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Propagate concept descriptions #392

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merged 2 commits into from
Oct 23, 2024
Merged

Propagate concept descriptions #392

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f54dc4e
Make sure that descriptions for concepts are propogated during ingest…
nanglo123 Oct 23, 2024
997d55c
Add description attribute to State class for petrinet amr, remove tra…
nanglo123 Oct 23, 2024
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12 changes: 8 additions & 4 deletions mira/modeling/amr/petrinet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,7 @@ def __init__(self, model: Model):
# on the key otherwise
vmap[key] = name = var.concept.name or str(key)
display_name = var.concept.display_name or name
description = var.concept.description
# State structure
# {
# 'id': str,
Expand All @@ -69,14 +70,16 @@ def __init__(self, model: Model):
# }
states_dict = {
'id': name,
'name': display_name,
'grounding': {
'name': display_name
}
if description:
states_dict['description'] = description
states_dict['grounding'] = {
'identifiers': {k: v for k, v in
var.concept.identifiers.items()
if k != 'biomodels.species'},
'modifiers': var.concept.context,
},
}
}
if var.concept.units:
states_dict['units'] = {
'expression': str(var.concept.units.expression),
Expand Down Expand Up @@ -404,6 +407,7 @@ class Units(BaseModel):
class State(BaseModel):
id: str
name: Optional[str] = None
description: Optional[str] = None
grounding: Optional[Dict] = None
units: Optional[Units] = None

Expand Down
13 changes: 8 additions & 5 deletions mira/modeling/amr/stockflow.py
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Expand Up @@ -72,16 +72,19 @@ def __init__(self, model: Model):
for key, var in model.variables.items():
vmap[key] = name = var.concept.name or str(key)
display_name = var.concept.display_name or name
description = var.concept.description
stocks_dict = {
'id': name,
'name': display_name,
'grounding': {
'name': display_name
}
if description:
stocks_dict['description'] = description
stocks_dict['grounding'] = {
'identifiers': {k: v for k, v in
var.concept.identifiers.items()
if k != 'biomodels.species'},
'modifiers': var.concept.context,
},
}
'modifiers': var.concept.context
}
if var.concept.units:
stocks_dict['units'] = {
'expression': str(var.concept.units.expression),
Expand Down
2 changes: 2 additions & 0 deletions mira/sources/amr/petrinet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -257,6 +257,7 @@ def state_to_concept(state):
# names
name = state['id']
display_name = state.get('name')
description = state.get("description")
grounding = state.get('grounding', {})
identifiers = grounding.get('identifiers', {})
context = grounding.get('modifiers', {})
Expand All @@ -265,6 +266,7 @@ def state_to_concept(state):
units_obj = Unit(expression=units_expr) if units_expr else None
return Concept(name=name,
display_name=display_name,
description=description,
identifiers=identifiers,
context=context,
units=units_obj)
2 changes: 1 addition & 1 deletion mira/sources/amr/stockflow.py
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Expand Up @@ -2,7 +2,7 @@
https://github.com/DARPA-ASKEM/Model-Representations/tree/main/stockflow.
"""
__all__ = ["template_model_from_amr_json",
"stock_to_concept"]
"stock_to_concept", "model_from_url"]

import sympy
import requests
Expand Down
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