extraction of the tar for the dump of crossref, and creation of the dataset

This commit is contained in:
Miriam Baglioni 2021-06-14 09:45:07 +02:00
parent dd997c49e0
commit 75780fc636
2 changed files with 126 additions and 0 deletions

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package eu.dnetlib.doiboost.crossref;
import java.io.BufferedOutputStream;
import java.net.URI;
import java.util.zip.GZIPOutputStream;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.mortbay.log.Log;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class ExtractCrossrefRecords {
public static void main(String[] args) throws Exception {
String hdfsServerUri;
String workingPath;
String crossrefFileNameTarGz;
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
ExtractCrossrefRecords.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/crossref_dump_reader.json")));
parser.parseArgument(args);
hdfsServerUri = parser.get("hdfsServerUri");
workingPath = parser.get("workingPath");
crossrefFileNameTarGz = parser.get("crossrefFileNameTarGz");
Path hdfsreadpath = new Path(hdfsServerUri.concat(workingPath).concat(crossrefFileNameTarGz));
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsServerUri.concat(workingPath));
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
FileSystem fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf);
FSDataInputStream crossrefFileStream = fs.open(hdfsreadpath);
try (TarArchiveInputStream tais = new TarArchiveInputStream(
new GzipCompressorInputStream(crossrefFileStream))) {
TarArchiveEntry entry = null;
while ((entry = tais.getNextTarEntry()) != null) {
if (entry.isDirectory()) {
} else {
try (
FSDataOutputStream out = fs
.create(new Path(workingPath.concat("filess/").concat(entry.getName()).concat(".gz")));
GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
IOUtils.copy(tais, gzipOs);
}
}
}
}
Log.info("Crossref dump reading completed");
}
}

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package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import org.apache.spark.{SparkConf, SparkContext}
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.JsonAST._
import org.json4s.jackson.JsonMethods._
import scala.io.Source
object GenerateCrossrefDatasetSpark {
val log: Logger = LoggerFactory.getLogger(GenerateCrossrefDatasetSpark.getClass)
implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
def extractDump(input:String):List[String] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
val a = (json \ "items").extract[JArray]
a.arr.map(s => compact(render(s)))
}
def crossrefElement(meta: String): CrossrefDT = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(meta)
val doi:String = (json \ "DOI").extract[String]
val timestamp: Long = (json \ "indexed" \ "timestamp").extract[Long]
new CrossrefDT(doi, meta, timestamp)
}
def main(args: Array[String]): Unit = {
val conf = new SparkConf
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json")).mkString)
parser.parseArgument(args)
val master = parser.get("master")
val sourcePath = parser.get("sourcePath")
val targetPath = parser.get("targetPath")
val spark: SparkSession = SparkSession.builder().config(conf)
.appName(GenerateCrossrefDatasetSpark.getClass.getSimpleName)
.master(master)
.getOrCreate()
import spark.implicits._
val sc: SparkContext = spark.sparkContext
sc.wholeTextFiles(sourcePath,2000).flatMap(d =>extractDump(d._2))
.map(meta => crossrefElement(meta))
.toDS()
.write.mode(SaveMode.Overwrite).save(targetPath)
}
}