produce a parquet file
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e254720377
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da65728afe
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@ -4,25 +4,25 @@ 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.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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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.AtomicLong;
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import java.util.stream.Collectors;
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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.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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@ -33,9 +33,6 @@ 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 com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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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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@ -43,8 +40,6 @@ public class BaseAnalyzerJob {
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private static final Logger log = LoggerFactory.getLogger(BaseAnalyzerJob.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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@ -65,122 +60,127 @@ public class BaseAnalyzerJob {
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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(conf, isSparkSessionManaged, spark -> processBaseRecords(spark, inputPath, outputPath));
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runWithSparkSession(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 outputPath) throws IOException {
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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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final Map<String, AtomicLong> fields = new HashMap<>();
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final Map<String, AtomicLong> types = new HashMap<>();
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final Map<String, AtomicLong> collections = new HashMap<>();
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final Map<String, AtomicLong> totals = new HashMap<>();
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analyze(fs, inputPath, fields, types, collections, totals, report);
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if (reimport) {
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fs.delete(new Path(dataPath), true);
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loadRecords(fs, inputPath, dataPath, report);
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}
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saveReport(fs, outputPath + "/fields", fields);
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saveReport(fs, outputPath + "/types", types);
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saveReport(fs, outputPath + "/collections", collections);
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saveReport(fs, outputPath + "/totals", totals);
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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 analyze(final FileSystem fs,
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private static void loadRecords(final FileSystem fs,
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final String inputPath,
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final Map<String, AtomicLong> fields,
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final Map<String, AtomicLong> types,
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final Map<String, AtomicLong> collections,
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final Map<String, AtomicLong> totals,
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final AggregatorReport report) throws JsonProcessingException, IOException, DocumentException {
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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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totals.put("Records", recordsCounter);
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final LongWritable key = new LongWritable();
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final Text value = new Text();
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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 = DocumentHelper.parseText(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("# Read records: " + i);
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log.info("# fields: " + fields.size());
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log.info("# types: " + types.size());
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log.info("# collections: " + collections.size());
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log.info("# totals: " + totals.size());
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}
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final List<String> recTypes = new ArrayList<>();
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for (final Object o : record.selectNodes("//*|//@*")) {
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incrementMapCounter(fields, ((Node) o).getPath());
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final String nodeName = ((Node) o).getName();
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if (o instanceof Element) {
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final Element n = (Element) o;
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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> 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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incrementMapCounter(collections, collName + ": " + OBJECT_MAPPER.writeValueAsString(map));
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}
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} else if ("type".equals(nodeName)) {
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recTypes.add("TYPE: " + n.getText().trim());
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} else if ("typenorm".equals(nodeName)) {
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recTypes.add("TYPE_NORM: " + n.getText().trim());
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}
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}
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}
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incrementMapCounter(types, recTypes.stream().sorted().distinct().collect(Collectors.joining(", ")));
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}
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}
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private static void incrementMapCounter(final Map<String, AtomicLong> map, final String key) {
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if (StringUtils.isNotBlank(key)) {
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if (map.containsKey(key)) {
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map.get(key).incrementAndGet();
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} else {
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map.put(key, new AtomicLong(1));
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}
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}
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}
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private static void saveReport(final FileSystem fs, final String outputPath, final Map<String, AtomicLong> fields)
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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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.keyClass(LongWritable.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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final BaseCollectorIterator iteraror = new BaseCollectorIterator(fs, new Path(inputPath), report);
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for (final Entry<String, AtomicLong> e : fields.entrySet()) {
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key.set(e.getKey());
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value.set(e.getKey() + ": " + e.getValue());
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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.fromSparkContext(spark.sparkContext())
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.sequenceFile(inputPath, LongWritable.class, Text.class)
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.map(s -> s._2)
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.map(BaseAnalyzerJob::extractInfo);
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spark.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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private static BaseRecordInfo extractInfo(final Text s) {
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try {
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final Document record = DocumentHelper.parseText(s.toString());
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final BaseRecordInfo info = new BaseRecordInfo();
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for (final Object o : record.selectNodes("//*|//@*")) {
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info.getPaths().add(((Node) o).getPath());
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final String nodeName = ((Node) o).getName();
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if (o instanceof Element) {
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final Element n = (Element) o;
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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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info.getCollections().put(collName, attrs);
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}
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} else if ("type".equals(nodeName)) {
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info.getTypes().add("TYPE: " + n.getText().trim());
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} else if ("typenorm".equals(nodeName)) {
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info.getTypes().add("TYPE_NORM: " + n.getText().trim());
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}
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}
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}
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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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@ -0,0 +1,42 @@
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package eu.dnetlib.dhp.collection.plugin.base;
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import java.io.Serializable;
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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.Set;
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public class BaseRecordInfo implements Serializable {
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private static final long serialVersionUID = -8848232018350074593L;
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private Set<String> paths = new LinkedHashSet<>();
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private Set<String> types = new LinkedHashSet<>();
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public Set<String> getPaths() {
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return this.paths;
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}
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public void setPaths(final Set<String> paths) {
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this.paths = paths;
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}
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public Set<String> getTypes() {
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return this.types;
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}
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public void setTypes(final Set<String> types) {
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this.types = types;
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}
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public Map<String, Map<String, String>> getCollections() {
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return this.collections;
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}
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public void setCollections(final Map<String, Map<String, String>> collections) {
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this.collections = collections;
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}
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private Map<String, Map<String, String>> collections = new HashMap<>();
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}
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@ -5,10 +5,22 @@
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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": "d",
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"paramLongName": "dataPath",
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"paramDescription": "the path of the loaded records",
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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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"paramName": "r",
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"paramLongName": "reimport",
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"paramDescription": "complete re-import",
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"paramRequired": true
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}
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]
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@ -4,26 +4,25 @@
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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>baseDataPath</name>
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<description>the path where to store BASE records</description>
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</property>
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<property>
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<name>baseReportsPath</name>
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<description>path where to store the reports</description>
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</property>
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<property>
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<name>baseReimportFlag</name>
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<description>flag to re-import the records from dump</description>
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</property>
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</parameters>
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<start to="deleteoutputpath"/>
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<start to="analyzeBaseRecords"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="deleteoutputpath">
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<fs>
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<delete path='${baseReportsPath}'/>
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<mkdir path='${baseReportsPath}'/>
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</fs>
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<ok to="analyzeBaseRecords"/>
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<error to="Kill"/>
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</action>
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<action name="analyzeBaseRecords">
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<spark xmlns="uri:oozie:spark-action:0.2">
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@ -43,7 +42,9 @@
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--conf spark.sql.shuffle.partitions=3840
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</spark-opts>
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<arg>--inputPath</arg><arg>${baseInputPath}</arg>
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<arg>--dataPath</arg><arg>${baseDataPath}</arg>
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<arg>--outputPath</arg><arg>${baseReportsPath}</arg>
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<arg>--reimport</arg><arg>${baseReimportFlag}</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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