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Merge branch 'develop' of github.com:SmartDataAnalytics/DL-Learner into develop
2 parents db4f6f1 + 42e7d00 commit 06845b0

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Lines changed: 1852 additions & 1650 deletions

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README renamed to README.md

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@@ -3,10 +3,10 @@ knowledge (usually in description logics, hence the "DL" in its name). Please
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check the website for details and examples. Post to the mailing list if help
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is needed.
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Website: http://dl-learner.org
7-
Bugs & Feature Requests: https://github.com/SmartDataAnalytics/DL-Learner/issues
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Mailing Lists: [DL-Learner Discussion](https://www.freelists.org/list/dl-learner-discussion)
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Latest Release: https://github.com/SmartDataAnalytics/DL-Learner/releases
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* Website: http://dl-learner.org
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* Bugs & Feature Requests: https://github.com/SmartDataAnalytics/DL-Learner/issues
8+
* Mailing Lists: [DL-Learner Discussion](https://www.freelists.org/list/dl-learner-discussion)
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* Latest Release: https://github.com/SmartDataAnalytics/DL-Learner/releases
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Documentation for DL-Learner:
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* please visit http://dl-learner.org for general information
@@ -16,7 +16,7 @@ Documentation for DL-Learner:
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* Docker: https://github.com/SmartDataAnalytics/DL-Learner/tree/develop/docker
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DL-Learner is Open Source and licensed under the GNU General Public License 3.
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(Copyright (c) 2007-2018, Jens Lehmann).
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(Copyright (c) 2007-2019, Jens Lehmann).
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DL-Learner uses several other libraries. An incomplete list is as follows:
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* [OWL API](https://owlcs.github.io/owlapi/) (licensed under LGPL)

‎components-core/pom.xml‎

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@@ -10,9 +10,13 @@
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<parent>
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<groupId>org.dllearner</groupId>
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<artifactId>dllearner-parent</artifactId>
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<version>1.3.1-SNAPSHOT</version>
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<version>1.4.1-SNAPSHOT</version>
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</parent>
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<properties>
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<automatic.module.name>org.dllearner</automatic.module.name>
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</properties>
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<profiles>
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<profile>
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<id>release</id>
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<dependency>
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<groupId>net.sourceforge.owlapi</groupId>
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<artifactId>org.semanticweb.hermit</artifactId>
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<exclusions>
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<exclusion>
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<groupId>commons-logging</groupId>
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<artifactId>commons-logging</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.geronimo.specs</groupId>
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<artifactId>geronimo-activation_1.1_spec</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.geronimo.specs</groupId>
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<artifactId>geronimo-javamail_1.4_spec</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.geronimo.specs</groupId>
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<artifactId>geronimo-stax-api_1.0_spec</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
@@ -404,6 +426,12 @@
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<dependency>
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<groupId>org.springframework</groupId>
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<artifactId>spring-beans</artifactId>
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<exclusions>
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<exclusion>
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<groupId>commons-logging</groupId>
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<artifactId>commons-logging</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>org.apache.lucene</groupId>
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<dependency>
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<groupId>com.thoughtworks.xstream</groupId>
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<artifactId>xstream</artifactId>
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<version>1.4.11.1</version>
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<version>1.4.13</version>
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<exclusions>
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<exclusion>
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<groupId>xpp3</groupId>
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<artifactId>xpp3_min</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<!--
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<dependency>
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</dependency>
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<!-- https://mvnrepository.com/artifact/org.tinyjee.jgraphx/jgraphx -->
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<!--
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<dependency>
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<groupId>org.tinyjee.jgraphx</groupId>
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<artifactId>jgraphx</artifactId>
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<version>3.4.1.3</version>
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</dependency>
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-->
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<!--
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<dependency>
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<artifactId>commons-httpclient</artifactId>
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<groupId>commons-httpclient</groupId>
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</exclusion>
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<exclusion>
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<artifactId>commons-beanutils-core</artifactId>
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<groupId>commons-beanutils</groupId>
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</exclusion>
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<exclusion>
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<groupId>commons-logging</groupId>
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<artifactId>commons-logging</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>edu.berkeley.compbio</groupId>
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<artifactId>jlibsvm</artifactId>
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<exclusions>
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<exclusion>
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<groupId>com.martiansoftware</groupId>
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<artifactId>JSAP</artifactId>
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</exclusion>
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<exclusion>
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<groupId>commons-logging</groupId>
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<artifactId>commons-logging</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<dependency>
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<groupId>org.reflections</groupId>
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<artifactId>reflections</artifactId>
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<version>0.9.11</version>
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<version>0.9.12</version>
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</dependency>
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<dependency>
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<artifactId>jaxws-api</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
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<version>2.12.1</version>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
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<version>2.12.1</version>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
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<version>${log4j.version}</version>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
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<version>${log4j.version}</version>
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</dependency>
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</dependencies>
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</project>

‎components-core/src/etc/overview.html‎

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<p>
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Project Homepage: <a href="http://dl-learner.org">http://dl-learner.org</a> <br />
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GitHub Website: <a href="https://github.com/AKSW/DL-Learner/">https://github.com/AKSW/DL-Learner/</a>
11+
GitHub Website: <a href="https://github.com/SmartDataAnalytics/DL-Learner/">https://github.com/AKSW/DL-Learner/</a>
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</p>
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<p><img src="https://raw.githubusercontent.com/github/media/master/octocats/blacktocat-16.png" border="0" alt="GitHub Logo" /></p>
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</body>
17-
</html>
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</html>

‎components-core/src/main/java/org/dllearner/core/AbstractReasonerComponent.java‎

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@@ -142,7 +142,7 @@ public abstract class AbstractReasonerComponent extends AbstractComponent implem
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@ConfigOption(description = "the underlying knowledge sources", required = true)
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protected Set<KnowledgeSource> sources;
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145-
public AbstractReasonerComponent(){
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public AbstractReasonerComponent(){
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}
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/**

‎components-core/src/main/java/org/dllearner/core/owl/AbstractHierarchy.java‎

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@@ -81,19 +81,26 @@ public SortedSet<T> getChildren(T entity, boolean direct) {
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SortedSet<T> result = hierarchyDown.get(entity);
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if(result == null) {
84-
logger.debug("Query for " + entity + " in hierarchy, but the entity is not contained in the (downward) hierarchy, e.g. because the entity does not exist or is ignored. Returning empty result instead.");
84+
logger.debug("Query for " + entity + " in hierarchy, but the entity is not contained in the (downward)" +
85+
" hierarchy, e.g. because the entity does not exist or is ignored. Returning empty result instead.");
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return new TreeSet<>();
8687
}
87-
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// create new set because we'll modify the set
90+
result = new TreeSet<>(result);
91+
92+
// depending on the reasoner implementation, the entity itself is trivially contained, so remove it here
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result.remove(entity);
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// recursive call for decendants
8996
if(!direct) { // get transitive children
9097
SortedSet<T> tmp = new TreeSet<>();
9198
for(T child : result){
9299
tmp.addAll(getChildren(child, direct));
93100
}
94101
result.addAll(tmp);
95102
}
96-
return new TreeSet<>(result);
103+
return result;
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}
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/* (non-Javadoc)
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112119
SortedSet<T> result = hierarchyUp.get(entity);
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114121
if(result == null) {
115-
logger.debug("Query for " + entity + " in hierarchy, but the entity is not contained in the (upward) hierarchy, e.g. because the entity does not exist or is ignored. Returning empty result instead.");
122+
logger.debug("Query for " + entity + " in hierarchy, but the entity is not contained in the (upward) " +
123+
"hierarchy, e.g. because the entity does not exist or is ignored. Returning empty result instead.");
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return new TreeSet<>();
117125
}
118-
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127+
// create new set because we'll modify the set
128+
result = new TreeSet<>(result);
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// depending on the reasoner implementation, the entity itself is trivially contained, so remove it here
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result.remove(entity);
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// recursive call for ancestors
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if(!direct) {
121135
SortedSet<T> tmp = new TreeSet<>();
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for(T parent : result){
@@ -125,7 +139,7 @@ public SortedSet<T> getParents(T entity, boolean direct) {
125139
result.addAll(tmp);
126140
}
127141

128-
return new TreeSet<>(result);
142+
return result;
129143
}
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/* (non-Javadoc)

‎components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java‎

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1818
*/
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package org.dllearner.core.owl;
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import java.util.HashSet;
22-
import java.util.Set;
23-
import java.util.SortedMap;
24-
import java.util.SortedSet;
25-
import java.util.TreeSet;
21+
import java.util.*;
22+
import java.util.stream.Collectors;
23+
import java.util.stream.Stream;
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import org.semanticweb.owlapi.model.OWLAxiom;
2826
import org.semanticweb.owlapi.model.OWLClass;
@@ -31,7 +29,6 @@
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import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
3230
import org.slf4j.Logger;
3331
import org.slf4j.LoggerFactory;
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import uk.ac.manchester.cs.owl.owlapi.OWLClassImpl;
3633
import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
3734

@@ -122,33 +119,56 @@ public boolean isSubclassOf(OWLClassExpression subClass, OWLClassExpression supe
122119

123120
@Override
124121
public ClassHierarchy clone() {
125-
return new ClassHierarchy(getHierarchyUp(), getHierarchyDown());
122+
return new ClassHierarchy(new TreeMap<>(getHierarchyUp()), new TreeMap<>(getHierarchyDown()));
126123
}
127-
128-
public Set<OWLAxiom> toOWLAxioms(){
129-
return toOWLAxioms(OWL_THING);
124+
125+
/**
126+
* Converts the class hierarchy to a set of subclass axioms.
127+
*
128+
* @return a set of subclass axioms
129+
*/
130+
public Set<OWLAxiom> toOWLAxioms() {
131+
return getEntities().stream().flatMap(cls ->
132+
Optional.ofNullable(getChildren(cls)).map(Collection::stream).orElseGet(Stream::empty)
133+
.map(sub -> df.getOWLSubClassOfAxiom(sub, cls))
134+
).collect(Collectors.toSet());
130135
}
131-
132-
public Set<OWLAxiom> toOWLAxioms(OWLClassExpression concept){
136+
137+
/**
138+
* Converts the class hierarchy starting from the given concept <code>ce</code> to a set of subclass axioms.
139+
*
140+
* @param ce the root
141+
* @return a set of subclass axioms
142+
*/
143+
public Set<OWLAxiom> toOWLAxioms(OWLClassExpression ce) {
133144
Set<OWLAxiom> axioms = new HashSet<>();
134-
Set<OWLClassExpression> subConcepts = getChildren(concept);
135-
if (subConcepts != null) {
136-
for (OWLClassExpression sub : subConcepts){
137-
axioms.add(df.getOWLSubClassOfAxiom(sub, concept));
138-
axioms.addAll(toOWLAxioms(sub));
145+
Set<OWLClassExpression> visited = new HashSet<>();
146+
Set<OWLClassExpression> subclasses = getChildren(ce);
147+
if (subclasses != null) {
148+
for (OWLClassExpression sub : subclasses) {
149+
axioms.add(df.getOWLSubClassOfAxiom(sub, ce));
150+
toOWLAxioms(sub, axioms, visited);
139151
}
140152
}
141153
return axioms;
142154
}
155+
156+
private void toOWLAxioms(OWLClassExpression ce, Set<OWLAxiom> axioms, Set<OWLClassExpression> visited){
157+
visited.add(ce);
158+
159+
Optional.ofNullable(getChildren(ce)).map(Collection::stream).orElseGet(Stream::empty)
160+
.filter(cls -> !visited.contains(cls))
161+
.forEach(sub -> {
162+
axioms.add(df.getOWLSubClassOfAxiom(sub, ce));
163+
toOWLAxioms(sub, axioms, visited);
164+
});
165+
}
143166

144167
public int getDepth2Root(OWLClassExpression concept){
145168
SortedSet<OWLClassExpression> superClasses = getParents(concept);
146-
int depth = 0;
169+
int depth = 1;
147170
if(superClasses != null){
148-
depth = 1;
149-
for(OWLClassExpression superClass : superClasses){
150-
depth += getDepth2Root(superClass);
151-
}
171+
depth += superClasses.stream().mapToInt(this::getDepth2Root).max().getAsInt();
152172
}
153173
return depth;
154174
}
@@ -172,4 +192,6 @@ public OWLClassExpression getTopConcept() {
172192
public OWLClassExpression getBottomConcept() {
173193
return OWL_NOTHING;
174194
}
195+
196+
175197
}

‎components-core/src/main/java/org/dllearner/core/owl/DatatypePropertyHierarchy.java‎

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@@ -20,6 +20,7 @@
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import java.util.SortedMap;
2222
import java.util.SortedSet;
23+
import java.util.TreeMap;
2324
import java.util.TreeSet;
2425

2526
import org.semanticweb.owlapi.model.OWLDataProperty;
@@ -93,6 +94,6 @@ public OWLDataProperty getBottomConcept() {
9394

9495
@Override
9596
public DatatypePropertyHierarchy clone() {
96-
return new DatatypePropertyHierarchy(getHierarchyUp(), getHierarchyDown());
97+
return new DatatypePropertyHierarchy(new TreeMap<>(getHierarchyUp()), new TreeMap<>(getHierarchyDown()));
9798
}
9899
}

‎components-core/src/main/java/org/dllearner/core/owl/ObjectPropertyHierarchy.java‎

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1818
*/
1919
package org.dllearner.core.owl;
2020

21-
import java.util.Set;
22-
import java.util.SortedMap;
23-
import java.util.SortedSet;
24-
import java.util.TreeSet;
21+
import java.util.*;
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2623
import org.semanticweb.owlapi.model.OWLObjectProperty;
2724
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
@@ -115,6 +112,6 @@ protected String toString(SortedMap<OWLObjectProperty, SortedSet<OWLObjectProper
115112

116113
@Override
117114
public ObjectPropertyHierarchy clone() {
118-
return new ObjectPropertyHierarchy(getHierarchyUp(), getHierarchyDown());
115+
return new ObjectPropertyHierarchy(new TreeMap<>(getHierarchyUp()), new TreeMap<>(getHierarchyDown()));
119116
}
120117
}

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