upgraded maven version of commons-lang

dnet-pace-core/pom.xml

@@ -27,17 +27,14 @@
 			<artifactId>gson</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>commons-lang</groupId>
+			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-lang</artifactId>
+			<artifactId>commons-lang3</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
 		</dependency>
-		<dependency>
+
-			<groupId>commons-collections</groupId>
-			<artifactId>commons-collections</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>org.antlr</groupId>
 			<artifactId>stringtemplate</artifactId>

dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/AbstractClusteringFunction.java

@@ -3,7 +3,7 @@ package eu.dnetlib.pace.clustering;
 import eu.dnetlib.pace.common.AbstractPaceFunctions;
 import eu.dnetlib.pace.config.Config;
 import eu.dnetlib.pace.model.Field;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import java.util.Collection;
 import java.util.HashSet;

dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/FieldFilter.java

@@ -6,7 +6,7 @@ import java.util.Map;
 import com.google.common.base.Predicate;
 
 import eu.dnetlib.pace.model.Field;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/KeywordsClustering.java

@@ -3,7 +3,7 @@ package eu.dnetlib.pace.clustering;
 import eu.dnetlib.pace.common.AbstractPaceFunctions;
 import eu.dnetlib.pace.config.Config;
 import eu.dnetlib.pace.model.Field;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import java.util.*;
 import java.util.stream.Collectors;

dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/LowercaseClustering.java

@@ -8,7 +8,7 @@ import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
 import eu.dnetlib.pace.config.Config;
 import eu.dnetlib.pace.model.Field;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 @ClusteringClass("lowercase")
 public class LowercaseClustering extends AbstractClusteringFunction {

dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/NGramUtils.java

@@ -2,7 +2,7 @@ package eu.dnetlib.pace.clustering;
 
 import java.util.Set;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import eu.dnetlib.pace.common.AbstractPaceFunctions;
 

dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/PersonClustering.java

@@ -5,7 +5,7 @@ import eu.dnetlib.pace.common.AbstractPaceFunctions;
 import eu.dnetlib.pace.config.Config;
 import eu.dnetlib.pace.model.Field;
 import eu.dnetlib.pace.model.Person;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import java.util.Collection;
 import java.util.List;

dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/SpaceTrimmingFieldValue.java

@@ -5,8 +5,8 @@ import java.util.List;
 import java.util.Map;
 
 import eu.dnetlib.pace.config.Config;
-import org.apache.commons.lang.RandomStringUtils;
+import org.apache.commons.lang3.RandomStringUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import com.google.common.collect.Lists;
 

dnet-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java

@@ -9,9 +9,8 @@ import eu.dnetlib.pace.clustering.NGramUtils;
 import eu.dnetlib.pace.model.Field;
 import eu.dnetlib.pace.model.FieldList;
 import eu.dnetlib.pace.model.FieldListImpl;
-import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import java.io.IOException;
 import java.io.StringWriter;
@@ -25,295 +24,293 @@ import java.util.stream.Collectors;
  * Set of common functions for the framework
  *
  * @author claudio
- *
  */
 public abstract class AbstractPaceFunctions {
 
-	//city map to be used when translating the city names into codes
+    //city map to be used when translating the city names into codes
-	private static Map<String,String> cityMap = AbstractPaceFunctions.loadMapFromClasspath("/eu/dnetlib/pace/config/city_map.csv");
+    private static Map<String, String> cityMap = AbstractPaceFunctions.loadMapFromClasspath("/eu/dnetlib/pace/config/city_map.csv");
 
-	//list of stopwords in different languages
+    //list of stopwords in different languages
-	protected static Set<String> stopwords_en = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_en.txt");
+    protected static Set<String> stopwords_en = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_en.txt");
-	protected static Set<String> stopwords_de = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_de.txt");
+    protected static Set<String> stopwords_de = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_de.txt");
-	protected static Set<String> stopwords_es = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_es.txt");
+    protected static Set<String> stopwords_es = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_es.txt");
-	protected static Set<String> stopwords_fr = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_fr.txt");
+    protected static Set<String> stopwords_fr = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_fr.txt");
-	protected static Set<String> stopwords_it = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_it.txt");
+    protected static Set<String> stopwords_it = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_it.txt");
-	protected static Set<String> stopwords_pt = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_pt.txt");
+    protected static Set<String> stopwords_pt = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_pt.txt");
 
-	//blacklist of ngrams: to avoid generic keys
+    //blacklist of ngrams: to avoid generic keys
-	protected static Set<String> ngramBlacklist = loadFromClasspath("/eu/dnetlib/pace/config/ngram_blacklist.txt");
+    protected static Set<String> ngramBlacklist = loadFromClasspath("/eu/dnetlib/pace/config/ngram_blacklist.txt");
 
-	private static final String alpha = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789 ";
+    private static final String alpha = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789 ";
-	private static final String aliases_from = "⁰¹²³⁴⁵⁶⁷⁸⁹⁺⁻⁼⁽⁾ⁿ₀₁₂₃₄₅₆₇₈₉₊₋₌₍₎àáâäæãåāèéêëēėęəîïíīįìôöòóœøōõûüùúūßśšłžźżçćčñń";
+    private static final String aliases_from = "⁰¹²³⁴⁵⁶⁷⁸⁹⁺⁻⁼⁽⁾ⁿ₀₁₂₃₄₅₆₇₈₉₊₋₌₍₎àáâäæãåāèéêëēėęəîïíīįìôöòóœøōõûüùúūßśšłžźżçćčñń";
-	private static final String aliases_to =   "0123456789+-=()n0123456789+-=()aaaaaaaaeeeeeeeeiiiiiioooooooouuuuussslzzzcccnn";
+    private static final String aliases_to = "0123456789+-=()n0123456789+-=()aaaaaaaaeeeeeeeeiiiiiioooooooouuuuussslzzzcccnn";
 
-	//doi prefix for normalization
+    //doi prefix for normalization
-	public final String DOI_PREFIX = "(https?:\\/\\/dx\\.doi\\.org\\/)|(doi:)";
+    public final String DOI_PREFIX = "(https?:\\/\\/dx\\.doi\\.org\\/)|(doi:)";
 
-	private Pattern numberPattern = Pattern.compile("-?\\d+(\\.\\d+)?");
+    private Pattern numberPattern = Pattern.compile("-?\\d+(\\.\\d+)?");
 
-	private Pattern hexUnicodePattern = Pattern.compile("\\\\u(\\p{XDigit}{4})");
+    private Pattern hexUnicodePattern = Pattern.compile("\\\\u(\\p{XDigit}{4})");
 
-	protected final static FieldList EMPTY_FIELD = new FieldListImpl();
+    protected final static FieldList EMPTY_FIELD = new FieldListImpl();
 
-	protected String concat(final List<String> l) {
+    protected String concat(final List<String> l) {
-		return Joiner.on(" ").skipNulls().join(l);
+        return Joiner.on(" ").skipNulls().join(l);
-	}
+    }
 
-	protected String cleanup(final String s) {
+    protected String cleanup(final String s) {
-		final String s0 = unicodeNormalization(s.toLowerCase());
+        final String s0 = unicodeNormalization(s.toLowerCase());
-		final String s1 = fixAliases(s0);
+        final String s1 = fixAliases(s0);
-		final String s2 = nfd(s1);
+        final String s2 = nfd(s1);
-		final String s3 = s2.replaceAll("&ndash;", " ");
+        final String s3 = s2.replaceAll("&ndash;", " ");
-		final String s4 = s3.replaceAll("&amp;", " ");
+        final String s4 = s3.replaceAll("&amp;", " ");
-		final String s5 = s4.replaceAll("&quot;", " ");
+        final String s5 = s4.replaceAll("&quot;", " ");
-		final String s6 = s5.replaceAll("&minus;", " ");
+        final String s6 = s5.replaceAll("&minus;", " ");
-		final String s7 = s6.replaceAll("([0-9]+)", " $1 ");
+        final String s7 = s6.replaceAll("([0-9]+)", " $1 ");
-		final String s8 = s7.replaceAll("[^\\p{ASCII}]", "");
+        final String s8 = s7.replaceAll("[^\\p{ASCII}]", "");
-		final String s9 = s8.replaceAll("[\\p{Punct}]", " ");
+        final String s9 = s8.replaceAll("[\\p{Punct}]", " ");
-		final String s10 = s9.replaceAll("\\n", " ");
+        final String s10 = s9.replaceAll("\\n", " ");
-		final String s11 = s10.replaceAll("(?m)\\s+", " ");
+        final String s11 = s10.replaceAll("(?m)\\s+", " ");
-		final String s12 = s11.trim();
+        final String s12 = s11.trim();
-		return s12;
+        return s12;
-	}
+    }
 
-	protected boolean checkNumbers(final String a, final String b) {
+    protected boolean checkNumbers(final String a, final String b) {
-		final String numbersA = getNumbers(a);
+        final String numbersA = getNumbers(a);
-		final String numbersB = getNumbers(b);
+        final String numbersB = getNumbers(b);
-		final String romansA = getRomans(a);
+        final String romansA = getRomans(a);
-		final String romansB = getRomans(b);
+        final String romansB = getRomans(b);
-		return !numbersA.equals(numbersB) || !romansA.equals(romansB);
+        return !numbersA.equals(numbersB) || !romansA.equals(romansB);
-	}
+    }
 
-	protected String getRomans(final String s) {
+    protected String getRomans(final String s) {
-		final StringBuilder sb = new StringBuilder();
+        final StringBuilder sb = new StringBuilder();
-		for (final String t : s.split(" ")) {
+        for (final String t : s.split(" ")) {
-			sb.append(isRoman(t) ? t : "");
+            sb.append(isRoman(t) ? t : "");
-		}
+        }
-		return sb.toString();
+        return sb.toString();
-	}
+    }
 
-	protected boolean isRoman(final String s) {
+    protected boolean isRoman(final String s) {
-		return s.replaceAll("^M{0,4}(CM|CD|D?C{0,3})(XC|XL|L?X{0,3})(IX|IV|V?I{0,3})$", "qwertyuiop").equals("qwertyuiop");
+        return s.replaceAll("^M{0,4}(CM|CD|D?C{0,3})(XC|XL|L?X{0,3})(IX|IV|V?I{0,3})$", "qwertyuiop").equals("qwertyuiop");
-	}
+    }
 
-	protected String getNumbers(final String s) {
+    protected String getNumbers(final String s) {
-		final StringBuilder sb = new StringBuilder();
+        final StringBuilder sb = new StringBuilder();
-		for (final String t : s.split(" ")) {
+        for (final String t : s.split(" ")) {
-			sb.append(isNumber(t)? t : "");
+            sb.append(isNumber(t) ? t : "");
-		}
+        }
-		return sb.toString();
+        return sb.toString();
-	}
+    }
 
-	public boolean isNumber(String strNum) {
+    public boolean isNumber(String strNum) {
-		if (strNum == null) {
+        if (strNum == null) {
-			return false;
+            return false;
-		}
+        }
-		return numberPattern.matcher(strNum).matches();
+        return numberPattern.matcher(strNum).matches();
-	}
+    }
 
-	protected static String fixAliases(final String s) {
+    protected static String fixAliases(final String s) {
-		final StringBuilder sb = new StringBuilder();
+        final StringBuilder sb = new StringBuilder();
-		for (final char ch : Lists.charactersOf(s)) {
+        for (final char ch : Lists.charactersOf(s)) {
-			final int i = StringUtils.indexOf(aliases_from, ch);
+            final int i = StringUtils.indexOf(aliases_from, ch);
-			sb.append(i >= 0 ? aliases_to.charAt(i) : ch);
+            sb.append(i >= 0 ? aliases_to.charAt(i) : ch);
-		}
+        }
-		return sb.toString();
+        return sb.toString();
-	}
+    }
 
-	protected String removeSymbols(final String s) {
+    protected String removeSymbols(final String s) {
-		final StringBuilder sb = new StringBuilder();
+        final StringBuilder sb = new StringBuilder();
 
-		for (final char ch : Lists.charactersOf(s)) {
+        for (final char ch : Lists.charactersOf(s)) {
-			sb.append(StringUtils.contains(alpha, ch) ? ch : " ");
+            sb.append(StringUtils.contains(alpha, ch) ? ch : " ");
-		}
+        }
-		return sb.toString().replaceAll("\\s+", " ");
+        return sb.toString().replaceAll("\\s+", " ");
-	}
+    }
 
-	protected String getFirstValue(final Field values) {
+    protected String getFirstValue(final Field values) {
-		return (values != null) && !Iterables.isEmpty(values) ? Iterables.getFirst(values, EMPTY_FIELD).stringValue() : "";
+        return (values != null) && !Iterables.isEmpty(values) ? Iterables.getFirst(values, EMPTY_FIELD).stringValue() : "";
-	}
+    }
 
-	protected boolean notNull(final String s) {
+    protected boolean notNull(final String s) {
-		return s != null;
+        return s != null;
-	}
+    }
 
-	protected String normalize(final String s) {
+    protected String normalize(final String s) {
-		return nfd(unicodeNormalization(s))
+        return nfd(unicodeNormalization(s))
-				.toLowerCase()
+                .toLowerCase()
-				// do not compact the regexes in a single expression, would cause StackOverflowError in case of large input strings
+                // do not compact the regexes in a single expression, would cause StackOverflowError in case of large input strings
-				.replaceAll("[^ \\w]+", "")
+                .replaceAll("[^ \\w]+", "")
-				.replaceAll("(\\p{InCombiningDiacriticalMarks})+", "")
+                .replaceAll("(\\p{InCombiningDiacriticalMarks})+", "")
-				.replaceAll("(\\p{Punct})+", " ")
+                .replaceAll("(\\p{Punct})+", " ")
-				.replaceAll("(\\d)+", " ")
+                .replaceAll("(\\d)+", " ")
-				.replaceAll("(\\n)+", " ")
+                .replaceAll("(\\n)+", " ")
-				.trim();
+                .trim();
-	}
+    }
 
-	public String nfd(final String s) {
+    public String nfd(final String s) {
-		return Normalizer.normalize(s, Normalizer.Form.NFD);
+        return Normalizer.normalize(s, Normalizer.Form.NFD);
-	}
+    }
 
-	public String unicodeNormalization(final String s) {
+    public String unicodeNormalization(final String s) {
 
-		Matcher m = hexUnicodePattern.matcher(s);
+        Matcher m = hexUnicodePattern.matcher(s);
-		StringBuffer buf = new StringBuffer(s.length());
+        StringBuffer buf = new StringBuffer(s.length());
-		while (m.find()) {
+        while (m.find()) {
-			String ch = String.valueOf((char) Integer.parseInt(m.group(1), 16));
+            String ch = String.valueOf((char) Integer.parseInt(m.group(1), 16));
-			m.appendReplacement(buf, Matcher.quoteReplacement(ch));
+            m.appendReplacement(buf, Matcher.quoteReplacement(ch));
-		}
+        }
-		m.appendTail(buf);
+        m.appendTail(buf);
-		return buf.toString();
+        return buf.toString();
-	}
+    }
 
-	protected String filterStopWords(final String s, final Set<String> stopwords) {
+    protected String filterStopWords(final String s, final Set<String> stopwords) {
-		final StringTokenizer st = new StringTokenizer(s);
+        final StringTokenizer st = new StringTokenizer(s);
-		final StringBuilder sb = new StringBuilder();
+        final StringBuilder sb = new StringBuilder();
-		while (st.hasMoreTokens()) {
+        while (st.hasMoreTokens()) {
-			final String token = st.nextToken();
+            final String token = st.nextToken();
-			if (!stopwords.contains(token)) {
+            if (!stopwords.contains(token)) {
-				sb.append(token);
+                sb.append(token);
-				sb.append(" ");
+                sb.append(" ");
-			}
+            }
-		}
+        }
-		return sb.toString().trim();
+        return sb.toString().trim();
-	}
+    }
 
-	public String filterAllStopWords(String s) {
+    public String filterAllStopWords(String s) {
 
-		s = filterStopWords(s, stopwords_en);
+        s = filterStopWords(s, stopwords_en);
-		s = filterStopWords(s, stopwords_de);
+        s = filterStopWords(s, stopwords_de);
-		s = filterStopWords(s, stopwords_it);
+        s = filterStopWords(s, stopwords_it);
-		s = filterStopWords(s, stopwords_fr);
+        s = filterStopWords(s, stopwords_fr);
-		s = filterStopWords(s, stopwords_pt);
+        s = filterStopWords(s, stopwords_pt);
-		s = filterStopWords(s, stopwords_es);
+        s = filterStopWords(s, stopwords_es);
 
-		return s;
+        return s;
-	}
+    }
 
-	protected Collection<String> filterBlacklisted(final Collection<String> set, final Set<String> ngramBlacklist) {
+    protected Collection<String> filterBlacklisted(final Collection<String> set, final Set<String> ngramBlacklist) {
-		final Set<String> newset = Sets.newLinkedHashSet();
+        final Set<String> newset = Sets.newLinkedHashSet();
-		for (final String s : set) {
+        for (final String s : set) {
-			if (!ngramBlacklist.contains(s)) {
+            if (!ngramBlacklist.contains(s)) {
-				newset.add(s);
+                newset.add(s);
-			}
+            }
-		}
+        }
-		return newset;
+        return newset;
-	}
+    }
 
-	public static Set<String> loadFromClasspath(final String classpath) {
+    public static Set<String> loadFromClasspath(final String classpath) {
-		final Set<String> h = Sets.newHashSet();
+        final Set<String> h = Sets.newHashSet();
-		try {
+        try {
-			for (final String s : IOUtils.readLines(NGramUtils.class.getResourceAsStream(classpath))) {
+            for (final String s : IOUtils.readLines(NGramUtils.class.getResourceAsStream(classpath))) {
-				h.add(s);
+                h.add(s);
-			}
+            }
-		} catch (final Throwable e) {
+        } catch (final Throwable e) {
-			return Sets.newHashSet();
+            return Sets.newHashSet();
-		}
+        }
-		return h;
+        return h;
-	}
+    }
 
-	public static Map<String, String> loadMapFromClasspath(final String classpath) {
+    public static Map<String, String> loadMapFromClasspath(final String classpath) {
-		final Map<String, String> m = new HashMap<>();
+        final Map<String, String> m = new HashMap<>();
-		try {
+        try {
-			for (final String s: IOUtils.readLines(AbstractPaceFunctions.class.getResourceAsStream(classpath))) {
+            for (final String s : IOUtils.readLines(AbstractPaceFunctions.class.getResourceAsStream(classpath))) {
-				//string is like this: code;word1;word2;word3
+                //string is like this: code;word1;word2;word3
-				String[] line = s.split(";");
+                String[] line = s.split(";");
-				String value = line[0];
+                String value = line[0];
-				for (int i=1; i<line.length;i++){
+                for (int i = 1; i < line.length; i++) {
-					m.put(line[i].toLowerCase(),value);
+                    m.put(line[i].toLowerCase(), value);
-				}
+                }
-			}
+            }
-		} catch (final Throwable e){
+        } catch (final Throwable e) {
-			return new HashMap<>();
+            return new HashMap<>();
-		}
+        }
-		return m;
+        return m;
-	}
+    }
 
-	public String removeKeywords(String s, Set<String> keywords) {
+    public String removeKeywords(String s, Set<String> keywords) {
 
-		s = " " + s + " ";
+        s = " " + s + " ";
-		for (String k: keywords ) {
+        for (String k : keywords) {
-			s = s.replaceAll(k.toLowerCase(), "");
+            s = s.replaceAll(k.toLowerCase(), "");
-		}
+        }
 
-		return s.trim();
+        return s.trim();
-	}
+    }
 
-    public double commonElementsPercentage(Set<String> s1, Set<String> s2){
+    public double commonElementsPercentage(Set<String> s1, Set<String> s2) {
 
-		int longer = (s1.size()>s2.size())?s1.size():s2.size();
+        double longer = Math.max(s1.size(), s2.size());
+        return (double) s1.stream().filter(s2::contains).count() / longer;
+    }
 
-		return (double)CollectionUtils.intersection(s1,s2).size()/(double)longer;
+    //convert the set of keywords to codes
-	}
+    public Set<String> toCodes(Set<String> keywords, Map<String, String> translationMap) {
+        return keywords.stream().map(s -> translationMap.get(s)).collect(Collectors.toSet());
+    }
 
-	//convert the set of keywords to codes
+    public Set<String> keywordsToCodes(Set<String> keywords, Map<String, String> translationMap) {
-	public Set<String> toCodes(Set<String> keywords, Map<String, String> translationMap) {
+        return toCodes(keywords, translationMap);
-		return keywords.stream().map(s -> translationMap.get(s)).collect(Collectors.toSet());
+    }
-	}
 
-	public Set<String> keywordsToCodes(Set<String> keywords, Map<String, String> translationMap) {
+    public Set<String> citiesToCodes(Set<String> keywords) {
-		return toCodes(keywords, translationMap);
+        return toCodes(keywords, cityMap);
-	}
+    }
 
-	public Set<String> citiesToCodes(Set<String> keywords) {
+    protected String firstLC(final String s) {
-		return toCodes(keywords, cityMap);
+        return StringUtils.substring(s, 0, 1).toLowerCase();
-	}
+    }
 
-	protected String firstLC(final String s) {
+    protected Iterable<String> tokens(final String s, final int maxTokens) {
-		return StringUtils.substring(s, 0, 1).toLowerCase();
+        return Iterables.limit(Splitter.on(" ").omitEmptyStrings().trimResults().split(s), maxTokens);
-	}
+    }
 
-	protected Iterable<String> tokens(final String s, final int maxTokens) {
+    public String normalizePid(String pid) {
-		return Iterables.limit(Splitter.on(" ").omitEmptyStrings().trimResults().split(s), maxTokens);
+        return pid.toLowerCase().replaceAll(DOI_PREFIX, "");
-	}
+    }
 
-	public String normalizePid(String pid) {
+    //get the list of keywords into the input string
-		return pid.toLowerCase().replaceAll(DOI_PREFIX, "");
+    public Set<String> getKeywords(String s1, Map<String, String> translationMap, int windowSize) {
-	}
 
-	//get the list of keywords into the input string
+        String s = s1;
-	public Set<String> getKeywords(String s1, Map<String, String> translationMap, int windowSize){
 
-		String s = s1;
+        List<String> tokens = Arrays.asList(s.toLowerCase().split(" "));
 
-		List<String> tokens = Arrays.asList(s.toLowerCase().split(" "));
+        Set<String> codes = new HashSet<>();
 
-		Set<String> codes = new HashSet<>();
+        if (tokens.size() < windowSize)
+            windowSize = tokens.size();
 
-		if (tokens.size()<windowSize)
+        int length = windowSize;
-			windowSize = tokens.size();
 
-		int length = windowSize;
+        while (length != 0) {
 
-		while (length != 0) {
+            for (int i = 0; i <= tokens.size() - length; i++) {
+                String candidate = concat(tokens.subList(i, i + length));
+                if (translationMap.containsKey(candidate)) {
+                    codes.add(candidate);
+                    s = s.replace(candidate, "").trim();
+                }
+            }
 
-			for (int i = 0; i<=tokens.size()-length; i++){
+            tokens = Arrays.asList(s.split(" "));
-				String candidate = concat(tokens.subList(i, i + length));
+            length -= 1;
-				if (translationMap.containsKey(candidate)) {
+        }
-					codes.add(candidate);
-					s = s.replace(candidate, "").trim();
-				}
-			}
 
-			tokens = Arrays.asList(s.split(" "));
+        return codes;
-			length-=1;
+    }
-		}
 
-		return codes;
+    public Set<String> getCities(String s1, int windowSize) {
-	}
+        return getKeywords(s1, cityMap, windowSize);
+    }
 
-	public Set<String> getCities(String s1, int windowSize) {
+    public static <T> String readFromClasspath(final String filename, final Class<T> clazz) {
-		return getKeywords(s1, cityMap, windowSize);
+        final StringWriter sw = new StringWriter();
-	}
+        try {
-
+            IOUtils.copy(clazz.getResourceAsStream(filename), sw);
-	public static <T> String readFromClasspath(final String filename, final Class<T> clazz) {
+            return sw.toString();
-		final StringWriter sw = new StringWriter();
+        } catch (final IOException e) {
-		try {
+            throw new RuntimeException("cannot load resource from classpath: " + filename);
-			IOUtils.copy(clazz.getResourceAsStream(filename), sw);
+        }
-			return sw.toString();
+    }
-		} catch (final IOException e) {
-			throw new RuntimeException("cannot load resource from classpath: " + filename);
-		}
-	}
 }

dnet-pace-core/src/main/java/eu/dnetlib/pace/config/WfConfig.java

@@ -4,7 +4,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
 import eu.dnetlib.pace.util.PaceException;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import java.io.IOException;
 import java.io.Serializable;

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java

@@ -1,8 +1,9 @@
 package eu.dnetlib.pace.model;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.base.Splitter;
 import com.google.common.collect.Lists;
-import com.google.gson.Gson;
 import eu.dnetlib.pace.config.Type;
 
 import java.io.Serializable;
@@ -103,7 +104,11 @@ public class FieldDef implements Serializable {
 
 	@Override
 	public String toString() {
-		return new Gson().toJson(this);
+		try {
+			return new ObjectMapper().writeValueAsString(this);
+		} catch (JsonProcessingException e) {
+			return null;
+		}
 	}
 
 }

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/FieldListImpl.java

@@ -1,11 +1,11 @@
 package eu.dnetlib.pace.model;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.base.Function;
 import com.google.common.base.Joiner;
-import com.google.common.base.Predicate;
 import com.google.common.collect.Iterables;
 import com.google.common.collect.Lists;
-import com.google.gson.Gson;
 import eu.dnetlib.pace.config.Type;
 
 import java.util.Collection;
@@ -283,7 +283,12 @@ public class FieldListImpl extends AbstractField implements FieldList {
 		case String:
 			return Joiner.on(" ").join(stringList());
 		case JSON:
-			final String json = new Gson().toJson(stringList());
+			String json;
+			try {
+				json = new ObjectMapper().writeValueAsString(this);
+			} catch (JsonProcessingException e) {
+				json = null;
+			}
 			return json;
 		default:
 			throw new IllegalArgumentException("Unknown type: " + getType().toString());

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/FieldValueImpl.java

@@ -2,12 +2,12 @@ package eu.dnetlib.pace.model;
 
 import java.net.MalformedURLException;
 import java.net.URL;
+import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
 import eu.dnetlib.pace.config.Type;
-import org.apache.commons.collections.iterators.SingletonIterator;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang.StringUtils;
 
 /**
  * The Class FieldValueImpl.
@@ -124,7 +124,7 @@ public class FieldValueImpl extends AbstractField implements FieldValue {
 	@Override
 	@SuppressWarnings("unchecked")
 	public Iterator<Field> iterator() {
-		return new SingletonIterator(this);
+		return Collections.singleton((Field) this).iterator();
 	}
 
 }

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Author.java

@@ -1,129 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import java.util.List;
-import java.util.Set;
-
-import org.apache.commons.lang.StringUtils;
-
-import com.google.common.collect.ComparisonChain;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Ordering;
-import com.google.common.collect.Sets;
-import com.google.gson.Gson;
-
-public class Author implements Comparable<Author> {
-
-	private String id;
-	private String fullname;
-	private String firstname;
-	private String secondnames;
-
-	private List<Match> matches = Lists.newArrayList();
-	private Set<Author> coauthors = Sets.newHashSet();
-	private SubjectsMap subjectsMap = new SubjectsMap();
-
-	public Author() {
-		super();
-	}
-
-	public Author(final Author a) {
-		this.id = a.getId();
-		this.fullname = a.getFullname();
-		this.firstname = a.getFirstname();
-		this.secondnames = a.getSecondnames();
-
-		this.matches = a.getMatches();
-		this.coauthors = a.getCoauthors();
-		this.subjectsMap = a.getSubjectsMap();
-	}
-
-	public boolean hasMatches() {
-		return (getMatches() != null) && !getMatches().isEmpty();
-	}
-
-	public boolean hasCoauthors() {
-		return (getCoauthors() != null) && !getCoauthors().isEmpty();
-	}
-
-	public boolean isWellFormed() {
-		return StringUtils.isNotBlank(getSecondnames()) && StringUtils.isNotBlank(getFirstname());
-	}
-
-	public String getId() {
-		return id;
-	}
-
-	public void setId(final String id) {
-		this.id = id;
-	}
-
-	public String getFullname() {
-		return fullname;
-	}
-
-	public void setFullname(final String fullname) {
-		this.fullname = fullname;
-	}
-
-	public String getFirstname() {
-		return firstname;
-	}
-
-	public void setFirstname(final String firstname) {
-		this.firstname = firstname;
-	}
-
-	public String getSecondnames() {
-		return secondnames;
-	}
-
-	public void setSecondnames(final String secondnames) {
-		this.secondnames = secondnames;
-	}
-
-	public List<Match> getMatches() {
-		return matches;
-	}
-
-	public void setMatches(final List<Match> matches) {
-		this.matches = matches;
-	}
-
-	public Set<Author> getCoauthors() {
-		return coauthors;
-	}
-
-	public void setCoauthors(final Set<Author> coauthors) {
-		this.coauthors = coauthors;
-	}
-
-	@Override
-	public String toString() {
-		return new Gson().toJson(this);
-	}
-
-	@Override
-	public int hashCode() {
-		return getId().hashCode();
-	}
-
-	@Override
-	public int compareTo(final Author o) {
-		return ComparisonChain.start()
-				.compare(this.getId(), o.getId(), Ordering.natural().nullsLast())
-				.result();
-	}
-
-	@Override
-	public boolean equals(final Object o) {
-		return (o instanceof Author) && getId().equals(((Author) o).getId());
-	}
-
-	public SubjectsMap getSubjectsMap() {
-		return subjectsMap;
-	}
-
-	public void setSubjectsMap(final SubjectsMap subjectsMap) {
-		this.subjectsMap = subjectsMap;
-	}
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/AuthorSet.java

@@ -1,37 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import com.google.gson.Gson;
-
-public class AuthorSet {
-
-	private String id;
-	private Authors authors;
-
-	public AuthorSet(final String id, final Authors authors) {
-		super();
-		this.id = id;
-		this.authors = authors;
-	}
-
-	public String getId() {
-		return id;
-	}
-
-	public void setId(final String id) {
-		this.id = id;
-	}
-
-	public Authors getAuthors() {
-		return authors;
-	}
-
-	public void setAuthors(final Authors authors) {
-		this.authors = authors;
-	}
-
-	@Override
-	public String toString() {
-		return new Gson().toJson(this);
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Authors.java

@@ -1,54 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import java.util.Collection;
-import java.util.HashSet;
-
-import com.google.common.collect.ComparisonChain;
-import com.google.common.collect.Ordering;
-import com.google.common.collect.Sets;
-import com.google.gson.Gson;
-
-public class Authors extends HashSet<Author> implements Comparable<Authors> {
-
-	private static final long serialVersionUID = -6878376220805286142L;
-
-	public Authors() {
-		super();
-	}
-
-	public Authors(final Collection<Author> authors) {
-		super(authors);
-	}
-
-	public Authors(final Author author) {
-		super(Sets.newHashSet(author));
-	}
-
-	@Override
-	public int compareTo(final Authors a) {
-		return ComparisonChain.start()
-				.compare(this.size(), a.size(), Ordering.natural().nullsLast())
-				.result();
-	}
-
-	@Override
-	public String toString() {
-		return new Gson().toJson(this);
-	}
-
-	@Override
-	public boolean equals(final Object o) {
-		final boolean res = o instanceof Authors;
-		return res && (Sets.intersection(this, (Authors) o).size() == this.size());
-	}
-
-	@Override
-	public int hashCode() {
-		int res = 0;
-		for (final Author a : this) {
-			res += a.hashCode();
-		}
-		return res;
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/CoAuthor.java

@@ -1,50 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import com.google.gson.Gson;
-import org.apache.commons.lang.StringUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-public class CoAuthor extends Author {
-
-	private static final Log log = LogFactory.getLog(CoAuthor.class);
-	private String anchorId = null;
-
-	public CoAuthor() {
-		super();
-	}
-
-	public CoAuthor(final Author author) {
-		super(author);
-	}
-
-	public boolean hasAnchorId() {
-		return StringUtils.isNotBlank(getAnchorId());
-	}
-
-	public String getAnchorId() {
-		return anchorId;
-	}
-
-	public void setAnchorId(final String anchorId) {
-		this.anchorId = anchorId;
-	}
-
-	@Override
-	public String toString() {
-		return new Gson().toJson(this);
-	}
-
-	@Override
-	public int hashCode() {
-		return getId() != null ? getId().hashCode() : getFullname().hashCode();
-	}
-
-	@Override
-	public boolean equals(final Object o) {
-		return (o instanceof CoAuthor) && StringUtils.isNotBlank(getId()) ?
-				getId().equals(((CoAuthor) o).getId()) :
-				getFullname().equals(((CoAuthor) o).getFullname());
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/CoAuthorSet.java

@@ -1,36 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import com.google.gson.Gson;
-
-public class CoAuthorSet {
-
-	private Author author;
-	private Authors coAuthors;
-
-	public CoAuthorSet(final Author author, final Authors coAuthors) {
-		super();
-		this.author = author;
-		this.coAuthors = coAuthors;
-	}
-
-	public Author getAuthor() {
-		return author;
-	}
-
-	public void setAuthor(final Author author) {
-		this.author = author;
-	}
-
-	public Authors getCoAuthors() {
-		return coAuthors;
-	}
-
-	public void setCoAuthors(final Authors coAuthors) {
-		this.coAuthors = coAuthors;
-	}
-
-	@Override
-	public String toString() {
-		return new Gson().toJson(this);
-	}
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/CoAuthorSetLite.java

@@ -1,40 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import java.util.Set;
-
-import com.google.gson.Gson;
-
-public class CoAuthorSetLite {
-
-	private String id;
-
-	private Set<String> coAuthors;
-
-	public CoAuthorSetLite(final String id, final Set<String> coAuthors) {
-		super();
-		this.id = id;
-		this.coAuthors = coAuthors;
-	}
-
-	public Set<String> getCoAuthors() {
-		return coAuthors;
-	}
-
-	public void setCoAuthors(final Set<String> coAuthors) {
-		this.coAuthors = coAuthors;
-	}
-
-	public String getId() {
-		return id;
-	}
-
-	public void setId(final String id) {
-		this.id = id;
-	}
-
-	@Override
-	public String toString() {
-		return new Gson().toJson(this);
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/CoAuthors.java

@@ -1,78 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import java.util.Collection;
-import java.util.HashSet;
-
-import com.google.common.base.Function;
-import com.google.common.collect.ComparisonChain;
-import com.google.common.collect.Ordering;
-import com.google.common.collect.Sets;
-import com.google.gson.Gson;
-
-public class CoAuthors extends HashSet<CoAuthor> implements Comparable<CoAuthors> {
-
-	private static final long serialVersionUID = 2525591524516562892L;
-
-	private Function<CoAuthors, Integer> hashFunction;
-
-	private static Function<CoAuthors, Integer> defaultHashFunction = new Function<CoAuthors, Integer>() {
-
-		@Override
-		public Integer apply(final CoAuthors input) {
-			int res = 0;
-			for (final CoAuthor a : input) {
-				res += a.hashCode();
-			}
-			return res;
-
-		}
-	};
-
-	public CoAuthors() {
-		super();
-	}
-
-	public CoAuthors(final Collection<CoAuthor> coauthors) {
-		super(coauthors);
-	}
-
-	public CoAuthors(final CoAuthor coauthor) {
-		super(Sets.newHashSet(coauthor));
-	}
-
-	public Function<CoAuthors, Integer> getHashFunction() {
-		return hashFunction;
-	}
-
-	public void setHashFunction(final Function<CoAuthors, Integer> hashFunction) {
-		this.hashFunction = hashFunction;
-	}
-
-	@Override
-	public int compareTo(final CoAuthors a) {
-		return ComparisonChain.start()
-				.compare(this.size(), a.size(), Ordering.natural().nullsLast())
-				.result();
-	}
-
-	@Override
-	public String toString() {
-		return new Gson().toJson(this);
-	}
-
-	@Override
-	public boolean equals(final Object o) {
-		final boolean res = o instanceof CoAuthors;
-		return res && (Sets.intersection(this, (CoAuthors) o).size() == this.size());
-	}
-
-	public String hashCodeString() {
-		return String.valueOf(hashCode());
-	}
-
-	@Override
-	public int hashCode() {
-		return (getHashFunction() != null) ? getHashFunction().apply(this) : defaultHashFunction.apply(this);
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/GTAuthor.java

@@ -1,196 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
-
-import com.google.common.base.Function;
-import com.google.common.collect.ComparisonChain;
-import com.google.common.collect.Iterables;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Maps;
-import com.google.common.collect.Ordering;
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
-
-public class GTAuthor implements Comparable<GTAuthor> {
-
-	private String id;
-	private Author author;
-	private Authors merged;
-	private CoAuthors coAuthors;
-	private boolean anchor;
-
-	public GTAuthor() {}
-
-	public GTAuthor(final String id, final Authors merged, final CoAuthors coAuthors, final boolean anchor) {
-		super();
-
-		if ((merged == null) || merged.isEmpty())
-			throw new IllegalArgumentException("empty merged author set, id: " + id);
-
-		this.author = pickAuthor(merged);
-		this.id = id;
-		this.merged = merged;
-		this.coAuthors = coAuthors;
-		this.anchor = anchor;
-	}
-
-	class AuthorFrequency extends Author {
-
-		private Integer frequency = new Integer(1);
-
-		public AuthorFrequency(final Author a) {
-			super(a);
-		}
-
-		public void increment() {
-			setFrequency(getFrequency() + 1);
-		}
-
-		public Integer getFrequency() {
-			return frequency;
-		}
-
-		public void setFrequency(final Integer frequency) {
-			this.frequency = frequency;
-		}
-	}
-
-	private Author pickAuthor(final Authors merged) {
-		final List<AuthorFrequency> freq = getFrequencies(merged);
-		Collections.sort(freq, Collections.reverseOrder(new Comparator<AuthorFrequency>() {
-
-			@Override
-			public int compare(final AuthorFrequency o1, final AuthorFrequency o2) {
-				return ComparisonChain.start().compare(o1.getFullname().length(), o2.getFullname().length()).compare(o1.getFrequency(), o2.getFrequency())
-						.result();
-			}
-		}));
-
-		return Iterables.getFirst(freq, null);
-	}
-
-	private List<AuthorFrequency> getFrequencies(final Authors merged) {
-		final Map<String, Integer> countMap = Maps.newHashMap();
-		for (final Author a : merged) {
-			final Integer count = countMap.get(a.getFullname());
-			if (count == null) {
-				countMap.put(a.getFullname(), new Integer(1));
-			} else {
-				countMap.put(a.getFullname(), count + 1);
-			}
-		}
-
-		return Lists.newArrayList(Iterables.transform(merged, new Function<Author, AuthorFrequency>() {
-
-			@Override
-			public AuthorFrequency apply(final Author a) {
-				final AuthorFrequency af = new AuthorFrequency(a);
-				final Integer freq = countMap.get(af.getFullname());
-				af.setFrequency(freq);
-				return af;
-			}
-		}));
-	}
-
-	public String getId() {
-		return id;
-	}
-
-	public void setId(final String id) {
-		this.id = id;
-	}
-
-	public Author getAuthor() {
-		return author;
-	}
-
-	public void setAuthor(final Author author) {
-		this.author = author;
-	}
-
-	public boolean hasMerged() {
-		return (getMerged() != null) && !getMerged().isEmpty();
-	}
-
-	public Authors getMerged() {
-		return merged;
-	}
-
-	public void setMerged(final Authors merged) {
-		this.merged = merged;
-	}
-
-	public boolean hasCoAuthors() {
-		return (getCoAuthors() != null) && !getCoAuthors().isEmpty();
-	}
-
-	public CoAuthors getCoAuthors() {
-		return coAuthors;
-	}
-
-	public void setCoAuthors(final CoAuthors coAuthors) {
-		this.coAuthors = coAuthors;
-	}
-
-	public boolean isAnchor() {
-		return anchor;
-	}
-
-	public void setAnchor(final boolean anchor) {
-		this.anchor = anchor;
-	}
-
-	public static GTAuthor fromJson(final String json) {
-		final Gson gson = new Gson();
-		return gson.fromJson(json, GTAuthor.class);
-	}
-
-	public static List<GTAuthor> fromOafJson(final List<String> json) {
-
-		final GsonBuilder gb = new GsonBuilder();
-		gb.registerTypeAdapter(GTAuthor.class, new GTAuthorOafSerialiser());
-		final Gson gson = gb.create();
-
-		return Lists.newArrayList(Iterables.transform(json, new Function<String, GTAuthor>() {
-			@Override
-			public GTAuthor apply(final String s) {
-				return gson.fromJson(s, GTAuthor.class);
-			}
-		}));
-	}
-
-	public static GTAuthor fromOafJson(final String json) {
-
-		final GsonBuilder gb = new GsonBuilder();
-		gb.registerTypeAdapter(GTAuthor.class, new GTAuthorOafSerialiser());
-		final Gson gson = gb.create();
-
-		return gson.fromJson(json, GTAuthor.class);
-	}
-
-	@Override
-	public String toString() {
-		return new Gson().toJson(this);
-	}
-
-	@Override
-	public int hashCode() {
-		return getId().hashCode();
-	}
-
-	@Override
-	public int compareTo(final GTAuthor o) {
-		return ComparisonChain.start()
-				.compare(this.getId(), o.getId(), Ordering.natural().nullsLast())
-				.result();
-	}
-
-	@Override
-	public boolean equals(final Object o) {
-		return (o instanceof GTAuthor) && getId().equals(((GTAuthor) o).getId());
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/GTAuthorOafSerialiser.java

@@ -1,104 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import java.lang.reflect.Type;
-
-import com.google.common.base.Function;
-import com.google.common.base.Joiner;
-import com.google.common.collect.Iterables;
-import com.google.common.collect.Lists;
-import com.google.gson.JsonDeserializationContext;
-import com.google.gson.JsonDeserializer;
-import com.google.gson.JsonElement;
-import com.google.gson.JsonObject;
-import com.google.gson.JsonParseException;
-
-public class GTAuthorOafSerialiser implements JsonDeserializer<GTAuthor> {
-
-	private static final String VALUE = "value";
-	private static final String SECONDNAMES = "secondnames";
-	private static final String FIRSTNAME = "firstname";
-	private static final String FULLNAME = "fullname";
-	private static final String ID = "id";
-	private static final String MERGEDPERSON = "mergedperson";
-	private static final String METADATA = "metadata";
-	private static final String ANCHOR_ID = "anchorId";
-	private static final String COAUTHOR = "coauthor";
-
-	@Override
-	public GTAuthor deserialize(final JsonElement json, final Type typeOfT, final JsonDeserializationContext context) throws JsonParseException {
-		final GTAuthor gta = new GTAuthor();
-
-		gta.setAuthor(getAuthor(json));
-		gta.setMerged(getMerged(json));
-
-		gta.setCoAuthors(getCoAuthors(json));
-
-		return gta;
-	}
-
-	private CoAuthors getCoAuthors(final JsonElement json) {
-		final JsonObject obj = json.getAsJsonObject();
-		if (!obj.has(COAUTHOR)) return null;
-		return new CoAuthors(Lists.newArrayList(Iterables.transform(obj.get(COAUTHOR).getAsJsonArray(),
-				new Function<JsonElement, CoAuthor>() {
-
-					@Override
-					public CoAuthor apply(final JsonElement in) {
-						final CoAuthor a = new CoAuthor(getAuthor(in));
-						final JsonObject jsonObject = in.getAsJsonObject();
-						if (jsonObject.has(ANCHOR_ID)) {
-							a.setAnchorId(jsonObject.get(ANCHOR_ID).getAsString());
-						}
-						return a;
-					}
-				})));
-	}
-
-	private Author getAuthor(final JsonElement json) {
-
-		final Author a = new Author();
-		a.setCoauthors(null);
-		a.setMatches(null);
-
-		final JsonObject jso = json.getAsJsonObject();
-
-		a.setId(jso.has(ID) ? jso.get(ID).getAsString() : null);
-
-		final JsonObject jsonObject = json.getAsJsonObject();
-		if (jsonObject.has(METADATA)) {
-			final JsonObject m = jsonObject.get(METADATA).getAsJsonObject();
-			a.setFullname(getValue(m, FULLNAME));
-			a.setFirstname(getValue(m, FIRSTNAME));
-			a.setSecondnames(getValues(m, SECONDNAMES));
-		}
-		return a;
-	}
-
-	private Authors getMerged(final JsonElement json) {
-		final JsonObject obj = json.getAsJsonObject();
-		if (!obj.has(MERGEDPERSON)) return null;
-		return new Authors(Lists.newArrayList(Iterables.transform(obj.get(MERGEDPERSON).getAsJsonArray(),
-				new Function<JsonElement, Author>() {
-
-					@Override
-					public Author apply(final JsonElement in) {
-						return getAuthor(in);
-					}
-				})));
-	}
-
-	private String getValues(final JsonObject m, final String fieldName) {
-		return m.has(fieldName) ? Joiner.on(" ").join(Iterables.transform(m.get(fieldName).getAsJsonArray(), new Function<JsonElement, String>() {
-
-			@Override
-			public String apply(final JsonElement in) {
-				return in.getAsJsonObject().get(VALUE).getAsString();
-			}
-		})) : null;
-	}
-
-	private String getValue(final JsonObject m, final String fieldName) {
-		return m.has(fieldName) ? m.get(fieldName).getAsJsonObject().get(VALUE).getAsString() : null;
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Group.java

@@ -1,44 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import java.util.List;
-
-import com.google.gson.Gson;
-
-public class Group {
-
-	private String id;
-	private int size;
-	private List<Result> results;
-
-	public Group() {}
-
-	public String getId() {
-		return id;
-	}
-
-	public void setId(final String id) {
-		this.id = id;
-	}
-
-	public int getSize() {
-		return size;
-	}
-
-	public void setSize(final int size) {
-		this.size = size;
-	}
-
-	public List<Result> getResults() {
-		return results;
-	}
-
-	public void setResults(final List<Result> results) {
-		this.results = results;
-	}
-
-	@Override
-	public String toString() {
-		return new Gson().toJson(this);
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/InvertedAuthor.java

@@ -1,41 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import java.util.Collection;
-
-import com.google.gson.Gson;
-
-public class InvertedAuthor {
-
-	private Author author;
-	private Collection<String> ids;
-
-	public InvertedAuthor() {}
-
-	public InvertedAuthor(final Author author, final Collection<String> ids) {
-		super();
-		this.author = author;
-		this.ids = ids;
-	}
-
-	public Author getAuthor() {
-		return author;
-	}
-
-	public void setAuthor(final Author author) {
-		this.author = author;
-	}
-
-	public Collection<String> getIds() {
-		return ids;
-	}
-
-	public void setIds(final Collection<String> ids) {
-		this.ids = ids;
-	}
-
-	@Override
-	public String toString() {
-		return new Gson().toJson(this);
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Match.java

@@ -1,31 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-public class Match extends Author {
-
-	private double score;
-
-	public Match() {
-		super();
-	}
-
-	public static Match from(final Author a) {
-		final Match m = new Match();
-		if (a.isWellFormed()) {
-			m.setFirstname(a.getFirstname());
-			m.setSecondnames(a.getSecondnames());
-		}
-		m.setFullname(a.getFullname());
-		m.setId(a.getId());
-
-		return m;
-	}
-
-	public double getScore() {
-		return score;
-	}
-
-	public void setScore(final double score) {
-		this.score = score;
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Result.java

@@ -1,72 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import java.util.List;
-
-import com.google.common.collect.ComparisonChain;
-import com.google.common.collect.Ordering;
-import com.google.gson.Gson;
-
-public class Result implements Comparable<Result> {
-
-	private String id;
-	private String originalId;
-	private String title;
-	private List<Author> authors;
-
-	private double meanDistance;
-
-	public Result() {}
-
-	public String getId() {
-		return id;
-	}
-
-	public void setId(final String id) {
-		this.id = id;
-	}
-
-	public String getOriginalId() {
-		return originalId;
-	}
-
-	public void setOriginalId(final String originalId) {
-		this.originalId = originalId;
-	}
-
-	public String getTitle() {
-		return title;
-	}
-
-	public void setTitle(final String title) {
-		this.title = title;
-	}
-
-	public List<Author> getAuthors() {
-		return authors;
-	}
-
-	public void setAuthors(final List<Author> authors) {
-		this.authors = authors;
-	}
-
-	@Override
-	public String toString() {
-		return new Gson().toJson(this);
-	}
-
-	@Override
-	public int compareTo(final Result o) {
-		return ComparisonChain.start()
-				.compare(this.getAuthors().size(), o.getAuthors().size(), Ordering.natural().nullsLast())
-				.result();
-	}
-
-	public double getMeanDistance() {
-		return meanDistance;
-	}
-
-	public void setMeanDistance(final double meanDistance) {
-		this.meanDistance = meanDistance;
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Subjects.java

@@ -1,10 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import java.util.HashMap;
-
-/**
- * Created by claudio on 07/03/16.
- */
-public class Subjects extends HashMap<String, Integer> {
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/SubjectsMap.java

@@ -1,35 +0,0 @@
-package eu.dnetlib.pace.model.gt;
-
-import java.util.HashMap;
-import java.util.Map.Entry;
-
-/**
- * Created by claudio on 07/03/16.
- */
-public class SubjectsMap extends HashMap<String, Subjects> {
-
-	public SubjectsMap mergeFrom(SubjectsMap sm) {
-
-		for(Entry<String, Subjects> e : sm.entrySet()) {
-			if (!this.containsKey(e.getKey())) {
-				Subjects sub = new Subjects();
-
-				sub.putAll(e.getValue());
-
-				this.put(e.getKey(), sub);
-			} else {
-				for (Entry<String, Integer> es : e.getValue().entrySet()) {
-					final Subjects subjects = this.get(e.getKey());
-					if (subjects.containsKey(es.getKey())) {
-						subjects.put(es.getKey(), es.getValue() + subjects.get(es.getKey()));
-					} else {
-						subjects.put(es.getKey(), new Integer(1));
-					}
-				}
-			}
-		}
-
-		return this;
-	}
-
-}

dnet-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerNormalizedName.java

@@ -5,7 +5,7 @@ import eu.dnetlib.pace.tree.support.AbstractComparator;
 import eu.dnetlib.pace.tree.support.ComparatorClass;
 
 import eu.dnetlib.pace.config.Config;
-import org.apache.commons.collections.CollectionUtils;
+
 
 import java.util.Map;
 import java.util.Set;

dnet-pace-core/src/main/java/eu/dnetlib/pace/tree/SubStringLevenstein.java

@@ -1,14 +1,14 @@
 package eu.dnetlib.pace.tree;
 
 import eu.dnetlib.pace.config.Config;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import com.wcohen.ss.AbstractStringDistance;
 import eu.dnetlib.pace.config.Type;
 import eu.dnetlib.pace.model.Field;
 import eu.dnetlib.pace.tree.support.AbstractComparator;
 import eu.dnetlib.pace.tree.support.ComparatorClass;
-import org.apache.commons.lang.StringUtils;
+
 
 import java.util.Map;
 

dnet-pace-core/src/main/java/eu/dnetlib/pace/tree/UrlMatcher.java

@@ -3,7 +3,7 @@ package eu.dnetlib.pace.tree;
 import eu.dnetlib.pace.config.Config;
 import eu.dnetlib.pace.model.Field;
 import eu.dnetlib.pace.tree.support.ComparatorClass;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import java.net.MalformedURLException;
 import java.net.URL;

dnet-pace-core/src/main/java/eu/dnetlib/pace/tree/YearMatch.java

@@ -4,7 +4,7 @@ import eu.dnetlib.pace.config.Config;
 import eu.dnetlib.pace.model.Field;
 import eu.dnetlib.pace.tree.support.AbstractComparator;
 import eu.dnetlib.pace.tree.support.ComparatorClass;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 
 import java.util.Map;
 

dnet-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java

@@ -1,14 +1,11 @@
 package eu.dnetlib.pace.tree.support;
 
 import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.model.*;
+import eu.dnetlib.pace.model.MapDocument;
-import eu.dnetlib.pace.model.gt.Match;
 import eu.dnetlib.pace.util.PaceException;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
-import java.io.Serializable;
-import java.util.Map;
 
 /**
  * The compare between two documents is given by the weighted mean of the field distances

dnet-pace-core/src/main/java/eu/dnetlib/pace/util/BlockProcessor.java

@@ -8,7 +8,7 @@ import eu.dnetlib.pace.tree.support.TreeProcessor;
 import eu.dnetlib.pace.model.Field;
 import eu.dnetlib.pace.model.MapDocument;
 import eu.dnetlib.pace.model.MapDocumentComparator;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 

dnet-pace-core/src/main/java/eu/dnetlib/pace/util/Capitalise.java

@@ -1,15 +1,15 @@
 package eu.dnetlib.pace.util;
 
-import org.apache.commons.lang.WordUtils;
 
 import com.google.common.base.Function;
+import org.apache.commons.lang3.text.WordUtils;
 
 public class Capitalise implements Function<String, String> {
 
-	private final char[] DELIM = { ' ', '-' };
+    private final char[] DELIM = {' ', '-'};
 
-	@Override
+    @Override
-	public String apply(final String s) {
+    public String apply(final String s) {
-		return WordUtils.capitalize(s.toLowerCase(), DELIM);
+        return WordUtils.capitalize(s.toLowerCase(), DELIM);
-	}
+    }
 };