Merge branch 'individual_inputs'

Accept clc and hbpc input files individually.
Remove brittle input directory API.

R/main.r

@@ -1,46 +1,58 @@
 #' @title Main
 #' @description Build all reports for input data in input directory
 #' @note This is the entry point for the application.
-#' @param input_dir path to directory that contains clc.csv or hbpc.csv
+#' @param ... paths to input files for clc, hbpc, or dementia reports
 #' @param config_path path to configuration file
 #' @param output_dir path to output directory. Defaults to input_dir
 #' @return boolean TRUE indicates successful run.
 #' @export
 #' 
-main <- function(input_dir, config_path, output_dir = NULL){
+main <- function(config_path, output_dir = NULL, ...){
+  cat("\nDEBUG\n")
+  cat(config_path)
+  cat("\nDEBUG\n")
+  cat(output_dir)
+  cat("\n")
+
+  input_args <- list(...)
+
   # Ignore warnings
   options(warn = -1) 
 
-  # Default to using same directory for input and output
-  if(is.null(output_dir)){ output_dir <- input_dir }
+  # Default to using working directory output
+  if(is.null(output_dir)){ output_dir <- getwd() }
 
   config <- read_config(config_path)
 
-  # Read in CLC and HBPC data frames
+  # Read in data
   cat("\n\n--- ReadingData\n")
-  clc_filename <- file.path(input_dir,"clc.csv")
-  hbpc_filename <- file.path(input_dir,"hbpc.csv")
+  clc_inpath <- input_args[['clc']] 
+  if(!is.null(clc_inpath) || clc_inpath != ''){
+    df_clc  <- read_clc_data(input_args[['clc']]) 
+  }
 
-  df_hbpc <- read_hbpc_data(hbpc_filename) 
-  df_clc  <- read_clc_data(clc_filename) 
+  hbpc_inpath <- input_args[['hbpc']]
+  if(!is.null(hbpc_inpath) || hbpc_inpath != ''){
+    df_hbpc <- read_hbpc_data(hbpc_inpath) 
+  }
 
-  # Process Data
+  # Process data
   if(!is.null(df_hbpc)){
     hbpc_df_list <- process_data(df_hbpc, envir=GOCC$HBPC)
+    report_all(hbpc_df_list, GOCC$HBPC, config, output_dir)
   }else{
-    cat(paste("\nHBPC input file", hbpc_filename, "not present or malformed.\n"))
+    cat(paste("\nHBPC input file", hbpc_inpath, "not present or malformed.\n"))
     hbpc_df_list <- list()
   }
 
   if(!is.null(df_clc)){
     clc_df_list <- process_data(df_clc, envir=GOCC$CLC)
+    report_all(clc_df_list,  GOCC$CLC,  config, output_dir)
   }else{
-    cat(paste("\nCLC input file", clc_filename, "not present or malformed.\n"))
+    cat(paste("\nCLC input file", clc_inpath, "not present or malformed.\n"))
     clc_df_list <- list()
   }
 
-  report_all(hbpc_df_list, GOCC$HBPC, config, output_dir)
-  report_all(clc_df_list,  GOCC$CLC,  config, output_dir)
 
   cat("\n\nEnd of Line\n\n")
 }

bin/gocc.sh

@@ -8,17 +8,18 @@ command -v Rscript 1> /dev/null 2>&1 || \
 read -r -d '' USE_MSG <<'HEREDOC'
 Usage:
   gocc.sh -h
-  gocc.sh input_dir config_file
-  gocc.sh -i [path to input dir] -c [path to config]
-  gocc.sh --input [path to input dir] --config [path to config]
+  gocc.sh [options]
+  gocc.sh [options] config_file  
 
 Input directory is expected to contain hbpc.csv and clc.csv files.
 
 Options:
   -h | --help   print help and exit
-  -i | --input  path to input directory
   -c | --config path to configuration file
   -o | --output path to output directory
+  --clc         path to clc report input csv file
+  --hbpc        path to hbpc report input csv file
+  --dementia    (unimplimented) path to dementia report input csv file
 HEREDOC
 
 # Parse args
@@ -29,10 +30,6 @@ while (( "$#" )); do
       echo "${USE_MSG}"
       exit 0
       ;;
-    -i|--input)
-      INPUT_DIR=$2
-      shift 2
-      ;;
     -c|--config)
       CONFIG_FILE=$2
       shift 2
@@ -41,6 +38,18 @@ while (( "$#" )); do
       OUTPUT_DIR=$2
       shift 2
       ;;
+    --clc)
+      CLC_INPUT=$2
+      shift 2
+      ;;
+    --hbpc)
+      HBPC_INPUT=$2
+      shift 2
+      ;;
+    --dementia)
+      DEMENTIA_INPUT=$2
+      shift 2
+      ;;
     --) # end argument parsing
       shift
       break
@@ -56,23 +65,16 @@ while (( "$#" )); do
   esac
 done
 
-# Sort out input directory and shift params if used
-if [[ -z $INPUT_DIR ]]; then
-  if [[ ${PARAMS[0]} ]]; then
-    INPUT_DIR="${PARAMS[0]}"
-    PARAMS=("${PARAMS[@]:1}")
-  else
-    echo "Aborting: Input directory required."
-    exit 1
-  fi
+# Check for input options
+if [[ -z ${CLC_INPUT} ]] && [[ -z ${HBPC_INPUT} ]] && [[ -z ${DEMENTIA_INPUT} ]]; then
+  echo "Aborting: Report input file required. See -h for input options."
+  exit 1
 fi
 
 # Sort out config file. 
 # Check 2nd param (unshifted case) then 1st param (shifted case)
 if [[ -z $CONFIG_FILE ]]; then
-  if [[ ${PARAMS[1]} ]]; then
-    CONFIG_FILE="${PARAMS[1]}"
-  elif [[ ${PARAMS[0]} ]]; then
+  if [[ ${PARAMS[0]} ]]; then
     CONFIG_FILE="${PARAMS[0]}"
   else
     echo "Aborting: Config file required."
@@ -87,8 +89,10 @@ fi
 echo "Creating ${OUTPUT_DIR} if it doesn't exist"
 mkdir -p "${OUTPUT_DIR}"
 
+INPUT_ARGS="clc='${CLC_INPUT}', hbpc='${HBPC_INPUT}', dementia='${DEMENTIA_INPUT}'"
+
 echo "Running GoCC R Package."
-EXPR="gocc::main('${INPUT_DIR}', '${CONFIG_FILE}', '${OUTPUT_DIR}')"
+EXPR="gocc::main(config_path='${CONFIG_FILE}', output_dir='${OUTPUT_DIR}', ${INPUT_ARGS})"
 echo "${EXPR}"
 Rscript --vanilla --default-packages=gocc -e "${EXPR}"