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wf to move orcid-no-doi dataset on the folder ready the import

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pull/98/head
Enrico Ottonello 3 years ago
parent 59ec5137e1
commit 27068aacd1
3 changed files with 101 additions and 35 deletions
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42
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_orcid_no_doi/oozie_app/workflow.xml
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@ -0,0 +1,42 @@
<workflow-app name="import_orcid_no_doi" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>inputPath</name>
<value>/data/orcid_activities_2020/no_doi_dataset</value>
<description>path where retrieve the already generated action set</description>
</property>
<property>
<name>outputPath</name>
<value>/data/orcid_activities_2020/test_import_orcid_no_doi</value>
<description>path where to store the action set</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="importOrcidNoDoi"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="importOrcidNoDoi">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${inputPath}/*</arg>
<arg>${outputPath}</arg>
</distcp>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

62
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java
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@ -16,19 +16,22 @@ import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
import org.apache.commons.compress.utils.Lists;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.orcid.AuthorData;
import eu.dnetlib.doiboost.orcid.xml.XMLRecordParserTest;
import jdk.nashorn.internal.ir.annotations.Ignore;
public class OrcidClientTest {
final String orcidId = "0000-0001-7291-3210";
final int REQ_LIMIT = 24;
final int REQ_MAX_TEST = 100;
final int RECORD_DOWNLOADED_COUNTER_LOG_INTERVAL = 10;
@ -41,14 +44,23 @@ public class OrcidClientTest {
final String REQUEST_TYPE_WORK = "work/47652866";
final String REQUEST_TYPE_WORKS = "works";
private static Path testPath;
@BeforeAll
private static void setUp() throws IOException {
testPath = Files.createTempDirectory(XMLRecordParserTest.class.getName());
System.out.println("using test path: " + testPath);
}
// curl -i -H "Accept: application/vnd.orcid+xml"
// -H 'Authorization: Bearer 78fdb232-7105-4086-8570-e153f4198e3d'
// 'https://api.orcid.org/v3.0/0000-0001-7291-3210/record'
@Test
private void downloadTest(String orcid) throws Exception {
public void downloadTest() throws Exception {
final String orcid = "0000-0001-7291-3210";
String record = testDownloadRecord(orcid, REQUEST_TYPE_RECORD);
String filename = "/tmp/downloaded_record_".concat(orcid).concat(".xml");
String filename = testPath + "/downloaded_record_".concat(orcid).concat(".xml");
File f = new File(filename);
OutputStream outStream = new FileOutputStream(f);
IOUtils.write(record.getBytes(), outStream);
@ -63,9 +75,10 @@ public class OrcidClientTest {
CloseableHttpResponse response = client.execute(httpGet);
long end = System.currentTimeMillis();
if (response.getStatusLine().getStatusCode() != 200) {
logToFile("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
logToFile(
testPath, "Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
}
logToFile(orcidId + " " + dataType + " " + (end - start) / 1000 + " seconds");
logToFile(testPath, orcidId + " " + dataType + " " + (end - start) / 1000 + " seconds");
return IOUtils.toString(response.getEntity().getContent());
} catch (Throwable e) {
e.printStackTrace();
@ -150,12 +163,13 @@ public class OrcidClientTest {
final String base64CompressedRecord = IOUtils
.toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64"));
final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
logToFile("\n\ndownloaded \n\n" + recordFromSeqFile);
logToFile(testPath, "\n\ndownloaded \n\n" + recordFromSeqFile);
final String downloadedRecord = testDownloadRecord("0000-0003-3028-6161", REQUEST_TYPE_RECORD);
assertTrue(recordFromSeqFile.equals(downloadedRecord));
}
@Test
@Disabled
public void lambdaFileReaderTest() throws Exception {
String last_update = "2021-01-12 00:00:06.685137";
TarArchiveInputStream input = new TarArchiveInputStream(
@ -198,17 +212,20 @@ public class OrcidClientTest {
entry = input.getNextTarEntry();
}
logToFile("modifiedNum : " + modifiedNum + " / " + rowNum);
logToFile(testPath, "modifiedNum : " + modifiedNum + " / " + rowNum);
}
public static void logToFile(String log)
throws IOException {
public static void logToFile(Path basePath, String log) throws IOException {
log = log.concat("\n");
Path path = Paths.get("/tmp/orcid_log.txt");
Path path = basePath.resolve("orcid_log.txt");
if (!Files.exists(path)) {
Files.createFile(path);
}
Files.write(path, log.getBytes(), StandardOpenOption.APPEND);
}
@Test
@Disabled
private void slowedDownDownloadTest() throws Exception {
String orcid = "0000-0001-5496-1243";
String record = slowedDownDownload(orcid);
@ -227,16 +244,17 @@ public class OrcidClientTest {
CloseableHttpResponse response = client.execute(httpGet);
long endReq = System.currentTimeMillis();
long reqSessionDuration = endReq - start;
logToFile("req time (millisec): " + reqSessionDuration);
logToFile(testPath, "req time (millisec): " + reqSessionDuration);
if (reqSessionDuration < 1000) {
logToFile("wait ....");
logToFile(testPath, "wait ....");
Thread.sleep(1000 - reqSessionDuration);
}
long end = System.currentTimeMillis();
long total = end - start;
logToFile("total time (millisec): " + total);
logToFile(testPath, "total time (millisec): " + total);
if (response.getStatusLine().getStatusCode() != 200) {
logToFile("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
logToFile(
testPath, "Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
}
return IOUtils.toString(response.getEntity().getContent());
} catch (Throwable e) {
@ -246,7 +264,7 @@ public class OrcidClientTest {
}
@Test
private void downloadWorkTest() throws Exception {
public void downloadWorkTest() throws Exception {
String orcid = "0000-0003-0015-1952";
String record = testDownloadRecord(orcid, REQUEST_TYPE_WORK);
String filename = "/tmp/downloaded_work_".concat(orcid).concat(".xml");
@ -256,7 +274,7 @@ public class OrcidClientTest {
}
@Test
private void downloadRecordTest() throws Exception {
public void downloadRecordTest() throws Exception {
String orcid = "0000-0001-5004-5918";
String record = testDownloadRecord(orcid, REQUEST_TYPE_RECORD);
String filename = "/tmp/downloaded_record_".concat(orcid).concat(".xml");
@ -266,7 +284,7 @@ public class OrcidClientTest {
}
@Test
private void downloadWorksTest() throws Exception {
public void downloadWorksTest() throws Exception {
String orcid = "0000-0001-5004-5918";
String record = testDownloadRecord(orcid, REQUEST_TYPE_WORKS);
String filename = "/tmp/downloaded_works_".concat(orcid).concat(".xml");
@ -276,7 +294,7 @@ public class OrcidClientTest {
}
@Test
private void downloadSingleWorkTest() throws Exception {
public void downloadSingleWorkTest() throws Exception {
String orcid = "0000-0001-5004-5918";
String record = testDownloadRecord(orcid, REQUEST_TYPE_WORK);
String filename = "/tmp/downloaded_work_47652866_".concat(orcid).concat(".xml");
@ -286,7 +304,7 @@ public class OrcidClientTest {
}
@Test
private void cleanAuthorListTest() throws Exception {
public void cleanAuthorListTest() throws Exception {
AuthorData a1 = new AuthorData();
a1.setOid("1");
a1.setName("n1");
@ -315,11 +333,11 @@ public class OrcidClientTest {
@Test
@Ignore
private void testUpdatedRecord() throws Exception {
public void testUpdatedRecord() throws Exception {
final String base64CompressedRecord = IOUtils
.toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64"));
final String record = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
logToFile("\n\nrecord updated \n\n" + record);
logToFile(testPath, "\n\nrecord updated \n\n" + record);
}
@Test
@ -327,6 +345,6 @@ public class OrcidClientTest {
private void testUpdatedWork() throws Exception {
final String base64CompressedWork = "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";
final String work = ArgumentApplicationParser.decompressValue(base64CompressedWork);
logToFile("\n\nwork updated \n\n" + work);
logToFile(testPath, "\n\nwork updated \n\n" + work);
}
}

32
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java
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@ -1,13 +1,14 @@
package eu.dnetlib.doiboost.orcid.xml;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
import java.util.Map;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
@ -18,7 +19,6 @@ import eu.dnetlib.dhp.schema.orcid.AuthorSummary;
import eu.dnetlib.dhp.schema.orcid.Work;
import eu.dnetlib.dhp.schema.orcid.WorkDetail;
import eu.dnetlib.doiboost.orcid.OrcidClientTest;
import eu.dnetlib.doiboost.orcid.SparkDownloadOrcidWorks;
import eu.dnetlib.doiboost.orcid.model.WorkData;
import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
@ -30,8 +30,15 @@ public class XMLRecordParserTest {
private static final String NS_COMMON = "common";
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static Path testPath;
@BeforeAll
private static void setUp() throws IOException {
testPath = Files.createTempDirectory(XMLRecordParserTest.class.getName());
}
@Test
private void testOrcidAuthorDataXMLParser() throws Exception {
public void testOrcidAuthorDataXMLParser() throws Exception {
String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_0000-0001-6828-479X.xml"));
@ -43,11 +50,11 @@ public class XMLRecordParserTest {
System.out.println("name: " + authorData.getName());
assertNotNull(authorData.getSurname());
System.out.println("surname: " + authorData.getSurname());
OrcidClientTest.logToFile(OBJECT_MAPPER.writeValueAsString(authorData));
OrcidClientTest.logToFile(testPath, OBJECT_MAPPER.writeValueAsString(authorData));
}
@Test
private void testOrcidXMLErrorRecordParser() throws Exception {
public void testOrcidXMLErrorRecordParser() throws Exception {
String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_error.xml"));
@ -60,7 +67,7 @@ public class XMLRecordParserTest {
}
@Test
private void testOrcidWorkDataXMLParser() throws Exception {
public void testOrcidWorkDataXMLParser() throws Exception {
String xml = IOUtils
.toString(
@ -72,12 +79,11 @@ public class XMLRecordParserTest {
assertNotNull(workData);
assertNotNull(workData.getOid());
System.out.println("oid: " + workData.getOid());
assertNotNull(workData.getDoi());
System.out.println("doi: " + workData.getDoi());
assertNull(workData.getDoi());
}
@Test
private void testOrcidOtherNamesXMLParser() throws Exception {
public void testOrcidOtherNamesXMLParser() throws Exception {
String xml = IOUtils
.toString(
@ -114,7 +120,7 @@ public class XMLRecordParserTest {
this.getClass().getResourceAsStream("record_0000-0001-5004-5918.xml"));
AuthorSummary authorSummary = XMLRecordParser.VTDParseAuthorSummary(xml.getBytes());
authorSummary.setBase64CompressData(ArgumentApplicationParser.compressArgument(xml));
OrcidClientTest.logToFile(JsonWriter.create(authorSummary));
OrcidClientTest.logToFile(testPath, JsonWriter.create(authorSummary));
}
@Test
@ -126,6 +132,6 @@ public class XMLRecordParserTest {
Work work = new Work();
work.setWorkDetail(workDetail);
work.setBase64CompressData(ArgumentApplicationParser.compressArgument(xml));
OrcidClientTest.logToFile(JsonWriter.create(work));
OrcidClientTest.logToFile(testPath, JsonWriter.create(work));
}
}

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