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dnet-hadoop
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fix conflicts

This commit is contained in:
Sandro La Bruzzo 2021-03-22 16:36:31 +01:00
parent 098914dcff 61a2551e74
commit c73072079d
149 changed files with 12924 additions and 2337 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
.gitignore vendored
View File

@ -7,6 +7,8 @@
*.iws
*~
.vscode
.metals
.bloop
.classpath
/*/.classpath
/*/*/.classpath
@ -24,4 +26,5 @@
spark-warehouse
/**/job-override.properties
/**/*.log
/**/.factorypath

29
dhp-common/pom.xml
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@ -6,7 +6,8 @@
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.2.4-SNAPSHOT</version>
<relativePath>../</relativePath>
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>dhp-common</artifactId>
@ -29,12 +30,6 @@
<artifactId>spark-sql_2.11</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
@ -59,11 +54,6 @@
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/com.rabbitmq/amqp-client -->
<dependency>
<groupId>com.rabbitmq</groupId>
<artifactId>amqp-client</artifactId>
</dependency>
<dependency>
<groupId>net.sf.saxon</groupId>
<artifactId>Saxon-HE</artifactId>
@ -104,6 +94,21 @@
<artifactId>dnet-pace-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
</dependency>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>mongo-java-driver</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>

71
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStore.java
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@ -2,12 +2,16 @@
package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import java.util.Date;
import java.util.Objects;
import java.util.UUID;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
@Entity
@Table(name = "mdstores")
@ -38,6 +42,13 @@ public class MDStore implements Serializable {
@Column(name = "api_id")
private String apiId;
@Column(name = "hdfs_path")
private String hdfsPath;
@Column(name = "creation_date")
@Temporal(TemporalType.TIMESTAMP)
private Date creationDate;
public String getId() {
return id;
}
@ -94,9 +105,28 @@ public class MDStore implements Serializable {
this.apiId = apiId;
}
public String getHdfsPath() {
return hdfsPath;
}
public void setHdfsPath(final String hdfsPath) {
this.hdfsPath = hdfsPath;
}
public Date getCreationDate() {
return creationDate;
}
public void setCreationDate(final Date creationDate) {
this.creationDate = creationDate;
}
public static MDStore newInstance(
final String format, final String layout, final String interpretation) {
return newInstance(format, layout, interpretation, null, null, null);
final String format,
final String layout,
final String interpretation,
final String hdfsBasePath) {
return newInstance(format, layout, interpretation, null, null, null, hdfsBasePath);
}
public static MDStore newInstance(
@ -105,15 +135,48 @@ public class MDStore implements Serializable {
final String interpretation,
final String dsName,
final String dsId,
final String apiId) {
final String apiId,
final String hdfsBasePath) {
final String mdId = "md-" + UUID.randomUUID();
final MDStore md = new MDStore();
md.setId("md-" + UUID.randomUUID());
md.setId(mdId);
md.setFormat(format);
md.setLayout(layout);
md.setInterpretation(interpretation);
md.setCreationDate(new Date());
md.setDatasourceName(dsName);
md.setDatasourceId(dsId);
md.setApiId(apiId);
md.setHdfsPath(String.format("%s/%s", hdfsBasePath, mdId));
return md;
}
@Override
public String toString() {
return String
.format(
"MDStore [id=%s, format=%s, layout=%s, interpretation=%s, datasourceName=%s, datasourceId=%s, apiId=%s, hdfsPath=%s, creationDate=%s]",
id, format, layout, interpretation, datasourceName, datasourceId, apiId, hdfsPath, creationDate);
}
@Override
public int hashCode() {
return Objects.hash(id);
}
@Override
public boolean equals(final Object obj) {
if (this == obj) {
return true;
}
if (!(obj instanceof MDStore)) {
return false;
}
final MDStore other = (MDStore) obj;
return Objects.equals(id, other.id);
}
}

23
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreCurrentVersion.java
View File

@ -2,6 +2,7 @@
package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import java.util.Objects;
import javax.persistence.Column;
import javax.persistence.Entity;
@ -48,4 +49,26 @@ public class MDStoreCurrentVersion implements Serializable {
public static MDStoreCurrentVersion newInstance(final MDStoreVersion v) {
return newInstance(v.getMdstore(), v.getId());
}
@Override
public String toString() {
return String.format("MDStoreCurrentVersion [mdstore=%s, currentVersion=%s]", mdstore, currentVersion);
}
@Override
public int hashCode() {
return Objects.hash(currentVersion, mdstore);
}
@Override
public boolean equals(final Object obj) {
if (this == obj) {
return true;
}
if (!(obj instanceof MDStoreCurrentVersion)) {
return false;
}
final MDStoreCurrentVersion other = (MDStoreCurrentVersion) obj;
return Objects.equals(currentVersion, other.currentVersion) && Objects.equals(mdstore, other.mdstore);
}
}

59
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreVersion.java
View File

@ -3,6 +3,7 @@ package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import java.util.Date;
import java.util.Objects;
import javax.persistence.Column;
import javax.persistence.Entity;
@ -38,15 +39,22 @@ public class MDStoreVersion implements Serializable {
@Column(name = "size")
private long size = 0;
public static MDStoreVersion newInstance(final String mdId, final boolean writing) {
final MDStoreVersion t = new MDStoreVersion();
t.setId(mdId + "-" + new Date().getTime());
t.setMdstore(mdId);
t.setLastUpdate(null);
t.setWriting(writing);
t.setReadCount(0);
t.setSize(0);
return t;
@Column(name = "hdfs_path")
private String hdfsPath;
public static MDStoreVersion newInstance(final String mdId, final boolean writing, final String hdfsBasePath) {
final MDStoreVersion v = new MDStoreVersion();
final String versionId = mdId + "-" + new Date().getTime();
v.setId(versionId);
v.setMdstore(mdId);
v.setLastUpdate(null);
v.setWriting(writing);
v.setReadCount(0);
v.setSize(0);
v.setHdfsPath(String.format("%s/%s/%s", hdfsBasePath, mdId, versionId));
return v;
}
public String getId() {
@ -96,4 +104,37 @@ public class MDStoreVersion implements Serializable {
public void setSize(final long size) {
this.size = size;
}
public String getHdfsPath() {
return hdfsPath;
}
public void setHdfsPath(final String hdfsPath) {
this.hdfsPath = hdfsPath;
}
@Override
public String toString() {
return String
.format(
"MDStoreVersion [id=%s, mdstore=%s, writing=%s, readCount=%s, lastUpdate=%s, size=%s, hdfsPath=%s]", id,
mdstore, writing, readCount, lastUpdate, size, hdfsPath);
}
@Override
public int hashCode() {
return Objects.hash(id);
}
@Override
public boolean equals(final Object obj) {
if (this == obj) {
return true;
}
if (!(obj instanceof MDStoreVersion)) {
return false;
}
final MDStoreVersion other = (MDStoreVersion) obj;
return Objects.equals(id, other.id);
}
}

51
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreWithInfo.java
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@ -3,6 +3,7 @@ package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import java.util.Date;
import java.util.Objects;
import javax.persistence.Column;
import javax.persistence.Entity;
@ -43,6 +44,10 @@ public class MDStoreWithInfo implements Serializable {
@Column(name = "current_version")
private String currentVersion;
@Column(name = "creation_date")
@Temporal(TemporalType.TIMESTAMP)
private Date creationDate;
@Column(name = "lastupdate")
@Temporal(TemporalType.TIMESTAMP)
private Date lastUpdate;
@ -53,6 +58,9 @@ public class MDStoreWithInfo implements Serializable {
@Column(name = "n_versions")
private long numberOfVersions = 0;
@Column(name = "hdfs_path")
private String hdfsPath;
public String getId() {
return id;
}
@ -117,6 +125,14 @@ public class MDStoreWithInfo implements Serializable {
this.currentVersion = currentVersion;
}
public Date getCreationDate() {
return creationDate;
}
public void setCreationDate(final Date creationDate) {
this.creationDate = creationDate;
}
public Date getLastUpdate() {
return lastUpdate;
}
@ -140,4 +156,39 @@ public class MDStoreWithInfo implements Serializable {
public void setNumberOfVersions(final long numberOfVersions) {
this.numberOfVersions = numberOfVersions;
}
public String getHdfsPath() {
return hdfsPath;
}
public void setHdfsPath(final String hdfsPath) {
this.hdfsPath = hdfsPath;
}
@Override
public String toString() {
return String
.format(
"MDStoreWithInfo [id=%s, format=%s, layout=%s, interpretation=%s, datasourceName=%s, datasourceId=%s, apiId=%s, currentVersion=%s, creationDate=%s, lastUpdate=%s, size=%s, numberOfVersions=%s, hdfsPath=%s]",
id, format, layout, interpretation, datasourceName, datasourceId, apiId, currentVersion, creationDate,
lastUpdate, size, numberOfVersions, hdfsPath);
}
@Override
public int hashCode() {
return Objects.hash(id);
}
@Override
public boolean equals(final Object obj) {
if (this == obj) {
return true;
}
if (!(obj instanceof MDStoreWithInfo)) {
return false;
}
final MDStoreWithInfo other = (MDStoreWithInfo) obj;
return Objects.equals(id, other.id);
}
}

14
dhp-common/src/main/java/eu/dnetlib/dhp/application/ApplicationUtils.java Normal file
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@ -0,0 +1,14 @@
package eu.dnetlib.dhp.application;
import java.io.*;
import java.util.Map;
import java.util.Properties;
import org.apache.hadoop.conf.Configuration;
import com.google.common.collect.Maps;
public class ApplicationUtils {
}

20
dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java
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@ -1,10 +1,7 @@
package eu.dnetlib.dhp.application;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.Serializable;
import java.io.StringWriter;
import java.io.*;
import java.util.*;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
@ -12,17 +9,21 @@ import java.util.zip.GZIPOutputStream;
import org.apache.commons.cli.*;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
public class ArgumentApplicationParser implements Serializable {
private static final Logger log = LoggerFactory.getLogger(ArgumentApplicationParser.class);
private final Options options = new Options();
private final Map<String, String> objectMap = new HashMap<>();
private final List<String> compressedValues = new ArrayList<>();
public ArgumentApplicationParser(final String json_configuration) throws Exception {
public ArgumentApplicationParser(final String json_configuration) throws IOException {
final ObjectMapper mapper = new ObjectMapper();
final OptionsParameter[] configuration = mapper.readValue(json_configuration, OptionsParameter[].class);
createOptionMap(configuration);
@ -33,7 +34,6 @@ public class ArgumentApplicationParser implements Serializable {
}
private void createOptionMap(final OptionsParameter[] configuration) {
Arrays
.stream(configuration)
.map(
@ -47,10 +47,6 @@ public class ArgumentApplicationParser implements Serializable {
return o;
})
.forEach(options::addOption);
// HelpFormatter formatter = new HelpFormatter();
// formatter.printHelp("myapp", null, options, null, true);
}
public static String decompressValue(final String abstractCompressed) {
@ -61,7 +57,7 @@ public class ArgumentApplicationParser implements Serializable {
IOUtils.copy(gis, stringWriter);
return stringWriter.toString();
} catch (Throwable e) {
System.out.println("Wrong value to decompress:" + abstractCompressed);
log.error("Wrong value to decompress:" + abstractCompressed);
throw new RuntimeException(e);
}
}
@ -74,7 +70,7 @@ public class ArgumentApplicationParser implements Serializable {
return java.util.Base64.getEncoder().encodeToString(out.toByteArray());
}
public void parseArgument(final String[] args) throws Exception {
public void parseArgument(final String[] args) throws ParseException {
CommandLineParser parser = new BasicParser();
CommandLine cmd = parser.parse(options, args);
Arrays

2
dhp-common/src/main/java/eu/dnetlib/collector/worker/model/ApiDescriptor.java → dhp-common/src/main/java/eu/dnetlib/dhp/collection/ApiDescriptor.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.collector.worker.model;
package eu.dnetlib.dhp.collection;
import java.util.HashMap;
import java.util.Map;

20
dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java
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@ -27,4 +27,24 @@ public class Constants {
coarCodeLabelMap.put("c_f1cf", "EMBARGO");
}
public static final String SEQUENCE_FILE_NAME = "/sequence_file";
public static final String REPORT_FILE_NAME = "/report";
public static final String MDSTORE_DATA_PATH = "/store";
public static final String MDSTORE_SIZE_PATH = "/size";
public static final String COLLECTION_MODE = "collectionMode";
public static final String METADATA_ENCODING = "metadataEncoding";
public static final String OOZIE_WF_PATH = "oozieWfPath";
public static final String DNET_MESSAGE_MGR_URL = "dnetMessageManagerURL";
public static final String MAX_NUMBER_OF_RETRY = "maxNumberOfRetry";
public static final String REQUEST_DELAY = "requestDelay";
public static final String RETRY_DELAY = "retryDelay";
public static final String CONNECT_TIMEOUT = "connectTimeOut";
public static final String READ_TIMEOUT = "readTimeOut";
public static final String CONTENT_TOTALITEMS = "TotalItems";
public static final String CONTENT_INVALIDRECORDS = "InvalidRecords";
public static final String CONTENT_TRANSFORMEDRECORDS = "transformedItems";
}

27
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MdstoreClient.java → dhp-common/src/main/java/eu/dnetlib/dhp/common/MdstoreClient.java
View File

@ -1,39 +1,60 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
package eu.dnetlib.dhp.common;
import java.io.Closeable;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
import java.util.stream.StreamSupport;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.bson.Document;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.collect.Iterables;
import com.mongodb.BasicDBObject;
import com.mongodb.MongoClient;
import com.mongodb.MongoClientURI;
import com.mongodb.QueryBuilder;
import com.mongodb.client.MongoCollection;
import com.mongodb.client.MongoDatabase;
public class MdstoreClient implements Closeable {
private static final Logger log = LoggerFactory.getLogger(MdstoreClient.class);
private final MongoClient client;
private final MongoDatabase db;
private static final String COLL_METADATA = "metadata";
private static final String COLL_METADATA_MANAGER = "metadataManager";
private static final Log log = LogFactory.getLog(MdstoreClient.class);
public MdstoreClient(final String baseUrl, final String dbName) {
this.client = new MongoClient(new MongoClientURI(baseUrl));
this.db = getDb(client, dbName);
}
public MongoCollection<Document> mdStore(final String mdId) {
BasicDBObject query = (BasicDBObject) QueryBuilder.start("mdId").is(mdId).get();
log.info("querying current mdId: {}", query.toJson());
final String currentId = Optional
.ofNullable(getColl(db, COLL_METADATA_MANAGER, true).find(query))
.map(r -> r.first())
.map(d -> d.getString("currentId"))
.orElseThrow(() -> new IllegalArgumentException("cannot find current mdstore id for: " + mdId));
log.info("currentId: {}", currentId);
return getColl(db, currentId, true);
}
public Map<String, String> validCollections(
final String mdFormat, final String mdLayout, final String mdInterpretation) {

72
dhp-common/src/main/java/eu/dnetlib/dhp/common/rest/DNetRestClient.java Normal file
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@ -0,0 +1,72 @@
package eu.dnetlib.dhp.common.rest;
import java.util.Arrays;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpUriRequest;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
public class DNetRestClient {
private static final Logger log = LoggerFactory.getLogger(DNetRestClient.class);
private static ObjectMapper mapper = new ObjectMapper();
public static <T> T doGET(final String url, Class<T> clazz) throws Exception {
final HttpGet httpGet = new HttpGet(url);
return doHTTPRequest(httpGet, clazz);
}
public static String doGET(final String url) throws Exception {
final HttpGet httpGet = new HttpGet(url);
return doHTTPRequest(httpGet);
}
public static <V> String doPOST(final String url, V objParam) throws Exception {
final HttpPost httpPost = new HttpPost(url);
if (objParam != null) {
final StringEntity entity = new StringEntity(mapper.writeValueAsString(objParam));
httpPost.setEntity(entity);
httpPost.setHeader("Accept", "application/json");
httpPost.setHeader("Content-type", "application/json");
}
return doHTTPRequest(httpPost);
}
public static <T, V> T doPOST(final String url, V objParam, Class<T> clazz) throws Exception {
return mapper.readValue(doPOST(url, objParam), clazz);
}
private static String doHTTPRequest(final HttpUriRequest r) throws Exception {
CloseableHttpClient client = HttpClients.createDefault();
log.info("performing HTTP request, method {} on URI {}", r.getMethod(), r.getURI().toString());
log
.info(
"request headers: {}",
Arrays
.asList(r.getAllHeaders())
.stream()
.map(h -> h.getName() + ":" + h.getValue())
.collect(Collectors.joining(",")));
CloseableHttpResponse response = client.execute(r);
return IOUtils.toString(response.getEntity().getContent());
}
private static <T> T doHTTPRequest(final HttpUriRequest r, Class<T> clazz) throws Exception {
return mapper.readValue(doHTTPRequest(r), clazz);
}
}

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;

30
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.*;
@ -67,6 +67,10 @@ public class VocabularyGroup implements Serializable {
private final Map<String, Vocabulary> vocs = new HashMap<>();
public Set<String> vocabularyNames() {
return vocs.keySet();
}
public void addVocabulary(final String id, final String name) {
vocs.put(id.toLowerCase(), new Vocabulary(id, name));
}
@ -118,7 +122,31 @@ public class VocabularyGroup implements Serializable {
return vocs.get(vocId.toLowerCase()).getSynonymAsQualifier(syn);
}
/**
* getSynonymAsQualifierCaseSensitive
*
* refelects the situation to check caseSensitive vocabulary
*/
public Qualifier getSynonymAsQualifierCaseSensitive(final String vocId, final String syn) {
if (StringUtils.isBlank(vocId)) {
return OafMapperUtils.unknown("", "");
}
return vocs.get(vocId).getSynonymAsQualifier(syn);
}
/**
* termExists
*
* two methods: without and with caseSensitive check
*/
public boolean termExists(final String vocId, final String id) {
return termExists(vocId, id, Boolean.FALSE);
}
public boolean termExists(final String vocId, final String id, final Boolean caseSensitive) {
if (Boolean.TRUE.equals(caseSensitive)) {
return vocabularyExists(vocId) && vocs.get(vocId).termExists(id);
}
return vocabularyExists(vocId) && vocs.get(vocId.toLowerCase()).termExists(id);
}

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;

64
dhp-common/src/main/java/eu/dnetlib/dhp/message/Message.java Normal file
View File

@ -0,0 +1,64 @@
package eu.dnetlib.dhp.message;
import java.io.Serializable;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;
public class Message implements Serializable {
private static final long serialVersionUID = 401753881204524893L;
public static String CURRENT_PARAM = "current";
public static String TOTAL_PARAM = "total";
private MessageType messageType;
private String workflowId;
private Map<String, String> body;
public Message() {
}
public Message(final MessageType messageType, final String workflowId) {
this(messageType, workflowId, new LinkedHashMap<>());
}
public Message(final MessageType messageType, final String workflowId, final Map<String, String> body) {
this.messageType = messageType;
this.workflowId = workflowId;
this.body = body;
}
public MessageType getMessageType() {
return messageType;
}
public void setMessageType(MessageType messageType) {
this.messageType = messageType;
}
public String getWorkflowId() {
return workflowId;
}
public void setWorkflowId(final String workflowId) {
this.workflowId = workflowId;
}
public Map<String, String> getBody() {
return body;
}
public void setBody(final Map<String, String> body) {
this.body = body;
}
@Override
public String toString() {
return String.format("Message [type=%s, workflowId=%s, body=%s]", messageType, workflowId, body);
}
}

94
dhp-common/src/main/java/eu/dnetlib/dhp/message/MessageSender.java Normal file
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@ -0,0 +1,94 @@
package eu.dnetlib.dhp.message;
import java.util.Map;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import org.apache.http.client.config.RequestConfig;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
public class MessageSender {
private static final Logger log = LoggerFactory.getLogger(MessageSender.class);
private static final int SOCKET_TIMEOUT_MS = 2000;
private static final int CONNECTION_REQUEST_TIMEOUT_MS = 2000;
private static final int CONNTECTION_TIMEOUT_MS = 2000;
private final ObjectMapper objectMapper = new ObjectMapper();
private final String dnetMessageEndpoint;
private final String workflowId;
private ExecutorService executorService = Executors.newCachedThreadPool();
public MessageSender(final String dnetMessageEndpoint, final String workflowId) {
this.workflowId = workflowId;
this.dnetMessageEndpoint = dnetMessageEndpoint;
}
public void sendMessage(final Message message) {
executorService.submit(() -> _sendMessage(message));
}
public void sendMessage(final Long current, final Long total) {
sendMessage(createOngoingMessage(current, total));
}
public void sendReport(final Map<String, String> report) {
sendMessage(new Message(MessageType.REPORT, workflowId, report));
}
private Message createOngoingMessage(final Long current, final Long total) {
final Message m = new Message(MessageType.ONGOING, workflowId);
m.getBody().put(Message.CURRENT_PARAM, current.toString());
if (total != null) {
m.getBody().put(Message.TOTAL_PARAM, total.toString());
}
return m;
}
private void _sendMessage(final Message message) {
try {
final String json = objectMapper.writeValueAsString(message);
final HttpPut req = new HttpPut(dnetMessageEndpoint);
req.setEntity(new StringEntity(json, ContentType.APPLICATION_JSON));
final RequestConfig requestConfig = RequestConfig
.custom()
.setConnectTimeout(CONNTECTION_TIMEOUT_MS)
.setConnectionRequestTimeout(CONNECTION_REQUEST_TIMEOUT_MS)
.setSocketTimeout(SOCKET_TIMEOUT_MS)
.build();
try (final CloseableHttpClient client = HttpClients
.custom()
.setDefaultRequestConfig(requestConfig)
.build();
final CloseableHttpResponse response = client.execute(req)) {
log.debug("Sent Message to " + dnetMessageEndpoint);
log.debug("MESSAGE:" + message);
} catch (final Throwable e) {
log.error("Error sending message to " + dnetMessageEndpoint + ", message content: " + message, e);
}
} catch (final JsonProcessingException e) {
log.error("Error sending message to " + dnetMessageEndpoint + ", message content: " + message, e);
}
}
}

21
dhp-common/src/main/java/eu/dnetlib/dhp/message/MessageType.java Normal file
View File

@ -0,0 +1,21 @@
package eu.dnetlib.dhp.message;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.lang3.StringUtils;
public enum MessageType implements Serializable {
ONGOING, REPORT;
public MessageType from(String value) {
return Optional
.ofNullable(value)
.map(StringUtils::upperCase)
.map(MessageType::valueOf)
.orElseThrow(() -> new IllegalArgumentException("unknown message type: " + value));
}
}

85
dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java
View File

@ -1,18 +1,29 @@
package eu.dnetlib.dhp.utils;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.*;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.codec.binary.Base64OutputStream;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.SaveMode;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Maps;
import com.jayway.jsonpath.JsonPath;
import net.minidev.json.JSONArray;
@ -21,6 +32,8 @@ import scala.collection.Seq;
public class DHPUtils {
private static final Logger log = LoggerFactory.getLogger(DHPUtils.class);
public static Seq<String> toSeq(List<String> list) {
return JavaConverters.asScalaIteratorConverter(list.iterator()).asScala().toSeq();
}
@ -79,4 +92,72 @@ public class DHPUtils {
return "";
}
}
public static final ObjectMapper MAPPER = new ObjectMapper();
public static void writeHdfsFile(final Configuration conf, final String content, final String path)
throws IOException {
log.info("writing file {}, size {}", path, content.length());
try (FileSystem fs = FileSystem.get(conf);
BufferedOutputStream os = new BufferedOutputStream(fs.create(new Path(path)))) {
os.write(content.getBytes(StandardCharsets.UTF_8));
os.flush();
}
}
public static String readHdfsFile(Configuration conf, String path) throws IOException {
log.info("reading file {}", path);
try (FileSystem fs = FileSystem.get(conf)) {
final Path p = new Path(path);
if (!fs.exists(p)) {
throw new FileNotFoundException(path);
}
return IOUtils.toString(fs.open(p));
}
}
public static <T> T readHdfsFileAs(Configuration conf, String path, Class<T> clazz) throws IOException {
return MAPPER.readValue(readHdfsFile(conf, path), clazz);
}
public static <T> void saveDataset(final Dataset<T> mdstore, final String targetPath) {
log.info("saving dataset in: {}", targetPath);
mdstore
.write()
.mode(SaveMode.Overwrite)
.format("parquet")
.save(targetPath);
}
public static Configuration getHadoopConfiguration(String nameNode) {
// ====== Init HDFS File System Object
Configuration conf = new Configuration();
// Set FileSystem URI
conf.set("fs.defaultFS", nameNode);
// 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.home.dir", "/");
return conf;
}
public static void populateOOZIEEnv(final Map<String, String> report) throws IOException {
File file = new File(System.getProperty("oozie.action.output.properties"));
Properties props = new Properties();
report.forEach((k, v) -> props.setProperty(k, v));
try (OutputStream os = new FileOutputStream(file)) {
props.store(os, "");
}
}
public static void populateOOZIEEnv(final String paramName, String value) throws IOException {
Map<String, String> report = Maps.newHashMap();
report.put(paramName, value);
populateOOZIEEnv(report);
}
}

76
dhp-common/src/main/java/eu/dnetlib/message/Message.java
View File

@ -1,76 +0,0 @@
package eu.dnetlib.message;
import java.io.IOException;
import java.util.Map;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
public class Message {
private String workflowId;
private String jobName;
private MessageType type;
private Map<String, String> body;
public static Message fromJson(final String json) throws IOException {
final ObjectMapper jsonMapper = new ObjectMapper();
return jsonMapper.readValue(json, Message.class);
}
public Message() {
}
public Message(String workflowId, String jobName, MessageType type, Map<String, String> body) {
this.workflowId = workflowId;
this.jobName = jobName;
this.type = type;
this.body = body;
}
public String getWorkflowId() {
return workflowId;
}
public void setWorkflowId(String workflowId) {
this.workflowId = workflowId;
}
public String getJobName() {
return jobName;
}
public void setJobName(String jobName) {
this.jobName = jobName;
}
public MessageType getType() {
return type;
}
public void setType(MessageType type) {
this.type = type;
}
public Map<String, String> getBody() {
return body;
}
public void setBody(Map<String, String> body) {
this.body = body;
}
@Override
public String toString() {
final ObjectMapper jsonMapper = new ObjectMapper();
try {
return jsonMapper.writeValueAsString(this);
} catch (JsonProcessingException e) {
return null;
}
}
}

47
dhp-common/src/main/java/eu/dnetlib/message/MessageConsumer.java
View File

@ -1,47 +0,0 @@
package eu.dnetlib.message;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.concurrent.LinkedBlockingQueue;
import com.rabbitmq.client.AMQP;
import com.rabbitmq.client.Channel;
import com.rabbitmq.client.DefaultConsumer;
import com.rabbitmq.client.Envelope;
public class MessageConsumer extends DefaultConsumer {
final LinkedBlockingQueue<Message> queueMessages;
/**
* Constructs a new instance and records its association to the passed-in channel.
*
* @param channel the channel to which this consumer is attached
* @param queueMessages
*/
public MessageConsumer(Channel channel, LinkedBlockingQueue<Message> queueMessages) {
super(channel);
this.queueMessages = queueMessages;
}
@Override
public void handleDelivery(
String consumerTag, Envelope envelope, AMQP.BasicProperties properties, byte[] body)
throws IOException {
final String json = new String(body, StandardCharsets.UTF_8);
Message message = Message.fromJson(json);
try {
this.queueMessages.put(message);
System.out.println("Receiving Message " + message);
} catch (InterruptedException e) {
if (message.getType() == MessageType.REPORT)
throw new RuntimeException("Error on sending message");
else {
// TODO LOGGING EXCEPTION
}
} finally {
getChannel().basicAck(envelope.getDeliveryTag(), false);
}
}
}

136
dhp-common/src/main/java/eu/dnetlib/message/MessageManager.java
View File

@ -1,136 +0,0 @@
package eu.dnetlib.message;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.TimeoutException;
import com.rabbitmq.client.Channel;
import com.rabbitmq.client.Connection;
import com.rabbitmq.client.ConnectionFactory;
public class MessageManager {
private final String messageHost;
private final String username;
private final String password;
private Connection connection;
private final Map<String, Channel> channels = new HashMap<>();
private boolean durable;
private boolean autodelete;
private final LinkedBlockingQueue<Message> queueMessages;
public MessageManager(
String messageHost,
String username,
String password,
final LinkedBlockingQueue<Message> queueMessages) {
this.queueMessages = queueMessages;
this.messageHost = messageHost;
this.username = username;
this.password = password;
}
public MessageManager(
String messageHost,
String username,
String password,
boolean durable,
boolean autodelete,
final LinkedBlockingQueue<Message> queueMessages) {
this.queueMessages = queueMessages;
this.messageHost = messageHost;
this.username = username;
this.password = password;
this.durable = durable;
this.autodelete = autodelete;
}
private Connection createConnection() throws IOException, TimeoutException {
ConnectionFactory factory = new ConnectionFactory();
factory.setHost(this.messageHost);
factory.setUsername(this.username);
factory.setPassword(this.password);
return factory.newConnection();
}
private Channel createChannel(
final Connection connection,
final String queueName,
final boolean durable,
final boolean autodelete)
throws Exception {
Map<String, Object> args = new HashMap<>();
args.put("x-message-ttl", 10000);
Channel channel = connection.createChannel();
channel.queueDeclare(queueName, durable, false, this.autodelete, args);
return channel;
}
private Channel getOrCreateChannel(final String queueName, boolean durable, boolean autodelete)
throws Exception {
if (channels.containsKey(queueName)) {
return channels.get(queueName);
}
if (this.connection == null) {
this.connection = createConnection();
}
channels.put(queueName, createChannel(this.connection, queueName, durable, autodelete));
return channels.get(queueName);
}
public void close() throws IOException {
channels
.values()
.forEach(
ch -> {
try {
ch.close();
} catch (Exception e) {
// TODO LOG
}
});
this.connection.close();
}
public boolean sendMessage(final Message message, String queueName) throws Exception {
try {
Channel channel = getOrCreateChannel(queueName, this.durable, this.autodelete);
channel.basicPublish("", queueName, null, message.toString().getBytes());
return true;
} catch (Throwable e) {
throw new RuntimeException(e);
}
}
public boolean sendMessage(
final Message message, String queueName, boolean durable_var, boolean autodelete_var)
throws Exception {
try {
Channel channel = getOrCreateChannel(queueName, durable_var, autodelete_var);
channel.basicPublish("", queueName, null, message.toString().getBytes());
return true;
} catch (Throwable e) {
throw new RuntimeException(e);
}
}
public void startConsumingMessage(
final String queueName, final boolean durable, final boolean autodelete) throws Exception {
Channel channel = createChannel(createConnection(), queueName, durable, autodelete);
channel.basicConsume(queueName, false, new MessageConsumer(channel, queueMessages));
}
}

6
dhp-common/src/main/java/eu/dnetlib/message/MessageType.java
View File

@ -1,6 +0,0 @@
package eu.dnetlib.message;
public enum MessageType {
ONGOING, REPORT
}

16
dhp-common/src/test/java/eu/dnetlib/dhp/model/mdstore/MetadataRecordTest.java
View File

@ -1,16 +0,0 @@
package eu.dnetlib.dhp.model.mdstore;
import static org.junit.jupiter.api.Assertions.assertTrue;
import org.junit.jupiter.api.Test;
public class MetadataRecordTest {
@Test
public void getTimestamp() {
MetadataRecord r = new MetadataRecord();
assertTrue(r.getDateOfCollection() > 0);
}
}

51
dhp-common/src/test/java/eu/dnetlib/message/MessageTest.java
View File

@ -1,51 +0,0 @@
package eu.dnetlib.message;
import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import org.junit.jupiter.api.Test;
public class MessageTest {
@Test
public void fromJsonTest() throws IOException {
Message m = new Message();
m.setWorkflowId("wId");
m.setType(MessageType.ONGOING);
m.setJobName("Collection");
Map<String, String> body = new HashMap<>();
body.put("parsedItem", "300");
body.put("ExecutionTime", "30s");
m.setBody(body);
System.out.println("m = " + m);
Message m1 = Message.fromJson(m.toString());
assertEquals(m1.getWorkflowId(), m.getWorkflowId());
assertEquals(m1.getType(), m.getType());
assertEquals(m1.getJobName(), m.getJobName());
assertNotNull(m1.getBody());
m1.getBody().keySet().forEach(it -> assertEquals(m1.getBody().get(it), m.getBody().get(it)));
assertEquals(m1.getJobName(), m.getJobName());
}
@Test
public void toStringTest() {
final String expectedJson = "{\"workflowId\":\"wId\",\"jobName\":\"Collection\",\"type\":\"ONGOING\",\"body\":{\"ExecutionTime\":\"30s\",\"parsedItem\":\"300\"}}";
Message m = new Message();
m.setWorkflowId("wId");
m.setType(MessageType.ONGOING);
m.setJobName("Collection");
Map<String, String> body = new HashMap<>();
body.put("parsedItem", "300");
body.put("ExecutionTime", "30s");
m.setBody(body);
assertEquals(expectedJson, m.toString());
}
}

5
dhp-schemas/pom.xml
View File

@ -67,6 +67,11 @@
<artifactId>guava</artifactId>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</dependency>
</dependencies>

27
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java
View File

@ -3,17 +3,19 @@ package eu.dnetlib.dhp.schema.common;
import static com.google.common.base.Preconditions.checkArgument;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.time.Instant;
import java.time.format.DateTimeFormatter;
import java.time.temporal.TemporalAccessor;
import java.util.Date;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.function.Function;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.Maps;
@ -252,13 +254,6 @@ public class ModelSupport {
.setRelation("isRelatedTo")
.setRelType("resultResult")
.setSubReltype("relationship"));
relationInverseMap
.put(
"resultResult_similarity_isAmongTopNSimilarDocuments", new RelationInverse()
.setInverse("hasAmongTopNSimilarDocuments")
.setRelation("isAmongTopNSimilarDocuments")
.setRelType("resultResult")
.setSubReltype("similarity"));
relationInverseMap
.put(
"resultResult_supplement_isSupplementTo", new RelationInverse()
@ -482,6 +477,20 @@ public class ModelSupport {
return ((OafEntity) t).getId();
}
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final NoSuchAlgorithmException e) {
throw new IllegalStateException(e);
}
}
public static String generateIdentifier(final String originalId, final String nsPrefix) {
return String.format("%s::%s", nsPrefix, md5(originalId));
}
public static String oldest(String dateA, String dateB) throws ParseException {
if (StringUtils.isBlank(dateA)) {

26
dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/MetadataRecord.java → dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/mdstore/MetadataRecord.java
View File

@ -1,11 +1,13 @@
package eu.dnetlib.dhp.model.mdstore;
package eu.dnetlib.dhp.schema.mdstore;
import java.io.Serializable;
import eu.dnetlib.dhp.utils.DHPUtils;
import eu.dnetlib.dhp.schema.common.ModelSupport;
/** This class models a record inside the new Metadata store collection on HDFS * */
/**
* This class models a record in a Metadata store collection on HDFS
*/
public class MetadataRecord implements Serializable {
/** The D-Net Identifier associated to the record */
@ -26,13 +28,13 @@ public class MetadataRecord implements Serializable {
private String body;
/** the date when the record has been stored */
private long dateOfCollection;
private Long dateOfCollection;
/** the date when the record has been stored */
private long dateOfTransformation;
private Long dateOfTransformation;
public MetadataRecord() {
this.dateOfCollection = System.currentTimeMillis();
}
public MetadataRecord(
@ -40,14 +42,14 @@ public class MetadataRecord implements Serializable {
String encoding,
Provenance provenance,
String body,
long dateOfCollection) {
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());
this.id = ModelSupport.generateIdentifier(originalId, this.provenance.getNsPrefix());
}
public String getId() {
@ -90,19 +92,19 @@ public class MetadataRecord implements Serializable {
this.body = body;
}
public long getDateOfCollection() {
public Long getDateOfCollection() {
return dateOfCollection;
}
public void setDateOfCollection(long dateOfCollection) {
public void setDateOfCollection(Long dateOfCollection) {
this.dateOfCollection = dateOfCollection;
}
public long getDateOfTransformation() {
public Long getDateOfTransformation() {
return dateOfTransformation;
}
public void setDateOfTransformation(long dateOfTransformation) {
public void setDateOfTransformation(Long dateOfTransformation) {
this.dateOfTransformation = dateOfTransformation;
}

2
dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/Provenance.java → dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/mdstore/Provenance.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.model.mdstore;
package eu.dnetlib.dhp.schema.mdstore;
import java.io.Serializable;

4
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/OafUtils.scala
View File

@ -15,11 +15,11 @@ object OafUtils {
}
def generateDataInfo(trust: String = "0.9", invisibile: Boolean = false): DataInfo = {
def generateDataInfo(trust: String = "0.9", invisible: Boolean = false): DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)
di.setInferred(false)
di.setInvisible(false)
di.setInvisible(invisible)
di.setTrust(trust)
di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions"))
di

3
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java
View File

@ -3,6 +3,7 @@ package eu.dnetlib.dhp.schema.oaf;
import static org.junit.jupiter.api.Assertions.*;
import java.time.format.DateTimeParseException;
import java.util.Arrays;
import java.util.List;
@ -94,7 +95,7 @@ public class MergeTest {
@Test
public void mergeRelationTestParseException() {
assertThrows(IllegalArgumentException.class, () -> {
assertThrows(DateTimeParseException.class, () -> {
Relation a = createRel(true, "2016-04-05");
Relation b = createRel(true, "2016-04-05");
a.mergeFrom(b);

38
dhp-workflows/dhp-aggregation/README.md
View File

@ -1,29 +1,27 @@
Description of the Module
--------------------------
This module defines a **collector worker application** that runs on Hadoop.
This module defines a set of oozie workflows for the **collection** and **transformation** of metadata records.
Both workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure
the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping
of each MDStore.
It is responsible for harvesting metadata using different plugins.
## Metadata collection
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).
The **metadata collection workflow** is responsible for harvesting metadata records from different protocols and responding to
different formats and to store them as on HDFS so that they can be further processed.
To work the collection worker need some parameter like:
### Collector Plugins
* **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
Different protocols are managed by dedicated Collector plugins, i.e. java programs implementing a defined interface:
##Plugins
* OAI Plugin
```eu.dnetlib.dhp.collection.plugin.CollectorPlugin```
## Usage
The list of the supported plugins:
* OAI Plugin: collects from OAI-PMH compatible endpoints
* MDStore plugin: collects from a given D-Net MetadataStore, (identified by moogodb URI, dbName, MDStoreID)
* MDStore dump plugin: collects from an MDStore dump stored on the HDFS location indicated by the `path` parameter
# Transformation Plugins
TODO

50
dhp-workflows/dhp-aggregation/pom.xml
View File

@ -7,10 +7,44 @@
<version>1.2.4-SNAPSHOT</version>
</parent>
<artifactId>dhp-aggregation</artifactId>
<build>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>${net.alchim31.maven.version}</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
@ -24,12 +58,6 @@
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
@ -58,6 +86,11 @@
<artifactId>jaxen</artifactId>
</dependency>
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-csv -->
<dependency>
<groupId>org.apache.commons</groupId>
@ -78,7 +111,10 @@
<artifactId>commons-compress</artifactId>
</dependency>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>mongo-java-driver</artifactId>
</dependency>
</dependencies>

83
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala Normal file
View File

@ -0,0 +1,83 @@
package eu.dnetlib.dhp.actionmanager.datacite
import org.apache.commons.io.IOUtils
import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest}
import org.apache.http.entity.StringEntity
import org.apache.http.impl.client.HttpClients
import java.io.IOException
abstract class AbstractRestClient extends Iterator[String]{
var buffer: List[String] = List()
var current_index:Int = 0
var scroll_value: Option[String] = None
var complete:Boolean = false
def extractInfo(input: String): Unit
protected def getBufferData(): Unit
def doHTTPGETRequest(url:String): String = {
val httpGet = new HttpGet(url)
doHTTPRequest(httpGet)
}
def doHTTPPOSTRequest(url:String, json:String): String = {
val httpPost = new HttpPost(url)
if (json != null) {
val entity = new StringEntity(json)
httpPost.setEntity(entity)
httpPost.setHeader("Accept", "application/json")
httpPost.setHeader("Content-type", "application/json")
}
doHTTPRequest(httpPost)
}
def hasNext: Boolean = {
buffer.nonEmpty && current_index < buffer.size
}
override def next(): String = {
val next_item:String = buffer(current_index)
current_index = current_index + 1
if (current_index == buffer.size)
getBufferData()
next_item
}
private def doHTTPRequest[A <: HttpUriRequest](r: A) :String ={
val client = HttpClients.createDefault
try {
var tries = 4
while (tries > 0) {
val response = client.execute(r)
if (response.getStatusLine.getStatusCode > 400) {
tries -= 1
}
else
return IOUtils.toString(response.getEntity.getContent)
}
""
} catch {
case e: Throwable =>
throw new RuntimeException("Error on executing request ", e)
} finally try client.close()
catch {
case e: IOException =>
throw new RuntimeException("Unable to close client ", e)
}
}
getBufferData()
}

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dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteAPIImporter.scala Normal file
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package eu.dnetlib.dhp.actionmanager.datacite
import org.json4s.{DefaultFormats, JValue}
import org.json4s.jackson.JsonMethods.{compact, parse, render}
class DataciteAPIImporter(timestamp: Long = 0, blocks: Long = 10) extends AbstractRestClient {
override def extractInfo(input: String): Unit = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(input)
buffer = (json \ "data").extract[List[JValue]].map(s => compact(render(s)))
val next_url = (json \ "links" \ "next").extractOrElse[String](null)
scroll_value = if (next_url != null && next_url.nonEmpty) Some(next_url) else None
if (scroll_value.isEmpty)
complete = true
current_index = 0
}
override def getBufferData(): Unit = {
if (!complete) {
val response = if (scroll_value.isDefined) doHTTPGETRequest(scroll_value.get) else doHTTPGETRequest(s"https://api.datacite.org/dois?page[cursor]=1&page[size]=$blocks&query=updated:[$timestamp%20TO%20*]")
extractInfo(response)
}
}
}

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dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala Normal file
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package eu.dnetlib.dhp.actionmanager.datacite
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Instance, KeyValue, Oaf, OafMapperUtils, OtherResearchProduct, Publication, Qualifier, Relation, Result, Software, StructuredProperty, Dataset => OafDataset}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
import java.nio.charset.CodingErrorAction
import java.text.SimpleDateFormat
import java.time.LocalDate
import java.time.format.DateTimeFormatter
import java.util.{Date, Locale}
import java.util.regex.Pattern
import scala.collection.JavaConverters._
import scala.io.{Codec, Source}
case class DataciteType(doi:String,timestamp:Long,isActive:Boolean, json:String ){}
case class NameIdentifiersType(nameIdentifierScheme: Option[String], schemeUri: Option[String], nameIdentifier: Option[String]) {}
case class CreatorType(nameType: Option[String], nameIdentifiers: Option[List[NameIdentifiersType]], name: Option[String], familyName: Option[String], givenName: Option[String], affiliation: Option[List[String]]) {}
case class TitleType(title: Option[String], titleType: Option[String], lang: Option[String]) {}
case class SubjectType(subject: Option[String], subjectScheme: Option[String]) {}
case class DescriptionType(descriptionType: Option[String], description: Option[String]) {}
case class FundingReferenceType(funderIdentifierType: Option[String], awardTitle: Option[String], awardUri: Option[String], funderName: Option[String], funderIdentifier: Option[String], awardNumber: Option[String]) {}
case class DateType(date: Option[String], dateType: Option[String]) {}
case class HostedByMapType(openaire_id: String, datacite_name: String, official_name: String, similarity: Option[Float]) {}
object DataciteToOAFTransformation {
implicit val codec: Codec = Codec("UTF-8")
codec.onMalformedInput(CodingErrorAction.REPLACE)
codec.onUnmappableCharacter(CodingErrorAction.REPLACE)
private val PID_VOCABULARY = "dnet:pid_types"
val COBJ_VOCABULARY = "dnet:publication_resource"
val RESULT_VOCABULARY = "dnet:result_typologies"
val ACCESS_MODE_VOCABULARY = "dnet:access_modes"
val DOI_CLASS = "doi"
val TITLE_SCHEME = "dnet:dataCite_title"
val SUBJ_CLASS = "keywords"
val SUBJ_SCHEME = "dnet:subject_classification_typologies"
val j_filter:List[String] = {
val s = Source.fromInputStream(getClass.getResourceAsStream("datacite_filter")).mkString
s.lines.toList
}
val mapper = new ObjectMapper()
val unknown_repository: HostedByMapType = HostedByMapType("openaire____::1256f046-bf1f-4afc-8b47-d0b147148b18", "Unknown Repository", "Unknown Repository", Some(1.0F))
val dataInfo: DataInfo = generateDataInfo("0.9")
val DATACITE_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue("openaire____::9e3be59865b2c1c335d32dae2fe7b254", "Datacite")
val hostedByMap: Map[String, HostedByMapType] = {
val s = Source.fromInputStream(getClass.getResourceAsStream("hostedBy_map.json")).mkString
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(s)
json.extract[Map[String, HostedByMapType]]
}
val df_en: DateTimeFormatter = DateTimeFormatter.ofPattern("[MM-dd-yyyy][MM/dd/yyyy][dd-MM-yy][dd-MMM-yyyy][dd/MMM/yyyy][dd-MMM-yy][dd/MMM/yy][dd-MM-yy][dd/MM/yy][dd-MM-yyyy][dd/MM/yyyy][yyyy-MM-dd][yyyy/MM/dd]", Locale.ENGLISH)
val df_it: DateTimeFormatter = DateTimeFormatter.ofPattern("[dd-MM-yyyy][dd/MM/yyyy]", Locale.ITALIAN)
val funder_regex:List[(Pattern, String)] = List(
(Pattern.compile("(info:eu-repo/grantagreement/ec/h2020/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE),"40|corda__h2020::"),
(Pattern.compile("(info:eu-repo/grantagreement/ec/fp7/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE),"40|corda_______::")
)
val Date_regex: List[Pattern] = List(
//Y-M-D
Pattern.compile("(18|19|20)\\d\\d([- /.])(0[1-9]|1[012])\\2(0[1-9]|[12][0-9]|3[01])", Pattern.MULTILINE),
//M-D-Y
Pattern.compile("((0[1-9]|1[012])|([1-9]))([- /.])(0[1-9]|[12][0-9]|3[01])([- /.])(18|19|20)?\\d\\d", Pattern.MULTILINE),
//D-M-Y
Pattern.compile("(?:(?:31(/|-|\\.)(?:0?[13578]|1[02]|(?:Jan|Mar|May|Jul|Aug|Oct|Dec)))\\1|(?:(?:29|30)(/|-|\\.)(?:0?[1,3-9]|1[0-2]|(?:Jan|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec))\\2))(?:(?:1[6-9]|[2-9]\\d)?\\d{2})|(?:29(/|-|\\.)(?:0?2|(?:Feb))\\3(?:(?:(?:1[6-9]|[2-9]\\d)?(?:0[48]|[2468][048]|[13579][26])|(?:(?:16|[2468][048]|[3579][26])00))))|(?:0?[1-9]|1\\d|2[0-8])(/|-|\\.)(?:(?:0?[1-9]|(?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep))|(?:1[0-2]|(?:Oct|Nov|Dec)))\\4(?:(?:1[6-9]|[2-9]\\d)?\\d{2})", Pattern.MULTILINE),
//Y
Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE)
)
def filter_json(json:String):Boolean = {
j_filter.exists(f => json.contains(f))
}
def toActionSet(item:Oaf) :(String, String) = {
val mapper = new ObjectMapper()
item match {
case dataset: OafDataset =>
val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
a.setClazz(classOf[OafDataset])
a.setPayload(dataset)
(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
case publication: Publication =>
val a: AtomicAction[Publication] = new AtomicAction[Publication]
a.setClazz(classOf[Publication])
a.setPayload(publication)
(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
case software: Software =>
val a: AtomicAction[Software] = new AtomicAction[Software]
a.setClazz(classOf[Software])
a.setPayload(software)
(software.getClass.getCanonicalName, mapper.writeValueAsString(a))
case orp: OtherResearchProduct =>
val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
a.setClazz(classOf[OtherResearchProduct])
a.setPayload(orp)
(orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
case relation: Relation =>
val a: AtomicAction[Relation] = new AtomicAction[Relation]
a.setClazz(classOf[Relation])
a.setPayload(relation)
(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
case _ =>
null
}
}
def embargo_end(embargo_end_date: String): Boolean = {
val dt = LocalDate.parse(embargo_end_date, DateTimeFormatter.ofPattern("[yyyy-MM-dd]"))
val td = LocalDate.now()
td.isAfter(dt)
}
def extract_date(input: String): Option[String] = {
val d = Date_regex.map(pattern => {
val matcher = pattern.matcher(input)
if (matcher.find())
matcher.group(0)
else
null
}
).find(s => s != null)
if (d.isDefined) {
val a_date = if (d.get.length == 4) s"01-01-${d.get}" else d.get
try {
return Some(LocalDate.parse(a_date, df_en).toString)
} catch {
case _: Throwable => try {
return Some(LocalDate.parse(a_date, df_it).toString)
} catch {
case _: Throwable => try {
return None
}
}
}
}
d
}
def getTypeQualifier(resourceType: String, resourceTypeGeneral: String, schemaOrg: String, vocabularies:VocabularyGroup): (Qualifier, Qualifier) = {
if (resourceType != null && resourceType.nonEmpty) {
val typeQualifier = vocabularies.getSynonymAsQualifier(COBJ_VOCABULARY, resourceType)
if (typeQualifier != null)
return (typeQualifier, vocabularies.getSynonymAsQualifier(RESULT_VOCABULARY, typeQualifier.getClassid))
}
if (schemaOrg != null && schemaOrg.nonEmpty) {
val typeQualifier = vocabularies.getSynonymAsQualifier(COBJ_VOCABULARY, schemaOrg)
if (typeQualifier != null)
return (typeQualifier, vocabularies.getSynonymAsQualifier(RESULT_VOCABULARY, typeQualifier.getClassid))
}
if (resourceTypeGeneral != null && resourceTypeGeneral.nonEmpty) {
val typeQualifier = vocabularies.getSynonymAsQualifier(COBJ_VOCABULARY, resourceTypeGeneral)
if (typeQualifier != null)
return (typeQualifier, vocabularies.getSynonymAsQualifier(RESULT_VOCABULARY, typeQualifier.getClassid))
}
null
}
def getResult(resourceType: String, resourceTypeGeneral: String, schemaOrg: String, vocabularies:VocabularyGroup): Result = {
val typeQualifiers: (Qualifier, Qualifier) = getTypeQualifier(resourceType, resourceTypeGeneral, schemaOrg, vocabularies)
if (typeQualifiers == null)
return null
val i = new Instance
i.setInstancetype(typeQualifiers._1)
typeQualifiers._2.getClassname match {
case "dataset" =>
val r = new OafDataset
r.setInstance(List(i).asJava)
return r
case "publication" =>
val r = new Publication
r.setInstance(List(i).asJava)
return r
case "software" =>
val r = new Software
r.setInstance(List(i).asJava)
return r
case "other" =>
val r = new OtherResearchProduct
r.setInstance(List(i).asJava)
return r
}
null
}
def available_date(input: String): Boolean = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(input)
val l: List[String] = for {
JObject(dates) <- json \\ "dates"
JField("dateType", JString(dateTypes)) <- dates
} yield dateTypes
l.exists(p => p.equalsIgnoreCase("available"))
}
def generateOAFDate(dt: String, q: Qualifier): StructuredProperty = {
OafMapperUtils.structuredProperty(dt, q, null)
}
def generateRelation(sourceId:String, targetId:String, relClass:String, cf:KeyValue, di:DataInfo) :Relation = {
val r = new Relation
r.setSource(sourceId)
r.setTarget(targetId)
r.setRelType("resultProject")
r.setRelClass(relClass)
r.setSubRelType("outcome")
r.setCollectedfrom(List(cf).asJava)
r.setDataInfo(di)
r
}
def get_projectRelation(awardUri:String, sourceId:String):List[Relation] = {
val match_pattern = funder_regex.find(s =>s._1.matcher(awardUri).find())
if (match_pattern.isDefined) {
val m =match_pattern.get._1
val p = match_pattern.get._2
val grantId = m.matcher(awardUri).replaceAll("$2")
val targetId = s"$p${DHPUtils.md5(grantId)}"
List(
generateRelation(sourceId, targetId,"isProducedBy", DATACITE_COLLECTED_FROM, dataInfo),
generateRelation(targetId, sourceId,"produces", DATACITE_COLLECTED_FROM, dataInfo)
)
}
else
List()
}
def generateOAF(input:String,ts:Long, dateOfCollection:Long, vocabularies: VocabularyGroup):List[Oaf] = {
if (filter_json(input))
return List()
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val resourceType = (json \ "attributes" \ "types" \ "resourceType").extractOrElse[String](null)
val resourceTypeGeneral = (json \ "attributes" \ "types" \ "resourceTypeGeneral").extractOrElse[String](null)
val schemaOrg = (json \ "attributes" \ "types" \ "schemaOrg").extractOrElse[String](null)
val doi = (json \ "attributes" \ "doi").extract[String]
if (doi.isEmpty)
return List()
//Mapping type based on vocabularies dnet:publication_resource and dnet:result_typologies
val result = getResult(resourceType, resourceTypeGeneral, schemaOrg, vocabularies)
if (result == null)
return List()
val doi_q = vocabularies.getSynonymAsQualifier(PID_VOCABULARY, "doi")
val pid = OafMapperUtils.structuredProperty(doi, doi_q, dataInfo)
result.setPid(List(pid).asJava)
result.setId(OafMapperUtils.createOpenaireId(50, s"datacite____::$doi", true))
result.setOriginalId(List(doi).asJava)
val d = new Date(dateOfCollection*1000)
val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
result.setDateofcollection(ISO8601FORMAT.format(d))
result.setDateoftransformation(ISO8601FORMAT.format(ts))
result.setDataInfo(dataInfo)
val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List())
val authors = creators.zipWithIndex.map { case (c, idx) =>
val a = new Author
a.setFullname(c.name.orNull)
a.setName(c.givenName.orNull)
a.setSurname(c.familyName.orNull)
if (c.nameIdentifiers!= null&& c.nameIdentifiers.isDefined && c.nameIdentifiers.get != null) {
a.setPid(c.nameIdentifiers.get.map(ni => {
val q = if (ni.nameIdentifierScheme.isDefined) vocabularies.getTermAsQualifier(PID_VOCABULARY, ni.nameIdentifierScheme.get.toLowerCase()) else null
if (ni.nameIdentifier!= null && ni.nameIdentifier.isDefined) {
OafMapperUtils.structuredProperty(ni.nameIdentifier.get, q, dataInfo)
}
else
null
}
)
.asJava)
}
if (c.affiliation.isDefined)
a.setAffiliation(c.affiliation.get.filter(af => af.nonEmpty).map(af => OafMapperUtils.field(af, dataInfo)).asJava)
a.setRank(idx + 1)
a
}
val titles:List[TitleType] = (json \\ "titles").extractOrElse[List[TitleType]](List())
result.setTitle(titles.filter(t => t.title.nonEmpty).map(t => {
if (t.titleType.isEmpty) {
OafMapperUtils.structuredProperty(t.title.get, "main title", "main title", TITLE_SCHEME, TITLE_SCHEME, null)
} else {
OafMapperUtils.structuredProperty(t.title.get, t.titleType.get, t.titleType.get, TITLE_SCHEME, TITLE_SCHEME, null)
}
}).asJava)
if(authors==null || authors.isEmpty || !authors.exists(a => a !=null))
return List()
result.setAuthor(authors.asJava)
val dates = (json \\ "dates").extract[List[DateType]]
val publication_year = (json \\ "publicationYear").extractOrElse[String](null)
val i_date = dates
.filter(d => d.date.isDefined && d.dateType.isDefined)
.find(d => d.dateType.get.equalsIgnoreCase("issued"))
.map(d => extract_date(d.date.get))
val a_date: Option[String] = dates
.filter(d => d.date.isDefined && d.dateType.isDefined && d.dateType.get.equalsIgnoreCase("available"))
.map(d => extract_date(d.date.get))
.find(d => d != null && d.isDefined)
.map(d => d.get)
if (a_date.isDefined) {
result.setEmbargoenddate(OafMapperUtils.field(a_date.get, null))
}
if (i_date.isDefined && i_date.get.isDefined) {
result.setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
}
else if (publication_year != null) {
result.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
}
result.setRelevantdate(dates.filter(d => d.date.isDefined && d.dateType.isDefined)
.map(d => (extract_date(d.date.get), d.dateType.get))
.filter(d => d._1.isDefined)
.map(d => (d._1.get, vocabularies.getTermAsQualifier("dnet:dataCite_date", d._2.toLowerCase())))
.filter(d => d._2 != null)
.map(d => generateOAFDate(d._1, d._2)).asJava)
val subjects = (json \\ "subjects").extract[List[SubjectType]]
result.setSubject(subjects.filter(s => s.subject.nonEmpty)
.map(s =>
OafMapperUtils.structuredProperty(s.subject.get, SUBJ_CLASS, SUBJ_CLASS, SUBJ_SCHEME, SUBJ_SCHEME, null)
).asJava)
result.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
val descriptions = (json \\ "descriptions").extract[List[DescriptionType]]
result.setDescription(
descriptions
.filter(d => d.description.isDefined).
map(d =>
OafMapperUtils.field(d.description.get, null)
).filter(s => s!=null).asJava)
val publisher = (json \\ "publisher").extractOrElse[String](null)
if (publisher != null)
result.setPublisher(OafMapperUtils.field(publisher, null))
val language: String = (json \\ "language").extractOrElse[String](null)
if (language != null)
result.setLanguage(vocabularies.getSynonymAsQualifier("dnet:languages", language))
val instance = result.getInstance().get(0)
val client = (json \ "relationships" \ "client" \\ "id").extractOpt[String]
val accessRights:List[String] = for {
JObject(rightsList) <- json \\ "rightsList"
JField("rightsUri", JString(rightsUri)) <- rightsList
} yield rightsUri
val aRights: Option[Qualifier] = accessRights.map(r => {
vocabularies.getSynonymAsQualifier(ACCESS_MODE_VOCABULARY, r)
}).find(q => q != null)
val access_rights_qualifier = if (aRights.isDefined) aRights.get else OafMapperUtils.qualifier("UNKNOWN", "not available", ACCESS_MODE_VOCABULARY, ACCESS_MODE_VOCABULARY)
if (client.isDefined) {
val hb = hostedByMap.getOrElse(client.get.toUpperCase(), unknown_repository)
instance.setHostedby(OafMapperUtils.keyValue(generateDSId(hb.openaire_id), hb.official_name))
instance.setCollectedfrom(DATACITE_COLLECTED_FROM)
instance.setUrl(List(s"https://dx.doi.org/$doi").asJava)
// instance.setAccessright(access_rights_qualifier)
//'http') and matches(., '.*(/licenses|/publicdomain|unlicense.org/|/legal-and-data-protection-notices|/download/license|/open-government-licence).*')]">
val license = accessRights
.find(r => r.startsWith("http") && r.matches(".*(/licenses|/publicdomain|unlicense\\.org/|/legal-and-data-protection-notices|/download/license|/open-government-licence).*"))
if (license.isDefined)
instance.setLicense(OafMapperUtils.field(license.get, null))
}
val awardUris:List[String] = for {
JObject(fundingReferences) <- json \\ "fundingReferences"
JField("awardUri", JString(awardUri)) <- fundingReferences
} yield awardUri
val relations:List[Relation] =awardUris.flatMap(a=> get_projectRelation(a, result.getId)).filter(r => r!= null)
if (relations!= null && relations.nonEmpty) {
List(result):::relations
}
else
List(result)
}
def generateDataInfo(trust: String): DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)
di.setInferred(false)
di.setInvisible(false)
di.setTrust(trust)
di.setProvenanceaction(OafMapperUtils.qualifier("sysimport:actionset", "sysimport:actionset", "dnet:provenanceActions", "dnet:provenanceActions"))
di
}
def generateDSId(input: String): String = {
val b = StringUtils.substringBefore(input, "::")
val a = StringUtils.substringAfter(input, "::")
s"10|$b::${DHPUtils.md5(a)}"
}
}

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package eu.dnetlib.dhp.actionmanager.datacite
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Oaf
import org.apache.hadoop.io.Text
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.hadoop.mapred.SequenceFileOutputFormat
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object ExportActionSetJobNode {
val log: Logger = LoggerFactory.getLogger(ExportActionSetJobNode.getClass)
def main(args: Array[String]): Unit = {
val conf = new SparkConf
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json")).mkString)
parser.parseArgument(args)
val master = parser.get("master")
val sourcePath = parser.get("sourcePath")
val targetPath = parser.get("targetPath")
val spark: SparkSession = SparkSession.builder().config(conf)
.appName(ExportActionSetJobNode.getClass.getSimpleName)
.master(master)
.getOrCreate()
implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val tEncoder:Encoder[(String,String)] = Encoders.tuple(Encoders.STRING,Encoders.STRING)
spark.read.load(sourcePath).as[Oaf]
.map(o =>DataciteToOAFTransformation.toActionSet(o))
.filter(o => o!= null)
.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
}
}

48
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala Normal file
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@ -0,0 +1,48 @@
package eu.dnetlib.dhp.actionmanager.datacite
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.mdstore.MetadataRecord
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.utils.ISLookupClientFactory
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object GenerateDataciteDatasetSpark {
val log: Logger = LoggerFactory.getLogger(GenerateDataciteDatasetSpark.getClass)
def main(args: Array[String]): Unit = {
val conf = new SparkConf
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json")).mkString)
parser.parseArgument(args)
val master = parser.get("master")
val sourcePath = parser.get("sourcePath")
val targetPath = parser.get("targetPath")
val isLookupUrl: String = parser.get("isLookupUrl")
log.info("isLookupUrl: {}", isLookupUrl)
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
log.info(s"vocabulary size is ${vocabularies.getTerms("dnet:languages").size()}")
val spark: SparkSession = SparkSession.builder().config(conf)
.appName(GenerateDataciteDatasetSpark.getClass.getSimpleName)
.master(master)
.getOrCreate()
implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord]
implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
import spark.implicits._
spark.read.load(sourcePath).as[DataciteType]
.filter(d => d.isActive)
.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies))
.filter(d => d != null)
.write.mode(SaveMode.Overwrite).save(targetPath)
}
}

169
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala Normal file
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@ -0,0 +1,169 @@
package eu.dnetlib.dhp.actionmanager.datacite
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import org.apache.hadoop.conf.Configuration
import org.apache.hadoop.fs.{FileSystem, LocalFileSystem, Path}
import org.apache.hadoop.hdfs.DistributedFileSystem
import org.apache.hadoop.io.{IntWritable, SequenceFile, Text}
import org.apache.spark.SparkContext
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.{Dataset, Encoder, SaveMode, SparkSession}
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.apache.spark.sql.functions.max
import org.slf4j.{Logger, LoggerFactory}
import java.time.format.DateTimeFormatter._
import java.time.{LocalDateTime, ZoneOffset}
import scala.io.Source
object ImportDatacite {
val log: Logger = LoggerFactory.getLogger(ImportDatacite.getClass)
def convertAPIStringToDataciteItem(input:String): DataciteType = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(input)
val doi = (json \ "attributes" \ "doi").extract[String].toLowerCase
val isActive = (json \ "attributes" \ "isActive").extract[Boolean]
val timestamp_string = (json \ "attributes" \ "updated").extract[String]
val dt = LocalDateTime.parse(timestamp_string, ISO_DATE_TIME)
DataciteType(doi = doi, timestamp = dt.toInstant(ZoneOffset.UTC).toEpochMilli/1000, isActive = isActive, json = input)
}
def main(args: Array[String]): Unit = {
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/import_from_api.json")).mkString)
parser.parseArgument(args)
val master = parser.get("master")
val hdfsuri = parser.get("namenode")
log.info(s"namenode is $hdfsuri")
val targetPath = parser.get("targetPath")
log.info(s"targetPath is $targetPath")
val dataciteDump = parser.get("dataciteDumpPath")
log.info(s"dataciteDump is $dataciteDump")
val hdfsTargetPath =new Path(targetPath)
log.info(s"hdfsTargetPath is $hdfsTargetPath")
val spark: SparkSession = SparkSession.builder()
.appName(ImportDatacite.getClass.getSimpleName)
.master(master)
.getOrCreate()
// ====== Init HDFS File System Object
val conf = new Configuration
// Set FileSystem URI
conf.set("fs.defaultFS", hdfsuri)
// Because of Maven
conf.set("fs.hdfs.impl", classOf[DistributedFileSystem].getName)
conf.set("fs.file.impl", classOf[LocalFileSystem].getName)
val sc:SparkContext = spark.sparkContext
sc.setLogLevel("ERROR")
import spark.implicits._
val dataciteAggregator: Aggregator[DataciteType, DataciteType, DataciteType] = new Aggregator[DataciteType, DataciteType, DataciteType] with Serializable {
override def zero: DataciteType = null
override def reduce(a: DataciteType, b: DataciteType): DataciteType = {
if (b == null)
return a
if (a == null)
return b
if(a.timestamp >b.timestamp) {
return a
}
b
}
override def merge(a: DataciteType, b: DataciteType): DataciteType = {
reduce(a,b)
}
override def bufferEncoder: Encoder[DataciteType] = implicitly[Encoder[DataciteType]]
override def outputEncoder: Encoder[DataciteType] = implicitly[Encoder[DataciteType]]
override def finish(reduction: DataciteType): DataciteType = reduction
}
val dump:Dataset[DataciteType] = spark.read.load(dataciteDump).as[DataciteType]
val ts = dump.select(max("timestamp")).first().getLong(0)
log.info(s"last Timestamp is $ts")
val cnt = writeSequenceFile(hdfsTargetPath, ts, conf)
log.info(s"Imported from Datacite API $cnt documents")
if (cnt > 0) {
val inputRdd:RDD[DataciteType] = sc.sequenceFile(targetPath, classOf[Int], classOf[Text])
.map(s => s._2.toString)
.map(s => convertAPIStringToDataciteItem(s))
spark.createDataset(inputRdd).write.mode(SaveMode.Overwrite).save(s"${targetPath}_dataset")
val ds:Dataset[DataciteType] = spark.read.load(s"${targetPath}_dataset").as[DataciteType]
dump
.union(ds)
.groupByKey(_.doi)
.agg(dataciteAggregator.toColumn)
.map(s=>s._2)
.repartition(4000)
.write.mode(SaveMode.Overwrite).save(s"${dataciteDump}_updated")
val fs = FileSystem.get(sc.hadoopConfiguration)
fs.delete(new Path(s"$dataciteDump"), true)
fs.rename(new Path(s"${dataciteDump}_updated"),new Path(s"$dataciteDump"))
}
}
private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration):Long = {
val client = new DataciteAPIImporter(timestamp*1000, 1000)
var i = 0
try {
val writer = SequenceFile.createWriter(conf, SequenceFile.Writer.file(hdfsTargetPath), SequenceFile.Writer.keyClass(classOf[IntWritable]), SequenceFile.Writer.valueClass(classOf[Text]))
try {
var start: Long = System.currentTimeMillis
var end: Long = 0
val key: IntWritable = new IntWritable(i)
val value: Text = new Text
while ( {
client.hasNext
}) {
key.set({
i += 1;
i - 1
})
value.set(client.next())
writer.append(key, value)
writer.hflush()
if (i % 1000 == 0) {
end = System.currentTimeMillis
val time = (end - start) / 1000.0F
println(s"Imported $i in $time seconds")
start = System.currentTimeMillis
}
}
} finally if (writer != null) writer.close()
}
i
}
}

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
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@ -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
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@ -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;
}
}

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java
View File

@ -17,8 +17,8 @@ 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;
import eu.dnetlib.dhp.collection.HttpConnector2;
/**
* Applies the parsing of a csv file and writes the Serialization of it in hdfs
@ -74,7 +74,7 @@ public class ReadCSV implements Closeable {
throws Exception {
this.conf = new Configuration();
this.conf.set("fs.defaultFS", hdfsNameNode);
HttpConnector httpConnector = new HttpConnector();
HttpConnector2 httpConnector = new HttpConnector2();
FileSystem fileSystem = FileSystem.get(this.conf);
Path hdfsWritePath = new Path(hdfsPath);
FSDataOutputStream fsDataOutputStream = null;

5
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java
View File

@ -14,13 +14,12 @@ 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;
import eu.dnetlib.dhp.collection.HttpConnector2;
/**
* Applies the parsing of an excel file and writes the Serialization of it in hdfs
*/
public class ReadExcel implements Closeable {
private static final Log log = LogFactory.getLog(ReadCSV.class);
private final Configuration conf;
@ -72,7 +71,7 @@ public class ReadExcel implements Closeable {
throws Exception {
this.conf = new Configuration();
this.conf.set("fs.defaultFS", hdfsNameNode);
HttpConnector httpConnector = new HttpConnector();
HttpConnector2 httpConnector = new HttpConnector2();
FileSystem fileSystem = FileSystem.get(this.conf);
Path hdfsWritePath = new Path(hdfsPath);
FSDataOutputStream fsDataOutputStream = null;

45
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/AggregationCounter.java Normal file
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@ -0,0 +1,45 @@
package eu.dnetlib.dhp.aggregation.common;
import java.io.Serializable;
import org.apache.spark.util.LongAccumulator;
public class AggregationCounter implements Serializable {
private LongAccumulator totalItems;
private LongAccumulator errorItems;
private LongAccumulator processedItems;
public AggregationCounter() {
}
public AggregationCounter(LongAccumulator totalItems, LongAccumulator errorItems, LongAccumulator processedItems) {
this.totalItems = totalItems;
this.errorItems = errorItems;
this.processedItems = processedItems;
}
public LongAccumulator getTotalItems() {
return totalItems;
}
public void setTotalItems(LongAccumulator totalItems) {
this.totalItems = totalItems;
}
public LongAccumulator getErrorItems() {
return errorItems;
}
public void setErrorItems(LongAccumulator errorItems) {
this.errorItems = errorItems;
}
public LongAccumulator getProcessedItems() {
return processedItems;
}
public void setProcessedItems(LongAccumulator processedItems) {
this.processedItems = processedItems;
}
}

47
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/AggregatorReport.java Normal file
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@ -0,0 +1,47 @@
package eu.dnetlib.dhp.aggregation.common;
import java.io.Closeable;
import java.io.IOException;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Objects;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.gson.Gson;
import eu.dnetlib.dhp.message.MessageSender;
import eu.dnetlib.dhp.utils.DHPUtils;
public class AggregatorReport extends LinkedHashMap<String, String> implements Closeable {
private static final Logger log = LoggerFactory.getLogger(AggregatorReport.class);
private MessageSender messageSender;
public AggregatorReport() {
}
public AggregatorReport(MessageSender messageSender) throws IOException {
this.messageSender = messageSender;
}
public void ongoing(Long current, Long total) {
messageSender.sendMessage(current, total);
}
@Override
public void close() throws IOException {
if (Objects.nonNull(messageSender)) {
log.info("closing report: ");
this.forEach((k, v) -> log.info("{} - {}", k, v));
Map<String, String> m = new HashMap<>();
m.put(getClass().getSimpleName().toLowerCase(), DHPUtils.MAPPER.writeValueAsString(values()));
messageSender.sendReport(m);
}
}
}

10
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/ReporterCallback.java Normal file
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@ -0,0 +1,10 @@
package eu.dnetlib.dhp.aggregation.common;
public interface ReporterCallback {
Long getCurrent();
Long getTotal();
}

41
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/ReportingJob.java Normal file
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@ -0,0 +1,41 @@
package eu.dnetlib.dhp.aggregation.common;
import java.util.TimerTask;
import java.util.concurrent.Executors;
import java.util.concurrent.ScheduledExecutorService;
import java.util.concurrent.TimeUnit;
public abstract class ReportingJob {
/**
* Frequency (seconds) for sending ongoing messages to report the collection task advancement
*/
public static final int ONGOING_REPORT_FREQUENCY = 5;
/**
* Initial delay (seconds) for sending ongoing messages to report the collection task advancement
*/
public static final int INITIAL_DELAY = 2;
private ScheduledExecutorService executor = Executors.newSingleThreadScheduledExecutor();
protected final AggregatorReport report;
public ReportingJob(AggregatorReport report) {
this.report = report;
}
protected void schedule(final ReporterCallback callback) {
executor.scheduleAtFixedRate(new TimerTask() {
@Override
public void run() {
report.ongoing(callback.getCurrent(), callback.getTotal());
}
}, INITIAL_DELAY, ONGOING_REPORT_FREQUENCY, TimeUnit.SECONDS);
}
protected void shutdown() {
executor.shutdown();
}
}

136
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/mdstore/MDStoreActionNode.java Normal file
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@ -0,0 +1,136 @@
package eu.dnetlib.dhp.aggregation.mdstore;
import static eu.dnetlib.dhp.common.Constants.*;
import static eu.dnetlib.dhp.utils.DHPUtils.*;
import java.net.URI;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.rest.DNetRestClient;
public class MDStoreActionNode {
private static final Logger log = LoggerFactory.getLogger(MDStoreActionNode.class);
enum MDAction {
NEW_VERSION, ROLLBACK, COMMIT, READ_LOCK, READ_UNLOCK
}
public static String NEW_VERSION_URI = "%s/mdstore/%s/newVersion";
public static final String COMMIT_VERSION_URL = "%s/version/%s/commit/%s";
public static final String ROLLBACK_VERSION_URL = "%s/version/%s/abort";
public static final String READ_LOCK_URL = "%s/mdstore/%s/startReading";
public static final String READ_UNLOCK_URL = "%s/version/%s/endReading";
private static final String MDSTOREVERSIONPARAM = "mdStoreVersion";
private static final String MDSTOREREADLOCKPARAM = "mdStoreReadLockVersion";
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser(
IOUtils
.toString(
MDStoreActionNode.class
.getResourceAsStream(
"/eu/dnetlib/dhp/collection/mdstore_action_parameters.json")));
argumentParser.parseArgument(args);
log.info("Java Xmx: {}m", Runtime.getRuntime().maxMemory() / (1024 * 1024));
final MDAction action = MDAction.valueOf(argumentParser.get("action"));
log.info("Current action is {}", action);
final String mdStoreManagerURI = argumentParser.get("mdStoreManagerURI");
log.info("mdStoreManagerURI is {}", mdStoreManagerURI);
switch (action) {
case NEW_VERSION: {
final String mdStoreID = argumentParser.get("mdStoreID");
if (StringUtils.isBlank(mdStoreID)) {
throw new IllegalArgumentException("missing or empty argument mdStoreId");
}
final MDStoreVersion currentVersion = DNetRestClient
.doGET(String.format(NEW_VERSION_URI, mdStoreManagerURI, mdStoreID), MDStoreVersion.class);
populateOOZIEEnv(MDSTOREVERSIONPARAM, MAPPER.writeValueAsString(currentVersion));
break;
}
case COMMIT: {
final String hdfsuri = argumentParser.get("namenode");
if (StringUtils.isBlank(hdfsuri)) {
throw new IllegalArgumentException("missing or empty argument namenode");
}
final String mdStoreVersion_params = argumentParser.get("mdStoreVersion");
final MDStoreVersion mdStoreVersion = MAPPER.readValue(mdStoreVersion_params, MDStoreVersion.class);
if (StringUtils.isBlank(mdStoreVersion.getId())) {
throw new IllegalArgumentException(
"invalid MDStoreVersion value current is " + mdStoreVersion_params);
}
Path hdfstoreSizepath = new Path(mdStoreVersion.getHdfsPath() + MDSTORE_SIZE_PATH);
try (
FileSystem fs = FileSystem.get(URI.create(hdfsuri), getHadoopConfiguration(hdfsuri));
FSDataInputStream inputStream = fs.open(hdfstoreSizepath)) {
final Long mdStoreSize = Long.parseLong(IOUtils.toString(inputStream));
fs.create(hdfstoreSizepath);
DNetRestClient
.doGET(
String.format(COMMIT_VERSION_URL, mdStoreManagerURI, mdStoreVersion.getId(), mdStoreSize));
}
break;
}
case ROLLBACK: {
final String mdStoreVersion_params = argumentParser.get("mdStoreVersion");
final MDStoreVersion mdStoreVersion = MAPPER.readValue(mdStoreVersion_params, MDStoreVersion.class);
if (StringUtils.isBlank(mdStoreVersion.getId())) {
throw new IllegalArgumentException(
"invalid MDStoreVersion value current is " + mdStoreVersion_params);
}
DNetRestClient.doGET(String.format(ROLLBACK_VERSION_URL, mdStoreManagerURI, mdStoreVersion.getId()));
break;
}
case READ_LOCK: {
final String mdStoreID = argumentParser.get("mdStoreID");
if (StringUtils.isBlank(mdStoreID)) {
throw new IllegalArgumentException("missing or empty argument mdStoreId");
}
final MDStoreVersion currentVersion = DNetRestClient
.doGET(String.format(READ_LOCK_URL, mdStoreManagerURI, mdStoreID), MDStoreVersion.class);
populateOOZIEEnv(MDSTOREREADLOCKPARAM, MAPPER.writeValueAsString(currentVersion));
break;
}
case READ_UNLOCK: {
final String mdStoreVersion_params = argumentParser.get("readMDStoreId");
final MDStoreVersion mdStoreVersion = MAPPER.readValue(mdStoreVersion_params, MDStoreVersion.class);
if (StringUtils.isBlank(mdStoreVersion.getId())) {
throw new IllegalArgumentException(
"invalid MDStoreVersion value current is " + mdStoreVersion_params);
}
DNetRestClient.doGET(String.format(READ_UNLOCK_URL, mdStoreManagerURI, mdStoreVersion.getId()));
break;
}
default:
throw new IllegalArgumentException("invalid action");
}
}
}

14
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorException.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorException.java
View File

@ -1,16 +1,16 @@
package eu.dnetlib.dhp.collection.worker;
package eu.dnetlib.dhp.collection;
public class DnetCollectorException extends Exception {
public class CollectorException extends Exception {
/** */
private static final long serialVersionUID = -290723075076039757L;
public DnetCollectorException() {
public CollectorException() {
super();
}
public DnetCollectorException(
public CollectorException(
final String message,
final Throwable cause,
final boolean enableSuppression,
@ -18,15 +18,15 @@ public class DnetCollectorException extends Exception {
super(message, cause, enableSuppression, writableStackTrace);
}
public DnetCollectorException(final String message, final Throwable cause) {
public CollectorException(final String message, final Throwable cause) {
super(message, cause);
}
public DnetCollectorException(final String message) {
public CollectorException(final String message) {
super(message);
}
public DnetCollectorException(final Throwable cause) {
public CollectorException(final Throwable cause) {
super(cause);
}
}

134
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java Normal file
View File

@ -0,0 +1,134 @@
package eu.dnetlib.dhp.collection;
import static eu.dnetlib.dhp.common.Constants.SEQUENCE_FILE_NAME;
import java.io.IOException;
import java.util.Optional;
import java.util.concurrent.atomic.AtomicInteger;
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.apache.hadoop.io.compress.DeflateCodec;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.aggregation.common.ReporterCallback;
import eu.dnetlib.dhp.aggregation.common.ReportingJob;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.rest.RestCollectorPlugin;
public class CollectorWorker extends ReportingJob {
private static final Logger log = LoggerFactory.getLogger(CollectorWorker.class);
private final ApiDescriptor api;
private final FileSystem fileSystem;
private final MDStoreVersion mdStoreVersion;
private final HttpClientParams clientParams;
public CollectorWorker(
final ApiDescriptor api,
final FileSystem fileSystem,
final MDStoreVersion mdStoreVersion,
final HttpClientParams clientParams,
final AggregatorReport report) {
super(report);
this.api = api;
this.fileSystem = fileSystem;
this.mdStoreVersion = mdStoreVersion;
this.clientParams = clientParams;
}
public void collect() throws UnknownCollectorPluginException, CollectorException, IOException {
final String outputPath = mdStoreVersion.getHdfsPath() + SEQUENCE_FILE_NAME;
log.info("outputPath path is {}", outputPath);
final CollectorPlugin plugin = getCollectorPlugin();
final AtomicInteger counter = new AtomicInteger(0);
scheduleReport(counter);
try (SequenceFile.Writer writer = SequenceFile
.createWriter(
fileSystem.getConf(),
SequenceFile.Writer.file(new Path(outputPath)),
SequenceFile.Writer.keyClass(IntWritable.class),
SequenceFile.Writer.valueClass(Text.class),
SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
final IntWritable key = new IntWritable(counter.get());
final Text value = new Text();
plugin
.collect(api, report)
.forEach(
content -> {
key.set(counter.getAndIncrement());
value.set(content);
try {
writer.append(key, value);
} catch (Throwable e) {
throw new RuntimeException(e);
}
});
} catch (Throwable e) {
report.put(e.getClass().getName(), e.getMessage());
throw new CollectorException(e);
} finally {
shutdown();
report.ongoing(counter.longValue(), counter.longValue());
}
}
private void scheduleReport(AtomicInteger counter) {
schedule(new ReporterCallback() {
@Override
public Long getCurrent() {
return counter.longValue();
}
@Override
public Long getTotal() {
return null;
}
});
}
private CollectorPlugin getCollectorPlugin() throws UnknownCollectorPluginException {
switch (CollectorPlugin.NAME.valueOf(api.getProtocol())) {
case oai:
return new OaiCollectorPlugin(clientParams);
case rest_json2xml:
return new RestCollectorPlugin(clientParams);
case other:
final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
.ofNullable(api.getParams().get("other_plugin_type"))
.map(CollectorPlugin.NAME.OTHER_NAME::valueOf)
.get();
switch (plugin) {
case mdstore_mongodb_dump:
return new MongoDbDumpCollectorPlugin(fileSystem);
case mdstore_mongodb:
return new MDStoreCollectorPlugin();
default:
throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
}
default:
throw new UnknownCollectorPluginException("protocol is not managed: " + api.getProtocol());
}
}
}

135
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorkerApplication.java Normal file
View File

@ -0,0 +1,135 @@
package eu.dnetlib.dhp.collection;
import static eu.dnetlib.dhp.common.Constants.*;
import static eu.dnetlib.dhp.utils.DHPUtils.*;
import java.io.IOException;
import java.util.Optional;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FileSystem;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.message.MessageSender;
/**
* CollectorWorkerApplication is the main class responsible to start the metadata collection process, storing the outcomes
* into HDFS. This application will be executed on the hadoop cluster, where invoked in the context of the metadata collection
* oozie workflow, it will receive all the input parameters necessary to instantiate the specific collection plugin and the
* relative specific configurations
*
* @author Sandro La Bruzzo, Claudio Atzori
*/
public class CollectorWorkerApplication {
private static final Logger log = LoggerFactory.getLogger(CollectorWorkerApplication.class);
private FileSystem fileSystem;
public CollectorWorkerApplication(FileSystem fileSystem) {
this.fileSystem = fileSystem;
}
/**
* @param args
*/
public static void main(final String[] args)
throws ParseException, IOException, UnknownCollectorPluginException, CollectorException {
final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser(
IOUtils
.toString(
CollectorWorkerApplication.class
.getResourceAsStream(
"/eu/dnetlib/dhp/collection/collector_worker_input_parameter.json")));
argumentParser.parseArgument(args);
log.info("Java Xmx: {}m", Runtime.getRuntime().maxMemory() / (1024 * 1024));
final String hdfsuri = argumentParser.get("namenode");
log.info("hdfsURI is {}", hdfsuri);
final String apiDescriptor = argumentParser.get("apidescriptor");
log.info("apiDescriptor is {}", apiDescriptor);
final String mdStoreVersion = argumentParser.get("mdStoreVersion");
log.info("mdStoreVersion is {}", mdStoreVersion);
final String dnetMessageManagerURL = argumentParser.get(DNET_MESSAGE_MGR_URL);
log.info("dnetMessageManagerURL is {}", dnetMessageManagerURL);
final String workflowId = argumentParser.get("workflowId");
log.info("workflowId is {}", workflowId);
final HttpClientParams clientParams = getClientParams(argumentParser);
final ApiDescriptor api = MAPPER.readValue(apiDescriptor, ApiDescriptor.class);
final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(hdfsuri));
new CollectorWorkerApplication(fileSystem)
.run(mdStoreVersion, clientParams, api, dnetMessageManagerURL, workflowId);
}
protected void run(String mdStoreVersion, HttpClientParams clientParams, ApiDescriptor api,
String dnetMessageManagerURL, String workflowId)
throws IOException, CollectorException, UnknownCollectorPluginException {
final MDStoreVersion currentVersion = MAPPER.readValue(mdStoreVersion, MDStoreVersion.class);
final MessageSender ms = new MessageSender(dnetMessageManagerURL, workflowId);
try (AggregatorReport report = new AggregatorReport(ms)) {
new CollectorWorker(api, fileSystem, currentVersion, clientParams, report).collect();
}
}
private static HttpClientParams getClientParams(ArgumentApplicationParser argumentParser) {
final HttpClientParams clientParams = new HttpClientParams();
clientParams
.setMaxNumberOfRetry(
Optional
.ofNullable(argumentParser.get(MAX_NUMBER_OF_RETRY))
.map(Integer::parseInt)
.orElse(HttpClientParams._maxNumberOfRetry));
log.info("maxNumberOfRetry is {}", clientParams.getMaxNumberOfRetry());
clientParams
.setRequestDelay(
Optional
.ofNullable(argumentParser.get(REQUEST_DELAY))
.map(Integer::parseInt)
.orElse(HttpClientParams._requestDelay));
log.info("requestDelay is {}", clientParams.getRequestDelay());
clientParams
.setRetryDelay(
Optional
.ofNullable(argumentParser.get(RETRY_DELAY))
.map(Integer::parseInt)
.orElse(HttpClientParams._retryDelay));
log.info("retryDelay is {}", clientParams.getRetryDelay());
clientParams
.setConnectTimeOut(
Optional
.ofNullable(argumentParser.get(CONNECT_TIMEOUT))
.map(Integer::parseInt)
.orElse(HttpClientParams._connectTimeOut));
log.info("connectTimeOut is {}", clientParams.getConnectTimeOut());
clientParams
.setReadTimeOut(
Optional
.ofNullable(argumentParser.get(READ_TIMEOUT))
.map(Integer::parseInt)
.orElse(HttpClientParams._readTimeOut));
log.info("readTimeOut is {}", clientParams.getReadTimeOut());
return clientParams;
}
}

284
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java
View File

@ -1,28 +1,26 @@
package eu.dnetlib.dhp.collection;
import static eu.dnetlib.dhp.common.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static eu.dnetlib.dhp.utils.DHPUtils.*;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.HashMap;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.expressions.Aggregator;
import org.apache.spark.util.LongAccumulator;
import org.dom4j.Document;
import org.dom4j.Node;
@ -30,19 +28,172 @@ import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.model.mdstore.Provenance;
import eu.dnetlib.message.Message;
import eu.dnetlib.message.MessageManager;
import eu.dnetlib.message.MessageType;
import eu.dnetlib.dhp.schema.mdstore.MetadataRecord;
import eu.dnetlib.dhp.schema.mdstore.Provenance;
import scala.Tuple2;
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/generate_native_input_parameters.json")));
parser.parseArgument(args);
final String provenanceArgument = parser.get("provenance");
log.info("Provenance is {}", provenanceArgument);
final Provenance provenance = MAPPER.readValue(provenanceArgument, Provenance.class);
final String dateOfCollectionArgs = parser.get("dateOfCollection");
log.info("dateOfCollection is {}", dateOfCollectionArgs);
final Long dateOfCollection = new Long(dateOfCollectionArgs);
String mdStoreVersion = parser.get("mdStoreVersion");
log.info("mdStoreVersion is {}", mdStoreVersion);
final MDStoreVersion currentVersion = MAPPER.readValue(mdStoreVersion, MDStoreVersion.class);
String readMdStoreVersionParam = parser.get("readMdStoreVersion");
log.info("readMdStoreVersion is {}", readMdStoreVersionParam);
final MDStoreVersion readMdStoreVersion = StringUtils.isBlank(readMdStoreVersionParam) ? null
: MAPPER.readValue(readMdStoreVersionParam, MDStoreVersion.class);
final String xpath = parser.get("xpath");
log.info("xpath is {}", xpath);
final String encoding = parser.get("encoding");
log.info("encoding is {}", encoding);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> createNativeMDStore(
spark, provenance, dateOfCollection, xpath, encoding, currentVersion, readMdStoreVersion));
}
private static void createNativeMDStore(SparkSession spark,
Provenance provenance,
Long dateOfCollection,
String xpath,
String encoding,
MDStoreVersion currentVersion,
MDStoreVersion readVersion) throws IOException {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final LongAccumulator totalItems = sc.sc().longAccumulator(CONTENT_TOTALITEMS);
final LongAccumulator invalidRecords = sc.sc().longAccumulator(CONTENT_INVALIDRECORDS);
final String seqFilePath = currentVersion.getHdfsPath() + SEQUENCE_FILE_NAME;
final JavaRDD<MetadataRecord> nativeStore = sc
.sequenceFile(seqFilePath, IntWritable.class, Text.class)
.map(
item -> parseRecord(
item._2().toString(),
xpath,
encoding,
provenance,
dateOfCollection,
totalItems,
invalidRecords))
.filter(Objects::nonNull)
.distinct();
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mdstore = spark.createDataset(nativeStore.rdd(), encoder);
final String targetPath = currentVersion.getHdfsPath() + MDSTORE_DATA_PATH;
if (readVersion != null) { // INCREMENTAL MODE
log.info("updating {} incrementally with {}", targetPath, readVersion.getHdfsPath());
Dataset<MetadataRecord> currentMdStoreVersion = spark
.read()
.load(readVersion.getHdfsPath() + MDSTORE_DATA_PATH)
.as(encoder);
TypedColumn<MetadataRecord, MetadataRecord> aggregator = new MDStoreAggregator().toColumn();
final Dataset<MetadataRecord> map = currentMdStoreVersion
.union(mdstore)
.groupByKey(
(MapFunction<MetadataRecord, String>) MetadataRecord::getId,
Encoders.STRING())
.agg(aggregator)
.map((MapFunction<Tuple2<String, MetadataRecord>, MetadataRecord>) Tuple2::_2, encoder);
map.select("id").takeAsList(100).forEach(s -> log.info(s.toString()));
saveDataset(map, targetPath);
} else {
saveDataset(mdstore, targetPath);
}
final Long total = spark.read().load(targetPath).count();
log.info("collected {} records for datasource '{}'", total, provenance.getDatasourceName());
writeHdfsFile(
spark.sparkContext().hadoopConfiguration(), total.toString(),
currentVersion.getHdfsPath() + MDSTORE_SIZE_PATH);
}
public static class MDStoreAggregator extends Aggregator<MetadataRecord, MetadataRecord, MetadataRecord> {
@Override
public MetadataRecord zero() {
return null;
}
@Override
public MetadataRecord reduce(MetadataRecord b, MetadataRecord a) {
return getLatestRecord(b, a);
}
@Override
public MetadataRecord merge(MetadataRecord b, MetadataRecord a) {
return getLatestRecord(b, a);
}
private MetadataRecord getLatestRecord(MetadataRecord b, MetadataRecord a) {
if (b == null)
return a;
if (a == null)
return b;
return (a.getDateOfCollection() > b.getDateOfCollection()) ? a : b;
}
@Override
public MetadataRecord finish(MetadataRecord r) {
return r;
}
@Override
public Encoder<MetadataRecord> bufferEncoder() {
return Encoders.bean(MetadataRecord.class);
}
@Override
public Encoder<MetadataRecord> outputEncoder() {
return Encoders.bean(MetadataRecord.class);
}
}
public static MetadataRecord parseRecord(
final String input,
final String xpath,
@ -64,112 +215,11 @@ public class GenerateNativeStoreSparkJob {
invalidRecords.add(1);
return null;
}
return new MetadataRecord(originalIdentifier, encoding, provenance, input, dateOfCollection);
return new MetadataRecord(originalIdentifier, encoding, provenance, document.asXML(), dateOfCollection);
} catch (Throwable e) {
if (invalidRecords != null)
invalidRecords.add(1);
e.printStackTrace();
return null;
}
}
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();
}
});
}
}

94
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/HttpClientParams.java Normal file
View File

@ -0,0 +1,94 @@
package eu.dnetlib.dhp.collection;
/**
* Bundles the http connection parameters driving the client behaviour.
*/
public class HttpClientParams {
// Defaults
public static int _maxNumberOfRetry = 3;
public static int _requestDelay = 0; // milliseconds
public static int _retryDelay = 10; // seconds
public static int _connectTimeOut = 10; // seconds
public static int _readTimeOut = 30; // seconds
/**
* Maximum number of allowed retires before failing
*/
private int maxNumberOfRetry;
/**
* Delay between request (Milliseconds)
*/
private int requestDelay;
/**
* Time to wait after a failure before retrying (Seconds)
*/
private int retryDelay;
/**
* Connect timeout (Seconds)
*/
private int connectTimeOut;
/**
* Read timeout (Seconds)
*/
private int readTimeOut;
public HttpClientParams() {
this(_maxNumberOfRetry, _requestDelay, _retryDelay, _connectTimeOut, _readTimeOut);
}
public HttpClientParams(int maxNumberOfRetry, int requestDelay, int retryDelay, int connectTimeOut,
int readTimeOut) {
this.maxNumberOfRetry = maxNumberOfRetry;
this.requestDelay = requestDelay;
this.retryDelay = retryDelay;
this.connectTimeOut = connectTimeOut;
this.readTimeOut = readTimeOut;
}
public int getMaxNumberOfRetry() {
return maxNumberOfRetry;
}
public void setMaxNumberOfRetry(int maxNumberOfRetry) {
this.maxNumberOfRetry = maxNumberOfRetry;
}
public int getRequestDelay() {
return requestDelay;
}
public void setRequestDelay(int requestDelay) {
this.requestDelay = requestDelay;
}
public int getRetryDelay() {
return retryDelay;
}
public void setRetryDelay(int retryDelay) {
this.retryDelay = retryDelay;
}
public void setConnectTimeOut(int connectTimeOut) {
this.connectTimeOut = connectTimeOut;
}
public int getConnectTimeOut() {
return connectTimeOut;
}
public int getReadTimeOut() {
return readTimeOut;
}
public void setReadTimeOut(int readTimeOut) {
this.readTimeOut = readTimeOut;
}
}

259
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/HttpConnector2.java Normal file
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@ -0,0 +1,259 @@
package eu.dnetlib.dhp.collection;
import static eu.dnetlib.dhp.utils.DHPUtils.*;
import java.io.IOException;
import java.io.InputStream;
import java.net.*;
import java.util.List;
import java.util.Map;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.http.HttpHeaders;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
/**
* Migrated from https://svn.driver.research-infrastructures.eu/driver/dnet45/modules/dnet-modular-collector-service/trunk/src/main/java/eu/dnetlib/data/collector/plugins/HttpConnector.java
*
* @author jochen, michele, andrea, alessia, claudio
*/
public class HttpConnector2 {
private static final Logger log = LoggerFactory.getLogger(HttpConnector2.class);
private static final String REPORT_PREFIX = "http:";
private HttpClientParams clientParams;
private String responseType = null;
private String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)";
public HttpConnector2() {
this(new HttpClientParams());
}
public HttpConnector2(HttpClientParams clientParams) {
this.clientParams = clientParams;
CookieHandler.setDefault(new CookieManager(null, CookiePolicy.ACCEPT_ALL));
}
/**
* @see HttpConnector2#getInputSource(java.lang.String, AggregatorReport)
*/
public InputStream getInputSourceAsStream(final String requestUrl) throws CollectorException {
return IOUtils.toInputStream(getInputSource(requestUrl));
}
/**
* @see HttpConnector2#getInputSource(java.lang.String, AggregatorReport)
*/
public String getInputSource(final String requestUrl) throws CollectorException {
return attemptDownloadAsString(requestUrl, 1, new AggregatorReport());
}
/**
* Given the URL returns the content via HTTP GET
*
* @param requestUrl the URL
* @param report the list of errors
* @return the content of the downloaded resource
* @throws CollectorException when retrying more than maxNumberOfRetry times
*/
public String getInputSource(final String requestUrl, AggregatorReport report)
throws CollectorException {
return attemptDownloadAsString(requestUrl, 1, report);
}
private String attemptDownloadAsString(final String requestUrl, final int retryNumber,
final AggregatorReport report) throws CollectorException {
try (InputStream s = attemptDownload(requestUrl, retryNumber, report)) {
return IOUtils.toString(s);
} catch (IOException e) {
log.error(e.getMessage(), e);
throw new CollectorException(e);
}
}
private InputStream attemptDownload(final String requestUrl, final int retryNumber,
final AggregatorReport report) throws CollectorException, IOException {
if (retryNumber > getClientParams().getMaxNumberOfRetry()) {
final String msg = String
.format(
"Max number of retries (%s/%s) exceeded, failing.",
retryNumber, getClientParams().getMaxNumberOfRetry());
log.error(msg);
throw new CollectorException(msg);
}
log.info("Request attempt {} [{}]", retryNumber, requestUrl);
InputStream input = null;
try {
if (getClientParams().getRequestDelay() > 0) {
backoffAndSleep(getClientParams().getRequestDelay());
}
final HttpURLConnection urlConn = (HttpURLConnection) new URL(requestUrl).openConnection();
urlConn.setInstanceFollowRedirects(false);
urlConn.setReadTimeout(getClientParams().getReadTimeOut() * 1000);
urlConn.setConnectTimeout(getClientParams().getConnectTimeOut() * 1000);
urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent);
if (log.isDebugEnabled()) {
logHeaderFields(urlConn);
}
int retryAfter = obtainRetryAfter(urlConn.getHeaderFields());
if (is2xx(urlConn.getResponseCode())) {
input = urlConn.getInputStream();
responseType = urlConn.getContentType();
return input;
}
if (is3xx(urlConn.getResponseCode())) {
// REDIRECTS
final String newUrl = obtainNewLocation(urlConn.getHeaderFields());
log.info(String.format("The requested url has been moved to %s", newUrl));
report
.put(
REPORT_PREFIX + urlConn.getResponseCode(),
String.format("Moved to: %s", newUrl));
urlConn.disconnect();
if (retryAfter > 0) {
backoffAndSleep(retryAfter);
}
return attemptDownload(newUrl, retryNumber + 1, report);
}
if (is4xx(urlConn.getResponseCode())) {
// CLIENT ERROR, DO NOT RETRY
report
.put(
REPORT_PREFIX + urlConn.getResponseCode(),
String
.format(
"%s error: %s", requestUrl, urlConn.getResponseMessage()));
throw new CollectorException("4xx error: request will not be repeated. " + report);
}
if (is5xx(urlConn.getResponseCode())) {
// SERVER SIDE ERRORS RETRY ONLY on 503
switch (urlConn.getResponseCode()) {
case HttpURLConnection.HTTP_UNAVAILABLE:
if (retryAfter > 0) {
log
.warn(
requestUrl + " - waiting and repeating request after suggested retry-after "
+ retryAfter + " sec.");
backoffAndSleep(retryAfter * 1000);
} else {
log
.warn(
requestUrl + " - waiting and repeating request after default delay of "
+ getClientParams().getRetryDelay() + " sec.");
backoffAndSleep(retryNumber * getClientParams().getRetryDelay() * 1000);
}
report.put(REPORT_PREFIX + urlConn.getResponseCode(), requestUrl);
urlConn.disconnect();
return attemptDownload(requestUrl, retryNumber + 1, report);
default:
report
.put(
REPORT_PREFIX + urlConn.getResponseCode(),
String
.format(
"%s Error: %s", requestUrl, urlConn.getResponseMessage()));
throw new CollectorException(urlConn.getResponseCode() + " error " + report);
}
}
throw new CollectorException(
String
.format(
"Unexpected status code: %s errors: %s", urlConn.getResponseCode(),
MAPPER.writeValueAsString(report)));
} catch (MalformedURLException | UnknownHostException e) {
log.error(e.getMessage(), e);
report.put(e.getClass().getName(), e.getMessage());
throw new CollectorException(e.getMessage(), e);
} catch (SocketTimeoutException | SocketException e) {
log.error(e.getMessage(), e);
report.put(e.getClass().getName(), e.getMessage());
backoffAndSleep(getClientParams().getRetryDelay() * retryNumber * 1000);
return attemptDownload(requestUrl, retryNumber + 1, report);
}
}
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 void backoffAndSleep(int sleepTimeMs) throws CollectorException {
log.info("I'm going to sleep for {}ms", sleepTimeMs);
try {
Thread.sleep(sleepTimeMs);
} catch (InterruptedException e) {
log.error(e.getMessage(), e);
throw new CollectorException(e);
}
}
private int obtainRetryAfter(final Map<String, List<String>> headerMap) {
for (String key : headerMap.keySet()) {
if ((key != null) && key.equalsIgnoreCase(HttpHeaders.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 CollectorException {
for (String key : headerMap.keySet()) {
if ((key != null) && key.equalsIgnoreCase(HttpHeaders.LOCATION) && (headerMap.get(key).size() > 0)) {
return headerMap.get(key).get(0);
}
}
throw new CollectorException("The requested url has been MOVED, but 'location' param is MISSING");
}
private boolean is2xx(final int statusCode) {
return statusCode >= 200 && statusCode <= 299;
}
private boolean is4xx(final int statusCode) {
return statusCode >= 400 && statusCode <= 499;
}
private boolean is3xx(final int statusCode) {
return statusCode >= 300 && statusCode <= 399;
}
private boolean is5xx(final int statusCode) {
return statusCode >= 500 && statusCode <= 599;
}
public String getResponseType() {
return responseType;
}
public HttpClientParams getClientParams() {
return clientParams;
}
public void setClientParams(HttpClientParams clientParams) {
this.clientParams = clientParams;
}
}

84
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/JsonUtils.java Normal file
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@ -0,0 +1,84 @@
package eu.dnetlib.dhp.collection;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
public class JsonUtils {
private static final Log log = LogFactory.getLog(JsonUtils.class);
public static final String wrapName = "recordWrap";
/**
* convert in JSON-KeyName 'whitespace(s)' to '_' and '/' to '_', '(' and ')' to ''
* check W3C XML syntax: https://www.w3.org/TR/2006/REC-xml11-20060816/#sec-starttags for valid tag names
* and work-around for the JSON to XML converting of org.json.XML-package.
*
* known bugs: doesn't prevent "key name":" ["sexy name",": penari","erotic dance"],
*
* @param jsonInput
* @return convertedJsonKeynameOutput
*/
public String syntaxConvertJsonKeyNames(String jsonInput) {
log.trace("before convertJsonKeyNames: " + jsonInput);
// pre-clean json - rid spaces of element names (misinterpreted as elements with attributes in xml)
// replace ' 's in JSON Namens with '_'
while (jsonInput.matches(".*\"([^\"]*)\\s+([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*)\\s+([^\"]*)\":", "\"$1_$2\":");
}
// replace forward-slash (sign '/' ) in JSON Names with '_'
while (jsonInput.matches(".*\"([^\"]*)/([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*)/([^\"]*)\":", "\"$1_$2\":");
}
// replace '(' in JSON Names with ''
while (jsonInput.matches(".*\"([^\"]*)[(]([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*)[(]([^\"]*)\":", "\"$1$2\":");
}
// replace ')' in JSON Names with ''
while (jsonInput.matches(".*\"([^\"]*)[)]([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*)[)]([^\"]*)\":", "\"$1$2\":");
}
// add prefix of startNumbers in JSON Keynames with 'n_'
while (jsonInput.matches(".*\"([^\"][0-9])([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"][0-9])([^\"]*)\":", "\"n_$1$2\":");
}
// add prefix of only numbers in JSON Keynames with 'm_'
while (jsonInput.matches(".*\"([0-9]+)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([0-9]+)\":", "\"m_$1\":");
}
// replace ':' between number like '2018-08-28T11:05:00Z' in JSON keynames with ''
while (jsonInput.matches(".*\"([^\"]*[0-9]):([0-9][^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*[0-9]):([0-9][^\"]*)\":", "\"$1$2\":");
}
// replace ',' in JSON Keynames with '.' to prevent , in xml tagnames.
// while (jsonInput.matches(".*\"([^\"]*),([^\"]*)\":.*")) {
// jsonInput = jsonInput.replaceAll("\"([^\"]*),([^\"]*)\":", "\"$1.$2\":");
// }
// replace '=' in JSON Keynames with '-'
while (jsonInput.matches(".*\"([^\"]*)=([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*)=([^\"]*)\":", "\"$1-$2\":");
}
log.trace("after syntaxConvertJsonKeyNames: " + jsonInput);
return jsonInput;
}
public String convertToXML(final String jsonRecord) {
String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
org.json.JSONObject jsonObject = new org.json.JSONObject(syntaxConvertJsonKeyNames(jsonRecord));
resultXml += org.json.XML.toString(jsonObject, wrapName); // wrap xml in single root element
log.trace("before inputStream: " + resultXml);
resultXml = XmlCleaner.cleanAllEntities(resultXml);
log.trace("after cleaning: " + resultXml);
return resultXml;
}
}

32
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/UnknownCollectorPluginException.java Normal file
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@ -0,0 +1,32 @@
package eu.dnetlib.dhp.collection;
public class UnknownCollectorPluginException extends Exception {
/** */
private static final long serialVersionUID = -290723075076039757L;
public UnknownCollectorPluginException() {
super();
}
public UnknownCollectorPluginException(
final String message,
final Throwable cause,
final boolean enableSuppression,
final boolean writableStackTrace) {
super(message, cause, enableSuppression, writableStackTrace);
}
public UnknownCollectorPluginException(final String message, final Throwable cause) {
super(message, cause);
}
public UnknownCollectorPluginException(final String message) {
super(message);
}
public UnknownCollectorPluginException(final Throwable cause) {
super(cause);
}
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/XmlCleaner.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/XmlCleaner.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.collection.worker.utils;
package eu.dnetlib.dhp.collection;
import java.util.HashMap;
import java.util.HashSet;

17
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
View File

@ -3,10 +3,21 @@ package eu.dnetlib.dhp.collection.plugin;
import java.util.stream.Stream;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.CollectorException;
public interface CollectorPlugin {
Stream<String> collect(ApiDescriptor api) throws DnetCollectorException;
enum NAME {
oai, other, rest_json2xml;
public enum OTHER_NAME {
mdstore_mongodb_dump, mdstore_mongodb
}
}
Stream<String> collect(ApiDescriptor api, AggregatorReport report) throws CollectorException;
}

58
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/mongodb/MDStoreCollectorPlugin.java Normal file
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@ -0,0 +1,58 @@
package eu.dnetlib.dhp.collection.plugin.mongodb;
import java.util.Optional;
import java.util.Spliterator;
import java.util.Spliterators;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;
import org.bson.Document;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.mongodb.client.MongoCollection;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.common.MdstoreClient;
public class MDStoreCollectorPlugin implements CollectorPlugin {
private static final Logger log = LoggerFactory.getLogger(MDStoreCollectorPlugin.class);
public static final String MONGODB_DBNAME = "mongodb_dbname";
public static final String MDSTORE_ID = "mdstore_id";
@Override
public Stream<String> collect(ApiDescriptor api, AggregatorReport report) throws CollectorException {
final String mongoBaseUrl = Optional
.ofNullable(api.getBaseUrl())
.orElseThrow(
() -> new CollectorException(
"missing mongodb baseUrl, expected in eu.dnetlib.dhp.collection.ApiDescriptor.baseUrl"));
log.info("mongoBaseUrl: {}", mongoBaseUrl);
final String dbName = Optional
.ofNullable(api.getParams().get(MONGODB_DBNAME))
.orElseThrow(() -> new CollectorException(String.format("missing parameter '%s'", MONGODB_DBNAME)));
log.info("dbName: {}", dbName);
final String mdId = Optional
.ofNullable(api.getParams().get(MDSTORE_ID))
.orElseThrow(() -> new CollectorException(String.format("missing parameter '%s'", MDSTORE_ID)));
log.info("mdId: {}", mdId);
final MdstoreClient client = new MdstoreClient(mongoBaseUrl, dbName);
final MongoCollection<Document> mdstore = client.mdStore(mdId);
long size = mdstore.count();
return StreamSupport
.stream(
Spliterators.spliterator(mdstore.find().iterator(), size, Spliterator.SIZED), false)
.map(doc -> doc.getString("body"));
}
}

54
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/mongodb/MongoDbDumpCollectorPlugin.java Normal file
View File

@ -0,0 +1,54 @@
package eu.dnetlib.dhp.collection.plugin.mongodb;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.nio.charset.Charset;
import java.util.Optional;
import java.util.stream.Stream;
import java.util.zip.GZIPInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.utils.DHPUtils;
public class MongoDbDumpCollectorPlugin implements CollectorPlugin {
public static final String PATH_PARAM = "path";
public static final String BODY_JSONPATH = "$.body";
public FileSystem fileSystem;
public MongoDbDumpCollectorPlugin(FileSystem fileSystem) {
this.fileSystem = fileSystem;
}
@Override
public Stream<String> collect(ApiDescriptor api, AggregatorReport report) throws CollectorException {
final Path path = Optional
.ofNullable(api.getParams().get("path"))
.map(Path::new)
.orElseThrow(() -> new CollectorException(String.format("missing parameter '%s'", PATH_PARAM)));
try {
if (!fileSystem.exists(path)) {
throw new CollectorException("path does not exist: " + path.toString());
}
return new BufferedReader(
new InputStreamReader(new GZIPInputStream(fileSystem.open(path)), Charset.defaultCharset()))
.lines()
.map(s -> DHPUtils.getJPathString(BODY_JSONPATH, s));
} catch (IOException e) {
throw new CollectorException(e);
}
}
}

33
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java
View File

@ -13,9 +13,11 @@ import com.google.common.base.Splitter;
import com.google.common.collect.Iterators;
import com.google.common.collect.Lists;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.HttpClientParams;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
public class OaiCollectorPlugin implements CollectorPlugin {
@ -26,8 +28,15 @@ public class OaiCollectorPlugin implements CollectorPlugin {
private OaiIteratorFactory oaiIteratorFactory;
private HttpClientParams clientParams;
public OaiCollectorPlugin(HttpClientParams clientParams) {
this.clientParams = clientParams;
}
@Override
public Stream<String> collect(final ApiDescriptor api) throws DnetCollectorException {
public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report)
throws CollectorException {
final String baseUrl = api.getBaseUrl();
final String mdFormat = api.getParams().get(FORMAT_PARAM);
final String setParam = api.getParams().get(OAI_SET_PARAM);
@ -46,26 +55,26 @@ public class OaiCollectorPlugin implements CollectorPlugin {
}
if (baseUrl == null || baseUrl.isEmpty()) {
throw new DnetCollectorException("Param 'baseurl' is null or empty");
throw new CollectorException("Param 'baseurl' is null or empty");
}
if (mdFormat == null || mdFormat.isEmpty()) {
throw new DnetCollectorException("Param 'mdFormat' is null or empty");
throw new CollectorException("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);
throw new CollectorException("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);
throw new CollectorException("Invalid date (YYYY-MM-DD): " + untilDate);
}
final Iterator<Iterator<String>> iters = sets
.stream()
.map(
set -> getOaiIteratorFactory()
.newIterator(baseUrl, mdFormat, set, fromDate, untilDate))
.newIterator(baseUrl, mdFormat, set, fromDate, untilDate, getClientParams(), report))
.iterator();
return StreamSupport
@ -79,4 +88,12 @@ public class OaiCollectorPlugin implements CollectorPlugin {
}
return oaiIteratorFactory;
}
public HttpClientParams getClientParams() {
return clientParams;
}
public void setClientParams(HttpClientParams clientParams) {
this.clientParams = clientParams;
}
}

83
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java
View File

@ -1,7 +1,9 @@
package eu.dnetlib.dhp.collection.plugin.oai;
import java.io.IOException;
import java.io.StringReader;
import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.Iterator;
@ -9,24 +11,28 @@ 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.DocumentHelper;
import org.dom4j.Node;
import org.dom4j.io.OutputFormat;
import org.dom4j.io.SAXReader;
import org.dom4j.io.XMLWriter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
import eu.dnetlib.dhp.collection.worker.utils.XmlCleaner;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.HttpConnector2;
import eu.dnetlib.dhp.collection.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 static final Logger log = LoggerFactory.getLogger(OaiIterator.class);
private final static String REPORT_PREFIX = "oai:";
private final Queue<String> queue = new PriorityBlockingQueue<>();
private final SAXReader reader = new SAXReader();
private final String baseUrl;
private final String set;
@ -35,7 +41,8 @@ public class OaiIterator implements Iterator<String> {
private final String untilDate;
private String token;
private boolean started;
private final HttpConnector httpConnector;
private final HttpConnector2 httpConnector;
private AggregatorReport report;
public OaiIterator(
final String baseUrl,
@ -43,7 +50,8 @@ public class OaiIterator implements Iterator<String> {
final String set,
final String fromDate,
final String untilDate,
final HttpConnector httpConnector) {
final HttpConnector2 httpConnector,
final AggregatorReport report) {
this.baseUrl = baseUrl;
this.mdFormat = mdFormat;
this.set = set;
@ -51,6 +59,7 @@ public class OaiIterator implements Iterator<String> {
this.untilDate = untilDate;
this.started = false;
this.httpConnector = httpConnector;
this.report = report;
}
private void verifyStarted() {
@ -58,7 +67,7 @@ public class OaiIterator implements Iterator<String> {
this.started = true;
try {
this.token = firstPage();
} catch (final DnetCollectorException e) {
} catch (final CollectorException e) {
throw new RuntimeException(e);
}
}
@ -80,7 +89,7 @@ public class OaiIterator implements Iterator<String> {
while (queue.isEmpty() && token != null && !token.isEmpty()) {
try {
token = otherPages(token);
} catch (final DnetCollectorException e) {
} catch (final CollectorException e) {
throw new RuntimeException(e);
}
}
@ -92,7 +101,7 @@ public class OaiIterator implements Iterator<String> {
public void remove() {
}
private String firstPage() throws DnetCollectorException {
private String firstPage() throws CollectorException {
try {
String url = baseUrl + "?verb=ListRecords&metadataPrefix=" + URLEncoder.encode(mdFormat, "UTF-8");
if (set != null && !set.isEmpty()) {
@ -108,7 +117,8 @@ public class OaiIterator implements Iterator<String> {
return downloadPage(url);
} catch (final UnsupportedEncodingException e) {
throw new DnetCollectorException(e);
report.put(e.getClass().getName(), e.getMessage());
throw new CollectorException(e);
}
}
@ -126,32 +136,35 @@ public class OaiIterator implements Iterator<String> {
return result.trim();
}
private String otherPages(final String resumptionToken) throws DnetCollectorException {
private String otherPages(final String resumptionToken) throws CollectorException {
try {
return downloadPage(
baseUrl
+ "?verb=ListRecords&resumptionToken="
+ URLEncoder.encode(resumptionToken, "UTF-8"));
} catch (final UnsupportedEncodingException e) {
throw new DnetCollectorException(e);
report.put(e.getClass().getName(), e.getMessage());
throw new CollectorException(e);
}
}
private String downloadPage(final String url) throws DnetCollectorException {
private String downloadPage(final String url) throws CollectorException {
final String xml = httpConnector.getInputSource(url);
final String xml = httpConnector.getInputSource(url, report);
Document doc;
try {
doc = reader.read(new StringReader(xml));
doc = DocumentHelper.parseText(xml);
} catch (final DocumentException e) {
log.warn("Error parsing xml, I try to clean it: " + xml, e);
log.warn("Error parsing xml, I try to clean it. {}", e.getMessage());
report.put(e.getClass().getName(), e.getMessage());
final String cleaned = XmlCleaner.cleanAllEntities(xml);
try {
doc = reader.read(new StringReader(cleaned));
doc = DocumentHelper.parseText(xml);
} catch (final DocumentException e1) {
final String resumptionToken = extractResumptionToken(xml);
if (resumptionToken == null) {
throw new DnetCollectorException("Error parsing cleaned document:" + cleaned, e1);
report.put(e1.getClass().getName(), e1.getMessage());
throw new CollectorException("Error parsing cleaned document:\n" + cleaned, e1);
}
return resumptionToken;
}
@ -159,19 +172,35 @@ public class OaiIterator implements Iterator<String> {
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);
final String code = errorNode.valueOf("@code").trim();
if ("noRecordsMatch".equalsIgnoreCase(code)) {
final String msg = "noRecordsMatch for oai call : " + url;
log.warn(msg);
report.put(REPORT_PREFIX + code, msg);
return null;
} else {
throw new DnetCollectorException(code + " - " + errorNode.getText());
final String msg = code + " - " + errorNode.getText();
report.put(REPORT_PREFIX + "error", msg);
throw new CollectorException(msg);
}
}
for (final Object o : doc.selectNodes("//*[local-name()='ListRecords']/*[local-name()='record']")) {
queue.add(((Node) o).asXML());
final StringWriter sw = new StringWriter();
final XMLWriter writer = new XMLWriter(sw, OutputFormat.createPrettyPrint());
try {
writer.write((Node) o);
queue.add(sw.toString());
} catch (IOException e) {
report.put(e.getClass().getName(), e.getMessage());
throw new CollectorException("Error parsing XML record:\n" + ((Node) o).asXML(), e);
}
}
return doc.valueOf("//*[local-name()='resumptionToken']");
}
public AggregatorReport getReport() {
return report;
}
}

16
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIteratorFactory.java
View File

@ -3,24 +3,28 @@ package eu.dnetlib.dhp.collection.plugin.oai;
import java.util.Iterator;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.HttpClientParams;
import eu.dnetlib.dhp.collection.HttpConnector2;
public class OaiIteratorFactory {
private HttpConnector httpConnector;
private HttpConnector2 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, getHttpConnector());
final String untilDate,
final HttpClientParams clientParams,
final AggregatorReport report) {
return new OaiIterator(baseUrl, mdFormat, set, fromDate, untilDate, getHttpConnector(clientParams), report);
}
private HttpConnector getHttpConnector() {
private HttpConnector2 getHttpConnector(HttpClientParams clientParams) {
if (httpConnector == null)
httpConnector = new HttpConnector();
httpConnector = new HttpConnector2(clientParams);
return httpConnector;
}
}

105
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestCollectorPlugin.java Normal file
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@ -0,0 +1,105 @@
package eu.dnetlib.dhp.collection.plugin.rest;
import java.util.Optional;
import java.util.Spliterator;
import java.util.Spliterators;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.HttpClientParams;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
/**
* TODO: delegate HTTP requests to the common HttpConnector2 implementation.
*
* @author js, Andreas Czerniak
* @date 2020-04-09
*
*/
public class RestCollectorPlugin implements CollectorPlugin {
public static final String RESULT_SIZE_VALUE_DEFAULT = "100";
private HttpClientParams clientParams;
public RestCollectorPlugin(HttpClientParams clientParams) {
this.clientParams = clientParams;
}
@Override
public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException {
final String baseUrl = api.getBaseUrl();
final String resumptionType = api.getParams().get("resumptionType");
final String resumptionParam = api.getParams().get("resumptionParam");
final String resumptionXpath = api.getParams().get("resumptionXpath");
final String resultTotalXpath = api.getParams().get("resultTotalXpath");
final String resultFormatParam = api.getParams().get("resultFormatParam");
final String resultFormatValue = api.getParams().get("resultFormatValue");
final String resultSizeParam = api.getParams().get("resultSizeParam");
final String queryParams = api.getParams().get("queryParams");
final String entityXpath = api.getParams().get("entityXpath");
final String authMethod = api.getParams().get("authMethod");
final String authToken = api.getParams().get("authToken");
final String resultSizeValue = Optional
.ofNullable(api.getParams().get("resultSizeValue"))
.filter(StringUtils::isNotBlank)
.orElse(RESULT_SIZE_VALUE_DEFAULT);
if (StringUtils.isBlank(baseUrl)) {
throw new CollectorException("Param 'baseUrl' is null or empty");
}
if (StringUtils.isBlank(resumptionType)) {
throw new CollectorException("Param 'resumptionType' is null or empty");
}
if (StringUtils.isBlank(resumptionParam)) {
throw new CollectorException("Param 'resumptionParam' is null or empty");
}
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");
}
final String resultOutputFormat = Optional
.ofNullable(api.getParams().get("resultOutputFormat"))
.map(String::toLowerCase)
.filter(StringUtils::isNotBlank)
.orElse(resultFormatValue.toLowerCase());
RestIterator it = new RestIterator(
getClientParams(),
baseUrl,
resumptionType,
resumptionParam,
resumptionXpath,
resultTotalXpath,
resultFormatParam,
resultFormatValue,
resultSizeParam,
resultSizeValue,
queryParams,
entityXpath,
authMethod,
authToken,
resultOutputFormat);
return StreamSupport
.stream(
Spliterators.spliteratorUnknownSize(it, Spliterator.ORDERED), false);
}
public HttpClientParams getClientParams() {
return clientParams;
}
}

412
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java Normal file
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@ -0,0 +1,412 @@
package eu.dnetlib.dhp.collection.plugin.rest;
import java.io.InputStream;
import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLEncoder;
import java.nio.charset.StandardCharsets;
import java.util.Iterator;
import java.util.Queue;
import java.util.concurrent.PriorityBlockingQueue;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import javax.xml.xpath.*;
import org.apache.avro.test.http.Http;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.HttpHeaders;
import org.apache.http.entity.ContentType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.HttpClientParams;
import eu.dnetlib.dhp.collection.JsonUtils;
/**
* log.info(...) equal to log.trace(...) in the application-logs
* <p>
* known bug: at resumptionType 'discover' if the (resultTotal % resultSizeValue) == 0 the collecting fails -> change the resultSizeValue
*
* @author Jochen Schirrwagen, Aenne Loehden, Andreas Czerniak
* @date 2020-04-09
*
*/
public class RestIterator implements Iterator<String> {
private static final Logger log = LoggerFactory.getLogger(RestIterator.class);
public static final String UTF_8 = "UTF-8";
private HttpClientParams clientParams;
private final String BASIC = "basic";
private JsonUtils jsonUtils;
private String baseUrl;
private String resumptionType;
private String resumptionParam;
private String resultFormatValue;
private String queryParams;
private int resultSizeValue;
private int resumptionInt = 0; // integer resumption token (first record to harvest)
private int resultTotal = -1;
private String resumptionStr = Integer.toString(resumptionInt); // string resumption token (first record to harvest
// or token scanned from results)
private InputStream resultStream;
private Transformer transformer;
private XPath xpath;
private String query;
private XPathExpression xprResultTotalPath;
private XPathExpression xprResumptionPath;
private XPathExpression xprEntity;
private String queryFormat;
private String querySize;
private String authMethod;
private String authToken;
private Queue<String> recordQueue = new PriorityBlockingQueue<String>();
private int discoverResultSize = 0;
private int pagination = 1;
/*
* While resultFormatValue is added to the request parameter, this is used to say that the results are retrieved in
* json. useful for cases when the target API expects a resultFormatValue != json, but the results are returned in
* json. An example is the EU Open Data Portal API: resultFormatValue=standard, results are in json format.
*/
private String resultOutputFormat;
/** RestIterator class
* compatible to version 1.3.33
*/
public RestIterator(
final HttpClientParams clientParams,
final String baseUrl,
final String resumptionType,
final String resumptionParam,
final String resumptionXpath,
final String resultTotalXpath,
final String resultFormatParam,
final String resultFormatValue,
final String resultSizeParam,
final String resultSizeValueStr,
final String queryParams,
final String entityXpath,
final String authMethod,
final String authToken,
final String resultOutputFormat) {
this.clientParams = clientParams;
this.jsonUtils = new JsonUtils();
this.baseUrl = baseUrl;
this.resumptionType = resumptionType;
this.resumptionParam = resumptionParam;
this.resultFormatValue = resultFormatValue;
this.resultSizeValue = Integer.valueOf(resultSizeValueStr);
this.queryParams = queryParams;
this.authMethod = authMethod;
this.authToken = authToken;
this.resultOutputFormat = resultOutputFormat;
queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue
: "";
querySize = StringUtils.isNotBlank(resultSizeParam) ? "&" + resultSizeParam + "=" + resultSizeValueStr : "";
try {
initXmlTransformation(resultTotalXpath, resumptionXpath, entityXpath);
} catch (Exception e) {
throw new IllegalStateException("xml transformation init failed: " + e.getMessage());
}
initQueue();
}
private void initXmlTransformation(String resultTotalXpath, String resumptionXpath, String entityXpath)
throws TransformerConfigurationException, XPathExpressionException {
transformer = TransformerFactory.newInstance().newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
xpath = XPathFactory.newInstance().newXPath();
xprResultTotalPath = xpath.compile(resultTotalXpath);
xprResumptionPath = xpath.compile(StringUtils.isBlank(resumptionXpath) ? "/" : resumptionXpath);
xprEntity = xpath.compile(entityXpath);
}
private void initQueue() {
query = baseUrl + "?" + queryParams + querySize + queryFormat;
log.info("REST calls starting with " + query);
}
private void disconnect() {
// TODO close inputstream
}
/*
* (non-Javadoc)
* @see java.util.Iterator#hasNext()
*/
@Override
public boolean hasNext() {
if (recordQueue.isEmpty() && query.isEmpty()) {
disconnect();
return false;
} else {
return true;
}
}
/*
* (non-Javadoc)
* @see java.util.Iterator#next()
*/
@Override
public String next() {
synchronized (recordQueue) {
while (recordQueue.isEmpty() && !query.isEmpty()) {
try {
query = downloadPage(query);
} catch (CollectorException e) {
log.debug("CollectorPlugin.next()-Exception: " + e);
throw new RuntimeException(e);
}
}
return recordQueue.poll();
}
}
/*
* download page and return nextQuery
*/
private String downloadPage(String query) throws CollectorException {
String resultJson;
String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
String nextQuery = "";
String emptyXml = resultXml + "<" + JsonUtils.wrapName + "></" + JsonUtils.wrapName + ">";
Node resultNode = null;
NodeList nodeList = null;
String qUrlArgument = "";
int urlOldResumptionSize = 0;
InputStream theHttpInputStream;
// check if cursor=* is initial set otherwise add it to the queryParam URL
if (resumptionType.equalsIgnoreCase("deep-cursor")) {
log.debug("check resumptionType deep-cursor and check cursor=*?" + query);
if (!query.contains("&cursor=")) {
query += "&cursor=*";
}
}
try {
log.info("requestig URL [{}]", query);
URL qUrl = new URL(query);
log.debug("authMethod :" + authMethod);
if ("bearer".equalsIgnoreCase(this.authMethod)) {
log.trace("authMethod before inputStream: " + resultXml);
HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + authToken);
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.getMimeType());
conn.setRequestMethod("GET");
theHttpInputStream = conn.getInputStream();
} else if (BASIC.equalsIgnoreCase(this.authMethod)) {
log.trace("authMethod before inputStream: " + resultXml);
HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Basic " + authToken);
conn.setRequestProperty(HttpHeaders.ACCEPT, ContentType.APPLICATION_XML.getMimeType());
conn.setRequestMethod("GET");
theHttpInputStream = conn.getInputStream();
} else {
theHttpInputStream = qUrl.openStream();
}
resultStream = theHttpInputStream;
if ("json".equals(resultOutputFormat)) {
resultJson = IOUtils.toString(resultStream, UTF_8);
resultXml = jsonUtils.convertToXML(resultJson);
resultStream = IOUtils.toInputStream(resultXml, UTF_8);
}
if (!(emptyXml).equalsIgnoreCase(resultXml)) {
resultNode = (Node) xpath.evaluate("/", new InputSource(resultStream), XPathConstants.NODE);
nodeList = (NodeList) xprEntity.evaluate(resultNode, XPathConstants.NODESET);
log.debug("nodeList.length: " + nodeList.getLength());
for (int i = 0; i < nodeList.getLength(); i++) {
StringWriter sw = new StringWriter();
transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
String toEnqueue = sw.toString();
if (toEnqueue == null || StringUtils.isBlank(toEnqueue) || emptyXml.equalsIgnoreCase(toEnqueue)) {
log.warn("The following record resulted in empty item for the feeding queue: " + resultXml);
} else {
recordQueue.add(sw.toString());
}
}
} else {
log.warn("resultXml is equal with emptyXml");
}
resumptionInt += resultSizeValue;
switch (resumptionType.toLowerCase()) {
case "scan": // read of resumptionToken , evaluate next results, e.g. OAI, iterate over items
resumptionStr = xprResumptionPath.evaluate(resultNode);
break;
case "count": // begin at one step for all records, iterate over items
resumptionStr = Integer.toString(resumptionInt);
break;
case "discover": // size of result items unknown, iterate over items (for openDOAR - 201808)
if (resultSizeValue < 2) {
throw new CollectorException("Mode: discover, Param 'resultSizeValue' is less than 2");
}
qUrlArgument = qUrl.getQuery();
String[] arrayQUrlArgument = qUrlArgument.split("&");
for (String arrayUrlArgStr : arrayQUrlArgument) {
if (arrayUrlArgStr.startsWith(resumptionParam)) {
String[] resumptionKeyValue = arrayUrlArgStr.split("=");
if (isInteger(resumptionKeyValue[1])) {
urlOldResumptionSize = Integer.parseInt(resumptionKeyValue[1]);
log.debug("discover OldResumptionSize from Url (int): " + urlOldResumptionSize);
} else {
log.debug("discover OldResumptionSize from Url (str): " + resumptionKeyValue[1]);
}
}
}
if (((emptyXml).equalsIgnoreCase(resultXml))
|| ((nodeList != null) && (nodeList.getLength() < resultSizeValue))) {
// resumptionStr = "";
if (nodeList != null) {
discoverResultSize += nodeList.getLength();
}
resultTotal = discoverResultSize;
} else {
resumptionStr = Integer.toString(resumptionInt);
resultTotal = resumptionInt + 1;
if (nodeList != null) {
discoverResultSize += nodeList.getLength();
}
}
log.info("discoverResultSize: {}", discoverResultSize);
break;
case "pagination":
case "page": // pagination, iterate over page numbers
pagination += 1;
if (nodeList != null) {
discoverResultSize += nodeList.getLength();
} else {
resultTotal = discoverResultSize;
pagination = discoverResultSize;
}
resumptionInt = pagination;
resumptionStr = Integer.toString(resumptionInt);
break;
case "deep-cursor": // size of result items unknown, iterate over items (for supporting deep cursor in
// solr)
// isn't relevant -- if (resultSizeValue < 2) {throw new CollectorServiceException("Mode:
// deep-cursor, Param 'resultSizeValue' is less than 2");}
resumptionStr = encodeValue(xprResumptionPath.evaluate(resultNode));
queryParams = queryParams.replace("&cursor=*", "");
// terminating if length of nodeList is 0
if ((nodeList != null) && (nodeList.getLength() < discoverResultSize)) {
resumptionInt += (nodeList.getLength() + 1 - resultSizeValue);
} else {
resumptionInt += (nodeList.getLength() - resultSizeValue); // subtract the resultSizeValue
// because the iteration is over
// real length and the
// resultSizeValue is added before
// the switch()
}
discoverResultSize = nodeList.getLength();
log
.debug(
"downloadPage().deep-cursor: resumptionStr=" + resumptionStr + " ; queryParams="
+ queryParams + " resumptionLengthIncreased: " + resumptionInt);
break;
default: // otherwise: abort
// resultTotal = resumptionInt;
break;
}
} catch (Exception e) {
log.error(e.getMessage(), e);
throw new IllegalStateException("collection failed: " + e.getMessage());
}
try {
if (resultTotal == -1) {
resultTotal = Integer.parseInt(xprResultTotalPath.evaluate(resultNode));
if (resumptionType.equalsIgnoreCase("page") && !BASIC.equalsIgnoreCase(authMethod)) {
resultTotal += 1;
} // to correct the upper bound
log.info("resultTotal was -1 is now: " + resultTotal);
}
} catch (Exception e) {
log.error(e.getMessage(), e);
throw new IllegalStateException("downloadPage resultTotal couldn't parse: " + e.getMessage());
}
log.debug("resultTotal: " + resultTotal);
log.debug("resInt: " + resumptionInt);
if (resumptionInt <= resultTotal) {
nextQuery = baseUrl + "?" + queryParams + querySize + "&" + resumptionParam + "=" + resumptionStr
+ queryFormat;
} else {
nextQuery = "";
// if (resumptionType.toLowerCase().equals("deep-cursor")) { resumptionInt -= 1; } // correct the
// resumptionInt and prevent a NullPointer Exception at mdStore
}
log.debug("nextQueryUrl: " + nextQuery);
return nextQuery;
}
private boolean isInteger(String s) {
boolean isValidInteger = false;
try {
Integer.parseInt(s);
// s is a valid integer
isValidInteger = true;
} catch (NumberFormatException ex) {
// s is not an integer
}
return isValidInteger;
}
// Method to encode a string value using `UTF-8` encoding scheme
private String encodeValue(String value) {
try {
return URLEncoder.encode(value, StandardCharsets.UTF_8.toString());
} catch (UnsupportedEncodingException ex) {
throw new RuntimeException(ex.getCause());
}
}
public String getResultFormatValue() {
return resultFormatValue;
}
public String getResultOutputFormat() {
return resultOutputFormat;
}
}

139
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorker.java
View File

@ -1,139 +0,0 @@
package eu.dnetlib.dhp.collection.worker;
import java.io.IOException;
import java.net.URI;
import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.atomic.AtomicInteger;
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 com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
import eu.dnetlib.message.Message;
import eu.dnetlib.message.MessageManager;
import eu.dnetlib.message.MessageType;
public class DnetCollectorWorker {
private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorker.class);
private final CollectorPluginFactory collectorPluginFactory;
private final ArgumentApplicationParser argumentParser;
private final MessageManager manager;
public DnetCollectorWorker(
final CollectorPluginFactory collectorPluginFactory,
final ArgumentApplicationParser argumentParser,
final MessageManager manager)
throws DnetCollectorException {
this.collectorPluginFactory = collectorPluginFactory;
this.argumentParser = argumentParser;
this.manager = manager;
}
public void collect() throws DnetCollectorException {
try {
final ObjectMapper jsonMapper = new ObjectMapper();
final ApiDescriptor api = jsonMapper.readValue(argumentParser.get("apidescriptor"), ApiDescriptor.class);
final CollectorPlugin plugin = collectorPluginFactory.getPluginByProtocol(api.getProtocol());
final String hdfsuri = argumentParser.get("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", argumentParser.get("userHDFS"));
System.setProperty("hadoop.home.dir", "/");
// Get the filesystem - HDFS
FileSystem.get(URI.create(hdfsuri), conf);
Path hdfswritepath = new Path(argumentParser.get("hdfsPath"));
log.info("Created path " + hdfswritepath.toString());
final Map<String, String> ongoingMap = new HashMap<>();
final Map<String, String> reportMap = new HashMap<>();
final AtomicInteger counter = new AtomicInteger(0);
try (SequenceFile.Writer writer = SequenceFile
.createWriter(
conf,
SequenceFile.Writer.file(hdfswritepath),
SequenceFile.Writer.keyClass(IntWritable.class),
SequenceFile.Writer.valueClass(Text.class))) {
final IntWritable key = new IntWritable(counter.get());
final Text value = new Text();
plugin
.collect(api)
.forEach(
content -> {
key.set(counter.getAndIncrement());
value.set(content);
if (counter.get() % 10 == 0) {
try {
ongoingMap.put("ongoing", "" + counter.get());
log
.debug(
"Sending message: "
+ manager
.sendMessage(
new Message(
argumentParser.get("workflowId"),
"Collection",
MessageType.ONGOING,
ongoingMap),
argumentParser.get("rabbitOngoingQueue"),
true,
false));
} catch (Exception e) {
log.error("Error on sending message ", e);
}
}
try {
writer.append(key, value);
} catch (IOException e) {
throw new RuntimeException(e);
}
});
}
ongoingMap.put("ongoing", "" + counter.get());
manager
.sendMessage(
new Message(
argumentParser.get("workflowId"), "Collection", MessageType.ONGOING, ongoingMap),
argumentParser.get("rabbitOngoingQueue"),
true,
false);
reportMap.put("collected", "" + counter.get());
manager
.sendMessage(
new Message(
argumentParser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
argumentParser.get("rabbitOngoingQueue"),
true,
false);
manager.close();
} catch (Throwable e) {
throw new DnetCollectorException("Error on collecting ", e);
}
}
}

49
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorkerApplication.java
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@ -1,49 +0,0 @@
package eu.dnetlib.dhp.collection.worker;
import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
import eu.dnetlib.message.MessageManager;
/**
* 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
*/
public class DnetCollectorWorkerApplication {
private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorkerApplication.class);
private static final CollectorPluginFactory collectorPluginFactory = new CollectorPluginFactory();
private static ArgumentApplicationParser argumentParser;
/** @param args */
public static void main(final String[] args) throws Exception {
argumentParser = new ArgumentApplicationParser(
IOUtils
.toString(
DnetCollectorWorker.class
.getResourceAsStream(
"/eu/dnetlib/collector/worker/collector_parameter.json")));
argumentParser.parseArgument(args);
log.info("hdfsPath =" + argumentParser.get("hdfsPath"));
log.info("json = " + argumentParser.get("apidescriptor"));
final MessageManager manager = new MessageManager(
argumentParser.get("rabbitHost"),
argumentParser.get("rabbitUser"),
argumentParser.get("rabbitPassword"),
false,
false,
null);
final DnetCollectorWorker worker = new DnetCollectorWorker(collectorPluginFactory, argumentParser, manager);
worker.collect();
}
}

19
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginErrorLogList.java
View File

@ -1,19 +0,0 @@
package eu.dnetlib.dhp.collection.worker.utils;
import java.util.LinkedList;
public class CollectorPluginErrorLogList extends LinkedList<String> {
private static final long serialVersionUID = -6925786561303289704L;
@Override
public String toString() {
String log = "";
int index = 0;
for (final String errorMessage : this) {
log += String.format("Retry #%s: %s / ", index++, errorMessage);
}
return log;
}
}

20
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginFactory.java
View File

@ -1,20 +0,0 @@
package eu.dnetlib.dhp.collection.worker.utils;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
public class CollectorPluginFactory {
public CollectorPlugin getPluginByProtocol(final String protocol) throws DnetCollectorException {
if (protocol == null)
throw new DnetCollectorException("protocol cannot be null");
switch (protocol.toLowerCase().trim()) {
case "oai":
return new OaiCollectorPlugin();
default:
throw new DnetCollectorException("UNknown protocol");
}
}
}

244
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/HttpConnector.java
View File

@ -1,244 +0,0 @@
package eu.dnetlib.dhp.collection.worker.utils;
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.lang.math.NumberUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
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 DnetCollectorException 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 DnetCollectorException 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;
}
}

29
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/DnetTransformationException.java Normal file
View File

@ -0,0 +1,29 @@
package eu.dnetlib.dhp.transformation;
public class DnetTransformationException extends Exception {
public DnetTransformationException() {
super();
}
public DnetTransformationException(
final String message,
final Throwable cause,
final boolean enableSuppression,
final boolean writableStackTrace) {
super(message, cause, enableSuppression, writableStackTrace);
}
public DnetTransformationException(final String message, final Throwable cause) {
super(message, cause);
}
public DnetTransformationException(final String message) {
super(message);
}
public DnetTransformationException(final Throwable cause) {
super(cause);
}
}

149
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java
View File

@ -1,15 +1,14 @@
package eu.dnetlib.dhp.transformation;
import static eu.dnetlib.dhp.common.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static eu.dnetlib.dhp.utils.DHPUtils.*;
import java.io.ByteArrayInputStream;
import java.util.HashMap;
import java.io.IOException;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
@ -17,22 +16,18 @@ import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.util.LongAccumulator;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
import eu.dnetlib.dhp.aggregation.common.AggregationCounter;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
import eu.dnetlib.dhp.transformation.vocabulary.VocabularyHelper;
import eu.dnetlib.dhp.utils.DHPUtils;
import eu.dnetlib.message.Message;
import eu.dnetlib.message.MessageManager;
import eu.dnetlib.message.MessageType;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.message.MessageSender;
import eu.dnetlib.dhp.schema.mdstore.MetadataRecord;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class TransformSparkJobNode {
@ -55,67 +50,85 @@ public class TransformSparkJobNode {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("input");
final String outputPath = parser.get("output");
final String workflowId = parser.get("workflowId");
final String trasformationRule = extractXSLTFromTR(
Objects.requireNonNull(DHPUtils.decompressString(parser.get("transformationRule"))));
final String mdstoreInputVersion = parser.get("mdstoreInputVersion");
final String mdstoreOutputVersion = parser.get("mdstoreOutputVersion");
final String rabbitUser = parser.get("rabbitUser");
final String rabbitPassword = parser.get("rabbitPassword");
final String rabbitHost = parser.get("rabbitHost");
final String rabbitReportQueue = parser.get("rabbitReportQueue");
final long dateOfCollection = new Long(parser.get("dateOfCollection"));
final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));
final MDStoreVersion nativeMdStoreVersion = MAPPER.readValue(mdstoreInputVersion, MDStoreVersion.class);
final String inputPath = nativeMdStoreVersion.getHdfsPath() + MDSTORE_DATA_PATH;
log.info("inputPath: {}", inputPath);
final MDStoreVersion cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, MDStoreVersion.class);
final String outputBasePath = cleanedMdStoreVersion.getHdfsPath();
log.info("outputBasePath: {}", outputBasePath);
final String isLookupUrl = parser.get("isLookupUrl");
log.info(String.format("isLookupUrl: %s", isLookupUrl));
final String dateOfTransformation = parser.get("dateOfTransformation");
log.info(String.format("dateOfTransformation: %s", dateOfTransformation));
final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
final VocabularyGroup vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService);
log.info("Retrieved {} vocabularies", vocabularies.vocabularyNames().size());
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
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 LongAccumulator errorItems = spark.sparkContext().longAccumulator("errorItems");
final LongAccumulator transformedItems = spark.sparkContext().longAccumulator("transformedItems");
final Map<String, Vocabulary> vocabularies = new HashMap<>();
vocabularies.put("dnet:languages", VocabularyHelper.getVocabularyFromAPI("dnet:languages"));
final TransformFunction transformFunction = new TransformFunction(
totalItems,
errorItems,
transformedItems,
trasformationRule,
dateOfCollection,
vocabularies);
mdstoreInput.map(transformFunction, encoder).write().format("parquet").save(outputPath);
if (rabbitHost != null) {
System.out.println("SEND FINAL REPORT");
final Map<String, String> reportMap = new HashMap<>();
reportMap.put("inputItem", "" + totalItems.value());
reportMap.put("invalidRecords", "" + errorItems.value());
reportMap.put("mdStoreSize", "" + transformedItems.value());
System.out.println(new Message(workflowId, "Transform", MessageType.REPORT, reportMap));
if (!test) {
final MessageManager manager = new MessageManager(rabbitHost, rabbitUser, rabbitPassword, false,
false,
null);
manager
.sendMessage(
new Message(workflowId, "Transform", MessageType.REPORT, reportMap),
rabbitReportQueue,
true,
false);
manager.close();
}
}
transformRecords(
parser.getObjectMap(), isLookupService, spark, inputPath, outputBasePath);
});
}
private static String extractXSLTFromTR(final String tr) throws DocumentException {
SAXReader reader = new SAXReader();
Document document = reader.read(new ByteArrayInputStream(tr.getBytes()));
Node node = document.selectSingleNode("//CODE/*[local-name()='stylesheet']");
return node.asXML();
public static void transformRecords(final Map<String, String> args, final ISLookUpService isLookUpService,
final SparkSession spark, final String inputPath, final String outputBasePath)
throws DnetTransformationException, IOException {
final LongAccumulator totalItems = spark.sparkContext().longAccumulator(CONTENT_TOTALITEMS);
final LongAccumulator errorItems = spark.sparkContext().longAccumulator(CONTENT_INVALIDRECORDS);
final LongAccumulator transformedItems = spark.sparkContext().longAccumulator(CONTENT_TRANSFORMEDRECORDS);
final AggregationCounter ct = new AggregationCounter(totalItems, errorItems, transformedItems);
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final String dnetMessageManagerURL = args.get(DNET_MESSAGE_MGR_URL);
log.info("dnetMessageManagerURL is {}", dnetMessageManagerURL);
final String workflowId = args.get("workflowId");
log.info("workflowId is {}", workflowId);
final MessageSender messageSender = new MessageSender(dnetMessageManagerURL, workflowId);
try (AggregatorReport report = new AggregatorReport(messageSender)) {
try {
final Dataset<MetadataRecord> mdstore = spark
.read()
.format("parquet")
.load(inputPath)
.as(encoder)
.map(
TransformationFactory.getTransformationPlugin(args, ct, isLookUpService),
encoder);
saveDataset(mdstore, outputBasePath + MDSTORE_DATA_PATH);
log.info("Transformed item " + ct.getProcessedItems().count());
log.info("Total item " + ct.getTotalItems().count());
log.info("Transformation Error item " + ct.getErrorItems().count());
final long mdStoreSize = spark.read().load(outputBasePath + MDSTORE_DATA_PATH).count();
writeHdfsFile(
spark.sparkContext().hadoopConfiguration(),
"" + mdStoreSize, outputBasePath + MDSTORE_SIZE_PATH);
} catch (Throwable e) {
log.error("error during record transformation", e);
report.put(TransformSparkJobNode.class.getSimpleName(), e.getMessage());
report.put(CONTENT_TOTALITEMS, ct.getTotalItems().value().toString());
report.put(CONTENT_INVALIDRECORDS, ct.getErrorItems().value().toString());
report.put(CONTENT_TRANSFORMEDRECORDS, ct.getProcessedItems().value().toString());
throw e;
}
}
}
}

69
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformationFactory.java Normal file
View File

@ -0,0 +1,69 @@
package eu.dnetlib.dhp.transformation;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.api.java.function.MapFunction;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.aggregation.common.AggregationCounter;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.mdstore.MetadataRecord;
import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class TransformationFactory {
private static final Logger log = LoggerFactory.getLogger(TransformationFactory.class);
public static final String TRULE_XQUERY = "for $x in collection('/db/DRIVER/TransformationRuleDSResources/TransformationRuleDSResourceType') where $x//RESOURCE_IDENTIFIER/@value = \"%s\" return $x//CODE/*[local-name() =\"stylesheet\"]";
public static MapFunction<MetadataRecord, MetadataRecord> getTransformationPlugin(
final Map<String, String> jobArgument, final AggregationCounter counters, final ISLookUpService isLookupService)
throws DnetTransformationException {
try {
final String transformationPlugin = jobArgument.get("transformationPlugin");
log.info("Transformation plugin required " + transformationPlugin);
switch (transformationPlugin) {
case "XSLT_TRANSFORM": {
final String transformationRuleId = jobArgument.get("transformationRuleId");
if (StringUtils.isBlank(transformationRuleId))
throw new DnetTransformationException("Missing Parameter transformationRule");
final VocabularyGroup vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService);
final String transformationRule = queryTransformationRuleFromIS(
transformationRuleId, isLookupService);
final long dateOfTransformation = new Long(jobArgument.get("dateOfTransformation"));
return new XSLTTransformationFunction(counters, transformationRule, dateOfTransformation,
vocabularies);
}
default:
throw new DnetTransformationException(
"transformation plugin does not exists for " + transformationPlugin);
}
} catch (Throwable e) {
throw new DnetTransformationException(e);
}
}
private static String queryTransformationRuleFromIS(final String transformationRuleId,
final ISLookUpService isLookUpService) throws Exception {
final String query = String.format(TRULE_XQUERY, transformationRuleId);
System.out.println("asking query to IS: " + query);
List<String> result = isLookUpService.quickSearchProfile(query);
if (result == null || result.isEmpty())
throw new DnetTransformationException(
"Unable to find transformation rule with name: " + transformationRuleId);
return result.get(0);
}
}

53
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/Term.java
View File

@ -1,53 +0,0 @@
package eu.dnetlib.dhp.transformation.vocabulary;
import java.io.Serializable;
public class Term implements Serializable {
private String englishName;
private String nativeName;
private String encoding;
private String code;
private String synonyms;
public String getEnglishName() {
return englishName;
}
public void setEnglishName(String englishName) {
this.englishName = englishName;
}
public String getNativeName() {
return nativeName;
}
public void setNativeName(String nativeName) {
this.nativeName = nativeName;
}
public String getEncoding() {
return encoding;
}
public void setEncoding(String encoding) {
this.encoding = encoding;
}
public String getCode() {
return code;
}
public void setCode(String code) {
this.code = code;
}
public String getSynonyms() {
return synonyms;
}
public void setSynonyms(String synonyms) {
this.synonyms = synonyms;
}
}

54
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/Vocabulary.java
View File

@ -1,54 +0,0 @@
package eu.dnetlib.dhp.transformation.vocabulary;
import java.io.Serializable;
import java.util.List;
public class Vocabulary implements Serializable {
private String id;
private String name;
private String description;
private String code;
private List<Term> terms;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getDescription() {
return description;
}
public void setDescription(String description) {
this.description = description;
}
public String getCode() {
return code;
}
public void setCode(String code) {
this.code = code;
}
public List<Term> getTerms() {
return terms;
}
public void setTerms(List<Term> terms) {
this.terms = terms;
}
}

24
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/vocabulary/VocabularyHelper.java
View File

@ -1,24 +0,0 @@
package eu.dnetlib.dhp.transformation.vocabulary;
import java.io.Serializable;
import java.net.URL;
import java.nio.charset.Charset;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class VocabularyHelper implements Serializable {
private static final String OPENAIRE_URL = "http://api.openaire.eu/vocabularies/%s.json";
public static Vocabulary getVocabularyFromAPI(final String vocabularyName) throws Exception {
final URL url = new URL(String.format(OPENAIRE_URL, vocabularyName));
final String response = IOUtils.toString(url, Charset.defaultCharset());
final ObjectMapper jsonMapper = new ObjectMapper();
final Vocabulary vocabulary = jsonMapper.readValue(response, Vocabulary.class);
return vocabulary;
}
}

33
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/functions/Cleaner.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/Cleaner.java
View File

@ -1,25 +1,25 @@
package eu.dnetlib.dhp.transformation.functions;
package eu.dnetlib.dhp.transformation.xslt;
import java.util.Map;
import java.util.Optional;
import static eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction.QNAME_BASE_URI;
import eu.dnetlib.dhp.transformation.vocabulary.Term;
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
import java.io.Serializable;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import net.sf.saxon.s9api.*;
import scala.Serializable;
public class Cleaner implements ExtensionFunction, Serializable {
private final Map<String, Vocabulary> vocabularies;
private final VocabularyGroup vocabularies;
public Cleaner(Map<String, Vocabulary> vocabularies) {
public Cleaner(final VocabularyGroup vocabularies) {
this.vocabularies = vocabularies;
}
@Override
public QName getName() {
return new QName("http://eu/dnetlib/trasform/extension", "clean");
return new QName(QNAME_BASE_URI + "/clean", "clean");
}
@Override
@ -30,23 +30,22 @@ public class Cleaner implements ExtensionFunction, Serializable {
@Override
public SequenceType[] getArgumentTypes() {
return new SequenceType[] {
SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ONE),
SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ZERO_OR_MORE),
SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ONE)
};
}
@Override
public XdmValue call(XdmValue[] xdmValues) throws SaxonApiException {
XdmValue r = xdmValues[0];
if (r.size() == 0) {
return new XdmAtomicValue("");
}
final String currentValue = xdmValues[0].itemAt(0).getStringValue();
final String vocabularyName = xdmValues[1].itemAt(0).getStringValue();
Optional<Term> cleanedValue = vocabularies
.get(vocabularyName)
.getTerms()
.stream()
.filter(it -> it.getNativeName().equalsIgnoreCase(currentValue))
.findAny();
Qualifier cleanedValue = vocabularies.getSynonymAsQualifier(vocabularyName, currentValue);
return new XdmAtomicValue(
cleanedValue.isPresent() ? cleanedValue.get().getCode() : currentValue);
cleanedValue != null ? cleanedValue.getClassid() : currentValue);
}
}

120
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/DateCleaner.java Normal file
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@ -0,0 +1,120 @@
package eu.dnetlib.dhp.transformation.xslt;
import static eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction.QNAME_BASE_URI;
import java.io.Serializable;
import java.time.LocalDate;
import java.time.format.DateTimeFormatter;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import net.sf.saxon.s9api.*;
public class DateCleaner implements ExtensionFunction, Serializable {
private final static List<Pattern> dateRegex = Arrays
.asList(
// Y-M-D
Pattern.compile("(18|19|20)\\d\\d([- /.])(0[1-9]|1[012])\\2(0[1-9]|[12][0-9]|3[01])", Pattern.MULTILINE),
// M-D-Y
Pattern
.compile(
"((0[1-9]|1[012])|([1-9]))([- /.])(0[1-9]|[12][0-9]|3[01])([- /.])(18|19|20)?\\d\\d",
Pattern.MULTILINE),
// D-M-Y
Pattern
.compile(
"(?:(?:31(/|-|\\.)(?:0?[13578]|1[02]|(?:Jan|Mar|May|Jul|Aug|Oct|Dec)))\\1|(?:(?:29|30)(/|-|\\.)(?:0?[1,3-9]|1[0-2]|(?:Jan|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec))\\2))(?:(?:1[6-9]|[2-9]\\d)?\\d{2})|(?:29(/|-|\\.)(?:0?2|(?:Feb))\\3(?:(?:(?:1[6-9]|[2-9]\\d)?(?:0[48]|[2468][048]|[13579][26])|(?:(?:16|[2468][048]|[3579][26])00))))|(?:0?[1-9]|1\\d|2[0-8])(/|-|\\.)(?:(?:0?[1-9]|(?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep))|(?:1[0-2]|(?:Oct|Nov|Dec)))\\4(?:(?:1[6-9]|[2-9]\\d)?\\d{2})",
Pattern.MULTILINE),
// Y
Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE));
private final static Pattern incompleteDateRegex = Pattern
.compile("^((18|19|20)\\d\\d){1}([- \\\\ \\/](0?[1-9]|1[012]))?", Pattern.MULTILINE);
private final static List<DateTimeFormatter> dformats = Arrays
.asList(
DateTimeFormatter
.ofPattern(
"[MM-dd-yyyy][MM/dd/yyyy][dd-MM-yy][dd-MMM-yyyy][dd/MMM/yyyy][dd-MMM-yy][dd/MMM/yy][dd-MM-yy][dd/MM/yy][dd-MM-yyyy][dd/MM/yyyy][yyyy-MM-dd][yyyy/MM/dd]",
Locale.ENGLISH),
DateTimeFormatter.ofPattern("[dd-MM-yyyy][dd/MM/yyyy]", Locale.ITALIAN));
public String clean(final String inputDate) {
Optional<String> cleanedDate = dateRegex
.stream()
.map(
p -> {
final Matcher matcher = p.matcher(inputDate);
if (matcher.find())
return matcher.group(0);
else
return null;
})
.filter(Objects::nonNull)
.map(m -> {
Optional<String> cleanDate = dformats
.stream()
.map(f -> {
try {
LocalDate parsedDate = LocalDate.parse(m, f);
if (parsedDate != null)
return parsedDate.toString();
else
return null;
} catch (Throwable e) {
return null;
}
}
)
.filter(Objects::nonNull)
.findAny();
return cleanDate.orElse(null);
})
.filter(Objects::nonNull)
.findAny();
if (cleanedDate.isPresent())
return cleanedDate.get();
final Matcher matcher = incompleteDateRegex.matcher(inputDate);
if (matcher.find()) {
final Integer year = Integer.parseInt(matcher.group(1));
final Integer month = Integer.parseInt(matcher.group(4) == null ? "01" : matcher.group(4));
return String.format("%d-%02d-01", year, month);
}
return null;
}
@Override
public QName getName() {
return new QName(QNAME_BASE_URI + "/dateISO", "dateISO");
}
@Override
public SequenceType getResultType() {
return SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ZERO_OR_ONE);
}
@Override
public SequenceType[] getArgumentTypes() {
return new SequenceType[] {
SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ZERO_OR_ONE)
};
}
@Override
public XdmValue call(XdmValue[] xdmValues) throws SaxonApiException {
XdmValue r = xdmValues[0];
if (r.size() == 0) {
return new XdmAtomicValue("");
}
final String currentValue = xdmValues[0].itemAt(0).getStringValue();
return new XdmAtomicValue(clean(currentValue));
}
}

49
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformFunction.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java
View File

@ -1,41 +1,39 @@
package eu.dnetlib.dhp.transformation;
package eu.dnetlib.dhp.transformation.xslt;
import java.io.ByteArrayInputStream;
import java.io.StringWriter;
import java.util.Map;
import java.nio.charset.StandardCharsets;
import javax.xml.transform.stream.StreamSource;
import org.apache.commons.io.IOUtils;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.util.LongAccumulator;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.transformation.functions.Cleaner;
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
import eu.dnetlib.dhp.aggregation.common.AggregationCounter;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.mdstore.MetadataRecord;
import net.sf.saxon.s9api.*;
public class TransformFunction implements MapFunction<MetadataRecord, MetadataRecord> {
public class XSLTTransformationFunction implements MapFunction<MetadataRecord, MetadataRecord> {
public final static String QNAME_BASE_URI = "http://eu/dnetlib/transform";
private final AggregationCounter aggregationCounter;
private final LongAccumulator totalItems;
private final LongAccumulator errorItems;
private final LongAccumulator transformedItems;
private final String transformationRule;
private final Cleaner cleanFunction;
private final long dateOfTransformation;
public TransformFunction(
LongAccumulator totalItems,
LongAccumulator errorItems,
LongAccumulator transformedItems,
public XSLTTransformationFunction(
final AggregationCounter aggregationCounter,
final String transformationRule,
long dateOfTransformation,
final Map<String, Vocabulary> vocabularies)
final VocabularyGroup vocabularies)
throws Exception {
this.totalItems = totalItems;
this.errorItems = errorItems;
this.transformedItems = transformedItems;
this.aggregationCounter = aggregationCounter;
this.transformationRule = transformationRule;
this.dateOfTransformation = dateOfTransformation;
cleanFunction = new Cleaner(vocabularies);
@ -43,32 +41,35 @@ public class TransformFunction implements MapFunction<MetadataRecord, MetadataRe
@Override
public MetadataRecord call(MetadataRecord value) {
totalItems.add(1);
aggregationCounter.getTotalItems().add(1);
try {
Processor processor = new Processor(false);
processor.registerExtensionFunction(cleanFunction);
processor.registerExtensionFunction(new DateCleaner());
final XsltCompiler comp = processor.newXsltCompiler();
XsltExecutable xslt = comp
.compile(new StreamSource(new ByteArrayInputStream(transformationRule.getBytes())));
.compile(new StreamSource(IOUtils.toInputStream(transformationRule, StandardCharsets.UTF_8)));
XdmNode source = processor
.newDocumentBuilder()
.build(new StreamSource(new ByteArrayInputStream(value.getBody().getBytes())));
.build(new StreamSource(IOUtils.toInputStream(value.getBody(), StandardCharsets.UTF_8)));
XsltTransformer trans = xslt.load();
trans.setInitialContextNode(source);
final StringWriter output = new StringWriter();
Serializer out = processor.newSerializer(output);
out.setOutputProperty(Serializer.Property.METHOD, "xml");
out.setOutputProperty(Serializer.Property.INDENT, "yes");
trans.setDestination(out);
trans.transform();
final String xml = output.toString();
value.setBody(xml);
value.setDateOfTransformation(dateOfTransformation);
transformedItems.add(1);
aggregationCounter.getProcessedItems().add(1);
return value;
} catch (Throwable e) {
errorItems.add(1);
return null;
aggregationCounter.getErrorItems().add(1);
throw new RuntimeException(e);
}
}
}

28
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite_filter Normal file
View File

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21
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json Normal file
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@ -0,0 +1,21 @@
[
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the source mdstore path",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "the target mdstore path",
"paramRequired": true
},
{
"paramName": "m",
"paramLongName": "master",
"paramDescription": "the master name",
"paramRequired": true
}
]

33
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json Normal file
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@ -0,0 +1,33 @@
[
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the source mdstore path",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "the target mdstore path",
"paramRequired": true
},
{
"paramName": "tr",
"paramLongName": "transformationRule",
"paramDescription": "the transformation Rule",
"paramRequired": true
},
{
"paramName": "m",
"paramLongName": "master",
"paramDescription": "the master name",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "isLookupUrl",
"paramDescription": "the isLookup URL",
"paramRequired": true
}
]

1032
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/hostedBy_map.json Normal file
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File diff suppressed because it is too large Load Diff

27
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/import_from_api.json Normal file
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@ -0,0 +1,27 @@
[
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "the path of the sequencial file to write",
"paramRequired": true
},
{
"paramName": "d",
"paramLongName": "dataciteDumpPath",
"paramDescription": "the path of the Datacite dump",
"paramRequired": true
},
{
"paramName": "n",
"paramLongName": "namenode",
"paramDescription": "the hive metastore uris",
"paramRequired": true
},
{
"paramName": "m",
"paramLongName": "master",
"paramDescription": "the master name",
"paramRequired": true
}
]

23
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/config-default.xml Normal file
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@ -0,0 +1,23 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

123
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml Normal file
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@ -0,0 +1,123 @@
<workflow-app name="Transformation_Workflow" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>mdstoreInputPath</name>
<description>the path of the input MDStore</description>
</property>
<property>
<name>mdstoreOutputPath</name>
<description>the path of the cleaned mdstore</description>
</property>
<property>
<name>nativeInputPath</name>
<description>the path of the input MDStore</description>
</property>
</parameters>
<start to="resume_from"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<decision name="resume_from">
<switch>
<case to="TransformJob">${wf:conf('resumeFrom') eq 'TransformJob'}</case>
<case to="ExportDataset">${wf:conf('resumeFrom') eq 'ExportDataset'}</case>
<default to="ImportDatacite"/>
</switch>
</decision>
<action name="ImportDatacite">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ImportDatacite</name>
<class>eu.dnetlib.dhp.actionmanager.datacite.ImportDatacite</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-t</arg><arg>${nativeInputPath}</arg>
<arg>-d</arg><arg>${mdstoreInputPath}</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="TransformJob"/>
<error to="Kill"/>
</action>
<action name="TransformJob">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>TransformJob</name>
<class>eu.dnetlib.dhp.actionmanager.datacite.GenerateDataciteDatasetSpark</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${mdstoreInputPath}</arg>
<arg>--targetPath</arg><arg>${mdstoreOutputPath}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>-tr</arg><arg>${isLookupUrl}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="DeletePathIfExists"/>
<error to="Kill"/>
</action>
<action name="DeletePathIfExists">
<fs>
<delete path='${mdstoreOutputPath}_raw_AS'/>
</fs>
<ok to="ExportDataset"/>
<error to="Kill"/>
</action>
<action name="ExportDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExportDataset</name>
<class>eu.dnetlib.dhp.actionmanager.datacite.ExportActionSetJobNode</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${mdstoreOutputPath}</arg>
<arg>--targetPath</arg><arg>${mdstoreOutputPath}_raw_AS</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

86
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/collection_input_parameters.json
View File

@ -1,86 +0,0 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "e",
"paramLongName": "encoding",
"paramDescription": "the encoding of the input record should be JSON or XML",
"paramRequired": true
},
{
"paramName": "d",
"paramLongName": "dateOfCollection",
"paramDescription": "the date when the record has been stored",
"paramRequired": true
},
{
"paramName": "p",
"paramLongName": "provenance",
"paramDescription": "the infos about the provenance of the collected records",
"paramRequired": true
},
{
"paramName": "x",
"paramLongName": "xpath",
"paramDescription": "the xpath to identify the record identifier",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "input",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "output",
"paramDescription": "the path of the result DataFrame on HDFS",
"paramRequired": true
},
{
"paramName": "ru",
"paramLongName": "rabbitUser",
"paramDescription": "the user to connect with RabbitMq for messaging",
"paramRequired": true
},
{
"paramName": "rp",
"paramLongName": "rabbitPassword",
"paramDescription": "the password to connect with RabbitMq for messaging",
"paramRequired": true
},
{
"paramName": "rh",
"paramLongName": "rabbitHost",
"paramDescription": "the host of the RabbitMq server",
"paramRequired": true
},
{
"paramName": "ro",
"paramLongName": "rabbitOngoingQueue",
"paramDescription": "the name of the ongoing queue",
"paramRequired": true
},
{
"paramName": "rr",
"paramLongName": "rabbitReportQueue",
"paramDescription": "the name of the report queue",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workflowId",
"paramDescription": "the identifier of the dnet Workflow",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "isTest",
"paramDescription": "the name of the report queue",
"paramRequired": false
}
]

62
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/collector_worker_input_parameter.json Normal file
View File

@ -0,0 +1,62 @@
[
{
"paramName": "a",
"paramLongName": "apidescriptor",
"paramDescription": "the JSON encoding of the API Descriptor",
"paramRequired": true
},
{
"paramName": "n",
"paramLongName": "namenode",
"paramDescription": "the Name Node URI",
"paramRequired": true
},
{
"paramName": "mv",
"paramLongName": "mdStoreVersion",
"paramDescription": "the MDStore Version bean",
"paramRequired": true
},
{
"paramName": "dm",
"paramLongName": "dnetMessageManagerURL",
"paramDescription": "the End point URL to send Messages",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workflowId",
"paramDescription": "the identifier of the dnet Workflow",
"paramRequired": true
},
{
"paramName": "mnr",
"paramLongName": "maxNumberOfRetry",
"paramDescription": "the maximum number of admitted connection retries",
"paramRequired": false
},
{
"paramName": "rqd",
"paramLongName": "requestDelay",
"paramDescription": "the delay (ms) between requests",
"paramRequired": false
},
{
"paramName": "rtd",
"paramLongName": "retryDelay",
"paramDescription": "the delay (ms) between retries",
"paramRequired": false
},
{
"paramName": "cto",
"paramLongName": "connectTimeOut",
"paramDescription": "the maximum allowed time (ms) to connect to the remote host",
"paramRequired": false
},
{
"paramName": "rto",
"paramLongName": "readTimeOut",
"paramDescription": "the maximum allowed time (ms) to receive content from the remote host",
"paramRequired": false
}
]

50
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/generate_native_input_parameters.json Normal file
View File

@ -0,0 +1,50 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "e",
"paramLongName": "encoding",
"paramDescription": "the encoding of the input record should be JSON or XML",
"paramRequired": true
},
{
"paramName": "d",
"paramLongName": "dateOfCollection",
"paramDescription": "the date when the record has been stored",
"paramRequired": true
},
{
"paramName": "p",
"paramLongName": "provenance",
"paramDescription": "the infos about the provenance of the collected records",
"paramRequired": true
},
{
"paramName": "x",
"paramLongName": "xpath",
"paramDescription": "the xpath to identify the record identifier",
"paramRequired": true
},
{
"paramName": "mv",
"paramLongName": "mdStoreVersion",
"paramDescription": "the Metadata Store Version Info",
"paramRequired": true
},
{
"paramName": "rmv",
"paramLongName": "readMdStoreVersion",
"paramDescription": "the Read Lock Metadata Store Version bean",
"paramRequired": false
},
{
"paramName": "w",
"paramLongName": "workflowId",
"paramDescription": "the identifier of the dnet Workflow",
"paramRequired": false
}
]

45
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/mdstore_action_parameters.json Normal file
View File

@ -0,0 +1,45 @@
[
{
"paramName": "a",
"paramLongName": "action",
"paramDescription": "the JSON encoding of the API Descriptor",
"paramRequired": true
},
{
"paramName": "mu",
"paramLongName": "mdStoreManagerURI",
"paramDescription": "the MDStore Manager URI",
"paramRequired": true
},
{
"paramName": "mi",
"paramLongName": "mdStoreID",
"paramDescription": "the Metadata Store ID",
"paramRequired": false
},
{
"paramName": "ms",
"paramLongName": "mdStoreSize",
"paramDescription": "the Metadata Store Size",
"paramRequired": false
},
{
"paramName": "mv",
"paramLongName": "mdStoreVersion",
"paramDescription": "the Metadata Version Bean",
"paramRequired": false
},
{
"paramName": "n",
"paramLongName": "namenode",
"paramDescription": "the Name Node URI",
"paramRequired": false
},
{
"paramName": "rm",
"paramLongName": "readMDStoreId",
"paramDescription": "the ID Locked to Read",
"paramRequired": false
}
]

22
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/config-default.xml Normal file
View File

@ -0,0 +1,22 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

212
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml
View File

@ -1,112 +1,212 @@
<workflow-app name="CollectionWorkflow" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sequenceFilePath</name>
<description>the path to store the sequence file of the native metadata collected</description>
</property>
<property>
<name>mdStorePath</name>
<description>the path of the native mdstore</description>
</property>
<property>
<name>apiDescription</name>
<description>A json encoding of the API Description class</description>
</property>
<property>
<name>dataSourceInfo</name>
<description>A json encoding of the Datasource Info</description>
</property>
<property>
<name>identifierPath</name>
<description>An xpath to retrieve the metadata idnentifier for the generation of DNet Identifier </description>
<description>An xpath to retrieve the metadata identifier for the generation of DNet Identifier </description>
</property>
<property>
<name>metadataEncoding</name>
<description> The type of the metadata XML/JSON</description>
</property>
<property>
<name>timestamp</name>
<description>The timestamp of the collection date</description>
</property>
<property>
<name>workflowId</name>
<description>The identifier of the workflow</description>
</property>
<property>
<name>mdStoreID</name>
<description>The identifier of the mdStore</description>
</property>
<property>
<name>mdStoreManagerURI</name>
<description>The URI of the MDStore Manager</description>
</property>
<property>
<name>dnetMessageManagerURL</name>
<description>The URI of the Dnet Message Manager</description>
</property>
<property>
<name>collectionMode</name>
<description>Should be REFRESH or INCREMENTAL</description>
</property>
<property>
<name>collection_java_xmx</name>
<value>-Xmx200m</value>
<description>Used to configure the heap size for the map JVM process. Should be 80% of mapreduce.map.memory.mb.</description>
</property>
</parameters>
<start to="DeleteMDStoresNative"/>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
</global>
<start to="collection_mode"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DeleteMDStoresNative">
<fs>
<mkdir path='${sequenceFilePath}'/>
<mkdir path='${mdStorePath}'/>
<delete path='${sequenceFilePath}'/>
<delete path='${mdStorePath}'/>
</fs>
<decision name="collection_mode">
<switch>
<case to="StartTransaction">${wf:conf('collectionMode') eq 'REFRESH'}</case>
<case to="BeginRead">${wf:conf('collectionMode') eq 'INCREMENTAL'}</case>
<default to="StartTransaction"/>
</switch>
</decision>
<action name="BeginRead">
<java>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<java-opts>${collection_java_xmx}</java-opts>
<arg>--action</arg><arg>READ_LOCK</arg>
<arg>--mdStoreID</arg><arg>${mdStoreID}</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
<capture-output/>
</java>
<ok to="StartTransaction"/>
<error to="Kill"/>
</action>
<action name="StartTransaction">
<java>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<java-opts>${collection_java_xmx}</java-opts>
<arg>--action</arg><arg>NEW_VERSION</arg>
<arg>--mdStoreID</arg><arg>${mdStoreID}</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
<capture-output/>
</java>
<ok to="CollectionWorker"/>
<error to="Kill"/>
</action>
<action name="CollectionWorker">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.collection.worker.DnetCollectorWorker</main-class>
<java-opts>-p</java-opts><java-opts>${sequenceFilePath}</java-opts>
<java-opts>-a</java-opts><java-opts>${apiDescription}</java-opts>
<java-opts>-n</java-opts><java-opts>${nameNode}</java-opts>
<java-opts>-rh</java-opts><java-opts>${rmq_host}</java-opts>
<java-opts>-ru</java-opts><java-opts>${rmq_user}</java-opts>
<java-opts>-rp</java-opts><java-opts>${rmq_pwd}</java-opts>
<java-opts>-rr</java-opts><java-opts>${rmq_report}</java-opts>
<java-opts>-ro</java-opts><java-opts>${rmq_ongoing}</java-opts>
<java-opts>-u</java-opts><java-opts>sandro.labruzzo</java-opts>
<java-opts>-w</java-opts><java-opts>${workflowId}</java-opts>
<main-class>eu.dnetlib.dhp.collection.CollectorWorkerApplication</main-class>
<java-opts>${collection_java_xmx}</java-opts>
<arg>--apidescriptor</arg><arg>${apiDescription}</arg>
<arg>--namenode</arg><arg>${nameNode}</arg>
<arg>--workflowId</arg><arg>${workflowId}</arg>
<arg>--dnetMessageManagerURL</arg><arg>${dnetMessageManagerURL}</arg>
<arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
<arg>--maxNumberOfRetry</arg><arg>${maxNumberOfRetry}</arg>
<arg>--requestDelay</arg><arg>${requestDelay}</arg>
<arg>--retryDelay</arg><arg>${retryDelay}</arg>
<arg>--connectTimeOut</arg><arg>${connectTimeOut}</arg>
<arg>--readTimeOut</arg><arg>${readTimeOut}</arg>
</java>
<ok to="GenerateNativeStoreSparkJob"/>
<error to="Kill"/>
<error to="FailCollection"/>
</action>
<action name="GenerateNativeStoreSparkJob">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn</master>
<mode>cluster</mode>
<name>GenerateNativeStoreSparkJob</name>
<name>Generate Native MetadataStore</name>
<class>eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob</class>
<jar>dhp-aggregations-1.0.0-SNAPSHOT.jar</jar>
<spark-opts>--num-executors 50 --conf spark.yarn.jars=&quot;hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2&quot;</spark-opts>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--encoding</arg><arg>${metadataEncoding}</arg>
<arg>--dateOfCollection</arg><arg>${timestamp}</arg>
<arg>--provenance</arg><arg>${dataSourceInfo}</arg>
<arg>--xpath</arg><arg>${identifierPath}</arg>
<arg>--input</arg><arg>${sequenceFilePath}</arg>
<arg>--output</arg><arg>${mdStorePath}</arg>
<arg>-rh</arg><arg>${rmq_host}</arg>
<arg>-ru</arg><arg>${rmq_user}</arg>
<arg>-rp</arg><arg>${rmq_pwd}</arg>
<arg>-rr</arg><arg>${rmq_report}</arg>
<arg>-ro</arg><arg>${rmq_ongoing}</arg>
<arg>-w</arg><arg>${workflowId}</arg>
<arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
<arg>--readMdStoreVersion</arg><arg>${wf:actionData('BeginRead')['mdStoreReadLockVersion']}</arg>
</spark>
<ok to="End"/>
<error to="DropInvalidStore"/>
<ok to="collection_mode_end"/>
<error to="FailCollection"/>
</action>
<action name="DropInvalidStore">
<fs>
<delete path='${mdStorePath}/../'/>
</fs>
<decision name="collection_mode_end">
<switch>
<case to="CommitVersion">${wf:conf('collectionMode') eq 'REFRESH'}</case>
<case to="EndRead">${wf:conf('collectionMode') eq 'INCREMENTAL'}</case>
<default to="CommitVersion"/>
</switch>
</decision>
<action name="EndRead">
<java>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<java-opts>${collection_java_xmx}</java-opts>
<arg>--action</arg><arg>READ_UNLOCK</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
<arg>--readMDStoreId</arg><arg>${wf:actionData('BeginRead')['mdStoreReadLockVersion']}</arg>
</java>
<ok to="CommitVersion"/>
<error to="Kill"/>
</action>
<action name="CommitVersion">
<java>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<java-opts>${collection_java_xmx}</java-opts>
<arg>--action</arg><arg>COMMIT</arg>
<arg>--namenode</arg><arg>${nameNode}</arg>
<arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<decision name="FailCollection">
<switch>
<case to="RollBack">${wf:conf('collectionMode') eq 'REFRESH'}</case>
<case to="EndReadRollBack">${wf:conf('collectionMode') eq 'INCREMENTAL'}</case>
<default to="RollBack"/>
</switch>
</decision>
<action name="EndReadRollBack">
<java>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<java-opts>${collection_java_xmx}</java-opts>
<arg>--action</arg><arg>READ_UNLOCK</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
<arg>--readMDStoreId</arg><arg>${wf:actionData('BeginRead')['mdStoreReadLockVersion']}</arg>
</java>
<ok to="RollBack"/>
<error to="Kill"/>
</action>
<action name="RollBack">
<java>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<java-opts>${collection_java_xmx}</java-opts>
<arg>--action</arg><arg>ROLLBACK</arg>
<arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
</java>
<ok to="Kill"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

12
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collector/worker/collector_parameter.json
View File

@ -1,12 +0,0 @@
[
{"paramName":"p", "paramLongName":"hdfsPath", "paramDescription": "the path where storing the sequential file", "paramRequired": true},
{"paramName":"a", "paramLongName":"apidescriptor", "paramDescription": "the JSON encoding of the API Descriptor", "paramRequired": true},
{"paramName":"n", "paramLongName":"namenode", "paramDescription": "the Name Node URI", "paramRequired": true},
{"paramName":"u", "paramLongName":"userHDFS", "paramDescription": "the user wich create the hdfs seq file", "paramRequired": true},
{"paramName":"ru", "paramLongName":"rabbitUser", "paramDescription": "the user to connect with RabbitMq for messaging", "paramRequired": true},
{"paramName":"rp", "paramLongName":"rabbitPassword", "paramDescription": "the password to connect with RabbitMq for messaging", "paramRequired": true},
{"paramName":"rh", "paramLongName":"rabbitHost", "paramDescription": "the host of the RabbitMq server", "paramRequired": true},
{"paramName":"ro", "paramLongName":"rabbitOngoingQueue", "paramDescription": "the name of the ongoing queue", "paramRequired": true},
{"paramName":"rr", "paramLongName":"rabbitReportQueue", "paramDescription": "the name of the report queue", "paramRequired": true},
{"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": true}
]

19
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/oozie_app/config-default.xml Normal file
View File

@ -0,0 +1,19 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

201
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/oozie_app/workflow.xml
View File

@ -1,76 +1,187 @@
<workflow-app name="Transformation_Workflow" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>mdstoreInputPath</name>
<description>the path of the input MDStore</description>
<name>mdStoreInputId</name>
<description>the identifier of the native MDStore</description>
</property>
<property>
<name>mdstoreOutputPath</name>
<name>mdStoreOutputId</name>
<description>the identifier of the cleaned MDStore</description>
</property>
<property>
<name>mdStoreManagerURI</name>
<description>the path of the cleaned mdstore</description>
</property>
<property>
<name>transformationRule</name>
<name>transformationRuleId</name>
<description>The transformation Rule to apply</description>
</property>
<property>
<name>timestamp</name>
<description>The timestamp of the collection date</description>
<name>transformationPlugin</name>
<value>XSLT_TRANSFORM</value>
<description>The transformation Plugin</description>
</property>
<property>
<name>dateOfTransformation</name>
<description>The timestamp of the transformation date</description>
</property>
<property>
<name>isLookupUrl</name>
<description>The IS lookUp service endopoint</description>
</property>
<property>
<name>workflowId</name>
<description>The identifier of the workflow</description>
</property>
<property>
<name>dnetMessageManagerURL</name>
<description>The URI of the Dnet Message Manager</description>
</property>
</parameters>
<start to="DeletePathIfExists"/>
<start to="BeginRead"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DeletePathIfExists">
<fs>
<mkdir path='${mdstoreOutputPath}'/>
<delete path='${mdstoreOutputPath}'/>
</fs>
<ok to="TransformJob"/>
<action name="BeginRead">
<java>
<configuration>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<arg>--action</arg><arg>READ_LOCK</arg>
<arg>--mdStoreID</arg><arg>${mdStoreInputId}</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
<capture-output/>
</java>
<ok to="StartTransaction"/>
<error to="Kill"/>
</action>
<action name="TransformJob">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn</master>
<mode>cluster</mode>
<name>MDBuilder</name>
<class>eu.dnetlib.dhp.transformation.TransformSparkJobNode</class>
<jar>dhp-aggregations-1.0.0-SNAPSHOT.jar</jar>
<spark-opts>--num-executors 50 --conf spark.yarn.jars=&quot;hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2&quot;</spark-opts>
<arg>--dateOfCollection</arg> <arg>${timestamp}</arg>
<arg>-mt</arg> <arg>yarn</arg>
<arg>--input</arg><arg>${mdstoreInputPath}</arg>
<arg>--output</arg><arg>${mdstoreOutputPath}</arg>
<arg>-w</arg><arg>${workflowId}</arg>
<arg>-tr</arg><arg>${transformationRule}</arg>
<arg>-ru</arg><arg>${rmq_user}</arg>
<arg>-rp</arg><arg>${rmq_pwd}</arg>
<arg>-rh</arg><arg>${rmq_host}</arg>
<arg>-ro</arg><arg>${rmq_ongoing}</arg>
<arg>-rr</arg><arg>${rmq_report}</arg>
</spark>
<ok to="End"/>
<error to="DropInvalidStore"/>
<action name="StartTransaction">
<java>
<configuration>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<arg>--action</arg><arg>NEW_VERSION</arg>
<arg>--mdStoreID</arg><arg>${mdStoreOutputId}</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
<capture-output/>
</java>
<ok to="TransformJob"/>
<error to="EndReadRollBack"/>
</action>
<action name="DropInvalidStore">
<fs>
<delete path='${mdstoreOutputPath}/../'/>
</fs>
<action name="TransformJob">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Transform MetadataStore</name>
<class>eu.dnetlib.dhp.transformation.TransformSparkJobNode</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--mdstoreOutputVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
<arg>--mdstoreInputVersion</arg><arg>${wf:actionData('BeginRead')['mdStoreReadLockVersion']}</arg>
<arg>--dateOfTransformation</arg><arg>${dateOfTransformation}</arg>
<arg>--transformationPlugin</arg><arg>${transformationPlugin}</arg>
<arg>--transformationRuleId</arg><arg>${transformationRuleId}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--workflowId</arg><arg>${workflowId}</arg>
<arg>--dnetMessageManagerURL</arg><arg>${dnetMessageManagerURL}</arg>
</spark>
<ok to="EndRead"/>
<error to="EndReadRollBack"/>
</action>
<action name="EndRead">
<java>
<configuration>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<arg>--action</arg><arg>READ_UNLOCK</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
<arg>--readMDStoreId</arg><arg>${wf:actionData('BeginRead')['mdStoreReadLockVersion']}</arg>
<capture-output/>
</java>
<ok to="CommitVersion"/>
<error to="Kill"/>
</action>
<action name="CommitVersion">
<java>
<configuration>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<arg>--action</arg><arg>COMMIT</arg>
<arg>--namenode</arg><arg>${nameNode}</arg>
<arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="EndReadRollBack">
<java>
<configuration>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<arg>--action</arg><arg>READ_UNLOCK</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
<arg>--readMDStoreId</arg><arg>${wf:actionData('BeginRead')['mdStoreReadLockVersion']}</arg>
<capture-output/>
</java>
<ok to="RollBack"/>
<error to="Kill"/>
</action>
<action name="RollBack">
<java>
<configuration>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>
<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
<arg>--action</arg><arg>ROLLBACK</arg>
<arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
</java>
<ok to="Kill"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

71
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/transformation_input_parameters.json
View File

@ -7,20 +7,39 @@
},
{
"paramName": "d",
"paramLongName": "dateOfCollection",
"paramLongName": "dateOfTransformation",
"paramDescription": "the date when the record has been stored",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "input",
"paramDescription": "the path of the sequencial file to read",
"paramLongName": "mdstoreInputVersion",
"paramDescription": "the mdStore Version bean of the Input",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "output",
"paramDescription": "the path of the result DataFrame on HDFS",
"paramLongName": "mdstoreOutputVersion",
"paramDescription": "the mdStore Version bean of the Output",
"paramRequired": true
},
{
"paramName": "tr",
"paramLongName": "transformationRuleId",
"paramDescription": "the transformation Rule to apply to the input MDStore",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "isLookupUrl",
"paramDescription": "the Information System Service LookUp URL",
"paramRequired": true
},
{
"paramName": "dm",
"paramLongName": "dnetMessageManagerURL",
"paramDescription": "the End point URL to send Messages",
"paramRequired": true
},
{
@ -30,45 +49,9 @@
"paramRequired": true
},
{
"paramName": "tr",
"paramLongName": "transformationRule",
"paramDescription": "the transformation Rule to apply to the input MDStore",
"paramName": "tp",
"paramLongName": "transformationPlugin",
"paramDescription": "the transformation plugin to apply",
"paramRequired": true
},
{
"paramName": "ru",
"paramLongName": "rabbitUser",
"paramDescription": "the user to connect with RabbitMq for messaging",
"paramRequired": true
},
{
"paramName": "rp",
"paramLongName": "rabbitPassword",
"paramDescription": "the password to connect with RabbitMq for messaging",
"paramRequired": true
},
{
"paramName": "rh",
"paramLongName": "rabbitHost",
"paramDescription": "the host of the RabbitMq server",
"paramRequired": true
},
{
"paramName": "ro",
"paramLongName": "rabbitOngoingQueue",
"paramDescription": "the name of the ongoing queue",
"paramRequired": true
},
{
"paramName": "rr",
"paramLongName": "rabbitReportQueue",
"paramDescription": "the name of the report queue",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "isTest",
"paramDescription": "the name of the report queue",
"paramRequired": false
}
]

8
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java
View File

@ -12,15 +12,15 @@ 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;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.HttpConnector2;
@Disabled
public class EXCELParserTest {
private static Path workingDir;
private HttpConnector httpConnector = new HttpConnector();
private HttpConnector2 httpConnector = new HttpConnector2();
private static final String URL = "http://cordis.europa.eu/data/reference/cordisref-H2020topics.xlsx";
@BeforeAll
@ -30,7 +30,7 @@ public class EXCELParserTest {
}
@Test
public void test1() throws CollectorServiceException, IOException, InvalidFormatException, ClassNotFoundException,
public void test1() throws CollectorException, IOException, InvalidFormatException, ClassNotFoundException,
IllegalAccessException, InstantiationException {
EXCELParser excelParser = new EXCELParser();

41
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java
View File

@ -1,41 +0,0 @@
package eu.dnetlib.dhp.actionmanager.project.httpconnector;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.http.conn.ssl.SSLConnectionSocketFactory;
import org.apache.http.ssl.SSLContextBuilder;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class HttpConnectorTest {
private static final Log log = LogFactory.getLog(HttpConnectorTest.class);
private static HttpConnector connector;
private static final String URL = "http://cordis.europa.eu/data/reference/cordisref-H2020topics.xlsx";
private static final String URL_MISCONFIGURED_SERVER = "https://www.alexandria.unisg.ch/cgi/oai2?verb=Identify";
private static final String URL_GOODSNI_SERVER = "https://air.unimi.it/oai/openaire?verb=Identify";
private static final SSLContextBuilder sslContextBuilder = new SSLContextBuilder();
private static SSLConnectionSocketFactory sslSocketFactory;
@BeforeAll
public static void setUp() {
connector = new HttpConnector();
}
@Test
public void testGetInputSource() throws CollectorServiceException {
System.out.println(connector.getInputSource(URL));
}
@Test
public void testGoodServers() throws CollectorServiceException {
System.out.println(connector.getInputSource(URL_GOODSNI_SERVER));
}
}

52
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/aggregation/AbstractVocabularyTest.java Normal file
View File

@ -0,0 +1,52 @@
package eu.dnetlib.dhp.aggregation;
import static org.mockito.Mockito.lenient;
import java.io.IOException;
import java.util.Collections;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.mockito.Mock;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.transformation.TransformationFactory;
import eu.dnetlib.dhp.transformation.TransformationJobTest;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public abstract class AbstractVocabularyTest {
@Mock
protected ISLookUpService isLookUpService;
protected VocabularyGroup vocabularies;
public void setUpVocabulary() throws ISLookUpException, IOException {
lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs());
lenient()
.when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY))
.thenReturn(synonyms());
vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService);
}
private static List<String> vocs() throws IOException {
return IOUtils
.readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/terms.txt"));
}
private static List<String> synonyms() throws IOException {
return IOUtils
.readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/synonyms.txt"));
}
protected void mockupTrasformationRule(final String trule, final String path) throws Exception {
final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path));
lenient()
.when(isLookUpService.quickSearchProfile(String.format(TransformationFactory.TRULE_XQUERY, trule)))
.thenReturn(Collections.singletonList(trValue));
}
}

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