Fix ode semantics

mira/dkg/model.py

@@ -2,11 +2,11 @@
 
 This submodule serves as an API for modeling
 """
-
+import json
 import uuid
 from pathlib import Path
 from textwrap import dedent
-from typing import Any, Dict, List, Literal, Optional, Set, Tuple, Type, Union
+from typing import Any, Dict, List, Literal, Optional, Set, Type, Union
 
 import pystow
 from fastapi import (
@@ -33,7 +33,8 @@
 from mira.modeling.bilayer import BilayerModel
 from mira.modeling.petri import PetriNetModel, PetriNetResponse
 from mira.modeling.viz import GraphicalModel
-from mira.sources.askenet.flux_span import reproduce_ode_semantics
+from mira.sources.askenet.flux_span import reproduce_ode_semantics, \
+    test_file_path
 from mira.sources.askenet.petrinet import template_model_from_askenet_json
 from mira.sources.bilayer import template_model_from_bilayer
 from mira.sources.biomodels import get_sbml_model
@@ -700,20 +701,23 @@ def askepetrinet_model_comparison(
 
 
 class FluxSpanQuery(BaseModel):
-    flux_span: Dict[str, Any] = Field(
+    model: Dict[str, Any] = Field(
         ...,
-        example={},  # fixme: create example
-        description="The flux span to recover the de-stratified model from",
+        example=json.load(test_file_path.open()),
+        description="The model to recover the ODE-semantics from.",
     )
 
 
-@model_blueprint.post("/flux_span", response_model=TemplateModel, tags=["modeling"])
-def flux_span(
+@model_blueprint.post("/reconstruct_ode_semnatics",
+                      response_model=TemplateModel,
+                      tags=["modeling"])
+def reproduce_ode_semantics_endpoint(
         query: FluxSpanQuery = Body(
             ...,
-            description="The flux span to recover the de-stratified model from"
+            description="Reproduce ODE semantics from a stratified model"
+                        "(flux span)."
         )
 ):
     """Get the flux span of a model"""
-    tm = reproduce_ode_semantics(query.flux_span)
+    tm = reproduce_ode_semantics(query.model)
     return tm

mira/sources/askenet/flux_span.py

@@ -16,7 +16,7 @@
 
 
 def reproduce_ode_semantics(flux_span):
-    """Reproduce ODE semantics from a flux span."""
+    """Reproduce ODE semantics from a stratified model (flux span)."""
 
     # First we make the original template model
     tm = template_model_from_askenet_json(flux_span)
@@ -98,7 +98,7 @@ def reproduce_ode_semantics(flux_span):
         # Find the rate law components in the original model
         rate_law = deepcopy(original_template.rate_law.args[0])
         # Now we need to map states to new states
-        concept_names = template.get_concept_names()
+        concept_names = {c.name for c in template.get_interactors()}
         for concept_name in concept_names:
             # Find the original concept
             original_concept = original_map[concept_name]

mira/sources/askenet/petrinet.py

@@ -10,6 +10,7 @@
 __all__ = ["model_from_url", "model_from_json_file", "template_model_from_askenet_json"]
 
 import json
+from copy import deepcopy
 
 import sympy
 import requests
@@ -170,8 +171,8 @@ def template_model_from_askenet_json(model_json) -> TemplateModel:
     # Loop
     for transition in model.get('transitions', []):
         transition_id = transition['id']  # required, str
-        inputs = transition.get('input', [])  # required, Array[str]
-        outputs = transition.get('output', [])  # required, Array[str]
+        inputs = deepcopy(transition.get('input', []))  # required, Array[str]
+        outputs = deepcopy(transition.get('output', []))  # required, Array[str]
         transition_grounding = transition.get('grounding', {})  # optional, Object
         transition_properties = transition.get('properties', {})  # optional, Object
         rate_obj = rates.get(transition_id, {})  # optional, Object

tests/test_model_api.py

@@ -673,13 +673,13 @@ def test_counts_to_dimensionless_amr(self):
         for initial in tm_dimless.initials.values():
             assert initial.concept.units.expression.args[0].equals(1)
 
-    def test_flux_span_endpoint(self):
+    def test_reconstruct_ode_semantics_endpoint(self):
         # Load test file
         from mira.sources.askenet.flux_span import test_file_path
-        flux_span = json.load(test_file_path.open())
+        strat_model = json.load(test_file_path.open())
         response = self.client.post(
-            "/api/flux_span",
-            json={"flux_span": flux_span}
+            "/api/reconstruct_ode_semnatics",
+            json={"model": strat_model}
         )
         self.assertEqual(200, response.status_code)