Cytoscape App and external Dependencies

[Mathias Kemeter]

Hi everyone,

I have developed a database connectivity app for SAP HANA, which requires the JDBC client for SAP HANA to be on the class path. With some trial&error I found, that the plugin works fine when I copy the ngdbc.jar (the JDBC client) to "/Applications/Cytoscape_v3.8.2/framework/lib/openjfx/mac".

Now, I would like to submit the app to the app store to make it more convenient (and visible) for users. Is there any best practice how to deal with the external dependency?

Many thanks,
Mathias

[Scooter Morris]

Hi Mathias,

   Sure -- what you need to do is to add (embed) the dependency to your jar, and the trick to doing that is all in your pom.xml.  There are a number of apps that embed dependencies -- one of mine, clusterMaker2, has quite a number of them, so you can take a look at the pom here: https://github.com/RBVI/clusterMaker2/blob/master/pom.xml  In particular, look at the <configuration><instructions> for the org.apache.felix plugin and then the <dependency> for org.ojalgo.  The net result of that will be a jar for your app that has all of your dependent jars included.

-- scooter

[Mathias Kemeter]

Thank you Scooter! Your suggestion almost worked. I am still facing issues, because my packaged dependency is a multi-release jar and for some reason it is fetching the incorrect release for my Java version. But I assume that this issue is not in any way related to Cytoscape specifics.

Regards,
Mathias

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[Mathias Kemeter]

Hi everyone,

this topic got staled a bit on my side. Now, I've found some time to dig deeper and found the following bug report, which is essentially describing the issue with my external dependency (..which happens to be the same SAP HANA driver mentioned in the bug report):
https://issues.apache.org/jira/browse/FELIX-6396

The bottom line is that multi-release jars are only supported with Karaf 4.3.1 upwards. 

Are there any plans for Cytoscape to move to OSGI 7 / Karaf 4.3.1?

Many thanks,

Mathias

[Mike Kucera]

Hi Mathias,

I am currently migrating the develop branch of Cytoscape 3.10 to Java 17, OSGi 7 and Karaf 4.3.3. 

This will be the platform used by Cytoscape 3.10. However 3.9 was just released recently, so it will be a while until 3.10 is released.

When I have the Cytoscape 3.10 build working can I ask you to test it with your App, to make sure the multi-release jars are working?

Thanks.

Mike.

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[Mathias Kemeter]

Many thanks! I am looking forward to 3.10 then :)

Sure, you can reach out. I am happy to test it with my app.

Regards,

Mathias

[Mathias Kemeter]

Hi everyone,

let me dig out this old thread as 3.10 has been released. Should this be working now? 

I was assuming, that I need to increase the Cytoscape API version to 3.10 and OSGI to 7 in my pom.xml. It seems both is not available on the Cytoscape Nexus.

Best regards,

Mathias

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[Mathias Kemeter]

Small update: I meanwhile changed my project to consume "api-bundle" instead of the individual API jars since for "api-bundle" there is a version 3.10.0 available. However, I am still receiving this error: 

Failed to read artifact descriptor for org.cytoscape:api-bundle:jar:3.10.0: org.cytoscape:api-parent:pom:3.10.0 was not found in https://nrnb-nexus.ucsd.edu/repository/cytoscape_releases/ during a previous attempt.

Is this an issue with my pom.xml?

Regards,

Mathias

[Scooter Morris]

Hi Mathias,

I've seen this before, and typically it means that in a previous attempt it failed and won't retry unless it's forced.  There's probably a flag for that, but I usually just go into my .m2 directory and delete the old attempt.

-- scooter

[Mathias Kemeter]

Hi Scooter,

that's actually what I tried first. I simply deleted .m2 completely. 

My understanding is that the 3.10 api-bundle refers to the 3.10 api-parent, which is not existing on the Nexus:

https://nrnb-nexus.ucsd.edu/#browse/search=keyword%3D3.10.0

Regards,

Mathias

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[Scooter Morris]

Hi Mathias,

You are correct -- we didn't get all of the bundles deployed for some reason.  I'll try to get that corrected by the team tomorrow.

-- scooter

[Mathias Kemeter]

Hi Scooter,

Many thanks! I can see that meanwhile more 3.10 artifacts are available. 

However, I am still having trouble with api-parent, which seems to be a dependency of application-api:

Failed to collect dependencies at org.cytoscape:application-api:jar:3.10.0: Failed to read artifact descriptor for org.cytoscape:application-api:jar:3.10.0

Regards,
Mathias

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[Mike Kucera]

Hi Mathias, 

Can you try again and let me know?

Thanks.

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[Mathias Kemeter]

Thanks Mike! It works on my end now and I can build my plug-in with the 3.10 bindings.

(Unfortunately my initial issue with the multi-release dependency is not yet solved, but that's a different thing)

Regards,

Mathias

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