2024-02-13 13:48:26 +01:00
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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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2024-02-14 10:37:39 +01:00
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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.AtomicInteger;
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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.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.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.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 -> processBaseRecords(spark, inputPath, outputPath));
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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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HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
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try (final FileSystem fs = FileSystem.get(new Configuration()); final AggregatorReport report = new AggregatorReport()) {
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final AtomicInteger recordsCounter = new AtomicInteger(0);
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final Map<String, AtomicInteger> fields = new HashMap<>();
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final Map<String, AtomicInteger> types = new HashMap<>();
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final Map<String, AtomicInteger> collections = new HashMap<>();
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analyze(fs, inputPath, recordsCounter, fields, types, collections, report);
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saveReport(fs, outputPath + "/total", Map.of("#records", recordsCounter));
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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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} 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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final String inputPath,
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final AtomicInteger recordsCounter,
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final Map<String, AtomicInteger> fields,
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final Map<String, AtomicInteger> types,
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final Map<String, AtomicInteger> collections,
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final AggregatorReport report) throws JsonProcessingException, IOException {
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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 % 10000) == 0) {
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log.info("# Read records: " + i);
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}
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final List<String> recTypes = new ArrayList<>();
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for (final Object o : record.selectNodes("//*[local-name()='metadata']//*")) {
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incrementMapCounter(fields, ((Node) o).getPath());
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final String nodeName = ((Node) o).getName();
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if ("collection".equals(nodeName)) {
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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)) {
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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: " + nodeName);
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} else if ("typenorm".equals(nodeName)) {
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recTypes.add("TYPE_NORM: " + nodeName);
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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, AtomicInteger> 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 AtomicInteger(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, AtomicInteger> 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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.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, AtomicInteger> 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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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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