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521 lines
22 KiB
Java
521 lines
22 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.Field;
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import eu.dnetlib.dhp.schema.oaf.Journal;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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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 AbstractMigrationExecutor implements Closeable {
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private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
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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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log.info("Processing datasources...");
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smdbe.execute("queryDatasources.sql", smdbe::processDatasource);
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log.info("Processing projects...");
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smdbe.execute("queryProjects.sql", smdbe::processProject);
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log.info("Processing orgs...");
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smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
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log.info("Processing relations ds <-> orgs ...");
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smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
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log.info("Processing projects <-> orgs ...");
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smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
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log.info("All done.");
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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(createOpenaireId(10, rs.getString("datasourceid")));
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ds.setOriginalId(Arrays.asList(rs.getString("datasourceid")));
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ds.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")));
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ds.setPid(new ArrayList<>());
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ds.setDateofcollection(asString(rs.getDate("dateofcollection")));
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ds.setDateoftransformation(null); // Value not returned by the SQL query
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ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB
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ds.setOaiprovenance(null); // Values not present in the DB
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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(field(rs.getString("officialname"), info));
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ds.setEnglishname(field(rs.getString("englishname"), info));
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ds.setWebsiteurl(field(rs.getString("websiteurl"), info));
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ds.setLogourl(field(rs.getString("logourl"), info));
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ds.setContactemail(field(rs.getString("contactemail"), info));
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ds.setNamespaceprefix(field(rs.getString("namespaceprefix"), info));
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ds.setLatitude(field(Double.toString(rs.getDouble("latitude")), info));
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ds.setLongitude(field(Double.toString(rs.getDouble("longitude")), info));
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ds.setDateofvalidation(field(asString(rs.getDate("dateofvalidation")), info));
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ds.setDescription(field(rs.getString("description"), info));
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ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info));
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ds.setOdnumberofitems(field(Double.toString(rs.getInt("odnumberofitems")), info));
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ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info));
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ds.setOdpolicies(field(rs.getString("odpolicies"), info));
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ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info));
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ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info));
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ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info));
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ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info));
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ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info));
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ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info));
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ds.setDataprovider(field(rs.getBoolean("dataprovider"), info));
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ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info));
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ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info));
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ds.setDatauploadtype(field(rs.getString("datauploadtype"), info));
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ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info));
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ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info));
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ds.setVersioning(field(rs.getBoolean("versioning"), info));
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ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info));
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ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info));
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ds.setPidsystems(field(rs.getString("pidsystems"), info));
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ds.setCertificates(field(rs.getString("certificates"), info));
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ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array
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ds.setJournal(prepareJournal(rs.getString("officialname"), rs.getString("journal"), info)); // Journal
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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
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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(createOpenaireId(40, rs.getString("projectid")));
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p.setOriginalId(Arrays.asList(rs.getString("projectid")));
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p.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")));
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p.setPid(new ArrayList<>());
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p.setDateofcollection(asString(rs.getDate("dateofcollection")));
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p.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
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p.setExtraInfo(new ArrayList<>()); // Values not present in the DB
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p.setOaiprovenance(null); // Values not present in the DB
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p.setWebsiteurl(field(rs.getString("websiteurl"), info));
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p.setCode(field(rs.getString("code"), info));
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p.setAcronym(field(rs.getString("acronym"), info));
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p.setTitle(field(rs.getString("title"), info));
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p.setStartdate(field(asString(rs.getDate("startdate")), info));
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p.setEnddate(field(asString(rs.getDate("enddate")), info));
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p.setCallidentifier(field(rs.getString("callidentifier"), info));
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p.setKeywords(field(rs.getString("keywords"), info));
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p.setDuration(field(Integer.toString(rs.getInt("duration")), info));
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p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info));
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p.setOamandatepublications(field(Boolean.toString(rs.getBoolean("oamandatepublications")), info));
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p.setEcarticle29_3(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(prepareListFields(rs.getArray("fundingtree"), info));
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p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype")));
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p.setOptional1(field(rs.getString("optional1"), info));
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p.setOptional2(field(rs.getString("optional2"), info));
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p.setJsonextrainfo(field(rs.getString("jsonextrainfo"), info));
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p.setContactfullname(field(rs.getString("contactfullname"), info));
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p.setContactfax(field(rs.getString("contactfax"), info));
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p.setContactphone(field(rs.getString("contactphone"), info));
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p.setContactemail(field(rs.getString("contactemail"), info));
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p.setSummary(field(rs.getString("summary"), info));
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p.setCurrency(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(createOpenaireId(20, rs.getString("organizationid")));
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o.setOriginalId(Arrays.asList(rs.getString("organizationid")));
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o.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")));
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o.setPid(new ArrayList<>());
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o.setDateofcollection(asString(rs.getDate("dateofcollection")));
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o.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
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o.setExtraInfo(new ArrayList<>()); // Values not present in the DB
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o.setOaiprovenance(null); // Values not present in the DB
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o.setLegalshortname(field("legalshortname", info));
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o.setLegalname(field("legalname", info));
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o.setAlternativeNames(new ArrayList<>()); // Values not returned by the SQL query
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o.setWebsiteurl(field("websiteurl", info));
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o.setLogourl(field("logourl", info));
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o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info));
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o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info));
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o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info));
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o.setEcresearchorganization(field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info));
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o.setEchighereducation(field(Boolean.toString(rs.getBoolean("echighereducation")), info));
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o.setEcinternationalorganizationeurinterests(field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info));
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o.setEcinternationalorganization(field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info));
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o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info));
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o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info));
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o.setEcnutscode(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 = createOpenaireId(20, rs.getString("organization"));
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final String dsId = createOpenaireId(10, rs.getString("datasource"));
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final List<KeyValue> collectedFrom = listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname"));
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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(collectedFrom);
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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(collectedFrom);
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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 {
|
|
final DataInfo info = prepareDataInfo(rs);
|
|
final String orgId = createOpenaireId(20, rs.getString("resporganization"));
|
|
final String projectId = createOpenaireId(40, rs.getString("project"));
|
|
final List<KeyValue> collectedFrom = listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname"));
|
|
|
|
final Relation r1 = new Relation();
|
|
r1.setRelType("projectOrganization");
|
|
r1.setSubRelType("participation");
|
|
r1.setRelClass("isParticipant");
|
|
r1.setSource(projectId);
|
|
r1.setTarget(orgId);
|
|
r1.setCollectedFrom(collectedFrom);
|
|
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(collectedFrom);
|
|
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 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 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null;
|
|
}
|
|
|
|
private List<Field<String>> prepareListFields(final Array array, final DataInfo info) {
|
|
try {
|
|
return listFields(info, (String[]) array.getArray());
|
|
} catch (final SQLException e) {
|
|
throw new RuntimeException("Invalid SQL array", e);
|
|
}
|
|
}
|
|
|
|
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 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;
|
|
}
|
|
|
|
private Journal prepareJournal(final String name, final String sj, final DataInfo info) {
|
|
if (StringUtils.isNotBlank(sj)) {
|
|
final String[] arr = sj.split("@@@");
|
|
if (arr.length == 3) {
|
|
final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null;
|
|
final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;;
|
|
final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;;
|
|
if (issn != null || eissn != null
|
|
|| lissn != null) { return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info); }
|
|
}
|
|
}
|
|
return null;
|
|
}
|
|
|
|
@Override
|
|
public void close() throws IOException {
|
|
super.close();
|
|
dbClient.close();
|
|
}
|
|
|
|
}
|