Nrthugu

I am trying to run this Knowledge Graph Evaluation project. Due to the migration of the maven repository, I had to do some modifications to the pom.xml dependencies and the other files. Now am running into the following error.

[ERROR] /home/manuelanayantarajeyaraj/Documents/Knowledge Extraction/KnowledgeGraphIdentification/nell_lazy/src/main/java/org/linqs/psl/kgi/LoadData.groovy:[62,89] 1. ERROR in /home/manuelanayantarajeyaraj/Documents/Knowledge Extraction/KnowledgeGraphIdentification/nell_lazy/src/main/java/org/linqs/psl/kgi/LoadData.groovy (at line 62)
DataStore data = new RDBMSDataStore(new H2DatabaseDriver(Type.Disk, './psl', true), new EmptyBundle());

^^^^^^^^^^^

Groovy:unable to resolve class EmptyBundle

The programs running under the following specs.
- Apache Maven 3.3.9
- Maven home: /usr/share/maven
- Groovy 2.5.4
- Java version: 1.8.0_181, vendor: Oracle Corporation
- Java home: /usr/lib/jvm/java-8-openjdk-amd64/jre

I tried to figure out how to resolve this error but had no luck whatsoever.

pom.xml

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

     xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">



  <modelVersion>4.0.0</modelVersion>

  <groupId>org.linqs.psl.kgi</groupId>

  <artifactId>kgi</artifactId>

  <version>1.0.-SNAPSHOT</version>

  <packaging>jar</packaging>

  <dependencies>

    <dependency>

      <groupId>org.linqs</groupId>

      <artifactId>psl-groovy</artifactId>

      <version>CANARY</version>

    </dependency>

    <dependency>

      <groupId>org.linqs</groupId>

      <artifactId>psl-dataloading</artifactId>

      <version>CANARY</version>

    </dependency>

    <dependency>

      <groupId>org.linqs</groupId>

      <artifactId>psl-textsim</artifactId>

      <version>CANARY</version>

    </dependency>

    <dependency>

      <groupId>org.linqs</groupId>

      <artifactId>psl-datasplitter</artifactId>

      <version>CANARY</version>

    </dependency>

    <dependency>

      <groupId>org.linqs</groupId>

      <artifactId>psl-experiment</artifactId>

      <version>CANARY</version>

    </dependency>

    <dependency>

      <groupId>org.linqs</groupId>

      <artifactId>psl-mosek</artifactId>

      <version>CANARY</version>

    </dependency>

    <dependency>

      <groupId>org.linqs</groupId>

      <artifactId>psl-optimize</artifactId>

      <version>CANARY</version>

    </dependency>

    <dependency>

      <groupId>org.linqs</groupId>

      <artifactId>psl-sampler</artifactId>

      <version>CANARY</version>

    </dependency>

    <dependency>

      <groupId>org.linqs</groupId>

      <artifactId>psl-weightlearning</artifactId>

      <version>CANARY</version>

    </dependency>

  </dependencies>

  <properties>

    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

  </properties>

  <repositories>

    <repository>

      <releases>

    <enabled>true</enabled>

    <updatePolicy>daily</updatePolicy>

    <checksumPolicy>fail</checksumPolicy>

      </releases>

      <id>psl-releases</id>

      <name>PSL Releases</name>

      <url>http://maven.linqs.org/maven/repositories/psl-releases/</url>

      <layout>default</layout>

    </repository>

    <repository>

      <releases>

    <enabled>true</enabled>

    <updatePolicy>daily</updatePolicy>

    <checksumPolicy>fail</checksumPolicy>

      </releases>

      <id>psl-thirdparty</id>

      <name>PSL Third Party</name>

      <url>http://maven.linqs.org/maven/repositories/psl-thirdparty/</url>

      <layout>default</layout>

    </repository>

  </repositories>

  <build>

    <plugins>

      <plugin>

        <artifactId>maven-compiler-plugin</artifactId>

        <version>3.1</version>

        <configuration>

            <compilerId>groovy-eclipse-compiler</compilerId>

        </configuration>

        <dependencies>

            <!-- https://mvnrepository.com/artifact/org.codehaus.groovy/groovy-eclipse-compiler -->

            <dependency>

                <groupId>org.codehaus.groovy</groupId>

                <artifactId>groovy-eclipse-compiler</artifactId>

                <version>2.9.2-01</version>

            </dependency>

            <!-- https://mvnrepository.com/artifact/org.codehaus.groovy/groovy-eclipse-batch -->

            <dependency>

                <groupId>org.codehaus.groovy</groupId>

                <artifactId>groovy-eclipse-batch</artifactId>

                <version>2.4.3-01</version>

            </dependency>

        </dependencies>

      </plugin>

      <plugin>

        <groupId>org.apache.maven.plugins</groupId>

        <artifactId>maven-eclipse-plugin</artifactId>

        <version>2.8</version>

        <configuration>

          <additionalProjectnatures>

            <projectnature>org.eclipse.jdt.groovy.core.groovyNature</projectnature>

          </additionalProjectnatures>

          <sourceIncludes>

              <sourceInclude>**/*.groovy</sourceInclude>

          </sourceIncludes>

        </configuration>

      </plugin>

      <plugin>

        <groupId>org.apache.maven.plugins</groupId>

        <artifactId>maven-surefire-plugin</artifactId>

        <version>2.9</version>

        <configuration>

          <enableAssertions>false</enableAssertions>

        </configuration>

      </plugin>

    </plugins>

  </build>

</project>

LoadData.groovy

package org.linqs.psl.kgi;



import org.slf4j.Logger; 

import org.slf4j.LoggerFactory; 



import org.linqs.psl.groovy.*;

import org.linqs.psl.config.*;

import org.linqs.psl.core.*;

import org.linqs.psl.core.inference.*;

import org.linqs.psl.ui.loading.*

import org.linqs.psl.evaluation.result.*;



import org.linqs.psl.database.DataStore; 

//import org.linqs.psl.database.Database; 

//import org.linqs.psl.database.DatabasePopulator; 

//import org.linqs.psl.database.DatabaseQuery; 

import org.linqs.psl.database.Partition; 

import org.linqs.psl.database.rdbms.RDBMSDataStore; 

import org.linqs.psl.database.rdbms.driver.H2DatabaseDriver; 

import org.linqs.psl.database.rdbms.driver.H2DatabaseDriver.Type; 



//import edu.emory.mathcs.utils.ConcurrencyUtils; 



import org.linqs.psl.model.term.ConstantType 

import org.linqs.psl.model.predicate.Predicate 

//import org.linqs.psl.model.predicate.StandardPredicate 

//import org.linqs.psl.model.term.GroundTerm 

//import org.linqs.psl.model.term.Variable 

import org.linqs.psl.model.atom.*



import java.io.*;

import java.util.*;

import java.util.HashSet;



import groovy.time.*;



Date start = new Date();



Logger log = LoggerFactory.getLogger(this.class);



//Where the data resides (first argument to this script)

def dataroot = args[0];



-->

DataStore data = new RDBMSDataStore(new H2DatabaseDriver(Type.Disk, './psl', true), new EmptyBundle());

PSLModel m = new PSLModel(this, data);





////////////////////////// predicate declaration ////////////////////////

System.out.println "[info] ttDECLARING PREDICATES...";



/*** Target Predicates ***/

m.add predicate: "Cat", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "Rel", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]





/*** Ontology Predicates ***/               

m.add predicate: "Sub", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "RSub", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "Mut", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "RMut", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "Inv", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "Domain", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "Range2", types: [ConstantType.UniqueID, ConstantType.UniqueID]



/*** Entity Resolution Predicates ***/

m.add predicate: "SameEntity", types: [ConstantType.UniqueID, ConstantType.UniqueID]





/*** Scoping Predicates ***/

m.add predicate: "ValCat", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "ValRel", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]





/*** Training Data Predicates ***/

m.add predicate: "PSeedCat", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "PSeedRel", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "NSeedCat", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "NSeedRel", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "TrCat", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "TrRel", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]







/*** Input Data Predicates ***/

m.add predicate: "CandCat", types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandRel", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandCat_General",  types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandRel_General", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandCat_CBL",  types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandRel_CBL", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandCat_CMC",  types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandRel_CMC", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandCat_CPL",  types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandRel_CPL", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandCat_Morph",  types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandRel_Morph", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandCat_SEAL",  types: [ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "CandRel_SEAL", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID]



m.add predicate: "PromCat", types: [ConstantType.UniqueID, ConstantType.UniqueID];



m.add predicate: "PromRel", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID];



m.add predicate: "PromCat_General", types: [ConstantType.UniqueID, ConstantType.UniqueID];



m.add predicate: "PromRel_General", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID];



m.add predicate: "PattCat", types: [ConstantType.UniqueID, ConstantType.UniqueID];



m.add predicate: "PattRel", types: [ConstantType.UniqueID, ConstantType.UniqueID, ConstantType.UniqueID];





/*** Load ontology atoms ***/

Partition ontology = DataStore.getPartition("10");



def ontoMap = [

        ((Predicate)Mut):dataroot+"165.onto-wbpg.db.Mut.txt",

        ((Predicate)Sub):dataroot+"165.onto-wbpg.db.Sub.txt",

        ((Predicate)RSub):dataroot+"165.onto-wbpg.db.RSub.txt",

                ((Predicate)Domain):dataroot+"165.onto-wbpg.db.Domain.txt",

        ((Predicate)Inv):dataroot+"165.onto-wbpg.db.Inv.txt",

        ((Predicate)Range2):dataroot+"165.onto-wbpg.db.Range2.txt",

        ((Predicate)RMut):dataroot+"165.onto-wbpg.db.RMut.txt"];



KGIUtils.loadPredicateAtoms(data, ontoMap, ontology)





/*** Load seed atoms ***/

Partition seeds = DataStore.getPartition("20");



def seedMap = [((Predicate)Cat):dataroot+"seed.165.cat.uniq.out",

           ((Predicate)Rel):dataroot+"seed.165.rel.uniq.out"];



KGIUtils.loadPredicateAtomsWithValue(data, seedMap, seeds)







/*** Load entity resolution atoms ***/

Partition entity_resolution = DataStore.getPartition("30");



def erMap = [((Predicate)SameEntity):dataroot+"NELL.08m.165.cesv.csv.SameEntity.out"]



KGIUtils.loadPredicateAtomsWithValue(data, erMap, entity_resolution)





/*** Load training atoms ***/

Partition training = DataStore.getPartition("40");



def trainMap = [((Predicate)Cat):dataroot+"label-train-uniq-raw-cat.db.TRAIN",

        ((Predicate)Rel):dataroot+"label-train-uniq-raw-rel.db.TRAIN"];



KGIUtils.loadPredicateAtomsWithValue(data, trainMap, training)



/*** Load candidate atoms ***/

Partition candidates = DataStore.getPartition("50");

Partition candidates_nosource = DataStore.getPartition("55");



def predCatMap = [((Predicate)CandCat_CBL):dataroot+"NELL.08m.165.cesv.csv.CandCat_CBL.out",

                 ((Predicate)CandCat_CMC):dataroot+"NELL.08m.165.cesv.csv.CandCat_CMC.out",

         ((Predicate)CandCat_CPL):dataroot+"NELL.08m.165.cesv.csv.CandCat_CPL.out",

         ((Predicate)CandCat_General):dataroot+"NELL.08m.165.cesv.csv.CandCat_General.out",

         ((Predicate)CandCat_Morph):dataroot+"NELL.08m.165.cesv.csv.CandCat_Morph.out",

         ((Predicate)CandCat_SEAL):dataroot+"NELL.08m.165.cesv.csv.CandCat_SEAL.out",

         ((Predicate)PattCat):dataroot+"NELL.08m.165.cesv.csv.PattCat.out",

         ((Predicate)PromCat_General):dataroot+"NELL.08m.165.esv.csv.PromCat_General.out"]



def predRelMap = [((Predicate)CandRel_CBL):dataroot+"NELL.08m.165.cesv.csv.CandRel_CBL.out",

                 ((Predicate)CandRel_CPL):dataroot+"NELL.08m.165.cesv.csv.CandRel_CPL.out",

         ((Predicate)CandRel_General):dataroot+"NELL.08m.165.cesv.csv.CandRel_General.out",

         ((Predicate)CandRel_SEAL):dataroot+"NELL.08m.165.cesv.csv.CandRel_SEAL.out",

         ((Predicate)PattRel):dataroot+"NELL.08m.165.cesv.csv.PattRel.out",

         ((Predicate)PromRel_General):dataroot+"NELL.08m.165.esv.csv.PromRel_General.out"];



def predNoSourceMap = [((Predicate)CandCat):dataroot+"NELL.08m.165.cesv.csv.CandCat.out",

                  ((Predicate)CandRel):dataroot+"NELL.08m.165.cesv.csv.CandRel.out"];



KGIUtils.loadPredicateAtomsWithValue(data, predCatMap, candidates)

KGIUtils.loadPredicateAtomsWithValue(data, predRelMap, candidates)

KGIUtils.loadPredicateAtomsWithValue(data, predNoSourceMap, candidates_nosource)





System.out.println("[info] data loading finished")



Date stop = new Date();



TimeDuration td = TimeCategory.minus( stop, start );

System.out.println td;

Any suggestions in this regard will be highly appreciated.