fix: completed instance schema for working examples

biosimulators · Feb 28, 2024 · 277130a · 277130a
1 parent 2dd6907
commit 277130a
Show file tree

Hide file tree

Showing 2 changed files with 20 additions and 38 deletions.
diff --git a/biosimulator_processes/processes/copasi_process.py b/biosimulator_processes/processes/copasi_process.py
@@ -155,6 +155,9 @@ def __init__(self, config=None, core=None):
         if isinstance(model_parameters, DataFrame):
             self.model_parameters_list = model_parameters.index.tolist()
             self.model_parameter_values = model_parameters['initial_value'].tolist()
+        else:
+            self.model_parameters_list = []
+            self.model_parameter_values = []
 
         # Get a list of reactions
         self.reaction_list = get_reactions(model=self.copasi_model_object).index.tolist()
@@ -189,11 +192,17 @@ def inputs(self):
                 '_apply': 'set',
             } for species_id in self.floating_species_list
         }
+        if self.model_parameters_list:
+            model_params_type = {
+                param_id: 'float' for param_id in self.model_parameters_list
+            }
+        else:
+            model_params_type = {}
+
         return {
             'time': 'float',
             'floating_species': floating_species_type,
-            'model_parameters': {
-                param_id: 'float' for param_id in self.model_parameters_list},
+            'model_parameters': model_params_type,
             'reactions': {
                 reaction_id: 'float' for reaction_id in self.reaction_list},
         }

diff --git a/notebooks/copasi_process_composer.ipynb b/notebooks/copasi_process_composer.ipynb
@@ -24,27 +24,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "c6c10dc5988e52d4",
    "metadata": {
-    "collapsed": false,
-    "ExecuteTime": {
-     "end_time": "2024-02-28T20:57:05.779779Z",
-     "start_time": "2024-02-28T20:57:03.764811Z"
-    }
+    "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "CobraProcess registered successfully.\n",
-      "CopasiProcess registered successfully.\n",
-      "SmoldynProcess registered successfully.\n",
-      "TelluriumProcess registered successfully.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import os \n",
     "from basico import *\n",
@@ -130,7 +115,7 @@
    "outputs": [],
    "source": [
     "root = os.path.abspath('..')\n",
-    "model_path = os.path.join(root, 'biosimulator_processes/model_files/Caravagna2010.xml')\n",
+    "model_path = os.path.join(root, 'biosimulator_processes/model_files/BIOMD0000000061_url.xml')\n",
     "\n",
     "instance = {\n",
     "    'copasi': {\n",
@@ -273,28 +258,15 @@
   },
   {
    "cell_type": "code",
-   "outputs": [
-    {
-     "data": {
-      "text/plain": "'The following types have been derived from both SEDML L1v4 and basico itself.\\n\\n        BASICO_MODEL_CHANGES_TYPE = {\\n            \\'species_changes\\': {   # <-- this is done like set_species(\\'B\\', kwarg=) where the inner most keys are the kwargs\\n                \\'species_name\\': {\\n                    \\'unit\\': \\'maybe[string]\\',\\n                    \\'initial_concentration\\': \\'maybe[float]\\',\\n                    \\'initial_particle_number\\': \\'maybe[float]\\',\\n                    \\'initial_expression\\': \\'maybe[string]\\',\\n                    \\'expression\\': \\'maybe[string]\\'\\n                }\\n            },\\n            \\'global_parameter_changes\\': {   # <-- this is done with set_parameters(PARAM, kwarg=). where the inner most keys are the kwargs\\n                \\'global_parameter_name\\': {\\n                    \\'initial_value\\': \\'maybe[float]\\',\\n                    \\'initial_expression\\': \\'maybe[string]\\',\\n                    \\'expression\\': \\'maybe[string]\\',\\n                    \\'status\\': \\'maybe[string]\\',\\n                    \\'type\\': \\'maybe[string]\\'  # (ie: fixed, assignment, reactions)\\n                }\\n            },\\n            \\'reaction_changes\\': {\\n                \\'reaction_name\\': {\\n                    \\'parameters\\': {\\n                        \\'reaction_parameter_name\\': \\'maybe[int]\\'  # (new reaction_parameter_name value)  <-- this is done with set_reaction_parameters(name=\"(REACTION_NAME).REACTION_NAME_PARAM\", value=VALUE)\\n                    },\\n                    \\'reaction_scheme\\': \\'maybe[string]\\'   # <-- this is done like set_reaction(name = \\'R1\\', scheme = \\'S + E + F = ES\\')\\n                }\\n            }\\n        }\\n'"
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "CHANGES_SCHEMA"
    ],
    "metadata": {
-    "collapsed": false,
-    "ExecuteTime": {
-     "end_time": "2024-02-28T20:57:27.860061Z",
-     "start_time": "2024-02-28T20:57:27.857520Z"
-    }
+    "collapsed": false
    },
    "id": "433d58bbe38402af",
-   "execution_count": 2
+   "execution_count": null
   },
   {
    "cell_type": "code",
@@ -343,7 +315,8 @@
    "metadata": {
     "collapsed": false
    },
-   "id": "8178d3c295764eb6"
+   "id": "8178d3c295764eb6",
+   "execution_count": null
   },
   {
    "cell_type": "code",