Fixed some errors regarding gpg

spsp

@@ -110,7 +110,7 @@ signFile() {
 encryptFile() {
     message="Encrypting file ${COL_LGREEN}$1${COL_RESET}..."
     printf "$message\n"
-    $GPGCMD --yes --always-trust -o $1.gpg -e -r $RECIPIENT $1
+    $GPGCMD --yes --batch --always-trust -o $1.gpg -e -r $RECIPIENT $1
     message="File is encrypted as ${COL_LYELLOW}$1.gpg${COL_RESET}!"
     printf "$message\n"
 }
@@ -137,12 +137,12 @@ if [ $# -gt 0 ]; then
 
     if [ "$1" == "--version" ] || [ "$1" == "-v" ] || [ "$1" == "version" ]; then
         showVersion
-        exit 1
+        exit 0
     fi
 
     if [ "$1" == "--help" ] || [ "$1" == "-H" ] || [ "$1" == "help" ]; then
         showHelp
-        exit 1
+        exit 0
     fi
 
     if [ "$1" == "init" ]; then
@@ -150,23 +150,23 @@ if [ $# -gt 0 ]; then
 
         if [ ! -x "$(command -v tar)" ]; then
             echo "Error: tar command is not available."
-            exit 0
+            exit 22
         fi
 
         if [ ! -x "$(command -v sftp)" ]; then
             echo "Error: sftp command is not available."
-            exit 0
+            exit 22
         fi
 
         if [ ! -f .env ]; then
             echo "No .env file found within current working directory $(pwd)"
             echo "Create a .env file before re-initializing"
-            exit 0
+            exit 2
         fi
 
         if [ ! -f spsp ]; then
             echo "No spsp file found within current working directory $(pwd)"
-            exit 0
+            exit 2
         fi
 
         echo "SPSP: Making spsp transfer-tool command available"
@@ -186,6 +186,7 @@ if [ $# -gt 0 ]; then
 
         CURRENTDATE=`date +"%Y-%m-%d"`
 
+        echo "############# $CURRENTDATE #############"
         echo "SPSP: Starting the transfer-tool..."
 
         OUTBOX=outbox
@@ -215,12 +216,24 @@ if [ $# -gt 0 ]; then
             touch $LOGFILE
         fi
 
+        if [ ! -x "$(command -v gpg)" ]; then
+            echo "Error: gpg command is not available, this error may happen when you use a CRON task. Modifying the PATH..."
+            export PATH=$PATH:/usr/local/bin
+            if [ ! -x "$(command -v gpg)" ]; then
+                echo "Error: gpg command is not available (no gpg instance is installed)."
+                exit 22
+            fi
+        fi
+
         if ! nc -w 1 -z ${HOST} 22 &> /dev/null;then 
             echo "[`date +"%T"`] local.ERROR: ${HOST}:22 is unreachable, please check your connection" >> $LOGFILE
             echo "SPSP: Error detected please check $LOGFILE"
-            exit 0
+            echo "########################################"
+            exit 55
         fi
 
+
+
         for DIRECTORY in *; do
             if [ -d "$DIRECTORY" ] && [ $DIRECTORY != $OUTBOX ] && [ $DIRECTORY != $SENT ] && [ $DIRECTORY != $LOGS ]; then
                 if ls $DIRECTORY/*.fastq* 1> /dev/null 2>&1 && [ -f $DIRECTORY/*.xlsx ]; then
@@ -233,53 +246,57 @@ if [ $# -gt 0 ]; then
                 else
                     echo "[`date +"%T"`] local.ERROR: Missing files (*.fastq/.fastq.gz and/or *.xlsx) inside ${DIRECTORY}" >> $LOGFILE
                     echo "SPSP: Error detected please check $LOGFILE"
-                    exit 0
+                    echo "########################################"
+                    exit 13
                 fi
             fi
         done
 
         for FILE in ./outbox/*; do
             if [ -f "$FILE" ]; then
-                echo "SPSP: Signing $FILE using SHA-256 algorithm..."
-                signFile $FILE &> /dev/null
-                echo "SPSP: $File is now signed!"
                 echo "SPSP: Encrypting $FILE using SPSP public key..."
-                encryptFile $FILE &> /dev/null
+                encryptFile $FILE
                 echo "SPSP: $FILE is now encrypted"
-                echo "SPSP: Removing unencrypted version of $FILE"
-                rm -rf $FILE
-                echo "SPSP: Deleted!"
-                if [ -f "$FILE.sha256" ] && [ -f "$FILE.gpg" ]; then
+                echo "SPSP: Signing $FILE using SHA-256 algorithm..."
+                signFile $FILE.gpg
+                echo "SPSP: $FILE is now signed!"
+                if [ -f "$FILE.gpg.sha256" ] && [ -f "$FILE.gpg" ]; then
                     echo "SPSP: Starting the transfer"
-                    transferFile $FILE.sha256 &> /dev/null
-                    transferFile $FILE.gpg &> /dev/null
+                    transferFile $FILE.gpg.sha256
+                    transferFile $FILE.gpg
                     echo "SPSP: $FILE has been transferred sucessfully!"
-                    mv $FILE.sha256 ./sent/.
+                    mv $FILE.gpg.sha256 ./sent/.
                     mv $FILE.gpg ./sent/.
+                    echo "SPSP: Removing unencrypted version of $FILE"
+                    rm -rf "$FILE"
+                    echo "SPSP: Deleted!"
                 else 
                     echo "[`date +"%T"`] local.ERROR: Missing the encrypted version or the signature for $FILE" >> $LOGFILE
                     echo "SPSP: Error detected please check $LOGFILE"
-                    exit 0
+                    echo "########################################"
+                    exit 2
                 fi
-                echo ""
             fi
         done
-        echo ""
         echo "SPSP: Process completed!"
+        echo "########################################"
 
     # Compress a folder given as an input
     elif [ "$1" == "compress" ]; then
         shift 1
         compressFolder $@
 
+    # Transfer a file given as an input
     elif [ "$1" == "transfer" ]; then
         shift 1
         transferFile $@
 
+    # Sign a afile given as an input
     elif [ "$1" == "sign" ]; then
         shift 1
         signFile $@
 
+    # Encrypt a folder/file given as an input
     elif [ "$1" == "encrypt" ]; then
         shift 1
         encryptFile $@