orcid-no-doi #43
|
|
@ -1,14 +1,15 @@
|
|||
|
||||
package eu.dnetlib.doiboost.orcid;
|
||||
|
||||
import java.io.BufferedReader;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStreamReader;
|
||||
import java.io.*;
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.Arrays;
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
|
||||
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.io.IOUtils;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FSDataInputStream;
|
||||
|
|
@ -16,6 +17,7 @@ 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.hadoop.io.compress.GzipCodec;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
import org.apache.http.impl.client.CloseableHttpClient;
|
||||
|
|
@ -27,10 +29,10 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|||
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 = 10000;
|
||||
static final int REQ_MAX_TEST = -1;
|
||||
static final int RECORD_PARSED_COUNTER_LOG_INTERVAL = 500;
|
||||
static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
|
||||
static final String lastUpdate = "2019-09-30 00:00:00";
|
||||
static final String lastUpdate = "2020-09-29 00:00:00";
|
||||
private String lambdaFileName;
|
||||
private String outputPath;
|
||||
private String token;
|
||||
|
|
@ -41,7 +43,7 @@ public class OrcidDownloader extends OrcidDSManager {
|
|||
orcidDownloader.parseLambdaFile();
|
||||
}
|
||||
|
||||
private String downloadRecord(String orcidId) {
|
||||
private String downloadRecord(String orcidId) throws IOException {
|
||||
try (CloseableHttpClient client = HttpClients.createDefault()) {
|
||||
HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record");
|
||||
httpGet.addHeader("Accept", "application/vnd.orcid+xml");
|
||||
|
|
@ -49,17 +51,23 @@ public class OrcidDownloader extends OrcidDSManager {
|
|||
CloseableHttpResponse response = client.execute(httpGet);
|
||||
if (response.getStatusLine().getStatusCode() != 200) {
|
||||
Log
|
||||
.warn(
|
||||
.info(
|
||||
"Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
|
||||
return new String("");
|
||||
}
|
||||
return IOUtils.toString(response.getEntity().getContent());
|
||||
|
||||
} catch (Throwable e) {
|
||||
Log.warn("Downloading " + orcidId, e.getMessage());
|
||||
|
||||
// return IOUtils.toString(response.getEntity().getContent());
|
||||
return xmlStreamToString(response.getEntity().getContent());
|
||||
}
|
||||
return new String("");
|
||||
}
|
||||
|
||||
private String xmlStreamToString(InputStream xmlStream) throws IOException {
|
||||
BufferedReader br = new BufferedReader(new InputStreamReader(xmlStream));
|
||||
String line;
|
||||
StringBuffer buffer = new StringBuffer();
|
||||
while ((line = br.readLine()) != null) {
|
||||
buffer.append(line);
|
||||
}
|
||||
return buffer.toString();
|
||||
}
|
||||
|
||||
public void parseLambdaFile() throws Exception {
|
||||
|
|
@ -76,46 +84,46 @@ public class OrcidDownloader extends OrcidDSManager {
|
|||
hdfsServerUri
|
||||
.concat(workingPath)
|
||||
.concat(outputPath)
|
||||
.concat("orcid_records.seq"));
|
||||
|
||||
.concat("updated_xml_authors.seq"));
|
||||
try (TarArchiveInputStream tais = new TarArchiveInputStream(
|
||||
new GzipCompressorInputStream(lambdaFileStream))) {
|
||||
TarArchiveEntry entry = null;
|
||||
StringBuilder sb = new StringBuilder();
|
||||
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;
|
||||
SequenceFile.Writer.valueClass(Text.class),
|
||||
SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new GzipCodec()))) {
|
||||
startDownload = System.currentTimeMillis();
|
||||
long startReqTmp = System.currentTimeMillis();
|
||||
while ((entry = tais.getNextTarEntry()) != null) {
|
||||
BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from tarInput
|
||||
String line;
|
||||
while ((line = br.readLine()) != null) {
|
||||
parsedRecordsCounter++;
|
||||
// skip headers line
|
||||
if (parsedRecordsCounter == 1) {
|
||||
continue;
|
||||
}
|
||||
String[] values = line.split(",");
|
||||
List<String> recordInfo = Arrays.asList(values);
|
||||
int nReqTmp = 0;
|
||||
long startReqTmp = System.currentTimeMillis();
|
||||
// skip headers line
|
||||
if (parsedRecordsCounter == 0) {
|
||||
parsedRecordsCounter++;
|
||||
continue;
|
||||
}
|
||||
parsedRecordsCounter++;
|
||||
String orcidId = recordInfo.get(0);
|
||||
if (isModified(orcidId, recordInfo.get(3))) {
|
||||
String record = downloadRecord(orcidId);
|
||||
downloadedRecordsCounter++;
|
||||
if (!record.isEmpty()) {
|
||||
String compressRecord = ArgumentApplicationParser.compressArgument(record);
|
||||
// String compressRecord = ArgumentApplicationParser.compressArgument(record);
|
||||
final Text key = new Text(recordInfo.get(0));
|
||||
final Text value = new Text(compressRecord);
|
||||
|
||||
try {
|
||||
final Text value = new Text(record);
|
||||
writer.append(key, value);
|
||||
savedRecordsCounter++;
|
||||
} catch (IOException e) {
|
||||
Log.warn("Writing to sequence file: " + e.getMessage());
|
||||
Log.warn(e);
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
} else {
|
||||
break;
|
||||
}
|
||||
long endReq = System.currentTimeMillis();
|
||||
nReqTmp++;
|
||||
|
|
@ -123,7 +131,7 @@ public class OrcidDownloader extends OrcidDSManager {
|
|||
long reqSessionDuration = endReq - startReqTmp;
|
||||
if (reqSessionDuration <= 1000) {
|
||||
Log
|
||||
.warn(
|
||||
.info(
|
||||
"\nreqSessionDuration: "
|
||||
+ reqSessionDuration
|
||||
+ " nReqTmp: "
|
||||
|
|
@ -135,10 +143,6 @@ public class OrcidDownloader extends OrcidDSManager {
|
|||
startReqTmp = System.currentTimeMillis();
|
||||
}
|
||||
}
|
||||
|
||||
// if (parsedRecordsCounter > REQ_MAX_TEST) {
|
||||
// break;
|
||||
// }
|
||||
if ((parsedRecordsCounter % RECORD_PARSED_COUNTER_LOG_INTERVAL) == 0) {
|
||||
Log
|
||||
.info(
|
||||
|
|
@ -148,9 +152,9 @@ public class OrcidDownloader extends OrcidDSManager {
|
|||
+ downloadedRecordsCounter
|
||||
+ " saved: "
|
||||
+ savedRecordsCounter);
|
||||
// if (parsedRecordsCounter > REQ_MAX_TEST) {
|
||||
// break;
|
||||
// }
|
||||
if (REQ_MAX_TEST != -1 && parsedRecordsCounter > REQ_MAX_TEST) {
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
long endDownload = System.currentTimeMillis();
|
||||
|
|
@ -158,8 +162,9 @@ public class OrcidDownloader extends OrcidDSManager {
|
|||
Log.info("Download time: " + ((downloadTime / 1000) / 60) + " minutes");
|
||||
}
|
||||
}
|
||||
lambdaFileStream.close();
|
||||
}
|
||||
Log.info("Download started at: " + new Date(startDownload).toString());
|
||||
Log.info("Download ended at: " + new Date(System.currentTimeMillis()).toString());
|
||||
Log.info("Parsed Records Counter: " + parsedRecordsCounter);
|
||||
Log.info("Downloaded Records Counter: " + downloadedRecordsCounter);
|
||||
Log.info("Saved Records Counter: " + savedRecordsCounter);
|
||||
|
|
@ -185,7 +190,7 @@ public class OrcidDownloader extends OrcidDSManager {
|
|||
token = parser.get("token");
|
||||
}
|
||||
|
||||
private boolean isModified(String orcidId, String modifiedDate) {
|
||||
public boolean isModified(String orcidId, String modifiedDate) {
|
||||
Date modifiedDateDt = null;
|
||||
Date lastUpdateDt = null;
|
||||
try {
|
||||
|
|
@ -195,7 +200,7 @@ public class OrcidDownloader extends OrcidDSManager {
|
|||
modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate);
|
||||
lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
|
||||
} catch (Exception e) {
|
||||
Log.warn("[" + orcidId + "] Parsing date: ", e.getMessage());
|
||||
Log.info("[" + orcidId + "] Parsing date: ", e.getMessage());
|
||||
return true;
|
||||
}
|
||||
return modifiedDateDt.after(lastUpdateDt);
|
||||
|
|
|
|||
|
|
@ -0,0 +1,166 @@
|
|||
|
||||
package eu.dnetlib.doiboost.orcid;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
|
||||
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.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaPairRDD;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.Function;
|
||||
import org.apache.spark.util.LongAccumulator;
|
||||
import org.mortbay.log.Log;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class SparkDownloadOrcidAuthors {
|
||||
|
||||
static Logger logger = LoggerFactory.getLogger(SparkDownloadOrcidAuthors.class);
|
||||
static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
|
||||
static final String lastUpdate = "2020-09-29 00:00:00";
|
||||
|
||||
public static void main(String[] args) throws IOException, Exception {
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkDownloadOrcidAuthors.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/doiboost/download_orcid_data.json")));
|
||||
parser.parseArgument(args);
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
final String workingPath = parser.get("workingPath");
|
||||
logger.info("workingPath: ", workingPath);
|
||||
final String outputPath = parser.get("outputPath");
|
||||
logger.info("outputPath: ", outputPath);
|
||||
final String token = parser.get("token");
|
||||
final String lambdaFileName = parser.get("lambdaFileName");
|
||||
logger.info("lambdaFileName: ", lambdaFileName);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
LongAccumulator parsedRecordsAcc = spark.sparkContext().longAccumulator("parsedRecords");
|
||||
LongAccumulator modifiedRecordsAcc = spark.sparkContext().longAccumulator("modifiedRecords");
|
||||
LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloadedRecords");
|
||||
|
||||
logger.info("Retrieving data from lamda sequence file");
|
||||
JavaPairRDD<Text, Text> lamdaFileRDD = sc
|
||||
.sequenceFile(workingPath + lambdaFileName, Text.class, Text.class);
|
||||
logger.info("Data retrieved: " + lamdaFileRDD.count());
|
||||
|
||||
Function<Tuple2<Text, Text>, Boolean> isModifiedAfterFilter = data -> {
|
||||
String orcidId = data._1().toString();
|
||||
String lastModifiedDate = data._2().toString();
|
||||
parsedRecordsAcc.add(1);
|
||||
if (isModified(orcidId, lastModifiedDate)) {
|
||||
modifiedRecordsAcc.add(1);
|
||||
return true;
|
||||
}
|
||||
return false;
|
||||
};
|
||||
|
||||
Function<Tuple2<Text, Text>, Tuple2<String, String>> downloadRecordFunction = data -> {
|
||||
String orcidId = data._1().toString();
|
||||
String lastModifiedDate = data._2().toString();
|
||||
final DownloadedRecordData downloaded = new DownloadedRecordData();
|
||||
downloaded.setOrcidId(orcidId);
|
||||
downloaded.setLastModifiedDate(lastModifiedDate);
|
||||
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);
|
||||
int statusCode = response.getStatusLine().getStatusCode();
|
||||
downloaded.setStatusCode(statusCode);
|
||||
if (statusCode != 200) {
|
||||
logger
|
||||
.info(
|
||||
"Downloading " + orcidId + " status code: "
|
||||
+ response.getStatusLine().getStatusCode());
|
||||
return downloaded.toTuple2();
|
||||
}
|
||||
downloadedRecordsAcc.add(1);
|
||||
long currentDownloaded = downloadedRecordsAcc.value();
|
||||
if ((currentDownloaded % 10000) == 0) {
|
||||
logger.info("Current downloaded: " + currentDownloaded);
|
||||
}
|
||||
downloaded
|
||||
.setCompressedData(
|
||||
ArgumentApplicationParser
|
||||
.compressArgument(IOUtils.toString(response.getEntity().getContent())));
|
||||
} catch (Throwable e) {
|
||||
logger.info("Downloading " + orcidId, e.getMessage());
|
||||
downloaded.setErrorMessage(e.getMessage());
|
||||
return downloaded.toTuple2();
|
||||
}
|
||||
return downloaded.toTuple2();
|
||||
};
|
||||
|
||||
sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true");
|
||||
|
||||
logger.info("Start execution ...");
|
||||
// List<Tuple2<Text, Text>> sampleList = lamdaFileRDD.take(500);
|
||||
// JavaRDD<Tuple2<Text, Text>> sampleRDD = sc.parallelize(sampleList);
|
||||
// sampleRDD
|
||||
JavaPairRDD<Text, Text> authorsModifiedRDD = lamdaFileRDD
|
||||
.filter(isModifiedAfterFilter);
|
||||
logger.info("Authors modified count: " + authorsModifiedRDD.count());
|
||||
logger.info("Start downloading ...");
|
||||
authorsModifiedRDD
|
||||
.map(downloadRecordFunction)
|
||||
.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
|
||||
.saveAsNewAPIHadoopFile(
|
||||
workingPath.concat(outputPath),
|
||||
Text.class,
|
||||
Text.class,
|
||||
SequenceFileOutputFormat.class,
|
||||
sc.hadoopConfiguration());
|
||||
logger.info("parsedRecordsAcc: " + parsedRecordsAcc.value().toString());
|
||||
logger.info("modifiedRecordsAcc: " + modifiedRecordsAcc.value().toString());
|
||||
logger.info("downloadedRecordsAcc: " + downloadedRecordsAcc.value().toString());
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
private static boolean isModified(String orcidId, String modifiedDate) {
|
||||
Date modifiedDateDt = null;
|
||||
Date lastUpdateDt = null;
|
||||
try {
|
||||
if (modifiedDate.length() != 19) {
|
||||
modifiedDate = modifiedDate.substring(0, 19);
|
||||
}
|
||||
modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate);
|
||||
lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
|
||||
} catch (Exception e) {
|
||||
logger.info("[" + orcidId + "] Parsing date: ", e.getMessage());
|
||||
return true;
|
||||
}
|
||||
return modifiedDateDt.after(lastUpdateDt);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,99 @@
|
|||
|
||||
package eu.dnetlib.doiboost.orcid;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.BufferedReader;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStreamReader;
|
||||
import java.net.URI;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
||||
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.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.hadoop.io.compress.GzipCodec;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.mortbay.log.Log;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
|
||||
public class SparkGenLastModifiedSeq {
|
||||
private static String hdfsServerUri;
|
||||
private static String workingPath;
|
||||
private static String outputPath;
|
||||
private static String lambdaFileName;
|
||||
|
||||
public static void main(String[] args) throws IOException, Exception {
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkGenLastModifiedSeq.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/doiboost/download_orcid_data.json")));
|
||||
parser.parseArgument(args);
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
hdfsServerUri = parser.get("hdfsServerUri");
|
||||
workingPath = parser.get("workingPath");
|
||||
outputPath = parser.get("outputPath");
|
||||
lambdaFileName = parser.get("lambdaFileName");
|
||||
String lambdaFileUri = hdfsServerUri.concat(workingPath).concat(lambdaFileName);
|
||||
|
||||
SparkConf sparkConf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
sparkConf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
int rowsNum = 0;
|
||||
Path output = new Path(
|
||||
hdfsServerUri
|
||||
.concat(workingPath)
|
||||
.concat(outputPath));
|
||||
Path hdfsreadpath = new Path(lambdaFileUri);
|
||||
Configuration conf = new Configuration();
|
||||
conf.set("fs.defaultFS", hdfsServerUri.concat(workingPath));
|
||||
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
|
||||
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
|
||||
FileSystem fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf);
|
||||
FSDataInputStream lambdaFileStream = fs.open(hdfsreadpath);
|
||||
try (TarArchiveInputStream tais = new TarArchiveInputStream(
|
||||
new GzipCompressorInputStream(lambdaFileStream))) {
|
||||
TarArchiveEntry entry = null;
|
||||
try (SequenceFile.Writer writer = SequenceFile
|
||||
.createWriter(
|
||||
conf,
|
||||
SequenceFile.Writer.file(output),
|
||||
SequenceFile.Writer.keyClass(Text.class),
|
||||
SequenceFile.Writer.valueClass(Text.class),
|
||||
SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new GzipCodec()))) {
|
||||
while ((entry = tais.getNextTarEntry()) != null) {
|
||||
BufferedReader br = new BufferedReader(new InputStreamReader(tais));
|
||||
String line;
|
||||
while ((line = br.readLine()) != null) {
|
||||
String[] values = line.split(",");
|
||||
List<String> recordInfo = Arrays.asList(values);
|
||||
String orcidId = recordInfo.get(0);
|
||||
final Text key = new Text(orcidId);
|
||||
final Text value = new Text(recordInfo.get(3));
|
||||
writer.append(key, value);
|
||||
rowsNum++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
Log.info("Saved rows from lamda csv tar file: " + rowsNum);
|
||||
});
|
||||
}
|
||||
}
|
||||
|
|
@ -1,165 +0,0 @@
|
|||
|
||||
package eu.dnetlib.doiboost.orcid;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
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.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.Function;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.util.LongAccumulator;
|
||||
import org.mortbay.log.Log;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class SparkOrcidGenerateAuthors {
|
||||
|
||||
static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
|
||||
static final String lastUpdate = "2019-09-30 00:00:00";
|
||||
|
||||
public static void main(String[] args) throws IOException, Exception {
|
||||
Logger logger = LoggerFactory.getLogger(SparkOrcidGenerateAuthors.class);
|
||||
logger.info("[ SparkOrcidGenerateAuthors STARTED]");
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkOrcidGenerateAuthors.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
final String workingPath = parser.get("workingPath");
|
||||
logger.info("workingPath: ", workingPath);
|
||||
final String outputAuthorsPath = parser.get("outputAuthorsPath");
|
||||
logger.info("outputAuthorsPath: ", outputAuthorsPath);
|
||||
final String token = parser.get("token");
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
LongAccumulator parsedRecordsAcc = sc.sc().longAccumulator("parsedRecords");
|
||||
LongAccumulator modifiedRecordsAcc = sc.sc().longAccumulator("modifiedRecords");
|
||||
LongAccumulator downloadedRecordsAcc = sc.sc().longAccumulator("downloadedRecords");
|
||||
LongAccumulator alreadyDownloadedRecords = sc.sc().longAccumulator("alreadyDownloadedRecords");
|
||||
JavaRDD<String> lamdaFileRDD = sc.textFile(workingPath + "lamdafiles");
|
||||
|
||||
JavaRDD<String> downloadedRDD = sc.textFile(workingPath + "downloaded");
|
||||
Function<String, String> getOrcidIdFunction = line -> {
|
||||
try {
|
||||
String[] values = line.split(",");
|
||||
return values[0].substring(1);
|
||||
} catch (Exception e) {
|
||||
return new String("");
|
||||
}
|
||||
};
|
||||
List<String> downloadedRecords = downloadedRDD.map(getOrcidIdFunction).collect();
|
||||
|
||||
Function<String, Boolean> isModifiedAfterFilter = line -> {
|
||||
String[] values = line.split(",");
|
||||
String orcidId = values[0];
|
||||
parsedRecordsAcc.add(1);
|
||||
if (isModified(orcidId, values[3])) {
|
||||
modifiedRecordsAcc.add(1);
|
||||
return true;
|
||||
}
|
||||
return false;
|
||||
};
|
||||
Function<String, Boolean> isNotDownloadedFilter = line -> {
|
||||
String[] values = line.split(",");
|
||||
String orcidId = values[0];
|
||||
if (downloadedRecords.contains(orcidId)) {
|
||||
alreadyDownloadedRecords.add(1);
|
||||
return false;
|
||||
}
|
||||
return true;
|
||||
};
|
||||
Function<String, Tuple2<String, String>> downloadRecordFunction = line -> {
|
||||
String[] values = line.split(",");
|
||||
String orcidId = values[0];
|
||||
String modifiedDate = values[3];
|
||||
return downloadRecord(orcidId, modifiedDate, token, downloadedRecordsAcc);
|
||||
};
|
||||
|
||||
lamdaFileRDD
|
||||
.filter(isModifiedAfterFilter)
|
||||
.filter(isNotDownloadedFilter)
|
||||
.map(downloadRecordFunction)
|
||||
.rdd()
|
||||
.saveAsTextFile(workingPath.concat(outputAuthorsPath));
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
private static boolean isModified(String orcidId, String modifiedDate) {
|
||||
Date modifiedDateDt = null;
|
||||
Date lastUpdateDt = null;
|
||||
try {
|
||||
if (modifiedDate.length() != 19) {
|
||||
modifiedDate = modifiedDate.substring(0, 19);
|
||||
}
|
||||
modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate);
|
||||
lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
|
||||
} catch (Exception e) {
|
||||
Log.warn("[" + orcidId + "] Parsing date: ", e.getMessage());
|
||||
return true;
|
||||
}
|
||||
return modifiedDateDt.after(lastUpdateDt);
|
||||
}
|
||||
|
||||
private static Tuple2<String, String> downloadRecord(String orcidId, String modifiedDate, String token,
|
||||
LongAccumulator downloadedRecordsAcc) {
|
||||
final DownloadedRecordData data = new DownloadedRecordData();
|
||||
data.setOrcidId(orcidId);
|
||||
data.setModifiedDate(modifiedDate);
|
||||
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);
|
||||
int statusCode = response.getStatusLine().getStatusCode();
|
||||
data.setStatusCode(statusCode);
|
||||
if (statusCode != 200) {
|
||||
Log
|
||||
.warn(
|
||||
"Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
|
||||
return data.toTuple2();
|
||||
}
|
||||
downloadedRecordsAcc.add(1);
|
||||
data
|
||||
.setCompressedData(
|
||||
ArgumentApplicationParser.compressArgument(IOUtils.toString(response.getEntity().getContent())));
|
||||
} catch (Throwable e) {
|
||||
Log.warn("Downloading " + orcidId, e.getMessage());
|
||||
data.setErrorMessage(e.getMessage());
|
||||
return data.toTuple2();
|
||||
}
|
||||
return data.toTuple2();
|
||||
}
|
||||
}
|
||||
|
|
@ -1,50 +0,0 @@
|
|||
|
||||
package eu.dnetlib.doiboost.orcid;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
|
||||
public class SparkPartitionLambdaFile {
|
||||
|
||||
public static void main(String[] args) throws IOException, Exception {
|
||||
Logger logger = LoggerFactory.getLogger(SparkOrcidGenerateAuthors.class);
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkOrcidGenerateAuthors.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
final String workingPath = parser.get("workingPath");
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
JavaRDD<String> lamdaFileRDD = sc.textFile(workingPath + "last_modified.csv");
|
||||
|
||||
lamdaFileRDD
|
||||
.repartition(20)
|
||||
.saveAsTextFile(workingPath.concat("lamdafiles"));
|
||||
});
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -3,8 +3,6 @@ package eu.dnetlib.doiboost.orcid.model;
|
|||
|
||||
import java.io.Serializable;
|
||||
|
||||
import org.apache.hadoop.io.Text;
|
||||
|
||||
import com.google.gson.JsonObject;
|
||||
|
||||
import scala.Tuple2;
|
||||
|
|
@ -12,7 +10,7 @@ import scala.Tuple2;
|
|||
public class DownloadedRecordData implements Serializable {
|
||||
|
||||
private String orcidId;
|
||||
private String modifiedDate;
|
||||
private String lastModifiedDate;
|
||||
private String statusCode;
|
||||
private String compressedData;
|
||||
private String errorMessage;
|
||||
|
|
@ -20,7 +18,7 @@ public class DownloadedRecordData implements Serializable {
|
|||
public Tuple2<String, String> toTuple2() {
|
||||
JsonObject data = new JsonObject();
|
||||
data.addProperty("statusCode", getStatusCode());
|
||||
data.addProperty("modifiedDate", getModifiedDate());
|
||||
data.addProperty("lastModifiedDate", getLastModifiedDate());
|
||||
if (getCompressedData() != null) {
|
||||
data.addProperty("compressedData", getCompressedData());
|
||||
}
|
||||
|
|
@ -66,11 +64,11 @@ public class DownloadedRecordData implements Serializable {
|
|||
this.compressedData = compressedData;
|
||||
}
|
||||
|
||||
public String getModifiedDate() {
|
||||
return modifiedDate;
|
||||
public String getLastModifiedDate() {
|
||||
return lastModifiedDate;
|
||||
}
|
||||
|
||||
public void setModifiedDate(String modifiedDate) {
|
||||
this.modifiedDate = modifiedDate;
|
||||
public void setLastModifiedDate(String lastModifiedDate) {
|
||||
this.lastModifiedDate = lastModifiedDate;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,4 +0,0 @@
|
|||
[{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path", "paramRequired": true},
|
||||
{"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true},
|
||||
{"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write the authors data", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -1,22 +0,0 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>hadoop-rm3.garr-pa1.d4science.org:8032</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://hadoop-rm1.garr-pa1.d4science.org:8020</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>queueName</name>
|
||||
<value>default</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -1,83 +0,0 @@
|
|||
<workflow-app name="Gen Orcid Authors" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>token</name>
|
||||
<description>access token</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>outputPath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="ResetWorkingPath"/>
|
||||
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="ResetWorkingPath">
|
||||
<fs>
|
||||
<delete path='${workingPath_activities}/authors'/>
|
||||
</fs>
|
||||
<ok to="Gen_Orcid_Authors"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Split_Lambda_File">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Split_Lambda_File</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkPartitionLambdaFile</class>
|
||||
<jar>dhp-doiboost-1.2.1-SNAPSHOT.jar</jar>
|
||||
<spark-opts>--num-executors 24 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory}
|
||||
</spark-opts>
|
||||
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||
<arg>-o</arg><arg>authors/</arg>
|
||||
<arg>-t</arg><arg>${token}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Gen_Orcid_Authors">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Gen_Orcid_Authors</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkOrcidGenerateAuthors</class>
|
||||
<jar>dhp-doiboost-1.2.1-SNAPSHOT.jar</jar>
|
||||
<spark-opts>--num-executors 20 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory}
|
||||
</spark-opts>
|
||||
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||
<arg>-o</arg><arg>authors/</arg>
|
||||
<arg>-t</arg><arg>${token}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -14,9 +14,63 @@
|
|||
</value>
|
||||
<description>the shell command that downloads the lambda file from orcid containing last orcid update informations</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorNumber</name>
|
||||
<value>20</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<value>7G</value>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<value>2G</value>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<value>1</value>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2MaxExecutors</name>
|
||||
<value>20</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozieActionShareLibForSpark2</name>
|
||||
<description>oozie action sharelib for spark 2.*</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||
<description>spark 2.* extra listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||
<description>spark 2.* sql query execution listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<description>spark 2.* yarn history server address</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<description>spark 2.* event log dir location</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="ResetWorkingPath"/>
|
||||
<global>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="DownloadOrcidAuthors"/>
|
||||
|
||||
|
||||
<kill name="Kill">
|
||||
|
|
@ -26,6 +80,7 @@
|
|||
<action name="ResetWorkingPath">
|
||||
<fs>
|
||||
<delete path='${workingPath}/downloads'/>
|
||||
<delete path='${workingPath}/last_modified.csv.tar'/>
|
||||
<mkdir path='${workingPath}/downloads'/>
|
||||
</fs>
|
||||
<ok to="DownloadLambdaFile"/>
|
||||
|
|
@ -41,24 +96,77 @@
|
|||
<argument>${shell_cmd}</argument>
|
||||
<capture-output/>
|
||||
</shell>
|
||||
<ok to="End"/>
|
||||
<ok to="DownloadUpdatedXMLAuthors"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="DownloadOrcidData">
|
||||
<action name="DownloadUpdatedXMLAuthors">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.orcid.OrcidDownloader</main-class>
|
||||
<arg>-d</arg><arg>${workingPathOrcid}/</arg>
|
||||
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||
<arg>-n</arg><arg>${nameNode}</arg>
|
||||
<arg>-f</arg><arg>last_modified.csv</arg>
|
||||
<arg>-o</arg><arg>download/</arg>
|
||||
<arg>-f</arg><arg>last_modified.csv.tar</arg>
|
||||
<arg>-o</arg><arg>downloads/</arg>
|
||||
<arg>-t</arg><arg>${token}</arg>
|
||||
</java>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="GenLastModifiedSeq">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>GenLastModifiedSeq</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkGenLastModifiedSeq</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--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>last_modified.csv.tar</arg>
|
||||
<arg>-o</arg><arg>last_modified.seq</arg>
|
||||
<arg>-t</arg><arg>-</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="DownloadOrcidAuthors">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>DownloadOrcidAuthors</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkDownloadOrcidAuthors</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--num-executors=${sparkExecutorNumber}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--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>last_modified.seq</arg>
|
||||
<arg>-o</arg><arg>downloads/updated_authors</arg>
|
||||
<arg>-t</arg><arg>${token}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -5,17 +5,24 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
|
|||
|
||||
import java.io.*;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.nio.file.Paths;
|
||||
import java.nio.file.StandardOpenOption;
|
||||
import java.text.ParseException;
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.Arrays;
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
|
||||
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.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.apache.spark.sql.catalyst.expressions.objects.AssertNotNull;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
|
|
@ -37,12 +44,49 @@ public class OrcidClientTest {
|
|||
// 'https://api.orcid.org/v3.0/0000-0001-7291-3210/record'
|
||||
|
||||
@Test
|
||||
public void downloadTest() throws Exception {
|
||||
String record = testDownloadRecord("0000-0001-6163-2042");
|
||||
File f = new File("/tmp/downloaded_0000-0001-6163-2042.xml");
|
||||
private void multipleDownloadTest() throws Exception {
|
||||
int toDownload = 1;
|
||||
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))) {
|
||||
downloadTest(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);
|
||||
String filename = "/tmp/downloaded_".concat(orcid).concat(".xml");
|
||||
File f = new File(filename);
|
||||
OutputStream outStream = new FileOutputStream(f);
|
||||
IOUtils.write(record.getBytes(), outStream);
|
||||
System.out.println("saved to tmp");
|
||||
}
|
||||
|
||||
private String testDownloadRecord(String orcidId) throws Exception {
|
||||
|
|
@ -50,7 +94,9 @@ public class OrcidClientTest {
|
|||
HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record");
|
||||
httpGet.addHeader("Accept", "application/vnd.orcid+xml");
|
||||
httpGet.addHeader("Authorization", "Bearer 78fdb232-7105-4086-8570-e153f4198e3d");
|
||||
logToFile("start connection: " + new Date(System.currentTimeMillis()).toString());
|
||||
CloseableHttpResponse response = client.execute(httpGet);
|
||||
logToFile("end connection: " + new Date(System.currentTimeMillis()).toString());
|
||||
if (response.getStatusLine().getStatusCode() != 200) {
|
||||
System.out
|
||||
.println("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
|
||||
|
|
@ -62,7 +108,7 @@ public class OrcidClientTest {
|
|||
return new String("");
|
||||
}
|
||||
|
||||
// @Test
|
||||
// @Test
|
||||
private void testLambdaFileParser() throws Exception {
|
||||
try (BufferedReader br = new BufferedReader(
|
||||
new InputStreamReader(this.getClass().getResourceAsStream("last_modified.csv")))) {
|
||||
|
|
@ -108,7 +154,7 @@ public class OrcidClientTest {
|
|||
}
|
||||
}
|
||||
|
||||
// @Test
|
||||
// @Test
|
||||
private void getRecordDatestamp() throws ParseException {
|
||||
Date toRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toRetrieveDate);
|
||||
Date toNotRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toNotRetrieveDate);
|
||||
|
|
@ -126,7 +172,7 @@ public class OrcidClientTest {
|
|||
System.out.println(valueDt.toString());
|
||||
}
|
||||
|
||||
// @Test
|
||||
// @Test
|
||||
@Ignore
|
||||
private void testModifiedDate() throws ParseException {
|
||||
testDate(toRetrieveDate);
|
||||
|
|
@ -134,14 +180,81 @@ public class OrcidClientTest {
|
|||
testDate(shortDate);
|
||||
}
|
||||
|
||||
// @Test
|
||||
@Ignore
|
||||
private void testReadBase64CompressedRecord() throws Exception {
|
||||
@Test
|
||||
public void testReadBase64CompressedRecord() throws Exception {
|
||||
final String base64CompressedRecord = IOUtils
|
||||
.toString(getClass().getResourceAsStream("0000-0001-6645-509X.compressed.base64"));
|
||||
.toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64"));
|
||||
final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
|
||||
System.out.println(recordFromSeqFile);
|
||||
final String downloadedRecord = testDownloadRecord("0000-0001-6645-509X");
|
||||
logToFile("\n\ndownloaded \n\n" + recordFromSeqFile);
|
||||
final String downloadedRecord = testDownloadRecord("0000-0003-3028-6161");
|
||||
assertTrue(recordFromSeqFile.equals(downloadedRecord));
|
||||
}
|
||||
|
||||
@Test
|
||||
private void lambdaFileReaderTest() throws Exception {
|
||||
TarArchiveInputStream input = new TarArchiveInputStream(
|
||||
new GzipCompressorInputStream(new FileInputStream("/develop/last_modified.csv.tar")));
|
||||
TarArchiveEntry entry = input.getNextTarEntry();
|
||||
BufferedReader br = null;
|
||||
StringBuilder sb = new StringBuilder();
|
||||
int rowNum = 0;
|
||||
int entryNum = 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);
|
||||
assertTrue(recordInfo.size() == 4);
|
||||
|
||||
rowNum++;
|
||||
if (rowNum == 1) {
|
||||
assertTrue(recordInfo.get(3).equals("last_modified"));
|
||||
} else if (rowNum == 2) {
|
||||
assertTrue(recordInfo.get(0).equals("0000-0002-0499-7333"));
|
||||
}
|
||||
}
|
||||
entryNum++;
|
||||
assertTrue(entryNum == 1);
|
||||
entry = input.getNextTarEntry();
|
||||
}
|
||||
}
|
||||
|
||||
@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);
|
||||
}
|
||||
|
||||
private void logToFile(String log)
|
||||
throws IOException {
|
||||
log = log.concat("\n");
|
||||
Path path = Paths.get("/tmp/orcid_log.txt");
|
||||
Files.write(path, log.getBytes(), StandardOpenOption.APPEND);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1 +0,0 @@
|
|||
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
|
||||
File diff suppressed because one or more lines are too long
Loading…
Reference in New Issue