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Add first version of BatchProcessor
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‎pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
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http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>org.scijava</groupId>
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<artifactId>pom-scijava</artifactId>
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<version>16.1.0</version>
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<relativePath />
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</parent>
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<artifactId>batch-processor</artifactId>
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<version>0.1.0-SNAPSHOT</version>
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<name>Batch Processor</name>
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<description>A Batch Processor for SciJava Modules and Scripts</description>
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<url>N/A</url>
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<inceptionYear>2017</inceptionYear>
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<organization>
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<name>None</name>
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<url>N/A</url>
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</organization>
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<licenses>
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<license>
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<name>Simplified BSD License</name>
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<distribution>repo</distribution>
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</license>
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</licenses>
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<developers>
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<!-- See https://imagej.net/Team -->
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<developer>
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<id>imagejan</id>
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<name>Jan Eglinger</name>
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<url>http://imagej.net/User:Eglinger</url>
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<roles>
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<role>founder</role>
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<role>lead</role>
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<role>developer</role>
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<role>debugger</role>
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<role>reviewer</role>
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<role>support</role>
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<role>maintainer</role>
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</roles>
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</developer>
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</developers>
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<contributors>
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<contributor>
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<name>Curtis Rueden</name>
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<url>http://imagej.net/User:Rueden</url>
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<roles><role>founder</role></roles>
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<properties><id>ctrueden</id></properties>
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</contributor>
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</contributors>
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<mailingLists>
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<mailingList>
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<name>ImageJ Forum</name>
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<archive>http://forum.imagej.net/</archive>
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</mailingList>
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</mailingLists>
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<scm>
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<connection>scm:git:git://github.com/imagejan/scijava-batch-processor</connection>
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<developerConnection>scm:git:git@github.com:imagejan/scijava-batch-processor</developerConnection>
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<tag>HEAD</tag>
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<url>https://github.com/imagejan/scijava-batch-processor</url>
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</scm>
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<issueManagement>
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<system>GitHub Issues</system>
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<url>https://github.com/imagejan/scijava-batch-processor/issues</url>
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</issueManagement>
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<ciManagement>
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<system>None</system>
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</ciManagement>
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<properties>
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<package-name>org.scijava</package-name>
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<main-class>org.scijava.batch.BatchProcessor</main-class>
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<license.licenseName>bsd_2</license.licenseName>
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<license.copyrightOwners>N/A</license.copyrightOwners>
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</properties>
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<repositories>
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<repository>
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<id>imagej.public</id>
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<url>http://maven.imagej.net/content/groups/public</url>
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</repository>
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</repositories>
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<dependencies>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-common</artifactId>
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</dependency>
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<dependency>
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<groupId>net.imagej</groupId>
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<artifactId>imagej</artifactId>
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</dependency>
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</dependencies>
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</project>

‎src/main/java/org/scijava/batch/BatchProcessor.java‎

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package org.scijava.batch;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.concurrent.ExecutionException;
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import java.util.concurrent.Future;
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import net.imagej.ImageJ;
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import org.scijava.command.Command;
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import org.scijava.command.DynamicCommand;
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import org.scijava.log.LogService;
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import org.scijava.module.Module;
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import org.scijava.module.ModuleException;
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import org.scijava.module.ModuleInfo;
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import org.scijava.module.ModuleItem;
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import org.scijava.module.ModuleService;
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import org.scijava.module.MutableModuleItem;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.script.ScriptInfo;
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import org.scijava.script.ScriptModule;
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import org.scijava.script.ScriptService;
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/**
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* Batch process a list of files in a folder by running a given script,
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* automatically providing the {@link File} input
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*
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* @author Jan Eglinger
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*/
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@Plugin(type = Command.class, label = "Batch Processor", initializer = "initScriptChoice", menuPath = "Process>Batch>SciJava Batch Processor")
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public class BatchProcessor extends DynamicCommand {
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// -- Parameters --
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@Parameter
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private LogService log;
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@Parameter
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private ModuleService modules;
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@Parameter
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private ScriptService scripts;
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@Parameter(label = "Input directory", style = "directory")
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private File inputFolder;
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@Parameter(label = "Script to run")
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private String scriptChoice;
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// -- Initializer methods --
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/**
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* Generate a list of all {@link ScriptInfo} objects that take a
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* {@link File} input, and populate the parameter choices with their
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* identifiers.
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*/
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protected void initScriptChoice() {
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MutableModuleItem<String> input = getInfo().getMutableInput("scriptChoice", String.class);
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List<String> choices = new ArrayList<>();
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for (ScriptInfo script : scripts.getScripts()) {
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try {
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if (modules.getSingleInput(script.createModule(), File.class) != null) {
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choices.add(script.getIdentifier());
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// choices.add(script.getPath());
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// TODO create map with readable names and modules
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}
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} catch (ModuleException exc) {
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log.warn("Could not create module for script: ", exc);
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}
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}
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input.setChoices(choices);
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}
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// -- Main method --
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@Override
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public void run() {
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ModuleInfo moduleInfo = modules.getModuleById(scriptChoice);
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ScriptModule module;
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try {
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module = (ScriptModule) moduleInfo.createModule();
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} catch (ModuleException exc) {
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log.error("Error during module creation", exc);
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return;
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}
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module.setContext(getContext());
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ModuleItem<File> fileInput = modules.getSingleInput(module, File.class);
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for (File file : inputFolder.listFiles()) {
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fileInput.setValue(module, file);
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module.resolveInput(fileInput.getName());
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Future<Module> instance = modules.run(module, true);
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try {
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log.info(instance.get());
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} catch (InterruptedException exc) {
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log.error("Error: interrupted module execution", exc);
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return;
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} catch (ExecutionException exc) {
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log.error("Error during module execution", exc);
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// continue loop
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}
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}
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}
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/** Test the batch processor. */
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public static void main(final String... args) throws Exception {
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// Launch ImageJ as usual.
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final ImageJ ij = net.imagej.Main.launch(args);
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ij.command().run(BatchProcessor.class, true);
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}
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}

‎src/main/resources/scripts/Testing/Test_Script.groovy‎

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#!groovy
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#@File inputFile
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#@String name
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#@LogService log
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log.info("Hello $name, now processing $inputFile")

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