added job to download from orcid the records modified after a fixed date, the info are taken from last_modified.csv on hdfs

This commit is contained in:
Enrico Ottonello 2020-05-08 14:49:39 +02:00
parent 1edcd53581
commit 9d812788e4
4 changed files with 257 additions and 0 deletions

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package eu.dnetlib.doiboost.orcid;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
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.mortbay.log.Log;
public class OrcidDownloader extends OrcidDSManager {
static final int REQ_LIMIT = 24;
static final int REQ_MAX_TEST = 100;
static final int RECORD_PARSED_COUNTER_LOG_INTERVAL = 50000;
static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss.";
static final String lastUpdate = "2019-09-30 00:00:00.000000";
private String lambdaFileName;
private String outputPath;
private String token;
public static void main(String[] args) throws IOException, Exception {
OrcidDownloader orcidDownloader = new OrcidDownloader();
orcidDownloader.loadArgs(args);
orcidDownloader.parseLambdaFile();
}
private String downloadRecord(String orcidId) throws Exception {
try (CloseableHttpClient client = HttpClients.createDefault()) {
HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record");
httpGet.addHeader("Accept", "application/vnd.orcid+xml");
httpGet.addHeader("Authorization", String.format("Bearer %s", token));
CloseableHttpResponse response = client.execute(httpGet);
if (response.getStatusLine().getStatusCode() != 200) {
Log.warn(
"Downloading "
+ orcidId
+ " status code: "
+ response.getStatusLine().getStatusCode());
return new String("");
}
return IOUtils.toString(response.getEntity().getContent());
} catch (Throwable e) {
Log.warn("Downloading " + orcidId, e);
}
return new String("");
}
public void parseLambdaFile() throws Exception {
int parsedRecordsCounter = 0;
int downloadedRecordsCounter = 0;
int savedRecordsCounter = 0;
long startDownload = 0;
Configuration conf = initConfigurationObject();
FileSystem fs = initFileSystemObject(conf);
String lambdaFileUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(lambdaFileName);
Path hdfsreadpath = new Path(lambdaFileUri);
FSDataInputStream lambdaFileStream = fs.open(hdfsreadpath);
Path hdfsoutputPath =
new Path(
hdfsServerUri
.concat(hdfsOrcidDefaultPath)
.concat(outputPath)
.concat("orcid_records.seq"));
try (SequenceFile.Writer writer =
SequenceFile.createWriter(
conf,
SequenceFile.Writer.file(hdfsoutputPath),
SequenceFile.Writer.keyClass(Text.class),
SequenceFile.Writer.valueClass(Text.class))) {
try (BufferedReader br = new BufferedReader(new InputStreamReader(lambdaFileStream))) {
String line;
int nReqTmp = 0;
startDownload = System.currentTimeMillis();
long startReqTmp = System.currentTimeMillis();
while ((line = br.readLine()) != null) {
parsedRecordsCounter++;
// skip headers line
if (parsedRecordsCounter == 1) {
continue;
}
String[] values = line.split(",");
List<String> recordInfo = Arrays.asList(values);
if (isModified(recordInfo.get(3))) {
String record = downloadRecord(recordInfo.get(0));
downloadedRecordsCounter++;
if (!record.isEmpty()) {
String compressRecord =
ArgumentApplicationParser.compressArgument(record);
final Text key = new Text(recordInfo.get(0));
final Text value = new Text(compressRecord);
try {
writer.append(key, value);
savedRecordsCounter++;
} catch (IOException e) {
Log.debug("Writing to sequence file: " + e.getMessage());
Log.debug(e);
throw new RuntimeException(e);
}
}
}
long endReq = System.currentTimeMillis();
nReqTmp++;
if (nReqTmp == REQ_LIMIT) {
long reqSessionDuration = endReq - startReqTmp;
if (reqSessionDuration <= 1000) {
Log.warn(
"\nreqSessionDuration: "
+ reqSessionDuration
+ " nReqTmp: "
+ nReqTmp
+ " wait ....");
Thread.sleep(1000 - reqSessionDuration);
} else {
nReqTmp = 0;
startReqTmp = System.currentTimeMillis();
}
}
// if (parsedRecordsCounter>REQ_MAX_TEST) {
// break;
// }
if ((parsedRecordsCounter % RECORD_PARSED_COUNTER_LOG_INTERVAL) == 0) {
Log.info("Current record parsed: " + parsedRecordsCounter);
Log.info("Current record downloaded: " + downloadedRecordsCounter);
Log.info("Current record saved: " + savedRecordsCounter);
}
}
long endDownload = System.currentTimeMillis();
long downloadTime = endDownload - startDownload;
Log.info("Download time: " + ((downloadTime / 1000) / 60) + " minutes");
}
}
lambdaFileStream.close();
Log.info("Download started at: " + new Date(startDownload).toString());
Log.info("Parsed Records Counter: " + parsedRecordsCounter);
Log.info("Downloaded Records Counter: " + downloadedRecordsCounter);
Log.info("Saved Records Counter: " + savedRecordsCounter);
}
private void loadArgs(String[] args) throws IOException, Exception {
final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
OrcidDownloader.class.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/download_orcid_data.json")));
parser.parseArgument(args);
hdfsServerUri = parser.get("hdfsServerUri");
Log.info("HDFS URI: " + hdfsServerUri);
hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath");
Log.info("Default Path: " + hdfsOrcidDefaultPath);
lambdaFileName = parser.get("lambdaFileName");
Log.info("Lambda File Name: " + lambdaFileName);
outputPath = parser.get("outputPath");
Log.info("Output Data: " + outputPath);
token = parser.get("token");
}
private boolean isModified(String modifiedDate) throws ParseException {
Date modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate);
Date lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
return modifiedDateDt.after(lastUpdateDt);
}
}

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[
{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
{"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true},
{"paramName":"f", "paramLongName":"lambdaFileName", "paramDescription": "the name of the lambda file", "paramRequired": true},
{"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true},
{"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true}
]

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<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>

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<workflow-app name="Orcid Download" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPathOrcid</name>
<description>the working dir base path</description>
</property>
<property>
<name>token</name>
<description>access token</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPathOrcid}/download'/>
<mkdir path='${workingPathOrcid}/download'/>
</fs>
<ok to="DownloadOrcidData"/>
<error to="Kill"/>
</action>
<action name="DownloadOrcidData">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidDownloader</main-class>
<arg>-d</arg><arg>${workingPathOrcid}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>last_modified.csv</arg>
<arg>-o</arg><arg>download/</arg>
<arg>-t</arg><arg>${token}</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>