Rearranged the precompiled examples into their own directory, edited makefiles...

Rearranged the precompiled examples into their own directory, edited makefiles to save the unprotected (stock) and protected executables.  Also adjustments to ps_analyze and makefiles to allow turning off steps of ps_analyze.

tools/ps_analyze.sh

@@ -8,6 +8,16 @@
 #     peasoup_analyze.sh <original_binary> <new_binary> <options>
 #
 
+check_step_option()
+{
+	echo $1|egrep "=off$|=on$" > /dev/null
+	if [ $? -ne 0 ]; then
+		echo Malformed option: $1;
+		exit -4;
+	fi
+	
+}
+
 
 #
 # check that the remaining options are validly parsable, and record what they are.
@@ -16,11 +26,44 @@ check_options()
 {
 
 	# 
-	# fill in better option parsing later.
-	#
+	# loop to process options.
+	# 
+
+	# Note that we use `"$@"' to let each command-line parameter expand to a 
+	# separate word. The quotes around `$@' are essential!
+	# We need TEMP as the `eval set --' would nuke the return value of getopt.
+	TEMP=`getopt -o s: --long step: -n 'ps_analyze.sh' -- "$@"`
+
+	# error check #
+	if [ $? != 0 ] ; then echo "Terminating..." >&2 ; exit -1 ; fi
+
+	# Note the quotes around `$TEMP': they are essential!
+	eval set -- "$TEMP"
+
+	while true ; do
+		case "$1" in
+		-s|--step) 
+			echo "found option --step with argument $2"
+			check_step_option $2
+			phases_off=" $phases_off $2 "
+			shift 2 
+			;;
+		--) 	shift 
+			break 
+			;;
+		*) 	echo "Internal error!" 
+		 	exit -2 
+			;;
+		esac
+	done
+
+	# report errors if found
 	if [ ! -z $1 ]; then
-		echo Cannot parse option $1
-		exit 1
+		echo Unparsed parameters:
+	fi
+	for arg do echo '--> '"\`$arg'" ; done
+	if [ ! -z $1 ]; then
+		exit -3;	
 	fi
 	
 }
@@ -31,19 +74,75 @@ check_options()
 #
 is_step_on()
 {
-	# for now, all steps are on 
+	step=$1
+
+	echo $phases_off|egrep "$step=off" > /dev/null
+	if [ $? -eq 0 ] ; then
+		return 0
+	fi
+
+	# for now, all steps are on unless explicitly set to off
 	return 1
 }
 
 #
-# get_step_error_code
+# is_step_error decide based on the step (in $1) and the exit code (in $2) if there was a failure.
 #
 is_step_error()
 {
-	#
-	# fill in with better info later
-	#
-	return 0
+	my_step=$1
+	my_error=$2
+
+
+	case $my_step in
+		# registering the program should return the variant ID, 0 or negative is error.
+		pdb_register)
+			if [ $my_error -gt 0 ]; then
+				return 0;
+			fi
+			return 1;
+		;;
+		# cloning the program should return the variant ID, 0 or negative is error.
+		clone)
+			if [ $my_error -gt 0 ]; then
+				return 0;
+			fi
+			return 1;
+		;;
+		*)
+			if [ $my_error -eq 0 ]; then
+				# if not otherwise specified, programs should return 0
+				return 0;
+			fi
+			return 1;
+	esac
+}
+
+#
+# return the severity of the error for the step in $1
+#
+stop_if_error()
+{
+	my_step=$1
+
+
+	case $my_step in
+		# getting the annotation file right is necessary-ish
+		meds_static)
+			return 1;
+		;;
+		# registering the program is necessary 
+		pdb_register)
+			return 2;
+		;;
+		# cloning is necessary 
+		clone)
+			return 3;
+		;;
+		# other steps are optional
+		*)
+			return 0;
+	esac
 }
 
 #
@@ -57,6 +156,7 @@ perform_step()
 
 	is_step_on $step
 	if [ $? -eq 0 ]; then 
+		echo Skipping step $step.
 		return 0
 	fi
 
@@ -74,11 +174,16 @@ perform_step()
 		command_exit=$?
 	fi
 	
-	echo command exit status for step $step is $command_exit
-
 	is_step_error $step $command_exit
 	if [ $? -ne 0 ]; then
-		echo command failed!
+		echo Done.  Command failed!
+
+		# check if we need to exit
+		stop_if_error $step
+		if [ $? -lt $error_threshold ]; then 
+			echo The $step step is necessary, but failed.  Exiting ps_analyze early.
+			exit -1;
+		fi
 	else
 		echo Done.  Successful.
 	fi
@@ -174,9 +279,6 @@ check_files()
 
 }
 
-
-ps_starttime=`date`
-
 #
 # turn on debugging output if it's requested.
 #
@@ -185,6 +287,18 @@ if [ ! -z "$VERBOSE" ]; then
 fi
 
 
+#
+# set the threshold value.  if a step errors with a more severe error (1=most severe, >1 lesser severe)
+# than the error_threshold, we exit.
+#
+error_threshold=1
+
+#
+# record when we started processing:
+#
+ps_starttime=`date`
+
+
 #
 # stepnum used for counting how many steps peasoup executes
 # 
@@ -307,6 +421,10 @@ if [ -f $newname.ncexe.annot  -a $varid -gt 0 ]; then
 	perform_step clone $SECURITY_TRANSFORMS_HOME/libIRDB/test/clone.exe $varid				
 	cloneid=$?
 
+	
+	#	
+	# we could skip this check and simplify ps_analyze if we say that cloning is necessary in is_step_error
+	#
 	if [ $cloneid -gt 0 ]; then
 		# do the basic tranforms we're performing for peasoup 
 		perform_step fix_calls $SECURITY_TRANSFORMS_HOME/libIRDB/test/fix_calls.exe $cloneid	

tools/ps_link.sh

@@ -6,7 +6,7 @@
 #
 for i in $*
 do
-	echo $i|egrep "^-";	# check for starting with a - 
+	echo $i|egrep "^-" > /dev/null;	# check for starting with a - 
 	if [ 0 -eq  $? ] ; then 
 		echo $i|egrep "^-o" > /dev/null;	# check for starting with a -o 
 		dasho=$?