aggregate_tables.R

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"))

output_dir <- system_conf$directories$output
aggtables_output_subdir <- file.path(output_dir, "aggregate_tables")
dir.create(aggtables_output_subdir, showWarnings = FALSE)

# in debug mode, csv files from the dir r_test_data_dir are used instead of db queries
debug_mode <- run_conf$debug

aggtables <- get_aggregate_table_names(system_conf)

# run the aggregate table scripts
for (aggtable in aggtables) {
  aggtable_file <- sprintf("%s.R", aggtable)
  source(file.path("aggregate_tables",aggtable_file, fsep = .Platform$file.sep))
  
  if (debug_mode == F) {
    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$port)
    create_tables(con,aggtables_output_subdir)
    close_con(con)
  } else {
    create_tables_debug(system_conf$directories$r_test_data_dir,aggtables_output_subdir)
  }
}