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9559_DBLP_
| Author | SHA1 | Date |
|---|---|---|
Serafeim Chatzopoulos
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842b309922 | |
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Serafeim Chatzopoulos
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b6e4d58817 |
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@ -0,0 +1,113 @@
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package eu.dnetlib.dhp.actionmanager.dblp;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.Arrays;
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import java.util.List;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.Dataset;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.Constants;
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import eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import scala.Tuple2;
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/**
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* Creates action sets for DBLP data
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*/
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public class PrepareDblpActionSets implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(PrepareDblpActionSets.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String ID_PREFIX = "50|doi_________::";
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public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
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public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
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public static final String BIP_INFERENCE_PROVENANCE = "bip:affiliation:crossref";
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public static <I extends Result> void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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PrepareDblpActionSets.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/dblp/input_actionset_parameter.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String dblpInputPath = parser.get("dblpInputPath");
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log.info("dblpInputPath: {}", dblpInputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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Constants.removeOutputDir(spark, outputPath);
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// TODO: add DBLP ID in ModelConstants
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List<KeyValue> collectedFromDBLP = OafMapperUtils
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.listKeyValues(ModelConstants.CROSSREF_ID, "DBLP");
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JavaPairRDD<Text, Text> dblpData = prepareDblpData(
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spark, dblpInputPath, collectedFromDBLP);
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dblpData
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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});
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}
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private static <I extends Result> JavaPairRDD<Text, Text> prepareDblpData(SparkSession spark,
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String inputPath,
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List<KeyValue> collectedFrom) {
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log.info("Reading DBLP XML data");
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//
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// TODO: load DBLP data into a Dataset
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Dataset<Row> df = spark
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.read()
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.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
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.json(inputPath);
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return df.map((MapFunction<Row, Result>) bs -> {
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Result result = new Result();
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// TODO: map DBLP data to Result objects
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return result;
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}, Encoders.bean(Result.class))
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.toJavaRDD()
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.map(p -> new AtomicAction(Result.class, p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))));
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}
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}
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@ -0,0 +1,20 @@
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[
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "when true will stop SparkSession after job execution",
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"paramRequired": false
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},
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{
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"paramName": "dip",
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"paramLongName": "dblpInputPath",
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"paramDescription": "the path to get the input data from DBLP",
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"paramRequired": true
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},
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{
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"paramName": "o",
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"paramLongName": "outputPath",
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"paramDescription": "the path of the new ActionSet",
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"paramRequired": true
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}
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]
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@ -0,0 +1,35 @@
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# --- You can override the following properties (if needed) coming from your ~/.dhp/application.properties ---
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# dhp.hadoop.frontend.temp.dir=/home/ilias.kanellos
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# dhp.hadoop.frontend.user.name=ilias.kanellos
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# dhp.hadoop.frontend.host.name=iis-cdh5-test-gw.ocean.icm.edu.pl
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# dhp.hadoop.frontend.port.ssh=22
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# oozieServiceLoc=http://iis-cdh5-test-m3:11000/oozie
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# jobTracker=yarnRM
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# nameNode=hdfs://nameservice1
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# oozie.execution.log.file.location = target/extract-and-run-on-remote-host.log
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# maven.executable=mvn
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# Some memory and driver settings for more demanding tasks
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sparkDriverMemory=10G
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sparkExecutorMemory=10G
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sparkExecutorCores=4
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sparkShufflePartitions=7680
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# The above is given differently in an example I found online
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oozie.action.sharelib.for.spark=spark2
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oozieActionShareLibForSpark2=spark2
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spark2YarnHistoryServerAddress=http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089
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spark2EventLogDir=/user/spark/spark2ApplicationHistory
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sparkSqlWarehouseDir=/user/hive/warehouse
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hiveMetastoreUris=thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083
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# This MAY avoid the no library used error
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oozie.use.system.libpath=true
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# Some stuff copied from openaire's jobs
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spark2ExtraListeners=com.cloudera.spark.lineage.NavigatorAppListener
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spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListener
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# The following is needed as a property of a workflow
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oozie.wf.application.path=${oozieTopWfApplicationPath}
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dblpInputPath=/data/dblp/dblp.xml.gz
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outputPath=/tmp/dblp-actionsets
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@ -0,0 +1,30 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>hiveMetastoreUris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>hiveJdbcUrl</name>
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<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
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</property>
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<property>
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<name>hiveDbName</name>
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<value>openaire</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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</configuration>
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@ -0,0 +1,107 @@
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<workflow-app name="BipAffiliations" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>dblpInputPath</name>
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<description>the path where to find the input data from DBLP</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the path where to store the actionset</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>oozieActionShareLibForSpark2</name>
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<description>oozie action sharelib for spark 2.*</description>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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<description>spark 2.* extra listeners classname</description>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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<description>spark 2.* sql query execution listeners classname</description>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<description>spark 2.* yarn history server address</description>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<description>spark 2.* event log dir location</description>
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</property>
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</parameters>
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="deleteoutputpath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="deleteoutputpath">
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<fs>
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<delete path="${outputPath}"/>
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<mkdir path="${outputPath}"/>
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<delete path="${workingDir}"/>
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<mkdir path="${workingDir}"/>
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</fs>
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<ok to="atomicactions"/>
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<error to="Kill"/>
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</action>
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<action name="atomicactions">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Produces the atomic action sets with the DBLP data</name>
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<class>eu.dnetlib.dhp.actionmanager.dblp.PrepareDblpActionSets</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--dblpInputPath</arg><arg>${dblpInputPath}</arg>
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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@ -0,0 +1,202 @@
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package eu.dnetlib.dhp.actionmanager.dblp;
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import static org.junit.jupiter.api.Assertions.*;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import javax.xml.crypto.Data;
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import eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob;
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import eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJobTest;
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import org.apache.commons.io.FileUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.Row;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Project;
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import eu.dnetlib.dhp.schema.oaf.Result;
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public class PrepareDblpActionSetsTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static SparkSession spark;
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private static Path workingDir;
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private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJobTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files
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.createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(SparkAtomicActionScoreJobTest.class.getSimpleName());
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conf.setMaster("local[*]");
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conf.set("spark.driver.host", "localhost");
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conf.set("hive.metastore.local", "true");
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conf.set("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
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spark = SparkSession
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.builder()
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.appName(SparkAtomicActionScoreJobTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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private void runJob(String dblpInputPath, String outputPath) throws Exception {
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PrepareDblpActionSets
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-dblpInputPath", dblpInputPath,
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"-outputPath", outputPath,
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});
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}
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@Test
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void testXmlParsing() throws Exception {
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String dblpInputPath = getClass()
|
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.getResource("/eu/dnetlib/dhp/actionmanager/dblp/dblp_dump_sample.xml")
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.getPath();
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String outputPath = workingDir.toString() + "/actionSet";
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// execute the job to generate the action sets for result scores
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runJob(dblpInputPath, outputPath);
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// TODO: use the data written in `outputPath` to perform tests
|
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// final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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//
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// JavaRDD<OafEntity> tmp = sc
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// .sequenceFile(outputPath, Text.class, Text.class)
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||||
// .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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// .map(aa -> ((OafEntity) aa.getPayload()));
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//
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// assertEquals(8, tmp.count());
|
||||
//
|
||||
// Dataset<OafEntity> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(OafEntity.class));
|
||||
// verificationDataset.createOrReplaceTempView("result");
|
||||
//
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||||
// Dataset<Row> testDataset = spark
|
||||
// .sql(
|
||||
// "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(28, testDataset.count());
|
||||
//
|
||||
// assertResultImpactScores(testDataset);
|
||||
// assertProjectImpactScores(testDataset);
|
||||
|
||||
}
|
||||
|
||||
void assertResultImpactScores(Dataset<Row> testDataset) {
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"6.63451994567e-09", testDataset
|
||||
.filter(
|
||||
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
|
||||
"and id = 'influence'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"0.348694533145", testDataset
|
||||
.filter(
|
||||
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
|
||||
"and id = 'popularity_alt'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"2.16094680115e-09", testDataset
|
||||
.filter(
|
||||
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
|
||||
"and id = 'popularity'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
}
|
||||
|
||||
void assertProjectImpactScores(Dataset<Row> testDataset) throws Exception {
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"0", testDataset
|
||||
.filter(
|
||||
"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
|
||||
"and id = 'numOfInfluentialResults'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"1", testDataset
|
||||
.filter(
|
||||
"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
|
||||
"and id = 'numOfPopularResults'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"25", testDataset
|
||||
.filter(
|
||||
"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
|
||||
"and id = 'totalImpulse'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"43", testDataset
|
||||
.filter(
|
||||
"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
|
||||
"and id = 'totalCitationCount'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
}
|
||||
}
|
||||
File diff suppressed because it is too large
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Reference in New Issue