updated builder and datamodel for spec

biosimulator_processes/data_model.py

@@ -27,7 +27,9 @@
     'BaseModel',
     'TimeCourseProcessConfigSchema',
     'ModelParameter',
-    'ProcessConfig'
+    'ProcessConfig',
+    'Port',
+    'State'
 ]
 
 
@@ -195,6 +197,22 @@ def set_value(cls):
 
 
 # --- TYPE REGISTRY
+class ProcessConfig(BaseModel):
+    value: Dict
+
+
+class Port(BaseModel):
+    value: Dict
+
+
+class State(BaseModel):
+    # THINK: builder_api LN.120: add_process. TODO: This should be parsable by the builder in add process.
+    _type: str
+    address: str
+    config: ProcessConfig
+    inputs: Port
+    outputs: Port
+
 
 # --- PROCESSES
 class ProcessConfigSchema(BaseModel):

biosimulator_processes/processes/copasi_process.py

@@ -16,7 +16,7 @@
 """
 
 
-from typing import Dict
+from typing import Dict, Union
 from pandas import DataFrame
 from basico import *
 # from basico import (
@@ -81,12 +81,17 @@ class CopasiProcess(Process):
 
     config_schema = TimeCourseProcessConfigSchema().model_dump()
 
-    def __init__(self, config: ProcessConfig=None, core=None):
+    def __init__(self,
+                 config: Union[CopasiProcessConfig, Dict] = None,
+                 core=None):
         super().__init__(config, core)
 
-
-        model_source = self.config['model']['model_source']['value']
-        self.model_changes = self.config['model'].get('model_changes', {})
+        if isinstance(self.config, dict):
+            model_source = self.config['model']['model_source']['value']
+            self.model_changes = self.config['model'].get('model_changes', {})
+        elif isinstance(self.config, CopasiProcessConfig):
+            model_source = self.config.model.model_source.value
+            self.model_changes = self.config.model.model_changes or {}
 
         # A. enter with model_file
         if '/' in model_source: