208 lines
6.2 KiB
Java
208 lines
6.2 KiB
Java
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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.LinkedHashSet;
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import java.util.Map;
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import java.util.Optional;
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import java.util.Set;
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import java.util.concurrent.atomic.AtomicLong;
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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.LongWritable;
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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.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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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.DocumentException;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Element;
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import org.dom4j.Node;
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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.aggregation.AggregatorReport;
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public class BaseAnalyzerJob {
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private static final Logger log = LoggerFactory.getLogger(BaseAnalyzerJob.class);
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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(
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BaseAnalyzerJob.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 dataPath = parser.get("dataPath");
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log.info("dataPath {}: ", dataPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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final boolean reimport = Boolean.parseBoolean(parser.get("reimport"));
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log.info("reimport {}: ", reimport);
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final SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf, isSparkSessionManaged, spark -> processBaseRecords(spark, inputPath, dataPath, outputPath, reimport));
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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 dataPath,
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final String outputPath,
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final boolean reimport) throws IOException {
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try (final FileSystem fs = FileSystem.get(new Configuration());
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final AggregatorReport report = new AggregatorReport()) {
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if (reimport) {
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loadRecords(fs, inputPath, dataPath, report);
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}
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// fs.delete(new Path(outputPath), true);
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extractInfo(spark, dataPath, outputPath);
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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 loadRecords(final FileSystem fs,
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final String inputPath,
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final String outputPath,
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final AggregatorReport report)
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throws Exception {
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final AtomicLong recordsCounter = new AtomicLong(0);
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final LongWritable key = new LongWritable();
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final Text value = new Text();
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try (final SequenceFile.Writer writer = SequenceFile
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.createWriter(
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fs.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
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.keyClass(LongWritable.class),
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SequenceFile.Writer
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.valueClass(Text.class),
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SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
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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 String record = iteraror.next();
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final long i = recordsCounter.incrementAndGet();
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if ((i % 10000) == 0) {
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log.info("# Loaded records: " + i);
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}
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key.set(i);
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value.set(record);
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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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log.info("# COMPLETED - Loaded records: " + recordsCounter.get());
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}
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}
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private static void extractInfo(final SparkSession spark,
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final String inputPath,
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final String targetPath) throws Exception {
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final JavaRDD<BaseRecordInfo> rdd = JavaSparkContext
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.fromSparkContext(spark.sparkContext())
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.sequenceFile(inputPath, LongWritable.class, Text.class)
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.map(s -> s._2.toString())
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.map(BaseAnalyzerJob::extractInfo);
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spark
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.createDataset(rdd.rdd(), Encoders.bean(BaseRecordInfo.class))
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.write()
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.mode(SaveMode.Overwrite)
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.format("parquet")
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.save(targetPath);
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}
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protected static BaseRecordInfo extractInfo(final String s) {
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try {
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final Document record = DocumentHelper.parseText(s);
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final BaseRecordInfo info = new BaseRecordInfo();
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final Set<String> paths = new LinkedHashSet<>();
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final Set<String> types = new LinkedHashSet<>();
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final Map<String, Map<String, String>> colls = new HashMap<>();
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for (final Object o : record.selectNodes("//*|//@*")) {
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paths.add(((Node) o).getPath());
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if (o instanceof Element) {
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final Element n = (Element) o;
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final String nodeName = n.getName();
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if ("collection".equals(nodeName)) {
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final String collName = n.getText().trim();
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if (StringUtils.isNotBlank(collName)) {
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final Map<String, String> attrs = new HashMap<>();
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for (final Object ao : n.attributes()) {
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attrs.put(((Attribute) ao).getName(), ((Attribute) ao).getValue());
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}
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colls.put(collName, attrs);
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}
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} else if ("type".equals(nodeName)) {
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types.add("TYPE: " + n.getText().trim());
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} else if ("typenorm".equals(nodeName)) {
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types.add("TYPE_NORM: " + n.getText().trim());
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}
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}
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}
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info.setId(record.valueOf("//*[local-name() = 'header']/*[local-name() = 'identifier']").trim());
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info.getTypes().addAll(types);
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info.getPaths().addAll(paths);
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info.setCollections(colls);
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return info;
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} catch (final DocumentException 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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