Commit 5484876a authored by Jasper Koehorst's avatar Jasper Koehorst
Browse files

init for java 17 default build

parent f817ec8b
#
# NOTICE: this is an auto-generated file
#
# This file sets the default parameters for manual `pnpm install`.
#
shamefully-hoist=true
plugins {
id 'org.springframework.boot' version '2.6.1'
id 'io.spring.dependency-management' version '1.0.11.RELEASE'
id 'java'
id 'com.vaadin' version '0.14.6.0'
id 'org.springframework.boot' version '2.6.2'
id 'io.spring.dependency-management' version '1.0.11.RELEASE'
id 'java'
id 'com.vaadin' version '0.14.7.3'
}
defaultTasks("clean", "build")
group = 'nl.munlock'
version = '1.0.1'
java {
toolchain {
languageVersion.set(JavaLanguageVersion.of(11))
}
}
group = 'com.example'
version = '0.0.1-SNAPSHOT'
sourceCompatibility = JavaVersion.VERSION_17
repositories {
mavenCentral()
mavenLocal()
maven { url "https://repo.gradle.org/gradle/libs-releases" }
maven { url "https://plugins.gradle.org/m2/" }
maven { url "https://maven.vaadin.com/vaadin-addons" }
}
ext {
set('vaadinVersion', "14.8.0")
set('log4j2Version', "2.16.0")
mavenCentral()
maven { url "https://maven.vaadin.com/vaadin-addons" }
}
configurations {
developmentOnly
runtimeClasspath {
extendsFrom developmentOnly
}
all {
resolutionStrategy.eachDependency { details ->
if (details.requested.group == 'org.apache.logging.log4j') {
details.useVersion '2.16.0'
details.because 'zero-day-exploits'
}
}
exclude group: 'log4j'
}
developmentOnly
runtimeClasspath {
extendsFrom developmentOnly
}
}
// Function to download and include URL jar files
def urlFile = { 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)
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)
}
test {
useJUnitPlatform()
}
dependencies {
implementation('com.vaadin:vaadin-spring-boot-starter') {
implementation('com.vaadin:vaadin-spring-boot-starter') {
// Webjars are only needed when running in Vaadin 13 compatibility mode
["spring-boot-starter-logging", "com.vaadin.webjar", "org.webjars.bowergithub.insites",
"org.webjars.bowergithub.polymer", "org.webjars.bowergithub.polymerelements",
"org.webjars.bowergithub.vaadin", "org.webjars.bowergithub.webcomponents"]
.forEach { group -> exclude(group: group) }
}
developmentOnly 'org.springframework.boot:spring-boot-devtools'
testImplementation('org.springframework.boot:spring-boot-starter-test') {
exclude group: 'org.junit.vintage', module: 'junit-vintage-engine'
}
implementation 'org.springframework.boot:spring-boot-starter-web'
implementation 'org.springframework.boot:spring-boot-starter-log4j2'
["com.vaadin.webjar", "org.webjars.bowergithub.insites",
"org.webjars.bowergithub.polymer", "org.webjars.bowergithub.polymerelements",
"org.webjars.bowergithub.vaadin", "org.webjars.bowergithub.webcomponents"]
.forEach { group -> exclude(group: group) }
}
developmentOnly 'org.springframework.boot:spring-boot-devtools'
testImplementation('org.springframework.boot:spring-boot-starter-test') {
exclude group: 'org.junit.vintage', module: 'junit-vintage-engine'
}
implementation 'org.vaadin.olli:file-download-wrapper:3.0.1'
// implementation 'org.springframework.boot:spring-boot-starter-web'
// implementation 'org.springframework.boot:spring-boot-starter-log4j2'
// Use JUnit test framework.
testImplementation 'junit:junit:4.13.2'
implementation 'org.vaadin.olli:file-download-wrapper:3.0.1'
// This dependency is used by the application.
implementation 'com.google.guava:guava:31.0.1-jre'
// Use JUnit test framework.
testImplementation 'junit:junit:4.13.2'
// irods dependency obtained locally
implementation urlFile('https://github.com/DICE-UNC/jargon/releases/download/4.3.0.2-RELEASE/jargon-core-4.3.0.2-RELEASE-jar-with-dependencies.jar', 'jargon-core-4.3.0.2-RELEASE-jar-with-dependencies')
// This dependency is used by the application.
implementation 'com.google.guava:guava:31.0.1-jre'
// unlock ontology obtained locally
implementation urlFile('http://download.systemsbiology.nl/unlock/UnlockOntology.jar', 'UnlockOntology')
// irods dependency obtained locally
implementation urlFile('https://github.com/DICE-UNC/jargon/releases/download/4.3.0.2-RELEASE/jargon-core-4.3.0.2-RELEASE-jar-with-dependencies.jar', 'jargon-core-4.3.0.2-RELEASE-jar-with-dependencies')
// kubernetes api
implementation 'io.kubernetes:client-java:14.0.0'
// unlock ontology obtained locally
implementation urlFile('http://download.systemsbiology.nl/unlock/UnlockOntology.jar', 'UnlockOntology')
// Excel parsers
implementation 'org.apache.poi:poi:5.0.0'
implementation 'org.apache.poi:poi-ooxml:5.0.0'
// kubernetes api
implementation 'io.kubernetes:client-java:14.0.0'
// Checker implementation
implementation 'org.checkerframework:checker-qual:3.18.1'
implementation group: 'com.esotericsoftware.yamlbeans', name: 'yamlbeans', version: '1.14'
// Excel parsers
implementation 'org.apache.poi:poi:5.0.0'
implementation 'org.apache.poi:poi-ooxml:5.0.0'
// https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-validation
implementation group: 'org.springframework.boot', name: 'spring-boot-starter-validation', version: '2.4.5'
// Checker implementation
implementation 'org.checkerframework:checker-qual:3.18.1'
implementation group: 'com.esotericsoftware.yamlbeans', name: 'yamlbeans', version: '1.14'
// Download button functionality
implementation 'org.vaadin.stefan:lazy-download-button:1.0.0'
// https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-core
implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '2.16.0'
// https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-validation
implementation group: 'org.springframework.boot', name: 'spring-boot-starter-validation', version: '2.4.5'
// Download button functionality
implementation 'org.vaadin.stefan:lazy-download-button:1.0.0'
// https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-core
implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '2.16.0'
}
dependencyManagement {
imports {
mavenBom "com.vaadin:vaadin-bom:${vaadinVersion}"
}
imports {
mavenBom "com.vaadin:vaadin-bom:$vaadinVersion"
}
}
test {
useJUnitPlatform()
useJUnitPlatform()
}
vaadin {
pnpmEnable = true
optimizeBundle = false
productionMode = false
}
\ No newline at end of file
pnpmEnable = false
}
{
"IRODSAdminUser": "adminuser",
"IRODSAdminPassword": "password",
"IRODSHost": "unlock-icat.irods.surfsara.nl",
"IRODSZone": "unlock",
"IRODSPort": 1247,
"IRODSSSLNegotiationPolicy": "CS_NEG_REQUIRE",
"IRODSAuthScheme": "STANDARD",
"certificateTrustStore": "/Users/jasperk/.irods_wur/keystore.jks",
"certificateTrustStorePassword": "randompassword",
"metadataXLSX": "./metadata.xlsx",
"debug": false
}
/******************************************************************************
* This file is auto-generated by Vaadin.
* If you want to customize the entry point, you can copy this file or create
* your own `index.ts` in your frontend directory.
* By default, the `index.ts` file should be in `./frontend/` folder.
*
* NOTE:
* - You need to restart the dev-server after adding the new `index.ts` file.
* After that, all modifications to `index.ts` are recompiled automatically.
* - `index.js` is also supported if you don't want to use TypeScript.
******************************************************************************/
// import Vaadin client-router to handle client-side and server-side navigation
import { Router } from '@vaadin/router';
// import Flow module to enable navigation to Vaadin server-side views
import { Flow } from '@vaadin/flow-frontend/Flow';
const { serverSideRoutes } = new Flow({
imports: () => import('../../build/frontend/generated-flow-imports')
});
const routes = [
// for client-side, place routes below (more info https://vaadin.com/docs/v15/flow/typescript/creating-routes.html)
// for server-side, the next magic line sends all unmatched routes:
...serverSideRoutes // IMPORTANT: this must be the last entry in the array
];
// Vaadin router needs an outlet in the index.html page to display views
const router = new Router(document.querySelector('#outlet'));
router.setRoutes(routes);
import './index';
import '@vaadin/flow-frontend/VaadinDevmodeGizmo.js';
vaadinVersion=14.7.3
\ No newline at end of file
vaadinVersion=14.7.3
#Thu Jan 30 08:04:25 EET 2020
distributionUrl=https\://services.gradle.org/distributions/gradle-7.3-all.zip
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.1-bin.zip
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
zipStoreBase=GRADLE_USER_HOME
#!/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.
#
#!/usr/bin/env sh
##############################################################################
#
# 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/.
#
##
## Gradle start up script for UN*X
##
##############################################################################
# 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
PRG="$0"
# Need this for relative symlinks.
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '/.*' > /dev/null; then
PRG="$link"
else
PRG=`dirname "$PRG"`"/$link"
fi
done
APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
SAVED="`pwd`"
cd "`dirname \"$PRG\"`/" >/dev/null
APP_HOME="`pwd -P`"
cd "$SAVED" >/dev/null
APP_NAME="Gradle"
APP_BASE_NAME=${0##*/}
APP_BASE_NAME=`basename "$0"`
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
DEFAULT_JVM_OPTS=""
# Use the maximum available, or set MAX_FD != -1 to use that value.
MAX_FD=maximum
MAX_FD="maximum"
warn () {
echo "$*"
} >&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 ;;
case "`uname`" in
CYGWIN* )
cygwin=true
;;
Darwin* )
darwin=true
;;
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
JAVACMD="$JAVA_HOME/jre/sh/java"
else
JAVACMD=$JAVA_HOME/bin/java
JAVACMD="$JAVA_HOME/bin/java"
fi
if [ ! -x "$JAVACMD" ] ; then
die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
......@@ -132,7 +81,7 @@ Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
else
JAVACMD=java
JAVACMD="java"
which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
Please set the JAVA_HOME variable in your environment to match the
......@@ -140,95 +89,84 @@ location of your Java installation."
fi
# Increase the maximum file descriptors if we can.
if ! "$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 $MAX_FD"
esac
if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
MAX_FD_LIMIT=`ulimit -H -n`
if [ $? -eq 0 ] ; then
if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
MAX_FD="$MAX_FD_LIMIT"
fi
ulimit -n $MAX_FD
if [ $? -ne 0 ] ; then
warn "Could not set maximum file descriptor limit: $MAX_FD"
fi
else
warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
fi
fi
# Collect all arguments for the java command, stacking in reverse order:
# * args from the command line
# * the main class name
# * -classpath
# * -D...appname settings
# * --module-path (only if needed)
# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
# For Cygwin or MSYS, switch paths to Windows format before running java
if "$cygwin" || "$msys" ; then
APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
JAVACMD=$( cygpath --unix "$JAVACMD" )
# For Darwin, add options to specify how the application appears in the dock
if $darwin; then
GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
fi
# For Cygwin, switch paths to Windows format before running java
if $cygwin ; then
APP_HOME=`cygpath --path --mixed "$APP_HOME"`
CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
JAVACMD=`cygpath --unix "$JAVACMD"`
# We build the pattern for arguments to be converted via cygpath
ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
SEP=""
for dir in $ROOTDIRSRAW ; do
ROOTDIRS="$ROOTDIRS$SEP$dir"
SEP="|"
done
OURCYGPATTERN="(^($ROOTDIRS))"
# Add a user-defined pattern to the cygpath arguments
if [ "$GRADLE_CYGPATTERN" != "" ] ; then
OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
fi
# 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" )
i=0
for arg in "$@" ; do
CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
else
eval `echo args$i`="\"$arg\""
fi
# Roll the args list around exactly as many times as the number of
# args, so each arg winds up back in the position where it started, but
# possibly modified.
#
# NB: a `for` loop captures its iteration list before it begins, so
# changing the positional parameters here affects neither the number of
# iterations, nor the values presented in `arg`.
shift # remove old arg
set -- "$@" "$arg" # push replacement arg
i=$((i+1))
done
case $i in
(0) set -- ;;
(1) set -- "$args0" ;;
(2) set -- "$args0" "$args1" ;;
(3) set -- "$args0" "$args1" "$args2" ;;
(4) set -- "$args0" "$args1" "$args2" "$args3" ;;
(5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
(6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
(7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
(8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
(9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
esac
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 $GRADLE_OPTS" |
xargs -n1 |
sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
tr '\n' ' '
)" '"$@"'
# Escape application args
save () {
for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
echo " "
}
APP_ARGS=$(save "$@")
# Collect all arguments for the java command, following the shell quoting and substitution rules
eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
cd "$(dirname "$0")"
fi
exec "$JAVACMD" "$@"
@rem
@rem Copyright 2015 the original author or authors.
@rem
@rem Licensed under the Apache License, Version 2.0 (the "License");
@rem you may not use this file except in compliance with the License.
@rem You may obtain a copy of the License at
@rem
@rem https://www.apache.org/licenses/LICENSE-2.0
@rem
@rem Unless required by applicable law or agreed to in writing, software