Shellharden to the rescue

b11f6c04 · David Hrbáč · 4e6e9282 · b11f6c04 · b11f6c04 · b11f6c04
Commit b11f6c04 authored 6 years ago by David Hrbáč
--- a/eb
+++ b/eb
@@ -19,7 +19,7 @@ if [ -z "$SING" ]; then
 fi
 WHO=$(whoami)
-EB=$(echo $EBVERSIONEASYBUILD)
+EB=$(echo "$EBVERSIONEASYBUILD")
 if [ -z "$EB" ]; then
   echo "EB version not defined"
   exit 1
@@ -38,7 +38,7 @@ if [[ ! -z `echo "$@" | grep "\-\-rm-module"` ]]; then
 fi
 if [[ ! -z `echo $@ | grep "\-\-find-dependency"` ]]; then
-   MODULE=$(echo $@ | sed "s|\-\-find-dependency||")
+   MODULE=$(echo "$@" | sed "s|\-\-find-dependency||")
   "$SCRIPTS_DIR/find-dependency.sh" "$MODULE"
   exit 0
 fi

--- a/scripts/find-dependency.sh
+++ b/scripts/find-dependency.sh
@@ -5,8 +5,8 @@ if [[ -z "$1" ]];then
    echo "Usage: find_dependency module_name"
    exit 1
 fi
-for P in `echo $MODULEPATH | tr ":" " "`; do
+for P in "$(echo "$MODULEPATH" | tr ":" " ")"; do
-    L=$(grep -E "(load|add)[[:punct:] ]*$1[^-[:alnum:]]*$" -R $P | sort)
+    L=$(grep -E "(load|add)[[:punct:] ]*$1[^-[:alnum:]]*$" -R "$P" | sort)
    if [[ ! -z "$L" ]]; then
 	LIST+=$L
        LIST+=$(echo -en "\n\b")
@@ -19,10 +19,10 @@ fi
 #for loop through lines only
 SAVEIFS=$IFS
 IFS=$(echo -en "\n\b")
-for MODULE_PATH in $LIST; do
+for MODULE_PATH in "$LIST"; do
-    MODULE_FIND=$(echo $MODULE_PATH | cut -d ':' -f 2 | grep -o -e "$1.*" | grep -o -e "[[:alnum:]/\._-]*")
+    MODULE_FIND=$(echo "$MODULE_PATH" | cut -d ':' -f 2 | grep -o -e "$1.*" | grep -o -e "[[:alnum:]/\._-]*")
-    MODULE_PATH=$(echo $MODULE_PATH | cut -d ':' -f 1)
+    MODULE_PATH=$(echo "$MODULE_PATH" | cut -d ':' -f 1)
-    MODULE_NAME=$(echo $MODULE_PATH | rev | cut -d '/' -f 1,2 | rev | sed 's/.lua//')
+    MODULE_NAME=$(echo "$MODULE_PATH" | rev | cut -d '/' -f 1,2 | rev | sed 's/.lua//')
    echo -e "\e[96m$MODULE_FIND \e[37m-> \e[93m$MODULE_NAME \e[37m($MODULE_PATH)"
 done
 IFS=$SAVEIFS

--- a/scripts/lib/find_dep
+++ b/scripts/lib/find_dep
 find_dep()
 {
-    for P in `echo $MODULEPATH | tr ":" " "`; do
+    for P in "$(echo "$MODULEPATH" | tr ":" " ")"; do
-        local L=$(grep -E "(load|add)[[:punct:] ]*$1[^-[:alnum:]]*$" -lR $P 2>/dev/null | sort)
+        local L="$(grep -E "(load|add)[[:punct:] ]*$1[^-[:alnum:]]*$" -lR "$P" 2>/dev/null | sort)"
        if [[ ! -z "$L" ]]; then
            LIST+=$L
            LIST+=$(echo -en "\n")
@@ -10,8 +10,8 @@ find_dep()
    if [[ -z "$LIST" ]];then
        return 1
    fi
-    for MODULE_PATH in $LIST; do
+    for MODULE_PATH in "$LIST"; do
-        local MODULE_NAME=$(echo $MODULE_PATH | rev | cut -d '/' -f 1,2 | rev | sed 's/.lua//')
+        local MODULE_NAME="$(echo "$MODULE_PATH" | rev | cut -d '/' -f 1,2 | rev | sed 's/.lua//')"
 	if [[ ! -z "$MODULE_NAME" ]]; then
 	    echo "$MODULE_NAME"
 	fi

--- a/scripts/lib/find_module_paths
+++ b/scripts/lib/find_module_paths
 find_module_paths()
 {
    echo -e "\n$1"
-    local ML=$(ml show $1 2>&1)
+    local ML="$(ml show "$1" 2>&1)"
    if [ $? != 0 ]; then
 	echo "Error: Module not found"
 	return 1
    fi
-    local MODROOT=$(echo "$ML" | grep "EBROOT" | cut -d ',' -f 2 | cut -d '"' -f 2)
+    local MODROOT="$(echo "$ML" | grep "EBROOT" | cut -d ',' -f 2 | cut -d '"' -f 2)"
    if [ ! -d "$MODROOT" ]; then
 	echo "Error: Non-standard installation, exiting..."
        exit 1
    fi
-    local MODFILE=$(echo "$ML" | head -n3 | grep "\/[^[:space:]]*:" | tr -d ': ')
+    local MODFILE="$(echo "$ML" | head -n3 | grep "\/[^[:space:]]*:" | tr -d ': ')"
    echo "    ROOT: $MODROOT"
-    if [ -L $MODFILE ]; then
+    if [ -L "$MODFILE" ]; then
-	local MODFILE2=$(readlink $MODFILE)
+	local MODFILE2="$(readlink "$MODFILE")"
 	echo "    MODL: $MODFILE"
        echo "    MODF: $MODFILE2"
-	if [ $(echo $MODROOT | rev | cut -d '/' -f 1) != $(echo $MODFILE2 | sed 's/.lua//' | rev | cut -d '/' -f 1) ] || [ $(echo $MODROOT | rev | cut -d '/' -f 1) != $(echo $MODFILE | sed 's/.lua//' | rev | cut -d '/' -f 1) ];then
+	if [ "$(echo "$MODROOT" | rev | cut -d '/' -f 1)" != "$(echo "$MODFILE2" | sed 's/.lua//' | rev | cut -d '/' -f 1)" ] || [ "$(echo "$MODROOT" | rev | cut -d '/' -f 1)" != "$(echo "$MODFILE" | sed 's/.lua//' | rev | cut -d '/' -f 1)" ];then
 	    echo -e "\nError: Non-standard installation, exiting..."
 	    exit 1
 	fi
    else
        echo "    MODF: $MODFILE"
-	if  [ $(echo $MODROOT | rev | cut -d '/' -f 1) != $(echo $MODFILE | sed 's/.lua//' | rev | cut -d '/' -f 1) ];then
+	if  [ "$(echo "$MODROOT" | rev | cut -d '/' -f 1)" != "$(echo "$MODFILE" | sed 's/.lua//' | rev | cut -d '/' -f 1)" ];then
 	    echo -e "\nError: Non-standard installation, exiting..."
 	    exit 1
        fi

--- a/scripts/lib/recursion
+++ b/scripts/lib/recursion
 recursion()
 {
-    local LIST=$(ml show $1 2>&1 | grep -E "load\(\"[[:alnum:]/\._-]*\"\)" | cut -d '"' -f2 | sort)
+    local LIST="$(ml show "$1" 2>&1 | grep -E "load\(\"[[:alnum:]/\._-]*\"\)" | cut -d '"' -f2 | sort)"
    if [[ -z "$LIST" ]];then
 	OUT="$1 $OUT"
 	echo -n "."
        return 0
    fi
-    for MODULE in $LIST; do
+    for MODULE in "$LIST"; do
-        local DUP=$(echo -e $OUT | grep "$MODULE")
+        local DUP="$(echo -e "$OUT" | grep "$MODULE")"
        if [[ -z "$DUP" ]];then
-            recursion $MODULE
+            recursion "$MODULE"
        fi
    done
    OUT="$1 $OUT"

--- a/scripts/lib/remove_module
+++ b/scripts/lib/remove_module
 remove_module()
 {
    echo -e "\nRemoving module: $1"
-    local ML=$(ml show $1 2>&1)
+    local ML="$(ml show "$1" 2>&1)"
    if [ $? != 0 ]; then
        echo "Error: Module not found"
        return 1
    fi
-    local MODROOT=$(echo "$ML" | grep "EBROOT" | cut -d ',' -f 2 | cut -d '"' -f 2)
+    local MODROOT="$(echo "$ML" | grep "EBROOT" | cut -d ',' -f 2 | cut -d '"' -f 2)"
-    local MODFILE=$(echo "$ML" | head -n3 | grep "\/[^[:space:]]*:" | tr -d ': ')
+    local MODFILE="$(echo "$ML" | head -n3 | grep "\/[^[:space:]]*:" | tr -d ': ')"
    echo -ne "[    ] Removing root directory:  $MODROOT"
-    rm -rf $MODROOT 2>&1 >/dev/null
+    rm -rf "$MODROOT" 2>&1 >/dev/null
    if [ $? == 0 ]; then
 	echo -e "\r[\e[32m OK \e[0m] Removing root directory:  $MODROOT"
    else
 	echo -e "\r[\e[31mFAIL\e[0m] Removing root directory:  $MODROOT"
    fi
-    if [ -L $MODFILE ]; then
+    if [ -L "$MODFILE" ]; then
-        local MODFILE2=$(readlink $MODFILE)
+        local MODFILE2="$(readlink "$MODFILE")"
    	echo -ne "[    ] Removing link to modfile: $MODFILE"
-	rm $MODFILE 2>&1 >/dev/null
+	rm "$MODFILE" 2>&1 >/dev/null
    	if [ $? == 0 ]; then
            echo -e "\r[\e[32m OK \e[0m] Removing link to modfile: $MODFILE"
 	else
            echo -e "\r[\e[31mFAIL\e[0m] Removing link to modfile: $MODFILE"
 	fi
 	echo -ne "[    ] Removing modfile:         $MODFILE2"
-        rm $MODFILE2 2>&1 >/dev/null
+        rm "$MODFILE2" 2>&1 >/dev/null
        if [ $? == 0 ]; then
            echo -e "\r[\e[32m OK \e[0m] Removing modfile:         $MODFILE2"
        else
@@ -33,7 +33,7 @@ remove_module()
        fi
    else
        echo -ne "[    ] Removing modfile: $MODFILE\r"
-        rm $MODFILE 2>&1 >/dev/null
+        rm "$MODFILE" 2>&1 >/dev/null
        if [ $? == 0 ]; then
            echo -e "[\e[32m OK \e[0m] Removing modfile: $MODFILE"
        else

--- a/scripts/post_install.sh
+++ b/scripts/post_install.sh
@@ -2,7 +2,7 @@
 # IT4Innovations 2018
 NAME=$(ml av EasyBuild -t 2>&1 | tail -1)
-VERSION=$(echo $NAME | cut -d '/' -f 2)
+VERSION=$(echo "$NAME" | cut -d '/' -f 2)
 echo -e "==\e[33m WARNING \e[0m!!! UPGRADE $NAME for IT4Innovations adjusting??? !!!\e[33m WARNING \e[0m"
 echo -n "== Do you really want to upgrade it? [yes/NO]: "
@@ -12,9 +12,9 @@ if [ "$CONTINUE" != "yes" ]; then
 fi
 echo -n "== eb -> eb.exe        [ "
-if [ ! -L /apps/all/EasyBuild/$VERSION/bin/eb ]; then
+if [ ! -L /apps/all/EasyBuild/"$VERSION"/bin/eb ]; then
-   if [ -f /apps/all/EasyBuild/$VERSION/bin/eb ];then
+   if [ -f /apps/all/EasyBuild/"$VERSION"/bin/eb ];then
-      mv /apps/all/EasyBuild/$VERSION/bin/eb /apps/all/EasyBuild/$VERSION/bin/eb.exe && echo -e "\e[32mOK \e[0m]" || echo -e "\e[31mFAIL \e[0m]"
+      mv /apps/all/EasyBuild/"$VERSION"/bin/eb /apps/all/EasyBuild/"$VERSION"/bin/eb.exe && echo -e "\e[32mOK \e[0m]" || echo -e "\e[31mFAIL \e[0m]"
   else
      echo -e "\e[33mPROBLEM \e[0m]"
   fi
@@ -23,24 +23,24 @@ else
 fi
 echo -n "== symlink eb          [ "
-if [ ! -f /apps/all/EasyBuild/$VERSION/bin/eb ];then
+if [ ! -f /apps/all/EasyBuild/"$VERSION"/bin/eb ];then
-   ln -s /apps/all/EasyBuild/upgrade/eb /apps/all/EasyBuild/$VERSION/bin/eb && echo -e "\e[32mOK \e[0m]" || echo -e "\e[31mFAIL\e[0m]"
+   ln -s /apps/all/EasyBuild/upgrade/eb /apps/all/EasyBuild/"$VERSION"/bin/eb && echo -e "\e[32mOK \e[0m]" || echo -e "\e[31mFAIL\e[0m]"
 else
   echo -e "\e[33mEXISTS \e[0m]"
 fi
 echo -n "== symlink python.py   [ "
 PY=$(ls /lib/ | grep python | sed "s|python||")
-if [ ! -f /apps/all/EasyBuild/$VERSION/lib/python$PY/site-packages/easybuild_framework-$VERSION-py$PY.egg/easybuild/toolchains/python.py ]; then
+if [ ! -f /apps/all/EasyBuild/"$VERSION/lib/python$PY/site-packages/easybuild_framework-$VERSION-py$PY".egg/easybuild/toolchains/python.py ]; then
-   ln -s /apps/all/EasyBuild/upgrade/python.py /apps/all/EasyBuild/$VERSION/lib/python$PY/site-packages/easybuild_framework-$VERSION-py$PY.egg/easybuild/toolchains/python.py && echo -e "\e[32mOK \e[0m]" || echo -e "\e[31mFAIL \e[0m]"
+   ln -s /apps/all/EasyBuild/upgrade/python.py /apps/all/EasyBuild/"$VERSION/lib/python$PY/site-packages/easybuild_framework-$VERSION-py$PY".egg/easybuild/toolchains/python.py && echo -e "\e[32mOK \e[0m]" || echo -e "\e[31mFAIL \e[0m]"
 else
   echo -e "\e[33mEXISTS \e[0m]"
 fi
 echo -n "== edit modulefile     [ "
-STATE=$(cat /apps/modules/all/EasyBuild/$VERSION.lua | grep sticky)
+STATE=$(cat /apps/modules/all/EasyBuild/"$VERSION".lua | grep sticky)
 if [ "$STATE" == "" ]; then
-   echo 'setenv("EASYBUILD_ROBOT_PATHS", "/apps/easybuild/easyconfigs-it4i:/apps/easybuild/easyconfigs-master/easybuild/easyconfigs:/apps/easybuild/easyconfigs-develop/easybuild/easyconfigs")' >> /apps/modules/all/EasyBuild/$VERSION.lua && echo 'setenv("EASYBUILD_INCLUDE_EASYBLOCKS", "/apps/easybuild/it4i-easyblocks/easyblocks/*/*.py")' >> /apps/modules/all/EasyBuild/$VERSION.lua && echo 'add_property("lmod", "sticky")' >> /apps/modules/all/EasyBuild/$VERSION.lua && echo -e "\e[32mOK \e[0m]" || echo -e "\e[31mFAIL\e[0m]"
+   echo 'setenv("EASYBUILD_ROBOT_PATHS", "/apps/easybuild/easyconfigs-it4i:/apps/easybuild/easyconfigs-master/easybuild/easyconfigs:/apps/easybuild/easyconfigs-develop/easybuild/easyconfigs")' >> /apps/modules/all/EasyBuild/"$VERSION".lua && echo 'setenv("EASYBUILD_INCLUDE_EASYBLOCKS", "/apps/easybuild/it4i-easyblocks/easyblocks/*/*.py")' >> /apps/modules/all/EasyBuild/"$VERSION".lua && echo 'add_property("lmod", "sticky")' >> /apps/modules/all/EasyBuild/"$VERSION".lua && echo -e "\e[32mOK \e[0m]" || echo -e "\e[31mFAIL\e[0m]"
 else
   echo -e "\e[33mEXISTS \e[0m]"
 fi

--- a/scripts/rm-module.sh
+++ b/scripts/rm-module.sh
 #!/bin/bash
 # IT4Innovations 2019
-DIRNAME=$(dirname $0)
+DIRNAME=$(dirname "$0")
-LIB_DIR="`dirname $0`/lib"
+LIB_DIR="$(dirname "$0")/lib"
 # Include functions
-. $LIB_DIR/find_dep
+. "$LIB_DIR"/find_dep
-. $LIB_DIR/find_module_paths
+. "$LIB_DIR"/find_module_paths
-. $LIB_DIR/recursion
+. "$LIB_DIR"/recursion
-. $LIB_DIR/remove_module
+. "$LIB_DIR"/remove_module
 # Display a usage message.
 usage () {
-    if [ -n "$*" ]; then
+    if [ -n "$@" ]; then
-       echo "usage error: $*"
+       echo "usage error: $@"
    fi
    cat <<EOF
 Usage: rm-module [OPTION ...] MODULE
@@ -32,7 +32,7 @@ ARGS=$(getopt --options shfo \
       --name "rm-module" -- "$@")
 GETOPT_STATUS=$?
-if [ $GETOPT_STATUS -ne 0 ]; then
+if [ "$GETOPT_STATUS" -ne 0 ]; then
    exit 6
 fi
@@ -62,7 +62,7 @@ if [[ -z "$1" ]];then
    exit 1
 fi
-MODULE=$(ml show $1 2>&1)
+MODULE=$(ml show "$1" 2>&1)
 if [ $? == 1 ];then
    echo "Error: can't find module $1"
@@ -72,10 +72,10 @@ fi
 MODULE=$(echo "$MODULE" | head -2 | tail -1 | tr -d ':' | rev | cut -d '/' -f 1,2 | rev | sed 's/.lua//')
 if [ "$SINGLE" ]; then
-    DEP=$(find_dep $MODULE)
+    DEP=$(find_dep "$MODULE")
    if [[ -z $DEP ]]; then
        echo -e "\r[\e[32mINDEPENDENT\e[0m] $MODULE"
-        find_module_paths $MODULE
+        find_module_paths "$MODULE"
 	if [[ -z "$FORCE" ]];then
            echo -ne "\nRemove module $MODULE? [yes/NO]: "
            read CONTINUE
@@ -83,7 +83,7 @@ if [ "$SINGLE" ]; then
                exit 0
            fi
        fi
-        remove_module $MODULE
+        remove_module "$MODULE"
 	exit 0
    else
        echo -e "\r[\e[31m DEPENDENT \e[0m] $MODULE"
@@ -92,16 +92,16 @@ if [ "$SINGLE" ]; then
 fi
 echo -n "Building module tree..."
-recursion $MODULE
+recursion "$MODULE"
 echo "done"
 REMOVELIST=""
-for MODULE in $OUT; do
+for MODULE in "$OUT"; do
    echo -n "[           ] $MODULE"
-    DEP=$(find_dep $MODULE)			#find all modules dependenton this one
+    DEP=$(find_dep "$MODULE")			#find all modules dependenton this one
-    for MOD in $REMOVELIST; do
+    for MOD in "$REMOVELIST"; do
-	DEP=$(echo "$DEP" | grep -v $MOD)	#erase modules which is on remove list
+	DEP=$(echo "$DEP" | grep -v "$MOD")	#erase modules which is on remove list
    done
    if [[ -z $DEP ]]; then
 	echo -e "\r[\e[32mINDEPENDENT\e[0m] $MODULE"
@@ -117,13 +117,13 @@ if [[ -z $REMOVELIST ]]; then
 fi
 echo -e "\nRemove list:"
-for MODULE in $REMOVELIST; do
+for MODULE in "$REMOVELIST"; do
-    find_module_paths $MODULE
+    find_module_paths "$MODULE"
 done
 if [ "$FORCE" ]; then
-    for MODULE in $REMOVELIST; do
+    for MODULE in "$REMOVELIST"; do
-        remove_module $MODULE
+        remove_module "$MODULE"
    done
    exit 0
 fi
@@ -137,7 +137,7 @@ if [ "$ONCE" ]; then
    fi
 fi
-for MODULE in $REMOVELIST; do
+for MODULE in "$REMOVELIST"; do
    if [[ -z "$ONCE" ]]; then
        echo -ne "\nRemove module $MODULE? [yes/NO]: "
        read CONTINUE
@@ -145,7 +145,7 @@ for MODULE in $REMOVELIST; do
            continue
        fi
    fi
-    remove_module $MODULE
+    remove_module "$MODULE"
 done
 exit 0