Hi Georg, Cytoscape not correctly resolving dependencies looks cumbersome. Do you know what more dependencies there could be? You can always download a server neo4j distribution, look into the /lib directory there and add all of these?
/peter G: neubauer.peter S: peter.neubauer P: +46 704 106975 L: http://www.linkedin.com/in/neubauer T: @peterneubauer Neo4j 2.0.0 - (graphs)-[:FOR]->(everyone)<http://blog.neo4j.org/2013/12/neo4j-20-ga-graphs-for-everyone.html> Do something useful - Teach your kids 1 hour code! <http://code.org/learn> On Wed, Jan 15, 2014 at 5:02 PM, Georg Summer <georg.sum...@gmail.com>wrote: > Neo4j Version: 2.0.0 > Cytoscape Version: 3.0.1 > Maven: 3.1.1 > Java: 1.7.0_45 OpenJDK Runtime Environment (IcedTea 2.4.3) (ArchLinux > build 7.u45_2.4.3-1-x86_64) > Eclipse: 4.3.1 > > > GOAL: The goal is to create an app for cytoscape 3.x (curr 3.0.1) that is > able to connect to an instance of neo4j. > > APPROACH: > 1. create a cytoscape 3.0.1 app based on the cytoscape tutorial from > http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Create_a_Bundle_App_Using_IDE > 2. make some menu entry that uses the EmbeddedGraphDatabaseService to > connect to an instance. > 3. add neo4j dependency to the pom.xml of the app > >> <dependency> >> <groupId>org.neo4j</groupId> > > <artifactId>neo4j</artifactId> >> <version>2.0.0</version> >> </dependency> > > 4. mvn clean install > 5. launch the app in Cytoscape > > RESULT: > Cytoscape 3 can not resolve the dependency and the app will not start. > > Suggested FIX 1: > http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/Cytoscape_3_App_Cookbook#Embedding_Dependencies > Use <Embed-Dependency> > >> <!-- 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> >> <!-- <Embed-Dependency>neo4j*;scope=compile|runtime</Embed-Dependency> >> --> >> <!-- <Embed-Transitive>true</Embed-Transitive> --> >> </instructions> >> </configuration> >> </plugin> > > > RESULT: While a neo4j jar is put into the app, the neo4j jar is empty and > does not resolve the dependencies. > > Naive Fix 2: > Normally one has to add more than one lib to the eclipse project. So I > tried that. > >> <dependency> >> <groupId>org.neo4j</groupId> >> <artifactId>neo4j-udc</artifactId> >> <version>2.0.0</version> >> </dependency> >> <dependency> >> <groupId>org.neo4j</groupId> >> <artifactId>neo4j-kernel</artifactId> >> <version>2.0.0</version> >> </dependency> >> <dependency> >> <groupId>org.neo4j</groupId> >> <artifactId>neo4j-lucene-index</artifactId> >> <version>2.0.0</version> >> </dependency> >> <dependency> >> <groupId>org.neo4j</groupId> >> <artifactId>neo4j-graph-algo</artifactId> >> <version>2.0.0</version> >> </dependency> > > > And so on. Embedding them as suggested in Fix 1 as well. > >> >> <Embed-Dependency>lucene-core,geronimo-jta_1.1_spec,scala-library,neo4j*,parboiled-scala_2.10,parboiled-core,concurrentlinkedhashmap-lru;scope=compile|runtime</Embed-Dependency> > > > All these sources are then included in the jar and when I deploy the app > in Cytoscape are recognized. > Why does it not fix the problem? Well Cytoscape demands more dependencies. > At the point of of it asking for org.apache.ant and javax.jms I stopped. > The <Embed-Transitive>true</Embed-Transitive> directive should take care > of that. > > > So I am a bit stuck. Does anyone have an idea how to make an Cytoscape 3 > App depending on Neo4j? > > > Georg > > -- > You received this message because you are subscribed to the Google Groups > "Neo4j" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to neo4j+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > -- You received this message because you are subscribed to the Google Groups "Neo4j" group. To unsubscribe from this group and stop receiving emails from it, send an email to neo4j+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
