org.osgi.framework.BundleException, How do I add and use dependencies in Cytoscape bundle app?

[Torgeir Ous]

Hi,

I'm making a Cytoscape app and want to use Solrj for searching multiple files (size up to 0.5GBf for each file). The problem is that I get a "org.osgi.framework.BundleException" when starting the app. I've added the dependency in pom.xml, but if I try importing something from SolrJ I get this error:

org.cytoscape.app.internal.exception.AppStartupException: Bundle start error

at org.cytoscape.app.internal.manager.BundleApp.start(BundleApp.java:84)

at org.cytoscape.app.internal.manager.AppManager.initializeApps(AppManager.java:347)

at org.cytoscape.app.internal.manager.AppManager.attemptInitialization(AppManager.java:230)

at org.cytoscape.app.internal.manager.AppManager.frameworkEvent(AppManager.java:222)

at org.apache.felix.framework.util.EventDispatcher.invokeFrameworkListenerCallback(EventDispatcher.java:835)

at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:785)

at org.apache.felix.framework.util.EventDispatcher.run(EventDispatcher.java:1088)

at org.apache.felix.framework.util.EventDispatcher.access$000(EventDispatcher.java:54)

at org.apache.felix.framework.util.EventDispatcher$1.run(EventDispatcher.java:101)

at java.lang.Thread.run(Thread.java:745)

Caused by: org.osgi.framework.BundleException: Unresolved constraint in bundle org.cytoscape.drugapp.drug-cyaction-app [113]: Unable to resolve 113.0: missing requirement [113.0] osgi.wiring.package; (osgi.wiring.package=org.apache.solr.client.solrj.impl)

at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:955)

at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:942)

at org.cytoscape.app.internal.manager.BundleApp.start(BundleApp.java:82)

... 9 more

What is the right approach to add and use dependencies in a Cytoscape bundle app?

Here is my pom.xml:

<?xml version="1.0" encoding="UTF-8"?>

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">

<properties>

<bundle.symbolicName>org.cytoscape.drugapp.drug-cyaction-app</bundle.symbolicName>

<bundle.namespace>org.cytoscape.drugapp</bundle.namespace>

</properties>

<modelVersion>4.0.0</modelVersion>

<groupId>org.cytoscape.drugapp</groupId>

<artifactId>drug-cyaction-app</artifactId>

<version>1.0-SNAPSHOT</version>

<name>${bundle.symbolicName} [${bundle.namespace}]</name>

<packaging>bundle</packaging>

<build>

<resources>

<resource>

<directory>src/main/resources</directory>

</resource>

</resources>

<!-- Cytoscape requires Java 1.8 -->

<plugins>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-compiler-plugin</artifactId>

<version>2.3.2</version>

<executions>

<execution>

<id>default-testCompile</id>

<phase>test-compile</phase>

<goals>

<goal>testCompile</goal>

</goals>

</execution>

<execution>

<id>default-compile</id>

<phase>compile</phase>

<goals>

<goal>compile</goal>

</goals>

</execution>

</executions>

<configuration>

<source>1.8</source>

<target>1.8</target>

<optimize>true</optimize>

<showWarnings>true</showWarnings>

<showDeprecation>true</showDeprecation>

<compilerArguments>

<Xmaxwarns>10000</Xmaxwarns>

<Xmaxerrs>10000</Xmaxerrs>

</compilerArguments>

</configuration>

</plugin>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-surefire-plugin</artifactId>

<version>2.7.1</version>

<configuration>

<redirectTestOutputToFile>true</redirectTestOutputToFile>

</configuration>

</plugin>

<!-- Generates the OSGi metadata based on the osgi.bnd file. -->

<plugin>

<groupId>org.apache.felix</groupId>

<artifactId>maven-bundle-plugin</artifactId>

<version>2.3.7</version>

<extensions>true</extensions>

<configuration>

<instructions>

<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>

<Bundle-Version>${project.version}</Bundle-Version>

<Export-Package>${bundle.namespace}</Export-Package>

<Private-Package>${bundle.namespace}.internal.*</Private-Package>

<Bundle-Activator>${bundle.namespace}.internal.CyActivator</Bundle-Activator>

</instructions>

</configuration>

</plugin>

</plugins>

</build>

<!-- Links to the Cytoscape Maven repositories. -->

<repositories>

<repository>

<id>cytoscape_snapshots</id>

<snapshots>

</snapshots>

<releases>

<enabled>false</enabled>

</releases>

<name>Cytoscape Snapshots</name>

<url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url>

</repository>

<repository>

<id>cytoscape_releases</id>

<snapshots>

<enabled>false</enabled>

</snapshots>

<releases>

</releases>

<name>Cytoscape Releases</name>

<url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>

</repository>

</repositories>

<!-- Dependencies needed to compile this project. -->

<dependencies>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>core-task-api</artifactId>

<version>3.3.0</version>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>layout-api</artifactId>

<version>3.3.0</version>

</dependency>

<dependency>

<groupId>org.osgi</groupId>

<artifactId>org.osgi.core</artifactId>

<version>4.2.0</version>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>service-api</artifactId>

<version>3.3.0</version>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>swing-application-api</artifactId>

<version>3.3.0</version>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>session-api</artifactId>

<version>3.3.0</version>

</dependency>

<dependency>

<groupId>org.apache.solr</groupId>

<artifactId>solr-solrj</artifactId>

<version>6.0.0</version>

</dependency>

<!-- Logging -->

<dependency>

<groupId>org.ops4j.pax.logging</groupId>

<artifactId>pax-logging-api</artifactId>

<version>1.5.2</version>

<scope>provided</scope>

</dependency>

</dependencies>

</project>

[piet molenaar]

Hi Torgeir,

This issue is described here: http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/Cytoscape_3_App_Cookbook#Including_packages_accessed_via_reflection_.28e.g._JDBC.2C_SAX_parsers.2C_XML_utilities.29

Hope this helps,

Piet

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[Torgeir Ous]

I tried the approach mentioned in your link and also this: http://wiki.cytoscape.org/HowToAddLibraryDependencies

but without success. I created a new project using the version 3.3.0 cyaction-app archetype, then followed both procedures from the links again and it still doesn't work.

I've added my pom-file and a file with output from running "mvn clean install". If someone can take a look or maybe show me how you guys are adding dependencies would be helpful. :)

By the way, I'm using cytoscape 3.3.0 and mvn 3.3.9.

-- UPDATE: I've narrowed it down to that for some reason I cant use any later release than Solr 4.3.1

Torgeir

[piet molenaar]

Hi Torgeir,

You have to add the dependencies to the bundle configuration instructions also: see for example one of my poms attached; note escpecially the part in the maven bundle plugin around line 80

Hope this helps,

Piet

On Thu, May 26, 2016 at 3:22 PM, Torgeir Ous <torge...@gmail.com> wrote:

I tried the approach mentioned in your link and also this: http://wiki.cytoscape.org/HowToAddLibraryDependencies

but without success. I created a new project using the version 3.3.0 cyaction-app archetype, then followed both procedures from the link again in it still doesn't work.

I've added my pom-file and a file with output from running "mvn clean install". If someone can take a look or maybe show me how you guys are adding dependencies would be helpful. :)

By the way, I'm using cytoscape 3.3.0 and mvn 3.3.9.

Torgeir

[Torgeir Ous]

I ended up updating maven-bundle-plugin from version 2.3.7 to 3.0.1 and that solved the problem.