diff --git a/biosimulator_processes/utils.py b/biosimulator_processes/utils.py index 072627ac2..f1e399989 100644 --- 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 index 95eaeb449..65cde9b04 100644 --- a/notebooks/copasi_process_composer.ipynb +++ b/notebooks/copasi_process_composer.ipynb @@ -653,6 +653,51 @@ "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": [], @@ -660,7 +705,7 @@ "metadata": { "collapsed": false }, - "id": "1ecc10e496abe9cb" + "id": "ed3c8d517ac54852" } ], "metadata": {