michele.artini
/
dnet-hadoop
forked from D-Net/dnet-hadoop
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

reformatted code according to the updated style descriptor

This commit is contained in:
Claudio Atzori 2020-04-28 11:23:29 +02:00
parent e6d68d1364
commit 6f5b899038
160 changed files with 1844 additions and 1497 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojo.java
View File

@ -4,6 +4,7 @@ package eu.dnetlib.maven.plugin.properties;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.maven.plugin.AbstractMojo;

4
dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectProperties.java
View File

@ -12,7 +12,6 @@
package eu.dnetlib.maven.plugin.properties;
import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
@ -25,6 +24,7 @@ import java.util.List;
import java.util.Map.Entry;
import java.util.Properties;
import java.util.Set;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.StringUtils;
@ -36,6 +36,8 @@ import org.springframework.core.io.DefaultResourceLoader;
import org.springframework.core.io.Resource;
import org.springframework.core.io.ResourceLoader;
import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
/**
* Writes project properties for the keys listed in specified properties files. Based on:
* http://site.kuali.org/maven/plugins/properties-maven-plugin/1.3.2/write-project-properties-mojo.html

1
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java
View File

@ -8,6 +8,7 @@ import static org.mockito.Mockito.lenient;
import java.io.*;
import java.util.Properties;
import org.apache.maven.plugin.MojoExecutionException;
import org.apache.maven.project.MavenProject;
import org.junit.jupiter.api.*;

1
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStore.java
View File

@ -3,6 +3,7 @@ package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import java.util.UUID;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;

1
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreCurrentVersion.java
View File

@ -2,6 +2,7 @@
package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;

1
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreVersion.java
View File

@ -3,6 +3,7 @@ package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import java.util.Date;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;

1
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreWithInfo.java
View File

@ -3,6 +3,7 @@ package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import java.util.Date;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;

4
dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java
View File

@ -1,7 +1,6 @@
package eu.dnetlib.dhp.application;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.Serializable;
@ -9,10 +8,13 @@ import java.io.StringWriter;
import java.util.*;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
import org.apache.commons.cli.*;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class ArgumentApplicationParser implements Serializable {
private final Options options = new Options();

1
dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java
View File

@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;

4
dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java
View File

@ -1,12 +1,14 @@
package eu.dnetlib.dhp.common;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
import java.util.Objects;
import java.util.function.Function;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
/** SparkSession utility methods. */
public class SparkSessionSupport {

3
dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/MetadataRecord.java
View File

@ -1,9 +1,10 @@
package eu.dnetlib.dhp.model.mdstore;
import eu.dnetlib.dhp.utils.DHPUtils;
import java.io.Serializable;
import eu.dnetlib.dhp.utils.DHPUtils;
/** This class models a record inside the new Metadata store collection on HDFS * */
public class MetadataRecord implements Serializable {

5
dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdUtilityParser.java
View File

@ -1,13 +1,14 @@
package eu.dnetlib.dhp.parser.utility;
import com.ximpleware.AutoPilot;
import com.ximpleware.VTDNav;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import com.ximpleware.AutoPilot;
import com.ximpleware.VTDNav;
/** Created by sandro on 9/29/16. */
public class VtdUtilityParser {

7
dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java
View File

@ -1,18 +1,21 @@
package eu.dnetlib.dhp.utils;
import com.jayway.jsonpath.JsonPath;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
import net.minidev.json.JSONArray;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.codec.binary.Base64OutputStream;
import org.apache.commons.codec.binary.Hex;
import com.jayway.jsonpath.JsonPath;
import net.minidev.json.JSONArray;
public class DHPUtils {
public static String md5(final String s) {

3
dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java
View File

@ -1,11 +1,12 @@
package eu.dnetlib.dhp.utils;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.cxf.jaxws.JaxWsProxyFactoryBean;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class ISLookupClientFactory {
private static final Log log = LogFactory.getLog(ISLookupClientFactory.class);

1
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java
View File

@ -5,6 +5,7 @@ import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.GregorianCalendar;
import net.sf.saxon.expr.XPathContext;
import net.sf.saxon.om.Item;
import net.sf.saxon.om.Sequence;

1
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java
View File

@ -4,6 +4,7 @@ package eu.dnetlib.dhp.utils.saxon;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;
import net.sf.saxon.expr.XPathContext;
import net.sf.saxon.om.Sequence;
import net.sf.saxon.trans.XPathException;

3
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java
View File

@ -1,13 +1,14 @@
package eu.dnetlib.dhp.utils.saxon;
import org.apache.commons.lang3.StringUtils;
import net.sf.saxon.expr.XPathContext;
import net.sf.saxon.om.Item;
import net.sf.saxon.om.Sequence;
import net.sf.saxon.trans.XPathException;
import net.sf.saxon.value.SequenceType;
import net.sf.saxon.value.StringValue;
import org.apache.commons.lang3.StringUtils;
public class PickFirst extends AbstractExtensionFunction {

2
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java
View File

@ -2,9 +2,11 @@
package eu.dnetlib.dhp.utils.saxon;
import java.io.StringReader;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.stream.StreamSource;
import net.sf.saxon.Configuration;
import net.sf.saxon.TransformerFactoryImpl;

5
dhp-common/src/main/java/eu/dnetlib/message/Message.java
View File

@ -1,11 +1,12 @@
package eu.dnetlib.message;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.IOException;
import java.util.Map;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
public class Message {
private String workflowId;

7
dhp-common/src/main/java/eu/dnetlib/message/MessageConsumer.java
View File

@ -1,13 +1,14 @@
package eu.dnetlib.message;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.concurrent.LinkedBlockingQueue;
import com.rabbitmq.client.AMQP;
import com.rabbitmq.client.Channel;
import com.rabbitmq.client.DefaultConsumer;
import com.rabbitmq.client.Envelope;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.concurrent.LinkedBlockingQueue;
public class MessageConsumer extends DefaultConsumer {

7
dhp-common/src/main/java/eu/dnetlib/message/MessageManager.java
View File

@ -1,15 +1,16 @@
package eu.dnetlib.message;
import com.rabbitmq.client.Channel;
import com.rabbitmq.client.Connection;
import com.rabbitmq.client.ConnectionFactory;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.TimeoutException;
import com.rabbitmq.client.Channel;
import com.rabbitmq.client.Connection;
import com.rabbitmq.client.ConnectionFactory;
public class MessageManager {
private final String messageHost;

4
dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelationMapper.java
View File

@ -1,11 +1,13 @@
package eu.dnetlib.scholexplorer.relation;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.Serializable;
import java.util.HashMap;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class RelationMapper extends HashMap<String, RelInfo> implements Serializable {
public static RelationMapper load() throws Exception {

1
dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java
View File

@ -9,6 +9,7 @@ import java.nio.file.Path;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.hadoop.conf.Configuration;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;

4
dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java
View File

@ -3,13 +3,15 @@ package eu.dnetlib.dhp.common;
import static org.mockito.Mockito.*;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
import java.util.function.Function;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
public class SparkSessionSupportTest {
@Nested

1
dhp-common/src/test/java/eu/dnetlib/message/MessageTest.java
View File

@ -6,6 +6,7 @@ import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import org.junit.jupiter.api.Test;
public class MessageTest {

6
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicAction.java
View File

@ -1,10 +1,12 @@
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 com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import eu.dnetlib.dhp.schema.oaf.Oaf;
@JsonDeserialize(using = AtomicActionDeserializer.class)
public class AtomicAction<T extends Oaf> implements Serializable {

4
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicActionDeserializer.java
View File

@ -1,14 +1,16 @@
package eu.dnetlib.dhp.schema.action;
import java.io.IOException;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.DeserializationContext;
import com.fasterxml.jackson.databind.JsonDeserializer;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import java.io.IOException;
public class AtomicActionDeserializer extends JsonDeserializer {

6
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java
View File

@ -1,12 +1,14 @@
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.Optional;
import java.util.function.Function;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.oaf.*;
/** Oaf model utility methods. */
public class ModelSupport {

3
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java
View File

@ -1,10 +1,11 @@
package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable;
import java.util.List;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Dataset extends Result implements Serializable {
private Field<String> storagedate;

4
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java
View File

@ -1,10 +1,12 @@
package eu.dnetlib.dhp.schema.oaf;
import com.fasterxml.jackson.annotation.JsonIgnore;
import java.io.Serializable;
import org.apache.commons.lang3.StringUtils;
import com.fasterxml.jackson.annotation.JsonIgnore;
public class GeoLocation implements Serializable {
private String point;

4
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java
View File

@ -1,10 +1,12 @@
package eu.dnetlib.dhp.schema.oaf;
import com.fasterxml.jackson.annotation.JsonIgnore;
import java.io.Serializable;
import org.apache.commons.lang3.StringUtils;
import com.fasterxml.jackson.annotation.JsonIgnore;
public class KeyValue implements Serializable {
private String key;

3
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java
View File

@ -1,10 +1,11 @@
package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable;
import java.util.List;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class OtherResearchProduct extends Result implements Serializable {
private List<Field<String>> contactperson;

3
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java
View File

@ -1,9 +1,10 @@
package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Publication extends Result implements Serializable {
// publication specific

4
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java
View File

@ -1,10 +1,12 @@
package eu.dnetlib.dhp.schema.oaf;
import com.fasterxml.jackson.annotation.JsonIgnore;
import java.io.Serializable;
import org.apache.commons.lang3.StringUtils;
import com.fasterxml.jackson.annotation.JsonIgnore;
public class Qualifier implements Serializable {
private String classid;

3
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java
View File

@ -1,10 +1,11 @@
package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable;
import java.util.List;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Software extends Result implements Serializable {
private List<Field<String>> documentationUrl;

6
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIDataset.java
View File

@ -1,14 +1,16 @@
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.HashMap;
import java.util.List;
import java.util.Map;
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 {
private String originalObjIdentifier;

6
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIPublication.java
View File

@ -1,12 +1,14 @@
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.util.*;
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 {
private String originalObjIdentifier;

6
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java
View File

@ -1,15 +1,17 @@
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.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
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 {
private String id;

7
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/action/AtomicActionTest.java
View File

@ -3,12 +3,15 @@ package eu.dnetlib.dhp.schema.action;
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 org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Relation;
/** @author claudio.atzori */
public class AtomicActionTest {

5
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java
View File

@ -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.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.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
public class ModelSupportTest {

1
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java
View File

@ -5,6 +5,7 @@ import static org.junit.jupiter.api.Assertions.*;
import java.util.Arrays;
import java.util.List;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;

11
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/scholexplorer/DLItest.java
View File

@ -1,16 +1,19 @@
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.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
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 {

25
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
View File

@ -1,9 +1,23 @@
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.collect.Iterables;
import com.google.common.collect.Lists;
import eu.dnetlib.actionmanager.rmi.ActionManagerException;
import eu.dnetlib.actionmanager.set.ActionManagerSet;
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.enabling.is.lookup.rmi.ISLookUpException;
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 {

3
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/LicenseComparator.java
View File

@ -1,9 +1,10 @@
package eu.dnetlib.dhp.actionmanager.migration;
import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
import java.util.Comparator;
import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
public class LicenseComparator implements Comparator<Qualifier> {
@Override

15
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java
View File

@ -1,12 +1,6 @@
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.FileOutputStream;
import java.io.OutputStream;
@ -15,6 +9,7 @@ import java.util.LinkedList;
import java.util.List;
import java.util.Properties;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.conf.Configuration;
@ -26,6 +21,14 @@ import org.apache.hadoop.util.ToolRunner;
import org.slf4j.Logger;
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 {
private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class);

11
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java
View File

@ -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.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.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
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 static final String UNKNOWN = "UNKNOWN";

25
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java
View File

@ -3,22 +3,12 @@ package eu.dnetlib.dhp.actionmanager.migration;
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.Serializable;
import java.util.LinkedList;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
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.slf4j.Logger;
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;
public class TransformActions implements Serializable {

10
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java
View File

@ -4,13 +4,10 @@ package eu.dnetlib.dhp.actionmanager.partition;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
@ -21,6 +18,11 @@ import org.apache.spark.sql.types.*;
import org.slf4j.Logger;
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. */
public class PartitionActionSetsByPayloadTypeJob {

3
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java
View File

@ -3,11 +3,12 @@ package eu.dnetlib.dhp.actionmanager.promote;
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.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Relation;
import java.util.function.BiFunction;
/** OAF model merging support. */
public class MergeAndGet {

15
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java
View File

@ -4,16 +4,11 @@ package eu.dnetlib.dhp.actionmanager.promote;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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.Optional;
import java.util.function.BiFunction;
import java.util.function.Function;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
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.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. */
public class PromoteActionPayloadForGraphTableJob {
private static final Logger logger = LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class);

6
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java
View File

@ -3,12 +3,11 @@ package eu.dnetlib.dhp.actionmanager.promote;
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.Optional;
import java.util.function.BiFunction;
import java.util.function.Function;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
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.TypedColumn;
import org.apache.spark.sql.expressions.Aggregator;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import scala.Tuple2;
/** Promote action payload functions. */

11
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java
View File

@ -6,16 +6,13 @@ import static org.apache.spark.sql.functions.*;
import static org.junit.jupiter.api.Assertions.assertIterableEquals;
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.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Job;
@ -33,6 +30,12 @@ import org.junit.jupiter.api.io.TempDir;
import org.mockito.Mock;
import org.mockito.Mockito;
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.collection.mutable.Seq;

6
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java
View File

@ -6,12 +6,14 @@ import static eu.dnetlib.dhp.actionmanager.promote.MergeAndGet.functionFor;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.*;
import java.util.function.BiFunction;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.*;
public class MergeAndGetTest {
@Nested

9
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java
View File

@ -4,9 +4,6 @@ package eu.dnetlib.dhp.actionmanager.promote;
import static org.junit.jupiter.api.Assertions.*;
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.nio.file.Files;
import java.nio.file.Path;
@ -16,6 +13,7 @@ import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
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.MethodSource;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
public class PromoteActionPayloadForGraphTableJobTest {
private static final ClassLoader cl = PromoteActionPayloadForGraphTableJobTest.class.getClassLoader();

6
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java
View File

@ -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.assertThrows;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.function.BiFunction;
import java.util.function.Function;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
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.Test;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf;
public class PromoteActionPayloadFunctionsTest {
private static SparkSession spark;

17
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java
View File

@ -1,18 +1,12 @@
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.nio.charset.StandardCharsets;
import java.util.HashMap;
import java.util.Map;
import java.util.Objects;
import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
@ -30,6 +24,15 @@ import org.dom4j.Document;
import org.dom4j.Node;
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 static MetadataRecord parseRecord(

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
View File

@ -1,9 +1,10 @@
package eu.dnetlib.dhp.collection.plugin;
import java.util.stream.Stream;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
import java.util.stream.Stream;
public interface CollectorPlugin {

14
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java
View File

@ -1,12 +1,6 @@
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.Iterator;
import java.util.List;
@ -15,6 +9,14 @@ import java.util.Spliterators;
import java.util.stream.Stream;
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 {
private static final String FORMAT_PARAM = "format";

8
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java
View File

@ -1,15 +1,13 @@
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.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.Iterator;
import java.util.Queue;
import java.util.concurrent.PriorityBlockingQueue;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -18,6 +16,10 @@ import org.dom4j.DocumentException;
import org.dom4j.Node;
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> {
private static final Log log = LogFactory.getLog(OaiIterator.class); // NOPMD by marko on

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIteratorFactory.java
View File

@ -1,9 +1,10 @@
package eu.dnetlib.dhp.collection.plugin.oai;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
import java.util.Iterator;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
public class OaiIteratorFactory {
private HttpConnector httpConnector;

19
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorker.java
View File

@ -1,19 +1,12 @@
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.net.URI;
import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.atomic.AtomicInteger;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
@ -23,6 +16,16 @@ import org.apache.hadoop.io.Text;
import org.slf4j.Logger;
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 {
private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorker.class);

7
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorkerApplication.java
View File

@ -1,12 +1,13 @@
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.collection.worker.utils.CollectorPluginFactory;
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

5
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/HttpConnector.java
View File

@ -1,7 +1,6 @@
package eu.dnetlib.dhp.collection.worker.utils;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
import java.io.IOException;
import java.io.InputStream;
import java.net.*;
@ -9,15 +8,19 @@ import java.security.GeneralSecurityException;
import java.security.cert.X509Certificate;
import java.util.List;
import java.util.Map;
import javax.net.ssl.HttpsURLConnection;
import javax.net.ssl.SSLContext;
import javax.net.ssl.TrustManager;
import javax.net.ssl.X509TrustManager;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.math.NumberUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
public class HttpConnector {
private static final Log log = LogFactory.getLog(HttpConnector.class);

15
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformFunction.java
View File

@ -1,16 +1,19 @@
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.transformation.functions.Cleaner;
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 org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.util.LongAccumulator;
public class TransformFunction implements MapFunction<MetadataRecord, MetadataRecord> {

18
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java
View File

@ -1,18 +1,11 @@
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.util.HashMap;
import java.util.Map;
import java.util.Objects;
import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.sql.Dataset;
@ -25,6 +18,15 @@ import org.dom4j.DocumentException;
import org.dom4j.Node;
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 static void main(String[] args) throws Exception {

5
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/functions/Cleaner.java
View File

@ -1,10 +1,11 @@
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.Optional;
import eu.dnetlib.dhp.transformation.vocabulary.Term;
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
import net.sf.saxon.s9api.*;
import scala.Serializable;

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/VocabularyHelper.java
View File

@ -1,12 +1,14 @@
package eu.dnetlib.dhp.transformation.vocabulary;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.Serializable;
import java.net.URL;
import java.nio.charset.Charset;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class VocabularyHelper implements Serializable {
private static final String OPENAIRE_URL = "http://api.openaire.eu/vocabularies/%s.json";

9
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java
View File

@ -3,18 +3,21 @@ package eu.dnetlib.dhp.collection;
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.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
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 eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.model.mdstore.Provenance;
public class CollectionJobTest {
private Path testDir;

11
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java
View File

@ -4,17 +4,20 @@ package eu.dnetlib.dhp.collector.worker;
import static org.junit.jupiter.api.Assertions.assertNotNull;
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 eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.collection.worker.DnetCollectorWorker;
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
import eu.dnetlib.message.Message;
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 {

15
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java
View File

@ -3,18 +3,14 @@ package eu.dnetlib.dhp.transformation;
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.nio.file.Files;
import java.nio.file.Path;
import java.util.HashMap;
import java.util.Map;
import javax.xml.transform.stream.StreamSource;
import net.sf.saxon.s9api.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.util.LongAccumulator;
import org.dom4j.Document;
@ -27,6 +23,13 @@ import org.junit.jupiter.api.io.TempDir;
import org.mockito.Mock;
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)
public class TransformationJobTest {

19
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java
View File

@ -1,19 +1,12 @@
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.Serializable;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.SaveMode;
@ -23,6 +16,16 @@ import org.dom4j.DocumentException;
import org.dom4j.Element;
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 {
protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()

5
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java
View File

@ -4,15 +4,18 @@ package eu.dnetlib.dhp.oa.dedup;
import static java.util.Collections.reverseOrder;
import static java.util.Map.Entry.comparingByValue;
import static java.util.stream.Collectors.toMap;
import static org.apache.commons.lang.StringUtils.endsWith;
import static org.apache.commons.lang.StringUtils.substringBefore;
import eu.dnetlib.dhp.schema.oaf.Field;
import java.time.Year;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.lang.StringUtils;
import eu.dnetlib.dhp.schema.oaf.Field;
public class DatePicker {
private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}";

13
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
View File

@ -1,13 +1,9 @@
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.Iterator;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
@ -15,6 +11,13 @@ import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
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;
public class DedupRecordFactory {

29
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java
View File

@ -1,8 +1,24 @@
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.wcohen.ss.JaroWinkler;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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.model.MapDocument;
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;
public class DedupUtility {

12
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java
View File

@ -1,15 +1,17 @@
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.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
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.Tuple2;

18
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
View File

@ -1,6 +1,16 @@
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.schema.common.EntityType;
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.ISLookUpService;
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 {

29
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java
View File

@ -1,23 +1,11 @@
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.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
@ -32,6 +20,21 @@ import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
import org.slf4j.Logger;
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;
public class SparkCreateMergeRels extends AbstractSparkAction {

28
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java
View File

@ -1,6 +1,21 @@
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.oa.dedup.model.Block;
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.MapDocument;
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;
public class SparkCreateSimRels extends AbstractSparkAction {

13
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
View File

@ -3,18 +3,19 @@ package eu.dnetlib.dhp.oa.dedup;
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.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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;
public class SparkPropagateRelation extends AbstractSparkAction {

4
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkReporter.java
View File

@ -1,11 +1,13 @@
package eu.dnetlib.dhp.oa.dedup;
import eu.dnetlib.pace.util.Reporter;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.apache.spark.util.LongAccumulator;
import eu.dnetlib.pace.util.Reporter;
import scala.Serializable;
import scala.Tuple2;

20
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java
View File

@ -1,16 +1,8 @@
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 org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileStatus;
@ -28,6 +20,16 @@ import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
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;
public class SparkUpdateEntity extends AbstractSparkAction {

9
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java
View File

@ -1,15 +1,18 @@
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.Serializable;
import java.util.Set;
import org.apache.commons.lang.StringUtils;
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 {
private Set<String> docIds;

6
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Block.java
View File

@ -1,8 +1,6 @@
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.util.ArrayList;
import java.util.Comparator;
@ -12,6 +10,10 @@ import java.util.stream.Collectors;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;
import com.google.common.collect.Lists;
import eu.dnetlib.pace.model.MapDocument;
public class Block implements Serializable {
private String key;

4
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/MergeAuthorTest.java
View File

@ -1,15 +1,17 @@
package eu.dnetlib.dhp.oa.dedup;
import eu.dnetlib.dhp.schema.oaf.Publication;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.codehaus.jackson.map.ObjectMapper;
import org.junit.jupiter.api.BeforeEach;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class MergeAuthorTest {
private List<Publication> publicationsToMerge;

13
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
View File

@ -2,19 +2,16 @@
package eu.dnetlib.dhp.oa.dedup;
import static java.nio.file.Files.createTempDirectory;
import static org.junit.jupiter.api.Assertions.assertEquals;
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.IOException;
import java.io.Serializable;
import java.net.URISyntaxException;
import java.nio.file.Paths;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
@ -31,6 +28,12 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.Mockito;
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;
@ExtendWith(MockitoExtension.class)

3
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java
View File

@ -1,10 +1,11 @@
package eu.dnetlib.dhp.oa.dedup.jpath;
import org.junit.jupiter.api.Test;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.util.MapDocumentUtil;
import org.junit.jupiter.api.Test;
public class JsonPathTest {

5
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DatePicker.java
View File

@ -4,15 +4,18 @@ package eu.dnetlib.dedup;
import static java.util.Collections.reverseOrder;
import static java.util.Map.Entry.comparingByValue;
import static java.util.stream.Collectors.toMap;
import static org.apache.commons.lang.StringUtils.endsWith;
import static org.apache.commons.lang.StringUtils.substringBefore;
import eu.dnetlib.dhp.schema.oaf.Field;
import java.time.Year;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.lang.StringUtils;
import eu.dnetlib.dhp.schema.oaf.Field;
public class DatePicker {
private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}";

15
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java
View File

@ -1,19 +1,22 @@
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 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.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;
public class DedupRecordFactory {

19
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupUtility.java
View File

@ -1,14 +1,6 @@
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.StringWriter;
import java.nio.charset.StandardCharsets;
@ -16,6 +8,7 @@ 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.io.IOUtils;
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.JavaSparkContext;
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;
public class DedupUtility {

10
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/Deduper.java
View File

@ -1,12 +1,9 @@
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.stream.Collectors;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
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.PairFunction;
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.Tuple2;

17
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java
View File

@ -1,15 +1,9 @@
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.List;
import org.apache.commons.io.IOUtils;
import org.apache.spark.api.java.JavaPairRDD;
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.Encoders;
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;
public class SparkCreateConnectedComponent {

10
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java
View File

@ -1,15 +1,17 @@
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.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
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 static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(

12
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java
View File

@ -1,18 +1,20 @@
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 org.apache.commons.io.IOUtils;
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.sql.Encoders;
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;
/**

4
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkReporter.java
View File

@ -1,13 +1,15 @@
package eu.dnetlib.dedup;
import eu.dnetlib.pace.util.Reporter;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.spark.util.LongAccumulator;
import eu.dnetlib.pace.util.Reporter;
import scala.Serializable;
import scala.Tuple2;

9
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/graph/ConnectedComponent.java
View File

@ -1,15 +1,18 @@
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.Serializable;
import java.util.Set;
import org.apache.commons.lang.StringUtils;
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 {
private Set<String> docIds;

15
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkPropagateRelationsJob.java
View File

@ -1,17 +1,20 @@
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 org.apache.commons.io.IOUtils;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
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;
public class SparkPropagateRelationsJob {

19
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkUpdateEntityJob.java
View File

@ -1,8 +1,19 @@
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.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
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.DLIUnknown;
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;
public class SparkUpdateEntityJob {

9
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveImporterJob.java
View File

@ -3,10 +3,8 @@ package eu.dnetlib.dhp.oa.graph.hive;
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 org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
@ -16,6 +14,11 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
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 {
private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJob.class);

51
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.oa.graph.raw;
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.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.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Context;
@ -29,24 +43,13 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
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 {
protected final Map<String, String> code2name;
protected static final Qualifier MAIN_TITLE_QUALIFIER =
qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
"main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
this.code2name = code2name;
@ -64,18 +67,17 @@ public abstract class AbstractMdRecordToOafMapper {
nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
final Document doc =
DocumentHelper.parseText(
xml.replaceAll(
final Document doc = DocumentHelper
.parseText(
xml
.replaceAll(
"http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3"));
final String type = doc.valueOf("//dr:CobjCategory/@type");
final KeyValue collectedFrom =
keyValue(
final KeyValue collectedFrom = keyValue(
createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true),
doc.valueOf("//oaf:collectedFrom/@name"));
final KeyValue hostedBy =
StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
? collectedFrom
: keyValue(
createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true),
@ -214,7 +216,8 @@ public abstract class AbstractMdRecordToOafMapper {
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
r.setCollectedfrom(Arrays.asList(collectedFrom));
r.setPid(
r
.setPid(
prepareListStructProps(
doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
@ -385,7 +388,8 @@ public abstract class AbstractMdRecordToOafMapper {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
res.add(
res
.add(
structuredProperty(
n.getText(),
n.valueOf("@classid"),
@ -398,8 +402,7 @@ public abstract class AbstractMdRecordToOafMapper {
}
protected OAIProvenance prepareOAIprovenance(final Document doc) {
final Node n =
doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
if (n == null) {
return null;

10
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/DispatchEntitiesApplication.java
View File

@ -3,11 +3,8 @@ package eu.dnetlib.dhp.oa.graph.raw;
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 org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
@ -19,6 +16,11 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
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 {
private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesApplication.class);

Some files were not shown because too many files have changed in this diff Show More