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Open-Systems-Pharmacology / OSPSuite.ReportingEngine

R implementation of the reporting engine
https://www.open-systems-pharmacology.org/OSPSuite.ReportingEngine/
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Qualification workflow crashes if log file is passed to the Qualification Runner #666

Open Yuri05 opened 2 years ago

Yuri05 commented 2 years ago

If a log file name is set, qualification workflow crashes with the error below Vancomycin-Model.zip

Unbehandelte Ausnahme: System.IO.FileLoadException: Die Datei oder Assembly "Microsoft.Extensions.Logging, Version=2.0.0.0, Culture=neutral, PublicKeyToken=adb9793829ddae60" oder eine Abh„ngigkeit davon wurde nicht gefunden. Die gefundene Manifestdefinition der Assembly stimmt nicht mit dem Assemblyverweis berein. (Ausnahme von HRESULT: 0x80131040)
   bei OSPSuite.Infrastructure.Services.LoggingBuilderExtensions.AddFile(ILoggingBuilder builder, String[] logFileFullPaths, LogLevel level, Boolean shared, String outputTemplate)
   bei OSPSuite.Infrastructure.Services.LoggingBuilderExtensions.AddFile(ILoggingBuilder builder, String logFileNameFileFullPath, LogLevel level, Boolean shared, String outputTemplate)
   bei QualificationRunner.Program.<>c__DisplayClass3_0.<initializeLogger>b__1(ILoggingBuilder builder)
   bei OSPSuite.Core.Extensions.FunctionExtensions.Compose[T](Func`2 f1, Func`2 f2, T value)
   bei OSPSuite.Infrastructure.Services.LoggerCreator.<>c__DisplayClass4_1.<setupLogger>b__1(ILoggingBuilder config)
   bei OSPSuite.Infrastructure.Services.LoggerCreator.<>c__DisplayClass4_0.<setupLogger>b__2(ILoggingBuilder x)
   bei Microsoft.Extensions.DependencyInjection.LoggingServiceCollectionExtensions.AddLogging(IServiceCollection services, Action`1 configure)
   bei Microsoft.Extensions.Logging.LoggerFactory.Create(Action`1 configure)
   bei OSPSuite.Infrastructure.Services.LoggerCreator.setupLogger(String categoryName)
   bei OSPSuite.Infrastructure.Services.LoggerCreator.<>c__DisplayClass3_0.<GetOrCreateLogger>b__0(String _)
   bei System.Collections.Concurrent.ConcurrentDictionary`2.GetOrAdd(TKey key, Func`2 valueFactory)
   bei OSPSuite.Infrastructure.Services.LoggerCreator.GetOrCreateLogger(String categoryName)
   bei OSPSuite.Infrastructure.Services.OSPSuiteLogger.AddToLog(String message, LogLevel logLevel, String categoryName)
   bei OSPSuite.Core.Services.LoggerExtensions.AddInfo(IOSPSuiteLogger logger, String message, String categoryName)
   bei QualificationRunner.Program.startCommand[TRunOptions](CLICommand`1 command)
   bei CommandLine.ParserResultExtensions.WithParsed[T](ParserResult`1 result, Action`1 action)
   bei QualificationRunner.Program.Main(String[] args)
[1] "Qualification Runner Duration: 0.1 minutes"
Error: lexical error: invalid char in json text.
                                       C:/SW-Dev/00/Vancomycin-Model/e
                     (right here) ------^

If the log file is set to NULL in the line below, the workflow continues. grafik

Yuri05 commented 2 years ago

With QualificationRunner 11.0.128 and PK-Sim 11.0.137: issue still there

pchelle commented 5 months ago

@Yuri05 is this still an issue ? I just tried the code updating to my computer paths and got the following:

info: QualificationRunner[0]
      Starting qualification workflow
dbug: QualificationRunner[0]
      Arguments:
Log file: C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation
      Log level: Debug
      Configuration file: C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/input/Evaluation_plan.json
      Output folder: C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input
      Run simulations: False
      Export project files: False

dbug: QualificationRunner[0]
      Force deleting output folder 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input'
dbug: QualificationRunner[0]
      Copying static files
info: QualificationRunner[0]
      Starting validation runs...
dbug: QualificationRunner[0]
      Starting qualification run for project 'Vancomycin'
dbug: QualificationRunner[0]
      Qualification configuration for project 'Vancomycin' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\temp\Vancomycin\config.json'
info: QualificationRunner[0]
      Starting qualification runs...
dbug: QualificationRunner[0]
      Starting qualification run for project 'Vancomycin'
dbug: QualificationRunner[0]
      Qualification configuration for project 'Vancomycin' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\temp\Vancomycin\config.json'
info: QualificationRunner[0]
      Qualification scenario finished in 00m:30s:76ms
info: QualificationRunner[0]
      Qualification Workflow finished
[1] "Qualification Runner Duration: 0.5 minutes"

After the run, there is no log in the path defined in logFile but one under: C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\temp\Vancomycin\log.txt

In case, I attached the content

here

[2024-03-11 11:00:06.193 PK-Sim DEBUG] Arguments:
Log file: C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\temp\Vancomycin\log.txt
Log file: C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation
Log level: Debug
Validate: True
Configuration file: C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\temp\Vancomycin\config.json
Run simulations: False
Export project files: False

 [2024-03-11 11:00:10.179 PK-Sim INFORMATION] Starting validation run... 
 [2024-03-11 11:00:10.187 PK-Sim DEBUG] Reading configuration from file 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\temp\Vancomycin\config.json' 
 [2024-03-11 11:00:10.502 Vancomycin DEBUG] Loading project from snapshot file 'C:\Design2Code\Qualification-Tests\Vancomycin-Model\evaluation\input\../../Vancomycin.json'... 
 [2024-03-11 11:00:10.898 Vancomycin DEBUG] Project Vancomycin loaded from snapshot file 'C:\Design2Code\Qualification-Tests\Vancomycin-Model\evaluation\input\../../Vancomycin.json'. 
 [2024-03-11 11:00:10.898 Vancomycin INFORMATION] Validation run terminated for Vancomycin 
 [2024-03-11 11:00:11.922 PK-Sim DEBUG] Arguments:
Log file: C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\temp\Vancomycin\log.txt
Log file: C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation
Log level: Debug
Validate: False
Configuration file: C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\temp\Vancomycin\config.json
Run simulations: False
Export project files: False

 [2024-03-11 11:00:15.620 PK-Sim INFORMATION] Starting qualification run... 
 [2024-03-11 11:00:15.628 PK-Sim DEBUG] Reading configuration from file 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\temp\Vancomycin\config.json' 
 [2024-03-11 11:00:15.936 Vancomycin DEBUG] Loading project from snapshot file 'C:\Design2Code\Qualification-Tests\Vancomycin-Model\evaluation\input\../../Vancomycin.json'... 
 [2024-03-11 11:00:16.353 Vancomycin DEBUG] Project Vancomycin loaded from snapshot file 'C:\Design2Code\Qualification-Tests\Vancomycin-Model\evaluation\input\../../Vancomycin.json'. 
 [2024-03-11 11:00:16.361 Vancomycin DEBUG] Loading project 'Vancomycin' from snapshot... 
 [2024-03-11 11:00:21.263 Vancomycin INFORMATION] Loading simulation 'Healy1987_1gBID' (1/4)... 
 [2024-03-11 11:00:23.693 Vancomycin INFORMATION] Loading simulation 'Healy1987_0.5gPer6h' (2/4)... 
 [2024-03-11 11:00:25.612 Vancomycin INFORMATION] Loading simulation 'Boeckh1988_1g' (3/4)... 
 [2024-03-11 11:00:27.681 Vancomycin INFORMATION] Loading simulation 'Boeckh 1988 Figure 1 0.5g' (4/4)... 
 [2024-03-11 11:00:29.686 Vancomycin DEBUG] Exporting project Vancomycin to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\Vancomycin' 
 [2024-03-11 11:00:30.611 Vancomycin DEBUG] Exporting simulation pkml to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\Vancomycin\Boeckh 1988 Figure 1 0.5g\Boeckh 1988 Figure 1 0.5g.pkml' 
 [2024-03-11 11:00:30.611 Vancomycin DEBUG] Simulation 'Boeckh 1988 Figure 1 0.5g' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\Vancomycin\Boeckh 1988 Figure 1 0.5g' 
 [2024-03-11 11:00:31.518 Vancomycin DEBUG] Exporting simulation pkml to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\Vancomycin\Boeckh1988_1g\Boeckh1988_1g.pkml' 
 [2024-03-11 11:00:31.518 Vancomycin DEBUG] Simulation 'Boeckh1988_1g' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\Vancomycin\Boeckh1988_1g' 
 [2024-03-11 11:00:32.308 Vancomycin DEBUG] Exporting simulation pkml to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\Vancomycin\Healy1987_0.5gPer6h\Healy1987_0.5gPer6h.pkml' 
 [2024-03-11 11:00:32.310 Vancomycin DEBUG] Simulation 'Healy1987_0.5gPer6h' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\Vancomycin\Healy1987_0.5gPer6h' 
 [2024-03-11 11:00:33.124 Vancomycin DEBUG] Exporting simulation pkml to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\Vancomycin\Healy1987_1gBID\Healy1987_1gBID.pkml' 
 [2024-03-11 11:00:33.124 Vancomycin DEBUG] Simulation 'Healy1987_1gBID' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\Vancomycin\Healy1987_1gBID' 
 [2024-03-11 11:00:33.126 Vancomycin DEBUG] Observed data 'Boekh 1988 - mean 0.5g - Vancomycin - IV - 0.5 g - Plasma - agg. (n=10)' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\ObservedData\Boekh 1988 - mean 0.5g - Vancomycin - IV - 0.5 g - Plasma - agg. (n=10).csv' 
 [2024-03-11 11:00:33.134 Vancomycin DEBUG] Observed data 'Boekh 1988 - mean 1g - Vancomycin - IV - 1 g - Plasma - agg. (n=10)' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\ObservedData\Boekh 1988 - mean 1g - Vancomycin - IV - 1 g - Plasma - agg. (n=10).csv' 
 [2024-03-11 11:00:33.134 Vancomycin DEBUG] Observed data 'Healy 1987 - mean 0.5g - Vancomycin - IV - 0.5 g - Plasma - agg. (n=11)' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\ObservedData\Healy 1987 - mean 0.5g - Vancomycin - IV - 0.5 g - Plasma - agg. (n=11).csv' 
 [2024-03-11 11:00:33.136 Vancomycin DEBUG] Observed data 'Healy 1987 - mean 1g - Vancomycin - IV - 1 g - Plasma - agg. (n=11)' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\ObservedData\Healy 1987 - mean 1g - Vancomycin - IV - 1 g - Plasma - agg. (n=11).csv' 
 [2024-03-11 11:00:33.146 Vancomycin DEBUG] Observed data 'Boekh 1988 - mean 1g - Vancomycin - IV - 1 g - Plasma - agg. (n=10)' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\ObservedData\Boekh 1988 - mean 1g - Vancomycin - IV - 1 g - Plasma - agg. (n=10).xlsx' 
 [2024-03-11 11:00:33.154 Vancomycin DEBUG] Observed data 'Healy 1987 - mean 1g - Vancomycin - IV - 1 g - Plasma - agg. (n=11)' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\ObservedData\Healy 1987 - mean 1g - Vancomycin - IV - 1 g - Plasma - agg. (n=11).xlsx' 
 [2024-03-11 11:00:33.154 Vancomycin DEBUG] Observed data 'Boekh 1988 - mean 0.5g - Vancomycin - IV - 0.5 g - Plasma - agg. (n=10)' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\ObservedData\Boekh 1988 - mean 0.5g - Vancomycin - IV - 0.5 g - Plasma - agg. (n=10).xlsx' 
 [2024-03-11 11:00:33.154 Vancomycin DEBUG] Observed data 'Healy 1987 - mean 0.5g - Vancomycin - IV - 0.5 g - Plasma - agg. (n=11)' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\ObservedData\Healy 1987 - mean 0.5g - Vancomycin - IV - 0.5 g - Plasma - agg. (n=11).xlsx' 
 [2024-03-11 11:00:33.616 Vancomycin DEBUG] Input data for Compound 'Vancomycin' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\Inputs\Vancomycin\Compound\Vancomycin.md' 
 [2024-03-11 11:00:33.679 Vancomycin DEBUG] Project mapping for 'Vancomycin' exported to 'C:/Design2Code/Qualification-Tests/Vancomycin-Model/evaluation/re_input\temp\Vancomycin\mapping.json' 
 [2024-03-11 11:00:33.695 Vancomycin INFORMATION] Project 'Vancomycin' exported for qualification in 00m:17s:326ms