joining entities using T x R x S method with groupByKey
This commit is contained in:
parent
1cd6899480
commit
799929c1e3
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@ -5,7 +5,7 @@
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<parent>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp</artifactId>
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<version>1.1.5-SNAPSHOT</version>
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<version>1.0.5-SNAPSHOT</version>
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<relativePath>../</relativePath>
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</parent>
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@ -1,118 +0,0 @@
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package eu.dnetlib.dhp.schema.dli;
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import java.io.Serializable;
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import java.util.List;
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public class Entity implements Serializable {
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private String identifier;
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private List<Pid> pid;
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private List<String> title;
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private List<String> date;
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private String typology;
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private List<String> authors;
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private List<Subject> subject;
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private String description;
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private String completionStatus;
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private List<Provenance> collectedFrom;
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private List<String> publisher;
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public String getIdentifier() {
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return identifier;
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}
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public void setIdentifier(String identifier) {
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this.identifier = identifier;
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}
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public List<Pid> getPid() {
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return pid;
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}
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public void setPid(List<Pid> pid) {
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this.pid = pid;
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}
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public List<String> getTitle() {
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return title;
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}
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public void setTitle(List<String> title) {
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this.title = title;
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}
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public List<String> getDate() {
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return date;
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}
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public void setDate(List<String> date) {
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this.date = date;
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}
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public String getTypology() {
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return typology;
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}
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public void setTypology(String typology) {
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this.typology = typology;
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}
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public List<String> getAuthors() {
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return authors;
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}
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public void setAuthors(List<String> authors) {
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this.authors = authors;
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}
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public List<Subject> getSubject() {
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return subject;
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}
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public void setSubject(List<Subject> subject) {
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this.subject = subject;
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}
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public String getDescription() {
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return description;
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}
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public void setDescription(String description) {
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this.description = description;
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}
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public List<Provenance> getCollectedFrom() {
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return collectedFrom;
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}
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public void setCollectedFrom(List<Provenance> collectedFrom) {
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this.collectedFrom = collectedFrom;
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}
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public List<String> getPublisher() {
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return publisher;
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}
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public void setPublisher(List<String> publisher) {
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this.publisher = publisher;
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}
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public String getCompletionStatus() {
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return completionStatus;
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}
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public void setCompletionStatus(String completionStatus) {
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this.completionStatus = completionStatus;
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}
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}
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@ -1,33 +0,0 @@
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package eu.dnetlib.dhp.schema.dli;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import org.apache.commons.lang3.StringUtils;
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public class Pid {
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private String pid;
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private String pidType;
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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 getPidType() {
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return pidType;
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}
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public void setPidType(String pidType) {
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this.pidType = pidType;
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}
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public String generateId() {
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if(StringUtils.isEmpty(pid) || StringUtils.isEmpty(pidType))
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return null;
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return DHPUtils.md5(String.format("%s::%s", pid, pidType));
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}
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}
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@ -1,35 +0,0 @@
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package eu.dnetlib.dhp.schema.dli;
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public class Provenance {
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private String datasourceId;
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private String datasourceName;
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private String completionStatus;
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public String getDatasourceId() {
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return datasourceId;
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}
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public void setDatasourceId(String datasourceId) {
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this.datasourceId = datasourceId;
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}
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public String getDatasourceName() {
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return datasourceName;
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}
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public void setDatasourceName(String datasourceName) {
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this.datasourceName = datasourceName;
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}
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public String getCompletionStatus() {
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return completionStatus;
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}
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public void setCompletionStatus(String completionStatus) {
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this.completionStatus = completionStatus;
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}
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}
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@ -1,47 +0,0 @@
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package eu.dnetlib.dhp.schema.dli;
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import java.io.Serializable;
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import java.util.List;
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public class Relation implements Serializable {
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private String source;
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private String target;
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private List<Provenance> provenance;
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private RelationSemantic semantic;
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public String getSource() {
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return source;
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}
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public void setSource(String source) {
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this.source = source;
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}
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public String getTarget() {
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return target;
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}
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public void setTarget(String target) {
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this.target = target;
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}
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public List<Provenance> getProvenance() {
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return provenance;
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}
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public void setProvenance(List<Provenance> provenance) {
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this.provenance = provenance;
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}
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public RelationSemantic getSemantic() {
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return semantic;
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}
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public void setSemantic(RelationSemantic semantic) {
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this.semantic = semantic;
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}
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}
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@ -1,16 +0,0 @@
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package eu.dnetlib.dhp.schema.dli;
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import java.io.Serializable;
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public class RelationSemantic extends Subject implements Serializable {
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public String inverse;
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public String getInverse() {
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return inverse;
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}
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public void setInverse(String inverse) {
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this.inverse = inverse;
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}
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}
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@ -1,35 +0,0 @@
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package eu.dnetlib.dhp.schema.dli;
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import java.io.Serializable;
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public class Subject implements Serializable {
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private String schema;
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private String value;
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public Subject() {
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}
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public Subject(String schema, String value) {
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this.schema = schema;
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this.value = value;
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}
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public String getSchema() {
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return schema;
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}
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public void setSchema(String schema) {
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this.schema = schema;
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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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@ -1,5 +1,4 @@
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sparkDriverMemory=7G
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sparkExecutorMemory=7G
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sparkExecutorMemoryOverhead=5G
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hive_db_name=claudio
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sourcePath=/tmp/db_openaireplus_services_beta.export.2019.11.06
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<groupId>org.apache.spark</groupId>
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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>com.jayway.jsonpath</groupId>
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<artifactId>json-path</artifactId>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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@ -1,4 +0,0 @@
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package eu.dnetlib.dhp.graph;
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public class EntityNode {
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}
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@ -1,20 +1,30 @@
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package eu.dnetlib.dhp.graph;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import java.io.Serializable;
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public class EntityRelEntity implements Serializable {
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private TypedRow source;
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private Relation relation;
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private TypedRow relation;
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private TypedRow target;
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public EntityRelEntity() {
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}
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public EntityRelEntity(TypedRow source) {
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this.source = source;
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}
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//helpers
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public Boolean hasMainEntity() {
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return getSource() != null & getRelation() == null & getTarget() == null;
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}
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public Boolean hasRelatedEntity() {
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return getSource() == null & getRelation() != null & getTarget() != null;
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}
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public TypedRow getSource() {
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return source;
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}
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@ -24,11 +34,11 @@ public class EntityRelEntity implements Serializable {
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return this;
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}
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public Relation getRelation() {
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public TypedRow getRelation() {
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return relation;
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}
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public EntityRelEntity setRelation(Relation relation) {
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public EntityRelEntity setRelation(TypedRow relation) {
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this.relation = relation;
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return this;
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}
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@ -42,12 +52,4 @@ public class EntityRelEntity implements Serializable {
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return this;
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}
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@Override
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public String toString() {
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try {
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return new ObjectMapper().writeValueAsString(this);
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} catch (JsonProcessingException e) {
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throw new RuntimeException(e);
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}
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}
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}
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@ -1,139 +1,119 @@
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package eu.dnetlib.dhp.graph;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.*;
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import com.google.common.collect.Iterables;
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import com.google.common.collect.Lists;
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import com.jayway.jsonpath.JsonPath;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.Optional;
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import org.apache.spark.api.java.function.PairFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import scala.Tuple2;
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import java.io.Serializable;
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import java.util.List;
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public class GraphJoiner implements Serializable {
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public static final int MAX_RELS = 100;
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public static final int MAX_RELS = 10;
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public void join(final SparkSession spark, final String inputPath, final String hiveDbName, final String outPath) {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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/*
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JavaPairRDD<String, TypedRow> entities = sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class))
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.map(oaf -> new TypedRow("publication", oaf))
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.mapToPair(toPair());
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final String entityIdPath = "$.id";
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*/
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JavaPairRDD<String, TypedRow> datasource = readPathEntity(sc, entityIdPath, inputPath, "datasource");
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JavaPairRDD<String, TypedRow> organization = readPathEntity(sc, entityIdPath, inputPath, "organization");
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JavaPairRDD<String, TypedRow> project = readPathEntity(sc, entityIdPath, inputPath, "project");
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JavaPairRDD<String, TypedRow> dataset = readPathEntity(sc, entityIdPath, inputPath, "dataset");
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JavaPairRDD<String, TypedRow> otherresearchproduct = readPathEntity(sc, entityIdPath, inputPath, "otherresearchproduct");
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JavaPairRDD<String, TypedRow> software = readPathEntity(sc, entityIdPath, inputPath, "software");
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JavaPairRDD<String, TypedRow> publication = readPathEntity(sc, entityIdPath, inputPath, "publication");
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JavaPairRDD<String, TypedRow> entities = sc.sequenceFile(inputPath + "/datasource", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Datasource.class))
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.map(oaf -> new TypedRow("datasource", oaf))
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.mapToPair(toPair())
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.union(sc.sequenceFile(inputPath + "/organization", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Organization.class))
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.map(oaf -> new TypedRow("organization", oaf))
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.mapToPair(toPair()))
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.union(sc.sequenceFile(inputPath + "/project", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Project.class))
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.map(oaf -> new TypedRow("project", oaf))
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.mapToPair(toPair()))
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.union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class))
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.map(oaf -> new TypedRow("dataset", oaf))
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.mapToPair(toPair()))
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.union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class))
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.map(oaf -> new TypedRow("otherresearchproduct", oaf))
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.mapToPair(toPair()))
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.union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class))
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.map(oaf -> new TypedRow("software", oaf))
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.mapToPair(toPair()));
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/*
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.union(sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class))
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.map(oaf -> new TypedRow("publication", oaf))
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.mapToPair(toPair()));
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final String entitiesPath = outPath + "/entities";
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datasource
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.union(organization)
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.union(project)
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.union(dataset)
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.union(otherresearchproduct)
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.union(software)
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.union(publication)
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.map(e -> new EntityRelEntity().setSource(e._2()))
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.map(e -> new ObjectMapper().writeValueAsString(e))
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.saveAsTextFile(entitiesPath, GzipCodec.class);
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*/
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JavaPairRDD<String, EntityRelEntity> entities = sc.textFile(entitiesPath)
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.map(t -> new ObjectMapper().readValue(t, EntityRelEntity.class))
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.mapToPair(t -> new Tuple2<>(t.getSource().getSource(), t));
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/*
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JavaRDD<Relation> rels = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class))
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.map(oaf -> new TypedRow("relation", oaf))
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.mapToPair(toPair())
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final JavaPairRDD<String, EntityRelEntity> relation = readPathRelation(sc, inputPath)
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.map(p -> new EntityRelEntity().setRelation(p))
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.mapToPair(p -> new Tuple2<>(p.getRelation().getSource(), p))
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.groupByKey()
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.map(t -> Iterables.limit(t._2(), MAX_RELS))
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.flatMap(t -> t.iterator())
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.map(t -> (Relation) t.getOaf());
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.map(p -> Iterables.limit(p._2(), MAX_RELS))
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.flatMap(p -> p.iterator())
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.mapToPair(p -> new Tuple2<>(p.getRelation().getTarget(), p));
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spark.createDataset(rels.rdd(), Encoders.bean(Relation.class))
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.write()
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.mode(SaveMode.Overwrite)
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.saveAsTable(hiveDbName + ".relation_100");
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*/
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final String joinByTargetPath = outPath + "/join_by_target";
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relation.join(entities)
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.map(s -> new EntityRelEntity()
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.setRelation(s._2()._1().getRelation())
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.setTarget(s._2()._2().getSource()))
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.map(e -> new ObjectMapper().writeValueAsString(e))
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.saveAsTextFile(joinByTargetPath, GzipCodec.class);
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JavaPairRDD<String, TypedRow> bounded_rels = spark.table(hiveDbName + ".relation_" + MAX_RELS)
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.as(Encoders.bean(Relation.class))
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.javaRDD()
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.map(r -> new TypedRow("relation", r))
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.mapToPair(toPair());
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// build the adjacency list: e -> r
|
||||
JavaPairRDD<String, Tuple2<TypedRow, Optional<TypedRow>>> adjacency_list = entities.leftOuterJoin(bounded_rels);
|
||||
JavaPairRDD<String, EntityRelEntity> bySource = sc.textFile(joinByTargetPath)
|
||||
.map(t -> new ObjectMapper().readValue(t, EntityRelEntity.class))
|
||||
.mapToPair(t -> new Tuple2<>(t.getRelation().getSource(), t));
|
||||
|
||||
JavaRDD<EntityRelEntity> linked_entities = adjacency_list
|
||||
.mapToPair(toPairTarget()) // make rel.targetid explicit so that we can join it
|
||||
.leftOuterJoin(entities) // again with the entities to get the target entity
|
||||
.map(l -> toEntityRelEntity(l)); // and map it to a more readable representation
|
||||
|
||||
spark.createDataFrame(linked_entities, EntityRelEntity.class)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.saveAsTable(hiveDbName + ".linked_entities");
|
||||
entities
|
||||
.union(bySource)
|
||||
.groupByKey() // by source id
|
||||
.map(p -> {
|
||||
final LinkedEntity e = new LinkedEntity();
|
||||
final List<Tuple> links = Lists.newArrayList();
|
||||
for(EntityRelEntity rel : p._2()) {
|
||||
if (rel.hasMainEntity() & e.getEntity() == null) {
|
||||
e.setEntity(rel.getSource());
|
||||
}
|
||||
if (rel.hasRelatedEntity()) {
|
||||
links.add(new Tuple()
|
||||
.setRelation(rel.getRelation())
|
||||
.setTarget(rel.getTarget()));
|
||||
}
|
||||
}
|
||||
e.setLinks(links);
|
||||
if (e.getEntity() == null) {
|
||||
throw new IllegalStateException("missing main entity on '" + p._1() + "'");
|
||||
}
|
||||
return e;
|
||||
})
|
||||
.map(e -> new ObjectMapper().writeValueAsString(e))
|
||||
.saveAsTextFile(outPath + "/linked_entities", GzipCodec.class);
|
||||
}
|
||||
|
||||
private EntityRelEntity toEntityRelEntity(Tuple2<String, Tuple2<Tuple2<String, Tuple2<TypedRow, Optional<TypedRow>>>, Optional<TypedRow>>> l) {
|
||||
// extract the entity source
|
||||
final EntityRelEntity res = new EntityRelEntity(l._2()._1()._2()._1());
|
||||
|
||||
if(l._2()._1()._2()._2().isPresent() && l._2()._2().isPresent()) {
|
||||
|
||||
// extract the relationship
|
||||
res.setRelation((Relation) l._2()._1()._2()._2().get().getOaf());
|
||||
|
||||
// extract the related entity
|
||||
res.setTarget(l._2()._2().get());
|
||||
}
|
||||
|
||||
return res;
|
||||
private JavaPairRDD<String, TypedRow> readPathEntity(final JavaSparkContext sc, final String idPath, final String inputPath, final String type) {
|
||||
return sc.sequenceFile(inputPath + "/" + type, Text.class, Text.class)
|
||||
.mapToPair((PairFunction<Tuple2<Text, Text>, String, TypedRow>) item -> {
|
||||
final String json = item._2().toString();
|
||||
final String id = JsonPath.read(json, idPath);
|
||||
return new Tuple2<>(id, new TypedRow(id, type, json));
|
||||
});
|
||||
}
|
||||
|
||||
private PairFunction<Tuple2<String, Tuple2<TypedRow, Optional<TypedRow>>>, String, Tuple2<String, Tuple2<TypedRow, Optional<TypedRow>>>> toPairTarget() {
|
||||
return e -> {
|
||||
Optional<TypedRow> o = e._2()._2();
|
||||
if (o.isPresent()) {
|
||||
return new Tuple2<>(((Relation) o.get().getOaf()).getTarget(), e);
|
||||
} else {
|
||||
return new Tuple2<>(null, e);
|
||||
}
|
||||
};
|
||||
}
|
||||
|
||||
private PairFunction<TypedRow, String, TypedRow> toPair() {
|
||||
return e -> {
|
||||
if (!"relation".equals(e.getType())) {
|
||||
return new Tuple2<>( ((OafEntity) e.getOaf()).getId(), e);
|
||||
} else {
|
||||
return new Tuple2<>( ((Relation) e.getOaf()).getSource(), e);
|
||||
}
|
||||
};
|
||||
private JavaRDD<TypedRow> readPathRelation(final JavaSparkContext sc, final String inputPath) {
|
||||
return sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
|
||||
.map(item -> {
|
||||
final String json = item._2().toString();
|
||||
final String source = JsonPath.read(json, "$.source");
|
||||
final String target = JsonPath.read(json, "$.target");
|
||||
return new TypedRow(source, target, "relation", json);
|
||||
});
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,29 @@
|
|||
package eu.dnetlib.dhp.graph;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.List;
|
||||
|
||||
public class LinkedEntity implements Serializable {
|
||||
|
||||
private TypedRow entity;
|
||||
|
||||
private List<Tuple> links;
|
||||
|
||||
public TypedRow getEntity() {
|
||||
return entity;
|
||||
}
|
||||
|
||||
public LinkedEntity setEntity(TypedRow entity) {
|
||||
this.entity = entity;
|
||||
return this;
|
||||
}
|
||||
|
||||
public List<Tuple> getLinks() {
|
||||
return links;
|
||||
}
|
||||
|
||||
public LinkedEntity setLinks(List<Tuple> links) {
|
||||
this.links = links;
|
||||
return this;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,69 +0,0 @@
|
|||
package eu.dnetlib.dhp.graph;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class RelatedEntity implements Serializable {
|
||||
|
||||
private String relType;
|
||||
|
||||
private String subRelType;
|
||||
|
||||
private String relClass;
|
||||
|
||||
private String type;
|
||||
|
||||
private String payload;
|
||||
|
||||
public RelatedEntity(String relType, String subRelType, String relClass, String type, String payload) {
|
||||
this.relType = relType;
|
||||
this.subRelType = subRelType;
|
||||
this.relClass = relClass;
|
||||
this.type = type;
|
||||
this.payload = payload;
|
||||
}
|
||||
|
||||
public String getRelType() {
|
||||
return relType;
|
||||
}
|
||||
|
||||
public RelatedEntity setRelType(String relType) {
|
||||
this.relType = relType;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getSubRelType() {
|
||||
return subRelType;
|
||||
}
|
||||
|
||||
public RelatedEntity setSubRelType(String subRelType) {
|
||||
this.subRelType = subRelType;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getRelClass() {
|
||||
return relClass;
|
||||
}
|
||||
|
||||
public RelatedEntity setRelClass(String relClass) {
|
||||
this.relClass = relClass;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getType() {
|
||||
return type;
|
||||
}
|
||||
|
||||
public RelatedEntity setType(String type) {
|
||||
this.type = type;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getPayload() {
|
||||
return payload;
|
||||
}
|
||||
|
||||
public RelatedEntity setPayload(String payload) {
|
||||
this.payload = payload;
|
||||
return this;
|
||||
}
|
||||
}
|
||||
|
|
@ -4,21 +4,27 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
|
||||
public class SparkGraphIndexingJob {
|
||||
|
||||
private final static String ENTITY_NODES_PATH = "/tmp/entity_node";
|
||||
private final static String OUTPUT_BASE_PATH = "/tmp/openaire_provision";
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkGraphIndexingJob.class.getResourceAsStream("/eu/dnetlib/dhp/graph/input_graph_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
final SparkConf conf = new SparkConf()
|
||||
.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
|
||||
.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
|
||||
|
||||
final SparkSession spark = SparkSession
|
||||
.builder()
|
||||
.config(conf)
|
||||
.appName(SparkGraphIndexingJob.class.getSimpleName())
|
||||
.master(parser.get("master"))
|
||||
.config("hive.metastore.uris", parser.get("hive_metastore_uris"))
|
||||
.enableHiveSupport()
|
||||
.getOrCreate();
|
||||
|
||||
|
|
@ -26,11 +32,12 @@ public class SparkGraphIndexingJob {
|
|||
final String hiveDbName = parser.get("hive_db_name");
|
||||
|
||||
final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
|
||||
if (fs.exists(new Path(ENTITY_NODES_PATH))) {
|
||||
fs.delete(new Path(ENTITY_NODES_PATH), true);
|
||||
if (fs.exists(new Path(OUTPUT_BASE_PATH))) {
|
||||
fs.delete(new Path(OUTPUT_BASE_PATH), true);
|
||||
fs.mkdirs(new Path(OUTPUT_BASE_PATH));
|
||||
}
|
||||
|
||||
new GraphJoiner().join(spark, inputPath, hiveDbName, ENTITY_NODES_PATH);
|
||||
new GraphJoiner().join(spark, inputPath, hiveDbName, OUTPUT_BASE_PATH);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,31 @@
|
|||
package eu.dnetlib.dhp.graph;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class Tuple implements Serializable {
|
||||
|
||||
private TypedRow relation;
|
||||
|
||||
private TypedRow target;
|
||||
|
||||
public TypedRow getRelation() {
|
||||
return relation;
|
||||
}
|
||||
|
||||
public Tuple setRelation(TypedRow relation) {
|
||||
this.relation = relation;
|
||||
return this;
|
||||
}
|
||||
|
||||
public TypedRow getTarget() {
|
||||
return target;
|
||||
}
|
||||
|
||||
public Tuple setTarget(TypedRow target) {
|
||||
this.target = target;
|
||||
return this;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,20 +1,46 @@
|
|||
package eu.dnetlib.dhp.graph;
|
||||
|
||||
import com.fasterxml.jackson.core.JsonProcessingException;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class TypedRow implements Serializable {
|
||||
private String type;
|
||||
private Oaf oaf;
|
||||
|
||||
public TypedRow(String type, Oaf oaf) {
|
||||
private String source;
|
||||
private String target;
|
||||
private String type;
|
||||
private String oaf;
|
||||
|
||||
public TypedRow() {
|
||||
}
|
||||
|
||||
public TypedRow(String source, String type, String oaf) {
|
||||
this.source = source;
|
||||
this.type = type;
|
||||
this.oaf = oaf;
|
||||
}
|
||||
|
||||
public TypedRow(String source, String target, String type, String oaf) {
|
||||
this(source, type, oaf);
|
||||
this.target = target;
|
||||
}
|
||||
|
||||
public String getSource() {
|
||||
return source;
|
||||
}
|
||||
|
||||
public TypedRow setSource(String source) {
|
||||
this.source = source;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getTarget() {
|
||||
return target;
|
||||
}
|
||||
|
||||
public TypedRow setTarget(String target) {
|
||||
this.target = target;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getType() {
|
||||
return type;
|
||||
}
|
||||
|
|
@ -24,21 +50,13 @@ public class TypedRow implements Serializable {
|
|||
return this;
|
||||
}
|
||||
|
||||
public Oaf getOaf() {
|
||||
public String getOaf() {
|
||||
return oaf;
|
||||
}
|
||||
|
||||
public TypedRow setOaf(Oaf oaf) {
|
||||
public TypedRow setOaf(String oaf) {
|
||||
this.oaf = oaf;
|
||||
return this;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
try {
|
||||
return new ObjectMapper().writeValueAsString(this);
|
||||
} catch (JsonProcessingException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,4 +23,12 @@
|
|||
<name>hive_db_name</name>
|
||||
<value>openaire</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18088</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<value>/user/spark/applicationHistory</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -16,6 +16,14 @@
|
|||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<description>spark 2.* yarn history server address</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<description>spark 2.* event log dir location</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="GraphJoinEntities"/>
|
||||
|
|
@ -33,7 +41,16 @@
|
|||
<name>GraphIndexing</name>
|
||||
<class>eu.dnetlib.dhp.graph.SparkGraphIndexingJob</class>
|
||||
<jar>dhp-graph-provision-${projectVersion}.jar</jar>
|
||||
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse" --conf spark.yarn.executor.memoryOverhead=${sparkExecutorMemoryOverhead}</spark-opts>
|
||||
<spark-opts>
|
||||
--executor-memory ${sparkExecutorMemory}
|
||||
--executor-cores ${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
|
||||
--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
|
||||
--conf spark.sql.warehouse.dir="/user/hive/warehouse"
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--hive_db_name</arg><arg>${hive_db_name}</arg>
|
||||
|
|
|
|||
Loading…
Reference in New Issue