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Merge pull request '[main] Rest collector plugin on hadoop supports a new param to pass request headers' (#467) from rest-collector-request-header-map2 into main 

Reviewed-on: #467
This commit is contained in:
Claudio Atzori 2024-08-05 09:34:24 +02:00
parent e0f58afd30 97c9706469
commit 5fc413a5df
6 changed files with 107 additions and 42 deletions
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26
dhp-common/pom.xml
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@ -70,10 +70,7 @@
<groupId>com.ibm.icu</groupId>
<artifactId>icu4j</artifactId>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-common</artifactId>
</dependency>
<dependency>
<groupId>com.github.sisyphsu</groupId>
<artifactId>dateparser</artifactId>
@ -163,7 +160,7 @@
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>${dhp-schemas.artifact}</artifactId>
<artifactId>dhp-schemas</artifactId>
</dependency>
<dependency>
@ -172,4 +169,23 @@
</dependency>
</dependencies>
<!-- dependencies required on JDK9+ because J2EE has been removed -->
<profiles>
<profile>
<id>spark-34</id>
<dependencies>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.2.11</version>
</dependency>
<dependency>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-ri</artifactId>
<version>2.3.3</version>
<type>pom</type>
</dependency>
</dependencies>
</profile>
</profiles>
</project>

12
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestCollectorPlugin.java
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@ -1,6 +1,7 @@
package eu.dnetlib.dhp.collection.plugin.rest;
import java.util.Map;
import java.util.Optional;
import java.util.Spliterator;
import java.util.Spliterators;
@ -9,6 +10,8 @@ import java.util.stream.StreamSupport;
import org.apache.commons.lang3.StringUtils;
import com.google.gson.Gson;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
@ -47,6 +50,9 @@ public class RestCollectorPlugin implements CollectorPlugin {
final String entityXpath = api.getParams().get("entityXpath");
final String authMethod = api.getParams().get("authMethod");
final String authToken = api.getParams().get("authToken");
final String requestHeaderMap = api.getParams().get("requestHeaderMap");
Gson gson = new Gson();
Map requestHeaders = gson.fromJson(requestHeaderMap, Map.class);
final String resultSizeValue = Optional
.ofNullable(api.getParams().get("resultSizeValue"))
.filter(StringUtils::isNotBlank)
@ -64,9 +70,6 @@ public class RestCollectorPlugin implements CollectorPlugin {
if (StringUtils.isBlank(resultFormatValue)) {
throw new CollectorException("Param 'resultFormatValue' is null or empty");
}
if (StringUtils.isBlank(queryParams)) {
throw new CollectorException("Param 'queryParams' is null or empty");
}
if (StringUtils.isBlank(entityXpath)) {
throw new CollectorException("Param 'entityXpath' is null or empty");
}
@ -92,7 +95,8 @@ public class RestCollectorPlugin implements CollectorPlugin {
entityXpath,
authMethod,
authToken,
resultOutputFormat);
resultOutputFormat,
requestHeaders);
return StreamSupport
.stream(

62
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
View File

@ -9,6 +9,7 @@ import java.net.URL;
import java.net.URLEncoder;
import java.nio.charset.StandardCharsets;
import java.util.Iterator;
import java.util.Map;
import java.util.Queue;
import java.util.concurrent.PriorityBlockingQueue;
@ -34,6 +35,8 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
@ -55,7 +58,7 @@ public class RestIterator implements Iterator<String> {
private final HttpClientParams clientParams;
private final String BASIC = "basic";
private final String AUTHBASIC = "basic";
private final String baseUrl;
private final String resumptionType;
@ -89,6 +92,11 @@ public class RestIterator implements Iterator<String> {
*/
private final String resultOutputFormat;
/*
* Can be used to set additional request headers, like for content negotiation
*/
private Map<String, String> requestHeaders;
/**
* RestIterator class compatible to version 1.3.33
*/
@ -107,7 +115,8 @@ public class RestIterator implements Iterator<String> {
final String entityXpath,
final String authMethod,
final String authToken,
final String resultOutputFormat) {
final String resultOutputFormat,
final Map<String, String> requestHeaders) {
this.clientParams = clientParams;
this.baseUrl = baseUrl;
@ -119,6 +128,7 @@ public class RestIterator implements Iterator<String> {
this.authMethod = authMethod;
this.authToken = authToken;
this.resultOutputFormat = resultOutputFormat;
this.requestHeaders = requestHeaders != null ? requestHeaders : Maps.newHashMap();
this.queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue
: "";
@ -231,25 +241,20 @@ public class RestIterator implements Iterator<String> {
final URL qUrl = new URL(query);
log.debug("authMethod: {}", this.authMethod);
if ("bearer".equalsIgnoreCase(this.authMethod)) {
log.trace("authMethod before inputStream: {}", resultXml);
final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + this.authToken);
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.getMimeType());
conn.setRequestMethod("GET");
theHttpInputStream = conn.getInputStream();
} else if (this.BASIC.equalsIgnoreCase(this.authMethod)) {
log.trace("authMethod before inputStream: {}", resultXml);
final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Basic " + this.authToken);
conn.setRequestProperty(HttpHeaders.ACCEPT, ContentType.APPLICATION_XML.getMimeType());
conn.setRequestMethod("GET");
theHttpInputStream = conn.getInputStream();
} else {
theHttpInputStream = qUrl.openStream();
if (this.authMethod == "bearer") {
log.trace("RestIterator.downloadPage():: authMethod before inputStream: " + resultXml);
requestHeaders.put("Authorization", "Bearer " + authToken);
// requestHeaders.put("Content-Type", "application/json");
} else if (AUTHBASIC.equalsIgnoreCase(this.authMethod)) {
log.trace("RestIterator.downloadPage():: authMethod before inputStream: " + resultXml);
requestHeaders.put("Authorization", "Basic " + authToken);
// requestHeaders.put("accept", "application/xml");
}
HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
conn.setRequestMethod("GET");
this.setRequestHeader(conn);
resultStream = conn.getInputStream();
this.resultStream = theHttpInputStream;
if ("json".equals(this.resultOutputFormat)) {
resultJson = IOUtils.toString(this.resultStream, StandardCharsets.UTF_8);
resultXml = JsonUtils.convertToXML(resultJson);
@ -380,7 +385,8 @@ public class RestIterator implements Iterator<String> {
try {
if (this.resultTotal == -1) {
this.resultTotal = Integer.parseInt(this.xprResultTotalPath.evaluate(resultNode));
if ("page".equalsIgnoreCase(this.resumptionType) && !this.BASIC.equalsIgnoreCase(this.authMethod)) {
if ("page".equalsIgnoreCase(this.resumptionType)
&& !this.AUTHBASIC.equalsIgnoreCase(this.authMethod)) {
this.resultTotal += 1;
} // to correct the upper bound
log.info("resultTotal was -1 is now: " + this.resultTotal);
@ -433,6 +439,22 @@ public class RestIterator implements Iterator<String> {
}
}
/**
* setRequestHeader
*
* setRequestProperty: Sets the general request property. If a property with the key already exists, overwrite its value with the new value.
* @param conn
*/
private void setRequestHeader(HttpURLConnection conn) {
if (requestHeaders != null) {
for (String key : requestHeaders.keySet()) {
conn.setRequestProperty(key, requestHeaders.get(key));
}
log.debug("Set Request Header with: " + requestHeaders);
}
}
public String getResultFormatValue() {
return this.resultFormatValue;
}

6
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java
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@ -39,8 +39,8 @@ public class OsfPreprintCollectorTest {
private final String resumptionType = "page";
private final String resumptionXpath = "/*/*[local-name()='links']/*[local-name()='next']";
private final String resultSizeParam = "";
private final String resultSizeValue = "";
private final String resultSizeParam = "page[size]";
private final String resultSizeValue = "100";
private final String resultFormatParam = "format";
private final String resultFormatValue = "json";
@ -74,7 +74,7 @@ public class OsfPreprintCollectorTest {
final AtomicInteger i = new AtomicInteger(0);
final Stream<String> stream = this.rcp.collect(this.api, new AggregatorReport());
stream.limit(200).forEach(s -> {
stream.limit(2000).forEach(s -> {
Assertions.assertTrue(s.length() > 0);
i.incrementAndGet();
log.info(s);

41
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/RestCollectorPluginTest.java
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@ -4,6 +4,11 @@
package eu.dnetlib.dhp.collection.plugin.rest;
import java.io.IOException;
import java.io.InputStream;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.HashMap;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Stream;
@ -12,6 +17,8 @@ import org.junit.jupiter.api.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.gson.Gson;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
@ -25,18 +32,18 @@ class RestCollectorPluginTest {
private static final Logger log = LoggerFactory.getLogger(RestCollectorPluginTest.class);
private final String baseUrl = "https://share.osf.io/api/v2/search/creativeworks/_search";
private final String resumptionType = "count";
private final String resumptionParam = "from";
private final String entityXpath = "//hits/hits";
private final String resumptionXpath = "//hits";
private final String resultTotalXpath = "//hits/total";
private final String resultFormatParam = "format";
private final String baseUrl = "https://ddh-openapi.worldbank.org/search";
private final String resumptionType = "discover";
private final String resumptionParam = "skip";
private final String entityXpath = "//*[local-name()='data']";
private final String resumptionXpath = "";
private final String resultTotalXpath = "//*[local-name()='count']";
private final String resultFormatParam = "";
private final String resultFormatValue = "json";
private final String resultSizeParam = "size";
private final String resultSizeParam = "top";
private final String resultSizeValue = "10";
// private String query = "q=%28sources%3ASocArXiv+AND+type%3Apreprint%29";
private final String query = "q=%28sources%3AengrXiv+AND+type%3Apreprint%29";
private final String query = "";
// private String query = "=(sources:engrXiv AND type:preprint)";
private final String protocolDescriptor = "rest_json2xml";
@ -56,6 +63,7 @@ class RestCollectorPluginTest {
params.put("resultSizeValue", resultSizeValue);
params.put("queryParams", query);
params.put("entityXpath", entityXpath);
params.put("requestHeaderMap", "{\"User-Agent\": \"OpenAIRE DEV\"}");
api.setBaseUrl(baseUrl);
api.setParams(params);
@ -78,4 +86,19 @@ class RestCollectorPluginTest {
log.info("{}", i.intValue());
Assertions.assertTrue(i.intValue() > 0);
}
@Disabled
@Test
void testUrl() throws IOException {
String url_s = "https://ddh-openapi.worldbank.org/search?&top=10";
URL url = new URL(url_s);
final HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestMethod("GET");
conn.setRequestProperty("User-Agent", "OpenAIRE");
Gson gson = new Gson();
System.out.println("Request header");
System.out.println(gson.toJson(conn.getHeaderFields()));
InputStream inputStream = conn.getInputStream();
}
}

2
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/RestIteratorTest.java
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@ -44,7 +44,7 @@ public class RestIteratorTest {
final RestIterator iterator = new RestIterator(clientParams, baseUrl, resumptionType, resumptionParam,
resumptionXpath, resultTotalXpath, resultFormatParam, resultFormatValue, resultSizeParam, resultSizeValue,
query, entityXpath, authMethod, authToken, resultOffsetParam);
query, entityXpath, authMethod, authToken, resultOffsetParam, null);
int i = 20;
while (iterator.hasNext() && i > 0) {
String result = iterator.next();