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katerina.i
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package eu.dnetlib.data.claims.migration.handler;
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import eu.dnetlib.data.claims.migration.ClaimValidation;
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import eu.dnetlib.data.claims.migration.entity.Result;
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katerina.i
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import eu.dnetlib.data.claims.migration.parser.DMFParser;
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import eu.dnetlib.data.claimsDemo.*;
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import org.apache.log4j.Logger;
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import org.xml.sax.SAXException;
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.xpath.XPathExpressionException;
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import java.io.BufferedWriter;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.sql.Timestamp;
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import java.util.Date;
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katerina.i
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/**
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* Created by kiatrop on 5/2/2016.
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*/
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public class DMFResultHandler {
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private static final Logger logger = Logger.getLogger(DMFResultHandler.class);
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SqlDAO sqlDAO = null;
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QueryGenerator queryGenerator = null;
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DMFParser dmfParser = null;
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/**
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* Given an openaire id decides the datasource that the result was collected from
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* Default datasource is openaire
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* @param openaireId
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* @return collectedFrom datasource
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*/
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public static String identifyCollectedFrom(String openaireId){
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if(openaireId==null){
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return null;
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}
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if(openaireId.contains("crossref")){
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return ClaimUtils.COLLECTED_FROM_CROSSREF;
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}else if (openaireId.contains("datacite")){
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return ClaimUtils.COLLECTED_FROM_DATACITE;
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} else if (openaireId.contains("orcid")){
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return ClaimUtils.COLLECTED_FROM_ORCID;
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}else{
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return ClaimUtils.COLLECTED_FROM_OPENAIRE;
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}
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}
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private String fetchDMFResult(String id) throws SQLStoreException, SQLException {
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ResultSet rs = sqlDAO.executePreparedQuery(queryGenerator.generateSelectDMFByIdQuery(id));
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return rs.getString("xml");
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}
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public Result fetchResultByDMF(String dmf) throws IOException, SAXException, ParserConfigurationException {
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return dmfParser.dmf2Result(dmf);
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}
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public Result fetchResultById(String id) throws SQLStoreException, SQLException, ParserConfigurationException, SAXException, IOException {
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//TODO check
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return fetchResultByDMF(fetchDMFResult(id));
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// return ParsingClaimUtils.getResultFromDMF(fetchDMFResult(id));
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}
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/**
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*
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* @param dmf
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* @return DOI from DMF - a *valid* one
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* @throws IOException
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* @throws SAXException
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* @throws ParserConfigurationException
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* @throws XPathExpressionException
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*/
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public String fetchDoiByDMF(String dmf) throws IOException, SAXException, ParserConfigurationException, XPathExpressionException {
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return checkDoiValidity(dmfParser.getDOIIdentifierFromDMF(dmf));
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}
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public String fetchOrcidWorkByDMF(String dmf) throws IOException, SAXException, ParserConfigurationException, XPathExpressionException {
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return dmfParser.getOrcidworkIdentifierFromDMF(dmf);
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}
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public String fetchEmbargoEndDateByDMF(String dmf) throws IOException, SAXException, ParserConfigurationException, XPathExpressionException {
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return dmfParser.getEmbargoEndDateFromDMF(dmf);
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}
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public String fetchAccessRights(String dmf) throws IOException, SAXException, ParserConfigurationException, XPathExpressionException {
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return dmfParser.getAccessRightsFromDMF(dmf);
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}
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/**
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*
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*
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* @param doi
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* @return DOI String : the given one if it's valid
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* @throws Exception
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*/
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public static String checkDoiValidity(String doi) {
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if(doi==null){
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return null;
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}
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String newDoi = doi;
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try{
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PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter("invalid_dois.txt", true)));
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boolean isValid= SearchUtils.isDoiValid(doi);
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if(!isValid&&(doi.length() - (doi.replace("_", "")).length() > 1)){
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String transformDoi = doi.replace("_", "-");
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isValid=SearchUtils.isDoiValid(transformDoi);
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if(isValid){
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Date date= new java.util.Date();
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out.println(new Timestamp(date.getTime())+" - Invalid doi: "+doi+" replaced with : "+transformDoi);
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newDoi=transformDoi;
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}
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}else if(!isValid&&(doi.length() - (doi.replace("_", "")).length() == 1)) {
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String transformDoi = doi.replace("_", "-");
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isValid=SearchUtils.isDoiValid(transformDoi);
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if(isValid){
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Date date= new java.util.Date();
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out.println(new Timestamp(date.getTime())+" - Invalid doi: "+doi+" replaced with : "+transformDoi);
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newDoi = transformDoi;
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}
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}else if(!isValid) {
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String transformDoi =doi.replaceAll("\\p{C}", "");
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isValid=SearchUtils.isDoiValid(transformDoi);
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if(isValid){
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Date date= new java.util.Date();
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out.println(new Timestamp(date.getTime())+" - Invalid doi: "+doi+" replaced with (zero-width-char): "+transformDoi);
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newDoi = transformDoi;
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}
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}
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out.close();
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}catch (IOException e) {
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logger.error("Couldn't write to file " + "invalid_dois.txt",e);
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}
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return newDoi;
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}
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public SqlDAO getSqlDAO() {
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return sqlDAO;
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}
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public void setSqlDAO(SqlDAO sqlDAO) {
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this.sqlDAO = sqlDAO;
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}
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public QueryGenerator getQueryGenerator() {
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return queryGenerator;
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}
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public void setQueryGenerator(QueryGenerator queryGenerator) {
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this.queryGenerator = queryGenerator;
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}
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public DMFParser getDmfParser() {
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return dmfParser;
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}
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public void setDmfParser(DMFParser dmfParser) {
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this.dmfParser = dmfParser;
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}
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}
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