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Michele De Bonis 2024-11-05 10:35:15 +01:00
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<recent name="$PROJECT_DIR$/dhp-raid/src/main/scala/eu/dnetlib/raid/clustering/dbscan" />
<recent name="$PROJECT_DIR$/src/main/scala" />
<recent name="$PROJECT_DIR$/src/main/scala/eu/dnetlib/walker" />
</key>
</component>
<component name="RunManager" selected="JUnit.RAiDInferenceTest">
<configuration name="Main" type="Application" factoryName="Application" temporary="true" nameIsGenerated="true">
<option name="MAIN_CLASS_NAME" value="org.example.Main" />
<module name="dhp-raid" />
<extension name="coverage">
<pattern>
<option name="PATTERN" value="org.example.*" />
<option name="ENABLED" value="true" />
</pattern>
</extension>
<method v="2">
<option name="Make" enabled="true" />
</method>
</configuration>
<configuration name="RAiDInferenceTest" type="JUnit" factoryName="JUnit" temporary="true" nameIsGenerated="true">
<module name="dhp-raid" />
<extension name="coverage">
<pattern>
<option name="PATTERN" value="eu.dnetlib.raid.*" />
<option name="ENABLED" value="true" />
</pattern>
</extension>
<option name="PACKAGE_NAME" value="eu.dnetlib.raid" />
<option name="MAIN_CLASS_NAME" value="eu.dnetlib.raid.RAiDInferenceTest" />
<option name="TEST_OBJECT" value="class" />
<method v="2">
<option name="Make" enabled="true" />
</method>
</configuration>
<configuration name="RAiDInferenceTest.createClusters" type="JUnit" factoryName="JUnit" temporary="true" nameIsGenerated="true">
<module name="dhp-raid" />
<extension name="coverage">
<pattern>
<option name="PATTERN" value="eu.dnetlib.raid.*" />
<option name="ENABLED" value="true" />
</pattern>
</extension>
<option name="PACKAGE_NAME" value="eu.dnetlib.raid" />
<option name="MAIN_CLASS_NAME" value="eu.dnetlib.raid.RAiDInferenceTest" />
<option name="METHOD_NAME" value="createClusters" />
<option name="TEST_OBJECT" value="method" />
<method v="2">
<option name="Make" enabled="true" />
</method>
</configuration>
<configuration name="RAiDInferenceTest.createRAiDEmbeddingsTest" type="JUnit" factoryName="JUnit" temporary="true" nameIsGenerated="true">
<module name="dhp-raid" />
<extension name="coverage">
<pattern>
<option name="PATTERN" value="eu.dnetlib.raid.*" />
<option name="ENABLED" value="true" />
</pattern>
</extension>
<option name="PACKAGE_NAME" value="eu.dnetlib.raid" />
<option name="MAIN_CLASS_NAME" value="eu.dnetlib.raid.RAiDInferenceTest" />
<option name="METHOD_NAME" value="createRAiDEmbeddingsTest" />
<option name="TEST_OBJECT" value="method" />
<method v="2">
<option name="Make" enabled="true" />
</method>
</configuration>
<recent_temporary>
<list>
<item itemvalue="JUnit.RAiDInferenceTest" />
<item itemvalue="JUnit.RAiDInferenceTest.createClusters" />
<item itemvalue="JUnit.RAiDInferenceTest.createRAiDEmbeddingsTest" />
<item itemvalue="Application.Main" />
</list>
</recent_temporary>
</component>
<component name="SpellCheckerSettings" RuntimeDictionaries="0" Folders="0" CustomDictionaries="0" DefaultDictionary="application-level" UseSingleDictionary="true" transferred="true" />
<component name="TaskManager">
<task active="true" id="Default" summary="Default task">
<changelist id="67528cef-c396-4288-9c84-8cedea88df9c" name="Changes" comment="" />
<created>1729084633471</created>
<option name="number" value="Default" />
<option name="presentableId" value="Default" />
<updated>1729084633471</updated>
<workItem from="1729084634987" duration="21063000" />
<workItem from="1729257864565" duration="95390000" />
<workItem from="1730275959282" duration="35702000" />
</task>
<servers />
</component>
<component name="TypeScriptGeneratedFilesManager">
<option name="version" value="3" />
</component>
</project>

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Module utilized by `dhp-workflows`.
Contains all required resources by this parent module:
* assembly XML definitions
* build shell scripts
* oozie package commands for uploading, running and monitoring oozie workflows

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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>eu.dnetlib</groupId>
<artifactId>dhp-build</artifactId>
<version>1.0.0-SNAPSHOT</version>
</parent>
<artifactId>dhp-build-assembly-resources</artifactId>
<packaging>jar</packaging>
<description>This module contains a set of scripts supporting the build lifecycle for the dnet-hadoop project</description>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>${maven.compiler.plugin.version}</version>
</plugin>
</plugins>
</build>
</project>

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dhp-build/dhp-build-assembly-resources/src/main/resources/assemblies/oozie-installer.xml Normal file
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<assembly
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
<id>oozie-installer</id>
<formats>
<format>dir</format>
</formats>
<fileSets>
<fileSet>
<filtered>true</filtered>
<directory>${project.build.directory}/assembly-resources/commands</directory>
<!--
dziala dla (lokalnie zasoby modulu):
<directory>src/main/resources</directory>
nie dziala dla:
<directory>classpath:/commands</directory>
<directory>commands</directory>
<directory>classpath/src/main/resources</directory>
-->
<outputDirectory>/</outputDirectory>
<includes>
<include>**/*</include>
</includes>
<fileMode>0755</fileMode>
<lineEnding>unix</lineEnding>
</fileSet>
</fileSets>
<baseDirectory>/</baseDirectory>
</assembly>

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<assembly
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
<id>tests</id>
<formats>
<format>jar</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<fileSets>
<fileSet>
<directory>${project.build.testOutputDirectory}
</directory>
<outputDirectory />
</fileSet>
</fileSets>
<!-- <dependencySets>
<dependencySet>
<useProjectArtifact>false</useProjectArtifact>
<outputDirectory>lib</outputDirectory>
</dependencySet>
</dependencySets>-->
</assembly>

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dhp-build/dhp-build-assembly-resources/src/main/resources/commands/get_working_dir.sh Normal file
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#!/bin/bash
hadoop fs -get ${workingDir}

5
dhp-build/dhp-build-assembly-resources/src/main/resources/commands/print_working_dir.sh Normal file
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#!/bin/bash
echo ""
echo "---->Contents of the working directory"
hadoop fs -ls ${workingDir}

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dhp-build/dhp-build-assembly-resources/src/main/resources/commands/readme.markdown Normal file
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Execute the scripts in the following order:
1. `upload_workflow.sh`
2. `run_workflow.sh`
3. `print_working_dir.sh` or `get_working_dir.sh`

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dhp-build/dhp-build-assembly-resources/src/main/resources/commands/run_workflow.sh Normal file
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#!/bin/bash
if [ $# = 0 ] ; then
oozie job -oozie ${oozieServiceLoc} -config job.properties -run
else
oozie job -oozie ${oozieServiceLoc} -config $1/job.properties -run
fi

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dhp-build/dhp-build-assembly-resources/src/main/resources/commands/upload_workflow.sh Normal file
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#!/bin/bash
exec 3>&1
BASH_XTRACEFD=3
set -x ## print every executed command
if [ $# = 0 ] ; then
target_dir_root=`pwd`'/${oozieAppDir}'
else
target_dir_root=`readlink -f $1`'/${oozieAppDir}'
fi
# initial phase, creating symbolic links to jars in all subworkflows
# currently disabled
#libDir=$target_dir_root'/lib'
#dirs=`find $target_dir_root/* -maxdepth 10 -type d`
#for dir in $dirs
#do
# if [ -f $dir/workflow.xml ]
# then
# echo "creating symbolic links to jars in directory: $dir/lib"
# if [ ! -d "$dir/lib" ]; then
# mkdir $dir/lib
# fi
# find $libDir -type f -exec ln -s \{\} $dir/lib \;
# fi
#done
#uploading
hadoop fs -rm -r ${sandboxDir}
hadoop fs -mkdir -p ${sandboxDir}
hadoop fs -mkdir -p ${workingDir}
hadoop fs -put $target_dir_root ${sandboxDir}

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dhp-build/dhp-build-assembly-resources/src/main/resources/project-default.properties Normal file
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#sandboxName when not provided explicitly will be generated
sandboxName=${sandboxName}
sandboxDir=/user/${dhp.hadoop.frontend.user.name}/${sandboxName}
workingDir=${sandboxDir}/working_dir
oozie.wf.application.path = ${nameNode}${sandboxDir}/${oozieAppDir}
oozieTopWfApplicationPath = ${oozie.wf.application.path}

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dhp-build/dhp-build-properties-maven-plugin/README.markdown Normal file
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Maven plugin module utilized by `dhp-workflows` for proper `job.properties` file building.
It is based on http://site.kuali.org/maven/plugins/properties-maven-plugin/1.3.2/write-project-properties-mojo.html and supplemented with:
* handling includePropertyKeysFromFiles property allowing writing only properties listed in given property files
As a final outcome only properties listed in `<include>` element and listed as a keys in files from `<includePropertyKeysFromFiles>` element will be written to output file.

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dhp-build/dhp-build-properties-maven-plugin/pom.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>eu.dnetlib</groupId>
<artifactId>dhp-build</artifactId>
<version>1.0.0-SNAPSHOT</version>
</parent>
<artifactId>dhp-build-properties-maven-plugin</artifactId>
<version>1.0.0-SNAPSHOT</version>
<packaging>maven-plugin</packaging>
<description>This module is a maven plugin implementing custom properties substitutions in the build lifecycle</description>
<dependencies>
<dependency>
<groupId>org.apache.maven</groupId>
<artifactId>maven-plugin-api</artifactId>
<version>3.6.3</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.maven</groupId>
<artifactId>maven-project</artifactId>
<version>2.2.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.maven</groupId>
<artifactId>maven-artifact</artifactId>
<version>2.2.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.kuali.maven.plugins</groupId>
<artifactId>properties-maven-plugin</artifactId>
<version>${properties.maven.plugin.version}</version>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>annotations</artifactId>
<version>3.0.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>3.0.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>${mockito-core.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<version>${mockito-core.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<directory>target</directory>
<outputDirectory>target/classes</outputDirectory>
<finalName>${project.artifactId}-${project.version}</finalName>
<testOutputDirectory>target/test-classes</testOutputDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>${maven.compiler.plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<id>attach-sources</id>
<phase>verify</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<configuration>
<detectLinks>true</detectLinks>
<!--<doclint>none</doclint>-->
</configuration>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-plugin-plugin</artifactId>
<version>3.2</version>
<configuration>
<skipErrorNoDescriptorsFound>true</skipErrorNoDescriptorsFound>
</configuration>
<executions>
<execution>
<id>mojo-descriptor</id>
<phase>process-classes</phase>
<goals>
<goal>descriptor</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>

76
dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojo.java Normal file
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package eu.dnetlib.maven.plugin.properties;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.maven.plugin.AbstractMojo;
import org.apache.maven.plugin.MojoExecutionException;
import org.apache.maven.plugin.MojoFailureException;
/**
* Generates oozie properties which were not provided from commandline.
*
* @author mhorst
* @goal generate-properties
*/
public class GenerateOoziePropertiesMojo extends AbstractMojo {
public static final String PROPERTY_NAME_WF_SOURCE_DIR = "workflow.source.dir";
public static final String PROPERTY_NAME_SANDBOX_NAME = "sandboxName";
private final String[] limiters = {
"dhp", "dnetlib", "eu"
};
@Override
public void execute() throws MojoExecutionException, MojoFailureException {
if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR)
&& !System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) {
String generatedSandboxName = generateSandboxName(
System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR));
if (generatedSandboxName != null) {
System.getProperties().setProperty(PROPERTY_NAME_SANDBOX_NAME, generatedSandboxName);
} else {
System.out
.println(
"unable to generate sandbox name from path: "
+ System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR));
}
}
}
/**
* Generates sandbox name from workflow source directory.
*
* @param wfSourceDir
* @return generated sandbox name
*/
private String generateSandboxName(String wfSourceDir) {
// utilize all dir names until finding one of the limiters
List<String> sandboxNameParts = new ArrayList<String>();
String[] tokens = StringUtils.split(wfSourceDir, File.separatorChar);
ArrayUtils.reverse(tokens);
if (tokens.length > 0) {
for (String token : tokens) {
for (String limiter : limiters) {
if (limiter.equals(token)) {
return sandboxNameParts.size() > 0
? StringUtils.join(sandboxNameParts.toArray())
: null;
}
}
if (sandboxNameParts.size() > 0) {
sandboxNameParts.add(0, File.separator);
}
sandboxNameParts.add(0, token);
}
return StringUtils.join(sandboxNameParts.toArray());
} else {
return null;
}
}
}

447
dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectProperties.java Normal file
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/**
* Licensed under the Educational Community 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
*
* <p>http://www.opensource.org/licenses/ecl2.php
*
* <p>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.
*/
package eu.dnetlib.maven.plugin.properties;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.Map.Entry;
import java.util.Properties;
import java.util.Set;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.maven.plugin.AbstractMojo;
import org.apache.maven.plugin.MojoExecutionException;
import org.apache.maven.plugin.MojoFailureException;
import org.apache.maven.project.MavenProject;
import org.springframework.core.io.DefaultResourceLoader;
import org.springframework.core.io.Resource;
import org.springframework.core.io.ResourceLoader;
import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
/**
* Writes project properties for the keys listed in specified properties files. Based on:
* http://site.kuali.org/maven/plugins/properties-maven-plugin/2.0.1/write-project-properties-mojo.html
*
* @author mhorst
* @goal write-project-properties
*/
public class WritePredefinedProjectProperties extends AbstractMojo {
private static final String CR = "\r";
private static final String LF = "\n";
private static final String TAB = "\t";
protected static final String PROPERTY_PREFIX_ENV = "env.";
private static final String ENCODING_UTF8 = "utf8";
/** @parameter property="properties.includePropertyKeysFromFiles" */
private String[] includePropertyKeysFromFiles;
/**
* @parameter default-value="${project}"
* @required
* @readonly
*/
protected MavenProject project;
/**
* The file that properties will be written to
*
* @parameter property="properties.outputFile"
* default-value="${project.build.directory}/properties/project.properties";
* @required
*/
protected File outputFile;
/**
* If true, the plugin will silently ignore any non-existent properties files, and the build will continue
*
* @parameter property="properties.quiet" default-value="true"
*/
private boolean quiet;
/**
* Comma separated list of characters to escape when writing property values. cr=carriage return, lf=linefeed,
* tab=tab. Any other values are taken literally.
*
* @parameter default-value="cr,lf,tab" property="properties.escapeChars"
*/
private String escapeChars;
/**
* If true, the plugin will include system properties when writing the properties file. System properties override
* both environment variables and project properties.
*
* @parameter default-value="false" property="properties.includeSystemProperties"
*/
private boolean includeSystemProperties;
/**
* If true, the plugin will include environment variables when writing the properties file. Environment variables
* are prefixed with "env". Environment variables override project properties.
*
* @parameter default-value="false" property="properties.includeEnvironmentVariables"
*/
private boolean includeEnvironmentVariables;
/**
* Comma separated set of properties to exclude when writing the properties file
*
* @parameter property="properties.exclude"
*/
private String exclude;
/**
* Comma separated set of properties to write to the properties file. If provided, only the properties matching
* those supplied here will be written to the properties file.
*
* @parameter property="properties.include"
*/
private String include;
/*
* (non-Javadoc)
* @see org.apache.maven.plugin.AbstractMojo#execute()
*/
@Override
@SuppressFBWarnings({
"NP_UNWRITTEN_FIELD", "UWF_UNWRITTEN_FIELD"
})
public void execute() throws MojoExecutionException, MojoFailureException {
Properties properties = new Properties();
// Add project properties
properties.putAll(project.getProperties());
if (includeEnvironmentVariables) {
// Add environment variables, overriding any existing properties with the same key
properties.putAll(getEnvironmentVariables());
}
if (includeSystemProperties) {
// Add system properties, overriding any existing properties with the same key
properties.putAll(System.getProperties());
}
// Remove properties as appropriate
trim(properties, exclude, include);
String comment = "# " + new Date() + "\n";
List<String> escapeTokens = getEscapeChars(escapeChars);
getLog().info("Creating " + outputFile);
writeProperties(outputFile, comment, properties, escapeTokens);
}
/**
* Provides environment variables.
*
* @return environment variables
*/
protected static Properties getEnvironmentVariables() {
Properties props = new Properties();
for (Entry<String, String> entry : System.getenv().entrySet()) {
props.setProperty(PROPERTY_PREFIX_ENV + entry.getKey(), entry.getValue());
}
return props;
}
/**
* Removes properties which should not be written.
*
* @param properties
* @param omitCSV
* @param includeCSV
* @throws MojoExecutionException
*/
protected void trim(Properties properties, String omitCSV, String includeCSV)
throws MojoExecutionException {
List<String> omitKeys = getListFromCSV(omitCSV);
for (String key : omitKeys) {
properties.remove(key);
}
List<String> includeKeys = getListFromCSV(includeCSV);
// mh: including keys from predefined properties
if (includePropertyKeysFromFiles != null && includePropertyKeysFromFiles.length > 0) {
for (String currentIncludeLoc : includePropertyKeysFromFiles) {
if (validate(currentIncludeLoc)) {
Properties p = getProperties(currentIncludeLoc);
for (String key : p.stringPropertyNames()) {
includeKeys.add(key);
}
}
}
}
if (includeKeys != null && !includeKeys.isEmpty()) {
// removing only when include keys provided
Set<String> keys = properties.stringPropertyNames();
for (String key : keys) {
if (!includeKeys.contains(key)) {
properties.remove(key);
}
}
}
}
/**
* Checks whether file exists.
*
* @param location
* @return true when exists, false otherwise.
*/
protected boolean exists(String location) {
if (StringUtils.isBlank(location)) {
return false;
}
File file = new File(location);
if (file.exists()) {
return true;
}
ResourceLoader loader = new DefaultResourceLoader();
Resource resource = loader.getResource(location);
return resource.exists();
}
/**
* Validates resource location.
*
* @param location
* @return true when valid, false otherwise
* @throws MojoExecutionException
*/
protected boolean validate(String location) throws MojoExecutionException {
boolean exists = exists(location);
if (exists) {
return true;
}
if (quiet) {
getLog().info("Ignoring non-existent properties file '" + location + "'");
return false;
} else {
throw new MojoExecutionException("Non-existent properties file '" + location + "'");
}
}
/**
* Provides input stream.
*
* @param location
* @return input stream
* @throws IOException
*/
protected InputStream getInputStream(String location) throws IOException {
File file = new File(location);
if (file.exists()) {
return new FileInputStream(location);
}
ResourceLoader loader = new DefaultResourceLoader();
Resource resource = loader.getResource(location);
return resource.getInputStream();
}
/**
* Creates properties for given location.
*
* @param location
* @return properties for given location
* @throws MojoExecutionException
*/
protected Properties getProperties(String location) throws MojoExecutionException {
InputStream in = null;
try {
Properties properties = new Properties();
in = getInputStream(location);
if (location.toLowerCase().endsWith(".xml")) {
properties.loadFromXML(in);
} else {
properties.load(in);
}
return properties;
} catch (IOException e) {
throw new MojoExecutionException("Error reading properties file " + location, e);
} finally {
IOUtils.closeQuietly(in);
}
}
/**
* Provides escape characters.
*
* @param escapeChars
* @return escape characters
*/
protected List<String> getEscapeChars(String escapeChars) {
List<String> tokens = getListFromCSV(escapeChars);
List<String> realTokens = new ArrayList<String>();
for (String token : tokens) {
String realToken = getRealToken(token);
realTokens.add(realToken);
}
return realTokens;
}
/**
* Provides real token.
*
* @param token
* @return real token
*/
protected String getRealToken(String token) {
if (token.equalsIgnoreCase("CR")) {
return CR;
} else if (token.equalsIgnoreCase("LF")) {
return LF;
} else if (token.equalsIgnoreCase("TAB")) {
return TAB;
} else {
return token;
}
}
/**
* Returns content.
*
* @param comment
* @param properties
* @param escapeTokens
* @return content
*/
protected String getContent(String comment, Properties properties, List<String> escapeTokens) {
List<String> names = new ArrayList<String>(properties.stringPropertyNames());
Collections.sort(names);
StringBuilder sb = new StringBuilder();
if (!StringUtils.isBlank(comment)) {
sb.append(comment);
}
for (String name : names) {
String value = properties.getProperty(name);
String escapedValue = escape(value, escapeTokens);
sb.append(name + "=" + escapedValue + "\n");
}
return sb.toString();
}
/**
* Writes properties to given file.
*
* @param file
* @param comment
* @param properties
* @param escapeTokens
* @throws MojoExecutionException
*/
protected void writeProperties(
File file, String comment, Properties properties, List<String> escapeTokens)
throws MojoExecutionException {
try {
String content = getContent(comment, properties, escapeTokens);
FileUtils.writeStringToFile(file, content, ENCODING_UTF8);
} catch (IOException e) {
throw new MojoExecutionException("Error creating properties file", e);
}
}
/**
* Escapes characters.
*
* @param s
* @param escapeChars
* @return
*/
protected String escape(String s, List<String> escapeChars) {
String result = s;
for (String escapeChar : escapeChars) {
result = result.replace(escapeChar, getReplacementToken(escapeChar));
}
return result;
}
/**
* Provides replacement token.
*
* @param escapeChar
* @return replacement token
*/
protected String getReplacementToken(String escapeChar) {
if (escapeChar.equals(CR)) {
return "\\r";
} else if (escapeChar.equals(LF)) {
return "\\n";
} else if (escapeChar.equals(TAB)) {
return "\\t";
} else {
return "\\" + escapeChar;
}
}
/**
* Returns list from csv.
*
* @param csv
* @return list of values generated from CSV
*/
protected static final List<String> getListFromCSV(String csv) {
if (StringUtils.isBlank(csv)) {
return new ArrayList<String>();
}
List<String> list = new ArrayList<String>();
String[] tokens = StringUtils.split(csv, ",");
for (String token : tokens) {
list.add(token.trim());
}
return list;
}
public void setIncludeSystemProperties(boolean includeSystemProperties) {
this.includeSystemProperties = includeSystemProperties;
}
public void setEscapeChars(String escapeChars) {
this.escapeChars = escapeChars;
}
public void setIncludeEnvironmentVariables(boolean includeEnvironmentVariables) {
this.includeEnvironmentVariables = includeEnvironmentVariables;
}
public void setExclude(String exclude) {
this.exclude = exclude;
}
public void setInclude(String include) {
this.include = include;
}
public void setQuiet(boolean quiet) {
this.quiet = quiet;
}
/**
* Sets property files for which keys properties should be included.
*
* @param includePropertyKeysFromFiles
*/
public void setIncludePropertyKeysFromFiles(String[] includePropertyKeysFromFiles) {
if (includePropertyKeysFromFiles != null) {
this.includePropertyKeysFromFiles = Arrays
.copyOf(includePropertyKeysFromFiles, includePropertyKeysFromFiles.length);
}
}
}

108
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojoTest.java Normal file
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package eu.dnetlib.maven.plugin.properties;
import static eu.dnetlib.maven.plugin.properties.GenerateOoziePropertiesMojo.PROPERTY_NAME_SANDBOX_NAME;
import static eu.dnetlib.maven.plugin.properties.GenerateOoziePropertiesMojo.PROPERTY_NAME_WF_SOURCE_DIR;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
import org.junit.jupiter.api.*;
/** @author mhorst, claudio.atzori */
public class GenerateOoziePropertiesMojoTest {
private static final GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
public void clearSystemProperties() {
System.clearProperty(PROPERTY_NAME_SANDBOX_NAME);
System.clearProperty(PROPERTY_NAME_WF_SOURCE_DIR);
}
@Test
public void testExecuteEmpty() throws Exception {
clearSystemProperties();
// execute
mojo.execute();
// assert
assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
@Test
public void testExecuteSandboxNameAlreadySet() throws Exception {
clearSystemProperties();
// given
String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
String sandboxName = "originalSandboxName";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
System.setProperty(PROPERTY_NAME_SANDBOX_NAME, sandboxName);
// execute
mojo.execute();
// assert
assertEquals(sandboxName, System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
@Test //fails
public void testExecuteEmptyWorkflowSourceDir() throws Exception {
clearSystemProperties();
// given
String workflowSourceDir = "";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
// execute
mojo.execute();
// assert
assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
@Test
public void testExecuteNullSandboxNameGenerated() throws Exception {
clearSystemProperties();
// given
String workflowSourceDir = "eu/dnetlib/dhp/";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
// execute
mojo.execute();
// assert
assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
@Test
public void testExecute() throws Exception {
clearSystemProperties();
// given
String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
// execute
mojo.execute();
// assert
assertEquals("wf/transformers", System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
@Test
public void testExecuteWithoutRoot() throws Exception {
clearSystemProperties();
// given
String workflowSourceDir = "wf/transformers";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
// execute
mojo.execute();
// assert
assertEquals("wf/transformers", System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
}

391
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java Normal file
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package eu.dnetlib.maven.plugin.properties;
import static eu.dnetlib.maven.plugin.properties.WritePredefinedProjectProperties.PROPERTY_PREFIX_ENV;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.doReturn;
import static org.mockito.Mockito.lenient;
import java.io.*;
import java.util.Properties;
import org.apache.maven.plugin.MojoExecutionException;
import org.apache.maven.project.MavenProject;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.api.io.TempDir;
import org.mockito.Mock;
import org.mockito.MockitoAnnotations;
import org.mockito.junit.jupiter.MockitoExtension;
/** @author mhorst, claudio.atzori */
@Disabled
@ExtendWith(MockitoExtension.class)
public class WritePredefinedProjectPropertiesTest {
@Mock
private MavenProject mavenProject;
private WritePredefinedProjectProperties mojo;
@TempDir File testFolder;
public void init(File testFolder) {
MockitoAnnotations.initMocks(this);
mojo = new WritePredefinedProjectProperties();
mojo.outputFile = getPropertiesFileLocation(testFolder);
mojo.project = mavenProject;
lenient().doReturn(new Properties()).when(mavenProject).getProperties();
}
// ----------------------------------- TESTS ---------------------------------------------
@Test
public void testExecuteEmpty() throws Exception {
init(testFolder);
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile());
assertEquals(0, storedProperties.size());
}
@Test
public void testExecuteWithProjectProperties() throws Exception {
init(testFolder);
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
doReturn(projectProperties).when(mavenProject).getProperties();
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile());
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
@Test()
public void testExecuteWithProjectPropertiesAndInvalidOutputFile(@TempDir File testFolder) {
init(testFolder);
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.outputFile = testFolder;
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws Exception {
init(testFolder);
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String excludedKey = "excludedPropertyKey";
String excludedValue = "excludedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(excludedKey, excludedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.setExclude(excludedKey);
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
@Test
public void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) throws Exception {
init(testFolder);
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.setInclude(includedKey);
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test
public void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) throws Exception {
init(testFolder);
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
File includedPropertiesFile = new File(testFolder, "included.properties");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.store(new FileWriter(includedPropertiesFile), null);
mojo.setIncludePropertyKeysFromFiles(new String[] {
includedPropertiesFile.getAbsolutePath()
});
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test
public void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder)
throws Exception {
init(testFolder);
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo
.setIncludePropertyKeysFromFiles(
new String[] {
"/eu/dnetlib/maven/plugin/properties/included.properties"
});
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test
public void testExecuteIncludingPropertyKeysFromBlankLocation() {
init(testFolder);
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.setIncludePropertyKeysFromFiles(new String[] {
""
});
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder)
throws Exception {
init(testFolder);
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
File includedPropertiesFile = new File(testFolder, "included.xml");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.storeToXML(new FileOutputStream(includedPropertiesFile), null);
mojo.setIncludePropertyKeysFromFiles(new String[] {
includedPropertiesFile.getAbsolutePath()
});
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test
public void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder)
throws Exception {
init(testFolder);
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
File includedPropertiesFile = new File(testFolder, "included.xml");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.store(new FileOutputStream(includedPropertiesFile), null);
mojo.setIncludePropertyKeysFromFiles(new String[] {
includedPropertiesFile.getAbsolutePath()
});
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception {
init(testFolder);
// given
mojo.setQuiet(true);
mojo.setIncludePropertyKeysFromFiles(new String[] {
"invalid location"
});
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(0, storedProperties.size());
}
@Test
public void testExecuteIncludingPropertyKeysFromInvalidFile() {
init(testFolder);
// given
mojo.setIncludePropertyKeysFromFiles(new String[] {
"invalid location"
});
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
init(testFolder);
// given
mojo.setIncludeEnvironmentVariables(true);
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
for (Object currentKey : storedProperties.keySet()) {
assertTrue(((String) currentKey).startsWith(PROPERTY_PREFIX_ENV));
}
}
@Test
public void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception {
init(testFolder);
// given
String key = "systemPropertyKey";
String value = "systemPropertyValue";
System.setProperty(key, value);
mojo.setIncludeSystemProperties(true);
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
@Test
public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder)
throws Exception {
init(testFolder);
// given
String key = "systemPropertyKey ";
String value = "systemPropertyValue";
System.setProperty(key, value);
mojo.setIncludeSystemProperties(true);
String escapeChars = "cr,lf,tab,|";
mojo.setEscapeChars(escapeChars);
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
assertFalse(storedProperties.containsKey(key));
assertTrue(storedProperties.containsKey(key.trim()));
assertEquals(value, storedProperties.getProperty(key.trim()));
}
// ----------------------------------- PRIVATE -------------------------------------------
private File getPropertiesFileLocation(File testFolder) {
return new File(testFolder, "test.properties");
}
private Properties getStoredProperties(File testFolder)
throws IOException {
Properties properties = new Properties();
properties.load(new FileInputStream(getPropertiesFileLocation(testFolder)));
return properties;
}
}

1
dhp-build/dhp-build-properties-maven-plugin/src/test/resources/eu/dnetlib/maven/plugin/properties/included.properties Normal file
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includedPropertyKey=irrelevantValue

2
dhp-build/dhp-build-properties-maven-plugin/test.properties Normal file
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# Tue Nov 05 10:06:34 CET 2024
projectPropertyKey=projectPropertyValue

48
dhp-build/dhp-code-style/pom.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>eu.dnetlib</groupId>
<artifactId>dhp-code-style</artifactId>
<version>1.0.0-SNAPSHOT</version>
<packaging>jar</packaging>
<description>This module contains resources supporting common code style conventions</description>
<distributionManagement>
<snapshotRepository>
<id>dnet45-snapshots</id>
<name>DNet45 Snapshots</name>
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-snapshots</url>
<layout>default</layout>
</snapshotRepository>
<repository>
<id>dnet45-releases</id>
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
</repository>
</distributionManagement>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.7.1</version>
</plugin>
</plugins>
</pluginManagement>
</build>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
</project>

252
dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_aosp.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<profiles version="10">
<profile kind="CodeFormatterProfile" name="Android" version="10">
<setting id="org.eclipse.jdt.core.formatter.align_type_members_on_columns" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_assignment" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_binary_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_compact_if" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_conditional_expression" value="80"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_enum_constants" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_multiple_fields" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_imports" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_package" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_field" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_first_class_body_declaration" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_imports" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_member_type" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_method" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_package" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_between_type_declarations" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_array_initializer" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_block" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_block_in_case" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_constructor_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_enum_constant" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_method_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_switch" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_type_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.comment.clear_blank_lines" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_comments" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_header" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_html" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_source_code" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.indent_parameter_description" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.indent_root_tags" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.line_length" value="120"/>
<setting id="org.eclipse.jdt.core.formatter.compact_else_if" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.continuation_indentation" value="2"/>
<setting id="org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer" value="2"/>
<setting id="org.eclipse.jdt.core.formatter.format_guardian_clause_on_one_line" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_type_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_breaks_compare_to_cases" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_empty_lines" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.indent_statements_compare_to_block" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_statements_compare_to_body" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indentation.size" value="4"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_opening_brace_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_at_end_of_file_if_missing" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_catch_in_try_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_closing_brace_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_while_in_do_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_constant" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_method_body" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_and_in_type_parameter" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_assignment_operator" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation_type_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_binary_operator" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_parameters" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_closing_brace_in_block" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_closing_paren_in_cast" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_assert" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_case" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_for" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_labeled_statement" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_allocation_expression" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_annotation" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_parameters" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_throws" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_constant_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_explicitconstructorcall_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_increments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_inits" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_parameters" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_throws" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_invocation_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_field_declarations" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_parameterized_type_reference" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_superinterfaces" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_ellipsis" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_brace_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_cast" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_catch" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_constructor_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_enum_constant" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_for" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_if" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_invocation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_parenthesized_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_switch" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_synchronized" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_prefix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_question_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_question_in_wildcard" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_unary_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_and_in_type_parameter" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_assignment_operator" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_binary_operator" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_brace_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_cast" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_constructor_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_for" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_if" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_invocation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_parenthesized_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_switch" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_synchronized" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_assert" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_default" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_for" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_labeled_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_array_initializer" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_throws" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_constant_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_declarations" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_explicitconstructorcall_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_ellipsis" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_anonymous_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_block" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_constructor_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_constant" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_switch" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_catch" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_constructor_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_if" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_invocation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_while" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_return" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_prefix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_unary_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_brackets_in_array_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_brackets_in_array_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_constructor_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.lineSplit" value="100"/>
<setting id="org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.tabulation.char" value="tab"/>
<setting id="org.eclipse.jdt.core.formatter.tabulation.size" value="4"/>
<setting id="org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.join_wrapped_lines" value="false"/>
</profile>
</profiles>

727
dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_dnet.xml Normal file
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@ -0,0 +1,727 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<profiles version="18">
<profile kind="CodeFormatterProfile" name="Android_custom" version="18">
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_ellipsis" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.parentheses_positions_in_for_statment" value="common_lines"/>
<setting id="org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_logical_operator" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_parameters" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.parentheses_positions_in_method_invocation" value="common_lines"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_imports" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement" value="common_lines"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_javadoc_comments" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.indentation.size" value="4"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.parentheses_positions_in_enum_constant_declaration" value="common_lines"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_increments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_arrow_in_switch_default" value="insert"/>
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</profile>
</profiles>

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dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_google.xml Normal file
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<profiles version="13">
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<setting id="org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode" value="enabled"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_field" value="1585"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_html" value="true"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer.count_dependent" value="16|5|80"/>
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<setting id="org.eclipse.jdt.core.formatter.comment.format_source_code" value="true"/>
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</profile>
</profiles>

30
dhp-build/pom.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>eu.dnetlib</groupId>
<artifactId>raid-inference</artifactId>
<version>1.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>dhp-build</artifactId>
<packaging>pom</packaging>
<description>This module is a container for the build tools used in dnet-hadoop</description>
<modules>
<module>dhp-code-style</module>
<module>dhp-build-assembly-resources</module>
<module>dhp-build-properties-maven-plugin</module>
</modules>
<pluginRepositories>
<pluginRepository>
<id>iis-releases</id>
<name>iis releases plugin repository</name>
<url>http://maven.ceon.pl/artifactory/iis-releases</url>
<layout>default</layout>
</pluginRepository>
</pluginRepositories>
</project>

6
dhp-raid/job-override.properties Normal file
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graphBasePath = /tmp/beta_provision/graph/06_graph_inferred
workingPath = /user/michele.debonis/raid_inference_test/working_dir
clustersPath = /user/michele.debonis/raid_inference_test/clusters
embeddingsPath = /user/michele.debonis/raid_inference_test/embeddings
raidConfPath = /user/michele.debonis/raid.conf.json
numPartitions = 1000

545
dhp-raid/pom.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>eu.dnetlib</groupId>
<artifactId>raid-inference</artifactId>
<version>1.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>dhp-raid</artifactId>
<version>1.0-SNAPSHOT</version>
<properties>
<java.version>1.8</java.version>
<scala.binary.version>2.11</scala.binary.version>
<scala.version>2.11.0</scala.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<scalatest.version>2.2.6</scalatest.version>
<encoding>UTF-8</encoding>
<hadoop-version>2.7.3</hadoop-version>
<spark.version>2.3.2</spark.version>
<redis.version>2.8.1</redis.version>
<dhp-schemas.version>8.0.1</dhp-schemas.version>
</properties>
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.binary.version}</artifactId>
<version>${spark.version}</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_${scala.binary.version}</artifactId>
<version>${spark.version}</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-mllib_${scala.binary.version}</artifactId>
<version>${spark.version}</version>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>${scala.version}</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>RELEASE</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
<version>2.4.0</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<version>${dhp-schemas.version}</version>
</dependency>
<dependency>
<groupId>de.lmu.ifi.dbs.elki</groupId>
<artifactId>elki</artifactId>
</dependency>
<dependency>
<groupId>com.github.haifengl</groupId>
<artifactId>smile-core</artifactId>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.4.4</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>process-resources</phase>
<goals>
<goal>compile</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<profiles>
<profile>
<id>oozie-package</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>1.4.1</version>
<executions>
<execution>
<id>enforce-connection-properties-file-existence</id>
<phase>initialize</phase>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireFilesExist>
<files>
<file>${dhpConnectionProperties}</file>
</files>
<message>
The file with connection properties could not be found. Please, create the ${dhpConnectionProperties} file or set the location to another already created file by using
-DdhpConnectionProperties property.
</message>
</requireFilesExist>
</rules>
<fail>true</fail>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy dependencies</id>
<phase>prepare-package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<includeScope>${oozie.package.dependencies.include.scope}</includeScope>
<excludeScope>${oozie.package.dependencies.exclude.scope}</excludeScope>
<silent>true</silent>
</configuration>
</execution>
</executions>
</plugin>
<!-- Plugin originally defined in attach-test-resources It was moved here to ensure that it will execute before priming -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<executions>
<execution>
<id>attach-test-resources-package</id>
<phase>prepare-package</phase>
<goals>
<goal>test-jar</goal>
</goals>
<configuration>
<skip>${oozie.package.skip.test.jar}</skip>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>eu.dnetlib.primer</groupId>
<artifactId>primer-maven-plugin</artifactId>
<version>1.2.0</version>
<executions>
<execution>
<id>priming</id>
<phase>prepare-package</phase>
<goals>
<goal>prime</goal>
</goals>
<configuration>
<classProviderFiles>
<classProviderFile>${project.build.directory}/dependency/*.jar</classProviderFile>
<classProviderFile>${project.build.directory}/*-tests.jar</classProviderFile>
<classProviderFile>${project.build.directory}/classes</classProviderFile>
</classProviderFiles>
<coansysPackageDir>${project.build.directory}/dependency</coansysPackageDir>
<destination>${project.build.directory}/${primed.dir}</destination>
<classpath>${workflow.source.dir}</classpath>
</configuration>
</execution>
</executions>
</plugin>
<!-- reading job.properties to use them in .sh scripts -->
<plugin>
<groupId>org.kuali.maven.plugins</groupId>
<artifactId>properties-maven-plugin</artifactId>
<version>${properties.maven.plugin.version}</version>
<dependencies>
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dhp-build-assembly-resources</artifactId>
<version>1.0.0-SNAPSHOT</version>
<!-- contains project-default.properties -->
</dependency>
</dependencies>
<executions>
<execution>
<id>reading-dhp-properties</id>
<phase>initialize</phase>
<goals>
<goal>read-project-properties</goal>
</goals>
<configuration>
<locations>
<location>${dhpConnectionProperties}</location>
</locations>
<quiet>false</quiet>
</configuration>
</execution>
<execution>
<id>read-default-properties</id>
<phase>prepare-package</phase>
<goals>
<goal>read-project-properties</goal>
</goals>
<configuration>
<locations>
<location>classpath:project-default.properties</location>
</locations>
<quiet>true</quiet>
</configuration>
</execution>
<execution>
<id>read-job-properties</id>
<phase>prepare-package</phase>
<goals>
<goal>read-project-properties</goal>
</goals>
<configuration>
<locations>
<param>${project.build.directory}/${primed.dir}/job.properties</param>
<param>job-override.properties</param>
</locations>
<quiet>true</quiet>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>eu.dnetlib</groupId>
<artifactId>dhp-build-properties-maven-plugin</artifactId>
<version>1.0.0-SNAPSHOT</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>generate-properties</goal>
<!-- generates sandboxName based on workflow.source.dir when not specified as commandline parameter -->
</goals>
<configuration>
</configuration>
</execution>
<execution>
<id>write-job-properties</id>
<phase>prepare-package</phase>
<goals>
<goal>write-project-properties</goal>
</goals>
<configuration>
<outputFile>target/${oozie.package.file.name}/job.properties</outputFile>
<!-- notice: dots are not allowed for job.properties! -->
<include>nameNode,jobTracker,queueName,importerQueueName,oozieLauncherQueueName,
workingDir,oozieTopWfApplicationPath,oozieServiceLoc,
sparkDriverMemory,sparkExecutorMemory,sparkExecutorCores,
oozie.wf.application.path,projectVersion,oozie.use.system.libpath,
oozieActionShareLibForSpark1,spark1YarnHistoryServerAddress,spark1EventLogDir,
oozieActionShareLibForSpark2,spark2YarnHistoryServerAddress,spark2EventLogDir,
sparkSqlWarehouseDir
</include>
<includeSystemProperties>true</includeSystemProperties>
<includePropertyKeysFromFiles>
<!-- <param>${workflow.source.dir}/job.properties</param> -->
<param>${project.build.directory}/${primed.dir}/job.properties</param>
<param>job-override.properties</param>
</includePropertyKeysFromFiles>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<version>2.1.11</version>
<executions>
<execution>
<goals>
<goal>revision</goal>
</goals>
</execution>
</executions>
<configuration>
<verbose>true</verbose>
<dateFormat>yyyy-MM-dd'T'HH:mm:ssZ</dateFormat>
<generateGitPropertiesFile>true</generateGitPropertiesFile>
<generateGitPropertiesFilename>target/${oozie.package.file.name}/${oozieAppDir}/version.properties</generateGitPropertiesFilename>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.0.0</version>
<dependencies>
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dhp-build-assembly-resources</artifactId>
<version>1.0.0-SNAPSHOT</version>
</dependency>
</dependencies>
<executions>
<execution>
<id>assembly-oozie-installer</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<finalName>${oozie.package.file.name}_shell_scripts</finalName>
<descriptorRefs>
<descriptorRef>oozie-installer</descriptorRef>
</descriptorRefs>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<!-- this plugin prepares oozie installer package-->
<artifactId>maven-antrun-plugin</artifactId>
<executions>
<!-- extracting shared resources phase -->
<execution>
<id>installer-copy-custom</id>
<phase>process-resources</phase>
<goals>
<goal>run</goal>
</goals>
<configuration>
<tasks>
<property name="assembly-resources.loc" value="${maven.dependency.eu.dnetlib.dhp.dhp-build-assembly-resources.jar.path}" />
<unjar src="${assembly-resources.loc}" dest="${project.build.directory}/assembly-resources" />
</tasks>
</configuration>
</execution>
<!-- packaging phase -->
<execution>
<phase>package</phase>
<configuration>
<tasks>
<!-- copying workflow resources -->
<mkdir dir="target/${oozie.package.file.name}" />
<mkdir dir="target/${oozie.package.file.name}/${oozieAppDir}" />
<copy todir="target/${oozie.package.file.name}/${oozieAppDir}">
<!-- <fileset dir="${workflow.source.dir}/${oozieAppDir}" /> replacing with primed dir location -->
<fileset dir="target/${primed.dir}/${oozieAppDir}" />
</copy>
<!-- copying all jars to oozie lib directory -->
<mkdir dir="target/${oozie.package.file.name}/${oozieAppDir}/lib" />
<copy todir="target/${oozie.package.file.name}/${oozieAppDir}/lib">
<fileset dir="${project.build.directory}/dependency" />
</copy>
<!-- copying current module lib -->
<copy todir="target/${oozie.package.file.name}/${oozieAppDir}/lib">
<fileset dir="${project.build.directory}">
<include name="*.jar" />
</fileset>
</copy>
<fixcrlf srcdir="target/${oozie.package.file.name}/${oozieAppDir}/" encoding="UTF-8" outputencoding="UTF-8" includes="**/*.sh,**/*.json,**/*.py,**/*.sql" eol="lf" />
<!-- creating tar.gz package -->
<tar destfile="target/${oozie.package.file.name}.tar.gz" compression="gzip" longfile="gnu">
<tarfileset dir="target/${oozie.package.file.name}" />
<tarfileset dir="target/${oozie.package.file.name}_shell_scripts" filemode="0755">
<include name="**/*.sh" />
</tarfileset>
<tarfileset dir="target/${oozie.package.file.name}_shell_scripts" filemode="0644">
<exclude name="**/*.sh" />
</tarfileset>
</tar>
<!-- cleanup -->
<delete dir="target/${oozie.package.file.name}" />
<delete dir="target/${oozie.package.file.name}_shell_scripts" />
</tasks>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>deploy</id>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.5.0</version>
<executions>
<execution>
<id>create-target-dir</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>ssh</executable>
<arguments>
<argument>${dhp.hadoop.frontend.user.name}@${dhp.hadoop.frontend.host.name}</argument>
<argument>-p ${dhp.hadoop.frontend.port.ssh}</argument>
<argument>-o StrictHostKeyChecking=no</argument>
<argument>rm -rf ${dhp.hadoop.frontend.temp.dir}/oozie-packages/${sandboxName}/${output.dir.name}/; mkdir -p ${dhp.hadoop.frontend.temp.dir}/oozie-packages/${sandboxName}/${output.dir.name}/</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>upload-oozie-package</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>scp</executable>
<arguments>
<argument>-P ${dhp.hadoop.frontend.port.ssh}</argument>
<argument>-o StrictHostKeyChecking=no</argument>
<argument>target/${oozie.package.file.name}.tar.gz</argument>
<argument>${dhp.hadoop.frontend.user.name}@${dhp.hadoop.frontend.host.name}:${dhp.hadoop.frontend.temp.dir}/oozie-packages/${sandboxName}/${output.dir.name}/${oozie.package.file.name}.tar.gz</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>extract-and-upload-to-hdfs</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>ssh</executable>
<!-- <outputFile>target/redirected_upload.log</outputFile> -->
<arguments>
<argument>${dhp.hadoop.frontend.user.name}@${dhp.hadoop.frontend.host.name}</argument>
<argument>-p ${dhp.hadoop.frontend.port.ssh}</argument>
<argument>-o StrictHostKeyChecking=no</argument>
<argument>cd ${dhp.hadoop.frontend.temp.dir}/oozie-packages/${sandboxName}/${output.dir.name}/; </argument>
<argument>tar -zxf oozie-package.tar.gz; </argument>
<argument>rm ${dhp.hadoop.frontend.temp.dir}/oozie-packages/${sandboxName}/${output.dir.name}/oozie-package.tar.gz; </argument>
<argument>./upload_workflow.sh</argument>
</arguments>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>run</id>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.5.0</version>
<executions>
<execution>
<id>run-job</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>ssh</executable>
<!-- this file will be used by test verification profile reading job identifier -->
<outputFile>${oozie.execution.log.file.location}</outputFile>
<arguments>
<argument>${dhp.hadoop.frontend.user.name}@${dhp.hadoop.frontend.host.name}</argument>
<argument>-p ${dhp.hadoop.frontend.port.ssh}</argument>
<argument>-o StrictHostKeyChecking=no</argument>
<argument>cd ${dhp.hadoop.frontend.temp.dir}/oozie-packages/${sandboxName}/${output.dir.name}/; </argument>
<argument>./run_workflow.sh</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>show-run-log-on-stdout</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>cat</executable>
<arguments>
<argument>${oozie.execution.log.file.location}</argument>
</arguments>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>

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package eu.dnetlib.raid.jobs;
import eu.dnetlib.raid.support.ArgumentApplicationParser;
import eu.dnetlib.raid.support.RAiDConfig;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.Serializable;
import java.util.stream.Collectors;
public abstract class AbstractSparkJob implements Serializable {
protected static final int NUM_PARTITIONS = 1000;
protected static final int SEED = 42;
protected static final String EMBEDDING_COL = "embedding";
protected static final String STRING_ID_COL = "id";
protected static final String LONG_ID_COL = "longId";
protected static final String RANDOM_WALK_COL = "random_walk";
protected static final String LABEL_ID_COL = "labelId";
protected static final String LABELS_COL = "labels";
protected static final String PARTITION_COL = "partition";
public ArgumentApplicationParser parser; // parameters for the spark action
public SparkSession spark; // the spark session
public AbstractSparkJob() {}
public AbstractSparkJob(ArgumentApplicationParser parser, SparkSession spark) {
this.parser = parser;
this.spark = spark;
}
abstract void run() throws Exception;
protected static SparkSession getSparkSession(SparkConf conf) {
return SparkSession.builder().config(conf).getOrCreate();
}
protected static <T> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
dataset.write().option("compression", "gzip").mode(mode).json(outPath);
}
protected static String readFileFromHDFS(String filePath) throws IOException {
Path path=new Path(filePath);
FileSystem fs = FileSystem.get(new Configuration());
BufferedReader br=new BufferedReader(new InputStreamReader(fs.open(path)));
try {
return String.join("", br.lines().collect(Collectors.toList()));
} finally {
br.close();
}
}
public static String readResource(String path, Class<? extends AbstractSparkJob> clazz) throws IOException {
return IOUtils.toString(clazz.getResourceAsStream(path));
}
protected static RAiDConfig loadRAiDConfig(String raidConfPath) throws IOException {
return RAiDConfig.load(
readFileFromHDFS(raidConfPath)
);
}
}

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dhp-raid/src/main/java/eu/dnetlib/raid/jobs/SparkCreateEmbeddings.java Normal file
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package eu.dnetlib.raid.jobs;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.raid.graph.GraphUtil;
import eu.dnetlib.raid.support.ArgumentApplicationParser;
import eu.dnetlib.raid.support.EdgeParam;
import eu.dnetlib.raid.support.RAiDConfig;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.graphx.Edge;
import org.apache.spark.ml.feature.Normalizer;
import org.apache.spark.ml.feature.Word2Vec;
import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.*;
import org.apache.spark.sql.catalyst.encoders.RowEncoder;
import org.apache.spark.sql.types.DataTypes;
import org.apache.spark.sql.types.StructField;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import static org.apache.spark.sql.functions.*;
public class SparkCreateEmbeddings extends AbstractSparkJob{
private static final Logger log = LoggerFactory.getLogger(SparkCreateEmbeddings.class);
private static final String ID_PATH = "$.id";
private static final String DELETEDBYINFERENCE_PATH = "$.dataInfo.deletedbyinference";
private static final Encoder<Relation> REL_BEAN_ENC = Encoders.bean(Relation.class);
public SparkCreateEmbeddings(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
}
public static void main(String[] args) throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
readResource("/jobs/parameters/createEmbeddings_parameters.json", SparkCreateEmbeddings.class)
);
parser.parseArgument(args);
SparkConf conf = new SparkConf();
new SparkCreateEmbeddings(
parser,
getSparkSession(conf)
).run();
}
@Override
public void run() throws Exception {
// read oozie parameters
final String graphBasePath = parser.get("graphBasePath");
final String workingPath = parser.get("workingPath");
final String outputPath = parser.get("outputPath");
final String raidConfPath = parser.get("raidConfPath");
final int numPartitions = Optional
.ofNullable(parser.get("numPartitions"))
.map(Integer::valueOf)
.orElse(NUM_PARTITIONS);
log.info("graphBasePath: '{}'", graphBasePath);
log.info("workingPath: '{}'", workingPath);
log.info("outputPath: '{}'", outputPath);
log.info("raidConfPath: '{}'", raidConfPath);
log.info("numPartitions: '{}'", numPartitions);
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
RAiDConfig config = loadRAiDConfig(raidConfPath);
Dataset<Row> nodeDS = prepareNodes(sc, graphBasePath, config);
log.info("Number of nodes: {}", nodeDS.count());
RDD<Tuple2<Object, String>> vertices = createVertices(nodeDS);
Dataset<Row> relations = spark
.read()
.schema(REL_BEAN_ENC.schema())
.json(graphBasePath + "/relation");
log.info("Number of relations: {}", relations.count());
Dataset<Row> labelDS = spark.createDataFrame(
new ArrayList<>(), DataTypes.createStructType(
new StructField[]{
DataTypes.createStructField(LONG_ID_COL, DataTypes.LongType, false),
DataTypes.createStructField(LABEL_ID_COL, DataTypes.StringType, false)
}));
for(EdgeParam edgeParam: config.getEdges()) {
RDD<Edge<String>> edges = createEdges(nodeDS, relations, edgeParam.getMetapath(), edgeParam.getName());
Dataset<Row> connectedComponents = GraphUtil.createConnectedComponents(spark, vertices, edges, 1);
//this is getting rid of those connected components of a single element (they are not meaningful ?)
Dataset<Row> counts = connectedComponents
.groupBy(LABEL_ID_COL)
.agg(functions.count(LABEL_ID_COL).alias("count"))
.filter(functions.col("count").gt(1));
connectedComponents = connectedComponents
.join(counts, connectedComponents.col(LABEL_ID_COL).equalTo(counts.col(LABEL_ID_COL)), "inner")
.select(connectedComponents.col(LONG_ID_COL), connectedComponents.col(LABEL_ID_COL));
labelDS = labelDS.union(connectedComponents);
}
Dataset<Row> labels = labelDS
.groupBy(col(LONG_ID_COL))
.agg(collect_list(labelDS.col(LABEL_ID_COL)).as(LABELS_COL));
Dataset<Row> result = nodeDS
.join(labels, nodeDS.col(LONG_ID_COL).equalTo(labels.col(LONG_ID_COL)), "left")
.select(col(STRING_ID_COL), col(LABELS_COL));
log.info("Labels generated: {}", result.count());
Dataset<Row> word2vecEmbeddings = new Word2Vec()
.setInputCol(LABELS_COL)
.setOutputCol("word2vec_" + EMBEDDING_COL)
.setVectorSize(config.getParams().getOrDefault("embeddingSize", 128).intValue())
.setStepSize(config.getParams().getOrDefault("learningRate", 0.01).doubleValue())
.setMinCount(config.getParams().getOrDefault("minCount", 1).intValue())
.setMaxIter(config.getParams().getOrDefault("maxIter", 10).intValue())
.fit(result)
.transform(result);
Dataset<Row> embeddings = new Normalizer()
.setInputCol("word2vec_" + EMBEDDING_COL)
.setOutputCol(EMBEDDING_COL)
.setP(2.0)
.transform(word2vecEmbeddings)
.select(col(STRING_ID_COL), col(EMBEDDING_COL));
embeddings.write().save(outputPath);
}
public Dataset<Row> prepareNodes(JavaSparkContext sc, String graphBasePath, RAiDConfig config) {
// create nodes
JavaRDD<String> nodes = sc.emptyRDD();
for (String nodeType: config.getNodes()) {
nodes = nodes.union(
sc.textFile(graphBasePath + "/" + nodeType)
.filter(json -> !((boolean) JsonPath.read(json, DELETEDBYINFERENCE_PATH)))
.map(json -> JsonPath.read(json, ID_PATH)));
}
return spark.createDataset(
nodes.zipWithIndex().map(n -> RowFactory.create(n._1(), n._2())).rdd(),
RowEncoder.apply(
DataTypes.createStructType(
new StructField[]{
DataTypes.createStructField(STRING_ID_COL, DataTypes.StringType, false),
DataTypes.createStructField(LONG_ID_COL, DataTypes.LongType, false)
})
));
}
public RDD<Tuple2<Object,String>> createVertices(Dataset<Row> nodeDS) {
return nodeDS
.toJavaRDD()
.map(row -> new Tuple2<>(row.get(1), row.getString(0)))
.rdd();
}
public RDD<Edge<String>> createEdges(Dataset<Row> nodeDS, Dataset<Row> relations, List<String> metapath, String edgeName) throws Exception {
Dataset<Row> edgesRow;
switch(metapath.size()) {
case 1:
edgesRow = relations
.where(col("relClass").equalTo(metapath.get(0)))
.select(col("source").as("src"), col("target").as("dst"), col("relClass"));
break;
case 2:
Dataset<Row> edges_1 = relations
.where(col("relClass").equalTo(metapath.get(0)))
.select(col("source").as("source_1"), col("target").as("target_1"));
Dataset<Row> edges_2 = relations
.where(col("relClass").equalTo(metapath.get(1)))
.select(col("source").as("source_2"), col("target").as("target_2"));
edgesRow = edges_1
.join(edges_2, edges_1.col("target_1").equalTo(edges_2.col("source_2")))
.select(col("source_1").as("src"), col("target_2").as("dst"))
.withColumn("relClass", lit(edgeName));
break;
default:
throw new Exception("Metapath size not allowed");
}
// join with nodes to get longs instead of string ids
return edgesRow
.join(nodeDS, edgesRow.col("src").equalTo(nodeDS.col(STRING_ID_COL)))
.select(col(LONG_ID_COL).as("src"), col("dst"), col("relClass"))
.join(nodeDS, edgesRow.col("dst").equalTo(nodeDS.col(STRING_ID_COL)))
.select(col("src"), col(LONG_ID_COL).as("dst"), col("relClass"))
.toJavaRDD()
.map(row ->
new Edge<>(
row.getLong(0),
row.getLong(1),
row.getString(2)
)
)
.rdd();
}
}

213
dhp-raid/src/main/java/eu/dnetlib/raid/jobs/SparkCreateEmbeddingsW2V.java Normal file
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package eu.dnetlib.raid.jobs;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.raid.graph.GraphUtil;
import eu.dnetlib.raid.support.ArgumentApplicationParser;
import eu.dnetlib.raid.support.EdgeParam;
import eu.dnetlib.raid.support.RAiDConfig;
import eu.dnetlib.raid.support.RandomWalkParam;
import eu.dnetlib.raid.walker.RandomWalk;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.ml.feature.Normalizer;
import org.apache.spark.ml.feature.Word2Vec;
import org.apache.spark.ml.feature.Word2VecModel;
import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.*;
import org.apache.spark.sql.catalyst.encoders.RowEncoder;
import org.apache.spark.sql.types.DataTypes;
import org.apache.spark.sql.types.Metadata;
import org.apache.spark.sql.types.StructField;
import org.apache.spark.sql.types.StructType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import static org.apache.spark.sql.functions.col;
import static org.apache.spark.sql.functions.lit;
public class SparkCreateEmbeddingsW2V extends AbstractSparkJob{
private static final Logger log = LoggerFactory.getLogger(SparkCreateEmbeddingsW2V.class);
private static final String ID_PATH = "$.id";
private static final String DELETEDBYINFERENCE_PATH = "$.dataInfo.deletedbyinference";
private static final Encoder<Relation> REL_BEAN_ENC = Encoders.bean(Relation.class);
public SparkCreateEmbeddingsW2V(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
}
public static void main(String[] args) throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
readResource("/jobs/parameters/createEmbeddings_parameters.json", SparkCreateEmbeddingsW2V.class)
);
parser.parseArgument(args);
SparkConf conf = new SparkConf();
new SparkCreateEmbeddingsW2V(
parser,
getSparkSession(conf)
).run();
}
@Override
public void run() throws Exception {
// read oozie parameters
final String graphBasePath = parser.get("graphBasePath");
final String workingPath = parser.get("workingPath");
final String outputPath = parser.get("outputPath");
final String raidConfPath = parser.get("raidConfPath");
final int numPartitions = Optional
.ofNullable(parser.get("numPartitions"))
.map(Integer::valueOf)
.orElse(NUM_PARTITIONS);
log.info("graphBasePath: '{}'", graphBasePath);
log.info("workingPath: '{}'", workingPath);
log.info("outputPath: '{}'", outputPath);
log.info("raidConfPath: '{}'", raidConfPath);
log.info("numPartitions: '{}'", numPartitions);
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
RAiDConfig config = loadRAiDConfig(raidConfPath);
// create nodes
JavaRDD<String> nodes = sc.emptyRDD();
for (String nodeType: config.getNodes()) {
nodes = nodes.union(
sc.textFile(graphBasePath + "/" + nodeType)
.filter(json -> !((boolean) JsonPath.read(json, DELETEDBYINFERENCE_PATH)))
.map(json -> JsonPath.read(json, ID_PATH)));
}
RDD<Row> nodeRDD = nodes.zipWithIndex().map(n -> RowFactory.create(n._1(), n._2())).rdd();
Dataset<Row> nodeDS = spark.createDataset(nodeRDD, RowEncoder.apply(
new StructType(
new StructField[]{
new StructField(STRING_ID_COL, DataTypes.StringType, false, Metadata.empty()),
new StructField(LONG_ID_COL, DataTypes.LongType, false, Metadata.empty())
})
));
log.info("Number of nodes: {}", nodeDS.count());
Dataset<Row> relations = spark
.read()
.schema(REL_BEAN_ENC.schema())
.json(graphBasePath + "/relation");
log.info("Number of relations: {}", relations.count());
// create random walks
Dataset<Row> randomWalks = spark.createDataFrame(
new ArrayList<>(), new StructType(
new StructField[]{
new StructField(RANDOM_WALK_COL, DataTypes.createArrayType(DataTypes.IntegerType), false, Metadata.empty())
}));
for(EdgeParam edgeParam: config.getEdges()) {
log.info("Creating '{}' edges with '{}' metapath", edgeParam.getName(), edgeParam.getMetapath());
Dataset<Row> edges = createEdges(nodeDS, relations, edgeParam.getMetapath());
log.info("Number of '{}' edges: {}", edgeParam.getName(), edges.count());
RandomWalkParam randomWalkParam = config.getRandomWalks().get(edgeParam.getName());
Dataset<Row> randomWalk = new RandomWalk()
.setNumWalk(randomWalkParam.getNumWalks())
.setWalkLength(randomWalkParam.getWalkLength())
.setQ(randomWalkParam.getQ())
.setP(randomWalkParam.getP())
.setOutputCol(RANDOM_WALK_COL)
.randomWalk(edges);
log.info("Number of random walks for '{}' edges: {}", edgeParam.getName(), randomWalk.count());
randomWalks = randomWalks.union(randomWalk);
}
randomWalks.cache();
log.info("Creating embeddings");
Word2VecModel word2VecModel = new Word2Vec()
.setMaxSentenceLength(config.getParams().getOrDefault("maxWalkLength", 100).intValue())
.setMinCount(config.getParams().getOrDefault("minCount", 2).intValue())
.setWindowSize(config.getParams().getOrDefault("windowSize", 5).intValue())
.setVectorSize(config.getParams().getOrDefault("embeddingSize", 128).intValue())
.setMaxIter(config.getParams().getOrDefault("maxIter", 20).intValue())
.setStepSize(config.getParams().getOrDefault("learningRate", 0.1).doubleValue())
.setSeed(SEED)
.setNumPartitions(numPartitions)
.setInputCol(RANDOM_WALK_COL)
.setOutputCol(EMBEDDING_COL)
.fit(randomWalks);
Dataset<Row> embeddings = word2VecModel
.getVectors()
.toDF(LONG_ID_COL, EMBEDDING_COL);
Normalizer normalizer = new Normalizer()
.setInputCol(EMBEDDING_COL)
.setOutputCol("normalized_" + EMBEDDING_COL)
.setP(2.0);
embeddings = normalizer
.transform(embeddings)
.select(col(LONG_ID_COL), col("normalized_" + EMBEDDING_COL).as(EMBEDDING_COL));
Dataset<Row> result = nodeDS
.join(embeddings, nodeDS.col(LONG_ID_COL).equalTo(embeddings.col(LONG_ID_COL)))
.select(col(STRING_ID_COL), col(EMBEDDING_COL));
log.info("Number of generated embeddings: {}", result.count());
result.write().save(outputPath);
}
public Dataset<Row> createEdges(Dataset<Row> nodeDS, Dataset<Row> relations, List<String> metapath) throws Exception {
Dataset<Row> edges;
switch(metapath.size()) {
case 1:
edges = relations
.where(col("relClass").equalTo(metapath.get(0)))
.select(col("source").as("src"), col("target").as("dst"));
break;
case 2:
Dataset<Row> edges_1 = relations
.where(col("relClass").equalTo(metapath.get(0)))
.select(col("source").as("source_1"), col("target").as("target_1"));
Dataset<Row> edges_2 = relations
.where(col("relClass").equalTo(metapath.get(1)))
.select(col("source").as("source_2"), col("target").as("target_2"));
edges = edges_1
.join(edges_2, edges_1.col("target_1").equalTo(edges_2.col("source_2")))
.select(col("source_1").as("src"), col("target_2").as("dst"));
break;
default:
throw new Exception("Metapath size not allowed");
}
// join with nodes to get longs instead of string ids
edges = edges
.join(nodeDS, edges.col("src").equalTo(nodeDS.col(STRING_ID_COL)))
.select(col(LONG_ID_COL).as("src"), col("dst"))
.join(nodeDS, edges.col("dst").equalTo(nodeDS.col(STRING_ID_COL)))
.select(col("src"), col(LONG_ID_COL).as("dst"))
.withColumn("weight", lit(1.0));
return GraphUtil.preProcess(edges, "src", "dst", "weight");
}
}

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package eu.dnetlib.raid.jobs;
import com.google.common.collect.Iterators;
import eu.dnetlib.raid.support.ArgumentApplicationParser;
import eu.dnetlib.raid.support.RAiDConfig;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapPartitionsFunction;
import org.apache.spark.ml.clustering.KMeans;
import org.apache.spark.ml.linalg.DenseVector;
import org.apache.spark.sql.*;
import org.apache.spark.sql.types.DataTypes;
import org.apache.spark.sql.types.StructField;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import smile.clustering.DBSCAN;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import static org.apache.spark.sql.functions.col;
public class SparkRAiDClustering extends AbstractSparkJob {
private static final Logger log = LoggerFactory.getLogger(SparkRAiDClustering.class);
public SparkRAiDClustering(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
}
public static void main(String[] args) throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
readResource("/jobs/parameters/createClusters_parameters.json", SparkCreateEmbeddingsW2V.class)
);
parser.parseArgument(args);
SparkConf conf = new SparkConf();
new SparkRAiDClustering(
parser,
getSparkSession(conf)
).run();
}
@Override
public void run() throws Exception {
// read oozie parameters
final String inputPath = parser.get("inputPath");
final String workingPath = parser.get("workingPath");
final String outputPath = parser.get("outputPath");
final String raidConfPath = parser.get("raidConfPath");
final int numPartitions = Optional
.ofNullable(parser.get("numPartitions"))
.map(Integer::valueOf)
.orElse(NUM_PARTITIONS);
log.info("inputPath: '{}'", inputPath);
log.info("workingPath: '{}'", workingPath);
log.info("outputPath: '{}'", outputPath);
log.info("raidConfPath: '{}'", raidConfPath);
log.info("numPartitions: '{}'", numPartitions);
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
RAiDConfig config = loadRAiDConfig(raidConfPath);
MapPartitionsFunction<Row, Row> dbScan = partition -> {
List<double[]> points = new ArrayList<>();
List<String> ids = new ArrayList<>();
int index = 0; //partition index
while (partition.hasNext()) {
Row row = partition.next();
index = row.getAs(PARTITION_COL);
double[] embedding = ((DenseVector) row.getAs(EMBEDDING_COL)).toArray();
ids.add(row.getString(row.fieldIndex(STRING_ID_COL)));
points.add(embedding);
}
if (points.size() > 0 ) {
DBSCAN<double[]> dbscan = DBSCAN.fit(
points.toArray(new double[0][]),
config.getParams().getOrDefault("minPts", 1).intValue(),
config.getParams().getOrDefault("epsilon", 0.1).doubleValue()
);
List<Row> results = new ArrayList<>();
for (int i = 0; i < dbscan.y.length; i++) {
int clusterId = dbscan.y[i] == Integer.MAX_VALUE ? -1 : index * 1000 + dbscan.y[i];
Row resultRow = RowFactory.create(ids.get(i), clusterId);
results.add(resultRow);
}
return results.iterator();
}
else {
return Iterators.emptyIterator();
}
};
final Dataset<Row> embeddings = spark.read().load(inputPath);
Dataset<Row> clusteredData = new KMeans()
.setK(numPartitions)
.setSeed(SEED)
.setFeaturesCol(EMBEDDING_COL)
.setPredictionCol(PARTITION_COL)
.setMaxIter(config.getParams().getOrDefault("partitioningMaxIter", 10).intValue())
.fit(embeddings)
.transform(embeddings)
.repartition(col(PARTITION_COL))
.mapPartitions(dbScan, Encoders.kryo(Row.class));
Dataset<Row> result = spark
.createDataFrame(clusteredData.rdd(), DataTypes.createStructType(new StructField[]{DataTypes.createStructField(STRING_ID_COL, DataTypes.StringType, false), DataTypes.createStructField(LABEL_ID_COL, DataTypes.IntegerType, false)}));
result.write().save(outputPath);
}
}

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package eu.dnetlib.raid.support;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.Serializable;
import java.io.StringWriter;
import java.util.*;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
public class ArgumentApplicationParser implements Serializable {
private final Options options = new Options();
private final Map<String, String> objectMap = new HashMap<>();
private final List<String> compressedValues = new ArrayList<>();
public ArgumentApplicationParser(final String json_configuration) throws Exception {
final ObjectMapper mapper = new ObjectMapper();
final OptionsParameter[] configuration = mapper.readValue(json_configuration, OptionsParameter[].class);
createOptionMap(configuration);
}
public ArgumentApplicationParser(final OptionsParameter[] configuration) {
createOptionMap(configuration);
}
private void createOptionMap(final OptionsParameter[] configuration) {
Arrays
.stream(configuration)
.map(
conf -> {
final Option o = new Option(conf.getParamName(), true, conf.getParamDescription());
o.setLongOpt(conf.getParamLongName());
o.setRequired(conf.isParamRequired());
if (conf.isCompressed()) {
compressedValues.add(conf.getParamLongName());
}
return o;
})
.forEach(options::addOption);
// HelpFormatter formatter = new HelpFormatter();
// formatter.printHelp("myapp", null, options, null, true);
}
public static String decompressValue(final String abstractCompressed) {
try {
byte[] byteArray = org.apache.commons.codec.binary.Base64.decodeBase64(abstractCompressed.getBytes());
GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(byteArray));
final StringWriter stringWriter = new StringWriter();
IOUtils.copy(gis, stringWriter);
return stringWriter.toString();
} catch (Throwable e) {
System.out.println("Wrong value to decompress:" + abstractCompressed);
throw new RuntimeException(e);
}
}
public static String compressArgument(final String value) throws Exception {
ByteArrayOutputStream out = new ByteArrayOutputStream();
GZIPOutputStream gzip = new GZIPOutputStream(out);
gzip.write(value.getBytes());
gzip.close();
return java.util.Base64.getEncoder().encodeToString(out.toByteArray());
}
public void parseArgument(final String[] args) throws Exception {
CommandLineParser parser = new BasicParser();
CommandLine cmd = parser.parse(options, args);
Arrays
.stream(cmd.getOptions())
.forEach(
it -> objectMap
.put(
it.getLongOpt(),
compressedValues.contains(it.getLongOpt())
? decompressValue(it.getValue())
: it.getValue()));
}
public String get(final String key) {
return objectMap.get(key);
}
public Map<String, String> getObjectMap() {
return objectMap;
}
}

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dhp-raid/src/main/java/eu/dnetlib/raid/support/EdgeParam.java Normal file
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package eu.dnetlib.raid.support;
import java.io.Serializable;
import java.util.List;
public class EdgeParam implements Serializable {
private String name;
private List<String> metapath;
public EdgeParam() {
}
public EdgeParam(String name, List<String> metapath) {
this.name = name;
this.metapath = metapath;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public List<String> getMetapath() {
return metapath;
}
public void setMetapath(List<String> metapath) {
this.metapath = metapath;
}
}

39
dhp-raid/src/main/java/eu/dnetlib/raid/support/OptionsParameter.java Normal file
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package eu.dnetlib.raid.support;
import java.io.Serializable;
public class OptionsParameter implements Serializable {
private String paramName;
private String paramLongName;
private String paramDescription;
private boolean paramRequired;
private boolean compressed;
public OptionsParameter() {
}
public String getParamName() {
return paramName;
}
public String getParamLongName() {
return paramLongName;
}
public String getParamDescription() {
return paramDescription;
}
public boolean isParamRequired() {
return paramRequired;
}
public boolean isCompressed() {
return compressed;
}
public void setCompressed(boolean compressed) {
this.compressed = compressed;
}
}

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dhp-raid/src/main/java/eu/dnetlib/raid/support/RAiDConfig.java Normal file
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package eu.dnetlib.raid.support;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.JsonIOException;
import java.io.IOException;
import java.io.Serializable;
import java.util.List;
import java.util.Map;
public class RAiDConfig implements Serializable {
private List<String> nodes; // list of nodes to be considered
private List<EdgeParam> edges; //list of edges to be created
private Map<String, RandomWalkParam> randomWalks; //list of random walk parameters
private Map<String, Number> params;
public RAiDConfig() {
}
public RAiDConfig(List<String> nodes, List<EdgeParam> edges, Map<String, RandomWalkParam> randomWalks, Map<String, Number> params) {
this.nodes = nodes;
this.edges = edges;
this.randomWalks = randomWalks;
this.params = params;
}
public List<String> getNodes() {
return nodes;
}
public void setNodes(List<String> nodes) {
this.nodes = nodes;
}
public List<EdgeParam> getEdges() {
return edges;
}
public void setEdges(List<EdgeParam> edges) {
this.edges = edges;
}
public Map<String, RandomWalkParam> getRandomWalks() {
return randomWalks;
}
public void setRandomWalks(Map<String, RandomWalkParam> randomWalks) {
this.randomWalks = randomWalks;
}
public Map<String, Number> getParams() {
return params;
}
public void setParams(Map<String, Number> params) {
this.params = params;
}
public static RAiDConfig load(final String json) {
final RAiDConfig config;
try {
config = new ObjectMapper().readValue(json, RAiDConfig.class);
return config;
} catch (IOException e) {
throw new JsonIOException("Error in parsing configuration json", e);
}
}
}

53
dhp-raid/src/main/java/eu/dnetlib/raid/support/RandomWalkParam.java Normal file
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package eu.dnetlib.raid.support;
import java.io.Serializable;
public class RandomWalkParam implements Serializable {
private double p;
private double q;
private int walkLength;
private int numWalks;
public RandomWalkParam() {
}
public RandomWalkParam(double p, double q, int walkLength, int numWalks) {
this.p = p;
this.q = q;
this.walkLength = walkLength;
this.numWalks = numWalks;
}
public double getP() {
return p;
}
public void setP(double p) {
this.p = p;
}
public double getQ() {
return q;
}
public void setQ(double q) {
this.q = q;
}
public int getWalkLength() {
return walkLength;
}
public void setWalkLength(int walkLength) {
this.walkLength = walkLength;
}
public int getNumWalks() {
return numWalks;
}
public void setNumWalks(int numWalks) {
this.numWalks = numWalks;
}
}

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dhp-raid/src/main/resources/jobs/parameters/createClusters_parameters.json Normal file
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[
{
"paramName": "i",
"paramLongName": "inputPath",
"paramDescription": "input embeddings",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "working directory for the computations",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "output path",
"paramRequired": true
},
{
"paramName": "rc",
"paramLongName": "raidConfPath",
"paramDescription": "RAiD configuration path",
"paramRequired": true
},
{
"paramName": "np",
"paramLongName": "numPartitions",
"paramDescription": "number of partitions for the spark job",
"paramRequired": false
}
]

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dhp-raid/src/main/resources/jobs/parameters/createEmbeddings_parameters.json Normal file
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[
{
"paramName": "g",
"paramLongName": "graphBasePath",
"paramDescription": "the input graph base path",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "working directory for the computations",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "output path",
"paramRequired": true
},
{
"paramName": "rc",
"paramLongName": "raidConfPath",
"paramDescription": "RAiD configuration path",
"paramRequired": true
},
{
"paramName": "np",
"paramLongName": "numPartitions",
"paramDescription": "number of partitions for the spark job",
"paramRequired": false
}
]

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dhp-raid/src/main/resources/raid/oozie_app/config-default.xml Normal file
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<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

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<workflow-app name="RAiD Inference WF" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>graphBasePath</name>
<description>path for the input graph</description>
</property>
<property>
<name>raidConfPath</name>
<description>configuration for RAiD inference</description>
</property>
<property>
<name>workingPath</name>
<description>path of the working directory</description>
</property>
<property>
<name>numPartitions</name>
<description>number of partitions for the spark files</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
<property>
<name>mapreduce.map.java.opts</name>
<value>-Xmx6144m</value>
</property>
<property>
<name>mapreduce.reduce.java.opts</name>
<value>-Xmx6144m</value>
</property>
</configuration>
</global>
<start to="CreateEmbeddings"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="CreateEmbeddings">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Create Embeddings</name>
<class>eu.dnetlib.raid.jobs.SparkCreateEmbeddings</class>
<jar>dhp-raid-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=32
--executor-memory=16G
--executor-cores=4
--driver-memory=8G
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
--conf spark.dynamicAllocation.enabled=true
</spark-opts>
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputPath</arg><arg>${embeddingsPath}</arg>
<arg>--raidConfPath</arg><arg>${raidConfPath}</arg>
<arg>--numPartitions</arg><arg>${numPartitions}</arg>
</spark>
<ok to="CreateClusters"/>
<error to="Kill"/>
</action>
<action name="CreateClusters">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Create Clusters</name>
<class>eu.dnetlib.raid.jobs.SparkRAiDClustering</class>
<jar>dhp-raid-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=32
--executor-memory=16G
--executor-cores=4
--driver-memory=8G
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
--conf spark.dynamicAllocation.enabled=true
</spark-opts>
<arg>--inputPath</arg><arg>${embeddingsPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputPath</arg><arg>${clustersPath}</arg>
<arg>--raidConfPath</arg><arg>${raidConfPath}</arg>
<arg>--numPartitions</arg><arg>${numPartitions}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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dhp-raid/src/main/scala/eu/dnetlib/raid/graph/AliasOps.scala Normal file
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package eu.dnetlib.raid.graph
import scala.collection.mutable.ArrayBuffer
/**
* alias method sampling
*/
object AliasOps {
def normalize(probabilities: Array[Double]): Array[Double] = {
val sum = probabilities.sum
probabilities.map(x => x / sum)
}
def setupAlias(probabilities: Array[Double]): (Array[Int], Array[Double]) = {
val K = probabilities.length
val J = Array.fill(K)(0)
val q = Array.fill(K)(0.0)
val smaller = new ArrayBuffer[Int]()
val larger = new ArrayBuffer[Int]()
probabilities.zipWithIndex.foreach { case (prob, kk) =>
q(kk) = K * prob
if (q(kk) < 1.0) {
smaller.append(kk)
} else {
larger.append(kk)
}
}
while (smaller.nonEmpty && larger.nonEmpty) {
val small = smaller.remove(smaller.length - 1)
val large = larger.remove(larger.length - 1)
J(small) = large
q(large) = q(large) + q(small) - 1.0
if (q(large) < 1.0) {
smaller.append(large)
} else {
larger.append(large)
}
}
(J, q)
}
def drawAlias(J: Array[Int], q: Array[Double]): Int = {
val K = J.length
val kk = math.floor(math.random * K).toInt
if (math.random < q(kk)) kk
else J(kk)
}
def main(args: Array[String]): Unit = {
val probabilities = Array(0.28, 0.32, 0.1, 0.3)
val jq = setupAlias(probabilities)
val res = new ArrayBuffer[Int]()
for (_ <- 0 until 1000) {
val index = drawAlias(jq._1, jq._2)
res.append(index)
}
for (i <- probabilities.indices) {
println(i + ": " + res.count(x => x == i))
}
}
}

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dhp-raid/src/main/scala/eu/dnetlib/raid/graph/GraphOps.scala Normal file
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package eu.dnetlib.raid.graph
import org.apache.spark.graphx._
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.SparkSession
/**
* initial graph with node alias and edge alias
*/
object GraphOps {
def setupEdgeAlias(p: Double = 1.0, q: Double = 1.0)(srcId: Long,
srcNeighbors: Array[(Long, Double)],
dstNeighbors: Array[(Long, Double)]): (Array[Int], Array[Double]) = {
val unNormalizedProbabilities = dstNeighbors.map { case (dstNeighborId, weight) =>
var unNormProb = weight / q
if (srcId == dstNeighborId) unNormProb = weight / p
else if (srcNeighbors.exists(_._1 == dstNeighborId)) unNormProb = weight
unNormProb
}
AliasOps.setupAlias(AliasOps.normalize(unNormalizedProbabilities))
}
def setupNodeAlias(neighbors: Array[(Long, Double)]): (Array[Int], Array[Double]) = {
val unNormalizedProbabilities = neighbors.map(_._2)
AliasOps.setupAlias(AliasOps.normalize(unNormalizedProbabilities))
}
def initTransitionProb(spark: SparkSession,
edges: RDD[Edge[EdgeAttr]],
vertices: RDD[(VertexId, NodeAttr)],
p: Double,
q: Double): Graph[NodeAttr, EdgeAttr] = {
val bcP = spark.sparkContext.broadcast(p)
val bcQ = spark.sparkContext.broadcast(q)
val graph = Graph.apply(vertices, edges).mapVertices[NodeAttr] {
case (_, nodeAttr) =>
val (j, q) = GraphOps.setupNodeAlias(nodeAttr.neighbors)
nodeAttr.J = j
nodeAttr.q = q
nodeAttr
}.mapTriplets {
edgeTriplet: EdgeTriplet[NodeAttr, EdgeAttr] =>
val (j, q) = GraphOps.setupEdgeAlias(bcP.value, bcQ.value)(
edgeTriplet.srcId,
edgeTriplet.srcAttr.neighbors,
edgeTriplet.dstAttr.neighbors)
edgeTriplet.attr.J = j
edgeTriplet.attr.q = q
edgeTriplet.attr.dstNeighbors = edgeTriplet.dstAttr.neighbors.map(_._1)
edgeTriplet.attr
}
graph
}
}

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dhp-raid/src/main/scala/eu/dnetlib/raid/graph/GraphUtil.scala Normal file
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package eu.dnetlib.raid.graph
import eu.dnetlib.raid.jobs.AbstractSparkJob
import org.apache.spark.api.java.JavaRDD
import org.apache.spark.api.java.JavaRDD.fromRDD
import org.apache.spark.graphx.{Edge, Graph, VertexId, VertexRDD}
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{DataFrame, Encoders, Row, RowFactory, SparkSession}
import org.apache.spark.sql.functions.{col, sum}
import org.apache.spark.sql.types.{LongType, StringType, StructField, StructType}
object GraphUtil {
// process the graph to make sure it can be fit into randomWalk
def preProcess(dataFrame: DataFrame, srcCol: String = "src", dstCol: String = "dst", weightCol: String = "weight"): DataFrame = {
val spark = dataFrame.sparkSession
import spark.implicits._
val filteredDF = dataFrame.filter(col(srcCol) =!= col(dstCol))
val uniqueEdges = filteredDF.map(x => {
val src = x.getAs[Long](srcCol)
val dst = x.getAs[Long](dstCol)
val weight = x.getAs[Double](weightCol)
val srcDst = Array(src, dst).sorted.mkString(",")
(srcDst, weight)
}).toDF("edge", "weight")
val weightedEdges = uniqueEdges.groupBy("edge").agg(
sum("weight")
).flatMap(x => {
val edge = x.getString(0).split(",").map(_.toLong)
val weight = x.getDouble(1)
Array((edge(0), edge(1), weight), (edge(1), edge(0), weight))
}).toDF(srcCol, dstCol, weightCol)
weightedEdges
}
def createConnectedComponents(spark: SparkSession, vertices: RDD[(Long, String)], edges: RDD[Edge[String]], maxIter: Int): DataFrame = {
val graph = Graph.apply(vertices,edges,"unknown")
val cc : RDD[Row] = graph.connectedComponents(maxIter).vertices.map(tuple => Row(tuple._1, tuple._2)).rdd
spark.createDataFrame(cc.rdd, StructType(Seq(
StructField("longId", LongType, nullable = false),
StructField("labelId", LongType, nullable = false)
)))
}
}

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package eu.dnetlib.raid
package object graph {
case class NodeAttr(var neighbors: Array[(Long, Double)] = Array.empty[(Long, Double)],
var J: Array[Int] = Array.empty[Int],
var q: Array[Double] = Array.empty[Double]) extends Serializable
case class EdgeAttr(var dstNeighbors: Array[Long] = Array.empty[Long],
var J: Array[Int] = Array.empty[Int],
var q: Array[Double] = Array.empty[Double]) extends Serializable
}

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package eu.dnetlib.raid.walker
import eu.dnetlib.raid.graph.{AliasOps, EdgeAttr, GraphOps, NodeAttr}
import org.apache.spark.graphx.{Edge, Graph}
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.DataFrame
import org.apache.spark.sql.functions.collect_list
import scala.collection.mutable.ArrayBuffer
class RandomWalk extends Serializable {
var p: Double = 1.0
var q: Double = 1.0
var numWalk: Int = 10
var walkLength: Int = 10
var bcMaxDegree: Int = 30
var weightLog: Boolean = false
var srcCol: String = "src"
var dstCol: String = "dst"
var weightCol: String = "weight"
var outputCol: String = "sequence"
/**
* initialize the graph
*
* @param dataFrame input dataFrame
*/
def initGraph(dataFrame: DataFrame): Graph[NodeAttr, EdgeAttr] = {
val spark = dataFrame.sparkSession
import spark.implicits._
val edges = dataFrame.map(x => {
val src = x.getAs[Long](srcCol)
val dst = x.getAs[Long](dstCol)
Edge(src, dst, EdgeAttr())
})
val vertices = dataFrame.groupBy(srcCol).agg(
collect_list(dstCol),
collect_list(weightCol)
).map(x => {
val src = x.getLong(0)
val dstSeq = x.getSeq[Long](1)
var weightSeq = x.getSeq[Double](2)
if (weightLog) weightSeq = weightSeq.map(x => math.log1p(x))
val dstWeight = dstSeq.zip(weightSeq).sortBy(_._2).reverse.take(bcMaxDegree)
(src, NodeAttr(neighbors = dstWeight.map(x => (x._1, x._2)).toArray))
})
GraphOps.initTransitionProb(spark, edges.rdd, vertices.rdd, p, q)
}
def setWeightLog(weightLog: Boolean): this.type = {
this.weightLog = weightLog
this
}
def setBcMaxDegree(bcMaxDegree: Int): this.type = {
this.bcMaxDegree = bcMaxDegree
this
}
def setP(p: Double): this.type = {
this.p = p
this
}
def setQ(p: Double): this.type = {
this.q = q
this
}
def setNumWalk(numWalk: Int): this.type = {
this.numWalk = numWalk
this
}
def setWalkLength(walkLength: Int): this.type = {
this.walkLength = walkLength
this
}
def setSrcCol(srcCol: String): this.type = {
this.srcCol = srcCol
this
}
def setDstCol(dstCol: String): this.type = {
this.dstCol = dstCol
this
}
def setWeightCol(weightCol: String): this.type = {
this.weightCol = weightCol
this
}
def setOutputCol(outputCol: String): this.type = {
this.outputCol = outputCol
this
}
def randomWalk(dataFrame: DataFrame): DataFrame = {
val spark = dataFrame.sparkSession
import spark.implicits._
val graph = initGraph(dataFrame)
val edges = graph.edges.map { x =>
(x.srcId + "," + x.dstId, x.attr)
}.repartition(1000).cache()
edges.first()
val vertices = graph.vertices.cache()
vertices.first()
var result: RDD[(String, ArrayBuffer[Long])] = null
for (_ <- 0 until numWalk) {
var path: RDD[(String, ArrayBuffer[Long])] = firstWalk(vertices)
path.first()
for (_ <- 1 until walkLength) {
path = edges.join(path).map { x =>
val edgeAttr = x._2._1
val pathBuffer = x._2._2
val nextNodeIndex = AliasOps.drawAlias(edgeAttr.J, edgeAttr.q)
val nextNode = edgeAttr.dstNeighbors(nextNodeIndex)
pathBuffer.append(nextNode)
val currId = pathBuffer.last
val prevId = pathBuffer(pathBuffer.length - 2)
(prevId + "," + currId, pathBuffer)
}
path.first()
}
if (result == null) {
result = path
result.first()
} else {
result = result.union(path)
result.first()
}
}
result.map { x => x._2.map(_.toString).toArray }.toDF(outputCol)
}
def firstWalk(vertices: RDD[(Long, NodeAttr)]): RDD[(String, ArrayBuffer[Long])] = {
val result = vertices.map { x =>
val nodeAttr = x._2
val startNode = x._1
val nextNodeIndex = AliasOps.drawAlias(nodeAttr.J, nodeAttr.q)
val nextNode = nodeAttr.neighbors(nextNodeIndex)._1
val buffer = new ArrayBuffer[Long]()
buffer.append(startNode)
buffer.append(nextNode)
(startNode + "," + nextNode, buffer)
}
result
}
}

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package eu.dnetlib.raid;
import eu.dnetlib.raid.jobs.AbstractSparkJob;
import eu.dnetlib.raid.jobs.SparkCreateEmbeddings;
import eu.dnetlib.raid.jobs.SparkRAiDClustering;
import eu.dnetlib.raid.support.ArgumentApplicationParser;
import eu.dnetlib.raid.support.RAiDConfig;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URISyntaxException;
import java.nio.file.Paths;
import java.util.stream.Collectors;
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
public class RAiDInferenceTest {
static SparkSession spark;
static RAiDConfig config;
static JavaSparkContext context;
final String graphBasePath = Paths
.get(RAiDInferenceTest.class.getResource("/eu/dnetlib/raid/examples/graph").toURI())
.toFile()
.getAbsolutePath();
final static String workingPath = "/tmp/working_dir";
final static String embeddingsPath = "/tmp/embeddings";
final static String clustersPath = "/tmp/clusters";
final static String numPartitions = "3";
final String raidConfPath = Paths
.get(RAiDInferenceTest.class.getResource("/eu/dnetlib/raid/config/raid.conf.json").toURI())
.toFile()
.getAbsolutePath();
public RAiDInferenceTest() throws URISyntaxException {
}
public static void cleanup() throws IOException {
//remove directories to clean workspace
FileUtils.deleteDirectory(new File(workingPath));
FileUtils.deleteDirectory(new File(clustersPath));
FileUtils.deleteDirectory(new File(embeddingsPath));
}
@BeforeAll
public void setup() throws IOException {
cleanup();
config = RAiDConfig.load(readFileFromHDFS(raidConfPath));
spark = SparkSession
.builder()
.appName("RAiD inference")
.master("local[*]")
.getOrCreate();
context = JavaSparkContext.fromSparkContext(spark.sparkContext());
}
@AfterAll
public static void finalCleanUp() throws IOException {
cleanup();
}
protected static String readFileFromHDFS(String filePath) throws IOException {
Path path=new Path(filePath);
FileSystem fs = FileSystem.get(new Configuration());
BufferedReader br=new BufferedReader(new InputStreamReader(fs.open(path)));
try {
return String.join("", br.lines().collect(Collectors.toList()));
} finally {
br.close();
}
}
public static String readResource(String path, Class<? extends AbstractSparkJob> clazz) throws IOException {
return IOUtils.toString(
clazz.getResourceAsStream(path));
}
@Test
@Order(1)
public void createRAiDEmbeddingsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(readResource("/jobs/parameters/createEmbeddings_parameters.json", SparkCreateEmbeddings.class));
parser.parseArgument(
new String[] {
"-g", graphBasePath,
"-rc", raidConfPath,
"-o", embeddingsPath,
"-w", workingPath,
"-np", numPartitions
});
new SparkCreateEmbeddings(
parser,
spark
).run();
}
@Test
@Order(2)
public void createClusters() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(readResource("/jobs/parameters/createClusters_parameters.json", SparkRAiDClustering.class));
parser.parseArgument(
new String[] {
"-i", embeddingsPath,
"-rc", raidConfPath,
"-o", clustersPath,
"-w", workingPath,
"-np", numPartitions
}
);
new SparkRAiDClustering(
parser,
spark
).run();
}
}

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{
"nodes": ["publication", "software", "dataset"],
"edges": [
{
"name": "coproduced",
"metapath": ["isProducedBy", "produces"]
},
{
"name": "coinstitution",
"metapath": ["hasAuthorInstitutionOf", "isAuthorInstitutionOf"]
},
{
"name": "part",
"metapath": ["IsPartOf"]
},
{
"name": "version",
"metapath": ["IsVersionOf"]
},
{
"name": "supplement",
"metapath": ["IsSupplementTo"]
}
],
"randomWalks": {
"coproduced": {"p": 1.0, "q": 2.0, "walkLength": 3, "numWalks": 10},
"coinstitution": {"p": 1.0, "q": 2.0, "walkLength": 3, "numWalks": 1},
"part": {"p": 1.0, "q": 0.25, "walkLength": 3, "numWalks": 2},
"version": {"p": 1.0, "q": 0.25, "walkLength": 4, "numWalks": 5},
"supplement": {"p": 1.0, "q": 0.25, "walkLength": 3, "numWalks": 3}
},
"params": {
"embeddingSize": 128,
"maxIter": 20,
"partitioningMaxIter": 50,
"learningRate": 0.01,
"epsilon": 0.5,
"minPts": 5
}
}

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{"dataInfo": {"deletedbyinference": false}, "author": [],"description": [ { "dataInfo": { "deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": { "classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions" }, "trust": "0.9" }, "value": "Description of dataset 1" }],"id": "50|dataset::1","pid": [],"subject": [],"title": [ { "dataInfo": { "deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": { "classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions" }, "trust": "0.9" }, "qualifier": { "classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title" }, "value": "Dataset 1" }]}
{"dataInfo": {"deletedbyinference": false}, "author": [],"description": [ { "dataInfo": { "deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": { "classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions" }, "trust": "0.9" }, "value": "Description of dataset 2" }],"id": "50|dataset::2","pid": [],"subject": [],"title": [ { "dataInfo": { "deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": { "classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions" }, "trust": "0.9" }, "qualifier": { "classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title" }, "value": "Dataset 2" }]}
{"dataInfo": {"deletedbyinference": false}, "author": [],"description": [ { "dataInfo": { "deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": { "classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions" }, "trust": "0.9" }, "value": "Description of dataset 3" }],"id": "50|dataset::3","pid": [],"subject": [],"title": [ { "dataInfo": { "deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": { "classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions" }, "trust": "0.9" }, "qualifier": { "classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title" }, "value": "Dataset 3" }]}

4
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{"dataInfo": {"deletedbyinference": false}, "author": [], "description": [{"dataInfo": {"deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9" }, "value": "Description of publication 1"}], "id": "50|publication::1", "pid": [], "title": [ { "dataInfo": { "deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9"}, "qualifier": { "classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"},"value": "Publication 1"}]}
{"dataInfo": {"deletedbyinference": false}, "author": [], "description": [{"dataInfo": {"deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9" }, "value": "Description of publication 2"}], "id": "50|publication::2", "pid": [], "title": [ { "dataInfo": { "deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9"}, "qualifier": { "classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"},"value": "Publication 2"}]}
{"dataInfo": {"deletedbyinference": false}, "author": [], "description": [{"dataInfo": {"deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9" }, "value": "Description of publication 3"}], "id": "50|publication::3", "pid": [], "title": [ { "dataInfo": { "deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9"}, "qualifier": { "classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"},"value": "Publication 3"}]}
{"dataInfo": {"deletedbyinference": false}, "author": [], "description": [{"dataInfo": {"deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9" }, "value": "Description of publication 4"}], "id": "50|publication::4", "pid": [], "title": [ { "dataInfo": { "deletedbyinference": false, "inferred": false, "invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9"}, "qualifier": { "classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"},"value": "Publication 4"}]}

29
dhp-raid/src/test/resources/eu/dnetlib/raid/examples/graph/relation Normal file
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4
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445
pom.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>eu.dnetlib</groupId>
<artifactId>raid-inference</artifactId>
<version>1.0.0-SNAPSHOT</version>
<packaging>pom</packaging>
<url>http://www.d-net.research-infrastructures.eu</url>
<licenses>
<license>
<name>The Apache Software License, Version 2.0</name>
<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
<distribution>repo</distribution>
<comments>A business-friendly OSS license</comments>
</license>
</licenses>
<scm>
<developerConnection>scm:git:https://code-repo.d4science.org/D-Net/raid-inference.git</developerConnection>
<tag>raid-inference-1.0.0</tag>
</scm>
<modules>
<module>dhp-raid</module>
<module>dhp-build</module>
</modules>
<issueManagement>
<system>Redmine</system>
<url>https://issue.openaire.research-infrastructures.eu/projects/openaire</url>
</issueManagement>
<distributionManagement>
<repository>
<id>dnet45-releases</id>
<name>D-Net 45 Releases</name>
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
<layout>default</layout>
</repository>
</distributionManagement>
<repositories>
<repository>
<id>dnet45-releases</id>
<name>D-Net 45 releases</name>
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
<layout>default</layout>
<snapshots>
<enabled>false</enabled>
</snapshots>
<releases>
<enabled>true</enabled>
</releases>
</repository>
<repository>
<id>dnet45-snapshots</id>
<name>D-Net 45 snapshots</name>
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-snapshots</url>
<layout>default</layout>
<snapshots>
<enabled>true</enabled>
</snapshots>
<releases>
<enabled>false</enabled>
</releases>
</repository>
<repository>
<id>dnet-deps</id>
<name>dnet-dependencies</name>
<url>https://maven.d4science.org/nexus/content/repositories/dnet-deps</url>
<layout>default</layout>
</repository>
<repository>
<id>cloudera</id>
<name>Cloudera Repository</name>
<url>https://repository.cloudera.com/artifactory/cloudera-repos</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>ceon</id>
<name>Ceon Repository</name>
<url>https://maven.ceon.pl/artifactory/repo</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
<build>
<directory>target</directory>
<outputDirectory>target/classes</outputDirectory>
<finalName>${project.artifactId}-${project.version}</finalName>
<testOutputDirectory>target/test-classes</testOutputDirectory>
<!--*************************************************-->
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.6.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<encoding>${project.build.sourceEncoding}</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.0.1</version>
<executions>
<execution>
<id>attach-sources</id>
<phase>verify</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.19.1</version>
<dependencies>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>${junit-jupiter.version}</version>
</dependency>
</dependencies>
<configuration>
<redirectTestOutputToFile>false</redirectTestOutputToFile>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.4</version>
<configuration>
<detectLinks>true</detectLinks>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.13</version>
<executions>
<execution>
<id>integration-test</id>
<goals>
<goal>integration-test</goal>
</goals>
</execution>
<execution>
<id>verify</id>
<goals>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.5.3</version>
</plugin>
</plugins>
</build>
<pluginRepositories>
<pluginRepository>
<id>iis-releases</id>
<name>iis releases plugin repository</name>
<url>http://maven.ceon.pl/artifactory/iis-releases</url>
<layout>default</layout>
</pluginRepository>
</pluginRepositories>
<properties>
<oozie.package.file.name>oozie-package</oozie.package.file.name>
<workflow.source.dir>src/test/resources/define/path/pointing/to/directory/holding/oozie_app</workflow.source.dir>
<oozieAppDir>oozie_app</oozieAppDir>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<google.gson.version>2.2.2</google.gson.version>
<google.guava.version>15.0</google.guava.version>
<spark.version>2.2.0</spark.version>
<!--<jackson.version>2.9.6</jackson.version>-->
<jackson.version>2.6.5</jackson.version>
<mockito-core.version>3.3.3</mockito-core.version>
<dhp-schemas.version>[8.0.1]</dhp-schemas.version>
<commons.lang.version>3.5</commons.lang.version>
<commons.io.version>2.4</commons.io.version>
<commons.collections.version>3.2.1</commons.collections.version>
<commons.logging.version>1.1.3</commons.logging.version>
<junit.version>4.9</junit.version>
<scala.version>2.11.8</scala.version>
<maven.javadoc.failOnError>false</maven.javadoc.failOnError>
<maven.compiler.plugin.version>3.6.0</maven.compiler.plugin.version>
<!-- from dhp-workflows -->
<queueName>default</queueName>
<importerQueueName>default</importerQueueName>
<oozieLauncherQueueName>default</oozieLauncherQueueName>
<primed.dir>primed</primed.dir>
<oozie.package.dependencies.include.scope>runtime</oozie.package.dependencies.include.scope>
<oozie.package.dependencies.exclude.scope />
<oozie.package.skip.test.jar>true</oozie.package.skip.test.jar>
<dhpConnectionProperties>${user.home}/.dhp/application.properties</dhpConnectionProperties>
<output.dir.name>${maven.build.timestamp}</output.dir.name>
<projectVersion>${project.version}</projectVersion>
<oozie.use.system.libpath>true</oozie.use.system.libpath>
<properties.maven.plugin.version>2.0.1</properties.maven.plugin.version>
<junit-jupiter.version>5.6.1</junit-jupiter.version>
<maven.dependency.eu.dnetlib.dhp.dhp-build-assembly-resources.jar.path>../dhp-build/dhp-build-assembly-resources/target/dhp-build-assembly-resources-${project.version}.jar</maven.dependency.eu.dnetlib.dhp.dhp-build-assembly-resources.jar.path>
</properties>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>edu.cmu</groupId>
<artifactId>secondstring</artifactId>
<version>1.0.0</version>
</dependency>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>stringtemplate</artifactId>
<version>3.2</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>${jackson.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-xml</artifactId>
<version>${jackson.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.module</groupId>
<artifactId>jackson-module-jsonSchema</artifactId>
<version>${jackson.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>${jackson.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>${jackson.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>${mockito-core.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<version>${mockito-core.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.6.1</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${google.guava.version}</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>${google.gson.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>${commons.lang.version}</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons.io.version}</version>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
<version>${commons.collections.version}</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>${commons.logging.version}</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
<version>${spark.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-graphx_2.11</artifactId>
<version>${spark.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
<version>${spark.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>${junit-jupiter.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>${scala.version}</version>
</dependency>
<dependency>
<groupId>org.apache.oozie</groupId>
<artifactId>oozie-client</artifactId>
<version>5.1.0</version>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
<version>2.4.0</version>
</dependency>
<dependency>
<groupId>com.ibm.icu</groupId>
<artifactId>icu4j</artifactId>
<version>70.1</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<version>${dhp-schemas.version}</version>
</dependency>
<dependency>
<groupId>de.lmu.ifi.dbs.elki</groupId>
<artifactId>elki</artifactId>
<version>0.7.5</version>
</dependency>
<dependency>
<groupId>com.github.haifengl</groupId>
<artifactId>smile-core</artifactId>
<version>2.5.3</version> <!-- usa la versione più recente disponibile -->
</dependency>
</dependencies>
</dependencyManagement>
<profiles>
</profiles>
</project>