This commit is contained in:
Enrico Ottonello 2020-04-22 14:50:50 +02:00
commit 5977f08e92
31 changed files with 1690 additions and 728 deletions

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@ -47,6 +47,16 @@
<artifactId>jaxen</artifactId>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-distcp</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-openaire-data-protos</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
@ -57,6 +67,44 @@
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-actionmanager-api</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-actionmanager-common</artifactId>
<exclusions>
<exclusion>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-openaireplus-mapping-utils</artifactId>
</exclusion>
<exclusion>
<groupId>saxonica</groupId>
<artifactId>saxon</artifactId>
</exclusion>
<exclusion>
<groupId>saxonica</groupId>
<artifactId>saxon-dom</artifactId>
</exclusion>
<exclusion>
<groupId>jgrapht</groupId>
<artifactId>jgrapht</artifactId>
</exclusion>
<exclusion>
<groupId>net.sf.ehcache</groupId>
<artifactId>ehcache</artifactId>
</exclusion>
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.*</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>apache</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
</project>

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@ -1,4 +1,4 @@
package eu.dnetlib.dhp.migration.actions;
package eu.dnetlib.dhp.actionmanager.migration;
import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
import java.util.Comparator;

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@ -1,4 +1,4 @@
package eu.dnetlib.dhp.migration.actions;
package eu.dnetlib.dhp.actionmanager.migration;
import com.google.common.base.Splitter;
import com.google.common.collect.Lists;
@ -9,35 +9,36 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import java.io.File;
import java.io.FileOutputStream;
import java.io.OutputStream;
import java.util.*;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
import java.util.Properties;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.tools.DistCp;
import org.apache.hadoop.tools.DistCpOptions;
import org.apache.hadoop.util.ToolRunner;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class MigrateActionSet {
private static final Log log = LogFactory.getLog(MigrateActionSet.class);
private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class);
private static final String SEPARATOR = "/";
private static final String TARGET_PATHS = "target_paths";
private static final String RAWSET_PREFIX = "rawset_";
private static Boolean DEFAULT_TRANSFORM_ONLY = false;
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
MigrateActionSet.class.getResourceAsStream(
"/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json")));
"/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json")));
parser.parseArgument(args);
new MigrateActionSet().run(parser);
@ -56,11 +57,11 @@ public class MigrateActionSet {
final String transform_only_s = parser.get("transform_only");
log.info("transform only param: " + transform_only_s);
log.info("transform only param: {}", transform_only_s);
final Boolean transformOnly = Boolean.valueOf(parser.get("transform_only"));
log.info("transform only: " + transformOnly);
log.info("transform only: {}", transformOnly);
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
@ -79,22 +80,19 @@ public class MigrateActionSet {
final List<Path> sourcePaths = getSourcePaths(sourceNN, isLookUp);
log.info(
String.format(
"paths to process:\n%s",
sourcePaths.stream()
.map(p -> p.toString())
.collect(Collectors.joining("\n"))));
"paths to process:\n{}",
sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n")));
for (Path source : sourcePaths) {
if (!sourceFS.exists(source)) {
log.warn(String.format("skipping unexisting path: %s", source));
log.warn("skipping unexisting path: {}", source);
} else {
LinkedList<String> pathQ =
Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath()));
final String rawSet = pathQ.pollLast();
log.info(String.format("got RAWSET: %s", rawSet));
log.info("got RAWSET: {}", rawSet);
if (StringUtils.isNotBlank(rawSet) && rawSet.startsWith(RAWSET_PREFIX)) {
@ -109,7 +107,7 @@ public class MigrateActionSet {
+ SEPARATOR
+ rawSet);
log.info(String.format("using TARGET PATH: %s", targetPath));
log.info("using TARGET PATH: {}", targetPath);
if (!transformOnly) {
if (targetFS.exists(targetPath)) {

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@ -1,4 +1,9 @@
package eu.dnetlib.dhp.migration.actions;
package eu.dnetlib.dhp.actionmanager.migration;
import static eu.dnetlib.data.proto.KindProtos.Kind.entity;
import static eu.dnetlib.data.proto.KindProtos.Kind.relation;
import static eu.dnetlib.data.proto.TypeProtos.*;
import static eu.dnetlib.data.proto.TypeProtos.Type.*;
import com.google.common.collect.Lists;
import com.googlecode.protobuf.format.JsonFormat;

View File

@ -0,0 +1,179 @@
package eu.dnetlib.dhp.actionmanager.migration;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Splitter;
import com.google.common.collect.Lists;
import com.google.protobuf.InvalidProtocolBufferException;
import eu.dnetlib.data.proto.OafProtos;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import java.io.IOException;
import java.io.Serializable;
import java.util.LinkedList;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
public class TransformActions implements Serializable {
private static final Logger log = LoggerFactory.getLogger(TransformActions.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String SEPARATOR = "/";
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
MigrateActionSet.class.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged =
Optional.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final String inputPaths = parser.get("inputPaths");
if (StringUtils.isBlank(inputPaths)) {
throw new RuntimeException("empty inputPaths");
}
log.info("inputPaths: {}", inputPaths);
final String targetBaseDir = getTargetBaseDir(isLookupUrl);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> transformActions(inputPaths, targetBaseDir, spark));
}
private static void transformActions(
String inputPaths, String targetBaseDir, SparkSession spark) throws IOException {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) {
LinkedList<String> pathQ =
Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath));
final String rawset = pathQ.pollLast();
final String actionSetDirectory = pathQ.pollLast();
final Path targetDirectory =
new Path(targetBaseDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawset);
if (fs.exists(targetDirectory)) {
log.info("found target directory '{}", targetDirectory);
fs.delete(targetDirectory, true);
log.info("deleted target directory '{}", targetDirectory);
}
log.info("transforming actions from '{}' to '{}'", sourcePath, targetDirectory);
sc.sequenceFile(sourcePath, Text.class, Text.class)
.map(
a ->
eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(
a._2().toString()))
.map(TransformActions::doTransform)
.filter(Objects::nonNull)
.mapToPair(
a ->
new Tuple2<>(
a.getClazz().toString(),
OBJECT_MAPPER.writeValueAsString(a)))
.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
.saveAsNewAPIHadoopFile(
targetDirectory.toString(),
Text.class,
Text.class,
SequenceFileOutputFormat.class,
sc.hadoopConfiguration());
}
}
private static AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa)
throws InvalidProtocolBufferException {
// dedup similarity relations had empty target value, don't migrate them
if (aa.getTargetValue().length == 0) {
return null;
}
final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue());
final Oaf oaf = ProtoConverter.convert(proto_oaf);
switch (proto_oaf.getKind()) {
case entity:
switch (proto_oaf.getEntity().getType()) {
case datasource:
return new AtomicAction<>(Datasource.class, (Datasource) oaf);
case organization:
return new AtomicAction<>(Organization.class, (Organization) oaf);
case project:
return new AtomicAction<>(Project.class, (Project) oaf);
case result:
final String resulttypeid =
proto_oaf
.getEntity()
.getResult()
.getMetadata()
.getResulttype()
.getClassid();
switch (resulttypeid) {
case "publication":
return new AtomicAction<>(Publication.class, (Publication) oaf);
case "software":
return new AtomicAction<>(Software.class, (Software) oaf);
case "other":
return new AtomicAction<>(
OtherResearchProduct.class, (OtherResearchProduct) oaf);
case "dataset":
return new AtomicAction<>(Dataset.class, (Dataset) oaf);
default:
// can be an update, where the resulttype is not specified
return new AtomicAction<>(Result.class, (Result) oaf);
}
default:
throw new IllegalArgumentException(
"invalid entity type: " + proto_oaf.getEntity().getType());
}
case relation:
return new AtomicAction<>(Relation.class, (Relation) oaf);
default:
throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind());
}
}
private static String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
String XQUERY =
"collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()";
return isLookUp.getResourceProfileByQuery(XQUERY);
}
}

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@ -0,0 +1,56 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "is",
"paramLongName": "isLookupUrl",
"paramDescription": "URL of the isLookUp Service",
"paramRequired": true
},
{
"paramName": "sn",
"paramLongName": "sourceNameNode",
"paramDescription": "nameNode of the source cluster",
"paramRequired": true
},
{
"paramName": "tn",
"paramLongName": "targetNameNode",
"paramDescription": "namoNode of the target cluster",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingDirectory",
"paramDescription": "working directory",
"paramRequired": true
},
{
"paramName": "nm",
"paramLongName": "distcp_num_maps",
"paramDescription": "maximum number of map tasks used in the distcp process",
"paramRequired": true
},
{
"paramName": "mm",
"paramLongName": "distcp_memory_mb",
"paramDescription": "memory for distcp action copying actionsets from remote cluster",
"paramRequired": true
},
{
"paramName": "tt",
"paramLongName": "distcp_task_timeout",
"paramDescription": "timeout for distcp copying actions from remote cluster",
"paramRequired": true
},
{
"paramName": "tr",
"paramLongName": "transform_only",
"paramDescription": "activate tranform-only mode. Only apply transformation step",
"paramRequired": true
}
]

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@ -0,0 +1,20 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "is",
"paramLongName": "isLookupUrl",
"paramDescription": "URL of the isLookUp Service",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "inputPaths",
"paramDescription": "URL of the isLookUp Service",
"paramRequired": true
}
]

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@ -10,7 +10,6 @@
</property>
<property>
<name>workingDirectory</name>
<value>/tmp/actionsets</value>
<description>working directory</description>
</property>
<property>
@ -44,6 +43,20 @@
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
@ -66,23 +79,27 @@
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to='migrate_actionsets' />
<start to="migrate_actionsets"/>
<action name='migrate_actionsets'>
<action name="migrate_actionsets">
<java>
<main-class>eu.dnetlib.dhp.migration.actions.MigrateActionSet</main-class>
<main-class>eu.dnetlib.dhp.actionmanager.migration.MigrateActionSet</main-class>
<java-opt>-Dmapred.task.timeout=${distcp_task_timeout}</java-opt>
<arg>-is</arg><arg>${isLookupUrl}</arg>
<arg>-sn</arg><arg>${sourceNN}</arg>
<arg>-tn</arg><arg>${nameNode}</arg>
<arg>-w</arg><arg>${workingDirectory}</arg>
<arg>-nm</arg><arg>${distcp_num_maps}</arg>
<arg>-mm</arg><arg>${distcp_memory_mb}</arg>
<arg>-tt</arg><arg>${distcp_task_timeout}</arg>
<arg>-tr</arg><arg>${transform_only}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--sourceNameNode</arg><arg>${sourceNN}</arg>
<arg>--targetNameNode</arg><arg>${nameNode}</arg>
<arg>--workingDirectory</arg><arg>${workingDirectory}</arg>
<arg>--distcp_num_maps</arg><arg>${distcp_num_maps}</arg>
<arg>--distcp_memory_mb</arg><arg>${distcp_memory_mb}</arg>
<arg>--distcp_task_timeout</arg><arg>${distcp_task_timeout}</arg>
<arg>--transform_only</arg><arg>${transform_only}</arg>
<capture-output/>
</java>
<ok to="transform_actions" />
@ -94,19 +111,18 @@
<master>yarn</master>
<mode>cluster</mode>
<name>transform_actions</name>
<class>eu.dnetlib.dhp.migration.actions.TransformActions</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<class>eu.dnetlib.dhp.actionmanager.migration.TransformActions</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores ${sparkExecutorCores}
--executor-memory ${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-mt</arg><arg>yarn</arg>
<arg>-is</arg><arg>${isLookupUrl}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--inputPaths</arg><arg>${wf:actionData('migrate_actionsets')['target_paths']}</arg>
</spark>
<ok to="end"/>

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@ -1,213 +0,0 @@
package eu.dnetlib.dhp.migration.actions;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Splitter;
import com.google.common.collect.Lists;
import com.google.protobuf.InvalidProtocolBufferException;
import eu.dnetlib.data.proto.OafProtos;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import java.io.IOException;
import java.io.Serializable;
import java.util.LinkedList;
import java.util.Objects;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
public class TransformActions implements Serializable {
private static final Log log = LogFactory.getLog(TransformActions.class);
private static final String SEPARATOR = "/";
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
MigrateActionSet.class.getResourceAsStream(
"/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json")));
parser.parseArgument(args);
new TransformActions().run(parser);
}
private void run(ArgumentApplicationParser parser) throws ISLookUpException, IOException {
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: " + isLookupUrl);
final String inputPaths = parser.get("inputPaths");
if (StringUtils.isBlank(inputPaths)) {
throw new RuntimeException("empty inputPaths");
}
log.info("inputPaths: " + inputPaths);
final String targetBaseDir = getTargetBaseDir(isLookupUrl);
try (SparkSession spark = getSparkSession(parser)) {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) {
LinkedList<String> pathQ =
Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath));
final String rawset = pathQ.pollLast();
final String actionSetDirectory = pathQ.pollLast();
final Path targetDirectory =
new Path(
targetBaseDir
+ SEPARATOR
+ actionSetDirectory
+ SEPARATOR
+ rawset);
if (fs.exists(targetDirectory)) {
log.info(String.format("found target directory '%s", targetDirectory));
fs.delete(targetDirectory, true);
log.info(String.format("deleted target directory '%s", targetDirectory));
}
log.info(
String.format(
"transforming actions from '%s' to '%s'",
sourcePath, targetDirectory));
sc.sequenceFile(sourcePath, Text.class, Text.class)
.map(
a ->
eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(
a._2().toString()))
.map(a -> doTransform(a))
.filter(Objects::isNull)
.filter(a -> a.getPayload() == null)
.map(a -> new ObjectMapper().writeValueAsString(a))
.saveAsTextFile(targetDirectory.toString(), GzipCodec.class);
}
}
}
private Text transformAction(eu.dnetlib.actionmanager.actions.AtomicAction aa)
throws InvalidProtocolBufferException, JsonProcessingException {
final Text out = new Text();
final ObjectMapper mapper = new ObjectMapper();
if (aa.getTargetValue() != null && aa.getTargetValue().length > 0) {
out.set(mapper.writeValueAsString(doTransform(aa)));
}
return out;
}
private AtomicAction<Relation> getRelationAtomicAction(String atomicaActionId) {
final String[] splitId = atomicaActionId.split("@");
String source = splitId[0];
String target = splitId[2];
String[] relSemantic = splitId[1].split("_");
Relation rel = new Relation();
rel.setSource(source);
rel.setTarget(target);
rel.setRelType(relSemantic[0]);
rel.setSubRelType(relSemantic[1]);
rel.setRelClass(relSemantic[2]);
DataInfo d = new DataInfo();
d.setDeletedbyinference(false);
d.setInferenceprovenance("deduplication");
d.setInferred(true);
d.setInvisible(false);
Qualifier provenanceaction = new Qualifier();
provenanceaction.setClassid("deduplication");
provenanceaction.setClassname("deduplication");
provenanceaction.setSchemeid("dnet:provenanceActions");
provenanceaction.setSchemename("dnet:provenanceActions");
d.setProvenanceaction(provenanceaction);
rel.setDataInfo(d);
return new AtomicAction<>(Relation.class, rel);
}
private AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa)
throws InvalidProtocolBufferException {
final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue());
final Oaf oaf = ProtoConverter.convert(proto_oaf);
switch (proto_oaf.getKind()) {
case entity:
switch (proto_oaf.getEntity().getType()) {
case datasource:
return new AtomicAction<>(Datasource.class, (Datasource) oaf);
case organization:
return new AtomicAction<>(Organization.class, (Organization) oaf);
case project:
return new AtomicAction<>(Project.class, (Project) oaf);
case result:
final String resulttypeid =
proto_oaf
.getEntity()
.getResult()
.getMetadata()
.getResulttype()
.getClassid();
switch (resulttypeid) {
case "publication":
return new AtomicAction<>(Publication.class, (Publication) oaf);
case "software":
return new AtomicAction<>(Software.class, (Software) oaf);
case "other":
return new AtomicAction<>(
OtherResearchProduct.class, (OtherResearchProduct) oaf);
case "dataset":
return new AtomicAction<>(Dataset.class, (Dataset) oaf);
default:
// can be an update, where the resulttype is not specified
return new AtomicAction<>(Result.class, (Result) oaf);
}
default:
throw new IllegalArgumentException(
"invalid entity type: " + proto_oaf.getEntity().getType());
}
case relation:
return new AtomicAction<>(Relation.class, (Relation) oaf);
default:
throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind());
}
}
private String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
String XQUERY =
"collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()";
return isLookUp.getResourceProfileByQuery(XQUERY);
}
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
SparkConf conf = new SparkConf();
return SparkSession.builder()
.appName(TransformActions.class.getSimpleName())
.master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
}
}

View File

@ -1,10 +0,0 @@
[
{"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true},
{"paramName":"sn", "paramLongName":"sourceNameNode", "paramDescription": "nameNode of the source cluster", "paramRequired": true},
{"paramName":"tn", "paramLongName":"targetNameNode", "paramDescription": "namoNode of the target cluster", "paramRequired": true},
{"paramName":"w", "paramLongName":"workingDirectory", "paramDescription": "working directory", "paramRequired": true},
{"paramName":"nm", "paramLongName":"distcp_num_maps", "paramDescription": "maximum number of map tasks used in the distcp process", "paramRequired": true},
{"paramName":"mm", "paramLongName":"distcp_memory_mb", "paramDescription": "memory for distcp action copying actionsets from remote cluster", "paramRequired": true},
{"paramName":"tt", "paramLongName":"distcp_task_timeout", "paramDescription": "timeout for distcp copying actions from remote cluster", "paramRequired": true},
{"paramName":"tr", "paramLongName":"transform_only", "paramDescription": "activate tranform-only mode. Only apply transformation step", "paramRequired": true}
]

View File

@ -1,5 +0,0 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true},
{"paramName":"i", "paramLongName":"inputPaths", "paramDescription": "URL of the isLookUp Service", "paramRequired": true}
]

View File

@ -14,9 +14,7 @@ import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
import org.apache.spark.SparkConf;
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.dom4j.Document;
@ -26,9 +24,6 @@ import org.dom4j.io.SAXReader;
abstract class AbstractSparkAction implements Serializable {
protected static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
protected static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
protected static final ObjectMapper OBJECT_MAPPER =
new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@ -89,29 +84,8 @@ abstract class AbstractSparkAction implements Serializable {
return SparkSession.builder().config(conf).getOrCreate();
}
protected static <T extends Oaf> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
dataset.map(
(MapFunction<T, String>) value -> OBJECT_MAPPER.writeValueAsString(value),
Encoders.STRING())
.write()
.option("compression", "gzip")
.mode(mode)
.text(outPath);
}
protected static DataInfo getDataInfo() {
DataInfo info = new DataInfo();
info.setDeletedbyinference(false);
info.setInferred(true);
info.setInvisible(false);
Qualifier provenanceAction = new Qualifier();
provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
info.setProvenanceaction(provenanceAction);
return info;
protected static <T> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
dataset.write().option("compression", "gzip").mode(mode).json(outPath);
}
protected static void removeOutputDir(SparkSession spark, String path) {

View File

@ -5,29 +5,29 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.pace.config.DedupConfig;
import java.util.Collection;
import java.util.Iterator;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
public class DedupRecordFactory {
private static final Logger log = LoggerFactory.getLogger(DedupRecordFactory.class);
protected static final ObjectMapper OBJECT_MAPPER =
new com.fasterxml.jackson.databind.ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
public static <T extends OafEntity> Dataset<T> createDedupRecord(
final SparkSession spark,
final String mergeRelsInputPath,
final String entitiesInputPath,
final Class<T> clazz,
final DedupConfig dedupConf) {
final Class<T> clazz) {
long ts = System.currentTimeMillis();
@ -54,40 +54,39 @@ public class DedupRecordFactory {
r -> new Tuple2<>(r.getSource(), r.getTarget()),
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
// <dedup_id, json_entity_merged>
return mergeRels
.joinWith(entities, mergeRels.col("_1").equalTo(entities.col("_1")), "left_outer")
.filter(
(FilterFunction<Tuple2<Tuple2<String, String>, Tuple2<String, T>>>)
value -> value._2() != null)
.joinWith(entities, mergeRels.col("_2").equalTo(entities.col("_1")), "inner")
.map(
(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, T>>, T>)
value -> value._2()._2(),
Encoders.kryo(clazz))
.groupByKey((MapFunction<T, String>) value -> value.getId(), Encoders.STRING())
(MapFunction<
Tuple2<Tuple2<String, String>, Tuple2<String, T>>,
Tuple2<String, T>>)
value -> new Tuple2<>(value._1()._1(), value._2()._2()),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)))
.groupByKey(
(MapFunction<Tuple2<String, T>, String>) entity -> entity._1(),
Encoders.STRING())
.mapGroups(
(MapGroupsFunction<String, T, T>)
(MapGroupsFunction<String, Tuple2<String, T>, T>)
(key, values) -> entityMerger(key, values, ts, clazz),
Encoders.bean(clazz));
}
private static <T extends OafEntity> T entityMerger(
String id, Iterator<T> entities, final long ts, Class<T> clazz) {
String id, Iterator<Tuple2<String, T>> entities, long ts, Class<T> clazz) {
try {
T entity = clazz.newInstance();
entity.setId(id);
if (entity.getDataInfo() == null) {
entity.setDataInfo(new DataInfo());
}
entity.getDataInfo().setTrust("0.9");
entity.setLastupdatetimestamp(ts);
final Collection<String> dates = Lists.newArrayList();
entities.forEachRemaining(
e -> {
entity.mergeFrom(e);
if (ModelSupport.isSubClass(e, Result.class)) {
Result r1 = (Result) e;
t -> {
T duplicate = t._2();
entity.mergeFrom(duplicate);
if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result r1 = (Result) duplicate;
Result er = (Result) entity;
er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor()));

View File

@ -11,6 +11,8 @@ import eu.dnetlib.pace.config.DedupConfig;
import java.io.IOException;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
@ -69,11 +71,14 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
save(
DedupRecordFactory.createDedupRecord(
spark, mergeRelPath, entityPath, clazz, dedupConf),
outputPath,
SaveMode.Overwrite);
DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz)
.map(
(MapFunction<OafEntity, String>)
value -> OBJECT_MAPPER.writeValueAsString(value),
Encoders.STRING())
.write()
.mode(SaveMode.Overwrite)
.json(outputPath);
}
}
}

View File

@ -6,6 +6,7 @@ import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent;
import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -34,7 +35,9 @@ import scala.Tuple2;
public class SparkCreateMergeRels extends AbstractSparkAction {
public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class);
public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
@ -145,13 +148,22 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
r.setRelClass(relClass);
r.setSubRelType("dedup");
DataInfo info = getDataInfo();
DataInfo info = new DataInfo();
info.setDeletedbyinference(false);
info.setInferred(true);
info.setInvisible(false);
info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
Qualifier provenanceAction = new Qualifier();
provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
info.setProvenanceaction(provenanceAction);
// TODO calculate the trust value based on the similarity score of the elements in the CC
// info.setTrust();
r.setDataInfo(getDataInfo());
r.setDataInfo(info);
return r;
}

View File

@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.dedup;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.dedup.model.Block;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -114,7 +115,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
r.setTarget(target);
r.setSubRelType("dedupSimilarity");
r.setRelClass("isSimilarTo");
r.setDataInfo(getDataInfo());
r.setDataInfo(new DataInfo());
switch (entity) {
case "result":

View File

@ -4,6 +4,7 @@ import static org.apache.spark.sql.functions.col;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -124,7 +125,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
return value -> {
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
if (rel.getDataInfo() == null) {
rel.setDataInfo(getDataInfo());
rel.setDataInfo(new DataInfo());
}
return rel;
};
@ -148,7 +149,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
Relation r = value._1()._2();
String id = value._2()._2();
if (r.getDataInfo() == null) {
r.setDataInfo(getDataInfo());
r.setDataInfo(new DataInfo());
}
r.getDataInfo().setDeletedbyinference(false);
switch (type) {
@ -172,7 +173,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
if (value._2() != null) {
Relation r = value._1()._2();
if (r.getDataInfo() == null) {
r.setDataInfo(getDataInfo());
r.setDataInfo(new DataInfo());
}
r.getDataInfo().setDeletedbyinference(true);
return r;

View File

@ -8,6 +8,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.util.MapDocumentUtil;
import java.io.File;
import java.io.IOException;
import java.io.Serializable;
@ -16,14 +17,20 @@ import java.nio.file.Paths;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension;
import scala.Tuple2;
@ExtendWith(MockitoExtension.class)
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
@ -41,7 +48,7 @@ public class SparkDedupTest implements Serializable {
private static final String testActionSetId = "test-orchestrator";
@BeforeAll
private static void cleanUp() throws IOException, URISyntaxException {
public static void cleanUp() throws IOException, URISyntaxException {
testGraphBasePath =
Paths.get(
@ -74,7 +81,7 @@ public class SparkDedupTest implements Serializable {
}
@BeforeEach
private void setUp() throws IOException, ISLookUpException {
public void setUp() throws IOException, ISLookUpException {
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
@ -96,6 +103,13 @@ public class SparkDedupTest implements Serializable {
IOUtils.toString(
SparkDedupTest.class.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
.thenReturn(
IOUtils.toString(
SparkDedupTest.class.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
}
@Test
@ -109,7 +123,6 @@ public class SparkDedupTest implements Serializable {
"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
parser.parseArgument(
new String[] {
"-mt", "local[*]",
"-i", testGraphBasePath,
"-asi", testActionSetId,
"-la", "lookupurl",
@ -126,9 +139,14 @@ public class SparkDedupTest implements Serializable {
spark.read()
.load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
.count();
long sw_simrel =
spark.read()
.load(testOutputBasePath + "/" + testActionSetId + "/software_simrel")
.count();
assertEquals(3288, orgs_simrel);
assertEquals(3432, orgs_simrel);
assertEquals(7260, pubs_simrel);
assertEquals(344, sw_simrel);
}
@Test
@ -142,7 +160,6 @@ public class SparkDedupTest implements Serializable {
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
parser.parseArgument(
new String[] {
"-mt", "local[*]",
"-i", testGraphBasePath,
"-asi", testActionSetId,
"-la", "lookupurl",
@ -159,9 +176,14 @@ public class SparkDedupTest implements Serializable {
spark.read()
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
.count();
long sw_mergerel =
spark.read()
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
.count();
assertEquals(1244, orgs_mergerel);
assertEquals(1276, orgs_mergerel);
assertEquals(1460, pubs_mergerel);
assertEquals(288, sw_mergerel);
}
@Test
@ -175,7 +197,6 @@ public class SparkDedupTest implements Serializable {
"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
parser.parseArgument(
new String[] {
"-mt", "local[*]",
"-i", testGraphBasePath,
"-asi", testActionSetId,
"-la", "lookupurl",
@ -198,9 +219,13 @@ public class SparkDedupTest implements Serializable {
+ testActionSetId
+ "/publication_deduprecord")
.count();
long sw_deduprecord =
jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord")
.count();
assertEquals(82, orgs_deduprecord);
assertEquals(66, pubs_deduprecord);
assertEquals(51, sw_deduprecord);
}
@Test
@ -214,7 +239,6 @@ public class SparkDedupTest implements Serializable {
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
parser.parseArgument(
new String[] {
"-mt", "local[*]",
"-i", testGraphBasePath,
"-w", testOutputBasePath,
"-o", testDedupGraphBasePath
@ -224,6 +248,9 @@ public class SparkDedupTest implements Serializable {
long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
long projects = jsc.textFile(testDedupGraphBasePath + "/project").count();
long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count();
long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count();
long mergedOrgs =
spark.read()
@ -245,13 +272,17 @@ public class SparkDedupTest implements Serializable {
.distinct()
.count();
assertEquals(897, publications);
assertEquals(831, publications);
assertEquals(835, organizations);
assertEquals(100, projects);
assertEquals(100, datasource);
assertEquals(200, softwares);
long deletedOrgs =
jsc.textFile(testDedupGraphBasePath + "/organization")
.filter(this::isDeletedByInference)
.count();
long deletedPubs =
jsc.textFile(testDedupGraphBasePath + "/publication")
.filter(this::isDeletedByInference)
@ -272,7 +303,6 @@ public class SparkDedupTest implements Serializable {
"/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
parser.parseArgument(
new String[] {
"-mt", "local[*]",
"-i", testGraphBasePath,
"-w", testOutputBasePath,
"-o", testDedupGraphBasePath
@ -283,6 +313,43 @@ public class SparkDedupTest implements Serializable {
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
assertEquals(826, relations);
// check deletedbyinference
final Dataset<Relation> mergeRels =
spark.read()
.load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*"))
.as(Encoders.bean(Relation.class));
final JavaPairRDD<String, String> mergedIds =
mergeRels
.where("relClass == 'merges'")
.select(mergeRels.col("target"))
.distinct()
.toJavaRDD()
.mapToPair(
(PairFunction<Row, String, String>)
r -> new Tuple2<String, String>(r.getString(0), "d"));
JavaRDD<String> toCheck =
jsc.textFile(testDedupGraphBasePath + "/relation")
.mapToPair(
json ->
new Tuple2<>(
MapDocumentUtil.getJPathString("$.source", json),
json))
.join(mergedIds)
.map(t -> t._2()._1())
.mapToPair(
json ->
new Tuple2<>(
MapDocumentUtil.getJPathString("$.target", json),
json))
.join(mergedIds)
.map(t -> t._2()._1());
long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
long updated = toCheck.count();
assertEquals(updated, deletedbyinference);
}
@AfterAll

View File

@ -0,0 +1,118 @@
{
"wf" : {
"threshold" : "0.99",
"dedupRun" : "001",
"entityType" : "result",
"subEntityType" : "resulttype",
"subEntityValue" : "dataset",
"orderField" : "title",
"queueMaxSize" : "2000",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "200",
"rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true"
},
"pace" : {
"clustering" : [
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree" : {
"start" : {
"fields": [
{
"field": "pid",
"comparator": "jsonListMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {
"jpath_value": "$.value",
"jpath_classid": "$.qualifier.classid"
}
}
],
"threshold": 0.5,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "layer2",
"undefined": "layer2",
"ignoreUndefined": "true"
},
"layer2" : {
"fields": [
{
"field": "title",
"comparator": "titleVersionMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
},
{
"field": "authors",
"comparator": "sizeMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 1.0,
"aggregation": "AND",
"positive": "layer3",
"negative": "NO_MATCH",
"undefined": "layer3",
"ignoreUndefined": "false"
},
"layer3" : {
"fields": [
{
"field": "title",
"comparator": "levensteinTitle",
"weight": 1.0,
"countIfUndefined": "true"
}
],
"threshold": 0.99,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
}
},
"model" : [
{
"name" : "doi",
"type" : "String",
"path" : "$.pid[@.qualifier.classid = 'doi'].value"
},
{
"name" : "pid",
"type" : "JSON",
"path" : "$.pid",
"overrideMatch" : "true"
},
{
"name" : "title",
"type" : "String",
"path" : "$.title[@.qualifier.classid = 'main title'].value",
"length" : 250,
"size" : 5
},
{
"name" : "authors",
"type" : "String",
"path" : "$.author[*].fullname",
"size" : 200
},
{
"name" : "resulttype",
"type" : "String",
"path" : "$.resulttype.classid"
}
],
"blacklists" : {},
"synonyms" : {}
}
}

View File

@ -0,0 +1,118 @@
{
"wf" : {
"threshold" : "0.99",
"dedupRun" : "001",
"entityType" : "result",
"subEntityType" : "resulttype",
"subEntityValue" : "otherresearchproduct",
"orderField" : "title",
"queueMaxSize" : "2000",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "200",
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true"
},
"pace" : {
"clustering" : [
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree" : {
"start" : {
"fields": [
{
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{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::97c2ec88f4aca7176ef1ac6c13f42cec", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::edadb7a520726c01cf2b5c0daecac464", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::f42cac35d9e8dd17b1a175afa512c13a", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::f6cf64f0efe65afec422b282218514b5", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::f7f3b7f8caf2520e2fcaa7f3a704ec03", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
{"subRelType": "affiliation", "relClass": "isAuthorInstitutionOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|doiboost____::29b88cdff7bd0a842b9c9f15f923bfc1", "lastupdatetimestamp": 0, "relType": "resultOrganization", "source": "20|microsoft___::fcc8d792603a72774ecbd9fe4504b3da", "collectedFrom": [{"dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "", "schemename": ""}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a", "value": "Microsoft Academic Graph"}]}
{"subRelType": "outcome", "relClass": "produces", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|erc_________::8511e17e153877fecd5a9a4ea8eb0969", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::07c370987d51b8273071fedf5931acf6"}
{"subRelType": "outcome", "relClass": "produces", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|erc_________::67b1c4d6876a12e265e965c1451a7f36", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::ae9a0c1b9384e04476ad3571d04be237"}
{"subRelType": "outcome", "relClass": "produces", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "50|od______1106::aabdb9c07beef7bdf7a93b6455f75e06", "lastupdatetimestamp": 0, "relType": "resultProject", "source": "40|corda_______::ae9a0c1b9384e04476ad3571d04be237"}

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@ -14,6 +14,7 @@
<SCAN_SEQUENCE>
<SCAN id="organization"/>
<SCAN id="publication"/>
<SCAN id="software"/>
</SCAN_SEQUENCE>
</DEDUPLICATION>
</CONFIGURATION>

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@ -2,8 +2,10 @@ package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang.StringUtils
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.JsonAST._
import org.json4s.jackson.JsonMethods._
import org.slf4j.Logger
@ -108,12 +110,58 @@ class Crossref2Oaf {
result.setLastupdatetimestamp((json \ "indexed" \ "timestamp").extract[Long])
result.setDateofcollection((json \ "indexed" \ "date-time").extract[String])
//result.setCollectedfrom()
result.setCollectedfrom(List(createCollectedFrom()).asJava)
// Publisher ( Name of work's publisher mapped into Result/Publisher)
val publisher = (json \ "publisher").extract[String]
result.setPublisher(asField(publisher))
// TITLE
val mainTitles = for {JString(title) <- json \ "title"} yield createSP(title, "main title", "dnet:dataCite_title")
val originalTitles = for {JString(title) <- json \ "original-title"} yield createSP(title, "alternative title", "dnet:dataCite_title")
val shortTitles = for {JString(title) <- json \ "short-title"} yield createSP(title, "alternative title", "dnet:dataCite_title")
result.setTitle((mainTitles ::: originalTitles ::: shortTitles).asJava)
// DESCRIPTION
val descriptionList = for {JString(description) <- json \ "abstract"} yield asField(description)
result.setDescription(descriptionList.asJava)
// Source
val sourceList = for {JString(source) <- json \ "source"} yield asField(source)
result.setSource(sourceList.asJava)
//RELEVANT DATE Mapping
val createdDate =generateDate((json \ "created" \"date-time").extract[String],(json \ "created"\"date-parts").extract[List[List[Int]]],"created", "dnet:dataCite_date" )
val postedDate =generateDate((json \ "posted" \"date-time").extractOrElse[String](null),(json \ "posted"\"date-parts").extract[List[List[Int]]],"available", "dnet:dataCite_date" )
val acceptedDate =generateDate((json \ "accepted" \"date-time").extractOrElse[String](null),(json \ "accepted"\"date-parts").extract[List[List[Int]]],"accepted", "dnet:dataCite_date" )
val publishedPrintDate =generateDate((json \ "published-print" \"date-time").extractOrElse[String](null),(json \ "published-print"\"date-parts").extract[List[List[Int]]],"published-print", "dnet:dataCite_date" )
val publishedOnlineDate =generateDate((json \ "published-online" \"date-time").extractOrElse[String](null),(json \ "published-online"\"date-parts").extract[List[List[Int]]],"published-online", "dnet:dataCite_date" )
result.setRelevantdate(List(createdDate ,postedDate, acceptedDate,publishedOnlineDate, publishedPrintDate).asJava)
result
}
def generateDate(dt: String, datePart: List[List[Int]], classId: String, schemeId: String): StructuredProperty = {
if (StringUtils.isNotBlank(dt))
return createSP(dt, classId, schemeId)
if (datePart != null && datePart.size == 1) {
val res = datePart.head
if (res.size == 3) {
val dp = f"${res.head}-${res(1)}%02d-${res(2)}%02d"
println(dp)
if (dp.length == 10) {
return createSP(dp, classId, schemeId)
}
}
}
null
}
def generateIdentifier(oaf: Result, doi: String): String = {
val id = DHPUtils.md5(doi.toLowerCase)
if (oaf.isInstanceOf[Dataset])
@ -121,6 +169,15 @@ class Crossref2Oaf {
s"50|${doiBoostNSPREFIX}${SEPARATOR}${id}"
}
def asField[T](value: T): Field[T] = {
val tmp = new Field[T]
tmp.setValue(value)
tmp
}
def generateDataInfo(): DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)
@ -140,6 +197,15 @@ class Crossref2Oaf {
}
def createCollectedFrom(): KeyValue = {
val cf = new KeyValue
cf.setValue(CROSSREF)
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5("crossref"))
cf
}
def createQualifier(cls: String, sch: String): Qualifier = {
val q = new Qualifier
q.setClassid(cls)

View File

@ -1,68 +1,107 @@
package eu.dnetlib.doiboost;
import static org.junit.jupiter.api.Assertions.*;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.doiboost.crossref.Crossref2Oaf;
import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF;
import java.io.IOException;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.junit.platform.commons.util.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.List;
public class DoiBoostTest {
Logger logger = LoggerFactory.getLogger(DoiBoostTest.class);
public void test() throws Exception {
// SparkDownloadContentFromCrossref.main(null);
//CrossrefImporter.main("-n file:///tmp -t file:///tmp/p.seq -ts 1586110000749".split(" "));
SparkMapDumpIntoOAF.main("-m local[*] -s file:///data/doiboost/crossref_dump.seq".split(" "));
// CrossrefImporter.main("-n file:///tmp -t file:///tmp/p.seq -ts 1586110000749".split("
// "));
SparkMapDumpIntoOAF.main(
"-m local[*] -s file:///data/doiboost/crossref_dump.seq".split(" "));
}
@Test
public void testConvertCrossRef2Oaf() throws IOException {
final String json = IOUtils.toString(getClass().getResourceAsStream("pc.json"));
ObjectMapper mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT);
Assertions.assertNotNull(json);
Assertions.assertFalse(StringUtils.isBlank(json));
assertNotNull(json);
assertFalse(StringUtils.isBlank(json));
Crossref2Oaf cf = new Crossref2Oaf();
final Result result = cf.convert(json, logger);
Assertions.assertNotNull(result);
assertNotNull(result);
assertNotNull(result.getDataInfo(), "Datainfo test not null Failed");
assertNotNull(
result.getDataInfo().getProvenanceaction(),
"DataInfo/Provenance test not null Failed");
assertFalse(
StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getClassid()),
"DataInfo/Provenance/classId test not null Failed");
assertFalse(
StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getClassname()),
"DataInfo/Provenance/className test not null Failed");
assertFalse(
StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getSchemeid()),
"DataInfo/Provenance/SchemeId test not null Failed");
assertFalse(
StringUtils.isBlank(result.getDataInfo().getProvenanceaction().getSchemename()),
"DataInfo/Provenance/SchemeName test not null Failed");
assertNotNull(result.getCollectedfrom(), "CollectedFrom test not null Failed");
assertTrue(result.getCollectedfrom().size() > 0);
assertTrue(
result.getCollectedfrom().stream()
.anyMatch(
c ->
c.getKey()
.equalsIgnoreCase(
"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")));
assertTrue(
result.getCollectedfrom().stream()
.anyMatch(c -> c.getValue().equalsIgnoreCase("crossref")));
assertTrue(
result.getRelevantdate().stream()
.anyMatch(d -> d.getQualifier().getClassid().equalsIgnoreCase("created")));
assertTrue(
result.getRelevantdate().stream()
.anyMatch(
d -> d.getQualifier().getClassid().equalsIgnoreCase("available")));
assertTrue(
result.getRelevantdate().stream()
.anyMatch(d -> d.getQualifier().getClassid().equalsIgnoreCase("accepted")));
assertTrue(
result.getRelevantdate().stream()
.anyMatch(
d ->
d.getQualifier()
.getClassid()
.equalsIgnoreCase("published-online")));
assertTrue(
result.getRelevantdate().stream()
.anyMatch(
d ->
d.getQualifier()
.getClassid()
.equalsIgnoreCase("published-print")));
logger.info(mapper.writeValueAsString(result));
}
@Test
public void testPath() throws Exception {
final String json = IOUtils.toString(getClass().getResourceAsStream("response.json"));
final List<String> res = JsonPath.read(json, "$.hits.hits[*]._source.blob");
System.out.println(res.size());
}
}

View File

@ -112,9 +112,35 @@
]
]
},
"published-print": {
"timestamp": 1446095513000,
"date-time": "2015-10-29T05:11:53Z",
"date-parts": [
[
2015,
2,
29
]
]
},
"published-online": {
"date-parts": [
[
2015,
2,
2
]
]
},
"title": [
"Genetic transformation of micropropagated shoots ofPinus radiataD.Don"
],
"original-title": [
"OR TITLE"
],
"short-title": [
"SHORT TITLE"
],
"group-title": "Plant Biology",
"subtype": "preprint"
}