: |
         python -m unittest discover -s tests

README.md

@@ -52,5 +52,13 @@ uv run pre-commit install
 ```
 
 
-#### Running tests:
+#### Running tests locally:
+Run these bash commands to establish your SynBioHub account for collection access. These are saved in GitHub secrets for the automated test suite.
+
+`export SBH_USERNAME=your_username`
+
+`export SBH_PASSWORD=your_password`
+
+Then run the tests with:
+
 `uv run python -m unittest discover -s tests`

notebooks/build_compiler_test.ipynb

@@ -12,72 +12,239 @@
     "from buildcompiler.abstract_translator import extract_toplevel_definition"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "238f2456",
+   "metadata": {},
+   "source": [
+    "## Multi-Design Lvl 1 Testing:"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,
    "id": "e60a9c84",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['qlSBuNBL', 'i0mwvNcgH']\n"
+     ]
+    }
+   ],
    "source": [
-    "design_doc = sbol2.Document()\n",
-    "design_doc.read(\"../tests/test_files/moclo_parts_circuit.xml\")\n",
-    "design = extract_toplevel_definition(design_doc)"
+    "design_path_list = [\n",
+    "    \"../tests/test_files/moclo_parts_circuit.xml\",\n",
+    "    \"../tests/test_files/mocloparts116.xml\",\n",
+    "]\n",
+    "design_defs = []\n",
+    "sbol_doc = sbol2.Document()\n",
+    "\n",
+    "for design in design_path_list:\n",
+    "    temp_doc = sbol2.Document()\n",
+    "    temp_doc.read(design)\n",
+    "\n",
+    "    design_defs.append(extract_toplevel_definition(temp_doc))\n",
+    "\n",
+    "    # sbol_doc.read(\"../tests/test_files/ExampleLvl2_design.xml\")\n",
+    "\n",
+    "print([design_def.displayId for design_def in design_defs])"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 3,
    "id": "90648527",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Indexing collection: https://synbiohub.org/user/Gon/impl_test/impl_test_collection/1\n",
+      "Indexing collection: https://synbiohub.org/user/Gon/Enzyme_Implementations/Enzyme_Implementations_collection/1\n"
+     ]
+    }
+   ],
    "source": [
-    "auth = \"51102d98-f852-4386-9ae8-7c5814d679c1\"\n",
+    "auth = \"c6f22554-f057-4b4f-a597-67041d9002e5\"\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",
-    "buildcompiler = BuildCompiler(collections, \"https://synbiohub.org\", auth, None)"
+    "buildcompiler = BuildCompiler(collections, \"https://synbiohub.org\", auth, sbol_doc)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "7c12e504",
+   "execution_count": 4,
+   "id": "19c5d2ff",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "https://synbiohub.org/user/Gon/Enzyme_Implementations/BbsI_impl/1 https://synbiohub.org/user/Gon/Enzyme_Implementations/BsaI_impl/1 https://synbiohub.org/user/Gon/Enzyme_Implementations/T4_Ligase_impl/1\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(buildcompiler.BbsI_impl, buildcompiler.BsaI_impl, buildcompiler.T4_ligase_impl)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "6ec9e2fe",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[<sbol2.implementation.Implementation object at 0x10d99bf20>, <sbol2.implementation.Implementation object at 0x10dadc230>]\n",
-      "[<sbol2.implementation.Implementation object at 0x10dadc140>]\n",
-      "matched pJ23100_AB_A_B with DVK_AE_A_E on fusion site A!\n",
-      "matched pB0034_BC_B_C with pJ23100_AB_A_B on fusion site B!\n",
-      "matched pE0030_CD_C_D with pB0034_BC_B_C on fusion site C!\n",
-      "matched final component pB0015_DE_D_E with pE0030_CD_C_D and DVK_AE_A_E on fusion sites (D, E)!\n",
       "Success with backbone: DVK_AE_A_E and plasmids: ['pJ23100_AB_A_B', 'pB0034_BC_B_C', 'pE0030_CD_C_D', 'pB0015_DE_D_E']\n",
-      "[Plasmid:\n",
-      "  Name: composite_1_A_B_C_D_E\n",
-      "  Plasmid Definition: https://SBOL2Build.org/composite_1/1\n",
+      "Success with backbone: DVK_AE_A_E and plasmids: ['pJ23116_AB_A_B', 'pB0034_BC_B_C', 'pE0030_CD_C_D', 'pB0015_DE_D_E']\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "({'https://sbolcanvas.org/qlSBuNBL/1': [Plasmid:\n",
+       "     Name: qlSBuNBL_composite_1_A_E\n",
+       "     Plasmid Definition: http://buildcompiler.org/qlSBuNBL_composite_1/1\n",
+       "     Strain Definitions: [None]\n",
+       "     Plasmid Implementations: ['http://buildcompiler.org/qlSBuNBL_composite_1_impl/1']\n",
+       "     Strain Implementations: [None]\n",
+       "     Fusion Sites: ['A', 'E']\n",
+       "     Antibiotic Resistance: Kanamycin],\n",
+       "  'https://sbolcanvas.org/i0mwvNcgH/1': [Plasmid:\n",
+       "     Name: i0mwvNcgH_composite_1_A_E\n",
+       "     Plasmid Definition: http://buildcompiler.org/i0mwvNcgH_composite_1/1\n",
+       "     Strain Definitions: [None]\n",
+       "     Plasmid Implementations: ['http://buildcompiler.org/i0mwvNcgH_composite_1_impl/1']\n",
+       "     Strain Implementations: [None]\n",
+       "     Fusion Sites: ['A', 'E']\n",
+       "     Antibiotic Resistance: Kanamycin]},\n",
+       " <sbol2.document.Document at 0x1110c3610>)"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "product_doc = sbol2.Document()\n",
+    "\n",
+    "buildcompiler.assembly_lvl1(design_defs, product_doc)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "00834b0c",
+   "metadata": {},
+   "source": [
+    "## LVL 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3e2272ff",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Gen\n",
+      "Gen1\n",
+      "Plasmid:\n",
+      "  Name: Gen_Gen1_plas_1_simple_A_E\n",
+      "  Plasmid Definition: http://buildcompiler.org/Gen_Gen1_plas_1_simple/1\n",
       "  Strain Definitions: [None]\n",
-      "  Plasmid Implementations: ['https://SBOL2Build.org/composite_1_impl/1']\n",
+      "  Plasmid Implementations: ['http://buildcompiler.org/Gen_Gen1_plas_1_impl/1']\n",
       "  Strain Implementations: [None]\n",
-      "  Fusion Sites: ['A', 'B', 'C', 'D', 'E']\n",
+      "  Fusion Sites: ['A', 'E']\n",
       "  Antibiotic Resistance: Kanamycin\n",
-      "]\n"
+      "\n",
+      "Plasmid:\n",
+      "  Name: Gen1_Gen1_plas_1_simple_E_F\n",
+      "  Plasmid Definition: http://buildcompiler.org/Gen1_Gen1_plas_1_simple/1\n",
+      "  Strain Definitions: [None]\n",
+      "  Plasmid Implementations: ['http://buildcompiler.org/Gen1_Gen1_plas_1_impl/1']\n",
+      "  Strain Implementations: [None]\n",
+      "  Fusion Sites: ['E', 'F']\n",
+      "  Antibiotic Resistance: Kanamycin\n",
+      "\n",
+      "Success with backbone: DVA_AF2_A_F and plasmids: ['Gen_Gen1_plas_1_simple_A_E', 'Gen1_Gen1_plas_1_simple_E_F']\n",
+      "Plasmid:\n",
+      "  Name: DVA_AF2_A_F\n",
+      "  Plasmid Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/DVA_AF2/1\n",
+      "  Strain Definitions: [None]\n",
+      "  Plasmid Implementations: ['https://synbiohub.org/user/Gon/impl_test/DVA_AF2_impl/1']\n",
+      "  Strain Implementations: None\n",
+      "  Fusion Sites: ['A', 'F']\n",
+      "  Antibiotic Resistance: Ampicillin\n",
+      "\n",
+      "Comparing gctt (Gen1_Gen1_plas_1_simple_extracted_part)to gcttand reverse: cgct (Gen1_Gen1_plas_1_simple_extracted_part)to ggag\n",
+      "Comparing cgct (DVA_AF2_extracted_backbone)to cgctand reverse: ggag (DVA_AF2_extracted_backbone)to ggag\n"
      ]
     }
    ],
    "source": [
-    "print(buildcompiler.restriction_enzyme_implementations)\n",
-    "print(buildcompiler.ligase_implementations)\n",
+    "lvl2_design_doc = sbol2.Document()\n",
+    "lvl2_design_doc.read(\"../tests/test_files/ExampleLvl2_design.xml\")\n",
     "\n",
-    "composite_plasmids = buildcompiler.assembly_lvl1(design, None)"
+    "\n",
+    "composite_plasmids, final_doc = buildcompiler.assembly_lvl2(\n",
+    "    lvl2_design_doc, product_name=\"lvl2\"\n",
+    ")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 7,
+   "id": "ba31c4c6",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[Plasmid:\n",
+      "  Name: lvl2_1_A_F\n",
+      "  Plasmid Definition: http://buildcompiler.org/lvl2_1/1\n",
+      "  Strain Definitions: [None]\n",
+      "  Plasmid Implementations: ['http://buildcompiler.org/lvl2_1_impl/1']\n",
+      "  Strain Implementations: [None]\n",
+      "  Fusion Sites: ['A', 'F']\n",
+      "  Antibiotic Resistance: Ampicillin\n",
+      "]\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "'Valid.'"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "print(composite_plasmids)\n",
+    "final_doc.write(\"lvl2_assembly.xml\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
    "id": "79fd0cb5",
    "metadata": {},
    "outputs": [],
@@ -109,46 +276,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "id": "8f4ea67c",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'composite_plasmids' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
-      "\u001b[31mNameError\u001b[39m                                 Traceback (most recent call last)",
-      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[6]\u001b[39m\u001b[32m, line 1\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m1\u001b[39m bacterial_transformation(\u001b[43mcomposite_plasmids\u001b[49m, chassis_implementation, chassis, final_doc)\n",
-      "\u001b[31mNameError\u001b[39m: name 'composite_plasmids' is not defined"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# bacterial_transformation(composite_plasmids, chassis_implementation, chassis, final_doc)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5553bfc3",
+   "id": "cd334add",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "'Valid.'"
-      ]
-     },
-     "execution_count": 12,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "# final_doc.write(\"fullbuild.xml\")"
-   ]
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {