forked from D-Net/dnet-hadoop
merge branch with master
This commit is contained in:
commit
ee13da9258
|
|
@ -1,2 +1,2 @@
|
|||
# dnet-hadoop
|
||||
Dnet-hadoop is a tool for
|
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Dnet-hadoop is the project that defined all the OOZIE workflows for the OpenAIRE Graph construction, processing, provisioning.
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|
|
@ -25,6 +25,11 @@
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|||
<groupId>com.github.sisyphsu</groupId>
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||||
<artifactId>dateparser</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>me.xuender</groupId>
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||||
<artifactId>unidecode</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
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||||
<groupId>org.apache.spark</groupId>
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||||
<artifactId>spark-core_2.11</artifactId>
|
||||
|
|
|
|||
|
|
@ -7,22 +7,19 @@ import java.time.format.DateTimeFormatter;
|
|||
import java.time.format.DateTimeParseException;
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import java.util.*;
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||||
import java.util.function.Function;
|
||||
import java.util.regex.Matcher;
|
||||
import java.util.regex.Pattern;
|
||||
import java.util.stream.Collectors;
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import java.util.stream.Stream;
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|
||||
import org.apache.commons.lang3.StringUtils;
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||||
import org.jetbrains.annotations.NotNull;
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||||
|
||||
import com.github.sisyphsu.dateparser.DateParserUtils;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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||||
import com.google.common.collect.Sets;
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||||
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||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
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||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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||||
import me.xuender.unidecode.Unidecode;
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||||
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||||
public class GraphCleaningFunctions extends CleaningFunctions {
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||||
|
||||
|
|
@ -194,11 +191,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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|||
.filter(Objects::nonNull)
|
||||
.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
|
||||
.filter(
|
||||
sp -> sp
|
||||
.getValue()
|
||||
.toLowerCase()
|
||||
.replaceAll(TITLE_FILTER_REGEX, "")
|
||||
.length() > TITLE_FILTER_RESIDUAL_LENGTH)
|
||||
sp -> {
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||||
final String title = sp
|
||||
.getValue()
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||||
.toLowerCase();
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final String residual = Unidecode
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||||
.decode(title)
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||||
.replaceAll(TITLE_FILTER_REGEX, "");
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return residual.length() > TITLE_FILTER_RESIDUAL_LENGTH;
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})
|
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.map(GraphCleaningFunctions::cleanValue)
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||||
.collect(Collectors.toList()));
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}
|
||||
|
|
|
|||
|
|
@ -4,12 +4,8 @@ package eu.dnetlib.dhp.schema.oaf.utils;
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import static org.junit.jupiter.api.Assertions.*;
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|
||||
import java.io.IOException;
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import java.time.LocalDate;
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import java.time.format.DateTimeFormatter;
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||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Locale;
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||||
import java.util.Optional;
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||||
import java.util.stream.Collectors;
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|
||||
import org.apache.commons.io.IOUtils;
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||||
|
|
@ -19,13 +15,32 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
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|||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import me.xuender.unidecode.Unidecode;
|
||||
|
||||
public class OafMapperUtilsTest {
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
|
||||
@Test
|
||||
public void testUnidecode() {
|
||||
|
||||
assertEquals("Liu Ben Mu hiruzuSen tawa", Unidecode.decode("六本木ヒルズ森タワ"));
|
||||
assertEquals("Nan Wu A Mi Tuo Fo", Unidecode.decode("南无阿弥陀佛"));
|
||||
assertEquals("Yi Tiao Hui Zou Lu De Yu", Unidecode.decode("一条会走路的鱼"));
|
||||
assertEquals("amidaniyorai", Unidecode.decode("あみだにょらい"));
|
||||
assertEquals("T`owrk`iayi", Unidecode.decode("Թուրքիայի"));
|
||||
assertEquals("Obzor tematiki", Unidecode.decode("Обзор тематики"));
|
||||
assertEquals("GERMANSKIE IaZYKI", Unidecode.decode("ГЕРМАНСКИЕ ЯЗЫКИ"));
|
||||
assertEquals("Diereunese tes ikanopoieses", Unidecode.decode("Διερεύνηση της ικανοποίησης"));
|
||||
assertEquals("lqDy l'wly@", Unidecode.decode("القضايا الأولية"));
|
||||
assertEquals("abc def ghi", Unidecode.decode("abc def ghi"));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testDateValidation() {
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,127 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.raw;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.FileNotFoundException;
|
||||
import java.util.Objects;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
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.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class PatchRelationsApplication {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(final String[] args) throws Exception {
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
Optional
|
||||
.ofNullable(
|
||||
PatchRelationsApplication.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json"))
|
||||
.orElseThrow(FileNotFoundException::new)));
|
||||
parser.parseArgument(args);
|
||||
|
||||
final Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
final String graphBasePath = parser.get("graphBasePath");
|
||||
log.info("graphBasePath: {}", graphBasePath);
|
||||
|
||||
final String workingDir = parser.get("workingDir");
|
||||
log.info("workingDir: {}", workingDir);
|
||||
|
||||
final String idMappingPath = parser.get("idMappingPath");
|
||||
log.info("idMappingPath: {}", idMappingPath);
|
||||
|
||||
final SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath));
|
||||
}
|
||||
|
||||
/**
|
||||
* Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the
|
||||
* mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location.
|
||||
*
|
||||
* @param spark the SparkSession
|
||||
* @param graphBasePath base graph path providing the set of relations to patch
|
||||
* @param workingDir intermediate storage location
|
||||
* @param idMappingPath dataset providing the old -> new identifier mapping
|
||||
*/
|
||||
private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir,
|
||||
final String idMappingPath) {
|
||||
|
||||
final String relationPath = graphBasePath + "/relation";
|
||||
|
||||
final Dataset<Relation> rels = Utils.readPath(spark, relationPath, Relation.class);
|
||||
final Dataset<RelationIdMapping> idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class);
|
||||
|
||||
log.info("relations: {}", rels.count());
|
||||
log.info("idMapping: {}", idMapping.count());
|
||||
|
||||
final Dataset<Relation> bySource = rels
|
||||
.joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left")
|
||||
.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
|
||||
final Relation r = t._1();
|
||||
Optional
|
||||
.ofNullable(t._2())
|
||||
.map(RelationIdMapping::getNewId)
|
||||
.ifPresent(r::setSource);
|
||||
return r;
|
||||
}, Encoders.bean(Relation.class));
|
||||
|
||||
bySource
|
||||
.joinWith(idMapping, bySource.col("target").equalTo(idMapping.col("oldId")), "left")
|
||||
.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
|
||||
final Relation r = t._1();
|
||||
Optional
|
||||
.ofNullable(t._2())
|
||||
.map(RelationIdMapping::getNewId)
|
||||
.ifPresent(r::setTarget);
|
||||
return r;
|
||||
}, Encoders.bean(Relation.class))
|
||||
.map(
|
||||
(MapFunction<Relation, String>) OBJECT_MAPPER::writeValueAsString,
|
||||
Encoders.STRING())
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.text(workingDir);
|
||||
|
||||
spark
|
||||
.read()
|
||||
.textFile(workingDir)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.text(relationPath);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.raw.common;
|
||||
|
||||
public class RelationIdMapping {
|
||||
|
||||
private String oldId;
|
||||
|
||||
private String newId;
|
||||
|
||||
public String getOldId() {
|
||||
return oldId;
|
||||
}
|
||||
|
||||
public void setOldId(final String oldId) {
|
||||
this.oldId = oldId;
|
||||
}
|
||||
|
||||
public String getNewId() {
|
||||
return newId;
|
||||
}
|
||||
|
||||
public void setNewId(final String newId) {
|
||||
this.newId = newId;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "g",
|
||||
"paramLongName": "graphBasePath",
|
||||
"paramDescription": "base graph path providing the set of relations to patch",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "w",
|
||||
"paramLongName": "workingDir",
|
||||
"paramDescription": "intermediate storage location",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "i",
|
||||
"paramLongName": "idMappingPath",
|
||||
"paramDescription": "dataset providing the old -> new identifier mapping",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -100,6 +100,16 @@
|
|||
<value></value>
|
||||
<description>a blacklist of nsprefixes (comma separeted)</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>shouldPatchRelations</name>
|
||||
<value>false</value>
|
||||
<description>activates the relation patching phase, driven by the content in ${idMappingPath}</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>idMappingPath</name>
|
||||
<value></value>
|
||||
<description>path pointing to the relations identifiers mapping dataset</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
|
|
@ -551,7 +561,6 @@
|
|||
<path start="merge_claims_relation"/>
|
||||
</fork>
|
||||
|
||||
|
||||
<action name="merge_claims_publication">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
|
|
@ -760,7 +769,42 @@
|
|||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="wait_merge" to="End"/>
|
||||
<join name="wait_merge" to="decisionPatchRelations"/>
|
||||
|
||||
<decision name="decisionPatchRelations">
|
||||
<switch>
|
||||
<case to="patchRelations">
|
||||
${(shouldPatchRelations eq "true") and
|
||||
(fs:exists(concat(concat(wf:conf('nameNode'),'/'),wf:conf('idMappingPath'))) eq "true")}
|
||||
</case>
|
||||
<default to="End"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<action name="patchRelations">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>PatchRelations</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.raw.PatchRelationsApplication</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory ${sparkExecutorMemory}
|
||||
--executor-cores ${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--graphBasePath</arg><arg>${graphOutputPath}</arg>
|
||||
<arg>--workingDir</arg><arg>${workingDir}/patch_relations</arg>
|
||||
<arg>--idMappingPath</arg><arg>${idMappingPath}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -1,11 +1,9 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.raw;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.cleanup;
|
||||
import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.fixVocabularyNames;
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
import java.io.IOException;
|
||||
|
|
@ -25,15 +23,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
|
|||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
|
||||
import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Author;
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||
import eu.dnetlib.dhp.schema.oaf.Instance;
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.Software;
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
|
||||
|
|
@ -74,7 +64,7 @@ public class MappersTest {
|
|||
|
||||
assertValidId(p.getId());
|
||||
|
||||
assertEquals(1, p.getOriginalId().size());
|
||||
assertEquals(2, p.getOriginalId().size());
|
||||
assertTrue(p.getOriginalId().contains("10.3897/oneeco.2.e13718"));
|
||||
|
||||
assertValidId(p.getCollectedfrom().get(0).getKey());
|
||||
|
|
@ -261,8 +251,8 @@ public class MappersTest {
|
|||
final Relation r2 = (Relation) list.get(2);
|
||||
|
||||
assertValidId(d.getId());
|
||||
assertEquals(1, d.getOriginalId().size());
|
||||
assertTrue(d.getOriginalId().contains("oai:zenodo.org:3234526"));
|
||||
assertEquals(2, d.getOriginalId().size());
|
||||
assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526")));
|
||||
assertValidId(d.getCollectedfrom().get(0).getKey());
|
||||
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
|
||||
assertTrue(d.getAuthor().size() > 0);
|
||||
|
|
@ -351,8 +341,11 @@ public class MappersTest {
|
|||
final Publication p = (Publication) list.get(0);
|
||||
|
||||
assertValidId(p.getId());
|
||||
assertTrue(p.getOriginalId().size() == 1);
|
||||
assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0));
|
||||
assertEquals(2, p.getOriginalId().size());
|
||||
|
||||
assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:pub.uni-bielefeld.de:2949739")));
|
||||
// assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0));
|
||||
|
||||
assertValidId(p.getCollectedfrom().get(0).getKey());
|
||||
assertTrue(p.getAuthor().size() > 0);
|
||||
|
||||
|
|
@ -413,7 +406,8 @@ public class MappersTest {
|
|||
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, d.getDataInfo().getProvenanceaction().getSchemename());
|
||||
|
||||
assertValidId(d.getId());
|
||||
assertTrue(d.getOriginalId().size() == 1);
|
||||
assertEquals(2, d.getOriginalId().size());
|
||||
|
||||
assertEquals("feabb67c-1fd1-423b-aec6-606d04ce53c6", d.getOriginalId().get(0));
|
||||
assertValidId(d.getCollectedfrom().get(0).getKey());
|
||||
|
||||
|
|
@ -567,31 +561,6 @@ public class MappersTest {
|
|||
assertNotNull(d.getInstance().get(0).getUrl());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testEnermaps() throws IOException {
|
||||
final String xml = IOUtils.toString(getClass().getResourceAsStream("enermaps.xml"));
|
||||
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
||||
|
||||
System.out.println("***************");
|
||||
System.out.println(new ObjectMapper().writeValueAsString(list));
|
||||
System.out.println("***************");
|
||||
|
||||
assertEquals(1, list.size());
|
||||
assertTrue(list.get(0) instanceof Dataset);
|
||||
|
||||
final Dataset d = (Dataset) list.get(0);
|
||||
|
||||
assertValidId(d.getId());
|
||||
assertValidId(d.getCollectedfrom().get(0).getKey());
|
||||
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
|
||||
assertEquals(1, d.getAuthor().size());
|
||||
assertEquals(1, d.getInstance().size());
|
||||
assertNotNull(d.getInstance().get(0).getUrl());
|
||||
assertNotNull(d.getContext());
|
||||
assertTrue(StringUtils.isNotBlank(d.getContext().get(0).getId()));
|
||||
assertEquals("enermaps::selection::tgs00004", d.getContext().get(0).getId());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testClaimFromCrossref() throws IOException {
|
||||
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_crossref.xml"));
|
||||
|
|
@ -673,6 +642,30 @@ public class MappersTest {
|
|||
System.out.println(p.getTitle().get(0).getValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testJairo() throws IOException {
|
||||
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_jairo.xml"));
|
||||
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
|
||||
|
||||
System.out.println("***************");
|
||||
System.out.println(new ObjectMapper().writeValueAsString(list));
|
||||
System.out.println("***************");
|
||||
|
||||
final Publication p = (Publication) list.get(0);
|
||||
assertValidId(p.getId());
|
||||
assertValidId(p.getCollectedfrom().get(0).getKey());
|
||||
|
||||
assertNotNull(p.getTitle());
|
||||
assertFalse(p.getTitle().isEmpty());
|
||||
assertTrue(p.getTitle().size() == 1);
|
||||
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
||||
|
||||
final Publication p_cleaned = cleanup(fixVocabularyNames(p));
|
||||
|
||||
assertNotNull(p_cleaned.getTitle());
|
||||
assertFalse(p_cleaned.getTitle().isEmpty());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testOdfFromHdfs() throws IOException {
|
||||
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_from_hdfs.xml"));
|
||||
|
|
@ -688,8 +681,8 @@ public class MappersTest {
|
|||
final Dataset p = (Dataset) list.get(0);
|
||||
|
||||
assertValidId(p.getId());
|
||||
assertTrue(p.getOriginalId().size() == 1);
|
||||
assertEquals("df76e73f-0483-49a4-a9bb-63f2f985574a", p.getOriginalId().get(0));
|
||||
assertEquals(2, p.getOriginalId().size());
|
||||
assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("df76e73f-0483-49a4-a9bb-63f2f985574a")));
|
||||
assertValidId(p.getCollectedfrom().get(0).getKey());
|
||||
assertTrue(p.getAuthor().size() > 0);
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,115 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.raw;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.util.List;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.AfterAll;
|
||||
import org.junit.jupiter.api.BeforeAll;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
|
||||
public class PatchRelationApplicationTest {
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
public static final String ID_MAPPING_PATH = "map/id_mapping.json";
|
||||
|
||||
private static SparkSession spark;
|
||||
|
||||
private static Path workingDir;
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(PatchRelationApplicationTest.class);
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files
|
||||
.createTempDirectory(PatchRelationApplicationTest.class.getSimpleName());
|
||||
log.info("using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(PatchRelationApplicationTest.class.getSimpleName());
|
||||
|
||||
conf.setMaster("local[*]");
|
||||
conf.set("spark.driver.host", "localhost");
|
||||
conf.set("hive.metastore.local", "true");
|
||||
conf.set("spark.ui.enabled", "false");
|
||||
conf.set("spark.sql.warehouse.dir", workingDir.toString());
|
||||
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
|
||||
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(PatchRelationApplicationTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
|
||||
FileUtils
|
||||
.copyInputStreamToFile(
|
||||
PatchRelationApplicationTest.class.getResourceAsStream("id_mapping.json"),
|
||||
workingDir.resolve(ID_MAPPING_PATH).toFile());
|
||||
|
||||
FileUtils
|
||||
.copyInputStreamToFile(
|
||||
PatchRelationApplicationTest.class.getResourceAsStream("relations_to_patch.json"),
|
||||
workingDir.resolve("graphBasePath/relation/rels.json").toFile());
|
||||
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testPatchRelationApplication() throws Exception {
|
||||
|
||||
final String graphBasePath = workingDir.toString() + "/graphBasePath";
|
||||
PatchRelationsApplication.main(new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-graphBasePath", graphBasePath,
|
||||
"-workingDir", workingDir.toString() + "/workingDir",
|
||||
"-idMappingPath", workingDir.toString() + "/" + ID_MAPPING_PATH
|
||||
});
|
||||
|
||||
final List<Relation> rels = spark
|
||||
.read()
|
||||
.textFile(graphBasePath + "/relation")
|
||||
.map(
|
||||
(MapFunction<String, Relation>) s -> OBJECT_MAPPER.readValue(s, Relation.class),
|
||||
Encoders.bean(Relation.class))
|
||||
.collectAsList();
|
||||
|
||||
assertEquals(6, rels.size());
|
||||
|
||||
assertEquals(0, getCount(rels, "1a"), "should be patched to 1b");
|
||||
assertEquals(0, getCount(rels, "2a"), "should be patched to 2b");
|
||||
|
||||
assertEquals(2, getCount(rels, "10a"), "not included in patching");
|
||||
assertEquals(2, getCount(rels, "20a"), "not included in patching");
|
||||
|
||||
assertEquals(2, getCount(rels, "15a"), "not included in patching");
|
||||
assertEquals(2, getCount(rels, "25a"), "not included in patching");
|
||||
|
||||
assertEquals(2, getCount(rels, "1b"), "patched from 1a");
|
||||
assertEquals(2, getCount(rels, "2b"), "patched from 2a");
|
||||
}
|
||||
|
||||
private long getCount(List<Relation> rels, final String id) {
|
||||
return rels.stream().filter(r -> r.getSource().equals(id) || r.getTarget().equals(id)).count();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,5 @@
|
|||
{"oldId": "1a", "newId": "1b"}
|
||||
{"oldId": "2a", "newId": "2b"}
|
||||
{"oldId": "3a", "newId": "3b"}
|
||||
{"oldId": "4a", "newId": "4b"}
|
||||
{"oldId": "5a", "newId": "5b"}
|
||||
|
|
@ -0,0 +1,70 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<record xmlns:dc="http://purl.org/dc/elements/1.1/"
|
||||
xmlns:dr="http://www.driver-repository.eu/namespace/dr"
|
||||
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
|
||||
xmlns:oaf="http://namespace.openaire.eu/oaf"
|
||||
xmlns:oai="http://www.openarchives.org/OAI/2.0/"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<header xmlns="http://namespace.openaire.eu/">
|
||||
<dri:objIdentifier>jairo_______::000012e58ed836576ef2a0d38b0f726f</dri:objIdentifier>
|
||||
<dri:recordIdentifier>oai:irdb.nii.ac.jp:01221:0000010198</dri:recordIdentifier>
|
||||
<dri:dateOfCollection/>
|
||||
<dri:mdFormat/>
|
||||
<dri:mdFormatInterpretation/>
|
||||
<dri:repositoryId/>
|
||||
<dr:objectIdentifier/>
|
||||
<dr:dateOfCollection>2021-05-10T11:31:09.424Z</dr:dateOfCollection>
|
||||
<dr:dateOfTransformation>2021-06-03T01:45:42.536Z</dr:dateOfTransformation>
|
||||
<oaf:datasourceprefix>jairo_______</oaf:datasourceprefix>
|
||||
</header>
|
||||
<metadata xmlns="http://namespace.openaire.eu/">
|
||||
<dc:title>多項式GCDを用いた復号法に関する研究</dc:title>
|
||||
<dc:creator>上原, 剛</dc:creator>
|
||||
<dc:creator>甲斐, 博</dc:creator>
|
||||
<dc:creator>野田, 松太郎</dc:creator>
|
||||
<dc:format>application/pdf</dc:format>
|
||||
<dc:identifier>http://hdl.handle.net/2433/25934</dc:identifier>
|
||||
<dc:language>jpn</dc:language>
|
||||
<dc:publisher>京都大学数理解析研究所</dc:publisher>
|
||||
<dc:subject classid="ndc" classname="ndc"
|
||||
schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">410</dc:subject>
|
||||
<dc:type>Departmental Bulletin Paper</dc:type>
|
||||
<dr:CobjCategory type="publication">0014</dr:CobjCategory>
|
||||
<oaf:dateAccepted>2004-10-01</oaf:dateAccepted>
|
||||
<oaf:projectid/>
|
||||
<oaf:collectedDatasourceid>openaire____::554c7c2873</oaf:collectedDatasourceid>
|
||||
<oaf:accessrights>OPEN</oaf:accessrights>
|
||||
<oaf:hostedBy id="openaire____::554c7c2873" name="JAIRO"/>
|
||||
<oaf:collectedFrom id="openaire____::554c7c2873" name="JAIRO"/>
|
||||
<oaf:identifier identifierType="handle">2433/25934</oaf:identifier>
|
||||
<oaf:identifier identifierType="ncid">AN00061013</oaf:identifier>
|
||||
<oaf:identifier identifierType="LandingPage">http://hdl.handle.net/2433/25934</oaf:identifier>
|
||||
<oaf:fulltext>http://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/25934/1/1395-16.pdf</oaf:fulltext>
|
||||
<oaf:journal ep="110" iss="" issn="1880-2818" sp="104" vol="1395">数理解析研究所講究録</oaf:journal>
|
||||
</metadata>
|
||||
<about>
|
||||
<provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">
|
||||
<originDescription altered="true" harvestDate="2021-05-10T11:31:09.424Z">
|
||||
<baseURL>https%3A%2F%2Firdb.nii.ac.jp%2Foai</baseURL>
|
||||
<identifier>oai:irdb.nii.ac.jp:01221:0000010198</identifier>
|
||||
<datestamp>2021-04-13T13:36:29Z</datestamp>
|
||||
<metadataNamespace/>
|
||||
<originDescription altered="true" harvestDate="2021-04-13T13:36:29Z">
|
||||
<baseURL>http://repository.kulib.kyoto-u.ac.jp/dspace-oai/request</baseURL>
|
||||
<identifier>oai:repository.kulib.kyoto-u.ac.jp:2433/25934</identifier>
|
||||
<datestamp>2012-07-12T14:15:41Z</datestamp>
|
||||
<metadataNamespace>http://irdb.nii.ac.jp/oai</metadataNamespace>
|
||||
</originDescription>
|
||||
</originDescription>
|
||||
</provenance>
|
||||
<oaf:datainfo>
|
||||
<oaf:inferred>false</oaf:inferred>
|
||||
<oaf:deletedbyinference>false</oaf:deletedbyinference>
|
||||
<oaf:trust>0.9</oaf:trust>
|
||||
<oaf:inferenceprovenance/>
|
||||
<oaf:provenanceaction classid="sysimport:crosswalk:repository"
|
||||
classname="sysimport:crosswalk:repository"
|
||||
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
|
||||
</oaf:datainfo>
|
||||
</about>
|
||||
</record>
|
||||
|
|
@ -0,0 +1,6 @@
|
|||
{"source":"1a","target":"10a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
|
||||
{"source":"10a","target":"1a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
|
||||
{"source":"2a","target":"20a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
|
||||
{"source":"20a","target":"2a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
|
||||
{"source":"15a","target":"25a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
|
||||
{"source":"25a","target":"15a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
|
||||
File diff suppressed because one or more lines are too long
|
|
@ -10,6 +10,7 @@ import java.util.Set;
|
|||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
|
|
@ -81,6 +82,7 @@ public class PrepareRelationsJob {
|
|||
|
||||
Set<String> relationFilter = Optional
|
||||
.ofNullable(parser.get("relationFilter"))
|
||||
.map(String::toLowerCase)
|
||||
.map(s -> Sets.newHashSet(Splitter.on(",").split(s)))
|
||||
.orElse(new HashSet<>());
|
||||
log.info("relationFilter: {}", relationFilter);
|
||||
|
|
@ -130,7 +132,7 @@ public class PrepareRelationsJob {
|
|||
|
||||
JavaRDD<Relation> rels = readPathRelationRDD(spark, inputRelationsPath)
|
||||
.filter(rel -> rel.getDataInfo().getDeletedbyinference() == false)
|
||||
.filter(rel -> relationFilter.contains(rel.getRelClass()) == false);
|
||||
.filter(rel -> relationFilter.contains(StringUtils.lowerCase(rel.getRelClass())) == false);
|
||||
|
||||
JavaRDD<Relation> pruned = pruneRels(
|
||||
pruneRels(
|
||||
|
|
|
|||
|
|
@ -16,7 +16,6 @@ import javax.xml.transform.*;
|
|||
import javax.xml.transform.dom.DOMSource;
|
||||
import javax.xml.transform.stream.StreamResult;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.spark.util.LongAccumulator;
|
||||
import org.dom4j.Document;
|
||||
|
|
@ -43,6 +42,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
|
|||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
|
||||
public class XmlRecordFactory implements Serializable {
|
||||
|
||||
|
|
|
|||
|
|
@ -7,8 +7,6 @@ import java.io.IOException;
|
|||
import java.io.StringReader;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.dhp.oa.provision.utils.ContextDef;
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentException;
|
||||
|
|
@ -25,6 +23,7 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
|
|||
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
|
||||
import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
|
||||
import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
|
|
@ -137,17 +136,18 @@ public class XmlRecordFactoryTest {
|
|||
@Test
|
||||
public void testEnermapsRecord() throws IOException, DocumentException {
|
||||
|
||||
String contextmap = "<entries><entry id=\"enermaps\" label=\"Energy Research\" name=\"context\" type=\"community\"/>" +
|
||||
"<entry id=\"enermaps::selection\" label=\"Featured dataset\" name=\"category\"/>"+
|
||||
"<entry id=\"enermaps::selection::tgs00004\" label=\"Dataset title\" name=\"concept\"/>"+
|
||||
"</entries>";
|
||||
String contextmap = "<entries><entry id=\"enermaps\" label=\"Energy Research\" name=\"context\" type=\"community\"/>"
|
||||
+
|
||||
"<entry id=\"enermaps::selection\" label=\"Featured dataset\" name=\"category\"/>" +
|
||||
"<entry id=\"enermaps::selection::tgs00004\" label=\"Dataset title\" name=\"concept\"/>" +
|
||||
"</entries>";
|
||||
|
||||
ContextMapper contextMapper = ContextMapper.fromXml(contextmap);
|
||||
XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation,
|
||||
otherDsTypeId);
|
||||
otherDsTypeId);
|
||||
|
||||
Dataset d = OBJECT_MAPPER
|
||||
.readValue(IOUtils.toString(getClass().getResourceAsStream("enermaps.json")), Dataset.class);
|
||||
.readValue(IOUtils.toString(getClass().getResourceAsStream("enermaps.json")), Dataset.class);
|
||||
|
||||
JoinedEntity je = new JoinedEntity<>(d);
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue