diff --git a/tools/do_p1transform.sh b/tools/do_p1transform.sh
deleted file mode 100755
index e322f44f163d30a13f3c28cee2b0e7e31abb74d5..0000000000000000000000000000000000000000
--- a/tools/do_p1transform.sh
+++ /dev/null
@@ -1,297 +0,0 @@
-#!/bin/bash -x
-#
-# do_p1transform.sh <originalBinary> <MEDS annotationFile> <cloneId> <BED_script>
-#
-# pre: we are in the top-level directory created by ps_analyze.sh
-#
-
-# input
-CLONE_ID=$1
-ORIGINAL_BINARY=$2
-MEDS_ANNOTATION_FILE=$3
-BED_SCRIPT=$4
-TIMEOUT_VALUE=$5
-
-shift 5
-PN_OPTIONS=$*
-
-# Maximum length of time to spend replaying inputs to get coverage
-COVERAGE_REPLAY_TIMEOUT=600
-# Timeout per replayer run
-REPLAYER_TIMEOUT=120
-TOP_LEVEL=`pwd`
-BASELINE_DIR=$TOP_LEVEL/replayer_baseline
-INPUT_CUTOFF=50
-
-mkdir $BASELINE_DIR
-
-STRATAFIED_BINARY=$TOP_LEVEL/a.stratafied
-
-# configuration variables
-P1_DIR=p1.xform
-CONCOLIC_DIR=concolic.files_a.stratafied_0001
-#EXECUTED_ADDRESSES=$CONCOLIC_DIR/executed_address_list.txt
-EXECUTED_ADDRESSES_CONCOLIC=concolic_coverage.txt;
-EXECUTED_ADDRESSES_MANUAL=manual_coverage.txt
-EXECUTED_ADDRESSES_FINAL=final.coverage.txt
-LIBC_FILTER=$PEASOUP_HOME/tools/libc_functions.txt
-BLACK_LIST=$P1_DIR/p1.filtered_out # list of functions to blacklist
-COVERAGE_FILE=$P1_DIR/p1.coverage
-P1THRESHOLD=0.75
-
-PN_BINARY=$SECURITY_TRANSFORMS_HOME/bin/p1transform.exe
-
-echo "P1: transforming binary: cloneid=$CLONE_ID bed_script=$BED_SCRIPT timeout_value=$TIMEOUT_VALUE options=$PN_OPTIONS"
-
-mkdir $P1_DIR
-
-# if C++ skip
-#file a.ncexe | grep -i static | grep -i link | grep -i execut
-#if [ $? -eq 0 ]; then
-# nm -a a.ncexe | grep __gnu_cxx
-# if [ $? -eq 0 ]; then
-# echo "P1: Statically-linked C++ program detected -- skipping"
-# exit 1
-# fi
-#else
-# ldd a.ncexe | grep "libstdc++"
-# if [ $? -eq 0 ]; then
-# echo "P1: Dynamically-linked C++ program detected -- skipping"
-# exit 1
-# fi
-#fi
-
-touch $EXECUTED_ADDRESSES_FINAL
-
-# generate coverage info for manually-specified tests (if any)
-$PEASOUP_HOME/tools/do_manual_cover.sh
-
-if [[ ! $? -eq 0 ]]; then
- echo "ERROR: Manual coverage failed"
- #continue for now, but don't encorporate manual coverage data.
-else
-# merge all execution traces if successfully run
- cat $EXECUTED_ADDRESSES_MANUAL >> $EXECUTED_ADDRESSES_FINAL
-fi
-echo "manual cover finished"
-
-echo "Replaying all .json files"
-input_cnt=0
-REPLAY_DEADLINE=$(( `date +'%s'` + $COVERAGE_REPLAY_TIMEOUT ))
-#run all .json inputs through the replayer starting with most recent
-for i in `ls -t $CONCOLIC_DIR/*.json`
-do
- rm -f exit_status stdout.* stderr.*
- rm -rf grace_replay/
-
- if [ `date +'%s'` -ge $REPLAY_DEADLINE ]; then
- break
- fi
-
- #FYI: I Believe this check is in the loop to avoid calling this program if grace completely
- #failed or was not called at all, but I can't remember. I recommend just leavin it for now.
-#check to see if the sym file exists, if not create it.
- if [ ! -e $TOP_LEVEL/a.sym ]; then
- $GRACE_HOME/concolic/src/util/linux/objdump_to_grace $STRATAFIED_BINARY
- fi
-
- input=`basename $i .json`
- #input_number=`echo $input | sed "s/.*input_//"`
- # abridged_number=`echo $input_number | sed 's/0*\(.*\)/\1/'`
-
- echo "timeout $REPLAYER_TIMEOUT "$GRACE_HOME/concolic/bin/replayer" --timeout=$REPLAYER_TIMEOUT --symbols=$TOP_LEVEL/a.sym --stdout=stdout.$input --stderr=stderr.$input --logfile=exit_status --engine=sdt $STRATAFIED_BINARY $i"
-
- #generate baseline from the stratafied program, if only to prevent discrepencies when a program prints its own name.
- #also I want to be as consistent as possible to avoid replayer issues.
- timeout $REPLAYER_TIMEOUT "$GRACE_HOME/concolic/bin/replayer" --timeout=$REPLAYER_TIMEOUT --symbols=$TOP_LEVEL/a.sym --stdout=stdout.$input --stderr=stderr.$input --logfile=exit_status --engine=sdt $STRATAFIED_BINARY $i
- if [ $? -ne 0 ]; then
- echo "Replay failed; ignoring input"
- mv $i $i.ignore
- continue;
- fi
-
- #the exit status file has long been a flag that replay worked, make sure it exists before continuing
- if [ ! -f exit_status ]; then
- echo "Failed to capture subject exit code; ignoring input"
- mv $i $i.ignore
- continue;
- fi
-
- status=`cat exit_status | grep "Subject exited" | sed "s/.*status //"`
-
- #don't consider inputs that cause the program to exit in exit codes 132-140 inclusive
- if [ "$status" -ge 132 ] && [ "$status" -le 140 ]; then
- echo "Ignoring input, bad exit status"
- mv $i $i.ignore
- continue
- fi
-
-
- #set up the baseline replayer directory, and move all replayer data into the directory
- mkdir $BASELINE_DIR/$input
-
- mv stdout.$input $BASELINE_DIR/$input/.
- mv stderr.$input $BASELINE_DIR/$input/.
- cat exit_status | grep "Subject exited with status" >tmp
- mv tmp $BASELINE_DIR/$input/exit_status
- mv grace_replay/ $BASELINE_DIR/$input/.
-
- #---------------Non-Determinism Check-------------------
-
- #replay again and check for divergence due to non-deterministic output
- # to force time-based nondeterminism, adjust clock ahead to a random time the next day
- ADJUST_TIME=$(($RANDOM % 30000 + 86490))
- echo "timeout $REPLAYER_TIMEOUT "$GRACE_HOME/concolic/bin/replayer" --timeout=$REPLAYER_TIMEOUT --adjust-time=$ADJUST_TIME --symbols=$TOP_LEVEL/a.sym --stdout=stdout.$input --stderr=stderr.$input --logfile=exit_status --engine=sdt --instruction_addresses=$i.coverage $STRATAFIED_BINARY $i"
-
- timeout $REPLAYER_TIMEOUT "$GRACE_HOME/concolic/bin/replayer" --timeout=$REPLAYER_TIMEOUT --adjust-time=$ADJUST_TIME --symbols=$TOP_LEVEL/a.sym --stdout=stdout.$input --stderr=stderr.$input --logfile=exit_status --engine=sdt --instruction_addresses=$i.coverage $STRATAFIED_BINARY $i
- if [ $? -ne 0 ]; then
- echo "Replay failed; ignoring input"
- mv $i $i.ignore
- rm -Rf $BASELINE_DIR/$input/
- continue;
- fi
-
- #create a temporary directory for the second replay values, so I can diff the directory structure.
- mkdir $BASELINE_DIR/${input}_tmp
-
- mv stdout.$input $BASELINE_DIR/${input}_tmp/.
- mv stderr.$input $BASELINE_DIR/${input}_tmp/.
- cat exit_status | grep "Subject exited with status" >tmp
- mv tmp $BASELINE_DIR/${input}_tmp/exit_status
- mv grace_replay/ $BASELINE_DIR/${input}_tmp/.
-
- diff -r $BASELINE_DIR/$input $BASELINE_DIR/${input}_tmp
- if [ ! $? -eq 0 ]; then
- echo "Replayer divergence detected for input: $input, rerunning replayer with -r"
-
- #destroy original baseline directory
- rm -r $BASELINE_DIR/$input
- #clean up the second replay baseline directory
- rm -r $BASELINE_DIR/${input}_tmp
-
- #rerun the replayer with -r
- #BEN NOTE: It is my understanding that once run with -r, when we actual replay a peasoup'ed version we
- #do not need to run with -r. I.e., replay is oblivious to whether or not we used -r.
- echo "timeout $REPLAYER_TIMEOUT "$GRACE_HOME/concolic/bin/replayer" --timeout=$REPLAYER_TIMEOUT --symbols=$TOP_LEVEL/a.sym --stdout=stdout.$input --stderr=stderr.$input --logfile=exit_status --engine=sdt -r $STRATAFIED_BINARY $i"
- timeout $REPLAYER_TIMEOUT "$GRACE_HOME/concolic/bin/replayer" --timeout=$REPLAYER_TIMEOUT --symbols=$TOP_LEVEL/a.sym --stdout=stdout.$input --stderr=stderr.$input --logfile=exit_status --engine=sdt -r $STRATAFIED_BINARY $i
- if [ $? -ne 0 ]; then
- echo "Replay with syscall capture failed; ignoring input"
- rm -Rf $BASELINE_DIR/$input/
- mv $i $i.ignore
- continue
- fi
-
- #recreate a temporary directory for the second replay value, so I can diff the directory structure with baseline.
- mkdir $BASELINE_DIR/${input}
-
- mv stdout.$input $BASELINE_DIR/${input}/.
- mv stderr.$input $BASELINE_DIR/${input}/.
- cat exit_status | grep "Subject exited with status" >tmp
- mv tmp $BASELINE_DIR/${input}/exit_status
- mv grace_replay/ $BASELINE_DIR/${input}/.
-
- #Run the replayer one more time without -r, to get a second run to compare against (-r is not necessary once it has been used once)
- echo "timeout $REPLAYER_TIMEOUT "$GRACE_HOME/concolic/bin/replayer" --timeout=$REPLAYER_TIMEOUT --symbols=$TOP_LEVEL/a.sym --stdout=stdout.$input --stderr=stderr.$input --logfile=exit_status --engine=sdt --instruction_addresses=$i.coverage $STRATAFIED_BINARY $i"
- timeout $REPLAYER_TIMEOUT "$GRACE_HOME/concolic/bin/replayer" --timeout=$REPLAYER_TIMEOUT --symbols=$TOP_LEVEL/a.sym --stdout=stdout.$input --stderr=stderr.$input --logfile=exit_status --engine=sdt --instruction_addresses=$i.coverage $STRATAFIED_BINARY $i
- if [ $? -ne 0 ]; then
- echo "Second replay with syscall capture failed; ignoring input"
- mv $i $i.ignore
- rm -rf $BASELINE_DIR/${input}
- continue
- fi
-
- #create a temporary directory for the second replay values, so I can diff the directory structure.
- mkdir $BASELINE_DIR/${input}_tmp
-
- mv stdout.$input $BASELINE_DIR/${input}_tmp/.
- mv stderr.$input $BASELINE_DIR/${input}_tmp/.
- cat exit_status | grep "Subject exited with status" >tmp
- mv tmp $BASELINE_DIR/${input}_tmp/exit_status
- mv grace_replay/ $BASELINE_DIR/${input}_tmp/.
-
-
- #Check for a divergence between the new baseline using -r and the rerun
- #If a divergence is detected, ignore the input (remove from baseline), and continue
- diff -r $BASELINE_DIR/$input $BASELINE_DIR/${input}_tmp
- if [ ! $? -eq 0 ]; then
- echo "Replayer divergence detected using -r for input: $input, ignoring input"
- #clean up the second replay baseline directory
- rm -r $BASELINE_DIR/${input}_tmp
- #remove original baseline run as well.
- rm -r $BASELINE_DIR/${input}
- continue
- fi
- fi #end of non-determinism check
-
- #at this point, the replayer should have produced baseline results that have been validated for non-determinism
-
- #clean up the second replay baseline directory
- rm -rf $BASELINE_DIR/${input}_tmp
-
- #increment input counter (counter indicates how many inputs have been validated)
- input_cnt=`expr $input_cnt + 1`
-done
-
-rm -f exit_status stdout.* stderr.*
-rm -rf grace_replay/
-
-echo "Finished replaying .json files: Replayed $input_cnt inputs"
-
-if [ "$input_cnt" -ne 0 ]; then
- echo "Choosing at most $INPUT_CUTOFF inputs with best coverage"
-
- GREEDY_COVER=`$GRACE_HOME/concolic/scripts/set_cover.py $INPUT_CUTOFF $CONCOLIC_DIR/*.coverage`
-
-
- input_cnt=`echo $GREEDY_COVER|wc -w`
-
- echo "Chose $input_cnt inputs"
-
- cat $GREEDY_COVER >> $EXECUTED_ADDRESSES_CONCOLIC
-
-# Remove inputs that were not chosen.
- for i in $BASELINE_DIR/*
- do
- if [[ ! "$GREEDY_COVER" =~ `basename $i` ]]; then
- rm -r $i
- fi
- done
-
-fi
-
-touch $EXECUTED_ADDRESSES_CONCOLIC
-
-cat $EXECUTED_ADDRESSES_CONCOLIC >> $EXECUTED_ADDRESSES_FINAL
-
-# sanity filter, keep only well formed addresses
-# also change a.stratafied to a.ncexe, which is the name for the main executable in IRDB
-cat $EXECUTED_ADDRESSES_FINAL | sed -e 's/\(.*0x.*\)/\1/' -e 's/^a\.stratafied+/a.ncexe+/' >tmp
-mv tmp $EXECUTED_ADDRESSES_FINAL
-
-sort $EXECUTED_ADDRESSES_FINAL | uniq > tmp
-mv tmp $EXECUTED_ADDRESSES_CONCOLIC
-
-echo "$SECURITY_TRANSFORMS_HOME/bin/cover $CLONE_ID $EXECUTED_ADDRESSES_FINAL $COVERAGE_FILE"
-# produce coverage file
-#$PEASOUP_HOME/tools/cover.sh $ORIGINAL_BINARY $MEDS_ANNOTATION_FILE $EXECUTED_ADDRESSES_FINAL $LIBC_FILTER $COVERAGE_FILE $BLACK_LIST
-$SECURITY_TRANSFORMS_HOME/bin/cover $CLONE_ID $EXECUTED_ADDRESSES_FINAL $COVERAGE_FILE
-
-#just in case something went wrong, touch the coverage file. An empty coverage file is permissible, but a missing one will cause PN to crash
-
-touch $COVERAGE_FILE
-
-
-c1="$PEASOUP_HOME/tools/my_timeout.sh $TIMEOUT_VALUE "
-c2="$PN_BINARY --variant_id=$CLONE_ID --bed_script=$BED_SCRIPT \
- --coverage_file=$COVERAGE_FILE --pn_threshold=$P1THRESHOLD \
- --blacklist=$LIBC_FILTER --shared_object_protection --no_p1_validate --align_stack $PN_OPTIONS"
-
-if [ ! -z $DEBUG_P1 ]; then
- gdb --args $c2
-else
- $c1 $c2
-fi
-
-
-
-