Cytoscape to Gephi

[lauraneckstein]

Expected Behavior

Current Behavior

When I try to import a graphml file from cytoscape I get this error. Help!

Possible Solution

Steps to Reproduce

Context

Your Environment

• Version used: Gephi 0.9.1
• Operating System: Mac OS Sierra

java.lang.RuntimeException: Can't modify the read-only 'id' column
at org.gephi.graph.impl.ElementImpl.checkReadOnlyColumn(ElementImpl.java:727)
at org.gephi.graph.impl.ElementImpl.setAttribute(ElementImpl.java:321)
at org.gephi.graph.impl.ElementImpl.setAttribute(ElementImpl.java:315)
at org.gephi.io.processor.plugin.AbstractProcessor.flushToElementAttributes(AbstractProcessor.java:194)
at org.gephi.io.processor.plugin.AbstractProcessor.flushToNode(AbstractProcessor.java:154)
at org.gephi.io.processor.plugin.DefaultProcessor.process(DefaultProcessor.java:169)
at org.gephi.io.processor.plugin.DefaultProcessor.process(DefaultProcessor.java:102)
at org.gephi.io.importer.impl.ImportControllerImpl.process(ImportControllerImpl.java:292)
at org.gephi.desktop.importer.DesktopImportControllerUI.finishImport(DesktopImportControllerUI.java:637)
at org.gephi.desktop.importer.DesktopImportControllerUI.access$200(DesktopImportControllerUI.java:102)
at org.gephi.desktop.importer.DesktopImportControllerUI$6.run(DesktopImportControllerUI.java:285)
[catch] at org.gephi.utils.longtask.api.LongTaskExecutor$RunningLongTask.run(LongTaskExecutor.java:274)
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)

[eduramiba]

Does this happen with latest 0.9.2 snapshot? https://github.com/gephi/gephi#nightly-builds

[lauraneckstein]

Yup, still getting : java.lang.RuntimeException: Can't modify the read-only 'id' column
at org.gephi.graph.impl.ElementImpl.checkReadOnlyColumn(ElementImpl.java:727)
at org.gephi.graph.impl.ElementImpl.setAttribute(ElementImpl.java:321)
at org.gephi.graph.impl.ElementImpl.setAttribute(ElementImpl.java:315)
at org.gephi.io.processor.plugin.AbstractProcessor.flushToElementAttributes(AbstractProcessor.java:259)
at org.gephi.io.processor.plugin.AbstractProcessor.flushToNode(AbstractProcessor.java:186)
at org.gephi.io.processor.plugin.DefaultProcessor.process(DefaultProcessor.java:181)
at org.gephi.io.processor.plugin.DefaultProcessor.process(DefaultProcessor.java:104)
at org.gephi.io.importer.impl.ImportControllerImpl.process(ImportControllerImpl.java:331)
at org.gephi.desktop.importer.DesktopImportControllerUI.finishImport(DesktopImportControllerUI.java:566)
at org.gephi.desktop.importer.DesktopImportControllerUI.access$000(DesktopImportControllerUI.java:104)
at org.gephi.desktop.importer.DesktopImportControllerUI$3.run(DesktopImportControllerUI.java:288)
[catch] at org.gephi.utils.longtask.api.LongTaskExecutor$RunningLongTask.run(LongTaskExecutor.java:274)
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:748)

[eduramiba]

Can you share a file to reproduce this please?

[lauraneckstein]

Kaplan Network.graphml.zip

[lauraneckstein]

updates? sorry, what does a milestone mean?

[eduramiba]

It will soon be fixed for version 0.9.2

[lauraneckstein]

how is this coming?

[eduramiba]

I will probably be able to check it later this week

[eduramiba]

Fixed for 0.9.2, please try with the latest 0.9.2 snapshot later: https://github.com/gephi/gephi#nightly-builds