forked from D-Net/dnet-hadoop
parser of orcid publication data from xml original dump
This commit is contained in:
parent
52f62d5d8c
commit
fcbb4c1489
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@ -84,6 +84,12 @@
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<artifactId>spark-sql_2.11</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-text</artifactId>
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<version>1.8</version>
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</dependency>
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</dependencies>
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@ -9,6 +9,7 @@ public class AuthorData implements Serializable {
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private String name;
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private String surname;
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private String creditName;
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private String otherName;
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private String errorCode;
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public String getErrorCode() {
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@ -50,4 +51,12 @@ public class AuthorData implements Serializable {
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public void setOid(String oid) {
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this.oid = oid;
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}
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public String getOtherName() {
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return otherName;
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}
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public void setOtherName(String otherName) {
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this.otherName = otherName;
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}
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}
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@ -0,0 +1,54 @@
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package eu.dnetlib.doiboost.orcidnodoi.model;
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import java.io.Serializable;
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import eu.dnetlib.doiboost.orcid.model.AuthorData;
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public class Contributor extends AuthorData implements Serializable {
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private String sequence;
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private String role;
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private boolean simpleMatch = false;
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private Double score = 0.0;
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private boolean bestMatch = false;
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public String getSequence() {
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return sequence;
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}
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public void setSequence(String sequence) {
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this.sequence = sequence;
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}
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public String getRole() {
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return role;
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}
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public void setRole(String role) {
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this.role = role;
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}
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public boolean isSimpleMatch() {
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return simpleMatch;
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}
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public void setSimpleMatch(boolean simpleMatch) {
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this.simpleMatch = simpleMatch;
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}
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public Double getScore() {
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return score;
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}
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public void setScore(Double score) {
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this.score = score;
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}
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public boolean isBestMatch() {
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return bestMatch;
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}
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public void setBestMatch(boolean bestMatch) {
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this.bestMatch = bestMatch;
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}
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}
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@ -0,0 +1,32 @@
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package eu.dnetlib.doiboost.orcidnodoi.model;
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public class ExternalId {
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private String type;
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private String value;
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private String relationShip;
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public String getType() {
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return type;
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}
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public void setType(String type) {
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this.type = type;
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}
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public String getValue() {
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return value;
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}
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public void setValue(String value) {
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this.value = value;
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}
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public String getRelationShip() {
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return relationShip;
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}
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public void setRelationShip(String relationShip) {
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this.relationShip = relationShip;
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}
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}
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@ -0,0 +1,32 @@
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package eu.dnetlib.doiboost.orcidnodoi.model;
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public class PublicationDate {
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private String year;
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private String month;
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private String day;
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public String getYear() {
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return year;
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}
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public void setYear(String year) {
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this.year = year;
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}
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public String getMonth() {
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return month;
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}
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public void setMonth(String month) {
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this.month = month;
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}
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public String getDay() {
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return day;
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}
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public void setDay(String day) {
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this.day = day;
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}
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}
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@ -0,0 +1,101 @@
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package eu.dnetlib.doiboost.orcidnodoi.model;
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import java.io.Serializable;
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import java.util.List;
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public class WorkDataNoDoi implements Serializable {
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private String oid;
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private String id;
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private String sourceName;
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private String type;
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private List<String> titles;
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private List<String> urls;
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List<ExternalId> extIds;
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List<PublicationDate> publicationDates;
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List<Contributor> contributors;
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public String getOid() {
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return oid;
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}
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public void setOid(String oid) {
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this.oid = oid;
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}
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public String getErrorCode() {
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return errorCode;
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}
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public void setErrorCode(String errorCode) {
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this.errorCode = errorCode;
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}
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private String errorCode;
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public String getId() {
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return id;
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}
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public void setId(String id) {
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this.id = id;
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}
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public List<String> getTitles() {
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return titles;
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}
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public void setTitles(List<String> titles) {
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this.titles = titles;
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}
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public String getSourceName() {
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return sourceName;
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}
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public void setSourceName(String sourceName) {
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this.sourceName = sourceName;
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}
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public String getType() {
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return type;
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}
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public void setType(String type) {
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this.type = type;
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}
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public List<String> getUrls() {
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return urls;
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}
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public void setUrls(List<String> urls) {
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this.urls = urls;
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}
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public List<ExternalId> getExtIds() {
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return extIds;
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}
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public void setExtIds(List<ExternalId> extIds) {
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this.extIds = extIds;
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}
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public List<PublicationDate> getPublicationDates() {
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return publicationDates;
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}
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public void setPublicationDates(List<PublicationDate> publicationDates) {
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this.publicationDates = publicationDates;
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}
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public List<Contributor> getContributors() {
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return contributors;
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}
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public void setContributors(List<Contributor> contributors) {
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this.contributors = contributors;
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}
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}
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@ -0,0 +1,216 @@
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package eu.dnetlib.doiboost.orcidnodoi.xml;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.ximpleware.*;
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import eu.dnetlib.dhp.parser.utility.VtdException;
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import eu.dnetlib.dhp.parser.utility.VtdUtilityParser;
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import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
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import eu.dnetlib.doiboost.orcidnodoi.model.ExternalId;
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import eu.dnetlib.doiboost.orcidnodoi.model.PublicationDate;
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import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
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public class XMLRecordParserNoDoi {
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private static final Logger logger = LoggerFactory.getLogger(XMLRecordParserNoDoi.class);
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private static final String NS_COMMON_URL = "http://www.orcid.org/ns/common";
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private static final String NS_COMMON = "common";
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private static final String NS_PERSON_URL = "http://www.orcid.org/ns/person";
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private static final String NS_PERSON = "person";
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private static final String NS_DETAILS_URL = "http://www.orcid.org/ns/personal-details";
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private static final String NS_DETAILS = "personal-details";
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private static final String NS_OTHER_URL = "http://www.orcid.org/ns/other-name";
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private static final String NS_OTHER = "other-name";
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private static final String NS_RECORD_URL = "http://www.orcid.org/ns/record";
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private static final String NS_RECORD = "record";
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private static final String NS_ERROR_URL = "http://www.orcid.org/ns/error";
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private static final String NS_WORK = "work";
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private static final String NS_WORK_URL = "http://www.orcid.org/ns/work";
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private static final String NS_ERROR = "error";
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public static WorkDataNoDoi VTDParseWorkData(byte[] bytes)
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throws VtdException, EncodingException, EOFException, EntityException, ParseException, XPathParseException,
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NavException, XPathEvalException {
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logger.info("parsing xml ...");
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final VTDGen vg = new VTDGen();
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vg.setDoc(bytes);
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vg.parse(true);
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final VTDNav vn = vg.getNav();
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final AutoPilot ap = new AutoPilot(vn);
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ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL);
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ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL);
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ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL);
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WorkDataNoDoi workData = new WorkDataNoDoi();
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final List<String> errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code");
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if (!errors.isEmpty()) {
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workData.setErrorCode(errors.get(0));
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return workData;
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}
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List<VtdUtilityParser.Node> workNodes = VtdUtilityParser
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.getTextValuesWithAttributes(ap, vn, "//work:work", Arrays.asList("path", "put-code"));
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if (!workNodes.isEmpty()) {
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final String oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1];
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workData.setOid(oid);
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final String id = (workNodes.get(0).getAttributes().get("put-code"));
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workData.setId(id);
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} else {
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return null;
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}
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final List<String> titles = VtdUtilityParser
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.getTextValue(
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ap, vn, "//common:title");
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if (!titles.isEmpty()) {
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workData.setTitles(titles);
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}
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final List<String> sourceNames = VtdUtilityParser
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.getTextValue(
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ap, vn, "//common:source-name");
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if (!sourceNames.isEmpty()) {
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workData.setSourceName(sourceNames.get(0));
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}
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final List<String> types = VtdUtilityParser
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.getTextValue(
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ap, vn, "//work:type");
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if (!types.isEmpty()) {
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workData.setType(types.get(0));
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}
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final List<String> urls = VtdUtilityParser
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.getTextValue(
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ap, vn, "//common:url");
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if (!urls.isEmpty()) {
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workData.setUrls(urls);
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}
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workData.setPublicationDates(getPublicationDates(vg, vn, ap));
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workData.setExtIds(getExternalIds(vg, vn, ap));
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workData.setContributors(getContributors(vg, vn, ap));
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return workData;
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}
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private static List<PublicationDate> getPublicationDates(VTDGen vg, VTDNav vn, AutoPilot ap)
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throws XPathParseException, NavException, XPathEvalException {
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List<PublicationDate> publicationDates = new ArrayList<PublicationDate>();
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int yearIndex = 0;
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ap.selectXPath("//common:publication-date/common:year");
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while (ap.evalXPath() != -1) {
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PublicationDate publicationDate = new PublicationDate();
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int t = vn.getText();
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if (t >= 0) {
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publicationDate.setYear(vn.toNormalizedString(t));
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publicationDates.add(yearIndex, publicationDate);
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yearIndex++;
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}
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}
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int monthIndex = 0;
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ap.selectXPath("//common:publication-date/common:month");
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while (ap.evalXPath() != -1) {
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int t = vn.getText();
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if (t >= 0) {
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publicationDates.get(monthIndex).setMonth(vn.toNormalizedString(t));
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monthIndex++;
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}
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}
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int dayIndex = 0;
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ap.selectXPath("//common:publication-date/common:day");
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while (ap.evalXPath() != -1) {
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int t = vn.getText();
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if (t >= 0) {
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publicationDates.get(dayIndex).setDay(vn.toNormalizedString(t));
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dayIndex++;
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}
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}
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return publicationDates;
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}
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private static List<ExternalId> getExternalIds(VTDGen vg, VTDNav vn, AutoPilot ap)
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throws XPathParseException, NavException, XPathEvalException {
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List<ExternalId> extIds = new ArrayList<ExternalId>();
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int typeIndex = 0;
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ap.selectXPath("//common:external-id/common:external-id-type");
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while (ap.evalXPath() != -1) {
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ExternalId extId = new ExternalId();
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int t = vn.getText();
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if (t >= 0) {
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extId.setType(vn.toNormalizedString(t));
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extIds.add(typeIndex, extId);
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typeIndex++;
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}
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}
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int valueIndex = 0;
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ap.selectXPath("//common:external-id/common:external-id-value");
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while (ap.evalXPath() != -1) {
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int t = vn.getText();
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if (t >= 0) {
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extIds.get(valueIndex).setValue(vn.toNormalizedString(t));
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valueIndex++;
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}
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}
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int relationshipIndex = 0;
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ap.selectXPath("//common:external-id/common:external-id-relationship");
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while (ap.evalXPath() != -1) {
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int t = vn.getText();
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if (t >= 0) {
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extIds.get(relationshipIndex).setRelationShip(vn.toNormalizedString(t));
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relationshipIndex++;
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}
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}
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if (typeIndex == valueIndex) {
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return extIds;
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}
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return new ArrayList<ExternalId>();
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}
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private static List<Contributor> getContributors(VTDGen vg, VTDNav vn, AutoPilot ap)
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throws XPathParseException, NavException, XPathEvalException {
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List<Contributor> contributors = new ArrayList<Contributor>();
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int nameIndex = 0;
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ap.selectXPath("//work:contributor/work:credit-name");
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while (ap.evalXPath() != -1) {
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Contributor contributor = new Contributor();
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int t = vn.getText();
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if (t >= 0) {
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contributor.setCreditName(vn.toNormalizedString(t));
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contributors.add(nameIndex, contributor);
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nameIndex++;
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}
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}
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int sequenceIndex = 0;
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ap.selectXPath("//work:contributor/work:contributor-attributes/work:contributor-sequence");
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while (ap.evalXPath() != -1) {
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int t = vn.getText();
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if (t >= 0) {
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contributors.get(sequenceIndex).setSequence(vn.toNormalizedString(t));
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sequenceIndex++;
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}
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}
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int roleIndex = 0;
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ap.selectXPath("//work:contributor/work:contributor-attributes/work:contributor-role");
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while (ap.evalXPath() != -1) {
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int t = vn.getText();
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if (t >= 0) {
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contributors.get(roleIndex).setRole(vn.toNormalizedString(t));
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roleIndex++;
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}
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}
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return contributors;
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}
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}
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@ -44,7 +44,7 @@ public class XMLRecordParserTest {
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String xml = IOUtils
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.toString(
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this.getClass().getResourceAsStream("activity_work_0000-0002-5982-8983.xml"));
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this.getClass().getResourceAsStream("activity_work_0000-0003-2760-1191.xml"));
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XMLRecordParser p = new XMLRecordParser();
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@ -0,0 +1,326 @@
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package eu.dnetlib.doiboost.orcidnodoi.xml;
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import com.ximpleware.NavException;
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import com.ximpleware.ParseException;
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import com.ximpleware.XPathEvalException;
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import com.ximpleware.XPathParseException;
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import eu.dnetlib.dhp.parser.utility.VtdException;
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import eu.dnetlib.doiboost.orcid.model.AuthorData;
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import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
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import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
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import jdk.nashorn.internal.ir.annotations.Ignore;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.text.similarity.JaccardSimilarity;
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import org.apache.commons.text.similarity.JaroWinklerSimilarity;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.IOException;
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import java.text.Normalizer;
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import java.util.*;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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|
||||
public class OrcidNoDoiTest {
|
||||
|
||||
private static final Logger logger = LoggerFactory.getLogger(OrcidNoDoiTest.class);
|
||||
|
||||
String nameA = "Khairy";
|
||||
String surnameA = "Abdel Dayem";
|
||||
String otherNameA = "Dayem MKA";
|
||||
String nameB = "K";
|
||||
String surnameB = "Abdel-Dayem";
|
||||
String orcidIdA = "0000-0003-2760-1191";
|
||||
Double threshold = 0.8;
|
||||
|
||||
@Test
|
||||
@Ignore
|
||||
private void similarityTest() throws Exception {
|
||||
logger.info("running testSimilarity ....");
|
||||
logger
|
||||
.info(
|
||||
"JaroWinklerSimilarity: "
|
||||
+ Double.toString(similarityJaroWinkler(nameA, surnameA, nameB, surnameB)));
|
||||
logger
|
||||
.info(
|
||||
"JaccardSimilarity: " + Double.toString(similarityJaccard(nameA, surnameA, nameB, surnameB)));
|
||||
}
|
||||
|
||||
@Test
|
||||
@Ignore
|
||||
private void bestMatchTest() throws Exception {
|
||||
logger.info("running bestMatchTest ....");
|
||||
String contributor = surnameB + ", " + nameB;
|
||||
logger.info("score: " + Double.toString(bestMatch(surnameA, nameA, contributor)));
|
||||
}
|
||||
|
||||
private static Double bestMatch(String authorSurname, String authorName, String contributor) {
|
||||
logger.debug(authorSurname + " " + authorName + " vs " + contributor);
|
||||
String[] contributorSplitted = contributor.split(" ");
|
||||
if (contributorSplitted.length == 0) {
|
||||
return 0.0;
|
||||
}
|
||||
final String contributorName = contributorSplitted[contributorSplitted.length - 1];
|
||||
String contributorSurname = "";
|
||||
if (contributorSplitted.length > 1) {
|
||||
StringJoiner joiner = new StringJoiner(" ");
|
||||
for (int i = 0; i < contributorSplitted.length - 1; i++) {
|
||||
joiner.add(contributorSplitted[i]);
|
||||
}
|
||||
contributorSurname = joiner.toString();
|
||||
}
|
||||
logger
|
||||
.debug(
|
||||
"contributorName: " + contributorName +
|
||||
" contributorSurname: " + contributorSurname);
|
||||
String authorNameNrm = normalize(authorName);
|
||||
String authorSurnameNrm = normalize(authorSurname);
|
||||
String contributorNameNrm = normalize(contributorName);
|
||||
String contributorSurnameNrm = normalize(contributorSurname);
|
||||
Double sm1 = similarity(authorNameNrm, authorSurnameNrm, contributorNameNrm, contributorSurnameNrm);
|
||||
Double sm2 = similarity(authorNameNrm, authorSurnameNrm, contributorSurnameNrm, contributorNameNrm);
|
||||
if (sm1.compareTo(sm2) >= 0) {
|
||||
return sm1;
|
||||
}
|
||||
return sm2;
|
||||
}
|
||||
|
||||
private static Double similarity(String nameA, String surnameA, String nameB, String surnameB) {
|
||||
Double score = similarityJaroWinkler(nameA, surnameA, nameB, surnameB);
|
||||
logger
|
||||
.debug(nameA + ", " + surnameA + " <> " + nameB + ", " + surnameB + " score: " + Double.toString(score));
|
||||
return score;
|
||||
}
|
||||
|
||||
private static Double similarityJaccard(String nameA, String surnameA, String nameB, String surnameB) {
|
||||
return new JaccardSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB)));
|
||||
}
|
||||
|
||||
private static Double similarityJaroWinkler(String nameA, String surnameA, String nameB, String surnameB) {
|
||||
return new JaroWinklerSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB)));
|
||||
}
|
||||
|
||||
private static String parse(String name, String surname) {
|
||||
return surname + " " + name;
|
||||
}
|
||||
|
||||
private static String normalize(final String s) {
|
||||
return nfd(s)
|
||||
.toLowerCase()
|
||||
// do not compact the regexes in a single expression, would cause StackOverflowError
|
||||
// in case
|
||||
// of large input strings
|
||||
.replaceAll("(\\W)+", " ")
|
||||
.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
|
||||
.replaceAll("(\\p{Punct})+", " ")
|
||||
.replaceAll("(\\d)+", " ")
|
||||
.replaceAll("(\\n)+", " ")
|
||||
.trim();
|
||||
}
|
||||
|
||||
private static String nfd(final String s) {
|
||||
return Normalizer.normalize(s, Normalizer.Form.NFD);
|
||||
}
|
||||
|
||||
@Test
|
||||
@Ignore
|
||||
public void readPublicationFieldsTest()
|
||||
throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
|
||||
logger.info("running loadPublicationFieldsTest ....");
|
||||
String xml = IOUtils
|
||||
.toString(
|
||||
OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0003-2760-1191.xml"));
|
||||
|
||||
if (xml == null) {
|
||||
logger.info("Resource not found");
|
||||
}
|
||||
XMLRecordParserNoDoi p = new XMLRecordParserNoDoi();
|
||||
if (p == null) {
|
||||
logger.info("XMLRecordParserNoDoi null");
|
||||
}
|
||||
WorkDataNoDoi workData = null;
|
||||
try {
|
||||
workData = p.VTDParseWorkData(xml.getBytes());
|
||||
} catch (Exception e) {
|
||||
logger.error("parsing xml", e);
|
||||
}
|
||||
assertNotNull(workData);
|
||||
assertNotNull(workData.getOid());
|
||||
logger.info("oid: " + workData.getOid());
|
||||
assertNotNull(workData.getTitles());
|
||||
logger.info("titles: ");
|
||||
workData.getTitles().forEach(t -> {
|
||||
logger.info(t);
|
||||
});
|
||||
logger.info("source: " + workData.getSourceName());
|
||||
logger.info("type: " + workData.getType());
|
||||
logger.info("urls: ");
|
||||
workData.getUrls().forEach(u -> {
|
||||
logger.info(u);
|
||||
});
|
||||
logger.info("publication date: ");
|
||||
workData.getPublicationDates().forEach(d -> {
|
||||
logger.info(d.getYear() + " - " + d.getMonth() + " - " + d.getDay());
|
||||
});
|
||||
logger.info("external id: ");
|
||||
workData.getExtIds().removeIf(e -> e.getRelationShip() != null && !e.getRelationShip().equals("self"));
|
||||
workData.getExtIds().forEach(e -> {
|
||||
logger.info(e.getType() + " - " + e.getValue() + " - " + e.getRelationShip());
|
||||
});
|
||||
logger.info("contributors: ");
|
||||
workData.getContributors().forEach(c -> {
|
||||
logger
|
||||
.info(
|
||||
c.getName() + " - " + c.getRole() + " - " + c.getSequence());
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
private void updateRanks(List<Contributor> contributors) {
|
||||
boolean seqFound = false;
|
||||
if (contributors
|
||||
.stream()
|
||||
.filter(
|
||||
c -> c.getRole() != null && c.getSequence() != null &&
|
||||
c.getRole().equals("author") && (c.getSequence().equals("first") ||
|
||||
c.getSequence().equals("additional")))
|
||||
.count() > 0) {
|
||||
seqFound = true;
|
||||
logger.info("sequence data found");
|
||||
}
|
||||
if (!seqFound) {
|
||||
List<Integer> seqIds = Arrays.asList(0);
|
||||
contributors.forEach(c -> {
|
||||
int currentSeq = seqIds.get(0) + 1;
|
||||
seqIds.set(0, currentSeq);
|
||||
c.setSequence(Integer.toString(seqIds.get(0)));
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
private void updateAuthorsSimpleMatch(List<Contributor> contributors, AuthorData author) {
|
||||
contributors.forEach(c -> {
|
||||
if (c.isSimpleMatch()) {
|
||||
logger.info("simple match on : " + c.getCreditName());
|
||||
c.setName(author.getName());
|
||||
c.setSurname(author.getSurname());
|
||||
c.setOid(author.getOid());
|
||||
}
|
||||
});
|
||||
updateRanks(contributors);
|
||||
}
|
||||
|
||||
private void updateAuthorsSimilarityMatch(List<Contributor> contributors, AuthorData author) {
|
||||
logger.info("inside updateAuthorsSimilarityMatch ...");
|
||||
contributors.forEach(c -> {
|
||||
logger
|
||||
.info(
|
||||
c.getOid() + " - " + c.getCreditName() + " - " +
|
||||
c.getName() + " - " + c.getSurname() + " - " +
|
||||
c.getRole() + " - " + c.getSequence() + " - best: " + c.isBestMatch() + " - simpe: "
|
||||
+ c.isSimpleMatch());
|
||||
});
|
||||
|
||||
contributors
|
||||
.stream()
|
||||
.filter(c -> c.isBestMatch())
|
||||
.forEach(c -> {
|
||||
logger.info("similarity match on : " + c.getCreditName());
|
||||
c.setName(author.getName());
|
||||
c.setSurname(author.getSurname());
|
||||
c.setOid(author.getOid());
|
||||
});
|
||||
updateRanks(contributors);
|
||||
}
|
||||
|
||||
@Test
|
||||
@Ignore
|
||||
public void authorSimilarityMatchTest() throws Exception {
|
||||
logger.info("running authorSimilarityMatchTest ....");
|
||||
authorMatchTest("activity_work_0000-0003-2760-1191-similarity.xml");
|
||||
}
|
||||
|
||||
@Test
|
||||
private void authorSimpleMatchTest() throws Exception {
|
||||
logger.info("running authorSimpleMatchTest ....");
|
||||
authorMatchTest("activity_work_0000-0003-2760-1191.xml");
|
||||
}
|
||||
|
||||
private void authorMatchTest(String orcidWork)
|
||||
throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
|
||||
AuthorData author = new AuthorData();
|
||||
author.setName(nameA);
|
||||
author.setSurname(surnameA);
|
||||
author.setOid(orcidIdA);
|
||||
String xml = IOUtils
|
||||
.toString(
|
||||
OrcidNoDoiTest.class.getResourceAsStream(orcidWork));
|
||||
|
||||
if (xml == null) {
|
||||
logger.info("Resource not found");
|
||||
}
|
||||
XMLRecordParserNoDoi p = new XMLRecordParserNoDoi();
|
||||
if (p == null) {
|
||||
logger.info("XMLRecordParserNoDoi null");
|
||||
}
|
||||
WorkDataNoDoi workData = null;
|
||||
try {
|
||||
workData = p.VTDParseWorkData(xml.getBytes());
|
||||
} catch (Exception e) {
|
||||
logger.error("parsing xml", e);
|
||||
}
|
||||
assertNotNull(workData);
|
||||
int matchCounter = 0;
|
||||
List<Integer> matchCounters = Arrays.asList(matchCounter);
|
||||
Contributor contributor = null;
|
||||
workData.getContributors().forEach(c -> {
|
||||
if (normalize(c.getCreditName()).contains(normalize(author.getName())) ||
|
||||
normalize(c.getCreditName()).contains(normalize(author.getSurname())) ||
|
||||
((author.getOtherName() != null)
|
||||
&& normalize(c.getCreditName()).contains(normalize(author.getOtherName())))) {
|
||||
matchCounters.set(0, matchCounters.get(0) + 1);
|
||||
c.setSimpleMatch(true);
|
||||
}
|
||||
});
|
||||
logger.info("match counter: " + Integer.toString(matchCounters.get(0)));
|
||||
if (matchCounters.get(0) == 1) {
|
||||
updateAuthorsSimpleMatch(workData.getContributors(), author);
|
||||
} else if (matchCounters.get(0) > 1) {
|
||||
Optional<Contributor> optCon = workData
|
||||
.getContributors()
|
||||
.stream()
|
||||
.filter(c -> c.isSimpleMatch())
|
||||
.map(c -> {
|
||||
c.setScore(bestMatch(nameA, surnameA, c.getCreditName()));
|
||||
logger.debug("nella map: " + c.getCreditName() + " score: " + c.getScore());
|
||||
return c;
|
||||
})
|
||||
.filter(c -> c.getScore() >= threshold)
|
||||
.max(Comparator.comparing(c -> c.getScore()));
|
||||
Contributor bestMatchContributor = null;
|
||||
if (optCon.isPresent()) {
|
||||
bestMatchContributor = optCon.get();
|
||||
bestMatchContributor.setBestMatch(true);
|
||||
logger.info("best match: " + bestMatchContributor.getCreditName());
|
||||
updateAuthorsSimilarityMatch(workData.getContributors(), author);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
logger.info("UPDATED contributors: ");
|
||||
workData.getContributors().forEach(c -> {
|
||||
logger
|
||||
.info(
|
||||
c.getOid() + " - " + c.getCreditName() + " - " +
|
||||
c.getName() + " - " + c.getSurname() + " - " +
|
||||
c.getRole() + " - " + c.getSequence());
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
//
|
||||
// orcid_RDD = sc.textFile(ORCID_DUMP_PATH)
|
||||
// no_doi_works_RDD = orcid_RDD.map(orcid_map).filter(lambda x:x is not None).map(lambda x: json.dumps(x)).saveAsTextFile(path=ORCID_OPENAIRE_PATH,compressionCodecClass="org.apache.hadoop.io.compress.GzipCodec")
|
||||
//
|
||||
|
|
@ -0,0 +1,106 @@
|
|||
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
|
||||
<work:work xmlns:address="http://www.orcid.org/ns/address"
|
||||
xmlns:email="http://www.orcid.org/ns/email" xmlns:history="http://www.orcid.org/ns/history"
|
||||
xmlns:employment="http://www.orcid.org/ns/employment"
|
||||
xmlns:education="http://www.orcid.org/ns/education"
|
||||
xmlns:other-name="http://www.orcid.org/ns/other-name"
|
||||
xmlns:deprecated="http://www.orcid.org/ns/deprecated"
|
||||
xmlns:funding="http://www.orcid.org/ns/funding"
|
||||
xmlns:research-resource="http://www.orcid.org/ns/research-resource"
|
||||
xmlns:service="http://www.orcid.org/ns/service"
|
||||
xmlns:researcher-url="http://www.orcid.org/ns/researcher-url"
|
||||
xmlns:distinction="http://www.orcid.org/ns/distinction"
|
||||
xmlns:internal="http://www.orcid.org/ns/internal"
|
||||
xmlns:membership="http://www.orcid.org/ns/membership"
|
||||
xmlns:person="http://www.orcid.org/ns/person"
|
||||
xmlns:personal-details="http://www.orcid.org/ns/personal-details"
|
||||
xmlns:bulk="http://www.orcid.org/ns/bulk" xmlns:common="http://www.orcid.org/ns/common"
|
||||
xmlns:record="http://www.orcid.org/ns/record" xmlns:keyword="http://www.orcid.org/ns/keyword"
|
||||
xmlns:activities="http://www.orcid.org/ns/activities"
|
||||
xmlns:qualification="http://www.orcid.org/ns/qualification"
|
||||
xmlns:external-identifier="http://www.orcid.org/ns/external-identifier"
|
||||
xmlns:error="http://www.orcid.org/ns/error"
|
||||
xmlns:preferences="http://www.orcid.org/ns/preferences"
|
||||
xmlns:invited-position="http://www.orcid.org/ns/invited-position"
|
||||
xmlns:work="http://www.orcid.org/ns/work"
|
||||
xmlns:peer-review="http://www.orcid.org/ns/peer-review" put-code="28776099"
|
||||
path="/0000-0003-2760-1191/work/28776099" visibility="public">
|
||||
<common:created-date>2016-12-12T23:02:05.233Z</common:created-date>
|
||||
<common:last-modified-date>2016-12-13T09:08:16.412Z</common:last-modified-date>
|
||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0002-9157-3431</common:uri>
|
||||
<common:path>0000-0002-9157-3431</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:source-orcid>
|
||||
<common:source-name>Europe PubMed Central</common:source-name>
|
||||
</common:source>
|
||||
<work:title>
|
||||
<common:title>Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which
|
||||
Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for
|
||||
ST-Segment-Elevation Myocardial Infarction.</common:title>
|
||||
</work:title>
|
||||
<work:citation>
|
||||
<work:citation-type>formatted-unspecified</work:citation-type>
|
||||
<work:citation-value>Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta
|
||||
Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016</work:citation-value>
|
||||
</work:citation>
|
||||
<work:type>journal-article</work:type>
|
||||
<common:publication-date>
|
||||
<common:year>2016</common:year>
|
||||
<common:month>11</common:month>
|
||||
</common:publication-date>
|
||||
<common:external-ids>
|
||||
<common:external-id>
|
||||
<common:external-id-type>pmid</common:external-id-type>
|
||||
<common:external-id-value>27899851</common:external-id-value>
|
||||
<common:external-id-normalized transient="true">27899851</common:external-id-normalized>
|
||||
<common:external-id-relationship>self</common:external-id-relationship>
|
||||
</common:external-id>
|
||||
<common:external-id>
|
||||
<common:external-id-type>pmc</common:external-id-type>
|
||||
<common:external-id-value>PMC5126442</common:external-id-value>
|
||||
<common:external-id-normalized transient="true"
|
||||
>PMC5126442</common:external-id-normalized>
|
||||
<common:external-id-relationship>self</common:external-id-relationship>
|
||||
</common:external-id>
|
||||
</common:external-ids>
|
||||
<common:url>http://europepmc.org/abstract/med/27899851</common:url>
|
||||
<work:contributors>
|
||||
<work:contributor>
|
||||
<work:credit-name>Abdel-Dayem K</work:credit-name>
|
||||
<work:contributor-attributes>
|
||||
<work:contributor-sequence>first</work:contributor-sequence>
|
||||
<work:contributor-role>author</work:contributor-role>
|
||||
</work:contributor-attributes>
|
||||
</work:contributor>
|
||||
<work:contributor>
|
||||
<work:credit-name>Eweda II</work:credit-name>
|
||||
<work:contributor-attributes>
|
||||
<work:contributor-sequence>first</work:contributor-sequence>
|
||||
<work:contributor-role>author</work:contributor-role>
|
||||
</work:contributor-attributes>
|
||||
</work:contributor>
|
||||
<work:contributor>
|
||||
<work:credit-name>El-Sherbiny A</work:credit-name>
|
||||
<work:contributor-attributes>
|
||||
<work:contributor-sequence>first</work:contributor-sequence>
|
||||
<work:contributor-role>author</work:contributor-role>
|
||||
</work:contributor-attributes>
|
||||
</work:contributor>
|
||||
<work:contributor>
|
||||
<work:credit-name>Dimitry MO</work:credit-name>
|
||||
<work:contributor-attributes>
|
||||
<work:contributor-sequence>first</work:contributor-sequence>
|
||||
<work:contributor-role>author</work:contributor-role>
|
||||
</work:contributor-attributes>
|
||||
</work:contributor>
|
||||
<work:contributor>
|
||||
<work:credit-name>Nammas W</work:credit-name>
|
||||
<work:contributor-attributes>
|
||||
<work:contributor-sequence>first</work:contributor-sequence>
|
||||
<work:contributor-role>author</work:contributor-role>
|
||||
</work:contributor-attributes>
|
||||
</work:contributor>
|
||||
</work:contributors>
|
||||
</work:work>
|
||||
|
|
@ -0,0 +1,113 @@
|
|||
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
|
||||
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<work:credit-name>Nammas W</work:credit-name>
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|
|
@ -0,0 +1,106 @@
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<common:title>Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which
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||||
Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for
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||||
ST-Segment-Elevation Myocardial Infarction.</common:title>
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</work:contributor>
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||||
</work:contributors>
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||||
</work:work>
|
||||
Loading…
Reference in New Issue