codeToRun.R

library(Strategus)
library(dplyr)

# Inputs to run (edit these for your CDM):
# ========================================= #
# If your database requires temp tables being created in a specific schema
if (!Sys.getenv("DATABASE_TEMP_SCHEMA") == "") {
  options(sqlRenderTempEmulationSchema = Sys.getenv("DATABASE_TEMP_SCHEMA"))
}

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

# fill in your connection details and path to driver
# see ?DatabaseConnector::createConnectionDetails for help for your 
# database platform
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 = Sys.getenv("DATABASE_DRIVER")
) 

# 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("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

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

analysisSpecifications <- ParallelLogger::loadSettingsFromJson(
  fileName = "./study_execution_jsons/validation.json"
)

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