diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..097f9f9 --- /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 f31ba61..ab6a1b2 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -34,22 +34,9 @@ jobs: distribution: 'temurin' java-version: ${{matrix.java}} - - name: Install dependencies and set up test config - shell: bash - run: | - export HOMEDIR=`pwd` - - # move to parent dir of homedir to install binaries etc - cd .. - - # set up jars - git clone https://github.com/kbase/jars - - cd $HOMEDIR - - name: Run tests run: | - make test-coverage + ./gradlew test - name: Upload coverage to Codecov uses: codecov/codecov-action@v3 diff --git a/Makefile b/Makefile deleted file mode 100644 index 8b5708e..0000000 --- a/Makefile +++ /dev/null @@ -1,88 +0,0 @@ -KB_TOP ?= /kb/deployment -KB_RUNTIME ?= /kb/runtime -JAVA_HOME ?= $KB_RUNTIME/java -AWE_WORKER_SCRIPT = $(KB_TOP)/bin/java_generic_script -JAR-PREFIX = kbase-common - -ANT = ant - -GITCOMMIT := $(shell git rev-parse --short HEAD) -EPOCH := $(shell date +%s) -#TODO use --points-at vs. --contains when git 1.7.10 available -TAGS := $(shell git tag --contains $(GITCOMMIT)) -TAG := $(shell python internal/checktags.py $(TAGS)) - -ERR := $(findstring Two valid tags for this commit, $(TAG)) - -ifneq ($(ERR), ) -$(error Tags are ambiguous for this commit: $(TAG)) -endif - -COMMON-JAR = $(JAR-PREFIX)-$(TAG) - -ifeq ($(TAG), ) -COMMON-JAR = $(JAR-PREFIX)-$(EPOCH)-$(GITCOMMIT) -endif - -# make sure our make test works -.PHONY : test - -default: build-libs build-docs - -build-libs: - $(ANT) compile -Dcompile.jarfile=$(COMMON-JAR) - -build-docs: build-libs - -rm -r docs - $(ANT) javadoc - -test: - $(ANT) test -Dcompile.jarfile=$(COMMON-JAR) - -test-coverage: - $(ANT) test_coverage -Dcompile.jarfile=$(COMMON-JAR) - -test-client: - @echo "no client" - -test-service: - @echo "no service" - -test-scripts: - @echo "no scripts to test" - -test-worker: - echo "$$($(AWE_WORKER_SCRIPT) kbase-common-0.0.8.jar:jackson-annotations-2.2.3.jar:jackson-core-2.2.3.jar:jackson-databind-2.2.3.jar 12345 us.kbase.common.awe.test.TempTask listToMap 5B5B226B31222C227632222C226B34222C227635225D5D 7B7D)" | grep status=done || exit 1 - echo "Test passed" - -deploy: deploy-worker - -deploy-client: - @echo "nothing to deploy" - -deploy-docs: - @echo "nothing to deploy" - -deploy-scripts: - @echo "nothing to deploy" - -deploy-worker: - echo '#!/bin/bash' > $(AWE_WORKER_SCRIPT) - echo 'export KB_TOP=$(KB_TOP)' >> $(AWE_WORKER_SCRIPT) - echo 'export KB_RUNTIME=$(KB_RUNTIME)' >> $(AWE_WORKER_SCRIPT) - echo 'export JAVA_HOME=$(JAVA_HOME)' >> $(AWE_WORKER_SCRIPT) - echo 'export PATH=$$KB_RUNTIME/bin:$$KB_TOP/bin:$$JAVA_HOME/bin:$$PATH' >> $(AWE_WORKER_SCRIPT) - echo 'JARS=$(KB_TOP)/lib/jars' >> $(AWE_WORKER_SCRIPT) - echo 'INITCP=$$JARS/kbase/common/kbase-common-0.0.8.jar:$$JARS/jackson/jackson-annotations-2.2.3.jar:$$JARS/jackson/jackson-core-2.2.3.jar:$$JARS/jackson/jackson-databind-2.2.3.jar' >> $(AWE_WORKER_SCRIPT) - echo 'FULLCP=$$(java -cp $$INITCP us.kbase.common.awe.task.JavaGenericScript $$1 kbase)' >> $(AWE_WORKER_SCRIPT) - echo 'java -cp $$FULLCP us.kbase.common.awe.task.JavaGenericScript $$2 $$3 $$4 $$5 $$6 $$7' >> $(AWE_WORKER_SCRIPT) - chmod 775 $(AWE_WORKER_SCRIPT) - -deploy-service: - @echo "nothing to deploy" - -jenkins: - $(ANT) jenkins - -clean: - $(ANT) clean diff --git a/build.gradle b/build.gradle new file mode 100644 index 0000000..bbc8c07 --- /dev/null +++ b/build.gradle @@ -0,0 +1,130 @@ +/* + * This file was generated by the Gradle 'init' task. + */ + +plugins { + id 'java' + id 'jacoco' + id 'maven-publish' +} + +group = 'com.github.kbase' + +// TODO GRADLE move files to standard gradle layout +// TODO GRADLE update docs +// TODO GRADLE update to jitpack built auth jar (javadoc as well) +// TODO GRADLE publish w/ jitpack when auth jar pulled from jitpack +// TODO BUILD get rid of dependency on Syslog4j, 10yo abandonware w/ CVEs + +repositories { + mavenCentral() +} + +compileJava { + // TODO BUILD remove when we no longer support java 8, use `options.release = 11` if needed + java.sourceCompatibility = JavaVersion.VERSION_1_8 + java.targetCompatibility = JavaVersion.VERSION_1_8 +} + +java { + withSourcesJar() + withJavadocJar() +} + +test { + forkEvery = 1 // seems to fix a race condition with the logging test + testLogging { + exceptionFormat = 'full' + showStandardStreams = true + } + finalizedBy jacocoTestReport +} + +jacocoTestReport { + reports { + xml.required = true + csv.required = true + } +} + +javadoc { + failOnError = false // big effort to fix this one + options { + // I don't know why this isn't working, but it's not worth spending time on right now + links "https://docs.oracle.com/javase/8/docs/api/" + } +} + +publishing { + publications { + maven(MavenPublication) { + from components.java + } + } +} + +sourceSets { + main { + java { + srcDirs = ["src"] + exclude '**/test/**' + exclude '**/testlogger/**' + } + } + test { + java { + srcDirs = ["src"] + include '**/test/**' + include '**/testlogger/**' + } + } +} + +def fromURL = { url, name -> + File file = new File("$buildDir/download/${name}.jar") + file.parentFile.mkdirs() + if (!file.exists()) { + new URL(url).withInputStream { downloadStream -> + file.withOutputStream { fileOut -> + fileOut << downloadStream + } + } + } + files(file.absolutePath) +} + +dependencies { + + // using older dependencies to not force upgrades on services that might not be able to + // handle them. Need to upgrade the services and then upgrade here + implementation 'com.fasterxml.jackson.core:jackson-annotations:2.9.9' + implementation 'com.fasterxml.jackson.core:jackson-databind:2.9.9' + implementation fromURL( + 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/auth/kbase-auth-0.4.2.jar', + 'kbase-auth-0.4.4' + ) + implementation 'org.apache.commons:commons-lang3:3.1' + implementation 'org.slf4j:slf4j-api:1.7.7' + implementation 'ch.qos.logback:logback-classic:1.1.2' + implementation 'org.ini4j:ini4j:0.5.2' + implementation 'javax.servlet:servlet-api:2.5' + implementation 'joda-time:joda-time:2.2' + // TODO CODE ideally we could rewrite java-common so it didn't have a runtime dependency on + // jetty + implementation 'org.eclipse.jetty.aggregate:jetty-all:7.0.0.v20091005' + // 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' + ) + // needed for syslog4j + implementation 'net.java.dev.jna:jna:3.4.0' + + testImplementation 'junit:junit:4.9' + testImplementation 'com.google.guava:guava:18.0' + testImplementation 'org.mockito:mockito-core:3.0.0' + testImplementation 'com.github.zafarkhaja:java-semver:0.9.0' + testImplementation 'commons-io:commons-io:2.4' + +} diff --git a/build.xml b/build.xml deleted file mode 100644 index c5585be..0000000 --- a/build.xml +++ /dev/null @@ -1,206 +0,0 @@ - - - - Build file for the comman KBase Java libs - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml new file mode 100644 index 0000000..4ac3234 --- /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 0000000..e644113 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 0000000..b82aa23 --- /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 0000000..1aa94a4 --- /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/internal/checktags.py b/internal/checktags.py deleted file mode 100644 index e56cc02..0000000 --- a/internal/checktags.py +++ /dev/null @@ -1,14 +0,0 @@ -import sys -import re - -VALID_TAG = re.compile("\d+.\d+.\d+") - -if __name__ == "__main__": - tag = "" - for t in sys.argv[1:]: - if VALID_TAG.match(t): - if tag != "": - print("Two valid tags for this commit: {} {}".format(tag, t)) - sys.exit(1) - tag = t - print(tag) diff --git a/settings.gradle b/settings.gradle new file mode 100644 index 0000000..f16f3a4 --- /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 = 'java_common'