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fixed error in the treeprocessor. it used th=-1 as default value, now it use th=1

This commit is contained in:
miconis 2020-09-29 12:01:25 +02:00
parent 9e8ea8f6ee
commit 5021e5048f
20 changed files with 768 additions and 23 deletions
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4
dnet-dedup-test/job-override.properties Normal file
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@ -0,0 +1,4 @@
entitiesPath = /tmp/graph_openorgs_and_corda/organization
workingPath = /tmp/openorgs_test/workingpath
dedupConfPath = /tmp/openorgs_test/organization.strict.conf.json
numPartitions = 40

32
dnet-dedup-test/src/main/java/eu/dnetlib/Deduper.java
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@ -1,5 +1,6 @@
package eu.dnetlib;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.hash.Hashing;
import eu.dnetlib.graph.GraphProcessor;
import eu.dnetlib.pace.config.DedupConfig;
@ -11,6 +12,7 @@ import eu.dnetlib.reporter.SparkReporter;
import eu.dnetlib.support.Block;
import eu.dnetlib.support.ConnectedComponent;
import eu.dnetlib.support.Relation;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.spark.api.java.JavaPairRDD;
@ -27,7 +29,9 @@ import org.apache.spark.sql.SparkSession;
import org.apache.spark.util.LongAccumulator;
import scala.Serializable;
import scala.Tuple2;
import scala.math.Ordering;
import java.nio.charset.Charset;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;
@ -36,6 +40,8 @@ public class Deduper implements Serializable {
private static final Log log = LogFactory.getLog(Deduper.class);
private static ObjectMapper mapper = new ObjectMapper();
public static JavaPairRDD<String, Block> createSortedBlocks(
JavaPairRDD<String, MapDocument> mapDocs, DedupConfig config) {
final String of = config.getWf().getOrderField();
@ -71,7 +77,7 @@ public class Deduper implements Serializable {
}
public static long hash(final String id) {
return Hashing.murmur3_128().hashString(id).asLong();
return Hashing.murmur3_128().hashString(id, Charset.defaultCharset()).asLong();
}
public static ConnectedComponent entityMerger(String key, Iterator<String> values) {
@ -79,7 +85,7 @@ public class Deduper implements Serializable {
ConnectedComponent cc = new ConnectedComponent();
cc.setCcId(key);
cc.setDocs(StreamSupport.stream(Spliterators.spliteratorUnknownSize(values, Spliterator.ORDERED), false)
.collect(Collectors.toSet()));
.collect(Collectors.toCollection(HashSet::new)));
return cc;
}
@ -115,6 +121,13 @@ public class Deduper implements Serializable {
// create blocks for deduplication
JavaPairRDD<String, Block> blocks = Deduper.createSortedBlocks(mapDocuments, dedupConf);
//TODO test purpose
blocks.foreach(b -> System.out.println("b = " + b));
blocks = blocks.filter(b -> b._1().equals("ghahos"));
// create relations by comparing only elements in the same group
JavaRDD<Relation> relations = Deduper.computeRelations(sc, blocks, dedupConf);
@ -145,15 +158,18 @@ public class Deduper implements Serializable {
.map(Relation::toEdgeRdd)
.rdd();
final Dataset<Relation> mergeRels = spark
.createDataset(
GraphProcessor
JavaRDD<ConnectedComponent> ccs = GraphProcessor
.findCCs(vertexes.rdd(), edgeRdd, maxIterations)
.toJavaRDD()
.toJavaRDD();
JavaRDD<Relation> mergeRel = ccs
.filter(k -> k.getDocs().size() > 1)
.flatMap(cc -> ccToMergeRel(cc, dedupConf))
.map(it -> new Relation(it._1(), it._2(), "mergeRel"))
.rdd(),
.map(it -> new Relation(it._1(), it._2(), "mergeRel"));
final Dataset<Relation> mergeRels = spark
.createDataset(
mergeRel.rdd(),
Encoders.bean(Relation.class));
mergeRels.write().mode(SaveMode.Overwrite).parquet(mergeRelsPath);

48
dnet-dedup-test/src/main/java/eu/dnetlib/jobs/AbstractSparkJob.java Normal file
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@ -0,0 +1,48 @@
package eu.dnetlib.jobs;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.utils.Utility;
import eu.dnetlib.support.ArgumentApplicationParser;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import java.io.IOException;
import java.io.Serializable;
abstract class AbstractSparkJob implements Serializable {
protected static final int NUM_PARTITIONS = 1000;
protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
public ArgumentApplicationParser parser; // parameters for the spark action
public SparkSession spark; // the spark session
public AbstractSparkJob() {}
public AbstractSparkJob(ArgumentApplicationParser parser, SparkSession spark) {
this.parser = parser;
this.spark = spark;
}
abstract void run();
protected static SparkSession getSparkSession(SparkConf conf) {
return SparkSession.builder().config(conf).getOrCreate();
}
protected static <T> void save(Dataset<T> dataset, String outPath, SaveMode mode) {
dataset.write().option("compression", "gzip").mode(mode).json(outPath);
}
protected static DedupConfig loadDedupConfig(String dedupConfPath) {
return DedupConfig.load(Utility.readFromClasspath("/eu/dnetlib/pace/config/organization.strict.conf.json", AbstractSparkJob.class));
}
}

63
dnet-dedup-test/src/main/java/eu/dnetlib/jobs/SparkCreateDedupEntity.java Normal file
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@ -0,0 +1,63 @@
package eu.dnetlib.jobs;
import eu.dnetlib.Deduper;
import eu.dnetlib.pace.utils.Utility;
import eu.dnetlib.support.ArgumentApplicationParser;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Optional;
public class SparkCreateDedupEntity extends AbstractSparkJob {
private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.jobs.SparkCreateDedupEntity.class);
public SparkCreateDedupEntity(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
}
public static void main(String[] args) throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
Utility.readFromClasspath("/eu/dnetlib/pace/createDedupEntity_parameters.json", SparkCreateDedupEntity.class)
);
parser.parseArgument(args);
SparkConf conf = new SparkConf();
new SparkCreateDedupEntity(
parser,
getSparkSession(conf)
).run();
}
@Override
public void run() {
// read oozie parameters
final String entitiesPath = parser.get("entitiesPath");
final String workingPath = parser.get("workingPath");
final String dedupConfPath = parser.get("dedupConfPath");
final int numPartitions = Optional
.ofNullable(parser.get("numPartitions"))
.map(Integer::valueOf)
.orElse(NUM_PARTITIONS);
log.info("entitiesPath: '{}'", entitiesPath);
log.info("workingPath: '{}'", workingPath);
log.info("dedupConfPath: '{}'", dedupConfPath);
log.info("numPartitions: '{}'", numPartitions);
Deduper.createDedupEntity(
loadDedupConfig(dedupConfPath),
workingPath + "/mergerels",
entitiesPath,
spark,
workingPath + "/dedupentity"
);
}
}

62
dnet-dedup-test/src/main/java/eu/dnetlib/jobs/SparkCreateMergeRels.java Normal file
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@ -0,0 +1,62 @@
package eu.dnetlib.jobs;
import eu.dnetlib.Deduper;
import eu.dnetlib.pace.utils.Utility;
import eu.dnetlib.support.ArgumentApplicationParser;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Optional;
public class SparkCreateMergeRels extends AbstractSparkJob {
private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class);
public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
}
public static void main(String[] args) throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
Utility.readFromClasspath("/eu/dnetlib/pace/createMergeRels_parameters.json", SparkCreateSimRels.class)
);
parser.parseArgument(args);
SparkConf conf = new SparkConf();
new SparkCreateSimRels(
parser,
getSparkSession(conf)
).run();
}
@Override
public void run() {
// read oozie parameters
final String entitiesPath = parser.get("entitiesPath");
final String workingPath = parser.get("workingPath");
final String dedupConfPath = parser.get("dedupConfPath");
final int numPartitions = Optional
.ofNullable(parser.get("numPartitions"))
.map(Integer::valueOf)
.orElse(NUM_PARTITIONS);
log.info("entitiesPath: '{}'", entitiesPath);
log.info("workingPath: '{}'", workingPath);
log.info("dedupConfPath: '{}'", dedupConfPath);
log.info("numPartitions: '{}'", numPartitions);
Deduper.createMergeRels(
loadDedupConfig(dedupConfPath),
entitiesPath,
workingPath + "/mergerels",
workingPath + "/simrels",
spark
);
}
}

62
dnet-dedup-test/src/main/java/eu/dnetlib/jobs/SparkCreateSimRels.java Normal file
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@ -0,0 +1,62 @@
package eu.dnetlib.jobs;
import eu.dnetlib.Deduper;
import eu.dnetlib.pace.utils.Utility;
import eu.dnetlib.support.ArgumentApplicationParser;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Optional;
public class SparkCreateSimRels extends AbstractSparkJob {
private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
}
public static void main(String[] args) throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
Utility.readFromClasspath("/eu/dnetlib/pace/parameters/createSimRels_parameters.json", SparkCreateSimRels.class)
);
parser.parseArgument(args);
SparkConf conf = new SparkConf();
new SparkCreateSimRels(
parser,
getSparkSession(conf)
).run();
}
@Override
public void run() {
// read oozie parameters
final String entitiesPath = parser.get("entitiesPath");
final String workingPath = parser.get("workingPath");
final String dedupConfPath = parser.get("dedupConfPath");
final int numPartitions = Optional
.ofNullable(parser.get("numPartitions"))
.map(Integer::valueOf)
.orElse(NUM_PARTITIONS);
log.info("entitiesPath: '{}'", entitiesPath);
log.info("workingPath: '{}'", workingPath);
log.info("dedupConfPath: '{}'", dedupConfPath);
log.info("numPartitions: '{}'", numPartitions);
Deduper.createSimRels(
loadDedupConfig(dedupConfPath),
spark,
entitiesPath,
workingPath + "/simrels"
);
}
}

95
dnet-dedup-test/src/main/java/eu/dnetlib/support/ArgumentApplicationParser.java Normal file
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@ -0,0 +1,95 @@
package eu.dnetlib.support;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.Serializable;
import java.io.StringWriter;
import java.util.*;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
public class ArgumentApplicationParser implements Serializable {
private final Options options = new Options();
private final Map<String, String> objectMap = new HashMap<>();
private final List<String> compressedValues = new ArrayList<>();
public ArgumentApplicationParser(final String json_configuration) throws Exception {
final ObjectMapper mapper = new ObjectMapper();
final OptionsParameter[] configuration = mapper.readValue(json_configuration, OptionsParameter[].class);
createOptionMap(configuration);
}
public ArgumentApplicationParser(final OptionsParameter[] configuration) {
createOptionMap(configuration);
}
private void createOptionMap(final OptionsParameter[] configuration) {
Arrays
.stream(configuration)
.map(
conf -> {
final Option o = new Option(conf.getParamName(), true, conf.getParamDescription());
o.setLongOpt(conf.getParamLongName());
o.setRequired(conf.isParamRequired());
if (conf.isCompressed()) {
compressedValues.add(conf.getParamLongName());
}
return o;
})
.forEach(options::addOption);
// HelpFormatter formatter = new HelpFormatter();
// formatter.printHelp("myapp", null, options, null, true);
}
public static String decompressValue(final String abstractCompressed) {
try {
byte[] byteArray = org.apache.commons.codec.binary.Base64.decodeBase64(abstractCompressed.getBytes());
GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(byteArray));
final StringWriter stringWriter = new StringWriter();
IOUtils.copy(gis, stringWriter);
return stringWriter.toString();
} catch (Throwable e) {
System.out.println("Wrong value to decompress:" + abstractCompressed);
throw new RuntimeException(e);
}
}
public static String compressArgument(final String value) throws Exception {
ByteArrayOutputStream out = new ByteArrayOutputStream();
GZIPOutputStream gzip = new GZIPOutputStream(out);
gzip.write(value.getBytes());
gzip.close();
return java.util.Base64.getEncoder().encodeToString(out.toByteArray());
}
public void parseArgument(final String[] args) throws Exception {
CommandLineParser parser = new BasicParser();
CommandLine cmd = parser.parse(options, args);
Arrays
.stream(cmd.getOptions())
.forEach(
it -> objectMap
.put(
it.getLongOpt(),
compressedValues.contains(it.getLongOpt())
? decompressValue(it.getValue())
: it.getValue()));
}
public String get(final String key) {
return objectMap.get(key);
}
public Map<String, String> getObjectMap() {
return objectMap;
}
}

9
dnet-dedup-test/src/main/java/eu/dnetlib/support/Block.java
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@ -89,6 +89,13 @@ public class Block implements Serializable {
return documents.size();
}
@Override
public String toString() {
return "Block{" +
"key='" + key + '\'' +
", size=" + documents.size() + '\'' +
", names=" + documents.stream().map(d -> d.getFieldMap().get("country").stringValue()).collect(Collectors.toList()) + '\'' +
'}';
}
}

7
dnet-dedup-test/src/main/java/eu/dnetlib/support/ConnectedComponent.java
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@ -2,6 +2,7 @@ package eu.dnetlib.support;
import java.io.IOException;
import java.io.Serializable;
import java.util.HashSet;
import java.util.Set;
import eu.dnetlib.pace.utils.Utility;
@ -14,14 +15,14 @@ import eu.dnetlib.pace.util.PaceException;
public class ConnectedComponent implements Serializable {
private Set<String> docs;
private HashSet<String> docs;
private String ccId;
public ConnectedComponent() {
}
public ConnectedComponent(Set<String> docs) {
this.docs = docs;
this.docs = new HashSet<>(docs);
createID();
}
@ -68,7 +69,7 @@ public class ConnectedComponent implements Serializable {
return docs;
}
public void setDocs(Set<String> docs) {
public void setDocs(HashSet<String> docs) {
this.docs = docs;
}

37
dnet-dedup-test/src/main/java/eu/dnetlib/support/OptionsParameter.java Normal file
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@ -0,0 +1,37 @@
package eu.dnetlib.support;
public class OptionsParameter {
private String paramName;
private String paramLongName;
private String paramDescription;
private boolean paramRequired;
private boolean compressed;
public OptionsParameter() {
}
public String getParamName() {
return paramName;
}
public String getParamLongName() {
return paramLongName;
}
public String getParamDescription() {
return paramDescription;
}
public boolean isParamRequired() {
return paramRequired;
}
public boolean isCompressed() {
return compressed;
}
public void setCompressed(boolean compressed) {
this.compressed = compressed;
}
}

9
dnet-dedup-test/src/main/java/eu/dnetlib/support/Relation.java
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@ -47,4 +47,13 @@ public class Relation implements Serializable {
public Edge<String> toEdgeRdd(){
return new Edge<>(Deduper.hash(source), Deduper.hash(target), type);
}
@Override
public String toString() {
return "Relation{" +
"source='" + source + '\'' +
", target='" + target + '\'' +
", type='" + type + '\'' +
'}';
}
}

18
dnet-dedup-test/src/main/resources/dedup/oozie_app/config-default.xml Normal file
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@ -0,0 +1,18 @@
<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>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

167
dnet-dedup-test/src/main/resources/dedup/oozie_app/workflow.xml Normal file
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@ -0,0 +1,167 @@
<workflow-app name="Deduplication WF" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>entitiesPath</name>
<description>the input entity path</description>
</property>
<property>
<name>workingPath</name>
<description>path for the working directory</description>
</property>
<property>
<name>numPartitions</name>
<description>number of partitions for the spark files</description>
</property>
<property>
<name>dedupConfPath</name>
<description>path for the dedup configuration file</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>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="resetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="resetWorkingPath">
<fs>
<delete path="${workingPath}"/>
</fs>
<ok to="CreateSimRels"/>
<error to="Kill"/>
</action>
<action name="CreateSimRels">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Create Similarity Relations</name>
<class>eu.dnetlib.jobs.SparkCreateSimRels</class>
<jar>dnet-dedup-test-${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.shuffle.partitions=3840
</spark-opts>
<arg>--entitiesPath</arg><arg>${entitiesPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--numPartitions</arg><arg>${numPartitions}</arg>
<arg>--dedupConfPath</arg><arg>${dedupConfPath}</arg>
</spark>
<ok to="CreateMergeRels"/>
<error to="Kill"/>
</action>
<action name="CreateMergeRels">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Create Merge Relations</name>
<class>eu.dnetlib.jobs.SparkCreateMergeRels</class>
<jar>dhp-dedup-test-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${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}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--entitiesPath</arg><arg>${entitiesPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--numPartitions</arg><arg>${numPartitions}</arg>
<arg>--dedupConfPath</arg><arg>${dedupConfPath}</arg>
</spark>
<ok to="CreateDedupEntities"/>
<error to="Kill"/>
</action>
<action name="CreateDedupEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Create Dedup Entities</name>
<class>eu.dnetlib.jobs.SparkCreateDedupEntity</class>
<jar>dhp-dedup-test-${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.shuffle.partitions=3840
</spark-opts>
<arg>--entitiesPath</arg><arg>${entitiesPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--numPartitions</arg><arg>${numPartitions}</arg>
<arg>--dedupConfPath</arg><arg>${dedupConfPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

68
dnet-dedup-test/src/test/java/eu/dnetlib/pace/DedupLocalTest.java
View File

@ -1,8 +1,12 @@
package eu.dnetlib.pace;
import eu.dnetlib.Deduper;
import eu.dnetlib.jobs.SparkCreateDedupEntity;
import eu.dnetlib.jobs.SparkCreateMergeRels;
import eu.dnetlib.jobs.SparkCreateSimRels;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.utils.Utility;
import eu.dnetlib.support.ArgumentApplicationParser;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.Before;
@ -16,12 +20,15 @@ public class DedupLocalTest extends DedupTestUtils {
DedupConfig config;
JavaSparkContext context;
final String entitiesPath = "/Users/miconis/Desktop/publications_to_fix.json";
final String entitiesPath = "/Users/miconis/IdeaProjects/DnetDedup/dnet-dedup/dnet-dedup-test/src/test/resources/eu/dnetlib/pace/examples/openorgs.to.fix.json";
final String workingPath = "/tmp/working_dir";
final String numPartitions = "10";
final String dedupConfPath = "/eu/dnetlib/pace/config/organization.strict.conf.json";
@Before
public void setup() {
config = DedupConfig.load(Utility.readFromClasspath("/eu/dnetlib/pace/config/publication.current.conf.json", DedupLocalTest.class));
config = DedupConfig.load(Utility.readFromClasspath("/eu/dnetlib/pace/config/organization.strict.conf.json", DedupLocalTest.class));
spark = SparkSession
.builder()
@ -32,6 +39,63 @@ public class DedupLocalTest extends DedupTestUtils {
}
@Test
public void createSimRelTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(Utility.readFromClasspath("/eu/dnetlib/pace/parameters/createSimRels_parameters.json", SparkCreateSimRels.class));
parser.parseArgument(
new String[] {
"-e", entitiesPath,
"-w", workingPath,
"-np", numPartitions,
"-dc", dedupConfPath
});
new SparkCreateSimRels(
parser,
spark
).run();
}
@Test
public void createMergeRelTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(Utility.readFromClasspath("/eu/dnetlib/pace/parameters/createMergeRels_parameters.json", SparkCreateMergeRels.class));
parser.parseArgument(
new String[] {
"-e", entitiesPath,
"-w", workingPath,
"-np", numPartitions,
"-dc", dedupConfPath
});
new SparkCreateMergeRels(
parser,
spark
).run();
}
@Test
public void createDedupEntityTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(Utility.readFromClasspath("/eu/dnetlib/pace/parameters/createDedupEntity_parameters.json", SparkCreateDedupEntity.class));
parser.parseArgument(
new String[] {
"-e", entitiesPath,
"-w", workingPath,
"-np", numPartitions,
"-dc", dedupConfPath
});
new SparkCreateDedupEntity(
parser,
spark
).run();
}
@Test
public void deduplicationTest() {

22
dnet-dedup-test/src/test/resources/eu/dnetlib/pace/config/organization.strict.conf.json
View File

@ -71,6 +71,13 @@
"weight": 1,
"countIfUndefined": "false",
"params": {}
},
{
"field": "rorid",
"comparator": "exactMatch",
"weight": 1,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 1,
@ -115,8 +122,8 @@
"aggregation": "AND",
"positive": "layer3",
"negative": "NO_MATCH",
"undefined": "layer3",
"ignoreUndefined": "true"
"undefined": "NO_MATCH",
"ignoreUndefined": "false"
},
"layer3": {
"fields": [
@ -184,11 +191,12 @@
}
},
"model" : [
{ "name" : "country", "type" : "String", "path" : "$.organization.metadata.country.classid"},
{ "name" : "legalshortname", "type" : "String", "path" : "$.organization.metadata.legalshortname.value"},
{ "name" : "legalname", "type" : "String", "path" : "$.organization.metadata.legalname.value" },
{ "name" : "websiteurl", "type" : "URL", "path" : "$.organization.metadata.websiteurl.value" },
{ "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='grid.ac')].value"},
{ "name" : "country", "type" : "String", "path" : "$.country.classid"},
{ "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"},
{ "name" : "legalname", "type" : "String", "path" : "$.legalname.value" },
{ "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" },
{ "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='GRID')].value"},
{ "name" : "rorid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='ROR')].value"},
{ "name" : "originalId", "type" : "String", "path" : "$.id" }
],
"blacklists" : {

6
dnet-dedup-test/src/test/resources/eu/dnetlib/pace/examples/openorgs.to.fix.json Normal file
View File

File diff suppressed because one or more lines are too long

26
dnet-dedup-test/src/test/resources/eu/dnetlib/pace/parameters/createDedupEntity_parameters.json Normal file
View File

@ -0,0 +1,26 @@
[
{
"paramName": "e",
"paramLongName": "entitiesPath",
"paramDescription": "the input entities",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "path of the working directory",
"paramRequired": true
},
{
"paramName": "np",
"paramLongName": "numPartitions",
"paramDescription": "number of partitions for the similarity relations intermediate phases",
"paramRequired": false
},
{
"paramName": "dc",
"paramLongName": "dedupConfPath",
"paramDescription": "path of the dedup configuration",
"paramRequired": false
}
]

26
dnet-dedup-test/src/test/resources/eu/dnetlib/pace/parameters/createMergeRels_parameters.json Normal file
View File

@ -0,0 +1,26 @@
[
{
"paramName": "e",
"paramLongName": "entitiesPath",
"paramDescription": "the input entities",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "path of the working directory",
"paramRequired": true
},
{
"paramName": "np",
"paramLongName": "numPartitions",
"paramDescription": "number of partitions for the similarity relations intermediate phases",
"paramRequired": false
},
{
"paramName": "dc",
"paramLongName": "dedupConfPath",
"paramDescription": "path of the dedup configuration",
"paramRequired": false
}
]

26
dnet-dedup-test/src/test/resources/eu/dnetlib/pace/parameters/createSimRels_parameters.json Normal file
View File

@ -0,0 +1,26 @@
[
{
"paramName": "e",
"paramLongName": "entitiesPath",
"paramDescription": "the input entities",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "path of the working directory",
"paramRequired": true
},
{
"paramName": "np",
"paramLongName": "numPartitions",
"paramDescription": "number of partitions for the similarity relations intermediate phases",
"paramRequired": false
},
{
"paramName": "dc",
"paramLongName": "dedupConfPath",
"paramDescription": "path of the dedup configuration",
"paramRequired": false
}
]

2
dnet-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeDef.java
View File

@ -51,7 +51,7 @@ public class TreeNodeDef implements Serializable {
fieldConf.getComparator() + " on " + fieldConf.getField() + " " + fields.indexOf(fieldConf),
new FieldStats(
weight,
Double.parseDouble(fieldConf.getParams().getOrDefault("threshold", "-1.0")),
Double.parseDouble(fieldConf.getParams().getOrDefault("threshold", "1.0")),
result,
fieldConf.isCountIfUndefined(),
doc1.getFieldMap().get(fieldConf.getField()),