forked from D-Net/dnet-hadoop
extraction of the tar for the dump of crossref, and creation of the dataset
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package eu.dnetlib.doiboost.crossref;
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import java.io.BufferedOutputStream;
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import java.net.URI;
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import java.util.zip.GZIPOutputStream;
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import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
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import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
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import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataInputStream;
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import org.apache.hadoop.fs.FSDataOutputStream;
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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.mortbay.log.Log;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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public class ExtractCrossrefRecords {
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public static void main(String[] args) throws Exception {
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String hdfsServerUri;
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String workingPath;
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String crossrefFileNameTarGz;
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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ExtractCrossrefRecords.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/crossref_dump_reader.json")));
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parser.parseArgument(args);
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hdfsServerUri = parser.get("hdfsServerUri");
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workingPath = parser.get("workingPath");
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crossrefFileNameTarGz = parser.get("crossrefFileNameTarGz");
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Path hdfsreadpath = new Path(hdfsServerUri.concat(workingPath).concat(crossrefFileNameTarGz));
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsServerUri.concat(workingPath));
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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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FileSystem fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf);
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FSDataInputStream crossrefFileStream = fs.open(hdfsreadpath);
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try (TarArchiveInputStream tais = new TarArchiveInputStream(
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new GzipCompressorInputStream(crossrefFileStream))) {
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TarArchiveEntry entry = null;
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while ((entry = tais.getNextTarEntry()) != null) {
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if (entry.isDirectory()) {
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} else {
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try (
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FSDataOutputStream out = fs
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.create(new Path(workingPath.concat("filess/").concat(entry.getName()).concat(".gz")));
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GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
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IOUtils.copy(tais, gzipOs);
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}
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}
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}
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}
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Log.info("Crossref dump reading completed");
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}
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}
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@ -0,0 +1,61 @@
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package eu.dnetlib.doiboost.crossref
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import org.apache.spark.{SparkConf, SparkContext}
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import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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import org.json4s
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import org.json4s.DefaultFormats
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import org.json4s.JsonAST._
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import org.json4s.jackson.JsonMethods._
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import scala.io.Source
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object GenerateCrossrefDatasetSpark {
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val log: Logger = LoggerFactory.getLogger(GenerateCrossrefDatasetSpark.getClass)
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implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
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def extractDump(input:String):List[String] = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(input)
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val a = (json \ "items").extract[JArray]
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a.arr.map(s => compact(render(s)))
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}
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def crossrefElement(meta: String): CrossrefDT = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(meta)
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val doi:String = (json \ "DOI").extract[String]
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val timestamp: Long = (json \ "indexed" \ "timestamp").extract[Long]
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new CrossrefDT(doi, meta, timestamp)
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}
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def main(args: Array[String]): Unit = {
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val conf = new SparkConf
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json")).mkString)
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parser.parseArgument(args)
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val master = parser.get("master")
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val sourcePath = parser.get("sourcePath")
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val targetPath = parser.get("targetPath")
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val spark: SparkSession = SparkSession.builder().config(conf)
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.appName(GenerateCrossrefDatasetSpark.getClass.getSimpleName)
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.master(master)
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.getOrCreate()
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import spark.implicits._
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val sc: SparkContext = spark.sparkContext
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sc.wholeTextFiles(sourcePath,2000).flatMap(d =>extractDump(d._2))
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.map(meta => crossrefElement(meta))
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.toDS()
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.write.mode(SaveMode.Overwrite).save(targetPath)
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}
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}
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