merge branch with master

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

@@ -1,10 +1,7 @@
 
 package eu.dnetlib.dhp.oa.graph.clean;
 
-import java.util.HashSet;
+import java.util.*;
-import java.util.LinkedHashMap;
-import java.util.Objects;
-import java.util.Set;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
@@ -18,7 +15,9 @@ 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<>();
 
@@ -79,7 +78,7 @@ public class CleaningFunctions {
 		return value;
 	}
 
-	protected static <T extends Oaf> T fixDefaults(T value) {
+	public static <T extends Oaf> T fixDefaults(T value) {
 		if (value instanceof Datasource) {
 			// nothing to clean here
 		} else if (value instanceof Project) {
@@ -112,6 +111,29 @@ 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())) {
@@ -125,10 +147,7 @@ public class CleaningFunctions {
 							.filter(sp -> !PID_BLACKLIST.contains(sp.getValue().trim().toLowerCase()))
 							.filter(sp -> Objects.nonNull(sp.getQualifier()))
 							.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
-							.map(sp -> {
+							.map(CleaningFunctions::normalizePidValue)
-								sp.setValue(StringUtils.trim(sp.getValue()));
-								return sp;
-							})
 							.collect(Collectors.toList()));
 			}
 			if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
@@ -211,6 +230,16 @@ 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) {
@@ -226,4 +255,24 @@ public class CleaningFunctions {
 				classid, classname, scheme, scheme);
 	}
 
+	/**
+	 * Utility method that normalises PID values on a per-type basis.
+	 * @param pid the PID whose value will be normalised.
+	 * @return the PID containing the normalised value.
+	 */
+	public static StructuredProperty normalizePidValue(StructuredProperty pid) {
+		String value = Optional
+			.ofNullable(pid.getValue())
+			.map(String::trim)
+			.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
+		switch (pid.getQualifier().getClassid()) {
+
+			// TODO add cleaning for more PID types as needed
+			case "doi":
+				pid.setValue(value.toLowerCase().replaceAll(DOI_URL_PREFIX_REGEX, ""));
+				break;
+		}
+		return pid;
+	}
+
 }