forked from D-Net/dnet-hadoop
This commit is contained in:
parent
2349bfd8b8
commit
4b0bd91012
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@ -0,0 +1,7 @@
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Merge remote-tracking branch 'upstream/master'
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# Please enter a commit message to explain why this merge is necessary,
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# especially if it merges an updated upstream into a topic branch.
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#
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# Lines starting with '#' will be ignored, and an empty message aborts
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# the commit.
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@ -1,11 +1,14 @@
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package eu.dnetlib.dhp.schema.common;
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import com.google.common.collect.Maps;
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import eu.dnetlib.dhp.schema.oaf.*;
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import java.util.Map;
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import java.util.Optional;
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import java.util.function.Function;
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import com.google.common.collect.Maps;
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import eu.dnetlib.dhp.schema.oaf.*;
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/** Oaf model utility methods. */
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public class ModelSupport {
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@ -51,7 +51,7 @@ import eu.dnetlib.dhp.schema.oaf.Software;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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implements Closeable {
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implements Closeable {
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private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class);
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@ -61,9 +61,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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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(MigrateDbEntitiesApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json")));
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IOUtils
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.toString(
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MigrateDbEntitiesApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json")));
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parser.parseArgument(args);
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@ -76,7 +77,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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final boolean processClaims = 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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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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@ -107,15 +108,15 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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}
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public MigrateDbEntitiesApplication(
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final String hdfsPath, final String dbUrl, final String dbUser, final String dbPassword)
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throws Exception {
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final String hdfsPath, final String dbUrl, final String dbUser, final String dbPassword)
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throws Exception {
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super(hdfsPath);
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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 Function<ResultSet, List<Oaf>> producer)
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throws Exception {
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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 Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf));
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@ -134,7 +135,10 @@ 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(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")));
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.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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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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@ -175,7 +179,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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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(prepareJournal(rs.getString("officialname"), rs.getString("journal"), info)); // Journal
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.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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@ -195,7 +199,10 @@ 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(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")));
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.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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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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@ -212,7 +219,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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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(field(Boolean.toString(rs.getBoolean("oamandatepublications")), info));
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.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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@ -249,7 +256,10 @@ 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(listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")));
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.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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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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@ -264,12 +274,14 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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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(field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info));
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.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
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.setEcinternationalorganizationeurinterests(field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info));
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.setEcinternationalorganizationeurinterests(
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field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info));
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o
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.setEcinternationalorganization(field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info));
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.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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o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info));
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@ -288,7 +300,8 @@ 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(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
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final List<KeyValue> collectedFrom = listKeyValues(
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createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
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final Relation r1 = new Relation();
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r1.setRelType("datasourceOrganization");
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@ -321,7 +334,8 @@ 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("resporganization"), true);
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final String projectId = createOpenaireId(40, rs.getString("project"), true);
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final List<KeyValue> collectedFrom = listKeyValues(createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
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final List<KeyValue> collectedFrom = listKeyValues(
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createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
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final Relation r1 = new Relation();
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r1.setRelType("projectOrganization");
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@ -351,10 +365,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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public List<Oaf> processClaims(final ResultSet rs) {
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final DataInfo info =
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dataInfo(false, null, false, false, qualifier("user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"), "0.9");
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final DataInfo info = dataInfo(
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false, null, false, false,
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qualifier("user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"), "0.9");
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final List<KeyValue> collectedFrom = listKeyValues(createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE");
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final List<KeyValue> collectedFrom = listKeyValues(
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createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE");
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try {
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@ -440,11 +456,15 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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final String inferenceprovenance = rs.getString("inferenceprovenance");
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final Boolean inferred = rs.getBoolean("inferred");
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final String trust = rs.getString("trust");
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return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, MigrationConstants.ENTITYREGISTRY_PROVENANCE_ACTION, trust);
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return dataInfo(
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deletedbyinference, inferenceprovenance, inferred, false,
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MigrationConstants.ENTITYREGISTRY_PROVENANCE_ACTION, trust);
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}
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private Qualifier prepareQualifierSplitting(final String s) {
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if (StringUtils.isBlank(s)) { return null; }
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if (StringUtils.isBlank(s)) {
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return null;
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}
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final String[] arr = s.split("@@@");
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return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null;
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}
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@ -458,19 +478,23 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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}
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private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) {
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if (StringUtils.isBlank(s)) { return null; }
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if (StringUtils.isBlank(s)) {
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return null;
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}
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final String[] parts = s.split("###");
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if (parts.length == 2) {
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final String value = parts[0];
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final String[] arr = parts[1].split("@@@");
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if (arr.length == 4) { return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); }
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if (arr.length == 4) {
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return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo);
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}
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}
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return null;
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}
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private List<StructuredProperty> prepareListOfStructProps(
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final Array array,
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final DataInfo dataInfo) throws SQLException {
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final Array array,
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final DataInfo dataInfo) throws SQLException {
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final List<StructuredProperty> res = new ArrayList<>();
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if (array != null) {
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for (final String s : (String[]) array.getArray()) {
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@ -489,8 +513,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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final String[] arr = sj.split("@@@");
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if (arr.length == 3) {
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final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0].trim() : null;
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final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1].trim() : null;;
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final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2].trim() : null;;
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final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1].trim() : null;
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;
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final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2].trim() : null;
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;
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if (issn != null || eissn != null || lissn != null) {
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return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info);
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}
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@ -504,5 +530,4 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
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super.close();
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dbClient.close();
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}
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}
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|
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@ -99,6 +99,7 @@ public class SparkResultToOrganizationFromIstRepoJob2 {
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String outputPath,
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Class<? extends Result> resultClazz,
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String resultType,
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Boolean saveGraph) {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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|
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@ -6,6 +6,12 @@
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"paramDescription": "the path of the sequencial file to read",
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"paramRequired": true
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},
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{
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"paramName":"sg",
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"paramLongName":"saveGraph",
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"paramDescription": "true if the new version of the graph must be saved",
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"paramRequired": false
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},
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{
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"paramName":"h",
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"paramLongName":"hive_metastore_uris",
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|
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@ -12,6 +12,10 @@
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<name>isLookupUrl</name>
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<description>the isLookup service endpoint</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the output path</description>
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</property>
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</parameters>
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<start to="reset-outputpath"/>
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@ -21,22 +25,72 @@
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</kill>
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<action name="reset-outputpath">
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<fs>
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<delete path='${workingDir}/resulttocommunitysemrel_propagation'/>
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<delete path='${outputPath}/relation'/>
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<delete path='${outputPath}/datasource'/>
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<delete path='${outputPath}/organization'/>
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<delete path='${outputPath}/project'/>
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<delete path='${outputPath}/publication'/>
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<delete path='${outputPath}/dataset'/>
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<delete path='${outputPath}/software'/>
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<delete path='${outputPath}/otherresearchproduct'/>
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<delete path='${workingDir}/preparedInfo'/>
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</fs>
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<ok to="copy_relation"/>
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<ok to="copy_entities"/>
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<error to="Kill"/>
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</action>
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<fork name="copy_entities">
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<path start="copy_relation"/>
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<path start="copy_organization"/>
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<path start="copy_projects"/>
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<path start="copy_datasources"/>
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</fork>
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<action name="copy_relation">
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<distcp xmlns="uri:oozie:distcp-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<arg>${nameNode}/${sourcePath}/relation</arg>
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<arg>${nameNode}/${workingDir}/projecttoresult_propagation/relation</arg>
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<arg>${nameNode}/${outputPath}/relation</arg>
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</distcp>
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<ok to="fork_prepare_assoc_step1"/>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_organization">
|
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<distcp xmlns="uri:oozie:distcp-action:0.2">
|
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<job-tracker>${jobTracker}</job-tracker>
|
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<name-node>${nameNode}</name-node>
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<arg>${nameNode}/${sourcePath}/organization</arg>
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<arg>${nameNode}/${outputPath}/organization</arg>
|
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</distcp>
|
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<ok to="copy_wait"/>
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<error to="Kill"/>
|
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</action>
|
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|
||||
<action name="copy_projects">
|
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<distcp xmlns="uri:oozie:distcp-action:0.2">
|
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<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/project</arg>
|
||||
<arg>${nameNode}/${outputPath}/project</arg>
|
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</distcp>
|
||||
<ok to="copy_wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_datasources">
|
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<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/datasource</arg>
|
||||
<arg>${nameNode}/${outputPath}/datasource</arg>
|
||||
</distcp>
|
||||
<ok to="copy_wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="copy_wait" to="fork_prepare_assoc_step1"/>
|
||||
|
||||
<fork name="fork_prepare_assoc_step1">
|
||||
<path start="join_prepare_publication"/>
|
||||
<path start="join_prepare_dataset"/>
|
||||
|
@ -67,7 +121,7 @@
|
|||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetCommunityAssoc</arg>
|
||||
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
</spark>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -215,7 +269,8 @@
|
|||
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/publication</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
|
||||
<arg>--saveGrap</arg><arg>${saveGraph</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -242,7 +297,8 @@
|
|||
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
|
||||
<arg>--saveGrap</arg><arg>${saveGraph</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -269,7 +325,8 @@
|
|||
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
|
||||
<arg>--saveGrap</arg><arg>${saveGraph</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -296,7 +353,8 @@
|
|||
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/software</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
|
||||
<arg>--saveGrap</arg><arg>${saveGraph</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
@ -88,6 +88,7 @@ public class Result2OrganizationJobTest {
|
|||
"",
|
||||
"-resultTableName",
|
||||
"eu.dnetlib.dhp.schema.oaf.Software",
|
||||
|
||||
"-saveGraph",
|
||||
"true",
|
||||
"-outputPath",
|
||||
|
@ -138,6 +139,7 @@ public class Result2OrganizationJobTest {
|
|||
"",
|
||||
"-resultTableName",
|
||||
"eu.dnetlib.dhp.schema.oaf.Software",
|
||||
|
||||
"-saveGraph",
|
||||
"true",
|
||||
"-outputPath",
|
||||
|
@ -211,6 +213,7 @@ public class Result2OrganizationJobTest {
|
|||
"",
|
||||
"-resultTableName",
|
||||
"eu.dnetlib.dhp.schema.oaf.Software",
|
||||
|
||||
"-saveGraph",
|
||||
"true",
|
||||
"-outputPath",
|
||||
|
|
Loading…
Reference in New Issue