moved class CleaningFunctions in the correct package. Remove newlines from titles, descriptions, subjects

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/CleaningFunctions.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.oa.graph.clean;
+package eu.dnetlib.dhp.schema.oaf;
 
 import java.util.*;
 import java.util.function.Function;
@@ -10,12 +10,12 @@ import org.apache.commons.lang3.StringUtils;
 import com.clearspring.analytics.util.Lists;
 
 import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.*;
 
 public class CleaningFunctions {
 
 	public static final String DOI_URL_PREFIX_REGEX = "(^http(s?):\\/\\/)(((dx\\.)?doi\\.org)|(handle\\.test\\.datacite\\.org))\\/";
 	public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/";
+	public static final String NEWLINES = "(?:\\n|\\r)";
 
 	public static final Set<String> PID_BLACKLIST = new HashSet<>();
 
@@ -76,7 +76,7 @@ public class CleaningFunctions {
 		return value;
 	}
 
-	protected static <T extends Oaf> T fixDefaults(T value) {
+	public static <T extends Oaf> T cleanup(T value) {
 		if (value instanceof Datasource) {
 			// nothing to clean here
 		} else if (value instanceof Project) {
@@ -109,6 +109,29 @@ public class CleaningFunctions {
 							.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
 							.filter(sp -> Objects.nonNull(sp.getQualifier()))
 							.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
+							.map(CleaningFunctions::removeNewLines)
+							.collect(Collectors.toList()));
+			}
+			if (Objects.nonNull(r.getTitle())) {
+				r
+					.setTitle(
+						r
+							.getTitle()
+							.stream()
+							.filter(Objects::nonNull)
+							.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
+							.map(CleaningFunctions::removeNewLines)
+							.collect(Collectors.toList()));
+			}
+			if (Objects.nonNull(r.getDescription())) {
+				r
+					.setDescription(
+						r
+							.getDescription()
+							.stream()
+							.filter(Objects::nonNull)
+							.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
+							.map(CleaningFunctions::removeNewLines)
 							.collect(Collectors.toList()));
 			}
 			if (Objects.nonNull(r.getPid())) {
@@ -205,6 +228,16 @@ public class CleaningFunctions {
 		return value;
 	}
 
+	protected static StructuredProperty removeNewLines(StructuredProperty s) {
+		s.setValue(s.getValue().replaceAll(NEWLINES, " "));
+		return s;
+	}
+
+	protected static Field<String> removeNewLines(Field<String> s) {
+		s.setValue(s.getValue().replaceAll(NEWLINES, " "));
+		return s;
+	}
+
 	// HELPERS
 
 	private static void fixVocabName(Qualifier q, String vocabularyName) {

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java

@@ -7,11 +7,10 @@ import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.stream.Collectors;
-import java.util.stream.Stream;
 
 import org.apache.commons.lang.StringUtils;
 
-import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.CleaningFunctions;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.dhp.utils.DHPUtils;

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java

@@ -4,12 +4,7 @@ package eu.dnetlib.dhp.schema.oaf.utils;
 import java.util.Comparator;
 import java.util.Optional;
 
-import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctions;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.OafEntity;
-import eu.dnetlib.dhp.schema.oaf.Organization;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import eu.dnetlib.dhp.schema.oaf.*;
 
 public class PidValueComparator implements Comparator<StructuredProperty> {
 

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java

@@ -2,6 +2,7 @@
 package eu.dnetlib.dhp.oa.graph.clean;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static eu.dnetlib.dhp.schema.oaf.CleaningFunctions.*;
 
 import java.util.Optional;
 
@@ -26,7 +27,6 @@ import eu.dnetlib.dhp.schema.oaf.Oaf;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
-import static eu.dnetlib.dhp.oa.graph.clean.CleaningFunctions.*;
 
 public class CleanGraphSparkJob {
 
@@ -89,7 +89,7 @@ public class CleanGraphSparkJob {
 		readTableFromPath(spark, inputPath, clazz)
 			.map((MapFunction<T, T>) value -> fixVocabularyNames(value), Encoders.bean(clazz))
 			.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
-			.map((MapFunction<T, T>) value -> fixDefaults(value), Encoders.bean(clazz))
+			.map((MapFunction<T, T>) value -> cleanup(value), Encoders.bean(clazz))
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java

@@ -16,9 +16,9 @@ import org.dom4j.Node;
 import com.google.common.collect.Lists;
 
 import eu.dnetlib.dhp.common.PacePerson;
-import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctions;
 import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
 import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.CleaningFunctions;
 
 public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java

@@ -12,7 +12,6 @@ import org.dom4j.Document;
 import org.dom4j.Node;
 
 import eu.dnetlib.dhp.common.PacePerson;
-import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctions;
 import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
 import eu.dnetlib.dhp.schema.oaf.*;
 

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java

@@ -19,10 +19,7 @@ import org.mockito.junit.jupiter.MockitoExtension;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.oaf.Qualifier;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 
@@ -89,7 +86,7 @@ public class CleaningFunctionTest {
 				.map(p -> p.getQualifier())
 				.allMatch(q -> pidTerms.contains(q.getClassid())));
 
-		Publication p_defaults = CleaningFunctions.fixDefaults(p_out);
+		Publication p_defaults = CleaningFunctions.cleanup(p_out);
 		assertEquals("CLOSED", p_defaults.getBestaccessright().getClassid());
 		assertNull(p_out.getPublisher());