codeToRun.R

# Install Strategus
# remotes::install_github("mi-erasmusmc/Strategus@v0.1.2")

# load Strategus
library(Strategus)

# Inputs to run (edit these for your CDM):
# ========================================= #
if (!Sys.getenv("DATABASE_TEMP_SCHEMA") == "") {
  options(sqlRenderTempEmulationSchema = Sys.getenv("DATABASE_TEMP_SCHEMA"))
}

database <- Sys.getenv("DATABASE") # your database name 

# reference for the connection used by Strategus
connectionDetailsReference <- paste0("DeepLearningComparison_", database)

# where to save the output - a directory in your environment
outputFolder <- "/output/"

# fill in your connection details and path to driver
connectionDetails <- DatabaseConnector::createConnectionDetails(
  dbms = Sys.getenv('DBMS'), 
  server = Sys.getenv("DATABASE_SERVER"), 
  user = Sys.getenv("DATABASE_USER"),
  password = Sys.getenv("DATABASE_PASSWORD"),
  port = Sys.getenv("DATABASE_PORT"),
  connectionString = Sys.getenv("DATABASE_CONNECTION_STRING"),
  pathToDriver = "/database_drivers"
) 

# A schema with write access to store cohort tables
workDatabaseSchema <- Sys.getenv("WORK_SCHEMA")

# name of cohort table that will be created for study
cohortTable <- Sys.getenv("STRATEGUS_COHORT_TABLE")

# schema where the cdm data is
cdmDatabaseSchema <- Sys.getenv("CDM_SCHEMA")

# Aggregated statistics with cell count less than this are removed before sharing results.
minCellCount <- 5


# Location to Strategus modules
# If you've ran Strategus studies before this directory should already exist.
# Note: this environmental variable should be set once for each compute node
Sys.setenv("INSTANTIATED_MODULES_FOLDER" = '/modules/')


# =========== END OF INPUTS ========== #

Strategus::storeConnectionDetails(
  connectionDetails = connectionDetails,
  connectionDetailsReference = connectionDetailsReference
)

executionSettings <- Strategus::createCdmExecutionSettings(
  connectionDetailsReference = connectionDetailsReference,
  workDatabaseSchema = workDatabaseSchema,
  cdmDatabaseSchema = cdmDatabaseSchema,
  cohortTableNames = CohortGenerator::getCohortTableNames(cohortTable = cohortTable),
  workFolder = file.path(outputFolder, "strategusWork"),
  resultsFolder = file.path(outputFolder, "strategusOutput"),
  minCellCount = minCellCount
)

json <- paste(readLines('./study_execution_jsons/deep_comp_study.json'), collapse = '\n')
analysisSpecifications <- ParallelLogger::convertJsonToSettings(json)

Strategus::execute(
  analysisSpecifications = analysisSpecifications,
  executionSettings = executionSettings,
  executionScriptFolder = file.path(outputFolder, "strategusExecution"),
  restart = F
)