Merge branch 'master' into fixes/fix-db-schema

genepi · Oct 3, 2023 · f2e4377 · f2e4377
2 parents 0874503 + 4f9ba91
commit f2e4377
Show file tree

Hide file tree

Showing 53 changed files with 3,834 additions and 3,981 deletions.
diff --git a/files/cloudgene-daemon b/files/cloudgene-daemon
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.5.4</version>
+	<version>2.6.3</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>
@@ -33,8 +33,8 @@
 		<java.version>1.8</java.version>
 		<restlet.version>2.3.12</restlet.version>
 		<hadoop.version>2.6.0-cdh5.16.1</hadoop.version>
-		<node.version>v8.11.4</node.version>
-		<npm.version>6.4.1</npm.version>
+		<node.version>v18.17.1</node.version>
+		<npm.version>9.6.7</npm.version>
 		<webapp>${basedir}/src/main/html/webapp</webapp>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
@@ -60,9 +60,9 @@
 		</repository>
 
 		<repository>
-			<id>jfrog-genepi-maven</id>
-			<name>jfrog-genepi-maven</name>
-			<url>https://genepi.jfrog.io/artifactory/maven/</url>
+			<id>genepi-maven</id>
+			<name>genepi-maven</name>
+			<url>https://genepi.i-med.ac.at/maven</url>
 		</repository>
 
 		<repository>
@@ -134,7 +134,7 @@
 		<dependency>
 			<groupId>com.h2database</groupId>
 			<artifactId>h2</artifactId>
-			<version>2.1.210</version>
+			<version>2.2.220</version>
 		</dependency>
 
 		<dependency>
@@ -188,14 +188,14 @@
 		<dependency>
 			<groupId>org.codehaus.groovy</groupId>
 			<artifactId>groovy-all</artifactId>
-			<version>3.0.9</version>
+			<version>3.0.17</version>
 			<type>pom</type>
 		</dependency>
 
 		<dependency>
 			<groupId>org.apache.ivy</groupId>
 			<artifactId>ivy</artifactId>
-			<version>2.5.1</version>
+			<version>2.5.2</version>
 		</dependency>
 
 		<!-- Logging -->
@@ -235,17 +235,18 @@
 		</dependency>
 
 		<dependency>
-			<groupId>com.esotericsoftware.yamlbeans</groupId>
-			<artifactId>yamlbeans</artifactId>
-			<version>1.15</version>
+		    <groupId>com.contrastsecurity</groupId>
+		    <artifactId>yamlbeans</artifactId>
+		    <version>1.17</version>
 		</dependency>
 
 		<dependency>
-			<groupId>org.apache.velocity</groupId>
-			<artifactId>velocity</artifactId>
-			<version>1.7</version>
+		    <groupId>org.apache.velocity</groupId>
+		    <artifactId>velocity-engine-core</artifactId>
+		    <version>2.3</version>
 		</dependency>
 
+
 		<dependency>
 			<groupId>com.nimbusds</groupId>
 			<artifactId>nimbus-jose-jwt</artifactId>
@@ -265,13 +266,6 @@
 			<version>1.6.2</version>
 		</dependency>
 
-
-		<dependency>
-			<groupId>com.jcraft</groupId>
-			<artifactId>jsch</artifactId>
-			<version>0.1.55</version>
-		</dependency>
-
 		<dependency>
 			<groupId>org.quartz-scheduler</groupId>
 			<artifactId>quartz</artifactId>
@@ -305,7 +299,7 @@
 		<dependency>
 			<groupId>com.google.guava</groupId>
 			<artifactId>guava</artifactId>
-			<version>31.0.1-jre</version>
+			<version>32.0.0-jre</version>
 		</dependency>
 
 		<dependency>
@@ -329,7 +323,7 @@
 		<dependency>
 			<groupId>org.bouncycastle</groupId>
 			<artifactId>bcprov-jdk15on</artifactId>
-			<version>1.58</version>
+			<version>1.70</version>
 			<scope>test</scope>
 		</dependency>
 
@@ -379,7 +373,7 @@
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
-			<version>4.8.1</version>
+			<version>4.13.1</version>
 			<scope>test</scope>
 		</dependency>
 
@@ -400,13 +394,6 @@
 			</exclusions>
 		</dependency>
 
-		<dependency>
-			<groupId>org.apache.sshd</groupId>
-			<artifactId>sshd-sftp</artifactId>
-			<version>0.9.0</version>
-			<scope>test</scope>
-		</dependency>
-
 	</dependencies>
 
 	<!-- **** Build **** -->