Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop

dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_dnet.xml

@@ -19,7 +19,7 @@
         <setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration" value="do not insert"/>
         <setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws" value="do not insert"/>
         <setting id="org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement" value="common_lines"/>
-        <setting id="org.eclipse.jdt.core.formatter.comment.format_javadoc_comments" value="true"/>
+        <setting id="org.eclipse.jdt.core.formatter.comment.format_javadoc_comments" value="false"/>
         <setting id="org.eclipse.jdt.core.formatter.indentation.size" value="4"/>
         <setting id="org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator" value="do not insert"/>
         <setting id="org.eclipse.jdt.core.formatter.parentheses_positions_in_enum_constant_declaration" value="common_lines"/>

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/MissingConceptDoiException.java

@@ -1,7 +1,8 @@
+
 package eu.dnetlib.dhp.common.api;
 
 public class MissingConceptDoiException extends Throwable {
-    public MissingConceptDoiException(String message) {
-        super(message);
-    }
+	public MissingConceptDoiException(String message) {
+		super(message);
+	}
 }

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java

@@ -12,14 +12,12 @@ import okhttp3.*;
 
 public class ZenodoAPIClient implements Serializable {
 
-
 	String urlString;
 	String bucket;
 
 	String deposition_id;
 	String access_token;
 
-
 	public static final MediaType MEDIA_TYPE_JSON = MediaType.parse("application/json; charset=utf-8");
 
 	private static final MediaType MEDIA_TYPE_ZIP = MediaType.parse("application/zip");
@@ -40,7 +38,9 @@ public class ZenodoAPIClient implements Serializable {
 		this.bucket = bucket;
 	}
 
-	public void setDeposition_id(String deposition_id){this.deposition_id = deposition_id;}
+	public void setDeposition_id(String deposition_id) {
+		this.deposition_id = deposition_id;
+	}
 
 	public ZenodoAPIClient(String urlString, String access_token) throws IOException {
 
@@ -182,10 +182,10 @@ public class ZenodoAPIClient implements Serializable {
 		OkHttpClient httpClient = new OkHttpClient();
 
 		Request request = new Request.Builder()
-				.url(urlString + "/" + deposition_id + "/actions/newversion")
-				.addHeader("Authorization", "Bearer " + access_token)
-				.post(RequestBody.create(MEDIA_TYPE_JSON, json))
-				.build();
+			.url(urlString + "/" + deposition_id + "/actions/newversion")
+			.addHeader("Authorization", "Bearer " + access_token)
+			.post(RequestBody.create(MEDIA_TYPE_JSON, json))
+			.build();
 
 		try (Response response = httpClient.newCall(request).execute()) {
 
@@ -205,9 +205,9 @@ public class ZenodoAPIClient implements Serializable {
 
 		ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(), ZenodoModelList.class);
 
-		for(ZenodoModel zm : zenodoModelList){
-			if (zm.getConceptrecid().equals(concept_rec_id)){
-				deposition_id =  zm.getId();
+		for (ZenodoModel zm : zenodoModelList) {
+			if (zm.getConceptrecid().equals(concept_rec_id)) {
+				deposition_id = zm.getId();
 				return;
 			}
 		}
@@ -220,11 +220,11 @@ public class ZenodoAPIClient implements Serializable {
 		OkHttpClient httpClient = new OkHttpClient();
 
 		Request request = new Request.Builder()
-				.url(urlString)
-				.addHeader("Content-Type", "application/json") // add request headers
-				.addHeader("Authorization", "Bearer " + access_token)
-				.get()
-				.build();
+			.url(urlString)
+			.addHeader("Content-Type", "application/json") // add request headers
+			.addHeader("Authorization", "Bearer " + access_token)
+			.get()
+			.build();
 
 		try (Response response = httpClient.newCall(request).execute()) {
 
@@ -241,11 +241,11 @@ public class ZenodoAPIClient implements Serializable {
 		OkHttpClient httpClient = new OkHttpClient();
 
 		Request request = new Request.Builder()
-				.url(url)
-				.addHeader("Content-Type", "application/json") // add request headers
-				.addHeader("Authorization", "Bearer " + access_token)
-				.get()
-				.build();
+			.url(url)
+			.addHeader("Content-Type", "application/json") // add request headers
+			.addHeader("Authorization", "Bearer " + access_token)
+			.get()
+			.build();
 
 		try (Response response = httpClient.newCall(request).execute()) {
 
@@ -255,12 +255,10 @@ public class ZenodoAPIClient implements Serializable {
 			// Get response body
 			ZenodoModel zenodoModel = new Gson().fromJson(response.body().string(), ZenodoModel.class);
 
-
 			return zenodoModel.getLinks().getBucket();
 
 		}
 
 	}
 
-
 }

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModelList.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.common.api.zenodo;
 
 import java.util.ArrayList;

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Funder.java

@@ -1,35 +1,36 @@
+
 package eu.dnetlib.dhp.schema.dump.oaf;
 
 import java.io.Serializable;
 
 public class Funder implements Serializable {
-    private String shortName;
+	private String shortName;
 
-    private String name;
+	private String name;
 
-    private String jurisdiction;
+	private String jurisdiction;
 
-    public String getJurisdiction() {
-        return jurisdiction;
-    }
+	public String getJurisdiction() {
+		return jurisdiction;
+	}
 
-    public void setJurisdiction(String jurisdiction) {
-        this.jurisdiction = jurisdiction;
-    }
+	public void setJurisdiction(String jurisdiction) {
+		this.jurisdiction = jurisdiction;
+	}
 
-    public String getShortName() {
-        return shortName;
-    }
+	public String getShortName() {
+		return shortName;
+	}
 
-    public void setShortName(String shortName) {
-        this.shortName = shortName;
-    }
+	public void setShortName(String shortName) {
+		this.shortName = shortName;
+	}
 
-    public String getName() {
-        return name;
-    }
+	public String getName() {
+		return name;
+	}
 
-    public void setName(String name) {
-        this.name = name;
-    }
+	public void setName(String name) {
+		this.name = name;
+	}
 }

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Instance.java

@@ -30,11 +30,11 @@ public class Instance implements Serializable {
 
 	private String type;
 
-	 private KeyValue hostedby;
+	private KeyValue hostedby;
 
 	private List<String> url;
 
-	 private KeyValue collectedfrom;
+	private KeyValue collectedfrom;
 
 	private String publicationdate;// dateofacceptance;
 

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Project.java

@@ -1,44 +1,45 @@
+
 package eu.dnetlib.dhp.schema.dump.oaf;
 
 import java.io.Serializable;
 
 public class Project implements Serializable {
-    protected String id;// OpenAIRE id
-    protected String code;
+	protected String id;// OpenAIRE id
+	protected String code;
 
-    protected String acronym;
+	protected String acronym;
 
-    protected String title;
+	protected String title;
 
-    public String getId() {
-        return id;
-    }
+	public String getId() {
+		return id;
+	}
 
-    public void setId(String id) {
-        this.id = id;
-    }
+	public void setId(String id) {
+		this.id = id;
+	}
 
-    public String getCode() {
-        return code;
-    }
+	public String getCode() {
+		return code;
+	}
 
-    public void setCode(String code) {
-        this.code = code;
-    }
+	public void setCode(String code) {
+		this.code = code;
+	}
 
-    public String getAcronym() {
-        return acronym;
-    }
+	public String getAcronym() {
+		return acronym;
+	}
 
-    public void setAcronym(String acronym) {
-        this.acronym = acronym;
-    }
+	public void setAcronym(String acronym) {
+		this.acronym = acronym;
+	}
 
-    public String getTitle() {
-        return title;
-    }
+	public String getTitle() {
+		return title;
+	}
 
-    public void setTitle(String title) {
-        this.title = title;
-    }
+	public void setTitle(String title) {
+		this.title = title;
+	}
 }

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Organization.java

@@ -10,7 +10,6 @@ import eu.dnetlib.dhp.schema.dump.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.dump.oaf.Qualifier;
 import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
 
-
 /**
  * To represent the generic organizaiton. It has the following parameters:
  * - private String legalshortname to store the legalshortname of the organizaiton

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java

@@ -366,48 +366,47 @@ public class ResultMapper implements Serializable {
 
 	private static Instance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i, boolean graph) {
 
-			Instance instance = new Instance();
+		Instance instance = new Instance();
 
-			if(!graph){
+		if (!graph) {
+			instance
+				.setCollectedfrom(
+					KeyValue
+						.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
+			instance
+				.setHostedby(
+					KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue()));
+		}
+
+		Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> opAr = Optional
+			.ofNullable(i.getAccessright());
+		if (opAr.isPresent()) {
+			if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) {
+				String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid());
 				instance
-						.setCollectedfrom(
-								KeyValue
-										.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
-				instance
-						.setHostedby(
-								KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue()));
+					.setAccessright(
+						AccessRight
+							.newInstance(
+								code,
+								Constants.coarCodeLabelMap.get(code),
+								Constants.COAR_ACCESS_RIGHT_SCHEMA));
 			}
+		}
 
-			Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> opAr = Optional
-					.ofNullable(i.getAccessright());
-			if (opAr.isPresent()) {
-				if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) {
-					String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid());
-					instance
-							.setAccessright(
-									AccessRight
-											.newInstance(
-													code,
-													Constants.coarCodeLabelMap.get(code),
-													Constants.COAR_ACCESS_RIGHT_SCHEMA));
-				}
-			}
-
-
-			Optional
-					.ofNullable(i.getLicense())
-					.ifPresent(value -> instance.setLicense(value.getValue()));
-			Optional
-					.ofNullable(i.getDateofacceptance())
-					.ifPresent(value -> instance.setPublicationdate(value.getValue()));
-			Optional
-					.ofNullable(i.getRefereed())
-					.ifPresent(value -> instance.setRefereed(value.getClassname()));
-			// .ifPresent(value -> instance.setRefereed(value.getValue()));
-			Optional
-					.ofNullable(i.getInstancetype())
-					.ifPresent(value -> instance.setType(value.getClassname()));
-			Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
+		Optional
+			.ofNullable(i.getLicense())
+			.ifPresent(value -> instance.setLicense(value.getValue()));
+		Optional
+			.ofNullable(i.getDateofacceptance())
+			.ifPresent(value -> instance.setPublicationdate(value.getValue()));
+		Optional
+			.ofNullable(i.getRefereed())
+			.ifPresent(value -> instance.setRefereed(value.getClassname()));
+		// .ifPresent(value -> instance.setRefereed(value.getValue()));
+		Optional
+			.ofNullable(i.getInstancetype())
+			.ifPresent(value -> instance.setType(value.getClassname()));
+		Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
 
 		return instance;
 	}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java

@@ -3,11 +3,13 @@ package eu.dnetlib.dhp.oa.graph.dump;
 
 import java.io.Serializable;
 import java.util.Optional;
+
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.*;
+
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.api.MissingConceptDoiException;
 import eu.dnetlib.dhp.common.api.ZenodoAPIClient;

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpGraphEntities.java

@@ -8,8 +8,6 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder;
-import eu.dnetlib.dhp.schema.dump.oaf.graph.Project;
 import org.apache.spark.SparkConf;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
@@ -24,6 +22,8 @@ import eu.dnetlib.dhp.oa.graph.dump.Utils;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.dump.oaf.*;
 import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
+import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder;
+import eu.dnetlib.dhp.schema.dump.oaf.graph.Project;
 import eu.dnetlib.dhp.schema.oaf.Field;
 import eu.dnetlib.dhp.schema.oaf.Journal;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkOrganizationRelation.java

@@ -1,5 +1,4 @@
 
-
 package eu.dnetlib.dhp.oa.graph.dump.graph;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java

@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.graph.dump;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
@@ -16,7 +17,9 @@ import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+
 import com.fasterxml.jackson.databind.ObjectMapper;
+
 import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit;
 import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
 

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/ExtractRelationFromEntityTest.java

@@ -38,7 +38,6 @@ public class ExtractRelationFromEntityTest {
 	private static final Logger log = LoggerFactory
 		.getLogger(ExtractRelationFromEntityTest.class);
 
-
 	@BeforeAll
 	public static void beforeAll() throws IOException {
 		workingDir = Files