fix: minor utils refacor

biosimulators · Feb 29, 2024 · 39f224d · 39f224d
1 parent ae00edc
commit 39f224d
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Showing 2 changed files with 47 additions and 2 deletions.
diff --git a/biosimulator_processes/utils.py b/biosimulator_processes/utils.py
@@ -161,7 +161,7 @@ def generate_copasi_parameter_scan_instance(
             instance_name=f'copasi_{n}',
             config=iteration_model_config
         )
-        for iter_name, iter_config in iteration_instance:
+        for iter_name, iter_config in iteration_instance.items():
             parameter_scan_instance[iter_name] = iteration_instance
 
     emitter_schema = generate_emitter_schema(floating_species='tree[float]', time='float')

diff --git a/notebooks/copasi_process_composer.ipynb b/notebooks/copasi_process_composer.ipynb
@@ -653,14 +653,59 @@
    "id": "9e11e97613ec9e16",
    "execution_count": 3
   },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from biosimulator_processes.utils import generate_copasi_parameter_scan_instance as param_scan"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-29T00:57:43.236081Z",
+     "start_time": "2024-02-29T00:57:42.393787Z"
+    }
+   },
+   "id": "1ecc10e496abe9cb",
+   "execution_count": 1
+  },
+  {
+   "cell_type": "code",
+   "outputs": [
+    {
+     "ename": "ValueError",
+     "evalue": "too many values to unpack (expected 2)",
+     "output_type": "error",
+     "traceback": [
+      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
+      "\u001B[0;31mValueError\u001B[0m                                Traceback (most recent call last)",
+      "Cell \u001B[0;32mIn[2], line 1\u001B[0m\n\u001B[0;32m----> 1\u001B[0m parameter_scan_instance \u001B[38;5;241m=\u001B[39m \u001B[43mparam_scan\u001B[49m\u001B[43m(\u001B[49m\u001B[43mnum_iterations\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;241;43m100\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mentry_config\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43m{\u001B[49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[38;5;124;43mbiomodel_id\u001B[39;49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[43m:\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[38;5;124;43mBIOMD0000000051\u001B[39;49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[43m}\u001B[49m\u001B[43m)\u001B[49m\n",
+      "File \u001B[0;32m~/Desktop/uchc_work/biosimulator-processes/biosimulator_processes/utils.py:164\u001B[0m, in \u001B[0;36mgenerate_copasi_parameter_scan_instance\u001B[0;34m(num_iterations, entry_config)\u001B[0m\n\u001B[1;32m    155\u001B[0m     iteration_model_config \u001B[38;5;241m=\u001B[39m generate_sed_model_config_schema(\n\u001B[1;32m    156\u001B[0m         entrypoint\u001B[38;5;241m=\u001B[39m{\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mbiomodel_id\u001B[39m\u001B[38;5;124m'\u001B[39m: \u001B[38;5;124m'\u001B[39m\u001B[38;5;124mBIOMD0000000051\u001B[39m\u001B[38;5;124m'\u001B[39m},\n\u001B[1;32m    157\u001B[0m         species_changes\u001B[38;5;241m=\u001B[39m{\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mExtracellular Glucose\u001B[39m\u001B[38;5;124m'\u001B[39m: {\u001B[38;5;124m'\u001B[39m\u001B[38;5;124minitial_concentration\u001B[39m\u001B[38;5;124m'\u001B[39m: origin_value\u001B[38;5;241m*\u001B[39m\u001B[38;5;241m*\u001B[39mn}},\n\u001B[1;32m    158\u001B[0m         parameter_changes\u001B[38;5;241m=\u001B[39m{\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcatp\u001B[39m\u001B[38;5;124m'\u001B[39m: {\u001B[38;5;124m'\u001B[39m\u001B[38;5;124minitial_value\u001B[39m\u001B[38;5;124m'\u001B[39m: (origin_value \u001B[38;5;241m-\u001B[39m n)\u001B[38;5;241m*\u001B[39m\u001B[38;5;241m*\u001B[39mn}}\n\u001B[1;32m    159\u001B[0m     )\n\u001B[1;32m    160\u001B[0m     iteration_instance \u001B[38;5;241m=\u001B[39m generate_single_copasi_process_instance(\n\u001B[1;32m    161\u001B[0m         instance_name\u001B[38;5;241m=\u001B[39m\u001B[38;5;124mf\u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcopasi_\u001B[39m\u001B[38;5;132;01m{\u001B[39;00mn\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m'\u001B[39m,\n\u001B[1;32m    162\u001B[0m         config\u001B[38;5;241m=\u001B[39miteration_model_config\n\u001B[1;32m    163\u001B[0m     )\n\u001B[0;32m--> 164\u001B[0m     \u001B[38;5;28;01mfor\u001B[39;00m iter_name, iter_config \u001B[38;5;129;01min\u001B[39;00m iteration_instance:\n\u001B[1;32m    165\u001B[0m         parameter_scan_instance[iter_name] \u001B[38;5;241m=\u001B[39m iteration_instance\n\u001B[1;32m    167\u001B[0m emitter_schema \u001B[38;5;241m=\u001B[39m generate_emitter_schema(floating_species\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mtree[float]\u001B[39m\u001B[38;5;124m'\u001B[39m, time\u001B[38;5;241m=\u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mfloat\u001B[39m\u001B[38;5;124m'\u001B[39m)\n",
+      "\u001B[0;31mValueError\u001B[0m: too many values to unpack (expected 2)"
+     ]
+    }
+   ],
+   "source": [
+    "parameter_scan_instance = param_scan(num_iterations=100, entry_config={'biomodel_id': 'BIOMD0000000051'})"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-29T00:58:43.335233Z",
+     "start_time": "2024-02-29T00:58:43.188913Z"
+    }
+   },
+   "id": "35ea2649d0f98801",
+   "execution_count": 2
+  },
   {
    "cell_type": "code",
    "outputs": [],
    "source": [],
    "metadata": {
     "collapsed": false
    },
-   "id": "1ecc10e496abe9cb"
+   "id": "ed3c8d517ac54852"
   }
  ],
  "metadata": {