adjusted reaction in example for copasi

biosimulator_processes/processes/copasi_process.py

@@ -17,6 +17,7 @@
 
 
 from typing import Dict
+from pandas import DataFrame
 from basico import (
     load_model,
     get_species,
@@ -111,7 +112,7 @@ class CopasiProcess(Process):
     config_schema = {
         'model': MODEL_TYPE,
         'biomodel_id': 'maybe[string]',  # <-- implies the lack of either model_file or model_reactions
-        'units': 'maybe[tree[string]]',
+        'units': 'tree[string]',
         'method': {
             '_type': 'string',
             '_default': 'deterministic'
@@ -138,25 +139,21 @@ def __init__(self, config=None, core=None):
             self.copasi_model_object = fetch_biomodel(model_id=source_model_id)
         # C. enter with a new model
         else:
-            self.copasi_model_object = new_model(name='CopasiProcess Model')
+            self.copasi_model_object = new_model(name='CopasiProcess Model', **self.config.get('units'))
 
         self.model_changes: Dict = self.config['model'].get('model_changes', {})
 
         # add reactions
-        reaction_changes: Dict = self.model_changes.get('reaction_changes')
-        if reaction_changes:
-            for reaction_name, reaction_spec in reaction_changes.items():
-                add_reaction(
-                    name=reaction_name,
-                    scheme=reaction_spec,
-                    model=self.copasi_model_object
-                )
+        reaction_changes: Dict = self.model_changes.get('reaction_changes', None)
+        if reaction_changes is not None:
+            for reaction_name, reaction_scheme in reaction_changes.items():
+                add_reaction(reaction_name, reaction_scheme, model=self.copasi_model_object)
 
         # Get the species (floating only)  TODO: add boundary species
         self.floating_species_list = get_species(model=self.copasi_model_object).index.tolist()
         self.floating_species_initial = get_species(model=self.copasi_model_object)['concentration'].tolist()
 
-        # Get the list of parameters and their values
+        # Get the list of parameters and their values (it is possible to run a model without any parameters)
         self.model_parameters_list = get_parameters(model=self.copasi_model_object).index.tolist()
         self.model_parameter_values = get_parameters(model=self.copasi_model_object)['initial_value'].tolist()
 

notebooks/copasi_process_composer.ipynb

@@ -174,23 +174,9 @@
    "source": [
     "workflow = Composite({\n",
     "    'state': instance\n",
-    "})\n",
-    "\n",
-    "# basico.set_report_dict('composite_process_model', task=T.TIME_COURSE)\n"
+    "})"
    ]
   },
-  {
-   "cell_type": "code",
-   "outputs": [],
-   "source": [
-    "basico.T.TIME_COURSE"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "5690cd2793a5a53b",
-   "execution_count": null
-  },
   {
    "cell_type": "markdown",
    "id": "6a402e48fbc30a5b",
@@ -213,18 +199,6 @@
     "workflow.run(10)"
    ]
   },
-  {
-   "cell_type": "code",
-   "outputs": [],
-   "source": [
-    "workflow.process_paths"
-   ],
-   "metadata": {
-    "collapsed": false
-   },
-   "id": "92246d0c4cdc0e51",
-   "execution_count": null
-  },
   {
    "cell_type": "markdown",
    "id": "d0ff3a2822a8fa2c",
@@ -291,7 +265,11 @@
     "        'address': 'local:copasi',\n",
     "        'config': {\n",
     "            'model': {\n",
-    "                'model_changes':\n",
+    "                'model_changes': {\n",
+    "                    'reaction_changes': {\n",
+    "                        'R1': 'A -> B'\n",
+    "                    }\n",
+    "                }\n",
     "            }\n",
     "        },\n",
     "        'inputs': {\n",