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,