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Open-Systems-Pharmacology / QualificationRunner

Qualification runner in charge of managing a qualification workflow
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No PKMLs generated by QualificationRunner for this qualification report #89

Closed abdullahhamadeh closed 3 years ago

abdullahhamadeh commented 3 years ago

Only XML files are generated in the reporting engine input folder

Yuri05 commented 3 years ago

Did you use version 10 of the QualiRunner? https://ci.appveyor.com/project/open-systems-pharmacology-ci/QualificationRunner/build/artifacts

abdullahhamadeh commented 3 years ago

I am able to generate the files with v9 but v10 is failing

image

I also can't see the log files that are referred to in the error message

Yuri05 commented 3 years ago

moving the issue to the QualiRunner-Repo

msevestre commented 3 years ago

Can you show me how you are calling the runnner? And which files are you using? I need to be able to reproduce

abdullahhamadeh commented 3 years ago

'C:/path/to/QualificationRunner 10.0.40/QualificationRunner.exe' -i 'C:/path/to/Qualification-DDI-CYP2C19-main/Qualification/Input/qualification_plan.json' -o 'C:/path/to/reporting engine input/' -p 'C:/Program Files/Open Systems Pharmacology/PK-Sim 9.1/'

msevestre commented 3 years ago

ok you are mixing v9 of PKSim and v10 of runner. Please install the latest portable version of PKSim and try again

https://ci.appveyor.com/project/open-systems-pharmacology-ci/pk-sim/build/artifacts

msevestre commented 3 years ago

using v10 of pksim I am getting what we expect image

@Yuri05 For the moment, PKSim is still running the simulation. I am going to make it optional (default true) so that we can turn that off (compatible with current Matlab reporting engine). Then when we have completely migrated to R, we can set the default to true?

Or is it ok to set the default to run = FALSE (and then we can just update the call in the matlarb reporting engine). I would prefer this solution. Let me know

abdullahhamadeh commented 3 years ago

@msevestre can you pls point me to v10 of pksim? I see only v9.1 here

msevestre commented 3 years ago

https://github.com/Open-Systems-Pharmacology/QualificationRunner/issues/89#issuecomment-921908695

abdullahhamadeh commented 3 years ago

oops, I need better glasses

msevestre commented 3 years ago

maybe you just need glasses :)

msevestre commented 3 years ago

beware. At the moment, it is also calculating the simulation which is not what you want. I am adding an option to the runner to turn that off. So once you are done with generating the pkml etc.. you should deleted all csv results files

Yuri05 commented 3 years ago

I am going to make it optional (default true) so that we can turn that off (compatible with current Matlab reporting engine). Then when we have completely migrated to R, we can set the default to true?

Would prefer this option for now. No need for the new version of Matlab-RE then and no unexpected side effects due to the change of the default :)

msevestre commented 3 years ago

see PR. Not possible with flag. So we need to update the code in reporting engine and add the -r flag

Yuri05 commented 3 years ago

V10 TODO list grows...

msevestre commented 3 years ago

LEt me see if I can declare the flag as nullable to catch when it's not set...and then say it's true

msevestre commented 3 years ago

ok I can't. But I'll create another termp flag "noRun" which by default will be false. Setting --norun will switch it to true

msevestre commented 3 years ago

All right. There is the flag --norun that will make sure we do not run the simulation. I am going to add it to the call in the new reporting engine