updated process_types script decs

biosimulators · Feb 28, 2024 · dedd260 · dedd260
1 parent 52c2727
commit dedd260
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diff --git a/biosimulator_processes/process_types.py b/biosimulator_processes/process_types.py
@@ -1,35 +1,34 @@
-"""The following types have been derived from both SEDML L1v4 and basico itself."""
+"""The following types have been derived from both SEDML L1v4 and basico itself.
 
-BASICO_MODEL_CHANGES_TYPE = {
-    'model_changes': {
-         'species_changes': {   # <-- this is done like set_species('B', kwarg=) where the inner most keys are the kwargs
-             'species_name': {
-                 'new_unit_for_species_name': 'maybe[string]',
-                 'new_initial_concentration_for_species_name': 'maybe[float]',
-                 'new_initial_particle_number_for_species_name': 'maybe[float]',
-                 'new_initial_expression_for_species_name': 'maybe[string]',
-                 'new_expression_for_species_name': 'maybe[string]'
-             }
-         },
-         'global_parameter_changes': {   # <-- this is done with set_parameters(PARAM, kwarg=). where the inner most keys are the kwargs
-             'global_parameter_name': {
-                 'new_initial_value_for_global_parameter_name': 'maybe[float]',
-                 'new_initial_expression_for_global_parameter_name': 'maybe[string]',
-                 'new_expression_for_global_parameter_name': 'maybe[string]',
-                 'new_status_for_global_parameter_name': 'maybe[string]',
-                 'new_type_for_global_parameter_name': 'maybe[string]'  # (ie: fixed, assignment, reactions)
-             }
-         },
-         'reaction_changes': {
-             'reaction_name': {
-                 'reaction_parameters': {
-                     'reaction_parameter_name': 'maybe[int]'  # (new reaction_parameter_name value)  <-- this is done with set_reaction_parameters(name="(REACTION_NAME).REACTION_NAME_PARAM", value=VALUE)
-                 },
-                 'reaction_scheme': 'maybe[string]'   # <-- this is done like set_reaction(name = 'R1', scheme = 'S + E + F = ES')
-             }
-         }
-    }
-}
+        BASICO_MODEL_CHANGES_TYPE = {
+            'species_changes': {   # <-- this is done like set_species('B', kwarg=) where the inner most keys are the kwargs
+                'species_name': {
+                    'unit': 'maybe[string]',
+                    'initial_concentration': 'maybe[float]',
+                    'initial_particle_number': 'maybe[float]',
+                    'initial_expression': 'maybe[string]',
+                    'expression': 'maybe[string]'
+                }
+            },
+            'global_parameter_changes': {   # <-- this is done with set_parameters(PARAM, kwarg=). where the inner most keys are the kwargs
+                'global_parameter_name': {
+                    'initial_value': 'maybe[float]',
+                    'initial_expression': 'maybe[string]',
+                    'expression': 'maybe[string]',
+                    'status': 'maybe[string]',
+                    'type': 'maybe[string]'  # (ie: fixed, assignment, reactions)
+                }
+            },
+            'reaction_changes': {
+                'reaction_name': {
+                    'parameters': {
+                        'reaction_parameter_name': 'maybe[int]'  # (new reaction_parameter_name value)  <-- this is done with set_reaction_parameters(name="(REACTION_NAME).REACTION_NAME_PARAM", value=VALUE)
+                    },
+                    'reaction_scheme': 'maybe[string]'   # <-- this is done like set_reaction(name = 'R1', scheme = 'S + E + F = ES')
+                }
+            }
+        }
+"""
 
 
 # The first 3 params are NOT optional below for a Model in SEDML. model_source has been adapted to mean point of residence
@@ -45,7 +44,14 @@
         '_default': 'composite_process_model'
     },
     'model_changes': {
-        '_type': 'tree[string]',
-        '_default': BASICO_MODEL_CHANGES_TYPE
+        '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]'
     }
 }
+
+
+# ^ 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.
diff --git a/biosimulator_processes/processes/copasi_process.py b/biosimulator_processes/processes/copasi_process.py
@@ -29,7 +29,7 @@ class CopasiProcess(Process):
         Entrypoints:
 
             A. SBML model file: 
-            B. Reactions (name: {scheme: reaction contents(also defines species))
+            B. Reactions (name: {scheme: reaction contents(also defines species)) 'model'.get('model_changes')
             C. Model search term (load preconfigured model from BioModels)
 
         Optional Parameters:
@@ -63,10 +63,7 @@ class CopasiProcess(Process):
                                 'reaction_scheme': 'string'   # <-- this is done like set_reaction(name = 'R1', scheme = 'S + E + F = ES')
                             }
                         }
-                        ^ 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.
+
                         
             B. 'method', changes the algorithm(s) used to solve the model
             C. 'units', (tree): quantity, volume, time, area, length
@@ -75,18 +72,18 @@ class CopasiProcess(Process):
 
             As per SEDML v4 specifications (section2.2.4), p.32:sed-ml-L1V4.
     """
-    # TODO: map this to SED syntax
+
     config_schema = {
-        'model': {  # <-- sourced from SEDML L1v4
+        'model': {
             '_type': 'tree[string]',
             '_default': MODEL_TYPE
         },
         'biomodel_id': 'string',  # <-- implies the lack of either model_file or model_reactions
+        'units': 'maybe[tree[string]]',
         'method': {
             '_type': 'string',
             '_default': 'lsoda'
-        },
-        'units': 'tree[string]'
+        }
     }
 
     def __init__(self, config=None, core=None):