forked from D-Net/dnet-hadoop
164 lines
6.6 KiB
Java
164 lines
6.6 KiB
Java
package eu.dnetlib.dhp.collection;
|
|
|
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
|
|
import eu.dnetlib.dhp.model.mdstore.Provenance;
|
|
import eu.dnetlib.message.Message;
|
|
import eu.dnetlib.message.MessageManager;
|
|
import eu.dnetlib.message.MessageType;
|
|
import java.io.ByteArrayInputStream;
|
|
import java.nio.charset.StandardCharsets;
|
|
import java.util.HashMap;
|
|
import java.util.Map;
|
|
import java.util.Objects;
|
|
import org.apache.commons.cli.*;
|
|
import org.apache.commons.io.IOUtils;
|
|
import org.apache.commons.lang3.StringUtils;
|
|
import org.apache.hadoop.io.IntWritable;
|
|
import org.apache.hadoop.io.Text;
|
|
import org.apache.spark.api.java.JavaPairRDD;
|
|
import org.apache.spark.api.java.JavaRDD;
|
|
import org.apache.spark.api.java.JavaSparkContext;
|
|
import org.apache.spark.sql.Dataset;
|
|
import org.apache.spark.sql.Encoder;
|
|
import org.apache.spark.sql.Encoders;
|
|
import org.apache.spark.sql.SparkSession;
|
|
import org.apache.spark.util.LongAccumulator;
|
|
import org.dom4j.Document;
|
|
import org.dom4j.Node;
|
|
import org.dom4j.io.SAXReader;
|
|
|
|
public class GenerateNativeStoreSparkJob {
|
|
|
|
public static MetadataRecord parseRecord(
|
|
final String input,
|
|
final String xpath,
|
|
final String encoding,
|
|
final Provenance provenance,
|
|
final Long dateOfCollection,
|
|
final LongAccumulator totalItems,
|
|
final LongAccumulator invalidRecords) {
|
|
|
|
if (totalItems != null) totalItems.add(1);
|
|
try {
|
|
SAXReader reader = new SAXReader();
|
|
Document document =
|
|
reader.read(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)));
|
|
Node node = document.selectSingleNode(xpath);
|
|
final String originalIdentifier = node.getText();
|
|
if (StringUtils.isBlank(originalIdentifier)) {
|
|
if (invalidRecords != null) invalidRecords.add(1);
|
|
return null;
|
|
}
|
|
return new MetadataRecord(
|
|
originalIdentifier, encoding, provenance, input, dateOfCollection);
|
|
} catch (Throwable e) {
|
|
if (invalidRecords != null) invalidRecords.add(1);
|
|
e.printStackTrace();
|
|
return null;
|
|
}
|
|
}
|
|
|
|
public static void main(String[] args) throws Exception {
|
|
|
|
final ArgumentApplicationParser parser =
|
|
new ArgumentApplicationParser(
|
|
IOUtils.toString(
|
|
GenerateNativeStoreSparkJob.class.getResourceAsStream(
|
|
"/eu/dnetlib/dhp/collection/collection_input_parameters.json")));
|
|
parser.parseArgument(args);
|
|
final ObjectMapper jsonMapper = new ObjectMapper();
|
|
final Provenance provenance =
|
|
jsonMapper.readValue(parser.get("provenance"), Provenance.class);
|
|
final long dateOfCollection = new Long(parser.get("dateOfCollection"));
|
|
|
|
final SparkSession spark =
|
|
SparkSession.builder()
|
|
.appName("GenerateNativeStoreSparkJob")
|
|
.master(parser.get("master"))
|
|
.getOrCreate();
|
|
|
|
final Map<String, String> ongoingMap = new HashMap<>();
|
|
final Map<String, String> reportMap = new HashMap<>();
|
|
|
|
final boolean test =
|
|
parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));
|
|
|
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
|
|
|
final JavaPairRDD<IntWritable, Text> inputRDD =
|
|
sc.sequenceFile(parser.get("input"), IntWritable.class, Text.class);
|
|
|
|
final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems");
|
|
|
|
final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords");
|
|
|
|
final MessageManager manager =
|
|
new MessageManager(
|
|
parser.get("rabbitHost"),
|
|
parser.get("rabbitUser"),
|
|
parser.get("rabbitPassword"),
|
|
false,
|
|
false,
|
|
null);
|
|
|
|
final JavaRDD<MetadataRecord> mappeRDD =
|
|
inputRDD.map(
|
|
item ->
|
|
parseRecord(
|
|
item._2().toString(),
|
|
parser.get("xpath"),
|
|
parser.get("encoding"),
|
|
provenance,
|
|
dateOfCollection,
|
|
totalItems,
|
|
invalidRecords))
|
|
.filter(Objects::nonNull)
|
|
.distinct();
|
|
|
|
ongoingMap.put("ongoing", "0");
|
|
if (!test) {
|
|
manager.sendMessage(
|
|
new Message(
|
|
parser.get("workflowId"),
|
|
"DataFrameCreation",
|
|
MessageType.ONGOING,
|
|
ongoingMap),
|
|
parser.get("rabbitOngoingQueue"),
|
|
true,
|
|
false);
|
|
}
|
|
|
|
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
|
|
final Dataset<MetadataRecord> mdstore = spark.createDataset(mappeRDD.rdd(), encoder);
|
|
final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords");
|
|
mdStoreRecords.add(mdstore.count());
|
|
ongoingMap.put("ongoing", "" + totalItems.value());
|
|
if (!test) {
|
|
manager.sendMessage(
|
|
new Message(
|
|
parser.get("workflowId"),
|
|
"DataFrameCreation",
|
|
MessageType.ONGOING,
|
|
ongoingMap),
|
|
parser.get("rabbitOngoingQueue"),
|
|
true,
|
|
false);
|
|
}
|
|
mdstore.write().format("parquet").save(parser.get("output"));
|
|
reportMap.put("inputItem", "" + totalItems.value());
|
|
reportMap.put("invalidRecords", "" + invalidRecords.value());
|
|
reportMap.put("mdStoreSize", "" + mdStoreRecords.value());
|
|
if (!test) {
|
|
manager.sendMessage(
|
|
new Message(
|
|
parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
|
|
parser.get("rabbitReportQueue"),
|
|
true,
|
|
false);
|
|
manager.close();
|
|
}
|
|
}
|
|
}
|