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Intel OpenVINO extension (#1)
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.github/workflows/build_jar.yml

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# This workflow will build the extension jar and retain the artifact.
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# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-gradle
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name: Build jar
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on: [workflow_dispatch]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up JDK 11
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uses: actions/setup-java@v2
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with:
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java-version: '11'
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distribution: 'adopt-hotspot'
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- name: Grant execute permission for gradlew
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run: chmod +x gradlew
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- name: Build with Gradle
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run: ./gradlew build -P toolchain=11
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- uses: actions/upload-artifact@v2
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with:
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name: libs
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path: build/libs
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retention-days: 1

.github/workflows/gradle.yml

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# This workflow will build a Java project with Gradle
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# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-gradle
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name: Java CI with Gradle
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on: [pull_request]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up JDK 11
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uses: actions/setup-java@v2
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with:
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java-version: '11'
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distribution: 'adopt-hotspot'
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- name: Grant execute permission for gradlew
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run: chmod +x gradlew
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- name: Build with Gradle
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run: ./gradlew build -P toolchain=11 --info

README.md

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# qupath-extension-openvino
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# QuPath OpenVINO extension
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Welcome to the Intel OpenVINO extension for [QuPath](http://qupath.github.io)!
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This adds support for inference optimization using [Intel OpenVINO for Java](https://github.com/openvinotoolkit/openvino_contrib/tree/master/modules/java_api) into QuPath.
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## Building
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### Extension + dependencies separately
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You can build the extension with
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```bash
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gradlew clean build copyDependencies
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```
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The output will be under `build/libs`.
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* `clean` removes anything old
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* `build` builds the QuPath extension as a *.jar* file and adds it to `libs`
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* `copyDependencies` copies the TensorFlow dependencies to the `libs` folder
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### Extension + dependencies together
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Alternatively, you can create a single *.jar* file that contains both the
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extension and all its dependencies with
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```bash
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gradlew clean shadowjar
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```
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## Installing
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The extension + its dependencies will all need to be available to QuPath inside
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QuPath's extensions folder.
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The easiest way to install the jars is to simply drag them on top of QuPath
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when it's running.
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You will then be prompted to ask whether you want to copy them to the
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appropriate folder.

build.gradle

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plugins {
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id 'java-library'
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// To create a shadow/fat jar, including dependencies
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id 'com.github.johnrengelman.shadow' version '7.0.0'
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// To manage included native libraries
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id 'org.bytedeco.gradle-javacpp-platform' version '1.5.4'
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}
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repositories {
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// Use this only for local development!
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// mavenLocal()
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mavenCentral()
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maven {
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url "https://maven.scijava.org/content/repositories/releases"
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}
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maven {
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url "https://maven.scijava.org/content/repositories/snapshots"
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}
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maven {
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url "https://openvino.jfrog.io/artifactory/openvino-gradle-dev-local"
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}
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}
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ext.moduleName = 'qupath.extension.openvino'
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description = 'QuPath extension to use Intel OpenVINO'
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version = "0.3.0"
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import org.gradle.internal.os.OperatingSystem
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println 'Operating system: ' + OperatingSystem.current()
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dependencies {
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def openvinoVersion = "2021.4"
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def qupathVersion = "0.3.0"
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def nativesCPP
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if (OperatingSystem.current().isMacOsX()) {
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nativesCPP = 'macosx-x86_64'
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} else if (OperatingSystem.current().isLinux()) {
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nativesCPP = 'linux-x86_64'
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} else if (OperatingSystem.current().isWindows()) {
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nativesCPP = 'windows-x86_64'
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} else {
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logger.warn('Unknown operating system!')
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}
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implementation "org.intel:openvino:${openvinoVersion}-${nativesCPP}"
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shadow "io.github.qupath:qupath-gui-fx:${qupathVersion}"
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shadow "org.slf4j:slf4j-api:1.7.30"
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testImplementation "io.github.qupath:qupath-gui-fx:${qupathVersion}"
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testImplementation "org.junit.jupiter:junit-jupiter-api:5.7.2"
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testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine'
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}
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processResources {
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from ("${projectDir}/LICENSE.txt") {
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into 'licenses/'
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}
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}
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tasks.register("copyDependencies", Copy) {
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description "Copy dependencies into the build directory for use elsewhere"
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group "QuPath"
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from configurations.default
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into 'build/libs'
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}
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/*
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* Ensure Java 11 compatibility
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*/
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java {
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toolchain {
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languageVersion = JavaLanguageVersion.of(11)
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}
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if (project.properties['sources'])
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withSourcesJar()
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if (project.properties['javadocs'])
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withJavadocJar()
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}
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/*
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* Create javadocs for all modules/packages in one place.
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* Use -PstrictJavadoc=true to fail on error with doclint (which is rather strict).
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*/
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def strictJavadoc = findProperty('strictJavadoc')
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if (!strictJavadoc) {
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tasks.withType(Javadoc) {
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options.addStringOption('Xdoclint:none', '-quiet')
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}
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}
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/*
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* Avoid 'Entry .gitkeep is a duplicate but no duplicate handling strategy has been set.'
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* when using withSourcesJar()
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*/
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tasks.withType(org.gradle.jvm.tasks.Jar) {
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duplicatesStrategy = DuplicatesStrategy.INCLUDE
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}
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tasks.named('test') {
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useJUnitPlatform()
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}

gradle/wrapper/gradle-wrapper.jar

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distributionBase=GRADLE_USER_HOME
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distributionPath=wrapper/dists
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distributionUrl=https\://services.gradle.org/distributions/gradle-7.1-bin.zip
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zipStoreBase=GRADLE_USER_HOME
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zipStorePath=wrapper/dists

gradlew

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#!/usr/bin/env sh
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#
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# Copyright 2015 the original author or authors.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# https://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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##############################################################################
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##
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## Gradle start up script for UN*X
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##
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##############################################################################
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# Attempt to set APP_HOME
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# Resolve links: $0 may be a link
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PRG="$0"
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# Need this for relative symlinks.
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while [ -h "$PRG" ] ; do
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ls=`ls -ld "$PRG"`
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link=`expr "$ls" : '.*-> \(.*\)$'`
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if expr "$link" : '/.*' > /dev/null; then
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PRG="$link"
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else
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PRG=`dirname "$PRG"`"/$link"
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fi
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done
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SAVED="`pwd`"
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cd "`dirname \"$PRG\"`/" >/dev/null
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APP_HOME="`pwd -P`"
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cd "$SAVED" >/dev/null
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APP_NAME="Gradle"
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APP_BASE_NAME=`basename "$0"`
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# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
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DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
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# Use the maximum available, or set MAX_FD != -1 to use that value.
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MAX_FD="maximum"
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warn () {
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echo "$*"
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}
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die () {
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echo
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echo "$*"
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echo
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exit 1
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}
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# OS specific support (must be 'true' or 'false').
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cygwin=false
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msys=false
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darwin=false
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nonstop=false
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case "`uname`" in
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CYGWIN* )
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cygwin=true
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;;
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Darwin* )
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darwin=true
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;;
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MINGW* )
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msys=true
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;;
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NONSTOP* )
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nonstop=true
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;;
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esac
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CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
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# Determine the Java command to use to start the JVM.
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if [ -n "$JAVA_HOME" ] ; then
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if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
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# IBM's JDK on AIX uses strange locations for the executables
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JAVACMD="$JAVA_HOME/jre/sh/java"
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else
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JAVACMD="$JAVA_HOME/bin/java"
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fi
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if [ ! -x "$JAVACMD" ] ; then
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die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
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Please set the JAVA_HOME variable in your environment to match the
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location of your Java installation."
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fi
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else
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JAVACMD="java"
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which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
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Please set the JAVA_HOME variable in your environment to match the
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location of your Java installation."
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fi
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# Increase the maximum file descriptors if we can.
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if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
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MAX_FD_LIMIT=`ulimit -H -n`
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if [ $? -eq 0 ] ; then
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if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
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MAX_FD="$MAX_FD_LIMIT"
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fi
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ulimit -n $MAX_FD
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if [ $? -ne 0 ] ; then
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warn "Could not set maximum file descriptor limit: $MAX_FD"
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fi
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else
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warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
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fi
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fi
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# For Darwin, add options to specify how the application appears in the dock
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if $darwin; then
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GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
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fi
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# For Cygwin or MSYS, switch paths to Windows format before running java
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if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
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APP_HOME=`cygpath --path --mixed "$APP_HOME"`
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CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
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JAVACMD=`cygpath --unix "$JAVACMD"`
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# We build the pattern for arguments to be converted via cygpath
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ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
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SEP=""
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for dir in $ROOTDIRSRAW ; do
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ROOTDIRS="$ROOTDIRS$SEP$dir"
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SEP="|"
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done
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OURCYGPATTERN="(^($ROOTDIRS))"
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# Add a user-defined pattern to the cygpath arguments
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if [ "$GRADLE_CYGPATTERN" != "" ] ; then
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OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
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fi
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# Now convert the arguments - kludge to limit ourselves to /bin/sh
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i=0
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for arg in "$@" ; do
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CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
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CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
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if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
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eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
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else
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eval `echo args$i`="\"$arg\""
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fi
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i=`expr $i + 1`
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done
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case $i in
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0) set -- ;;
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1) set -- "$args0" ;;
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2) set -- "$args0" "$args1" ;;
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3) set -- "$args0" "$args1" "$args2" ;;
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4) set -- "$args0" "$args1" "$args2" "$args3" ;;
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5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
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6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
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7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
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8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
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9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
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esac
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fi
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# Escape application args
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save () {
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for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
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echo " "
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}
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APP_ARGS=`save "$@"`
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# Collect all arguments for the java command, following the shell quoting and substitution rules
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eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
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exec "$JAVACMD" "$@"

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