261 lines
9.0 KiB
Java
261 lines
9.0 KiB
Java
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package eu.dnetlib.doiboost.orcid;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import java.io.*;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.nio.file.StandardOpenOption;
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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.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.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.apache.spark.sql.catalyst.expressions.objects.AssertNotNull;
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import org.junit.jupiter.api.Test;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import jdk.nashorn.internal.ir.annotations.Ignore;
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public class OrcidClientTest {
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final String orcidId = "0000-0001-7291-3210";
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final int REQ_LIMIT = 24;
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final int REQ_MAX_TEST = 100;
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final int RECORD_DOWNLOADED_COUNTER_LOG_INTERVAL = 10;
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final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
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final String toRetrieveDate = "2020-05-06 23:59:46.031145";
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String toNotRetrieveDate = "2019-09-29 23:59:59.000000";
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String lastUpdate = "2019-09-30 00:00:00";
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String shortDate = "2020-05-06 16:06:11";
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// curl -i -H "Accept: application/vnd.orcid+xml"
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// -H 'Authorization: Bearer 78fdb232-7105-4086-8570-e153f4198e3d'
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// 'https://api.orcid.org/v3.0/0000-0001-7291-3210/record'
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@Test
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private void multipleDownloadTest() throws Exception {
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int toDownload = 1;
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long start = System.currentTimeMillis();
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OrcidDownloader downloader = new OrcidDownloader();
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TarArchiveInputStream input = new TarArchiveInputStream(
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new GzipCompressorInputStream(new FileInputStream("/tmp/last_modified.csv.tar")));
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TarArchiveEntry entry = input.getNextTarEntry();
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BufferedReader br = null;
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StringBuilder sb = new StringBuilder();
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int rowNum = 0;
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int entryNum = 0;
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int modified = 0;
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while (entry != null) {
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br = new BufferedReader(new InputStreamReader(input)); // 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.toString().split(",");
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List<String> recordInfo = Arrays.asList(values);
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String orcidId = recordInfo.get(0);
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if (downloader.isModified(orcidId, recordInfo.get(3))) {
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downloadTest(orcidId);
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modified++;
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}
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rowNum++;
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if (modified > toDownload) {
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break;
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}
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}
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entryNum++;
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entry = input.getNextTarEntry();
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}
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long end = System.currentTimeMillis();
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logToFile("start test: " + new Date(start).toString());
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logToFile("end test: " + new Date(end).toString());
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}
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@Test
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private void downloadTest(String orcid) throws Exception {
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String record = testDownloadRecord(orcid);
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String filename = "/tmp/downloaded_".concat(orcid).concat(".xml");
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File f = new File(filename);
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OutputStream outStream = new FileOutputStream(f);
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IOUtils.write(record.getBytes(), outStream);
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}
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private String testDownloadRecord(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", "Bearer 78fdb232-7105-4086-8570-e153f4198e3d");
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logToFile("start connection: " + new Date(System.currentTimeMillis()).toString());
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CloseableHttpResponse response = client.execute(httpGet);
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logToFile("end connection: " + new Date(System.currentTimeMillis()).toString());
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if (response.getStatusLine().getStatusCode() != 200) {
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System.out
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.println("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
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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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e.printStackTrace();
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}
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return new String("");
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}
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// @Test
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private void testLambdaFileParser() throws Exception {
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try (BufferedReader br = new BufferedReader(
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new InputStreamReader(this.getClass().getResourceAsStream("last_modified.csv")))) {
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String line;
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int counter = 0;
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int nReqTmp = 0;
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long startDownload = System.currentTimeMillis();
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long startReqTmp = System.currentTimeMillis();
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while ((line = br.readLine()) != null) {
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counter++;
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// skip headers line
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if (counter == 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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testDownloadRecord(recordInfo.get(0));
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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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System.out
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.println(
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"\nreqSessionDuration: " + reqSessionDuration + " nReqTmp: " + nReqTmp + " 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 (counter > REQ_MAX_TEST) {
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break;
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}
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if ((counter % RECORD_DOWNLOADED_COUNTER_LOG_INTERVAL) == 0) {
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System.out.println("Current record downloaded: " + counter);
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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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System.out.println("Download time: " + ((downloadTime / 1000) / 60) + " minutes");
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}
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}
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// @Test
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private void getRecordDatestamp() throws ParseException {
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Date toRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toRetrieveDate);
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Date toNotRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toNotRetrieveDate);
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Date lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
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assertTrue(toRetrieveDateDt.after(lastUpdateDt));
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assertTrue(!toNotRetrieveDateDt.after(lastUpdateDt));
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}
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private void testDate(String value) throws ParseException {
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System.out.println(value.toString());
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if (value.length() != 19) {
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value = value.substring(0, 19);
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}
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Date valueDt = new SimpleDateFormat(DATE_FORMAT).parse(value);
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System.out.println(valueDt.toString());
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}
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// @Test
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@Ignore
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private void testModifiedDate() throws ParseException {
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testDate(toRetrieveDate);
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testDate(toNotRetrieveDate);
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testDate(shortDate);
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}
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@Test
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public void testReadBase64CompressedRecord() throws Exception {
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final String base64CompressedRecord = IOUtils
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.toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64"));
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final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
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logToFile("\n\ndownloaded \n\n" + recordFromSeqFile);
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final String downloadedRecord = testDownloadRecord("0000-0003-3028-6161");
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assertTrue(recordFromSeqFile.equals(downloadedRecord));
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}
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@Test
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private void lambdaFileReaderTest() throws Exception {
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TarArchiveInputStream input = new TarArchiveInputStream(
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new GzipCompressorInputStream(new FileInputStream("/develop/last_modified.csv.tar")));
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TarArchiveEntry entry = input.getNextTarEntry();
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BufferedReader br = null;
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StringBuilder sb = new StringBuilder();
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int rowNum = 0;
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int entryNum = 0;
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while (entry != null) {
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br = new BufferedReader(new InputStreamReader(input)); // 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.toString().split(",");
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List<String> recordInfo = Arrays.asList(values);
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assertTrue(recordInfo.size() == 4);
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rowNum++;
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if (rowNum == 1) {
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assertTrue(recordInfo.get(3).equals("last_modified"));
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} else if (rowNum == 2) {
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assertTrue(recordInfo.get(0).equals("0000-0002-0499-7333"));
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}
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}
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entryNum++;
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assertTrue(entryNum == 1);
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entry = input.getNextTarEntry();
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}
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}
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@Test
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private void lambdaFileCounterTest() throws Exception {
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final String lastUpdate = "2020-09-29 00:00:00";
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OrcidDownloader downloader = new OrcidDownloader();
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TarArchiveInputStream input = new TarArchiveInputStream(
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new GzipCompressorInputStream(new FileInputStream("/tmp/last_modified.csv.tar")));
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TarArchiveEntry entry = input.getNextTarEntry();
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BufferedReader br = null;
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StringBuilder sb = new StringBuilder();
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int rowNum = 0;
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int entryNum = 0;
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int modified = 0;
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while (entry != null) {
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br = new BufferedReader(new InputStreamReader(input)); // 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.toString().split(",");
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List<String> recordInfo = Arrays.asList(values);
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String orcidId = recordInfo.get(0);
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if (downloader.isModified(orcidId, recordInfo.get(3))) {
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modified++;
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}
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rowNum++;
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}
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entryNum++;
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entry = input.getNextTarEntry();
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}
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logToFile("rowNum: " + rowNum);
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logToFile("modified: " + modified);
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}
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private void logToFile(String log)
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throws IOException {
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log = log.concat("\n");
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Path path = Paths.get("/tmp/orcid_log.txt");
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Files.write(path, log.getBytes(), StandardOpenOption.APPEND);
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}
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}
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