updated index mapping to include orcid
This commit is contained in:
Sandro La Bruzzo
parent
ab1842e5dc
commit
4f07dba68f
|
|
@ -1,158 +0,0 @@
|
|||
package eu.dnetlib.dhp.sx.graph.scholix;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
public class ScholixFlat {
|
||||
private String identifier;
|
||||
private String relationType;
|
||||
private String sourceId;
|
||||
private String sourceType;
|
||||
private String sourceSubType;
|
||||
private List<String> sourcePid;
|
||||
private List<String> sourcePidType;
|
||||
private List<String> sourcePublisher;
|
||||
private String targetId;
|
||||
private String targetType;
|
||||
private String targetSubType;
|
||||
private List<String> targetPid;
|
||||
private List<String> targetPidType;
|
||||
private List<String> targetPublisher;
|
||||
private List<String> linkProviders;
|
||||
private String publicationDate;
|
||||
private String blob;
|
||||
|
||||
public String getIdentifier() {
|
||||
return identifier;
|
||||
}
|
||||
|
||||
public void setIdentifier(String identifier) {
|
||||
this.identifier = identifier;
|
||||
}
|
||||
|
||||
public String getRelationType() {
|
||||
return relationType;
|
||||
}
|
||||
|
||||
public void setRelationType(String relationType) {
|
||||
this.relationType = relationType;
|
||||
}
|
||||
public String getSourceId() {
|
||||
return sourceId;
|
||||
}
|
||||
|
||||
public void setSourceId(String sourceId) {
|
||||
this.sourceId = sourceId;
|
||||
}
|
||||
|
||||
public String getSourceType() {
|
||||
return sourceType;
|
||||
}
|
||||
|
||||
public void setSourceType(String sourceType) {
|
||||
this.sourceType = sourceType;
|
||||
}
|
||||
|
||||
public String getSourceSubType() {
|
||||
return sourceSubType;
|
||||
}
|
||||
|
||||
public void setSourceSubType(String sourceSubType) {
|
||||
this.sourceSubType = sourceSubType;
|
||||
}
|
||||
|
||||
public List<String> getSourcePid() {
|
||||
return sourcePid;
|
||||
}
|
||||
|
||||
public void setSourcePid(List<String> sourcePid) {
|
||||
this.sourcePid = sourcePid;
|
||||
}
|
||||
|
||||
public List<String> getSourcePidType() {
|
||||
return sourcePidType;
|
||||
}
|
||||
|
||||
public void setSourcePidType(List<String> sourcePidType) {
|
||||
this.sourcePidType = sourcePidType;
|
||||
}
|
||||
|
||||
public List<String> getSourcePublisher() {
|
||||
return sourcePublisher;
|
||||
}
|
||||
|
||||
public void setSourcePublisher(List<String> sourcePublisher) {
|
||||
this.sourcePublisher = sourcePublisher;
|
||||
}
|
||||
|
||||
public String getTargetId() {
|
||||
return targetId;
|
||||
}
|
||||
|
||||
public void setTargetId(String targetId) {
|
||||
this.targetId = targetId;
|
||||
}
|
||||
|
||||
public String getTargetType() {
|
||||
return targetType;
|
||||
}
|
||||
|
||||
public void setTargetType(String targetType) {
|
||||
this.targetType = targetType;
|
||||
}
|
||||
|
||||
public String getTargetSubType() {
|
||||
return targetSubType;
|
||||
}
|
||||
|
||||
public void setTargetSubType(String targetSubType) {
|
||||
this.targetSubType = targetSubType;
|
||||
}
|
||||
|
||||
public List<String> getTargetPid() {
|
||||
return targetPid;
|
||||
}
|
||||
|
||||
public void setTargetPid(List<String> targetPid) {
|
||||
this.targetPid = targetPid;
|
||||
}
|
||||
|
||||
public List<String> getTargetPidType() {
|
||||
return targetPidType;
|
||||
}
|
||||
|
||||
public void setTargetPidType(List<String> targetPidType) {
|
||||
this.targetPidType = targetPidType;
|
||||
}
|
||||
|
||||
public List<String> getTargetPublisher() {
|
||||
return targetPublisher;
|
||||
}
|
||||
|
||||
public void setTargetPublisher(List<String> targetPublisher) {
|
||||
this.targetPublisher = targetPublisher;
|
||||
}
|
||||
|
||||
public List<String> getLinkProviders() {
|
||||
return linkProviders;
|
||||
}
|
||||
|
||||
public void setLinkProviders(List<String> linkProviders) {
|
||||
this.linkProviders = linkProviders;
|
||||
}
|
||||
|
||||
public String getPublicationDate() {
|
||||
return publicationDate;
|
||||
}
|
||||
|
||||
public void setPublicationDate(String publicationDate) {
|
||||
this.publicationDate = publicationDate;
|
||||
}
|
||||
|
||||
public String getBlob() {
|
||||
return blob;
|
||||
}
|
||||
|
||||
public void setBlob(String blob) {
|
||||
this.blob = blob;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,6 +1,14 @@
|
|||
package eu.dnetlib.dhp.sx.graph.scholix
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.{Dataset, OtherResearchProduct, Publication, Relation, Result, Software, StructuredProperty}
|
||||
import eu.dnetlib.dhp.schema.oaf.{
|
||||
Dataset,
|
||||
OtherResearchProduct,
|
||||
Publication,
|
||||
Relation,
|
||||
Result,
|
||||
Software,
|
||||
StructuredProperty
|
||||
}
|
||||
import eu.dnetlib.dhp.schema.sx.scholix._
|
||||
import eu.dnetlib.dhp.schema.sx.summary.{AuthorPid, CollectedFromType, SchemeValue, ScholixSummary, Typology}
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
|
|
@ -263,14 +271,16 @@ object ScholixUtils extends Serializable {
|
|||
|
||||
if (summaryObject.getAuthor != null && !summaryObject.getAuthor.isEmpty) {
|
||||
val l: List[ScholixEntityId] =
|
||||
summaryObject.getAuthor.asScala.map(a => {
|
||||
summaryObject.getAuthor.asScala
|
||||
.map(a => {
|
||||
if (a.getORCID != null)
|
||||
new ScholixEntityId(
|
||||
a.getFullname,
|
||||
List(new ScholixIdentifier(a.getORCID, "ORCID", s"https://orcid.org/${a.getORCID}")).asJava
|
||||
)
|
||||
else new ScholixEntityId(a.getFullname, null)
|
||||
}).toList
|
||||
})
|
||||
.toList
|
||||
if (l.nonEmpty)
|
||||
r.setCreator(l.asJava)
|
||||
}
|
||||
|
|
|
|||
|
|
@ -11,6 +11,7 @@ import org.junit.jupiter.api.Test;
|
|||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.schema.sx.scholix.Scholix;
|
||||
import eu.dnetlib.dhp.schema.sx.scholix.ScholixFlat;
|
||||
|
||||
public class ScholixFlatTest {
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,91 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx.graph.dump;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.*;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.api.MissingConceptDoiException;
|
||||
import eu.dnetlib.dhp.common.api.ZenodoAPIClient;
|
||||
|
||||
public class SendToZenodoHDFS implements Serializable {
|
||||
|
||||
private static final String NEW = "new"; // to be used for a brand new deposition in zenodo
|
||||
private static final String VERSION = "version"; // to be used to upload a new version of a published deposition
|
||||
private static final String UPDATE = "update"; // to upload content to an open deposition not published
|
||||
|
||||
public static void main(final String[] args) throws Exception, MissingConceptDoiException {
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SendToZenodoHDFS.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/sx/graph/dump/upload_zenodo.json")));
|
||||
|
||||
parser.parseArgument(args);
|
||||
|
||||
final String hdfsPath = parser.get("hdfsPath");
|
||||
final String hdfsNameNode = parser.get("nameNode");
|
||||
final String access_token = parser.get("accessToken");
|
||||
final String connection_url = parser.get("connectionUrl");
|
||||
final String metadata = parser.get("metadata");
|
||||
final String depositionType = parser.get("depositionType");
|
||||
final String concept_rec_id = Optional
|
||||
.ofNullable(parser.get("conceptRecordId"))
|
||||
.orElse(null);
|
||||
|
||||
final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null);
|
||||
|
||||
Configuration conf = new Configuration();
|
||||
conf.set("fs.defaultFS", hdfsNameNode);
|
||||
|
||||
FileSystem fileSystem = FileSystem.get(conf);
|
||||
|
||||
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
|
||||
.listFiles(
|
||||
new Path(hdfsPath), true);
|
||||
ZenodoAPIClient zenodoApiClient = new ZenodoAPIClient(connection_url, access_token);
|
||||
switch (depositionType) {
|
||||
case NEW:
|
||||
zenodoApiClient.newDeposition();
|
||||
break;
|
||||
case VERSION:
|
||||
if (concept_rec_id == null) {
|
||||
throw new MissingConceptDoiException("No concept record id has been provided");
|
||||
}
|
||||
zenodoApiClient.newVersion(concept_rec_id);
|
||||
break;
|
||||
case UPDATE:
|
||||
if (depositionId == null) {
|
||||
throw new MissingConceptDoiException("No deposition id has been provided");
|
||||
}
|
||||
zenodoApiClient.uploadOpenDeposition(depositionId);
|
||||
break;
|
||||
default:
|
||||
throw new RuntimeException("No available entries");
|
||||
}
|
||||
|
||||
while (fileStatusListIterator.hasNext()) {
|
||||
LocatedFileStatus fileStatus = fileStatusListIterator.next();
|
||||
|
||||
Path p = fileStatus.getPath();
|
||||
String pString = p.toString();
|
||||
if (!pString.endsWith("_SUCCESS")) {
|
||||
String name = pString.substring(pString.lastIndexOf("/") + 1);
|
||||
|
||||
FSDataInputStream inputStream = fileSystem.open(p);
|
||||
// zenodoApiClient.uploadIS(inputStream, name);
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
if (!metadata.equals("")) {
|
||||
zenodoApiClient.sendMretadata(metadata);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
[
|
||||
{
|
||||
"paramName": "dt",
|
||||
"paramLongName": "depositionType",
|
||||
"paramDescription": "the type of the deposition (new, version, update)",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "cri",
|
||||
"paramLongName": "conceptRecordId",
|
||||
"paramDescription": "The id of the concept record for a new version",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "di",
|
||||
"paramLongName": "depositionId",
|
||||
"paramDescription": "the id of an open deposition which has not been published",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "hdfsp",
|
||||
"paramLongName": "hdfsPath",
|
||||
"paramDescription": "the path of the folder tofind files to send to Zenodo",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "nn",
|
||||
"paramLongName": "nameNode",
|
||||
"paramDescription": "the name node",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "at",
|
||||
"paramLongName": "accessToken",
|
||||
"paramDescription": "the access token for the deposition",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "cu",
|
||||
"paramLongName": "connectionUrl",
|
||||
"paramDescription": "the url to connect to deposit",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "m",
|
||||
"paramLongName": "metadata",
|
||||
"paramDescription": "metadata associated to the deposition",
|
||||
"paramRequired": false
|
||||
}
|
||||
]
|
||||
|
|
@ -8,148 +8,36 @@
|
|||
<name>targetPath</name>
|
||||
<description>the final graph path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>relationFilter</name>
|
||||
<description>Filter relation semantic</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>maxNumberOfPid</name>
|
||||
<description>filter relation with at least #maxNumberOfPid</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>dumpCitations</name>
|
||||
<value>false</value>
|
||||
<description>should dump citation relations</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="ImportDatasetEntities"/>
|
||||
<start to="make_tar"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="ImportDatasetEntities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Import JSONRDD to Dataset kryo</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkConvertRDDtoDataset</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=3000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||
<arg>--filterRelation</arg><arg>${relationFilter}</arg>
|
||||
</spark>
|
||||
<ok to="CreateSummaries"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
<action name="CreateSummaries">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert Entities to summaries</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkCreateSummaryObject</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=20000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}/entities</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/provision/summaries</arg>
|
||||
</spark>
|
||||
<ok to="CreateScholix"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="CreateScholix">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Generate Scholix Dataset</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkCreateScholix</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=30000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--summaryPath</arg><arg>${targetPath}/provision/summaries</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/provision/scholix</arg>
|
||||
<arg>--relationPath</arg><arg>${targetPath}/relation</arg>
|
||||
<arg>--dumpCitations</arg><arg>${dumpCitations}</arg>
|
||||
</spark>
|
||||
<ok to="DropJSONPath"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="DropJSONPath">
|
||||
<fs>
|
||||
<delete path='${targetPath}/json'/>
|
||||
<mkdir path='${targetPath}/json/'/>
|
||||
</fs>
|
||||
<ok to="SerializeScholix"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="SerializeScholix">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Serialize scholix to JSON</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=6000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}/provision/scholix/scholix</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/json/scholix_json</arg>
|
||||
<arg>--objectType</arg><arg>scholix</arg>
|
||||
<arg>--maxPidNumberFilter</arg><arg>maxNumberOfPid</arg>
|
||||
</spark>
|
||||
<ok to="make_tar"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="make_tar">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.common.MakeTarArchive</main-class>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--hdfsPath</arg><arg>${targetPath}</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
</java>
|
||||
<ok to="send_zenodo"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="send_zenodo">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.sx.graph.dump.SendToZenodoHDFS</main-class>
|
||||
<arg>--hdfsPath</arg><arg>${targetPath}/tar</arg>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}/json</arg>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--accessToken</arg><arg>${accessToken}</arg>
|
||||
<arg>--connectionUrl</arg><arg>${connectionUrl}</arg>
|
||||
<arg>--metadata</arg><arg>${metadata}</arg>
|
||||
<arg>--conceptRecordId</arg><arg>${conceptRecordId}</arg>
|
||||
<arg>--depositionType</arg><arg>${depositionType}</arg>
|
||||
<arg>--depositionId</arg><arg>${depositionId}</arg>
|
||||
</java>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
|
|
@ -103,7 +103,7 @@ public class DropAndCreateESIndex {
|
|||
Objects
|
||||
.requireNonNull(
|
||||
DropAndCreateESIndex.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/sx/provision/scholix_index.json")));
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/sx/provision/scholix_index_flat.json")));
|
||||
|
||||
log.info("creating Index SCHOLIX");
|
||||
final HttpPut put = new HttpPut(String.format(url, ip, index, "scholix"));
|
||||
|
|
|
|||
|
|
@ -42,7 +42,8 @@ public class SparkIndexCollectionOnES {
|
|||
.toString(
|
||||
Objects
|
||||
.requireNonNull(
|
||||
DropAndCreateESIndex.class.getResourceAsStream("/eu/dnetlib/dhp/sx/provision/cluster.json")));
|
||||
SparkIndexCollectionOnES.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/sx/provision/cluster.json")));
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
final Map<String, String> clusterMap = new ObjectMapper().readValue(clusterJson, Map.class);
|
||||
|
|
|
|||
|
|
@ -14,7 +14,7 @@
|
|||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="DropAndCreateIndex"/>
|
||||
<start to="indexScholix"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,77 @@
|
|||
{
|
||||
"mappings": {
|
||||
"properties": {
|
||||
"blob": {
|
||||
"type": "binary",
|
||||
"index": false
|
||||
},
|
||||
"identifier": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"linkProviders": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"publicationDate": {
|
||||
"type": "date"
|
||||
},
|
||||
"relationType": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"sourceId": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"sourcePid": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"sourcePidType": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"sourcePublisher": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"sourceSubType": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"sourceType": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"targetId": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"targetPid": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"targetPidType": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"targetPublisher": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"targetSubType": {
|
||||
"type": "keyword"
|
||||
},
|
||||
"targetType": {
|
||||
"type": "keyword"
|
||||
}
|
||||
}
|
||||
},
|
||||
"settings": {
|
||||
"index": {
|
||||
"refresh_interval": "600s",
|
||||
"number_of_shards": "48",
|
||||
"translog": {
|
||||
"sync_interval": "15s",
|
||||
"durability": "ASYNC"
|
||||
},
|
||||
"analysis": {
|
||||
"analyzer": {
|
||||
"analyzer_keyword": {
|
||||
"filter": "lowercase",
|
||||
"tokenizer": "keyword"
|
||||
}
|
||||
}
|
||||
},
|
||||
"number_of_replicas": "0"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,146 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx;
|
||||
|
||||
import static eu.dnetlib.dhp.sx.provision.DropAndCreateESIndex.APPLICATION_JSON;
|
||||
import static eu.dnetlib.dhp.sx.provision.DropAndCreateESIndex.STATUS_CODE_TEXT;
|
||||
|
||||
import java.io.*;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Paths;
|
||||
import java.util.Base64;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
import java.util.Objects;
|
||||
import java.util.zip.GZIPInputStream;
|
||||
import java.util.zip.GZIPOutputStream;
|
||||
|
||||
import org.apache.commons.codec.binary.Base64InputStream;
|
||||
import org.apache.commons.codec.binary.Base64OutputStream;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpDelete;
|
||||
import org.apache.http.client.methods.HttpPut;
|
||||
import org.apache.http.entity.StringEntity;
|
||||
import org.apache.http.impl.client.CloseableHttpClient;
|
||||
import org.apache.http.impl.client.HttpClients;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.elasticsearch.spark.rdd.api.java.JavaEsSpark;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.schema.sx.scholix.Scholix;
|
||||
import eu.dnetlib.dhp.schema.sx.scholix.ScholixFlat;
|
||||
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils;
|
||||
import eu.dnetlib.dhp.sx.provision.DropAndCreateESIndex;
|
||||
import eu.dnetlib.dhp.sx.provision.SparkIndexCollectionOnES;
|
||||
|
||||
public class FlatIndexTest {
|
||||
@Test
|
||||
public void dropAndCreateIndex() {
|
||||
|
||||
Logger log = LoggerFactory.getLogger(getClass().getName());
|
||||
|
||||
final String url = "http://localhost:9200/dli_scholix";
|
||||
|
||||
try (CloseableHttpClient client = HttpClients.createDefault()) {
|
||||
|
||||
HttpDelete delete = new HttpDelete(url);
|
||||
|
||||
CloseableHttpResponse response = client.execute(delete);
|
||||
|
||||
log.info("deleting Index SCHOLIX");
|
||||
log.info(STATUS_CODE_TEXT, response.getStatusLine());
|
||||
} catch (IOException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
|
||||
try (CloseableHttpClient client = HttpClients.createDefault()) {
|
||||
|
||||
final String scholixConf = IOUtils
|
||||
.toString(
|
||||
Objects
|
||||
.requireNonNull(
|
||||
DropAndCreateESIndex.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/sx/provision/scholix_index_flat.json")));
|
||||
|
||||
log.info("creating Index SCHOLIX");
|
||||
final HttpPut put = new HttpPut(url);
|
||||
|
||||
final StringEntity entity = new StringEntity(scholixConf);
|
||||
put.setEntity(entity);
|
||||
put.setHeader("Accept", APPLICATION_JSON);
|
||||
put.setHeader("Content-type", APPLICATION_JSON);
|
||||
|
||||
final CloseableHttpResponse response = client.execute(put);
|
||||
log.info(STATUS_CODE_TEXT, response.getStatusLine());
|
||||
} catch (IOException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
private String compressString(final String input) {
|
||||
try {
|
||||
ByteArrayOutputStream os = new ByteArrayOutputStream();
|
||||
Base64OutputStream b64os = new Base64OutputStream(os);
|
||||
GZIPOutputStream gzip = new GZIPOutputStream(b64os);
|
||||
gzip.write(input.getBytes(StandardCharsets.UTF_8));
|
||||
gzip.close();
|
||||
b64os.close();
|
||||
return new String(os.toByteArray(), StandardCharsets.UTF_8);
|
||||
} catch (Throwable t) {
|
||||
t.printStackTrace();
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
private String uncompress(final String compressed) throws Exception {
|
||||
Base64InputStream bis = new Base64InputStream(new ByteArrayInputStream(compressed.getBytes()));
|
||||
GZIPInputStream gzip = new GZIPInputStream(bis);
|
||||
return IOUtils.toString(gzip);
|
||||
}
|
||||
|
||||
public void testFeedIndex() throws Exception {
|
||||
|
||||
InputStream gzipStream = new GZIPInputStream(
|
||||
getClass().getResourceAsStream("/eu/dnetlib/dhp/sx/provision/scholix_dump.gz"));
|
||||
Reader decoder = new InputStreamReader(gzipStream, "UTF-8");
|
||||
BufferedReader buffered = new BufferedReader(decoder);
|
||||
final ObjectMapper mapper = new ObjectMapper();
|
||||
GZIPOutputStream gzip = new GZIPOutputStream(Files.newOutputStream(Paths.get("/tmp/scholix_flat.gz")));
|
||||
String line = buffered.readLine();
|
||||
while (line != null) {
|
||||
|
||||
final Scholix s = mapper.readValue(line, Scholix.class);
|
||||
final ScholixFlat flat = ScholixUtils.flattenizeScholix(s, compressString(line));
|
||||
gzip.write(mapper.writeValueAsString(flat).concat("\n").getBytes(StandardCharsets.UTF_8));
|
||||
line = buffered.readLine();
|
||||
}
|
||||
gzip.close();
|
||||
|
||||
SparkConf conf = new SparkConf()
|
||||
.setAppName(SparkIndexCollectionOnES.class.getSimpleName())
|
||||
.setMaster("local[*]");
|
||||
final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
|
||||
|
||||
try (final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext())) {
|
||||
|
||||
JavaRDD<String> inputRdd = sc.textFile("/tmp/scholix_flat.gz");
|
||||
|
||||
Map<String, String> esCfg = new HashMap<>();
|
||||
esCfg.put("es.nodes", "localhost");
|
||||
esCfg.put("es.mapping.id", "identifier");
|
||||
esCfg.put("es.batch.write.retry.count", "8");
|
||||
esCfg.put("es.batch.write.retry.wait", "60s");
|
||||
esCfg.put("es.batch.size.entries", "200");
|
||||
esCfg.put("es.nodes.wan.only", "true");
|
||||
JavaEsSpark.saveJsonToEs(inputRdd, "scholix", esCfg);
|
||||
}
|
||||
}
|
||||
}
|
||||
Binary file not shown.
Binary file not shown.
Loading…
Reference in New Issue