Test case simultaneous PEtab and SBML event

petabtests/cases/v2.0.0/sbml/0030/0030.py

@@ -0,0 +1,118 @@
+from inspect import cleandoc
+
+from petab.v2.C import *
+from petab.v2 import Problem
+from petabtests import (
+    PetabV2TestCase,
+    antimony_to_sbml_str,
+)
+from pathlib import Path
+
+DESCRIPTION = cleandoc("""
+## Objective
+
+This case tests simultaneous re-initialization of compartment size and
+contained species when an SBML event triggers at the exact same
+time-point as a PEtab condition.
+
+## Model
+
+A species `S`, defined in terms of concentrations, with `dS/dt = p = 1`,
+in a compartment `C`. `S` and `C` are changed via the condition table.
+
+There is a PEtab condition triggered at `t=10`, which is triggered
+at the exact time as an SBML event that re-initializes the compartment
+volume after the condition table is applied.
+""")
+
+# problem --------------------------------------------------------------------
+
+sbml_file = Path(__file__).parent / "model.xml"
+
+vol0 = 4
+conc0 = 2
+conc10 = 8
+dSdt = 1
+vol10 = (conc0 + 10 * dSdt) + vol0  # = 16
+
+ant_model = f"""
+model petab_test_0030
+    compartment C = {vol0}
+
+    species S in C = 3 # this is overwritten by the condition table
+
+    p = {dSdt}
+    S' = p
+
+    at time >= 10, fromTrigger=false: C = C * 2 # this is executed after PEtab condition
+end
+"""
+sbml_file.write_text(antimony_to_sbml_str(ant_model))
+
+problem = Problem()
+problem.add_observable("obs_C", "C", noise_formula="1")
+problem.add_observable("obs_amount_S", "S * C", noise_formula="1")
+problem.add_observable("obs_conc_S", "S", noise_formula="1")
+
+problem.add_parameter("p", lb=0, ub=10, nominal_value=1)
+
+problem.add_experiment("experiment1", 0, "condition1", 10, "condition2")
+# at t=0
+problem.add_condition(
+    "condition1",
+    "condition1",
+    S=conc0,
+)
+# t=10
+problem.add_condition(
+    "condition2",
+    "condition2",
+    S="S + C",
+    C=conc10,
+)
+
+ts = [0, 5, 10, 15]
+for t in ts:
+    for obs in ["obs_C", "obs_amount_S", "obs_conc_S"]:
+        problem.add_measurement(
+            obs, experiment_id="experiment1", time=t, measurement=t
+        )
+
+# solutions ------------------------------------------------------------------
+
+simulation_df = problem.measurement_df.copy(deep=True).rename(
+    columns={MEASUREMENT: SIMULATION}
+)
+simulation_df[SIMULATION] = [
+    # vol, amount, conc
+    # --- t=0 ---
+    vol0,
+    conc0 * vol0,
+    conc0,
+    # --- t=5 ---
+    vol0,
+    (conc0 + 5 * dSdt) * vol0,
+    (conc0 + 5 * dSdt),
+    # --- t=10 ---
+    # condition table:
+    # 8, 16 * 8 = 128 , 12 + 4 = 16
+    # event (triggered at same time as PEtab condition)
+    # volume is changed by event, amount is preserved, conc changes
+    # C = 8 * 2 = 16, 128, 8
+    vol10,
+    conc10 * vol10,
+    conc10,
+    # --- t=15 ---
+    vol10,
+    (conc10 + 5 * dSdt) * vol10,
+    (conc10 + 5 * dSdt)
+]
+
+case = PetabV2TestCase.from_problem(
+    id=30,
+    brief="Simultaneous trigger of PEtab condition and SBML event.",
+    description=DESCRIPTION,
+    model=sbml_file,
+    problem=problem,
+    simulation_df=simulation_df,
+)

petabtests/cases/v2.0.0/sbml/0030/README.md

@@ -0,0 +1,16 @@
+# PEtab test case 0030
+
+## Objective
+
+This case tests simultaneous re-initialization of compartment size and
+contained species when an SBML event triggers at the exact same
+time-point as a PEtab condition.
+
+## Model
+
+A species `S`, defined in terms of concentrations, with `dS/dt = p = 1`,
+in a compartment `C`. `S` and `C` are changed via the condition table.
+
+There is a PEtab condition triggered at `t=10`, which is triggered
+at the exact time as an SBML event that re-initializes the compartment
+volume after the condition table is applied.

petabtests/cases/v2.0.0/sbml/0030/_0030.yaml

@@ -0,0 +1,17 @@
+condition_files:
+- _conditions.tsv
+experiment_files:
+- _experiments.tsv
+format_version: 2.0.0
+mapping_files:
+- _mapping.tsv
+measurement_files:
+- _measurements.tsv
+model_files:
+  model_0:
+    language: sbml
+    location: _model.xml
+observable_files:
+- _observables.tsv
+parameter_files:
+- _parameters.tsv

petabtests/cases/v2.0.0/sbml/0030/_0030_solution.yaml

@@ -0,0 +1,7 @@
+chi2: 51836.0
+llh: -25929.027262398453
+simulation_files:
+- _simulations.tsv
+tol_chi2: 0.001
+tol_llh: 0.001
+tol_simulations: 0.001

petabtests/cases/v2.0.0/sbml/0030/_conditions.tsv

@@ -0,0 +1,4 @@
+conditionId	targetId	targetValue
+condition1	S	2.0
+condition2	S	C + S
+condition2	C	8.0

petabtests/cases/v2.0.0/sbml/0030/_experiments.tsv

@@ -0,0 +1,3 @@
+experimentId	time	conditionId
+experiment1	0.0	condition1
+experiment1	10.0	condition2

petabtests/cases/v2.0.0/sbml/0030/_mapping.tsv

@@ -0,0 +1,3 @@
+petabEntityId	modelEntityId	name
+condition1		condition1
+condition2		condition2

petabtests/cases/v2.0.0/sbml/0030/_measurements.tsv

@@ -0,0 +1,13 @@
+modelId	observableId	experimentId	time	measurement	observableParameters	noiseParameters
+	obs_C	experiment1	0.0	0.0		
+	obs_amount_S	experiment1	0.0	0.0		
+	obs_conc_S	experiment1	0.0	0.0		
+	obs_C	experiment1	5.0	5.0		
+	obs_amount_S	experiment1	5.0	5.0		
+	obs_conc_S	experiment1	5.0	5.0		
+	obs_C	experiment1	10.0	10.0		
+	obs_amount_S	experiment1	10.0	10.0		
+	obs_conc_S	experiment1	10.0	10.0		
+	obs_C	experiment1	15.0	15.0		
+	obs_amount_S	experiment1	15.0	15.0		
+	obs_conc_S	experiment1	15.0	15.0		

petabtests/cases/v2.0.0/sbml/0030/_model.xml

@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v3.1.1 with libSBML version 5.20.5. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
+  <model metaid="petab_test_0030" id="petab_test_0030">
+    <listOfCompartments>
+      <compartment id="C" spatialDimensions="3" size="4" constant="false"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S" compartment="C" initialConcentration="3" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="p" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfRules>
+      <rateRule variable="S">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <ci> p </ci>
+        </math>
+      </rateRule>
+    </listOfRules>
+    <listOfEvents>
+      <event id="_E0" useValuesFromTriggerTime="false">
+        <trigger initialValue="true" persistent="true">
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <geq/>
+              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
+              <cn type="integer"> 10 </cn>
+            </apply>
+          </math>
+        </trigger>
+        <listOfEventAssignments>
+          <eventAssignment variable="C">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
+              <apply>
+                <times/>
+                <ci> C </ci>
+                <cn type="integer"> 2 </cn>
+              </apply>
+            </math>
+          </eventAssignment>
+        </listOfEventAssignments>
+      </event>
+    </listOfEvents>
+  </model>
+</sbml>

petabtests/cases/v2.0.0/sbml/0030/_observables.tsv

@@ -0,0 +1,4 @@
+observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
+obs_C		C	1.00000000000000	normal		
+obs_amount_S		C*S	1.00000000000000	normal		
+obs_conc_S		S	1.00000000000000	normal		

petabtests/cases/v2.0.0/sbml/0030/_parameters.tsv

@@ -0,0 +1,2 @@
+parameterId	lowerBound	upperBound	nominalValue	estimate	priorDistribution	priorParameters
+p	0.0	10.0	1.0	true		

petabtests/cases/v2.0.0/sbml/0030/_simulations.tsv

@@ -0,0 +1,13 @@
+modelId	observableId	experimentId	time	simulation	observableParameters	noiseParameters
+	obs_C	experiment1	0.0	4		
+	obs_amount_S	experiment1	0.0	8		
+	obs_conc_S	experiment1	0.0	2		
+	obs_C	experiment1	5.0	4		
+	obs_amount_S	experiment1	5.0	28		
+	obs_conc_S	experiment1	5.0	7		
+	obs_C	experiment1	10.0	16		
+	obs_amount_S	experiment1	10.0	128		
+	obs_conc_S	experiment1	10.0	8		
+	obs_C	experiment1	15.0	16		
+	obs_amount_S	experiment1	15.0	208		
+	obs_conc_S	experiment1	15.0	13		

petabtests/cases/v2.0.0/sbml/0030/model.xml

@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v3.1.1 with libSBML version 5.20.5. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
+  <model metaid="petab_test_0030" id="petab_test_0030">
+    <listOfCompartments>
+      <compartment id="C" spatialDimensions="3" size="4" constant="false"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S" compartment="C" initialConcentration="3" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="p" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfRules>
+      <rateRule variable="S">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <ci> p </ci>
+        </math>
+      </rateRule>
+    </listOfRules>
+    <listOfEvents>
+      <event id="_E0" useValuesFromTriggerTime="false">
+        <trigger initialValue="true" persistent="true">
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <geq/>
+              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
+              <cn type="integer"> 10 </cn>
+            </apply>
+          </math>
+        </trigger>
+        <listOfEventAssignments>
+          <eventAssignment variable="C">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
+              <apply>
+                <times/>
+                <ci> C </ci>
+                <cn type="integer"> 2 </cn>
+              </apply>
+            </math>
+          </eventAssignment>
+        </listOfEventAssignments>
+      </event>
+    </listOfEvents>
+  </model>
+</sbml>

petabtests/cases/v2.0.0/sbml/README.md

@@ -110,3 +110,7 @@ Simulation. None t0 condition applied at time-point without measurements.
 
 Simulation. Non-zero simulation start time
 
+# [0030](0030/)
+
+Simultaneous trigger of PEtab condition and SBML event.
+