Merge pull request 'aggregation_on_hadoop' (#91) from sandro.labruzzo/dnet-hadoop:aggregation_on_hadoop into hadoop_aggregator
okpull/94/head
commit
2da8bf7429
@ -0,0 +1,45 @@
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package eu.dnetlib.dhp.aggregation.common;
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import java.io.Serializable;
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import org.apache.spark.util.LongAccumulator;
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public class AggregationCounter implements Serializable {
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private LongAccumulator totalItems;
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private LongAccumulator errorItems;
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private LongAccumulator processedItems;
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public AggregationCounter() {
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}
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public AggregationCounter(LongAccumulator totalItems, LongAccumulator errorItems, LongAccumulator processedItems) {
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this.totalItems = totalItems;
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this.errorItems = errorItems;
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this.processedItems = processedItems;
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}
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public LongAccumulator getTotalItems() {
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return totalItems;
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}
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public void setTotalItems(LongAccumulator totalItems) {
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this.totalItems = totalItems;
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}
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public LongAccumulator getErrorItems() {
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return errorItems;
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}
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public void setErrorItems(LongAccumulator errorItems) {
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this.errorItems = errorItems;
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}
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public LongAccumulator getProcessedItems() {
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return processedItems;
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}
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public void setProcessedItems(LongAccumulator processedItems) {
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this.processedItems = processedItems;
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}
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}
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@ -0,0 +1,93 @@
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package eu.dnetlib.dhp.collection.worker;
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import java.io.IOException;
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import java.net.URI;
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import java.util.concurrent.atomic.AtomicInteger;
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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.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.collector.worker.model.ApiDescriptor;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
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import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
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public class CollectorWorker {
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private static final Logger log = LoggerFactory.getLogger(CollectorWorker.class);
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private final CollectorPluginFactory collectorPluginFactory;
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private final ApiDescriptor api;
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private final String hdfsuri;
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private final String hdfsPath;
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public CollectorWorker(
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final CollectorPluginFactory collectorPluginFactory,
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final ApiDescriptor api,
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final String hdfsuri,
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final String hdfsPath) {
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this.collectorPluginFactory = collectorPluginFactory;
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this.api = api;
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this.hdfsuri = hdfsuri;
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this.hdfsPath = hdfsPath;
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}
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public void collect() throws CollectorException {
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try {
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final CollectorPlugin plugin = collectorPluginFactory.getPluginByProtocol(api.getProtocol());
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// ====== Init HDFS File System Object
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Configuration conf = new Configuration();
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// Set FileSystem URI
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conf.set("fs.defaultFS", hdfsuri);
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// Because of Maven
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conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
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conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
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System.setProperty("hadoop.home.dir", "/");
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// Get the filesystem - HDFS
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FileSystem.get(URI.create(hdfsuri), conf);
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Path hdfswritepath = new Path(hdfsPath);
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log.info("Created path " + hdfswritepath.toString());
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final AtomicInteger counter = new AtomicInteger(0);
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try (SequenceFile.Writer writer = SequenceFile
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.createWriter(
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conf,
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SequenceFile.Writer.file(hdfswritepath),
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SequenceFile.Writer.keyClass(IntWritable.class),
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SequenceFile.Writer.valueClass(Text.class))) {
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final IntWritable key = new IntWritable(counter.get());
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final Text value = new Text();
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plugin
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.collect(api)
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.forEach(
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content -> {
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key.set(counter.getAndIncrement());
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value.set(content);
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try {
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writer.append(key, value);
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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});
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}
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} catch (Throwable e) {
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throw new CollectorException("Error on collecting ", e);
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}
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}
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}
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@ -0,0 +1,55 @@
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package eu.dnetlib.dhp.collection.worker;
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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 com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.collector.worker.model.ApiDescriptor;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
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/**
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* DnetCollectortWorkerApplication is the main class responsible to start the Dnet Collection into HDFS. This module
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* will be executed on the hadoop cluster and taking in input some parameters that tells it which is the right collector
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* plugin to use and where store the data into HDFS path
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*
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* @author Sandro La Bruzzo
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*/
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public class CollectorWorkerApplication {
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private static final Logger log = LoggerFactory.getLogger(CollectorWorkerApplication.class);
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private static final CollectorPluginFactory collectorPluginFactory = new CollectorPluginFactory();
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/**
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* @param args
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*/
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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CollectorWorker.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/collection/collector_parameter.json")));
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argumentParser.parseArgument(args);
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final String hdfsuri = argumentParser.get("namenode");
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log.info("hdfsURI is {}", hdfsuri);
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final String hdfsPath = argumentParser.get("hdfsPath");
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log.info("hdfsPath is {}" + hdfsPath);
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final String apiDescriptor = argumentParser.get("apidescriptor");
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log.info("apiDescriptor is {}" + apiDescriptor);
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final ObjectMapper jsonMapper = new ObjectMapper();
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final ApiDescriptor api = jsonMapper.readValue(apiDescriptor, ApiDescriptor.class);
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final CollectorWorker worker = new CollectorWorker(collectorPluginFactory, api, hdfsuri, hdfsPath);
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worker.collect();
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}
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}
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@ -1,139 +0,0 @@
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package eu.dnetlib.dhp.collection.worker;
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import java.io.IOException;
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import java.net.URI;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.concurrent.atomic.AtomicInteger;
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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.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.collector.worker.model.ApiDescriptor;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
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import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
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import eu.dnetlib.message.Message;
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import eu.dnetlib.message.MessageManager;
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import eu.dnetlib.message.MessageType;
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public class DnetCollectorWorker {
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private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorker.class);
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private final CollectorPluginFactory collectorPluginFactory;
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private final ArgumentApplicationParser argumentParser;
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private final MessageManager manager;
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public DnetCollectorWorker(
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final CollectorPluginFactory collectorPluginFactory,
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final ArgumentApplicationParser argumentParser,
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final MessageManager manager)
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throws DnetCollectorException {
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this.collectorPluginFactory = collectorPluginFactory;
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this.argumentParser = argumentParser;
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this.manager = manager;
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}
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public void collect() throws DnetCollectorException {
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try {
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final ObjectMapper jsonMapper = new ObjectMapper();
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final ApiDescriptor api = jsonMapper.readValue(argumentParser.get("apidescriptor"), ApiDescriptor.class);
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final CollectorPlugin plugin = collectorPluginFactory.getPluginByProtocol(api.getProtocol());
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final String hdfsuri = argumentParser.get("namenode");
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// ====== Init HDFS File System Object
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Configuration conf = new Configuration();
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// Set FileSystem URI
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conf.set("fs.defaultFS", hdfsuri);
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// Because of Maven
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conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
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conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
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System.setProperty("HADOOP_USER_NAME", argumentParser.get("userHDFS"));
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System.setProperty("hadoop.home.dir", "/");
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// Get the filesystem - HDFS
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FileSystem.get(URI.create(hdfsuri), conf);
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Path hdfswritepath = new Path(argumentParser.get("hdfsPath"));
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log.info("Created path " + hdfswritepath.toString());
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final Map<String, String> ongoingMap = new HashMap<>();
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final Map<String, String> reportMap = new HashMap<>();
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final AtomicInteger counter = new AtomicInteger(0);
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try (SequenceFile.Writer writer = SequenceFile
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.createWriter(
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conf,
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SequenceFile.Writer.file(hdfswritepath),
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SequenceFile.Writer.keyClass(IntWritable.class),
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SequenceFile.Writer.valueClass(Text.class))) {
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final IntWritable key = new IntWritable(counter.get());
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final Text value = new Text();
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plugin
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.collect(api)
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.forEach(
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content -> {
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key.set(counter.getAndIncrement());
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value.set(content);
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if (counter.get() % 10 == 0) {
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try {
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ongoingMap.put("ongoing", "" + counter.get());
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log
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.debug(
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"Sending message: "
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+ manager
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.sendMessage(
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new Message(
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argumentParser.get("workflowId"),
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"Collection",
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MessageType.ONGOING,
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ongoingMap),
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argumentParser.get("rabbitOngoingQueue"),
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true,
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false));
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} catch (Exception e) {
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log.error("Error on sending message ", e);
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}
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}
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try {
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writer.append(key, value);
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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});
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}
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ongoingMap.put("ongoing", "" + counter.get());
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manager
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.sendMessage(
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new Message(
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argumentParser.get("workflowId"), "Collection", MessageType.ONGOING, ongoingMap),
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argumentParser.get("rabbitOngoingQueue"),
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true,
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false);
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reportMap.put("collected", "" + counter.get());
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manager
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.sendMessage(
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new Message(
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argumentParser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
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argumentParser.get("rabbitOngoingQueue"),
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true,
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false);
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manager.close();
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} catch (Throwable e) {
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throw new DnetCollectorException("Error on collecting ", e);
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}
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}
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}
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@ -1,49 +0,0 @@
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package eu.dnetlib.dhp.collection.worker;
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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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|
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
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import eu.dnetlib.message.MessageManager;
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|
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/**
|
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* DnetCollectortWorkerApplication is the main class responsible to start the Dnet Collection into HDFS. This module
|
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* will be executed on the hadoop cluster and taking in input some parameters that tells it which is the right collector
|
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* plugin to use and where store the data into HDFS path
|
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*
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* @author Sandro La Bruzzo
|
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*/
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public class DnetCollectorWorkerApplication {
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private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorkerApplication.class);
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private static final CollectorPluginFactory collectorPluginFactory = new CollectorPluginFactory();
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private static ArgumentApplicationParser argumentParser;
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/** @param args */
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public static void main(final String[] args) throws Exception {
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argumentParser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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DnetCollectorWorker.class
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.getResourceAsStream(
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"/eu/dnetlib/collector/worker/collector_parameter.json")));
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argumentParser.parseArgument(args);
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log.info("hdfsPath =" + argumentParser.get("hdfsPath"));
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log.info("json = " + argumentParser.get("apidescriptor"));
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final MessageManager manager = new MessageManager(
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argumentParser.get("rabbitHost"),
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argumentParser.get("rabbitUser"),
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argumentParser.get("rabbitPassword"),
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false,
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false,
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null);
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final DnetCollectorWorker worker = new DnetCollectorWorker(collectorPluginFactory, argumentParser, manager);
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worker.collect();
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}
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}
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@ -0,0 +1,29 @@
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package eu.dnetlib.dhp.transformation;
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public class DnetTransformationException extends Exception {
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public DnetTransformationException() {
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super();
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}
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public DnetTransformationException(
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final String message,
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final Throwable cause,
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final boolean enableSuppression,
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final boolean writableStackTrace) {
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super(message, cause, enableSuppression, writableStackTrace);
|
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}
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|
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public DnetTransformationException(final String message, final Throwable cause) {
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super(message, cause);
|
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}
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|
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public DnetTransformationException(final String message) {
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super(message);
|
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}
|
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|
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public DnetTransformationException(final Throwable cause) {
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super(cause);
|
||||
}
|
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}
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@ -0,0 +1,69 @@
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package eu.dnetlib.dhp.transformation;
|
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|
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import java.util.List;
|
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import java.util.Map;
|
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|
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import org.apache.commons.lang3.StringUtils;
|
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import org.apache.spark.api.java.function.MapFunction;
|
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import org.slf4j.Logger;
|
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import org.slf4j.LoggerFactory;
|
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|
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import eu.dnetlib.dhp.aggregation.common.AggregationCounter;
|
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
|
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import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
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import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction;
|
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
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|
||||
public class TransformationFactory {
|
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|
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private static final Logger log = LoggerFactory.getLogger(TransformationFactory.class);
|
||||
public static final String TRULE_XQUERY = "for $x in collection('/db/DRIVER/TransformationRuleDSResources/TransformationRuleDSResourceType') where $x//TITLE = \"%s\" return $x//CODE/text()";
|
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|
||||
public static MapFunction<MetadataRecord, MetadataRecord> getTransformationPlugin(
|
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final Map<String, String> jobArgument, final AggregationCounter counters, final ISLookUpService isLookupService)
|
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throws DnetTransformationException {
|
||||
|
||||
try {
|
||||
final String transformationPlugin = jobArgument.get("transformationPlugin");
|
||||
|
||||
log.info("Transformation plugin required " + transformationPlugin);
|
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switch (transformationPlugin) {
|
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case "XSLT_TRANSFORM": {
|
||||
final String transformationRuleName = jobArgument.get("transformationRuleTitle");
|
||||
if (StringUtils.isBlank(transformationRuleName))
|
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throw new DnetTransformationException("Missing Parameter transformationRule");
|
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final VocabularyGroup vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService);
|
||||
|
||||
final String transformationRule = queryTransformationRuleFromIS(
|
||||
transformationRuleName, isLookupService);
|
||||
|
||||
final long dateOfTransformation = new Long(jobArgument.get("dateOfTransformation"));
|
||||
return new XSLTTransformationFunction(counters, transformationRule, dateOfTransformation,
|
||||
vocabularies);
|
||||
|
||||
}
|
||||
default:
|
||||
throw new DnetTransformationException(
|
||||
"transformation plugin does not exists for " + transformationPlugin);
|
||||
|
||||
}
|
||||
|
||||
} catch (Throwable e) {
|
||||
throw new DnetTransformationException(e);
|
||||
}
|
||||
}
|
||||
|
||||
private static String queryTransformationRuleFromIS(final String transformationRuleName,
|
||||
final ISLookUpService isLookUpService) throws Exception {
|
||||
final String query = String.format(TRULE_XQUERY, transformationRuleName);
|
||||
log.info("asking query to IS: " + query);
|
||||
List<String> result = isLookUpService.quickSearchProfile(query);
|
||||
|
||||
if (result == null || result.isEmpty())
|
||||
throw new DnetTransformationException(
|
||||
"Unable to find transformation rule with name: " + transformationRuleName);
|
||||
return result.get(0);
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,6 @@
|
||||
[
|
||||
{"paramName":"p", "paramLongName":"hdfsPath", "paramDescription": "the path where storing the sequential file", "paramRequired": true},
|
||||
{"paramName":"a", "paramLongName":"apidescriptor", "paramDescription": "the JSON encoding of the API Descriptor", "paramRequired": true},
|
||||
{"paramName":"n", "paramLongName":"namenode", "paramDescription": "the Name Node URI", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": false}
|
||||
]
|
||||
@ -0,0 +1,18 @@
|
||||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>yarnRM</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://nameservice1</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
</configuration>
|
||||
@ -1,12 +0,0 @@
|
||||
[
|
||||
{"paramName":"p", "paramLongName":"hdfsPath", "paramDescription": "the path where storing the sequential file", "paramRequired": true},
|
||||
{"paramName":"a", "paramLongName":"apidescriptor", "paramDescription": "the JSON encoding of the API Descriptor", "paramRequired": true},
|
||||
{"paramName":"n", "paramLongName":"namenode", "paramDescription": "the Name Node URI", "paramRequired": true},
|
||||
{"paramName":"u", "paramLongName":"userHDFS", "paramDescription": "the user wich create the hdfs seq file", "paramRequired": true},
|
||||
{"paramName":"ru", "paramLongName":"rabbitUser", "paramDescription": "the user to connect with RabbitMq for messaging", "paramRequired": true},
|
||||
{"paramName":"rp", "paramLongName":"rabbitPassword", "paramDescription": "the password to connect with RabbitMq for messaging", "paramRequired": true},
|
||||
{"paramName":"rh", "paramLongName":"rabbitHost", "paramDescription": "the host of the RabbitMq server", "paramRequired": true},
|
||||
{"paramName":"ro", "paramLongName":"rabbitOngoingQueue", "paramDescription": "the name of the ongoing queue", "paramRequired": true},
|
||||
{"paramName":"rr", "paramLongName":"rabbitReportQueue", "paramDescription": "the name of the report queue", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": true}
|
||||
]
|
||||
@ -0,0 +1,18 @@
|
||||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>yarnRM</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://nameservice1</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
</configuration>
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
Loading…
Reference in New Issue