diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..097f9f98 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,9 @@ +# +# https://help.github.com/articles/dealing-with-line-endings/ +# +# Linux start script should use lf +/gradlew text eol=lf + +# These are Windows script files and should use crlf +*.bat text eol=crlf + diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 945d77d6..079d5c0d 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -24,21 +24,14 @@ jobs: include: # the current production setup - java: '8' - codecov: true mongo: 'mongodb-linux-x86_64-3.6.13' wired_tiger: 'false' - ant_test: 'test' + gradle_test: 'test' # test all code w/ java 11 - - java: '11' - codecov: true - mongo: 'mongodb-linux-x86_64-3.6.13' - wired_tiger: 'false' - ant_test: 'test' - # test the latest 3X version of mongo against just the mongo storage code - java: '11' mongo: 'mongodb-linux-x86_64-3.6.23' wired_tiger: 'true' - ant_test: 'test_mongo_storage' + gradle_test: 'test' steps: - uses: actions/checkout@v3 @@ -56,10 +49,6 @@ jobs: # move to parent dir of homedir to install binaries etc cd .. - # set up jars - git clone https://github.com/kbase/jars - export JARSDIR=$(pwd)/jars/lib/jars/ - # set up mongo wget -q http://fastdl.mongodb.org/linux/${{matrix.mongo}}.tgz tar xfz ${{matrix.mongo}}.tgz @@ -68,7 +57,6 @@ jobs: # set up test config cd $HOMEDIR cp -n test.cfg.example test.cfg - sed -i "s#^test.jars.dir.*#test.jars.dir=$JARSDIR#" test.cfg sed -i "s#^test.temp.dir=.*#test.temp.dir=temp_test_dir#" test.cfg sed -i "s#^test.mongo.exe.*#test.mongo.exe=$MONGOD#" test.cfg sed -i "s#^test.mongo.useWiredTiger.*#test.mongo.useWiredTiger=${{matrix.wired_tiger}}#" test.cfg @@ -77,10 +65,9 @@ jobs: - name: Run tests shell: bash run: | - ant ${{matrix.ant_test}} + gradle ${{matrix.gradle_test}} - name: Upload coverage to Codecov - if: matrix.codecov uses: codecov/codecov-action@v3 with: token: ${{ secrets.CODECOV_TOKEN }} diff --git a/Dockerfile b/Dockerfile index 103b3461..fd2899b7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,10 +1,23 @@ FROM kbase/sdkbase2 as build -COPY . /tmp/groups -RUN cd /tmp \ - && git clone https://github.com/kbase/jars \ - && cd groups \ - && ant buildwar +WORKDIR /tmp/groups + +# dependencies take a while to D/L, so D/L & cache before the build so code changes don't cause +# a new D/L +# can't glob *gradle because of the .gradle dir +COPY build.gradle gradlew settings.gradle /tmp/groups/ +COPY gradle/ /tmp/groups/gradle/ +RUN ./gradlew dependencies + +# Now build the code +COPY deployment/ /tmp/groups/deployment/ +COPY jettybase/ /tmp/groups/jettybase/ +COPY src /tmp/groups/src/ +COPY war /tmp/groups/war/ +# for the git commit +COPY .git /tmp/groups/.git/ +RUN ./gradlew war + FROM kbase/kb_jre:latest @@ -15,6 +28,7 @@ ARG BRANCH=develop COPY --from=build /tmp/groups/deployment/ /kb/deployment/ COPY --from=build /tmp/groups/jettybase/ /kb/deployment/jettybase/ +COPY --from=build /tmp/groups/build/libs/groups.war /kb/deployment/jettybase/webapps/ROOT.war # The BUILD_DATE value seem to bust the docker cache when the timestamp changes, move to # the end @@ -30,6 +44,9 @@ ENV KB_DEPLOYMENT_CONFIG=/kb/deployment/conf/deployment.cfg RUN chmod -R a+rwx /kb/deployment/conf /kb/deployment/jettybase/ +# TODO BUILD update to no longer use dockerize and take env vars (e.g. like Collections). +# TODO BUILD Use subsections in the ini file / switch to TOML + ENTRYPOINT [ "/kb/deployment/bin/dockerize" ] # Here are some default params passed to dockerize. They would typically diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index 6973d6b2..67576215 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -1,5 +1,9 @@ # KBase Groups Service release notes +## 0.1.7 + +* The build tool has been switched from Ant to Gradle. + ## 0.1.6 ### Admin notes: diff --git a/build.gradle b/build.gradle new file mode 100644 index 00000000..7365ba76 --- /dev/null +++ b/build.gradle @@ -0,0 +1,167 @@ +/* + * This file was generated by the Gradle 'init' task. + */ + +plugins { + id 'java' + id 'war' + id 'jacoco' + id 'org.ajoberstar.grgit' version '4.1.1' +} + +// TODO NOW run tests from Eclipse w/o specifying classpath manually & remove sourceSets & classpath +// TODO NOW update any ant refs in docs to gradle + +repositories { + mavenCentral() +} + +task buildGitCommitFile { + doLast { + def commitId = grgit.head().id + // is there a variable for builddir/classes/java/main? + file("$buildDir/classes/java/main/us/kbase/groups/gitcommit").text = commitId + } +} + +compileJava { + // TODO BUILD remove when we no longer support java 8, use `options.release = 11` if needed + java.sourceCompatibility = JavaVersion.VERSION_1_8 + java.targetCompatibility = JavaVersion.VERSION_1_8 + finalizedBy buildGitCommitFile +} + +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 + /* + * TODO TEST split mongo wrapper tests out. + * Set up GHA to run the full test suite with a single version of mongo and run the + * mongo tests with matrixed mongo versions. + * Since the tests only take a minute or two this isn't high ROI. + */ + systemProperty "KBASE_GROUPS_TEST_CONFIG", "./test.cfg" + maxHeapSize = "3G" + testLogging { + exceptionFormat = 'full' + showStandardStreams = true + } + finalizedBy jacocoTestReport +} + +// TODO TEST add a test that starts the server in a docker container and checks some simple cmds + +jacocoTestReport { + reports { + xml.required = true + csv.required = true + } +} + +war { + webXml = file('war/web.xml') +} + +// Custom java project layout +sourceSets { + main { + java { + srcDirs = ["src"] + exclude '**/test/**' + } + } + test { + java { + srcDirs = ["src"] + include '**/test/**' + } + resources { + srcDirs = ["src"] + include "**/*wsjars" + } + } +} + +configurations { + // can't directly access testImplementation, so extend and access + testimpl.extendsFrom testImplementation +} + +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 { + + compileOnly 'javax.servlet:javax.servlet-api:3.0.1' + + implementation fromURL( + 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/auth/kbase-auth-0.4.4.jar', + 'kbase-auth-0.4.4' + ) + implementation fromURL( + 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/workspace/WorkspaceClient-0.8.0.jar', + 'WorkspaceClient-0.8.0' + ) + implementation fromURL( + 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/catalog/kbase-catalog-client-2.1.3.jar', + 'kbase-catalog-client-2.1.3' + ) + implementation fromURL( + 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/common/kbase-common-0.0.25.jar', + 'kbase-common-0.0.25' + ) + // Pull from jars repo vs a maven repository to avoid the JNA dependency + // TODO DEPS 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' + ) + implementation 'ch.qos.logback:logback-classic:1.1.2' + implementation 'org.ini4j:ini4j:0.5.2' + implementation 'org.mongodb:mongo-java-driver:3.8.2' + implementation 'org.apache.kafka:kafka-clients:2.1.0' + implementation 'com.google.guava:guava:18.0' + implementation 'org.slf4j:slf4j-api:1.7.25' + implementation 'com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.5.4' + implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jdk8:2.5.4' + implementation 'org.glassfish.jersey.containers:jersey-container-servlet:2.23.2' + implementation 'org.glassfish.jersey.media:jersey-media-json-jackson:2.23.2' + implementation 'com.github.zafarkhaja:java-semver:0.9.0' + + testImplementation fromURL( + 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/auth2/kbase-auth2-test-shadow-all-0.7.0.jar', + 'kbase-auth2-test-shadow-all-0.7.0' + ) + testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.1.10' + testImplementation 'junit:junit:4.12' + testImplementation 'org.mockito:mockito-core:3.0.0' + testImplementation('org.mock-server:mockserver-netty:5.4.1') { + // otherwise a newer jackson implementation is brought in and tests make a poo poo + // TODO BUILD on upgrade switch to the no dependencies version + exclude group: "com.fasterxml.jackson.core" + } + testImplementation 'org.eclipse.jetty:jetty-servlet:9.3.11.v20160721' +} + +task showTestClassPath { + doLast { + configurations.testimpl.each { println it } + } +} + diff --git a/build.xml b/build.xml deleted file mode 100644 index 39084fd0..00000000 --- a/build.xml +++ /dev/null @@ -1,361 +0,0 @@ - - - - Build file for the KBase Groups Service - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml new file mode 100644 index 00000000..4ac3234a --- /dev/null +++ b/gradle/libs.versions.toml @@ -0,0 +1,2 @@ +# This file was generated by the Gradle 'init' task. +# https://docs.gradle.org/current/userguide/platforms.html#sub::toml-dependencies-format diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar new file mode 100644 index 00000000..e6441136 Binary files /dev/null and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties new file mode 100644 index 00000000..b82aa23a --- /dev/null +++ b/gradle/wrapper/gradle-wrapper.properties @@ -0,0 +1,7 @@ +distributionBase=GRADLE_USER_HOME +distributionPath=wrapper/dists +distributionUrl=https\://services.gradle.org/distributions/gradle-8.7-bin.zip +networkTimeout=10000 +validateDistributionUrl=true +zipStoreBase=GRADLE_USER_HOME +zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew new file mode 100755 index 00000000..1aa94a42 --- /dev/null +++ b/gradlew @@ -0,0 +1,249 @@ +#!/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/HEAD/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 + +# 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 "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit + +# Use the maximum available, or set MAX_FD != -1 to use that value. +MAX_FD=maximum + +warn () { + echo "$*" +} >&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 "$JAVACMD" "$@" diff --git a/settings.gradle b/settings.gradle new file mode 100644 index 00000000..751f4065 --- /dev/null +++ b/settings.gradle @@ -0,0 +1,8 @@ +/* + * This file was generated by the Gradle 'init' task. + * + * The settings file is used to specify which projects to include in your build. + * For more detailed information on multi-project builds, please refer to https://docs.gradle.org/8.7/userguide/multi_project_builds.html in the Gradle documentation. + */ + +rootProject.name = 'groups' diff --git a/src/us/kbase/groups/config/GroupsConfig.java b/src/us/kbase/groups/config/GroupsConfig.java index ef1213fa..b752f09b 100644 --- a/src/us/kbase/groups/config/GroupsConfig.java +++ b/src/us/kbase/groups/config/GroupsConfig.java @@ -133,6 +133,7 @@ private GroupsConfig( logger = new NullLogger(); } else { // may want to allow configuring the logger name, but YAGNI + JsonServerSyslog.setStaticUseSyslog(false); logger = new JsonServerSysLogAutoLogger(new JsonServerSyslog( LOG_NAME, null, JsonServerSyslog.LOG_LEVEL_INFO, true)); }