Fixes #152 Update to SimModel 4.0.0.52 causes a PK-Sim test to fail (#…

…2357)

Co-authored-by: Yuri05 <[email protected]>

src/Db/Diff/PKSimDB_diff.txt

@@ -1,6 +1,12 @@
-CREATE TABLE [tab_active_transport_types]([transport_type] TEXT PRIMARY KEY NOT NULL REFERENCES [tab_process_types]([process_type]) ON UPDATE CASCADE) WITHOUT ROWID;
-INSERT INTO tab_active_transport_types(transport_type) VALUES('BiDirectional');
-INSERT INTO tab_active_transport_types(transport_type) VALUES('Efflux');
-INSERT INTO tab_active_transport_types(transport_type) VALUES('Influx');
-INSERT INTO tab_active_transport_types(transport_type) VALUES('PgpLike');
-UPDATE tab_transport_directions SET display_name='Influx Lumen to Mucosa/Intracellular' WHERE transport_direction='InfluxLumenToMucosaIntracellular';
+UPDATE tab_calculation_method_rates SET formula='V>0 ? Liquid/V : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_FillLevel';
+UPDATE tab_calculation_method_rates SET formula='alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_Outflow_Caecum';
+UPDATE tab_calculation_method_rates SET formula='alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_Outflow_ColonAscendens';
+UPDATE tab_calculation_method_rates SET formula='alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_Outflow_ColonDescendens';
+UPDATE tab_calculation_method_rates SET formula='alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_Outflow_ColonSigmoid';
+UPDATE tab_calculation_method_rates SET formula='alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_Outflow_ColonTransversum';
+UPDATE tab_calculation_method_rates SET formula='alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_Outflow_Duodenum';
+UPDATE tab_calculation_method_rates SET formula='alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_Outflow_LowerIleum';
+UPDATE tab_calculation_method_rates SET formula='alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_Outflow_LowerJejunum';
+UPDATE tab_calculation_method_rates SET formula='alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_Outflow_Rectum';
+UPDATE tab_calculation_method_rates SET formula='alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_Outflow_UpperIleum';
+UPDATE tab_calculation_method_rates SET formula='alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0' WHERE calculation_method='Lumen_PKSim' AND formula_rate='PARAM_Outflow_UpperJejunum';

src/Db/Dump/PKSimDB_dump.txt

@@ -3877,7 +3877,7 @@ INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Area','PI*(
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_DrugAbsorption_para','OralApplicationsEnabled ? P_int_para*Aeff*(EffectiveLumenConcentration-(NOT SinkCondition_para ? fu*DrugMucosa : 0)) : 0','Amount per time');
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_DrugAbsorption_trans','OralApplicationsEnabled ? P_int_trans*Aeff*(P_int_trans_lum_cell_factor*EffectiveLumenConcentration-(NOT SinkCondition_trans ? P_int_trans_cell_lum_factor*fu/K_cell_pls*DrugMucosa : 0)) : 0','Amount per time');
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_EffectiveSurfaceArea','Ageom*AeffFactor*AeffVariabilityFactor','Area');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_FillLevel','Liquid/V','Dimensionless');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_FillLevel','V>0 ? Liquid/V : 0','Dimensionless');
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_FillLevelFlagFlag','(FillLevel<0.9?1:1/(1+exp((FillLevel-1)/0.01)))','Dimensionless');
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Inflow_Caecum','0*V','Flow');
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Inflow_ColonAscendens','0.00098426*V','Flow');
@@ -3945,18 +3945,18 @@ INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_OralMassAbs
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_OralMassAbsorbed_RHS_rect','PassiveRates_para+PassiveRates_trans-(ActiveRates_para_IN+ActiveRates_trans_IN)+ActiveRates_para_OUT+ActiveRates_trans_OUT','Amount per time');
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_OralMassAbsorbed_RHS_uil','PassiveRates_para+PassiveRates_trans-(ActiveRates_para_IN+ActiveRates_trans_IN)+ActiveRates_para_OUT+ActiveRates_trans_OUT','Amount per time');
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_OralMassAbsorbed_RHS_uje','PassiveRates_para+PassiveRates_trans-(ActiveRates_para_IN+ActiveRates_trans_IN)+ActiveRates_para_OUT+ActiveRates_trans_OUT','Amount per time');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_Caecum','(k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V)','Inversed time');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_ColonAscendens','(k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V)','Inversed time');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_ColonDescendens','(k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V)','Inversed time');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_ColonSigmoid','(k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V)','Inversed time');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_ColonTransversum','(k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V)','Inversed time');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_Duodenum','(k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V)','Inversed time');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_LowerIleum','(k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V)','Inversed time');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_LowerJejunum','(k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V)','Inversed time');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_Rectum','(k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V)','Inversed time');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_Caecum','alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0','Inversed time');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_ColonAscendens','alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0','Inversed time');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_ColonDescendens','alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0','Inversed time');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_ColonSigmoid','alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0','Inversed time');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_ColonTransversum','alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0','Inversed time');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_Duodenum','alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0','Inversed time');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_LowerIleum','alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0','Inversed time');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_LowerJejunum','alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0','Inversed time');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_Rectum','alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0','Inversed time');
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_Stomach','0','Inversed time');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_UpperIleum','(k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V)','Inversed time');
-INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_UpperJejunum','(k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V)','Inversed time');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_UpperIleum','alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0','Inversed time');
+INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_Outflow_UpperJejunum','alpha*V > 0 ? (k_p*alpha_p*V_p+inflow-k*alpha*V)/(alpha*V) : 0','Inversed time');
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_pH_from_pH_fasted','pH_fasted','Dimensionless');
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_SITT_Factor','P1*SITT+P2','Dimensionless');
 INSERT INTO tab_calculation_method_rates VALUES('Lumen_PKSim','PARAM_VolumeGut','V_duo + V_uje + V_lje + V_uil + V_lil + V_cae','Volume');

tests/PKSim.Tests/IntegrationTests/SimulationSpecs.cs

@@ -156,7 +156,7 @@ public override void GlobalContext()
          _allPopulations = populationsRepo.All().ToList();
       }
 
-      [Observation, Ignore("To be un-ignored when SimModel is updated")]
+      [Observation]
       public async Task should_be_able_to_simulate_the_simulation()
       {
          var errors = new List<string>();