From 59d53f0e4d97c60142fd7553ba5011855228dd9b Mon Sep 17 00:00:00 2001
From: Andrew Brown <andrew.g.brown@usda.gov>
Date: Thu, 5 May 2022 20:38:57 -0700
Subject: [PATCH] Functions that take multiple files are auto-quoted by default
 #55

---
 PY2R/automation.py            | 13 ++++++++++++-
 PY2R/scripts/image_analysis.R |  2 +-
 PY2R/scripts/lidar_analysis.R |  4 ++--
 R/image_analysis.R            |  2 +-
 R/lidar_analysis.R            |  4 ++--
 5 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/PY2R/automation.py b/PY2R/automation.py
index c7f28f455..95b4a5044 100644
--- a/PY2R/automation.py
+++ b/PY2R/automation.py
@@ -99,7 +99,7 @@ def function_block(line, ff):
                   + "\n"
               )
               ff.write("  }" + "\n")
-            elif '"' not in para and ("wd" in para or "inputs" in para):
+            elif '"' not in para and "wd" in para:
               ff.write("  if (!missing(" + para + ")) {" + "\n")
               ff.write(
                   '    args <- paste(args, paste0("--'
@@ -110,6 +110,17 @@ def function_block(line, ff):
                   + "\n"
               )
               ff.write("  }" + "\n")
+            elif '"' not in para and "inputs" in para:
+              ff.write("  if (!is.null(" + para + ")) {" + "\n")
+              ff.write(
+                  '    args <- paste(args, paste0("--'
+                  + para
+                  + '=", wbt_file_path('
+                  + para
+                  + ")))"
+                  + "\n"
+              )
+              ff.write("  }" + "\n")
             elif '"' not in para:
               ff.write("  if (!is.null(" + para + ")) {" + "\n")
               ff.write(
diff --git a/PY2R/scripts/image_analysis.R b/PY2R/scripts/image_analysis.R
index 7a3d6d3f6..84767020a 100644
--- a/PY2R/scripts/image_analysis.R
+++ b/PY2R/scripts/image_analysis.R
@@ -360,7 +360,7 @@ wbt_mosaic <- function(output, inputs=NULL, method="nn", wd=NULL, verbose_mode=F
   args <- ""
   args <- paste(args, paste0("--output=", wbt_file_path(output)))
   if (!is.null(inputs)) {
-    args <- paste(args, paste0("--inputs=", inputs))
+    args <- paste(args, paste0("--inputs=", wbt_file_path(inputs)))
   }
   if (!is.null(method)) {
     args <- paste(args, paste0("--method=", method))
diff --git a/PY2R/scripts/lidar_analysis.R b/PY2R/scripts/lidar_analysis.R
index 1ce64eeef..4292f27d1 100644
--- a/PY2R/scripts/lidar_analysis.R
+++ b/PY2R/scripts/lidar_analysis.R
@@ -451,7 +451,7 @@ wbt_las_to_zlidar <- function(inputs=NULL, outdir=NULL, compress="brotli", level
   wbt_init()
   args <- ""
   if (!is.null(inputs)) {
-    args <- paste(args, paste0("--inputs=", inputs))
+    args <- paste(args, paste0("--inputs=", wbt_file_path(inputs)))
   }
   if (!is.null(outdir)) {
     args <- paste(args, paste0("--outdir=", outdir))
@@ -2194,7 +2194,7 @@ wbt_zlidar_to_las <- function(inputs=NULL, outdir=NULL, wd=NULL, verbose_mode=FA
   wbt_init()
   args <- ""
   if (!is.null(inputs)) {
-    args <- paste(args, paste0("--inputs=", inputs))
+    args <- paste(args, paste0("--inputs=", wbt_file_path(inputs)))
   }
   if (!is.null(outdir)) {
     args <- paste(args, paste0("--outdir=", outdir))
diff --git a/R/image_analysis.R b/R/image_analysis.R
index 7a3d6d3f6..84767020a 100644
--- a/R/image_analysis.R
+++ b/R/image_analysis.R
@@ -360,7 +360,7 @@ wbt_mosaic <- function(output, inputs=NULL, method="nn", wd=NULL, verbose_mode=F
   args <- ""
   args <- paste(args, paste0("--output=", wbt_file_path(output)))
   if (!is.null(inputs)) {
-    args <- paste(args, paste0("--inputs=", inputs))
+    args <- paste(args, paste0("--inputs=", wbt_file_path(inputs)))
   }
   if (!is.null(method)) {
     args <- paste(args, paste0("--method=", method))
diff --git a/R/lidar_analysis.R b/R/lidar_analysis.R
index 1ce64eeef..4292f27d1 100644
--- a/R/lidar_analysis.R
+++ b/R/lidar_analysis.R
@@ -451,7 +451,7 @@ wbt_las_to_zlidar <- function(inputs=NULL, outdir=NULL, compress="brotli", level
   wbt_init()
   args <- ""
   if (!is.null(inputs)) {
-    args <- paste(args, paste0("--inputs=", inputs))
+    args <- paste(args, paste0("--inputs=", wbt_file_path(inputs)))
   }
   if (!is.null(outdir)) {
     args <- paste(args, paste0("--outdir=", outdir))
@@ -2194,7 +2194,7 @@ wbt_zlidar_to_las <- function(inputs=NULL, outdir=NULL, wd=NULL, verbose_mode=FA
   wbt_init()
   args <- ""
   if (!is.null(inputs)) {
-    args <- paste(args, paste0("--inputs=", inputs))
+    args <- paste(args, paste0("--inputs=", wbt_file_path(inputs)))
   }
   if (!is.null(outdir)) {
     args <- paste(args, paste0("--outdir=", outdir))