forked from D-Net/dnet-hadoop
classes to implement the dump of the whole graph.
This commit is contained in:
parent
8d4327b292
commit
6d0f08277b
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@ -0,0 +1,30 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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import java.io.Serializable;
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public class Constants implements Serializable {
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// collectedFrom va con isProvidedBy -> becco da ModelSupport
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public static final String IS_HOSTED_BY = "isHostedBy";
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public static final String HOSTS = "hosts";
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public static final String IS_FUNDED_BY = "isFundedBy";
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public static final String FUNDS = "funds";
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public static final String FUNDINGS = "fundings";
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// community result uso isrelatedto
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public static final String RESULT_ENTITY = "result";
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public static final String DATASOURCE_ENTITY = "datasource";
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public static final String CONTEXT_ENTITY = "context";
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public static final String ORGANIZATION_ENTITY = "organization";
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public static final String PROJECT_ENTITY = "project";
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public static final String CONTEXT_ID = "00";
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public static final String CONTEXT_NS_PREFIX = "context____";
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public static final String HARVESTED = "Harvested";
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public static final String DEFAULT_TRUST = "0.9";
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}
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@ -1,4 +1,80 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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public class ContextInfo {
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import java.io.Serializable;
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import java.util.List;
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public class ContextInfo implements Serializable {
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private String id;
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private String description;
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private String type;
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private String zenodocommunity;
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private String name;
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private List<String> projectList;
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private List<String> datasourceList;
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private List<String> subject;
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public List<String> getSubject() {
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return subject;
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}
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public void setSubject(List<String> subject) {
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this.subject = subject;
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}
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public String getName() {
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return name;
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}
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public void setName(String name) {
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this.name = name;
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}
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public String getId() {
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return id;
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}
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public void setId(String id) {
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this.id = id;
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}
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public 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 String getType() {
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return type;
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}
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public void setType(String type) {
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this.type = type;
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}
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public String getZenodocommunity() {
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return zenodocommunity;
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}
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public void setZenodocommunity(String zenodocommunity) {
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this.zenodocommunity = zenodocommunity;
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}
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public List<String> getProjectList() {
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return projectList;
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}
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public void setProjectList(List<String> projectList) {
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this.projectList = projectList;
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}
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public List<String> getDatasourceList() {
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return datasourceList;
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}
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public void setDatasourceList(List<String> datasourceList) {
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this.datasourceList = datasourceList;
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}
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}
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@ -1,77 +1,104 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import java.io.BufferedWriter;
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import java.io.IOException;
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import java.io.OutputStreamWriter;
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import java.io.Serializable;
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import java.nio.charset.StandardCharsets;
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import java.util.List;
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import java.util.Optional;
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import java.util.function.Consumer;
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import java.util.function.Function;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import javax.rmi.CORBA.Util;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchCommunity;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataOutputStream;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.Serializable;
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import java.util.Optional;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchCommunity;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative;
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public class SparkCreateContextEntities implements Serializable {
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public class CreateContextEntities implements Serializable {
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//leggo i context dall'is e mi faccio la mappa id -> contextinfo
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// leggo i context dall'is e mi faccio la mappa id -> contextinfo
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//creo le entities con le info generali
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// creo le entities con le info generali
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//creo le relazioni con le info in projectList e datasourceList. Le relazioni sono di tipo isRelatedTo da una parte e dall'altra
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private static final Logger log = LoggerFactory.getLogger(CreateContextEntities.class);
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private final Configuration conf;
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private final BufferedWriter writer;
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//prendo un parametro community_organization per creare relazioni fra community ed organizzazioni . n.b. l'id dell'organizzazione
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//e' non deduplicato => bisogna risolverlo e prendere i dedup id distinti
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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CreateContextEntities.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameters.json"));
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private static final Logger log = LoggerFactory.getLogger(SparkCreateContextEntities.class);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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SparkCreateContextEntities.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final String hdfsPath = parser.get("hdfsPath");
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log.info("hdfsPath: {}", hdfsPath);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String hdfsNameNode = parser.get("nameNode");
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log.info("nameNode: {}", hdfsNameNode);
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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String isLookUpUrl = parser.get("isLookUpUrl");
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log.info("isLookUpUrl: {}", isLookUpUrl);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final CreateContextEntities cce = new CreateContextEntities(hdfsPath, hdfsNameNode);
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final String isLookUpUrl = parser.get("isLookUpUrl");
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log.info("isLookUpUrl: {}", isLookUpUrl);
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log.info("Processing contexts...");
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cce.execute(Process::getEntity, isLookUpUrl);
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QueryInformationSystem queryInformationSystem = new QueryInformationSystem();
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queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl));
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CommunityMap communityMap = queryInformationSystem.getCommunityMap();
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}
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createEntities(communityMap, outputPath + "/context");
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public CreateContextEntities(String hdfsPath, String hdfsNameNode) throws IOException {
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this.conf = new Configuration();
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this.conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(this.conf);
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Path hdfsWritePath = new Path(hdfsPath);
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FSDataOutputStream fsDataOutputStream = null;
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if (fileSystem.exists(hdfsWritePath)) {
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fsDataOutputStream = fileSystem.append(hdfsWritePath);
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} else {
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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}
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}
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this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
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private static void createEntities(CommunityMap communityMap, String s) {
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communityMap.keySet().stream()
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.map(key -> {
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ResearchInitiative community;
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ContextInfo cinfo = communityMap.get(key);
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if(cinfo.getType().equals("community")){
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community = new ResearchCommunity();
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}else{
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community = new ResearchInitiative();
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}
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return community;
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})
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}
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}
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public <R extends ResearchInitiative> void execute(final Function<ContextInfo, R> producer, String isLookUpUrl)
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throws Exception {
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QueryInformationSystem queryInformationSystem = new QueryInformationSystem();
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queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl));
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final Consumer<ContextInfo> consumer = ci -> writeEntity(producer.apply(ci));
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queryInformationSystem.getContextInformation(consumer);
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}
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protected <R extends ResearchInitiative> void writeEntity(final R r) {
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try {
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writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r));
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writer.newLine();
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} catch (final Exception 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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package eu.dnetlib.dhp.oa.graph.dump.graph;
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public class CreateContextRelation {
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import java.io.BufferedWriter;
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import java.io.IOException;
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import java.io.OutputStreamWriter;
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import java.io.Serializable;
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import java.nio.charset.StandardCharsets;
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import java.util.List;
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import java.util.Optional;
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import java.util.function.Consumer;
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import java.util.function.Function;
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import eu.dnetlib.dhp.schema.oaf.Datasource;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataOutputStream;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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public class CreateContextRelation implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(CreateContextEntities.class);
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private final Configuration conf;
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private final BufferedWriter writer;
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private final QueryInformationSystem queryInformationSystem;
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private static final String CONTEX_RELATION_DATASOURCE = "contentproviders";
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private static final String CONTEX_RELATION_PROJECT = "projects";
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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CreateContextRelation.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String hdfsPath = parser.get("hdfsPath");
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log.info("hdfsPath: {}", hdfsPath);
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final String hdfsNameNode = parser.get("nameNode");
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log.info("nameNode: {}", hdfsNameNode);
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final String isLookUpUrl = parser.get("isLookUpUrl");
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log.info("isLookUpUrl: {}", isLookUpUrl);
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final CreateContextRelation cce = new CreateContextRelation(hdfsPath, hdfsNameNode, isLookUpUrl);
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log.info("Creating relation for datasource...");
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cce.execute(Process::getRelation, CONTEX_RELATION_DATASOURCE, ModelSupport.getIdPrefix(Datasource.class));
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log.info("Creating relations for projects... ");
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cce.execute(Process::getRelation, CONTEX_RELATION_PROJECT, ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class));
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}
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public CreateContextRelation(String hdfsPath, String hdfsNameNode, String isLookUpUrl)
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throws IOException, ISLookUpException {
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this.conf = new Configuration();
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this.conf.set("fs.defaultFS", hdfsNameNode);
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queryInformationSystem = new QueryInformationSystem();
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queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl));
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queryInformationSystem.execContextRelationQuery();
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FileSystem fileSystem = FileSystem.get(this.conf);
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Path hdfsWritePath = new Path(hdfsPath);
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FSDataOutputStream fsDataOutputStream = null;
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if (fileSystem.exists(hdfsWritePath)) {
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fsDataOutputStream = fileSystem.append(hdfsWritePath);
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} else {
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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}
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this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
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}
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public void execute(final Function<ContextInfo, List<Relation>> producer, String category, String prefix) throws Exception {
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final Consumer<ContextInfo> consumer = ci -> producer.apply(ci).forEach(c -> writeEntity(c));
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queryInformationSystem.getContextRelation(consumer, category, prefix);
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}
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protected void writeEntity(final Relation r) {
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try {
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writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r));
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writer.newLine();
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} catch (final Exception 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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@ -1,16 +1,18 @@
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package eu.dnetlib.dhp.oa.graph.dump.graph;
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import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.dump.oaf.ControlledField;
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import eu.dnetlib.dhp.schema.dump.oaf.Country;
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import eu.dnetlib.dhp.schema.dump.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.dump.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.io.StringReader;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.schema.dump.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.Journal;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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@ -20,234 +22,452 @@ import org.dom4j.DocumentException;
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import org.dom4j.Node;
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import org.dom4j.io.SAXReader;
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import java.io.Serializable;
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import java.io.StringReader;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import javax.swing.text.html.Option;
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public class DumpGraph implements Serializable {
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public class DumpGraphEntities implements Serializable {
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public void run(Boolean isSparkSessionManaged,
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String inputPath,
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String outputPath,
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Class<? extends OafEntity> inputClazz,
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CommunityMap communityMap) {
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SparkConf conf = new SparkConf();
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switch (ModelSupport.idPrefixMap.get(inputClazz)) {
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case "50":
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DumpProducts d = new DumpProducts();
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d.run(isSparkSessionManaged, inputPath, outputPath, communityMap, inputClazz, Result.class, true);
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break;
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case "40":
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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Utils.removeOutputDir(spark, outputPath);
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projectMap(spark, inputPath, outputPath, inputClazz);
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});
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break;
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case "20":
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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Utils.removeOutputDir(spark, outputPath);
|
||||
organizationMap(spark, inputPath, outputPath, inputClazz);
|
||||
|
||||
});
|
||||
break;
|
||||
case "10":
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
datasourceMap(spark, inputPath, outputPath, inputClazz);
|
||||
|
||||
});
|
||||
break;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static <E extends OafEntity> void datasourceMap(SparkSession spark, String inputPath, String outputPath, Class<E> inputClazz) {
|
||||
Utils
|
||||
.readPath(spark, inputPath, inputClazz)
|
||||
.map(d -> mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) d), Encoders.bean(Datasource.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
|
||||
|
||||
public void run(Boolean isSparkSessionManaged,
|
||||
String inputPath,
|
||||
String outputPath,
|
||||
Class<? extends OafEntity> inputClazz,
|
||||
CommunityMap communityMap) {
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
switch (ModelSupport.idPrefixMap.get(inputClazz)){
|
||||
case "50":
|
||||
DumpProducts d = new DumpProducts();
|
||||
d.run(isSparkSessionManaged,inputPath,outputPath,communityMap, inputClazz, true);
|
||||
break;
|
||||
case "40":
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
projectMap(spark, inputPath, outputPath, inputClazz);
|
||||
private static <E extends OafEntity> void projectMap(SparkSession spark, String inputPath, String outputPath,
|
||||
Class<E> inputClazz) {
|
||||
Utils
|
||||
.readPath(spark, inputPath, inputClazz)
|
||||
.map(p -> mapProject((eu.dnetlib.dhp.schema.oaf.Project) p), Encoders.bean(Project.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
|
||||
});
|
||||
break;
|
||||
case "20":
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
organizationMap(spark, inputPath, outputPath, inputClazz);
|
||||
private static Datasource mapDatasource(eu.dnetlib.dhp.schema.oaf.Datasource d) {
|
||||
Datasource datasource = new Datasource();
|
||||
|
||||
});
|
||||
break;
|
||||
}
|
||||
}
|
||||
datasource.setId(d.getId());
|
||||
|
||||
private static <E extends OafEntity> void projectMap(SparkSession spark, String inputPath, String outputPath, Class<E> inputClazz) {
|
||||
Utils.readPath(spark, inputPath, inputClazz)
|
||||
.map(p -> mapProject((eu.dnetlib.dhp.schema.oaf.Project)p), Encoders.bean(Project.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
Optional.ofNullable(d.getOriginalId()).ifPresent(oId -> datasource.setOriginalId(oId));
|
||||
|
||||
private static Project mapProject(eu.dnetlib.dhp.schema.oaf.Project p) {
|
||||
Project project = new Project();
|
||||
Optional.ofNullable(d.getPid())
|
||||
.ifPresent(pids -> pids.stream().map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
|
||||
.collect(Collectors.toList()));
|
||||
|
||||
project.setCollectedfrom(Optional.ofNullable(p.getCollectedfrom())
|
||||
.map(cf -> cf.stream().map(coll -> coll.getValue()).collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
Optional.ofNullable(d.getDatasourcetype())
|
||||
.ifPresent(dsType -> datasource.setDatasourcetype(ControlledField.newInstance(dsType.getClassid(), dsType.getClassname())));
|
||||
|
||||
Optional.ofNullable(p.getId())
|
||||
.ifPresent(id -> project.setId(id));
|
||||
Optional.ofNullable(d.getOpenairecompatibility())
|
||||
.ifPresent(v -> datasource.setOpenairecompatibility(v.getClassname()));
|
||||
|
||||
Optional.ofNullable(p.getWebsiteurl())
|
||||
.ifPresent(w -> project.setWebsiteurl(w.getValue()));
|
||||
Optional.ofNullable(d.getOfficialname())
|
||||
.ifPresent(oname -> datasource.setOfficialname(oname.getValue()));
|
||||
|
||||
Optional.ofNullable(p.getCode())
|
||||
.ifPresent(code -> project.setCode(code.getValue()));
|
||||
Optional.ofNullable(d.getEnglishname())
|
||||
.ifPresent(ename -> datasource.setEnglishname(ename.getValue()));
|
||||
|
||||
Optional.ofNullable(p.getAcronym())
|
||||
.ifPresent(acronynim -> project.setAcronym(acronynim.getValue()));
|
||||
Optional.ofNullable(d.getWebsiteurl())
|
||||
.ifPresent(wsite -> datasource.setWebsiteurl(wsite.getValue()));
|
||||
|
||||
Optional.ofNullable(p.getTitle())
|
||||
.ifPresent(title -> project.setTitle(title.getValue()));
|
||||
Optional.ofNullable(d.getLogourl())
|
||||
.ifPresent(lurl -> datasource.setLogourl(lurl.getValue()));
|
||||
|
||||
Optional.ofNullable(p.getStartdate())
|
||||
.ifPresent(sdate -> project.setStartdate(sdate.getValue()));
|
||||
Optional.ofNullable(d.getDateofvalidation())
|
||||
.ifPresent(dval -> datasource.setDateofvalidation(dval.getValue()));
|
||||
|
||||
Optional.ofNullable(p.getEnddate())
|
||||
.ifPresent(edate -> project.setEnddate(edate.getValue()));
|
||||
Optional.ofNullable(d.getDescription())
|
||||
.ifPresent(dex -> datasource.setDescription(dex.getValue()));
|
||||
|
||||
Optional.ofNullable(p.getCallidentifier())
|
||||
.ifPresent(cide -> project.setCallidentifier(cide.getValue()));
|
||||
Optional.ofNullable(d.getSubjects())
|
||||
.ifPresent(sbjs -> datasource.setSubjects(sbjs.stream().map(sbj -> sbj.getValue()).collect(Collectors.toList())));
|
||||
|
||||
Optional.ofNullable(p.getKeywords())
|
||||
.ifPresent(key -> project.setKeywords(key.getValue()));
|
||||
Optional.ofNullable(d.getOdpolicies())
|
||||
.ifPresent(odp->datasource.setPolicies(Arrays.asList(odp.getValue())));
|
||||
|
||||
Optional.ofNullable(p.getDuration())
|
||||
.ifPresent(duration -> project.setDuration(duration.getValue()));
|
||||
Optional.ofNullable(d.getOdlanguages())
|
||||
.ifPresent(langs -> datasource.setLanguages(langs.stream().map(lang -> lang.getValue()).collect(Collectors.toList())));
|
||||
|
||||
Optional<Field<String>> omandate = Optional.ofNullable(p.getOamandatepublications());
|
||||
Optional<Field<String>> oecsc39 = Optional.ofNullable(p.getEcsc39());
|
||||
boolean mandate = false;
|
||||
if(omandate.isPresent()){
|
||||
if (!omandate.get().getValue().equals("N")){
|
||||
mandate = true;
|
||||
}
|
||||
}
|
||||
if(oecsc39.isPresent()){
|
||||
if(!oecsc39.get().getValue().equals("N")){
|
||||
mandate = true;
|
||||
}
|
||||
}
|
||||
Optional.ofNullable(d.getOdcontenttypes())
|
||||
.ifPresent(ctypes -> datasource.setContenttypes(ctypes.stream().map(ctype -> ctype.getValue()).collect(Collectors.toList())));
|
||||
|
||||
project.setOpenaccessmandateforpublications(mandate);
|
||||
project.setOpenaccessmandatefordataset(false);
|
||||
Optional.ofNullable(d.getReleasestartdate())
|
||||
.ifPresent(rd -> datasource.setReleasestartdate(rd.getValue()));
|
||||
|
||||
Optional.ofNullable(p.getEcarticle29_3())
|
||||
.ifPresent(oamandate -> project.setOpenaccessmandatefordataset(oamandate.getValue().equals("Y")));
|
||||
Optional.ofNullable(d.getReleaseenddate())
|
||||
.ifPresent(ed -> datasource.setReleaseenddate(ed.getValue()));
|
||||
|
||||
project.setSubject(Optional.ofNullable(p.getSubjects())
|
||||
.map(subjs -> subjs.stream().map(s -> s.getValue()).collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
Optional.ofNullable(d.getMissionstatementurl())
|
||||
.ifPresent(ms -> datasource.setMissionstatementurl(ms.getValue()));
|
||||
|
||||
Optional.ofNullable(p.getSummary())
|
||||
.ifPresent(summary -> project.setSummary(summary.getValue()));
|
||||
Optional.ofNullable(d.getDatabaseaccesstype())
|
||||
.ifPresent(ar -> datasource.setAccessrights(ar.getValue()));
|
||||
|
||||
Optional<Float> ofundedamount = Optional.ofNullable(p.getFundedamount());
|
||||
Optional<Field<String>> ocurrency = Optional.ofNullable(p.getCurrency());
|
||||
Optional<Float> ototalcost = Optional.ofNullable(p.getTotalcost());
|
||||
Optional.ofNullable(d.getDatauploadtype())
|
||||
.ifPresent(dut -> datasource.setUploadrights(dut.getValue()));
|
||||
|
||||
if(ocurrency.isPresent()){
|
||||
if(ofundedamount.isPresent()){
|
||||
if(ototalcost.isPresent()){
|
||||
project.setGranted(Granted.newInstance(ocurrency.get().getValue(), ototalcost.get(), ofundedamount.get()));
|
||||
}else{
|
||||
project.setGranted(Granted.newInstance(ocurrency.get().getValue(), ofundedamount.get()));
|
||||
}
|
||||
}
|
||||
}
|
||||
Optional.ofNullable(d.getDatabaseaccessrestriction())
|
||||
.ifPresent(dar ->datasource.setDatabaseaccessrestriction(dar.getValue()));
|
||||
|
||||
project.setProgramme(Optional.ofNullable(p.getProgramme())
|
||||
.map(programme -> programme.stream().map(pg -> Programme.newInstance(pg.getCode(), pg.getDescription()))
|
||||
.collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
Optional.ofNullable(d.getDatauploadrestriction())
|
||||
.ifPresent(dur -> datasource.setDatauploadrestriction(dur.getValue()));
|
||||
|
||||
project.setFunding(Optional.ofNullable(p.getFundingtree())
|
||||
.map(value -> value.stream()
|
||||
.map(fundingtree -> getFunder(fundingtree.getValue())).collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
return project;
|
||||
}
|
||||
Optional.ofNullable(d.getVersioning())
|
||||
.ifPresent(v->datasource.setVersioning(v.getValue()));
|
||||
|
||||
public static Funder getFunder(String fundingtree){
|
||||
Optional.ofNullable(d.getCitationguidelineurl())
|
||||
.ifPresent(cu -> datasource.setCitationguidelineurl(cu.getValue()));
|
||||
|
||||
Funder f = new Funder();
|
||||
final Document doc;
|
||||
try {
|
||||
doc = new SAXReader().read(new StringReader(fundingtree));
|
||||
f.setShortName(((org.dom4j.Node) (doc.selectNodes("//funder/shortname").get(0))).getText());
|
||||
f.setName(((org.dom4j.Node) (doc.selectNodes("//funder/name").get(0))).getText());
|
||||
f.setJurisdiction(((org.dom4j.Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText());
|
||||
f.setId(((org.dom4j.Node) (doc.selectNodes("//funder/id").get(0))).getText());
|
||||
List<Levels> fundings = new ArrayList<>();
|
||||
int level = 0;
|
||||
List<org.dom4j.Node> nodes = doc.selectNodes("//funding_level_"+level);
|
||||
while(nodes.size() > 0 ) {
|
||||
for(org.dom4j.Node n: nodes) {
|
||||
Levels funding_stream = new Levels();
|
||||
funding_stream.setLevel(String.valueOf(level));
|
||||
List node = n.selectNodes("./name");
|
||||
funding_stream.setName(((org.dom4j.Node)node.get(0)).getText());
|
||||
node = n.selectNodes("./id");
|
||||
funding_stream.setId(((org.dom4j.Node)node.get(0)).getText());
|
||||
node = n.selectNodes("./description");
|
||||
funding_stream.setDescription(((Node)node.get(0)).getText());
|
||||
fundings.add(funding_stream);
|
||||
Optional.ofNullable(d.getPidsystems())
|
||||
.ifPresent(ps -> datasource.setPidsystems(ps.getValue()));
|
||||
|
||||
}
|
||||
level += 1;
|
||||
nodes = doc.selectNodes("//funding_level_"+level);
|
||||
}
|
||||
if(fundings.size() > 0 ) {
|
||||
f.setFunding_levels(fundings);
|
||||
}
|
||||
Optional.ofNullable(d.getCertificates())
|
||||
.ifPresent(c -> datasource.setCertificates(c.getValue()));
|
||||
|
||||
return f;
|
||||
} catch (DocumentException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
return f;
|
||||
Optional.ofNullable(d.getPolicies())
|
||||
.ifPresent(ps -> datasource.setPolicies(ps.stream().map(p -> p.getValue()).collect(Collectors.toList())));
|
||||
|
||||
}
|
||||
Optional.ofNullable(d.getJournal())
|
||||
.ifPresent(j -> datasource.setJournal(getContainer(j)));
|
||||
|
||||
private static <E extends OafEntity> void organizationMap(SparkSession spark, String inputPath, String outputPath, Class<E> inputClazz) {
|
||||
Utils.readPath(spark, inputPath,inputClazz)
|
||||
.map(o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization)o), Encoders.bean(Organization.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
return datasource;
|
||||
|
||||
private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org){
|
||||
Organization organization = new Organization();
|
||||
}
|
||||
|
||||
Optional.ofNullable(org.getLegalshortname())
|
||||
.ifPresent(value -> organization.setLegalshortname(value.getValue()));
|
||||
private static Container getContainer(Journal j) {
|
||||
Container c = new Container();
|
||||
|
||||
Optional.ofNullable(org.getLegalname())
|
||||
.ifPresent(value -> organization.setLegalname(value.getValue()));
|
||||
Optional.ofNullable(j.getName())
|
||||
.ifPresent(n->c.setName(n));
|
||||
|
||||
Optional.ofNullable(org.getWebsiteurl())
|
||||
.ifPresent(value -> organization.setWebsiteurl(value.getValue()));
|
||||
Optional.ofNullable(j.getIssnPrinted())
|
||||
.ifPresent(issnp -> c.setIssnPrinted(issnp));
|
||||
|
||||
Optional.ofNullable(org.getAlternativeNames())
|
||||
.ifPresent(value -> organization.setAlternativenames(value.stream()
|
||||
.map( v-> v.getValue()).collect(Collectors.toList())));
|
||||
Optional.ofNullable(j.getIssnOnline())
|
||||
.ifPresent(issno -> c.setIssnOnline(issno));
|
||||
|
||||
Optional.ofNullable(org.getCountry())
|
||||
.ifPresent(value -> organization.setCountry(Qualifier.newInstance(value.getClassid(), value.getClassname())));
|
||||
Optional.ofNullable(j.getIssnLinking())
|
||||
.ifPresent(isnl -> c.setIssnLinking(isnl));
|
||||
|
||||
Optional.ofNullable(org.getId())
|
||||
.ifPresent(value -> organization.setId(value));
|
||||
Optional.ofNullable(j.getEp())
|
||||
.ifPresent(ep -> c.setEp(ep));
|
||||
|
||||
Optional.ofNullable(org.getPid())
|
||||
.ifPresent(value -> organization.setPid(
|
||||
value.stream().map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())).collect(Collectors.toList())
|
||||
));
|
||||
Optional.ofNullable(j.getIss())
|
||||
.ifPresent(iss -> c.setIss(iss));
|
||||
|
||||
organization.setCollectedfrom(Optional.ofNullable(org.getCollectedfrom())
|
||||
.map(value -> value.stream()
|
||||
.map(cf -> KeyValue.newInstance(cf.getKey(),cf.getValue())).collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
Optional.ofNullable(j.getSp())
|
||||
.ifPresent(sp -> c.setSp(sp));
|
||||
|
||||
return organization;
|
||||
}
|
||||
Optional.ofNullable(j.getVol())
|
||||
.ifPresent(vol -> c.setVol(vol));
|
||||
|
||||
Optional.ofNullable(j.getEdition())
|
||||
.ifPresent(edition -> c.setEdition(edition));
|
||||
|
||||
Optional.ofNullable(j.getConferencedate())
|
||||
.ifPresent(cdate -> c.setConferencedate(cdate));
|
||||
|
||||
Optional.ofNullable(j.getConferenceplace())
|
||||
.ifPresent(cplace -> c.setConferenceplace(cplace));
|
||||
|
||||
return c;
|
||||
}
|
||||
|
||||
private static Project mapProject(eu.dnetlib.dhp.schema.oaf.Project p) {
|
||||
Project project = new Project();
|
||||
|
||||
// project
|
||||
// .setCollectedfrom(
|
||||
// Optional
|
||||
// .ofNullable(p.getCollectedfrom())
|
||||
// .map(
|
||||
// cf -> cf
|
||||
// .stream()
|
||||
// .map(coll -> KeyValue.newInstance(coll.getKey(), coll.getValue()))
|
||||
// .collect(Collectors.toList()))
|
||||
// .orElse(new ArrayList<>()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getId())
|
||||
.ifPresent(id -> project.setId(id));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getWebsiteurl())
|
||||
.ifPresent(w -> project.setWebsiteurl(w.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getCode())
|
||||
.ifPresent(code -> project.setCode(code.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getAcronym())
|
||||
.ifPresent(acronynim -> project.setAcronym(acronynim.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getTitle())
|
||||
.ifPresent(title -> project.setTitle(title.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getStartdate())
|
||||
.ifPresent(sdate -> project.setStartdate(sdate.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getEnddate())
|
||||
.ifPresent(edate -> project.setEnddate(edate.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getCallidentifier())
|
||||
.ifPresent(cide -> project.setCallidentifier(cide.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getKeywords())
|
||||
.ifPresent(key -> project.setKeywords(key.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getDuration())
|
||||
.ifPresent(duration -> project.setDuration(duration.getValue()));
|
||||
|
||||
Optional<Field<String>> omandate = Optional.ofNullable(p.getOamandatepublications());
|
||||
Optional<Field<String>> oecsc39 = Optional.ofNullable(p.getEcsc39());
|
||||
boolean mandate = false;
|
||||
if (omandate.isPresent()) {
|
||||
if (omandate.get().getValue().equals("true")) {
|
||||
mandate = true;
|
||||
}
|
||||
}
|
||||
if (oecsc39.isPresent()) {
|
||||
if (oecsc39.get().getValue().equals("true")) {
|
||||
mandate = true;
|
||||
}
|
||||
}
|
||||
|
||||
project.setOpenaccessmandateforpublications(mandate);
|
||||
project.setOpenaccessmandatefordataset(false);
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getEcarticle29_3())
|
||||
.ifPresent(oamandate -> project.setOpenaccessmandatefordataset(oamandate.getValue().equals("true")));
|
||||
|
||||
project
|
||||
.setSubject(
|
||||
Optional
|
||||
.ofNullable(p.getSubjects())
|
||||
.map(subjs -> subjs.stream().map(s -> s.getValue()).collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getSummary())
|
||||
.ifPresent(summary -> project.setSummary(summary.getValue()));
|
||||
|
||||
Optional<Float> ofundedamount = Optional.ofNullable(p.getFundedamount());
|
||||
Optional<Field<String>> ocurrency = Optional.ofNullable(p.getCurrency());
|
||||
Optional<Float> ototalcost = Optional.ofNullable(p.getTotalcost());
|
||||
|
||||
if (ocurrency.isPresent()) {
|
||||
if (ofundedamount.isPresent()) {
|
||||
if (ototalcost.isPresent()) {
|
||||
project
|
||||
.setGranted(
|
||||
Granted.newInstance(ocurrency.get().getValue(), ototalcost.get(), ofundedamount.get()));
|
||||
} else {
|
||||
project.setGranted(Granted.newInstance(ocurrency.get().getValue(), ofundedamount.get()));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
project
|
||||
.setProgramme(
|
||||
Optional
|
||||
.ofNullable(p.getProgramme())
|
||||
.map(
|
||||
programme -> programme
|
||||
.stream()
|
||||
.map(pg -> Programme.newInstance(pg.getCode(), pg.getDescription()))
|
||||
.collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
|
||||
project
|
||||
.setFunding(
|
||||
Optional
|
||||
.ofNullable(p.getFundingtree())
|
||||
.map(
|
||||
value -> value
|
||||
.stream()
|
||||
.map(fundingtree -> getFunder(fundingtree.getValue()))
|
||||
.collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
return project;
|
||||
}
|
||||
|
||||
public static Funder getFunder(String fundingtree) {
|
||||
|
||||
Funder f = new Funder();
|
||||
final Document doc;
|
||||
try {
|
||||
doc = new SAXReader().read(new StringReader(fundingtree));
|
||||
f.setShortName(((org.dom4j.Node) (doc.selectNodes("//funder/shortname").get(0))).getText());
|
||||
f.setName(((org.dom4j.Node) (doc.selectNodes("//funder/name").get(0))).getText());
|
||||
f.setJurisdiction(((org.dom4j.Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText());
|
||||
// f.setId(((org.dom4j.Node) (doc.selectNodes("//funder/id").get(0))).getText());
|
||||
|
||||
String id = "";
|
||||
String description = "";
|
||||
// List<Levels> fundings = new ArrayList<>();
|
||||
int level = 0;
|
||||
List<org.dom4j.Node> nodes = doc.selectNodes("//funding_level_" + level);
|
||||
while (nodes.size() > 0) {
|
||||
for (org.dom4j.Node n : nodes) {
|
||||
// Levels funding_stream = new Levels();
|
||||
// funding_stream.setLevel(String.valueOf(level));
|
||||
// List node = n.selectNodes("./name");
|
||||
// funding_stream.setName(((org.dom4j.Node)node.get(0)).getText());
|
||||
List node = n.selectNodes("./id");
|
||||
id = ((org.dom4j.Node) node.get(0)).getText();
|
||||
id = id.substring(id.indexOf("::") + 2);
|
||||
// funding_stream.setId(((org.dom4j.Node)node.get(0)).getText());
|
||||
node = n.selectNodes("./description");
|
||||
description += ((Node) node.get(0)).getText() + " - ";
|
||||
// funding_stream.setDescription(((Node)node.get(0)).getText());
|
||||
// fundings.add(funding_stream);
|
||||
|
||||
}
|
||||
level += 1;
|
||||
nodes = doc.selectNodes("//funding_level_" + level);
|
||||
}
|
||||
// if(fundings.size() > 0 ) {
|
||||
// f.setFunding_levels(fundings);
|
||||
// }
|
||||
if (!id.equals("")) {
|
||||
Fundings fundings = new Fundings();
|
||||
fundings.setId(id);
|
||||
fundings.setDescription(description.substring(0, description.length() - 3).trim());
|
||||
f.setFunding_stream(fundings);
|
||||
}
|
||||
|
||||
return f;
|
||||
} catch (DocumentException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
return f;
|
||||
|
||||
}
|
||||
|
||||
private static <E extends OafEntity> void organizationMap(SparkSession spark, String inputPath, String outputPath,
|
||||
Class<E> inputClazz) {
|
||||
Utils
|
||||
.readPath(spark, inputPath, inputClazz)
|
||||
.map(o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), Encoders.bean(Organization.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
|
||||
private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) {
|
||||
Organization organization = new Organization();
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getLegalshortname())
|
||||
.ifPresent(value -> organization.setLegalshortname(value.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getLegalname())
|
||||
.ifPresent(value -> organization.setLegalname(value.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getWebsiteurl())
|
||||
.ifPresent(value -> organization.setWebsiteurl(value.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getAlternativeNames())
|
||||
.ifPresent(
|
||||
value -> organization
|
||||
.setAlternativenames(
|
||||
value
|
||||
.stream()
|
||||
.map(v -> v.getValue())
|
||||
.collect(Collectors.toList())));
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getCountry())
|
||||
.ifPresent(
|
||||
value -> organization.setCountry(Qualifier.newInstance(value.getClassid(), value.getClassname())));
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getId())
|
||||
.ifPresent(value -> organization.setId(value));
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getPid())
|
||||
.ifPresent(
|
||||
value -> organization
|
||||
.setPid(
|
||||
value
|
||||
.stream()
|
||||
.map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
|
||||
.collect(Collectors.toList())));
|
||||
|
||||
|
||||
|
||||
return organization;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,207 @@
|
|||
package eu.dnetlib.dhp.oa.graph.dump.graph;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.Node;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FlatMapFunction;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.*;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
public class Extractor implements Serializable {
|
||||
|
||||
public void run(Boolean isSparkSessionManaged,
|
||||
String inputPath,
|
||||
String outputPath,
|
||||
Class<? extends Result> inputClazz,
|
||||
CommunityMap communityMap) {
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
extractRelationResult(spark, inputPath, outputPath, inputClazz, communityMap);
|
||||
});
|
||||
}
|
||||
|
||||
|
||||
|
||||
// private static void extractRelationProjects(SparkSession spark, String inputPath, String outputPath){
|
||||
// Utils.readPath(spark, inputPath, Project.class)
|
||||
// .flatMap((FlatMapFunction<Project, Relation>) project ->{
|
||||
// List<Relation> relList = new ArrayList<>();
|
||||
// Optional.ofNullable(project.getCollectedfrom())
|
||||
// .ifPresent(cfl ->
|
||||
// cfl.forEach(cf -> {
|
||||
// Provenance provenance = Provenance.newInstance(cf.getDataInfo().getProvenanceaction().getClassname(),
|
||||
// cf.getDataInfo().getTrust());
|
||||
//
|
||||
// relList.add(getRelation(project.getId(), cf.getKey(),
|
||||
// Constants.PROJECT_ENTITY, Constants.DATASOURCE_ENTITY, Constants.IS_FUNDED_BY,
|
||||
// Constants.FUNDINGS, provenance));
|
||||
// relList.add(getRelation(cf.getKey(), project.getId(),
|
||||
// Constants.DATASOURCE_ENTITY, Constants.PROJECT_ENTITY, Constants.FUNDS,
|
||||
// Constants.FUNDINGS, provenance));
|
||||
// }));
|
||||
// return relList.iterator();
|
||||
// }, Encoders.bean(Relation.class))
|
||||
// .write()
|
||||
// .option("Compression", "gzip")
|
||||
// .mode(SaveMode.Append)
|
||||
// .json(outputPath);
|
||||
// }
|
||||
|
||||
|
||||
private <R extends Result> void extractRelationResult(SparkSession spark,
|
||||
String inputPath,
|
||||
String outputPath,
|
||||
Class<R> inputClazz,
|
||||
CommunityMap communityMap) {
|
||||
|
||||
Set<Integer> hashCodes = new HashSet<>();
|
||||
|
||||
Utils
|
||||
.readPath(spark, inputPath, inputClazz)
|
||||
.flatMap((FlatMapFunction<R, Relation>) value -> {
|
||||
List<Relation> relationList = new ArrayList<>();
|
||||
Optional
|
||||
.ofNullable(value.getInstance())
|
||||
.ifPresent(inst -> inst.forEach(instance -> {
|
||||
Optional
|
||||
.ofNullable(instance.getCollectedfrom())
|
||||
.ifPresent(cf ->
|
||||
getRelatioPair(value, relationList, cf,
|
||||
ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)
|
||||
);
|
||||
Optional
|
||||
.ofNullable(instance.getHostedby())
|
||||
.ifPresent(hb -> getRelatioPair(value, relationList, hb,
|
||||
Constants.IS_HOSTED_BY, Constants.HOSTS , hashCodes) );
|
||||
}));
|
||||
Set<String> communities = communityMap.keySet();
|
||||
Optional
|
||||
.ofNullable(value.getContext())
|
||||
.ifPresent(contexts -> contexts.forEach(context -> {
|
||||
String id = context.getId();
|
||||
if (id.contains(":")) {
|
||||
id = id.substring(0, id.indexOf(":"));
|
||||
}
|
||||
if (communities.contains(id)) {
|
||||
String contextId = Utils.getContextId(id);
|
||||
Provenance provenance = Optional
|
||||
.ofNullable(context.getDataInfo())
|
||||
.map(
|
||||
dinfo -> Optional
|
||||
.ofNullable(dinfo.get(0).getProvenanceaction())
|
||||
.map(
|
||||
paction -> Provenance
|
||||
.newInstance(
|
||||
paction.getClassid(),
|
||||
dinfo.get(0).getTrust()))
|
||||
.orElse(null))
|
||||
.orElse(null);
|
||||
Relation r = getRelation(
|
||||
value.getId(), contextId,
|
||||
Constants.RESULT_ENTITY,
|
||||
Constants.CONTEXT_ENTITY,
|
||||
ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, provenance);
|
||||
if(!hashCodes.contains(r.hashCode())){
|
||||
relationList
|
||||
.add(r);
|
||||
hashCodes.add(r.hashCode());
|
||||
}
|
||||
r = getRelation(
|
||||
contextId, value.getId(),
|
||||
Constants.CONTEXT_ENTITY,
|
||||
Constants.RESULT_ENTITY,
|
||||
ModelConstants.RELATIONSHIP,
|
||||
ModelConstants.IS_RELATED_TO, provenance);
|
||||
if(!hashCodes.contains(r.hashCode())){
|
||||
relationList
|
||||
.add(
|
||||
r);
|
||||
hashCodes.add(r.hashCode());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}));
|
||||
|
||||
return relationList.iterator();
|
||||
}, Encoders.bean(Relation.class))
|
||||
.write()
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Overwrite)
|
||||
.json(outputPath);
|
||||
|
||||
}
|
||||
|
||||
private static <R extends Result> void getRelatioPair(R value, List<Relation> relationList, KeyValue cf,
|
||||
String result_dtasource, String datasource_result,
|
||||
Set<Integer> hashCodes) {
|
||||
Provenance provenance = Optional
|
||||
.ofNullable(cf.getDataInfo())
|
||||
.map(
|
||||
dinfo -> Optional
|
||||
.ofNullable(dinfo.getProvenanceaction())
|
||||
.map(
|
||||
paction -> Provenance
|
||||
.newInstance(
|
||||
paction.getClassid(),
|
||||
dinfo.getTrust()))
|
||||
.orElse(Provenance.newInstance(Constants.HARVESTED, Constants.DEFAULT_TRUST)))
|
||||
.orElse(Provenance.newInstance(Constants.HARVESTED, Constants.DEFAULT_TRUST));
|
||||
Relation r = getRelation(
|
||||
value.getId(),
|
||||
cf.getKey(), Constants.RESULT_ENTITY, Constants.DATASOURCE_ENTITY,
|
||||
result_dtasource, ModelConstants.PROVISION,
|
||||
provenance);
|
||||
if(!hashCodes.contains(r.hashCode())){
|
||||
relationList
|
||||
.add(r);
|
||||
hashCodes.add(r.hashCode());
|
||||
}
|
||||
|
||||
r = getRelation(
|
||||
cf.getKey(), value.getId(),
|
||||
Constants.DATASOURCE_ENTITY, Constants.RESULT_ENTITY,
|
||||
datasource_result, ModelConstants.PROVISION,
|
||||
provenance);
|
||||
|
||||
if(!hashCodes.contains(r.hashCode())){
|
||||
relationList
|
||||
.add(r);
|
||||
hashCodes.add(r.hashCode());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static Relation getRelation(String source, String target, String sourceType, String targetType,
|
||||
String relName, String relType, Provenance provenance) {
|
||||
Relation r = new Relation();
|
||||
r.setSource(Node.newInstance(source, sourceType));
|
||||
r.setTarget(Node.newInstance(target, targetType));
|
||||
r.setReltype(RelType.newInstance(relName, relType));
|
||||
r.setProvenance(provenance);
|
||||
return r;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.resulttocommunityfromorganization;
|
||||
package eu.dnetlib.dhp.oa.graph.dump.graph;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
|
|
|
|||
|
|
@ -0,0 +1,71 @@
|
|||
package eu.dnetlib.dhp.oa.graph.dump.graph;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Constants;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
public class Process implements Serializable {
|
||||
|
||||
public static <R extends ResearchInitiative> R getEntity(ContextInfo ci) {
|
||||
try {
|
||||
ResearchInitiative ri;
|
||||
if (ci.getType().equals("community")) {
|
||||
ri = new ResearchCommunity();
|
||||
((ResearchCommunity) ri).setSubject(ci.getSubject());
|
||||
ri.setType(Constants.RESEARCH_COMMUNITY);
|
||||
} else {
|
||||
ri = new ResearchInitiative();
|
||||
ri.setType(Constants.RESEARCH_INFRASTRUCTURE);
|
||||
}
|
||||
ri.setId(Utils.getContextId(ci.getId()));
|
||||
ri.setOriginalId(ci.getId());
|
||||
|
||||
ri.setDescription(ci.getDescription());
|
||||
ri.setName(ci.getName());
|
||||
ri.setZenodo_community(Constants.ZENODO_COMMUNITY_PREFIX + ci.getZenodocommunity());
|
||||
return (R) ri;
|
||||
|
||||
} catch (final Exception e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
public static List<Relation> getRelation(ContextInfo ci) {
|
||||
try {
|
||||
|
||||
List<Relation> relationList = new ArrayList<>();
|
||||
ci
|
||||
.getDatasourceList()
|
||||
.forEach(ds -> {
|
||||
Relation direct = new Relation();
|
||||
Relation inverse = new Relation();
|
||||
String nodeType = ModelSupport.idPrefixEntity.get(ds.substring(0, 2));
|
||||
direct.setSource(Node.newInstance(Utils.getContextId(ci.getId()), "context"));
|
||||
direct.setTarget(Node.newInstance(ds, nodeType));
|
||||
direct.setReltype(RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP));
|
||||
direct.setProvenance(Provenance.newInstance("Harvested", "09"));
|
||||
relationList.add(direct);
|
||||
|
||||
inverse.setTarget(Node.newInstance(Utils.getContextId(ci.getId()), "context"));
|
||||
inverse.setSource(Node.newInstance(ds, nodeType));
|
||||
inverse.setReltype(RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP));
|
||||
inverse.setProvenance(Provenance.newInstance("Harvested", "09"));
|
||||
relationList.add(inverse);
|
||||
|
||||
});
|
||||
|
||||
return relationList;
|
||||
|
||||
} catch (final Exception e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,37 +1,73 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump;
|
||||
package eu.dnetlib.dhp.oa.graph.dump.graph;
|
||||
|
||||
import java.io.StringReader;
|
||||
import java.util.List;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.SQLException;
|
||||
import java.sql.Statement;
|
||||
import java.util.*;
|
||||
import java.util.function.Consumer;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentException;
|
||||
import org.dom4j.Element;
|
||||
import org.dom4j.Node;
|
||||
import org.dom4j.io.SAXReader;
|
||||
import org.jetbrains.annotations.NotNull;
|
||||
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
|
||||
public class QueryInformationSystem {
|
||||
|
||||
private ISLookUpService isLookUp;
|
||||
private List<String> contextRelationResult;
|
||||
|
||||
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
|
||||
+
|
||||
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
|
||||
" and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') "
|
||||
+
|
||||
" and $x//context/param[./@name = 'status']/text() = 'all' " +
|
||||
" return " +
|
||||
"<community> " +
|
||||
"{$x//CONFIGURATION/context/@id}" +
|
||||
"{$x//CONFIGURATION/context/@label}" +
|
||||
"</community>";
|
||||
"$x//context";
|
||||
|
||||
public CommunityMap getCommunityMap()
|
||||
throws ISLookUpException {
|
||||
return getMap(isLookUp.quickSearchProfile(XQUERY));
|
||||
private static final String XQUERY_ENTITY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
|
||||
+
|
||||
"where $x//context[./@type='community' or ./@type = 'ri'] and $x//context/param[./@name = 'status']/text() = 'all' return "
|
||||
+
|
||||
"concat(data($x//context/@id) , '@@', $x//context/param[./@name =\"name\"]/text(), '@@', " +
|
||||
"$x//context/param[./@name=\"description\"]/text(), '@@', $x//context/param[./@name = \"subject\"]/text(), '@@', "
|
||||
+
|
||||
"$x//context/param[./@name = \"zenodoCommunity\"]/text(), '@@', $x//context/@type)";
|
||||
|
||||
public void getContextInformation(final Consumer<ContextInfo> consumer) throws ISLookUpException {
|
||||
|
||||
isLookUp
|
||||
.quickSearchProfile(XQUERY_ENTITY)
|
||||
.forEach(c -> {
|
||||
ContextInfo cinfo = new ContextInfo();
|
||||
String[] cSplit = c.split("@@");
|
||||
cinfo.setId(cSplit[0]);
|
||||
cinfo.setName(cSplit[1]);
|
||||
cinfo.setDescription(cSplit[2]);
|
||||
if (!cSplit[3].trim().equals("")){
|
||||
cinfo.setSubject(Arrays.asList(cSplit[3].split(",")));
|
||||
}
|
||||
cinfo.setZenodocommunity(cSplit[4]);
|
||||
cinfo.setType(cSplit[5]);
|
||||
consumer.accept(cinfo);
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
public List<String> getContextRelationResult() {
|
||||
return contextRelationResult;
|
||||
}
|
||||
|
||||
public void setContextRelationResult(List<String> contextRelationResult) {
|
||||
this.contextRelationResult = contextRelationResult;
|
||||
}
|
||||
|
||||
public ISLookUpService getIsLookUp() {
|
||||
|
|
@ -42,22 +78,62 @@ public class QueryInformationSystem {
|
|||
this.isLookUp = isLookUpService;
|
||||
}
|
||||
|
||||
private CommunityMap getMap(List<String> communityMap) {
|
||||
final CommunityMap map = new CommunityMap();
|
||||
public void execContextRelationQuery() throws ISLookUpException {
|
||||
contextRelationResult = isLookUp.quickSearchProfile(XQUERY);
|
||||
|
||||
communityMap.stream().forEach(xml -> {
|
||||
}
|
||||
|
||||
public void getContextRelation(final Consumer<ContextInfo> consumer, String category, String prefix) {
|
||||
|
||||
contextRelationResult.forEach(xml -> {
|
||||
ContextInfo cinfo = new ContextInfo();
|
||||
final Document doc;
|
||||
|
||||
try {
|
||||
|
||||
doc = new SAXReader().read(new StringReader(xml));
|
||||
Element root = doc.getRootElement();
|
||||
map.put(root.attribute("id").getValue(), root.attribute("label").getValue());
|
||||
cinfo.setId(root.attributeValue("id"));
|
||||
|
||||
Iterator it = root.elementIterator();
|
||||
while (it.hasNext()) {
|
||||
Element el = (Element) it.next();
|
||||
if(el.getName().equals("category")){
|
||||
String categoryId = el.attributeValue("id");
|
||||
categoryId = categoryId.substring(categoryId.lastIndexOf("::") + 2);
|
||||
if (categoryId.equals(category)) {
|
||||
cinfo.setDatasourceList(getCategoryList(el, prefix));
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
consumer.accept(cinfo);
|
||||
} catch (DocumentException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
});
|
||||
|
||||
return map;
|
||||
}
|
||||
|
||||
@NotNull
|
||||
private List<String> getCategoryList(Element el, String prefix) {
|
||||
List<String> datasourceList = new ArrayList<>();
|
||||
for(Object node : el.selectNodes(".//param")){
|
||||
Node n = (Node)node;
|
||||
if(n.valueOf("./@name").equals("openaireId")){
|
||||
datasourceList.add(prefix + "|" + n.getText());
|
||||
}
|
||||
}
|
||||
|
||||
// cat_iterator = el.elementIterator();
|
||||
// while (cat_iterator.hasNext()) {
|
||||
// Element catEl = (Element) cat_iterator.next();
|
||||
// if (catEl.getName().equals("param") && catEl.attribute("name").getValue().equals("openaireId")) {
|
||||
// datasourceList.add(catEl.getText());
|
||||
// }
|
||||
// }
|
||||
return datasourceList;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,83 @@
|
|||
package eu.dnetlib.dhp.oa.graph.dump.graph;
|
||||
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.Optional;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
public class SparkCollectAndSave implements Serializable {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkCollectAndSave.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
SparkCollectAndSave.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.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 + "/result");
|
||||
run(spark, inputPath, outputPath);
|
||||
|
||||
});
|
||||
|
||||
|
||||
}
|
||||
|
||||
private static void run(SparkSession spark, String inputPath, String outputPath) {
|
||||
Utils.readPath(spark, inputPath + "/result/publication", Result.class)
|
||||
.union(Utils.readPath(spark, inputPath + "/result/dataset", Result.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/result/otherresearchproduct" , Result.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/result/software", Result.class))
|
||||
.write()
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Overwrite)
|
||||
.json(outputPath);
|
||||
|
||||
Utils.readPath(spark, inputPath +"/relation/publication", Relation.class)
|
||||
.union(Utils.readPath(spark, inputPath + "/relation/dataset", Relation.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/relation/orp", Relation.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/relation/software", Relation.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/relation/contextOrg", Relation.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/relation/context", Relation.class))
|
||||
.write()
|
||||
.mode(SaveMode.Append)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath + "/relation");
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -1,84 +1,59 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump.graph;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.QueryInformationSystem;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.ControlledField;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Country;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
import org.apache.avro.generic.GenericData;
|
||||
import java.io.Serializable;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentException;
|
||||
import org.dom4j.Node;
|
||||
import org.dom4j.io.SAXReader;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import javax.swing.text.html.Option;
|
||||
import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
|
||||
import java.io.Serializable;
|
||||
import java.io.StringReader;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.QueryInformationSystem;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
public class SparkDumpEntitiesJob implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkDumpEntitiesJob.class);
|
||||
|
||||
public class SparkDumpJob implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkDumpCommunityProducts.class);
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
SparkDumpEntitiesJob.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/dump_whole/input_parameters.json"));
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
SparkDumpJob.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json"));
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
|
||||
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);
|
||||
|
||||
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 inputPath = parser.get("sourcePath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
final String resultClassName = parser.get("resultTableName");
|
||||
log.info("resultTableName: {}", resultClassName);
|
||||
|
||||
final String resultClassName = parser.get("resultTableName");
|
||||
log.info("resultTableName: {}", resultClassName);
|
||||
final String isLookUpUrl = parser.get("isLookUpUrl");
|
||||
log.info("isLookUpUrl: {}", isLookUpUrl);
|
||||
|
||||
final String isLookUpUrl = parser.get("isLookUpUrl");
|
||||
log.info("isLookUpUrl: {}", isLookUpUrl);
|
||||
Class<? extends OafEntity> inputClazz = (Class<? extends OafEntity>) Class.forName(resultClassName);
|
||||
|
||||
Class<? extends OafEntity> inputClazz = (Class<? extends OafEntity>) Class.forName(resultClassName);
|
||||
|
||||
QueryInformationSystem queryInformationSystem = new QueryInformationSystem();
|
||||
queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl));
|
||||
CommunityMap communityMap = queryInformationSystem.getCommunityMap();
|
||||
|
||||
DumpGraph dg = new DumpGraph();
|
||||
dg.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMap);
|
||||
|
||||
|
||||
}
|
||||
QueryInformationSystem queryInformationSystem = new QueryInformationSystem();
|
||||
queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl));
|
||||
CommunityMap communityMap = queryInformationSystem.getCommunityMap();
|
||||
|
||||
DumpGraphEntities dg = new DumpGraphEntities();
|
||||
dg.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMap);
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,4 +1,108 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump.graph;
|
||||
|
||||
public class SparkDumpRelationJob {
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.Node;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
|
||||
public class SparkDumpRelationJob implements Serializable {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkDumpRelationJob.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
SparkDumpEntitiesJob.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/dump_whole/input_relationdump_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);
|
||||
dumpRelation(spark, inputPath, outputPath);
|
||||
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
private static void dumpRelation(SparkSession spark, String inputPath, String outputPath) {
|
||||
Utils
|
||||
.readPath(spark, inputPath, Relation.class)
|
||||
.map(relation -> {
|
||||
eu.dnetlib.dhp.schema.dump.oaf.graph.Relation rel = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation();
|
||||
rel
|
||||
.setSource(
|
||||
Node
|
||||
.newInstance(
|
||||
relation.getSource(),
|
||||
ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2))));
|
||||
|
||||
rel
|
||||
.setTarget(
|
||||
Node
|
||||
.newInstance(
|
||||
relation.getTarget(),
|
||||
ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2))));
|
||||
|
||||
rel
|
||||
.setReltype(
|
||||
RelType
|
||||
.newInstance(
|
||||
relation.getRelClass(),
|
||||
relation.getSubRelType()));
|
||||
|
||||
Optional
|
||||
.ofNullable(relation.getDataInfo())
|
||||
.ifPresent(
|
||||
datainfo -> rel
|
||||
.setProvenance(
|
||||
Provenance
|
||||
.newInstance(datainfo.getProvenanceaction().getClassname(), datainfo.getTrust())));
|
||||
|
||||
return rel;
|
||||
|
||||
}, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class))
|
||||
.write()
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Overwrite)
|
||||
.json(outputPath);
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,4 +1,62 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump.graph;
|
||||
|
||||
public class SparkExtractRelationFromEntities {
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.*;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.QueryInformationSystem;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
|
||||
public class SparkExtractRelationFromEntities implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkExtractRelationFromEntities.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
SparkExtractRelationFromEntities.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/dump/input_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);
|
||||
|
||||
final String resultClassName = parser.get("resultTableName");
|
||||
log.info("resultTableName: {}", resultClassName);
|
||||
|
||||
final String isLookUpUrl = parser.get("isLookUpUrl");
|
||||
log.info("isLookUpUrl: {}", isLookUpUrl);
|
||||
|
||||
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
||||
|
||||
QueryInformationSystem queryInformationSystem = new QueryInformationSystem();
|
||||
queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl));
|
||||
CommunityMap communityMap = queryInformationSystem.getCommunityMap();
|
||||
|
||||
Extractor extractor = new Extractor();
|
||||
extractor.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMap);
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,4 +1,145 @@
|
|||
package eu.dnetlib.dhp.oa.graph.dump.graph;
|
||||
|
||||
public class SparkOrganizationRelation {
|
||||
}
|
||||
import com.google.gson.Gson;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.Node;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType;
|
||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
|
||||
import org.apache.avro.generic.GenericData;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FSDataOutputStream;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.apache.spark.SparkConf;
|
||||
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.ForeachFunction;
|
||||
|
||||
import org.apache.spark.sql.*;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.IOException;
|
||||
import java.io.OutputStreamWriter;
|
||||
import java.io.Serializable;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.util.*;
|
||||
import java.util.concurrent.atomic.AtomicReference;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
public class SparkOrganizationRelation implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkOrganizationRelation.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
SparkOrganizationRelation.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/dump_whole/input_organization_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);
|
||||
|
||||
|
||||
final OrganizationMap organizationMap = new Gson().fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class);
|
||||
log.info("organization map : {}", new Gson().toJson(organizationMap));
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
AtomicReference<Set<String>> relationSet = null;
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
writeRelations(spark, extractRelation(spark, inputPath, organizationMap), outputPath, organizationMap);
|
||||
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
private static void writeRelations(SparkSession spark, Set<String> rels, String outputPath, OrganizationMap organizationMap) {
|
||||
|
||||
List<eu.dnetlib.dhp.schema.dump.oaf.graph.Relation> relList = new ArrayList<>();
|
||||
|
||||
rels.forEach(oId -> {
|
||||
organizationMap.get(oId).forEach(community -> {
|
||||
eu.dnetlib.dhp.schema.dump.oaf.graph.Relation direct = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation();
|
||||
eu.dnetlib.dhp.schema.dump.oaf.graph.Relation inverse = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation();
|
||||
String id = Utils.getContextId(community);
|
||||
direct.setSource(Node.newInstance(id, "context"));
|
||||
direct.setTarget(Node.newInstance(oId, ModelSupport.idPrefixEntity.get(oId.substring(0, 2))));
|
||||
direct.setReltype(RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP));
|
||||
direct.setProvenance(Provenance.newInstance("Harvested", "0.9"));
|
||||
relList.add(direct);
|
||||
inverse.setTarget(Node.newInstance(id, "context"));
|
||||
inverse.setSource(Node.newInstance(oId, ModelSupport.idPrefixEntity.get(oId.substring(0, 2))));
|
||||
inverse.setReltype(RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP));
|
||||
inverse.setProvenance(Provenance.newInstance("Harvested", "0.9"));
|
||||
relList.add(inverse);
|
||||
|
||||
});
|
||||
|
||||
});
|
||||
|
||||
spark.createDataset(relList, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
|
||||
|
||||
|
||||
private static Set<String> extractRelation(SparkSession spark, String inputPath, OrganizationMap organizationMap) {
|
||||
Dataset<Relation> tmp = Utils.readPath(spark, inputPath, Relation.class);
|
||||
Set<String> organizationSet = organizationMap.keySet();
|
||||
Set<String> toCreateRels = new HashSet<>();
|
||||
|
||||
tmp.foreach((ForeachFunction<Relation>) relation -> {
|
||||
Optional<DataInfo> odInfo = Optional.ofNullable(relation.getDataInfo());
|
||||
if (odInfo.isPresent()) {
|
||||
if (!odInfo.get().getDeletedbyinference()) {
|
||||
if(relation.getRelClass().equals(ModelConstants.MERGES)){
|
||||
String oId = relation.getTarget();
|
||||
if (organizationSet.contains(oId)) {
|
||||
organizationSet.remove(oId);
|
||||
toCreateRels.add(relation.getSource());
|
||||
}
|
||||
}
|
||||
}
|
||||
}});
|
||||
|
||||
toCreateRels.addAll(organizationSet);
|
||||
return toCreateRels;
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue