This commit is contained in:
Miriam Baglioni 2023-05-02 15:47:06 +02:00
parent 6ba43a1b67
commit 011b7737ad
7 changed files with 856 additions and 210 deletions

View File

@ -8,6 +8,7 @@ import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
@ -65,21 +66,21 @@ public class SparkDumpCommunityProducts implements Serializable {
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
String communityMapPath = parser.get("communityMapPath");
String communityMapPath = Optional
.ofNullable(parser.get("communityMapPath"))
.orElse(null);
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
String finalCommunityMapPath = communityMapPath;
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
resultDump(
spark, inputPath, outputPath, finalCommunityMapPath, inputClazz);
spark, inputPath, outputPath, communityMapPath, inputClazz);
});
}
@ -91,12 +92,15 @@ public class SparkDumpCommunityProducts implements Serializable {
String communityMapPath,
Class<I> inputClazz) {
CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
CommunityMap communityMap = null;
if (!StringUtils.isEmpty(communityMapPath))
communityMap = Utils.getCommunityMap(spark, communityMapPath);
CommunityMap finalCommunityMap = communityMap;
Utils
.readPath(spark, inputPath, inputClazz)
.map(
(MapFunction<I, CommunityResult>) value -> execMap(value, communityMap),
(MapFunction<I, CommunityResult>) value -> execMap(value, finalCommunityMap),
Encoders.bean(CommunityResult.class))
.filter((FilterFunction<CommunityResult>) value -> value != null)
.map(
@ -119,26 +123,27 @@ public class SparkDumpCommunityProducts implements Serializable {
|| Boolean.TRUE.equals(odInfo.get().getInvisible())) {
return null;
}
Set<String> communities = communityMap.keySet();
if (communityMap != null) {
Set<String> communities = communityMap.keySet();
Optional<List<Context>> inputContext = Optional
.ofNullable(((eu.dnetlib.dhp.schema.oaf.Result) value).getContext());
if (!inputContext.isPresent()) {
return null;
}
List<String> toDumpFor = inputContext.get().stream().map(c -> {
if (communities.contains(c.getId())) {
return c.getId();
Optional<List<Context>> inputContext = Optional
.ofNullable(((eu.dnetlib.dhp.schema.oaf.Result) value).getContext());
if (!inputContext.isPresent()) {
return null;
}
if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) {
return c.getId().substring(0, c.getId().indexOf("::"));
List<String> toDumpFor = inputContext.get().stream().map(c -> {
if (communities.contains(c.getId())) {
return c.getId();
}
if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) {
return c.getId().substring(0, c.getId().indexOf("::"));
}
return null;
}).filter(Objects::nonNull).collect(Collectors.toList());
if (toDumpFor.isEmpty()) {
return null;
}
return null;
}).filter(Objects::nonNull).collect(Collectors.toList());
if (toDumpFor.isEmpty()) {
return null;
}
return (O) ResultMapper.map(value, communityMap, Constants.DUMPTYPE.COMMUNITY.getType());
}

View File

@ -1,9 +1,29 @@
package eu.dnetlib.dhp.oa.graph.dump.country;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.*;
import javax.rmi.CORBA.Util;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Constants;
import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
@ -17,119 +37,100 @@ import eu.dnetlib.dhp.oa.graph.dump.subset.selectionconstraints.SelectionConstra
import eu.dnetlib.dhp.oa.model.graph.GraphResult;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import org.apache.commons.io.IOUtils;
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.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
import javax.rmi.CORBA.Util;
import java.io.Serializable;
import java.util.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
/**
* @author miriam.baglioni
* @Date 27/04/23
* Selects the results having in the country the given country
*/
public class SparkFindResultWithCountry implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkFindResultWithCountry.class);
private static final Logger log = LoggerFactory.getLogger(SparkFindResultWithCountry.class);
public static final String COMPRESSION = "compression";
public static final String GZIP = "gzip";
public static final String COMPRESSION = "compression";
public static final String GZIP = "gzip";
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkFindResultWithCountry.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json"));
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkFindResultWithCountry.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/result_country_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
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);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String resultType = parser.get("resultType");
log.info("resultType: {}", resultType);
final String resultType = parser.get("resultType");
log.info("resultType: {}", resultType);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final String preparedInfoPath = parser.get("resultWithCountry");
Class<? extends eu.dnetlib.dhp.schema.oaf.Result> inputClazz = (Class<? extends eu.dnetlib.dhp.schema.oaf.Result>) Class
.forName(resultClassName);
final String preparedInfoPath = parser.get("resultWithCountry");
run(
isSparkSessionManaged, inputPath, outputPath, inputClazz,
resultType, preparedInfoPath);
}
private static void run(Boolean isSparkSessionManaged, String inputPath, String outputPath,
Class<? extends eu.dnetlib.dhp.schema.oaf.Result> inputClazz = (Class<? extends eu.dnetlib.dhp.schema.oaf.Result>) Class
.forName(resultClassName);
Class<? extends eu.dnetlib.dhp.schema.oaf.Result> inputClazz, String resultType, String preparedInfoPath) {
SparkConf conf = new SparkConf();
run(
isSparkSessionManaged, inputPath, outputPath, inputClazz,
resultType, preparedInfoPath);
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath + "/original/" + resultType);
}
resultDump(
spark, inputPath, outputPath, inputClazz, resultType, preparedInfoPath);
});
private static void run(Boolean isSparkSessionManaged, String inputPath, String outputPath,
}
Class<? extends eu.dnetlib.dhp.schema.oaf.Result> inputClazz, String resultType, String preparedInfoPath) {
SparkConf conf = new SparkConf();
public static <I extends eu.dnetlib.dhp.schema.oaf.Result> void resultDump(
SparkSession spark,
String inputPath,
String outputPath,
Class<I> inputClazz,
String resultType,
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath + "/original/" + resultType);
String preparedInfoPath) {
resultDump(
spark, inputPath, outputPath, inputClazz, resultType, preparedInfoPath);
});
Dataset<String> resultsWithCountry = spark.read().textFile(preparedInfoPath).distinct();
}
Dataset<I> result = Utils
.readPath(spark, inputPath, inputClazz)
.filter(
(FilterFunction<I>) r -> !r.getDataInfo().getInvisible() && !r.getDataInfo().getDeletedbyinference());
public static <I extends eu.dnetlib.dhp.schema.oaf.Result> void resultDump(
SparkSession spark,
String inputPath,
String outputPath,
Class<I> inputClazz,
resultsWithCountry
.joinWith(result, resultsWithCountry.col("value").equalTo(result.col("id")))
.map((MapFunction<Tuple2<String, I>, I>) t2 -> t2._2(), Encoders.bean(inputClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + "/original/" + resultType);
String resultType,
String preparedInfoPath) {
Dataset<String> resultsWithCountry = Utils.readPath(spark, preparedInfoPath, String.class).distinct();
Dataset<I> result = Utils
.readPath(spark, inputPath, inputClazz);
resultsWithCountry.joinWith(result, resultsWithCountry.col("value").equalTo(result.col("id")))
.map((MapFunction<Tuple2<String,I>, I>) t2 -> t2._2(), Encoders.bean(inputClazz) )
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + "/original/" + resultType);
}
}
}

View File

@ -1,9 +1,12 @@
package eu.dnetlib.dhp.oa.graph.dump.country;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.io.StringReader;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -19,14 +22,13 @@ import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;
import java.io.Serializable;
import java.io.StringReader;
import java.util.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
/**
* @author miriam.baglioni
* @Date 27/04/23
@ -34,124 +36,136 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
* or that have that country in the country list
*/
public class SparkFindResultsRelatedToCountry implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkFindResultsRelatedToCountry.class);
private static final Logger log = LoggerFactory.getLogger(SparkFindResultsRelatedToCountry.class);
public static final String COMPRESSION = "compression";
public static final String GZIP = "gzip";
public static final String COMPRESSION = "compression";
public static final String GZIP = "gzip";
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkFindResultsRelatedToCountry.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json"));
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkFindResultsRelatedToCountry.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/result_related_country_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
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);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String country = parser.get("country");
final String country = parser.get("country");
run(
isSparkSessionManaged, inputPath, outputPath, country);
}
run(
isSparkSessionManaged, inputPath, outputPath, country);
private static void run(Boolean isSparkSessionManaged, String inputPath, String outputPath,
String country) {
SparkConf conf = new SparkConf();
}
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
findRelatedEntities(
spark, inputPath, outputPath, country);
});
private static void run(Boolean isSparkSessionManaged, String inputPath, String outputPath,
String country) {
SparkConf conf = new SparkConf();
}
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
findRelatedEntities(
spark, inputPath, outputPath, country);
});
public static <I extends eu.dnetlib.dhp.schema.oaf.Result> void findRelatedEntities(
SparkSession spark,
String inputPath,
String outputPath,
String country) {
}
Dataset<Project> projectsInCountry = Utils
.readPath(spark, inputPath + "/project", Project.class)
.filter((FilterFunction<Project>) p -> isCountryInFunderJurisdiction(p.getFundingtree(), country));
public static <I extends eu.dnetlib.dhp.schema.oaf.Result> void findRelatedEntities(
SparkSession spark,
String inputPath,
String outputPath,
String country) {
Dataset<Relation> relsProjectResults = Utils
.readPath(spark, inputPath + "/relation", Relation.class)
.filter(
(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
r.getRelClass().equals(ModelConstants.PRODUCES));
Dataset<Project> projectsInCountry = Utils.readPath(spark, inputPath + "/project", Project.class)
.filter((FilterFunction<Project>) p -> isCountryInFunderJurisdiction(p.getFundingtree(), country));
projectsInCountry
.joinWith(relsProjectResults, projectsInCountry.col("id").equalTo(relsProjectResults.col("source")))
.map((MapFunction<Tuple2<Project, Relation>, String>) t2 -> t2._2().getTarget(), Encoders.STRING())
.write()
.option(COMPRESSION, GZIP)
.mode(SaveMode.Overwrite)
.text(outputPath);
Dataset<Relation> relsProjectResults = Utils.readPath(spark, inputPath + "/relation", Relation.class)
.filter((FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
r.getRelClass().equals(ModelConstants.PRODUCES));
Dataset<Organization> organizationsInCountry = Utils
.readPath(spark, inputPath + "/organization", Organization.class)
.filter((FilterFunction<Organization>) o -> o.getCountry().getClassid().equals(country));
projectsInCountry.joinWith(relsProjectResults, projectsInCountry.col("id").equalTo(relsProjectResults.col("source")))
.map((MapFunction<Tuple2<Project, Relation>, String>) t2 -> t2._2().getTarget(), Encoders.STRING())
.write()
.option(COMPRESSION, GZIP)
.mode(SaveMode.Overwrite)
.json(outputPath );
Dataset<Relation> relsOrganizationResults = Utils
.readPath(spark, inputPath + "/relation", Relation.class)
.filter(
(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
r.getRelClass().equals(ModelConstants.HAS_AUTHOR_INSTITUTION));
organizationsInCountry
.joinWith(
relsOrganizationResults,
organizationsInCountry.col("id").equalTo(relsOrganizationResults.col("source")))
.map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getTarget(), Encoders.STRING())
.write()
.option(COMPRESSION, GZIP)
.mode(SaveMode.Append)
.text(outputPath);
Dataset<Organization> organizationsInCountry = Utils.readPath(spark, inputPath + "/organization", Organization.class)
.filter((FilterFunction<Organization>) o -> o.getCountry().getClassid().equals(country));
selectResultWithCountry(spark, inputPath, outputPath, country, "publication", Publication.class);
selectResultWithCountry(
spark, inputPath, outputPath, country, "dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
selectResultWithCountry(spark, inputPath, outputPath, country, "software", Software.class);
selectResultWithCountry(
spark, inputPath, outputPath, country, "otherresearchproduct", OtherResearchProduct.class);
Dataset<Relation> relsOrganizationResults = Utils.readPath(spark, inputPath + "/relation", Relation.class)
.filter((FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
r.getRelClass().equals(ModelConstants.IS_AUTHOR_INSTITUTION_OF));
}
organizationsInCountry.joinWith(relsOrganizationResults, organizationsInCountry.col("id").equalTo(relsOrganizationResults.col("source")))
.map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getTarget(), Encoders.STRING())
.write()
.option(COMPRESSION, GZIP)
.mode(SaveMode.Append)
.json(outputPath );
selectResultWithCountry(spark, inputPath, outputPath, country, "publication", Publication.class);
selectResultWithCountry(spark, inputPath, outputPath, country, "dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
selectResultWithCountry(spark, inputPath, outputPath, country, "software", Software.class);
selectResultWithCountry(spark, inputPath, outputPath, country, "otherresearchproduct", OtherResearchProduct.class);
}
private static <R extends Result> void selectResultWithCountry(SparkSession spark, String inputPath, String outputPath, String country, String type, Class<R> inputClazz) {
Utils.readPath(spark, inputPath + "/" + type, inputClazz)
.filter((FilterFunction<R>) p -> !p.getDataInfo().getDeletedbyinference() && !p.getDataInfo().getInvisible() &&
p.getCountry().stream().anyMatch(c -> c.getClassid().equals(country)))
.map((MapFunction<R, String>) p -> p.getId(), Encoders.STRING() )
.write()
.option(COMPRESSION, GZIP)
.mode(SaveMode.Append)
.json(outputPath);
}
private static boolean isCountryInFunderJurisdiction(List<Field<String>> fundingtrees, String country) {
try {
final SAXReader reader = new SAXReader();
reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
for (Field<String> fundingtree: fundingtrees){
final Document doc = reader.read(new StringReader(fundingtree.getValue()));
if(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText().equals(country)){
return true;
}
}
return false;
} catch (DocumentException | SAXException e) {
throw new IllegalArgumentException(e);
}
}
private static <R extends Result> void selectResultWithCountry(SparkSession spark, String inputPath,
String outputPath, String country, String type, Class<R> inputClazz) {
Utils
.readPath(spark, inputPath + "/" + type, inputClazz)
.filter(
(FilterFunction<R>) p -> !p.getDataInfo().getDeletedbyinference() && !p.getDataInfo().getInvisible() &&
p.getCountry() != null &&
p.getCountry().stream().anyMatch(c -> c.getClassid().equals(country)))
.map((MapFunction<R, String>) p -> p.getId(), Encoders.STRING())
.write()
.option(COMPRESSION, GZIP)
.mode(SaveMode.Append)
.text(outputPath);
}
private static boolean isCountryInFunderJurisdiction(List<Field<String>> fundingtrees, String country) {
try {
final SAXReader reader = new SAXReader();
reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
for (Field<String> fundingtree : fundingtrees) {
final Document doc = reader.read(new StringReader(fundingtree.getValue()));
if (((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText().equals(country)) {
return true;
}
}
return false;
} catch (DocumentException | SAXException e) {
throw new IllegalArgumentException(e);
}
}
}

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@ -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>

View File

@ -0,0 +1,525 @@
<workflow-app name="sub-dump_subset" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
<property>
<name>country</name>
<description>the country for which to produce the dump</description>
</property>
<property>
<name>hiveDbName</name>
<description>the target hive database name</description>
</property>
<property>
<name>hiveJdbcUrl</name>
<description>hive server jdbc url</description>
</property>
<property>
<name>hiveMetastoreUris</name>
<description>hive server metastore URIs</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>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="save_community_map" />
<action name="save_community_map">
<java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap</main-class>
<arg>--outputPath</arg><arg>${workingDir}/communityMap</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</java>
<ok to="find_results_for_country"/>
<error to="Kill"/>
</action>
<action name="find_results_for_country">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table publication </name>
<class>eu.dnetlib.dhp.oa.graph.dump.country.SparkFindResultsRelatedToCountry</class>
<jar>dump-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${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>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/resultsInCountry</arg>
<arg>--country</arg><arg>${country}</arg>
</spark>
<ok to="fork_select"/>
<error to="Kill"/>
</action>
<fork name="fork_select">
<path start="select_publication"/>
<path start="select_dataset"/>
<path start="select_orp"/>
<path start="select_software"/>
</fork>
<action name="select_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table publication </name>
<class>eu.dnetlib.dhp.oa.graph.dump.country.SparkFindResultWithCountry</class>
<jar>dump-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=7G
--executor-cores=2
--driver-memory=7G
--conf spark.sql.shuffle.partitions=3840
--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>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--resultWithCountry</arg><arg>${workingDir}/resultsInCountry</arg>
<arg>--resultType</arg><arg>publication</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="select_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table dataset </name>
<class>eu.dnetlib.dhp.oa.graph.dump.country.SparkFindResultWithCountry</class>
<jar>dump-${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=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--resultType</arg><arg>dataset</arg>
<arg>--resultWithCountry</arg><arg>${workingDir}/resultsInCountry</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="select_orp">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table ORP </name>
<class>eu.dnetlib.dhp.oa.graph.dump.country.SparkFindResultWithCountry</class>
<jar>dump-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${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>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--resultType</arg><arg>otherresearchproduct</arg>
<arg>--resultWithCountry</arg><arg>${workingDir}/resultsInCountry</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="select_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table software </name>
<class>eu.dnetlib.dhp.oa.graph.dump.country.SparkFindResultWithCountry</class>
<jar>dump-${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=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--resultType</arg><arg>software</arg>
<arg>--resultWithCountry</arg><arg>${workingDir}/resultsInCountry</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<join name="join_dump" to="select_subset"/>
<action name="select_subset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Select valid table relation </name>
<class>eu.dnetlib.dhp.oa.graph.dump.subset.SparkSelectSubset</class>
<jar>dump-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${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}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--removeSet</arg><arg>${removeSet}</arg>
</spark>
<ok to="fork_dump_community"/>
<error to="Kill"/>
</action>
<fork name="fork_dump_community">
<path start="dump_publication"/>
<path start="dump_dataset"/>
<path start="dump_orp"/>
<path start="dump_software"/>
</fork>
<action name="dump_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table publication for community/funder related products</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
<jar>dump-${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=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}/original/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/dump/publication</arg>
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
</spark>
<ok to="join_dump_comm"/>
<error to="Kill"/>
</action>
<action name="dump_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table dataset for community/funder related products</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
<jar>dump-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${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>--sourcePath</arg><arg>${outputPath}/original/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/dump/dataset</arg>
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
</spark>
<ok to="join_dump_comm"/>
<error to="Kill"/>
</action>
<action name="dump_orp">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table ORP for community related products</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
<jar>dump-${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=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}/original/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/dump/otherresearchproduct</arg>
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
</spark>
<ok to="join_dump_comm"/>
<error to="Kill"/>
</action>
<action name="dump_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table software for community related products</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
<jar>dump-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${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>--sourcePath</arg><arg>${outputPath}/original/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/dump/software</arg>
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
</spark>
<ok to="join_dump_comm"/>
<error to="Kill"/>
</action>
<join name="join_dump_comm" to="prepareResultProject"/>
<action name="prepareResultProject">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Prepare association result subset of project info</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject</class>
<jar>dump-${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=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}/original</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark>
<ok to="fork_extendWithProject"/>
<error to="Kill"/>
</action>
<fork name="fork_extendWithProject">
<path start="extend_publication"/>
<path start="extend_dataset"/>
<path start="extend_orp"/>
<path start="extend_software"/>
</fork>
<action name="extend_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extend dumped publications with information about project</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
<jar>dump-${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=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/dump/publication</arg>
<arg>--outputPath</arg><arg>${outputPath}/dump/publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark>
<ok to="join_extend"/>
<error to="Kill"/>
</action>
<action name="extend_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extend dumped dataset with information about project</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
<jar>dump-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${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>--sourcePath</arg><arg>${workingDir}/dump/dataset</arg>
<arg>--outputPath</arg><arg>${outputPath}/dump/dataset</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark>
<ok to="join_extend"/>
<error to="Kill"/>
</action>
<action name="extend_orp">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extend dumped ORP with information about project</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
<jar>dump-${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=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/dump/otherresearchproduct</arg>
<arg>--outputPath</arg><arg>${outputPath}/dump/otherresearchproduct</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark>
<ok to="join_extend"/>
<error to="Kill"/>
</action>
<action name="extend_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extend dumped software with information about project</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
<jar>dump-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${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>--sourcePath</arg><arg>${workingDir}/dump/software</arg>
<arg>--outputPath</arg><arg>${outputPath}/dump/software</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark>
<ok to="join_extend"/>
<error to="Kill"/>
</action>
<join name="join_extend" to="End"/>
<kill name="Kill">
<message>Sub-workflow dump complete failed with error message ${wf:errorMessage()}
</message>
</kill>
<end name="End" />
</workflow-app>

View File

@ -0,0 +1,42 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName": "c",
"paramLongName": "resultWithCountry",
"paramDescription": "the path of the id of results associated to a given country",
"paramRequired": true
},
{
"paramName":"tn",
"paramLongName":"resultTableName",
"paramDescription": "the name of the result table we are currently working on",
"paramRequired": true
},
{
"paramName":"rt",
"paramLongName":"resultType",
"paramDescription": "",
"paramRequired": true
}
]

View File

@ -0,0 +1,29 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName": "c",
"paramLongName": "country",
"paramDescription": "the path of the association result projectlist",
"paramRequired": true
}
]