forked from D-Net/dnet-hadoop
openorgs pids
This commit is contained in:
parent
c364b329c4
commit
2c2311b062
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@ -244,7 +244,7 @@ public abstract class AbstractDbApplication extends AbstractMigrationApplication
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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.setPid(prepareListOfStructProps(rs.getArray("pid"), info));
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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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@ -0,0 +1,64 @@
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package eu.dnetlib.dhp.oa.graph.raw;
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import org.apache.commons.io.IOUtils;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.DbClient;
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import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
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public class MigrateCordaOrgsApplication extends AbstractDbApplication {
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private static final Logger log = LoggerFactory.getLogger(MigrateCordaOrgsApplication.class);
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public static final String SOURCE_TYPE = "source_type";
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public static final String TARGET_TYPE = "target_type";
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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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MigrateCordaOrgsApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_openorgs_parameters.json")));
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parser.parseArgument(args);
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final String dbUrl = parser.get("postgresUrl");
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log.info("postgresUrl: {}", dbUrl);
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final String dbUser = parser.get("postgresUser");
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log.info("postgresUser: {}", dbUser);
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final String dbPassword = parser.get("postgresPassword");
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log.info("postgresPassword: xxx");
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final String isLookupUrl = parser.get("isLookupUrl");
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log.info("isLookupUrl: {}", isLookupUrl);
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final String hdfsPath = parser.get("hdfsPath");
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log.info("hdfsPath: {}", hdfsPath);
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try (final MigrateCordaOrgsApplication mapper = new MigrateCordaOrgsApplication(hdfsPath, dbUrl, dbUser,
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dbPassword, isLookupUrl)) {
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log.info("Processing CORDA orgs...");
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mapper.execute("queryCordaOrganizations.sql", mapper::processOrganization);
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}
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log.info("All done.");
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}
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public MigrateCordaOrgsApplication(final String hdfsPath, final String dbUrl, final String dbUser,
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final String dbPassword, final String isLookupUrl)
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throws Exception {
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super(hdfsPath, dbUrl, dbUser, dbPassword, isLookupUrl);
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}
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protected MigrateCordaOrgsApplication(final DbClient dbClient, final VocabularyGroup vocs) { // ONLY FOT TESTS
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super(dbClient, vocs);
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}
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}
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@ -1,9 +1,26 @@
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<workflow-app name="import OpenOrgs" xmlns="uri:oozie:workflow:0.5">
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<workflow-app name="create RAW Graph (openorgs and cordaorgs)" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>graphOutputPath</name>
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<description>the target path to store raw graph</description>
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</property>
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<property>
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<name>contentPath</name>
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<description>path location to store (or reuse) content from the aggregator</description>
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</property>
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<property>
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<name>postgresURL</name>
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<description>the postgres URL to access to the database</description>
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</property>
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<property>
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<name>postgresUser</name>
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<description>the user postgres</description>
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</property>
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<property>
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<name>postgresPassword</name>
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<description>the password postgres</description>
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</property>
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<property>
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<name>postgresOpenOrgsURL</name>
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<description>the postgres URL to access to the OpenOrgs database</description>
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@ -15,6 +32,19 @@
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<property>
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<name>postgresOpenOrgsPassword</name>
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<description>the password of OpenOrgs database</description>
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</property>
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<property>
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<name>dbSchema</name>
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<value>beta</value>
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<description>the database schema according to the D-Net infrastructure (beta or production)</description>
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</property>
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<property>
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<name>mongoURL</name>
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<description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
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</property>
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<property>
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<name>mongoDb</name>
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<description>mongo database</description>
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</property>
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<property>
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<name>isLookupUrl</name>
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@ -76,13 +106,18 @@
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</configuration>
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</global>
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<start to="ImportDB_openorgs"/>
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<start to="start_import"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ImportDB_openorgs">
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<fork name="start_import">
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<path start="ImportDB_corda_orgs"/>
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<path start="ImportDB_openorgs"/>
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</fork>
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<action name="ImportDB_openorgs">
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<java>
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<prepare>
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<delete path="${contentPath}/db_openorgs"/>
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@ -94,9 +129,76 @@
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<arg>--postgresPassword</arg><arg>${postgresOpenOrgsPassword}</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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</java>
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<ok to="wait_import"/>
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<error to="Kill"/>
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</action>
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<action name="ImportDB_corda_orgs">
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<java>
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<prepare>
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<delete path="${contentPath}/db_records"/>
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</prepare>
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<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateCordaOrgsApplication</main-class>
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<arg>--hdfsPath</arg><arg>${contentPath}/db_cordaorgs</arg>
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<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
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<arg>--postgresUser</arg><arg>${postgresUser}</arg>
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<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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</java>
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<ok to="wait_import"/>
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<error to="Kill"/>
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</action>
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<join name="wait_import" to="GenerateEntities"/>
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<action name="GenerateEntities">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>GenerateEntities</name>
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<class>eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory ${sparkExecutorMemory}
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--executor-cores ${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePaths</arg><arg>${contentPath}/db_openorgs,${contentPath}/db_cordaorgs</arg>
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<arg>--targetPath</arg><arg>${workingDir}/entities</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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</spark>
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<ok to="GenerateGraph"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateGraph">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>GenerateGraph</name>
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<class>eu.dnetlib.dhp.oa.graph.raw.DispatchEntitiesApplication</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory ${sparkExecutorMemory}
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--executor-cores ${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--sourcePath</arg><arg>${workingDir}/entities</arg>
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<arg>--graphRawPath</arg><arg>${graphOutputPath}</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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</workflow-app>
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@ -0,0 +1,32 @@
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SELECT
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o.id AS organizationid,
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o.legalshortname AS legalshortname,
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o.legalname AS legalname,
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ARRAY[]::text[] AS alternativenames,
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o.websiteurl AS websiteurl,
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o.logourl AS logourl,
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o.ec_legalbody AS eclegalbody,
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o.ec_legalperson AS eclegalperson,
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o.ec_nonprofit AS ecnonprofit,
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o.ec_researchorganization AS ecresearchorganization,
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o.ec_highereducation AS echighereducation,
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o.ec_internationalorganizationeurinterests AS ecinternationalorganizationeurinterests,
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o.ec_internationalorganization AS ecinternationalorganization,
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o.ec_enterprise AS ecenterprise,
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o.ec_smevalidated AS ecsmevalidated,
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o.ec_nutscode AS ecnutscode,
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o.dateofcollection AS dateofcollection,
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o.lastupdate AS dateoftransformation,
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false AS inferred,
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false AS deletedbyinference,
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o.trust AS trust,
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'' AS inferenceprovenance,
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d.id AS collectedfromid,
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d.officialname AS collectedfromname,
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o.country || '@@@dnet:countries' AS country,
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'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction,
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ARRAY[]::text[] AS pid
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FROM dsm_organizations o
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LEFT OUTER JOIN dsm_datasources d ON (d.id = o.collectedfrom)
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WHERE o.id like 'corda__%'
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