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moved collector worker

This commit is contained in:
Sandro La Bruzzo 2019-04-03 16:05:16 +02:00
parent c2ecbf5572
commit ded6aef5e1
33 changed files with 1486 additions and 60 deletions
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16
dhp-applications/dhp-collector-worker/README.md Normal file
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Description of the Module
--------------------------
This module defines a **collector worker application** that run on Hadoop.
It is responsible of harvesting metadata using different plugin, that should be passed as arguments
in the main class
##Plugins
* OAI Plugin
## Api Descriptor
TODO
## Usage
TODO

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dhp-applications/dhp-collector-worker/pom.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<!-- Inherit defaults from Spring Boot -->
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-applications</artifactId>
<version>1.0.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>
<groupId>eu.dnetlib</groupId>
<artifactId>dhp-collector-worker</artifactId>
<version>1.0.0</version>
<repositories>
<repository>
<id>cloudera</id>
<name>Cloudera Repository</name>
<url>https://repository.cloudera.com/artifactory/cloudera-repos</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-client</artifactId>
<version>2.6.0-cdh5.9.2</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
</dependency>
<dependency>
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
<dhp.hadoop.version>2.6.0-${dhp.cdh.version}</dhp.hadoop.version>
<dhp.spark.version>2.2.0</dhp.spark.version>
<scala.version>2.11.8</scala.version>
</properties>
</project>

30
dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/DnetCollectorException.java Normal file
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package eu.dnetlib.collector.worker;
public class DnetCollectorException extends Exception {
/**
*
*/
private static final long serialVersionUID = -290723075076039757L;
public DnetCollectorException() {
super();
}
public DnetCollectorException(final String message, final Throwable cause, final boolean enableSuppression, final boolean writableStackTrace) {
super(message, cause, enableSuppression, writableStackTrace);
}
public DnetCollectorException(final String message, final Throwable cause) {
super(message, cause);
}
public DnetCollectorException(final String message) {
super(message);
}
public DnetCollectorException(final Throwable cause) {
super(cause);
}
}

121
dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/DnetCollectorWorkerApplication.java Normal file
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package eu.dnetlib.collector.worker;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.collector.worker.plugins.CollectorPlugin;
import eu.dnetlib.collector.worker.utils.CollectorPluginEnumerator;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.CommandLineRunner;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
import java.io.IOException;
import java.net.URI;
import java.util.concurrent.atomic.AtomicInteger;
/**
*
* DnetCollectortWorkerApplication is the main class responsible to start
* the Dnet Collection into HDFS.
* This module will be executed on the hadoop cluster and taking in input some parameters
* that tells it which is the right collector plugin to use and where store the data into HDFS path
*
*
* @author Sandro La Bruzzo
*/
@SpringBootApplication
public class DnetCollectorWorkerApplication implements CommandLineRunner {
private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorkerApplication.class);
@Autowired
private CollectorPluginEnumerator collectorPluginEnumerator;
/**
*
* @param args
*/
public static void main(final String[] args) {
SpringApplication.run(DnetCollectorWorkerApplication.class, args);
}
/**
* This module expect two arguments:
* path hdfs where store the sequential file.
* Json serialization of {@link ApiDescriptor}
*/
@Override
public void run(final String... args) throws Exception {
if (args.length == 0) { return; }
if (args.length != 3) { throw new DnetCollectorException("Invalid number of parameters, expected: hdfs_path and json_api_description"); }
//TODO : migrate to https://commons.apache.org/proper/commons-cli/usage.html
final String hdfsPath = args[0];
log.info("hdfsPath ="+hdfsPath);
final String json = args[1];
final String nameNode = args[2];
log.info("json = "+json);
final ObjectMapper jsonMapper = new ObjectMapper();
final ApiDescriptor api = jsonMapper.readValue(json, ApiDescriptor.class);
final CollectorPlugin plugin = collectorPluginEnumerator.getPluginByProtocol(api.getProtocol());
final String hdfsuri =nameNode;
// ====== Init HDFS File System Object
Configuration conf = new Configuration();
// Set FileSystem URI
conf.set("fs.defaultFS", hdfsuri);
// Because of Maven
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
System.setProperty("HADOOP_USER_NAME", "sandro.labruzzo");
System.setProperty("hadoop.home.dir", "/");
//Get the filesystem - HDFS
FileSystem fs = FileSystem.get(URI.create(hdfsuri), conf);
Path hdfswritepath = new Path(hdfsPath);
log.info("Created path "+hdfswritepath.toString());
try(SequenceFile.Writer writer = SequenceFile.createWriter(conf,
SequenceFile.Writer.file(hdfswritepath), SequenceFile.Writer.keyClass(IntWritable.class),
SequenceFile.Writer.valueClass(Text.class))) {
final AtomicInteger counter = new AtomicInteger(0);
final IntWritable key = new IntWritable(counter.get());
final Text value = new Text();
plugin.collect(api).forEach(content -> {
key.set(counter.getAndIncrement());
value.set(content);
try {
writer.append(key, value);
} catch (IOException e) {
throw new RuntimeException(e);
}
});
}
}
}

50
dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/model/ApiDescriptor.java Normal file
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package eu.dnetlib.collector.worker.model;
import java.util.HashMap;
import java.util.Map;
//TODO sholud be moved on dhp-common
public class ApiDescriptor {
private String id;
private String baseUrl;
private String protocol;
private Map<String, String> params = new HashMap<>();
public String getBaseUrl() {
return baseUrl;
}
public void setBaseUrl(final String baseUrl) {
this.baseUrl = baseUrl;
}
public String getId() {
return id;
}
public void setId(final String id) {
this.id = id;
}
public Map<String, String> getParams() {
return params;
}
public void setParams(final HashMap<String, String> params) {
this.params = params;
}
public String getProtocol() {
return protocol;
}
public void setProtocol(final String protocol) {
this.protocol = protocol;
}
}

11
dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/plugins/CollectorPlugin.java Normal file
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package eu.dnetlib.collector.worker.plugins;
import java.util.stream.Stream;
import eu.dnetlib.collector.worker.DnetCollectorException;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
public interface CollectorPlugin {
Stream<String> collect(ApiDescriptor api) throws DnetCollectorException;
}

66
dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/plugins/oai/OaiCollectorPlugin.java Normal file
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package eu.dnetlib.collector.worker.plugins.oai;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Spliterator;
import java.util.Spliterators;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import com.google.common.base.Splitter;
import com.google.common.collect.Iterators;
import com.google.common.collect.Lists;
import eu.dnetlib.collector.worker.DnetCollectorException;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.collector.worker.plugins.CollectorPlugin;
import eu.dnetlib.collector.worker.utils.DnetWorkerCollector;
@Component
@DnetWorkerCollector("oai")
public class OaiCollectorPlugin implements CollectorPlugin {
private static final String FORMAT_PARAM = "format";
private static final String OAI_SET_PARAM = "set";
private static final Object OAI_FROM_DATE_PARAM = "fromDate";
private static final Object OAI_UNTIL_DATE_PARAM = "untilDate";
@Autowired
private OaiIteratorFactory oaiIteratorFactory;
@Override
public Stream<String> collect(final ApiDescriptor api) throws DnetCollectorException {
final String baseUrl = api.getBaseUrl();
final String mdFormat = api.getParams().get(FORMAT_PARAM);
final String setParam = api.getParams().get(OAI_SET_PARAM);
final String fromDate = api.getParams().get(OAI_FROM_DATE_PARAM);
final String untilDate = api.getParams().get(OAI_UNTIL_DATE_PARAM);
final List<String> sets = new ArrayList<>();
if (setParam != null) {
sets.addAll(Lists.newArrayList(Splitter.on(",").omitEmptyStrings().trimResults().split(setParam)));
}
if (sets.isEmpty()) {
// If no set is defined, ALL the sets must be harvested
sets.add("");
}
if (baseUrl == null || baseUrl.isEmpty()) { throw new DnetCollectorException("Param 'baseurl' is null or empty"); }
if (mdFormat == null || mdFormat.isEmpty()) { throw new DnetCollectorException("Param 'mdFormat' is null or empty"); }
if (fromDate != null && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) { throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + fromDate); }
if (untilDate != null && !untilDate.matches("\\d{4}-\\d{2}-\\d{2}")) { throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + untilDate); }
final Iterator<Iterator<String>> iters = sets.stream()
.map(set -> oaiIteratorFactory.newIterator(baseUrl, mdFormat, set, fromDate, untilDate))
.iterator();
return StreamSupport.stream(Spliterators.spliteratorUnknownSize(Iterators.concat(iters), Spliterator.ORDERED), false);
}
}

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dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/plugins/oai/OaiIterator.java Normal file
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package eu.dnetlib.collector.worker.plugins.oai;
import java.io.StringReader;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.Iterator;
import java.util.Queue;
import java.util.concurrent.PriorityBlockingQueue;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import eu.dnetlib.collector.worker.DnetCollectorException;
import eu.dnetlib.collector.worker.utils.HttpConnector;
import eu.dnetlib.collector.worker.utils.XmlCleaner;
public class OaiIterator implements Iterator<String> {
private static final Log log = LogFactory.getLog(OaiIterator.class); // NOPMD by marko on 11/24/08 5:02 PM
private final Queue<String> queue = new PriorityBlockingQueue<>();
private final SAXReader reader = new SAXReader();
private final String baseUrl;
private final String set;
private final String mdFormat;
private final String fromDate;
private final String untilDate;
private String token;
private boolean started;
private final HttpConnector httpConnector;
public OaiIterator(final String baseUrl, final String mdFormat, final String set, final String fromDate, final String untilDate,
final HttpConnector httpConnector) {
this.baseUrl = baseUrl;
this.mdFormat = mdFormat;
this.set = set;
this.fromDate = fromDate;
this.untilDate = untilDate;
this.started = false;
this.httpConnector = httpConnector;
}
private void verifyStarted() {
if (!this.started) {
this.started = true;
try {
this.token = firstPage();
} catch (final DnetCollectorException e) {
throw new RuntimeException(e);
}
}
}
@Override
public boolean hasNext() {
synchronized (queue) {
verifyStarted();
return !queue.isEmpty();
}
}
@Override
public String next() {
synchronized (queue) {
verifyStarted();
final String res = queue.poll();
while (queue.isEmpty() && token != null && !token.isEmpty()) {
try {
token = otherPages(token);
} catch (final DnetCollectorException e) {
throw new RuntimeException(e);
}
}
return res;
}
}
@Override
public void remove() {}
private String firstPage() throws DnetCollectorException {
try {
String url = baseUrl + "?verb=ListRecords&metadataPrefix=" + URLEncoder.encode(mdFormat, "UTF-8");
if (set != null && !set.isEmpty()) {
url += "&set=" + URLEncoder.encode(set, "UTF-8");
}
if (fromDate != null && fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
url += "&from=" + URLEncoder.encode(fromDate, "UTF-8");
}
if (untilDate != null && untilDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
url += "&until=" + URLEncoder.encode(untilDate, "UTF-8");
}
log.info("Start harvesting using url: " + url);
return downloadPage(url);
} catch (final UnsupportedEncodingException e) {
throw new DnetCollectorException(e);
}
}
private String extractResumptionToken(final String xml) {
final String s = StringUtils.substringAfter(xml, "<resumptionToken");
if (s == null) { return null; }
final String result = StringUtils.substringBetween(s, ">", "</");
if (result == null) { return null; }
return result.trim();
}
private String otherPages(final String resumptionToken) throws DnetCollectorException {
try {
return downloadPage(baseUrl + "?verb=ListRecords&resumptionToken=" + URLEncoder.encode(resumptionToken, "UTF-8"));
} catch (final UnsupportedEncodingException e) {
throw new DnetCollectorException(e);
}
}
private String downloadPage(final String url) throws DnetCollectorException {
final String xml = httpConnector.getInputSource(url);
Document doc;
try {
doc = reader.read(new StringReader(xml));
} catch (final DocumentException e) {
log.warn("Error parsing xml, I try to clean it: " + xml, e);
final String cleaned = XmlCleaner.cleanAllEntities(xml);
try {
doc = reader.read(new StringReader(cleaned));
} catch (final DocumentException e1) {
final String resumptionToken = extractResumptionToken(xml);
if (resumptionToken == null) { throw new DnetCollectorException("Error parsing cleaned document:" + cleaned, e1); }
return resumptionToken;
}
}
final Node errorNode = doc.selectSingleNode("/*[local-name()='OAI-PMH']/*[local-name()='error']");
if (errorNode != null) {
final String code = errorNode.valueOf("@code");
if ("noRecordsMatch".equalsIgnoreCase(code.trim())) {
log.warn("noRecordsMatch for oai call: " + url);
return null;
} else {
throw new DnetCollectorException(code + " - " + errorNode.getText());
}
}
for (final Object o : doc.selectNodes("//*[local-name()='ListRecords']/*[local-name()='record']")) {
queue.add(((Node) o).asXML());
}
return doc.valueOf("//*[local-name()='resumptionToken']");
}
}

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dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/plugins/oai/OaiIteratorFactory.java Normal file
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package eu.dnetlib.collector.worker.plugins.oai;
import java.util.Iterator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import eu.dnetlib.collector.worker.utils.HttpConnector;
@Component
public class OaiIteratorFactory {
@Autowired
private HttpConnector httpConnector;
public Iterator<String> newIterator(final String baseUrl, final String mdFormat, final String set, final String fromDate, final String untilDate) {
return new OaiIterator(baseUrl, mdFormat, set, fromDate, untilDate, httpConnector);
}
}

24
dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/utils/CollectorPluginEnumerator.java Normal file
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package eu.dnetlib.collector.worker.utils;
import java.util.List;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import eu.dnetlib.collector.worker.plugins.CollectorPlugin;
@Component
public class CollectorPluginEnumerator {
@Autowired
private List<CollectorPlugin> plugins;
public CollectorPlugin getPluginByProtocol(final String protocol) {
return plugins.stream()
.filter(p -> p.getClass().isAnnotationPresent(DnetWorkerCollector.class))
.filter(p -> p.getClass().getAnnotation(DnetWorkerCollector.class).value().equalsIgnoreCase(protocol))
.findFirst()
.get();
}
}

19
dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/utils/CollectorPluginErrorLogList.java Normal file
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package eu.dnetlib.collector.worker.utils;
import java.util.LinkedList;
public class CollectorPluginErrorLogList extends LinkedList<String> {
private static final long serialVersionUID = -6925786561303289704L;
@Override
public String toString() {
String log = new String();
int index = 0;
for (final String errorMessage : this) {
log += String.format("Retry #%s: %s / ", index++, errorMessage);
}
return log;
}
}

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dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/utils/DnetWorkerCollector.java Normal file
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package eu.dnetlib.collector.worker.utils;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.TYPE)
public @interface DnetWorkerCollector {
String value();
}

226
dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/utils/HttpConnector.java Normal file
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package eu.dnetlib.collector.worker.utils;
import java.io.IOException;
import java.io.InputStream;
import java.net.CookieHandler;
import java.net.CookieManager;
import java.net.CookiePolicy;
import java.net.HttpURLConnection;
import java.net.URL;
import java.security.GeneralSecurityException;
import java.security.cert.X509Certificate;
import java.util.List;
import java.util.Map;
import javax.net.ssl.HttpsURLConnection;
import javax.net.ssl.SSLContext;
import javax.net.ssl.TrustManager;
import javax.net.ssl.X509TrustManager;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.math.NumberUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.stereotype.Component;
import eu.dnetlib.collector.worker.DnetCollectorException;
@Component
public class HttpConnector {
private static final Log log = LogFactory.getLog(HttpConnector.class);
private int maxNumberOfRetry = 6;
private int defaultDelay = 120; // seconds
private int readTimeOut = 120; // seconds
private String responseType = null;
private final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)";
public HttpConnector() {
CookieHandler.setDefault(new CookieManager(null, CookiePolicy.ACCEPT_ALL));
}
/**
* Given the URL returns the content via HTTP GET
*
* @param requestUrl
* the URL
* @return the content of the downloaded resource
* @throws CollectorServiceException
* when retrying more than maxNumberOfRetry times
*/
public String getInputSource(final String requestUrl) throws DnetCollectorException {
return attemptDownlaodAsString(requestUrl, 1, new CollectorPluginErrorLogList());
}
/**
* Given the URL returns the content as a stream via HTTP GET
*
* @param requestUrl
* the URL
* @return the content of the downloaded resource as InputStream
* @throws CollectorServiceException
* when retrying more than maxNumberOfRetry times
*/
public InputStream getInputSourceAsStream(final String requestUrl) throws DnetCollectorException {
return attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList());
}
private String attemptDownlaodAsString(final String requestUrl, final int retryNumber, final CollectorPluginErrorLogList errorList)
throws DnetCollectorException {
try {
final InputStream s = attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList());
try {
return IOUtils.toString(s);
} catch (final IOException e) {
log.error("error while retrieving from http-connection occured: " + requestUrl, e);
Thread.sleep(defaultDelay * 1000);
errorList.add(e.getMessage());
return attemptDownlaodAsString(requestUrl, retryNumber + 1, errorList);
} finally {
IOUtils.closeQuietly(s);
}
} catch (final InterruptedException e) {
throw new DnetCollectorException(e);
}
}
private InputStream attemptDownload(final String requestUrl, final int retryNumber, final CollectorPluginErrorLogList errorList)
throws DnetCollectorException {
if (retryNumber > maxNumberOfRetry) { throw new DnetCollectorException("Max number of retries exceeded. Cause: \n " + errorList); }
log.debug("Downloading " + requestUrl + " - try: " + retryNumber);
try {
InputStream input = null;
try {
final HttpURLConnection urlConn = (HttpURLConnection) new URL(requestUrl).openConnection();
urlConn.setInstanceFollowRedirects(false);
urlConn.setReadTimeout(readTimeOut * 1000);
urlConn.addRequestProperty("User-Agent", userAgent);
if (log.isDebugEnabled()) {
logHeaderFields(urlConn);
}
final int retryAfter = obtainRetryAfter(urlConn.getHeaderFields());
if (retryAfter > 0 && urlConn.getResponseCode() == HttpURLConnection.HTTP_UNAVAILABLE) {
log.warn("waiting and repeating request after " + retryAfter + " sec.");
Thread.sleep(retryAfter * 1000);
errorList.add("503 Service Unavailable");
urlConn.disconnect();
return attemptDownload(requestUrl, retryNumber + 1, errorList);
} else if (urlConn.getResponseCode() == HttpURLConnection.HTTP_MOVED_PERM || urlConn.getResponseCode() == HttpURLConnection.HTTP_MOVED_TEMP) {
final String newUrl = obtainNewLocation(urlConn.getHeaderFields());
log.debug("The requested url has been moved to " + newUrl);
errorList.add(String.format("%s %s. Moved to: %s", urlConn.getResponseCode(), urlConn.getResponseMessage(), newUrl));
urlConn.disconnect();
return attemptDownload(newUrl, retryNumber + 1, errorList);
} else if (urlConn.getResponseCode() != HttpURLConnection.HTTP_OK) {
log.error(String.format("HTTP error: %s %s", urlConn.getResponseCode(), urlConn.getResponseMessage()));
Thread.sleep(defaultDelay * 1000);
errorList.add(String.format("%s %s", urlConn.getResponseCode(), urlConn.getResponseMessage()));
urlConn.disconnect();
return attemptDownload(requestUrl, retryNumber + 1, errorList);
} else {
input = urlConn.getInputStream();
responseType = urlConn.getContentType();
return input;
}
} catch (final IOException e) {
log.error("error while retrieving from http-connection occured: " + requestUrl, e);
Thread.sleep(defaultDelay * 1000);
errorList.add(e.getMessage());
return attemptDownload(requestUrl, retryNumber + 1, errorList);
}
} catch (final InterruptedException e) {
throw new DnetCollectorException(e);
}
}
private void logHeaderFields(final HttpURLConnection urlConn) throws IOException {
log.debug("StatusCode: " + urlConn.getResponseMessage());
for (final Map.Entry<String, List<String>> e : urlConn.getHeaderFields().entrySet()) {
if (e.getKey() != null) {
for (final String v : e.getValue()) {
log.debug(" key: " + e.getKey() + " - value: " + v);
}
}
}
}
private int obtainRetryAfter(final Map<String, List<String>> headerMap) {
for (final String key : headerMap.keySet()) {
if (key != null && key.toLowerCase().equals("retry-after") && headerMap.get(key).size() > 0
&& NumberUtils.isNumber(headerMap.get(key).get(0))) { return Integer.parseInt(headerMap.get(key).get(0)) + 10; }
}
return -1;
}
private String obtainNewLocation(final Map<String, List<String>> headerMap) throws DnetCollectorException {
for (final String key : headerMap.keySet()) {
if (key != null && key.toLowerCase().equals("location") && headerMap.get(key).size() > 0) { return headerMap.get(key).get(0); }
}
throw new DnetCollectorException("The requested url has been MOVED, but 'location' param is MISSING");
}
/**
* register for https scheme; this is a workaround and not intended for the use in trusted environments
*/
public void initTrustManager() {
final X509TrustManager tm = new X509TrustManager() {
@Override
public void checkClientTrusted(final X509Certificate[] xcs, final String string) {}
@Override
public void checkServerTrusted(final X509Certificate[] xcs, final String string) {}
@Override
public X509Certificate[] getAcceptedIssuers() {
return null;
}
};
try {
final SSLContext ctx = SSLContext.getInstance("TLS");
ctx.init(null, new TrustManager[] { tm }, null);
HttpsURLConnection.setDefaultSSLSocketFactory(ctx.getSocketFactory());
} catch (final GeneralSecurityException e) {
log.fatal(e);
throw new IllegalStateException(e);
}
}
public int getMaxNumberOfRetry() {
return maxNumberOfRetry;
}
public void setMaxNumberOfRetry(final int maxNumberOfRetry) {
this.maxNumberOfRetry = maxNumberOfRetry;
}
public int getDefaultDelay() {
return defaultDelay;
}
public void setDefaultDelay(final int defaultDelay) {
this.defaultDelay = defaultDelay;
}
public int getReadTimeOut() {
return readTimeOut;
}
public void setReadTimeOut(final int readTimeOut) {
this.readTimeOut = readTimeOut;
}
public String getResponseType() {
return responseType;
}
}

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dhp-applications/dhp-collector-worker/src/main/java/eu/dnetlib/collector/worker/utils/XmlCleaner.java Normal file
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package eu.dnetlib.collector.worker.utils;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.regex.Pattern;
/**
* @author jochen, Andreas Czerniak
*
*/
public class XmlCleaner {
/**
* Pattern for numeric entities.
*/
private static Pattern validCharacterEntityPattern = Pattern.compile("^&#x?\\d{2,4};"); //$NON-NLS-1$
// private static Pattern validCharacterEntityPattern = Pattern.compile("^&#?\\d{2,4};"); //$NON-NLS-1$
// see https://www.w3.org/TR/REC-xml/#charsets , not only limited to &#11;
private static Pattern invalidControlCharPattern = Pattern.compile("&#x?1[0-9a-fA-F];");
/**
* Pattern that negates the allowable XML 4 byte unicode characters. Valid are: #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] |
* [#x10000-#x10FFFF]
*/
private static Pattern invalidCharacterPattern = Pattern.compile("[^\t\r\n\u0020-\uD7FF\uE000-\uFFFD]"); //$NON-NLS-1$
// Map entities to their unicode equivalent
private static Set<String> goodEntities = new HashSet<>();
private static Map<String, String> badEntities = new HashMap<>();
static {
// pre-defined XML entities
goodEntities.add("&quot;"); //$NON-NLS-1$ // quotation mark
goodEntities.add("&amp;"); //$NON-NLS-1$ // ampersand
goodEntities.add("&lt;"); //$NON-NLS-1$ // less-than sign
goodEntities.add("&gt;"); //$NON-NLS-1$ // greater-than sign
// control entities
// badEntities.put("&#11;", "");
badEntities.put("&#127;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#128;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#129;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#130;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#131;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#132;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#133;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#134;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#135;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#136;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#137;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#138;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#139;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#140;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#141;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#142;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#143;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#144;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#145;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#146;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#147;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#148;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#149;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#150;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#151;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#152;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#153;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#154;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#155;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#156;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#157;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#158;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
badEntities.put("&#159;", " "); //$NON-NLS-1$ //$NON-NLS-2$ // illegal HTML character
// misc entities
badEntities.put("&euro;", "\u20AC"); //$NON-NLS-1$ //$NON-NLS-2$ // euro
badEntities.put("&lsquo;", "\u2018"); //$NON-NLS-1$ //$NON-NLS-2$ // left single quotation mark
badEntities.put("&rsquo;", "\u2019"); //$NON-NLS-1$ //$NON-NLS-2$ // right single quotation mark
// Latin 1 entities
badEntities.put("&nbsp;", "\u00A0"); //$NON-NLS-1$ //$NON-NLS-2$ // no-break space
badEntities.put("&iexcl;", "\u00A1"); //$NON-NLS-1$ //$NON-NLS-2$ // inverted exclamation mark
badEntities.put("&cent;", "\u00A2"); //$NON-NLS-1$ //$NON-NLS-2$ // cent sign
badEntities.put("&pound;", "\u00A3"); //$NON-NLS-1$ //$NON-NLS-2$ // pound sign
badEntities.put("&curren;", "\u00A4"); //$NON-NLS-1$ //$NON-NLS-2$ // currency sign
badEntities.put("&yen;", "\u00A5"); //$NON-NLS-1$ //$NON-NLS-2$ // yen sign
badEntities.put("&brvbar;", "\u00A6"); //$NON-NLS-1$ //$NON-NLS-2$ // broken vertical bar
badEntities.put("&sect;", "\u00A7"); //$NON-NLS-1$ //$NON-NLS-2$ // section sign
badEntities.put("&uml;", "\u00A8"); //$NON-NLS-1$ //$NON-NLS-2$ // diaeresis
badEntities.put("&copy;", "\u00A9"); //$NON-NLS-1$ //$NON-NLS-2$ // copyright sign
badEntities.put("&ordf;", "\u00AA"); //$NON-NLS-1$ //$NON-NLS-2$ // feminine ordinal indicator
badEntities.put("&laquo;", "\u00AB"); //$NON-NLS-1$ //$NON-NLS-2$ // left-pointing double angle quotation mark
badEntities.put("&not;", "\u00AC"); //$NON-NLS-1$ //$NON-NLS-2$ // not sign
badEntities.put("&shy;", "\u00AD"); //$NON-NLS-1$ //$NON-NLS-2$ // soft hyphen
badEntities.put("&reg;", "\u00AE"); //$NON-NLS-1$ //$NON-NLS-2$ // registered sign
badEntities.put("&macr;", "\u00AF"); //$NON-NLS-1$ //$NON-NLS-2$ // macron
badEntities.put("&deg;", "\u00B0"); //$NON-NLS-1$ //$NON-NLS-2$ // degree sign
badEntities.put("&plusmn;", "\u00B1"); //$NON-NLS-1$ //$NON-NLS-2$ // plus-minus sign
badEntities.put("&sup2;", "\u00B2"); //$NON-NLS-1$ //$NON-NLS-2$ // superscript two
badEntities.put("&sup3;", "\u00B3"); //$NON-NLS-1$ //$NON-NLS-2$ // superscript three
badEntities.put("&acute;", "\u00B4"); //$NON-NLS-1$ //$NON-NLS-2$ // acute accent
badEntities.put("&micro;", "\u00B5"); //$NON-NLS-1$ //$NON-NLS-2$ // micro sign
badEntities.put("&para;", "\u00B6"); //$NON-NLS-1$ //$NON-NLS-2$ // pilcrow sign
badEntities.put("&middot;", "\u00B7"); //$NON-NLS-1$ //$NON-NLS-2$ // middle dot
badEntities.put("&cedil;", "\u00B8"); //$NON-NLS-1$ //$NON-NLS-2$ // cedilla
badEntities.put("&sup1;", "\u00B9"); //$NON-NLS-1$ //$NON-NLS-2$ // superscript one
badEntities.put("&ordm;", "\u00BA"); //$NON-NLS-1$ //$NON-NLS-2$ // masculine ordinal indicator
badEntities.put("&raquo;", "\u00BB"); //$NON-NLS-1$ //$NON-NLS-2$ // right-pointing double angle quotation mark
badEntities.put("&frac14;", "\u00BC"); //$NON-NLS-1$ //$NON-NLS-2$ // vulgar fraction one quarter
badEntities.put("&frac12;", "\u00BD"); //$NON-NLS-1$ //$NON-NLS-2$ // vulgar fraction one half
badEntities.put("&frac34;", "\u00BE"); //$NON-NLS-1$ //$NON-NLS-2$ // vulgar fraction three quarters
badEntities.put("&iquest;", "\u00BF"); //$NON-NLS-1$ //$NON-NLS-2$ // inverted question mark
badEntities.put("&Agrave;", "\u00C0"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with grave
badEntities.put("&Aacute;", "\u00C1"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with acute
badEntities.put("&Acirc;", "\u00C2"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with circumflex
badEntities.put("&Atilde;", "\u00C3"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with tilde
badEntities.put("&Auml;", "\u00C4"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with diaeresis
badEntities.put("&Aring;", "\u00C5"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter A with ring above
badEntities.put("&AElig;", "\u00C6"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter AE
badEntities.put("&Ccedil;", "\u00C7"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter C with cedilla
badEntities.put("&Egrave;", "\u00C8"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with grave
badEntities.put("&Eacute;", "\u00C9"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with acute
badEntities.put("&Ecirc;", "\u00CA"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with circumflex
badEntities.put("&Euml;", "\u00CB"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter E with diaeresis
badEntities.put("&Igrave;", "\u00CC"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with grave
badEntities.put("&Iacute;", "\u00CD"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with acute
badEntities.put("&Icirc;", "\u00CE"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with circumflex
badEntities.put("&Iuml;", "\u00CF"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter I with diaeresis
badEntities.put("&ETH;", "\u00D0"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter ETH
badEntities.put("&Ntilde;", "\u00D1"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter N with tilde
badEntities.put("&Ograve;", "\u00D2"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with grave
badEntities.put("&Oacute;", "\u00D3"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with acute
badEntities.put("&Ocirc;", "\u00D4"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with circumflex
badEntities.put("&Otilde;", "\u00D5"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with tilde
badEntities.put("&Ouml;", "\u00D6"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with diaeresis
badEntities.put("&times;", "\u00D7"); //$NON-NLS-1$ //$NON-NLS-2$ // multiplication sign
badEntities.put("&Oslash;", "\u00D8"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter O with stroke
badEntities.put("&Ugrave;", "\u00D9"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with grave
badEntities.put("&Uacute;", "\u00DA"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with acute
badEntities.put("&Ucirc;", "\u00DB"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with circumflex
badEntities.put("&Uuml;", "\u00DC"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter U with diaeresis
badEntities.put("&Yacute;", "\u00DD"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter Y with acute
badEntities.put("&THORN;", "\u00DE"); //$NON-NLS-1$ //$NON-NLS-2$ // latin capital letter THORN
badEntities.put("&szlig;", "\u00DF"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter sharp s
badEntities.put("&agrave;", "\u00E0"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with grave
badEntities.put("&aacute;", "\u00E1"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with acute
badEntities.put("&acirc;", "\u00E2"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with circumflex
badEntities.put("&atilde;", "\u00E3"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with tilde
badEntities.put("&auml;", "\u00E4"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with diaeresis
badEntities.put("&aring;", "\u00E5"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter a with ring above
badEntities.put("&aelig;", "\u00E6"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter ae
badEntities.put("&ccedil;", "\u00E7"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter c with cedilla
badEntities.put("&egrave;", "\u00E8"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with grave
badEntities.put("&eacute;", "\u00E9"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with acute
badEntities.put("&ecirc;", "\u00EA"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with circumflex
badEntities.put("&euml;", "\u00EB"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter e with diaeresis
badEntities.put("&igrave;", "\u00EC"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with grave
badEntities.put("&iacute;", "\u00ED"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with acute
badEntities.put("&icirc;", "\u00EE"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with circumflex
badEntities.put("&iuml;", "\u00EF"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter i with diaeresis
badEntities.put("&eth;", "\u00F0"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter eth
badEntities.put("&ntilde;", "\u00F1"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter n with tilde
badEntities.put("&ograve;", "\u00F2"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with grave
badEntities.put("&oacute;", "\u00F3"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with acute
badEntities.put("&ocirc;", "\u00F4"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with circumflex
badEntities.put("&otilde;", "\u00F5"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with tilde
badEntities.put("&ouml;", "\u00F6"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with diaeresis
badEntities.put("&divide;", "\u00F7"); //$NON-NLS-1$ //$NON-NLS-2$ // division sign
badEntities.put("&oslash;", "\u00F8"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter o with stroke
badEntities.put("&ugrave;", "\u00F9"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with grave
badEntities.put("&uacute;", "\u00FA"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with acute
badEntities.put("&ucirc;", "\u00FB"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with circumflex
badEntities.put("&uuml;", "\u00FC"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter u with diaeresis
badEntities.put("&yacute;", "\u00FD"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter y with acute
badEntities.put("&thorn;", "\u00FE"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter thorn
badEntities.put("&yuml;", "\u00FF"); //$NON-NLS-1$ //$NON-NLS-2$ // latin small letter y with diaeresis
}
/**
* For each entity in the input that is not allowed in XML, replace the entity with its unicode equivalent or remove it. For each
* instance of a bare {@literal &}, replace it with {@literal &amp;<br/>
* } XML only allows 4 entities: {@literal &amp;amp;}, {@literal &amp;quot;}, {@literal &amp;lt;} and {@literal &amp;gt;}.
*
* @param broken
* the string to handle entities
* @return the string with entities appropriately fixed up
*/
static public String cleanAllEntities(final String broken) {
if (broken == null) { return null; }
String working = invalidControlCharPattern.matcher(broken).replaceAll("");
working = invalidCharacterPattern.matcher(working).replaceAll("");
int cleanfrom = 0;
while (true) {
int amp = working.indexOf('&', cleanfrom);
// If there are no more amps then we are done
if (amp == -1) {
break;
}
// Skip references of the kind &#ddd;
if (validCharacterEntityPattern.matcher(working.substring(amp)).find()) {
cleanfrom = working.indexOf(';', amp) + 1;
continue;
}
int i = amp + 1;
while (true) {
// if we are at the end of the string then just escape the '&';
if (i >= working.length()) { return working.substring(0, amp) + "&amp;" + working.substring(amp + 1); //$NON-NLS-1$
}
// if we have come to a ; then we have an entity
// If it is something that xml can't handle then replace it.
final char c = working.charAt(i);
if (c == ';') {
final String entity = working.substring(amp, i + 1);
final String replace = handleEntity(entity);
working = working.substring(0, amp) + replace + working.substring(i + 1);
break;
}
// Did we end an entity without finding a closing ;
// Then treat it as an '&' that needs to be replaced with &amp;
if (!Character.isLetterOrDigit(c)) {
working = working.substring(0, amp) + "&amp;" + working.substring(amp + 1); //$NON-NLS-1$
amp = i + 4; // account for the 4 extra characters
break;
}
i++;
}
cleanfrom = amp + 1;
}
if (Pattern.compile("<<").matcher(working).find()) {
working = working.replaceAll("<<", "&lt;&lt;");
}
if (Pattern.compile(">>").matcher(working).find()) {
working = working.replaceAll(">>", "&gt;&gt;");
}
return working;
}
/**
* Replace entity with its unicode equivalent, if it is not a valid XML entity. Otherwise strip it out. XML only allows 4 entities:
* &amp;amp;, &amp;quot;, &amp;lt; and &amp;gt;.
*
* @param entity
* the entity to be replaced
* @return the substitution for the entity, either itself, the unicode equivalent or an empty string.
*/
private static String handleEntity(final String entity) {
if (goodEntities.contains(entity)) { return entity; }
final String replace = badEntities.get(entity);
if (replace != null) { return replace; }
return replace != null ? replace : "";
}
}

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dhp-applications/dhp-collector-worker/src/test/java/eu/dnetlib/collector/worker/DnetCollectorWorkerApplicationTests.java Normal file
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package eu.dnetlib.collector.worker;
import static org.junit.Assert.assertNotNull;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.CommandLineRunner;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.context.ApplicationContext;
import org.springframework.test.context.junit4.SpringRunner;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.collector.worker.utils.CollectorPluginEnumerator;
@RunWith(SpringRunner.class)
@SpringBootTest
public class DnetCollectorWorkerApplicationTests {
@Autowired
private ApplicationContext ctx;
@Test
public void testFindPlugin() throws Exception {
final CollectorPluginEnumerator collectorPluginEnumerator = ctx.getBean(CollectorPluginEnumerator.class);
assertNotNull(collectorPluginEnumerator.getPluginByProtocol("oai"));
assertNotNull(collectorPluginEnumerator.getPluginByProtocol("OAI"));
}
@Test
public void testCollectionOAI() throws Exception {
final ApiDescriptor api = new ApiDescriptor();
api.setId("oai");
api.setProtocol("oai");
api.setBaseUrl("http://www.revista.vocesdelaeducacion.com.mx/index.php/index/oai");
api.getParams().put("format", "oai_dc");
ObjectMapper mapper = new ObjectMapper();
System.out.println(mapper.writeValueAsString(api));
}
}

39
dhp-applications/dhp-mdstore-manager-app/pom.xml
View File

@ -3,30 +3,31 @@
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-mdstore-manager-app</artifactId>
<version>1.1.0-SNAPSHOT</version>
<!-- Inherit defaults from Spring Boot -->
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.1.3.RELEASE</version>
<relativePath></relativePath>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-applications</artifactId>
<version>1.0.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<!-- <repositories> <repository> <id>dnet-deps</id> <name>dnet-dependencies</name>
<url>http://maven.research-infrastructures.eu/nexus/content/repositories/dnet-deps</url>
<layout>default</layout> </repository> <repository> <id>dnet45-releases</id>
<name>D-Net 45 Releases</name> <url>http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases</url>
<layout>default</layout> <snapshots> <enabled>true</enabled> </snapshots>
</repository> <repository> <id>dnet45-snapshots</id> <name>D-Net 45 Snapshots</name>
<url>http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-snapshots</url>
<layout>default</layout> <snapshots> <enabled>true</enabled> </snapshots>
<!-- <repositories> <repository> <id>dnet-deps</id> <name>dnet-dependencies</name>
<url>http://maven.research-infrastructures.eu/nexus/content/repositories/dnet-deps</url>
<layout>default</layout> </repository> <repository> <id>dnet45-releases</id>
<name>D-Net 45 Releases</name> <url>http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases</url>
<layout>default</layout> <snapshots> <enabled>true</enabled> </snapshots>
</repository> <repository> <id>dnet45-snapshots</id> <name>D-Net 45 Snapshots</name>
<url>http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-snapshots</url>
<layout>default</layout> <snapshots> <enabled>true</enabled> </snapshots>
</repository> </repositories> -->
<!-- Add typical dependencies for a web application -->
<dependencies>
<dependency>
@ -84,16 +85,6 @@
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<configuration>
<executable>true</executable>
</configuration>
</plugin>
</plugins>
</build>
</project>

4
dhp-applications/dhp-mdstore-manager-app/src/main/resources/application.properties
View File

@ -2,8 +2,8 @@ spring.main.banner-mode = console
logging.level.root = INFO
spring.datasource.url=jdbc:postgresql://localhost:5432/mdstoremanager
spring.datasource.username=
spring.datasource.password=
spring.datasource.username=dnet
spring.datasource.password=dnetPwd
spring.jpa.properties.hibernate.dialect = org.hibernate.dialect.PostgreSQLDialect

35
dhp-applications/pom.xml
View File

@ -5,11 +5,46 @@
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.0.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<artifactId>dhp-applications</artifactId>
<packaging>pom</packaging>
<modules>
<module>dhp-mdstore-manager-app</module>
<module>dhp-collector-worker</module>
</modules>
<dependencyManagement>
<dependencies>
<dependency>
<!-- Import dependency management from Spring Boot -->
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-dependencies</artifactId>
<version>2.1.3.RELEASE</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>1.0.0-SNAPSHOT</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<configuration>
<executable>true</executable>
</configuration>
</plugin>
</plugins>
</build>
</project>

1
dhp-common/pom.xml
View File

@ -8,6 +8,7 @@
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.0.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<artifactId>dhp-common</artifactId>

105
dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/MetadataRecord.java Normal file
View File

@ -0,0 +1,105 @@
package eu.dnetlib.dhp.model.mdstore;
import eu.dnetlib.dhp.utils.DHPUtils;
import org.apache.commons.lang3.StringUtils;
import java.io.Serializable;
/**
* This class models a record inside the new MetadataStore
*
*/
public class MetadataRecord implements Serializable {
private String id;
private String originalId;
private String encoding;
private Provenance provenance;
private String body;
private long dateOfCollection;
public MetadataRecord() {
this.dateOfCollection = System.currentTimeMillis();
}
public MetadataRecord(String originalId, String encoding, Provenance provenance, String body, long dateOfCollection) {
this.originalId = originalId;
this.encoding = encoding;
this.provenance = provenance;
this.body = body;
this.dateOfCollection = dateOfCollection;
this.id = DHPUtils.generateIdentifier(originalId,this.provenance.getNsPrefix());
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getOriginalId() {
return originalId;
}
public void setOriginalId(String originalId) {
this.originalId = originalId;
}
public String getEncoding() {
return encoding;
}
public void setEncoding(String encoding) {
this.encoding = encoding;
}
public Provenance getProvenance() {
return provenance;
}
public void setProvenance(Provenance provenance) {
this.provenance = provenance;
}
public String getBody() {
return body;
}
public void setBody(String body) {
this.body = body;
}
public long getDateOfCollection() {
return dateOfCollection;
}
public void setDateOfCollection(long dateOfCollection) {
this.dateOfCollection = dateOfCollection;
}
@Override
public boolean equals(Object o) {
if (!(o instanceof MetadataRecord)) {
return false;
}
return ((MetadataRecord) o).getId().equalsIgnoreCase(id);
}
@Override
public int hashCode() {
return id.hashCode();
}
}

56
dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/Provenance.java Normal file
View File

@ -0,0 +1,56 @@
package eu.dnetlib.dhp.model.mdstore;
import java.io.Serializable;
/**
* @author Sandro La Bruzzo
*
* Provenace class models the provenance of the record in the metadataStore
* It contains the identifier and the name of the datasource that gives the
* record
*
*/
public class Provenance implements Serializable {
private String datasourceId;
private String datasourceName;
private String nsPrefix;
public Provenance() {
}
public Provenance(String datasourceId, String datasourceName, String nsPrefix) {
this.datasourceId = datasourceId;
this.datasourceName = datasourceName;
this.nsPrefix = nsPrefix;
}
public String getDatasourceId() {
return datasourceId;
}
public void setDatasourceId(String datasourceId) {
this.datasourceId = datasourceId;
}
public String getDatasourceName() {
return datasourceName;
}
public void setDatasourceName(String datasourceName) {
this.datasourceName = datasourceName;
}
public String getNsPrefix() {
return nsPrefix;
}
public void setNsPrefix(String nsPrefix) {
this.nsPrefix = nsPrefix;
}
}

25
dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java Normal file
View File

@ -0,0 +1,25 @@
package eu.dnetlib.dhp.utils;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.lang3.StringUtils;
import java.security.MessageDigest;
public class DHPUtils {
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes("UTF-8"));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
System.err.println("Error creating id");
return null;
}
}
public static String generateIdentifier(final String originalId, final String nsPrefix) {
return String.format("%s::%s",nsPrefix, DHPUtils.md5(originalId));
}
}

15
dhp-common/src/test/java/eu/dnetlib/dhp/model/mdstore/MetadataRecordTest.java Normal file
View File

@ -0,0 +1,15 @@
package eu.dnetlib.dhp.model.mdstore;
import org.junit.Test;
import static org.junit.Assert.assertTrue;
public class MetadataRecordTest {
@Test
public void getTimestamp() {
MetadataRecord r = new MetadataRecord();
assertTrue(r.getDateOfCollection() >0);
}
}

1
dhp-schemas/pom.xml
View File

@ -8,6 +8,7 @@
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.0.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<artifactId>dhp-schemas</artifactId>

6
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java
View File

@ -50,10 +50,6 @@ public class GenerateNativeStoreSparkJob {
}
}
public static void main(String[] args) throws Exception {
Options options = new Options();
@ -113,7 +109,7 @@ public class GenerateNativeStoreSparkJob {
final SparkSession spark = SparkSession
.builder()
.appName("GenerateNativeStoreSparkJob")
.master("yarn")
.master("local")
.getOrCreate();
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());

47
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/TransformSparkJobNode.java
View File

@ -1,4 +1,51 @@
package eu.dnetlib.dhp.collection;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.transformation.TransformFunction;
import org.apache.commons.cli.*;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.util.LongAccumulator;
public class TransformSparkJobNode {
public static void main(String[] args) throws ParseException {
Options options = new Options();
options.addOption(Option.builder("i")
.longOpt("input")
.required(true)
.desc("input path of the sequence file")
.hasArg() // This option has an argument.
.build());
options.addOption(Option.builder("o")
.longOpt("output")
.required(true)
.desc("output path of the mdstore")
.hasArg()
.build());
final CommandLineParser parser = new DefaultParser();
final CommandLine cmd = parser.parse( options, args);
final String inputPath = cmd.getOptionValue("i");
final String outputPath = cmd.getOptionValue("o");
final SparkSession spark = SparkSession
.builder()
.appName("GenerateNativeStoreSparkJob")
.master("local")
.getOrCreate();
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mdstoreInput = spark.read().format("parquet").load(inputPath).as(encoder);
final LongAccumulator totalItems = spark.sparkContext().longAccumulator("TotalItems");
final TransformFunction mfunc = new TransformFunction(totalItems);
mdstoreInput.map(mfunc, encoder).write().format("parquet").save(outputPath);
System.out.println("totalItems = " + totalItems.value());
}
}

12
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformFunction.java
View File

@ -1,13 +1,21 @@
package eu.dnetlib.dhp.collection;
package eu.dnetlib.dhp.transformation;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.util.LongAccumulator;
public class TransformFunction implements MapFunction<MetadataRecord, MetadataRecord> {
private final LongAccumulator totalItems;
public TransformFunction(LongAccumulator totalItems) {
this.totalItems= totalItems;
}
@Override
public MetadataRecord call(MetadataRecord value) throws Exception {
return null;
totalItems.add(1);
return value;
}
}

2
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/oozie/workflows/oozie_collection_workflows.xml
View File

@ -20,7 +20,7 @@
<description>A json encoding of the Datasource Info</description>
</property>
<property>
<name>identifierPath</name>
<name>identifierXPath</name>
<description>An xpath to retrieve the metadata idnentifier for the generation of DNet Identifier </description>
</property>

21
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java
View File

@ -15,13 +15,23 @@ public class CollectionJobTest {
@Test
public void test () throws Exception {
Provenance provenance = new Provenance("pippo", "puppa", "ns_prefix");
// GenerateNativeStoreSparkJob.main(new String[] {"XML", ""+System.currentTimeMillis(), new ObjectMapper().writeValueAsString(provenance), "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']","/home/sandro/Downloads/mdstore_oai","/home/sandro/Downloads/mdstore_result"});
GenerateNativeStoreSparkJob.main(new String[] {"-e", "XML","-d", ""+System.currentTimeMillis(),"-p", new ObjectMapper().writeValueAsString(provenance), "-x","./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']","-i","/home/sandro/Downloads/oai_1","-o","/home/sandro/Downloads/mdstore_result"});
System.out.println(new ObjectMapper().writeValueAsString(provenance));
}
@Test
public void transformTest () throws Exception {
TransformSparkJobNode.main(new String[]{"-o","/home/sandro/Downloads/mdstore_cleande","-i","/home/sandro/Downloads/mdstore_result"});
}
@Test
public void testGenerationMetadataRecord() throws Exception {
@ -29,6 +39,7 @@ public class CollectionJobTest {
MetadataRecord record = GenerateNativeStoreSparkJob.parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", "ns_prefix"), System.currentTimeMillis(), null,null);
assert record != null;
System.out.println(record.getId());
System.out.println(record.getOriginalId());
@ -42,9 +53,11 @@ public class CollectionJobTest {
final String xml = IOUtils.toString(this.getClass().getResourceAsStream("./record.xml"));
MetadataRecord record = GenerateNativeStoreSparkJob.parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", "ns_prefix"), System.currentTimeMillis(), null,null);
MetadataRecord record1 = GenerateNativeStoreSparkJob.parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", "ns_prefix"), System.currentTimeMillis(), null,null);
assert record != null;
record.setBody("ciao");
assert record1 != null;
record1.setBody("mondo");
Assert.assertTrue(record.equals(record1));
Assert.assertEquals(record, record1);
}

4
dhp-workflows/dhp-collector-worker/target/maven-archiver/pom.properties
View File

@ -1,4 +0,0 @@
#Created by Apache Maven 3.6.0
version=1.0.0
groupId=eu.dnetlib
artifactId=dhp-collector-worker

2
dhp-workflows/pom.xml
View File

@ -5,11 +5,11 @@
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.0.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<artifactId>dhp-workflows</artifactId>
<packaging>pom</packaging>
<modules>
<module>dhp-collector-worker</module>
<module>dhp-aggregation</module>
</modules>

21
pom.xml
View File

@ -23,7 +23,7 @@
<!--<module>dhp-build</module>-->
<module>dhp-common</module>
<module>dhp-workflows</module>
<module>dhp-applications</module>
<module>dhp-applications</module>
</modules>
<issueManagement>
@ -37,9 +37,9 @@
</ciManagement>
<scm>
<connection>scm:git:ssh://git@github.com/???</connection>
<developerConnection>scm:git:ssh://git@github.com/???.git</developerConnection>
<url>https://github.com/???</url>
<connection>scm:git:ssh://git@github.com/dnet-team/dnet-hadoop.git</connection>
<developerConnection>scm:git:ssh://git@github.com:dnet-team/dnet-hadoop.git</developerConnection>
<url>https://github.com/dnet-team/dnet-hadoop</url>
<tag>HEAD</tag>
</scm>
@ -135,22 +135,16 @@
<artifactId>commons-cli</artifactId>
<version>1.4</version>
</dependency>
</dependencies>
</dependencyManagement>
<build>
<directory>target</directory>
<outputDirectory>target/classes</outputDirectory>
<finalName>${project.artifactId}-${project.version}</finalName>
<testOutputDirectory>target/test-classes</testOutputDirectory>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
@ -191,7 +185,6 @@
<redirectTestOutputToFile>true</redirectTestOutputToFile>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
@ -200,27 +193,21 @@
<detectLinks>true</detectLinks>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself. -->
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.5.3</version>
</plugin>
</plugins>