added data model demo

biosimulators · Mar 1, 2024 · 7d19249 · 7d19249
1 parent 42c3c84
commit 7d19249
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diff --git a/biosimulator_processes/data_model.py b/biosimulator_processes/data_model.py
@@ -29,7 +29,7 @@
 # TODO: You may be able to resolve this warning by setting `model_config['protected_namespaces'] = ()`.
 class BaseModel(Base):
     model_config = ConfigDict(arbitrary_types_allowed=True)
-    protected_namespaces: Tuple = Field(default=())
+    # protected_namespaces: Tuple = Field(default=())
 
 
 class SpeciesChanges(BaseModel):  # <-- this is done like set_species('B', kwarg=) where the inner most keys are the kwargs
@@ -61,7 +61,7 @@ class ReactionChanges(BaseModel):
     reaction_scheme: Union[NoneType, str] = Field(default=None)
 
 
-class ModelChanges:
+class ModelChanges(BaseModel):
     species_changes: Union[NoneType, List[SpeciesChanges]] = Field(default=None)
     global_parameter_changes: Union[NoneType, List[GlobalParameterChanges]] = Field(default=None)
     reaction_changes: Union[NoneType, List[ReactionChanges]] = Field(default=None)
@@ -72,7 +72,7 @@ class ModelSource(BaseModel):
 
 
 class BiomodelId(ModelSource):
-    value: str = Field(default='')
+    value: str
 
     @classmethod
     @field_validator('value')
@@ -82,7 +82,7 @@ def check_value(cls, v):
 
 
 class ModelFilepath(BaseModel):
-    value: str = Field(default='')
+    value: str
 
     @classmethod
     @field_validator('value')
@@ -96,15 +96,13 @@ class Model(BaseModel):
 
         Parameters:
             model_id: `str`
-            input_source: `str`
             model_source: `Union[biosimulator_processes.data_model.ModelFilepath, biosimulator_processes.data_model.BiomodelId]`
             model_language: `str`
             model_name: `str`
             model_changes: `biosimulator_processes.data_model.ModelChanges`
     """
     model_id: str = Field(default='')
-    input_source: str  # <-- user input
-    model_source: Union[ModelFilepath, BiomodelId]  # <-- SED type validated by constructor
+    model_source: str  # <-- SED type validated by constructor
     model_language: str = Field(default='sbml')
     model_name: str = Field(default='Unnamed Composite Process Model')
     model_changes: ModelChanges
@@ -113,19 +111,34 @@ class Model(BaseModel):
     @field_validator('model_source')
     def set_value(cls):
         """Verify that the model source is set to only either a path or a biomodels id"""
-        if '/' in cls.input_source:
-            return ModelFilepath(value=cls.input_source)
-        elif 'BIO' in cls.input_source:
-            return BiomodelId(value=cls.input_source)
+        # if '/' in cls.model_source:
+        #     return ModelFilepath(value=cls.model_source)
+        # elif 'BIO' in cls.input_source:
+        #     return BiomodelId(value=cls.model_source)
+        if '/' not in cls.model_source or 'BIO' not in cls.model_source:
+            raise AttributeError('You must pass either a model filepath or valid biomodel id.')
+        else:
+            return cls.model_source
 
 
 class ProcessConfigSchema(BaseModel):
-    config: Dict
+    config: Dict = Field(default={})
 
 
-class CopasiProcessConfigSchema(ProcessConfigSchema):
-    model: Union[Dict, Model]
+class CopasiProcessConfigSchema(BaseModel):
     method: str = Field(default='deterministic')
+    model: Union[Model, Dict]
+
+    @classmethod
+    @field_serializer('model')
+    def serialize_model(cls):
+        return cls.model.model_dump()
+
+    '''@classmethod
+    @field_validator('model')
+    def set_model(cls):
+        if isinstance(cls.model, Model):
+            return cls.model.model_dump()'''
 
 
 class PortSchema(BaseModel):

diff --git a/notebooks/data_model_demo.ipynb b/notebooks/data_model_demo.ipynb
@@ -7,8 +7,8 @@
    "metadata": {
     "collapsed": true,
     "ExecuteTime": {
-     "end_time": "2024-03-01T16:58:02.687656Z",
-     "start_time": "2024-03-01T16:58:02.684480Z"
+     "end_time": "2024-03-01T17:36:11.752324Z",
+     "start_time": "2024-03-01T17:36:11.749069Z"
     }
    },
    "outputs": [],
@@ -69,13 +69,14 @@
     }
    ],
    "source": [
-    "from biosimulator_processes.data_model import *"
+    "from biosimulator_processes.data_model import *\n",
+    "from process_bigraph import pf"
    ],
    "metadata": {
     "collapsed": false,
     "ExecuteTime": {
-     "end_time": "2024-03-01T16:58:04.483343Z",
-     "start_time": "2024-03-01T16:58:02.800619Z"
+     "end_time": "2024-03-01T17:36:13.415658Z",
+     "start_time": "2024-03-01T17:36:11.894800Z"
     }
    },
    "id": "3cd5053431aed7e1",
@@ -85,21 +86,125 @@
    "cell_type": "code",
    "outputs": [],
    "source": [
+    "speciesChangesA = SpeciesChanges(\n",
+    "    species_name='A',\n",
+    "    initial_concentration=20.017\n",
+    ")\n",
     "\n",
+    "speciesChangesB = SpeciesChanges(\n",
+    "    species_name='B',\n",
+    "    expression='A + B = C'\n",
+    ")\n",
     "\n",
+    "process_changes = ModelChanges(\n",
+    "   species_changes=[speciesChangesA, speciesChangesB]\n",
+    ")\n",
+    "\n",
+    "# process_biomodel_id = BiomodelId(value='BIOMD0000000861')\n",
     "\n",
     "process_model = Model(\n",
     "    model_id='BioModel',\n",
-    "    input_source='BIOMD0000000861',\n",
+    "    model_source='BIOMD0000000861',\n",
     "    model_name='Bachmann2011',\n",
-    "    model_changes=''\n",
+    "    model_changes=process_changes\n",
     ")"
    ],
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-01T17:36:13.418537Z",
+     "start_time": "2024-03-01T17:36:13.415607Z"
+    }
    },
    "id": "6bf18cbc74f1f95f",
-   "execution_count": null
+   "execution_count": 3
+  },
+  {
+   "cell_type": "code",
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "biosimulator_processes.data_model.Model"
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "type(process_model)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-01T17:36:15.889304Z",
+     "start_time": "2024-03-01T17:36:15.883583Z"
+    }
+   },
+   "id": "6dd932af0c8358aa",
+   "execution_count": 4
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "copasi_process = CopasiProcessConfigSchema(\n",
+    "    model=process_model,\n",
+    "    method='stochastic'\n",
+    ")"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-01T17:36:16.365986Z",
+     "start_time": "2024-03-01T17:36:16.363866Z"
+    }
+   },
+   "id": "909c4fc3a751659",
+   "execution_count": 5
+  },
+  {
+   "cell_type": "code",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{ 'method': 'stochastic',\n",
+      "  'model': { 'model_changes': { 'global_parameter_changes': None,\n",
+      "                                'reaction_changes': None,\n",
+      "                                'species_changes': [ { 'expression': None,\n",
+      "                                                       'initial_concentration': 20.017,\n",
+      "                                                       'initial_expression': None,\n",
+      "                                                       'initial_particle_number': None,\n",
+      "                                                       'species_name': 'A',\n",
+      "                                                       'unit': None},\n",
+      "                                                     { 'expression': 'A + B = '\n",
+      "                                                                     'C',\n",
+      "                                                       'initial_concentration': None,\n",
+      "                                                       'initial_expression': None,\n",
+      "                                                       'initial_particle_number': None,\n",
+      "                                                       'species_name': 'B',\n",
+      "                                                       'unit': None}]},\n",
+      "             'model_id': 'BioModel',\n",
+      "             'model_language': 'sbml',\n",
+      "             'model_name': 'Bachmann2011',\n",
+      "             'model_source': 'sdfadf'}}\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(pf(copasi_process.model_dump()))"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-01T17:36:16.957634Z",
+     "start_time": "2024-03-01T17:36:16.954386Z"
+    }
+   },
+   "id": "2be623d00e2fc495",
+   "execution_count": 6
   },
   {
    "cell_type": "code",
@@ -108,7 +213,7 @@
    "metadata": {
     "collapsed": false
    },
-   "id": "6dd932af0c8358aa"
+   "id": "7bca99082a8df8ef"
   }
  ],
  "metadata": {