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Open-Systems-Pharmacology / PK-Sim

PK-Sim® is a comprehensive software tool for whole-body physiologically based pharmacokinetic modeling
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After change in compound file by adding a clearance or removing and replace I have frequently this bug. #2884

Open hanssmit777 opened 6 months ago

hanssmit777 commented 6 months ago

Application: PK-Sim® 11.2.142

Object reference not set to an instance of an object.

Stack trace:

at OSPSuite.Core.Domain.SimulationQuantitySelection.Clone()
   at OSPSuite.Core.Domain.OutputMapping.Clone()
   at OSPSuite.Core.Domain.OutputMappings.<>c.<UpdatePropertiesFrom>b__1_0(OutputMapping x)
   at System.Linq.Enumerable.WhereSelectListIterator`2.MoveNext()
   at System.Collections.Generic.List`1.InsertRange(Int32 index, IEnumerable`1 collection)
   at OSPSuite.Core.Domain.OutputMappings.UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager)
   at PKSim.Core.Model.Simulation.UpdatePropertiesFrom(IUpdatable sourceObject, ICloneManager cloneManager)
   at OSPSuite.Core.Domain.Services.CloneManagerStrategy.Clone[T](T objectToClone)
   at PKSim.Core.Services.Cloner.createClone[T](T objectToClone, ICloneManager cloneManager)
   at PKSim.Core.Services.Cloner.CloneForModel[T](T objectToClone)
   at PKSim.Presentation.Presenters.Simulations.ConfigureSimulationPresenterBase`1.createSimulationToConfigureBasedOn()
   at PKSim.Presentation.Presenters.Simulations.ConfigureSimulationPresenterBase`1.configureSimulation(Simulation simulation, ISubPresenterItem subPresenterItem, Action actionToPerformBeforeDisplayingView)
   at PKSim.Presentation.Presenters.Simulations.ConfigureSimulationPresenterBase`1.ConfigureSimulationWithBuildingBlock(Simulation simulation, IPKSimBuildingBlock templateBuildingBlock)
   at PKSim.Presentation.Services.ConfigureSimulationTask.<>c__DisplayClass9_0.<Configure>b__0(IConfigureSimulationPresenter x)
   at PKSim.Presentation.Services.ConfigureSimulationTask.configure(Simulation simulationToConfigure, Func`2 configureAction)
   at PKSim.Presentation.Services.ConfigureSimulationTask.Configure(Simulation simulationToConfigure, IPKSimBuildingBlock buildingBlockToActivate)
   at PKSim.Presentation.Services.SimulationTask.UpdateUsedBuildingBlockInSimulation[TBuildingBlock](TBuildingBlock templateBuildingBlock, UsedBuildingBlock usedBuildingBlock, Simulation simulation)
   at PKSim.Presentation.UICommands.UpdateBuildingBlockInSimulationUICommand`1.Execute()
   at OSPSuite.Presentation.UICommands.UICommandExtensions.ExecuteWithinExceptionHandler(IUICommand uiCommand, IEventPublisher eventPublisher, IChangePropagator changePropagator)
Yuri05 commented 6 months ago

Can you please provide a more detailed workflow and also attach an example project (if possible)?

hanssmit777 commented 6 months ago

Hello Juri. Sure will do so I have done a full install validation after installing osp.

Kind regards Hans

I will reply from my work email, see cc

Op vr 22 mrt 2024 10:57 schreef Juri Solodenko @.***>:

Can you please provide a more detailed workflow and also attach an example project (if possible)?

— Reply to this email directly, view it on GitHub https://github.com/Open-Systems-Pharmacology/PK-Sim/issues/2884#issuecomment-2014738274, or unsubscribe https://github.com/notifications/unsubscribe-auth/AON5FGWJ6BRJCXD4MFNQ2ALYZP6A3AVCNFSM6AAAAABFC2Y3OWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJUG4ZTQMRXGQ . You are receiving this because you authored the thread.Message ID: @.***>

Yuri05 commented 6 months ago

If you want to upload any attachments to your upcoming answer: please do it directly on GitHub. (when answering via email, attachments get lost)

hanssmit777 commented 6 months ago

Will do

Op vr 22 mrt 2024 14:33 schreef Juri Solodenko @.***>:

If you want to upload any attachments to your upcoming answer: please do it directly on GitHub. (when answering via email, attachments get lost)

— Reply to this email directly, view it on GitHub https://github.com/Open-Systems-Pharmacology/PK-Sim/issues/2884#issuecomment-2015108222, or unsubscribe https://github.com/notifications/unsubscribe-auth/AON5FGVWYBRUFXU4HOITJZLYZQXJBAVCNFSM6AAAAABFC2Y3OWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJVGEYDQMRSGI . You are receiving this because you authored the thread.Message ID: @.***>

hanssmit777 commented 6 months ago

So what I do: i create a new simulation, compound file, dosing info, species selected and if available add observed data. Usually what happens is I can run, adjust to assess parameters and alter them BUT if I configure following a run for assessing a parameter changes the system appears to not see the new input and since I altered the previous input (eg i change a invitro parameter and add a new one), the old input seems not present and hangs stating reference not set. I am now generating simulation form a file, one compound, little added data. No issues.. Application: PK-Sim® 11.2.142

Object reference not set to an instance of an object.

Stack trace:

at OSPSuite.Core.Domain.SimulationQuantitySelection.Clone()
   at OSPSuite.Core.Domain.OutputMapping.Clone()
   at OSPSuite.Core.Domain.OutputMappings.<>c.<UpdatePropertiesFrom>b__1_0(OutputMapping x)
   at System.Linq.Enumerable.WhereSelectListIterator`2.MoveNext()
   at System.Collections.Generic.List`1.InsertRange(Int32 index, IEnumerable`1 collection)
   at OSPSuite.Core.Domain.OutputMappings.UpdatePropertiesFrom(IUpdatable source, ICloneManager cloneManager)
   at PKSim.Core.Model.Simulation.UpdatePropertiesFrom(IUpdatable sourceObject, ICloneManager cloneManager)
   at OSPSuite.Core.Domain.Services.CloneManagerStrategy.Clone[T](T objectToClone)
   at PKSim.Core.Services.Cloner.createClone[T](T objectToClone, ICloneManager cloneManager)
   at PKSim.Core.Services.Cloner.CloneForModel[T](T objectToClone)
   at PKSim.Presentation.Presenters.Simulations.ConfigureSimulationPresenterBase`1.createSimulationToConfigureBasedOn()
   at PKSim.Presentation.Presenters.Simulations.ConfigureSimulationPresenterBase`1.configureSimulation(Simulation simulation, ISubPresenterItem subPresenterItem, Action actionToPerformBeforeDisplayingView)
   at PKSim.Presentation.Presenters.Simulations.ConfigureSimulationPresenterBase`1.ConfigureSimulation(Simulation simulation)
   at PKSim.Presentation.Services.ConfigureSimulationTask.<>c__DisplayClass8_0.<Configure>b__0(IConfigureSimulationPresenter x)
   at PKSim.Presentation.Services.ConfigureSimulationTask.configure(Simulation simulationToConfigure, Func`2 configureAction)
   at PKSim.Presentation.Services.ConfigureSimulationTask.Configure(Simulation simulationToConfigure)
   at PKSim.Presentation.UICommands.ConfigureSimulationCommand.PerformExecute()
   at OSPSuite.Presentation.UICommands.ObjectUICommand`1.Execute()
   at OSPSuite.Presentation.UICommands.UICommandExtensions.ExecuteWithinExceptionHandler(IUICommand uiCommand, IEventPublisher eventPublisher, IChangePropagator changePropagator)
hanssmit777 commented 6 months ago

sorry for the confusion, the added PKSIM feedback was from simulation on a larger file, more compound files and more dog data..

Yuri05 commented 6 months ago

I cannot reproduce. Is it possible to upload a project where you face the problem?

hanssmit777 commented 6 months ago

Just ran in similar error today. I will have to anonamise the file and share it tomorrow.

Op ma 25 mrt 2024 18:35 schreef Juri Solodenko @.***>:

I cannot reproduce. Is it possible to upload a project where you face the problem?

— Reply to this email directly, view it on GitHub https://github.com/Open-Systems-Pharmacology/PK-Sim/issues/2884#issuecomment-2018542804, or unsubscribe https://github.com/notifications/unsubscribe-auth/AON5FGTLHE6EC7RY7XUCMRLY2BN5VAVCNFSM6AAAAABFC2Y3OWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJYGU2DEOBQGQ . You are receiving this because you authored the thread.Message ID: @.***>

msevestre commented 2 months ago

@hanssmit777 Any info here please?