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package eu.dnetlib.data.mapreduce.hbase.lodExport.utils;
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import eu.dnetlib.data.mapreduce.util.LicenseComparator;
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import eu.dnetlib.data.proto.DatasourceProtos.Datasource.Metadata;
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import eu.dnetlib.data.proto.FieldTypeProtos;
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import eu.dnetlib.data.proto.FieldTypeProtos.StringField;
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import eu.dnetlib.data.proto.FieldTypeProtos.Author;
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import eu.dnetlib.data.proto.FieldTypeProtos.StructuredProperty;
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import eu.dnetlib.data.proto.OafProtos.Oaf;
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import eu.dnetlib.data.proto.OafProtos.OafEntity;
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import eu.dnetlib.data.proto.OafProtos.OafRel;
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import eu.dnetlib.data.proto.OrganizationProtos.Organization;
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import eu.dnetlib.data.proto.ProjectProtos.Project;
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import eu.dnetlib.data.proto.ResultProtos.Result;
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import eu.dnetlib.data.proto.ResultProtos.Result.Instance;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Set;
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/**
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* @author eri Simple serializer that parses input Oaf Protos and prepares them
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* for sqoop
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*/
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public class Serializer {
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private static final String TEXT_PATTERN = "[^a-zA-Z0-9 .-_:/@+=-]";
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private static final String ID_PATTERN = "[^a-zA-Z0-9.:/_-]";
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private static final String DOI_PATTERN = ".*\\/(10.)";
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public static String serialize(Oaf oaf, String DELIM) {
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switch (oaf.getKind()) {
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case entity:
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OafEntity valueEntity = oaf.getEntity();
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switch (valueEntity.getType()) {
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case datasource:
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return buildDatasource(valueEntity, DELIM);
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case organization:
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return buildOrganization(valueEntity, DELIM);
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case project:
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return buildProject(valueEntity, DELIM);
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case result:
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return buildResult(valueEntity, DELIM);
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default:
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break;
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}
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break;
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case relation:
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OafRel valueRel = oaf.getRel();
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return serialize(valueRel, DELIM);
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}
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return null;
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}
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public static void extractRelations(Oaf oaf, String DELIM, Set<String> relations) {
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OafEntity valueEntity = oaf.getEntity();
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switch (valueEntity.getType()) {
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case result:
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getResultDatasources(valueEntity, DELIM, relations);
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getDedups(valueEntity, DELIM, relations);
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case datasource:
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getDedups(valueEntity, DELIM, relations);
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/*
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case person:
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getDedups(valueEntity, DELIM, relations);
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*/
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case organization:
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getDedups(valueEntity, DELIM, relations);
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default:
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}
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}
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public static String serialize(OafRel Rel, String DELIM) {
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StringBuilder buff;
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switch (Rel.getRelType()) {
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case datasourceOrganization:
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buff = new StringBuilder();
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buff.append(Rel.getRelType().name()).append(DELIM).append("datasource").append(DELIM).append(cleanId(Rel.getSource())).append(DELIM)
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.append("organization").append(DELIM).append(cleanId(Rel.getTarget())).append(DELIM).append("\n");
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return buff.toString();
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case resultResult:
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buff = new StringBuilder();
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buff.append(Rel.getRelType().name()).append(DELIM).append("result").append(DELIM).append(cleanId(Rel.getSource())).append(DELIM)
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.append("result").append(DELIM).append(cleanId(Rel.getTarget())).append(DELIM);
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return buff.toString();
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case organizationOrganization:
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buff = new StringBuilder();
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buff.append(Rel.getRelType().name()).append(DELIM).append("organization").append(DELIM).append(cleanId(Rel.getSource())).append(DELIM)
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.append("organization").append(DELIM).append(cleanId(Rel.getTarget())).append(DELIM);
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return buff.toString();
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case projectOrganization:
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buff = new StringBuilder();
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buff.append(Rel.getRelType().name()).append(DELIM).append("project").append(DELIM).append(cleanId(Rel.getSource())).append(DELIM)
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.append("organization").append(DELIM).append(cleanId(Rel.getTarget())).append(DELIM);
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return buff.toString();
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case resultOrganization:
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buff = new StringBuilder();
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buff.append(Rel.getRelType().name()).append(DELIM).append("result").append(DELIM).append(cleanId(Rel.getSource())).append(DELIM)
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.append("organization").append(DELIM).append(cleanId(Rel.getTarget())).append(DELIM);
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return buff.toString();
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//TODO - SOS RELATION RESULT PROJECT IS INVERTED! SOURCE IS PROJECT, TARGET IS RESULT
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case resultProject:
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buff = new StringBuilder();
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buff.append(Rel.getRelType().name()).append(DELIM).append("result").append(DELIM).append(cleanId(Rel.getTarget())).append(DELIM)
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.append("project").append(DELIM).append(cleanId(Rel.getSource())).append(DELIM);
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return buff.toString();
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default:
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}
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return "";
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}
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private static String getHeader(OafEntity data, String DELIM) {
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String SEPERATOR = ";";
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StringBuilder buff = new StringBuilder();
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// EntityType
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buff.append(data.getType().name()).append(DELIM);
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// OpenaireID
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buff.append(cleanId(data.getId())).append(DELIM);
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// dateOfTransformation
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// TODO CRITERIA FOR IDENTIFYING UPDATED RECORDS
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buff.append(cleanId(data.getDateoftransformation())).append(DELIM);
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// dateOfCollection
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buff.append(clean(data.getDateofcollection())).append(DELIM);
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String dataStr = new String();
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// originalId
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for (String oid : data.getOriginalIdList()) {
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dataStr += cleanDoi(oid) + SEPERATOR; //oid is not openaireid, clean instead of cleanid
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}
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buff.append(dataStr).append(DELIM);
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return buff.toString();
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}
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private static String buildDatasource(OafEntity data, String DELIM) {
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String SEPERATOR = ";";
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StringBuilder buff = new StringBuilder();
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buff.append(getHeader(data, DELIM));
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Metadata metadata = data.getDatasource().getMetadata();
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//Datasourcetype
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buff.append(clean(metadata.getDatasourcetype().getClassname())).append(DELIM);
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//Openairecompatibility
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buff.append(clean(metadata.getOpenairecompatibility().getClassname())).append(DELIM);
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//OfficialName
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buff.append(clean(metadata.getOfficialname().getValue())).append(DELIM);
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// Englishname
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buff.append(clean(metadata.getEnglishname().getValue())).append(DELIM);
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//Websiteurl
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buff.append(clean(metadata.getWebsiteurl().getValue())).append(DELIM);
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//LogoURL
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buff.append(clean(metadata.getLogourl().getValue())).append(DELIM);
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//Contactemail
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buff.append(clean(metadata.getContactemail().getValue())).append(DELIM);
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//Namespaceprefix
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buff.append(clean(metadata.getNamespaceprefix().getValue())).append(DELIM);
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// latitude
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buff.append(clean(metadata.getLatitude().getValue())).append(DELIM);
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// longtitude
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buff.append(clean(metadata.getLongitude().getValue())).append(DELIM);
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// dateofvalidation,
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buff.append(clean(metadata.getDateofvalidation().getValue())).append(DELIM);
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//Description
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buff.append(clean(metadata.getDescription().getValue())).append(DELIM);
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//subjects
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String subj = new String();
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for (StructuredProperty s : metadata.getSubjectsList()) {
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subj += clean(s.getValue()) + SEPERATOR;
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}
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//subjectList
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buff.append(clean(subj)).append(DELIM);
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//Number of items
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buff.append(clean(metadata.getOdnumberofitems().getValue())).append(DELIM);
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//Date of number of items
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buff.append(clean(metadata.getOdnumberofitemsdate().getValue())).append(DELIM);
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// Policies
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buff.append(clean(metadata.getOdpolicies().getValue())).append(DELIM);
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//languages
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String dataStr = new String();
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for (StringField lang : metadata.getOdlanguagesList()) {
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dataStr += clean(lang.getValue()) + SEPERATOR;
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}
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buff.append(dataStr).append(DELIM);
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;
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// Content type
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dataStr = " ";
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for (StringField c : metadata.getOdcontenttypesList()) {
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dataStr += clean(c.getValue()) + SEPERATOR;
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}
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buff.append(dataStr).append(DELIM);
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//Access info package
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dataStr = " ";
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for (StringField c : metadata.getAccessinfopackageList()) {
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dataStr += clean(c.getValue()) + SEPERATOR;
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}
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buff.append(dataStr).append(DELIM);
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//Release start date
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buff.append(clean(metadata.getReleasestartdate().getValue())).append(DELIM);
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//Release end date
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buff.append(clean(metadata.getReleaseenddate().getValue())).append(DELIM);
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//Mission statement url
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buff.append(clean(metadata.getMissionstatementurl().getValue())).append(DELIM);
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//Data provider
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buff.append(clean(String.valueOf(metadata.getDataprovider().getValue()))).append(DELIM);
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//Service provider
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buff.append(clean(String.valueOf(metadata.getServiceprovider().getValue()))).append(DELIM);
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//Database access type
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buff.append(clean(metadata.getDatabaseaccessrestriction().getValue())).append(DELIM);
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//Data upload type
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buff.append(clean(metadata.getDatauploadtype().getValue())).append(DELIM);
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//Data upload restrictions
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buff.append(clean(metadata.getDatauploadrestriction().getValue())).append(DELIM);
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//Versioning
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buff.append(clean(String.valueOf(metadata.getVersioning().getValue()))).append(DELIM);
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//Citation guideline url
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buff.append(clean(metadata.getCitationguidelineurl().getValue())).append(DELIM);
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//Quality management kind
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buff.append(clean(metadata.getQualitymanagementkind().getValue())).append(DELIM);
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//PID systems
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buff.append(clean(metadata.getPidsystems().getValue())).append(DELIM);
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//Certificates
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buff.append(clean(metadata.getCertificates().getValue())).append(DELIM);
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//Policies
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dataStr = " ";
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for (FieldTypeProtos.KeyValue property : metadata.getPoliciesList()) {
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dataStr += clean(property.getValue()) + SEPERATOR;
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}
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buff.append(dataStr).append(DELIM);
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buff.append(getTrust(data)).append(DELIM);
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return buff.toString();
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}
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private static String buildOrganization(OafEntity data, String DELIM) {
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String SEPERATOR = ";";
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StringBuilder buff = new StringBuilder();
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buff.append(getHeader(data, DELIM));
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Organization organization = data.getOrganization();
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Organization.Metadata metadata = organization.getMetadata();
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//getLegalshortname
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buff.append(clean(metadata.getLegalshortname().getValue())).append(DELIM);
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// `name`,
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buff.append(clean(metadata.getLegalname().getValue())).append(DELIM);
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//website URL
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String[] split = metadata.getWebsiteurl().getValue().split(",");
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String dataStr = new String();
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for (String s : split) {
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dataStr += s.replace(DELIM, " ") + SEPERATOR;
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}
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buff.append(dataStr).append(DELIM);
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//logourl
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buff.append(clean(metadata.getLogourl().getValue())).append(DELIM);
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// `country`,
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buff.append(clean(metadata.getCountry().getClassid())).append(DELIM);
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buff.append(getTrust(data)).append(DELIM);
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return buff.toString();
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}
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static String getTrust(OafEntity data) {
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for (FieldTypeProtos.ExtraInfo info : data.getExtraInfoList()) {
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return (info.getTrust());
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}
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return " ";
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}
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private static String buildResult(OafEntity data, String DELIM) {
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String SEPERATOR = ";";
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Result.Metadata metadata = data.getResult().getMetadata();
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338
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339
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StringBuilder buff = new StringBuilder();
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341
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buff.append(getHeader(data, DELIM));
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// titleString
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String dataStr = new String();
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for (int i = 0; i < metadata.getTitleList().size(); i++) {
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StructuredProperty title = metadata.getTitleList().get(i);
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dataStr = clean(title.getValue());
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break;
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}
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// pubtitle
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buff.append(clean(dataStr)).append(DELIM);
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// date of acceptance CHANGED THIS TO DATE FORMAT
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buff.append(clean(metadata.getDateofacceptance().getValue())).append(DELIM);
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// publisher
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buff.append(clean(metadata.getPublisher().getValue())).append(DELIM);
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361
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362
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//PID
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dataStr = " ";
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for (StructuredProperty p : data.getPidList()) {
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dataStr += clean(p.getValue()) + SEPERATOR;
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}
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368
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buff.append(dataStr).append(DELIM);
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370
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//language
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buff.append(clean(metadata.getLanguage().getClassid())).append(DELIM);
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373
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// RelevantDate
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dataStr = " ";
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375
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for (StructuredProperty p : metadata.getRelevantdateList()) {
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dataStr += clean(p.getValue());
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break;
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}
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380
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381
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buff.append(dataStr).append(DELIM);
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382
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383
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//Subject
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dataStr = " ";
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for (StructuredProperty subj : metadata.getSubjectList()) {
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386
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387
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if (subj.getValue() != null && !subj.getValue().isEmpty()) {
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dataStr += clean(subj.getValue()) + SEPERATOR;
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}
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390
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}
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391
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392
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buff.append(dataStr).append(DELIM);
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393
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394
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//TODO ExternalReference
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395
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396
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buff.append(" ").append(DELIM);
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397
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398
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//Source
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399
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dataStr = " ";
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400
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for (StringField s : metadata.getSourceList()) {
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401
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dataStr += clean(s.getValue()) + SEPERATOR;
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402
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}
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403
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404
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buff.append(dataStr).append(DELIM);
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405
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406
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//TODO Format
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buff.append(" ").append(DELIM);
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408
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409
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//Context
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dataStr = " ";
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411
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for (Result.Context s : metadata.getContextList()) {
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dataStr += clean(s.getId()) + SEPERATOR;
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}
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buff.append(dataStr).append(DELIM);
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416
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//country
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417
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418
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String country = " ";
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419
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for (FieldTypeProtos.Qualifier c : metadata.getCountryList()) {
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country += clean(c.getClassid()) + SEPERATOR;
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}
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423
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buff.append(country).append(DELIM);
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425
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426
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//Best License
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427
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buff.append(getBestLicense(data.getResult())).append(DELIM);
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428
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429
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//Description
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dataStr = " ";
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431
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432
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for (StringField desc : metadata.getDescriptionList()) {
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433
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dataStr += clean(desc.getValue());
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434
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break;
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435
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}
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436
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437
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buff.append(dataStr).append(DELIM);
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438
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439
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//Journal
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440
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buff.append(clean(metadata.getJournal().getName())).append(DELIM); //#null#!
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441
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442
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443
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// TODO ERI SOS : HERE IN GET JOUTNAL. GET DATA INFO I CAN FIND PROVENANCE AND SIMILARITY
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444
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445
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// TODO isRelatedTo
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446
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447
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// resource type
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448
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buff.append(clean(metadata.getResourcetype().getClassname())).append(DELIM);
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449
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// device
|
450
|
buff.append(clean(metadata.getDevice().getValue())).append(DELIM);
|
451
|
// size
|
452
|
buff.append(clean(metadata.getSize().getValue())).append(DELIM);
|
453
|
// version
|
454
|
buff.append(clean(metadata.getVersion().getValue())).append(DELIM);
|
455
|
|
456
|
// metadata update
|
457
|
buff.append(clean(metadata.getLastmetadataupdate().getValue())).append(DELIM);
|
458
|
// metadata version
|
459
|
buff.append(clean(metadata.getMetadataversionnumber().getValue())).append(DELIM);
|
460
|
|
461
|
// year
|
462
|
buff.append(clean(getYearInt(metadata.getDateofacceptance().getValue()))).append(DELIM);
|
463
|
|
464
|
// type
|
465
|
buff.append(clean(metadata.getResulttype().getClassname())).append(DELIM);
|
466
|
|
467
|
buff.append(getTrust(data)).append(DELIM);
|
468
|
|
469
|
//Authors
|
470
|
dataStr = " ";
|
471
|
for(Author p : metadata.getAuthorList()){
|
472
|
dataStr += clean(p.getFullname()) + SEPERATOR;
|
473
|
}
|
474
|
|
475
|
buff.append(dataStr).append(DELIM);
|
476
|
|
477
|
return buff.toString();
|
478
|
}
|
479
|
|
480
|
|
481
|
private static String buildProject(OafEntity data, String DELIM) {
|
482
|
String SEPERATOR = ";";
|
483
|
|
484
|
StringBuilder buff = new StringBuilder();
|
485
|
|
486
|
buff.append(getHeader(data, DELIM));
|
487
|
Project.Metadata metadata = data.getProject().getMetadata();
|
488
|
|
489
|
|
490
|
//Code
|
491
|
buff.append(metadata.getCode().getValue()).append(DELIM);
|
492
|
// `Websiteurl`,
|
493
|
buff.append(clean(metadata.getWebsiteurl().getValue())).append(DELIM);
|
494
|
//TODO here
|
495
|
|
496
|
// `Acronym`,
|
497
|
buff.append(clean(metadata.getAcronym().getValue())).append(DELIM);
|
498
|
|
499
|
//Title
|
500
|
buff.append(clean(metadata.getTitle().getValue())).append(DELIM);
|
501
|
|
502
|
// Startdate
|
503
|
buff.append(clean(metadata.getStartdate().getValue())).append(DELIM);
|
504
|
|
505
|
// Enddate
|
506
|
buff.append(clean(metadata.getEnddate().getValue())).append(DELIM);
|
507
|
|
508
|
//`Call identifer`
|
509
|
buff.append(clean(metadata.getCallidentifier().getValue())).append(DELIM);
|
510
|
|
511
|
//`KeyWords`
|
512
|
buff.append(clean(metadata.getKeywords().getValue())).append(DELIM);
|
513
|
|
514
|
//`Duration`
|
515
|
buff.append(clean(metadata.getDuration().getValue())).append(DELIM);
|
516
|
|
517
|
//esc39
|
518
|
buff.append(clean(metadata.getEcsc39().getValue())).append(DELIM);
|
519
|
|
520
|
//`Contracttype`
|
521
|
buff.append(clean(metadata.getContracttype().getClassname())).append(DELIM);
|
522
|
|
523
|
//`OA mandate pubs` TODO DOES NOT EXIST
|
524
|
buff.append(clean(metadata.getOamandatepublications().getValue())).append(DELIM);
|
525
|
//`Subjects`
|
526
|
String dataStr = new String();
|
527
|
for (StructuredProperty s : metadata.getSubjectsList()) {
|
528
|
|
529
|
dataStr += clean(s.getValue()) + SEPERATOR;
|
530
|
}
|
531
|
buff.append(dataStr).append(DELIM);
|
532
|
|
533
|
//`EC293`
|
534
|
buff.append(clean(metadata.getEcarticle293().getValue())).append(DELIM);
|
535
|
|
536
|
List<StringField> fundList = metadata.getFundingtreeList();
|
537
|
|
538
|
if (!fundList.isEmpty()) // `funding_lvl0`,
|
539
|
{//TODO funder + 3 funding levels
|
540
|
/* funder text,
|
541
|
funding_lvl0 text,
|
542
|
funding_lvl1 text,
|
543
|
funding_lvl2 text,
|
544
|
funding_lvl3 text,*/
|
545
|
buff.append(FundingParser.getFundingInfo(fundList.get(0).getValue(), DELIM));
|
546
|
} else {
|
547
|
|
548
|
buff.append(FundingParser.getFundingInfo("", DELIM));
|
549
|
}
|
550
|
|
551
|
buff.append(getTrust(data)).append(DELIM);
|
552
|
|
553
|
return buff.toString();
|
554
|
|
555
|
}
|
556
|
|
557
|
private static void getResultDatasources(OafEntity valueEntity, String DELIM, Set<String> returnList) {
|
558
|
String SEPERATOR = ";";
|
559
|
|
560
|
Result result = valueEntity.getResult();
|
561
|
|
562
|
if (valueEntity.getId().contains("dedup")) return;
|
563
|
|
564
|
//TODO hosted by
|
565
|
for (Instance instance : (result.getInstanceList())) {
|
566
|
String hostedBy = instance.getHostedby().getKey();
|
567
|
|
568
|
if (hostedBy != null && !hostedBy.isEmpty()) {
|
569
|
returnList.add("resultDatasource" + DELIM + "result" + DELIM +
|
570
|
cleanId(valueEntity.getId()) + DELIM + "datasource" + DELIM + cleanId(hostedBy) + DELIM);
|
571
|
}
|
572
|
}
|
573
|
|
574
|
//TODO collected froms
|
575
|
for (FieldTypeProtos.KeyValue collectedFromValue : (valueEntity.getCollectedfromList())) {
|
576
|
String collectedFrom = collectedFromValue.getKey();
|
577
|
if (collectedFrom != null && !collectedFrom.isEmpty())
|
578
|
returnList.add(("resultDatasource" + DELIM
|
579
|
+ "result" + DELIM + cleanId(valueEntity.getId()) + DELIM
|
580
|
+ "datasource" + DELIM + cleanId(collectedFrom) + DELIM));
|
581
|
|
582
|
}
|
583
|
|
584
|
|
585
|
}
|
586
|
|
587
|
|
588
|
public static String cleanId(String value) {
|
589
|
if (value == null) {
|
590
|
return " ";
|
591
|
}
|
592
|
|
593
|
// DO NOT CHANGE THIS: IT REMOVES ID PREFIX ( 5|datacite____::
|
594
|
// to datacite____:: )
|
595
|
// AND REPLACES OCCURENCES OF DELIM CHARS IN DATA
|
596
|
value = value.replaceFirst(".*\\|", "");
|
597
|
value = value.replaceAll(ID_PATTERN, "");
|
598
|
value = value.replace("#", " ");
|
599
|
value = value.replace("\n", " ");
|
600
|
return value;
|
601
|
}
|
602
|
|
603
|
private static String clean(String value) {
|
604
|
if (value == null) {
|
605
|
return " ";
|
606
|
}
|
607
|
|
608
|
|
609
|
// TODO DO NOT CHANGE THIS: IT REMOVES ID PREFIX ( 5|datacite____::
|
610
|
value = value.replaceAll("[\"\\r\\\\;]", "");
|
611
|
value = value.replace("\\", "");
|
612
|
value = value.replaceAll(TEXT_PATTERN, " ");
|
613
|
|
614
|
value = value.replace(">", " ");
|
615
|
value = value.replace("<", " ");
|
616
|
value = value.replace("\"", " ");
|
617
|
value = value.replace("\\", " ");
|
618
|
value = value.replace("'", " ");
|
619
|
value = value.replace("«", " ");
|
620
|
value = value.replace("»", " ");
|
621
|
value = value.replace("#", " ");
|
622
|
value = value.replace("\\", " ");
|
623
|
value = value.replace("\n", " ");
|
624
|
value = value.replace(",", "");
|
625
|
value = value.replace("#", "");
|
626
|
value = value.replace(";", "");
|
627
|
|
628
|
|
629
|
return value;
|
630
|
}
|
631
|
|
632
|
private static String cleanDoi(String value) {
|
633
|
value = value.replaceAll(DOI_PATTERN, "");
|
634
|
value = value.replace("#", " ");
|
635
|
value = value.replace("\n", " ");
|
636
|
return value;
|
637
|
}
|
638
|
|
639
|
|
640
|
//TODO make them in pairs
|
641
|
private static void getDedups(OafEntity valueEntity, String DELIM, Set<String> returnList) {
|
642
|
if (!valueEntity.getChildrenList().isEmpty() && valueEntity.getId().contains("dedup")) {
|
643
|
ArrayList<String> entries = new ArrayList<String>();
|
644
|
|
645
|
for (OafEntity child : valueEntity.getChildrenList()) {
|
646
|
if (child.getType() == valueEntity.getType() && !child.getId().contains("dedup")) {
|
647
|
// if it is result, then its the deduplication
|
648
|
entries.add(cleanId(child.getId()));
|
649
|
}
|
650
|
}
|
651
|
|
652
|
for (int i = 0; i < entries.size() - 1; i++) {
|
653
|
for (int j = i + 1; j < entries.size(); j++) {
|
654
|
returnList.add("dedup" + DELIM +
|
655
|
valueEntity.getType().name() + DELIM +
|
656
|
entries.get(i) + DELIM +
|
657
|
valueEntity.getType().name() + DELIM +
|
658
|
entries.get(j) + DELIM);
|
659
|
}
|
660
|
}
|
661
|
|
662
|
}
|
663
|
|
664
|
}
|
665
|
|
666
|
|
667
|
private static String getYearInt(String data) {
|
668
|
if (data == null || data.isEmpty() || data.equals("-1")) {
|
669
|
return " ";
|
670
|
}
|
671
|
String[] split = data.split("-");
|
672
|
|
673
|
if (split == null || split.length == 0) {
|
674
|
return " ";
|
675
|
}
|
676
|
|
677
|
|
678
|
return split[0];
|
679
|
|
680
|
|
681
|
}
|
682
|
|
683
|
|
684
|
private static String getBestLicense(Result result) {
|
685
|
FieldTypeProtos.Qualifier bestLicense = null;
|
686
|
LicenseComparator lc = new LicenseComparator();
|
687
|
for (Instance instance : (result.getInstanceList())) {
|
688
|
if (lc.compare(bestLicense, instance.getAccessright()) > 0) {
|
689
|
bestLicense = instance.getAccessright();
|
690
|
}
|
691
|
}
|
692
|
if (bestLicense != null) {
|
693
|
return bestLicense.getClassname();
|
694
|
} else {
|
695
|
return null;
|
696
|
}
|
697
|
}
|
698
|
|
699
|
|
700
|
}
|