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dnet-hadoop
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upgraded maven version of commons-lang

This commit is contained in:
Sandro La Bruzzo 2020-02-10 12:38:40 +01:00
parent 5c8f6febee
commit 46727f5c76
35 changed files with 277 additions and 1233 deletions
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9
dnet-pace-core/pom.xml
View File

@ -27,17 +27,14 @@
<artifactId>gson</artifactId>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<groupId>org.apache.commons</groupId>
<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>

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/AbstractClusteringFunction.java
View File

@ -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;

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/FieldFilter.java
View File

@ -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;

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/KeywordsClustering.java
View File

@ -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;

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/LowercaseClustering.java
View File

@ -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 {

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/NGramUtils.java
View File

@ -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;

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/PersonClustering.java
View File

@ -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;

4
dnet-pace-core/src/main/java/eu/dnetlib/pace/clustering/SpaceTrimmingFieldValue.java
View File

@ -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.lang.StringUtils;
import org.apache.commons.lang3.RandomStringUtils;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.Lists;

9
dnet-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java
View File

@ -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;
@ -25,7 +24,6 @@ import java.util.stream.Collectors;
* Set of common functions for the framework
*
* @author claudio
*
*/
public abstract class AbstractPaceFunctions {
@ -242,9 +240,8 @@ public abstract class AbstractPaceFunctions {
public double commonElementsPercentage(Set<String> s1, Set<String> s2) {
int longer = (s1.size()>s2.size())?s1.size():s2.size();
return (double)CollectionUtils.intersection(s1,s2).size()/(double)longer;
double longer = Math.max(s1.size(), s2.size());
return (double) s1.stream().filter(s2::contains).count() / longer;
}
//convert the set of keywords to codes

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/config/WfConfig.java
View File

@ -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;

9
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java
View File

@ -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;
}
}
}

11
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/FieldListImpl.java
View File

@ -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());

6
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/FieldValueImpl.java
View File

@ -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.lang.StringUtils;
import org.apache.commons.lang3.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();
}
}

129
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Author.java
View File

@ -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;
}
}

37
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/AuthorSet.java
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@ -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);
}
}

54
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Authors.java
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@ -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;
}
}

50
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/CoAuthor.java
View File

@ -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());
}
}

36
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/CoAuthorSet.java
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@ -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);
}
}

40
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/CoAuthorSetLite.java
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@ -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);
}
}

78
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/CoAuthors.java
View File

@ -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);
}
}

196
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/GTAuthor.java
View File

@ -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());
}
}

104
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/GTAuthorOafSerialiser.java
View File

@ -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;
}
}

44
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Group.java
View File

@ -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);
}
}

41
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/InvertedAuthor.java
View File

@ -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);
}
}

31
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Match.java
View File

@ -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;
}
}

72
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Result.java
View File

@ -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;
}
}

10
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/Subjects.java
View File

@ -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> {
}

35
dnet-pace-core/src/main/java/eu/dnetlib/pace/model/gt/SubjectsMap.java
View File

@ -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;
}
}

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerNormalizedName.java
View File

@ -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;

4
dnet-pace-core/src/main/java/eu/dnetlib/pace/tree/SubStringLevenstein.java
View File

@ -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;

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/tree/UrlMatcher.java
View File

@ -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;

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/tree/YearMatch.java
View File

@ -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;

5
dnet-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java
View File

@ -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.gt.Match;
import eu.dnetlib.pace.model.MapDocument;
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

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/util/BlockProcessor.java
View File

@ -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;

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/util/Capitalise.java
View File

@ -1,8 +1,8 @@
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> {