reports.R

library(plyr)
library(dplyr)

source(file.path("function_libraries","config_file_funcs.R", fsep = .Platform$file.sep))
source(file.path("config_setup.R", fsep = .Platform$file.sep)) # sets the path to the run config to use
run_conf <-get_run_config(config_run_path)
system_conf <- get_system_config(file.path("config_system.json"))

# in debug mode, csv files from the dir r_test_data_dir are used instead of db queries
debug_mode <- run_conf$debug
if (debug_mode == T) {
  source(file.path("function_libraries","csv_sources.R", fsep = .Platform$file.sep))
  test_data_dir <- system_conf$directories$r_test_data_dir
  domain_table <- get_domain_table_from_csv (test_data_dir)
} else {
  source(file.path("function_libraries","db_queries.R", fsep = .Platform$file.sep))
  con <- get_con(dbname=system_conf$database$dbname,
                 user=system_conf$database$user,
                 pass=system_conf$database$pass,
                 host=system_conf$database$host, 
                 port=system_conf$database$port)
  domain_table <- get_domain_table(con)
}
domains_for_run <- get_domains_for_run(domain_table,run_conf)

if (length(domains_for_run) == 0) {
  warning("No domains matched config file domain section, nothing to run on.")
} else {
  reports <- get_report_module_names(run_conf)
  aggregate_tables_dir <- file.path(system_conf$directories$output,"aggregate_tables")
  tmp_report_pdf_dir <- file.path(system_conf$directories$tmp,"report_pdfs")
  dir.create(tmp_report_pdf_dir, showWarnings = FALSE)
  
  report_pdfs <- vector()
  # run the report modules
  for (report in reports) {
    print(sprintf("Running report module: %s", report))
    report_file <- sprintf("%s.R", report)
    report_options <- get_report_options(run_conf,report)
    source(file.path("report_modules",report_file, fsep = .Platform$file.sep))
    
    if (debug_mode == F) {
      module_pdfs <- render(con,domains_for_run,report_options,aggregate_tables_dir,tmp_report_pdf_dir)
    } else {
      module_pdfs <- render_debug(test_data_dir,domains_for_run,report_options,aggregate_tables_dir,tmp_report_pdf_dir)
    }
    report_pdfs <- c(report_pdfs,module_pdfs)
  }
  
  report_file_name <- file.path(system_conf$directories$output,paste(run_conf$reports$report_file_name,"pdf",sep="."))
  system2(command = "pdftk",args = c(shQuote(report_pdfs), "cat output", shQuote(report_file_name)))
}

if (debug_mode == F) {
  close_con(con)
}