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Merge pull request 'aggregation_on_hadoop' (#90) from sandro.labruzzo/dnet-hadoop:aggregation_on_hadoop into hadoop_aggregator 

Wonderfull code... You're the Best Sandro
This commit is contained in:
Sandro La Bruzzo 2021-01-26 16:00:47 +01:00
parent f1a852f278 a54848a59c
commit 150a617bd1
24 changed files with 136 additions and 426 deletions
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2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java → dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
package eu.dnetlib.dhp.common.vocabulary;
import java.io.Serializable;
import java.util.HashMap;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java → dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
package eu.dnetlib.dhp.common.vocabulary;
import java.io.Serializable;
import java.util.*;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyTerm.java → dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyTerm.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
package eu.dnetlib.dhp.common.vocabulary;
import java.io.Serializable;

31
dhp-workflows/dhp-aggregation/README.md
View File

@ -2,28 +2,15 @@ Description of the Module
--------------------------
This module defines a **collector worker application** that runs on Hadoop.
It is responsible for harvesting metadata using different plugins.
It is responsible for harvesting metadata using different collector plugins and transformation into the common metadata model.
The collector worker uses a message queue to inform the progress
of the harvesting action (using a message queue for sending **ONGOING** messages) furthermore,
It gives, at the end of the job, some information about the status
of the collection i.e Number of records collected(using a message queue for sending **REPORT** messages).
To work the collection worker need some parameter like:
* **hdfsPath**: the path where storing the sequential file
* **apidescriptor**: the JSON encoding of the API Descriptor
* **namenode**: the Name Node URI
* **userHDFS**: the user wich create the hdfs seq file
* **rabbitUser**: the user to connect with RabbitMq for messaging
* **rabbitPassWord**: the password to connect with RabbitMq for messaging
* **rabbitHost**: the host of the RabbitMq server
* **rabbitOngoingQueue**: the name of the ongoing queue
* **rabbitReportQueue**: the name of the report queue
* **workflowId**: the identifier of the dnet Workflow
##Plugins
# Collector Plugins
* OAI Plugin
## Usage
TODO
# Transformation Plugins
TODO
# Usage
TODO

20
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/CollectorPluginErrorLogList.java
View File

@ -1,20 +0,0 @@
package eu.dnetlib.dhp.actionmanager.project.httpconnector;
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 (String errorMessage : this) {
log += String.format("Retry #%s: %s / ", index++, errorMessage);
}
return log;
}
}

20
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/CollectorServiceException.java
View File

@ -1,20 +0,0 @@
package eu.dnetlib.dhp.actionmanager.project.httpconnector;
public class CollectorServiceException extends Exception {
private static final long serialVersionUID = 7523999812098059764L;
public CollectorServiceException(String string) {
super(string);
}
public CollectorServiceException(String string, Throwable exception) {
super(string, exception);
}
public CollectorServiceException(Throwable exception) {
super(exception);
}
}

240
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnector.java
View File

@ -1,240 +0,0 @@
package eu.dnetlib.dhp.actionmanager.project.httpconnector;
import java.io.IOException;
import java.io.InputStream;
import java.net.*;
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.lang3.math.NumberUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
/**
* @author jochen, michele, andrea
*/
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 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 CollectorServiceException {
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 CollectorServiceException {
return attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList());
}
private String attemptDownlaodAsString(final String requestUrl, final int retryNumber,
final CollectorPluginErrorLogList errorList)
throws CollectorServiceException {
try {
InputStream s = attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList());
try {
return IOUtils.toString(s);
} catch (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 (InterruptedException e) {
throw new CollectorServiceException(e);
}
}
private InputStream attemptDownload(final String requestUrl, final int retryNumber,
final CollectorPluginErrorLogList errorList)
throws CollectorServiceException {
if (retryNumber > maxNumberOfRetry) {
throw new CollectorServiceException("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);
}
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 (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 (InterruptedException e) {
throw new CollectorServiceException(e);
}
}
private void logHeaderFields(final HttpURLConnection urlConn) throws IOException {
log.debug("StatusCode: " + urlConn.getResponseMessage());
for (Map.Entry<String, List<String>> e : urlConn.getHeaderFields().entrySet()) {
if (e.getKey() != null) {
for (String v : e.getValue()) {
log.debug(" key: " + e.getKey() + " - value: " + v);
}
}
}
}
private int obtainRetryAfter(final Map<String, List<String>> headerMap) {
for (String key : headerMap.keySet()) {
if ((key != null) && key.toLowerCase().equals("retry-after") && (headerMap.get(key).size() > 0)
&& NumberUtils.isCreatable(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 CollectorServiceException {
for (String key : headerMap.keySet()) {
if ((key != null) && key.toLowerCase().equals("location") && (headerMap.get(key).size() > 0)) {
return headerMap.get(key).get(0);
}
}
throw new CollectorServiceException("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 (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;
}
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java
View File

@ -17,7 +17,7 @@ import org.apache.hadoop.fs.Path;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.project.httpconnector.HttpConnector;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
/**

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java
View File

@ -4,6 +4,7 @@ package eu.dnetlib.dhp.actionmanager.project.utils;
import java.io.*;
import java.nio.charset.StandardCharsets;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -14,7 +15,7 @@ import org.apache.hadoop.fs.Path;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.project.httpconnector.HttpConnector;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
/**

198
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java
View File

@ -43,6 +43,106 @@ public class GenerateNativeStoreSparkJob {
private static final Logger log = LoggerFactory.getLogger(GenerateNativeStoreSparkJob.class);
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
GenerateNativeStoreSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/collection/collection_input_parameters.json")));
parser.parseArgument(args);
final ObjectMapper jsonMapper = new ObjectMapper();
final Provenance provenance = jsonMapper.readValue(parser.get("provenance"), Provenance.class);
final long dateOfCollection = new Long(parser.get("dateOfCollection"));
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final Map<String, String> ongoingMap = new HashMap<>();
final Map<String, String> reportMap = new HashMap<>();
final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final JavaPairRDD<IntWritable, Text> inputRDD = sc
.sequenceFile(parser.get("input"), IntWritable.class, Text.class);
final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems");
final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords");
final MessageManager manager = new MessageManager(
parser.get("rabbitHost"),
parser.get("rabbitUser"),
parser.get("rabbitPassword"),
false,
false,
null);
final JavaRDD<MetadataRecord> mappeRDD = inputRDD
.map(
item -> parseRecord(
item._2().toString(),
parser.get("xpath"),
parser.get("encoding"),
provenance,
dateOfCollection,
totalItems,
invalidRecords))
.filter(Objects::nonNull)
.distinct();
ongoingMap.put("ongoing", "0");
if (!test) {
manager
.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mdstore = spark.createDataset(mappeRDD.rdd(), encoder);
final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords");
mdStoreRecords.add(mdstore.count());
ongoingMap.put("ongoing", "" + totalItems.value());
if (!test) {
manager
.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
mdstore.write().format("parquet").save(parser.get("output"));
reportMap.put("inputItem", "" + totalItems.value());
reportMap.put("invalidRecords", "" + invalidRecords.value());
reportMap.put("mdStoreSize", "" + mdStoreRecords.value());
if (!test) {
manager
.sendMessage(
new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
parser.get("rabbitReportQueue"),
true,
false);
manager.close();
}
});
}
public static MetadataRecord parseRecord(
final String input,
final String xpath,
@ -73,103 +173,5 @@ public class GenerateNativeStoreSparkJob {
}
}
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
GenerateNativeStoreSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/collection/collection_input_parameters.json")));
parser.parseArgument(args);
final ObjectMapper jsonMapper = new ObjectMapper();
final Provenance provenance = jsonMapper.readValue(parser.get("provenance"), Provenance.class);
final long dateOfCollection = new Long(parser.get("dateOfCollection"));
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final Map<String, String> ongoingMap = new HashMap<>();
final Map<String, String> reportMap = new HashMap<>();
final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final JavaPairRDD<IntWritable, Text> inputRDD = sc
.sequenceFile(parser.get("input"), IntWritable.class, Text.class);
final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems");
final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords");
final MessageManager manager = new MessageManager(
parser.get("rabbitHost"),
parser.get("rabbitUser"),
parser.get("rabbitPassword"),
false,
false,
null);
final JavaRDD<MetadataRecord> mappeRDD = inputRDD
.map(
item -> parseRecord(
item._2().toString(),
parser.get("xpath"),
parser.get("encoding"),
provenance,
dateOfCollection,
totalItems,
invalidRecords))
.filter(Objects::nonNull)
.distinct();
ongoingMap.put("ongoing", "0");
if (!test) {
manager
.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mdstore = spark.createDataset(mappeRDD.rdd(), encoder);
final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords");
mdStoreRecords.add(mdstore.count());
ongoingMap.put("ongoing", "" + totalItems.value());
if (!test) {
manager
.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
mdstore.write().format("parquet").save(parser.get("output"));
reportMap.put("inputItem", "" + totalItems.value());
reportMap.put("invalidRecords", "" + invalidRecords.value());
reportMap.put("mdStoreSize", "" + mdStoreRecords.value());
if (!test) {
manager
.sendMessage(
new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
parser.get("rabbitReportQueue"),
true,
false);
manager.close();
}
});
}
}

7
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java
View File

@ -6,14 +6,15 @@ import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.actionmanager.project.httpconnector.CollectorServiceException;
import eu.dnetlib.dhp.actionmanager.project.httpconnector.HttpConnector;
import eu.dnetlib.dhp.actionmanager.project.utils.EXCELParser;
@Disabled
@ -30,7 +31,7 @@ public class EXCELParserTest {
}
@Test
public void test1() throws CollectorServiceException, IOException, InvalidFormatException, ClassNotFoundException,
public void test1() throws DnetCollectorException, IOException, InvalidFormatException, ClassNotFoundException,
IllegalAccessException, InstantiationException {
EXCELParser excelParser = new EXCELParser();

6
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java
View File

@ -1,6 +1,8 @@
package eu.dnetlib.dhp.actionmanager.project.httpconnector;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.http.conn.ssl.SSLConnectionSocketFactory;
@ -29,12 +31,12 @@ public class HttpConnectorTest {
@Test
public void testGetInputSource() throws CollectorServiceException {
public void testGetInputSource() throws DnetCollectorException {
System.out.println(connector.getInputSource(URL));
}
@Test
public void testGoodServers() throws CollectorServiceException {
public void testGoodServers() throws DnetCollectorException {
System.out.println(connector.getInputSource(URL_GOODSNI_SERVER));
}

4
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/ext_simple.xsl
View File

@ -1,7 +1,7 @@
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:oai="http://www.openarchives.org/OAI/2.0/"
xmlns:oaf="http://namespace.openaire.eu/oaf"
xmlns:eg="http://eu/dnetlib/trasform/extension"
xmlns:dnetFunction="http://eu/dnetlib/trasform/extension"
version="2.0"
exclude-result-prefixes="xsl">
<xsl:template match="/">
@ -9,7 +9,7 @@
<xsl:copy-of select="//oai:header"/>
<metadata>
<xsl:for-each select="//*[local-name()='subject']">
<subject><xsl:value-of select="eg:clean(.,'dnet:languages')"/></subject>
<subject><xsl:value-of select="dnetFunction:clean(.,'dnet:languages')"/></subject>
</xsl:for-each>
</metadata>
<oaf:about>

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java
View File

@ -21,7 +21,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java
View File

@ -7,7 +7,7 @@ import java.util.HashMap;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableConsumer;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Qualifier;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -38,7 +38,7 @@ import org.dom4j.DocumentFactory;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.LicenseComparator;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Author;

5
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
View File

@ -3,7 +3,6 @@ package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
@ -12,8 +11,6 @@ import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
@ -27,7 +24,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
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@ -57,7 +57,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.DbClient;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.oa.graph.raw.common.VerifyNsPrefixPredicate;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
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@ -18,7 +18,7 @@ import org.dom4j.Node;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.common.PacePerson;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Field;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
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@ -19,7 +19,7 @@ import org.dom4j.Node;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.common.PacePerson;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Field;

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java
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@ -18,7 +18,7 @@ import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Result;

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java
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@ -16,7 +16,7 @@ import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
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@ -22,7 +22,7 @@ import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Dataset;

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java
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@ -27,7 +27,7 @@ import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.*;
@ExtendWith(MockitoExtension.class)