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Merge branch 'hotfix-1.1.22'
2 parents aadd54a + 88e992f commit 4538868

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‎pom.xml‎

Lines changed: 23 additions & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -5,15 +5,15 @@
55
<name>baseCode</name>
66
<groupId>baseCode</groupId>
77
<artifactId>baseCode</artifactId>
8-
<version>1.1.21</version>
8+
<version>1.1.22</version>
99
<inceptionYear>2003</inceptionYear>
1010
<description>
1111
<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
1212
</description>
13-
<url>https://github.com/pavlidisLab/basecode</url>
13+
<url>https://github.com/PavlidisLab/baseCode</url>
1414
<organization>
15-
<name>UBC Michael Smith Laboratories</name>
16-
<url>http://www.msl.ubc.ca/</url>
15+
<name>Pavlidis Lab</name>
16+
<url>https://pavlab.msl.ubc.ca/</url>
1717
</organization>
1818
<packaging>jar</packaging>
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<issueManagement>
@@ -27,7 +27,7 @@
2727
<licenses>
2828
<license>
2929
<name>The Apache Software License, Version 2.0</name>
30-
<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
30+
<url>https://www.apache.org/licenses/LICENSE-2.0.txt</url>
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<distribution>repo</distribution>
3232
</license>
3333
</licenses>
@@ -81,7 +81,7 @@
8181
<dependency>
8282
<groupId>commons-io</groupId>
8383
<artifactId>commons-io</artifactId>
84-
<version>2.15.1</version>
84+
<version>2.16.1</version>
8585
</dependency>
8686
<dependency>
8787
<groupId>org.apache.commons</groupId>
@@ -144,45 +144,7 @@
144144
<dependency>
145145
<groupId>org.apache.jena</groupId>
146146
<artifactId>jena-core</artifactId>
147-
<version>2.7.4</version>
148-
<exclusions>
149-
<exclusion>
150-
<groupId>log4j</groupId>
151-
<artifactId>log4j</artifactId>
152-
</exclusion>
153-
<exclusion>
154-
<groupId>org.slf4j</groupId>
155-
<artifactId>slf4j-log4j12</artifactId>
156-
</exclusion>
157-
</exclusions>
158-
</dependency>
159-
<!-- Be careful with versions of lucene -->
160-
<!-- jena-text uses lucene 4.x.. Not ready for this. -->
161-
<!-- <dependency> <groupId>org.apache.jena</groupId> <artifactId>jena-text</artifactId> <version>1.0.0-SNAPSHOT</version>
162-
</dependency> -->
163-
<dependency>
164-
<groupId>org.apache.jena</groupId>
165-
<artifactId>jena-larq</artifactId>
166-
<version>1.0.0-incubating</version>
167-
<exclusions>
168-
<exclusion>
169-
<groupId>log4j</groupId>
170-
<artifactId>log4j</artifactId>
171-
</exclusion>
172-
<exclusion>
173-
<groupId>org.slf4j</groupId>
174-
<artifactId>slf4j-log4j12</artifactId>
175-
</exclusion>
176-
<exclusion>
177-
<artifactId>icu4j</artifactId>
178-
<groupId>com.ibm.icu</groupId>
179-
</exclusion>
180-
</exclusions>
181-
</dependency>
182-
<dependency>
183-
<groupId>org.apache.jena</groupId>
184-
<artifactId>jena-arq</artifactId>
185-
<version>2.9.4</version> <!-- latest release is 2.10.1, but not compatible with larq? -->
147+
<version>2.13.0</version>
186148
<exclusions>
187149
<exclusion>
188150
<groupId>log4j</groupId>
@@ -264,16 +226,28 @@
264226
<version>4.11.0</version>
265227
<scope>test</scope>
266228
</dependency>
229+
<dependency>
230+
<groupId>org.assertj</groupId>
231+
<artifactId>assertj-core</artifactId>
232+
<version>3.25.3</version>
233+
<scope>test</scope>
234+
</dependency>
235+
<dependency>
236+
<groupId>org.apache.logging.log4j</groupId>
237+
<artifactId>log4j-api</artifactId>
238+
<version>2.23.1</version>
239+
<scope>test</scope>
240+
</dependency>
267241
<dependency>
268242
<groupId>org.apache.logging.log4j</groupId>
269243
<artifactId>log4j-core</artifactId>
270-
<version>2.21.1</version>
244+
<version>2.23.1</version>
271245
<scope>test</scope>
272246
</dependency>
273247
<dependency>
274248
<groupId>org.apache.logging.log4j</groupId>
275249
<artifactId>log4j-slf4j-impl</artifactId>
276-
<version>2.21.1</version>
250+
<version>2.23.1</version>
277251
<scope>test</scope>
278252
</dependency>
279253
</dependencies>
@@ -341,7 +315,7 @@
341315
<plugin>
342316
<groupId>com.amashchenko.maven.plugin</groupId>
343317
<artifactId>gitflow-maven-plugin</artifactId>
344-
<version>1.16.0</version>
318+
<version>1.21.0</version>
345319
<configuration>
346320
<!-- Do not push to remote -->
347321
<pushRemote>false</pushRemote>
@@ -444,7 +418,7 @@
444418
<plugin>
445419
<groupId>org.apache.maven.plugins</groupId>
446420
<artifactId>maven-project-info-reports-plugin</artifactId>
447-
<version>3.1.2</version>
421+
<version>3.2.2</version>
448422
<reportSets>
449423
<reportSet>
450424
<reports>

‎src/ontology.properties‎ renamed to ‎src/basecode.properties‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -37,4 +37,7 @@ url.fmaOntology=http://purl.obolibrary.org/obo/fma.owl
3737

3838
ontology.index.dir=
3939
ontology.cache.dir=
40-
ncbo.api.key=
40+
ncbo.api.key=
41+
42+
rserve.start.command=
43+
rlibpath=

‎src/ubic/basecode/ontology/jena/AbstractOntologyMemoryBackedService.java‎

Lines changed: 0 additions & 91 deletions
This file was deleted.

‎src/ubic/basecode/ontology/jena/AbstractOntologyResource.java‎

Lines changed: 3 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -25,37 +25,25 @@
2525
import ubic.basecode.ontology.model.OntologyResource;
2626

2727
import javax.annotation.Nullable;
28-
import java.util.Comparator;
2928
import java.util.Objects;
3029

31-
import static java.util.Comparator.*;
32-
3330
/**
3431
* @author pavlidis
3532
*/
3633
abstract class AbstractOntologyResource implements OntologyResource {
3734

3835
protected static final Logger log = LoggerFactory.getLogger( AbstractOntologyResource.class );
3936

40-
private static final Comparator<OntologyResource> comparator = Comparator
41-
.comparing( OntologyResource::getScore, nullsLast( reverseOrder() ) )
42-
.thenComparing( OntologyResource::getUri, nullsLast( naturalOrder() ) );
43-
4437
private final OntResource res;
45-
@Nullable
46-
private final Double score;
4738

4839
private String _label;
4940
private boolean _isLabelNull = false;
5041

51-
protected AbstractOntologyResource( OntResource resource ) {
52-
this.res = resource;
53-
this.score = null;
54-
}
42+
private String _label;
43+
private boolean _isLabelNull = false;
5544

56-
public AbstractOntologyResource( OntResource resource, double score ) {
45+
protected AbstractOntologyResource( OntResource resource ) {
5746
this.res = resource;
58-
this.score = score;
5947
}
6048

6149
@Override
@@ -97,17 +85,6 @@ public boolean isObsolete() {
9785
return res.hasLiteral( OWL2.deprecated, true );
9886
}
9987

100-
@Override
101-
@Nullable
102-
public Double getScore() {
103-
return score;
104-
}
105-
106-
@Override
107-
public int compareTo( OntologyResource other ) {
108-
return Objects.compare( this, other, comparator );
109-
}
110-
11188
@Override
11289
public boolean equals( Object obj ) {
11390
if ( this == obj ) return true;

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