update script

annotator-sample-command.sh

@@ -35,14 +35,10 @@ echo -e "$nullaway_config_path\t$scanner_config_path" > sample/annotator-out/pat
 
 # run the annotator
 java -jar annotator-core-1.3.15.jar \
-    -bc "cd $(pwd) && ./gradlew sample:compileJava" \
+    -bc "cd $(pwd)/sample && ./gradlew compileJava" \
     -d "$annotator_out_dir" \
     -n javax.annotation.Nullable \
     -cp sample/annotator-out/paths.tsv \
     -cn NULLAWAY \
     -i com.uber.nullaway.annotations.Initializer \
     -sre org.jspecify.annotations.NullUnmarked
-
-
-
-

sample/annotator-out/0/class_records.tsv

@@ -0,0 +1,2 @@
+class	path
+edu.ucr.cs.riple.annotator.sample.Test	/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java

sample/annotator-out/0/errors.tsv

@@ -0,0 +1,3 @@
+message_type	message	enc_class	enc_member	offset	path	target_kind	target_class	target_method	target_param	target_index	target_path
+ASSIGN_FIELD_NULLABLE	assigning @Nullable expression to @NonNull field	edu.ucr.cs.riple.annotator.sample.Test	f2	1269	/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java	FIELD	edu.ucr.cs.riple.annotator.sample.Test	null	f2	null	/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java
+ASSIGN_FIELD_NULLABLE	assigning @Nullable expression to @NonNull field	edu.ucr.cs.riple.annotator.sample.Test	m4()	1649	/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java	FIELD	edu.ucr.cs.riple.annotator.sample.Test	null	f6	null	/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java

sample/annotator-out/0/field_impacted_region_map.tsv

@@ -0,0 +1,13 @@
+REGION_CLASS	REGION_MEMBER	USED_MEMBER	USED_CLASS	SOURCE_TYPE
+edu.ucr.cs.riple.annotator.sample.Test	f5	f4	edu.ucr.cs.riple.annotator.sample.Test	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	f4	f4	edu.ucr.cs.riple.annotator.sample.Test	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m1()	f1	edu.ucr.cs.riple.annotator.sample.Test	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m1()	f1	edu.ucr.cs.riple.annotator.sample.Test	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m1()	f2	edu.ucr.cs.riple.annotator.sample.Test	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m1()	f6	edu.ucr.cs.riple.annotator.sample.Test	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m2()	f3	edu.ucr.cs.riple.annotator.sample.Test	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m2()	f3	edu.ucr.cs.riple.annotator.sample.Test	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m2()	f2	edu.ucr.cs.riple.annotator.sample.Test	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m2()	f6	edu.ucr.cs.riple.annotator.sample.Test	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m3()	f5	edu.ucr.cs.riple.annotator.sample.Test	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m4()	f6	edu.ucr.cs.riple.annotator.sample.Test	SOURCE

sample/annotator-out/0/field_init.tsv

@@ -0,0 +1 @@
+kind	class	method	param	index	uri	field

sample/annotator-out/0/fixes.tsv

@@ -0,0 +1,3 @@
+kind	class	method	param	index	uri	reason	annotation	rootClass	rootMethod
+FIELD	edu.ucr.cs.riple.annotator.sample.Test	null	f2	null	/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java	ASSIGN_FIELD_NULLABLE	nullable	edu.ucr.cs.riple.annotator.sample.Test	f2
+FIELD	edu.ucr.cs.riple.annotator.sample.Test	null	f6	null	/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java	ASSIGN_FIELD_NULLABLE	nullable	edu.ucr.cs.riple.annotator.sample.Test	m4()

sample/annotator-out/0/method_impacted_region_map.tsv

@@ -0,0 +1,8 @@
+REGION_CLASS	REGION_MEMBER	USED_MEMBER	USED_CLASS	SOURCE_TYPE
+edu.ucr.cs.riple.annotator.sample.Test	f6	Object()	java.lang.Object	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m1()	toString()	java.lang.Object	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m1()	toString()	java.lang.Object	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m1()	toString()	java.lang.Object	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m2()	hashCode()	java.lang.Object	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m2()	hashCode()	java.lang.Object	SOURCE
+edu.ucr.cs.riple.annotator.sample.Test	m2()	hashCode()	java.lang.Object	SOURCE

sample/annotator-out/0/method_records.tsv

@@ -0,0 +1,5 @@
+id	class	method	parent	flags	annotations	visibility	non-primitive-return	path
+1	edu.ucr.cs.riple.annotator.sample.Test	m1()	0	[]		package	true	/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java
+2	edu.ucr.cs.riple.annotator.sample.Test	m2()	0	[]		package	false	/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java
+3	edu.ucr.cs.riple.annotator.sample.Test	m3()	0	[]		package	true	/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java
+4	edu.ucr.cs.riple.annotator.sample.Test	m4()	0	[]		package	false	/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java

sample/annotator-out/0/nonnull_elements.tsv

@@ -0,0 +1 @@
+kind	class	method	param	index	uri

sample/annotator-out/0/serialization_version.txt

@@ -0,0 +1 @@
+3

sample/annotator-out/log.txt

@@ -0,0 +1,4 @@
+Total number of nodes=9
+Total number of Requested builds=15
+Total time=27453
+Total time spent on builds=30329

sample/annotator-out/nullaway.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><serialization><suggest active="true" enclosing="true"/><fieldInitInfo active="true"/><path>/Users/nima/Developer/NullAwayAnnotator/sample/annotator-out/0</path><uuid>6da8e068-1258-4990-807c-fe64a5e9679f</uuid></serialization>

sample/annotator-out/paths.tsv

@@ -0,0 +1 @@
+/Users/nima/Developer/NullAwayAnnotator/sample/annotator-out/nullaway.xml	/Users/nima/Developer/NullAwayAnnotator/sample/annotator-out/scanner.xml

sample/annotator-out/reports.json

@@ -0,0 +1 @@
+{"REPORTS":[{"VARIABLES":["f2"],"LOCAL EFFECT":1,"KIND":"FIELD","TREE":[],"CLASS":"edu.ucr.cs.riple.annotator.sample.Test","FINISHED":true,"OVERALL EFFECT":1,"Upper Bound EFFECT":0,"Lower Bound EFFECT":0,"PATH":/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java},{"VARIABLES":["f6"],"LOCAL EFFECT":1,"KIND":"FIELD","TREE":[],"CLASS":"edu.ucr.cs.riple.annotator.sample.Test","FINISHED":true,"OVERALL EFFECT":1,"Upper Bound EFFECT":0,"Lower Bound EFFECT":0,"PATH":/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java},{"VARIABLES":["f4"],"LOCAL EFFECT":0,"KIND":"FIELD","TREE":[],"CLASS":"edu.ucr.cs.riple.annotator.sample.Test","FINISHED":true,"OVERALL EFFECT":0,"Upper Bound EFFECT":0,"Lower Bound EFFECT":0,"PATH":/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java},{"VARIABLES":["f5"],"LOCAL EFFECT":0,"KIND":"FIELD","TREE":[],"CLASS":"edu.ucr.cs.riple.annotator.sample.Test","FINISHED":true,"OVERALL EFFECT":0,"Upper Bound EFFECT":0,"Lower Bound EFFECT":0,"PATH":/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java},{"VARIABLES":["f3"],"LOCAL EFFECT":-1,"KIND":"FIELD","TREE":[],"CLASS":"edu.ucr.cs.riple.annotator.sample.Test","FINISHED":true,"OVERALL EFFECT":-1,"Upper Bound EFFECT":0,"Lower Bound EFFECT":0,"PATH":/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java},{"VARIABLES":["f1"],"LOCAL EFFECT":-1,"KIND":"FIELD","TREE":[],"CLASS":"edu.ucr.cs.riple.annotator.sample.Test","FINISHED":true,"OVERALL EFFECT":-1,"Upper Bound EFFECT":0,"Lower Bound EFFECT":0,"PATH":/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java},{"LOCAL EFFECT":-1,"KIND":"METHOD","TREE":[],"CLASS":"edu.ucr.cs.riple.annotator.sample.Test","FINISHED":true,"OVERALL EFFECT":-1,"Upper Bound EFFECT":0,"Lower Bound EFFECT":0,"PATH":/Users/nima/Developer/NullAwayAnnotator/sample/src/main/java/edu/ucr/cs/riple/annotator/sample/Test.java,"METHOD":"m3()"}]}

sample/annotator-out/scanner.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><scanner><serialization active="false"/><uuid>37900c23-dad7-460e-abc9-8bfc62dccc1a</uuid><path>/Users/nima/Developer/NullAwayAnnotator/sample/annotator-out/0</path><processor><LOMBOK active="true"/></processor><annotations/></scanner>

sample/gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,7 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.9-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists

sample/gradlew

@@ -0,0 +1,252 @@
+#!/bin/sh
+
+#
+# Copyright © 2015-2021 the original authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
+##############################################################################
+#
+#   Gradle start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
+##############################################################################
+
+# Attempt to set APP_HOME
+
+# Resolve links: $0 may be a link
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
+done
+
+# This is normally unused
+# shellcheck disable=SC2034
+APP_BASE_NAME=${0##*/}
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s
+' "$PWD" ) || exit
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD=maximum
+
+warn () {
+    echo "$*"
+} >&2
+
+die () {
+    echo
+    echo "$*"
+    echo
+    exit 1
+} >&2
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD=$JAVA_HOME/jre/sh/java
+    else
+        JAVACMD=$JAVA_HOME/bin/java
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD=java
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+fi
+
+# Increase the maximum file descriptors if we can.
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
+fi
+
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
+        fi
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
+    done
+fi
+
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
+
+exec "$JAVACMD" "$@"

settings.gradle

@@ -29,4 +29,3 @@ include 'injector'
 include 'library-model-loader'
 include 'checks'
 include 'checks:ban-mutable-static'
-include 'sample'