forked from D-Net/dnet-hadoop
added job to download from orcid the records modified after a fixed date, the info are taken from last_modified.csv on hdfs
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package eu.dnetlib.doiboost.orcid;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.text.ParseException;
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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.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.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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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 = 100;
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static final int RECORD_PARSED_COUNTER_LOG_INTERVAL = 50000;
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static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss.";
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static final String lastUpdate = "2019-09-30 00:00:00.000000";
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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 Exception {
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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.warn(
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"Downloading "
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+ orcidId
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+ " status code: "
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+ 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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} catch (Throwable e) {
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Log.warn("Downloading " + orcidId, e);
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}
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return new String("");
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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(hdfsOrcidDefaultPath).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 =
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new Path(
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hdfsServerUri
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.concat(hdfsOrcidDefaultPath)
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.concat(outputPath)
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.concat("orcid_records.seq"));
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try (SequenceFile.Writer writer =
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SequenceFile.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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try (BufferedReader br = new BufferedReader(new InputStreamReader(lambdaFileStream))) {
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String line;
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int nReqTmp = 0;
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startDownload = System.currentTimeMillis();
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long startReqTmp = System.currentTimeMillis();
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while ((line = br.readLine()) != null) {
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parsedRecordsCounter++;
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// skip headers line
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if (parsedRecordsCounter == 1) {
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continue;
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}
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String[] values = line.split(",");
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List<String> recordInfo = Arrays.asList(values);
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if (isModified(recordInfo.get(3))) {
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String record = downloadRecord(recordInfo.get(0));
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downloadedRecordsCounter++;
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if (!record.isEmpty()) {
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String compressRecord =
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ArgumentApplicationParser.compressArgument(record);
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final Text key = new Text(recordInfo.get(0));
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final Text value = new Text(compressRecord);
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try {
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writer.append(key, value);
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savedRecordsCounter++;
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} catch (IOException e) {
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Log.debug("Writing to sequence file: " + e.getMessage());
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Log.debug(e);
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throw new RuntimeException(e);
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}
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}
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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.warn(
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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>REQ_MAX_TEST) {
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// break;
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// }
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if ((parsedRecordsCounter % RECORD_PARSED_COUNTER_LOG_INTERVAL) == 0) {
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Log.info("Current record parsed: " + parsedRecordsCounter);
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Log.info("Current record downloaded: " + downloadedRecordsCounter);
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Log.info("Current record saved: " + savedRecordsCounter);
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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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lambdaFileStream.close();
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Log.info("Download started at: " + new Date(startDownload).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 =
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new ArgumentApplicationParser(
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IOUtils.toString(
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OrcidDownloader.class.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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hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath");
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Log.info("Default Path: " + hdfsOrcidDefaultPath);
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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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private boolean isModified(String modifiedDate) throws ParseException {
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Date modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate);
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Date lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
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return modifiedDateDt.after(lastUpdateDt);
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}
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}
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@ -0,0 +1,7 @@
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[
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{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
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{"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true},
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{"paramName":"f", "paramLongName":"lambdaFileName", "paramDescription": "the name of the lambda file", "paramRequired": true},
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{"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true},
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{"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true}
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]
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@ -0,0 +1,22 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.java</name>
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<value>spark2</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.map.java.opts</name>
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<value>-Xmx4g</value>
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</property>
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</configuration>
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@ -0,0 +1,45 @@
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<workflow-app name="Orcid Download" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>workingPathOrcid</name>
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<description>the working dir base path</description>
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</property>
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<property>
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<name>token</name>
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<description>access token</description>
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</property>
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</parameters>
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<start to="ResetWorkingPath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ResetWorkingPath">
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<fs>
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<delete path='${workingPathOrcid}/download'/>
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<mkdir path='${workingPathOrcid}/download'/>
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</fs>
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<ok to="DownloadOrcidData"/>
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<error to="Kill"/>
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</action>
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<action name="DownloadOrcidData">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.orcid.OrcidDownloader</main-class>
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<arg>-d</arg><arg>${workingPathOrcid}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>last_modified.csv</arg>
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<arg>-o</arg><arg>download/</arg>
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<arg>-t</arg><arg>${token}</arg>
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</java>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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