forked from D-Net/dnet-hadoop
Fix relations in migration
Fix pom.xml in dhp-stats-update
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parent
3616d0f88d
commit
a5d7007005
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@ -1,4 +1,3 @@
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package eu.dnetlib.dhp.oa.graph.raw;
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import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.asString;
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@ -11,23 +10,6 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listKeyValues;
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import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
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import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
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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 java.util.function.Function;
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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.oa.graph.raw.common.AbstractMigrationApplication;
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import eu.dnetlib.dhp.oa.graph.raw.common.DbClient;
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@ -49,6 +31,21 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.Software;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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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 java.util.function.Function;
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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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public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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implements Closeable {
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@ -60,11 +57,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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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
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.toString(
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MigrateDbEntitiesApplication.class
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.getResourceAsStream(
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final ArgumentApplicationParser parser =
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new ArgumentApplicationParser(
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IOUtils.toString(
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MigrateDbEntitiesApplication.class.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json")));
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parser.parseArgument(args);
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@ -75,10 +71,11 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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final String hdfsPath = parser.get("hdfsPath");
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final boolean processClaims = parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims");
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final boolean processClaims =
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parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims");
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try (final MigrateDbEntitiesApplication smdbe = new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser,
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dbPassword)) {
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try (final MigrateDbEntitiesApplication smdbe =
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new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser, dbPassword)) {
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if (processClaims) {
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log.info("Processing claims...");
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smdbe.execute("queryClaims.sql", smdbe::processClaims);
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@ -118,7 +115,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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public void execute(final String sqlFile, final Function<ResultSet, List<Oaf>> producer)
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throws Exception {
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final String sql = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile));
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final String sql =
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IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile));
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final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf));
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@ -135,8 +133,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true));
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ds.setOriginalId(Arrays.asList(rs.getString("datasourceid")));
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ds
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.setCollectedfrom(
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ds.setCollectedfrom(
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listKeyValues(
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createOpenaireId(10, rs.getString("collectedfromid"), true),
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rs.getString("collectedfromname")));
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@ -179,8 +176,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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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
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.setJournal(
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ds.setJournal(
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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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@ -200,8 +196,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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p.setId(createOpenaireId(40, rs.getString("projectid"), true));
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p.setOriginalId(Arrays.asList(rs.getString("projectid")));
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p
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.setCollectedfrom(
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p.setCollectedfrom(
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listKeyValues(
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createOpenaireId(10, rs.getString("collectedfromid"), true),
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rs.getString("collectedfromname")));
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@ -220,8 +215,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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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
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.setOamandatepublications(
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p.setOamandatepublications(
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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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@ -258,8 +252,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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o.setId(createOpenaireId(20, rs.getString("organizationid"), true));
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o.setOriginalId(Arrays.asList(rs.getString("organizationid")));
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o
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.setCollectedfrom(
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o.setCollectedfrom(
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listKeyValues(
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createOpenaireId(10, rs.getString("collectedfromid"), true),
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rs.getString("collectedfromname")));
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@ -276,15 +269,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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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
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.setEcresearchorganization(
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o.setEcresearchorganization(
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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
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.setEcinternationalorganizationeurinterests(
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o.setEcinternationalorganizationeurinterests(
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field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info));
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o
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.setEcinternationalorganization(
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o.setEcinternationalorganization(
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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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@ -304,7 +294,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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final DataInfo info = prepareDataInfo(rs);
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final String orgId = createOpenaireId(20, rs.getString("organization"), true);
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final String dsId = createOpenaireId(10, rs.getString("datasource"), true);
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final List<KeyValue> collectedFrom = listKeyValues(
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final List<KeyValue> collectedFrom =
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listKeyValues(
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createOpenaireId(10, rs.getString("collectedfromid"), true),
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rs.getString("collectedfromname"));
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@ -339,14 +330,15 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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final DataInfo info = prepareDataInfo(rs);
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final String orgId = createOpenaireId(20, rs.getString("resporganization"), true);
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final String projectId = createOpenaireId(40, rs.getString("project"), true);
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final List<KeyValue> collectedFrom = listKeyValues(
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final List<KeyValue> collectedFrom =
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listKeyValues(
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createOpenaireId(10, rs.getString("collectedfromid"), true),
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rs.getString("collectedfromname"));
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final Relation r1 = new Relation();
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r1.setRelType("projectOrganization");
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r1.setSubRelType("participation");
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r1.setRelClass("isParticipant");
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r1.setRelClass("hasParticipant");
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r1.setSource(projectId);
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r1.setTarget(orgId);
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r1.setCollectedfrom(collectedFrom);
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@ -356,7 +348,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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final Relation r2 = new Relation();
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r2.setRelType("projectOrganization");
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r2.setSubRelType("participation");
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r2.setRelClass("hasParticipant");
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r2.setRelClass("isParticipant");
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r2.setSource(orgId);
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r2.setTarget(projectId);
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r2.setCollectedfrom(collectedFrom);
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@ -371,7 +363,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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public List<Oaf> processClaims(final ResultSet rs) {
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final DataInfo info = dataInfo(
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final DataInfo info =
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dataInfo(
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false,
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null,
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false,
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@ -380,8 +373,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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"user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"),
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"0.9");
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final List<KeyValue> collectedFrom = listKeyValues(
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createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE");
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final List<KeyValue> collectedFrom =
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listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE");
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try {
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@ -409,8 +402,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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return Arrays.asList(r);
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} else {
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final String sourceId = createOpenaireId(rs.getString("source_type"), rs.getString("source_id"), false);
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final String targetId = createOpenaireId(rs.getString("target_type"), rs.getString("target_id"), false);
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final String sourceId =
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createOpenaireId(rs.getString("source_type"), rs.getString("source_id"), false);
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final String targetId =
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createOpenaireId(rs.getString("target_type"), rs.getString("target_id"), false);
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final Relation r1 = new Relation();
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final Relation r2 = new Relation();
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