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package eu.dnetlib.data.claims.migration;
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import eu.dnetlib.data.claims.migration.entity.*;
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import eu.dnetlib.data.claims.migration.handler.*;
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import eu.dnetlib.data.claimsDemo.ClaimUtils;
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import eu.dnetlib.data.claimsDemo.SQLStoreException;
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import org.apache.log4j.BasicConfigurator;
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import org.apache.log4j.Level;
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import org.apache.log4j.Logger;
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import org.springframework.context.ApplicationContext;
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import org.springframework.context.support.ClassPathXmlApplicationContext;
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import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
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import java.io.*;
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import java.math.BigInteger;
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import java.security.MessageDigest;
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import java.sql.Timestamp;
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import java.util.ArrayList;
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import java.util.Date;
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import java.util.List;
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/**
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* Created by kiatrop on 4/2/2016.
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*/
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public class Migration {
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private static final Logger logger = Logger.getLogger(Migration.class);
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RelationHandler relationHandler = null;
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ContextRelationHandler contextRelationHandler = null;
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ProjectHandler projectHandler = null;
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DMFContextHandler dmfContextHandler = null;
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DMFResultHandler dmfResultHandler = null;
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IndexResultHandler indexResultHandler = null;
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ExternalRecordHandler externalRecordHandler = null;
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ResultHandler resultHandler = null;
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ClaimHandler claimHandler = null;
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ClaimValidation claimValidation = new ClaimValidation();
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public Migration() {
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ApplicationContext context = new ClassPathXmlApplicationContext("eu/dnetlib/data/claims/migration/springContext-claimsDemo.xml");
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relationHandler = context.getBean(RelationHandler.class);
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contextRelationHandler = context.getBean(ContextRelationHandler.class);
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projectHandler = context.getBean(ProjectHandler.class);
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dmfContextHandler = context.getBean(DMFContextHandler.class);
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dmfResultHandler = context.getBean(DMFResultHandler.class);
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externalRecordHandler = context.getBean(ExternalRecordHandler.class);
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indexResultHandler = context.getBean(IndexResultHandler.class);
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resultHandler = context.getBean(ResultHandler.class);
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claimHandler = context.getBean(ClaimHandler.class);
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claimValidation = context.getBean(ClaimValidation.class);
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}
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public List<Claim> createRelationsClaims() throws Exception, SQLStoreException {
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List<Relation> relations = relationHandler.fetchAllRelations();
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List<Claim> claims = new ArrayList<Claim>();
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for (Relation relation : relations) {
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Claim claim= new Claim();
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claim.setUserMail(relation.getClaimedBy());
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claim.setDate(relation.getClaimDate());
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claim.setId(relation.getClaimId());
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System.out.println("Claim id:" + claim.getId());
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OpenaireEntity source = null;
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//first work with the Source
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if (relation.getSourceType().equals(ClaimUtils.PROJECT)) {
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source= buildProject(relation.getSourceId(),relation.getClaimId());
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claim.setSourceType(ClaimUtils.PROJECT);
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} else if (relation.getSourceType().equals(ClaimUtils.CONTEXT)) {
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Context context = dmfContextHandler.fetchContextByIdFromDmf(relation.getSourceId());
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source = context;
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claim.setSourceType(ClaimUtils.CONTEXT);
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} else if (relation.getSourceType().equals(ClaimUtils.DATASET) || relation.getSourceType().equals(ClaimUtils.PUBLICATION)) {
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Result result = buildResult(relation.getDmf(), relation.getCollectedFrom(), relation.getSourceId(), relation.getClaimId());
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source = result;
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claim.setSourceType(result.getResultType());
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}
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claim.setSource(source);
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Result target = null;
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if (relation.getTargetType().equals(ClaimUtils.DATASET) || relation.getTargetType().equals(ClaimUtils.PUBLICATION)) {
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target = buildResult(relation.getDmf(), relation.getCollectedFrom(), relation.getTargetId(), relation.getClaimId());
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}
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if( target != null) {
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claim.setTarget(target);
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claim.setTargetType(target.getResultType());
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}
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if(claimValidation.validateClaim(claim)){ // is valid
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// System.out.println(claim);
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claims.add(claim);
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}
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}
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return claims;
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}
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public void createAndSaveRelationsClaims(boolean save) throws Exception, SQLStoreException {
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/*for stats*/
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List<Claim> claimsOp= new ArrayList<Claim>();
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List<Claim> claimsCr= new ArrayList<Claim>();
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List<Claim> claimsDat= new ArrayList<Claim>();
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List<Claim> claimsOrc= new ArrayList<Claim>();
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Integer targetOp=0;
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Integer targetCr=0;
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Integer targetDat=0;
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Integer targetOrc=0;
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Integer sourceRes=0;
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Integer sourceOp=0;
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Integer sourceCr=0;
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Integer sourceDat=0;
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Integer sourceOrc=0;
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Integer projects=0;
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Integer contexts=0;
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Integer totalClaims=0;
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List<Relation> relations = relationHandler.fetchAllRelations();
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List<Claim> claims = new ArrayList<Claim>();
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logger.info("Relation size: "+relations.size());
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for (Relation relation : relations) {
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try {
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Claim claim = new Claim();
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claim.setUserMail(relation.getClaimedBy());
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claim.setDate(relation.getClaimDate());
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claim.setId(relation.getClaimId());
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logger.info("Claim id:" + claim.getId());
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OpenaireEntity source = null;
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//first work with the Source
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if (relation.getSourceType().equals(ClaimUtils.PROJECT)) {
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source = buildProject(relation.getSourceId(), relation.getClaimId());
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claim.setSourceType(ClaimUtils.PROJECT);
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} else if (relation.getSourceType().equals(ClaimUtils.CONTEXT)) {
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Context context = dmfContextHandler.fetchContextByIdFromDmf(relation.getSourceId());
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source = context;
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claim.setSourceType(ClaimUtils.CONTEXT);
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} else if (relation.getSourceType().equals(ClaimUtils.DATASET) || relation.getSourceType().equals(ClaimUtils.PUBLICATION)) {
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Result result = buildResult(relation.getDmf(), relation.getCollectedFrom(), relation.getSourceId(), relation.getClaimId());
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source = result;
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claim.setSourceType(result.getResultType());
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}
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claim.setSource(source);
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Result target = null;
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if (relation.getTargetType().equals(ClaimUtils.DATASET) || relation.getTargetType().equals(ClaimUtils.PUBLICATION)) {
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target = buildResult(relation.getDmf(), relation.getCollectedFrom(), relation.getTargetId(), relation.getClaimId());
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}
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if (target != null) {
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claim.setTarget(target);
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claim.setTargetType(target.getResultType());
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}
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if (claimValidation.validateClaim(claim)) { // is valid
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if(save) {
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claim = claimHandler.exportMedatataForClaim(claim);
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claimHandler.saveClaim(claim);
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}
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/*for stats*/
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if(((Result)claim.getTarget()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_CROSSREF)){
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targetCr++;
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}else if(((Result)claim.getTarget()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_DATACITE)){
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targetDat++;
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}else if(((Result)claim.getTarget()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_ORCID)){
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targetOrc++;
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}else {
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targetOp++;
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}
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if(claim.getSourceType().equals(ClaimUtils.PUBLICATION)||claim.getSourceType().equals(ClaimUtils.DATASET)){
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sourceRes++;
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if(((Result)claim.getSource()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_CROSSREF)){
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sourceCr++;
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}else if(((Result)claim.getSource()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_DATACITE)){
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sourceDat++;
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}else if(((Result)claim.getSource()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_ORCID)){
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sourceOrc++;
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}else {
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sourceOp++;
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}
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}else if(claim.getSourceType().equals(ClaimUtils.PROJECT)) {
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projects++;
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}else if(claim.getSourceType().equals(ClaimUtils.CONTEXT)){
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contexts++;
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}
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}
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}catch (Exception e){
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e.printStackTrace();
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logger.error("Exception: "+e.getMessage());
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}
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}
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/*for stats*/
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System.out.println("\n\nTargets:\n\nCrossref : "+targetCr+ " DataCite :"+targetDat+" Orcid : "+targetOrc+" OpenAire : "+targetOp);
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System.out.println("\n\nSources:\n\nAll : "+sourceRes+" Crossref : "+sourceCr+ " DataCite :"+sourceDat+" Orcid : "+sourceOrc+" OpenAire : "+sourceOp);
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System.out.println("\n\nTotalClaims: "+totalClaims+" Projects: "+projects+ " Contexts :"+contexts);
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}
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public List<Claim> createContextRelationClaims() throws Exception, SQLStoreException {
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List<ContextRelation> relations = contextRelationHandler.fetchAllConceptRelations();
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List<Claim> claims = new ArrayList<Claim>();
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for (ContextRelation relation : relations) {
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Claim claim= new Claim();
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claim.setId(relation.getClaimId());
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claim.setUserMail(relation.getClaimedBy());
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claim.setDate(relation.getClaimDate());
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System.out.println("Claim id:" + claim.getId());
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//first work with the Source
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Context context = dmfContextHandler.extractContextFromDMF(relation.getContextDmf());
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claim.setSourceType(ClaimUtils.CONTEXT);
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claim.setSource(context);
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Result target = buildResult(relation.getResultDmf(), relation.getCollectedFrom(), relation.getResultId(), relation.getClaimId());
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if( target != null){
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| 230 |
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claim.setTarget(target);
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| 231 |
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claim.setTargetType(target.getResultType());
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| 232 |
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}
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| 233 |
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if(claimValidation.validateClaim(claim)){ // is valid
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claims.add(claim);
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}
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}
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return claims;
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}
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public void createAndSaveContextRelationClaims(Boolean save) throws Exception, SQLStoreException {
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| 243 |
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/*for stats*/
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| 244 |
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List<Claim> claimsOp= new ArrayList<Claim>();
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| 245 |
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List<Claim> claimsCr= new ArrayList<Claim>();
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| 246 |
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List<Claim> claimsDat= new ArrayList<Claim>();
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| 247 |
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List<Claim> claimsOrc= new ArrayList<Claim>();
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| 248 |
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Integer targetOp=0;
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| 249 |
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Integer targetCr=0;
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| 250 |
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Integer targetDat=0;
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| 251 |
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Integer targetOrc=0;
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| 252 |
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Integer sourceRes=0;
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| 253 |
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Integer sourceOp=0;
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| 254 |
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Integer sourceCr=0;
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| 255 |
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Integer sourceDat=0;
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| 256 |
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Integer sourceOrc=0;
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| 257 |
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Integer projects=0;
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| 258 |
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Integer contexts=0;
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| 259 |
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Integer totalClaims=0;
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List<ContextRelation> relations = contextRelationHandler.fetchAllConceptRelations();
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| 262 |
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// List<Claim> claims = new ArrayList<Claim>();
|
| 263 |
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for (ContextRelation relation : relations) {
|
| 264 |
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| 265 |
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Claim claim= new Claim();
|
| 266 |
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claim.setId(relation.getClaimId());
|
| 267 |
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claim.setUserMail(relation.getClaimedBy());
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| 268 |
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claim.setDate(relation.getClaimDate());
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| 269 |
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logger.info("Claim id:" + claim.getId());
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| 270 |
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| 271 |
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//first work with the Source
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| 272 |
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Context context = dmfContextHandler.extractContextFromDMF(relation.getContextDmf());
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| 273 |
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claim.setSourceType(ClaimUtils.CONTEXT);
|
| 274 |
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claim.setSource(context);
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| 275 |
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| 276 |
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Result target = buildResult(relation.getResultDmf(), relation.getCollectedFrom(), relation.getResultId(), relation.getClaimId());
|
| 277 |
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if( target != null){
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| 278 |
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claim.setTarget(target);
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| 279 |
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claim.setTargetType(target.getResultType());
|
| 280 |
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}
|
| 281 |
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if(claimValidation.validateClaim(claim)){ // is valid
|
| 282 |
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if(save){
|
| 283 |
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claim = claimHandler.exportMedatataForClaim(claim);
|
| 284 |
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claimHandler.saveClaim(claim);
|
| 285 |
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}
|
| 286 |
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| 287 |
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/*for stats*/
|
| 288 |
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if(((Result)claim.getTarget()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_CROSSREF)){
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| 289 |
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targetCr++;
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| 290 |
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}else if(((Result)claim.getTarget()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_DATACITE)){
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| 291 |
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targetDat++;
|
| 292 |
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}else if(((Result)claim.getTarget()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_ORCID)){
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| 293 |
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targetOrc++;
|
| 294 |
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}else {
|
| 295 |
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targetOp++;
|
| 296 |
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}
|
| 297 |
|
|
if(claim.getSourceType().equals(ClaimUtils.PUBLICATION)||claim.getSourceType().equals(ClaimUtils.DATASET)){
|
| 298 |
|
|
sourceRes++;
|
| 299 |
|
|
if(((Result)claim.getSource()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_CROSSREF)){
|
| 300 |
|
|
sourceCr++;
|
| 301 |
|
|
}else if(((Result)claim.getSource()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_DATACITE)){
|
| 302 |
|
|
sourceDat++;
|
| 303 |
|
|
}else if(((Result)claim.getSource()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_ORCID)){
|
| 304 |
|
|
sourceOrc++;
|
| 305 |
|
|
}else {
|
| 306 |
|
|
sourceOp++;
|
| 307 |
|
|
}
|
| 308 |
|
|
}else if(claim.getSourceType().equals(ClaimUtils.PROJECT)) {
|
| 309 |
|
|
projects++;
|
| 310 |
|
|
}else if(claim.getSourceType().equals(ClaimUtils.CONTEXT)){
|
| 311 |
|
|
contexts++;
|
| 312 |
|
|
}
|
| 313 |
|
|
}
|
| 314 |
|
|
|
| 315 |
|
|
|
| 316 |
|
|
}
|
| 317 |
|
|
|
| 318 |
|
|
/*for stats*/
|
| 319 |
|
|
System.out.println("\n\nTargets:\n\nCrossref : "+targetCr+ " DataCite :"+targetDat+" Orcid : "+targetOrc+" OpenAire : "+targetOp);
|
| 320 |
|
|
System.out.println("\n\nSources:\n\nAll : "+sourceRes+" Crossref : "+sourceCr+ " DataCite :"+sourceDat+" Orcid : "+sourceOrc+" OpenAire : "+sourceOp);
|
| 321 |
|
|
System.out.println("\n\nTotalClaims: "+totalClaims+" Projects: "+projects+ " Contexts :"+contexts);
|
| 322 |
|
|
|
| 323 |
|
|
}
|
| 324 |
|
|
|
| 325 |
41254
|
argiro.kok
|
/**
|
| 326 |
41621
|
argiro.kok
|
*Returns a project from Openaire.
|
| 327 |
|
|
* In case the project id has a "welcometrust" prefix changes it to "wt__________", before search for it in the index.
|
| 328 |
|
|
*
|
| 329 |
|
|
* @param projectId
|
| 330 |
|
|
* @param claimId
|
| 331 |
|
|
* @return Project
|
| 332 |
|
|
* @throws Exception
|
| 333 |
|
|
*/
|
| 334 |
46918
|
argiro.kok
|
public Project buildProject(String projectId, String claimId) throws Exception {
|
| 335 |
47219
|
argiro.kok
|
String id = projectId;
|
| 336 |
41621
|
argiro.kok
|
if(projectId != null && projectId.contains("welcometrust")){
|
| 337 |
47219
|
argiro.kok
|
id=projectId.replace("welcometrust","wt__________");
|
| 338 |
41621
|
argiro.kok
|
}
|
| 339 |
49865
|
argiro.kok
|
Project project = projectHandler.fetchProjectByID(id, false);
|
| 340 |
41621
|
argiro.kok
|
if (project == null) {
|
| 341 |
49865
|
argiro.kok
|
project = projectHandler.fetchProjectByID(id, true);
|
| 342 |
|
|
}
|
| 343 |
|
|
if (project == null) {
|
| 344 |
41621
|
argiro.kok
|
try{
|
| 345 |
49865
|
argiro.kok
|
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(claimValidation.getPathToSaveReport()+"missing_projects.txt", true)));
|
| 346 |
41621
|
argiro.kok
|
Date date= new java.util.Date();
|
| 347 |
47219
|
argiro.kok
|
out.println(new Timestamp(date.getTime())+" ProjectId: "+id+ " ClaimId: "+claimId);
|
| 348 |
41621
|
argiro.kok
|
out.close();
|
| 349 |
|
|
}catch (IOException e) {
|
| 350 |
47219
|
argiro.kok
|
logger.error("Couldn't write to file " + "missing_projects.txt",e);
|
| 351 |
41621
|
argiro.kok
|
}
|
| 352 |
|
|
}
|
| 353 |
|
|
return project;
|
| 354 |
|
|
|
| 355 |
|
|
}
|
| 356 |
|
|
/**
|
| 357 |
41350
|
argiro.kok
|
* *If there is a dmf, the result is extracted from the external sources (crossRef, Datacite, Orcid)
|
| 358 |
41254
|
argiro.kok
|
* Otherwise Result is extracted from Openaire
|
| 359 |
41350
|
argiro.kok
|
* @param dmf
|
| 360 |
|
|
* @param collectedFrom
|
| 361 |
|
|
* @param resultId
|
| 362 |
|
|
* @param claimId
|
| 363 |
41254
|
argiro.kok
|
* @return Result or null
|
| 364 |
|
|
*/
|
| 365 |
41350
|
argiro.kok
|
private Result buildResult(String dmf, String collectedFrom, String resultId, String claimId){
|
| 366 |
41254
|
argiro.kok
|
Result result = null;
|
| 367 |
41444
|
argiro.kok
|
String external_id= null; // testing
|
| 368 |
41621
|
argiro.kok
|
if((dmf !=null && collectedFrom != null)&& !collectedFrom.equals(ClaimUtils.COLLECTED_FROM_OPENAIRE)){
|
| 369 |
41213
|
katerina.i
|
|
| 370 |
41350
|
argiro.kok
|
if (collectedFrom.equals(ClaimUtils.COLLECTED_FROM_CROSSREF)) {
|
| 371 |
41254
|
argiro.kok
|
try {
|
| 372 |
41350
|
argiro.kok
|
String doi= dmfResultHandler.fetchDoiByDMF(dmf);
|
| 373 |
41444
|
argiro.kok
|
external_id=doi;
|
| 374 |
41254
|
argiro.kok
|
if(doi != null) {
|
| 375 |
|
|
result = externalRecordHandler.fetchResultfromCrossref(doi);
|
| 376 |
|
|
}
|
| 377 |
|
|
} catch (Exception e) {
|
| 378 |
47219
|
argiro.kok
|
logger.error("Error fetching result from Crossref",e);
|
| 379 |
41444
|
argiro.kok
|
}
|
| 380 |
41213
|
katerina.i
|
|
| 381 |
41350
|
argiro.kok
|
} else if (collectedFrom.equals(ClaimUtils.COLLECTED_FROM_ORCID)) {
|
| 382 |
41254
|
argiro.kok
|
try {
|
| 383 |
41350
|
argiro.kok
|
String orcidwork= dmfResultHandler.fetchOrcidWorkByDMF(dmf);
|
| 384 |
41444
|
argiro.kok
|
external_id=orcidwork;
|
| 385 |
41350
|
argiro.kok
|
if(orcidwork != null) {
|
| 386 |
41254
|
argiro.kok
|
result = externalRecordHandler.fetchResultfromOrcid(orcidwork);
|
| 387 |
|
|
}
|
| 388 |
|
|
} catch (Exception e) {
|
| 389 |
47219
|
argiro.kok
|
logger.error("Error fetching result from Orcid",e);
|
| 390 |
41254
|
argiro.kok
|
}
|
| 391 |
41350
|
argiro.kok
|
} else if (collectedFrom.equals(ClaimUtils.COLLECTED_FROM_DATACITE)) {
|
| 392 |
41254
|
argiro.kok
|
try {
|
| 393 |
41350
|
argiro.kok
|
String doi= dmfResultHandler.fetchDoiByDMF(dmf);
|
| 394 |
41444
|
argiro.kok
|
external_id=doi;
|
| 395 |
41254
|
argiro.kok
|
if(doi != null) {
|
| 396 |
|
|
result = externalRecordHandler.fetchResultfromDatacite(doi);
|
| 397 |
|
|
}
|
| 398 |
|
|
} catch (Exception e) {
|
| 399 |
47219
|
argiro.kok
|
logger.error("Error fetching result from Datacite",e);
|
| 400 |
41254
|
argiro.kok
|
}
|
| 401 |
|
|
}
|
| 402 |
41449
|
argiro.kok
|
if(result == null){
|
| 403 |
|
|
//report missing external results
|
| 404 |
41350
|
argiro.kok
|
try{
|
| 405 |
47008
|
argiro.kok
|
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(claimValidation.getPathToSaveReport()+"missing_results_external_sources.txt", true)));
|
| 406 |
41350
|
argiro.kok
|
Date date= new java.util.Date();
|
| 407 |
41444
|
argiro.kok
|
out.println(new Timestamp(date.getTime())+" OpenaireId: "+resultId+ " collectedFrom: "+collectedFrom +" externalId: "+external_id+" claimId: "+claimId);
|
| 408 |
41350
|
argiro.kok
|
out.close();
|
| 409 |
|
|
}catch (IOException e) {
|
| 410 |
47219
|
argiro.kok
|
logger.error("Couldn't write to file " + "missing_results_external_sources.txt",e);
|
| 411 |
41350
|
argiro.kok
|
}
|
| 412 |
41449
|
argiro.kok
|
//give a second chance - search index
|
| 413 |
|
|
result = buildOpenaireResult(resultId,claimId);
|
| 414 |
41450
|
argiro.kok
|
if(result!=null) {
|
| 415 |
41449
|
argiro.kok
|
try {
|
| 416 |
47008
|
argiro.kok
|
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(claimValidation.getPathToSaveReport()+"external_results_found_inOpenaire.txt", true)));
|
| 417 |
41449
|
argiro.kok
|
Date date = new java.util.Date();
|
| 418 |
|
|
out.println(new Timestamp(date.getTime()) + " OpenaireId: " + resultId + " collectedFrom: " + collectedFrom + " externalId: " + external_id + " claimId: " + claimId);
|
| 419 |
|
|
out.close();
|
| 420 |
|
|
} catch (IOException e) {
|
| 421 |
47219
|
argiro.kok
|
logger.error("Couldn't write to file " + "external_results_found_inOpenaire.txt",e);
|
| 422 |
41449
|
argiro.kok
|
}
|
| 423 |
|
|
}
|
| 424 |
41350
|
argiro.kok
|
|
| 425 |
41254
|
argiro.kok
|
}
|
| 426 |
41449
|
argiro.kok
|
if(result!=null){
|
| 427 |
|
|
// if result found enriched with access rights/ embargo date from DMF
|
| 428 |
|
|
try {
|
| 429 |
|
|
result.setAccessRights(dmfResultHandler.fetchAccessRights(dmf));
|
| 430 |
|
|
result.setEmbargoEndDate(dmfResultHandler.fetchEmbargoEndDateByDMF(dmf));
|
| 431 |
|
|
} catch (Exception e) {
|
| 432 |
47219
|
argiro.kok
|
logger.error("Error fetching Access or Embargo end date from DMF",e);
|
| 433 |
41449
|
argiro.kok
|
}
|
| 434 |
|
|
}
|
| 435 |
|
|
} else { //If dmf/ collecteFrom is null or is collected from openaire search in the index
|
| 436 |
41350
|
argiro.kok
|
result = buildOpenaireResult(resultId,claimId);
|
| 437 |
41254
|
argiro.kok
|
}
|
| 438 |
41200
|
katerina.i
|
|
| 439 |
|
|
|
| 440 |
41254
|
argiro.kok
|
return result;
|
| 441 |
|
|
}
|
| 442 |
|
|
|
| 443 |
|
|
/**
|
| 444 |
|
|
*
|
| 445 |
41350
|
argiro.kok
|
* @param resultId
|
| 446 |
|
|
* @param claimId
|
| 447 |
41254
|
argiro.kok
|
* @return target Result from Openaire or null
|
| 448 |
|
|
*/
|
| 449 |
41350
|
argiro.kok
|
public Result buildOpenaireResult(String resultId, String claimId ){
|
| 450 |
41254
|
argiro.kok
|
|
| 451 |
|
|
Result result = null;
|
| 452 |
41350
|
argiro.kok
|
try {
|
| 453 |
49865
|
argiro.kok
|
result = indexResultHandler.fetchPublicationById(resultId, false);
|
| 454 |
41350
|
argiro.kok
|
} catch (Exception e) {
|
| 455 |
47219
|
argiro.kok
|
logger.error("Error fetching result from Openaire",e);
|
| 456 |
49865
|
argiro.kok
|
System.out.println("Error fetching result from Openaire");
|
| 457 |
41350
|
argiro.kok
|
}
|
| 458 |
|
|
|
| 459 |
41254
|
argiro.kok
|
//If it is not found in the index
|
| 460 |
|
|
if (result == null) {
|
| 461 |
41450
|
argiro.kok
|
//give a second chance as dedup
|
| 462 |
49865
|
argiro.kok
|
// try {
|
| 463 |
|
|
// result = indexResultHandler.fetchDedupResultById(resultId);
|
| 464 |
|
|
// } catch (Exception e) {
|
| 465 |
|
|
// logger.error("Error fetching dedup Result",e);
|
| 466 |
|
|
// }
|
| 467 |
|
|
//give a second chance in production
|
| 468 |
41450
|
argiro.kok
|
try {
|
| 469 |
49865
|
argiro.kok
|
result = indexResultHandler.fetchPublicationById(resultId, true);
|
| 470 |
41450
|
argiro.kok
|
} catch (Exception e) {
|
| 471 |
49865
|
argiro.kok
|
logger.error("Error fetching result from Openaire",e);
|
| 472 |
|
|
System.out.println("Error fetching result from Openaire");
|
| 473 |
41254
|
argiro.kok
|
}
|
| 474 |
49865
|
argiro.kok
|
if (result == null) {
|
| 475 |
|
|
try {
|
| 476 |
|
|
result = indexResultHandler.fetchDatasetById(resultId, false);
|
| 477 |
|
|
} catch (Exception e) {
|
| 478 |
|
|
logger.error("Error fetching result from Openaire",e);
|
| 479 |
|
|
System.out.println("Error fetching result from Openaire");
|
| 480 |
|
|
}
|
| 481 |
|
|
}
|
| 482 |
|
|
if (result == null) {
|
| 483 |
|
|
try {
|
| 484 |
|
|
result = indexResultHandler.fetchDatasetById(resultId, true);
|
| 485 |
|
|
} catch (Exception e) {
|
| 486 |
|
|
logger.error("Error fetching result from Openaire",e);
|
| 487 |
|
|
System.out.println("Error fetching result from Openaire");
|
| 488 |
|
|
}
|
| 489 |
|
|
}
|
| 490 |
|
|
if (result == null) {
|
| 491 |
|
|
try {
|
| 492 |
|
|
result = indexResultHandler.fetchDedupById(resultId, false);
|
| 493 |
|
|
} catch (Exception e) {
|
| 494 |
|
|
logger.error("Error fetching result from Openaire",e);
|
| 495 |
|
|
System.out.println("Error fetching result from Openaire");
|
| 496 |
|
|
}
|
| 497 |
|
|
}
|
| 498 |
|
|
// if (result == null) {
|
| 499 |
|
|
// try {
|
| 500 |
|
|
// result = indexResultHandler.fetchDedupById(resultId, true);
|
| 501 |
|
|
// } catch (Exception e) {
|
| 502 |
|
|
// logger.error("Error fetching result from Openaire",e);
|
| 503 |
|
|
// System.out.println("Error fetching result from Openaire");
|
| 504 |
|
|
// }
|
| 505 |
|
|
// }
|
| 506 |
41450
|
argiro.kok
|
if (result != null) {
|
| 507 |
|
|
try {
|
| 508 |
47008
|
argiro.kok
|
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(claimValidation.getPathToSaveReport()+"dedup_results_found.txt", true)));
|
| 509 |
41450
|
argiro.kok
|
Date date = new java.util.Date();
|
| 510 |
|
|
out.println(new Timestamp(date.getTime()) + " OpenaireId: " + resultId + " claimId: " + claimId);
|
| 511 |
|
|
out.close();
|
| 512 |
|
|
} catch (IOException e) {
|
| 513 |
47219
|
argiro.kok
|
logger.error("Couldn't write to file " + "external_results_found_inOpenaire.txt",e);
|
| 514 |
41450
|
argiro.kok
|
}
|
| 515 |
|
|
}else {
|
| 516 |
|
|
//report it as missing
|
| 517 |
|
|
try {
|
| 518 |
47008
|
argiro.kok
|
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(claimValidation.getPathToSaveReport()+"missing_results.txt", true)));
|
| 519 |
41450
|
argiro.kok
|
Date date = new java.util.Date();
|
| 520 |
|
|
out.println(new Timestamp(date.getTime()) + " OpenaireId: " + resultId + " ClaimId: " + claimId);
|
| 521 |
|
|
out.close();
|
| 522 |
|
|
} catch (IOException e) {
|
| 523 |
47219
|
argiro.kok
|
logger.error("Couldn't write to file " + "missing_results.txt",e);
|
| 524 |
41450
|
argiro.kok
|
}
|
| 525 |
|
|
}
|
| 526 |
|
|
|
| 527 |
41350
|
argiro.kok
|
}else{
|
| 528 |
|
|
//FOUND report results that came from datacite but are publications
|
| 529 |
|
|
//TODO deal with them as externals?
|
| 530 |
|
|
|
| 531 |
|
|
if(result.getProvenanceaction() != null && result.getProvenanceaction().equals("user:claim:datacite")&&result.getOai()!=null){
|
| 532 |
|
|
try{
|
| 533 |
47008
|
argiro.kok
|
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(claimValidation.getPathToSaveReport()+"datacite_claim_results.txt", true)));
|
| 534 |
41350
|
argiro.kok
|
Date date= new java.util.Date();
|
| 535 |
41444
|
argiro.kok
|
out.println(new Timestamp(date.getTime())+" openaireId:"+resultId+" aoi: " +result.getOai() +" provenanceactions: "+result.getProvenanceaction()+" type: "+result.getResultType()+ " ClaimId: "+claimId);
|
| 536 |
41350
|
argiro.kok
|
out.close();
|
| 537 |
|
|
try {
|
| 538 |
|
|
result= externalRecordHandler.fetchResultfromDatacite(result.getOai());
|
| 539 |
|
|
result.setOpenaireId(resultId);
|
| 540 |
|
|
}catch(Exception e){
|
| 541 |
47219
|
argiro.kok
|
logger.error("Couldn't get Result from Datacite "+result.getOai(),e);
|
| 542 |
41350
|
argiro.kok
|
}
|
| 543 |
|
|
}catch (IOException e) {
|
| 544 |
47219
|
argiro.kok
|
logger.error("Couldn't write to file " + "datacite_claim_results.txt",e);
|
| 545 |
41350
|
argiro.kok
|
}
|
| 546 |
|
|
|
| 547 |
|
|
}
|
| 548 |
41200
|
katerina.i
|
}
|
| 549 |
|
|
|
| 550 |
41254
|
argiro.kok
|
return result;
|
| 551 |
41200
|
katerina.i
|
}
|
| 552 |
|
|
|
| 553 |
41350
|
argiro.kok
|
|
| 554 |
|
|
/**
|
| 555 |
|
|
* For each claim of the list
|
| 556 |
|
|
* if there are results in the relation exports their metadaa file
|
| 557 |
|
|
* Save the claim in DB
|
| 558 |
|
|
* @param claims
|
| 559 |
|
|
* @throws Exception
|
| 560 |
|
|
*/
|
| 561 |
47219
|
argiro.kok
|
private void saveClaims(List<Claim> claims) throws Exception, SQLStoreException {
|
| 562 |
41350
|
argiro.kok
|
for(Claim claim : claims){
|
| 563 |
41791
|
argiro.kok
|
/* if(claim.getTargetType().equals(ClaimUtils.DATASET)||claim.getTargetType().equals(ClaimUtils.PUBLICATION)){
|
| 564 |
41350
|
argiro.kok
|
String path = resultHandler.exportMetadataFileForResult((Result)claim.getTarget());
|
| 565 |
41408
|
argiro.kok
|
((Result) claim.getTarget()).setRecordPath(path);
|
| 566 |
41350
|
argiro.kok
|
}
|
| 567 |
|
|
if(claim.getSourceType().equals(ClaimUtils.DATASET)||claim.getSourceType().equals(ClaimUtils.PUBLICATION)){
|
| 568 |
|
|
String path = resultHandler.exportMetadataFileForResult((Result)claim.getSource());
|
| 569 |
41408
|
argiro.kok
|
((Result) claim.getSource()).setRecordPath(path);
|
| 570 |
41791
|
argiro.kok
|
}*/
|
| 571 |
|
|
claim = claimHandler.exportMedatataForClaim(claim);
|
| 572 |
41350
|
argiro.kok
|
claimHandler.saveClaim(claim);
|
| 573 |
|
|
}
|
| 574 |
|
|
|
| 575 |
|
|
}
|
| 576 |
|
|
|
| 577 |
41791
|
argiro.kok
|
|
| 578 |
|
|
|
| 579 |
47008
|
argiro.kok
|
public static void main(String[] args) throws IOException {
|
| 580 |
49865
|
argiro.kok
|
BasicConfigurator.configure();
|
| 581 |
|
|
logger.setLevel(Level.DEBUG);
|
| 582 |
41350
|
argiro.kok
|
Migration migration = new Migration();
|
| 583 |
|
|
try {
|
| 584 |
49865
|
argiro.kok
|
// migration.claimHandler.getQueryGenerator().setMigrationTable("claims_view");
|
| 585 |
|
|
// migration.createAndSaveRelationsClaims(true);
|
| 586 |
|
|
// migration.createAndSaveContextRelationClaims(true);
|
| 587 |
41444
|
argiro.kok
|
|
| 588 |
49865
|
argiro.kok
|
migration.claimHandler.getQueryGenerator().setMigrationTable("export_last_claims");
|
| 589 |
|
|
migration.createAndSaveRelationsClaims(true);
|
| 590 |
|
|
migration.createAndSaveContextRelationClaims(true);
|
| 591 |
41350
|
argiro.kok
|
|
| 592 |
49865
|
argiro.kok
|
|
| 593 |
41350
|
argiro.kok
|
} catch (Exception e) {
|
| 594 |
47219
|
argiro.kok
|
logger.error("Error in migration",e);
|
| 595 |
|
|
} catch (SQLStoreException e) {
|
| 596 |
41350
|
argiro.kok
|
e.printStackTrace();
|
| 597 |
|
|
}
|
| 598 |
47008
|
argiro.kok
|
|
| 599 |
41200
|
katerina.i
|
}
|
| 600 |
41350
|
argiro.kok
|
public void printStatistics(List<Claim> claims){
|
| 601 |
41254
|
argiro.kok
|
|
| 602 |
41350
|
argiro.kok
|
//testing
|
| 603 |
|
|
List<Claim> claimsOp= new ArrayList<Claim>();
|
| 604 |
|
|
List<Claim> claimsCr= new ArrayList<Claim>();
|
| 605 |
|
|
List<Claim> claimsDat= new ArrayList<Claim>();
|
| 606 |
|
|
List<Claim> claimsOrc= new ArrayList<Claim>();
|
| 607 |
|
|
Integer targetOp=0;
|
| 608 |
|
|
Integer targetCr=0;
|
| 609 |
|
|
Integer targetDat=0;
|
| 610 |
|
|
Integer targetOrc=0;
|
| 611 |
|
|
Integer sourceRes=0;
|
| 612 |
|
|
Integer sourceOp=0;
|
| 613 |
|
|
Integer sourceCr=0;
|
| 614 |
|
|
Integer sourceDat=0;
|
| 615 |
|
|
Integer sourceOrc=0;
|
| 616 |
|
|
Integer projects=0;
|
| 617 |
|
|
Integer contexts=0;
|
| 618 |
|
|
Integer totalClaims=0;
|
| 619 |
|
|
for(Claim claim: claims){
|
| 620 |
41444
|
argiro.kok
|
// System.out.println(claim.toString());
|
| 621 |
41350
|
argiro.kok
|
if(((Result)claim.getTarget()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_CROSSREF)){
|
| 622 |
|
|
targetCr++;
|
| 623 |
|
|
}else if(((Result)claim.getTarget()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_DATACITE)){
|
| 624 |
|
|
targetDat++;
|
| 625 |
|
|
}else if(((Result)claim.getTarget()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_ORCID)){
|
| 626 |
|
|
targetOrc++;
|
| 627 |
|
|
}else {
|
| 628 |
|
|
targetOp++;
|
| 629 |
|
|
}
|
| 630 |
|
|
if(claim.getSourceType().equals(ClaimUtils.PUBLICATION)||claim.getSourceType().equals(ClaimUtils.DATASET)){
|
| 631 |
|
|
sourceRes++;
|
| 632 |
|
|
if(((Result)claim.getSource()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_CROSSREF)){
|
| 633 |
|
|
sourceCr++;
|
| 634 |
|
|
}else if(((Result)claim.getSource()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_DATACITE)){
|
| 635 |
|
|
sourceDat++;
|
| 636 |
|
|
}else if(((Result)claim.getSource()).getCollectedFrom().equals(ClaimUtils.COLLECTED_FROM_ORCID)){
|
| 637 |
|
|
sourceOrc++;
|
| 638 |
|
|
}else {
|
| 639 |
|
|
sourceOp++;
|
| 640 |
|
|
}
|
| 641 |
|
|
}else if(claim.getSourceType().equals(ClaimUtils.PROJECT)) {
|
| 642 |
|
|
projects++;
|
| 643 |
|
|
}else if(claim.getSourceType().equals(ClaimUtils.CONTEXT)){
|
| 644 |
|
|
contexts++;
|
| 645 |
|
|
}
|
| 646 |
|
|
}
|
| 647 |
|
|
totalClaims=claims.size();
|
| 648 |
|
|
System.out.println("\n\nTargets:\n\nCrossref : "+targetCr+ " DataCite :"+targetDat+" Orcid : "+targetOrc+" OpenAire : "+targetOp);
|
| 649 |
|
|
System.out.println("\n\nSources:\n\nAll : "+sourceRes+" Crossref : "+sourceCr+ " DataCite :"+sourceDat+" Orcid : "+sourceOrc+" OpenAire : "+sourceOp);
|
| 650 |
|
|
System.out.println("\n\nTotalClaims: "+totalClaims+" Projects: "+projects+ " Contexts :"+contexts);
|
| 651 |
41254
|
argiro.kok
|
|
| 652 |
41350
|
argiro.kok
|
}
|
| 653 |
|
|
|
| 654 |
|
|
|
| 655 |
41200
|
katerina.i
|
}
|