test list

python/data/tests-list/gzip/README.md

@@ -0,0 +1,23 @@
+## Running `gzip` bugs
+
+After running the container you need to follow the following
+steps to prepare `SOSRepair` for running:
+
+1. Copy `makeout`, `compile.sh`, `test.sh` and `tests-list` to
+the container's `/experiment/`.
+2. Copy `settings.py` to the container's `/opt/sosrepair/sosrepair`.
+3. In the container, reconfigure the project with coverage flags:
+```
+cd /experiment/src
+./configure "CFLAGS=-m32 -fprofile-arcs -ftest-coverage" "CXXFLAGS=-m32 -fprofile-arcs -ftest-coverage" "LDFLAGS=-m32 -lgcov"
+make clean
+make
+```
+4. Run `/opt/sosrepair/prepare/setup.sh`.
+5. Set proper permissions by running `sudo chmod -R 777 /opt/sosrepair/sosrepair`.
+6. Setup environment variables:
+```
+export PYTHONPATH="/opt/sosrepair/bindings:${PYTHONPATH}"
+export CPATH=":/opt/sosrepair/include"
+export PATH="/opt/sosrepair/bin:$PATH"
+```

python/data/tests-list/gzip/compile.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+TIME_LIMIT=60
+HERE_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+PATCH_EXE=$1
+PATCH_DIR=$(dirname "$PATCH_EXE")
+PROJECT_DIR="$HERE_DIR/src"
+
+# Remove the object file for the affected source code file
+# cp "$PATCH_DIR/inflate.c" "$PROJECT_DIR/inflate.c" && \
+pushd "$PROJECT_DIR" && \
+rm -f inflate.o && \
+
+# Clear the results of any test executions for any previous patches
+# pushd tests && \
+# make clean && \
+# popd && \
+
+# Rebuild the rest of the project
+timeout $TIME_LIMIT make || exit 1

python/data/tests-list/gzip/copy.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+
+CONTAINER=$1
+BUG=$2
+
+docker cp compile.sh $CONTAINER:/experiment/
+docker cp $BUG/test.sh $CONTAINER:/experiment/
+docker cp $BUG/tests-list.txt $CONTAINER:/experiment/
+docker cp $BUG/settings.py $CONTAINER:/opt/sosrepair/sosrepair/

python/data/tests-list/gzip/gzip-bug-2009-08-16-3fe0caeada-39a362ae9d/settings.py

@@ -0,0 +1,80 @@
+"""
+This file includes all the settings that could be modified for running SearchRepair/SOSRepair
+
+* LIBCLANG_PATH: The path to libclang build. It should be either a .so or .dylib file.
+* GENERATE_DB_PATH: The path where the DB should be built from. SR will enumerate all C files in this path to build the
+ DB
+* Z3_COMMAND: The z3 command on this machine.
+* LARGEST_SNIPPET: The maximum number of lines that is considered as a snippet.
+* SMALLEST_SNIPPET: The minimum number of lines that is considered as a snippet.
+* DATABASE: Information about the database.
+* LOGGING: Settings for logging.
+* MAX_SUSPICIOUS_LINES: The number of suspicious lines tried before giving up.
+* VALID_TYPES: The variable types that are right now supported by SR.
+------ Settings related to file under repair -------
+* TESTS_LIST: The path to a list of the tests that could be run on the file
+* TEST_SCRIPT: The path to a script that will run the test
+* COMPILE_SCRIPT: The path to a script that will compile the code
+* FAULTY_CODE: The path to the faulty code (a C file)
+* COMPILE_EXTRA_ARGS: The list of necessary arguments that should be passed to clang to properly parse the code
+* MAKE_OUTPUT: The output of running `make` stored in a file (for the purpose of finding necessary arguments for compilation
+automatically)
+* METHOD_RANGE: The tuple of beginning and end of method with the fault (limits the search to the area)
+* SOSREPAIR: If set to False it will only run SearchRepair features
+* NUMBER_OF_TIMES_RERUNNING_TESTS: The number of times that the tests should be run to assure patch's correctness
+* EXCLUDE_SCANF: If removing/replacing scanf in buggy code is going to be a problem, set this to True
+"""
+__author__ = 'Afsoon Afzal'
+
+import logging
+
+
+LIBCLANG_PATH = '/opt/sosrepair/llvm/lib/libclang.so'
+
+GENERATE_DB_PATH = '/experiment/src'
+
+Z3_COMMAND = '/opt/sosrepair/bin/z3'
+
+LARGEST_SNIPPET = 7
+SMALLEST_SNIPPET = 3
+
+DATABASE = {
+    'db_name': 'testdocker',
+    'user': 'docker',
+    'password': '1234'
+}
+
+LOGGING = {
+    'filename': 'logs/repair.log',
+    'level': logging.DEBUG
+}
+
+logging.basicConfig(**LOGGING)
+
+MAX_SUSPICIOUS_LINES = 10
+
+VALID_TYPES = ['int', 'short', 'long', 'char', 'float', 'double', 'long long', 'size_t']
+
+TESTS_LIST = "/experiment/tests-list.txt"
+TEST_SCRIPT = "/experiment/test.sh"
+TEST_SCRIPT_TYPE = "/bin/bash"
+COMPILE_SCRIPT = "/experiment/compile.sh"
+FAULTY_CODE = "/experiment/src/inflate.c"
+
+
+COMPILE_EXTRA_ARGS = [
+                    "-I/usr/include",
+]
+
+MAKE_OUTPUT = "/experiment/makeout"
+
+METHOD_RANGE = (300, 492)
+# IF SOS+
+# METHOD_RANGE = (338, 339)
+
+SOSREPAIR = True
+
+NUMBER_OF_TIMES_RERUNNING_TESTS = 1
+EXCLUDE_SCANF = False
+
+BULK_RUN_PATH = ""

python/data/tests-list/gzip/gzip-bug-2009-08-16-3fe0caeada-39a362ae9d/test.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+TEST_ID=$1
+DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+
+
+run_test()
+{
+    cd $DIR/src
+        timeout 5 perl $DIR/gzip-run-tests.pl $1
+    RESULT=$?
+    if [ $RESULT = 0 ] ; then
+	echo "PASS"
+    else
+	echo "FAIL"
+    fi
+    cd ..
+    return 0
+}
+case $TEST_ID in
+    p1) run_test 1 && exit 0 ;; 
+    p2) run_test 4 && exit 0 ;; 
+    n1) run_test 3 && exit 0 ;; 
+esac
+exit 1

python/data/tests-list/gzip/gzip-bug-2009-08-16-3fe0caeada-39a362ae9d/tests-list.txt

@@ -0,0 +1,3 @@
+n1
+p1
+p2

python/data/tests-list/gzip/gzip-bug-2009-09-26-a1d3d4019d-f17cbd13a1/notes.md

@@ -0,0 +1,5 @@
+For running SOS+ on this bug, we manually helped in finding
+correct set of live variables. Variable `ifd` is global variable
+therefore not considered by SOS+ as a live variable.
+We manually changed code in `fault_localization/suspicious_block.py`
+to include `ifd` as a variable.

python/data/tests-list/gzip/gzip-bug-2009-09-26-a1d3d4019d-f17cbd13a1/settings.py

@@ -0,0 +1,80 @@
+"""
+This file includes all the settings that could be modified for running SearchRepair/SOSRepair
+
+* LIBCLANG_PATH: The path to libclang build. It should be either a .so or .dylib file.
+* GENERATE_DB_PATH: The path where the DB should be built from. SR will enumerate all C files in this path to build the
+ DB
+* Z3_COMMAND: The z3 command on this machine.
+* LARGEST_SNIPPET: The maximum number of lines that is considered as a snippet.
+* SMALLEST_SNIPPET: The minimum number of lines that is considered as a snippet.
+* DATABASE: Information about the database.
+* LOGGING: Settings for logging.
+* MAX_SUSPICIOUS_LINES: The number of suspicious lines tried before giving up.
+* VALID_TYPES: The variable types that are right now supported by SR.
+------ Settings related to file under repair -------
+* TESTS_LIST: The path to a list of the tests that could be run on the file
+* TEST_SCRIPT: The path to a script that will run the test
+* COMPILE_SCRIPT: The path to a script that will compile the code
+* FAULTY_CODE: The path to the faulty code (a C file)
+* COMPILE_EXTRA_ARGS: The list of necessary arguments that should be passed to clang to properly parse the code
+* MAKE_OUTPUT: The output of running `make` stored in a file (for the purpose of finding necessary arguments for compilation
+automatically)
+* METHOD_RANGE: The tuple of beginning and end of method with the fault (limits the search to the area)
+* SOSREPAIR: If set to False it will only run SearchRepair features
+* NUMBER_OF_TIMES_RERUNNING_TESTS: The number of times that the tests should be run to assure patch's correctness
+* EXCLUDE_SCANF: If removing/replacing scanf in buggy code is going to be a problem, set this to True
+"""
+__author__ = 'Afsoon Afzal'
+
+import logging
+
+
+LIBCLANG_PATH = '/opt/sosrepair/llvm/lib/libclang.so'
+
+GENERATE_DB_PATH = '/experiment/src'
+
+Z3_COMMAND = '/opt/sosrepair/bin/z3'
+
+LARGEST_SNIPPET = 7
+SMALLEST_SNIPPET = 3
+
+DATABASE = {
+    'db_name': 'testdocker',
+    'user': 'docker',
+    'password': '1234'
+}
+
+LOGGING = {
+    'filename': 'logs/repair.log',
+    'level': logging.DEBUG
+}
+
+logging.basicConfig(**LOGGING)
+
+MAX_SUSPICIOUS_LINES = 10
+
+VALID_TYPES = ['int', 'short', 'long', 'char', 'float', 'double', 'long long', 'size_t']
+
+TESTS_LIST = "/experiment/tests-list.txt"
+TEST_SCRIPT = "/experiment/test.sh"
+TEST_SCRIPT_TYPE = "/bin/bash"
+COMPILE_SCRIPT = "/experiment/compile.sh"
+FAULTY_CODE = "/experiment/src/gzip.c"
+
+
+COMPILE_EXTRA_ARGS = [
+                    "-I/usr/include",
+]
+
+MAKE_OUTPUT = "/experiment/makeout"
+
+METHOD_RANGE = (608, 692)
+# IF SOS+
+# METHOD_RANGE = (653, 654)
+
+SOSREPAIR = True
+
+NUMBER_OF_TIMES_RERUNNING_TESTS = 1
+EXCLUDE_SCANF = False
+
+BULK_RUN_PATH = ""

python/data/tests-list/gzip/gzip-bug-2009-09-26-a1d3d4019d-f17cbd13a1/test.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+TEST_ID=$1
+DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+
+
+run_test()
+{
+    cd $DIR/src
+        timeout 5 /usr/bin/perl $DIR/gzip-run-tests.pl $1
+    RESULT=$?
+    if [ $RESULT = 0 ] ; then
+	echo "PASS"
+    else
+	echo "FAIL"
+    fi
+    cd ..
+    return 0
+}
+case $TEST_ID in
+    p1) run_test 1 && exit 0 ;; 
+    p2) run_test 3 && exit 0 ;; 
+    p3) run_test 4 && exit 0 ;; 
+    n1) run_test 7 && exit 0 ;; 
+esac
+exit 1

python/data/tests-list/gzip/gzip-bug-2009-09-26-a1d3d4019d-f17cbd13a1/tests-list.txt

@@ -0,0 +1,4 @@
+n1
+p1
+p2
+p3

python/data/tests-list/gzip/gzip-bug-2009-10-09-1a085b1446-118a107f2d/settings.py

@@ -0,0 +1,80 @@
+"""
+This file includes all the settings that could be modified for running SearchRepair/SOSRepair
+
+* LIBCLANG_PATH: The path to libclang build. It should be either a .so or .dylib file.
+* GENERATE_DB_PATH: The path where the DB should be built from. SR will enumerate all C files in this path to build the
+ DB
+* Z3_COMMAND: The z3 command on this machine.
+* LARGEST_SNIPPET: The maximum number of lines that is considered as a snippet.
+* SMALLEST_SNIPPET: The minimum number of lines that is considered as a snippet.
+* DATABASE: Information about the database.
+* LOGGING: Settings for logging.
+* MAX_SUSPICIOUS_LINES: The number of suspicious lines tried before giving up.
+* VALID_TYPES: The variable types that are right now supported by SR.
+------ Settings related to file under repair -------
+* TESTS_LIST: The path to a list of the tests that could be run on the file
+* TEST_SCRIPT: The path to a script that will run the test
+* COMPILE_SCRIPT: The path to a script that will compile the code
+* FAULTY_CODE: The path to the faulty code (a C file)
+* COMPILE_EXTRA_ARGS: The list of necessary arguments that should be passed to clang to properly parse the code
+* MAKE_OUTPUT: The output of running `make` stored in a file (for the purpose of finding necessary arguments for compilation
+automatically)
+* METHOD_RANGE: The tuple of beginning and end of method with the fault (limits the search to the area)
+* SOSREPAIR: If set to False it will only run SearchRepair features
+* NUMBER_OF_TIMES_RERUNNING_TESTS: The number of times that the tests should be run to assure patch's correctness
+* EXCLUDE_SCANF: If removing/replacing scanf in buggy code is going to be a problem, set this to True
+"""
+__author__ = 'Afsoon Afzal'
+
+import logging
+
+
+LIBCLANG_PATH = '/opt/sosrepair/llvm/lib/libclang.so'
+
+GENERATE_DB_PATH = '/experiment/src'
+
+Z3_COMMAND = '/opt/sosrepair/bin/z3'
+
+LARGEST_SNIPPET = 7
+SMALLEST_SNIPPET = 3
+
+DATABASE = {
+    'db_name': 'testdocker',
+    'user': 'docker',
+    'password': '1234'
+}
+
+LOGGING = {
+    'filename': 'logs/repair.log',
+    'level': logging.DEBUG
+}
+
+logging.basicConfig(**LOGGING)
+
+MAX_SUSPICIOUS_LINES = 10
+
+VALID_TYPES = ['int', 'short', 'long', 'char', 'float', 'double', 'long long', 'size_t']
+
+TESTS_LIST = "/experiment/tests-list.txt"
+TEST_SCRIPT = "/experiment/test.sh"
+TEST_SCRIPT_TYPE = "/bin/bash"
+COMPILE_SCRIPT = "/experiment/compile.sh"
+FAULTY_CODE = "/experiment/src/gzip.c"
+
+
+COMPILE_EXTRA_ARGS = [
+                    "-I/usr/include",
+]
+
+MAKE_OUTPUT = "/experiment/makeout"
+
+METHOD_RANGE = (1254, 1438)
+# IF SOS+
+# METHOD_RANGE = (1269,1270)
+
+SOSREPAIR = True
+
+NUMBER_OF_TIMES_RERUNNING_TESTS = 1
+EXCLUDE_SCANF = False
+
+BULK_RUN_PATH = ""

python/data/tests-list/gzip/gzip-bug-2009-10-09-1a085b1446-118a107f2d/test.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+TEST_ID=$1
+DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+
+
+run_test()
+{
+    cd $DIR/src
+        timeout 5 perl $DIR/gzip-run-tests.pl $1
+    RESULT=$?
+    if [ $RESULT = 0 ] ; then
+	echo "PASS"
+    else
+	echo "FAIL"
+    fi
+    cd ..
+    return 0
+}
+case $TEST_ID in
+    p1) run_test 1 && exit 0 ;; 
+    p2) run_test 3 && exit 0 ;; 
+    p3) run_test 4 && exit 0 ;; 
+    p4) run_test 7 && exit 0 ;; 
+    p5) run_test 9 && exit 0 ;; 
+    n1) run_test 8 && exit 0 ;; 
+esac
+exit 1

python/data/tests-list/gzip/gzip-bug-2009-10-09-1a085b1446-118a107f2d/tests-list.txt

@@ -0,0 +1,6 @@
+n1
+p1
+p2
+p3
+p4
+p5

python/data/tests-list/gzip/gzip-bug-2010-02-19-3eb6091d69-884ef6d16c/settings.py

@@ -0,0 +1,80 @@
+"""
+This file includes all the settings that could be modified for running SearchRepair/SOSRepair
+
+* LIBCLANG_PATH: The path to libclang build. It should be either a .so or .dylib file.
+* GENERATE_DB_PATH: The path where the DB should be built from. SR will enumerate all C files in this path to build the
+ DB
+* Z3_COMMAND: The z3 command on this machine.
+* LARGEST_SNIPPET: The maximum number of lines that is considered as a snippet.
+* SMALLEST_SNIPPET: The minimum number of lines that is considered as a snippet.
+* DATABASE: Information about the database.
+* LOGGING: Settings for logging.
+* MAX_SUSPICIOUS_LINES: The number of suspicious lines tried before giving up.
+* VALID_TYPES: The variable types that are right now supported by SR.
+------ Settings related to file under repair -------
+* TESTS_LIST: The path to a list of the tests that could be run on the file
+* TEST_SCRIPT: The path to a script that will run the test
+* COMPILE_SCRIPT: The path to a script that will compile the code
+* FAULTY_CODE: The path to the faulty code (a C file)
+* COMPILE_EXTRA_ARGS: The list of necessary arguments that should be passed to clang to properly parse the code
+* MAKE_OUTPUT: The output of running `make` stored in a file (for the purpose of finding necessary arguments for compilation
+automatically)
+* METHOD_RANGE: The tuple of beginning and end of method with the fault (limits the search to the area)
+* SOSREPAIR: If set to False it will only run SearchRepair features
+* NUMBER_OF_TIMES_RERUNNING_TESTS: The number of times that the tests should be run to assure patch's correctness
+* EXCLUDE_SCANF: If removing/replacing scanf in buggy code is going to be a problem, set this to True
+"""
+__author__ = 'Afsoon Afzal'
+
+import logging
+
+
+LIBCLANG_PATH = '/opt/sosrepair/llvm/lib/libclang.so'
+
+GENERATE_DB_PATH = '/experiment/src'
+
+Z3_COMMAND = '/opt/sosrepair/bin/z3'
+
+LARGEST_SNIPPET = 7
+SMALLEST_SNIPPET = 3
+
+DATABASE = {
+    'db_name': 'testdocker',
+    'user': 'docker',
+    'password': '1234'
+}
+
+LOGGING = {
+    'filename': 'logs/repair.log',
+    'level': logging.DEBUG
+}
+
+logging.basicConfig(**LOGGING)
+
+MAX_SUSPICIOUS_LINES = 10
+
+VALID_TYPES = ['int', 'short', 'long', 'char', 'float', 'double', 'long long', 'size_t']
+
+TESTS_LIST = "/experiment/tests-list.txt"
+TEST_SCRIPT = "/experiment/test.sh"
+TEST_SCRIPT_TYPE = "/bin/bash"
+COMPILE_SCRIPT = "/experiment/compile.sh"
+FAULTY_CODE = "/experiment/src/gzip.c"
+
+
+COMPILE_EXTRA_ARGS = [
+                    "-I/usr/include",
+]
+
+MAKE_OUTPUT = "/experiment/makeout"
+
+METHOD_RANGE = (409, 585)
+# IF SOS+
+# METHOD_RANGE = (546, 547)
+
+SOSREPAIR = True
+
+NUMBER_OF_TIMES_RERUNNING_TESTS = 1
+EXCLUDE_SCANF = False
+
+BULK_RUN_PATH = ""

python/data/tests-list/gzip/gzip-bug-2010-02-19-3eb6091d69-884ef6d16c/test.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+TEST_ID=$1
+DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+
+
+run_test()
+{
+    cd $DIR/src
+        timeout 5 perl $DIR/gzip-run-tests.pl $1
+    RESULT=$?
+    if [ $RESULT = 0 ] ; then
+	echo "PASS"
+    else
+	echo "FAIL"
+    fi
+    cd ..
+    return 0
+}
+case $TEST_ID in
+    p1) run_test 1 && exit 0 ;; 
+    p2) run_test 3 && exit 0 ;; 
+    p3) run_test 4 && exit 0 ;; 
+    p4) run_test 5 && exit 0 ;; 
+    p5) run_test 7 && exit 0 ;; 
+    p6) run_test 8 && exit 0 ;; 
+    p7) run_test 9 && exit 0 ;; 
+    p8) run_test 12 && exit 0 ;; 
+    n1) run_test 6 && exit 0 ;; 
+esac
+exit 1

python/data/tests-list/gzip/gzip-bug-2010-02-19-3eb6091d69-884ef6d16c/tests-list.txt

@@ -0,0 +1,9 @@
+n1
+p1
+p2
+p3
+p4
+p5
+p6
+p7
+p8

python/data/tests-list/gzip/makeout

@@ -0,0 +1,79 @@
+Making all in lib
+make[1]: Entering directory `/experiment/src/lib'
+  GEN      arg-nonnull.h
+  GEN      c++defs.h
+  GEN      configmake.h
+  GEN      warn-on-use.h
+  GEN      fcntl.h
+  GEN      stdio.h
+  GEN      string.h
+  GEN      sys/stat.h
+  GEN      sys/time.h
+  GEN      time.h
+  GEN      unistd.h
+  GEN      wchar.h
+  GEN      wctype.h
+make  all-recursive
+make[2]: Entering directory `/experiment/src/lib'
+make[3]: Entering directory `/experiment/src/lib'
+  GEN      charset.alias
+  GEN      ref-add.sed
+  GEN      ref-del.sed
+  CC       exitfail.o
+  CC       freadahead.o
+  CC       freading.o
+  CC       localcharset.o
+  CC       close-stream.o
+  CC       xalloc-die.o
+  CC       closein.o
+  CC       closeout.o
+  CC       creat-safer.o
+  CC       dup-safer.o
+  CC       fcntl.o
+  CC       fd-safer.o
+  CC       fflush.o
+  CC       fpurge.o
+  CC       fseeko.o
+  CC       gettime.o
+  CC       open-safer.o
+  CC       pipe-safer.o
+  CC       quotearg.o
+  CC       utimens.o
+  CC       xmalloc.o
+  CC       yesno.o
+  AR       libgzip.a
+make[3]: Leaving directory `/experiment/src/lib'
+make[2]: Leaving directory `/experiment/src/lib'
+make[1]: Leaving directory `/experiment/src/lib'
+Making all in doc
+make[1]: Entering directory `/experiment/src/doc'
+make[1]: Nothing to be done for `all'.
+make[1]: Leaving directory `/experiment/src/doc'
+make[1]: Entering directory `/experiment/src'
+  CC       bits.o
+  CC       crypt.o
+  CC       deflate.o
+  CC       gzip.o
+  CC       inflate.o
+  CC       lzw.o
+  CC       trees.o
+  CC       unlzh.o
+  CC       unlzw.o
+  CC       unpack.o
+  CC       unzip.o
+  CC       util.o
+  CC       zip.o
+  GEN      gunzip
+  GEN      gzexe
+  GEN      zcat
+  GEN      zcmp
+  GEN      zdiff
+  GEN      zegrep
+  GEN      zfgrep
+  GEN      zforce
+  GEN      zgrep
+  GEN      zless
+  GEN      zmore
+  GEN      znew
+  CCLD     gzip
+make[1]: Leaving directory `/experiment/src'

python/data/tests-list/gzip/test.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+TEST_ID=$1
+DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+
+
+run_test()
+{
+    cd $DIR/src
+        timeout 5 perl $DIR/gzip-run-tests.pl $1
+    RESULT=$?
+    if [ $RESULT = 0 ] ; then
+	echo "PASS"
+    else
+	echo "FAIL"
+    fi
+    cd ..
+    return 0
+}
+case $TEST_ID in
+    p1) run_test 1 && exit 0 ;; 
+    p2) run_test 4 && exit 0 ;; 
+    n1) run_test 3 && exit 0 ;; 
+esac
+exit 1