updated utils function to implement entrypoint

biosimulator_processes/process_types.py

@@ -33,8 +33,8 @@
 
 # The first 3 params are NOT optional below for a Model in SEDML. model_source has been adapted to mean point of residence
 MODEL_TYPE = {
-    'model_id': 'string',    # could be used as the BioModels id
-    'model_source': 'string',    # could be used as the "model_file" below (SEDML l1V4 uses URIs); what if it was 'model_source': 'sbml:model_filepath'  ?
+    'model_id': 'string',
+    'model_source': 'string',    # could be used as the "model_file" or "biomodel_id" below (SEDML l1V4 uses URIs); what if it was 'model_source': 'sbml:model_filepath'  ?
     'model_language': {    # could be used to load a different model language supported by COPASI/basico
         '_type': 'string',
         '_default': 'sbml'    # perhaps concatenate this with 'model_source'.value? I.E: 'model_source': 'MODEL_LANGUAGE:MODEL_FILEPATH' <-- this would facilitate verifying correct model fp types.
@@ -47,11 +47,6 @@
         'species_changes': 'tree[string]',   # <-- this is done like set_species('B', kwarg=) where the inner most keys are the kwargs
         'global_parameter_changes': 'tree[string]',  # <-- this is done with set_parameters(PARAM, kwarg=). where the inner most keys are the kwargs
         'reaction_changes': 'tree[string]'
-    }
+    },
+    'model_units': 'tree[string]'
 }
-
-
-# ^ Here, the model changes would be applied in either two ways:
-#  A. (model_file/biomodel_id is passed): after model instatiation in the constructor
-#  B. (no model_file or biomodel_id is passed): used to extract reactions. Since adding reactions to an empty model technically
-#   is an act of "changing" the model (empty -> context), it is safe to say that you must pass 'model': {'model_changes': etc...} instead.

biosimulator_processes/processes/copasi_process.py

@@ -71,7 +71,7 @@ class CopasiProcess(Process):
                         'reaction_changes': {
                             'reaction_name': {
                                 'reaction_parameters': {
-                                    reaction_parameter_name: 'int'  # (new reaction_parameter_name value)  <-- this is done with set_reaction_parameters(name="(REACTION_NAME).REACTION_NAME_PARAM", value=VALUE)
+                                    reaction_parameter_name: 'float'  # (new reaction_parameter_name value)  <-- this is done with set_reaction_parameters(name="(REACTION_NAME).REACTION_NAME_PARAM", value=VALUE)
                                 }, 
                                 'reaction_scheme': 'string'   # <-- this is done like set_reaction(name = 'R1', scheme = 'S + E + F = ES')
                             }
@@ -111,8 +111,6 @@ class CopasiProcess(Process):
 
     config_schema = {
         'model': MODEL_TYPE,
-        'biomodel_id': 'maybe[string]',  # <-- implies the lack of either model_file or model_reactions
-        'units': 'tree[string]',
         'method': {
             '_type': 'string',
             '_default': 'deterministic'

biosimulator_processes/utils.py

@@ -1,6 +1,7 @@
 from typing import Dict
 from basico import biomodels, load_model_from_string
 from process_bigraph import Composite, pf
+from pydantic import BaseModel
 
 
 def fetch_biomodel_by_term(term: str, index: int = 0):
@@ -101,6 +102,12 @@ def generate_emitter_schema(
         emitter_type: str = "ram-emitter",
         **emit_values_schema
 ) -> Dict:
+    """
+        Args:
+            **emit_values_schema:`kwargs`: values to be emitted by the address
+
+
+    """
     return {
         '_type': 'step',
         'address': 'local:ram-emitter',
@@ -211,12 +218,9 @@ def generate_sed_model_config_schema(
     }
 
     for param_name, param_val in entrypoint.items():
-        if 'biomodel' in param_name.lower():
-            instance_schema[param_name] = param_val
-        elif 'model_source' in param_name.lower():
-            instance_schema['model'][param_name] = {
-                param_name: param_val
-            }
+        instance_schema['model'][param_name] = {
+            param_name: param_val
+        }
 
     return instance_schema