Updated many dependencies.

owlcollab · May 11, 2020 · 34d29f0 · 34d29f0
1 parent 5518cab
commit 34d29f0
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Showing 6 changed files with 19 additions and 32 deletions.
diff --git a/Golr-Client/pom.xml b/Golr-Client/pom.xml
@@ -37,7 +37,7 @@
 		<dependency>
 			<groupId>org.apache.httpcomponents</groupId>
 			<artifactId>httpclient</artifactId>
-			<version>4.3.6</version>
+			<version>4.5.12</version>
 		</dependency>
 	</dependencies>
 </project>
diff --git a/OWLTools-Core/pom.xml b/OWLTools-Core/pom.xml
@@ -102,10 +102,6 @@
 			<groupId>com.google.code.gson</groupId>
 			<artifactId>gson</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>jline</groupId>
-			<artifactId>jline</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>org.geneontology</groupId>
 			<artifactId>expression-materializing-reasoner</artifactId>
@@ -118,7 +114,7 @@
 		<dependency>
 			<groupId>org.geneontology</groupId>
 			<artifactId>obographs</artifactId>
-			<version>0.1.0</version>
+			<version>0.2.1</version>
 		</dependency>
 		<dependency>
 			<groupId>com.google.guava</groupId>

diff --git a/OWLTools-Parent/pom.xml b/OWLTools-Parent/pom.xml
@@ -18,8 +18,8 @@
 	</issueManagement>
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-		<owlapi.version>4.5.6</owlapi.version>
-		<slf4j.version>1.7.10</slf4j.version>
+		<owlapi.version>4.5.6</owlapi.version> <!-- Needs fix to upgrade to 4.5.16; see failing test-->
+		<slf4j.version>1.7.30</slf4j.version>
 	</properties>
 
 	<build>
@@ -131,7 +131,7 @@
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
-			<version>4.12</version>
+			<version>4.13</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
@@ -173,7 +173,7 @@
 			<dependency>
 				<groupId>net.sourceforge.owlapi</groupId>
 				<artifactId>org.semanticweb.hermit</artifactId>
-				<version>1.3.8.413</version>
+				<version>1.4.5.456</version>
 			</dependency>
 			<dependency>
 				<groupId>org.bbop</groupId>
@@ -188,7 +188,7 @@
 			<dependency>
 				<groupId>org.apache.ant</groupId>
 				<artifactId>ant</artifactId>
-				<version>1.8.2</version>
+				<version>1.10.7</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.commons</groupId>
@@ -209,22 +209,22 @@
 			<dependency>
 				<groupId>commons-io</groupId>
 				<artifactId>commons-io</artifactId>
-				<version>2.2</version>
+				<version>2.6</version>
 			</dependency>
 			<dependency>
 				<groupId>commons-collections</groupId>
 				<artifactId>commons-collections</artifactId>
-				<version>3.2.1-fixit</version> <!-- This version does not contain a zero day exploit class InvokeTransformer -->
+				<version>3.2.2</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.commons</groupId>
 				<artifactId>commons-lang3</artifactId>
-				<version>3.1</version>
+				<version>3.10</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.commons</groupId>
 				<artifactId>commons-math3</artifactId>
-				<version>3.3</version>
+				<version>3.6.1</version>
 			</dependency>
 			<dependency>
 				<groupId>org.semanticweb.elk</groupId>
@@ -234,24 +234,13 @@
 			<dependency>
 				<groupId>com.google.code.gson</groupId>
 				<artifactId>gson</artifactId>
-				<version>2.2.4</version>
+				<version>2.8.6</version>
 			</dependency>
 			<dependency>
 				<groupId>rhino</groupId>
 				<artifactId>js</artifactId>
 				<version>1.7R2</version>
 			</dependency>
-			<dependency>
-				<groupId>jline</groupId>
-				<artifactId>jline</artifactId>
-				<version>0.9.93</version>
-				<exclusions>
-					<exclusion>
-						<groupId>junit</groupId>
-						<artifactId>junit</artifactId>
-					</exclusion>
-				</exclusions>
-			</dependency>
 			<dependency>
 				<groupId>org.geneontology</groupId>
 				<artifactId>expression-materializing-reasoner</artifactId>
@@ -270,7 +259,7 @@
 			<dependency>
 				<groupId>com.google.guava</groupId>
 				<artifactId>guava</artifactId>
-				<version>18.0</version>
+				<version>29.0-jre</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.jena</groupId>

diff --git a/OWLTools-Sim/pom.xml b/OWLTools-Sim/pom.xml
@@ -56,7 +56,7 @@
 		<dependency>
 			<groupId>com.googlecode.javaewah</groupId>
 			<artifactId>JavaEWAH</artifactId>
-			<version>0.7.7</version>
+			<version>1.1.7</version>
 		</dependency>
 	</dependencies>
 </project>
diff --git a/OWLTools-Sim/src/main/java/owltools/sim2/FastOwlSim.java b/OWLTools-Sim/src/main/java/owltools/sim2/FastOwlSim.java
@@ -41,6 +41,8 @@
 import com.googlecode.javaewah.EWAHCompressedBitmap;
 import com.googlecode.javaewah.IntIterator;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
+
 /**
  * Faster implementation of OwlSim
  * 
@@ -2102,7 +2104,7 @@ public void loadLCSCache(String fileName) throws IOException {
 
 		FileInputStream s = new FileInputStream(fileName);
 		//List<String> lines = IOUtils.readLines(s);
-		LineIterator itr = IOUtils.lineIterator(s, null);
+		LineIterator itr = IOUtils.lineIterator(s, UTF_8);
 		while (itr.hasNext()) {
 			String line = itr.nextLine();
 			String[] vals = line.split("\t");

diff --git a/OWLTools-Solr/pom.xml b/OWLTools-Solr/pom.xml
@@ -33,7 +33,7 @@
 		<dependency>
 			<artifactId>solr-solrj</artifactId>
 			<groupId>org.apache.solr</groupId>
-			<version>3.6.0</version>
+			<version>3.6.2</version>
 			<exclusions>
 				<exclusion>
 					<artifactId>slf4j-api</artifactId>
@@ -48,7 +48,7 @@
 		<dependency>
 			<groupId>org.yaml</groupId>
 			<artifactId>snakeyaml</artifactId>
-			<version>1.10</version>
+			<version>1.26</version>
 		</dependency>
 		<dependency>
 			<groupId>com.google.code.gson</groupId>