package eu.dnetlib.doiboost.orcid; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.text.SimpleDateFormat; import java.util.Date; import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.Function; import org.apache.spark.util.LongAccumulator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData; import scala.Tuple2; public class SparkDownloadOrcidAuthors { static Logger logger = LoggerFactory.getLogger(SparkDownloadOrcidAuthors.class); static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; static final String lastUpdate = "2020-09-29 00:00:00"; public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( SparkDownloadOrcidAuthors.class .getResourceAsStream( "/eu/dnetlib/dhp/doiboost/download_orcid_data.json"))); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional .ofNullable(parser.get("isSparkSessionManaged")) .map(Boolean::valueOf) .orElse(Boolean.TRUE); logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String workingPath = parser.get("workingPath"); logger.info("workingPath: {}", workingPath); final String outputPath = parser.get("outputPath"); logger.info("outputPath: {}", outputPath); final String token = parser.get("token"); final String lambdaFileName = parser.get("lambdaFileName"); logger.info("lambdaFileName: {}", lambdaFileName); SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, spark -> { JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); LongAccumulator parsedRecordsAcc = spark.sparkContext().longAccumulator("parsed_records"); LongAccumulator modifiedRecordsAcc = spark.sparkContext().longAccumulator("to_download_records"); LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloaded_records"); LongAccumulator errorHTTP403Acc = spark.sparkContext().longAccumulator("error_HTTP_403"); LongAccumulator errorHTTP409Acc = spark.sparkContext().longAccumulator("error_HTTP_409"); LongAccumulator errorHTTP503Acc = spark.sparkContext().longAccumulator("error_HTTP_503"); LongAccumulator errorHTTP525Acc = spark.sparkContext().longAccumulator("error_HTTP_525"); LongAccumulator errorHTTPGenericAcc = spark.sparkContext().longAccumulator("error_HTTP_Generic"); logger.info("Retrieving data from lamda sequence file"); JavaPairRDD lamdaFileRDD = sc .sequenceFile(workingPath + lambdaFileName, Text.class, Text.class); logger.info("Data retrieved: " + lamdaFileRDD.count()); Function, Boolean> isModifiedAfterFilter = data -> { String orcidId = data._1().toString(); String lastModifiedDate = data._2().toString(); parsedRecordsAcc.add(1); if (isModified(orcidId, lastModifiedDate)) { modifiedRecordsAcc.add(1); return true; } return false; }; Function, Tuple2> downloadRecordFunction = data -> { String orcidId = data._1().toString(); String lastModifiedDate = data._2().toString(); final DownloadedRecordData downloaded = new DownloadedRecordData(); downloaded.setOrcidId(orcidId); downloaded.setLastModifiedDate(lastModifiedDate); try (CloseableHttpClient client = HttpClients.createDefault()) { HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); httpGet.addHeader("Accept", "application/vnd.orcid+xml"); httpGet.addHeader("Authorization", String.format("Bearer %s", token)); long startReq = System.currentTimeMillis(); CloseableHttpResponse response = client.execute(httpGet); long endReq = System.currentTimeMillis(); long reqTime = endReq - startReq; if (reqTime < 1000) { Thread.sleep(1000 - reqTime); } int statusCode = response.getStatusLine().getStatusCode(); downloaded.setStatusCode(statusCode); if (statusCode != 200) { switch (statusCode) { case 403: errorHTTP403Acc.add(1); case 409: errorHTTP409Acc.add(1); case 503: errorHTTP503Acc.add(1); throw new RuntimeException("Orcid request rate limit reached (HTTP 503)"); case 525: errorHTTP525Acc.add(1); default: errorHTTPGenericAcc.add(1); logger .info( "Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); } return downloaded.toTuple2(); } downloadedRecordsAcc.add(1); downloaded .setCompressedData( ArgumentApplicationParser .compressArgument(IOUtils.toString(response.getEntity().getContent()))); } catch (Throwable e) { logger.info("Downloading " + orcidId, e.getMessage()); downloaded.setErrorMessage(e.getMessage()); return downloaded.toTuple2(); } return downloaded.toTuple2(); }; sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true"); logger.info("Start execution ..."); JavaPairRDD authorsModifiedRDD = lamdaFileRDD.filter(isModifiedAfterFilter); logger.info("Authors modified count: " + authorsModifiedRDD.count()); logger.info("Start downloading ..."); authorsModifiedRDD .repartition(10) .map(downloadRecordFunction) .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) .saveAsNewAPIHadoopFile( workingPath.concat(outputPath), Text.class, Text.class, SequenceFileOutputFormat.class, sc.hadoopConfiguration()); logger.info("parsedRecordsAcc: " + parsedRecordsAcc.value().toString()); logger.info("modifiedRecordsAcc: " + modifiedRecordsAcc.value().toString()); logger.info("downloadedRecordsAcc: " + downloadedRecordsAcc.value().toString()); logger.info("errorHTTP403Acc: " + errorHTTP403Acc.value().toString()); logger.info("errorHTTP409Acc: " + errorHTTP409Acc.value().toString()); logger.info("errorHTTP503Acc: " + errorHTTP503Acc.value().toString()); logger.info("errorHTTP525Acc: " + errorHTTP525Acc.value().toString()); logger.info("errorHTTPGenericAcc: " + errorHTTPGenericAcc.value().toString()); }); } private static boolean isModified(String orcidId, String modifiedDate) { Date modifiedDateDt; Date lastUpdateDt; try { if (modifiedDate.length() != 19) { modifiedDate = modifiedDate.substring(0, 19); } modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate); lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); } catch (Exception e) { logger.info("[" + orcidId + "] Parsing date: ", e.getMessage()); return true; } return modifiedDateDt.after(lastUpdateDt); } }