Merge branch 'beta' into consistency_keep_mergerels
This commit is contained in:
commit
7b403a920f
|
|
@ -1,98 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.merge;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.util.Objects;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
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.*;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
|
||||
public class DispatchEntitiesSparkJob {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesSparkJob.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
Objects
|
||||
.requireNonNull(
|
||||
DispatchEntitiesSparkJob.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/merge/dispatch_entities_parameters.json")));
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
String inputPath = parser.get("inputPath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
boolean filterInvisible = Boolean.valueOf(parser.get("filterInvisible"));
|
||||
log.info("filterInvisible: {}", filterInvisible);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
|
||||
dispatchEntities(spark, inputPath, outputPath, filterInvisible);
|
||||
});
|
||||
}
|
||||
|
||||
private static void dispatchEntities(
|
||||
SparkSession spark,
|
||||
String inputPath,
|
||||
String outputPath,
|
||||
boolean filterInvisible) {
|
||||
|
||||
Dataset<String> df = spark.read().textFile(inputPath);
|
||||
|
||||
ModelSupport.oafTypes.entrySet().parallelStream().forEach(entry -> {
|
||||
String entityType = entry.getKey();
|
||||
Class<?> clazz = entry.getValue();
|
||||
|
||||
if (!entityType.equalsIgnoreCase("relation")) {
|
||||
Dataset<Row> entityDF = spark
|
||||
.read()
|
||||
.schema(Encoders.bean(clazz).schema())
|
||||
.json(
|
||||
df
|
||||
.filter((FilterFunction<String>) s -> s.startsWith(clazz.getName()))
|
||||
.map(
|
||||
(MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"),
|
||||
Encoders.STRING()));
|
||||
|
||||
if (filterInvisible) {
|
||||
entityDF = entityDF.filter("dataInfo.invisible != true");
|
||||
}
|
||||
|
||||
entityDF
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath + "/" + entityType);
|
||||
}
|
||||
});
|
||||
}
|
||||
}
|
||||
|
|
@ -2,36 +2,28 @@
|
|||
package eu.dnetlib.dhp.oa.merge;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
|
||||
import static org.apache.spark.sql.functions.col;
|
||||
import static org.apache.spark.sql.functions.when;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.List;
|
||||
import java.util.Objects;
|
||||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
import java.util.concurrent.ExecutionException;
|
||||
import java.util.concurrent.ForkJoinPool;
|
||||
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.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.api.java.function.ReduceFunction;
|
||||
import org.apache.spark.sql.*;
|
||||
import org.apache.spark.sql.expressions.Aggregator;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.jayway.jsonpath.Configuration;
|
||||
import com.jayway.jsonpath.DocumentContext;
|
||||
import com.jayway.jsonpath.JsonPath;
|
||||
import com.jayway.jsonpath.Option;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.schema.common.EntityType;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
|
||||
import scala.Tuple2;
|
||||
|
||||
|
|
@ -39,13 +31,9 @@ import scala.Tuple2;
|
|||
* Groups the graph content by entity identifier to ensure ID uniqueness
|
||||
*/
|
||||
public class GroupEntitiesSparkJob {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class);
|
||||
|
||||
private static final String ID_JPATH = "$.id";
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
private static final Encoder<OafEntity> OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
|
|
@ -66,9 +54,15 @@ public class GroupEntitiesSparkJob {
|
|||
String graphInputPath = parser.get("graphInputPath");
|
||||
log.info("graphInputPath: {}", graphInputPath);
|
||||
|
||||
String checkpointPath = parser.get("checkpointPath");
|
||||
log.info("checkpointPath: {}", checkpointPath);
|
||||
|
||||
String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
boolean filterInvisible = Boolean.valueOf(parser.get("filterInvisible"));
|
||||
log.info("filterInvisible: {}", filterInvisible);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
|
|
@ -78,126 +72,95 @@ public class GroupEntitiesSparkJob {
|
|||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
|
||||
groupEntities(spark, graphInputPath, outputPath);
|
||||
groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible);
|
||||
});
|
||||
}
|
||||
|
||||
private static void groupEntities(
|
||||
SparkSession spark,
|
||||
String inputPath,
|
||||
String outputPath) {
|
||||
String checkpointPath,
|
||||
String outputPath,
|
||||
boolean filterInvisible) {
|
||||
|
||||
final TypedColumn<OafEntity, OafEntity> aggregator = new GroupingAggregator().toColumn();
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
spark
|
||||
.read()
|
||||
.textFile(toSeq(listEntityPaths(inputPath, sc)))
|
||||
.map((MapFunction<String, OafEntity>) GroupEntitiesSparkJob::parseOaf, Encoders.kryo(OafEntity.class))
|
||||
.filter((FilterFunction<OafEntity>) e -> StringUtils.isNotBlank(ModelSupport.idFn().apply(e)))
|
||||
.groupByKey((MapFunction<OafEntity, String>) oaf -> ModelSupport.idFn().apply(oaf), Encoders.STRING())
|
||||
.agg(aggregator)
|
||||
Dataset<OafEntity> allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC);
|
||||
|
||||
for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
|
||||
String entity = e.getKey().name();
|
||||
Class<? extends OafEntity> entityClass = e.getValue();
|
||||
String entityInputPath = inputPath + "/" + entity;
|
||||
|
||||
if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) {
|
||||
continue;
|
||||
}
|
||||
|
||||
allEntities = allEntities
|
||||
.union(
|
||||
((Dataset<OafEntity>) spark
|
||||
.read()
|
||||
.schema(Encoders.bean(entityClass).schema())
|
||||
.json(entityInputPath)
|
||||
.filter("length(id) > 0")
|
||||
.as(Encoders.bean(entityClass)))
|
||||
.map((MapFunction<OafEntity, OafEntity>) r -> r, OAFENTITY_KRYO_ENC));
|
||||
}
|
||||
|
||||
Dataset<?> groupedEntities = allEntities
|
||||
.groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
|
||||
.reduceGroups((ReduceFunction<OafEntity>) (b, a) -> OafMapperUtils.mergeEntities(b, a))
|
||||
.map(
|
||||
(MapFunction<Tuple2<String, OafEntity>, String>) t -> t._2().getClass().getName() +
|
||||
"|" + OBJECT_MAPPER.writeValueAsString(t._2()),
|
||||
Encoders.STRING())
|
||||
(MapFunction<Tuple2<String, OafEntity>, Tuple2<String, OafEntity>>) t -> new Tuple2(
|
||||
t._2().getClass().getName(), t._2()),
|
||||
Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC));
|
||||
|
||||
// pivot on "_1" (classname of the entity)
|
||||
// created columns containing only entities of the same class
|
||||
for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
|
||||
String entity = e.getKey().name();
|
||||
Class<? extends OafEntity> entityClass = e.getValue();
|
||||
|
||||
groupedEntities = groupedEntities
|
||||
.withColumn(
|
||||
entity,
|
||||
when(col("_1").equalTo(entityClass.getName()), col("_2")));
|
||||
}
|
||||
|
||||
groupedEntities
|
||||
.drop("_1", "_2")
|
||||
.write()
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Overwrite)
|
||||
.text(outputPath);
|
||||
}
|
||||
.option("compression", "gzip")
|
||||
.save(checkpointPath);
|
||||
|
||||
public static class GroupingAggregator extends Aggregator<OafEntity, OafEntity, OafEntity> {
|
||||
ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size());
|
||||
|
||||
@Override
|
||||
public OafEntity zero() {
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public OafEntity reduce(OafEntity b, OafEntity a) {
|
||||
return mergeAndGet(b, a);
|
||||
}
|
||||
|
||||
private OafEntity mergeAndGet(OafEntity b, OafEntity a) {
|
||||
if (Objects.nonNull(a) && Objects.nonNull(b)) {
|
||||
return OafMapperUtils.mergeEntities(b, a);
|
||||
}
|
||||
return Objects.isNull(a) ? b : a;
|
||||
}
|
||||
|
||||
@Override
|
||||
public OafEntity merge(OafEntity b, OafEntity a) {
|
||||
return mergeAndGet(b, a);
|
||||
}
|
||||
|
||||
@Override
|
||||
public OafEntity finish(OafEntity j) {
|
||||
return j;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Encoder<OafEntity> bufferEncoder() {
|
||||
return Encoders.kryo(OafEntity.class);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Encoder<OafEntity> outputEncoder() {
|
||||
return Encoders.kryo(OafEntity.class);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static OafEntity parseOaf(String s) {
|
||||
|
||||
DocumentContext dc = JsonPath
|
||||
.parse(s, Configuration.defaultConfiguration().addOptions(Option.SUPPRESS_EXCEPTIONS));
|
||||
final String id = dc.read(ID_JPATH);
|
||||
if (StringUtils.isNotBlank(id)) {
|
||||
|
||||
String prefix = StringUtils.substringBefore(id, "|");
|
||||
switch (prefix) {
|
||||
case "10":
|
||||
return parse(s, Datasource.class);
|
||||
case "20":
|
||||
return parse(s, Organization.class);
|
||||
case "40":
|
||||
return parse(s, Project.class);
|
||||
case "50":
|
||||
String resultType = dc.read("$.resulttype.classid");
|
||||
switch (resultType) {
|
||||
case "publication":
|
||||
return parse(s, Publication.class);
|
||||
case "dataset":
|
||||
return parse(s, eu.dnetlib.dhp.schema.oaf.Dataset.class);
|
||||
case "software":
|
||||
return parse(s, Software.class);
|
||||
case "other":
|
||||
return parse(s, OtherResearchProduct.class);
|
||||
default:
|
||||
throw new IllegalArgumentException(String.format("invalid resultType: '%s'", resultType));
|
||||
}
|
||||
default:
|
||||
throw new IllegalArgumentException(String.format("invalid id prefix: '%s'", prefix));
|
||||
}
|
||||
} else {
|
||||
throw new IllegalArgumentException(String.format("invalid oaf: '%s'", s));
|
||||
}
|
||||
}
|
||||
|
||||
private static <T extends OafEntity> OafEntity parse(String s, Class<T> clazz) {
|
||||
try {
|
||||
return OBJECT_MAPPER.readValue(s, clazz);
|
||||
} catch (IOException e) {
|
||||
throw new IllegalArgumentException(e);
|
||||
}
|
||||
}
|
||||
|
||||
private static List<String> listEntityPaths(String inputPath, JavaSparkContext sc) {
|
||||
return HdfsSupport
|
||||
.listFiles(inputPath, sc.hadoopConfiguration())
|
||||
ModelSupport.entityTypes
|
||||
.entrySet()
|
||||
.stream()
|
||||
.filter(f -> !f.toLowerCase().contains("relation"))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
.map(e -> parPool.submit(() -> {
|
||||
String entity = e.getKey().name();
|
||||
Class<? extends OafEntity> entityClass = e.getValue();
|
||||
|
||||
spark
|
||||
.read()
|
||||
.load(checkpointPath)
|
||||
.select(col(entity).as("value"))
|
||||
.filter("value IS NOT NULL")
|
||||
.as(OAFENTITY_KRYO_ENC)
|
||||
.map((MapFunction<OafEntity, OafEntity>) r -> r, (Encoder<OafEntity>) Encoders.bean(entityClass))
|
||||
.filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE")
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath + "/" + entity);
|
||||
}))
|
||||
.collect(Collectors.toList())
|
||||
.forEach(t -> {
|
||||
try {
|
||||
t.get();
|
||||
} catch (InterruptedException | ExecutionException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
});
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,26 +0,0 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "i",
|
||||
"paramLongName": "inputPath",
|
||||
"paramDescription": "the source path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "o",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "path of the output graph",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "fi",
|
||||
"paramLongName": "filterInvisible",
|
||||
"paramDescription": "if true filters out invisible entities",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -8,13 +8,25 @@
|
|||
{
|
||||
"paramName": "gin",
|
||||
"paramLongName": "graphInputPath",
|
||||
"paramDescription": "the graph root path",
|
||||
"paramDescription": "the input graph root path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "cp",
|
||||
"paramLongName": "checkpointPath",
|
||||
"paramDescription": "checkpoint directory",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "out",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the output merged graph root path",
|
||||
"paramDescription": "the output graph root path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "fi",
|
||||
"paramLongName": "filterInvisible",
|
||||
"paramDescription": "if true filters out invisible entities",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -81,7 +81,7 @@ case class SparkModel(conf: DedupConfig) {
|
|||
MapDocumentUtil.truncateList(
|
||||
MapDocumentUtil.getJPathList(fdef.getPath, documentContext, fdef.getType),
|
||||
fdef.getSize
|
||||
).toArray
|
||||
).asScala
|
||||
|
||||
case Type.StringConcat =>
|
||||
val jpaths = CONCAT_REGEX.split(fdef.getPath)
|
||||
|
|
|
|||
|
|
@ -1,6 +1,23 @@
|
|||
|
||||
package eu.dnetlib.pace.util;
|
||||
|
||||
/*
|
||||
* Diff Match and Patch
|
||||
* Copyright 2018 The diff-match-patch Authors.
|
||||
* https://github.com/google/diff-match-patch
|
||||
*
|
||||
* Licensed under the Apache License, Version 2.0 (the "License");
|
||||
* you may not use this file except in compliance with the License.
|
||||
* You may obtain a copy of the License at
|
||||
*
|
||||
* http://www.apache.org/licenses/LICENSE-2.0
|
||||
*
|
||||
* Unless required by applicable law or agreed to in writing, software
|
||||
* distributed under the License is distributed on an "AS IS" BASIS,
|
||||
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
* See the License for the specific language governing permissions and
|
||||
* limitations under the License.
|
||||
*/
|
||||
/*
|
||||
* Diff Match and Patch
|
||||
* Copyright 2018 The diff-match-patch Authors.
|
||||
|
|
|
|||
|
|
@ -80,16 +80,15 @@ public class PrepareAffiliationRelations implements Serializable {
|
|||
// load and parse affiliation relations from HDFS
|
||||
Dataset<Row> df = spark
|
||||
.read()
|
||||
.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:ARRAY<STRING>,`Confidence`:DOUBLE>>")
|
||||
.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
|
||||
.json(inputPath);
|
||||
|
||||
// unroll nested arrays
|
||||
df = df
|
||||
.withColumn("matching", functions.explode(new Column("Matchings")))
|
||||
.withColumn("rorid", functions.explode(new Column("matching.RORid")))
|
||||
.select(
|
||||
new Column("DOI").as("doi"),
|
||||
new Column("rorid"),
|
||||
new Column("matching.RORid").as("rorid"),
|
||||
new Column("matching.Confidence").as("confidence"));
|
||||
|
||||
// prepare action sets for affiliation relations
|
||||
|
|
@ -121,8 +120,10 @@ public class PrepareAffiliationRelations implements Serializable {
|
|||
qualifier,
|
||||
Double.toString(row.getAs("confidence")));
|
||||
|
||||
List<KeyValue> collectedfrom = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
|
||||
|
||||
// return bi-directional relations
|
||||
return getAffiliationRelationPair(paperId, affId, dataInfo).iterator();
|
||||
return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
|
||||
|
||||
})
|
||||
.map(p -> new AtomicAction(Relation.class, p))
|
||||
|
|
@ -133,7 +134,8 @@ public class PrepareAffiliationRelations implements Serializable {
|
|||
|
||||
}
|
||||
|
||||
private static List<Relation> getAffiliationRelationPair(String paperId, String affId, DataInfo dataInfo) {
|
||||
private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,
|
||||
DataInfo dataInfo) {
|
||||
return Arrays
|
||||
.asList(
|
||||
OafMapperUtils
|
||||
|
|
@ -143,7 +145,7 @@ public class PrepareAffiliationRelations implements Serializable {
|
|||
ModelConstants.RESULT_ORGANIZATION,
|
||||
ModelConstants.AFFILIATION,
|
||||
ModelConstants.HAS_AUTHOR_INSTITUTION,
|
||||
null,
|
||||
collectedfrom,
|
||||
dataInfo,
|
||||
null),
|
||||
OafMapperUtils
|
||||
|
|
@ -153,7 +155,7 @@ public class PrepareAffiliationRelations implements Serializable {
|
|||
ModelConstants.RESULT_ORGANIZATION,
|
||||
ModelConstants.AFFILIATION,
|
||||
ModelConstants.IS_AUTHOR_INSTITUTION_OF,
|
||||
null,
|
||||
collectedfrom,
|
||||
dataInfo,
|
||||
null));
|
||||
}
|
||||
|
|
|
|||
|
|
@ -31,5 +31,5 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
|
|||
# The following is needed as a property of a workflow
|
||||
oozie.wf.application.path=${oozieTopWfApplicationPath}
|
||||
|
||||
inputPath=/user/schatz/affiliations/data-v3.1.json
|
||||
outputPath=/tmp/crossref-affiliations-output-v3.1
|
||||
inputPath=/data/bip-affiliations/data.json
|
||||
outputPath=/tmp/crossref-affiliations-output-v5
|
||||
|
|
|
|||
|
|
@ -1,4 +1,9 @@
|
|||
{
|
||||
"ETHZ.UNIGENF": {
|
||||
"openaire_id": "opendoar____::1400",
|
||||
"datacite_name": "Uni Genf",
|
||||
"official_name": "Archive ouverte UNIGE"
|
||||
},
|
||||
"GESIS.RKI": {
|
||||
"openaire_id": "re3data_____::r3d100010436",
|
||||
"datacite_name": "Forschungsdatenzentrum am Robert Koch Institut",
|
||||
|
|
|
|||
|
|
@ -101,7 +101,7 @@ public class PrepareAffiliationRelationsTest {
|
|||
// );
|
||||
// }
|
||||
// count the number of relations
|
||||
assertEquals(16, tmp.count());
|
||||
assertEquals(20, tmp.count());
|
||||
|
||||
Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
|
||||
dataset.createOrReplaceTempView("result");
|
||||
|
|
@ -112,7 +112,7 @@ public class PrepareAffiliationRelationsTest {
|
|||
// verify that we have equal number of bi-directional relations
|
||||
Assertions
|
||||
.assertEquals(
|
||||
8, execVerification
|
||||
10, execVerification
|
||||
.filter(
|
||||
"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
|
||||
.collectAsList()
|
||||
|
|
@ -120,14 +120,14 @@ public class PrepareAffiliationRelationsTest {
|
|||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
8, execVerification
|
||||
10, execVerification
|
||||
.filter(
|
||||
"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
|
||||
.collectAsList()
|
||||
.size());
|
||||
|
||||
// check confidence value of a specific relation
|
||||
String sourceDOI = "10.1105/tpc.8.3.343";
|
||||
String sourceDOI = "10.1061/(asce)0733-9399(2002)128:7(759)";
|
||||
|
||||
final String sourceOpenaireId = ID_PREFIX
|
||||
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", sourceDOI));
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
{"DOI":"10.1061\/(asce)0733-9399(2002)128:7(759)","Matchings":[{"RORid":["https:\/\/ror.org\/01teme464"],"Confidence":0.73},{"RORid":["https:\/\/ror.org\/03yxnpp24"],"Confidence":0.7071067812}]}
|
||||
{"DOI":"10.1105\/tpc.8.3.343","Matchings":[{"RORid":["https:\/\/ror.org\/02k40bc56"],"Confidence":0.7071067812}]}
|
||||
{"DOI":"10.1161\/01.cir.0000013305.01850.37","Matchings":[{"RORid":["https:\/\/ror.org\/00qjgza05"],"Confidence":1}]}
|
||||
{"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":["https:\/\/ror.org\/05apxxy63"],"Confidence":1},{"RORid":["https:\/\/ror.org\/035xkbk20"],"Confidence":1}]}
|
||||
{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":["https:\/\/ror.org\/04j198w64"],"Confidence":0.58}]}
|
||||
{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":["https:\/\/ror.org\/057xtrt18"],"Confidence":0.7071067812}]}
|
||||
{"DOI":"10.1061\/(asce)0733-9399(2002)128:7(759)","Matchings":[{"RORid":"https:\/\/ror.org\/03yxnpp24","Confidence":0.7071067812},{"RORid":"https:\/\/ror.org\/01teme464","Confidence":0.89}]}
|
||||
{"DOI":"10.1105\/tpc.8.3.343","Matchings":[{"RORid":"https:\/\/ror.org\/02k40bc56","Confidence":0.7071067812}]}
|
||||
{"DOI":"10.1161\/01.cir.0000013305.01850.37","Matchings":[{"RORid":"https:\/\/ror.org\/00qjgza05","Confidence":1}]}
|
||||
{"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":"https:\/\/ror.org\/035xkbk20","Confidence":1},{"RORid":"https:\/\/ror.org\/05apxxy63","Confidence":1}]}
|
||||
{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":"https:\/\/ror.org\/04j198w64","Confidence":0.82}]}
|
||||
{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(588)","Matchings":[{"RORid":"https:\/\/ror.org\/03m8km719","Confidence":0.8660254038},{"RORid":"https:\/\/ror.org\/02aze4h65","Confidence":0.87}]}
|
||||
{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":"https:\/\/ror.org\/057xtrt18","Confidence":0.7071067812}]}
|
||||
|
|
@ -2,7 +2,9 @@
|
|||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
|
@ -27,10 +29,14 @@ public class TrustUtils {
|
|||
static {
|
||||
mapper = new ObjectMapper();
|
||||
try {
|
||||
dedupConfig = mapper
|
||||
.readValue(
|
||||
DedupConfig.class.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/dedupConfig/dedupConfig.json"),
|
||||
DedupConfig.class);
|
||||
dedupConfig = DedupConfig
|
||||
.load(
|
||||
IOUtils
|
||||
.toString(
|
||||
DedupConfig.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/dedupConfig/dedupConfig.json"),
|
||||
StandardCharsets.UTF_8));
|
||||
|
||||
deduper = new SparkDeduper(dedupConfig);
|
||||
} catch (final IOException e) {
|
||||
log.error("Error loading dedupConfig, e");
|
||||
|
|
@ -57,7 +63,7 @@ public class TrustUtils {
|
|||
return TrustUtils.rescale(score, threshold);
|
||||
} catch (final Exception e) {
|
||||
log.error("Error computing score between results", e);
|
||||
return BrokerConstants.MIN_TRUST;
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -126,31 +126,7 @@
|
|||
--conf spark.sql.shuffle.partitions=15000
|
||||
</spark-opts>
|
||||
<arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
</spark>
|
||||
<ok to="dispatch_entities"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_entities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch grouped entitities</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--conf spark.executor.memoryOverhead=${sparkExecutorMemoryOverhead}
|
||||
--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}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--checkpointPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}</arg>
|
||||
<arg>--filterInvisible</arg><arg>${filterInvisible}</arg>
|
||||
</spark>
|
||||
|
|
|
|||
|
|
@ -117,14 +117,14 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
return Lists.newArrayList();
|
||||
}
|
||||
|
||||
final DataInfo info = prepareDataInfo(doc, invisible);
|
||||
final DataInfo entityInfo = prepareDataInfo(doc, invisible);
|
||||
final long lastUpdateTimestamp = new Date().getTime();
|
||||
|
||||
final List<Instance> instances = prepareInstances(doc, info, collectedFrom, hostedBy);
|
||||
final List<Instance> instances = prepareInstances(doc, entityInfo, collectedFrom, hostedBy);
|
||||
|
||||
final String type = getResultType(doc, instances);
|
||||
|
||||
return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
|
||||
return createOafs(doc, type, instances, collectedFrom, entityInfo, lastUpdateTimestamp);
|
||||
} catch (DocumentException e) {
|
||||
log.error("Error with record:\n" + xml);
|
||||
return Lists.newArrayList();
|
||||
|
|
@ -184,13 +184,15 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
|
||||
final List<Oaf> oafs = Lists.newArrayList(entity);
|
||||
|
||||
final DataInfo relationInfo = prepareDataInfo(doc, false);
|
||||
|
||||
if (!oafs.isEmpty()) {
|
||||
Set<Oaf> rels = Sets.newHashSet();
|
||||
|
||||
rels.addAll(addProjectRels(doc, entity));
|
||||
rels.addAll(addOtherResultRels(doc, entity));
|
||||
rels.addAll(addRelations(doc, entity));
|
||||
rels.addAll(addAffiliations(doc, entity));
|
||||
rels.addAll(addProjectRels(doc, entity, relationInfo));
|
||||
rels.addAll(addOtherResultRels(doc, entity, relationInfo));
|
||||
rels.addAll(addRelations(doc, entity, relationInfo));
|
||||
rels.addAll(addAffiliations(doc, entity, relationInfo));
|
||||
|
||||
oafs.addAll(rels);
|
||||
}
|
||||
|
|
@ -243,7 +245,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
|
||||
private List<Oaf> addProjectRels(
|
||||
final Document doc,
|
||||
final OafEntity entity) {
|
||||
final OafEntity entity, DataInfo info) {
|
||||
|
||||
final List<Oaf> res = new ArrayList<>();
|
||||
|
||||
|
|
@ -262,18 +264,21 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
.add(
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate));
|
||||
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity.getCollectedfrom(),
|
||||
info, entity.getLastupdatetimestamp(), validationdDate, null));
|
||||
res
|
||||
.add(
|
||||
OafMapperUtils
|
||||
.getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate));
|
||||
.getRelation(
|
||||
projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity.getCollectedfrom(), info,
|
||||
entity.getLastupdatetimestamp(), validationdDate, null));
|
||||
}
|
||||
}
|
||||
|
||||
return res;
|
||||
}
|
||||
|
||||
private List<Oaf> addRelations(Document doc, OafEntity entity) {
|
||||
private List<Oaf> addRelations(Document doc, OafEntity entity, DataInfo info) {
|
||||
|
||||
final List<Oaf> rels = Lists.newArrayList();
|
||||
|
||||
|
|
@ -301,14 +306,16 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
.add(
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
entity.getId(), targetId, relType, subRelType, relClass, entity,
|
||||
validationDate));
|
||||
entity.getId(), targetId, relType, subRelType, relClass,
|
||||
entity.getCollectedfrom(), info,
|
||||
entity.getLastupdatetimestamp(), validationDate, null));
|
||||
rels
|
||||
.add(
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
targetId, entity.getId(), relType, subRelType, relClassInverse, entity,
|
||||
validationDate));
|
||||
targetId, entity.getId(), relType, subRelType, relClassInverse,
|
||||
entity.getCollectedfrom(), info,
|
||||
entity.getLastupdatetimestamp(), validationDate, null));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -316,7 +323,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
return rels;
|
||||
}
|
||||
|
||||
private List<Oaf> addAffiliations(Document doc, OafEntity entity) {
|
||||
private List<Oaf> addAffiliations(Document doc, OafEntity entity, DataInfo info) {
|
||||
final List<Oaf> rels = Lists.newArrayList();
|
||||
|
||||
for (Object o : doc.selectNodes("//datacite:affiliation[@affiliationIdentifierScheme='ROR']")) {
|
||||
|
|
@ -345,14 +352,14 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
OafMapperUtils
|
||||
.getRelation(
|
||||
resultId, orgId, RESULT_ORGANIZATION, AFFILIATION, HAS_AUTHOR_INSTITUTION,
|
||||
entity.getCollectedfrom(), entity.getDataInfo(), entity.getLastupdatetimestamp(), null,
|
||||
entity.getCollectedfrom(), info, entity.getLastupdatetimestamp(), null,
|
||||
properties));
|
||||
rels
|
||||
.add(
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
orgId, resultId, RESULT_ORGANIZATION, AFFILIATION, IS_AUTHOR_INSTITUTION_OF,
|
||||
entity.getCollectedfrom(), entity.getDataInfo(), entity.getLastupdatetimestamp(), null,
|
||||
entity.getCollectedfrom(), info, entity.getLastupdatetimestamp(), null,
|
||||
properties));
|
||||
}
|
||||
}
|
||||
|
|
@ -361,7 +368,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
|
||||
protected abstract List<Oaf> addOtherResultRels(
|
||||
final Document doc,
|
||||
final OafEntity entity);
|
||||
final OafEntity entity, DataInfo info);
|
||||
|
||||
private void populateResultFields(
|
||||
final Result r,
|
||||
|
|
|
|||
|
|
@ -4,7 +4,6 @@ package eu.dnetlib.dhp.oa.graph.raw;
|
|||
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
|
||||
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
|
||||
|
||||
import java.io.UnsupportedEncodingException;
|
||||
import java.net.URLDecoder;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashSet;
|
||||
|
|
@ -292,7 +291,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
@Override
|
||||
protected List<Oaf> addOtherResultRels(
|
||||
final Document doc,
|
||||
final OafEntity entity) {
|
||||
final OafEntity entity, DataInfo info) {
|
||||
|
||||
final String docId = entity.getId();
|
||||
final List<Oaf> res = new ArrayList<>();
|
||||
|
|
@ -308,11 +307,13 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
res
|
||||
.add(
|
||||
getRelation(
|
||||
docId, otherId, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, entity));
|
||||
docId, otherId, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, entity.getCollectedfrom(), info,
|
||||
entity.getLastupdatetimestamp(), null, null));
|
||||
res
|
||||
.add(
|
||||
getRelation(
|
||||
otherId, docId, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, entity));
|
||||
otherId, docId, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, entity.getCollectedfrom(), info,
|
||||
entity.getLastupdatetimestamp(), null, null));
|
||||
}
|
||||
}
|
||||
return res;
|
||||
|
|
|
|||
|
|
@ -5,15 +5,11 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
|
|||
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
|
||||
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty;
|
||||
|
||||
import java.io.UnsupportedEncodingException;
|
||||
import java.net.MalformedURLException;
|
||||
import java.net.URL;
|
||||
import java.net.URLDecoder;
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.commons.validator.routines.UrlValidator;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.Element;
|
||||
import org.dom4j.Node;
|
||||
|
|
@ -27,7 +23,6 @@ import eu.dnetlib.dhp.schema.common.RelationInverse;
|
|||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
|
||||
|
||||
public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
||||
|
||||
|
|
@ -397,7 +392,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
@Override
|
||||
protected List<Oaf> addOtherResultRels(
|
||||
final Document doc,
|
||||
final OafEntity entity) {
|
||||
final OafEntity entity, DataInfo info) {
|
||||
|
||||
final String docId = entity.getId();
|
||||
|
||||
|
|
@ -413,7 +408,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
final String relType = ((Node) o).valueOf("@relationType");
|
||||
String otherId = guessRelatedIdentifier(idType, originalId);
|
||||
if (StringUtils.isNotBlank(otherId)) {
|
||||
res.addAll(getRelations(relType, docId, otherId, entity));
|
||||
res.addAll(getRelations(relType, docId, otherId, entity, info));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -434,18 +429,20 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
}
|
||||
|
||||
protected List<Oaf> getRelations(final String reltype, final String entityId, final String otherId,
|
||||
final OafEntity entity) {
|
||||
final OafEntity entity, DataInfo info) {
|
||||
final List<Oaf> res = new ArrayList<>();
|
||||
RelationInverse rel = ModelSupport.findRelation(reltype);
|
||||
if (rel != null) {
|
||||
res
|
||||
.add(
|
||||
getRelation(
|
||||
entityId, otherId, rel.getRelType(), rel.getSubReltype(), rel.getRelClass(), entity));
|
||||
entityId, otherId, rel.getRelType(), rel.getSubReltype(), rel.getRelClass(),
|
||||
entity.getCollectedfrom(), info, entity.getLastupdatetimestamp(), null, null));
|
||||
res
|
||||
.add(
|
||||
getRelation(
|
||||
otherId, entityId, rel.getRelType(), rel.getSubReltype(), rel.getInverseRelClass(), entity));
|
||||
otherId, entityId, rel.getRelType(), rel.getSubReltype(), rel.getInverseRelClass(),
|
||||
entity.getCollectedfrom(), info, entity.getLastupdatetimestamp(), null, null));
|
||||
|
||||
}
|
||||
return res;
|
||||
|
|
|
|||
|
|
@ -96,30 +96,7 @@
|
|||
--conf spark.sql.shuffle.partitions=15000
|
||||
</spark-opts>
|
||||
<arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
</spark>
|
||||
<ok to="dispatch_entities"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_entities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch grouped entities</name>
|
||||
<class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--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>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--checkpointPath</arg><arg>${workingPath}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}</arg>
|
||||
<arg>--filterInvisible</arg><arg>${filterInvisible}</arg>
|
||||
</spark>
|
||||
|
|
|
|||
|
|
@ -1,16 +1,15 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.group;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.nio.file.Paths;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
|
|
@ -19,118 +18,108 @@ import org.apache.spark.sql.Encoders;
|
|||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.*;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import java.io.IOException;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.nio.file.Paths;
|
||||
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||
public class GroupEntitiesSparkJobTest {
|
||||
|
||||
private static SparkSession spark;
|
||||
private static SparkSession spark;
|
||||
|
||||
private static ObjectMapper mapper = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
private static ObjectMapper mapper = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
|
||||
private static Path workingDir;
|
||||
private Path dataInputPath;
|
||||
private static Path workingDir;
|
||||
private Path dataInputPath;
|
||||
|
||||
private Path groupEntityPath;
|
||||
private Path dispatchEntityPath;
|
||||
private Path checkpointPath;
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName());
|
||||
private Path outputPath;
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName());
|
||||
conf.setMaster("local");
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
spark = SparkSession.builder().config(conf).getOrCreate();
|
||||
}
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName());
|
||||
|
||||
@BeforeEach
|
||||
public void beforeEach() throws IOException, URISyntaxException {
|
||||
dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI());
|
||||
groupEntityPath = workingDir.resolve("grouped_entity");
|
||||
dispatchEntityPath = workingDir.resolve("dispatched_entity");
|
||||
}
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName());
|
||||
conf.setMaster("local");
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
spark = SparkSession.builder().config(conf).getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
spark.stop();
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
}
|
||||
@BeforeEach
|
||||
public void beforeEach() throws IOException, URISyntaxException {
|
||||
dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI());
|
||||
checkpointPath = workingDir.resolve("grouped_entity");
|
||||
outputPath = workingDir.resolve("dispatched_entity");
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(1)
|
||||
void testGroupEntities() throws Exception {
|
||||
GroupEntitiesSparkJob.main(new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-graphInputPath",
|
||||
dataInputPath.toString(),
|
||||
"-outputPath",
|
||||
groupEntityPath.toString()
|
||||
});
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
spark.stop();
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
}
|
||||
|
||||
Dataset<Result> output = spark
|
||||
.read()
|
||||
.textFile(groupEntityPath.toString())
|
||||
.map((MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING())
|
||||
.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
|
||||
@Test
|
||||
@Order(1)
|
||||
void testGroupEntities() throws Exception {
|
||||
GroupEntitiesSparkJob.main(new String[]{
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-graphInputPath",
|
||||
dataInputPath.toString(),
|
||||
"-checkpointPath",
|
||||
checkpointPath.toString(),
|
||||
"-outputPath",
|
||||
outputPath.toString(),
|
||||
"-filterInvisible",
|
||||
Boolean.FALSE.toString()
|
||||
});
|
||||
|
||||
assertEquals(
|
||||
1,
|
||||
output
|
||||
.filter(
|
||||
(FilterFunction<Result>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
|
||||
.equals(r.getId()) &&
|
||||
r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
|
||||
.count());
|
||||
}
|
||||
Dataset<OafEntity> checkpointTable = spark
|
||||
.read()
|
||||
.load(checkpointPath.toString())
|
||||
.selectExpr("COALESCE(*)")
|
||||
.as(Encoders.kryo(OafEntity.class));
|
||||
|
||||
@Test
|
||||
@Order(2)
|
||||
void testDispatchEntities() throws Exception {
|
||||
DispatchEntitiesSparkJob.main(new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-inputPath",
|
||||
groupEntityPath.toString(),
|
||||
"-outputPath",
|
||||
dispatchEntityPath.resolve(".").toString(),
|
||||
"-filterInvisible",
|
||||
Boolean.TRUE.toString()
|
||||
});
|
||||
|
||||
Dataset<Result> output = spark
|
||||
.read()
|
||||
.textFile(
|
||||
DHPUtils
|
||||
.toSeq(
|
||||
HdfsSupport
|
||||
.listFiles(dispatchEntityPath.toString(), spark.sparkContext().hadoopConfiguration())))
|
||||
.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
|
||||
assertEquals(
|
||||
1,
|
||||
checkpointTable
|
||||
.filter(
|
||||
(FilterFunction<OafEntity>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
|
||||
.equals(r.getId()) &&
|
||||
r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
|
||||
.count());
|
||||
|
||||
assertEquals(3, output.count());
|
||||
assertEquals(
|
||||
2,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("publication"))
|
||||
.count());
|
||||
assertEquals(
|
||||
1,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("dataset"))
|
||||
.count());
|
||||
}
|
||||
}
|
||||
|
||||
Dataset<Result> output = spark
|
||||
.read()
|
||||
.textFile(
|
||||
DHPUtils
|
||||
.toSeq(
|
||||
HdfsSupport
|
||||
.listFiles(outputPath.toString(), spark.sparkContext().hadoopConfiguration())))
|
||||
.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
|
||||
|
||||
assertEquals(3, output.count());
|
||||
assertEquals(
|
||||
2,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("publication"))
|
||||
.count());
|
||||
assertEquals(
|
||||
1,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("dataset"))
|
||||
.count());
|
||||
}
|
||||
}
|
||||
|
|
@ -49,7 +49,7 @@ public class DownloadCsvTest {
|
|||
@Test
|
||||
void getUnibiFileTest() throws CollectorException, IOException, ClassNotFoundException {
|
||||
|
||||
String fileURL = "https://pub.uni-bielefeld.de/download/2944717/2944718/issn_gold_oa_version_4.csv";
|
||||
String fileURL = "https://pub.uni-bielefeld.de/download/2944717/2944718/issn_gold_oa_version_5.csv";
|
||||
|
||||
final String outputFile = workingDir + "/unibi_gold.json";
|
||||
new DownloadCSV()
|
||||
|
|
|
|||
|
|
@ -1067,6 +1067,28 @@ class MappersTest {
|
|||
System.out.println("***************");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testD4ScienceTraining() throws IOException {
|
||||
final String xml = IOUtils
|
||||
.toString(Objects.requireNonNull(getClass().getResourceAsStream("d4science-1-training.xml")));
|
||||
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
||||
final OtherResearchProduct trainingMaterial = (OtherResearchProduct) list.get(0);
|
||||
System.out.println("***************");
|
||||
System.out.println(new ObjectMapper().writeValueAsString(trainingMaterial));
|
||||
System.out.println("***************");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testD4ScienceDataset() throws IOException {
|
||||
final String xml = IOUtils
|
||||
.toString(Objects.requireNonNull(getClass().getResourceAsStream("d4science-2-dataset.xml")));
|
||||
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
||||
final Dataset trainingMaterial = (Dataset) list.get(0);
|
||||
System.out.println("***************");
|
||||
System.out.println(new ObjectMapper().writeValueAsString(trainingMaterial));
|
||||
System.out.println("***************");
|
||||
}
|
||||
|
||||
@Test
|
||||
void testNotWellFormed() throws IOException {
|
||||
final String xml = IOUtils
|
||||
|
|
|
|||
|
|
@ -0,0 +1,93 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<oai:record 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/">
|
||||
<oai:header>
|
||||
<dri:objIdentifier>alessia_____::104c2d4ba8878c16fa824dce5b1bea57</dri:objIdentifier>
|
||||
<dri:recordIdentifier>12d8f77e-d66f-46f5-8d88-af7db23bc4c9</dri:recordIdentifier>
|
||||
<dri:dateOfCollection>2023-09-08T10:12:35.864+02:00</dri:dateOfCollection>
|
||||
<oaf:datasourceprefix>alessia_____</oaf:datasourceprefix>
|
||||
<dr:dateOfTransformation>2023-09-08T11:31:45.692+02:00</dr:dateOfTransformation>
|
||||
</oai:header>
|
||||
<oai:metadata>
|
||||
<datacite:resource
|
||||
xmlns:datacite="http://datacite.org/schema/kernel-4"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
|
||||
<datacite:identifier identifierType="URL">http://data.d4science.org/ctlg/ResourceCatalogue/visual_analytics_for_data_scientists</datacite:identifier>
|
||||
<datacite:alternateIdentifiers/>
|
||||
<datacite:creators>
|
||||
<datacite:creator>
|
||||
<datacite:creatorName>BRAGHIERI MARCO</datacite:creatorName>
|
||||
</datacite:creator>
|
||||
</datacite:creators>
|
||||
<datacite:titles>
|
||||
<datacite:title>Visual Analytics for Data Scientists</datacite:title>
|
||||
</datacite:titles>
|
||||
<datacite:publisher>SoBigData++</datacite:publisher>
|
||||
<datacite:publicationYear/>
|
||||
<datacite:dates>
|
||||
<datacite:date dateType="Issued"/>
|
||||
</datacite:dates>
|
||||
<datacite:resourceType resourceTypeGeneral="TrainingMaterial">TrainingMaterial</datacite:resourceType>
|
||||
<datacite:descriptions>
|
||||
<datacite:description descriptionType="Abstract">Participants to this module shall
|
||||
- Learn the principles and rules underlying the design of visual data
|
||||
representations and human-computer interactions
|
||||
- Understand, adapt and apply representative visual analytics methods and systems for diverse types
|
||||
of data and problems
|
||||
- Analyse and evaluate the structure and properties
|
||||
of data to select or devise appropriate methods for data exploration
|
||||
- Combine visualization, interactive techniques, and computational
|
||||
processing to develop practical data analysis for problem solving
|
||||
|
||||
(This teaching material on Visual Analytics for Data Scientists is part of a MSc module at City University London).
|
||||
|
||||
The author did not intend to violate any copyright on figures or content. In case you are the legal owner of any copyrighted content, please contact info@sobigdata.eu and we will immediately remove it</datacite:description>
|
||||
</datacite:descriptions>
|
||||
<datacite:subjects>
|
||||
<datacite:subject>Visual analytics</datacite:subject>
|
||||
</datacite:subjects>
|
||||
<datacite:formats>
|
||||
<datacite:format>Slides</datacite:format>
|
||||
<datacite:format>Other</datacite:format>
|
||||
<datacite:format>PDF</datacite:format>
|
||||
<datacite:format>PDF</datacite:format>
|
||||
<datacite:format>PDF</datacite:format>
|
||||
<datacite:format>PDF</datacite:format>
|
||||
<datacite:format>PDF</datacite:format>
|
||||
<datacite:format>PDF</datacite:format>
|
||||
<datacite:format>PDF</datacite:format>
|
||||
<datacite:format>PDF</datacite:format>
|
||||
<datacite:format>PDF</datacite:format>
|
||||
<datacite:format>PDF</datacite:format>
|
||||
<datacite:format>ZIP</datacite:format>
|
||||
</datacite:formats>
|
||||
</datacite:resource>
|
||||
<oaf:accessrights>OPEN</oaf:accessrights>
|
||||
<dr:CobjCategory type="other">0010</dr:CobjCategory>
|
||||
<oaf:dateAccepted/>
|
||||
<oaf:hostedBy id="alessia_____::alessia" name="Alessia"/>
|
||||
<oaf:collectedFrom id="alessia_____::alessia" name="Alessia"/>
|
||||
<oaf:license>other-open</oaf:license>
|
||||
<oaf:projectid>corda__h2020::871042</oaf:projectid>
|
||||
</oai:metadata>
|
||||
<about xmlns:dc="http://purl.org/dc/elements/1.1/"
|
||||
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<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="2023-09-08T10:12:35.864+02:00">
|
||||
<baseURL>https%3A%2F%2Fapi.d4science.org%2Fcatalogue%2Fitems</baseURL>
|
||||
<identifier/>
|
||||
<datestamp/>
|
||||
<metadataNamespace/>
|
||||
</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"
|
||||
classname="Harvested" schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
|
||||
</oaf:datainfo>
|
||||
</about>
|
||||
</oai:record>
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<oai:record 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/">
|
||||
<oai:header>
|
||||
<dri:objIdentifier>alessia_____::028879484548f4e1c630e1c503e35231</dri:objIdentifier>
|
||||
<dri:recordIdentifier>4fed018e-c2ff-4afa-b7b5-1ca1beebf850</dri:recordIdentifier>
|
||||
<dri:dateOfCollection>2023-09-08T12:14:27.615+02:00</dri:dateOfCollection>
|
||||
<oaf:datasourceprefix>alessia_____</oaf:datasourceprefix>
|
||||
<dr:dateOfTransformation>2023-09-08T12:14:51.7+02:00</dr:dateOfTransformation>
|
||||
</oai:header>
|
||||
<oai:metadata>
|
||||
<datacite:resource
|
||||
xmlns:datacite="http://datacite.org/schema/kernel-4"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
|
||||
<datacite:identifier identifierType="URL">http://data.d4science.org/ctlg/ResourceCatalogue/city-to-city_migration</datacite:identifier>
|
||||
<datacite:alternateIdentifiers>
|
||||
<datacite:alternateIdentifier type="URL"/>
|
||||
</datacite:alternateIdentifiers>
|
||||
<datacite:creators>
|
||||
<datacite:creator>
|
||||
<datacite:creatorName>Pappalardo, Luca</datacite:creatorName>
|
||||
<datacite:affiliation/>
|
||||
<datacite:nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org">0000-0002-1547-6007</datacite:nameIdentifier>
|
||||
</datacite:creator>
|
||||
</datacite:creators>
|
||||
<datacite:titles>
|
||||
<datacite:title>City-to-city migration</datacite:title>
|
||||
</datacite:titles>
|
||||
<datacite:publisher>SoBigData++</datacite:publisher>
|
||||
<datacite:publicationYear/>
|
||||
<datacite:dates>
|
||||
<datacite:date dateType="Issued">2018-02-15</datacite:date>
|
||||
</datacite:dates>
|
||||
<datacite:resourceType resourceTypeGeneral="Dataset">Dataset</datacite:resourceType>
|
||||
<datacite:descriptions>
|
||||
<datacite:description descriptionType="Abstract">Census data recording the migration of people between metropolitan areas in
|
||||
the US</datacite:description>
|
||||
</datacite:descriptions>
|
||||
<datacite:subjects>
|
||||
<datacite:subject>Human Mobility data</datacite:subject>
|
||||
</datacite:subjects>
|
||||
<datacite:formats/>
|
||||
</datacite:resource>
|
||||
<oaf:accessrights>OPEN</oaf:accessrights>
|
||||
<dr:CobjCategory type="dataset">0021</dr:CobjCategory>
|
||||
<oaf:dateAccepted>2018-02-15</oaf:dateAccepted>
|
||||
<oaf:hostedBy id="alessia_____::alessia" name="Alessia"/>
|
||||
<oaf:collectedFrom id="alessia_____::alessia" name="Alessia"/>
|
||||
<oaf:license>AFL-3.0</oaf:license>
|
||||
<oaf:projectid>corda__h2020::871042</oaf:projectid>
|
||||
</oai:metadata>
|
||||
<about xmlns:dc="http://purl.org/dc/elements/1.1/"
|
||||
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<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="2023-09-08T12:14:27.615+02:00">
|
||||
<baseURL>https%3A%2F%2Fapi.d4science.org%2Fcatalogue%2Fitems</baseURL>
|
||||
<identifier/>
|
||||
<datestamp/>
|
||||
<metadataNamespace/>
|
||||
</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"
|
||||
classname="Harvested" schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
|
||||
</oaf:datainfo>
|
||||
</about>
|
||||
</oai:record>
|
||||
|
|
@ -24,10 +24,7 @@ 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.Datasource;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
|
||||
public class XmlRecordFactoryTest {
|
||||
|
||||
|
|
@ -196,4 +193,51 @@ public class XmlRecordFactoryTest {
|
|||
assertEquals("dnet:pid_types", ((Element) pids.get(0)).attribute("schemeid").getValue());
|
||||
assertEquals("dnet:pid_types", ((Element) pids.get(0)).attribute("schemename").getValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testD4ScienceTraining() throws DocumentException, IOException {
|
||||
final ContextMapper contextMapper = new ContextMapper();
|
||||
|
||||
final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
|
||||
XmlConverterJob.schemaLocation);
|
||||
|
||||
final OtherResearchProduct p = OBJECT_MAPPER
|
||||
.readValue(
|
||||
IOUtils.toString(getClass().getResourceAsStream("d4science-1-training.json")),
|
||||
OtherResearchProduct.class);
|
||||
|
||||
final String xml = xmlRecordFactory.build(new JoinedEntity<>(p));
|
||||
|
||||
assertNotNull(xml);
|
||||
|
||||
final Document doc = new SAXReader().read(new StringReader(xml));
|
||||
|
||||
assertNotNull(doc);
|
||||
System.out.println(doc.asXML());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testD4ScienceDataset() throws DocumentException, IOException {
|
||||
final ContextMapper contextMapper = new ContextMapper();
|
||||
|
||||
final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
|
||||
XmlConverterJob.schemaLocation);
|
||||
|
||||
final OtherResearchProduct p = OBJECT_MAPPER
|
||||
.readValue(
|
||||
IOUtils.toString(getClass().getResourceAsStream("d4science-2-dataset.json")),
|
||||
OtherResearchProduct.class);
|
||||
|
||||
final String xml = xmlRecordFactory.build(new JoinedEntity<>(p));
|
||||
|
||||
assertNotNull(xml);
|
||||
|
||||
final Document doc = new SAXReader().read(new StringReader(xml));
|
||||
|
||||
assertNotNull(doc);
|
||||
System.out.println(doc.asXML());
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
|
|
@ -39,7 +39,8 @@
|
|||
<switch>
|
||||
<!-- The default will be set as the normal start, a.k.a. get-doi-synonyms -->
|
||||
<!-- If any different condition is set, go to the corresponding start -->
|
||||
<case to="non-iterative-rankings">${wf:conf('resume') eq "rankings-start"}</case>
|
||||
<case to="spark-cc">${wf:conf('resume') eq "cc"}</case>
|
||||
<case to="spark-ram">${wf:conf('resume') eq "ram"}</case>
|
||||
<case to="spark-impulse">${wf:conf('resume') eq "impulse"}</case>
|
||||
<case to="spark-pagerank">${wf:conf('resume') eq "pagerank"}</case>
|
||||
<case to="spark-attrank">${wf:conf('resume') eq "attrank"}</case>
|
||||
|
|
@ -89,18 +90,11 @@
|
|||
<file>${nameNode}${wfAppPath}/create_openaire_ranking_graph.py#create_openaire_ranking_graph.py</file>
|
||||
</spark>
|
||||
|
||||
<ok to="non-iterative-rankings" />
|
||||
<ok to="spark-cc"/>
|
||||
<error to="openaire-graph-error" />
|
||||
|
||||
</action>
|
||||
|
||||
<!-- Citation Count and RAM are calculated in parallel-->
|
||||
<fork name="non-iterative-rankings">
|
||||
<path start="spark-cc"/>
|
||||
<!-- <path start="spark-impulse"/> -->
|
||||
<path start="spark-ram"/>
|
||||
</fork>
|
||||
|
||||
<!-- Run Citation Count calculation -->
|
||||
<action name="spark-cc">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
|
@ -129,7 +123,7 @@
|
|||
<file>${wfAppPath}/bip-ranker/CC.py#CC.py</file>
|
||||
</spark>
|
||||
|
||||
<ok to="join-non-iterative-rankings" />
|
||||
<ok to="spark-ram" />
|
||||
<error to="cc-fail" />
|
||||
|
||||
</action>
|
||||
|
|
@ -165,14 +159,11 @@
|
|||
<file>${wfAppPath}/bip-ranker/TAR.py#TAR.py</file>
|
||||
</spark>
|
||||
|
||||
<ok to="join-non-iterative-rankings" />
|
||||
<ok to="spark-impulse" />
|
||||
<error to="ram-fail" />
|
||||
|
||||
</action>
|
||||
|
||||
<!-- Join non-iterative methods -->
|
||||
<join name="join-non-iterative-rankings" to="spark-impulse"/>
|
||||
|
||||
<action name="spark-impulse">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
|
|
|
|||
10
pom.xml
10
pom.xml
|
|
@ -112,6 +112,16 @@
|
|||
<url>https://maven.d4science.org/nexus/content/repositories/dnet-deps</url>
|
||||
<layout>default</layout>
|
||||
</repository>
|
||||
<repository>
|
||||
<id>maven-restlet</id>
|
||||
<name>Restlet repository</name>
|
||||
<url>https://maven.restlet.talend.com</url>
|
||||
</repository>
|
||||
<repository>
|
||||
<id>conjars</id>
|
||||
<name>conjars</name>
|
||||
<url>https://conjars.wensel.net/repo/</url>
|
||||
</repository>
|
||||
</repositories>
|
||||
|
||||
<dependencies>
|
||||
|
|
|
|||
Loading…
Reference in New Issue