Implement display name and update scenario

gyorilab · Jul 6, 2023 · 21d1911 · 21d1911
1 parent 84cd710
commit 21d1911
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Showing 6 changed files with 56 additions and 46 deletions.
diff --git a/mira/metamodel/templates.py b/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(

diff --git a/mira/modeling/askenet/petrinet.py b/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()

diff --git a/mira/sources/askenet/petrinet.py b/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)

diff --git a/notebooks/hackathon_2023.07/scenario1_a.json b/notebooks/hackathon_2023.07/scenario1_a.json
@@ -173,10 +173,6 @@
     }
    ],
    "parameters": [
-    {
-     "id": "beta_s",
-     "value": 1.0
-    },
     {
      "id": "N",
      "value": 5600000.0,
@@ -186,16 +182,20 @@
      }
     },
     {
-     "id": "t_0",
-     "value": 89.0
+     "id": "beta_c",
+     "value": 0.4
+    },
+    {
+     "id": "beta_s",
+     "value": 1.0
     },
     {
      "id": "kappa",
      "value": 0.45454545454545453
     },
     {
-     "id": "beta_c",
-     "value": 0.4
+     "id": "t_0",
+     "value": 89.0
     },
     {
      "id": "delta",
@@ -205,14 +205,6 @@
       "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
      }
     },
-    {
-     "id": "gamma",
-     "value": 0.09090909090909091,
-     "units": {
-      "expression": "1/day",
-      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
-     }
-    },
     {
      "id": "alpha",
      "value": 6.4e-05,
@@ -221,6 +213,14 @@
       "expression_mathml": "<cn>1</cn>"
      }
     },
+    {
+     "id": "gamma",
+     "value": 0.09090909090909091,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
     {
      "id": "rho",
      "value": 0.1111111111111111,

diff --git a/notebooks/hackathon_2023.07/scenario1_c.json b/notebooks/hackathon_2023.07/scenario1_c.json
@@ -174,20 +174,20 @@
    ],
    "parameters": [
     {
-     "id": "beta_s",
-     "value": 1.0
+     "id": "beta_c",
+     "value": 0.4
     },
     {
-     "id": "t_0",
-     "value": 89.0
+     "id": "beta_s",
+     "value": 1.0
     },
     {
      "id": "kappa",
      "value": 0.45454545454545453
     },
     {
-     "id": "beta_c",
-     "value": 0.4
+     "id": "t_0",
+     "value": 89.0
     },
     {
      "id": "delta",
@@ -197,14 +197,6 @@
       "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
      }
     },
-    {
-     "id": "gamma",
-     "value": 0.09090909090909091,
-     "units": {
-      "expression": "1/day",
-      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
-     }
-    },
     {
      "id": "alpha",
      "value": 6.4e-05,
@@ -213,6 +205,14 @@
       "expression_mathml": "<cn>1</cn>"
      }
     },
+    {
+     "id": "gamma",
+     "value": 0.09090909090909091,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
     {
      "id": "rho",
      "value": 0.1111111111111111,

diff --git a/notebooks/hackathon_2023.07/scenario1_d.json b/notebooks/hackathon_2023.07/scenario1_d.json
@@ -174,20 +174,20 @@
    ],
    "parameters": [
     {
-     "id": "beta_s",
-     "value": 1.0
+     "id": "beta_c",
+     "value": 0.4
     },
     {
-     "id": "t_0",
-     "value": 89.0
+     "id": "beta_s",
+     "value": 1.0
     },
     {
      "id": "kappa",
      "value": 0.45454545454545453
     },
     {
-     "id": "beta_c",
-     "value": 0.4
+     "id": "t_0",
+     "value": 89.0
     },
     {
      "id": "delta",
@@ -197,14 +197,6 @@
       "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
      }
     },
-    {
-     "id": "gamma",
-     "value": 0.09090909090909091,
-     "units": {
-      "expression": "1/day",
-      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
-     }
-    },
     {
      "id": "alpha",
      "value": 6.4e-05,
@@ -213,6 +205,14 @@
       "expression_mathml": "<cn>1</cn>"
      }
     },
+    {
+     "id": "gamma",
+     "value": 0.09090909090909091,
+     "units": {
+      "expression": "1/day",
+      "expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
+     }
+    },
     {
      "id": "rho",
      "value": 0.1111111111111111,