Fix some integration test issues.

Author: mikekucera

EnrichmentMapIntegrationTest/pom.xml

@@ -45,25 +45,6 @@
 							</artifactItems>
 						</configuration>
 					</execution>
-					<execution>
-						<id>unpack-api-docs</id>
-						<phase>generate-test-resources</phase>
-						<goals>
-							<goal>unpack</goal>
-						</goals>
-						<configuration>
-							<artifactItems>
-								<artifactItem>
-									<groupId>org.cytoscape</groupId>
-									<artifactId>swing-app-api</artifactId>
-									<version>${cy3.version}</version>
-									<includes>package-list</includes>
-									<type>javadoc</type>
-									<outputDirectory>target/dependencies</outputDirectory>
-								</artifactItem>
-							</artifactItems>
-						</configuration>
-					</execution>
 				</executions>
 			</plugin>
 			<plugin>
@@ -247,28 +228,30 @@
 			<version>${cy3.version}</version>
 			<scope>test</scope>
 		</dependency>
-
 		<dependency>
 			<groupId>org.cytoscape</groupId>
 			<artifactId>ding-presentation-impl</artifactId>
 			<version>${cy3.version}</version>
 			<scope>test</scope>
 		</dependency>
-
 		<dependency>
 			<groupId>org.cytoscape</groupId>
 			<artifactId>vizmap-gui-impl</artifactId>
 			<version>${cy3.version}</version>
 			<scope>test</scope>
 		</dependency>
-
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>vizmap-gui-core-impl</artifactId>
+			<version>${cy3.version}</version>
+			<scope>test</scope>
+		</dependency>
 		<dependency>
 			<groupId>org.cytoscape</groupId>
 			<artifactId>session-impl</artifactId>
 			<version>${cy3.version}</version>
 			<scope>test</scope>
 		</dependency>
-
 		<dependency>
 			<groupId>org.cytoscape</groupId>
 			<artifactId>io-impl</artifactId>
@@ -287,6 +270,37 @@
 			<version>${cy3.version}</version>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>swing-util-impl</artifactId>
+			<version>${cy3.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.cytoscape.distribution</groupId>
+			<artifactId>application-metadata-impl</artifactId>
+			<version>${cy3.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>api-bundle</artifactId>
+			<version>${cy3.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.cytoscape.distribution</groupId>
+			<artifactId>third-party</artifactId>
+			<version>${cy3.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>util-impl</artifactId>
+			<version>${cy3.version}</version>
+			<scope>test</scope>
+		</dependency>
+
 
 		<!-- Pax Exam Dependencies -->
 

EnrichmentMapIntegrationTest/src/test/java/org/baderlab/csplugins/enrichmentmap/integration/PaxExamConfiguration.java

@@ -1,12 +1,6 @@
 package org.baderlab.csplugins.enrichmentmap.integration;
 
-import static org.ops4j.pax.exam.CoreOptions.frameworkStartLevel;
-import static org.ops4j.pax.exam.CoreOptions.junitBundles;
-import static org.ops4j.pax.exam.CoreOptions.maven;
-import static org.ops4j.pax.exam.CoreOptions.mavenBundle;
-import static org.ops4j.pax.exam.CoreOptions.options;
-import static org.ops4j.pax.exam.CoreOptions.systemProperty;
-import static org.ops4j.pax.exam.CoreOptions.vmOption;
+import static org.ops4j.pax.exam.CoreOptions.*;
 import static org.ops4j.pax.exam.karaf.options.KarafDistributionOption.karafDistributionConfiguration;
 
 import org.ops4j.pax.exam.Configuration;
@@ -25,7 +19,7 @@ public Option[] config() {
 
 		// These have to match what's in the pom.xml files.
 		final String cyVersion = "3.7.1"; 
-		final String emVersion = "3.3.1-SNAPSHOT";
+		final String emVersion = "3.3.5-SNAPSHOT";
 		final String karafVersion = "4.2.1";
 		final String groupId   = "org.baderlab.csplugins";
 		final String appBundle = "EnrichmentMap";
@@ -42,10 +36,10 @@ public Option[] config() {
 			frameworkStartLevel(50),
 
 			// Specify all of our repositories
-//				repository("http://code.cytoscape.org/nexus/content/repositories/snapshots/"),
-//				repository("http://code.cytoscape.org/nexus/content/repositories/releases/"),
-//				repository("http://code.cytoscape.org/nexus/content/repositories/thirdparty/"),
-
+			repository("https://nrnb-nexus.ucsd.edu/repository/cytoscape_releases/"),
+			repository("https://nrnb-nexus.ucsd.edu/repository/cytoscape_snapshots/"),
+			repository("https://nrnb-nexus.ucsd.edu/repository/cytoscape_thirdparty/"),
+			
 			// Misc. bundles required to run minimal Cytoscape
 			mavenBundle().groupId("org.apache.servicemix.specs").artifactId("org.apache.servicemix.specs.jaxb-api-2.1").version("1.2.0").startLevel(3),
 			mavenBundle().groupId("org.apache.servicemix.bundles").artifactId("org.apache.servicemix.bundles.jaxb-impl").version("2.1.6_1").startLevel(3),