Cytoscape 3.9.1 problem with opening xlsx files?

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Bernhard Mlecnik

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Aug 11, 2022, 10:26:03 AM8/11/22

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Hi all, do you know if there is an issue with opening xlsx/xls files in Cytoscape 3.9.x

I get this error when opening e.g. a table from xlsx. It seems not to recognize the xlsx ending of the file?

Thanks

System:

Ubuntu 20.04.4 LTS

Kernel 5.11.4-051104-generic x86_64

karaf@Cytoscape 3.9.1()>

java.lang.IllegalStateException: Don't know how to read file:/home/user/data.xlsx
at org.cytoscape.io.internal.read.GenericReaderManager.getReader(GenericReaderManager.java:137) ~[?:?]
at org.cytoscape.io.internal.read.CyTableReaderManagerImpl.getReader(CyTableReaderManagerImpl.java:34) ~[?:?]
at org.cytoscape.tableimport.internal.task.AbstractLoadTableTask.loadTable(AbstractLoadTableTask.java:53) ~[?:?]
at org.cytoscape.tableimport.internal.task.LoadTableFileTask.run(LoadTableFileTask.java:44) ~[?:?]
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321) ~[!/:?]
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:352) [!/:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) [?:?]
at java.util.concurrent.FutureTask.run(FutureTask.java:264) [?:?]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
at java.lang.Thread.run(Thread.java:829) [?:?]
java.lang.IllegalStateException: Don't know how to read file:/home/berni/AhnenCytoscapeImport.xlsx
at org.cytoscape.io.internal.read.GenericReaderManager.getReader(GenericReaderManager.java:137)
at org.cytoscape.io.internal.read.CyTableReaderManagerImpl.getReader(CyTableReaderManagerImpl.java:34)
at org.cytoscape.tableimport.internal.task.AbstractLoadTableTask.loadTable(AbstractLoadTableTask.java:53)
at org.cytoscape.tableimport.internal.task.LoadTableFileTask.run(LoadTableFileTask.java:44)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:352)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)

Scooter Morris

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Aug 11, 2022, 10:29:46 AM8/11/22

to cytoscape-helpdesk

Hi Bernhard,

As far as I know, there's no issues with reading xlsx files. Can you tell us what commands you are using? It looks to me like Cytoscape is not correctly figuring out that it's supposed to be reading Excel.