fix: updated datamodel schema

biosimulators · Mar 1, 2024 · 42c3c84 · 42c3c84
1 parent b8bd971
commit 42c3c84
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Showing 2 changed files with 52 additions and 24 deletions.
diff --git a/biosimulator_processes/data_model.py b/biosimulator_processes/data_model.py
@@ -34,20 +34,20 @@ class BaseModel(Base):
 
 class SpeciesChanges(BaseModel):  # <-- this is done like set_species('B', kwarg=) where the inner most keys are the kwargs
     species_name: str
-    unit: str
-    initial_concentration: float
-    initial_particle_number: float
-    initial_expression: str
-    expression: str
+    unit: Union[str, NoneType] = Field(default=None)
+    initial_concentration: Union[float, NoneType] = Field(default=None)
+    initial_particle_number: Union[float, NoneType] = Field(default=None)
+    initial_expression: Union[str, NoneType] = Field(default=None)
+    expression: Union[str, NoneType] = Field(default=None)
 
 
 class GlobalParameterChanges(BaseModel):  # <-- this is done with set_parameters(PARAM, kwarg=). where the inner most keys are the kwargs
     parameter_name: str
-    initial_value: float
-    initial_expression: str
-    expression: str
-    status: str
-    param_type: str  # ie: fixed, assignment, reactions, etc
+    initial_value: Union[float, NoneType] = Field(default=None)
+    initial_expression: Union[str, NoneType] = Field(default=None)
+    expression: Union[str, NoneType] = Field(default=None)
+    status: Union[str, NoneType] = Field(default=None)
+    param_type: Union[str, NoneType] = Field(default=None)  # ie: fixed, assignment, reactions, etc
 
 
 class ReactionParameter(BaseModel):
@@ -57,22 +57,22 @@ class ReactionParameter(BaseModel):
 
 class ReactionChanges(BaseModel):
     reaction_name: str
-    reaction_parameters: Dict[str, ReactionParameter]
-    reaction_scheme: str
+    reaction_parameters: Union[NoneType, Dict[str, ReactionParameter]] = Field(default=None)
+    reaction_scheme: Union[NoneType, str] = Field(default=None)
 
 
 class ModelChanges:
-    species_changes: List[SpeciesChanges]
-    global_parameter_changes: List[GlobalParameterChanges]
-    reaction_changes: List[ReactionChanges]
+    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)
 
 
 class ModelSource(BaseModel):
-    value: str = None
+    value: str
 
 
 class BiomodelId(ModelSource):
-    value: str = None
+    value: str = Field(default='')
 
     @classmethod
     @field_validator('value')
@@ -82,7 +82,7 @@ def check_value(cls, v):
 
 
 class ModelFilepath(BaseModel):
-    value: str = None
+    value: str = Field(default='')
 
     @classmethod
     @field_validator('value')
@@ -92,7 +92,16 @@ def check_value(cls, v):
 
 
 class Model(BaseModel):
-    """The data model declaration for process configuration schemas that support SED"""
+    """The data model declaration for process configuration schemas that support SED.
+
+        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

diff --git a/notebooks/data_model_demo.ipynb b/notebooks/data_model_demo.ipynb
@@ -7,8 +7,8 @@
    "metadata": {
     "collapsed": true,
     "ExecuteTime": {
-     "end_time": "2024-03-01T16:48:23.151735Z",
-     "start_time": "2024-03-01T16:48:23.148684Z"
+     "end_time": "2024-03-01T16:58:02.687656Z",
+     "start_time": "2024-03-01T16:58:02.684480Z"
     }
    },
    "outputs": [],
@@ -74,8 +74,8 @@
    "metadata": {
     "collapsed": false,
     "ExecuteTime": {
-     "end_time": "2024-03-01T16:48:24.895974Z",
-     "start_time": "2024-03-01T16:48:23.425420Z"
+     "end_time": "2024-03-01T16:58:04.483343Z",
+     "start_time": "2024-03-01T16:58:02.800619Z"
     }
    },
    "id": "3cd5053431aed7e1",
@@ -84,12 +84,31 @@
   {
    "cell_type": "code",
    "outputs": [],
-   "source": [],
+   "source": [
+    "\n",
+    "\n",
+    "\n",
+    "process_model = Model(\n",
+    "    model_id='BioModel',\n",
+    "    input_source='BIOMD0000000861',\n",
+    "    model_name='Bachmann2011',\n",
+    "    model_changes=''\n",
+    ")"
+   ],
    "metadata": {
     "collapsed": false
    },
    "id": "6bf18cbc74f1f95f",
    "execution_count": null
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "6dd932af0c8358aa"
   }
  ],
  "metadata": {