reformatted code according to the updated style descriptor
This commit is contained in:
parent
e6d68d1364
commit
6f5b899038
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@ -4,6 +4,7 @@ package eu.dnetlib.maven.plugin.properties;
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import java.io.File;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.List;
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import org.apache.commons.lang.ArrayUtils;
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import org.apache.commons.lang.ArrayUtils;
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import org.apache.commons.lang.StringUtils;
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import org.apache.commons.lang.StringUtils;
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import org.apache.maven.plugin.AbstractMojo;
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import org.apache.maven.plugin.AbstractMojo;
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@ -12,7 +12,6 @@
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package eu.dnetlib.maven.plugin.properties;
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package eu.dnetlib.maven.plugin.properties;
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import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
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import java.io.File;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileInputStream;
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import java.io.IOException;
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import java.io.IOException;
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@ -25,6 +24,7 @@ import java.util.List;
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import java.util.Map.Entry;
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import java.util.Map.Entry;
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import java.util.Properties;
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import java.util.Properties;
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import java.util.Set;
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import java.util.Set;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang.StringUtils;
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import org.apache.commons.lang.StringUtils;
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@ -36,6 +36,8 @@ import org.springframework.core.io.DefaultResourceLoader;
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import org.springframework.core.io.Resource;
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import org.springframework.core.io.Resource;
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import org.springframework.core.io.ResourceLoader;
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import org.springframework.core.io.ResourceLoader;
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import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
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/**
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/**
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* Writes project properties for the keys listed in specified properties files. Based on:
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* Writes project properties for the keys listed in specified properties files. Based on:
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* http://site.kuali.org/maven/plugins/properties-maven-plugin/1.3.2/write-project-properties-mojo.html
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* http://site.kuali.org/maven/plugins/properties-maven-plugin/1.3.2/write-project-properties-mojo.html
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@ -8,6 +8,7 @@ import static org.mockito.Mockito.lenient;
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import java.io.*;
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import java.io.*;
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import java.util.Properties;
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import java.util.Properties;
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import org.apache.maven.plugin.MojoExecutionException;
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import org.apache.maven.plugin.MojoExecutionException;
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import org.apache.maven.project.MavenProject;
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import org.apache.maven.project.MavenProject;
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import org.junit.jupiter.api.*;
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import org.junit.jupiter.api.*;
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@ -3,6 +3,7 @@ package eu.dnetlib.data.mdstore.manager.common.model;
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import java.io.Serializable;
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import java.io.Serializable;
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import java.util.UUID;
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import java.util.UUID;
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import javax.persistence.Column;
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import javax.persistence.Column;
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import javax.persistence.Entity;
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import javax.persistence.Entity;
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import javax.persistence.Id;
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import javax.persistence.Id;
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@ -2,6 +2,7 @@
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package eu.dnetlib.data.mdstore.manager.common.model;
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package eu.dnetlib.data.mdstore.manager.common.model;
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import java.io.Serializable;
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import java.io.Serializable;
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import javax.persistence.Column;
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import javax.persistence.Column;
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import javax.persistence.Entity;
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import javax.persistence.Entity;
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import javax.persistence.Id;
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import javax.persistence.Id;
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@ -3,6 +3,7 @@ package eu.dnetlib.data.mdstore.manager.common.model;
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import java.io.Serializable;
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import java.io.Serializable;
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import java.util.Date;
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import java.util.Date;
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import javax.persistence.Column;
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import javax.persistence.Column;
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import javax.persistence.Entity;
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import javax.persistence.Entity;
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import javax.persistence.Id;
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import javax.persistence.Id;
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@ -3,6 +3,7 @@ package eu.dnetlib.data.mdstore.manager.common.model;
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import java.io.Serializable;
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import java.io.Serializable;
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import java.util.Date;
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import java.util.Date;
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import javax.persistence.Column;
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import javax.persistence.Column;
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import javax.persistence.Entity;
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import javax.persistence.Entity;
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import javax.persistence.Id;
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import javax.persistence.Id;
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@ -1,7 +1,6 @@
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package eu.dnetlib.dhp.application;
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package eu.dnetlib.dhp.application;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.Serializable;
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import java.io.Serializable;
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@ -9,10 +8,13 @@ import java.io.StringWriter;
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import java.util.*;
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import java.util.*;
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import java.util.zip.GZIPInputStream;
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import java.util.zip.GZIPInputStream;
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import java.util.zip.GZIPOutputStream;
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import java.util.zip.GZIPOutputStream;
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import org.apache.commons.cli.*;
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import org.apache.commons.cli.*;
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import org.apache.commons.codec.binary.Base64;
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import org.apache.commons.codec.binary.Base64;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.IOUtils;
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import com.fasterxml.jackson.databind.ObjectMapper;
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public class ArgumentApplicationParser implements Serializable {
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public class ArgumentApplicationParser implements Serializable {
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private final Options options = new Options();
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private final Options options = new Options();
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@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException;
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import java.util.Arrays;
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import java.util.Arrays;
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import java.util.List;
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import java.util.List;
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import java.util.stream.Collectors;
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import java.util.stream.Collectors;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileStatus;
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import org.apache.hadoop.fs.FileStatus;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.FileSystem;
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@ -1,12 +1,14 @@
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package eu.dnetlib.dhp.common;
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package eu.dnetlib.dhp.common;
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import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
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import java.util.Objects;
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import java.util.Objects;
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import java.util.function.Function;
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import java.util.function.Function;
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import org.apache.spark.SparkConf;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.SparkSession;
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import org.apache.spark.sql.SparkSession;
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import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
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/** SparkSession utility methods. */
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/** SparkSession utility methods. */
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public class SparkSessionSupport {
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public class SparkSessionSupport {
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@ -1,9 +1,10 @@
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package eu.dnetlib.dhp.model.mdstore;
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package eu.dnetlib.dhp.model.mdstore;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import java.io.Serializable;
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import java.io.Serializable;
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import eu.dnetlib.dhp.utils.DHPUtils;
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/** This class models a record inside the new Metadata store collection on HDFS * */
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/** This class models a record inside the new Metadata store collection on HDFS * */
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public class MetadataRecord implements Serializable {
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public class MetadataRecord implements Serializable {
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@ -1,13 +1,14 @@
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package eu.dnetlib.dhp.parser.utility;
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package eu.dnetlib.dhp.parser.utility;
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import com.ximpleware.AutoPilot;
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import com.ximpleware.VTDNav;
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import java.util.ArrayList;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashMap;
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import java.util.List;
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import java.util.List;
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import java.util.Map;
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import java.util.Map;
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import com.ximpleware.AutoPilot;
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import com.ximpleware.VTDNav;
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/** Created by sandro on 9/29/16. */
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/** Created by sandro on 9/29/16. */
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public class VtdUtilityParser {
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public class VtdUtilityParser {
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@ -1,18 +1,21 @@
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package eu.dnetlib.dhp.utils;
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package eu.dnetlib.dhp.utils;
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import com.jayway.jsonpath.JsonPath;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.ByteArrayOutputStream;
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import java.nio.charset.StandardCharsets;
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import java.nio.charset.StandardCharsets;
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import java.security.MessageDigest;
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import java.security.MessageDigest;
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import java.util.zip.GZIPInputStream;
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import java.util.zip.GZIPInputStream;
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import java.util.zip.GZIPOutputStream;
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import java.util.zip.GZIPOutputStream;
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import net.minidev.json.JSONArray;
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import org.apache.commons.codec.binary.Base64;
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import org.apache.commons.codec.binary.Base64;
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import org.apache.commons.codec.binary.Base64OutputStream;
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import org.apache.commons.codec.binary.Base64OutputStream;
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import org.apache.commons.codec.binary.Hex;
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import org.apache.commons.codec.binary.Hex;
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import com.jayway.jsonpath.JsonPath;
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import net.minidev.json.JSONArray;
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public class DHPUtils {
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public class DHPUtils {
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public static String md5(final String s) {
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public static String md5(final String s) {
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@ -1,11 +1,12 @@
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package eu.dnetlib.dhp.utils;
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package eu.dnetlib.dhp.utils;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.commons.logging.LogFactory;
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import org.apache.cxf.jaxws.JaxWsProxyFactoryBean;
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import org.apache.cxf.jaxws.JaxWsProxyFactoryBean;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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public class ISLookupClientFactory {
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public class ISLookupClientFactory {
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private static final Log log = LogFactory.getLog(ISLookupClientFactory.class);
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private static final Log log = LogFactory.getLog(ISLookupClientFactory.class);
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@ -5,6 +5,7 @@ import java.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.text.SimpleDateFormat;
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import java.util.Calendar;
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import java.util.Calendar;
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import java.util.GregorianCalendar;
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import java.util.GregorianCalendar;
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import net.sf.saxon.expr.XPathContext;
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import net.sf.saxon.expr.XPathContext;
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import net.sf.saxon.om.Item;
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import net.sf.saxon.om.Item;
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import net.sf.saxon.om.Sequence;
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import net.sf.saxon.om.Sequence;
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@ -4,6 +4,7 @@ package eu.dnetlib.dhp.utils.saxon;
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import java.text.ParseException;
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import java.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.text.SimpleDateFormat;
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import java.util.Date;
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import java.util.Date;
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import net.sf.saxon.expr.XPathContext;
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import net.sf.saxon.expr.XPathContext;
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import net.sf.saxon.om.Sequence;
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import net.sf.saxon.om.Sequence;
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import net.sf.saxon.trans.XPathException;
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import net.sf.saxon.trans.XPathException;
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@ -1,13 +1,14 @@
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package eu.dnetlib.dhp.utils.saxon;
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package eu.dnetlib.dhp.utils.saxon;
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import org.apache.commons.lang3.StringUtils;
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import net.sf.saxon.expr.XPathContext;
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import net.sf.saxon.expr.XPathContext;
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import net.sf.saxon.om.Item;
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import net.sf.saxon.om.Item;
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import net.sf.saxon.om.Sequence;
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import net.sf.saxon.om.Sequence;
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import net.sf.saxon.trans.XPathException;
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import net.sf.saxon.trans.XPathException;
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import net.sf.saxon.value.SequenceType;
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import net.sf.saxon.value.SequenceType;
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import net.sf.saxon.value.StringValue;
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import net.sf.saxon.value.StringValue;
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import org.apache.commons.lang3.StringUtils;
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public class PickFirst extends AbstractExtensionFunction {
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public class PickFirst extends AbstractExtensionFunction {
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package eu.dnetlib.dhp.utils.saxon;
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package eu.dnetlib.dhp.utils.saxon;
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import java.io.StringReader;
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import java.io.StringReader;
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import javax.xml.transform.Transformer;
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import javax.xml.transform.Transformer;
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import javax.xml.transform.TransformerException;
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import javax.xml.transform.TransformerException;
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import javax.xml.transform.stream.StreamSource;
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import javax.xml.transform.stream.StreamSource;
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import net.sf.saxon.Configuration;
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import net.sf.saxon.Configuration;
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import net.sf.saxon.TransformerFactoryImpl;
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import net.sf.saxon.TransformerFactoryImpl;
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package eu.dnetlib.message;
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package eu.dnetlib.message;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import java.io.IOException;
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import java.io.IOException;
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import java.util.Map;
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import java.util.Map;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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public class Message {
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public class Message {
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private String workflowId;
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private String workflowId;
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package eu.dnetlib.message;
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package eu.dnetlib.message;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import java.util.concurrent.LinkedBlockingQueue;
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import com.rabbitmq.client.AMQP;
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import com.rabbitmq.client.AMQP;
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import com.rabbitmq.client.Channel;
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import com.rabbitmq.client.Channel;
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import com.rabbitmq.client.DefaultConsumer;
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import com.rabbitmq.client.DefaultConsumer;
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import com.rabbitmq.client.Envelope;
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import com.rabbitmq.client.Envelope;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import java.util.concurrent.LinkedBlockingQueue;
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public class MessageConsumer extends DefaultConsumer {
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public class MessageConsumer extends DefaultConsumer {
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package eu.dnetlib.message;
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package eu.dnetlib.message;
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import com.rabbitmq.client.Channel;
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import com.rabbitmq.client.Connection;
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import com.rabbitmq.client.ConnectionFactory;
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import java.io.IOException;
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import java.io.IOException;
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import java.util.HashMap;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.Map;
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import java.util.concurrent.LinkedBlockingQueue;
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import java.util.concurrent.LinkedBlockingQueue;
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import java.util.concurrent.TimeoutException;
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import java.util.concurrent.TimeoutException;
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import com.rabbitmq.client.Channel;
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import com.rabbitmq.client.Connection;
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import com.rabbitmq.client.ConnectionFactory;
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public class MessageManager {
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public class MessageManager {
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private final String messageHost;
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private final String messageHost;
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@ -1,11 +1,13 @@
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package eu.dnetlib.scholexplorer.relation;
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package eu.dnetlib.scholexplorer.relation;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import java.io.Serializable;
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import java.io.Serializable;
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import java.util.HashMap;
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import java.util.HashMap;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.IOUtils;
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import com.fasterxml.jackson.databind.ObjectMapper;
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public class RelationMapper extends HashMap<String, RelInfo> implements Serializable {
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public class RelationMapper extends HashMap<String, RelInfo> implements Serializable {
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public static RelationMapper load() throws Exception {
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public static RelationMapper load() throws Exception {
|
||||||
|
|
|
@ -9,6 +9,7 @@ import java.nio.file.Path;
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.hadoop.conf.Configuration;
|
import org.apache.hadoop.conf.Configuration;
|
||||||
import org.junit.jupiter.api.Nested;
|
import org.junit.jupiter.api.Nested;
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
|
@ -3,13 +3,15 @@ package eu.dnetlib.dhp.common;
|
||||||
|
|
||||||
import static org.mockito.Mockito.*;
|
import static org.mockito.Mockito.*;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
|
|
||||||
import java.util.function.Function;
|
import java.util.function.Function;
|
||||||
|
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
import org.apache.spark.sql.SparkSession;
|
import org.apache.spark.sql.SparkSession;
|
||||||
import org.junit.jupiter.api.Nested;
|
import org.junit.jupiter.api.Nested;
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
|
||||||
|
|
||||||
public class SparkSessionSupportTest {
|
public class SparkSessionSupportTest {
|
||||||
|
|
||||||
@Nested
|
@Nested
|
||||||
|
|
|
@ -6,6 +6,7 @@ import static org.junit.jupiter.api.Assertions.*;
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.util.HashMap;
|
import java.util.HashMap;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
public class MessageTest {
|
public class MessageTest {
|
||||||
|
|
|
@ -1,10 +1,12 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.action;
|
package eu.dnetlib.dhp.schema.action;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
|
||||||
@JsonDeserialize(using = AtomicActionDeserializer.class)
|
@JsonDeserialize(using = AtomicActionDeserializer.class)
|
||||||
public class AtomicAction<T extends Oaf> implements Serializable {
|
public class AtomicAction<T extends Oaf> implements Serializable {
|
||||||
|
|
||||||
|
|
|
@ -1,14 +1,16 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.action;
|
package eu.dnetlib.dhp.schema.action;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
|
||||||
import com.fasterxml.jackson.core.JsonParser;
|
import com.fasterxml.jackson.core.JsonParser;
|
||||||
import com.fasterxml.jackson.core.JsonProcessingException;
|
import com.fasterxml.jackson.core.JsonProcessingException;
|
||||||
import com.fasterxml.jackson.databind.DeserializationContext;
|
import com.fasterxml.jackson.databind.DeserializationContext;
|
||||||
import com.fasterxml.jackson.databind.JsonDeserializer;
|
import com.fasterxml.jackson.databind.JsonDeserializer;
|
||||||
import com.fasterxml.jackson.databind.JsonNode;
|
import com.fasterxml.jackson.databind.JsonNode;
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
import java.io.IOException;
|
|
||||||
|
|
||||||
public class AtomicActionDeserializer extends JsonDeserializer {
|
public class AtomicActionDeserializer extends JsonDeserializer {
|
||||||
|
|
||||||
|
|
|
@ -1,12 +1,14 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.common;
|
package eu.dnetlib.dhp.schema.common;
|
||||||
|
|
||||||
import com.google.common.collect.Maps;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
import java.util.Optional;
|
import java.util.Optional;
|
||||||
import java.util.function.Function;
|
import java.util.function.Function;
|
||||||
|
|
||||||
|
import com.google.common.collect.Maps;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
|
||||||
/** Oaf model utility methods. */
|
/** Oaf model utility methods. */
|
||||||
public class ModelSupport {
|
public class ModelSupport {
|
||||||
|
|
||||||
|
|
|
@ -1,10 +1,11 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.oaf;
|
package eu.dnetlib.dhp.schema.oaf;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
|
|
||||||
public class Dataset extends Result implements Serializable {
|
public class Dataset extends Result implements Serializable {
|
||||||
|
|
||||||
private Field<String> storagedate;
|
private Field<String> storagedate;
|
||||||
|
|
|
@ -1,10 +1,12 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.oaf;
|
package eu.dnetlib.dhp.schema.oaf;
|
||||||
|
|
||||||
import com.fasterxml.jackson.annotation.JsonIgnore;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.JsonIgnore;
|
||||||
|
|
||||||
public class GeoLocation implements Serializable {
|
public class GeoLocation implements Serializable {
|
||||||
|
|
||||||
private String point;
|
private String point;
|
||||||
|
|
|
@ -1,10 +1,12 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.oaf;
|
package eu.dnetlib.dhp.schema.oaf;
|
||||||
|
|
||||||
import com.fasterxml.jackson.annotation.JsonIgnore;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.JsonIgnore;
|
||||||
|
|
||||||
public class KeyValue implements Serializable {
|
public class KeyValue implements Serializable {
|
||||||
|
|
||||||
private String key;
|
private String key;
|
||||||
|
|
|
@ -1,10 +1,11 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.oaf;
|
package eu.dnetlib.dhp.schema.oaf;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
|
|
||||||
public class OtherResearchProduct extends Result implements Serializable {
|
public class OtherResearchProduct extends Result implements Serializable {
|
||||||
|
|
||||||
private List<Field<String>> contactperson;
|
private List<Field<String>> contactperson;
|
||||||
|
|
|
@ -1,9 +1,10 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.oaf;
|
package eu.dnetlib.dhp.schema.oaf;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
|
|
||||||
public class Publication extends Result implements Serializable {
|
public class Publication extends Result implements Serializable {
|
||||||
|
|
||||||
// publication specific
|
// publication specific
|
||||||
|
|
|
@ -1,10 +1,12 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.oaf;
|
package eu.dnetlib.dhp.schema.oaf;
|
||||||
|
|
||||||
import com.fasterxml.jackson.annotation.JsonIgnore;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.JsonIgnore;
|
||||||
|
|
||||||
public class Qualifier implements Serializable {
|
public class Qualifier implements Serializable {
|
||||||
|
|
||||||
private String classid;
|
private String classid;
|
||||||
|
|
|
@ -1,10 +1,11 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.oaf;
|
package eu.dnetlib.dhp.schema.oaf;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
|
|
||||||
public class Software extends Result implements Serializable {
|
public class Software extends Result implements Serializable {
|
||||||
|
|
||||||
private List<Field<String>> documentationUrl;
|
private List<Field<String>> documentationUrl;
|
||||||
|
|
|
@ -1,14 +1,16 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.scholexplorer;
|
package eu.dnetlib.dhp.schema.scholexplorer;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.HashMap;
|
import java.util.HashMap;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||||
|
|
||||||
public class DLIDataset extends Dataset {
|
public class DLIDataset extends Dataset {
|
||||||
|
|
||||||
private String originalObjIdentifier;
|
private String originalObjIdentifier;
|
||||||
|
|
|
@ -1,12 +1,14 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.scholexplorer;
|
package eu.dnetlib.dhp.schema.scholexplorer;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.util.*;
|
import java.util.*;
|
||||||
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||||
|
|
||||||
public class DLIPublication extends Publication implements Serializable {
|
public class DLIPublication extends Publication implements Serializable {
|
||||||
|
|
||||||
private String originalObjIdentifier;
|
private String originalObjIdentifier;
|
||||||
|
|
|
@ -1,15 +1,17 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.scholexplorer;
|
package eu.dnetlib.dhp.schema.scholexplorer;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.HashMap;
|
import java.util.HashMap;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
|
||||||
public class DLIUnknown extends Oaf implements Serializable {
|
public class DLIUnknown extends Oaf implements Serializable {
|
||||||
|
|
||||||
private String id;
|
private String id;
|
||||||
|
|
|
@ -3,12 +3,15 @@ package eu.dnetlib.dhp.schema.action;
|
||||||
|
|
||||||
import static org.junit.jupiter.api.Assertions.*;
|
import static org.junit.jupiter.api.Assertions.*;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
|
||||||
/** @author claudio.atzori */
|
/** @author claudio.atzori */
|
||||||
public class AtomicActionTest {
|
public class AtomicActionTest {
|
||||||
|
|
||||||
|
|
|
@ -4,11 +4,12 @@ package eu.dnetlib.dhp.schema.common;
|
||||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||||
|
|
||||||
|
import org.junit.jupiter.api.Nested;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
import org.junit.jupiter.api.Nested;
|
|
||||||
import org.junit.jupiter.api.Test;
|
|
||||||
|
|
||||||
public class ModelSupportTest {
|
public class ModelSupportTest {
|
||||||
|
|
||||||
|
|
|
@ -5,6 +5,7 @@ import static org.junit.jupiter.api.Assertions.*;
|
||||||
|
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import org.junit.jupiter.api.BeforeEach;
|
import org.junit.jupiter.api.BeforeEach;
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
|
|
@ -1,16 +1,19 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.scholexplorer;
|
package eu.dnetlib.dhp.schema.scholexplorer;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.Collections;
|
||||||
|
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
import com.fasterxml.jackson.core.JsonProcessingException;
|
import com.fasterxml.jackson.core.JsonProcessingException;
|
||||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
import com.fasterxml.jackson.databind.SerializationFeature;
|
import com.fasterxml.jackson.databind.SerializationFeature;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
import java.io.IOException;
|
|
||||||
import java.util.Arrays;
|
|
||||||
import java.util.Collections;
|
|
||||||
import org.junit.jupiter.api.Test;
|
|
||||||
|
|
||||||
public class DLItest {
|
public class DLItest {
|
||||||
|
|
||||||
|
|
|
@ -1,9 +1,23 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.actionmanager;
|
package eu.dnetlib.dhp.actionmanager;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.io.StringReader;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.NoSuchElementException;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
|
import org.dom4j.Document;
|
||||||
|
import org.dom4j.Element;
|
||||||
|
import org.dom4j.io.SAXReader;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
import com.google.common.base.Splitter;
|
import com.google.common.base.Splitter;
|
||||||
import com.google.common.collect.Iterables;
|
import com.google.common.collect.Iterables;
|
||||||
import com.google.common.collect.Lists;
|
import com.google.common.collect.Lists;
|
||||||
|
|
||||||
import eu.dnetlib.actionmanager.rmi.ActionManagerException;
|
import eu.dnetlib.actionmanager.rmi.ActionManagerException;
|
||||||
import eu.dnetlib.actionmanager.set.ActionManagerSet;
|
import eu.dnetlib.actionmanager.set.ActionManagerSet;
|
||||||
import eu.dnetlib.actionmanager.set.ActionManagerSet.ImpactTypes;
|
import eu.dnetlib.actionmanager.set.ActionManagerSet.ImpactTypes;
|
||||||
|
@ -11,17 +25,6 @@ import eu.dnetlib.dhp.actionmanager.partition.PartitionActionSetsByPayloadTypeJo
|
||||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||||
import java.io.Serializable;
|
|
||||||
import java.io.StringReader;
|
|
||||||
import java.util.ArrayList;
|
|
||||||
import java.util.List;
|
|
||||||
import java.util.NoSuchElementException;
|
|
||||||
import java.util.stream.Collectors;
|
|
||||||
import org.dom4j.Document;
|
|
||||||
import org.dom4j.Element;
|
|
||||||
import org.dom4j.io.SAXReader;
|
|
||||||
import org.slf4j.Logger;
|
|
||||||
import org.slf4j.LoggerFactory;
|
|
||||||
|
|
||||||
public class ISClient implements Serializable {
|
public class ISClient implements Serializable {
|
||||||
|
|
||||||
|
|
|
@ -1,9 +1,10 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.actionmanager.migration;
|
package eu.dnetlib.dhp.actionmanager.migration;
|
||||||
|
|
||||||
import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
|
|
||||||
import java.util.Comparator;
|
import java.util.Comparator;
|
||||||
|
|
||||||
|
import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
|
||||||
|
|
||||||
public class LicenseComparator implements Comparator<Qualifier> {
|
public class LicenseComparator implements Comparator<Qualifier> {
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
|
|
|
@ -1,12 +1,6 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.actionmanager.migration;
|
package eu.dnetlib.dhp.actionmanager.migration;
|
||||||
|
|
||||||
import com.google.common.base.Splitter;
|
|
||||||
import com.google.common.collect.Lists;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
|
||||||
import java.io.File;
|
import java.io.File;
|
||||||
import java.io.FileOutputStream;
|
import java.io.FileOutputStream;
|
||||||
import java.io.OutputStream;
|
import java.io.OutputStream;
|
||||||
|
@ -15,6 +9,7 @@ import java.util.LinkedList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Properties;
|
import java.util.Properties;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
import org.apache.hadoop.conf.Configuration;
|
import org.apache.hadoop.conf.Configuration;
|
||||||
|
@ -26,6 +21,14 @@ import org.apache.hadoop.util.ToolRunner;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import com.google.common.base.Splitter;
|
||||||
|
import com.google.common.collect.Lists;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||||
|
|
||||||
public class MigrateActionSet {
|
public class MigrateActionSet {
|
||||||
|
|
||||||
private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class);
|
private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class);
|
||||||
|
|
|
@ -6,16 +6,19 @@ import static eu.dnetlib.data.proto.KindProtos.Kind.relation;
|
||||||
import static eu.dnetlib.data.proto.TypeProtos.*;
|
import static eu.dnetlib.data.proto.TypeProtos.*;
|
||||||
import static eu.dnetlib.data.proto.TypeProtos.Type.*;
|
import static eu.dnetlib.data.proto.TypeProtos.Type.*;
|
||||||
|
|
||||||
import com.google.common.collect.Lists;
|
|
||||||
import com.googlecode.protobuf.format.JsonFormat;
|
|
||||||
import eu.dnetlib.data.proto.*;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Optional;
|
import java.util.Optional;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
|
||||||
|
import com.google.common.collect.Lists;
|
||||||
|
import com.googlecode.protobuf.format.JsonFormat;
|
||||||
|
|
||||||
|
import eu.dnetlib.data.proto.*;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
|
||||||
public class ProtoConverter implements Serializable {
|
public class ProtoConverter implements Serializable {
|
||||||
|
|
||||||
public static final String UNKNOWN = "UNKNOWN";
|
public static final String UNKNOWN = "UNKNOWN";
|
||||||
|
|
|
@ -3,22 +3,12 @@ package eu.dnetlib.dhp.actionmanager.migration;
|
||||||
|
|
||||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import com.google.common.base.Splitter;
|
|
||||||
import com.google.common.collect.Lists;
|
|
||||||
import com.google.protobuf.InvalidProtocolBufferException;
|
|
||||||
import eu.dnetlib.data.proto.OafProtos;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.util.LinkedList;
|
import java.util.LinkedList;
|
||||||
import java.util.Objects;
|
import java.util.Objects;
|
||||||
import java.util.Optional;
|
import java.util.Optional;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
import org.apache.hadoop.fs.FileSystem;
|
import org.apache.hadoop.fs.FileSystem;
|
||||||
|
@ -30,6 +20,19 @@ import org.apache.spark.api.java.JavaSparkContext;
|
||||||
import org.apache.spark.sql.SparkSession;
|
import org.apache.spark.sql.SparkSession;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
import com.google.common.base.Splitter;
|
||||||
|
import com.google.common.collect.Lists;
|
||||||
|
import com.google.protobuf.InvalidProtocolBufferException;
|
||||||
|
|
||||||
|
import eu.dnetlib.data.proto.OafProtos;
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class TransformActions implements Serializable {
|
public class TransformActions implements Serializable {
|
||||||
|
|
|
@ -4,13 +4,10 @@ package eu.dnetlib.dhp.actionmanager.partition;
|
||||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||||
import static org.apache.spark.sql.functions.*;
|
import static org.apache.spark.sql.functions.*;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.actionmanager.ISClient;
|
|
||||||
import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Optional;
|
import java.util.Optional;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.hadoop.io.Text;
|
import org.apache.hadoop.io.Text;
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
|
@ -21,6 +18,11 @@ import org.apache.spark.sql.types.*;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.actionmanager.ISClient;
|
||||||
|
import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob;
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||||
|
|
||||||
/** Partitions given set of action sets by payload type. */
|
/** Partitions given set of action sets by payload type. */
|
||||||
public class PartitionActionSetsByPayloadTypeJob {
|
public class PartitionActionSetsByPayloadTypeJob {
|
||||||
|
|
||||||
|
|
|
@ -3,11 +3,12 @@ package eu.dnetlib.dhp.actionmanager.promote;
|
||||||
|
|
||||||
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
|
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
|
||||||
|
|
||||||
|
import java.util.function.BiFunction;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
|
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
import java.util.function.BiFunction;
|
|
||||||
|
|
||||||
/** OAF model merging support. */
|
/** OAF model merging support. */
|
||||||
public class MergeAndGet {
|
public class MergeAndGet {
|
||||||
|
|
|
@ -4,16 +4,11 @@ package eu.dnetlib.dhp.actionmanager.promote;
|
||||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||||
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
|
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
|
|
||||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import java.util.Objects;
|
import java.util.Objects;
|
||||||
import java.util.Optional;
|
import java.util.Optional;
|
||||||
import java.util.function.BiFunction;
|
import java.util.function.BiFunction;
|
||||||
import java.util.function.Function;
|
import java.util.function.Function;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
|
@ -24,6 +19,14 @@ import org.apache.spark.sql.SparkSession;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
|
||||||
|
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
|
||||||
/** Applies a given action payload file to graph table of compatible type. */
|
/** Applies a given action payload file to graph table of compatible type. */
|
||||||
public class PromoteActionPayloadForGraphTableJob {
|
public class PromoteActionPayloadForGraphTableJob {
|
||||||
private static final Logger logger = LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class);
|
private static final Logger logger = LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class);
|
||||||
|
|
|
@ -3,12 +3,11 @@ package eu.dnetlib.dhp.actionmanager.promote;
|
||||||
|
|
||||||
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
|
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
||||||
import java.util.Objects;
|
import java.util.Objects;
|
||||||
import java.util.Optional;
|
import java.util.Optional;
|
||||||
import java.util.function.BiFunction;
|
import java.util.function.BiFunction;
|
||||||
import java.util.function.Function;
|
import java.util.function.Function;
|
||||||
|
|
||||||
import org.apache.spark.api.java.function.FilterFunction;
|
import org.apache.spark.api.java.function.FilterFunction;
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
import org.apache.spark.sql.Dataset;
|
import org.apache.spark.sql.Dataset;
|
||||||
|
@ -16,6 +15,9 @@ import org.apache.spark.sql.Encoder;
|
||||||
import org.apache.spark.sql.Encoders;
|
import org.apache.spark.sql.Encoders;
|
||||||
import org.apache.spark.sql.TypedColumn;
|
import org.apache.spark.sql.TypedColumn;
|
||||||
import org.apache.spark.sql.expressions.Aggregator;
|
import org.apache.spark.sql.expressions.Aggregator;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
/** Promote action payload functions. */
|
/** Promote action payload functions. */
|
||||||
|
|
|
@ -6,16 +6,13 @@ import static org.apache.spark.sql.functions.*;
|
||||||
import static org.junit.jupiter.api.Assertions.assertIterableEquals;
|
import static org.junit.jupiter.api.Assertions.assertIterableEquals;
|
||||||
import static scala.collection.JavaConversions.mutableSeqAsJavaList;
|
import static scala.collection.JavaConversions.mutableSeqAsJavaList;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.actionmanager.ISClient;
|
|
||||||
import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.nio.file.Files;
|
import java.nio.file.Files;
|
||||||
import java.nio.file.Path;
|
import java.nio.file.Path;
|
||||||
import java.nio.file.Paths;
|
import java.nio.file.Paths;
|
||||||
import java.util.*;
|
import java.util.*;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.hadoop.conf.Configuration;
|
import org.apache.hadoop.conf.Configuration;
|
||||||
import org.apache.hadoop.io.Text;
|
import org.apache.hadoop.io.Text;
|
||||||
import org.apache.hadoop.mapreduce.Job;
|
import org.apache.hadoop.mapreduce.Job;
|
||||||
|
@ -33,6 +30,12 @@ import org.junit.jupiter.api.io.TempDir;
|
||||||
import org.mockito.Mock;
|
import org.mockito.Mock;
|
||||||
import org.mockito.Mockito;
|
import org.mockito.Mockito;
|
||||||
import org.mockito.junit.jupiter.MockitoExtension;
|
import org.mockito.junit.jupiter.MockitoExtension;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.actionmanager.ISClient;
|
||||||
|
import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
import scala.collection.mutable.Seq;
|
import scala.collection.mutable.Seq;
|
||||||
|
|
||||||
|
|
|
@ -6,12 +6,14 @@ import static eu.dnetlib.dhp.actionmanager.promote.MergeAndGet.functionFor;
|
||||||
import static org.junit.jupiter.api.Assertions.*;
|
import static org.junit.jupiter.api.Assertions.*;
|
||||||
import static org.mockito.Mockito.*;
|
import static org.mockito.Mockito.*;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import java.util.function.BiFunction;
|
import java.util.function.BiFunction;
|
||||||
|
|
||||||
import org.junit.jupiter.api.Nested;
|
import org.junit.jupiter.api.Nested;
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
|
||||||
public class MergeAndGetTest {
|
public class MergeAndGetTest {
|
||||||
|
|
||||||
@Nested
|
@Nested
|
||||||
|
|
|
@ -4,9 +4,6 @@ package eu.dnetlib.dhp.actionmanager.promote;
|
||||||
import static org.junit.jupiter.api.Assertions.*;
|
import static org.junit.jupiter.api.Assertions.*;
|
||||||
import static org.junit.jupiter.params.provider.Arguments.arguments;
|
import static org.junit.jupiter.params.provider.Arguments.arguments;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.nio.file.Files;
|
import java.nio.file.Files;
|
||||||
import java.nio.file.Path;
|
import java.nio.file.Path;
|
||||||
|
@ -16,6 +13,7 @@ import java.util.List;
|
||||||
import java.util.Objects;
|
import java.util.Objects;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
import java.util.stream.Stream;
|
import java.util.stream.Stream;
|
||||||
|
|
||||||
import org.apache.commons.io.FileUtils;
|
import org.apache.commons.io.FileUtils;
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
|
@ -27,6 +25,11 @@ import org.junit.jupiter.params.ParameterizedTest;
|
||||||
import org.junit.jupiter.params.provider.Arguments;
|
import org.junit.jupiter.params.provider.Arguments;
|
||||||
import org.junit.jupiter.params.provider.MethodSource;
|
import org.junit.jupiter.params.provider.MethodSource;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
|
||||||
public class PromoteActionPayloadForGraphTableJobTest {
|
public class PromoteActionPayloadForGraphTableJobTest {
|
||||||
private static final ClassLoader cl = PromoteActionPayloadForGraphTableJobTest.class.getClassLoader();
|
private static final ClassLoader cl = PromoteActionPayloadForGraphTableJobTest.class.getClassLoader();
|
||||||
|
|
||||||
|
|
|
@ -4,13 +4,12 @@ package eu.dnetlib.dhp.actionmanager.promote;
|
||||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||||
import static org.junit.jupiter.api.Assertions.assertThrows;
|
import static org.junit.jupiter.api.Assertions.assertThrows;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Objects;
|
import java.util.Objects;
|
||||||
import java.util.function.BiFunction;
|
import java.util.function.BiFunction;
|
||||||
import java.util.function.Function;
|
import java.util.function.Function;
|
||||||
|
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
import org.apache.spark.sql.Dataset;
|
import org.apache.spark.sql.Dataset;
|
||||||
import org.apache.spark.sql.Encoders;
|
import org.apache.spark.sql.Encoders;
|
||||||
|
@ -20,6 +19,9 @@ import org.junit.jupiter.api.BeforeAll;
|
||||||
import org.junit.jupiter.api.Nested;
|
import org.junit.jupiter.api.Nested;
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
|
||||||
public class PromoteActionPayloadFunctionsTest {
|
public class PromoteActionPayloadFunctionsTest {
|
||||||
|
|
||||||
private static SparkSession spark;
|
private static SparkSession spark;
|
||||||
|
|
|
@ -1,18 +1,12 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.collection;
|
package eu.dnetlib.dhp.collection;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
|
||||||
import eu.dnetlib.dhp.model.mdstore.Provenance;
|
|
||||||
import eu.dnetlib.message.Message;
|
|
||||||
import eu.dnetlib.message.MessageManager;
|
|
||||||
import eu.dnetlib.message.MessageType;
|
|
||||||
import java.io.ByteArrayInputStream;
|
import java.io.ByteArrayInputStream;
|
||||||
import java.nio.charset.StandardCharsets;
|
import java.nio.charset.StandardCharsets;
|
||||||
import java.util.HashMap;
|
import java.util.HashMap;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
import java.util.Objects;
|
import java.util.Objects;
|
||||||
|
|
||||||
import org.apache.commons.cli.*;
|
import org.apache.commons.cli.*;
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
@ -30,6 +24,15 @@ import org.dom4j.Document;
|
||||||
import org.dom4j.Node;
|
import org.dom4j.Node;
|
||||||
import org.dom4j.io.SAXReader;
|
import org.dom4j.io.SAXReader;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
||||||
|
import eu.dnetlib.dhp.model.mdstore.Provenance;
|
||||||
|
import eu.dnetlib.message.Message;
|
||||||
|
import eu.dnetlib.message.MessageManager;
|
||||||
|
import eu.dnetlib.message.MessageType;
|
||||||
|
|
||||||
public class GenerateNativeStoreSparkJob {
|
public class GenerateNativeStoreSparkJob {
|
||||||
|
|
||||||
public static MetadataRecord parseRecord(
|
public static MetadataRecord parseRecord(
|
||||||
|
|
|
@ -1,9 +1,10 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.collection.plugin;
|
package eu.dnetlib.dhp.collection.plugin;
|
||||||
|
|
||||||
|
import java.util.stream.Stream;
|
||||||
|
|
||||||
import eu.dnetlib.collector.worker.model.ApiDescriptor;
|
import eu.dnetlib.collector.worker.model.ApiDescriptor;
|
||||||
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
|
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
|
||||||
import java.util.stream.Stream;
|
|
||||||
|
|
||||||
public interface CollectorPlugin {
|
public interface CollectorPlugin {
|
||||||
|
|
||||||
|
|
|
@ -1,12 +1,6 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.collection.plugin.oai;
|
package eu.dnetlib.dhp.collection.plugin.oai;
|
||||||
|
|
||||||
import com.google.common.base.Splitter;
|
|
||||||
import com.google.common.collect.Iterators;
|
|
||||||
import com.google.common.collect.Lists;
|
|
||||||
import eu.dnetlib.collector.worker.model.ApiDescriptor;
|
|
||||||
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
|
|
||||||
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
|
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.Iterator;
|
import java.util.Iterator;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
@ -15,6 +9,14 @@ import java.util.Spliterators;
|
||||||
import java.util.stream.Stream;
|
import java.util.stream.Stream;
|
||||||
import java.util.stream.StreamSupport;
|
import java.util.stream.StreamSupport;
|
||||||
|
|
||||||
|
import com.google.common.base.Splitter;
|
||||||
|
import com.google.common.collect.Iterators;
|
||||||
|
import com.google.common.collect.Lists;
|
||||||
|
|
||||||
|
import eu.dnetlib.collector.worker.model.ApiDescriptor;
|
||||||
|
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
|
||||||
|
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
|
||||||
|
|
||||||
public class OaiCollectorPlugin implements CollectorPlugin {
|
public class OaiCollectorPlugin implements CollectorPlugin {
|
||||||
|
|
||||||
private static final String FORMAT_PARAM = "format";
|
private static final String FORMAT_PARAM = "format";
|
||||||
|
|
|
@ -1,15 +1,13 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.collection.plugin.oai;
|
package eu.dnetlib.dhp.collection.plugin.oai;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
|
|
||||||
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
|
|
||||||
import eu.dnetlib.dhp.collection.worker.utils.XmlCleaner;
|
|
||||||
import java.io.StringReader;
|
import java.io.StringReader;
|
||||||
import java.io.UnsupportedEncodingException;
|
import java.io.UnsupportedEncodingException;
|
||||||
import java.net.URLEncoder;
|
import java.net.URLEncoder;
|
||||||
import java.util.Iterator;
|
import java.util.Iterator;
|
||||||
import java.util.Queue;
|
import java.util.Queue;
|
||||||
import java.util.concurrent.PriorityBlockingQueue;
|
import java.util.concurrent.PriorityBlockingQueue;
|
||||||
|
|
||||||
import org.apache.commons.lang.StringUtils;
|
import org.apache.commons.lang.StringUtils;
|
||||||
import org.apache.commons.logging.Log;
|
import org.apache.commons.logging.Log;
|
||||||
import org.apache.commons.logging.LogFactory;
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
@ -18,6 +16,10 @@ import org.dom4j.DocumentException;
|
||||||
import org.dom4j.Node;
|
import org.dom4j.Node;
|
||||||
import org.dom4j.io.SAXReader;
|
import org.dom4j.io.SAXReader;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
|
||||||
|
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
|
||||||
|
import eu.dnetlib.dhp.collection.worker.utils.XmlCleaner;
|
||||||
|
|
||||||
public class OaiIterator implements Iterator<String> {
|
public class OaiIterator implements Iterator<String> {
|
||||||
|
|
||||||
private static final Log log = LogFactory.getLog(OaiIterator.class); // NOPMD by marko on
|
private static final Log log = LogFactory.getLog(OaiIterator.class); // NOPMD by marko on
|
||||||
|
|
|
@ -1,9 +1,10 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.collection.plugin.oai;
|
package eu.dnetlib.dhp.collection.plugin.oai;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
|
|
||||||
import java.util.Iterator;
|
import java.util.Iterator;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
|
||||||
|
|
||||||
public class OaiIteratorFactory {
|
public class OaiIteratorFactory {
|
||||||
|
|
||||||
private HttpConnector httpConnector;
|
private HttpConnector httpConnector;
|
||||||
|
|
|
@ -1,19 +1,12 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.collection.worker;
|
package eu.dnetlib.dhp.collection.worker;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.collector.worker.model.ApiDescriptor;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
|
|
||||||
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
|
|
||||||
import eu.dnetlib.message.Message;
|
|
||||||
import eu.dnetlib.message.MessageManager;
|
|
||||||
import eu.dnetlib.message.MessageType;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.net.URI;
|
import java.net.URI;
|
||||||
import java.util.HashMap;
|
import java.util.HashMap;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
import java.util.concurrent.atomic.AtomicInteger;
|
import java.util.concurrent.atomic.AtomicInteger;
|
||||||
|
|
||||||
import org.apache.hadoop.conf.Configuration;
|
import org.apache.hadoop.conf.Configuration;
|
||||||
import org.apache.hadoop.fs.FileSystem;
|
import org.apache.hadoop.fs.FileSystem;
|
||||||
import org.apache.hadoop.fs.Path;
|
import org.apache.hadoop.fs.Path;
|
||||||
|
@ -23,6 +16,16 @@ import org.apache.hadoop.io.Text;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.collector.worker.model.ApiDescriptor;
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
|
||||||
|
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
|
||||||
|
import eu.dnetlib.message.Message;
|
||||||
|
import eu.dnetlib.message.MessageManager;
|
||||||
|
import eu.dnetlib.message.MessageType;
|
||||||
|
|
||||||
public class DnetCollectorWorker {
|
public class DnetCollectorWorker {
|
||||||
|
|
||||||
private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorker.class);
|
private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorker.class);
|
||||||
|
|
|
@ -1,12 +1,13 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.collection.worker;
|
package eu.dnetlib.dhp.collection.worker;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
|
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
|
||||||
import eu.dnetlib.message.MessageManager;
|
import eu.dnetlib.message.MessageManager;
|
||||||
import org.apache.commons.io.IOUtils;
|
|
||||||
import org.slf4j.Logger;
|
|
||||||
import org.slf4j.LoggerFactory;
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* DnetCollectortWorkerApplication is the main class responsible to start the Dnet Collection into HDFS. This module
|
* DnetCollectortWorkerApplication is the main class responsible to start the Dnet Collection into HDFS. This module
|
||||||
|
|
|
@ -1,7 +1,6 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.collection.worker.utils;
|
package eu.dnetlib.dhp.collection.worker.utils;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.io.InputStream;
|
import java.io.InputStream;
|
||||||
import java.net.*;
|
import java.net.*;
|
||||||
|
@ -9,15 +8,19 @@ import java.security.GeneralSecurityException;
|
||||||
import java.security.cert.X509Certificate;
|
import java.security.cert.X509Certificate;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
|
||||||
import javax.net.ssl.HttpsURLConnection;
|
import javax.net.ssl.HttpsURLConnection;
|
||||||
import javax.net.ssl.SSLContext;
|
import javax.net.ssl.SSLContext;
|
||||||
import javax.net.ssl.TrustManager;
|
import javax.net.ssl.TrustManager;
|
||||||
import javax.net.ssl.X509TrustManager;
|
import javax.net.ssl.X509TrustManager;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.commons.lang.math.NumberUtils;
|
import org.apache.commons.lang.math.NumberUtils;
|
||||||
import org.apache.commons.logging.Log;
|
import org.apache.commons.logging.Log;
|
||||||
import org.apache.commons.logging.LogFactory;
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
|
||||||
|
|
||||||
public class HttpConnector {
|
public class HttpConnector {
|
||||||
|
|
||||||
private static final Log log = LogFactory.getLog(HttpConnector.class);
|
private static final Log log = LogFactory.getLog(HttpConnector.class);
|
||||||
|
|
|
@ -1,16 +1,19 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.transformation;
|
package eu.dnetlib.dhp.transformation;
|
||||||
|
|
||||||
|
import java.io.ByteArrayInputStream;
|
||||||
|
import java.io.StringWriter;
|
||||||
|
import java.util.Map;
|
||||||
|
|
||||||
|
import javax.xml.transform.stream.StreamSource;
|
||||||
|
|
||||||
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
|
import org.apache.spark.util.LongAccumulator;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
||||||
import eu.dnetlib.dhp.transformation.functions.Cleaner;
|
import eu.dnetlib.dhp.transformation.functions.Cleaner;
|
||||||
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
|
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
|
||||||
import java.io.ByteArrayInputStream;
|
|
||||||
import java.io.StringWriter;
|
|
||||||
import java.util.Map;
|
|
||||||
import javax.xml.transform.stream.StreamSource;
|
|
||||||
import net.sf.saxon.s9api.*;
|
import net.sf.saxon.s9api.*;
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
|
||||||
import org.apache.spark.util.LongAccumulator;
|
|
||||||
|
|
||||||
public class TransformFunction implements MapFunction<MetadataRecord, MetadataRecord> {
|
public class TransformFunction implements MapFunction<MetadataRecord, MetadataRecord> {
|
||||||
|
|
||||||
|
|
|
@ -1,18 +1,11 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.transformation;
|
package eu.dnetlib.dhp.transformation;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
|
||||||
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
|
|
||||||
import eu.dnetlib.dhp.transformation.vocabulary.VocabularyHelper;
|
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
|
||||||
import eu.dnetlib.message.Message;
|
|
||||||
import eu.dnetlib.message.MessageManager;
|
|
||||||
import eu.dnetlib.message.MessageType;
|
|
||||||
import java.io.ByteArrayInputStream;
|
import java.io.ByteArrayInputStream;
|
||||||
import java.util.HashMap;
|
import java.util.HashMap;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
import java.util.Objects;
|
import java.util.Objects;
|
||||||
|
|
||||||
import org.apache.commons.cli.*;
|
import org.apache.commons.cli.*;
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.spark.sql.Dataset;
|
import org.apache.spark.sql.Dataset;
|
||||||
|
@ -25,6 +18,15 @@ import org.dom4j.DocumentException;
|
||||||
import org.dom4j.Node;
|
import org.dom4j.Node;
|
||||||
import org.dom4j.io.SAXReader;
|
import org.dom4j.io.SAXReader;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
||||||
|
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
|
||||||
|
import eu.dnetlib.dhp.transformation.vocabulary.VocabularyHelper;
|
||||||
|
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||||
|
import eu.dnetlib.message.Message;
|
||||||
|
import eu.dnetlib.message.MessageManager;
|
||||||
|
import eu.dnetlib.message.MessageType;
|
||||||
|
|
||||||
public class TransformSparkJobNode {
|
public class TransformSparkJobNode {
|
||||||
|
|
||||||
public static void main(String[] args) throws Exception {
|
public static void main(String[] args) throws Exception {
|
||||||
|
|
|
@ -1,10 +1,11 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.transformation.functions;
|
package eu.dnetlib.dhp.transformation.functions;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.transformation.vocabulary.Term;
|
|
||||||
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
|
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
import java.util.Optional;
|
import java.util.Optional;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.transformation.vocabulary.Term;
|
||||||
|
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
|
||||||
import net.sf.saxon.s9api.*;
|
import net.sf.saxon.s9api.*;
|
||||||
import scala.Serializable;
|
import scala.Serializable;
|
||||||
|
|
||||||
|
|
|
@ -1,12 +1,14 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.transformation.vocabulary;
|
package eu.dnetlib.dhp.transformation.vocabulary;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.net.URL;
|
import java.net.URL;
|
||||||
import java.nio.charset.Charset;
|
import java.nio.charset.Charset;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
public class VocabularyHelper implements Serializable {
|
public class VocabularyHelper implements Serializable {
|
||||||
|
|
||||||
private static final String OPENAIRE_URL = "http://api.openaire.eu/vocabularies/%s.json";
|
private static final String OPENAIRE_URL = "http://api.openaire.eu/vocabularies/%s.json";
|
||||||
|
|
|
@ -3,18 +3,21 @@ package eu.dnetlib.dhp.collection;
|
||||||
|
|
||||||
import static org.junit.jupiter.api.Assertions.*;
|
import static org.junit.jupiter.api.Assertions.*;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
|
||||||
import eu.dnetlib.dhp.model.mdstore.Provenance;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.nio.file.Files;
|
import java.nio.file.Files;
|
||||||
import java.nio.file.Path;
|
import java.nio.file.Path;
|
||||||
|
|
||||||
import org.apache.commons.io.FileUtils;
|
import org.apache.commons.io.FileUtils;
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.junit.jupiter.api.AfterEach;
|
import org.junit.jupiter.api.AfterEach;
|
||||||
import org.junit.jupiter.api.BeforeEach;
|
import org.junit.jupiter.api.BeforeEach;
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
||||||
|
import eu.dnetlib.dhp.model.mdstore.Provenance;
|
||||||
|
|
||||||
public class CollectionJobTest {
|
public class CollectionJobTest {
|
||||||
|
|
||||||
private Path testDir;
|
private Path testDir;
|
||||||
|
|
|
@ -4,17 +4,20 @@ package eu.dnetlib.dhp.collector.worker;
|
||||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||||
import static org.mockito.Mockito.*;
|
import static org.mockito.Mockito.*;
|
||||||
|
|
||||||
|
import java.io.File;
|
||||||
|
|
||||||
|
import org.junit.jupiter.api.AfterEach;
|
||||||
|
import org.junit.jupiter.api.BeforeEach;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
import eu.dnetlib.collector.worker.model.ApiDescriptor;
|
import eu.dnetlib.collector.worker.model.ApiDescriptor;
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
import eu.dnetlib.dhp.collection.worker.DnetCollectorWorker;
|
import eu.dnetlib.dhp.collection.worker.DnetCollectorWorker;
|
||||||
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
|
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
|
||||||
import eu.dnetlib.message.Message;
|
import eu.dnetlib.message.Message;
|
||||||
import eu.dnetlib.message.MessageManager;
|
import eu.dnetlib.message.MessageManager;
|
||||||
import java.io.File;
|
|
||||||
import org.junit.jupiter.api.AfterEach;
|
|
||||||
import org.junit.jupiter.api.BeforeEach;
|
|
||||||
import org.junit.jupiter.api.Test;
|
|
||||||
|
|
||||||
public class DnetCollectorWorkerApplicationTests {
|
public class DnetCollectorWorkerApplicationTests {
|
||||||
|
|
||||||
|
|
|
@ -3,18 +3,14 @@ package eu.dnetlib.dhp.transformation;
|
||||||
|
|
||||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
|
||||||
import eu.dnetlib.dhp.transformation.functions.Cleaner;
|
|
||||||
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
|
|
||||||
import eu.dnetlib.dhp.transformation.vocabulary.VocabularyHelper;
|
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
|
||||||
import java.io.StringWriter;
|
import java.io.StringWriter;
|
||||||
import java.nio.file.Files;
|
import java.nio.file.Files;
|
||||||
import java.nio.file.Path;
|
import java.nio.file.Path;
|
||||||
import java.util.HashMap;
|
import java.util.HashMap;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
|
||||||
import javax.xml.transform.stream.StreamSource;
|
import javax.xml.transform.stream.StreamSource;
|
||||||
import net.sf.saxon.s9api.*;
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.spark.util.LongAccumulator;
|
import org.apache.spark.util.LongAccumulator;
|
||||||
import org.dom4j.Document;
|
import org.dom4j.Document;
|
||||||
|
@ -27,6 +23,13 @@ import org.junit.jupiter.api.io.TempDir;
|
||||||
import org.mockito.Mock;
|
import org.mockito.Mock;
|
||||||
import org.mockito.junit.jupiter.MockitoExtension;
|
import org.mockito.junit.jupiter.MockitoExtension;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
||||||
|
import eu.dnetlib.dhp.transformation.functions.Cleaner;
|
||||||
|
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
|
||||||
|
import eu.dnetlib.dhp.transformation.vocabulary.VocabularyHelper;
|
||||||
|
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||||
|
import net.sf.saxon.s9api.*;
|
||||||
|
|
||||||
@ExtendWith(MockitoExtension.class)
|
@ExtendWith(MockitoExtension.class)
|
||||||
public class TransformationJobTest {
|
public class TransformationJobTest {
|
||||||
|
|
||||||
|
|
|
@ -1,19 +1,12 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup;
|
package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.io.StringReader;
|
import java.io.StringReader;
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
import org.apache.spark.sql.Dataset;
|
import org.apache.spark.sql.Dataset;
|
||||||
import org.apache.spark.sql.SaveMode;
|
import org.apache.spark.sql.SaveMode;
|
||||||
|
@ -23,6 +16,16 @@ import org.dom4j.DocumentException;
|
||||||
import org.dom4j.Element;
|
import org.dom4j.Element;
|
||||||
import org.dom4j.io.SAXReader;
|
import org.dom4j.io.SAXReader;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||||
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
|
|
||||||
abstract class AbstractSparkAction implements Serializable {
|
abstract class AbstractSparkAction implements Serializable {
|
||||||
|
|
||||||
protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
|
protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
|
||||||
|
|
|
@ -4,15 +4,18 @@ package eu.dnetlib.dhp.oa.dedup;
|
||||||
import static java.util.Collections.reverseOrder;
|
import static java.util.Collections.reverseOrder;
|
||||||
import static java.util.Map.Entry.comparingByValue;
|
import static java.util.Map.Entry.comparingByValue;
|
||||||
import static java.util.stream.Collectors.toMap;
|
import static java.util.stream.Collectors.toMap;
|
||||||
|
|
||||||
import static org.apache.commons.lang.StringUtils.endsWith;
|
import static org.apache.commons.lang.StringUtils.endsWith;
|
||||||
import static org.apache.commons.lang.StringUtils.substringBefore;
|
import static org.apache.commons.lang.StringUtils.substringBefore;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Field;
|
|
||||||
import java.time.Year;
|
import java.time.Year;
|
||||||
import java.util.*;
|
import java.util.*;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.commons.lang.StringUtils;
|
import org.apache.commons.lang.StringUtils;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||||
|
|
||||||
public class DatePicker {
|
public class DatePicker {
|
||||||
|
|
||||||
private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}";
|
private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}";
|
||||||
|
|
|
@ -1,13 +1,9 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup;
|
package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import com.google.common.collect.Lists;
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import java.util.Collection;
|
import java.util.Collection;
|
||||||
import java.util.Iterator;
|
import java.util.Iterator;
|
||||||
|
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
import org.apache.spark.api.java.function.MapGroupsFunction;
|
import org.apache.spark.api.java.function.MapGroupsFunction;
|
||||||
import org.apache.spark.sql.Dataset;
|
import org.apache.spark.sql.Dataset;
|
||||||
|
@ -15,6 +11,13 @@ import org.apache.spark.sql.Encoders;
|
||||||
import org.apache.spark.sql.SparkSession;
|
import org.apache.spark.sql.SparkSession;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
import com.google.common.collect.Lists;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class DedupRecordFactory {
|
public class DedupRecordFactory {
|
||||||
|
|
|
@ -1,8 +1,24 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup;
|
package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
|
import java.io.StringReader;
|
||||||
|
import java.security.MessageDigest;
|
||||||
|
import java.text.Normalizer;
|
||||||
|
import java.util.*;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
|
import org.apache.commons.codec.binary.Hex;
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.apache.spark.SparkContext;
|
||||||
|
import org.apache.spark.util.LongAccumulator;
|
||||||
|
import org.dom4j.Document;
|
||||||
|
import org.dom4j.DocumentException;
|
||||||
|
import org.dom4j.Element;
|
||||||
|
import org.dom4j.io.SAXReader;
|
||||||
|
|
||||||
import com.google.common.collect.Sets;
|
import com.google.common.collect.Sets;
|
||||||
import com.wcohen.ss.JaroWinkler;
|
import com.wcohen.ss.JaroWinkler;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Author;
|
import eu.dnetlib.dhp.schema.oaf.Author;
|
||||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||||
|
@ -12,19 +28,6 @@ import eu.dnetlib.pace.clustering.BlacklistAwareClusteringCombiner;
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
import eu.dnetlib.pace.model.MapDocument;
|
import eu.dnetlib.pace.model.MapDocument;
|
||||||
import eu.dnetlib.pace.model.Person;
|
import eu.dnetlib.pace.model.Person;
|
||||||
import java.io.StringReader;
|
|
||||||
import java.security.MessageDigest;
|
|
||||||
import java.text.Normalizer;
|
|
||||||
import java.util.*;
|
|
||||||
import java.util.stream.Collectors;
|
|
||||||
import org.apache.commons.codec.binary.Hex;
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
|
||||||
import org.apache.spark.SparkContext;
|
|
||||||
import org.apache.spark.util.LongAccumulator;
|
|
||||||
import org.dom4j.Document;
|
|
||||||
import org.dom4j.DocumentException;
|
|
||||||
import org.dom4j.Element;
|
|
||||||
import org.dom4j.io.SAXReader;
|
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class DedupUtility {
|
public class DedupUtility {
|
||||||
|
|
|
@ -1,15 +1,17 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup;
|
package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
|
import org.apache.spark.api.java.JavaPairRDD;
|
||||||
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
|
import org.apache.spark.util.LongAccumulator;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.oa.dedup.model.Block;
|
import eu.dnetlib.dhp.oa.dedup.model.Block;
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
import eu.dnetlib.pace.model.MapDocument;
|
import eu.dnetlib.pace.model.MapDocument;
|
||||||
import eu.dnetlib.pace.util.BlockProcessor;
|
import eu.dnetlib.pace.util.BlockProcessor;
|
||||||
import java.util.Map;
|
|
||||||
import java.util.stream.Collectors;
|
|
||||||
import org.apache.spark.api.java.JavaPairRDD;
|
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
|
||||||
import org.apache.spark.util.LongAccumulator;
|
|
||||||
import scala.Serializable;
|
import scala.Serializable;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
|
|
|
@ -1,6 +1,16 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup;
|
package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.sql.SaveMode;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import org.dom4j.DocumentException;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
import eu.dnetlib.dhp.schema.common.EntityType;
|
import eu.dnetlib.dhp.schema.common.EntityType;
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
@ -11,14 +21,6 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
import java.io.IOException;
|
|
||||||
import org.apache.commons.io.IOUtils;
|
|
||||||
import org.apache.spark.SparkConf;
|
|
||||||
import org.apache.spark.sql.SaveMode;
|
|
||||||
import org.apache.spark.sql.SparkSession;
|
|
||||||
import org.dom4j.DocumentException;
|
|
||||||
import org.slf4j.Logger;
|
|
||||||
import org.slf4j.LoggerFactory;
|
|
||||||
|
|
||||||
public class SparkCreateDedupRecord extends AbstractSparkAction {
|
public class SparkCreateDedupRecord extends AbstractSparkAction {
|
||||||
|
|
||||||
|
|
|
@ -1,23 +1,11 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup;
|
package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
import com.google.common.hash.Hashing;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent;
|
|
||||||
import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor;
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
||||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
|
||||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.Iterator;
|
import java.util.Iterator;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
import org.apache.spark.api.java.JavaPairRDD;
|
import org.apache.spark.api.java.JavaPairRDD;
|
||||||
|
@ -32,6 +20,21 @@ import org.apache.spark.sql.SparkSession;
|
||||||
import org.dom4j.DocumentException;
|
import org.dom4j.DocumentException;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import com.google.common.hash.Hashing;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent;
|
||||||
|
import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||||
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
|
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class SparkCreateMergeRels extends AbstractSparkAction {
|
public class SparkCreateMergeRels extends AbstractSparkAction {
|
||||||
|
|
|
@ -1,6 +1,21 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup;
|
package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.api.java.JavaPairRDD;
|
||||||
|
import org.apache.spark.api.java.JavaRDD;
|
||||||
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
|
import org.apache.spark.api.java.function.PairFunction;
|
||||||
|
import org.apache.spark.sql.Encoders;
|
||||||
|
import org.apache.spark.sql.SaveMode;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import org.dom4j.DocumentException;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
import eu.dnetlib.dhp.oa.dedup.model.Block;
|
import eu.dnetlib.dhp.oa.dedup.model.Block;
|
||||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
|
@ -13,19 +28,6 @@ import eu.dnetlib.pace.model.FieldListImpl;
|
||||||
import eu.dnetlib.pace.model.FieldValueImpl;
|
import eu.dnetlib.pace.model.FieldValueImpl;
|
||||||
import eu.dnetlib.pace.model.MapDocument;
|
import eu.dnetlib.pace.model.MapDocument;
|
||||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||||
import java.io.IOException;
|
|
||||||
import org.apache.commons.io.IOUtils;
|
|
||||||
import org.apache.spark.SparkConf;
|
|
||||||
import org.apache.spark.api.java.JavaPairRDD;
|
|
||||||
import org.apache.spark.api.java.JavaRDD;
|
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
|
||||||
import org.apache.spark.api.java.function.PairFunction;
|
|
||||||
import org.apache.spark.sql.Encoders;
|
|
||||||
import org.apache.spark.sql.SaveMode;
|
|
||||||
import org.apache.spark.sql.SparkSession;
|
|
||||||
import org.dom4j.DocumentException;
|
|
||||||
import org.slf4j.Logger;
|
|
||||||
import org.slf4j.LoggerFactory;
|
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class SparkCreateSimRels extends AbstractSparkAction {
|
public class SparkCreateSimRels extends AbstractSparkAction {
|
||||||
|
|
|
@ -3,18 +3,19 @@ package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
import static org.apache.spark.sql.functions.col;
|
import static org.apache.spark.sql.functions.col;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
|
import org.apache.spark.sql.*;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||||
import org.apache.commons.io.IOUtils;
|
|
||||||
import org.apache.spark.SparkConf;
|
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
|
||||||
import org.apache.spark.sql.*;
|
|
||||||
import org.slf4j.Logger;
|
|
||||||
import org.slf4j.LoggerFactory;
|
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class SparkPropagateRelation extends AbstractSparkAction {
|
public class SparkPropagateRelation extends AbstractSparkAction {
|
||||||
|
|
|
@ -1,11 +1,13 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup;
|
package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
import eu.dnetlib.pace.util.Reporter;
|
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
|
||||||
import org.apache.spark.util.LongAccumulator;
|
import org.apache.spark.util.LongAccumulator;
|
||||||
|
|
||||||
|
import eu.dnetlib.pace.util.Reporter;
|
||||||
import scala.Serializable;
|
import scala.Serializable;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
|
|
|
@ -1,16 +1,8 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup;
|
package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
||||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
|
||||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.hadoop.conf.Configuration;
|
import org.apache.hadoop.conf.Configuration;
|
||||||
import org.apache.hadoop.fs.FileStatus;
|
import org.apache.hadoop.fs.FileStatus;
|
||||||
|
@ -28,6 +20,16 @@ import org.apache.spark.sql.Row;
|
||||||
import org.apache.spark.sql.SparkSession;
|
import org.apache.spark.sql.SparkSession;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||||
|
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class SparkUpdateEntity extends AbstractSparkAction {
|
public class SparkUpdateEntity extends AbstractSparkAction {
|
||||||
|
|
|
@ -1,15 +1,18 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup.graph;
|
package eu.dnetlib.dhp.oa.dedup.graph;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.oa.dedup.DedupUtility;
|
|
||||||
import eu.dnetlib.pace.util.PaceException;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.util.Set;
|
import java.util.Set;
|
||||||
|
|
||||||
import org.apache.commons.lang.StringUtils;
|
import org.apache.commons.lang.StringUtils;
|
||||||
import org.codehaus.jackson.annotate.JsonIgnore;
|
import org.codehaus.jackson.annotate.JsonIgnore;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.oa.dedup.DedupUtility;
|
||||||
|
import eu.dnetlib.pace.util.PaceException;
|
||||||
|
|
||||||
public class ConnectedComponent implements Serializable {
|
public class ConnectedComponent implements Serializable {
|
||||||
|
|
||||||
private Set<String> docIds;
|
private Set<String> docIds;
|
||||||
|
|
|
@ -1,8 +1,6 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup.model;
|
package eu.dnetlib.dhp.oa.dedup.model;
|
||||||
|
|
||||||
import com.google.common.collect.Lists;
|
|
||||||
import eu.dnetlib.pace.model.MapDocument;
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.Comparator;
|
import java.util.Comparator;
|
||||||
|
@ -12,6 +10,10 @@ import java.util.stream.Collectors;
|
||||||
import java.util.stream.Stream;
|
import java.util.stream.Stream;
|
||||||
import java.util.stream.StreamSupport;
|
import java.util.stream.StreamSupport;
|
||||||
|
|
||||||
|
import com.google.common.collect.Lists;
|
||||||
|
|
||||||
|
import eu.dnetlib.pace.model.MapDocument;
|
||||||
|
|
||||||
public class Block implements Serializable {
|
public class Block implements Serializable {
|
||||||
|
|
||||||
private String key;
|
private String key;
|
||||||
|
|
|
@ -1,15 +1,17 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup;
|
package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.codehaus.jackson.map.ObjectMapper;
|
import org.codehaus.jackson.map.ObjectMapper;
|
||||||
import org.junit.jupiter.api.BeforeEach;
|
import org.junit.jupiter.api.BeforeEach;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||||
|
|
||||||
public class MergeAuthorTest {
|
public class MergeAuthorTest {
|
||||||
|
|
||||||
private List<Publication> publicationsToMerge;
|
private List<Publication> publicationsToMerge;
|
||||||
|
|
|
@ -2,19 +2,16 @@
|
||||||
package eu.dnetlib.dhp.oa.dedup;
|
package eu.dnetlib.dhp.oa.dedup;
|
||||||
|
|
||||||
import static java.nio.file.Files.createTempDirectory;
|
import static java.nio.file.Files.createTempDirectory;
|
||||||
|
|
||||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||||
import static org.mockito.Mockito.lenient;
|
import static org.mockito.Mockito.lenient;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
|
||||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
|
||||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
|
||||||
import java.io.File;
|
import java.io.File;
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.net.URISyntaxException;
|
import java.net.URISyntaxException;
|
||||||
import java.nio.file.Paths;
|
import java.nio.file.Paths;
|
||||||
|
|
||||||
import org.apache.commons.io.FileUtils;
|
import org.apache.commons.io.FileUtils;
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
|
@ -31,6 +28,12 @@ import org.junit.jupiter.api.extension.ExtendWith;
|
||||||
import org.mockito.Mock;
|
import org.mockito.Mock;
|
||||||
import org.mockito.Mockito;
|
import org.mockito.Mockito;
|
||||||
import org.mockito.junit.jupiter.MockitoExtension;
|
import org.mockito.junit.jupiter.MockitoExtension;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||||
|
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
@ExtendWith(MockitoExtension.class)
|
@ExtendWith(MockitoExtension.class)
|
||||||
|
|
|
@ -1,10 +1,11 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.dedup.jpath;
|
package eu.dnetlib.dhp.oa.dedup.jpath;
|
||||||
|
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
import eu.dnetlib.pace.model.MapDocument;
|
import eu.dnetlib.pace.model.MapDocument;
|
||||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||||
import org.junit.jupiter.api.Test;
|
|
||||||
|
|
||||||
public class JsonPathTest {
|
public class JsonPathTest {
|
||||||
|
|
||||||
|
|
|
@ -4,15 +4,18 @@ package eu.dnetlib.dedup;
|
||||||
import static java.util.Collections.reverseOrder;
|
import static java.util.Collections.reverseOrder;
|
||||||
import static java.util.Map.Entry.comparingByValue;
|
import static java.util.Map.Entry.comparingByValue;
|
||||||
import static java.util.stream.Collectors.toMap;
|
import static java.util.stream.Collectors.toMap;
|
||||||
|
|
||||||
import static org.apache.commons.lang.StringUtils.endsWith;
|
import static org.apache.commons.lang.StringUtils.endsWith;
|
||||||
import static org.apache.commons.lang.StringUtils.substringBefore;
|
import static org.apache.commons.lang.StringUtils.substringBefore;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Field;
|
|
||||||
import java.time.Year;
|
import java.time.Year;
|
||||||
import java.util.*;
|
import java.util.*;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.commons.lang.StringUtils;
|
import org.apache.commons.lang.StringUtils;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||||
|
|
||||||
public class DatePicker {
|
public class DatePicker {
|
||||||
|
|
||||||
private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}";
|
private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}";
|
||||||
|
|
|
@ -1,19 +1,22 @@
|
||||||
|
|
||||||
package eu.dnetlib.dedup;
|
package eu.dnetlib.dedup;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import com.google.common.collect.Lists;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
|
||||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
|
||||||
import java.util.Collection;
|
import java.util.Collection;
|
||||||
|
|
||||||
import org.apache.spark.api.java.JavaPairRDD;
|
import org.apache.spark.api.java.JavaPairRDD;
|
||||||
import org.apache.spark.api.java.JavaRDD;
|
import org.apache.spark.api.java.JavaRDD;
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
import org.apache.spark.api.java.function.PairFunction;
|
import org.apache.spark.api.java.function.PairFunction;
|
||||||
import org.apache.spark.sql.Encoders;
|
import org.apache.spark.sql.Encoders;
|
||||||
import org.apache.spark.sql.SparkSession;
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
import com.google.common.collect.Lists;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
|
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class DedupRecordFactory {
|
public class DedupRecordFactory {
|
||||||
|
|
|
@ -1,14 +1,6 @@
|
||||||
|
|
||||||
package eu.dnetlib.dedup;
|
package eu.dnetlib.dedup;
|
||||||
|
|
||||||
import com.google.common.collect.Sets;
|
|
||||||
import com.wcohen.ss.JaroWinkler;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Author;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
|
||||||
import eu.dnetlib.pace.clustering.BlacklistAwareClusteringCombiner;
|
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
|
||||||
import eu.dnetlib.pace.model.MapDocument;
|
|
||||||
import eu.dnetlib.pace.model.Person;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.io.StringWriter;
|
import java.io.StringWriter;
|
||||||
import java.nio.charset.StandardCharsets;
|
import java.nio.charset.StandardCharsets;
|
||||||
|
@ -16,6 +8,7 @@ import java.security.MessageDigest;
|
||||||
import java.text.Normalizer;
|
import java.text.Normalizer;
|
||||||
import java.util.*;
|
import java.util.*;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.commons.codec.binary.Hex;
|
import org.apache.commons.codec.binary.Hex;
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
@ -27,6 +20,16 @@ import org.apache.spark.SparkContext;
|
||||||
import org.apache.spark.api.java.JavaRDD;
|
import org.apache.spark.api.java.JavaRDD;
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
import org.apache.spark.util.LongAccumulator;
|
import org.apache.spark.util.LongAccumulator;
|
||||||
|
|
||||||
|
import com.google.common.collect.Sets;
|
||||||
|
import com.wcohen.ss.JaroWinkler;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Author;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
import eu.dnetlib.pace.clustering.BlacklistAwareClusteringCombiner;
|
||||||
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
|
import eu.dnetlib.pace.model.MapDocument;
|
||||||
|
import eu.dnetlib.pace.model.Person;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class DedupUtility {
|
public class DedupUtility {
|
||||||
|
|
|
@ -1,12 +1,9 @@
|
||||||
|
|
||||||
package eu.dnetlib.dedup;
|
package eu.dnetlib.dedup;
|
||||||
|
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
|
||||||
import eu.dnetlib.pace.model.MapDocument;
|
|
||||||
import eu.dnetlib.pace.util.BlockProcessor;
|
|
||||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
|
||||||
import java.util.*;
|
import java.util.*;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import org.apache.commons.logging.Log;
|
import org.apache.commons.logging.Log;
|
||||||
import org.apache.commons.logging.LogFactory;
|
import org.apache.commons.logging.LogFactory;
|
||||||
import org.apache.spark.api.java.JavaPairRDD;
|
import org.apache.spark.api.java.JavaPairRDD;
|
||||||
|
@ -16,6 +13,11 @@ import org.apache.spark.api.java.function.Function2;
|
||||||
import org.apache.spark.api.java.function.PairFlatMapFunction;
|
import org.apache.spark.api.java.function.PairFlatMapFunction;
|
||||||
import org.apache.spark.api.java.function.PairFunction;
|
import org.apache.spark.api.java.function.PairFunction;
|
||||||
import org.apache.spark.util.LongAccumulator;
|
import org.apache.spark.util.LongAccumulator;
|
||||||
|
|
||||||
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
|
import eu.dnetlib.pace.model.MapDocument;
|
||||||
|
import eu.dnetlib.pace.util.BlockProcessor;
|
||||||
|
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||||
import scala.Serializable;
|
import scala.Serializable;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
|
|
|
@ -1,15 +1,9 @@
|
||||||
|
|
||||||
package eu.dnetlib.dedup;
|
package eu.dnetlib.dedup;
|
||||||
|
|
||||||
import com.google.common.hash.Hashing;
|
|
||||||
import eu.dnetlib.dedup.graph.ConnectedComponent;
|
|
||||||
import eu.dnetlib.dedup.graph.GraphProcessor;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
|
||||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.spark.api.java.JavaPairRDD;
|
import org.apache.spark.api.java.JavaPairRDD;
|
||||||
import org.apache.spark.api.java.JavaRDD;
|
import org.apache.spark.api.java.JavaRDD;
|
||||||
|
@ -21,6 +15,15 @@ import org.apache.spark.rdd.RDD;
|
||||||
import org.apache.spark.sql.Dataset;
|
import org.apache.spark.sql.Dataset;
|
||||||
import org.apache.spark.sql.Encoders;
|
import org.apache.spark.sql.Encoders;
|
||||||
import org.apache.spark.sql.SparkSession;
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
|
||||||
|
import com.google.common.hash.Hashing;
|
||||||
|
|
||||||
|
import eu.dnetlib.dedup.graph.ConnectedComponent;
|
||||||
|
import eu.dnetlib.dedup.graph.GraphProcessor;
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
|
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class SparkCreateConnectedComponent {
|
public class SparkCreateConnectedComponent {
|
||||||
|
|
|
@ -1,15 +1,17 @@
|
||||||
|
|
||||||
package eu.dnetlib.dedup;
|
package eu.dnetlib.dedup;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.spark.api.java.JavaRDD;
|
import org.apache.spark.api.java.JavaRDD;
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
import org.apache.spark.sql.SparkSession;
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||||
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
|
|
||||||
public class SparkCreateDedupRecord {
|
public class SparkCreateDedupRecord {
|
||||||
public static void main(String[] args) throws Exception {
|
public static void main(String[] args) throws Exception {
|
||||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||||
|
|
|
@ -1,18 +1,20 @@
|
||||||
|
|
||||||
package eu.dnetlib.dedup;
|
package eu.dnetlib.dedup;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
||||||
import eu.dnetlib.pace.config.DedupConfig;
|
|
||||||
import eu.dnetlib.pace.model.MapDocument;
|
|
||||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.spark.api.java.JavaPairRDD;
|
import org.apache.spark.api.java.JavaPairRDD;
|
||||||
import org.apache.spark.api.java.JavaRDD;
|
import org.apache.spark.api.java.JavaRDD;
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
import org.apache.spark.sql.Encoders;
|
import org.apache.spark.sql.Encoders;
|
||||||
import org.apache.spark.sql.SparkSession;
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.pace.config.DedupConfig;
|
||||||
|
import eu.dnetlib.pace.model.MapDocument;
|
||||||
|
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
|
|
|
@ -1,13 +1,15 @@
|
||||||
|
|
||||||
package eu.dnetlib.dedup;
|
package eu.dnetlib.dedup;
|
||||||
|
|
||||||
import eu.dnetlib.pace.util.Reporter;
|
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
|
||||||
import org.apache.commons.logging.Log;
|
import org.apache.commons.logging.Log;
|
||||||
import org.apache.commons.logging.LogFactory;
|
import org.apache.commons.logging.LogFactory;
|
||||||
import org.apache.spark.util.LongAccumulator;
|
import org.apache.spark.util.LongAccumulator;
|
||||||
|
|
||||||
|
import eu.dnetlib.pace.util.Reporter;
|
||||||
import scala.Serializable;
|
import scala.Serializable;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
|
|
|
@ -1,15 +1,18 @@
|
||||||
|
|
||||||
package eu.dnetlib.dedup.graph;
|
package eu.dnetlib.dedup.graph;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dedup.DedupUtility;
|
|
||||||
import eu.dnetlib.pace.util.PaceException;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.util.Set;
|
import java.util.Set;
|
||||||
|
|
||||||
import org.apache.commons.lang.StringUtils;
|
import org.apache.commons.lang.StringUtils;
|
||||||
import org.codehaus.jackson.annotate.JsonIgnore;
|
import org.codehaus.jackson.annotate.JsonIgnore;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dedup.DedupUtility;
|
||||||
|
import eu.dnetlib.pace.util.PaceException;
|
||||||
|
|
||||||
public class ConnectedComponent implements Serializable {
|
public class ConnectedComponent implements Serializable {
|
||||||
|
|
||||||
private Set<String> docIds;
|
private Set<String> docIds;
|
||||||
|
|
|
@ -1,17 +1,20 @@
|
||||||
|
|
||||||
package eu.dnetlib.dedup.sx;
|
package eu.dnetlib.dedup.sx;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
import org.apache.spark.sql.*;
|
import org.apache.spark.sql.*;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class SparkPropagateRelationsJob {
|
public class SparkPropagateRelationsJob {
|
||||||
|
|
|
@ -1,8 +1,19 @@
|
||||||
|
|
||||||
package eu.dnetlib.dedup.sx;
|
package eu.dnetlib.dedup.sx;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.hadoop.io.compress.GzipCodec;
|
||||||
|
import org.apache.spark.api.java.JavaPairRDD;
|
||||||
|
import org.apache.spark.api.java.JavaRDD;
|
||||||
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
|
import org.apache.spark.api.java.function.PairFunction;
|
||||||
|
import org.apache.spark.sql.*;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
@ -11,14 +22,6 @@ import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset;
|
||||||
import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication;
|
import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication;
|
||||||
import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown;
|
import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown;
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||||
import java.io.IOException;
|
|
||||||
import org.apache.commons.io.IOUtils;
|
|
||||||
import org.apache.hadoop.io.compress.GzipCodec;
|
|
||||||
import org.apache.spark.api.java.JavaPairRDD;
|
|
||||||
import org.apache.spark.api.java.JavaRDD;
|
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
|
||||||
import org.apache.spark.api.java.function.PairFunction;
|
|
||||||
import org.apache.spark.sql.*;
|
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
|
||||||
public class SparkUpdateEntityJob {
|
public class SparkUpdateEntityJob {
|
||||||
|
|
|
@ -3,10 +3,8 @@ package eu.dnetlib.dhp.oa.graph.hive;
|
||||||
|
|
||||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
|
||||||
import java.util.Optional;
|
import java.util.Optional;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
|
@ -16,6 +14,11 @@ import org.apache.spark.sql.SparkSession;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
|
||||||
public class GraphHiveImporterJob {
|
public class GraphHiveImporterJob {
|
||||||
|
|
||||||
private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJob.class);
|
private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJob.class);
|
||||||
|
|
|
@ -1,3 +1,4 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.graph.raw;
|
package eu.dnetlib.dhp.oa.graph.raw;
|
||||||
|
|
||||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
|
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
|
||||||
|
@ -10,6 +11,19 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance;
|
||||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
|
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
|
||||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
|
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
|
||||||
|
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.Date;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Map;
|
||||||
|
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.dom4j.Document;
|
||||||
|
import org.dom4j.DocumentFactory;
|
||||||
|
import org.dom4j.DocumentHelper;
|
||||||
|
import org.dom4j.Node;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.oa.graph.raw.common.MigrationConstants;
|
import eu.dnetlib.dhp.oa.graph.raw.common.MigrationConstants;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Author;
|
import eu.dnetlib.dhp.schema.oaf.Author;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Context;
|
import eu.dnetlib.dhp.schema.oaf.Context;
|
||||||
|
@ -29,440 +43,429 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Software;
|
import eu.dnetlib.dhp.schema.oaf.Software;
|
||||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
import java.util.ArrayList;
|
|
||||||
import java.util.Arrays;
|
|
||||||
import java.util.Date;
|
|
||||||
import java.util.HashMap;
|
|
||||||
import java.util.List;
|
|
||||||
import java.util.Map;
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
|
||||||
import org.dom4j.Document;
|
|
||||||
import org.dom4j.DocumentFactory;
|
|
||||||
import org.dom4j.DocumentHelper;
|
|
||||||
import org.dom4j.Node;
|
|
||||||
|
|
||||||
public abstract class AbstractMdRecordToOafMapper {
|
public abstract class AbstractMdRecordToOafMapper {
|
||||||
|
|
||||||
protected final Map<String, String> code2name;
|
protected final Map<String, String> code2name;
|
||||||
|
|
||||||
protected static final Qualifier MAIN_TITLE_QUALIFIER =
|
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
|
||||||
qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
|
"main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
|
||||||
|
|
||||||
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
|
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
|
||||||
this.code2name = code2name;
|
this.code2name = code2name;
|
||||||
}
|
}
|
||||||
|
|
||||||
public List<Oaf> processMdRecord(final String xml) {
|
public List<Oaf> processMdRecord(final String xml) {
|
||||||
try {
|
try {
|
||||||
final Map<String, String> nsContext = new HashMap<>();
|
final Map<String, String> nsContext = new HashMap<>();
|
||||||
nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
|
nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
|
||||||
nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
|
nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
|
||||||
nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
|
nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
|
||||||
nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
|
nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
|
||||||
nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
|
nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
|
||||||
nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
|
nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
|
||||||
nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
|
nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
|
||||||
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
|
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
|
||||||
|
|
||||||
final Document doc =
|
final Document doc = DocumentHelper
|
||||||
DocumentHelper.parseText(
|
.parseText(
|
||||||
xml.replaceAll(
|
xml
|
||||||
"http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3"));
|
.replaceAll(
|
||||||
|
"http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3"));
|
||||||
final String type = doc.valueOf("//dr:CobjCategory/@type");
|
|
||||||
final KeyValue collectedFrom =
|
final String type = doc.valueOf("//dr:CobjCategory/@type");
|
||||||
keyValue(
|
final KeyValue collectedFrom = keyValue(
|
||||||
createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true),
|
createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true),
|
||||||
doc.valueOf("//oaf:collectedFrom/@name"));
|
doc.valueOf("//oaf:collectedFrom/@name"));
|
||||||
final KeyValue hostedBy =
|
final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
|
||||||
StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
|
? collectedFrom
|
||||||
? collectedFrom
|
: keyValue(
|
||||||
: keyValue(
|
createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true),
|
||||||
createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true),
|
doc.valueOf("//oaf:hostedBy/@name"));
|
||||||
doc.valueOf("//oaf:hostedBy/@name"));
|
|
||||||
|
final DataInfo info = prepareDataInfo(doc);
|
||||||
final DataInfo info = prepareDataInfo(doc);
|
final long lastUpdateTimestamp = new Date().getTime();
|
||||||
final long lastUpdateTimestamp = new Date().getTime();
|
|
||||||
|
return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||||
return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
} catch (final Exception e) {
|
||||||
} catch (final Exception e) {
|
throw new RuntimeException(e);
|
||||||
throw new RuntimeException(e);
|
}
|
||||||
}
|
}
|
||||||
}
|
|
||||||
|
protected List<Oaf> createOafs(
|
||||||
protected List<Oaf> createOafs(
|
final Document doc,
|
||||||
final Document doc,
|
final String type,
|
||||||
final String type,
|
final KeyValue collectedFrom,
|
||||||
final KeyValue collectedFrom,
|
final KeyValue hostedBy,
|
||||||
final KeyValue hostedBy,
|
final DataInfo info,
|
||||||
final DataInfo info,
|
final long lastUpdateTimestamp) {
|
||||||
final long lastUpdateTimestamp) {
|
|
||||||
|
final List<Oaf> oafs = new ArrayList<>();
|
||||||
final List<Oaf> oafs = new ArrayList<>();
|
|
||||||
|
switch (type.toLowerCase()) {
|
||||||
switch (type.toLowerCase()) {
|
case "":
|
||||||
case "":
|
case "publication":
|
||||||
case "publication":
|
final Publication p = new Publication();
|
||||||
final Publication p = new Publication();
|
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||||
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
p.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER);
|
||||||
p.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER);
|
p.setJournal(prepareJournal(doc, info));
|
||||||
p.setJournal(prepareJournal(doc, info));
|
oafs.add(p);
|
||||||
oafs.add(p);
|
break;
|
||||||
break;
|
case "dataset":
|
||||||
case "dataset":
|
final Dataset d = new Dataset();
|
||||||
final Dataset d = new Dataset();
|
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||||
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
d.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER);
|
||||||
d.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER);
|
d.setStoragedate(prepareDatasetStorageDate(doc, info));
|
||||||
d.setStoragedate(prepareDatasetStorageDate(doc, info));
|
d.setDevice(prepareDatasetDevice(doc, info));
|
||||||
d.setDevice(prepareDatasetDevice(doc, info));
|
d.setSize(prepareDatasetSize(doc, info));
|
||||||
d.setSize(prepareDatasetSize(doc, info));
|
d.setVersion(prepareDatasetVersion(doc, info));
|
||||||
d.setVersion(prepareDatasetVersion(doc, info));
|
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
|
||||||
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
|
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
|
||||||
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
|
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
|
||||||
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
|
oafs.add(d);
|
||||||
oafs.add(d);
|
break;
|
||||||
break;
|
case "software":
|
||||||
case "software":
|
final Software s = new Software();
|
||||||
final Software s = new Software();
|
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||||
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
s.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER);
|
||||||
s.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER);
|
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
|
||||||
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
|
s.setLicense(prepareSoftwareLicenses(doc, info));
|
||||||
s.setLicense(prepareSoftwareLicenses(doc, info));
|
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
|
||||||
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
|
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
|
||||||
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
|
oafs.add(s);
|
||||||
oafs.add(s);
|
break;
|
||||||
break;
|
case "otherresearchproducts":
|
||||||
case "otherresearchproducts":
|
default:
|
||||||
default:
|
final OtherResearchProduct o = new OtherResearchProduct();
|
||||||
final OtherResearchProduct o = new OtherResearchProduct();
|
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||||
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
o.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER);
|
||||||
o.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER);
|
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
|
||||||
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
|
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
|
||||||
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
|
o.setTool(prepareOtherResearchProductTools(doc, info));
|
||||||
o.setTool(prepareOtherResearchProductTools(doc, info));
|
oafs.add(o);
|
||||||
oafs.add(o);
|
break;
|
||||||
break;
|
}
|
||||||
}
|
|
||||||
|
if (!oafs.isEmpty()) {
|
||||||
if (!oafs.isEmpty()) {
|
oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
||||||
oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
||||||
oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
}
|
||||||
}
|
|
||||||
|
return oafs;
|
||||||
return oafs;
|
}
|
||||||
}
|
|
||||||
|
private List<Oaf> addProjectRels(
|
||||||
private List<Oaf> addProjectRels(
|
final Document doc,
|
||||||
final Document doc,
|
final KeyValue collectedFrom,
|
||||||
final KeyValue collectedFrom,
|
final DataInfo info,
|
||||||
final DataInfo info,
|
final long lastUpdateTimestamp) {
|
||||||
final long lastUpdateTimestamp) {
|
|
||||||
|
final List<Oaf> res = new ArrayList<>();
|
||||||
final List<Oaf> res = new ArrayList<>();
|
|
||||||
|
final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false);
|
||||||
final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false);
|
|
||||||
|
for (final Object o : doc.selectNodes("//oaf:projectid")) {
|
||||||
for (final Object o : doc.selectNodes("//oaf:projectid")) {
|
|
||||||
|
final String originalId = ((Node) o).getText();
|
||||||
final String originalId = ((Node) o).getText();
|
|
||||||
|
if (StringUtils.isNotBlank(originalId)) {
|
||||||
if (StringUtils.isNotBlank(originalId)) {
|
final String projectId = createOpenaireId(40, originalId, true);
|
||||||
final String projectId = createOpenaireId(40, originalId, true);
|
|
||||||
|
final Relation r1 = new Relation();
|
||||||
final Relation r1 = new Relation();
|
r1.setRelType("resultProject");
|
||||||
r1.setRelType("resultProject");
|
r1.setSubRelType("outcome");
|
||||||
r1.setSubRelType("outcome");
|
r1.setRelClass("isProducedBy");
|
||||||
r1.setRelClass("isProducedBy");
|
r1.setSource(docId);
|
||||||
r1.setSource(docId);
|
r1.setTarget(projectId);
|
||||||
r1.setTarget(projectId);
|
r1.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||||
r1.setCollectedfrom(Arrays.asList(collectedFrom));
|
r1.setDataInfo(info);
|
||||||
r1.setDataInfo(info);
|
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
res.add(r1);
|
||||||
res.add(r1);
|
|
||||||
|
final Relation r2 = new Relation();
|
||||||
final Relation r2 = new Relation();
|
r2.setRelType("resultProject");
|
||||||
r2.setRelType("resultProject");
|
r2.setSubRelType("outcome");
|
||||||
r2.setSubRelType("outcome");
|
r2.setRelClass("produces");
|
||||||
r2.setRelClass("produces");
|
r2.setSource(projectId);
|
||||||
r2.setSource(projectId);
|
r2.setTarget(docId);
|
||||||
r2.setTarget(docId);
|
r2.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||||
r2.setCollectedfrom(Arrays.asList(collectedFrom));
|
r2.setDataInfo(info);
|
||||||
r2.setDataInfo(info);
|
r2.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
r2.setLastupdatetimestamp(lastUpdateTimestamp);
|
res.add(r2);
|
||||||
res.add(r2);
|
}
|
||||||
}
|
}
|
||||||
}
|
|
||||||
|
return res;
|
||||||
return res;
|
}
|
||||||
}
|
|
||||||
|
protected abstract List<Oaf> addOtherResultRels(
|
||||||
protected abstract List<Oaf> addOtherResultRels(
|
final Document doc,
|
||||||
final Document doc,
|
final KeyValue collectedFrom,
|
||||||
final KeyValue collectedFrom,
|
final DataInfo info,
|
||||||
final DataInfo info,
|
final long lastUpdateTimestamp);
|
||||||
final long lastUpdateTimestamp);
|
|
||||||
|
private void populateResultFields(
|
||||||
private void populateResultFields(
|
final Result r,
|
||||||
final Result r,
|
final Document doc,
|
||||||
final Document doc,
|
final KeyValue collectedFrom,
|
||||||
final KeyValue collectedFrom,
|
final KeyValue hostedBy,
|
||||||
final KeyValue hostedBy,
|
final DataInfo info,
|
||||||
final DataInfo info,
|
final long lastUpdateTimestamp) {
|
||||||
final long lastUpdateTimestamp) {
|
r.setDataInfo(info);
|
||||||
r.setDataInfo(info);
|
r.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
r.setLastupdatetimestamp(lastUpdateTimestamp);
|
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
|
||||||
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
|
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
|
||||||
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
|
r.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||||
r.setCollectedfrom(Arrays.asList(collectedFrom));
|
r
|
||||||
r.setPid(
|
.setPid(
|
||||||
prepareListStructProps(
|
prepareListStructProps(
|
||||||
doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
|
doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
|
||||||
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
|
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
|
||||||
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
|
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
|
||||||
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||||
r.setOaiprovenance(prepareOAIprovenance(doc));
|
r.setOaiprovenance(prepareOAIprovenance(doc));
|
||||||
r.setAuthor(prepareAuthors(doc, info));
|
r.setAuthor(prepareAuthors(doc, info));
|
||||||
r.setLanguage(prepareLanguages(doc));
|
r.setLanguage(prepareLanguages(doc));
|
||||||
r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||||
r.setSubject(prepareSubjects(doc, info));
|
r.setSubject(prepareSubjects(doc, info));
|
||||||
r.setTitle(prepareTitles(doc, info));
|
r.setTitle(prepareTitles(doc, info));
|
||||||
r.setRelevantdate(prepareRelevantDates(doc, info));
|
r.setRelevantdate(prepareRelevantDates(doc, info));
|
||||||
r.setDescription(prepareDescriptions(doc, info));
|
r.setDescription(prepareDescriptions(doc, info));
|
||||||
r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info));
|
r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info));
|
||||||
r.setPublisher(preparePublisher(doc, info));
|
r.setPublisher(preparePublisher(doc, info));
|
||||||
r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
|
r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
|
||||||
r.setSource(prepareSources(doc, info));
|
r.setSource(prepareSources(doc, info));
|
||||||
r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||||
r.setFormat(prepareFormats(doc, info));
|
r.setFormat(prepareFormats(doc, info));
|
||||||
r.setContributor(prepareContributors(doc, info));
|
r.setContributor(prepareContributors(doc, info));
|
||||||
r.setResourcetype(prepareResourceType(doc, info));
|
r.setResourcetype(prepareResourceType(doc, info));
|
||||||
r.setCoverage(prepareCoverages(doc, info));
|
r.setCoverage(prepareCoverages(doc, info));
|
||||||
r.setContext(prepareContexts(doc, info));
|
r.setContext(prepareContexts(doc, info));
|
||||||
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||||
r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
|
r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
|
||||||
}
|
}
|
||||||
|
|
||||||
private List<Context> prepareContexts(final Document doc, final DataInfo info) {
|
private List<Context> prepareContexts(final Document doc, final DataInfo info) {
|
||||||
final List<Context> list = new ArrayList<>();
|
final List<Context> list = new ArrayList<>();
|
||||||
for (final Object o : doc.selectNodes("//oaf:concept")) {
|
for (final Object o : doc.selectNodes("//oaf:concept")) {
|
||||||
final String cid = ((Node) o).valueOf("@id");
|
final String cid = ((Node) o).valueOf("@id");
|
||||||
if (StringUtils.isNotBlank(cid)) {
|
if (StringUtils.isNotBlank(cid)) {
|
||||||
final Context c = new Context();
|
final Context c = new Context();
|
||||||
c.setId(cid);
|
c.setId(cid);
|
||||||
c.setDataInfo(Arrays.asList(info));
|
c.setDataInfo(Arrays.asList(info));
|
||||||
list.add(c);
|
list.add(c);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
return list;
|
return list;
|
||||||
}
|
}
|
||||||
|
|
||||||
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
|
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<Instance> prepareInstances(
|
protected abstract List<Instance> prepareInstances(
|
||||||
Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby);
|
Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby);
|
||||||
|
|
||||||
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
|
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info);
|
protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info);
|
protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info);
|
protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info);
|
protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
|
protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
|
protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
|
protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
|
protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract Qualifier prepareLanguages(Document doc);
|
protected abstract Qualifier prepareLanguages(Document doc);
|
||||||
|
|
||||||
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
|
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<Field<String>> prepareOtherResearchProductTools(
|
protected abstract List<Field<String>> prepareOtherResearchProductTools(
|
||||||
Document doc, DataInfo info);
|
Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
|
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
|
||||||
Document doc, DataInfo info);
|
Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
|
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
|
||||||
Document doc, DataInfo info);
|
Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
|
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
|
protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<StructuredProperty> prepareSoftwareLicenses(Document doc, DataInfo info);
|
protected abstract List<StructuredProperty> prepareSoftwareLicenses(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
|
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
|
||||||
Document doc, DataInfo info);
|
Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
|
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract Field<String> prepareDatasetMetadataVersionNumber(Document doc, DataInfo info);
|
protected abstract Field<String> prepareDatasetMetadataVersionNumber(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
|
protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info);
|
protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
|
protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
|
protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
|
||||||
|
|
||||||
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
|
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
|
||||||
|
|
||||||
private Journal prepareJournal(final Document doc, final DataInfo info) {
|
private Journal prepareJournal(final Document doc, final DataInfo info) {
|
||||||
final Node n = doc.selectSingleNode("//oaf:journal");
|
final Node n = doc.selectSingleNode("//oaf:journal");
|
||||||
if (n != null) {
|
if (n != null) {
|
||||||
final String name = n.getText();
|
final String name = n.getText();
|
||||||
final String issnPrinted = n.valueOf("@issn");
|
final String issnPrinted = n.valueOf("@issn");
|
||||||
final String issnOnline = n.valueOf("@eissn");
|
final String issnOnline = n.valueOf("@eissn");
|
||||||
final String issnLinking = n.valueOf("@lissn");
|
final String issnLinking = n.valueOf("@lissn");
|
||||||
final String ep = n.valueOf("@ep");
|
final String ep = n.valueOf("@ep");
|
||||||
final String iss = n.valueOf("@iss");
|
final String iss = n.valueOf("@iss");
|
||||||
final String sp = n.valueOf("@sp");
|
final String sp = n.valueOf("@sp");
|
||||||
final String vol = n.valueOf("@vol");
|
final String vol = n.valueOf("@vol");
|
||||||
final String edition = n.valueOf("@edition");
|
final String edition = n.valueOf("@edition");
|
||||||
if (StringUtils.isNotBlank(name)) {
|
if (StringUtils.isNotBlank(name)) {
|
||||||
return journal(
|
return journal(
|
||||||
name,
|
name,
|
||||||
issnPrinted,
|
issnPrinted,
|
||||||
issnOnline,
|
issnOnline,
|
||||||
issnLinking,
|
issnLinking,
|
||||||
ep,
|
ep,
|
||||||
iss,
|
iss,
|
||||||
sp,
|
sp,
|
||||||
vol,
|
vol,
|
||||||
edition,
|
edition,
|
||||||
null,
|
null,
|
||||||
null,
|
null,
|
||||||
info);
|
info);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
return null;
|
return null;
|
||||||
}
|
}
|
||||||
|
|
||||||
protected Qualifier prepareQualifier(
|
protected Qualifier prepareQualifier(
|
||||||
final Node node, final String xpath, final String schemeId, final String schemeName) {
|
final Node node, final String xpath, final String schemeId, final String schemeName) {
|
||||||
final String classId = node.valueOf(xpath);
|
final String classId = node.valueOf(xpath);
|
||||||
final String className = code2name.get(classId);
|
final String className = code2name.get(classId);
|
||||||
return qualifier(classId, className, schemeId, schemeName);
|
return qualifier(classId, className, schemeId, schemeName);
|
||||||
}
|
}
|
||||||
|
|
||||||
protected List<StructuredProperty> prepareListStructProps(
|
protected List<StructuredProperty> prepareListStructProps(
|
||||||
final Node node,
|
final Node node,
|
||||||
final String xpath,
|
final String xpath,
|
||||||
final String xpathClassId,
|
final String xpathClassId,
|
||||||
final String schemeId,
|
final String schemeId,
|
||||||
final String schemeName,
|
final String schemeName,
|
||||||
final DataInfo info) {
|
final DataInfo info) {
|
||||||
final List<StructuredProperty> res = new ArrayList<>();
|
final List<StructuredProperty> res = new ArrayList<>();
|
||||||
for (final Object o : node.selectNodes(xpath)) {
|
for (final Object o : node.selectNodes(xpath)) {
|
||||||
final Node n = (Node) o;
|
final Node n = (Node) o;
|
||||||
final String classId = n.valueOf(xpathClassId);
|
final String classId = n.valueOf(xpathClassId);
|
||||||
final String className = code2name.get(classId);
|
final String className = code2name.get(classId);
|
||||||
res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info));
|
res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info));
|
||||||
}
|
}
|
||||||
return res;
|
return res;
|
||||||
}
|
}
|
||||||
|
|
||||||
protected List<StructuredProperty> prepareListStructProps(
|
protected List<StructuredProperty> prepareListStructProps(
|
||||||
final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) {
|
final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) {
|
||||||
final List<StructuredProperty> res = new ArrayList<>();
|
final List<StructuredProperty> res = new ArrayList<>();
|
||||||
for (final Object o : node.selectNodes(xpath)) {
|
for (final Object o : node.selectNodes(xpath)) {
|
||||||
final Node n = (Node) o;
|
final Node n = (Node) o;
|
||||||
res.add(structuredProperty(n.getText(), qualifier, info));
|
res.add(structuredProperty(n.getText(), qualifier, info));
|
||||||
}
|
}
|
||||||
return res;
|
return res;
|
||||||
}
|
}
|
||||||
|
|
||||||
protected List<StructuredProperty> prepareListStructProps(
|
protected List<StructuredProperty> prepareListStructProps(
|
||||||
final Node node, final String xpath, final DataInfo info) {
|
final Node node, final String xpath, final DataInfo info) {
|
||||||
final List<StructuredProperty> res = new ArrayList<>();
|
final List<StructuredProperty> res = new ArrayList<>();
|
||||||
for (final Object o : node.selectNodes(xpath)) {
|
for (final Object o : node.selectNodes(xpath)) {
|
||||||
final Node n = (Node) o;
|
final Node n = (Node) o;
|
||||||
res.add(
|
res
|
||||||
structuredProperty(
|
.add(
|
||||||
n.getText(),
|
structuredProperty(
|
||||||
n.valueOf("@classid"),
|
n.getText(),
|
||||||
n.valueOf("@classname"),
|
n.valueOf("@classid"),
|
||||||
n.valueOf("@schemeid"),
|
n.valueOf("@classname"),
|
||||||
n.valueOf("@schemename"),
|
n.valueOf("@schemeid"),
|
||||||
info));
|
n.valueOf("@schemename"),
|
||||||
}
|
info));
|
||||||
return res;
|
}
|
||||||
}
|
return res;
|
||||||
|
}
|
||||||
protected OAIProvenance prepareOAIprovenance(final Document doc) {
|
|
||||||
final Node n =
|
protected OAIProvenance prepareOAIprovenance(final Document doc) {
|
||||||
doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
|
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
|
||||||
|
|
||||||
if (n == null) {
|
if (n == null) {
|
||||||
return null;
|
return null;
|
||||||
}
|
}
|
||||||
|
|
||||||
final String identifier = n.valueOf("./*[local-name()='identifier']");
|
final String identifier = n.valueOf("./*[local-name()='identifier']");
|
||||||
final String baseURL = n.valueOf("./*[local-name()='baseURL']");
|
final String baseURL = n.valueOf("./*[local-name()='baseURL']");
|
||||||
;
|
;
|
||||||
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");
|
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");
|
||||||
;
|
;
|
||||||
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
|
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
|
||||||
final String datestamp = n.valueOf("./*[local-name()='datestamp']");
|
final String datestamp = n.valueOf("./*[local-name()='datestamp']");
|
||||||
;
|
;
|
||||||
final String harvestDate = n.valueOf("@harvestDate");
|
final String harvestDate = n.valueOf("@harvestDate");
|
||||||
;
|
;
|
||||||
|
|
||||||
return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
|
return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
|
||||||
}
|
}
|
||||||
|
|
||||||
protected DataInfo prepareDataInfo(final Document doc) {
|
protected DataInfo prepareDataInfo(final Document doc) {
|
||||||
final Node n = doc.selectSingleNode("//oaf:datainfo");
|
final Node n = doc.selectSingleNode("//oaf:datainfo");
|
||||||
|
|
||||||
if (n == null) {
|
if (n == null) {
|
||||||
return dataInfo(
|
return dataInfo(
|
||||||
false, null, false, false, MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS, "0.9");
|
false, null, false, false, MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS, "0.9");
|
||||||
}
|
}
|
||||||
|
|
||||||
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
|
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
|
||||||
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
|
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
|
||||||
final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");
|
final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");
|
||||||
final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
|
final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
|
||||||
|
|
||||||
final boolean deletedbyinference = Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference"));
|
final boolean deletedbyinference = Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference"));
|
||||||
final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
|
final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
|
||||||
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
|
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
|
||||||
final String trust = n.valueOf("./oaf:trust");
|
final String trust = n.valueOf("./oaf:trust");
|
||||||
|
|
||||||
return dataInfo(
|
return dataInfo(
|
||||||
deletedbyinference,
|
deletedbyinference,
|
||||||
inferenceprovenance,
|
inferenceprovenance,
|
||||||
inferred,
|
inferred,
|
||||||
false,
|
false,
|
||||||
qualifier(paClassId, paClassName, paSchemeId, paSchemeName),
|
qualifier(paClassId, paClassName, paSchemeId, paSchemeName),
|
||||||
trust);
|
trust);
|
||||||
}
|
}
|
||||||
|
|
||||||
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
|
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
|
||||||
return field(node.valueOf(xpath), info);
|
return field(node.valueOf(xpath), info);
|
||||||
}
|
}
|
||||||
|
|
||||||
protected List<Field<String>> prepareListFields(
|
protected List<Field<String>> prepareListFields(
|
||||||
final Node node, final String xpath, final DataInfo info) {
|
final Node node, final String xpath, final DataInfo info) {
|
||||||
return listFields(info, prepareListString(node, xpath));
|
return listFields(info, prepareListString(node, xpath));
|
||||||
}
|
}
|
||||||
|
|
||||||
protected List<String> prepareListString(final Node node, final String xpath) {
|
protected List<String> prepareListString(final Node node, final String xpath) {
|
||||||
final List<String> res = new ArrayList<>();
|
final List<String> res = new ArrayList<>();
|
||||||
for (final Object o : node.selectNodes(xpath)) {
|
for (final Object o : node.selectNodes(xpath)) {
|
||||||
final String s = ((Node) o).getText().trim();
|
final String s = ((Node) o).getText().trim();
|
||||||
if (StringUtils.isNotBlank(s)) {
|
if (StringUtils.isNotBlank(s)) {
|
||||||
res.add(s);
|
res.add(s);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
return res;
|
return res;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
|
@ -3,11 +3,8 @@ package eu.dnetlib.dhp.oa.graph.raw;
|
||||||
|
|
||||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
import java.util.Optional;
|
import java.util.Optional;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
|
@ -19,6 +16,11 @@ import org.apache.spark.sql.SparkSession;
|
||||||
import org.slf4j.Logger;
|
import org.slf4j.Logger;
|
||||||
import org.slf4j.LoggerFactory;
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
|
||||||
public class DispatchEntitiesApplication {
|
public class DispatchEntitiesApplication {
|
||||||
|
|
||||||
private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesApplication.class);
|
private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesApplication.class);
|
||||||
|
|
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Reference in New Issue