all actions from download lambda file to merge updated data into one wf
This commit is contained in:
parent
efe4c2a9c5
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b2de598c1a
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@ -1,208 +0,0 @@
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package eu.dnetlib.doiboost.orcid;
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import java.io.*;
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import java.text.SimpleDateFormat;
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import java.util.Arrays;
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import java.util.Date;
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import java.util.List;
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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.FileSystem;
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import org.apache.hadoop.fs.Path;
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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.GzipCodec;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.apache.http.impl.client.CloseableHttpClient;
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import org.apache.http.impl.client.HttpClients;
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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 OrcidDownloader extends OrcidDSManager {
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static final int REQ_LIMIT = 24;
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static final int REQ_MAX_TEST = -1;
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static final int RECORD_PARSED_COUNTER_LOG_INTERVAL = 500;
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static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
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static final String lastUpdate = "2020-09-29 00:00:00";
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private String lambdaFileName;
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private String outputPath;
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private String token;
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public static void main(String[] args) throws IOException, Exception {
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OrcidDownloader orcidDownloader = new OrcidDownloader();
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orcidDownloader.loadArgs(args);
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orcidDownloader.parseLambdaFile();
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}
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private String downloadRecord(String orcidId) throws IOException {
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try (CloseableHttpClient client = HttpClients.createDefault()) {
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HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record");
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httpGet.addHeader("Accept", "application/vnd.orcid+xml");
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httpGet.addHeader("Authorization", String.format("Bearer %s", token));
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CloseableHttpResponse response = client.execute(httpGet);
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if (response.getStatusLine().getStatusCode() != 200) {
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Log
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.info(
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"Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
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return new String("");
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}
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// return IOUtils.toString(response.getEntity().getContent());
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return xmlStreamToString(response.getEntity().getContent());
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}
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}
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private String xmlStreamToString(InputStream xmlStream) throws IOException {
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BufferedReader br = new BufferedReader(new InputStreamReader(xmlStream));
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String line;
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StringBuffer buffer = new StringBuffer();
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while ((line = br.readLine()) != null) {
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buffer.append(line);
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}
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return buffer.toString();
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}
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public void parseLambdaFile() throws Exception {
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int parsedRecordsCounter = 0;
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int downloadedRecordsCounter = 0;
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int savedRecordsCounter = 0;
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long startDownload = 0;
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Configuration conf = initConfigurationObject();
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FileSystem fs = initFileSystemObject(conf);
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String lambdaFileUri = hdfsServerUri.concat(workingPath).concat(lambdaFileName);
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Path hdfsreadpath = new Path(lambdaFileUri);
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FSDataInputStream lambdaFileStream = fs.open(hdfsreadpath);
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Path hdfsoutputPath = new Path(
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hdfsServerUri
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.concat(workingPath)
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.concat(outputPath)
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.concat("updated_xml_authors.seq"));
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try (TarArchiveInputStream tais = new TarArchiveInputStream(
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new GzipCompressorInputStream(lambdaFileStream))) {
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TarArchiveEntry entry = null;
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StringBuilder sb = new StringBuilder();
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try (SequenceFile.Writer writer = SequenceFile
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.createWriter(
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conf,
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SequenceFile.Writer.file(hdfsoutputPath),
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SequenceFile.Writer.keyClass(Text.class),
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SequenceFile.Writer.valueClass(Text.class),
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SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new GzipCodec()))) {
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startDownload = System.currentTimeMillis();
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while ((entry = tais.getNextTarEntry()) != null) {
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BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from tarInput
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String line;
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while ((line = br.readLine()) != null) {
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String[] values = line.split(",");
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List<String> recordInfo = Arrays.asList(values);
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int nReqTmp = 0;
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long startReqTmp = System.currentTimeMillis();
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// skip headers line
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if (parsedRecordsCounter == 0) {
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parsedRecordsCounter++;
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continue;
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}
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parsedRecordsCounter++;
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String orcidId = recordInfo.get(0);
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if (isModified(orcidId, recordInfo.get(3))) {
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String record = downloadRecord(orcidId);
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downloadedRecordsCounter++;
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if (!record.isEmpty()) {
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// String compressRecord = ArgumentApplicationParser.compressArgument(record);
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final Text key = new Text(recordInfo.get(0));
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final Text value = new Text(record);
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writer.append(key, value);
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savedRecordsCounter++;
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}
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} else {
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break;
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}
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long endReq = System.currentTimeMillis();
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nReqTmp++;
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if (nReqTmp == REQ_LIMIT) {
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long reqSessionDuration = endReq - startReqTmp;
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if (reqSessionDuration <= 1000) {
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Log
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.info(
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"\nreqSessionDuration: "
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+ reqSessionDuration
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+ " nReqTmp: "
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+ nReqTmp
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+ " wait ....");
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Thread.sleep(1000 - reqSessionDuration);
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} else {
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nReqTmp = 0;
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startReqTmp = System.currentTimeMillis();
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}
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}
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if ((parsedRecordsCounter % RECORD_PARSED_COUNTER_LOG_INTERVAL) == 0) {
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Log
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.info(
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"Current parsed: "
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+ parsedRecordsCounter
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+ " downloaded: "
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+ downloadedRecordsCounter
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+ " saved: "
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+ savedRecordsCounter);
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if (REQ_MAX_TEST != -1 && parsedRecordsCounter > REQ_MAX_TEST) {
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break;
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}
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}
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}
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long endDownload = System.currentTimeMillis();
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long downloadTime = endDownload - startDownload;
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Log.info("Download time: " + ((downloadTime / 1000) / 60) + " minutes");
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}
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}
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}
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Log.info("Download started at: " + new Date(startDownload).toString());
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Log.info("Download ended at: " + new Date(System.currentTimeMillis()).toString());
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Log.info("Parsed Records Counter: " + parsedRecordsCounter);
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Log.info("Downloaded Records Counter: " + downloadedRecordsCounter);
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Log.info("Saved Records Counter: " + savedRecordsCounter);
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}
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private void loadArgs(String[] args) throws IOException, Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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OrcidDownloader.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/download_orcid_data.json")));
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parser.parseArgument(args);
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hdfsServerUri = parser.get("hdfsServerUri");
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Log.info("HDFS URI: " + hdfsServerUri);
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workingPath = parser.get("workingPath");
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Log.info("Default Path: " + workingPath);
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lambdaFileName = parser.get("lambdaFileName");
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Log.info("Lambda File Name: " + lambdaFileName);
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outputPath = parser.get("outputPath");
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Log.info("Output Data: " + outputPath);
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token = parser.get("token");
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}
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public boolean isModified(String orcidId, String modifiedDate) {
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Date modifiedDateDt = null;
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Date lastUpdateDt = null;
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try {
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if (modifiedDate.length() != 19) {
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modifiedDate = modifiedDate.substring(0, 19);
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}
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modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate);
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lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
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} catch (Exception e) {
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Log.info("[" + orcidId + "] Parsing date: ", e.getMessage());
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return true;
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}
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return modifiedDateDt.after(lastUpdateDt);
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}
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}
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@ -34,7 +34,7 @@ public class SparkDownloadOrcidAuthors {
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static Logger logger = LoggerFactory.getLogger(SparkDownloadOrcidAuthors.class);
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static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
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static final String lastUpdate = "2020-09-29 00:00:00";
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static final String lastUpdate = "2020-11-18 00:00:05";
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public static void main(String[] args) throws IOException, Exception {
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@ -69,6 +69,7 @@ public class SparkDownloadOrcidAuthors {
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LongAccumulator modifiedRecordsAcc = spark.sparkContext().longAccumulator("to_download_records");
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LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloaded_records");
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LongAccumulator errorHTTP403Acc = spark.sparkContext().longAccumulator("error_HTTP_403");
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LongAccumulator errorHTTP404Acc = spark.sparkContext().longAccumulator("error_HTTP_404");
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LongAccumulator errorHTTP409Acc = spark.sparkContext().longAccumulator("error_HTTP_409");
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LongAccumulator errorHTTP503Acc = spark.sparkContext().longAccumulator("error_HTTP_503");
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LongAccumulator errorHTTP525Acc = spark.sparkContext().longAccumulator("error_HTTP_525");
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@ -113,6 +114,8 @@ public class SparkDownloadOrcidAuthors {
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switch (statusCode) {
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case 403:
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errorHTTP403Acc.add(1);
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case 404:
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errorHTTP404Acc.add(1);
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case 409:
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errorHTTP409Acc.add(1);
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case 503:
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@ -149,7 +152,7 @@ public class SparkDownloadOrcidAuthors {
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logger.info("Authors modified count: " + authorsModifiedRDD.count());
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logger.info("Start downloading ...");
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authorsModifiedRDD
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.repartition(10)
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.repartition(100)
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.map(downloadRecordFunction)
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.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
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.saveAsNewAPIHadoopFile(
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@ -158,10 +161,12 @@ public class SparkDownloadOrcidAuthors {
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Text.class,
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SequenceFileOutputFormat.class,
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sc.hadoopConfiguration());
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logger.info("parsedRecordsAcc: " + parsedRecordsAcc.value().toString());
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logger.info("modifiedRecordsAcc: " + modifiedRecordsAcc.value().toString());
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logger.info("downloadedRecordsAcc: " + downloadedRecordsAcc.value().toString());
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logger.info("errorHTTP403Acc: " + errorHTTP403Acc.value().toString());
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logger.info("errorHTTP404Acc: " + errorHTTP404Acc.value().toString());
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logger.info("errorHTTP409Acc: " + errorHTTP409Acc.value().toString());
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logger.info("errorHTTP503Acc: " + errorHTTP503Acc.value().toString());
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logger.info("errorHTTP525Acc: " + errorHTTP525Acc.value().toString());
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@ -43,7 +43,7 @@ public class SparkDownloadOrcidWorks {
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public static final String ORCID_XML_DATETIME_FORMAT = "yyyy-MM-dd'T'HH:mm:ss.SSS'Z'";
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public static final DateTimeFormatter ORCID_XML_DATETIMEFORMATTER = DateTimeFormatter
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.ofPattern(ORCID_XML_DATETIME_FORMAT);
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public static final String lastUpdateValue = "2020-09-29 00:00:00";
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public static final String lastUpdateValue = "2020-11-18 00:00:05";
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public static void main(String[] args) throws IOException, Exception {
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@ -89,6 +89,7 @@ public class SparkDownloadOrcidWorks {
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.longAccumulator("error_parsing_xml_found");
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LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloaded_records");
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LongAccumulator errorHTTP403Acc = spark.sparkContext().longAccumulator("error_HTTP_403");
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LongAccumulator errorHTTP404Acc = spark.sparkContext().longAccumulator("error_HTTP_404");
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LongAccumulator errorHTTP409Acc = spark.sparkContext().longAccumulator("error_HTTP_409");
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LongAccumulator errorHTTP503Acc = spark.sparkContext().longAccumulator("error_HTTP_503");
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LongAccumulator errorHTTP525Acc = spark.sparkContext().longAccumulator("error_HTTP_525");
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@ -163,6 +164,8 @@ public class SparkDownloadOrcidWorks {
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switch (statusCode) {
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case 403:
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errorHTTP403Acc.add(1);
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case 404:
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errorHTTP404Acc.add(1);
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case 409:
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errorHTTP409Acc.add(1);
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case 503:
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@ -186,29 +189,19 @@ public class SparkDownloadOrcidWorks {
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.compressArgument(IOUtils.toString(response.getEntity().getContent())));
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} catch (Throwable e) {
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logger.info("Downloading " + orcidId, e.getMessage());
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if (downloaded.getStatusCode() == 503) {
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throw new RuntimeException("Orcid request rate limit reached (HTTP 503)");
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}
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downloaded.setErrorMessage(e.getMessage());
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return downloaded.toTuple2();
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}
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return downloaded.toTuple2();
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};
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// sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true");
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updatedAuthorsRDD
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.flatMap(retrieveWorkUrlFunction)
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.repartition(100)
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.map(downloadWorkFunction)
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.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
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.saveAsTextFile(workingPath.concat(outputPath), GzipCodec.class);
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// .saveAsNewAPIHadoopFile(
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// workingPath.concat(outputPath),
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// Text.class,
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// Text.class,
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// SequenceFileOutputFormat.class,
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// sc.hadoopConfiguration());
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logger.info("updatedAuthorsAcc: " + updatedAuthorsAcc.value().toString());
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logger.info("parsedAuthorsAcc: " + parsedAuthorsAcc.value().toString());
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logger.info("parsedWorksAcc: " + parsedWorksAcc.value().toString());
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@ -36,12 +36,12 @@ public class SparkUpdateOrcidAuthors {
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.setSerializationInclusion(JsonInclude.Include.NON_NULL);
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public static void main(String[] args) throws IOException, Exception {
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Logger logger = LoggerFactory.getLogger(SparkUpdateOrcidDatasets.class);
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Logger logger = LoggerFactory.getLogger(SparkUpdateOrcidAuthors.class);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkUpdateOrcidDatasets.class
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SparkUpdateOrcidAuthors.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/download_orcid_data.json")));
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parser.parseArgument(args);
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@ -95,7 +95,7 @@ public class SparkUpdateOrcidAuthors {
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authorSummary = XMLRecordParser
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.VTDParseAuthorSummary(xmlAuthor.getBytes());
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authorSummary.setStatusCode(statusCode);
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authorSummary.setDownloadDate("2020-11-18 00:00:05.644768");
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authorSummary.setDownloadDate("2020-12-15 00:00:01.000000");
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authorSummary.setBase64CompressData(compressedData);
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return authorSummary;
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} catch (Exception e) {
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@ -105,7 +105,7 @@ public class SparkUpdateOrcidAuthors {
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}
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} else {
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authorSummary.setStatusCode(statusCode);
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authorSummary.setDownloadDate("2020-11-18 00:00:05.644768");
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authorSummary.setDownloadDate("2020-12-15 00:00:01.000000");
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errorCodeAuthorsFoundAcc.add(1);
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}
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return authorSummary;
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@ -1,317 +0,0 @@
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package eu.dnetlib.doiboost.orcid;
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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.Objects;
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import java.util.Optional;
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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.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.Function;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.util.LongAccumulator;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.annotation.JsonInclude;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.orcid.AuthorSummary;
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import eu.dnetlib.dhp.schema.orcid.Work;
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import eu.dnetlib.dhp.schema.orcid.WorkDetail;
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import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
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import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
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import scala.Tuple2;
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public class SparkUpdateOrcidDatasets {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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.setSerializationInclusion(JsonInclude.Include.NON_NULL);
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public static void main(String[] args) throws IOException, Exception {
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Logger logger = LoggerFactory.getLogger(SparkUpdateOrcidDatasets.class);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkUpdateOrcidDatasets.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/download_orcid_data.json")));
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parser.parseArgument(args);
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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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final String workingPath = parser.get("workingPath");
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// final String outputPath = parser.get("outputPath");
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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LongAccumulator oldAuthorsFoundAcc = spark
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.sparkContext()
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.longAccumulator("old_authors_found");
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LongAccumulator updatedAuthorsFoundAcc = spark
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.sparkContext()
|
||||
.longAccumulator("updated_authors_found");
|
||||
LongAccumulator newAuthorsFoundAcc = spark
|
||||
.sparkContext()
|
||||
.longAccumulator("new_authors_found");
|
||||
LongAccumulator errorCodeAuthorsFoundAcc = spark
|
||||
.sparkContext()
|
||||
.longAccumulator("error_code_authors_found");
|
||||
LongAccumulator errorLoadingAuthorsJsonFoundAcc = spark
|
||||
.sparkContext()
|
||||
.longAccumulator("error_loading_authors_json_found");
|
||||
LongAccumulator errorParsingAuthorsXMLFoundAcc = spark
|
||||
.sparkContext()
|
||||
.longAccumulator("error_parsing_authors_xml_found");
|
||||
|
||||
LongAccumulator oldWorksFoundAcc = spark
|
||||
.sparkContext()
|
||||
.longAccumulator("old_works_found");
|
||||
LongAccumulator updatedWorksFoundAcc = spark
|
||||
.sparkContext()
|
||||
.longAccumulator("updated_works_found");
|
||||
LongAccumulator newWorksFoundAcc = spark
|
||||
.sparkContext()
|
||||
.longAccumulator("new_works_found");
|
||||
LongAccumulator errorCodeWorksFoundAcc = spark
|
||||
.sparkContext()
|
||||
.longAccumulator("error_code_works_found");
|
||||
LongAccumulator errorLoadingWorksJsonFoundAcc = spark
|
||||
.sparkContext()
|
||||
.longAccumulator("error_loading_works_json_found");
|
||||
LongAccumulator errorParsingWorksXMLFoundAcc = spark
|
||||
.sparkContext()
|
||||
.longAccumulator("error_parsing_works_xml_found");
|
||||
|
||||
// JavaPairRDD<Text, Text> xmlSummariesRDD = sc
|
||||
// .sequenceFile(workingPath.concat("xml/authors/xml_authors.seq"), Text.class, Text.class);
|
||||
// xmlSummariesRDD
|
||||
// .map(seq -> {
|
||||
// AuthorSummary authorSummary = XMLRecordParser
|
||||
// .VTDParseAuthorSummary(seq._2().toString().getBytes());
|
||||
// authorSummary
|
||||
// .setBase64CompressData(ArgumentApplicationParser.compressArgument(seq._2().toString()));
|
||||
// return authorSummary;
|
||||
// })
|
||||
// .filter(authorSummary -> authorSummary != null)
|
||||
// .map(authorSummary -> JsonWriter.create(authorSummary))
|
||||
// .saveAsTextFile(workingPath.concat("orcid_dataset/authors"), GzipCodec.class);
|
||||
//
|
||||
// JavaPairRDD<Text, Text> xmlWorksRDD = sc
|
||||
// .sequenceFile(workingPath.concat("xml/works/*"), Text.class, Text.class);
|
||||
//
|
||||
// xmlWorksRDD
|
||||
// .map(seq -> {
|
||||
// WorkDetail workDetail = XMLRecordParserNoDoi.VTDParseWorkData(seq._2().toString().getBytes());
|
||||
// Work work = new Work();
|
||||
// work.setWorkDetail(workDetail);
|
||||
// work.setBase64CompressData(ArgumentApplicationParser.compressArgument(seq._2().toString()));
|
||||
// return work;
|
||||
// })
|
||||
// .filter(work -> work != null)
|
||||
// .map(work -> JsonWriter.create(work))
|
||||
// .saveAsTextFile(workingPath.concat("orcid_dataset/works"), GzipCodec.class);
|
||||
|
||||
// Function<Tuple2<Text, Text>, AuthorSummary> retrieveAuthorSummaryFunction = data -> {
|
||||
// AuthorSummary authorSummary = new AuthorSummary();
|
||||
// String orcidId = data._1().toString();
|
||||
// String jsonData = data._2().toString();
|
||||
// JsonElement jElement = new JsonParser().parse(jsonData);
|
||||
// String statusCode = getJsonValue(jElement, "statusCode");
|
||||
// String downloadDate = getJsonValue(jElement, "lastModifiedDate");
|
||||
// if (statusCode.equals("200")) {
|
||||
// String compressedData = getJsonValue(jElement, "compressedData");
|
||||
// if (StringUtils.isEmpty(compressedData)) {
|
||||
// errorLoadingAuthorsJsonFoundAcc.add(1);
|
||||
// } else {
|
||||
// String xmlAuthor = ArgumentApplicationParser.decompressValue(compressedData);
|
||||
// try {
|
||||
// authorSummary = XMLRecordParser
|
||||
// .VTDParseAuthorSummary(xmlAuthor.getBytes());
|
||||
// authorSummary.setStatusCode(statusCode);
|
||||
// authorSummary.setDownloadDate("2020-11-18 00:00:05.644768");
|
||||
// authorSummary.setBase64CompressData(compressedData);
|
||||
// return authorSummary;
|
||||
// } catch (Exception e) {
|
||||
// logger.error("parsing xml " + orcidId + " [" + jsonData + "]", e);
|
||||
// errorParsingAuthorsXMLFoundAcc.add(1);
|
||||
// }
|
||||
// }
|
||||
// } else {
|
||||
// authorSummary.setStatusCode(statusCode);
|
||||
// authorSummary.setDownloadDate("2020-11-18 00:00:05.644768");
|
||||
// errorCodeAuthorsFoundAcc.add(1);
|
||||
// }
|
||||
// return authorSummary;
|
||||
// };
|
||||
//
|
||||
// Dataset<AuthorSummary> downloadedAuthorSummaryDS = spark
|
||||
// .createDataset(
|
||||
// sc
|
||||
// .sequenceFile(workingPath + "downloads/updated_authors/*", Text.class, Text.class)
|
||||
// .map(retrieveAuthorSummaryFunction)
|
||||
// .rdd(),
|
||||
// Encoders.bean(AuthorSummary.class));
|
||||
// Dataset<AuthorSummary> currentAuthorSummaryDS = spark
|
||||
// .createDataset(
|
||||
// sc
|
||||
// .textFile(workingPath.concat("orcid_dataset/authors/*"))
|
||||
// .map(item -> OBJECT_MAPPER.readValue(item, AuthorSummary.class))
|
||||
// .rdd(),
|
||||
// Encoders.bean(AuthorSummary.class));
|
||||
// currentAuthorSummaryDS
|
||||
// .joinWith(
|
||||
// downloadedAuthorSummaryDS,
|
||||
// currentAuthorSummaryDS
|
||||
// .col("authorData.oid")
|
||||
// .equalTo(downloadedAuthorSummaryDS.col("authorData.oid")),
|
||||
// "full_outer")
|
||||
// .map(value -> {
|
||||
// Optional<AuthorSummary> opCurrent = Optional.ofNullable(value._1());
|
||||
// Optional<AuthorSummary> opDownloaded = Optional.ofNullable(value._2());
|
||||
// if (!opCurrent.isPresent()) {
|
||||
// newAuthorsFoundAcc.add(1);
|
||||
// return opDownloaded.get();
|
||||
// }
|
||||
// if (!opDownloaded.isPresent()) {
|
||||
// oldAuthorsFoundAcc.add(1);
|
||||
// return opCurrent.get();
|
||||
// }
|
||||
// if (opCurrent.isPresent() && opDownloaded.isPresent()) {
|
||||
// updatedAuthorsFoundAcc.add(1);
|
||||
// return opDownloaded.get();
|
||||
// }
|
||||
// return null;
|
||||
// },
|
||||
// Encoders.bean(AuthorSummary.class))
|
||||
// .filter(Objects::nonNull)
|
||||
// .toJavaRDD()
|
||||
// .map(authorSummary -> OBJECT_MAPPER.writeValueAsString(authorSummary))
|
||||
// .saveAsTextFile(workingPath.concat("orcid_dataset/new_authors"), GzipCodec.class);
|
||||
//
|
||||
// logger.info("oldAuthorsFoundAcc: " + oldAuthorsFoundAcc.value().toString());
|
||||
// logger.info("newAuthorsFoundAcc: " + newAuthorsFoundAcc.value().toString());
|
||||
// logger.info("updatedAuthorsFoundAcc: " + updatedAuthorsFoundAcc.value().toString());
|
||||
// logger.info("errorCodeFoundAcc: " + errorCodeAuthorsFoundAcc.value().toString());
|
||||
// logger.info("errorLoadingJsonFoundAcc: " + errorLoadingAuthorsJsonFoundAcc.value().toString());
|
||||
// logger.info("errorParsingXMLFoundAcc: " + errorParsingAuthorsXMLFoundAcc.value().toString());
|
||||
|
||||
Function<String, Work> retrieveWorkFunction = jsonData -> {
|
||||
Work work = new Work();
|
||||
JsonElement jElement = new JsonParser().parse(jsonData);
|
||||
String statusCode = getJsonValue(jElement, "statusCode");
|
||||
work.setStatusCode(statusCode);
|
||||
String downloadDate = getJsonValue(jElement, "lastModifiedDate");
|
||||
work.setDownloadDate("2020-11-18 00:00:05.644768");
|
||||
if (statusCode.equals("200")) {
|
||||
String compressedData = getJsonValue(jElement, "compressedData");
|
||||
if (StringUtils.isEmpty(compressedData)) {
|
||||
errorLoadingWorksJsonFoundAcc.add(1);
|
||||
} else {
|
||||
String xmlWork = ArgumentApplicationParser.decompressValue(compressedData);
|
||||
try {
|
||||
WorkDetail workDetail = XMLRecordParserNoDoi
|
||||
.VTDParseWorkData(xmlWork.getBytes());
|
||||
work.setWorkDetail(workDetail);
|
||||
work.setBase64CompressData(compressedData);
|
||||
return work;
|
||||
} catch (Exception e) {
|
||||
logger.error("parsing xml [" + jsonData + "]", e);
|
||||
errorParsingWorksXMLFoundAcc.add(1);
|
||||
}
|
||||
}
|
||||
} else {
|
||||
errorCodeWorksFoundAcc.add(1);
|
||||
}
|
||||
return work;
|
||||
};
|
||||
|
||||
Dataset<Work> downloadedWorksDS = spark
|
||||
.createDataset(
|
||||
sc
|
||||
.textFile(workingPath + "downloads/updated_works/*")
|
||||
.map(s -> {
|
||||
return s.substring(21, s.length() - 1);
|
||||
})
|
||||
.map(retrieveWorkFunction)
|
||||
.rdd(),
|
||||
Encoders.bean(Work.class));
|
||||
Dataset<Work> currentWorksDS = spark
|
||||
.createDataset(
|
||||
sc
|
||||
.textFile(workingPath.concat("orcid_dataset/works/*"))
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Work.class))
|
||||
.rdd(),
|
||||
Encoders.bean(Work.class));
|
||||
currentWorksDS
|
||||
.joinWith(
|
||||
downloadedWorksDS,
|
||||
currentWorksDS
|
||||
.col("workDetail.id")
|
||||
.equalTo(downloadedWorksDS.col("workDetail.id"))
|
||||
.and(
|
||||
currentWorksDS
|
||||
.col("workDetail.oid")
|
||||
.equalTo(downloadedWorksDS.col("workDetail.oid"))),
|
||||
"full_outer")
|
||||
.map(value -> {
|
||||
Optional<Work> opCurrent = Optional.ofNullable(value._1());
|
||||
Optional<Work> opDownloaded = Optional.ofNullable(value._2());
|
||||
if (!opCurrent.isPresent()) {
|
||||
newWorksFoundAcc.add(1);
|
||||
return opDownloaded.get();
|
||||
}
|
||||
if (!opDownloaded.isPresent()) {
|
||||
oldWorksFoundAcc.add(1);
|
||||
return opCurrent.get();
|
||||
}
|
||||
if (opCurrent.isPresent() && opDownloaded.isPresent()) {
|
||||
updatedWorksFoundAcc.add(1);
|
||||
return opDownloaded.get();
|
||||
}
|
||||
return null;
|
||||
},
|
||||
Encoders.bean(Work.class))
|
||||
.filter(Objects::nonNull)
|
||||
.toJavaRDD()
|
||||
.map(work -> OBJECT_MAPPER.writeValueAsString(work))
|
||||
.saveAsTextFile(workingPath.concat("orcid_dataset/new_works"), GzipCodec.class);
|
||||
|
||||
logger.info("oldWorksFoundAcc: " + oldWorksFoundAcc.value().toString());
|
||||
logger.info("newWorksFoundAcc: " + newWorksFoundAcc.value().toString());
|
||||
logger.info("updatedWorksFoundAcc: " + updatedWorksFoundAcc.value().toString());
|
||||
logger.info("errorCodeWorksFoundAcc: " + errorCodeWorksFoundAcc.value().toString());
|
||||
logger.info("errorLoadingJsonWorksFoundAcc: " + errorLoadingWorksJsonFoundAcc.value().toString());
|
||||
logger.info("errorParsingXMLWorksFoundAcc: " + errorParsingWorksXMLFoundAcc.value().toString());
|
||||
|
||||
});
|
||||
}
|
||||
|
||||
private static String getJsonValue(JsonElement jElement, String property) {
|
||||
if (jElement.getAsJsonObject().has(property)) {
|
||||
JsonElement name = null;
|
||||
name = jElement.getAsJsonObject().get(property);
|
||||
if (name != null && !name.isJsonNull()) {
|
||||
return name.getAsString();
|
||||
}
|
||||
}
|
||||
return "";
|
||||
}
|
||||
}
|
||||
|
|
@ -35,12 +35,12 @@ public class SparkUpdateOrcidWorks {
|
|||
.setSerializationInclusion(JsonInclude.Include.NON_NULL);
|
||||
|
||||
public static void main(String[] args) throws IOException, Exception {
|
||||
Logger logger = LoggerFactory.getLogger(SparkUpdateOrcidDatasets.class);
|
||||
Logger logger = LoggerFactory.getLogger(SparkUpdateOrcidWorks.class);
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkUpdateOrcidDatasets.class
|
||||
SparkUpdateOrcidWorks.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/doiboost/download_orcid_data.json")));
|
||||
parser.parseArgument(args);
|
||||
|
|
@ -83,7 +83,7 @@ public class SparkUpdateOrcidWorks {
|
|||
String statusCode = getJsonValue(jElement, "statusCode");
|
||||
work.setStatusCode(statusCode);
|
||||
String downloadDate = getJsonValue(jElement, "lastModifiedDate");
|
||||
work.setDownloadDate("2020-11-18 00:00:05.644768");
|
||||
work.setDownloadDate("2020-12-15 00:00:01.000000");
|
||||
if (statusCode.equals("200")) {
|
||||
String compressedData = getJsonValue(jElement, "compressedData");
|
||||
if (StringUtils.isEmpty(compressedData)) {
|
||||
|
|
|
|||
|
|
@ -1,22 +0,0 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>yarnRM</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://nameservice1</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.java</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.map.java.opts</name>
|
||||
<value>-Xmx4g</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -1,9 +1,25 @@
|
|||
<workflow-app name="Orcid Updates Download" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>spark2UpdateStepMaxExecutors</name>
|
||||
<value>50</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.java</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.map.java.opts</name>
|
||||
<value>-Xmx4g</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>token</name>
|
||||
<description>access token</description>
|
||||
|
|
@ -30,7 +46,7 @@
|
|||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2MaxExecutors</name>
|
||||
<name>spark2DownloadingMaxExecutors</name>
|
||||
<value>10</value>
|
||||
</property>
|
||||
<property>
|
||||
|
|
@ -58,6 +74,8 @@
|
|||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
|
|
@ -66,18 +84,16 @@
|
|||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="ResetWorkingPath"/>
|
||||
|
||||
|
||||
<start to="ResetLambda"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="ResetWorkingPath">
|
||||
|
||||
<action name="ResetLambda">
|
||||
<fs>
|
||||
<delete path='${workingPath}/downloads'/>
|
||||
<delete path='${workingPath}/last_modified.csv.tar'/>
|
||||
<mkdir path='${workingPath}/downloads'/>
|
||||
<delete path='${workingPath}/last_modified.seq'/>
|
||||
</fs>
|
||||
<ok to="DownloadLambdaFile"/>
|
||||
<error to="Kill"/>
|
||||
|
|
@ -92,7 +108,7 @@
|
|||
<argument>${shell_cmd}</argument>
|
||||
<capture-output/>
|
||||
</shell>
|
||||
<ok to="DownloadUpdatedXMLAuthors"/>
|
||||
<ok to="GenLastModifiedSeq"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
|
@ -118,7 +134,16 @@
|
|||
<arg>-o</arg><arg>last_modified.seq</arg>
|
||||
<arg>-t</arg><arg>-</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<ok to="ResetDownloads"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ResetDownloads">
|
||||
<fs>
|
||||
<delete path='${workingPath}/downloads/updated_authors'/>
|
||||
<delete path='${workingPath}/downloads/updated_works'/>
|
||||
</fs>
|
||||
<ok to="DownloadOrcidAuthors"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
|
@ -131,7 +156,7 @@
|
|||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--conf spark.dynamicAllocation.enabled=true
|
||||
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
|
||||
--conf spark.dynamicAllocation.maxExecutors=${spark2DownloadingMaxExecutors}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
|
|
@ -145,7 +170,7 @@
|
|||
<arg>-o</arg><arg>downloads/updated_authors</arg>
|
||||
<arg>-t</arg><arg>${token}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<ok to="DownloadOrcidWorks"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
|
@ -158,7 +183,7 @@
|
|||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--conf spark.dynamicAllocation.enabled=true
|
||||
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
|
||||
--conf spark.dynamicAllocation.maxExecutors=${spark2DownloadingMaxExecutors}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
|
|
@ -172,6 +197,95 @@
|
|||
<arg>-o</arg><arg>downloads/updated_works</arg>
|
||||
<arg>-t</arg><arg>${token}</arg>
|
||||
</spark>
|
||||
<ok to="UpdateOrcidAuthors"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="UpdateOrcidAuthors">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>UpdateOrcidAuthors</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkUpdateOrcidAuthors</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--conf spark.dynamicAllocation.enabled=true
|
||||
--conf spark.dynamicAllocation.maxExecutors=${spark2UpdateStepMaxExecutors}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
</spark-opts>
|
||||
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||
<arg>-n</arg><arg>${nameNode}</arg>
|
||||
<arg>-f</arg><arg>-</arg>
|
||||
<arg>-o</arg><arg>-</arg>
|
||||
<arg>-t</arg><arg>-</arg>
|
||||
</spark>
|
||||
<ok to="UpdateOrcidWorks"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="UpdateOrcidWorks">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>UpdateOrcidWorks</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkUpdateOrcidWorks</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--conf spark.dynamicAllocation.enabled=true
|
||||
--conf spark.dynamicAllocation.maxExecutors=${spark2UpdateStepMaxExecutors}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
</spark-opts>
|
||||
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||
<arg>-n</arg><arg>${nameNode}</arg>
|
||||
<arg>-f</arg><arg>-</arg>
|
||||
<arg>-o</arg><arg>-</arg>
|
||||
<arg>-t</arg><arg>-</arg>
|
||||
</spark>
|
||||
<ok to="promoteOrcidAuthorsDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="promoteOrcidAuthorsDataset">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${workingPath}/orcid_dataset/authors"/>
|
||||
<mkdir path="${workingPath}/orcid_dataset/authors"/>
|
||||
</prepare>
|
||||
<arg>${workingPath}/orcid_dataset/new_authors/*</arg>
|
||||
<arg>${workingPath}/orcid_dataset/authors</arg>
|
||||
</distcp>
|
||||
<ok to="promoteOrcidWorksDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="promoteOrcidWorksDataset">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${workingPath}/orcid_dataset/works"/>
|
||||
<mkdir path="${workingPath}/orcid_dataset/works"/>
|
||||
</prepare>
|
||||
<arg>${workingPath}/orcid_dataset/new_works/*</arg>
|
||||
<arg>${workingPath}/orcid_dataset/works</arg>
|
||||
</distcp>
|
||||
<ok to="CleanWorkingPath"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="CleanWorkingPath">
|
||||
<fs>
|
||||
<delete path='${workingPath}/orcid_dataset/new_authors'/>
|
||||
<delete path='${workingPath}/orcid_dataset/new_works'/>
|
||||
</fs>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
|
|
|||
|
|
@ -51,43 +51,6 @@ public class OrcidClientTest {
|
|||
// -H 'Authorization: Bearer 78fdb232-7105-4086-8570-e153f4198e3d'
|
||||
// 'https://api.orcid.org/v3.0/0000-0001-7291-3210/record'
|
||||
|
||||
@Test
|
||||
private void multipleDownloadTest() throws Exception {
|
||||
int toDownload = 10;
|
||||
long start = System.currentTimeMillis();
|
||||
OrcidDownloader downloader = new OrcidDownloader();
|
||||
TarArchiveInputStream input = new TarArchiveInputStream(
|
||||
new GzipCompressorInputStream(new FileInputStream("/tmp/last_modified.csv.tar")));
|
||||
TarArchiveEntry entry = input.getNextTarEntry();
|
||||
BufferedReader br = null;
|
||||
StringBuilder sb = new StringBuilder();
|
||||
int rowNum = 0;
|
||||
int entryNum = 0;
|
||||
int modified = 0;
|
||||
while (entry != null) {
|
||||
br = new BufferedReader(new InputStreamReader(input)); // Read directly from tarInput
|
||||
String line;
|
||||
while ((line = br.readLine()) != null) {
|
||||
String[] values = line.toString().split(",");
|
||||
List<String> recordInfo = Arrays.asList(values);
|
||||
String orcidId = recordInfo.get(0);
|
||||
if (downloader.isModified(orcidId, recordInfo.get(3))) {
|
||||
slowedDownDownload(orcidId);
|
||||
modified++;
|
||||
}
|
||||
rowNum++;
|
||||
if (modified > toDownload) {
|
||||
break;
|
||||
}
|
||||
}
|
||||
entryNum++;
|
||||
entry = input.getNextTarEntry();
|
||||
}
|
||||
long end = System.currentTimeMillis();
|
||||
logToFile("start test: " + new Date(start).toString());
|
||||
logToFile("end test: " + new Date(end).toString());
|
||||
}
|
||||
|
||||
@Test
|
||||
private void downloadTest(String orcid) throws Exception {
|
||||
String record = testDownloadRecord(orcid, REQUEST_TYPE_RECORD);
|
||||
|
|
@ -228,37 +191,6 @@ public class OrcidClientTest {
|
|||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
private void lambdaFileCounterTest() throws Exception {
|
||||
final String lastUpdate = "2020-09-29 00:00:00";
|
||||
OrcidDownloader downloader = new OrcidDownloader();
|
||||
TarArchiveInputStream input = new TarArchiveInputStream(
|
||||
new GzipCompressorInputStream(new FileInputStream("/tmp/last_modified.csv.tar")));
|
||||
TarArchiveEntry entry = input.getNextTarEntry();
|
||||
BufferedReader br = null;
|
||||
StringBuilder sb = new StringBuilder();
|
||||
int rowNum = 0;
|
||||
int entryNum = 0;
|
||||
int modified = 0;
|
||||
while (entry != null) {
|
||||
br = new BufferedReader(new InputStreamReader(input)); // Read directly from tarInput
|
||||
String line;
|
||||
while ((line = br.readLine()) != null) {
|
||||
String[] values = line.toString().split(",");
|
||||
List<String> recordInfo = Arrays.asList(values);
|
||||
String orcidId = recordInfo.get(0);
|
||||
if (downloader.isModified(orcidId, recordInfo.get(3))) {
|
||||
modified++;
|
||||
}
|
||||
rowNum++;
|
||||
}
|
||||
entryNum++;
|
||||
entry = input.getNextTarEntry();
|
||||
}
|
||||
logToFile("rowNum: " + rowNum);
|
||||
logToFile("modified: " + modified);
|
||||
}
|
||||
|
||||
public static void logToFile(String log)
|
||||
throws IOException {
|
||||
log = log.concat("\n");
|
||||
|
|
|
|||
Loading…
Reference in New Issue