prepared a job to analyze the BASE records
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package eu.dnetlib.dhp.collection.plugin.base;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Optional;
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import java.util.concurrent.atomic.AtomicInteger;
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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.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.io.IntWritable;
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import org.apache.hadoop.io.SequenceFile;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.DeflateCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.Attribute;
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import org.dom4j.Document;
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import org.dom4j.Element;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.ror.GenerateRorActionSetJob;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
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public class BaseAnalyzerJob {
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private static final Logger log = LoggerFactory.getLogger(GenerateRorActionSetJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(final String[] args) throws Exception {
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final String jsonConfiguration = IOUtils
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.toString(GenerateRorActionSetJob.class
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.getResourceAsStream("/eu/dnetlib/dhp/collection/plugin/base/action_set_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.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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final String inputPath = parser.get("inputPath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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final SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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removeOutputDir(spark, outputPath);
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processBaseRecords(spark, inputPath, outputPath);
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});
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}
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private static void removeOutputDir(final SparkSession spark, final String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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private static void processBaseRecords(final SparkSession spark,
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final String inputPath,
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final String outputPath) throws IOException {
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try (final FileSystem fs = FileSystem.get(new Configuration()); final AggregatorReport report = new AggregatorReport()) {
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final Map<String, String> collections = new HashMap<>();
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collect(fs, inputPath, outputPath + "/temp", collections, report);
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finalReport(fs, outputPath + "/final", collections);
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} catch (final Throwable e) {
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throw new RuntimeException(e);
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}
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}
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private static void collect(final FileSystem fs,
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final String inputPath,
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final String outputPath,
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final Map<String, String> collections,
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final AggregatorReport report) throws JsonProcessingException, IOException {
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try (final SequenceFile.Writer writer = SequenceFile
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.createWriter(fs.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
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.keyClass(IntWritable.class), SequenceFile.Writer
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.valueClass(Text.class), SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
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final AtomicInteger recordsCounter = new AtomicInteger(0);
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final AtomicInteger collectionsCounter = new AtomicInteger(0);
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final BaseCollectorIterator iteraror = new BaseCollectorIterator(fs, new Path(inputPath), report);
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while (iteraror.hasNext()) {
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final Document record = iteraror.next();
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final int i = recordsCounter.incrementAndGet();
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if ((i % 1000) == 0) {
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log.info("# Read records: " + i);
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}
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for (final Object o : record.selectNodes("//*[local-name() = 'collection']")) {
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final Element n = (Element) o;
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final String collName = n.getText().trim();
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if (StringUtils.isNotBlank(collName) && !collections.containsKey(collName)) {
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final Map<String, String> map = new HashMap<>();
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for (final Object ao : n.attributes()) {
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map.put(((Attribute) ao).getName(), ((Attribute) ao).getValue());
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}
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final String attrs = OBJECT_MAPPER.writeValueAsString(map);
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collections.put(collName, attrs);
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final IntWritable key = new IntWritable(collectionsCounter.incrementAndGet());
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final Text value = new Text(collName + ": " + attrs);
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try {
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writer.append(key, value);
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} catch (final Throwable e1) {
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throw new RuntimeException(e1);
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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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private static void finalReport(final FileSystem fs, final String outputPath, final Map<String, String> collections)
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throws JsonProcessingException, IOException {
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try (final SequenceFile.Writer writer = SequenceFile
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.createWriter(fs.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
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.keyClass(IntWritable.class), SequenceFile.Writer
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.valueClass(Text.class), SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
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final Text key = new Text();
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final Text value = new Text();
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for (final Entry<String, String> e : collections.entrySet()) {
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key.set(e.getKey());
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value.set(e.getKey() + ": " + e.getValue());
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try {
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writer.append(key, value);
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} catch (final Throwable e1) {
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throw new RuntimeException(e1);
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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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{
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"paramName": "i",
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"paramLongName": "inputPath",
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"paramDescription": "the path of the BASE dump",
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"paramRequired": true
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},
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{
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"paramName": "o",
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"paramLongName": "outputPath",
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"paramDescription": "the path of the generated report",
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"paramRequired": true
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}
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]
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@ -0,0 +1,58 @@
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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>hive_metastore_uris</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>spark2YarnHistoryServerAddress</name>
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<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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<property>
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<name>sparkExecutorNumber</name>
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<value>4</value>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<value>/user/spark/spark2ApplicationHistory</value>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<value>15G</value>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<value>6G</value>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<value>1</value>
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</property>
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</configuration>
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@ -0,0 +1,53 @@
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<workflow-app name="Analyze_BASE_Records" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>baseInputPath</name>
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<description>the path of the BASE dump</description>
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</property>
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<property>
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<name>reportsPath</name>
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<description>path where to store the reports</description>
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</property>
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</parameters>
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<start to="deleteoutputpath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="deleteoutputpath">
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<fs>
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<delete path='${reportsPath}'/>
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<mkdir path='${reportsPath}'/>
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</fs>
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<ok to="analyzeBaseRecords"/>
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<error to="Kill"/>
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</action>
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<action name="analyzeBaseRecords">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>AnalyzeBaseRecords</name>
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<class>eu.dnetlib.dhp.collection.plugin.base.BaseAnalyzerJob</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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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=3840
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</spark-opts>
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<arg>--inputPath</arg><arg>${baseInputPath}</arg>
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<arg>--outputPath</arg><arg>${reportsPath}</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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