fixes, move packagename

dice-group · Apr 1, 2021 · 13c257f · 13c257f
1 parent 596b074
commit 13c257f
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Showing 28 changed files with 136 additions and 92 deletions.
diff --git a/exampleconfig.yml b/exampleconfig.yml
@@ -25,6 +25,4 @@ maxGenerateConcepts: 100
 maxConceptLength: 8
 maxDepth: 1
 removeLiterals: true
-namespace: http://dbpedia.org/ontology/
-concepts:
-  - positive: Album  and (artist some Agent)
+namespace: http://dbpedia.org/ontology/
diff --git a/pom.xml b/pom.xml
@@ -26,8 +26,8 @@
         </developer>
     </developers>
     <properties>
-        <maven.compiler.source>1.8</maven.compiler.source>
-        <maven.compiler.target>1.8</maven.compiler.target>
+        <maven.compiler.source>11</maven.compiler.source>
+        <maven.compiler.target>11</maven.compiler.target>
         <log4j.version>2.13.3</log4j.version>
     </properties>
 
@@ -101,7 +101,6 @@
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>org.semanticweb.hermit</artifactId>
             <version>1.4.5.519</version>
-            <scope>test</scope>
         </dependency>
 
         <dependency>
@@ -144,7 +143,6 @@
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>org.semanticweb.hermit</artifactId>
             <version>1.4.5.519</version>
-            <scope>compile</scope>
         </dependency>
     </dependencies>
 
@@ -161,4 +159,69 @@
             <url>http://maven.aksw.org/archiva/repository/snapshots</url>
         </repository>
     </repositories>
+
+    <build>
+
+        <plugins>
+            <plugin>
+                <artifactId>maven-dependency-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <phase>install</phase>
+                        <goals>
+                            <goal>copy-dependencies</goal>
+                        </goals>
+                        <configuration>
+                            <outputDirectory>${project.build.directory}/lib</outputDirectory>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+             <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>3.2.1</version>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                        <configuration>
+                            <shadedArtifactAttached>true</shadedArtifactAttached>
+                            <transformers>
+                                <transformer implementation=
+                                                     "org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                    <mainClass>org.dice_group.lpbenchgen.Main</mainClass>
+                                </transformer>
+                            </transformers>
+                            <filters>
+                                <filter>
+                                    <artifact>*:*</artifact>
+                                    <excludes>
+                                        <exclude>META-INF/*.SF</exclude>
+                                        <exclude>META-INF/*.DSA</exclude>
+                                        <exclude>META-INF/*.RSA</exclude>
+                                    </excludes>
+                                </filter>
+                            </filters>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.8.1</version>
+                <configuration>
+                    <source>11</source>
+                    <target>11</target>
+                    <encoding>UTF-8</encoding>
+                    <compilerArgs>
+                        <arg>-parameters</arg>
+                    </compilerArgs>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
 </project>
diff --git a/.../java/org/dice_group/LPBenchGen/Main.java → .../java/org/dice_group/lpbenchgen/Main.java b/.../java/org/dice_group/LPBenchGen/Main.java → .../java/org/dice_group/lpbenchgen/Main.java
@@ -1,8 +1,8 @@
-package org.dice_group.LPBenchGen;
+package org.dice_group.lpbenchgen;
 
 
-import com.fasterxml.jackson.core.JsonProcessingException;
-import org.dice_group.LPBenchGen.lp.LPGenerator;
+import org.apache.jena.query.ARQ;
+import org.dice_group.lpbenchgen.lp.LPGenerator;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 
 import java.io.IOException;
@@ -26,6 +26,8 @@ public static void main(String[] args) throws OWLOntologyCreationException, IOEx
             printHelp();
         }
         else {
+            //somehow we need to do this manually otherwise the jar will not do it for weird reasons I do not understand.
+            ARQ.init();
             String name="";
             String config="";
             if(args[0].equals("--name")){
@@ -54,14 +56,15 @@ public static void main(String[] args) throws OWLOntologyCreationException, IOEx
      * Print help.
      */
     public static void printHelp(){
-        String help =" obscene --config <CONFIG.YML> --name <BENCHMARK-NAME> \n" +
+        String help =" lpbenchgen --config <CONFIG.YML> --name <BENCHMARK-NAME> \n" +
                 "\n\twill create learning problems and an ontology " +
                 "\n\tbased upon a SPARQL endpoint and a base ontology" +
                 "\n\tfor each concept in <CONFIG.YML> a learning problem will be created" +
                 "\n\tand the corresponding Individuals will be added to the ontology" +
                 "\n\tfurther on a certain amount of random Individuals will be added as well which will be retrieved using the types" +
                 "\n\tstated in <CONFIG.YML>" +
                 "\n\n\tOutput at <BENCHMARK-NAME>-lp.json and <BENCHMARK-NAME>-ontology.owl";
+        System.out.println(help);
     }
 
 }
diff --git a/...n/cleaner/OntologyInconsistentFinder.java → ...n/cleaner/OntologyInconsistentFinder.java b/...n/cleaner/OntologyInconsistentFinder.java → ...n/cleaner/OntologyInconsistentFinder.java
@@ -1,4 +1,4 @@
-package org.dice_group.LPBenchGen.cleaner;
+package org.dice_group.lpbenchgen.cleaner;
 
 import com.google.common.collect.Sets;
 import org.apache.jena.query.*;
@@ -15,7 +15,6 @@
 import java.io.FileOutputStream;
 import java.util.*;
 import java.util.concurrent.atomic.AtomicInteger;
-import java.util.concurrent.atomic.AtomicReference;
 
 /**
  * The type Ontology inconsistent finder.

diff --git a/...ce_group/LPBenchGen/cleaner/TreeNode.java → ...ce_group/lpbenchgen/cleaner/TreeNode.java b/...ce_group/LPBenchGen/cleaner/TreeNode.java → ...ce_group/lpbenchgen/cleaner/TreeNode.java
@@ -1,6 +1,4 @@
-package org.dice_group.LPBenchGen.cleaner;
-
-import org.semanticweb.owlapi.model.OWLClass;
+package org.dice_group.lpbenchgen.cleaner;
 
 import java.util.ArrayList;
 import java.util.List;

diff --git a/...roup/LPBenchGen/config/Configuration.java → ...roup/lpbenchgen/config/Configuration.java b/...roup/LPBenchGen/config/Configuration.java → ...roup/lpbenchgen/config/Configuration.java
@@ -1,7 +1,6 @@
-package org.dice_group.LPBenchGen.config;
+package org.dice_group.lpbenchgen.config;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
-import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
 

diff --git a/...roup/LPBenchGen/config/PosNegExample.java → ...roup/lpbenchgen/config/PosNegExample.java b/...roup/LPBenchGen/config/PosNegExample.java → ...roup/lpbenchgen/config/PosNegExample.java
@@ -1,4 +1,4 @@
-package org.dice_group.LPBenchGen.config;
+package org.dice_group.lpbenchgen.config;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
 import org.semanticweb.owlapi.model.OWLClassExpression;

diff --git a/.../dice_group/LPBenchGen/dl/ABoxFiller.java → .../dice_group/lpbenchgen/dl/ABoxFiller.java b/.../dice_group/LPBenchGen/dl/ABoxFiller.java → .../dice_group/lpbenchgen/dl/ABoxFiller.java
@@ -1,16 +1,14 @@
-package org.dice_group.LPBenchGen.dl;
+package org.dice_group.lpbenchgen.dl;
 
-import com.google.common.collect.Lists;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryFactory;
 import org.apache.jena.query.ResultSet;
-import org.apache.jena.sparql.algebra.optimize.VariableUsageVisitor;
 import org.apache.jena.sparql.core.Var;
 import org.apache.jena.sparql.syntax.ElementWalker;
-import org.dice_group.LPBenchGen.sparql.IndividualRetriever;
-import org.dice_group.LPBenchGen.sparql.QueryTripleMappingVisitor;
-import org.dice_group.LPBenchGen.sparql.VariableCollector;
-import org.dice_group.LPBenchGen.sparql.visitors.QueryRemoveUselessTriplesVisitor;
+import org.dice_group.lpbenchgen.sparql.IndividualRetriever;
+import org.dice_group.lpbenchgen.sparql.QueryTripleMappingVisitor;
+import org.dice_group.lpbenchgen.sparql.VariableCollector;
+import org.dice_group.lpbenchgen.sparql.visitors.QueryRemoveUselessTriplesVisitor;
 import org.semanticweb.owlapi.model.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

diff --git a/...PBenchGen/dl/ConceptLengthCalculator.java → ...pbenchgen/dl/ConceptLengthCalculator.java b/...PBenchGen/dl/ConceptLengthCalculator.java → ...pbenchgen/dl/ConceptLengthCalculator.java
@@ -1,4 +1,4 @@
-package org.dice_group.LPBenchGen.dl;
+package org.dice_group.lpbenchgen.dl;
 
 import org.semanticweb.owlapi.dlsyntax.renderer.DLSyntaxObjectRenderer;
 import org.semanticweb.owlapi.model.*;

diff --git a/.../dice_group/LPBenchGen/dl/OWL2SPARQL.java → .../dice_group/lpbenchgen/dl/OWL2SPARQL.java b/.../dice_group/LPBenchGen/dl/OWL2SPARQL.java → .../dice_group/lpbenchgen/dl/OWL2SPARQL.java
@@ -1,4 +1,4 @@
-package org.dice_group.LPBenchGen.dl;
+package org.dice_group.lpbenchgen.dl;
 
 import com.google.common.collect.HashMultimap;
 import com.google.common.collect.Multimap;
@@ -14,7 +14,6 @@
 import org.apache.jena.query.Syntax;
 import org.apache.jena.sparql.algebra.Algebra;
 import org.apache.jena.sparql.algebra.Op;
-import org.eclipse.rdf4j.model.vocabulary.XSD;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.dlsyntax.renderer.DLSyntaxObjectRenderer;
 import org.semanticweb.owlapi.io.ToStringRenderer;

diff --git a/...up/LPBenchGen/dl/OWLAxiomVisitorBase.java → ...up/lpbenchgen/dl/OWLAxiomVisitorBase.java b/...up/LPBenchGen/dl/OWLAxiomVisitorBase.java → ...up/lpbenchgen/dl/OWLAxiomVisitorBase.java
@@ -1,4 +1,4 @@
-package org.dice_group.LPBenchGen.dl;
+package org.dice_group.lpbenchgen.dl;
 
 import org.semanticweb.owlapi.model.*;
 import uk.ac.manchester.cs.owl.owlapi.OWLObjectSomeValuesFromImpl;

diff --git a/...oup/LPBenchGen/dl/OWLNegationCreator.java → ...oup/lpbenchgen/dl/OWLNegationCreator.java b/...oup/LPBenchGen/dl/OWLNegationCreator.java → ...oup/lpbenchgen/dl/OWLNegationCreator.java
@@ -1,12 +1,11 @@
-package org.dice_group.LPBenchGen.dl;
+package org.dice_group.lpbenchgen.dl;
 
 
 import com.google.common.collect.Lists;
 import org.semanticweb.owlapi.model.*;
 import uk.ac.manchester.cs.owl.owlapi.*;
 
 import java.util.ArrayList;
-import java.util.HashSet;
 import java.util.Collection;
 import java.util.List;
 

diff --git a/...BenchGen/dl/OWLSPARQLPositiveCreator.java → ...benchgen/dl/OWLSPARQLPositiveCreator.java b/...BenchGen/dl/OWLSPARQLPositiveCreator.java → ...benchgen/dl/OWLSPARQLPositiveCreator.java
@@ -1,4 +1,4 @@
-package org.dice_group.LPBenchGen.dl;
+package org.dice_group.lpbenchgen.dl;
 
 /**
  * The type Owlsparql positive creator.

diff --git a/.../LPBenchGen/dl/OWLTBoxConceptCreator.java → .../lpbenchgen/dl/OWLTBoxConceptCreator.java b/.../LPBenchGen/dl/OWLTBoxConceptCreator.java → .../lpbenchgen/dl/OWLTBoxConceptCreator.java
@@ -1,4 +1,4 @@
-package org.dice_group.LPBenchGen.dl;
+package org.dice_group.lpbenchgen.dl;
 
 import java.util.Collection;
 

diff --git a/...Gen/dl/OWLTBoxPatternPositiveCreator.java → ...gen/dl/OWLTBoxPatternPositiveCreator.java b/...Gen/dl/OWLTBoxPatternPositiveCreator.java → ...gen/dl/OWLTBoxPatternPositiveCreator.java
@@ -1,13 +1,11 @@
-package org.dice_group.LPBenchGen.dl;
+package org.dice_group.lpbenchgen.dl;
 
-import org.dice_group.LPBenchGen.dl.visitors.Pattern2ExprVisitor;
+import org.dice_group.lpbenchgen.dl.visitors.Pattern2ExprVisitor;
 import org.semanticweb.owlapi.model.OWLClassExpression;
 import org.semanticweb.owlapi.model.OWLOntology;
 
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
-import java.util.Random;
 
 /**
  * The type Owlt box pattern positive creator.

diff --git a/...LPBenchGen/dl/OWLTBoxPositiveCreator.java → ...lpbenchgen/dl/OWLTBoxPositiveCreator.java b/...LPBenchGen/dl/OWLTBoxPositiveCreator.java → ...lpbenchgen/dl/OWLTBoxPositiveCreator.java
@@ -1,9 +1,7 @@
-package org.dice_group.LPBenchGen.dl;
+package org.dice_group.lpbenchgen.dl;
 
 import com.google.common.collect.Lists;
-import com.google.common.collect.Sets;
-import org.dice_group.LPBenchGen.sparql.IndividualRetriever;
-import org.semanticweb.HermiT.Configuration;
+import org.dice_group.lpbenchgen.sparql.IndividualRetriever;
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.owlapi.model.*;
 import org.slf4j.Logger;
@@ -12,7 +10,6 @@
 import uk.ac.manchester.cs.owl.owlapi.OWLObjectComplementOfImpl;
 import uk.ac.manchester.cs.owl.owlapi.OWLObjectIntersectionOfImpl;
 import uk.ac.manchester.cs.owl.owlapi.OWLObjectSomeValuesFromImpl;
-import org.semanticweb.owlapi.reasoner.Node;
 
 import java.util.*;
 
@@ -86,16 +83,19 @@ public Collection<String> createDistinctConcepts(int noOfConcepts){
                 toSmallCount++;
                 continue;
             }
-            if(!retriever.retrieveIndividualsForConcept(concept, 1, 5).isEmpty()) {
+            try {
+                if (!retriever.retrieveIndividualsForConcept(concept, 1, 5).isEmpty()) {
 
-                ret.add(parser.render(concept));
-                if(ret.size()>=noOfConcepts){
-                    break;
+                    ret.add(parser.render(concept));
+                    if (ret.size() >= noOfConcepts) {
+                        break;
+                    }
+                } else {
+                    noResults++;
                 }
-            }else{
-                noResults++;
+            }catch(Exception e){
+                e.printStackTrace();
             }
-
         }
         List<String> ret2= new ArrayList<String>(ret);
         LOGGER.info("Final {} concepts. [{} to small, {} with no results/timeout]", ret2.size(), toSmallCount, noResults);

diff --git a/.../org/dice_group/LPBenchGen/dl/Parser.java → .../org/dice_group/lpbenchgen/dl/Parser.java b/.../org/dice_group/LPBenchGen/dl/Parser.java → .../org/dice_group/lpbenchgen/dl/Parser.java
@@ -1,4 +1,4 @@
-package org.dice_group.LPBenchGen.dl;
+package org.dice_group.lpbenchgen.dl;
 
 import com.google.common.collect.Sets;
 import org.semanticweb.owlapi.apibinding.OWLManager;
@@ -8,7 +8,6 @@
 import org.semanticweb.owlapi.manchestersyntax.renderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
 import org.semanticweb.owlapi.manchestersyntax.renderer.ManchesterOWLSyntaxPrefixNameShortFormProvider;
 import org.semanticweb.owlapi.model.*;
-import org.semanticweb.owlapi.util.BidirectionalShortFormProvider;
 import org.semanticweb.owlapi.util.BidirectionalShortFormProviderAdapter;
 import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
 

diff --git a/.../visitors/ConceptSubClassesExchanger.java → .../visitors/ConceptSubClassesExchanger.java b/.../visitors/ConceptSubClassesExchanger.java → .../visitors/ConceptSubClassesExchanger.java
@@ -1,4 +1,4 @@
-package org.dice_group.LPBenchGen.dl.visitors;
+package org.dice_group.lpbenchgen.dl.visitors;
 
 import org.semanticweb.owlapi.dlsyntax.renderer.DLSyntaxObjectRenderer;
 import org.semanticweb.owlapi.model.*;

diff --git a/...hGen/dl/visitors/Pattern2ExprVisitor.java → ...hgen/dl/visitors/Pattern2ExprVisitor.java b/...hGen/dl/visitors/Pattern2ExprVisitor.java → ...hgen/dl/visitors/Pattern2ExprVisitor.java
@@ -1,4 +1,4 @@
-package org.dice_group.LPBenchGen.dl.visitors;
+package org.dice_group.lpbenchgen.dl.visitors;
 
 import org.semanticweb.owlapi.model.*;
 

diff --git a/...dice_group/LPBenchGen/lp/LPGenerator.java → ...dice_group/lpbenchgen/lp/LPGenerator.java b/...dice_group/LPBenchGen/lp/LPGenerator.java → ...dice_group/lpbenchgen/lp/LPGenerator.java
@@ -1,14 +1,14 @@
-package org.dice_group.LPBenchGen.lp;
+package org.dice_group.lpbenchgen.lp;
 
 import com.google.common.collect.Lists;
-import org.dice_group.LPBenchGen.config.Configuration;
-import org.dice_group.LPBenchGen.config.PosNegExample;
-import org.dice_group.LPBenchGen.dl.ABoxFiller;
-import org.dice_group.LPBenchGen.dl.OWLNegationCreator;
-import org.dice_group.LPBenchGen.dl.OWLTBoxPositiveCreator;
-import org.dice_group.LPBenchGen.dl.Parser;
-import org.dice_group.LPBenchGen.dl.visitors.ConceptSubClassesExchanger;
-import org.dice_group.LPBenchGen.sparql.IndividualRetriever;
+import org.dice_group.lpbenchgen.config.Configuration;
+import org.dice_group.lpbenchgen.config.PosNegExample;
+import org.dice_group.lpbenchgen.dl.ABoxFiller;
+import org.dice_group.lpbenchgen.dl.OWLNegationCreator;
+import org.dice_group.lpbenchgen.dl.OWLTBoxPositiveCreator;
+import org.dice_group.lpbenchgen.dl.Parser;
+import org.dice_group.lpbenchgen.dl.visitors.ConceptSubClassesExchanger;
+import org.dice_group.lpbenchgen.sparql.IndividualRetriever;
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.owlapi.formats.TurtleDocumentFormat;
 import org.semanticweb.owlapi.model.*;

diff --git a/...g/dice_group/LPBenchGen/lp/LPProblem.java → ...g/dice_group/lpbenchgen/lp/LPProblem.java b/...g/dice_group/LPBenchGen/lp/LPProblem.java → ...g/dice_group/lpbenchgen/lp/LPProblem.java
@@ -1,4 +1,4 @@
-package org.dice_group.LPBenchGen.lp;
+package org.dice_group.lpbenchgen.lp;
 
 import org.semanticweb.owlapi.model.OWLClassExpression;
 import org.semanticweb.owlapi.model.OWLDataProperty;