Tests pass

.gitattributes

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+#
+# https://help.github.com/articles/dealing-with-line-endings/
+#
+# These are explicitly windows files and should use crlf
+*.bat           text eol=crlf
+

build.gradle

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+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * This generated file contains a sample Java application project to get you started.
+ * For more details take a look at the 'Building Java & JVM projects' chapter in the Gradle
+ * User Manual available at https://docs.gradle.org/7.4.2/userguide/building_java_projects.html
+ */
+
+plugins {
+	id 'java'
+	id 'war'
+	id 'jacoco'
+}
+
+repositories {
+	mavenCentral()
+}
+
+compileJava {
+	options.release = 8
+}
+
+test {
+	/* 
+	 * TODO TEST Figure out why tests fail without this and remove. Might have something to do
+	 * with the stfuLoggers() call in many of the tests, might kill logging for tests that
+	 * require it
+	 * Although it seems to make Mongo start up correctly as well which is odd
+	 */
+	forkEvery = 1
+	systemProperty "AUTH2_TEST_CONFIG", "./test.cfg"
+	testLogging {
+		exceptionFormat = 'full'
+		showStandardStreams = true
+	}
+}
+
+// Custom java project layout
+sourceSets {
+	main {
+		java {
+			srcDirs = ["src"]
+			exclude '**/test/**'
+		}
+	}
+	test {
+		java {
+			srcDirs = ["src"]
+			include '**/test/**'
+		}
+		resources {
+			srcDirs = ["src"]
+			include "**/*.testdata"
+			include "**/authjars"
+		}
+	}
+}
+
+war {
+	webXml = file('war/web.xml')
+}
+
+def fromURL = { url, name ->
+	File file = new File("$buildDir/download/${name}.jar")
+	file.parentFile.mkdirs()
+	if (!file.exists()) {
+		new URL(url).withInputStream { downloadStream ->
+			file.withOutputStream { fileOut ->
+				fileOut << downloadStream
+			}
+		}
+	}
+	files(file.absolutePath)
+}
+
+dependencies {
+
+	// ### General application dependencies ###
+
+	implementation 'commons-codec:commons-codec:1.8'
+	implementation 'commons-validator:commons-validator:1.5.1'
+	implementation 'com.google.guava:guava:18.0'
+	implementation 'org.ini4j:ini4j:0.5.2'
+	implementation 'com.beust:jcommander:1.48'
+	implementation 'org.mongodb:mongo-java-driver:3.8.2'
+	implementation 'com.github.spullara.mustache.java:compiler:0.9.3'
+	implementation 'com.nulab-inc:zxcvbn:1.2.2'
+	implementation 'nl.basjes.parse.useragent:yauaa:1.3'
+	implementation 'com.fasterxml.jackson.core:jackson-annotations:2.5.4'
+	implementation 'com.fasterxml.jackson.core:jackson-databind:2.5.4'
+	implementation 'com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.5.4'
+	implementation 'com.github.zafarkhaja:java-semver:0.9.0'
+	implementation 'org.glassfish.jersey.containers:jersey-container-servlet:2.23.2'
+	implementation 'org.glassfish.jersey.media:jersey-media-json-jackson:2.23.2'
+	implementation 'org.glassfish.jersey.ext:jersey-mvc-mustache:2.23.2'
+	implementation 'javax.persistence:persistence-api:1.0'
+	implementation 'javax.servlet:javax.servlet-api:3.0.1'
+	implementation 'javax.xml.bind:jaxb-api:2.4.0-b180830.0359'
+
+
+	// ### Logging dependencies ###
+	implementation fromURL(
+		'https://github.com/kbase/jars/raw/master/lib/jars/kbase/common/kbase-common-0.0.22.jar',
+		'kbase-common-0.0.22'
+	)
+	implementation 'ch.qos.logback:logback-classic:1.1.2'
+	implementation 'org.slf4j:slf4j-api:1.7.25'
+	// Syslog4j 0.9.46 doesn't appear to be available on Maven. It apparently lives in 
+	// a JetBrains artifact server, but that's too much trouble and there's only one version there
+	// anyway.
+	// https://mvnrepository.com/artifact/org.jetbrains/syslog4j/0.9.46
+	// Need to rework the java common logger to not use syslog4j at all since it's abandonware
+	// and has a ton of CVEs, even in the newer versions.
+	implementation fromURL(
+		'https://github.com/kbase/jars/raw/master/lib/jars/syslog4j/syslog4j-0.9.46.jar',
+		'syslog4j-0.9.46'
+	)
+	// needed for syslog
+	implementation 'net.java.dev.jna:jna:3.4.0'
+
+	// ### Test ###
+
+	testImplementation 'commons-io:commons-io:2.4'
+	testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.1.10'
+	testImplementation 'junit:junit:4.12'
+	testImplementation 'org.mock-server:mockserver-netty:3.10.4'
+	testImplementation 'org.eclipse.jetty:jetty-server:9.3.11.v20160721'
+	testImplementation 'org.eclipse.jetty:jetty-servlet:9.3.11.v20160721'
+	testImplementation 'io.github.java-diff-utils:java-diff-utils:2.2.0'
+	testImplementation 'de.danielbechler:java-object-diff:0.94'
+	testImplementation 'org.jsoup:jsoup:1.10.2'
+	testImplementation 'org.mockito:mockito-core:3.0.0'
+}

gradle/wrapper/gradle-wrapper.properties

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+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-bin.zip
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists

gradlew

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+#!/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.
+#
+
+##############################################################################
+#
+#   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/master/subprojects/plugins/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
+
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
+
+APP_NAME="Gradle"
+APP_BASE_NAME=${0##*/}
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD=maximum
+
+warn () {
+    echo "$*"
+} >&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: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD=java
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        ulimit -n "$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
+
+# Collect all arguments for the java command;
+#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+#     shell script including quotes and variable substitutions, so put them in
+#     double quotes to make sure that they get re-expanded; and
+#   * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# 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

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+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * The settings file is used to specify which projects to include in your build.
+ *
+ * Detailed information about configuring a multi-project build in Gradle can be found
+ * in the user manual at https://docs.gradle.org/7.4.2/userguide/multi_project_builds.html
+ */
+
+rootProject.name = 'auth2'