updated utils generator

biosimulators · Feb 28, 2024 · f2b711c · f2b711c
1 parent 501693c
commit f2b711c
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Showing 2 changed files with 84 additions and 42 deletions.
diff --git a/biosimulator_processes/utils.py b/biosimulator_processes/utils.py
@@ -45,12 +45,9 @@ def generate_emitter_schema(
         '_type': 'step',
         'address': 'local:ram-emitter',
         'config': {
-            'emit': {
-                'floating_species': 'tree[float]',
-                'time': 'float',
-            },
+            'emit': {**emit_values_schema},
         },
-        'inputs': {
+        'inputs': {  # TODO: make this generalized
             'floating_species': ['floating_species_store'],
             'time': ['time_store'],
         }
@@ -73,7 +70,8 @@ def generate_composite_copasi_process_instance(instance_name: str, config: Dict,
         Args:
             instance_name:`str`: name of the new instance referenced by PBG.
             config:`Dict`: see `biosimulator_processes.processes.copasi_process.CopasiProcess`
-            add_emitter:`
+            add_emitter:`bool`: Adds emitter schema configured for CopasiProcess IO store if `True`. Defaults
+                to `True`.
     """
     instance = {}
     instance[instance_name] = {
@@ -91,38 +89,10 @@ def generate_composite_copasi_process_instance(instance_name: str, config: Dict,
             'time': ['time_store'],
         }
     }
+    if add_emitter:
+        instance['emitter'] = generate_copasi_process_emitter_schema()
 
-    return {
-        instance_name: {
-            '_type': 'process',
-            'address': 'local:copasi',
-            'config': config,
-            'inputs': {
-                'floating_species': ['floating_species_store'],
-                'model_parameters': ['model_parameters_store'],
-                'time': ['time_store'],
-                'reactions': ['reactions_store']
-            },
-            'outputs': {
-                'floating_species': ['floating_species_store'],
-                'time': ['time_store'],
-            }
-        },
-        'emitter': {
-            '_type': 'step',
-            'address': 'local:ram-emitter',
-            'config': {
-                'emit': {
-                    'floating_species': 'tree[float]',
-                    'time': 'float',
-                },
-            },
-            'inputs': {
-                'floating_species': ['floating_species_store'],
-                'time': ['time_store'],
-            }
-        }
-    }
+    return instance
 
 
 
diff --git a/notebooks/copasi_process_composer.ipynb b/notebooks/copasi_process_composer.ipynb
@@ -16,8 +16,8 @@
    "id": "initial_id",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2024-02-28T21:35:30.970032Z",
-     "start_time": "2024-02-28T21:35:30.965409Z"
+     "end_time": "2024-02-28T22:21:50.630537Z",
+     "start_time": "2024-02-28T22:21:50.627788Z"
     }
    },
    "outputs": [],
@@ -34,8 +34,8 @@
    "metadata": {
     "collapsed": false,
     "ExecuteTime": {
-     "end_time": "2024-02-28T21:35:36.900035Z",
-     "start_time": "2024-02-28T21:35:34.590082Z"
+     "end_time": "2024-02-28T22:21:52.425406Z",
+     "start_time": "2024-02-28T22:21:50.700424Z"
     }
    },
    "outputs": [
@@ -475,14 +475,86 @@
    "id": "3b8a27c7dd246d02",
    "execution_count": 1
   },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from biosimulator_processes.utils import generate_composite_copasi_process_instance as copasi_instance"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-28T22:25:33.366994Z",
+     "start_time": "2024-02-28T22:25:32.646371Z"
+    }
+   },
+   "id": "57712e54678bcb70",
+   "execution_count": 1
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "model_config = {\n",
+    "    'model': {\n",
+    "        'model_changes': {\n",
+    "            'reaction_changes': {\n",
+    "                'R1': 'A -> B'\n",
+    "            }\n",
+    "        }\n",
+    "    }\n",
+    "}\n",
+    "\n",
+    "\n",
+    "instance = copasi_instance(\n",
+    "    instance_name='copasi_A',\n",
+    "    config=model_config,\n",
+    "    add_emitter=True\n",
+    ")"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-28T22:25:51.771960Z",
+     "start_time": "2024-02-28T22:25:51.763524Z"
+    }
+   },
+   "id": "482579fdd5bb4350",
+   "execution_count": 2
+  },
+  {
+   "cell_type": "code",
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "{'copasi_A': {'_type': 'process',\n  'address': 'local:copasi',\n  'config': {'model': {'model_changes': {'reaction_changes': {'R1': 'A -> B'}}}},\n  'inputs': {'floating_species': ['floating_species_store'],\n   'model_parameters': ['model_parameters_store'],\n   'time': ['time_store'],\n   'reactions': ['reactions_store']},\n  'outputs': {'floating_species': ['floating_species_store'],\n   'time': ['time_store']}},\n 'emitter': {'_type': 'step',\n  'address': 'local:ram-emitter',\n  'config': {'emit': {'floating_species': 'tree[float]', 'time': 'float'}},\n  'inputs': {'floating_species': ['floating_species_store'],\n   'time': ['time_store']}}}"
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "instance"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-28T22:25:53.779628Z",
+     "start_time": "2024-02-28T22:25:53.774909Z"
+    }
+   },
+   "id": "9e11e97613ec9e16",
+   "execution_count": 3
+  },
   {
    "cell_type": "code",
    "outputs": [],
    "source": [],
    "metadata": {
     "collapsed": false
    },
-   "id": "57712e54678bcb70"
+   "id": "1ecc10e496abe9cb"
   }
  ],
  "metadata": {