Merge pull request #190 from indralab/hackathon

Improvements and hackathon scenario

mira/metamodel/io.py

@@ -2,7 +2,7 @@
 
 import json
 import sympy
-from .template_model import TemplateModel
+from .template_model import TemplateModel, SympyExprStr
 
 
 def model_from_json_file(fname) -> TemplateModel:
@@ -42,6 +42,8 @@ def expression_to_mathml(expression: sympy.Expr, *args, **kwargs) -> str:
     Here we pay attention to not style underscores and numeric suffixes
     in special ways.
     """
+    if isinstance(expression, SympyExprStr):
+        expression = expression.args[0]
     mappings = {}
     for sym in expression.atoms(sympy.Symbol):
         name = '|' + str(sym).replace('_', 'QQQ') + '|'

mira/metamodel/schema.json

@@ -30,6 +30,11 @@
           "description": "The name of the concept.",
           "type": "string"
         },
+        "display_name": {
+          "title": "Display Name",
+          "description": "An optional display name for the concept. If not provided, the name can be used for display purposes.",
+          "type": "string"
+        },
         "description": {
           "title": "Description",
           "description": "An optional description of the concept.",
@@ -470,6 +475,11 @@
           "description": "The name of the concept.",
           "type": "string"
         },
+        "display_name": {
+          "title": "Display Name",
+          "description": "An optional display name for the concept. If not provided, the name can be used for display purposes.",
+          "type": "string"
+        },
         "description": {
           "title": "Description",
           "description": "An optional description of the concept.",
@@ -516,8 +526,7 @@
         }
       },
       "required": [
-        "name",
-        "value"
+        "name"
       ]
     },
     "Initial": {
@@ -548,6 +557,11 @@
           "description": "The name of the concept.",
           "type": "string"
         },
+        "display_name": {
+          "title": "Display Name",
+          "description": "An optional display name for the concept. If not provided, the name can be used for display purposes.",
+          "type": "string"
+        },
         "description": {
           "title": "Description",
           "description": "An optional description of the concept.",

mira/metamodel/template_model.py

@@ -31,7 +31,7 @@ class Distribution(BaseModel):
 
 class Parameter(Concept):
     """A Parameter is a special type of Concept that carries a value."""
-    value: float = Field(
+    value: Optional[float] = Field(
         default_factory=None, description="Value of the parameter.")
 
     distribution: Optional[Distribution] = Field(

mira/metamodel/templates.py

@@ -124,6 +124,10 @@ class Concept(BaseModel):
     """
 
     name: str = Field(..., description="The name of the concept.")
+    display_name: str = \
+        Field(None, description="An optional display name for the concept. "
+                                "If not provided, the name can be used for "
+                                "display purposes.")
     description: Optional[str] = \
         Field(None, description="An optional description of the concept.")
     identifiers: Mapping[str, str] = Field(

mira/modeling/__init__.py

@@ -108,8 +108,8 @@ def assemble_variable(
         return var
 
     def assemble_parameter(self, template: Template, tkey) -> ModelParameter:
-        rate_parameters = self.template_model.get_parameters_from_rate_law(
-            template.rate_law)
+        rate_parameters = sorted(
+            self.template_model.get_parameters_from_rate_law(template.rate_law))
 
         if rate_parameters:
             model_parameters = []
@@ -133,8 +133,8 @@ def assemble_parameter(self, template: Template, tkey) -> ModelParameter:
 
     def make_model(self):
         for name, observable in self.template_model.observables.items():
-            params = observable.get_parameter_names(
-                self.template_model.parameters)
+            params = sorted(
+                observable.get_parameter_names(self.template_model.parameters))
             self.observables[observable.name] = \
                 ModelObservable(observable, params)
             for key in params:

mira/modeling/askenet/petrinet.py

@@ -55,6 +55,7 @@ def __init__(self, model: Model):
             # Use the variable's concept name if possible but fall back
             # on the key otherwise
             vmap[key] = name = var.concept.name or str(key)
+            display_name = var.concept.display_name or name
             # State structure
             # {
             #   'id': str,
@@ -63,7 +64,7 @@ def __init__(self, model: Model):
             # }
             states_dict = {
                 'id': name,
-                'name': name,
+                'name': display_name,
                 'grounding': {
                     'identifiers': {k: v for k, v in
                                     var.concept.identifiers.items()
@@ -258,10 +259,11 @@ def to_json_file(self, fname, name=None, description=None,
         kwargs :
             Additional keyword arguments to pass to :func:`json.dump`.
         """
+        indent = kwargs.pop('indent', 1)
         js = self.to_json(name=name, description=description,
                           model_version=model_version)
         with open(fname, 'w') as fh:
-            json.dump(js, fh, **kwargs)
+            json.dump(js, fh, indent=indent, **kwargs)
 
 
 class Initial(BaseModel):

mira/sources/askenet/petrinet.py

@@ -226,7 +226,11 @@ def state_to_concept(state):
     #     }
     #   }
     # }
-    name = state.get('name') or state['id']
+    # Note that in the shared representation we have id and name
+    # whereas for Concepts in MIRA we have names and display
+    # names
+    name = state['id']
+    display_name = state.get('name')
     grounding = state.get('grounding', {})
     identifiers = grounding.get('identifiers', {})
     context = grounding.get('modifiers', {})
@@ -239,6 +243,7 @@ def state_to_concept(state):
             units_expr = sympy.parse_expr(expr, local_dict=UNIT_SYMBOLS)
             units_obj = Unit(expression=units_expr)
     return Concept(name=name,
+                   display_name=display_name,
                    identifiers=identifiers,
                    context=context,
                    units=units_obj)

mira/sources/sbml/processor.py

@@ -190,6 +190,14 @@ def _lookup_concepts_filtered(species_ids) -> List[Concept]:
             product_species = [species.species for species in reaction.products]
 
             rate_law = reaction.getKineticLaw()
+            # Some rate laws define parameters locally and so we need to
+            # extract them and add them to the global parameter list
+            for parameter in rate_law.parameters:
+                all_parameters[parameter.id] = {'value': parameter.value,
+                                                'description': parameter.name if parameter.name else None,
+                                                'units': self.get_object_units(parameter)}
+                parameter_symbols[clean_formula(parameter.id)] = \
+                    sympy.Symbol(clean_formula(parameter.id))
 
             rate_expr = sympy.parse_expr(clean_formula(rate_law.formula),
                                          local_dict=all_locals)