Merge branch 'hotfix-1.1.2'

PavlidisLab · Dec 14, 2021 · 49bca56 · 49bca56
2 parents c36cc70 + a636dde
commit 49bca56
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Showing 3 changed files with 38 additions and 33 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1.1</version>
+	<version>1.1.2</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
@@ -150,6 +150,16 @@
 			<groupId>org.apache.jena</groupId>
 			<artifactId>jena-core</artifactId>
 			<version>2.7.4</version>
+			<exclusions>
+				<exclusion>
+					<groupId>log4j</groupId>
+					<artifactId>log4j</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.slf4j</groupId>
+					<artifactId>slf4j-log4j12</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<!-- Be careful with versions of lucene -->
 		<!-- jena-text uses lucene 4.x.. Not ready for this. -->
@@ -159,11 +169,31 @@
 			<groupId>org.apache.jena</groupId>
 			<artifactId>jena-larq</artifactId>
 			<version>1.0.0-incubating</version>
+			<exclusions>
+				<exclusion>
+					<groupId>log4j</groupId>
+					<artifactId>log4j</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.slf4j</groupId>
+					<artifactId>slf4j-log4j12</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.jena</groupId>
 			<artifactId>jena-arq</artifactId>
 			<version>2.9.4</version> <!-- latest release is 2.10.1, but not compatible with larq? -->
+			<exclusions>
+				<exclusion>
+					<groupId>log4j</groupId>
+					<artifactId>log4j</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.slf4j</groupId>
+					<artifactId>slf4j-log4j12</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 
 		<!-- Lucene -->
@@ -308,13 +338,6 @@
 				</configuration>
 			</plugin>
 		</plugins>
-		<extensions>
-			<extension>
-				<groupId>org.apache.maven.wagon</groupId>
-				<artifactId>wagon-ssh-external</artifactId>
-				<version>3.4.3</version>
-			</extension>
-		</extensions>
 	</build>
 	<reporting>
 		<plugins>
@@ -400,23 +423,6 @@
 			</plugin>
 		</plugins>
 	</reporting>
-	<distributionManagement>
-		<site>
-			<id>broca</id>
-			<name>broca</name>
-			<url>scpexe://otto.pavlab.chibi.ubc.ca:/space/gemmaData/baseCode-site</url>
-		</site>
-		<repository>
-			<id>repo</id>
-			<name>Pavlab</name>
-			<url>scpexe://otto.pavlab.chibi.ubc.ca:/space/maven2</url>
-		</repository>
-		<snapshotRepository>
-			<id>repo</id>
-			<name>Pavlab</name>
-			<url>scpexe://otto.pavlab.chibi.ubc.ca:/space/maven2</url>
-		</snapshotRepository>
-	</distributionManagement>
 	<repositories>
 		<repository>
 			<id>pavlab</id>

diff --git a/test/log4j.properties b/test/log4j.properties
diff --git a/test/ubic/basecode/ontology/ncbo/AnnotatorClientTest.java b/test/ubic/basecode/ontology/ncbo/AnnotatorClientTest.java
@@ -20,13 +20,20 @@
 
 import java.util.Collection;
 
+import org.junit.Assume;
+import org.junit.Before;
 import org.junit.Test;
 
 /**
  * @author Paul
  */
 public class AnnotatorClientTest {
 
+    @Before
+    public void setUp() {
+        Assume.assumeTrue( "", System.getProperty( "ncbo.api.key" ) != null );
+    }
+
     @Test
     public void test() throws Exception {
         Collection<AnnotatorResponse> results = AnnotatorClient.findTerm( "cancer" );