clueGO - saving a session is not working

[Assa Yeroslaviz]

Hi,

I am having troubles saving and/or opening a session of clueGO.

I'm using the clueGO v. 2.2.6 on an iMac with Cytoscape 3.3.0

when I try to save a session I get this error:

When I afterwards try to upload the session:

I have seen, that there are similar problems in earlier version ( I have seen it in the earlier forum). Is there a fix for that now?

thanks

Assa

[Bernhard]

Hi Assa, can you please run Cytoscape from a terminal and reproduce the error and post the terminal output to see what happened?
Thanks

[Assa Yeroslaviz]

Ok. I did it.

this is the error I get when trying to save the clueGO session:

java.lang.NullPointerException

at fr.upmc.ici.cluegoplugin.cluego.internal.task.SaveClueGOSessionTask.run(SaveClueGOSessionTask.java:216)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:326)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:355)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

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

this is the  error I get when trying to load the saved file:

java.util.zip.ZipException: error in opening zip file

at java.util.zip.ZipFile.open(Native Method)

at java.util.zip.ZipFile.<init>(ZipFile.java:219)

at java.util.zip.ZipFile.<init>(ZipFile.java:149)

at java.util.zip.ZipFile.<init>(ZipFile.java:163)

at fr.upmc.ici.cluegoplugin.cluego.internal.task.OpenClueGOSessionTask$OpenClueGOSessionWithoutWarningTask.run(OpenClueGOSessionTask.java:172)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:342)

at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:355)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

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

But I guess this is due to the fact, that the file is not correctly saved.

any ideas?

thanks

Assa

[Bernhard]

Hi Assa, I tried to reproduce the problem. I used C. elegans data and saved a simple network and it worked. We just updated the C. elegans data with the latest info.
- Could you move you C elegans Source folder from the ClueGOConfiguration folder and download C. elegans again?
- Could you retry to save the Network you created?
- If it still doesn't work, could you post here the steps you used to create the network before you saved it?
Thanks

[Assa Yeroslaviz]

Hi Bernhard,

I have circumvented the problem. I have downloaded Cytoscpae verion 3.4.0 and tried it again. I was able to start ClueGO, save and load a saved session. For now it is working fine 

Just a question for the future - does ClueGO also saves the all networks created in the cytoscape session (or only the clueGO networks)? 

thanks for the help.

Assa

[Bernhard]

Hi Assa, good to know that it works; at least for now :). Let me know if you get new issues with saving the project, it can for sure be that there are still some bugs somewhere.
ClueGO saves the Cytoscape session (.cys) into the .cluego file (which is in fact just a zip file containing all data you used in ClueGO (and data to be able to reconstruct the ClueGO session)) plus the cytoscape session. So theoretically you should get back the same session that you saved before and also all cytoscape networks you did outside of ClueGO. The only problematic thing is when you manually modify a ClueGO network like deleting an edge or node, not using the delete function of ClueGO/Pedia. Then you will get problems saving the ClueGO session.
Best