first entities
This commit is contained in:
parent
4885d36b3b
commit
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package eu.dnetlib.dhp.skgif.model;
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/**
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* @author miriam.baglioni
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* @Date 04/09/23
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*/
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public enum AccessRight {
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OPEN("open"),
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CLOSED("closed"),
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EMBARGO("embargo"),
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RESTRICTED("restricted"),
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UNAVAILABLE("unavailable");
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public final String label;
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private AccessRight(String label) {
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this.label = label;
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}
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}
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package eu.dnetlib.dhp.skgif.model;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import java.io.Serializable;
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/**
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* @author miriam.baglioni
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* @Date 05/09/23
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*/
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public class Affiliation implements Serializable {
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private String organization;
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@JsonProperty("start_date")
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private String startDate;
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@JsonProperty("end_date")
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private String endDate;
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public String getOrganization() {
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return organization;
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}
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public void setOrganization(String organization) {
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this.organization = organization;
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}
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public String getStartDate() {
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return startDate;
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}
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public void setStartDate(String startDate) {
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this.startDate = startDate;
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}
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public String getEndDate() {
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return endDate;
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}
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public void setEndDate(String endDate) {
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this.endDate = endDate;
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}
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}
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@ -0,0 +1,86 @@
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package eu.dnetlib.dhp.skgif.model;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import java.io.Serializable;
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/**
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* @author miriam.baglioni
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* @Date 01/09/23
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*/
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public class Biblio implements Serializable {
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private String issue;
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@JsonProperty("start_page")
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private String startPage;
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@JsonProperty("end_page")
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private String endPage;
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private String volume;
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private String edition;
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private String number;
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private String publisher;
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private String series;
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public String getIssue() {
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return issue;
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}
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public void setIssue(String issue) {
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this.issue = issue;
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}
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public String getStartPage() {
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return startPage;
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}
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public void setStartPage(String startPage) {
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this.startPage = startPage;
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}
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public String getEndPage() {
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return endPage;
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}
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public void setEndPage(String endPage) {
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this.endPage = endPage;
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}
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public String getVolume() {
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return volume;
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}
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public void setVolume(String volume) {
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this.volume = volume;
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}
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public String getEdition() {
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return edition;
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}
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public void setEdition(String edition) {
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this.edition = edition;
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}
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public String getNumber() {
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return number;
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}
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public void setNumber(String number) {
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this.number = number;
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}
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public String getPublisher() {
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return publisher;
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}
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public void setPublisher(String publisher) {
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this.publisher = publisher;
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}
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public String getSeries() {
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return series;
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}
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public void setSeries(String series) {
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this.series = series;
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}
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}
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package eu.dnetlib.dhp.skgif.model;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import java.io.Serializable;
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import java.util.List;
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/**
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* @author miriam.baglioni
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* @Date 01/09/23
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*/
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public class Contribution implements Serializable {
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private String person;
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@JsonProperty("declared_affiliations")
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private List<String> declaredAffiliation;
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private List<String> roles;
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private Integer rank;
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public String getPerson() {
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return person;
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}
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public void setPerson(String person) {
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this.person = person;
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}
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public List<String> getDeclaredAffiliation() {
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return declaredAffiliation;
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}
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public void setDeclaredAffiliation(List<String> declaredAffiliation) {
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this.declaredAffiliation = declaredAffiliation;
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}
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public List<String> getRoles() {
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return roles;
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}
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public void setRoles(List<String> roles) {
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this.roles = roles;
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}
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public Integer getRank() {
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return rank;
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}
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public void setRank(Integer rank) {
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this.rank = rank;
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}
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}
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package eu.dnetlib.dhp.skgif.model;
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import java.io.Serializable;
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/**
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* @author miriam.baglioni
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* @Date 01/09/23
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*/
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public class Dates implements Serializable {
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private String value;
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private String type;
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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 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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}
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package eu.dnetlib.dhp.skgif.model;
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import java.io.Serializable;
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/**
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* @author miriam.baglioni
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* @Date 01/09/23
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*/
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public class Identifier implements Serializable {
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private String scheme;
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private String value;
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public String getScheme() {
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return scheme;
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}
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public void setScheme(String scheme) {
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this.scheme = scheme;
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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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}
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package eu.dnetlib.dhp.skgif.model;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import java.io.Serializable;
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import java.net.URL;
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import java.util.List;
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/**
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* @author miriam.baglioni
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* @Date 01/09/23
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*/
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public class Manifestation implements Serializable {
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@JsonProperty("product_local_type")
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private String productLocalType;
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@JsonProperty("product_local_type_schema")
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private String productLocalTypeSchema;
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private List<Dates> dates;
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@JsonProperty("peer_review")
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private String peerReview;
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@JsonProperty("metadata_curation")
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private String metadataCuration;
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private URL url;
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private String pid;
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@JsonProperty("access_right")
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private String accessRight;
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private String licence;
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@JsonProperty("licance_schema")
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private String licenceSchema;
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private Biblio biblio;
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private String venue;
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@JsonProperty("hosting_datasource")
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private String hostingDatasource;
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public String getProductLocalType() {
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return productLocalType;
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}
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public void setProductLocalType(String productLocalType) {
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this.productLocalType = productLocalType;
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}
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public String getProductLocalTypeSchema() {
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return productLocalTypeSchema;
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}
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public void setProductLocalTypeSchema(String productLocalTypeSchema) {
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this.productLocalTypeSchema = productLocalTypeSchema;
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}
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public List<Dates> getDates() {
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return dates;
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}
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public void setDates(List<Dates> dates) {
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this.dates = dates;
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}
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public String getPeerReview() {
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return peerReview;
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}
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public void setPeerReview(String peerReview) {
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this.peerReview = peerReview;
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}
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public String getMetadataCuration() {
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return metadataCuration;
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}
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public void setMetadataCuration(String metadataCuration) {
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this.metadataCuration = metadataCuration;
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}
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public URL getUrl() {
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return url;
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}
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public void setUrl(URL url) {
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this.url = url;
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}
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public String getPid() {
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return pid;
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}
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public void setPid(String pid) {
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this.pid = pid;
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}
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public String getAccessRight() {
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return accessRight;
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}
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public void setAccessRight(String accessRight) {
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this.accessRight = accessRight;
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}
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public String getLicence() {
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return licence;
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}
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public void setLicence(String licence) {
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this.licence = licence;
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}
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public String getLicenceSchema() {
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return licenceSchema;
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}
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public void setLicenceSchema(String licenceSchema) {
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this.licenceSchema = licenceSchema;
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}
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public Biblio getBiblio() {
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return biblio;
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}
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public void setBiblio(Biblio biblio) {
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this.biblio = biblio;
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}
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public String getVenue() {
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return venue;
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}
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public void setVenue(String venue) {
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this.venue = venue;
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}
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public String getHostingDatasource() {
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return hostingDatasource;
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}
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public void setHostingDatasource(String hostingDatasource) {
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this.hostingDatasource = hostingDatasource;
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}
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}
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package eu.dnetlib.dhp.skgif.model;
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/**
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* @author miriam.baglioni
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* @Date 04/09/23
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*/
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public enum MetadataCuration {
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YES("yes"),
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NO("no"),
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UNAVAILABLE("unavailable");
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public final String label;
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private MetadataCuration(String label) {
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this.label = label;
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}
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}
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package eu.dnetlib.dhp.skgif.model;
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/**
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* @author miriam.baglioni
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* @Date 04/09/23
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*/
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public enum PeerReview {
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PEER_REVIEWED("peer reviewed"),
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NON_PEER_REVIEWED("open"),
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DOUBLE_BLIND("double-blind"),
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SINGLE_BLIND("single-blind"),
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UNAVAILABLE("unavailable");
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public final String label;
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private PeerReview(String label) {
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this.label = label;
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}
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}
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package eu.dnetlib.dhp.skgif.model;
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import org.codehaus.jackson.annotate.JsonProperty;
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import java.io.Serializable;
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import java.util.List;
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/**
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* @author miriam.baglioni
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* @Date 05/09/23
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*/
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public class Persons implements Serializable {
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@JsonProperty("local_identifier")
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private String localIdentifier;
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private List<Identifier> identifiers;
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@JsonProperty("given_name")
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private String givenName;
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@JsonProperty("family_name")
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private String familyName;
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private String agent;
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@JsonProperty("declared_affiliations")
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private List<Affiliation>declaredAffiliations;
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public String getLocalIdentifier() {
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return localIdentifier;
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}
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public void setLocalIdentifier(String localIdentifier) {
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this.localIdentifier = localIdentifier;
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}
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public List<Identifier> getIdentifiers() {
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return identifiers;
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}
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public void setIdentifiers(List<Identifier> identifiers) {
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this.identifiers = identifiers;
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}
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public String getGivenName() {
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return givenName;
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}
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public void setGivenName(String givenName) {
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this.givenName = givenName;
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}
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public String getFamilyName() {
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return familyName;
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}
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public void setFamilyName(String familyName) {
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this.familyName = familyName;
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}
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public String getAgent() {
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return agent;
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}
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public void setAgent(String agent) {
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this.agent = agent;
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}
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public List<Affiliation> getDeclaredAffiliations() {
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return declaredAffiliations;
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}
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public void setDeclaredAffiliations(List<Affiliation> declaredAffiliations) {
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this.declaredAffiliations = declaredAffiliations;
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}
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}
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package eu.dnetlib.dhp.skgif.model;
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import java.io.Serializable;
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/**
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* @author miriam.baglioni
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* @Date 01/09/23
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*/
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public class Provenance implements Serializable {
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private String type;
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private double trust;
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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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||||
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||||
public double getTrust() {
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||||
return trust;
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||||
}
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||||
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||||
public void setTrust(double trust) {
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||||
this.trust = trust;
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||||
}
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}
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package eu.dnetlib.dhp.skgif.model;
|
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|
||||
import java.io.Serializable;
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|
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/**
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* @author miriam.baglioni
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* @Date 05/09/23
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*/
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public enum RelationType implements Serializable {
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OUTCOME("outcome"),
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AFFILIATION("hasAuthorInstitution"),
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SUPPLEMENT("IsSupplementedBy"),
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DOCUMENTS("IsDocumentedBy"),
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PART("IsPartOf"),
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VERSION("IsNewVersioneOf");
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public final String label;
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private RelationType(String label) {
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this.label = label;
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}
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}
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package eu.dnetlib.dhp.skgif.model;
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import com.fasterxml.jackson.annotation.JsonProperty;
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|
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import java.io.Serializable;
|
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import java.util.List;
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||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 01/09/23
|
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*/
|
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public class Relations implements Serializable {
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@JsonProperty("relation_type")
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private String relationType;
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@JsonProperty("product_list")
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||||
private List<String> productList;
|
||||
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||||
public String getRelationType() {
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||||
return relationType;
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||||
}
|
||||
|
||||
public void setRelationType(String relationType) {
|
||||
this.relationType = relationType;
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}
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|
||||
public List<String> getProductList() {
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||||
return productList;
|
||||
}
|
||||
|
||||
public void setProductList(List<String> productList) {
|
||||
this.productList = productList;
|
||||
}
|
||||
}
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|
|
@ -0,0 +1,116 @@
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package eu.dnetlib.dhp.skgif.model;
|
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|
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import com.fasterxml.jackson.annotation.JsonProperty;
|
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|
||||
import java.io.Serializable;
|
||||
import java.util.List;
|
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|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 01/09/23
|
||||
*/
|
||||
public class ResearchProduct implements Serializable {
|
||||
@JsonProperty("local_identifier")
|
||||
private String localIdentifier;
|
||||
private List<Identifier> identifiers;
|
||||
private List<String> titles;
|
||||
private List<String> abstracts;
|
||||
@JsonProperty("product_type")
|
||||
private String productType;
|
||||
private List<Topic> topics;
|
||||
private List<Contribution> contributions;
|
||||
private List<Manifestation> manifestations;
|
||||
@JsonProperty("relevant_organizations")
|
||||
private List<String> relevantOrganizations;
|
||||
private List<String> funding;
|
||||
@JsonProperty("related_products")
|
||||
private List<Relations> relatedProducts;
|
||||
|
||||
public String getLocalIdentifier() {
|
||||
return localIdentifier;
|
||||
}
|
||||
|
||||
public void setLocalIdentifier(String localIdentifier) {
|
||||
this.localIdentifier = localIdentifier;
|
||||
}
|
||||
|
||||
public List<Identifier> getIdentifiers() {
|
||||
return identifiers;
|
||||
}
|
||||
|
||||
public void setIdentifiers(List<Identifier> identifiers) {
|
||||
this.identifiers = identifiers;
|
||||
}
|
||||
|
||||
public List<String> getTitles() {
|
||||
return titles;
|
||||
}
|
||||
|
||||
public void setTitles(List<String> titles) {
|
||||
this.titles = titles;
|
||||
}
|
||||
|
||||
public List<String> getAbstracts() {
|
||||
return abstracts;
|
||||
}
|
||||
|
||||
public void setAbstracts(List<String> abstracts) {
|
||||
this.abstracts = abstracts;
|
||||
}
|
||||
|
||||
public String getProductType() {
|
||||
return productType;
|
||||
}
|
||||
|
||||
public void setProductType(String productType) {
|
||||
this.productType = productType;
|
||||
}
|
||||
|
||||
public List<Topic> getTopics() {
|
||||
return topics;
|
||||
}
|
||||
|
||||
public void setTopics(List<Topic> topics) {
|
||||
this.topics = topics;
|
||||
}
|
||||
|
||||
public List<Contribution> getContributions() {
|
||||
return contributions;
|
||||
}
|
||||
|
||||
public void setContributions(List<Contribution> contributions) {
|
||||
this.contributions = contributions;
|
||||
}
|
||||
|
||||
public List<Manifestation> getManifestations() {
|
||||
return manifestations;
|
||||
}
|
||||
|
||||
public void setManifestations(List<Manifestation> manifestations) {
|
||||
this.manifestations = manifestations;
|
||||
}
|
||||
|
||||
public List<String> getRelevantOrganizations() {
|
||||
return relevantOrganizations;
|
||||
}
|
||||
|
||||
public void setRelevantOrganizations(List<String> relevantOrganizations) {
|
||||
this.relevantOrganizations = relevantOrganizations;
|
||||
}
|
||||
|
||||
public List<String> getFunding() {
|
||||
return funding;
|
||||
}
|
||||
|
||||
public void setFunding(List<String> funding) {
|
||||
this.funding = funding;
|
||||
}
|
||||
|
||||
public List<Relations> getRelatedProducts() {
|
||||
return relatedProducts;
|
||||
}
|
||||
|
||||
public void setRelatedProducts(List<Relations> relatedProducts) {
|
||||
this.relatedProducts = relatedProducts;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
package eu.dnetlib.dhp.skgif.model;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 01/09/23
|
||||
*/
|
||||
public enum ResearchTypes {
|
||||
LITERATURE("literature"),
|
||||
RESEARCH_DATA("research data"),
|
||||
RESEARCH_SOFTWARE("research software"),
|
||||
OTHER("other");
|
||||
|
||||
public final String label;
|
||||
|
||||
private ResearchTypes(String label) {
|
||||
this.label = label;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,28 @@
|
|||
package eu.dnetlib.dhp.skgif.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 01/09/23
|
||||
*/
|
||||
public class Topic implements Serializable {
|
||||
private String topic;
|
||||
private Provenance provenance;
|
||||
|
||||
public String getTopic() {
|
||||
return topic;
|
||||
}
|
||||
|
||||
public void setTopic(String topic) {
|
||||
this.topic = topic;
|
||||
}
|
||||
|
||||
public Provenance getProvenance() {
|
||||
return provenance;
|
||||
}
|
||||
|
||||
public void setProvenance(Provenance provenance) {
|
||||
this.provenance = provenance;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.common;
|
||||
package eu.dnetlib.dhp.common;
|
||||
|
||||
import java.io.BufferedInputStream;
|
||||
import java.io.IOException;
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi;
|
||||
package eu.dnetlib.dhp.common.zenodoapi;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi;
|
||||
package eu.dnetlib.dhp.common.zenodoapi;
|
||||
|
||||
public class MissingConceptDoiException extends Throwable {
|
||||
public MissingConceptDoiException(String message) {
|
||||
|
|
@ -1,31 +1,20 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi;
|
||||
package eu.dnetlib.dhp.common.zenodoapi;
|
||||
|
||||
import java.io.*;
|
||||
import java.net.HttpURLConnection;
|
||||
import java.net.URI;
|
||||
import java.net.URL;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
import org.apache.http.HttpHeaders;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
import org.apache.http.client.methods.HttpPost;
|
||||
import org.apache.http.client.methods.HttpPut;
|
||||
import org.apache.http.client.utils.URIBuilder;
|
||||
import org.apache.http.entity.ContentType;
|
||||
import org.apache.http.entity.InputStreamEntity;
|
||||
import org.apache.http.entity.StringEntity;
|
||||
import org.apache.http.impl.client.CloseableHttpClient;
|
||||
// import org.apache.http.impl.client.HttpClients;
|
||||
import org.apache.http.util.EntityUtils;
|
||||
import org.jetbrains.annotations.NotNull;
|
||||
|
||||
import com.google.gson.Gson;
|
||||
|
||||
import eu.dnetlib.dhp.oa.zenodoapi.model.ZenodoModel;
|
||||
import eu.dnetlib.dhp.oa.zenodoapi.model.ZenodoModelList;
|
||||
import eu.dnetlib.dhp.common.zenodoapi.model.ZenodoModel;
|
||||
import eu.dnetlib.dhp.common.zenodoapi.model.ZenodoModelList;
|
||||
import okhttp3.*;
|
||||
|
||||
public class ZenodoAPIClient implements Serializable {
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi.model;
|
||||
package eu.dnetlib.dhp.common.zenodoapi.model;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi.model;
|
||||
package eu.dnetlib.dhp.common.zenodoapi.model;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi.model;
|
||||
package eu.dnetlib.dhp.common.zenodoapi.model;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi.model;
|
||||
package eu.dnetlib.dhp.common.zenodoapi.model;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi.model;
|
||||
package eu.dnetlib.dhp.common.zenodoapi.model;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi.model;
|
||||
package eu.dnetlib.dhp.common.zenodoapi.model;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi.model;
|
||||
package eu.dnetlib.dhp.common.zenodoapi.model;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi.model;
|
||||
package eu.dnetlib.dhp.common.zenodoapi.model;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi.model;
|
||||
package eu.dnetlib.dhp.common.zenodoapi.model;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.zenodoapi.model;
|
||||
package eu.dnetlib.dhp.common.zenodoapi.model;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
|
|
@ -15,7 +15,7 @@ import org.slf4j.Logger;
|
|||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.common.MakeTarArchive;
|
||||
import eu.dnetlib.dhp.common.MakeTarArchive;
|
||||
|
||||
public class MakeTar implements Serializable {
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,126 @@
|
|||
package eu.dnetlib.dhp.skgif;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.skgif.model.RelationType;
|
||||
import eu.dnetlib.dhp.skgif.model.Relations;
|
||||
import eu.dnetlib.dhp.skgif.model.ResearchProduct;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.api.java.function.MapGroupsFunction;
|
||||
import org.apache.spark.sql.*;
|
||||
import org.apache.spark.sql.types.StructType;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import scala.Tuple2;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.*;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 05/09/23
|
||||
*/
|
||||
public class ExtendResult implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(ExtendResult.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
PrepareResultRelation.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/dump/extend_result_parameters.json"));
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
|
||||
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
extendResult(spark, inputPath, outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static void extendResult(SparkSession spark, String inputPath, String outputPath) {
|
||||
ObjectMapper mapper = new ObjectMapper();
|
||||
Dataset<ResearchProduct> result = spark.read().json(inputPath + "/result")
|
||||
.as(Encoders.bean(ResearchProduct.class));
|
||||
final StructType structureSchema = new StructType()
|
||||
.fromDDL("`resultId` STRING, `target` STRING, `resultClass` STRING");
|
||||
|
||||
Dataset<Row> relations = spark
|
||||
.read()
|
||||
.schema(structureSchema)
|
||||
.json(inputPath + "/preparedRelations");
|
||||
|
||||
result.joinWith(relations, result.col("localIdentifier")
|
||||
.equalTo(relations.col("resultId")), "left")
|
||||
.groupByKey((MapFunction<Tuple2<ResearchProduct, Row>, String>)t2 -> t2._1().getLocalIdentifier(),Encoders.STRING() )
|
||||
.mapGroups((MapGroupsFunction<String, Tuple2<ResearchProduct, Row>, ResearchProduct>) (key,it) -> {
|
||||
Tuple2<ResearchProduct, Row> first = it.next();
|
||||
ResearchProduct rp = first._1();
|
||||
addRels(rp, first._2());
|
||||
it.forEachRemaining(t2 -> addRels(rp, t2._2()));
|
||||
return rp;
|
||||
}, Encoders.bean(ResearchProduct.class))
|
||||
.map((MapFunction<ResearchProduct, String>) r -> mapper.writeValueAsString(r), Encoders.STRING())
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.text(outputPath);
|
||||
|
||||
}
|
||||
|
||||
private static void addRels(ResearchProduct rp, Row row) {
|
||||
String relClass = row.getAs("relClass");
|
||||
Map<String, List<String>> relations = new HashMap<>();
|
||||
if(relClass.equals(RelationType.OUTCOME.label)){
|
||||
if(!Optional.ofNullable(rp.getFunding()).isPresent()){
|
||||
rp.setFunding(new ArrayList<>());
|
||||
}
|
||||
rp.getFunding().add(row.getAs("target"));
|
||||
}else if(relClass.equals(RelationType.AFFILIATION)){
|
||||
if(!Optional.ofNullable(rp.getRelevantOrganizations()).isPresent())
|
||||
rp.setRelevantOrganizations(new ArrayList<>());
|
||||
rp.getRelevantOrganizations().add(row.getAs("target"));
|
||||
}else{
|
||||
if(!relations.containsKey(relClass)){
|
||||
relations.put(relClass, new ArrayList<>());
|
||||
}
|
||||
relations.get(relClass).add(row.getAs("target"));
|
||||
}
|
||||
if(relations.size() > 0) {
|
||||
rp.setRelatedProducts(new ArrayList<>());
|
||||
for (String key: relations.keySet()){
|
||||
Relations rel = new Relations();
|
||||
rel.setRelationType(key);
|
||||
rel.setProductList(relations.get(key));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,93 @@
|
|||
package eu.dnetlib.dhp.skgif;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.sql.*;
|
||||
import org.apache.spark.sql.types.StructType;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import java.io.Serializable;
|
||||
import java.util.*;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 04/09/23
|
||||
*/
|
||||
public class PrepareResultRelation implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(PrepareResultRelation.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
PrepareResultRelation.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/dump/result_relation_parameters.json"));
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
prepareResultRelationList(spark, inputPath, outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static void prepareResultRelationList(SparkSession spark, String inputPath, String outputPath) {
|
||||
final StructType structureSchema = new StructType()
|
||||
.fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>");
|
||||
Dataset<Relation> relation = spark.read().json(inputPath).as(Encoders.bean(Relation.class))
|
||||
.filter("dataInfo.deletedbyinference != true and dataInfo.invisible != true")
|
||||
.filter("relClass == 'hasAuthorInstitution' or relClass == 'outcome' or " +
|
||||
"relClass == 'IsSupplementedBy' or relClass == 'IsDocumentedBy' or relClass == 'IsPartOf' " +
|
||||
"relClass == IsNewVersionOf");
|
||||
|
||||
org.apache.spark.sql.Dataset<Row> df = spark.createDataFrame(new ArrayList<Row>(), structureSchema);
|
||||
List<String> entities = Arrays
|
||||
.asList(
|
||||
"publication", "dataset", "otherresearchproduct", "software");
|
||||
for (String e : entities)
|
||||
df = df
|
||||
.union(
|
||||
spark
|
||||
.read()
|
||||
.schema(structureSchema)
|
||||
.json(inputPath + "/" + e)
|
||||
.filter("dataInfo.deletedbyinference != true and dataInfo.invisible != true"));
|
||||
|
||||
relation.joinWith(df, relation.col("source").equalTo(df.col("id")))
|
||||
.select(
|
||||
new Column("id").as("resultId"),
|
||||
new Column("target"),
|
||||
new Column("relClass"))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.json(outputPath);
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,282 @@
|
|||
package eu.dnetlib.dhp.skgif;
|
||||
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.dump.csv.AuthorResult;
|
||||
import eu.dnetlib.dhp.oa.model.ResultPid;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.skgif.exception.NoAllowedTypeException;
|
||||
import eu.dnetlib.dhp.skgif.exception.NoTitleFoundException;
|
||||
import eu.dnetlib.dhp.skgif.model.*;
|
||||
import eu.dnetlib.dhp.skgif.model.AccessRight;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import scala.Tuple2;
|
||||
import scala.reflect.internal.Trees;
|
||||
|
||||
import javax.management.RuntimeErrorException;
|
||||
import java.io.Serializable;
|
||||
import java.net.MalformedURLException;
|
||||
import java.net.URL;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static eu.dnetlib.dhp.oa.graph.dump.ResultMapper.*;
|
||||
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 01/09/23
|
||||
*/
|
||||
public class ResultMapper implements Serializable {
|
||||
|
||||
public static <E extends Result> ResearchProduct map(
|
||||
E input)
|
||||
throws Exception{
|
||||
|
||||
ResearchProduct out = new ResearchProduct();
|
||||
|
||||
Optional<Qualifier> ort = Optional.ofNullable(input.getResulttype());
|
||||
if (ort.isPresent()) {
|
||||
try {
|
||||
out.setLocalIdentifier(input.getId());
|
||||
mapPid(out, input);
|
||||
mapTitle(out, input);
|
||||
mapAbstract(out, input);
|
||||
mapType(out, input);
|
||||
mapTopic(out, input);
|
||||
mapContribution(out, input);
|
||||
|
||||
if(!Optional.ofNullable(out.getTitles()).isPresent() ||
|
||||
!Optional.ofNullable(out.getContributions()).isPresent())
|
||||
return null;
|
||||
//TODO map the manifestation directly from the instances
|
||||
//it is not completed
|
||||
mapManifestation(out, input);
|
||||
|
||||
|
||||
//TODO extend the mapping to consider relations between these entities and the results
|
||||
// private List<String> relevantOrganizations;
|
||||
// private List<String> funding;
|
||||
// private List<Relations> relatedProducts;
|
||||
|
||||
} catch (ClassCastException cce) {
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
return null;
|
||||
|
||||
}
|
||||
|
||||
private static <E extends Result> void mapManifestation(ResearchProduct out, E input) {
|
||||
out.setManifestations( input.getInstance().stream().parallel()
|
||||
.map(i -> {
|
||||
try {
|
||||
return getManifestation(i);
|
||||
} catch (MalformedURLException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}).collect(Collectors.toList()));
|
||||
}
|
||||
|
||||
private static Manifestation getManifestation(Instance i) throws MalformedURLException {
|
||||
Manifestation manifestation = new Manifestation();
|
||||
manifestation.setProductLocalType(i.getInstancetype().getClassname());
|
||||
manifestation.setProductLocalTypeSchema(i.getInstancetype().getSchemename());
|
||||
Dates dates = new Dates();
|
||||
dates.setType("publishing");
|
||||
dates.setValue(i.getDateofacceptance().getValue());
|
||||
manifestation.setDates(Arrays.asList(dates));
|
||||
switch(i.getRefereed().getClassid()){
|
||||
case "0000":
|
||||
manifestation.setPeerReview(PeerReview.UNAVAILABLE.label);
|
||||
break;
|
||||
case "0001":
|
||||
manifestation.setPeerReview(PeerReview.PEER_REVIEWED.label);
|
||||
break;
|
||||
case "0002":
|
||||
manifestation.setPeerReview(PeerReview.NON_PEER_REVIEWED.label);
|
||||
break;
|
||||
}
|
||||
manifestation.setMetadataCuration(MetadataCuration.UNAVAILABLE.label);
|
||||
//TODO filter out the URL that refer to pids. If nothing remains, decide what to do
|
||||
manifestation.setUrl(new URL(i.getUrl().get(0)));
|
||||
if(Optional.ofNullable(i.getPid()).isPresent()){
|
||||
manifestation.setPid(i.getPid().get(0).getValue());
|
||||
}
|
||||
switch(i.getAccessright().getClassid()){
|
||||
case"OPEN":
|
||||
case"OPEN DATA":
|
||||
case "OPEN SOURCE":
|
||||
manifestation.setAccessRight(AccessRight.OPEN.label);
|
||||
break;
|
||||
case "CLOSED":
|
||||
manifestation.setAccessRight(AccessRight.CLOSED.label);
|
||||
break;
|
||||
case "RESTRICTED":
|
||||
manifestation.setAccessRight(AccessRight.RESTRICTED.label);
|
||||
break;
|
||||
case"EMBARGO":
|
||||
case "12MONTHS":
|
||||
case "6MONTHS":
|
||||
manifestation.setAccessRight(AccessRight.EMBARGO.label);
|
||||
break;
|
||||
default:
|
||||
manifestation.setAccessRight(AccessRight.UNAVAILABLE.label);
|
||||
}
|
||||
if(Optional.ofNullable(i.getLicense()).isPresent())
|
||||
manifestation.setLicence(i.getLicense().getValue());
|
||||
//TODO to fill the biblio in case it is a journal, we need to join with the datasource and verify the type
|
||||
Biblio biblio = null;
|
||||
manifestation.setHostingDatasource(i.getHostedby().getKey());
|
||||
//TODO verify if the result is published in ojournal or conferences. In that case the venue is the identifier
|
||||
//of the journal/conference. In case it is not, the venue is the datasource
|
||||
if(biblio == null){
|
||||
manifestation.setVenue(i.getHostedby().getKey());
|
||||
}else{
|
||||
manifestation.setVenue("insert the id of the venue");
|
||||
}
|
||||
return manifestation;
|
||||
}
|
||||
|
||||
private static Tuple2<String, Boolean> getOrcid(List<StructuredProperty> pid) {
|
||||
if (!Optional.ofNullable(pid).isPresent())
|
||||
return null;
|
||||
if (pid.size() == 0)
|
||||
return null;
|
||||
for (StructuredProperty p : pid) {
|
||||
if (p.getQualifier().getClassid().equals(ModelConstants.ORCID)) {
|
||||
return new Tuple2<>(p.getValue(), Boolean.TRUE);
|
||||
}
|
||||
}
|
||||
for (StructuredProperty p : pid) {
|
||||
if (p.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING)) {
|
||||
return new Tuple2<>(p.getValue(), Boolean.FALSE);
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
private static <E extends Result> void mapContribution(ResearchProduct out, E input) {
|
||||
if(Optional.ofNullable(input.getAuthor()).isPresent()){
|
||||
int count = 0;
|
||||
for (Author a : input.getAuthor()) {
|
||||
count += 1;
|
||||
Contribution contribution = new Contribution();
|
||||
if(Optional.ofNullable(a.getPid()).isPresent()){
|
||||
Tuple2<String, Boolean> orcid = getOrcid(a.getPid());
|
||||
if(orcid != null){
|
||||
contribution.setPerson(DHPUtils.md5(orcid._1() + orcid._2()));
|
||||
}else{
|
||||
if(Optional.ofNullable(a.getRank()).isPresent()){
|
||||
contribution.setPerson(DHPUtils.md5(input.getId() + a.getRank()));
|
||||
}else{
|
||||
contribution.setPerson(DHPUtils.md5(input.getId() + count));
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// "contributions": [
|
||||
// {
|
||||
// "person": "person_123",
|
||||
// "declared_affiliations": ["org_1", "org_3"],
|
||||
// "rank": 1,
|
||||
// "roles": ["writing-original-draft", "conceptualization"]
|
||||
// }
|
||||
// ]
|
||||
}
|
||||
|
||||
private static <E extends Result> void mapTopic(ResearchProduct out, E input) {
|
||||
if(Optional.ofNullable(input.getSubject()).isPresent()){
|
||||
out.setTopics(input.getSubject().stream().parallel().map(s -> {
|
||||
Topic topic = new Topic();
|
||||
topic.setTopic(getIdentifier(s));
|
||||
Provenance provenance = new Provenance();
|
||||
provenance.setTrust(Double.valueOf(s.getDataInfo().getTrust()));
|
||||
provenance.setType(s.getDataInfo().getInferenceprovenance());
|
||||
topic.setProvenance(provenance);
|
||||
return topic;
|
||||
}).collect(Collectors.toList()));
|
||||
}
|
||||
}
|
||||
|
||||
private static String getIdentifier(StructuredProperty s) {
|
||||
return DHPUtils.md5(s.getQualifier().getClassid() + s.getValue());
|
||||
}
|
||||
|
||||
private static <E extends Result> void mapType(ResearchProduct out, E input) throws NoAllowedTypeException{
|
||||
switch (input.getResulttype().getClassid()){
|
||||
case "publication":
|
||||
out.setProductType(ResearchTypes.LITERATURE.label);
|
||||
break;
|
||||
case"dataset":
|
||||
out.setProductType(ResearchTypes.RESEARCH_DATA.label);
|
||||
break;
|
||||
case"software":
|
||||
out.setProductType(ResearchTypes.RESEARCH_SOFTWARE.label);
|
||||
break;
|
||||
case"other":
|
||||
out.setProductType(ResearchTypes.OTHER.label);
|
||||
break;
|
||||
default:
|
||||
throw new ClassCastException("Result type not present or not allowed");
|
||||
}
|
||||
}
|
||||
|
||||
private static void mapPid(ResearchProduct out, Result input) {
|
||||
Optional
|
||||
.ofNullable(input.getPid())
|
||||
.ifPresent(
|
||||
value -> out
|
||||
.setIdentifiers(
|
||||
value
|
||||
.stream()
|
||||
.map(
|
||||
p -> {
|
||||
Identifier identifier = new Identifier();
|
||||
identifier.setValue(p.getValue());
|
||||
identifier.setScheme(p.getQualifier().getSchemeid());
|
||||
return identifier;
|
||||
})
|
||||
.collect(Collectors.toList())));
|
||||
}
|
||||
|
||||
private static void mapTitle(ResearchProduct out, Result input) throws NoTitleFoundException {
|
||||
Optional<List<StructuredProperty>> otitle = Optional.ofNullable(input.getTitle());
|
||||
if (otitle.isPresent()) {
|
||||
List<StructuredProperty> iTitle = otitle
|
||||
.get()
|
||||
.stream()
|
||||
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
|
||||
.collect(Collectors.toList());
|
||||
if (!iTitle.isEmpty()) {
|
||||
out.setTitles(Arrays.asList(iTitle.get(0).getValue()));
|
||||
return;
|
||||
}
|
||||
|
||||
iTitle = otitle
|
||||
.get()
|
||||
.stream()
|
||||
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
|
||||
.collect(Collectors.toList());
|
||||
if (!iTitle.isEmpty()) {
|
||||
out.setTitles(Arrays.asList(iTitle.get(0).getValue()));
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
private static void mapAbstract(ResearchProduct out, Result input) {
|
||||
final List<String> descriptionList = new ArrayList<>();
|
||||
Optional
|
||||
.ofNullable(input.getDescription())
|
||||
.ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue())));
|
||||
out.setAbstracts(descriptionList);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
|
||||
package eu.dnetlib.dhp.skgif.exception;
|
||||
|
||||
public class NoAllowedTypeException extends Exception {
|
||||
public NoAllowedTypeException() {
|
||||
super();
|
||||
}
|
||||
|
||||
public NoAllowedTypeException(
|
||||
final String message,
|
||||
final Throwable cause,
|
||||
final boolean enableSuppression,
|
||||
final boolean writableStackTrace) {
|
||||
super(message, cause, enableSuppression, writableStackTrace);
|
||||
}
|
||||
|
||||
public NoAllowedTypeException(final String message, final Throwable cause) {
|
||||
super(message, cause);
|
||||
}
|
||||
|
||||
public NoAllowedTypeException(final String message) {
|
||||
super(message);
|
||||
}
|
||||
|
||||
public NoAllowedTypeException(final Throwable cause) {
|
||||
super(cause);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
|
||||
package eu.dnetlib.dhp.skgif.exception;
|
||||
|
||||
public class NoTitleFoundException extends Exception {
|
||||
public NoTitleFoundException() {
|
||||
super();
|
||||
}
|
||||
|
||||
public NoTitleFoundException(
|
||||
final String message,
|
||||
final Throwable cause,
|
||||
final boolean enableSuppression,
|
||||
final boolean writableStackTrace) {
|
||||
super(message, cause, enableSuppression, writableStackTrace);
|
||||
}
|
||||
|
||||
public NoTitleFoundException(final String message, final Throwable cause) {
|
||||
super(message, cause);
|
||||
}
|
||||
|
||||
public NoTitleFoundException(final String message) {
|
||||
super(message);
|
||||
}
|
||||
|
||||
public NoTitleFoundException(final Throwable cause) {
|
||||
super(cause);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -17,8 +17,8 @@ import org.junit.jupiter.api.Test;
|
|||
import com.google.gson.Gson;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
|
||||
import eu.dnetlib.dhp.oa.zenodoapi.MissingConceptDoiException;
|
||||
import eu.dnetlib.dhp.oa.zenodoapi.ZenodoAPIClient;
|
||||
import eu.dnetlib.dhp.common.zenodoapi.MissingConceptDoiException;
|
||||
import eu.dnetlib.dhp.common.zenodoapi.ZenodoAPIClient;
|
||||
|
||||
@Disabled
|
||||
public class ZenodoUploadTest {
|
||||
|
|
|
|||
Loading…
Reference in New Issue