compilation after merging

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java

@@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
 
 		return projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> {
 			Project project = new Project();
-			//project.setId(bipProjectScores.getProjectId());
+			project.setId(bipProjectScores.getProjectId());
 			project.setMeasures(bipProjectScores.toMeasures());
 			return project;
 		}, Encoders.bean(Project.class))

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/MoveResult.java

@@ -30,7 +30,7 @@ public class MoveResult implements Serializable {
 	public static void main(String[] args) throws Exception {
 		String jsonConfiguration = IOUtils
 			.toString(
-					MoveResult.class
+				MoveResult.class
 					.getResourceAsStream(
 						"/eu/dnetlib/dhp/wf/subworkflows/input_moveresult_parameters.json"));
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.bulktag.actions;
 
 import java.io.Serializable;
@@ -8,31 +9,31 @@ import java.util.List;
  * @Date 22/01/24
  */
 public class Action implements Serializable {
-    private String clazz;
+	private String clazz;
-     private String method;
+	private String method;
-     private List<Parameters> params;
+	private List<Parameters> params;
 
-    public String getClazz() {
+	public String getClazz() {
-        return clazz;
+		return clazz;
-    }
+	}
 
-    public void setClazz(String clazz) {
+	public void setClazz(String clazz) {
-        this.clazz = clazz;
+		this.clazz = clazz;
-    }
+	}
 
-    public String getMethod() {
+	public String getMethod() {
-        return method;
+		return method;
-    }
+	}
 
-    public void setMethod(String method) {
+	public void setMethod(String method) {
-        this.method = method;
+		this.method = method;
-    }
+	}
 
-    public List<Parameters> getParams() {
+	public List<Parameters> getParams() {
-        return params;
+		return params;
-    }
+	}
 
-    public void setParams(List<Parameters> params) {
+	public void setParams(List<Parameters> params) {
-        this.params = params;
+		this.params = params;
-    }
+	}
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.bulktag.actions;
 
 import java.io.Serializable;
@@ -8,47 +9,47 @@ import java.io.Serializable;
  */
 public class ExecSubstringAction implements Serializable {
 
-    private String value;
+	private String value;
-    private String from;
+	private String from;
-    private String to;
+	private String to;
 
-    public String getValue() {
+	public String getValue() {
-        return value;
+		return value;
-    }
+	}
 
-    public void setValue(String value) {
+	public void setValue(String value) {
-        this.value = value;
+		this.value = value;
-    }
+	}
 
-    public String getFrom() {
+	public String getFrom() {
-        return from;
+		return from;
-    }
+	}
 
-    public void setFrom(String from) {
+	public void setFrom(String from) {
-        this.from = from;
+		this.from = from;
-    }
+	}
 
-    public String getTo() {
+	public String getTo() {
-        return to;
+		return to;
-    }
+	}
 
-    public void setTo(String to) {
+	public void setTo(String to) {
-        this.to = to;
+		this.to = to;
-    }
+	}
 
-    public String execSubstring(){
+	public String execSubstring() {
-        int to = Integer.valueOf(this.to);
+		int to = Integer.valueOf(this.to);
-        int from = Integer.valueOf(this.from);
+		int from = Integer.valueOf(this.from);
 
-        if(to < from || from > this.value.length())
+		if (to < from || from > this.value.length())
-            return "";
+			return "";
 
-        if(from < 0)
+		if (from < 0)
-            from = 0;
+			from = 0;
-        if (to > this.value.length())
+		if (to > this.value.length())
-            to =  this.value.length();
+			to = this.value.length();
 
-        return  this.value.substring(from, to);
+		return this.value.substring(from, to);
 
-    }
+	}
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.bulktag.actions;
 
 import java.io.Serializable;
@@ -8,23 +9,22 @@ import java.io.Serializable;
  */
 public class MapModel implements Serializable {
 
-    private String path;
+	private String path;
-    private Action action;
+	private Action action;
 
+	public String getPath() {
+		return path;
+	}
 
-    public String getPath() {
+	public void setPath(String path) {
-        return path;
+		this.path = path;
-    }
+	}
 
-    public void setPath(String path) {
+	public Action getAction() {
-        this.path = path;
+		return action;
-    }
+	}
 
-    public Action getAction() {
+	public void setAction(Action action) {
-        return action;
+		this.action = action;
-    }
+	}
-
-    public void setAction(Action action) {
-        this.action = action;
-    }
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.bulktag.actions;
 
 import java.io.Serializable;
@@ -7,22 +8,22 @@ import java.io.Serializable;
  * @Date 22/01/24
  */
 public class Parameters implements Serializable {
-    private String paramName;
+	private String paramName;
-    private String paramValue;
+	private String paramValue;
 
-    public String getParamName() {
+	public String getParamName() {
-        return paramName;
+		return paramName;
-    }
+	}
 
-    public void setParamName(String paramName) {
+	public void setParamName(String paramName) {
-        this.paramName = paramName;
+		this.paramName = paramName;
-    }
+	}
 
-    public String getParamValue() {
+	public String getParamValue() {
-        return paramValue;
+		return paramValue;
-    }
+	}
 
-    public void setParamValue(String paramValue) {
+	public void setParamValue(String paramValue) {
-        this.paramValue = paramValue;
+		this.paramValue = paramValue;
-    }
+	}
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java

@@ -1,11 +1,11 @@
 
 package eu.dnetlib.dhp.bulktag.community;
 
-import eu.dnetlib.dhp.bulktag.actions.MapModel;
-
 import java.io.Serializable;
 import java.util.HashMap;
 
+import eu.dnetlib.dhp.bulktag.actions.MapModel;
+
 public class ProtoMap extends HashMap<String, MapModel> implements Serializable {
 
 	public ProtoMap() {

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java

@@ -10,9 +10,6 @@ import java.lang.reflect.Method;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import com.jayway.jsonpath.PathNotFoundException;
-import eu.dnetlib.dhp.bulktag.actions.MapModel;
-import eu.dnetlib.dhp.bulktag.actions.Parameters;
 import org.apache.commons.lang3.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -20,7 +17,10 @@ import org.slf4j.LoggerFactory;
 import com.google.gson.Gson;
 import com.jayway.jsonpath.DocumentContext;
 import com.jayway.jsonpath.JsonPath;
+import com.jayway.jsonpath.PathNotFoundException;
 
+import eu.dnetlib.dhp.bulktag.actions.MapModel;
+import eu.dnetlib.dhp.bulktag.actions.Parameters;
 import eu.dnetlib.dhp.bulktag.eosc.EoscIFTag;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
@@ -40,7 +40,8 @@ public class ResultTagger implements Serializable {
 		return (tmp != clist.size());
 	}
 
-	private Map<String, List<String>> getParamMap(final Result result, Map<String, MapModel> params) throws NoSuchMethodException, InvocationTargetException {
+	private Map<String, List<String>> getParamMap(final Result result, Map<String, MapModel> params)
+		throws NoSuchMethodException, InvocationTargetException {
 		Map<String, List<String>> param = new HashMap<>();
 		String json = new Gson().toJson(result, Result.class);
 		DocumentContext jsonContext = JsonPath.parse(json);
@@ -54,30 +55,34 @@ public class ResultTagger implements Serializable {
 			try {
 				String path = mapModel.getPath();
 				Object obj = jsonContext.read(path);
-				List<String> pathValue ;
+				List<String> pathValue;
-				if(obj instanceof java.lang.String)
+				if (obj instanceof java.lang.String)
-					pathValue = Arrays.asList((String)obj);
+					pathValue = Arrays.asList((String) obj);
 				else
-					pathValue = (List<String>)obj;
+					pathValue = (List<String>) obj;
-				if(Optional.ofNullable(mapModel.getAction()).isPresent()){
+				if (Optional.ofNullable(mapModel.getAction()).isPresent()) {
 					Class<?> c = Class.forName(mapModel.getAction().getClazz());
 					Object class_instance = c.newInstance();
 					Method setField = c.getMethod("setValue", String.class);
 					setField.invoke(class_instance, pathValue.get(0));
-					for(Parameters p : mapModel.getAction().getParams()){
+					for (Parameters p : mapModel.getAction().getParams()) {
 						setField = c.getMethod("set" + p.getParamName(), String.class);
 						setField.invoke(class_instance, p.getParamValue());
 					}
 
-					param.put(key,Arrays.asList((String)c.getMethod(mapModel.getAction().getMethod()).invoke(class_instance)));
+					param
+						.put(
+							key, Arrays
+								.asList((String) c.getMethod(mapModel.getAction().getMethod()).invoke(class_instance)));
 
 				}
 
-				else{
+				else {
 					param.put(key, pathValue);
 				}
 
-			} catch (PathNotFoundException | ClassNotFoundException | InstantiationException | IllegalAccessException e) {
+			} catch (PathNotFoundException | ClassNotFoundException | InstantiationException
+				| IllegalAccessException e) {
 				param.put(key, new ArrayList<>());
 			}
 		}
@@ -86,9 +91,8 @@ public class ResultTagger implements Serializable {
 	}
 
 	public <R extends Result> R enrichContextCriteria(
-		final R result, final CommunityConfiguration conf, final Map<String, MapModel> criteria) throws InvocationTargetException, NoSuchMethodException {
+		final R result, final CommunityConfiguration conf, final Map<String, MapModel> criteria)
-
+		throws InvocationTargetException, NoSuchMethodException {
-
 
 		// Verify if the entity is deletedbyinference. In case verify if to clean the context list
 		// from all the zenodo communities

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java

@@ -33,25 +33,25 @@ public class BulkTagJobTest {
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
 	public static final String pathMap = "{\"author\":{\"path\":\"$['author'][*]['fullname']\"}," +
-			" \"title\":{\"path\":\"$['title'][*]['value']\"}, "+
+		" \"title\":{\"path\":\"$['title'][*]['value']\"}, " +
-			" \"orcid\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']\"} , " +
+		" \"orcid\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']\"} , " +
-			" \"orcid_pending\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']\"} ,"+
+		" \"orcid_pending\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']\"} ,"
-			"\"contributor\" : {\"path\":\"$['contributor'][*]['value']\"},"+
+		+
-			" \"description\" : {\"path\":\"$['description'][*]['value']\"},"+
+		"\"contributor\" : {\"path\":\"$['contributor'][*]['value']\"}," +
-			" \"subject\" :{\"path\":\"$['subject'][*]['value']\"}, " +
+		" \"description\" : {\"path\":\"$['description'][*]['value']\"}," +
-			" \"fos\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"} , "+
+		" \"subject\" :{\"path\":\"$['subject'][*]['value']\"}, " +
-			"\"sdg\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"}," +
+		" \"fos\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"} , " +
-			"\"journal\":{\"path\":\"$['journal'].name\"}," +
+		"\"sdg\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"}," +
-			"\"hostedby\":{\"path\":\"$['instance'][*]['hostedby']['key']\"}," +
+		"\"journal\":{\"path\":\"$['journal'].name\"}," +
-			"\"collectedfrom\":{\"path\":\"$['instance'][*]['collectedfrom']['key']\"}," +
+		"\"hostedby\":{\"path\":\"$['instance'][*]['hostedby']['key']\"}," +
-			"\"publisher\":{\"path\":\"$['publisher'].value\"}," +
+		"\"collectedfrom\":{\"path\":\"$['instance'][*]['collectedfrom']['key']\"}," +
-			"\"publicationyear\":{\"path\":\"$['dateofacceptance'].value\", " +
+		"\"publisher\":{\"path\":\"$['publisher'].value\"}," +
-			" \"action\":{\"clazz\":\"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction\"," +
+		"\"publicationyear\":{\"path\":\"$['dateofacceptance'].value\", " +
-		                 "\"method\":\"execSubstring\","+
+		" \"action\":{\"clazz\":\"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction\"," +
-		                 "\"params\":[" +
+		"\"method\":\"execSubstring\"," +
-						 "{\"paramName\":\"From\",  \"paramValue\":0}, " +
+		"\"params\":[" +
-		                     "{\"paramName\":\"To\",\"paramValue\":4}]}}}";
+		"{\"paramName\":\"From\",  \"paramValue\":0}, " +
-
+		"{\"paramName\":\"To\",\"paramValue\":4}]}}}";
 
 	private static SparkSession spark;
 
@@ -1609,60 +1609,94 @@ public class BulkTagJobTest {
 		Assertions.assertEquals(0, spark.sql(query).count());
 	}
 
-
 	@Test
 	void pubdateTest() throws Exception {
 
-
 		final String pathMap = BulkTagJobTest.pathMap;
 		SparkBulkTagJob
-				.main(
+			.main(
-						new String[] {
+				new String[] {
-								"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-								"-sourcePath",
+					"-sourcePath",
-								getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/").getPath(),
+					getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/").getPath(),
-								"-taggingConf",
+					"-taggingConf",
-								IOUtils
+					IOUtils
-										.toString(
+						.toString(
-										BulkTagJobTest.class
+							BulkTagJobTest.class
-												.getResourceAsStream(
+								.getResourceAsStream(
-														"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml")),
+									"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml")),
-								"-outputPath", workingDir.toString() + "/",
+					"-outputPath", workingDir.toString() + "/",
-								"-pathMap", pathMap
+					"-pathMap", pathMap
-						});
+				});
 
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Dataset> tmp = sc
-				.textFile(workingDir.toString() + "/dataset")
+			.textFile(workingDir.toString() + "/dataset")
-				.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
+			.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
 
 		Assertions.assertEquals(10, tmp.count());
 		org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
-				.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
+			.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
 
 		verificationDataset.createOrReplaceTempView("dataset");
 
-
 		String query = "select id, MyT.id community, MyD.provenanceaction.classid "
-				+ "from dataset "
+			+ "from dataset "
-				+ "lateral view explode(context) c as MyT "
+			+ "lateral view explode(context) c as MyT "
-				+ "lateral view explode(MyT.datainfo) d as MyD "
+			+ "lateral view explode(MyT.datainfo) d as MyD "
-				+ "where MyD.inferenceprovenance = 'bulktagging'";
+			+ "where MyD.inferenceprovenance = 'bulktagging'";
 
 		org.apache.spark.sql.Dataset<Row> queryResult = spark.sql(query);
 		queryResult.show(false);
 		Assertions.assertEquals(5, queryResult.count());
 
-		Assertions.assertEquals(1, queryResult.filter((FilterFunction<Row>)  r -> r.getAs("id").equals("50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529")).count());
+		Assertions
-		Assertions.assertEquals(1, queryResult.filter((FilterFunction<Row>)  r -> r.getAs("id").equals("50|od______3989::2f4f3c820c450bd08dac08d07cc82dcf")).count());
+			.assertEquals(
-		Assertions.assertEquals(1, queryResult.filter((FilterFunction<Row>)  r -> r.getAs("id").equals("50|od______3989::7fcbe3a03280663cddebfd3cb9203177")).count());
+				1,
-		Assertions.assertEquals(1, queryResult.filter((FilterFunction<Row>)  r -> r.getAs("id").equals("50|od______3989::d791339867bec6d3eb2104deeb4e4961")).count());
+				queryResult
-		Assertions.assertEquals(1, queryResult.filter((FilterFunction<Row>)  r -> r.getAs("id").equals("50|od______3989::d90d3a1f64ad264b5ebed8a35b280343")).count());
+					.filter(
-
+						(FilterFunction<Row>) r -> r
+							.getAs("id")
+							.equals("50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529"))
+					.count());
+		Assertions
+			.assertEquals(
+				1,
+				queryResult
+					.filter(
+						(FilterFunction<Row>) r -> r
+							.getAs("id")
+							.equals("50|od______3989::2f4f3c820c450bd08dac08d07cc82dcf"))
+					.count());
+		Assertions
+			.assertEquals(
+				1,
+				queryResult
+					.filter(
+						(FilterFunction<Row>) r -> r
+							.getAs("id")
+							.equals("50|od______3989::7fcbe3a03280663cddebfd3cb9203177"))
+					.count());
+		Assertions
+			.assertEquals(
+				1,
+				queryResult
+					.filter(
+						(FilterFunction<Row>) r -> r
+							.getAs("id")
+							.equals("50|od______3989::d791339867bec6d3eb2104deeb4e4961"))
+					.count());
+		Assertions
+			.assertEquals(
+				1,
+				queryResult
+					.filter(
+						(FilterFunction<Row>) r -> r
+							.getAs("id")
+							.equals("50|od______3989::d90d3a1f64ad264b5ebed8a35b280343"))
+					.count());
 
 	}
 
-
-
 }