forked from D-Net/dnet-hadoop
488 lines
21 KiB
Java
488 lines
21 KiB
Java
package eu.dnetlib.dhp.migration;
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import java.io.Closeable;
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import java.io.IOException;
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import java.sql.Array;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Date;
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import java.util.List;
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import java.util.function.Consumer;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Datasource;
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import eu.dnetlib.dhp.schema.oaf.Organization;
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import eu.dnetlib.dhp.schema.oaf.Project;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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public class MigrateDbEntitiesApplication extends AbstractMigrateApplication implements Closeable {
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private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = MigrationUtils
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.qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenance_actions", "dnet:provenance_actions");
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private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class);
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private final DbClient dbClient;
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private final long lastUpdateTimestamp;
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(MigrateDbEntitiesApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json")));
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parser.parseArgument(args);
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final String dbUrl = parser.get("postgresUrl");
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final String dbUser = parser.get("postgresUser");
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final String dbPassword = parser.get("postgresPassword");
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final String hdfsPath = parser.get("hdfsPath");
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final String hdfsNameNode = parser.get("namenode");
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final String hdfsUser = parser.get("hdfsUser");
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try (final MigrateDbEntitiesApplication smdbe = new MigrateDbEntitiesApplication(hdfsPath, hdfsNameNode, hdfsUser, dbUrl, dbUser, dbPassword)) {
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smdbe.execute("queryDatasources.sql", smdbe::processDatasource);
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smdbe.execute("queryProjects.sql", smdbe::processProject);
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smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
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smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
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smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
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}
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}
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public MigrateDbEntitiesApplication(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String dbUrl, final String dbUser,
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final String dbPassword) throws Exception {
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super(hdfsPath, hdfsNameNode, hdfsUser);
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this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
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this.lastUpdateTimestamp = new Date().getTime();
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}
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public void execute(final String sqlFile, final Consumer<ResultSet> consumer) throws Exception {
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final String sql = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/migration/sql/" + sqlFile));
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dbClient.processResults(sql, consumer);
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}
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public void processDatasource(final ResultSet rs) {
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try {
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final DataInfo info = prepareDataInfo(rs);
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final Datasource ds = new Datasource();
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ds.setId(MigrationUtils.createOpenaireId("10", rs.getString("datasourceid")));
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ds.setOriginalId(Arrays.asList(rs.getString("datasourceid")));
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ds.setCollectedfrom(MigrationUtils.listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")));
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ds.setPid(null); // List<StructuredProperty> // TODO
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ds.setDateofcollection(rs.getDate("dateofcollection").toString());
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ds.setDateoftransformation(null); // TODO
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ds.setExtraInfo(null); // TODO
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ds.setOaiprovenance(null); // TODO
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ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype")));
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ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility")));
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ds.setOfficialname(MigrationUtils.field(rs.getString("officialname"), info));
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ds.setEnglishname(MigrationUtils.field(rs.getString("englishname"), info));
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ds.setWebsiteurl(MigrationUtils.field(rs.getString("websiteurl"), info));
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ds.setLogourl(MigrationUtils.field(rs.getString("logourl"), info));
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ds.setContactemail(MigrationUtils.field(rs.getString("contactemail"), info));
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ds.setNamespaceprefix(MigrationUtils.field(rs.getString("namespaceprefix"), info));
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ds.setLatitude(MigrationUtils.field(Double.toString(rs.getDouble("latitude")), info));
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ds.setLongitude(MigrationUtils.field(Double.toString(rs.getDouble("longitude")), info));
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ds.setDateofvalidation(MigrationUtils.field(rs.getDate("dateofvalidation").toString(), info));
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ds.setDescription(MigrationUtils.field(rs.getString("description"), info));
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ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info));
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ds.setOdnumberofitems(MigrationUtils.field(Double.toString(rs.getInt("odnumberofitems")), info));
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ds.setOdnumberofitemsdate(MigrationUtils.field(rs.getDate("odnumberofitemsdate").toString(), info));
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ds.setOdpolicies(MigrationUtils.field(rs.getString("odpolicies"), info));
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ds.setOdlanguages(MigrationUtils.listFields(info, rs.getArray("odlanguages")));
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ds.setOdcontenttypes(MigrationUtils.listFields(info, rs.getArray("odcontenttypes")));
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ds.setAccessinfopackage(MigrationUtils.listFields(info, rs.getArray("accessinfopackage")));
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ds.setReleasestartdate(MigrationUtils.field(rs.getDate("releasestartdate").toString(), info));
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ds.setReleaseenddate(MigrationUtils.field(rs.getDate("releaseenddate").toString(), info));
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ds.setMissionstatementurl(MigrationUtils.field(rs.getString("missionstatementurl"), info));
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ds.setDataprovider(MigrationUtils.field(rs.getBoolean("dataprovider"), info));
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ds.setServiceprovider(MigrationUtils.field(rs.getBoolean("serviceprovider"), info));
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ds.setDatabaseaccesstype(MigrationUtils.field(rs.getString("databaseaccesstype"), info));
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ds.setDatauploadtype(MigrationUtils.field(rs.getString("datauploadtype"), info));
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ds.setDatabaseaccessrestriction(MigrationUtils.field(rs.getString("databaseaccessrestriction"), info));
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ds.setDatauploadrestriction(MigrationUtils.field(rs.getString("datauploadrestriction"), info));
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ds.setVersioning(MigrationUtils.field(rs.getBoolean("versioning"), info));
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ds.setCitationguidelineurl(MigrationUtils.field(rs.getString("citationguidelineurl"), info));
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ds.setQualitymanagementkind(MigrationUtils.field(rs.getString("qualitymanagementkind"), info));
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ds.setPidsystems(MigrationUtils.field(rs.getString("pidsystems"), info));
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ds.setCertificates(MigrationUtils.field(rs.getString("certificates"), info));
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ds.setPolicies(null); // List<KeyValue> // TODO
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ds.setJournal(null); // Journal // TODO
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ds.setDataInfo(info);
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ds.setLastupdatetimestamp(lastUpdateTimestamp);
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// rs.getString("datasourceid");
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rs.getArray("identities");
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// rs.getString("officialname");
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// rs.getString("englishname");
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// rs.getString("contactemail");
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// rs.getString("openairecompatibility"); // COMPLEX ...@@@...
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// rs.getString("websiteurl");
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// rs.getString("logourl");
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// rs.getArray("accessinfopackage");
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// rs.getDouble("latitude");
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// rs.getDouble("longitude");
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// rs.getString("namespaceprefix");
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// rs.getInt("odnumberofitems"); // NULL
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// rs.getDate("odnumberofitemsdate"); // NULL
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// rs.getArray("subjects");
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// rs.getString("description");
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// rs.getString("odpolicies"); // NULL
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// rs.getArray("odlanguages");
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// rs.getArray("odcontenttypes");
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// rs.getBoolean("inferred"); // false
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// rs.getBoolean("deletedbyinference");// false
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// rs.getDouble("trust"); // 0.9
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// rs.getString("inferenceprovenance"); // NULL
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// rs.getDate("dateofcollection");
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// rs.getDate("dateofvalidation");
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// rs.getDate("releasestartdate");
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// rs.getDate("releaseenddate");
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// rs.getString("missionstatementurl");
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// rs.getBoolean("dataprovider");
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// rs.getBoolean("serviceprovider");
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// rs.getString("databaseaccesstype");
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// rs.getString("datauploadtype");
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// rs.getString("databaseaccessrestriction");
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// rs.getString("datauploadrestriction");
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// rs.getBoolean("versioning");
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// rs.getString("citationguidelineurl");
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// rs.getString("qualitymanagementkind");
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// rs.getString("pidsystems");
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// rs.getString("certificates");
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rs.getArray("policies");
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// rs.getString("collectedfromid");
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// rs.getString("collectedfromname");
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// rs.getString("datasourcetype"); // COMPLEX XXX@@@@....
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// rs.getString("provenanceaction"); //
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// 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions'
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// AS provenanceaction,
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rs.getString("journal"); // CONCAT(d.issn, '@@@', d.eissn, '@@@', d.lissn) AS journal
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emitOaf(ds);
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} catch (final Exception e) {
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throw new RuntimeException(e);
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}
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}
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public void processProject(final ResultSet rs) {
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try {
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final DataInfo info = prepareDataInfo(rs);
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final Project p = new Project();
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p.setId(MigrationUtils.createOpenaireId("40", rs.getString("projectid")));
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p.setOriginalId(Arrays.asList(rs.getString("projectid")));
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p.setCollectedfrom(MigrationUtils.listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")));
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p.setPid(null); // List<StructuredProperty> // TODO
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p.setDateofcollection(rs.getDate("dateofcollection").toString());
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p.setDateoftransformation(rs.getDate("dateoftransformation").toString());
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p.setExtraInfo(null); // List<ExtraInfo> //TODO
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p.setOaiprovenance(null); // OAIProvenance /TODO
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p.setWebsiteurl(MigrationUtils.field(rs.getString("websiteurl"), info));
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p.setCode(MigrationUtils.field(rs.getString("code"), info));
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p.setAcronym(MigrationUtils.field(rs.getString("acronym"), info));
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p.setTitle(MigrationUtils.field(rs.getString("title"), info));
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p.setStartdate(MigrationUtils.field(rs.getDate("startdate").toString(), info));
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p.setEnddate(MigrationUtils.field(rs.getDate("enddate").toString(), info));
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p.setCallidentifier(MigrationUtils.field(rs.getString("callidentifier"), info));
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p.setKeywords(MigrationUtils.field(rs.getString("keywords"), info));
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p.setDuration(MigrationUtils.field(Integer.toString(rs.getInt("duration")), info));
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p.setEcsc39(MigrationUtils.field(Boolean.toString(rs.getBoolean("ecsc39")), info));
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p.setOamandatepublications(MigrationUtils.field(Boolean.toString(rs.getBoolean("oamandatepublications")), info));
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p.setEcarticle29_3(MigrationUtils.field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info));
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p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info));
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p.setFundingtree(null); // List<Field<String>> //TODO
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p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype")));
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p.setOptional1(MigrationUtils.field(rs.getString("optional1"), info));
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p.setOptional2(MigrationUtils.field(rs.getString("optional2"), info));
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p.setJsonextrainfo(MigrationUtils.field(rs.getString("jsonextrainfo"), info));
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p.setContactfullname(MigrationUtils.field(rs.getString("contactfullname"), info));
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p.setContactfax(MigrationUtils.field(rs.getString("contactfax"), info));
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p.setContactphone(MigrationUtils.field(rs.getString("contactphone"), info));
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p.setContactemail(MigrationUtils.field(rs.getString("contactemail"), info));
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p.setSummary(MigrationUtils.field(rs.getString("summary"), info));
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p.setCurrency(MigrationUtils.field(rs.getString("currency"), info));
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p.setTotalcost(new Float(rs.getDouble("totalcost")));
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p.setFundedamount(new Float(rs.getDouble("fundedamount")));
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p.setDataInfo(info);
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p.setLastupdatetimestamp(lastUpdateTimestamp);
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// rs.getString("projectid");
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// rs.getString("code");
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// rs.getString("websiteurl");
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// rs.getString("acronym");
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// rs.getString("title");
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// rs.getDate("startdate");
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// rs.getDate("enddate");
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// rs.getString("callidentifier");
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// rs.getString("keywords");
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// rs.getInt("duration");
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// rs.getBoolean("ecsc39");
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// rs.getBoolean("oamandatepublications");
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// rs.getBoolean("ecarticle29_3");
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// rs.getDate("dateofcollection");
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// rs.getDate("dateoftransformation");
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// rs.getBoolean("inferred");
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// rs.getBoolean("deletedbyinference");
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// rs.getDouble("trust");
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// rs.getString("inferenceprovenance");
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// rs.getString("optional1");
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// rs.getString("optional2");
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// rs.getString("jsonextrainfo");
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// rs.getString("contactfullname");
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// rs.getString("contactfax");
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// rs.getString("contactphone");
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// rs.getString("contactemail");
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// rs.getString("summary");
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// rs.getString("currency");
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// rs.getDouble("totalcost");
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// rs.getDouble("fundedamount");
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// rs.getString("collectedfromid");
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// rs.getString("collectedfromname");
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rs.getString("contracttype"); // COMPLEX
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rs.getString("provenanceaction"); // COMPLEX
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rs.getArray("pid");
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rs.getArray("subjects");
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rs.getArray("fundingtree");
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emitOaf(p);
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} catch (final Exception e) {
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throw new RuntimeException(e);
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}
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}
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public void processOrganization(final ResultSet rs) {
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try {
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final DataInfo info = prepareDataInfo(rs);
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final Organization o = new Organization();
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o.setId(MigrationUtils.createOpenaireId("20", rs.getString("organizationid"))); // String id) {
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o.setOriginalId(Arrays.asList(rs.getString("organizationid")));
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o.setCollectedfrom(MigrationUtils.listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")));
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o.setPid(null); // List<StructuredProperty> // TODO
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o.setDateofcollection(rs.getDate("dateofcollection").toString());
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o.setDateoftransformation(rs.getDate("dateoftransformation").toString());
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o.setExtraInfo(null); // List<ExtraInfo> // TODO
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o.setOaiprovenance(null); // OAIProvenance // TODO
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o.setLegalshortname(MigrationUtils.field("legalshortname", info));
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o.setLegalname(MigrationUtils.field("legalname", info));
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o.setAlternativeNames(new ArrayList<>());
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o.setWebsiteurl(MigrationUtils.field("websiteurl", info));
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o.setLogourl(MigrationUtils.field("logourl", info));
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o.setEclegalbody(MigrationUtils.field(Boolean.toString(rs.getBoolean("eclegalbody")), info));
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o.setEclegalperson(MigrationUtils.field(Boolean.toString(rs.getBoolean("eclegalperson")), info));
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o.setEcnonprofit(MigrationUtils.field(Boolean.toString(rs.getBoolean("ecnonprofit")), info));
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o.setEcresearchorganization(MigrationUtils.field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info));
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o.setEchighereducation(MigrationUtils.field(Boolean.toString(rs.getBoolean("echighereducation")), info));
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o.setEcinternationalorganizationeurinterests(MigrationUtils
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.field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info));
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o.setEcinternationalorganization(MigrationUtils.field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info));
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o.setEcenterprise(MigrationUtils.field(Boolean.toString(rs.getBoolean("ecenterprise")), info));
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o.setEcsmevalidated(MigrationUtils.field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info));
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o.setEcnutscode(MigrationUtils.field(Boolean.toString(rs.getBoolean("ecnutscode")), info));
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o.setCountry(prepareQualifierSplitting(rs.getString("country")));
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o.setDataInfo(info);
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o.setLastupdatetimestamp(lastUpdateTimestamp);
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// rs.getString("organizationid");
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// rs.getString("legalshortname");
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// rs.getString("legalname");
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// rs.getString("websiteurl");
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// rs.getString("logourl");
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// rs.getBoolean("eclegalbody");
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// rs.getBoolean("eclegalperson");
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// rs.getBoolean("ecnonprofit");
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// rs.getBoolean("ecresearchorganization");
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// rs.getBoolean("echighereducation");
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// rs.getBoolean("ecinternationalorganizationeurinterests");
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// rs.getBoolean("ecinternationalorganization");
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// rs.getBoolean("ecenterprise");
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// rs.getBoolean("ecsmevalidated");
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// rs.getBoolean("ecnutscode");
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// rs.getDate("dateofcollection");
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// rs.getDate("dateoftransformation");
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// rs.getBoolean("inferred");
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// rs.getBoolean("deletedbyinference");
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// rs.getDouble("trust");
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// rs.getString("inferenceprovenance");
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// rs.getString("collectedfromid");
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// rs.getString("collectedfromname");
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// rs.getString("country");
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rs.getString("provenanceaction");
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rs.getArray("pid");
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emitOaf(o);
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} catch (final Exception e) {
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throw new RuntimeException(e);
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}
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}
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public void processDatasourceOrganization(final ResultSet rs) {
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try {
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final DataInfo info = prepareDataInfo(rs);
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final String orgId = MigrationUtils.createOpenaireId("20", rs.getString("organization"));
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final String dsId = MigrationUtils.createOpenaireId("10", rs.getString("datasource"));
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final Relation r1 = new Relation();
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r1.setRelType("datasourceOrganization");
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r1.setSubRelType("provision");
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r1.setRelClass("isProvidedBy");
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r1.setSource(dsId);
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r1.setTarget(orgId);
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r1.setCollectedFrom(null);// TODO
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r1.setDataInfo(info);
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r1.setLastupdatetimestamp(lastUpdateTimestamp);
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emitOaf(r1);
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final Relation r2 = new Relation();
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r2.setRelType("datasourceOrganization");
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r2.setSubRelType("provision");
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r2.setRelClass("provides");
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r2.setSource(orgId);
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r2.setTarget(dsId);
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r2.setCollectedFrom(null); // TODO
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r2.setDataInfo(info);
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r1.setLastupdatetimestamp(lastUpdateTimestamp);
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emitOaf(r2);
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// rs.getString("datasource");
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// rs.getString("organization");
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// rs.getDate("startdate"); // NULL
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// rs.getDate("enddate"); // NULL
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// rs.getBoolean("inferred"); // false
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// rs.getBoolean("deletedbyinference"); // false
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// rs.getDouble("trust"); // 0.9
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// rs.getString("inferenceprovenance"); // NULL
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// rs.getString("semantics"); // 'providedBy@@@provided
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// by@@@dnet:datasources_organizations_typologies@@@dnet:datasources_organizations_typologies' AS
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// semantics,
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// rs.getString("provenanceaction"); // d.provenanceaction || '@@@' || d.provenanceaction ||
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// '@@@dnet:provenanceActions@@@dnet:provenanceActions' AS provenanceaction
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} catch (final Exception e) {
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throw new RuntimeException(e);
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}
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}
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public void processProjectOrganization(final ResultSet rs) {
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try {
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final DataInfo info = prepareDataInfo(rs);
|
|
final String orgId = MigrationUtils.createOpenaireId("20", rs.getString("resporganization"));
|
|
final String projectId = MigrationUtils.createOpenaireId("40", rs.getString("project"));
|
|
|
|
final Relation r1 = new Relation();
|
|
r1.setRelType("projectOrganization");
|
|
r1.setSubRelType("participation");
|
|
r1.setRelClass("isParticipant");
|
|
r1.setSource(projectId);
|
|
r1.setTarget(orgId);
|
|
r1.setCollectedFrom(null);// TODO
|
|
r1.setDataInfo(info);
|
|
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
|
emitOaf(r1);
|
|
|
|
final Relation r2 = new Relation();
|
|
r2.setRelType("projectOrganization");
|
|
r2.setSubRelType("participation");
|
|
r2.setRelClass("hasParticipant");
|
|
r2.setSource(orgId);
|
|
r2.setTarget(projectId);
|
|
r2.setCollectedFrom(null); // TODO
|
|
r2.setDataInfo(info);
|
|
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
|
emitOaf(r2);
|
|
|
|
// rs.getString("project");
|
|
// rs.getString("resporganization");
|
|
// rs.getInt("participantnumber");
|
|
// rs.getDouble("contribution");
|
|
// rs.getDate("startdate");// null
|
|
// rs.getDate("enddate");// null
|
|
// rs.getBoolean("inferred");// false
|
|
// rs.getBoolean("deletedbyinference"); // false
|
|
// rs.getDouble("trust");
|
|
// rs.getString("inferenceprovenance"); // NULL
|
|
// rs.getString("semantics"); // po.semanticclass || '@@@' || po.semanticclass ||
|
|
// '@@@dnet:project_organization_relations@@@dnet:project_organization_relations' AS semantics,
|
|
// rs.getString("provenanceaction"); //
|
|
// 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions'
|
|
// AS provenanceaction
|
|
|
|
} catch (final Exception e) {
|
|
throw new RuntimeException(e);
|
|
}
|
|
}
|
|
|
|
private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException {
|
|
final Boolean deletedbyinference = rs.getBoolean("deletedbyinference");
|
|
final String inferenceprovenance = rs.getString("inferenceprovenance");
|
|
final Boolean inferred = rs.getBoolean("inferred");
|
|
final String trust = rs.getString("trust");
|
|
return MigrationUtils.dataInfo(deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust);
|
|
}
|
|
|
|
private Qualifier prepareQualifierSplitting(final String s) {
|
|
if (StringUtils.isBlank(s)) { return null; }
|
|
final String[] arr = s.split("@@@");
|
|
return arr.length == 4 ? MigrationUtils.qualifier(arr[0], arr[1], arr[2], arr[3]) : null;
|
|
}
|
|
|
|
private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) {
|
|
if (StringUtils.isBlank(s)) { return null; }
|
|
final String[] parts = s.split("###");
|
|
if (parts.length == 2) {
|
|
final String value = parts[0];
|
|
final String[] arr = parts[1].split("@@@");
|
|
if (arr.length == 4) { return MigrationUtils.structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); }
|
|
}
|
|
return null;
|
|
}
|
|
|
|
private List<StructuredProperty> prepareListOfStructProps(final Array array, final DataInfo dataInfo) throws SQLException {
|
|
final List<StructuredProperty> res = new ArrayList<>();
|
|
if (array != null) {
|
|
for (final String s : (String[]) array.getArray()) {
|
|
final StructuredProperty sp = prepareStructProp(s, dataInfo);
|
|
if (sp != null) {
|
|
res.add(sp);
|
|
}
|
|
}
|
|
}
|
|
|
|
return res;
|
|
}
|
|
|
|
@Override
|
|
public void close() throws IOException {
|
|
super.close();
|
|
dbClient.close();
|
|
}
|
|
|
|
}
|