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Merge pull request 'bipFinder at the level of the result' (#173) from bipFinder into beta 

Reviewed-on: #173
This commit is contained in:
Miriam Baglioni 2021-12-22 15:48:03 +01:00
parent 8d18500069 0807fdb65a
commit bf52a1847b
24 changed files with 152 additions and 1798 deletions
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86
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java
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@ -1,86 +0,0 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.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 com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.Result;
/**
* Just collects all the atomic actions produced for the different results and saves them in
* outputpath for the ActionSet
*/
public class CollectAndSave implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
Objects
.requireNonNull(
CollectAndSave.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.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);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
collectAndSave(spark, inputPath, outputPath);
});
}
private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
sc
.sequenceFile(inputPath + "/publication", Text.class, Text.class)
.union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class))
.union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class))
.union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
}

28
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java
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@ -1,28 +0,0 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
/**
* Subset of the information of the generic results that are needed to create the atomic action
*/
public class PreparedResult implements Serializable {
private String id; // openaire id
private String value; // doi
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

88
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java
View File

@ -1,6 +1,7 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import static eu.dnetlib.dhp.actionmanager.bipmodel.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
@ -15,7 +16,6 @@ import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
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;
@ -24,11 +24,15 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize;
import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import scala.Tuple2;
/**
@ -46,7 +50,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
.toString(
SparkAtomicActionScoreJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json"));
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
@ -65,14 +69,6 @@ public class SparkAtomicActionScoreJob implements Serializable {
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
final String bipScorePath = parser.get("bipScorePath");
log.info("bipScorePath: {}", bipScorePath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
Class<I> inputClazz = (Class<I>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
runWithSparkSession(
@ -80,12 +76,11 @@ public class SparkAtomicActionScoreJob implements Serializable {
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz);
prepareResults(spark, inputPath, outputPath);
});
}
private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath,
String bipScorePath, Class<I> inputClazz) {
private static <I extends Result> void prepareResults(SparkSession spark, String bipScorePath, String outputPath) {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -101,41 +96,19 @@ public class SparkAtomicActionScoreJob implements Serializable {
return bs;
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class));
Dataset<I> results = readPath(spark, inputPath, inputClazz);
results.createOrReplaceTempView("result");
Dataset<PreparedResult> preparedResult = spark
.sql(
"select pIde.value value, id " +
"from result " +
"lateral view explode (pid) p as pIde " +
"where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'")
.as(Encoders.bean(PreparedResult.class));
bipScores
.joinWith(
preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")),
"inner")
.map((MapFunction<Tuple2<BipScore, PreparedResult>, BipScore>) value -> {
BipScore ret = value._1();
ret.setId(value._2().getId());
return ret;
}, Encoders.bean(BipScore.class))
.groupByKey((MapFunction<BipScore, String>) BipScore::getId, Encoders.STRING())
.mapGroups((MapGroupsFunction<String, BipScore, Result>) (k, it) -> {
Result ret = new Result();
ret.setDataInfo(getDataInfo());
BipScore first = it.next();
ret.setId(first.getId());
ret.setMeasures(getMeasure(first));
it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value)));
.map((MapFunction<BipScore, Result>) bs -> {
Result ret = new Result();
ret.setId(bs.getId());
ret.setMeasures(getMeasure(bs));
return ret;
}, Encoders.bean(Result.class))
.toJavaRDD()
.map(p -> new AtomicAction(inputClazz, p))
.map(p -> new AtomicAction(Result.class, p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
@ -159,7 +132,21 @@ public class SparkAtomicActionScoreJob implements Serializable {
KeyValue kv = new KeyValue();
kv.setValue(unit.getValue());
kv.setKey(unit.getKey());
kv.setDataInfo(getDataInfo());
kv
.setDataInfo(
OafMapperUtils
.dataInfo(
false,
UPDATE_DATA_INFO_TYPE,
true,
false,
OafMapperUtils
.qualifier(
UPDATE_MEASURE_BIP_CLASS_ID,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
""));
return kv;
})
.collect(Collectors.toList()));
@ -168,21 +155,6 @@ public class SparkAtomicActionScoreJob implements Serializable {
.collect(Collectors.toList());
}
private static DataInfo getDataInfo() {
DataInfo di = new DataInfo();
di.setInferred(false);
di.setInvisible(false);
di.setDeletedbyinference(false);
di.setTrust("");
Qualifier qualifier = new Qualifier();
qualifier.setClassid("sysimport:actionset");
qualifier.setClassname("Harvested");
qualifier.setSchemename("dnet:provenanceActions");
qualifier.setSchemeid("dnet:provenanceActions");
di.setProvenanceaction(qualifier);
return di;
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/BipDeserialize.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
package eu.dnetlib.dhp.actionmanager.bipmodel;
import java.io.Serializable;
import java.util.ArrayList;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/BipScore.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
package eu.dnetlib.dhp.actionmanager.bipmodel;
import java.io.Serializable;
import java.util.List;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/Constants.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/Constants.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
package eu.dnetlib.dhp.actionmanager.bipmodel;
import java.util.Optional;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/KeyValue.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
package eu.dnetlib.dhp.actionmanager.bipmodel;
import java.io.Serializable;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/Score.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
package eu.dnetlib.dhp.actionmanager.bipmodel;
import java.io.Serializable;
import java.util.List;

10
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java
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@ -1,8 +1,8 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*;
import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.UPDATE_CLASS_NAME;
import static eu.dnetlib.dhp.actionmanager.bipmodel.Constants.*;
import static eu.dnetlib.dhp.actionmanager.bipmodel.Constants.UPDATE_CLASS_NAME;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
@ -11,7 +11,6 @@ import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.hdfs.client.HdfsUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
@ -24,8 +23,8 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.BipDeserialize;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.BipScore;
import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize;
import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelConstants;
@ -89,6 +88,7 @@ public class PrepareBipFinder implements Serializable {
BipScore bs = new BipScore();
bs.setId(key);
bs.setScoreList(entry.get(key));
return bs;
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class))
.map((MapFunction<BipScore, Result>) v -> {

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java
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@ -1,7 +1,7 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*;
import static eu.dnetlib.dhp.actionmanager.bipmodel.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java
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@ -1,7 +1,7 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*;
import static eu.dnetlib.dhp.actionmanager.bipmodel.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;

28
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipDeserialize.java
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@ -1,28 +0,0 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
/**
* Class that maps the model of the bipFinder! input data.
* Only needed for deserialization purposes
*/
public class BipDeserialize extends HashMap<String, List<Score>> implements Serializable {
public BipDeserialize() {
super();
}
public List<Score> get(String key) {
if (super.get(key) == null) {
return new ArrayList<>();
}
return super.get(key);
}
}

30
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipScore.java
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@ -1,30 +0,0 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
import java.io.Serializable;
import java.util.List;
/**
* Rewriting of the bipFinder input data by extracting the identifier of the result (doi)
*/
public class BipScore implements Serializable {
private String id; // doi
private List<Score> scoreList; // unit as given in the inputfile
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<Score> getScoreList() {
return scoreList;
}
public void setScoreList(List<Score> scoreList) {
this.scoreList = scoreList;
}
}

26
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/KeyValue.java
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@ -1,26 +0,0 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
import java.io.Serializable;
public class KeyValue implements Serializable {
private String key;
private String value;
public String getKey() {
return key;
}
public void setKey(String key) {
this.key = key;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

30
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/Score.java
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@ -1,30 +0,0 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
import java.io.Serializable;
import java.util.List;
/**
* represents the score in the input file
*/
public class Score implements Serializable {
private String id;
private List<KeyValue> unit;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<KeyValue> getUnit() {
return unit;
}
public void setUnit(List<KeyValue> unit) {
this.unit = unit;
}
}

32
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json
View File

@ -1,32 +0,0 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "rtn",
"paramLongName": "resultTableName",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "bsp",
"paramLongName": "bipScorePath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
]

30
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/config-default.xml Normal file
View File

@ -0,0 +1,30 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>hiveMetastoreUris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hiveJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
</property>
<property>
<name>hiveDbName</name>
<value>openaire</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

171
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml
View File

@ -13,8 +13,61 @@
<name>outputPath</name>
<description>the path where to store the actionset</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<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>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="deleteoutputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
@ -30,14 +83,8 @@
<error to="Kill"/>
</action>
<fork name="atomicactions">
<path start="atomicactions_publication"/>
<path start="atomicactions_dataset"/>
<path start="atomicactions_orp"/>
<path start="atomicactions_software"/>
</fork>
<action name="atomicactions_publication">
<action name="atomicactions">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
@ -54,118 +101,14 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/publication</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for datasets</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_orp">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for orp</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for software</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/software</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<join name="join_aa" to="collectandsave"/>
<action name="collectandsave">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>saves all the aa produced for the several types of results in the as output path</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.CollectAndSave</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${workingDir}</arg>
<arg>--inputPath</arg><arg>${bipScorePath}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

218
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java
View File

@ -28,6 +28,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Result;
public class SparkAtomicActionScoreJobTest {
@ -69,13 +70,9 @@ public class SparkAtomicActionScoreJobTest {
}
@Test
void matchOne() throws Exception {
void testMatch() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json")
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores_oid.json")
.getPath();
SparkAtomicActionScoreJob
@ -84,234 +81,57 @@ public class SparkAtomicActionScoreJobTest {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
JavaRDD<Result> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
.map(aa -> ((Result) aa.getPayload()));
assertEquals(1, tmp.count());
assertEquals(4, tmp.count());
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Result> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Result.class));
verificationDataset.createOrReplaceTempView("result");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"Select p.id oaid, mes.id, mUnit.value from result p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(2, execVerification.count());
Assertions.assertEquals(12, execVerification.count());
Assertions
.assertEquals(
"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb",
execVerification.select("oaid").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
"1.47565045883e-08",
execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
"0.227515392",
execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0));
}
@Test
void matchOneWithTwo() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json")
.getPath();
SparkAtomicActionScoreJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
assertEquals(1, tmp.count());
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(4, execVerification.count());
Assertions
.assertEquals(
"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb",
execVerification.select("oaid").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
2,
execVerification.filter("id = 'influence'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'popularity'").count());
List<Row> tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList();
String tmp_influence = tmp_ds.get(0).getString(0);
assertTrue(
"1.47565045883e-08".equals(tmp_influence) ||
"1.98956540239e-08".equals(tmp_influence));
tmp_influence = tmp_ds.get(1).getString(0);
assertTrue(
"1.47565045883e-08".equals(tmp_influence) ||
"1.98956540239e-08".equals(tmp_influence));
assertNotEquals(tmp_ds.get(1).getString(0), tmp_ds.get(0).getString(0));
}
@Test
void matchTwo() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json")
.getPath();
SparkAtomicActionScoreJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
assertEquals(2, tmp.count());
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(4, execVerification.count());
Assertions
.assertEquals(
2,
execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count());
Assertions
.assertEquals(
2,
execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'influence'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'popularity'").count());
Assertions
.assertEquals(
"1.47565045883e-08",
execVerification
"6.63451994567e-09", execVerification
.filter(
"oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " +
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
"and id = 'influence'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"1.98956540239e-08",
execVerification
"0.348694533145", execVerification
.filter(
"oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " +
"and id = 'influence'")
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
"and id = 'popularity_alt'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"0.282046161584",
execVerification
"2.16094680115e-09", execVerification
.filter(
"oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " +
"and id = 'popularity'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"0.227515392",
execVerification
.filter(
"oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " +
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
"and id = 'popularity'")
.select("value")
.collectAsList()

1101
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json
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4
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores_oid.json Normal file
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@ -0,0 +1,4 @@
{"50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1": [{"id": "influence", "unit": [{"value": "6.63451994567e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.348694533145", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "2.16094680115e-09", "key": "score"}]}]}
{"50|dedup_wf_001::05b1f8ce98702f69d07aa5f0429de1e3": [{"id": "influence", "unit": [{"value": "6.25057357279e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "7.0208", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "2.40234462244e-08", "key": "score"}]}]}
{"50|dedup_wf_001::08823c8f5c3ca2eae523817036cdda67": [{"id": "influence", "unit": [{"value": "5.54921449123e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "3.53012887452e-10", "key": "score"}]}]}
{"50|dedup_wf_001::0e72b399325d6efcbe3271891a1dfe4c": [{"id": "influence", "unit": [{"value": "1.63466096315e-08", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "20.9870879741", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "5.49501495323e-08", "key": "score"}]}]}

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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json
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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json
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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json
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