From e21854237f602e5692eb53318725e3e1d389d601 Mon Sep 17 00:00:00 2001
From: alexPatrie <alexanderpatrie@gmail.com>
Date: Fri, 1 Mar 2024 14:00:57 -0500
Subject: [PATCH] updated model params for datamodel

---
 biosimulator_processes/data_model.py |  9 +++++----
 notebooks/builder_composer.ipynb     | 22 ++++++++++++++++++----
 2 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/biosimulator_processes/data_model.py b/biosimulator_processes/data_model.py
index 2d784290b..ed18f907a 100644
--- a/biosimulator_processes/data_model.py
+++ b/biosimulator_processes/data_model.py
@@ -106,6 +106,7 @@ class Model(BaseModel):
     model_language: str = Field(default='sbml')
     model_name: str = Field(default='Unnamed Composite Process Model')
     model_changes: ModelChanges
+    model_units: Union[Dict[str, str], None] = None
 
     @field_validator('model_source')
     @classmethod
@@ -261,7 +262,7 @@ class SedModel(FromDict):
     # 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',
-        '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_source': 'dict[string]',  # '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.
@@ -271,9 +272,9 @@ class SedModel(FromDict):
             '_default': 'composite_process_model'
         },
         'model_changes': {
-            '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]'
+            'species_changes': 'maybe[tree[string]]',   # <-- this is done like set_species('B', kwarg=) where the inner most keys are the kwargs
+            'global_parameter_changes': 'maybe[tree[string]]',  # <-- this is done with set_parameters(PARAM, kwarg=). where the inner most keys are the kwargs
+            'reaction_changes': 'maybe[tree[string]]'
         },
         'model_units': 'tree[string]'
     }
diff --git a/notebooks/builder_composer.ipynb b/notebooks/builder_composer.ipynb
index ae47495aa..2739da12c 100644
--- a/notebooks/builder_composer.ipynb
+++ b/notebooks/builder_composer.ipynb
@@ -263,14 +263,28 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "['__abstractmethods__',\n '__annotations__',\n '__class__',\n '__class_getitem__',\n '__class_vars__',\n '__copy__',\n '__deepcopy__',\n '__delattr__',\n '__dict__',\n '__dir__',\n '__doc__',\n '__eq__',\n '__fields__',\n '__fields_set__',\n '__format__',\n '__ge__',\n '__get_pydantic_core_schema__',\n '__get_pydantic_json_schema__',\n '__getattr__',\n '__getattribute__',\n '__getstate__',\n '__gt__',\n '__hash__',\n '__init__',\n '__init_subclass__',\n '__iter__',\n '__le__',\n '__lt__',\n '__module__',\n '__ne__',\n '__new__',\n '__pretty__',\n '__private_attributes__',\n '__pydantic_complete__',\n '__pydantic_core_schema__',\n '__pydantic_custom_init__',\n '__pydantic_decorators__',\n '__pydantic_extra__',\n '__pydantic_fields_set__',\n '__pydantic_generic_metadata__',\n '__pydantic_init_subclass__',\n '__pydantic_parent_namespace__',\n '__pydantic_post_init__',\n '__pydantic_private__',\n '__pydantic_root_model__',\n '__pydantic_serializer__',\n '__pydantic_validator__',\n '__reduce__',\n '__reduce_ex__',\n '__repr__',\n '__repr_args__',\n '__repr_name__',\n '__repr_str__',\n '__rich_repr__',\n '__setattr__',\n '__setstate__',\n '__signature__',\n '__sizeof__',\n '__slots__',\n '__str__',\n '__subclasshook__',\n '__weakref__',\n '_abc_impl',\n '_calculate_keys',\n '_check_frozen',\n '_copy_and_set_values',\n '_get_value',\n '_iter',\n 'construct',\n 'copy',\n 'dict',\n 'from_orm',\n 'json',\n 'method',\n 'model',\n 'model_computed_fields',\n 'model_config',\n 'model_construct',\n 'model_copy',\n 'model_dump',\n 'model_dump_json',\n 'model_extra',\n 'model_fields',\n 'model_fields_set',\n 'model_json_schema',\n 'model_parametrized_name',\n 'model_post_init',\n 'model_rebuild',\n 'model_validate',\n 'model_validate_json',\n 'model_validate_strings',\n 'parse_file',\n 'parse_obj',\n 'parse_raw',\n 'schema',\n 'schema_json',\n 'serialize_model',\n 'update_forward_refs',\n 'validate']"
+     },
+     "execution_count": 28,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "dir()"
+    "dir(process_config)"
    ],
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-01T18:55:44.251693Z",
+     "start_time": "2024-03-01T18:55:44.243963Z"
+    }
    },
-   "id": "a8bc9415d6ac47ad"
+   "id": "a8bc9415d6ac47ad",
+   "execution_count": 28
   },
   {
    "cell_type": "code",