Impurity annotation

.github/workflows/make.yml

@@ -19,5 +19,8 @@ jobs:
         run: sudo apt -y install shfmt shellcheck devscripts
       - name: Install markdownlint
         run: npm install markdownlint-cli2 --global
+      - name: Install Python `uv`
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
       - name: style check
-        run: make style-check
+        run: |
+          make style-check

.gitignore

@@ -16,7 +16,13 @@ Thumbs.db
 
 # subdirectory with source repositories
 tests/src
-subject-programs/src
+subject-programs/src-grt/
+subject-programs/src-upstream/
+# temporary
+subject-programs/src-upstream-OLD/
+subject-programs/src-upstream-GOOD/
+subject-programs/src-grt-SAVE/
+subject-programs/files.diff
 
 # subdirectory created by scripts/mutation-randoop.sh and scripts/mutation-evosuite.sh
 scripts/jarfiles
@@ -25,7 +31,7 @@ scripts/build/
 scripts/results/
 checkbashisms
 
-# output from runnin jacoco
+# output from running jacoco
 jacoco.exec
 
 # Obtained via Git

.python-version

@@ -1 +1 @@
-3.14
+3.10

pyproject.toml

@@ -1,3 +1,7 @@
+[build-system]
+requires = ["uv_build >= 0.9.11, <0.10.0"]
+build-backend = "uv_build"
+
 [project]
 name = "grt-testing"
 version = "0.1.0"
@@ -13,5 +17,7 @@ dependencies = [
 [dependency-groups]
 dev = [
     "pymarkdownlnt>=0.9.33",
+    "pyyaml>=6.0.3",
     "ty>=0.0.1a31",
 ]
+# dynamic = ["version"]

scripts/Makefile

@@ -1,6 +1,7 @@
 MAKEFILE_DIR := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
 
 all: \
+    build/checker-framework/checker/dist/checker-qual.jar \
     build/evosuite-1.2.0.jar \
     build/evosuite-standalone-runtime-1.2.0.jar \
     build/hamcrest-core-1.3.jar \
@@ -64,13 +65,21 @@ build/junit-4.12.jar:
 
 build/hamcrest-core-1.3.jar:
 	mkdir -p build
-	cp ../subject-programs/hamcrest-core-1.3.jar build/
+	cp ../subject-programs/jars/hamcrest-core-1.3.jar build/
 
 build/major/bin/ant-replacecall:
 	LATEST_RELEASE=$$(curl -s https://api.github.com/repos/randoop/grt-replacecall/releases/latest | grep -o '"tag_name": "[^"]*' | cut -d'"' -f4) && \
 	wget "https://github.com/randoop/grt-replacecall/releases/download/$${LATEST_RELEASE}/ant-replacecall" && \
 	mv ant-replacecall build/major/bin/
 
+build/checker-framework/checker/dist/checker-qual.jar:
+	mkdir -p build
+	CFVER=3.50.0 && \
+	cd build && wget "https://github.com/typetools/checker-framework/releases/download/checker-framework-$${CFVER}/checker-framework-$${CFVER}.zip" && \
+	unzip -o checker-framework-$${CFVER}.zip && \
+	rm -rf checker-framework && \
+	mv checker-framework-$${CFVER} checker-framework
+
 build/defects4j:
 	mkdir -p build
 	cd build && git clone https://github.com/rjust/defects4j && cd defects4j && cpanm --installdeps . && ./init.sh

scripts/mutation-evosuite.sh

@@ -172,7 +172,7 @@ echo
 SRC_BASE_DIR="$(realpath "$SCRIPT_DIR/../subject-programs/src/$SUBJECT_PROGRAM")"
 
 # Path to the jar file of the subject program.
-SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/$SUBJECT_PROGRAM.jar")
+SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/jars/$SUBJECT_PROGRAM.jar")
 
 # Number of classes in given jar file.
 NUM_CLASSES=$(jar -tf "$SRC_JAR" | grep -c '.class')
@@ -318,7 +318,7 @@ case "$SUBJECT_PROGRAM" in
       "$SRC_BASE_DIR/lib/jaxen-core.jar" \
       "$SRC_BASE_DIR/lib/jaxen-jdom.jar" \
       "$SRC_BASE_DIR/lib/saxpath.jar" \
-      "$SCRIPT_DIR/../subject-programs/jaxen-1.1.6.jar"
+      "$SCRIPT_DIR/../subject-programs/jars/jaxen-1.1.6.jar"
     ;;
 
   "joda-time-2.3")

scripts/mutation-randoop.sh

@@ -56,12 +56,12 @@ set -o pipefail
 Generator=Randoop
 generator=randoop
 SCRIPT_DIR="$(CDPATH='' cd -- "$(dirname -- "$0")" && pwd -P)"
-SCRIPT_NAME=$(basename -- "$0")
-MAJOR_HOME=$(realpath "${SCRIPT_DIR}/build/major/")                     # Major home directory, for mutation testing
-RANDOOP_JAR=$(realpath "${SCRIPT_DIR}/build/randoop-all-4.3.4.jar")     # Randoop jar file
-JACOCO_AGENT_JAR=$(realpath "${SCRIPT_DIR}/build/jacocoagent.jar")      # For Bloodhound
-JACOCO_CLI_JAR=$(realpath "${SCRIPT_DIR}/build/jacococli.jar")          # For coverage report generation
-REPLACECALL_JAR=$(realpath "${SCRIPT_DIR}/build/replacecall-4.3.4.jar") # For replacing undesired method calls
+MAJOR_HOME=$(realpath "${SCRIPT_DIR}/build/major/")                                                # Major home directory, for mutation testing
+RANDOOP_JAR=$(realpath "${SCRIPT_DIR}/build/randoop-all-4.3.4.jar")                                # Randoop jar file
+JACOCO_AGENT_JAR=$(realpath "${SCRIPT_DIR}/build/jacocoagent.jar")                                 # For Bloodhound
+JACOCO_CLI_JAR=$(realpath "${SCRIPT_DIR}/build/jacococli.jar")                                     # For coverage report generation
+REPLACECALL_JAR=$(realpath "${SCRIPT_DIR}/build/replacecall-4.3.4.jar")                            # For replacing undesired method calls
+CHECKER_QUAL_JAR=$(realpath "${SCRIPT_DIR}/build/checker-framework/checker/dist/checker-qual.jar") # For Randoop Impurity
 
 . "$SCRIPT_DIR/defs.sh" # Define shell functions.
 
@@ -70,6 +70,7 @@ require_file "$RANDOOP_JAR"
 require_file "$JACOCO_AGENT_JAR"
 require_file "$JACOCO_CLI_JAR"
 require_file "$REPLACECALL_JAR"
+require_file "$CHECKER_QUAL_JAR"
 
 \usejdk8
 JAVA_VER=$(java -version 2>&1 | awk -F '"' '/version/ {print $2}' | awk -F '.' '{sub("^$", "0", $2); print ($1=="1")?$2:$1}')
@@ -219,8 +220,18 @@ echo
 # Path to the base directory of the source code.
 SRC_BASE_DIR="$(realpath "$SCRIPT_DIR/../subject-programs/src/$SUBJECT_PROGRAM")"
 
-# Path to the jar file of the subject program.
-SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/$SUBJECT_PROGRAM.jar")
+if [[ " ${RANDOOP_FEATURES[*]} " =~ " GRT_FUZZING " ]]; then
+  # If randoop features contain "GRT_FUZZING", use annotated subject program jar.
+  ANNOTATED_JAR="$SCRIPT_DIR/../subject-programs/annotated-jars/$SUBJECT_PROGRAM.jar"
+  if [ ! -f "$ANNOTATED_JAR" ]; then
+    echo "${SCRIPT_NAME}: error: GRT_FUZZING enabled but annotated JAR not found: $ANNOTATED_JAR" >&2
+    exit 2
+  fi
+  SRC_JAR=$(realpath "$ANNOTATED_JAR")
+else
+  # Else, use the original subject program jar.
+  SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/jars/$SUBJECT_PROGRAM.jar")
+fi
 
 # Number of classes in given jar file.
 NUM_CLASSES=$(jar -tf "$SRC_JAR" | grep -c '.class')
@@ -353,7 +364,7 @@ case "$SUBJECT_PROGRAM" in
       "$SRC_BASE_DIR/lib/jaxen-core.jar" \
       "$SRC_BASE_DIR/lib/jaxen-jdom.jar" \
       "$SRC_BASE_DIR/lib/saxpath.jar" \
-      "$SCRIPT_DIR/../subject-programs/jaxen-1.1.6.jar"
+      "$SCRIPT_DIR/../subject-programs/jars/jaxen-1.1.6.jar"
     ;;
 
   "joda-time-2.3")
@@ -456,7 +467,7 @@ RANDOOP_BASE_COMMAND=(
   -Xbootclasspath/a:"$JACOCO_AGENT_JAR:$REPLACECALL_JAR"
   -javaagent:"$JACOCO_AGENT_JAR"
   -javaagent:"$REPLACECALL_COMMAND"
-  -classpath "$RANDOOP_CLASSPATH:$RANDOOP_JAR"
+  -classpath "$RANDOOP_CLASSPATH:$RANDOOP_JAR:$CHECKER_QUAL_JAR"
   randoop.main.Main
   gentests
   --testjar="$TARGET_JAR"

subject-programs/README

@@ -1,3 +1,8 @@
+Run Python scripts in this directory via:
+
+uv run SCRIPTNAME
+
+
 This directory contains compiled versions (jar files) of projects that the GRT
 paper used as subject programs.  The paper's Table II lists 32 projects.  We
 have located 30 of them.

subject-programs/README.build

@@ -12,8 +12,8 @@ Maven (mvn) builds
 ------------------
 If the project uses Maven to build, usually indicated by a pom.xml file in
 the root, a useful build command is:
-```
-  mvn -B clean package -Dmaven.test.failure.ignore -Dmaven.javadoc.skip |& tee mvn-output.txt
+```sh
+  mvn -B clean package -Dmaven.test.failure.ignore -Dmaven.javadoc.skip 2>&1 | tee mvn-output.txt
 ```
 
 The failure.ignore option allows the .jar file to be built even if there are
@@ -24,67 +24,67 @@ The resulting .jar file will be in the target subdirectory.
 
 Test directory            Build instructions
 ------------------------------------------------------------
-a4j-1.0b:                 ant createJar   (result is in dist subdir)
-asm-5.0.1:                (uses mvn)
-bcel-5.2:                 ant jar         (result is in target subdir)
-ClassViewer-5.0.5b:       ant build       (result is in root directory)
-commons-cli-1.2:          (uses mvn)
-commons-codec-1.9:        (uses mvn)
-commons-collections4-4.0: (uses mvn)
-commons-compress-1.8:     (uses mvn)
-commons-lang3-3.0:        (uses mvn)
-commons-math3-3.2:        (uses mvn)
-commons-primitives-1.0:   ant jar         (result is in target subdir)
+a4j-1.0b                  ant createJar   (result is in dist subdir)
+asm-5.0.1                 (uses mvn)
+bcel-5.2                  ant jar         (result is in target subdir)
+ClassViewer-5.0.5b        ant build       (result is in root directory)
+commons-cli-1.2           (uses mvn)
+commons-codec-1.9         (uses mvn)
+commons-collections4-4.0  (uses mvn)
+commons-compress-1.8      (uses mvn)
+commons-lang3-3.0         (uses mvn)
+commons-math3-3.2         (uses mvn)
+commons-primitives-1.0    ant jar         (result is in target subdir)
 dcParseArgs-10.2008       ant createJar   (result is in dist subdir)
 easymock-3.2              (uses mvn)      (result is in easymock/target subdir)
 fixsuite-r48              ant jar         (result is in jar subdir)
 guava-16.0.1              (uses mvn)
 hamcrest-core-1.3         ant core        (result is in build subdir)
 javassist-3.19            ant jar         (result is in root directory)
-jaxax.mail-1.5.1:         (uses mvn)
-jaxen-1.1.6:              (uses mvn)
-jcommander-1.35:          (uses mvn)
-jdom-1.0:                 ./build.sh      (result is in build subdir)
-joda-time-2.3:            (uses mvn)
-JSAP-2.1:                 ant jar         (result is in dist subdir)
-jvc-1.1:                  ant tools       (result is in dist subdir)
-nekomud-r16:              ant             (result is in dist subdir)
-pmd-core-5.2.2:           cd pmd-core; mvn -B clean package -Dmaven.test.skip -Dmaven.javadoc.skip -DjavaccBuildNotRequired
-sat4j.core-2.3.5:         (uses mvn)      (result is in org.sat4j.core/target)
-shiro-core-1.2.3:         (uses mvn - but 'cd core' first)
-slf4j-api-1.7.12:         (uses mvn - but 'cd slf4j-api' first)
-tiny-sql-2.26:            ./build.sh      (result is in classes subdir)
+jaxax.mail-1.5.1          (uses mvn)
+jaxen-1.1.6               (uses mvn)
+jcommander-1.35           (uses mvn)
+jdom-1.0                  ./build.sh      (result is in build subdir)
+joda-time-2.3             (uses mvn)
+JSAP-2.1                  ant jar         (result is in dist subdir)
+jvc-1.1                   ant tools       (result is in dist subdir)
+nekomud-r16               ant             (result is in dist subdir)
+pmd-core-5.2.2            cd pmd-core; mvn -B clean package -Dmaven.test.skip -Dmaven.javadoc.skip -DjavaccBuildNotRequired
+sat4j.core-2.3.5          (uses mvn)      (result is in org.sat4j.core/target)
+shiro-core-1.2.3          (uses mvn - but 'cd core' first)
+slf4j-api-1.7.12          (uses mvn - but 'cd slf4j-api' first)
+tiny-sql-2.26             ./build.sh      (result is in classes subdir)
 
 
 software (version)             original source
 ------------------------------------------------------------------------------------------------------------------------
-Amazon AWS 4 Java (1.0b)       //sourceforge.net/projects/a4j/files/latest/download/a4j-1.0b1.zip
-ASM (5.0.1)                    //repo1.maven.org/maven2/org/ow2/asm/asm/5.0.1/asm-5.0.1-sources.jar
-Apache BCEL (5.2)              //github.com/apache/commons-bcel/archive/refs/tags/BCEL_5_2.zip
+Amazon AWS 4 Java (1.0b)       https://sourceforge.net/projects/a4j/files/latest/download/a4j-1.0b1.zip
+ASM (5.0.1)                    https://repo1.maven.org/maven2/org/ow2/asm/asm/5.0.1/asm-5.0.1-sources.jar
+Apache BCEL (5.2)              https://github.com/apache/commons-bcel/archive/refs/tags/BCEL_5_2.zip
 ClassViewer (5.0.5b)           svn checkout -r 28  https://svn.code.sf.net/p/classviewer/code/trunk ClassViewer
-Apache Commons Cli (1.2)       //archive.apache.org/dist/commons/cli/source/commons-cli-1.2-src.zip
-Apache C. Codec (1.9)          //archive.apache.org/dist/commons/codec/source/commons-codec-1.9-src.zip
-Apache C. Collection (4.0)     //archive.apache.org/dist/commons/collections/source/commons-collections4-4.0-src.zip
-Apache C. Compress (1.8)       //archive.apache.org/dist/commons/compress/source/commons-compress-1.8-src.zip
-Apache C. Lang (3.0)           //archive.apache.org/dist/commons/lang/source/commons-lang3-3.0-src.zip
-Apache C. Math (3.2)           //archive.apache.org/dist/commons/math/source/commons-math3-3.2-src.zip
-Apache C. Primitive (1.0)      //archive.apache.org/dist/commons/primitives/source/commons-primitives-1.0-src.zip
-Dcparseargs (10/2008)          //sourceforge.net/projects/dcparseargs/files/Source/First%20upload/dcParseArgs_src.tar.bz2
-Easymock (3.2)                 //github.com/easymock/easymock/archive/refs/tags/easymock-3.2.zip
+Apache Commons Cli (1.2)       https://archive.apache.org/dist/commons/cli/source/commons-cli-1.2-src.zip
+Apache C. Codec (1.9)          https://archive.apache.org/dist/commons/codec/source/commons-codec-1.9-src.zip
+Apache C. Collection (4.0)     https://archive.apache.org/dist/commons/collections/source/commons-collections4-4.0-src.zip
+Apache C. Compress (1.8)       https://archive.apache.org/dist/commons/compress/source/commons-compress-1.8-src.zip
+Apache C. Lang (3.0)           https://archive.apache.org/dist/commons/lang/source/commons-lang3-3.0-src.zip
+Apache C. Math (3.2)           https://archive.apache.org/dist/commons/math/source/commons-math3-3.2-src.zip
+Apache C. Primitive (1.0)      https://archive.apache.org/dist/commons/primitives/source/commons-primitives-1.0-src.zip
+Dcparseargs (10/2008)          https://sourceforge.net/projects/dcparseargs/files/Source/First%20upload/dcParseArgs_src.tar.bz2
+Easymock (3.2)                 https://github.com/easymock/easymock/archive/refs/tags/easymock-3.2.zip
 Fixsuite (R48)                 svn checkout https://svn.code.sf.net/p/fixsuite/code/trunk fixsuite-r48
-Guava (16.0.1)                 //repo1.maven.org/maven2/com/google/guava/guava/16.0.1/guava-16.0.1-sources.jar
-Hamcrest-core (1.3)            //github.com/hamcrest/JavaHamcrest/archive/refs/tags/hamcrest-java-1.3.zip
-Javassit (3.19)                //github.com/jboss-javassist/javassist/archive/refs/tags/rel_3_19_0_ga.zip
-Javax Mail (1.5.1)             //repo1.maven.org/maven2/com/sun/mail/javax.mail/1.5.1/javax.mail-1.5.1-sources.jar
-Jaxen (1.1.6)                  //repo1.maven.org/maven2/jaxen/jaxen/1.1.6/jaxen-1.1.6-sources.jar
+Guava (16.0.1)                 https://repo1.maven.org/maven2/com/google/guava/guava/16.0.1/guava-16.0.1-sources.jar
+Hamcrest-core (1.3)            https://github.com/hamcrest/JavaHamcrest/archive/refs/tags/hamcrest-java-1.3.zip
+Javassit (3.19)                https://github.com/jboss-javassist/javassist/archive/refs/tags/rel_3_19_0_ga.zip
+Javax Mail (1.5.1)             https://repo1.maven.org/maven2/com/sun/mail/javax.mail/1.5.1/javax.mail-1.5.1-sources.jar
+Jaxen (1.1.6)                  https://repo1.maven.org/maven2/jaxen/jaxen/1.1.6/jaxen-1.1.6-sources.jar
 Jcommander (1.35)              [email protected]:cbeust/jcommander.git (git co jcommander-1.35)
-Jdom (1.0)                     //www.jdom.org/dist/binary/archive/jdom-1.0.zip
-Joda Time (2.3)                //github.com/JodaOrg/joda-time/archive/refs/tags/v2.3.zip
-Java Simple Arg. Parser (2.1)  //sourceforge.net/projects/jsap/files/jsap/2.1/JSAP-2.1-src.zip
-Java View Control (1.1)        //sourceforge.net/projects/javaviewcontrol/files/javaviewcontrol/jvc-1.1.tar.gz
-Multi-User Dungeon server R16  svn checkout https://svn.code.sf.net/p/nekomud/code/trunk nekomud-r16
-Pmd DCD 5.2.2                  [email protected]:pmd/pmd.git (git co pmd_releases/5.2.2)
+Jdom (1.0)                     https://www.jdom.org/dist/binary/archive/jdom-1.0.zip
+Joda Time (2.3)                https://github.com/JodaOrg/joda-time/archive/refs/tags/v2.3.zip
+Java Simple Arg. Parser (2.1)  https://sourceforge.net/projects/jsap/files/jsap/2.1/JSAP-2.1-src.zip
+Java View Control (1.1)        https://sourceforge.net/projects/javaviewcontrol/files/javaviewcontrol/jvc-1.1.tar.gz
+Multi-User Dungeon server (R16)  svn checkout https://svn.code.sf.net/p/nekomud/code/trunk nekomud-r16
+Pmd DCD (5.2.2)                  [email protected]:pmd/pmd.git (git co pmd_releases/5.2.2)
 SAT4J Core (2.3.5)             https://gitlab.ow2.org/sat4j/sat4j.git (git co 2_3_5)
-Apache Shiro-core (1.2.6)      //archive.apache.org/dist/shiro/1.2.3/shiro-root-1.2.3-source-release.zip
-Slf4j-api (1.7.12)             //github.com/qos-ch/slf4j/releases/tag/v_1.7.12/slf4j-v_1.7.12.zip
-Tiny Sql (2.26)                //sourceforge.net/projects/tinysql/files/tinySQL2.26/V2.26/tinySQL-2.26.zip
+Apache Shiro-core (1.2.6)      https://archive.apache.org/dist/shiro/1.2.3/shiro-root-1.2.3-source-release.zip
+Slf4j-api (1.7.12)             https://github.com/qos-ch/slf4j/releases/tag/v_1.7.12/slf4j-v_1.7.12.zip
+Tiny Sql (2.26)                https://sourceforge.net/projects/tinysql/files/tinySQL2.26/V2.26/tinySQL-2.26.zip