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This commit is contained in:
Claudio Atzori 2024-06-26 11:40:16 +02:00
parent 786c217085
commit 023099a921
31 changed files with 665 additions and 1645 deletions
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113
dhp-workflows/dhp-graph-provision/pom.xml
View File

@ -18,7 +18,7 @@
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<phase>process-resources</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
@ -59,12 +59,6 @@
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>dom4j</groupId>
@ -160,6 +154,26 @@
<groupId>org.apache.zookeeper</groupId>
<artifactId>zookeeper</artifactId>
</exclusion>
<exclusion>
<artifactId>ant</artifactId>
<groupId>org.apache.ant</groupId>
</exclusion>
<exclusion>
<artifactId>antlr4-runtime</artifactId>
<groupId>org.antlr</groupId>
</exclusion>
<exclusion>
<artifactId>woodstox-core</artifactId>
<groupId>com.fasterxml.woodstox</groupId>
</exclusion>
<exclusion>
<artifactId>log4j</artifactId>
<groupId>*</groupId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
@ -206,5 +220,90 @@
</dependencies>
<profiles>
<profile>
<id>spark-24</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.4.0</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/sparksolr-3</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>spark-34</id>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.4.0</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/sparksolr-4</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>spark-35</id>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.4.0</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/sparksolr-4</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>

3
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/ProvisionConstants.java
View File

@ -14,4 +14,7 @@ public class ProvisionConstants {
return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
}
public static final String PUBLIC_ALIAS_NAME = "public";
public static final String SHADOW_ALIAS_NAME = "shadow";
}

65
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
View File

@ -9,6 +9,7 @@ import org.apache.commons.io.IOUtils;
import org.apache.solr.client.solrj.SolrResponse;
import org.apache.solr.client.solrj.SolrServerException;
import org.apache.solr.client.solrj.impl.CloudSolrClient;
import org.apache.solr.client.solrj.request.CollectionAdminRequest;
import org.apache.solr.client.solrj.response.UpdateResponse;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -23,7 +24,7 @@ public class SolrAdminApplication implements Closeable {
private static final Logger log = LoggerFactory.getLogger(SolrAdminApplication.class);
enum Action {
DELETE_BY_QUERY, COMMIT
DELETE_BY_QUERY, COMMIT, UPDATE_ALIASES
}
private final CloudSolrClient solrClient;
@ -39,9 +40,6 @@ public class SolrAdminApplication implements Closeable {
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final String format = parser.get("format");
log.info("format: {}", format);
final Action action = Action.valueOf(parser.get("action"));
log.info("action: {}", action);
@ -59,11 +57,21 @@ public class SolrAdminApplication implements Closeable {
final String zkHost = isLookup.getZkHost();
log.info("zkHost: {}", zkHost);
final String collection = ProvisionConstants.getCollectionName(format);
log.info("collection: {}", collection);
final String publicFormat = parser.get("publicFormat");
log.info("publicFormat: {}", publicFormat);
final String shadowFormat = parser.get("shadowFormat");
log.info("shadowFormat: {}", shadowFormat);
// get collection names from metadata format profiles names
final String publicCollection = ProvisionConstants.getCollectionName(publicFormat);
log.info("publicCollection: {}", publicCollection);
final String shadowCollection = ProvisionConstants.getCollectionName(shadowFormat);
log.info("shadowCollection: {}", shadowCollection);
try (SolrAdminApplication app = new SolrAdminApplication(zkHost)) {
app.execute(action, collection, query, commit);
app.execute(action, query, commit, publicCollection, shadowCollection);
}
}
@ -72,22 +80,29 @@ public class SolrAdminApplication implements Closeable {
this.solrClient = new CloudSolrClient.Builder(zk.getHosts(), zk.getChroot()).build();
}
public SolrResponse commit(String collection) throws IOException, SolrServerException {
return execute(Action.COMMIT, collection, null, true);
public SolrResponse commit(String shadowCollection) throws IOException, SolrServerException {
return execute(Action.COMMIT, null, true, null, shadowCollection);
}
public SolrResponse execute(Action action, String collection, String query, boolean commit)
public SolrResponse execute(Action action, String query, boolean commit,
String publicCollection, String shadowCollection)
throws IOException, SolrServerException {
switch (action) {
case DELETE_BY_QUERY:
UpdateResponse rsp = solrClient.deleteByQuery(collection, query);
UpdateResponse rsp = solrClient.deleteByQuery(shadowCollection, query);
if (commit) {
solrClient.commit(collection);
return solrClient.commit(shadowCollection);
}
return rsp;
case COMMIT:
return solrClient.commit(collection);
return solrClient.commit(shadowCollection);
case UPDATE_ALIASES:
this.updateAliases(publicCollection, shadowCollection);
return null;
default:
throw new IllegalArgumentException("action not managed: " + action);
}
@ -98,4 +113,28 @@ public class SolrAdminApplication implements Closeable {
solrClient.close();
}
private void updateAliases(String publicCollection, String shadowCollection)
throws SolrServerException, IOException {
// delete current aliases
this.deleteAlias(ProvisionConstants.PUBLIC_ALIAS_NAME);
this.deleteAlias(ProvisionConstants.SHADOW_ALIAS_NAME);
// create aliases
this.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, publicCollection);
this.createAlias(ProvisionConstants.SHADOW_ALIAS_NAME, shadowCollection);
}
public SolrResponse deleteAlias(String aliasName) throws SolrServerException, IOException {
CollectionAdminRequest.DeleteAlias deleteAliasRequest = CollectionAdminRequest.deleteAlias(aliasName);
return deleteAliasRequest.process(solrClient);
}
public SolrResponse createAlias(String aliasName, String collection) throws IOException, SolrServerException {
CollectionAdminRequest.CreateAlias createAliasRequest = CollectionAdminRequest
.createAlias(aliasName, collection);
return createAliasRequest.process(solrClient);
}
}

19
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJob.java
View File

@ -36,7 +36,7 @@ public class SolrRecordDumpJob extends AbstractSolrRecordTransformJob {
private final String inputPath;
private final String format;
private final String shadowFormat;
private final String outputPath;
@ -61,8 +61,8 @@ public class SolrRecordDumpJob extends AbstractSolrRecordTransformJob {
final String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath);
final String format = parser.get("format");
log.info("format: {}", format);
final String shadowFormat = parser.get("shadowFormat");
log.info("shadowFormat: {}", shadowFormat);
final String outputPath = Optional
.ofNullable(parser.get("outputPath"))
@ -95,27 +95,24 @@ public class SolrRecordDumpJob extends AbstractSolrRecordTransformJob {
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl));
new SolrRecordDumpJob(spark, inputPath, format, outputPath).run(isLookup);
new SolrRecordDumpJob(spark, inputPath, shadowFormat, outputPath).run(isLookup);
});
}
public SolrRecordDumpJob(SparkSession spark, String inputPath, String format, String outputPath) {
public SolrRecordDumpJob(SparkSession spark, String inputPath, String shadowFormat, String outputPath) {
this.spark = spark;
this.inputPath = inputPath;
this.format = format;
this.shadowFormat = shadowFormat;
this.outputPath = outputPath;
}
public void run(ISLookupClient isLookup) throws ISLookUpException, TransformerException {
final String fields = isLookup.getLayoutSource(format);
final String fields = isLookup.getLayoutSource(shadowFormat);
log.info("fields: {}", fields);
final String xslt = isLookup.getLayoutTransformer();
final String dsId = isLookup.getDsId(format);
log.info("dsId: {}", dsId);
final String indexRecordXslt = getLayoutTransformer(format, fields, xslt);
final String indexRecordXslt = getLayoutTransformer(shadowFormat, fields, xslt);
log.info("indexRecordTransformer {}", indexRecordXslt);
final Encoder<TupleWrapper> encoder = Encoders.bean(TupleWrapper.class);

24
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java
View File

@ -25,6 +25,7 @@ import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
import eu.dnetlib.dhp.sparksolr.DHPSolrSupport;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -39,6 +40,8 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
private final String format;
private final String shadowCollection;
private final int batchSize;
private final SparkSession spark;
@ -62,8 +65,11 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
final String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath);
final String format = parser.get("format");
log.info("format: {}", format);
final String shadowFormat = parser.get("shadowFormat");
log.info("shadowFormat: {}", shadowFormat);
final String shadowCollection = ProvisionConstants.getCollectionName(shadowFormat);
log.info("shadowCollection: {}", shadowCollection);
final Integer batchSize = Optional
.ofNullable(parser.get("batchSize"))
@ -84,15 +90,17 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl));
new XmlIndexingJob(spark, inputPath, format, batchSize)
new XmlIndexingJob(spark, inputPath, shadowFormat, shadowCollection, batchSize)
.run(isLookup);
});
}
public XmlIndexingJob(SparkSession spark, String inputPath, String format, Integer batchSize) {
public XmlIndexingJob(SparkSession spark, String inputPath, String format, String shadowCollection,
Integer batchSize) {
this.spark = spark;
this.inputPath = inputPath;
this.format = format;
this.shadowCollection = shadowCollection;
this.batchSize = batchSize;
}
@ -102,12 +110,6 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
final String xslt = isLookup.getLayoutTransformer();
final String dsId = isLookup.getDsId(format);
log.info("dsId: {}", dsId);
final String collection = ProvisionConstants.getCollectionName(format);
log.info("collection: {}", collection);
final String zkHost = isLookup.getZkHost();
log.info("zkHost: {}", zkHost);
@ -129,7 +131,7 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
.javaRDD()
.map(
t -> new StreamingInputDocumentFactory().parseDocument(t.getXml(), t.getJson()));
SolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd());
DHPSolrSupport.indexDocs(zkHost, shadowCollection, batchSize, docs.rdd());
}
}

2
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/StreamingInputDocumentFactory.java
View File

@ -213,7 +213,7 @@ public class StreamingInputDocumentFactory implements Serializable {
}
writer.close();
indexDocument.addField(INDEX_RESULT, results.toString());
indexDocument.addField(INDEX_JSON_RESULT, json);
//indexDocument.addField(INDEX_JSON_RESULT, json);
} finally {
outputFactory.remove();
eventFactory.remove();

3
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java
View File

@ -5,14 +5,11 @@ import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.removePrefix;
import static eu.dnetlib.dhp.oa.provision.utils.XmlSerializationUtils.escapeXml;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import javax.swing.text.html.Option;
import org.apache.commons.lang3.StringUtils;
import org.stringtemplate.v4.ST;

7
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java
View File

@ -170,8 +170,8 @@ public class XmlSerializationUtils {
return sb.toString();
}
// <measure id="views" count="0" datasource="infrastruct_::f66f1bd369679b5b077dcdf006089556||OpenAIRE" />
// <measure id="downloads" count="0" datasource="infrastruct_::f66f1bd369679b5b077dcdf006089556||OpenAIRE" />
// <measure views="0" datasource="infrastruct_::f66f1bd369679b5b077dcdf006089556||OpenAIRE" />
// <measure downloads="0" datasource="infrastruct_::f66f1bd369679b5b077dcdf006089556||OpenAIRE" />
public static String usageMeasureAsXmlElement(String name, Measure measure) {
StringBuilder sb = new StringBuilder();
for (KeyValue kv : measure.getUnit()) {
@ -179,8 +179,7 @@ public class XmlSerializationUtils {
.append("<")
.append(name)
.append(" ")
.append(attr("id", measure.getId()))
.append(attr("count", kv.getValue()))
.append(attr(measure.getId(), kv.getValue()))
.append(attr("datasource", kv.getKey()))
.append(" />");
}

4
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/oozie_app/workflow.xml
View File

@ -69,13 +69,13 @@
</configuration>
</global>
<start to="irish_oaipmh_provision"/>
<start to="oaiphm_provision"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="irish_oaipmh_provision">
<action name="irish_oaiphm_provision">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>

2
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json
View File

@ -13,7 +13,7 @@
},
{
"paramName": "f",
"paramLongName": "format",
"paramLongName": "shadowFormat",
"paramDescription": "MDFormat name found in the IS profile",
"paramRequired": true
},

4
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json
View File

@ -13,8 +13,8 @@
},
{
"paramName": "f",
"paramLongName": "format",
"paramDescription": "MDFormat name found in the IS profile",
"paramLongName": "shadowFormat",
"paramDescription": "MDFormat name found in the IS profile bound to the shadow index collection to feed",
"paramRequired": true
},
{

19
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json
View File

@ -5,12 +5,6 @@
"paramDescription": "the URL to the ISLookUp Service",
"paramRequired": true
},
{
"paramName": "f",
"paramLongName": "format",
"paramDescription": "metadata format profile name",
"paramRequired": true
},
{
"paramName": "a",
"paramLongName": "action",
@ -28,5 +22,18 @@
"paramLongName": "commit",
"paramDescription": "should the action be followed by a commit?",
"paramRequired": false
},
{
"paramName": "pf",
"paramLongName": "publicFormat",
"paramDescription": "the name of the public metadata format profile - used to create an alias",
"paramRequired": false
},
{
"paramName": "sf",
"paramLongName": "shadowFormat",
"paramDescription": "the name of the shadow metadata format profile - used to create an alias",
"paramRequired": false
}
]

34
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
View File

@ -35,9 +35,13 @@
<description>maximum number of relations allowed for a each entity grouping by target</description>
</property>
<property>
<name>format</name>
<name>shadowFormat</name>
<description>metadata format name (DMF|TMF)</description>
</property>
<property>
<name>publicFormat</name>
<description>the public metadata format - used to create the public collection alias</description>
</property>
<property>
<name>batchSize</name>
<description>number of records to be included in each indexing request</description>
@ -133,6 +137,7 @@
<case to="create_payloads">${wf:conf('resumeFrom') eq 'create_payloads'}</case>
<case to="drop_solr_collection">${wf:conf('resumeFrom') eq 'drop_solr_collection'}</case>
<case to="to_solr_index">${wf:conf('resumeFrom') eq 'to_solr_index'}</case>
<case to="update_solr_aliases">${wf:conf('resumeFrom') eq 'update_solr_aliases'}</case>
<default to="prepare_relations"/>
</switch>
</decision>
@ -641,8 +646,8 @@
</configuration>
<main-class>eu.dnetlib.dhp.oa.provision.SolrAdminApplication</main-class>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--format</arg><arg>${format}</arg>
<arg>--action</arg><arg>DELETE_BY_QUERY</arg>
<arg>--shadowFormat</arg><arg>${shadowFormat}</arg>
<arg>--query</arg><arg>${solrDeletionQuery}</arg>
<arg>--commit</arg><arg>true</arg>
</java>
@ -672,7 +677,7 @@
</spark-opts>
<arg>--inputPath</arg><arg>${workingDir}/xml_json</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--format</arg><arg>${format}</arg>
<arg>--shadowFormat</arg><arg>${shadowFormat}</arg>
<arg>--batchSize</arg><arg>${batchSize}</arg>
</spark>
<ok to="commit_solr_collection"/>
@ -689,7 +694,7 @@
</configuration>
<main-class>eu.dnetlib.dhp.oa.provision.SolrAdminApplication</main-class>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--format</arg><arg>${format}</arg>
<arg>--shadowFormat</arg><arg>${shadowFormat}</arg>
<arg>--action</arg><arg>COMMIT</arg>
</java>
<ok to="End"/>
@ -714,12 +719,31 @@
</spark-opts>
<arg>--inputPath</arg><arg>${workingDir}/xml_json</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--format</arg><arg>${format}</arg>
<arg>--shadowFormat</arg><arg>${shadowFormat}</arg>
<arg>--outputPath</arg><arg>${workingDir}/solr_documents</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<!-- Action that updates the solr core aliases - out of order execution, only using the 'resume_from' param -->
<action name="update_solr_aliases">
<java>
<configuration>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>
<main-class>eu.dnetlib.dhp.oa.provision.SolrAdminApplication</main-class>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--action</arg><arg>UPDATE_ALIASES</arg>
<arg>--publicFormat</arg><arg>${publicFormat}</arg>
<arg>--shadowFormat</arg><arg>${shadowFormat}</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

12
dhp-workflows/dhp-graph-provision/src/main/sparksolr-3/eu/dnetlib/dhp/sparksolr/DHPSolrSupport.java Normal file
View File

@ -0,0 +1,12 @@
package eu.dnetlib.dhp.sparksolr;
import com.lucidworks.spark.util.SolrSupport;
import org.apache.solr.common.SolrInputDocument;
import org.apache.spark.rdd.RDD;
public class DHPSolrSupport {
static public void indexDocs(String zkhost, String collection, int batchSize, RDD<SolrInputDocument> docs) {
SolrSupport.indexDocs(zkhost, collection, batchSize, docs);
}
}

12
dhp-workflows/dhp-graph-provision/src/main/sparksolr-4/eu/dnetlib/dhp/sparksolr/DHPSolrSupport.java Normal file
View File

@ -0,0 +1,12 @@
package eu.dnetlib.dhp.sparksolr;
import com.lucidworks.spark.util.SolrSupport;
import org.apache.solr.common.SolrInputDocument;
import org.apache.spark.rdd.RDD;
public class DHPSolrSupport {
static public void indexDocs(String zkhost, String collection, int batchSize, RDD<SolrInputDocument> docs) {
SolrSupport.indexDocs(zkhost, collection, batchSize, com.lucidworks.spark.BatchSizeType.NUM_DOCS, docs);
}
}

12
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJobTest.java
View File

@ -67,7 +67,7 @@ public class PrepareRelationsJobTest {
@Test
void testRunPrepareRelationsJob(@TempDir Path testPath) throws Exception {
final int maxRelations = 20;
final int maxRelations = 5;
PrepareRelationsJob
.main(
new String[] {
@ -86,7 +86,7 @@ public class PrepareRelationsJobTest {
.as(Encoders.bean(Relation.class))
.cache();
assertEquals(maxRelations, out.count());
assertEquals(44, out.count());
Dataset<Row> freq = out
.toDF()
@ -101,12 +101,8 @@ public class PrepareRelationsJobTest {
long affiliation = getRows(freq, AFFILIATION).get(0).getAs("count");
assertEquals(outcome, participation);
assertTrue(outcome > affiliation);
assertTrue(participation > affiliation);
assertEquals(7, outcome);
assertEquals(7, participation);
assertEquals(6, affiliation);
assertEquals(outcome, affiliation);
assertEquals(4, affiliation);
}
protected List<Row> getRows(Dataset<Row> freq, String col) {

33
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java
View File

@ -4,16 +4,20 @@ package eu.dnetlib.dhp.oa.provision;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import org.apache.solr.client.solrj.request.SolrPing;
import org.apache.solr.client.solrj.response.CollectionAdminResponse;
import org.apache.solr.client.solrj.response.SolrPingResponse;
import org.apache.solr.client.solrj.response.UpdateResponse;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
class SolrAdminApplicationTest extends SolrTest {
@Test
void testPing() throws Exception {
SolrPingResponse pingResponse = miniCluster.getSolrClient().ping();
final SolrPing ping = new SolrPing();
ping.getParams().set("collection", ProvisionConstants.SHADOW_ALIAS_NAME);
SolrPingResponse pingResponse = ping.process(miniCluster.getSolrClient());
log.info("pingResponse: '{}'", pingResponse.getStatus());
assertEquals(0, pingResponse.getStatus());
}
@ -24,7 +28,7 @@ class SolrAdminApplicationTest extends SolrTest {
SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost());
UpdateResponse rsp = (UpdateResponse) admin
.execute(SolrAdminApplication.Action.DELETE_BY_QUERY, DEFAULT_COLLECTION, "*:*", false);
.execute(SolrAdminApplication.Action.DELETE_BY_QUERY, "*:*", false, null, SHADOW_COLLECTION);
assertEquals(0, rsp.getStatus());
}
@ -34,9 +38,30 @@ class SolrAdminApplicationTest extends SolrTest {
SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost());
UpdateResponse rsp = (UpdateResponse) admin.commit(DEFAULT_COLLECTION);
UpdateResponse rsp = (UpdateResponse) admin.commit(SHADOW_COLLECTION);
assertEquals(0, rsp.getStatus());
}
@Test
void testAdminApplication_CREATE_ALIAS() throws Exception {
SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost());
CollectionAdminResponse rsp = (CollectionAdminResponse) admin
.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, SHADOW_COLLECTION);
assertEquals(0, rsp.getStatus());
}
@Test
void testAdminApplication_DELETE_ALIAS() throws Exception {
SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost());
CollectionAdminResponse rsp = (CollectionAdminResponse) admin.deleteAlias(ProvisionConstants.PUBLIC_ALIAS_NAME);
assertEquals(0, rsp.getStatus());
}
}

134
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
View File

@ -1,21 +1,40 @@
package eu.dnetlib.dhp.oa.provision;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.embedded.JettyConfig;
import org.apache.solr.client.solrj.impl.CloudSolrClient;
import org.apache.solr.client.solrj.request.CollectionAdminRequest;
import org.apache.solr.client.solrj.request.ConfigSetAdminRequest;
import org.apache.solr.client.solrj.request.QueryRequest;
import org.apache.solr.client.solrj.response.CollectionAdminResponse;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.cloud.MiniSolrCloudCluster;
import org.apache.solr.common.SolrDocument;
import org.apache.solr.common.params.CollectionParams;
import org.apache.solr.common.params.CommonParams;
import org.apache.solr.common.params.CoreAdminParams;
import org.apache.solr.common.params.ModifiableSolrParams;
import org.apache.solr.common.util.NamedList;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.api.io.TempDir;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
@ -23,7 +42,18 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class)
public class SolrConfigExploreTest extends SolrExploreTest {
public class SolrConfigExploreTest {
protected static final Logger log = LoggerFactory.getLogger(SolrConfigExploreTest.class);
protected static final String SHADOW_FORMAT = "c1";
protected static final String SHADOW_COLLECTION = SHADOW_FORMAT + "-index-openaire";
protected static final String PUBLIC_FORMAT = "c2";
protected static final String PUBLIC_COLLECTION = PUBLIC_FORMAT + "-index-openaire";
protected static final String CONFIG_NAME = "testConfig";
protected static SolrAdminApplication admin;
protected static SparkSession spark;
@ -35,15 +65,17 @@ public class SolrConfigExploreTest extends SolrExploreTest {
@Mock
private ISLookupClient isLookupClient;
@TempDir
public static Path workingDir;
protected static MiniSolrCloudCluster miniCluster;
@BeforeEach
public void prepareMocks() throws ISLookUpException, IOException {
isLookupClient.setIsLookup(isLookUpService);
int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort();
Mockito
.when(isLookupClient.getDsId(Mockito.anyString()))
.thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl");
Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort));
Mockito
.when(isLookupClient.getLayoutSource(Mockito.anyString()))
@ -54,7 +86,7 @@ public class SolrConfigExploreTest extends SolrExploreTest {
}
@BeforeAll
public static void before() {
public static void setup() throws Exception {
SparkConf conf = new SparkConf();
conf.setAppName(XmlIndexingJobTest.class.getSimpleName());
@ -70,15 +102,75 @@ public class SolrConfigExploreTest extends SolrExploreTest {
spark = SparkSession
.builder()
.appName(XmlIndexingJobTest.class.getSimpleName())
.appName(SolrConfigExploreTest.class.getSimpleName())
.config(conf)
.getOrCreate();
// random unassigned HTTP port
final int jettyPort = 0;
final JettyConfig jettyConfig = JettyConfig.builder().setPort(jettyPort).build();
log.info(String.format("working directory: %s", workingDir.toString()));
System.setProperty("solr.log.dir", workingDir.resolve("logs").toString());
// create a MiniSolrCloudCluster instance
miniCluster = new MiniSolrCloudCluster(2, workingDir.resolve("solr"), jettyConfig);
// Upload Solr configuration directory to ZooKeeper
String solrZKConfigDir = "src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig";
File configDir = new File(solrZKConfigDir);
miniCluster.uploadConfigSet(configDir.toPath(), CONFIG_NAME);
// override settings in the solrconfig include
System.setProperty("solr.tests.maxBufferedDocs", "100000");
System.setProperty("solr.tests.maxIndexingThreads", "-1");
System.setProperty("solr.tests.ramBufferSizeMB", "100");
// use non-test classes so RandomizedRunner isn't necessary
System.setProperty("solr.tests.mergeScheduler", "org.apache.lucene.index.ConcurrentMergeScheduler");
System.setProperty("solr.directoryFactory", "solr.RAMDirectoryFactory");
System.setProperty("solr.lock.type", "single");
log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString());
log
.info(
CollectionAdminRequest.ClusterStatus
.getClusterStatus()
.process(miniCluster.getSolrClient())
.toString());
NamedList<Object> res = createCollection(
miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
res.forEach(o -> log.info(o.toString()));
// miniCluster.getSolrClient().setDefaultCollection(SHADOW_COLLECTION);
res = createCollection(
miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
res.forEach(o -> log.info(o.toString()));
admin = new SolrAdminApplication(miniCluster.getZkClient().getZkServerAddress());
CollectionAdminResponse rsp = (CollectionAdminResponse) admin
.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
assertEquals(0, rsp.getStatus());
rsp = (CollectionAdminResponse) admin.createAlias(ProvisionConstants.SHADOW_ALIAS_NAME, SHADOW_COLLECTION);
assertEquals(0, rsp.getStatus());
log
.info(
CollectionAdminRequest.ClusterStatus
.getClusterStatus()
.process(miniCluster.getSolrClient())
.toString());
}
@AfterAll
public static void tearDown() {
public static void tearDown() throws Exception {
spark.stop();
miniCluster.shutdown();
FileUtils.deleteDirectory(workingDir.toFile());
}
@Test
@ -86,8 +178,10 @@ public class SolrConfigExploreTest extends SolrExploreTest {
String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
new XmlIndexingJob(spark, inputPath, FORMAT, batchSize).run(isLookupClient);
Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
.run(isLookupClient);
Assertions
.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
String[] queryStrings = {
"cancer",
@ -101,14 +195,14 @@ public class SolrConfigExploreTest extends SolrExploreTest {
query.add(CommonParams.Q, q);
query.set("debugQuery", "on");
log.info("Submit query to Solr with params: {}", query.toString());
QueryResponse rsp = miniCluster.getSolrClient().query(query);
log.info("Submit query to Solr with params: {}", query);
QueryResponse rsp = miniCluster.getSolrClient().query(ProvisionConstants.SHADOW_ALIAS_NAME, query);
// System.out.println(rsp.getHighlighting());
// System.out.println(rsp.getExplainMap());
for (SolrDocument doc : rsp.getResults()) {
System.out
.println(
log
.info(
doc.get("score") + "\t" +
doc.get("__indexrecordidentifier") + "\t" +
doc.get("resultidentifier") + "\t" +
@ -122,4 +216,18 @@ public class SolrConfigExploreTest extends SolrExploreTest {
}
}
}
protected static NamedList<Object> createCollection(CloudSolrClient client, String name, int numShards,
int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
ModifiableSolrParams modParams = new ModifiableSolrParams();
modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name());
modParams.set("name", name);
modParams.set("numShards", numShards);
modParams.set("replicationFactor", replicationFactor);
modParams.set("collection.configName", configName);
modParams.set("maxShardsPerNode", maxShardsPerNode);
QueryRequest request = new QueryRequest(modParams);
request.setPath("/admin/collections");
return client.request(request);
}
}

21
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
View File

@ -2,24 +2,15 @@
package eu.dnetlib.dhp.oa.provision;
import java.io.IOException;
import java.io.StringReader;
import java.net.URI;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.common.SolrDocument;
import org.apache.solr.common.SolrInputField;
import org.apache.solr.common.params.CommonParams;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.dom4j.io.SAXReader;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
@ -50,9 +41,6 @@ public class SolrConfigTest extends SolrTest {
int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort();
Mockito
.when(isLookupClient.getDsId(Mockito.anyString()))
.thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl");
Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort));
Mockito
.when(isLookupClient.getLayoutSource(Mockito.anyString()))
@ -95,9 +83,10 @@ public class SolrConfigTest extends SolrTest {
String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
new XmlIndexingJob(spark, inputPath, FORMAT, batchSize)
new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
.run(isLookupClient);
Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
Assertions
.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
String[] queryStrings = {
"cancer",
@ -109,8 +98,8 @@ public class SolrConfigTest extends SolrTest {
SolrQuery query = new SolrQuery();
query.add(CommonParams.Q, q);
log.info("Submit query to Solr with params: {}", query.toString());
QueryResponse rsp = miniCluster.getSolrClient().query(query);
log.info("Submit query to Solr with params: {}", query);
QueryResponse rsp = miniCluster.getSolrClient().query(ProvisionConstants.SHADOW_ALIAS_NAME, query);
for (SolrDocument doc : rsp.getResults()) {
System.out

52
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java
View File

@ -34,58 +34,6 @@ public abstract class SolrExploreTest {
@TempDir
public static Path workingDir;
@BeforeAll
public static void setup() throws Exception {
// random unassigned HTTP port
final int jettyPort = 0;
final JettyConfig jettyConfig = JettyConfig.builder().setPort(jettyPort).build();
log.info(String.format("working directory: %s", workingDir.toString()));
System.setProperty("solr.log.dir", workingDir.resolve("logs").toString());
// create a MiniSolrCloudCluster instance
miniCluster = new MiniSolrCloudCluster(2, workingDir.resolve("solr"), jettyConfig);
// Upload Solr configuration directory to ZooKeeper
String solrZKConfigDir = "src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig";
File configDir = new File(solrZKConfigDir);
miniCluster.uploadConfigSet(configDir.toPath(), CONFIG_NAME);
// override settings in the solrconfig include
System.setProperty("solr.tests.maxBufferedDocs", "100000");
System.setProperty("solr.tests.maxIndexingThreads", "-1");
System.setProperty("solr.tests.ramBufferSizeMB", "100");
// use non-test classes so RandomizedRunner isn't necessary
System.setProperty("solr.tests.mergeScheduler", "org.apache.lucene.index.ConcurrentMergeScheduler");
System.setProperty("solr.directoryFactory", "solr.RAMDirectoryFactory");
System.setProperty("solr.lock.type", "single");
log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString());
log
.info(
CollectionAdminRequest.ClusterStatus
.getClusterStatus()
.process(miniCluster.getSolrClient())
.toString());
NamedList<Object> res = createCollection(
miniCluster.getSolrClient(), DEFAULT_COLLECTION, 4, 2, 20, CONFIG_NAME);
res.forEach(o -> log.info(o.toString()));
miniCluster.getSolrClient().setDefaultCollection(DEFAULT_COLLECTION);
log
.info(
CollectionAdminRequest.ClusterStatus
.getClusterStatus()
.process(miniCluster.getSolrClient())
.toString());
}
@AfterAll
public static void shutDown() throws Exception {
miniCluster.shutdown();

3
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJobTest.java
View File

@ -91,9 +91,6 @@ class SolrRecordDumpJobTest {
public void prepareMocks() throws ISLookUpException, IOException {
isLookupClient.setIsLookup(isLookUpService);
Mockito
.when(isLookupClient.getDsId(Mockito.anyString()))
.thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl");
Mockito
.when(isLookupClient.getLayoutSource(Mockito.anyString()))
.thenReturn(IOUtils.toString(getClass().getResourceAsStream("fields.xml")));

31
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrTest.java
View File

@ -1,6 +1,8 @@
package eu.dnetlib.dhp.oa.provision;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.File;
import java.nio.file.Path;
@ -10,6 +12,7 @@ import org.apache.solr.client.solrj.impl.CloudSolrClient;
import org.apache.solr.client.solrj.request.CollectionAdminRequest;
import org.apache.solr.client.solrj.request.ConfigSetAdminRequest;
import org.apache.solr.client.solrj.request.QueryRequest;
import org.apache.solr.client.solrj.response.CollectionAdminResponse;
import org.apache.solr.cloud.MiniSolrCloudCluster;
import org.apache.solr.common.params.CollectionParams;
import org.apache.solr.common.params.CoreAdminParams;
@ -21,14 +24,21 @@ import org.junit.jupiter.api.io.TempDir;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import sun.security.provider.SHA;
public abstract class SolrTest {
protected static final Logger log = LoggerFactory.getLogger(SolrTest.class);
protected static final String FORMAT = "test";
protected static final String DEFAULT_COLLECTION = FORMAT + "-index-openaire";
protected static final String SHADOW_FORMAT = "c1";
protected static final String SHADOW_COLLECTION = SHADOW_FORMAT + "-index-openaire";
protected static final String PUBLIC_FORMAT = "c2";
protected static final String PUBLIC_COLLECTION = PUBLIC_FORMAT + "-index-openaire";
protected static final String CONFIG_NAME = "testConfig";
protected static SolrAdminApplication admin;
protected static MiniSolrCloudCluster miniCluster;
@TempDir
@ -72,10 +82,21 @@ public abstract class SolrTest {
.toString());
NamedList<Object> res = createCollection(
miniCluster.getSolrClient(), DEFAULT_COLLECTION, 4, 2, 20, CONFIG_NAME);
miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
res.forEach(o -> log.info(o.toString()));
miniCluster.getSolrClient().setDefaultCollection(DEFAULT_COLLECTION);
// miniCluster.getSolrClient().setDefaultCollection(SHADOW_COLLECTION);
res = createCollection(
miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
res.forEach(o -> log.info(o.toString()));
admin = new SolrAdminApplication(miniCluster.getZkClient().getZkServerAddress());
CollectionAdminResponse rsp = (CollectionAdminResponse) admin
.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
assertEquals(0, rsp.getStatus());
rsp = (CollectionAdminResponse) admin.createAlias(ProvisionConstants.SHADOW_ALIAS_NAME, SHADOW_COLLECTION);
assertEquals(0, rsp.getStatus());
log
.info(
@ -83,12 +104,12 @@ public abstract class SolrTest {
.getClusterStatus()
.process(miniCluster.getSolrClient())
.toString());
}
@AfterAll
public static void shutDown() throws Exception {
miniCluster.shutdown();
admin.close();
FileUtils.deleteDirectory(workingDir.toFile());
}

62
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java
View File

@ -10,6 +10,7 @@ import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.SolrResponse;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.common.params.CommonParams;
import org.apache.spark.SparkConf;
@ -50,9 +51,6 @@ public class XmlIndexingJobTest extends SolrTest {
int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort();
Mockito
.when(isLookupClient.getDsId(Mockito.anyString()))
.thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl");
Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort));
Mockito
.when(isLookupClient.getLayoutSource(Mockito.anyString()))
@ -103,37 +101,62 @@ public class XmlIndexingJobTest extends SolrTest {
long nRecord = records.count();
new XmlIndexingJob(spark, inputPath, FORMAT, batchSize).run(isLookupClient);
new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
.run(isLookupClient);
assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
assertEquals(0, miniCluster.getSolrClient().commit(SHADOW_COLLECTION).getStatus());
QueryResponse rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "*:*"));
QueryResponse rsp = miniCluster
.getSolrClient()
.query(
ProvisionConstants.SHADOW_ALIAS_NAME,
new SolrQuery().add(CommonParams.Q, "*:*"));
assertEquals(
nRecord, rsp.getResults().getNumFound(),
"the number of indexed records should be equal to the number of input records");
rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "isgreen:true"));
rsp = miniCluster
.getSolrClient()
.query(
ProvisionConstants.SHADOW_ALIAS_NAME,
new SolrQuery().add(CommonParams.Q, "isgreen:true"));
assertEquals(
4, rsp.getResults().getNumFound(),
"the number of indexed records having isgreen = true");
rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "openaccesscolor:bronze"));
rsp = miniCluster
.getSolrClient()
.query(
ProvisionConstants.SHADOW_ALIAS_NAME,
new SolrQuery().add(CommonParams.Q, "openaccesscolor:bronze"));
assertEquals(
2, rsp.getResults().getNumFound(),
"the number of indexed records having openaccesscolor = bronze");
rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "isindiamondjournal:true"));
rsp = miniCluster
.getSolrClient()
.query(
ProvisionConstants.SHADOW_ALIAS_NAME,
new SolrQuery().add(CommonParams.Q, "isindiamondjournal:true"));
assertEquals(
0, rsp.getResults().getNumFound(),
"the number of indexed records having isindiamondjournal = true");
rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "publiclyfunded:true"));
rsp = miniCluster
.getSolrClient()
.query(
ProvisionConstants.SHADOW_ALIAS_NAME,
new SolrQuery().add(CommonParams.Q, "publiclyfunded:true"));
assertEquals(
0, rsp.getResults().getNumFound(),
"the number of indexed records having publiclyfunded = true");
rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "peerreviewed:true"));
rsp = miniCluster
.getSolrClient()
.query(
ProvisionConstants.SHADOW_ALIAS_NAME,
new SolrQuery().add(CommonParams.Q, "peerreviewed:true"));
assertEquals(
35, rsp.getResults().getNumFound(),
"the number of indexed records having peerreviewed = true");
@ -141,6 +164,7 @@ public class XmlIndexingJobTest extends SolrTest {
rsp = miniCluster
.getSolrClient()
.query(
ProvisionConstants.SHADOW_ALIAS_NAME,
new SolrQuery()
.add(CommonParams.Q, "objidentifier:\"57a035e5b1ae::236d6d8c1e03368b5ae72acfeeb11bbc\"")
.add(CommonParams.FL, "__json"));
@ -158,6 +182,22 @@ public class XmlIndexingJobTest extends SolrTest {
log.info((String) json.get());
admin
.execute(
SolrAdminApplication.Action.UPDATE_ALIASES, null, false,
SHADOW_COLLECTION, PUBLIC_COLLECTION);
rsp = miniCluster
.getSolrClient()
.query(
ProvisionConstants.PUBLIC_ALIAS_NAME,
new SolrQuery()
.add(CommonParams.Q, "objidentifier:\"57a035e5b1ae::236d6d8c1e03368b5ae72acfeeb11bbc\"")
.add(CommonParams.FL, "__json"));
assertEquals(
1, rsp.getResults().getNumFound(),
"the number of indexed records having the given identifier, found in the public collection");
}
}

8
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
View File

@ -9,7 +9,6 @@ import java.io.StringReader;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.commons.math3.optim.AbstractOptimizationProblem;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Element;
@ -52,12 +51,7 @@ public class XmlRecordFactoryTest {
assertNotNull(doc);
System.out.println(doc.asXML());
assertEquals("10", doc.valueOf("//measure[@id = 'downloads']/@count"));
assertEquals("fakeds", doc.valueOf("//measure[@id = 'downloads']/@datasource"));
assertEquals(0, doc.selectNodes("//measure[@id = 'views']").size());
// System.out.println(doc.asXML());
assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid"));
assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending"));

586
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/edith-demo/10.1098-rsta.2020.0257.xml
View File

@ -1,586 +0,0 @@
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characterization of cardiovascular diseases, since it can identify abnormalities in structure
and function of the myocardium non-invasively and without the need for ionizing radiation.
However, in clinical practice, it is commonly acquired as a collection of separated and
independent 2D image planes, which limits its accuracy in 3D analysis. This paper presents a
completely automated pipeline for generating patient-specific 3D biventricular heart models from
cine magnetic resonance (MR) slices. Our pipeline automatically selects the relevant cine MR
images, segments them using a deep learning-based method to extract the heart contours, and
aligns the contours in 3D space correcting possible misalignments due to breathing or subject
motion first using the intensity and contours information from the cine data and next with the
help of a statistical shape model. Finally, the sparse 3D representation of the contours is used
to generate a smooth 3D biventricular mesh. The computational pipeline is applied and evaluated
in a CMR dataset of 20 healthy subjects. Our results show an average reduction of misalignment
artefacts from 1.82 ± 1.60 mm to 0.72 ± 0.73 mm over 20 subjects, in terms of distance from the
final reconstructed mesh. The high-resolution 3D biventricular meshes obtained with our
computational pipeline are used for simulations of electrical activation patterns, showing
agreement with non-invasive electrocardiographic imaging. The automatic methodologies presented
here for patient-specific MR imaging-based 3D biventricular representations contribute to the
efficient realization of precision medicine, enabling the enhanced interpretability of clinical
data, the digital twin vision through patient-specific image-based modelling and simulation, and
augmented reality applications.
This article is part of the theme issue ‘Advanced computation in cardiovascular physiology: new
challenges and opportunities’.
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dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/edith-demo/10.2196-33081-ethics.xml
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<description>Background: The concept of digital twins has great potential for transforming the existing health care system by making it more personalized. As a convergence of health care, artificial intelligence, and information and communication technologies, personalized health care services that are developed under the concept of digital twins raise a myriad of ethical issues. Although some of the ethical issues are known to researchers working on digital health and personalized medicine, currently, there is no comprehensive review that maps the major ethical risks of digital twins for personalized health care services. Objective This study aims to fill the research gap by identifying the major ethical risks of digital twins for personalized health care services. We first propose a working definition for digital twins for personalized health care services to facilitate future discussions on the ethical issues related to these emerging digital health services. We then develop a process-oriented ethical map to identify the major ethical risks in each of the different data processing phases. MethodsWe resorted to the literature on eHealth, personalized medicine, precision medicine, and information engineering to identify potential issues and developed a process-oriented ethical map to structure the inquiry in a more systematic way. The ethical map allows us to see how each of the major ethical concerns emerges during the process of transforming raw data into valuable information. Developers of a digital twin for personalized health care service may use this map to identify ethical risks during the development stage in a more systematic way and can proactively address them. ResultsThis paper provides a working definition of digital twins for personalized health care services by identifying 3 features that distinguish the new application from other eHealth services. On the basis of the working definition, this paper further layouts 10 major operational problems and the corresponding ethical risks. ConclusionsIt is challenging to address all the major ethical risks that a digital twin for a personalized health care service might encounter proactively without a conceptual map at hand. The process-oriented ethical map we propose here can assist the developers of digital twins for personalized health care services in analyzing ethical risks in a more systematic manner. </description>
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material-consuming step. In this article, a physico-chemical model of in vitro mRNA
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quantitative validation workflow. Statistically significant parameters are identified as part of
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with a deviation of less than 1%. The advantages of continuous production are pointed out
compared to batchwise in vitro transcription by optimization of the space–time yield.
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7
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml
View File

@ -68,15 +68,12 @@
<FIELD copy="true" indexable="false" name="externalreflabel" result="false" stat="false" tokenizable="true" xpath="distinct-values(//*[local-name()='entity']/*//children/externalreference/label)"/>
<FIELD copy="true" indexable="true" name="resultidentifier" result="false" stat="false" type="string_ci" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/children/instance/webresource/*[local-name()='url'])"/>
<FIELD copy="true" indexable="false" name="resultsource" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/source)"/>
<FIELD indexable="true" multivalued="false" name="isgreen" result="false" stat="false" type="boolean" value="//*[local-name()='entity']/*[local-name()='result']/isgreen"/>
<FIELD indexable="true" multivalued="false" name="openaccesscolor" result="false" stat="false" tokenizable="false" value="//*[local-name()='entity']/*[local-name()='result']/openaccesscolor"/>
<FIELD indexable="true" multivalued="false" name="isindiamondjournal" result="false" stat="false" type="boolean" value="//*[local-name()='entity']/*[local-name()='result']/isindiamondjournal"/>
<FIELD indexable="true" multivalued="false" name="publiclyfunded" result="false" stat="false" type="boolean" value="//*[local-name()='entity']/*[local-name()='result']/publiclyfunded"/>
<FIELD indexable="true" multivalued="false" name="peerreviewed" result="false" stat="false" type="boolean" value="some $refereed in //*[local-name()='entity']/*[local-name()='result']/children/instance/*[local-name()='refereed']/@classid satisfies ($refereed = '0001')"/>
<FIELD indexable="true" multivalued="false" name="haslicense" result="false" stat="false" type="boolean" value="some $license in //*[local-name()='entity']/*[local-name()='result']/children/instance/*[local-name()='license']/text() satisfies (string-length($license) &gt; 0)"/>
<FIELD indexable="true" name="eoscifguidelines" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name() = 'result']/eoscifguidelines/@code)"/><!-- FOS and SDGs non tokenizable for faceted search-->
<FIELD indexable="true" name="fos" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/subject[@classid='FOS'])"/>
<FIELD indexable="true" name="foslabel" result="false" stat="false" tokenizable="false" value="concat(./text(), '||', replace(./text(), '^\d+\s', ''))" xpath="//*[local-name()='entity']/*[local-name()='result']/subject[@classid='FOS']"/>
@ -93,6 +90,7 @@
<FIELD indexable="true" name="relorganizationid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to[@type='organization'])"/>
<FIELD copy="true" indexable="true" name="relorganizationname" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='organization']/legalname)"/>
<FIELD copy="true" indexable="true" name="relorganizationshortname" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='organization']/legalshortname)"/>
<FIELD indexable="true" name="relorganization" result="false" stat="false" tokenizable="false" value="distinct-values(concat(./to, '||', ./legalname))" xpath="//*[local-name()='entity']/*//rel[./to/@type='organization']"/>
<FIELD indexable="true" name="relresultid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to[@type='publication' or @type='dataset' or @type='software' or @type='otherresearchproduct'])"/>
<FIELD indexable="true" name="relresulttype" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to/@type)"/>
<FIELD indexable="true" name="relclass" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to/@class)"/>
@ -122,6 +120,7 @@
<FIELD indexable="true" name="categoryid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/context/category/@id)"/>
<FIELD indexable="true" name="conceptname" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/context/category//concept/@label)"/><!-- new index field for country info from different xpaths for any type of entity -->
<FIELD indexable="true" name="country" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*/country/@classid | //*[local-name()='entity']/*//rel[./to/@type='organization']/country/@classid | //*[local-name()='entity']//funder/@jurisdiction)"/>
<FIELD indexable="true" name="countrynojurisdiction" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*/country/@classid | //*[local-name()='entity']/*//rel[./to/@type='organization']/country/@classid)"/>
<FIELD indexable="false" name="oafentity" result="true" stat="false" tokenizable="false" xpath="//*[local-name() = 'entity']"/><!-- impact indicators -->
<FIELD copy="false" indexable="true" multivalued="false" name="influence" result="false" stat="false" type="pfloat" xpath="//measure[@id='influence']/@score/number()"/>
<FIELD copy="false" indexable="true" multivalued="false" name="influence_class" result="false" stat="false" type="string" xpath="//measure[@id='influence']/@class/string()"/>

86
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json
View File

@ -8,26 +8,6 @@
}
],
"measures": [
{
"id": "downloads",
"unit": [
{
"key": "fakeds",
"value": "10",
"dataInfo": null
}
]
},
{
"id": "views",
"unit": [
{
"key": "fakedss",
"value": "0",
"dataInfo": null
}
]
},
{
"id": "influence",
"unit": [
@ -451,26 +431,7 @@
"value": "VIRTA"
}
],
"context": [
{
"id": "eosc",
"dataInfo": [
{
"invisible": false,
"inferred": false,
"deletedbyinference": false,
"trust": "0.9",
"inferenceprovenance": "",
"provenanceaction": {
"classid": "sysimport:crosswalk",
"classname": "sysimport:crosswalk",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
}
}
]
}
],
"context": [],
"contributor": [],
"country": [],
"coverage": [],
@ -559,24 +520,6 @@
"value": "4.62970429725e-08"
}
]
},
{
"id": "downloads",
"unit": [
{
"key": "fakeds",
"value": "10"
}
]
},
{
"id": "views",
"unit": [
{
"key": "fakeds",
"value": "10"
}
]
}
],
"pid": [
@ -712,7 +655,9 @@
},
"value": ""
},
"url": ["http://dx.doi.org/10.1109/TED.2018.2853550"]
"url": [
"http://dx.doi.org/10.1109/TED.2018.2853550"
]
},
{
"pid": [
@ -848,7 +793,9 @@
},
"value": "CC-BY"
},
"url": ["http://dx.doi.org/10.1109/TED.2018.2853550"]
"url": [
"http://dx.doi.org/10.1109/TED.2018.2853550"
]
},
{
"pid": [
@ -984,7 +931,9 @@
},
"value": ""
},
"url": ["http://dx.doi.org/10.1109/TED.2018.2853551"]
"url": [
"http://dx.doi.org/10.1109/TED.2018.2853551"
]
},
{
"pid": [
@ -1253,7 +1202,8 @@
},
"value": ""
},
"url": []
"url": [
]
},
{
"pid": [
@ -1383,7 +1333,9 @@
},
"value": ""
},
"url": [""]
"url": [
""
]
},
{
"pid": [
@ -1513,7 +1465,9 @@
},
"value": ""
},
"url": ["asdasd://not a URL"]
"url": [
"asdasd://not a URL"
]
}
],
"journal": {
@ -1607,9 +1561,7 @@
"schemeid": "dnet:result_typologies",
"schemename": "dnet:result_typologies"
},
"source": [
{"value": "Bulletin of the National Technical University \"KhPI\" A series of \"Information and Modeling\"; № 1 (3) (2020):"}
],
"source": [ { "value" : "Bulletin of the National Technical University \"KhPI\" A series of \"Information and Modeling\"; № 1 (3) (2020):" } ],
"subject": [
{
"dataInfo": {

339
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema
View File

@ -194,228 +194,173 @@
<fieldType name="tints" class="solr.TrieIntField" positionIncrementGap="0" docValues="true" multiValued="true" precisionStep="8"/>
<fieldType name="tlong" class="solr.TrieLongField" positionIncrementGap="0" docValues="true" precisionStep="8"/>
<fieldType name="tlongs" class="solr.TrieLongField" positionIncrementGap="0" docValues="true" multiValued="true" precisionStep="8"/>
<!-- Indexed fields -->
<field name="__all" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="__deleted" type="boolean" default="false" omitNorms="true" omitTermFreqAndPositions="true" indexed="true" stored="false"/>
<field name="__dsid" type="string" omitNorms="true" omitTermFreqAndPositions="true" indexed="true" stored="true"/>
<field name="__dsversion" type="pdate" omitNorms="true" omitTermFreqAndPositions="true" indexed="true" stored="true"/>
<field name="__indexrecordidentifier" type="string" multiValued="false" indexed="true" required="true" stored="true"/>
<field name="__result" type="string" docValues="false" multiValued="false" indexed="false" stored="true"/>
<field name="__json" type="string" docValues="false" multiValued="false" indexed="false" stored="true"/>
<field name="__result" type="string" docValues="false" multiValued="false" indexed="false" stored="true"/>
<field name="_root_" type="string" docValues="false" indexed="true" stored="false"/>
<field name="_version_" type="long" multiValued="false" indexed="true" stored="true"/>
<field name="authorid" type="string_ci" multiValued="true" indexed="true" stored="false"/>
<field name="authoridtype" type="string_ci" multiValued="true" indexed="true" stored="false"/>
<field name="categoryid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="categoryname" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="collectedfrom" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="collectedfromdatasourceid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="collectedfromname" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="community" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="communityid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="communityname" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="conceptid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="conceptname" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="contextid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="contextname" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="contexttype" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="country" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="datasourcecompatibilityid" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="datasourcecompatibilityname" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="datasourceenglishname" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="authorid" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="categoryid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="citation_count" type="pint" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="citation_count_class" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="collectedfromdatasourceid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="collectedfromname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="community" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="communityid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="conceptname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="contextid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="contextname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="country" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="countrynojurisdiction" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="datasourcecompatibilityid" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="datasourcecompatibilityname" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="datasourceenglishname" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="datasourcejurisdiction" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="datasourceodcontenttypes" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="datasourceoddescription" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="datasourceodlanguages" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="datasourceodsubjects" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="datasourceofficialname" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="datasourcesubject" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
<field name="datasourceodcontenttypes" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="datasourceoddescription" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="datasourceodlanguages" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="datasourceodsubjects" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="datasourceofficialname" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="datasourcesubject" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="datasourcethematic" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="datasourcetypename" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="datasourcetypeuiid" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="datasourcetypeuiname" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="dateofcollection" type="pdate" multiValued="false" indexed="true" stored="false"/>
<field name="deletedbyinference" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="datasourcetypename" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="datasourcetypeuiid" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="datasourcetypeuiname" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="dateofcollection" type="date" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="deletedbyinference" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="eoscdatasourcetype" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="eoscifguidelines" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="eosctype" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="externalrefclass" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="externalrefid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="externalreflabel" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="externalrefsite" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="funder" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="funderid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="funderjurisdiction" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="fundername" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="funderoriginalname" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="fundershortname" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel0_description" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel0_id" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel0_name" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel1_description" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel1_id" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel1_name" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel2_description" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel2_id" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel2_name" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="inferenceprovenance" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="inferred" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="instancetypename" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="oafentity" type="string" multiValued="true" indexed="false" stored="false"/>
<field name="oaftype" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="objidentifier" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="organizationalternativenames" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
<field name="organizationcountryname" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="organizationdupid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="organizationecenterprise" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="organizationecinternationalorganization" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="organizationecinternationalorganizationeurinterests" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="organizationeclegalbody" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="organizationeclegalperson" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="organizationecnonprofit" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="organizationecnutscode" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="organizationecresearchorganization" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="organizationecsmevalidated" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="organizationlegalname" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
<field name="organizationlegalshortname" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
<field name="originalid" type="string_ci" multiValued="true" indexed="true" stored="false"/>
<field name="pid" type="string_ci" multiValued="true" indexed="true" stored="false"/>
<field name="pidclassid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="pidclassname" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="projectacronym" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
<field name="projectcallidentifier" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="projectcode" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
<field name="projectcode_nt" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="projectcontracttypename" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="projectduration" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="projectecarticle29_3" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="projectecsc39" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="projectenddate" type="pdate" multiValued="false" indexed="true" stored="false"/>
<field name="projectendyear" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="projectkeywords" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="projectoamandatepublications" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="projectstartdate" type="pdate" multiValued="false" indexed="true" stored="false"/>
<field name="projectstartyear" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="projectsubject" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="projecttitle" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
<field name="provenanceactionclassid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relclass" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relcollectedfromid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relcollectedfromname" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relcontracttypeid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relcontracttypename" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="reldatasourcecompatibilityid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relfunder" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relfunderid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relfunderjurisdiction" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relfundername" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relfundershortname" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel0_id" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel0_name" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel1_id" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel1_name" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel2_id" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel2_name" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relinferenceprovenance" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relinferred" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relorganizationcountryid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relorganizationcountryname" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="relorganizationid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relorganizationname" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="relorganizationshortname" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="relproject" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relprojectcode" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relprojectid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relprojectname" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relprojecttitle" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="relprovenanceactionclassid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relresultid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="relresulttype" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="reltrust" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="resultacceptanceyear" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="resultaccessright" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="resultauthor" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="resultauthor_nt" type="string_ci" multiValued="true" indexed="true" stored="false"/>
<field name="resultbestaccessright" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="resultdateofacceptance" type="pdate" multiValued="false" indexed="true" stored="false"/>
<field name="resultdescription" type="text_en" multiValued="true" indexed="true" stored="false"/>
<field name="resultdupid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="resultembargoenddate" type="pdate" multiValued="false" indexed="true" stored="false"/>
<field name="resultembargoendyear" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="resulthostingdatasource" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="resulthostingdatasourceid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="resulthostingdatasourcename" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="resultidentifier" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="resultlanguagename" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="resultlicense" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="resultpublisher" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="resultsource" type="text_common" multiValued="true" indexed="true" stored="false"/>
<field name="resultsubject" type="text_en" multiValued="true" indexed="true" stored="false"/>
<field name="resultsubjectclass" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="resulttitle" type="text_en" multiValued="true" indexed="true" stored="false"/>
<field name="resulttypeid" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="resulttypename" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="semrelid" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="externalreflabel" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="fos" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="foslabel" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="funder" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="funderid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="fundershortname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel0_description" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel0_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel0_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel1_description" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel1_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel1_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel2_description" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel2_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="fundinglevel2_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="haslicense" type="boolean" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="impulse" type="pint" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="impulse_class" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="influence" type="pfloat" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="influence_class" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="instancetypename" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="isgreen" type="boolean" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="isindiamondjournal" type="boolean" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="oafentity" type="string" docValues="false" multiValued="true" indexed="false" stored="false"/>
<field name="oaftype" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="objidentifier" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="openaccesscolor" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="orcidtypevalue" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="organizationalternativenames" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="organizationdupid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="organizationlegalname" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="organizationlegalshortname" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="originalid" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="peerreviewed" type="boolean" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="pid" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="pidclassid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="popularity" type="pfloat" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="popularity_alt" type="pfloat" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="popularity_alt_class" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="popularity_class" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="projectacronym" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="projectcallidentifier" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="projectcode" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="projectcode_nt" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="projectduration" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="projectecsc39" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="projectenddate" type="date" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="projectendyear" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="projectkeywords" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="projectoamandatepublications" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="projectstartdate" type="date" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="projectstartyear" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="projecttitle" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="projecttitle_alternative" type="text_en" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="provenanceactionclassid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="publiclyfunded" type="boolean" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="relclass" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relcontracttypename" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="reldatasourcecompatibilityid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relfunder" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relfunderid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relfundershortname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel0_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel0_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel1_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel1_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel2_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relfundinglevel2_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relorganizationcountryid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relorganizationcountryname" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relorganizationid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relorganizationname" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relorganizationshortname" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relproject" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relprojectcode" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relprojectid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relprojectname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relprojecttitle" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relresultid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="relresulttype" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="resultacceptanceyear" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="resultauthor" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="resultbestaccessright" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="resultdateofacceptance" type="date" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="resultdescription" type="text_en" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="resultdupid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="resultembargoenddate" type="date" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="resultembargoendyear" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="resulthostingdatasource" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="resulthostingdatasourceid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="resultidentifier" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="resultlanguagename" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="resultpublisher" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="resultsource" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="resultsubject" type="text_en" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="resulttitle" type="text_en" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="resulttypeid" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
<field name="sdg" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="semrelid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="status" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
<field name="text" type="text_common" indexed="false" stored="false"/>
<field name="trust" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="versioning" type="string" multiValued="true" indexed="true" stored="false"/>
<field name="isgreen" type="boolean" multiValued="false" indexed="true" stored="false"/>
<field name="openaccesscolor" type="string" multiValued="false" indexed="true" stored="false"/>
<field name="isindiamondjournal" type="boolean" multiValued="false" indexed="true" stored="false"/>
<field name="publiclyfunded" type="boolean" multiValued="false" indexed="true" stored="false"/>
<field name="peerreviewed" type="boolean" multiValued="false" indexed="true" stored="false"/>
<!-- Copy field definitions follow: -->
<!-- Data source -->
<copyField source="datasourceenglishname" dest="__all"/>
<copyField source="datasourceoddescription" dest="__all"/>
<copyField source="datasourceodsubjects" dest="__all"/>
<copyField source="datasourceofficialname" dest="__all"/>
<copyField source="datasourcesubject" dest="__all"/>
<!-- Organization -->
<copyField source="externalreflabel" dest="__all"/>
<copyField source="fundinglevel0_description" dest="__all"/>
<copyField source="fundinglevel1_description" dest="__all"/>
<copyField source="fundinglevel2_description" dest="__all"/>
<copyField source="organizationalternativenames" dest="__all"/>
<copyField source="organizationecenterprise" dest="__all"/>
<copyField source="organizationecinternationalorganization" dest="__all"/>
<copyField source="organizationecinternationalorganizationeurinterests" dest="__all"/>
<copyField source="organizationeclegalbody" dest="__all"/>
<copyField source="organizationeclegalperson" dest="__all"/>
<copyField source="organizationecnonprofit" dest="__all"/>
<copyField source="organizationecnutscode" dest="__all"/>
<copyField source="organizationecresearchorganization" dest="__all"/>
<copyField source="organizationecsmevalidated" dest="__all"/>
<copyField source="organizationlegalname" dest="__all"/>
<copyField source="organizationlegalshortname" dest="__all"/>
<!-- Project -->
<copyField source="projectacronym" dest="__all"/>
<copyField source="projectcode" dest="__all"/>
<copyField source="projectkeywords" dest="__all"/>
<copyField source="projecttitle" dest="__all"/>
<!-- Result -->
<copyField source="resultpublisher" dest="__all"/>
<copyField source="resultsource" dest="__all"/>
<copyField source="resultidentifier" dest="__all"/>
<copyField source="resultauthor" dest="__all"/>
<copyField source="resulttitle" dest="__all"/>
<copyField source="resultdescription" dest="__all"/>
<copyField source="resultsubject" dest="__all"/>
<copyField source="resultacceptanceyear" dest="__all"/>
<!-- Other -->
<copyField source="externalreflabel" dest="__all"/>
<copyField source="fundinglevel0_description" dest="__all"/>
<copyField source="fundinglevel1_description" dest="__all"/>
<copyField source="fundinglevel2_description" dest="__all"/>
<copyField source="projecttitle_alternative" dest="__all"/>
<copyField source="relcontracttypename" dest="__all"/>
<copyField source="relorganizationcountryname" dest="__all"/>
<copyField source="relorganizationname" dest="__all"/>
<copyField source="relorganizationshortname" dest="__all"/>
<copyField source="relprojecttitle" dest="__all"/>
<copyField source="relprojectname" dest="__all"/>
<copyField source="relprojecttitle" dest="__all"/>
<copyField source="resultacceptanceyear" dest="__all"/>
<copyField source="resultauthor" dest="__all"/>
<copyField source="resultdescription" dest="__all"/>
<copyField source="resultidentifier" dest="__all"/>
<copyField source="resultpublisher" dest="__all"/>
<copyField source="resultsource" dest="__all"/>
<copyField source="resulttitle" dest="__all"/>
</schema>