Merge pull request 'Implements pivots table update oozie workflow' (#376) from update_pivots_table into beta
Reviewed-on: #376
This commit is contained in:
commit
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package eu.dnetlib.dhp.oozie;
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import com.google.common.io.Resources;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import org.apache.commons.lang3.time.DurationFormatUtils;
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import org.apache.commons.text.StringSubstitutor;
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import org.apache.spark.SparkConf;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.net.URL;
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import java.nio.charset.StandardCharsets;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.Optional;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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public class RunSQLSparkJob {
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private static final Logger log = LoggerFactory.getLogger(RunSQLSparkJob.class);
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private final ArgumentApplicationParser parser;
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public RunSQLSparkJob(ArgumentApplicationParser parser) {
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this.parser = parser;
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}
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public static void main(String[] args) throws Exception {
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Map<String, String> params = new HashMap<>();
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for (int i = 0; i < args.length - 1; i++) {
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if (args[i].startsWith("--")) {
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params.put(args[i].substring(2), args[++i]);
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}
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}
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/*
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* String jsonConfiguration = IOUtils .toString( Objects .requireNonNull( RunSQLSparkJob.class
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* .getResourceAsStream( "/eu/dnetlib/dhp/oozie/run_sql_parameters.json"))); final ArgumentApplicationParser
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* parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args);
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*/
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Boolean isSparkSessionManaged = Optional
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.ofNullable(params.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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URL url = com.google.common.io.Resources.getResource(params.get("sql"));
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String raw_sql = Resources.toString(url, StandardCharsets.UTF_8);
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String sql = StringSubstitutor.replace(raw_sql, params);
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log.info("sql: {}", sql);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", params.get("hiveMetastoreUris"));
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runWithSparkHiveSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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for (String statement : sql.split(";\\s*/\\*\\s*EOS\\s*\\*/\\s*")) {
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log.info("executing: {}", statement);
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long startTime = System.currentTimeMillis();
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spark.sql(statement).show();
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log
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.info(
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"executed in {}",
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DurationFormatUtils.formatDuration(System.currentTimeMillis() - startTime, "HH:mm:ss.S"));
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}
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});
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}
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}
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[
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "when true will stop SparkSession after job execution",
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"paramRequired": false
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},
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{
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"paramName": "hmu",
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"paramLongName": "hiveMetastoreUris",
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"paramDescription": "the hive metastore uris",
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"paramRequired": true
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},
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{
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"paramName": "sql",
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"paramLongName": "sql",
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"paramDescription": "sql script to execute",
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"paramRequired": true
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}
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]
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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<property>
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<name>hiveMetastoreUris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>sparkSqlWarehouseDir</name>
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<value>/user/hive/warehouse</value>
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</property>
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</configuration>
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CREATE TABLE `${pivot_history_db}`.`dataset_new` STORED AS PARQUET AS
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WITH pivots (
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SELECT property.value AS id, '${new_graph_date}' AS usedIn FROM `${new_graph_db}`.`relation`
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LEFT SEMI JOIN `${new_graph_db}`.`dataset` ON relation.source = dataset.id
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LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot'
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UNION
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SELECT id, usedIn FROM `${pivot_history_db}`.`dataset` LATERAL VIEW EXPLODE(usages) AS usedIn
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)
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SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages
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FROM pivots
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GROUP BY id; /*EOS*/
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CREATE TABLE `${pivot_history_db}`.`publication_new` STORED AS PARQUET AS
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WITH pivots (
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SELECT property.value AS id, '${new_graph_date}' AS usedIn FROM `${new_graph_db}`.`relation`
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LEFT SEMI JOIN `${new_graph_db}`.`publication` ON relation.source = publication.id
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LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot'
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UNION
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SELECT id, usedIn FROM `${pivot_history_db}`.`publication` LATERAL VIEW EXPLODE(usages) AS usedIn
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)
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SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages
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FROM pivots
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GROUP BY id; /*EOS*/
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CREATE TABLE `${pivot_history_db}`.`software_new` STORED AS PARQUET AS
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WITH pivots (
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SELECT property.value AS id, '${new_graph_date}' AS usedIn FROM `${new_graph_db}`.`relation`
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LEFT SEMI JOIN `${new_graph_db}`.`software` ON relation.source = software.id
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LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot'
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UNION
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SELECT id, usedIn FROM `${pivot_history_db}`.`software` LATERAL VIEW EXPLODE(usages) AS usedIn
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)
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SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages
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FROM pivots
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GROUP BY id; /*EOS*/
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CREATE TABLE `${pivot_history_db}`.`otherresearchproduct_new` STORED AS PARQUET AS
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WITH pivots (
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SELECT property.value AS id, '${new_graph_date}' AS usedIn FROM `${new_graph_db}`.`relation`
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LEFT SEMI JOIN `${new_graph_db}`.`otherresearchproduct` ON relation.source = otherresearchproduct.id
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LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot'
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UNION
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SELECT id, usedIn FROM `${pivot_history_db}`.`otherresearchproduct` LATERAL VIEW EXPLODE(usages) AS usedIn
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)
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SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages
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FROM pivots
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GROUP BY id; /*EOS*/
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DROP TABLE IF EXISTS `${pivot_history_db}`.`dataset_old`; /*EOS*/
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ALTER TABLE `${pivot_history_db}`.`dataset` RENAME TO `${pivot_history_db}`.`dataset_old`; /*EOS*/
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ALTER TABLE `${pivot_history_db}`.`dataset_new` RENAME TO `${pivot_history_db}`.`dataset`; /*EOS*/
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DROP TABLE IF EXISTS `${pivot_history_db}`.`publication_old`; /*EOS*/
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ALTER TABLE `${pivot_history_db}`.`publication` RENAME TO `${pivot_history_db}`.`publication_old`; /*EOS*/
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ALTER TABLE `${pivot_history_db}`.`publication_new` RENAME TO `${pivot_history_db}`.`publication`; /*EOS*/
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DROP TABLE IF EXISTS `${pivot_history_db}`.`software_old`; /*EOS*/
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ALTER TABLE `${pivot_history_db}`.`software` RENAME TO `${pivot_history_db}`.`software_old`; /*EOS*/
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ALTER TABLE `${pivot_history_db}`.`software_new` RENAME TO `${pivot_history_db}`.`software`; /*EOS*/
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DROP TABLE IF EXISTS `${pivot_history_db}`.`otherresearchproduct_old`; /*EOS*/
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ALTER TABLE `${pivot_history_db}`.`otherresearchproduct` RENAME TO `${pivot_history_db}`.`otherresearchproduct_old`; /*EOS*/
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ALTER TABLE `${pivot_history_db}`.`otherresearchproduct_new` RENAME TO `${pivot_history_db}`.`otherresearchproduct`; /*EOS*/
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<workflow-app name="Update pivot history" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<!-- properties used in SQL -->
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<property>
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<name>pivot_history_db</name>
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<!-- <value>openaire_beta_pivots_test</value> -->
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<description>Pivot history DB on hive</description>
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</property>
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<property>
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<name>new_graph_db</name>
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<!--<value>openaire_beta_20231208</value> -->
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<description>New graph DB on hive</description>
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</property>
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<property>
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<name>new_graph_date</name>
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<!-- <value>20231208</value> -->
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<description>Creation date of new graph db</description>
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</property>
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<!-- RunSQLSparkJob properties -->
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<property>
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<name>hiveMetastoreUris</name>
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<description>hive server metastore URIs</description>
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</property>
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<property>
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<name>sparkSqlWarehouseDir</name>
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</property>
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<!-- General oozie workflow properties -->
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<property>
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<name>sparkClusterOpts</name>
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<value>--conf spark.network.timeout=600 --conf spark.extraListeners= --conf spark.sql.queryExecutionListeners= --conf spark.yarn.historyServer.address=http://iis-cdh5-test-m3.ocean.icm.edu.pl:18088 --conf spark.eventLog.dir=hdfs://nameservice1/user/spark/applicationHistory</value>
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<description>spark cluster-wide options</description>
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</property>
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<property>
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<name>sparkResourceOpts</name>
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<value>--executor-memory=3G --conf spark.executor.memoryOverhead=3G --executor-cores=6 --driver-memory=8G --driver-cores=4</value>
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<description>spark resource options</description>
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</property>
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<property>
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<name>sparkApplicationOpts</name>
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<value>--conf spark.sql.shuffle.partitions=3840</value>
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<description>spark resource options</description>
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</property>
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</parameters>
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="UpgradePivotHistory"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="UpgradePivotHistory">
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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>Upgrade Pivot History</name>
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<class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
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<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
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<spark-opts>
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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${sparkClusterOpts}
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${sparkResourceOpts}
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${sparkApplicationOpts}
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</spark-opts>
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<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
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<arg>--sql</arg><arg>eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/sql.sql</arg>
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<arg>--pivot_history_db</arg><arg>${pivot_history_db}</arg>
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<arg>--new_graph_db</arg><arg>${new_graph_db}</arg>
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<arg>--new_graph_date</arg><arg>${new_graph_date}</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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