Merge branch 'master' of https://github.com/genepi/cloudgene into rel…

…ease-2.7.0-tis

.settings/org.eclipse.jdt.core.prefs

@@ -1,5 +1,8 @@
 eclipse.preferences.version=1
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
 org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
+org.eclipse.jdt.core.compiler.release=disabled
 org.eclipse.jdt.core.compiler.source=1.8

README.md

@@ -1,8 +1,7 @@
 Cloudgene
 =========
 
-[![Build Status](https://travis-ci.org/genepi/cloudgene.svg?branch=master)](https://travis-ci.org/genepi/cloudgene)
-[![codecov](https://codecov.io/gh/genepi/cloudgene/branch/master/graph/badge.svg)](https://codecov.io/gh/genepi/cloudgene)
+[![Build Status](https://github.com/genepi/cloudgene/actions/workflows/maven-test.yml/badge.svg)](https://github.com/genepi/cloudgene/actions/workflows/maven-test.yml)
 [![GitHub release](https://img.shields.io/github/release/genepi/cloudgene.svg)](https://GitHub.com/genepi/cloudgene/releases/)
 
 

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.6.3</version>
+	<version>2.7.0</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>
@@ -94,19 +94,17 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
-
 		<dependency>
-			<groupId>genepi</groupId>
-			<artifactId>genepi-db</artifactId>
-			<version>1.2.1</version>
-			<exclusions>
-				<exclusion>
-					<groupId>log4j</groupId>
-					<artifactId>log4j</artifactId>
-				</exclusion>
-			</exclusions>
-		</dependency>
-
+				<groupId>commons-dbutils</groupId>
+				<artifactId>commons-dbutils</artifactId>
+				<version>1.7</version>
+			</dependency>
+
+			<dependency>
+				<groupId>commons-dbcp</groupId>
+				<artifactId>commons-dbcp</artifactId>
+				<version>1.4</version>
+			</dependency>
 		<dependency>
 			<groupId>genepi</groupId>
 			<artifactId>genepi-hadoop</artifactId>
@@ -136,7 +134,7 @@
 		<dependency>
 			<groupId>com.h2database</groupId>
 			<artifactId>h2</artifactId>
-			<version>2.1.210</version>
+			<version>2.2.220</version>
 		</dependency>
 
 		<dependency>
@@ -197,7 +195,7 @@
 		<dependency>
 			<groupId>org.apache.ivy</groupId>
 			<artifactId>ivy</artifactId>
-			<version>2.5.1</version>
+			<version>2.5.2</version>
 		</dependency>
 
 		<!-- Logging -->
@@ -237,17 +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>
@@ -300,7 +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>
@@ -324,7 +323,7 @@
 		<dependency>
 			<groupId>org.bouncycastle</groupId>
 			<artifactId>bcprov-jdk15on</artifactId>
-			<version>1.58</version>
+			<version>1.70</version>
 			<scope>test</scope>
 		</dependency>
 
@@ -374,7 +373,7 @@
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
-			<version>4.8.1</version>
+			<version>4.13.1</version>
 			<scope>test</scope>
 		</dependency>