Exception handling and timing for execution

[anthonysena]

Aims to address #141 to provide better exception handling for execution. This work depends on the completion of #145. I've provided a reprex below to show how this is currently working.

A few notes:

• Making use of purrr::safely works nicely to capture errors and to provide a summary of the entirety of the execution. The only potential downside is that we don't seem to get a stack trace (but this may be due to my contrived example that will eventually be the basis for a test case).
• I'm not currently emitting the errors when they occur which may make the logs confusing - an alternative may be to use ParallelLogger::logError in the case that an error is encountered during the iteration over all module execution.
• We may want to control this behavior via a parameter to the execute function such that we may want to stop upon an error.

Reprex

# Create a simple class that throws an error upon execution
ExceptionThrowerModule <- R6::R6Class(
  classname = "ExceptionThrowerModule",
  inherit = Strategus:::StrategusModule,
  public = list(
    #' @description Initialize the module
    initialize = function() {
      super$initialize()
    },
    execute = function(connectionDetails, analysisSpecifications, executionSettings) {
      super$execute(connectionDetails, analysisSpecifications, executionSettings)
      checkmate::assertClass(executionSettings, "CdmExecutionSettings")
      stop("THROWING EXCEPTION")
    }
  )
)

# Create a simple class that prints a message
SimpleModule <- R6::R6Class(
  classname = "SimpleModule",
  inherit = Strategus:::StrategusModule,
  public = list(
    #' @description Initialize the module
    initialize = function() {
      super$initialize()
    },
    execute = function(connectionDetails, analysisSpecifications, executionSettings) {
      super$execute(connectionDetails, analysisSpecifications, executionSettings)
      checkmate::assertClass(executionSettings, "CdmExecutionSettings")
      private$.message("Hello World")
    }
  )
)


# Create a simple analysis spec with this module
etm <- ExceptionThrowerModule$new()
etmSpecs <- etm$createModuleSpecifications(list(foo = "bar"))

sm <- SimpleModule$new()
smSpecs <- sm$createModuleSpecifications(list(foo = "bar"))

analysisSpecifications <- Strategus::createEmptyAnalysisSpecificiations() |>
  Strategus::addModuleSpecifications(smSpecs) |>
  Strategus::addModuleSpecifications(etmSpecs) |>
  Strategus::addModuleSpecifications(smSpecs)

# Execute the study
executionSettings <- Strategus::createCdmExecutionSettings(
  workDatabaseSchema = "main",
  cdmDatabaseSchema = "main",
  cohortTableNames = CohortGenerator::getCohortTableNames(cohortTable = "strategus_test"),
  workFolder = file.path(getwd(), "workFolder"),
  resultsFolder = file.path(getwd(), "resultsFolder"),
  minCellCount = 5
)

connectionDetails <- Eunomia::getEunomiaConnectionDetails()
Strategus::execute(
  analysisSpecifications = analysisSpecifications,
  executionSettings = executionSettings,
  connectionDetails = connectionDetails
)
#> Currently in a tryCatch or withCallingHandlers block, so unable to add global calling handlers. ParallelLogger will not capture R messages, errors, and warnings, only explicit calls to ParallelLogger. (This message will not be shown again this R session)
#> Connecting using SQLite driver
#> EXECUTING: SimpleModule
#> Hello World
#> EXECUTING: ExceptionThrowerModule
#> EXECUTING: SimpleModule
#> Hello World
#> 
#> 
#> -- EXECUTION SUMMARY -----------------------------------------------------------
#> 
#> v SimpleModule
#> 
#> x ExceptionThrowerModule ERROR: THROWING EXCEPTION
#> 
#> v SimpleModule

^{Created on 2024-07-16 with reprex v2.1.0}