cannot export edge or note tables in 2.3.1

[cov...@mail.nih.gov]

Having difficulty exporting either node or edge tables in Cytoscape 3.2.1. Searching blogs indicates that right click
anywhere in table begins the process. But no luck. Using export > table > default.edge generates an empty file.
Cntl-A and Cntl-V into an excel file does not work either.
Suggestions would be most appreciated.

Thanks,
David

[Tim Hull]

The way to do it should be File-Export-Table... Not sure why that isn't working - I just tried it with the bundled galFiltered.cys file and it works fine exporting to CSV format. Can you give more details about what you're trying to export and what you're seeing? It would help if you had an example file that demonstrates the problem...

Let us know...

Tim

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[cov...@mail.nih.gov]

Tim,
Thanks for the reply. The attached image is a png image of what I am trying to export. There are a number of subnetworks available for viewing, and I have selected test_new2.csv(8). From the screenshot, this consists of 309 nodes and 361 edges. The edge appears in the Table Panel at the bottom. When I attempt to export>table>test_new2.csv(8) default edge, I get a zero length table. When I export test_new2.csv default edge, I get the 18204 edges in the top level network. In the pull-down menu for which network item to export, all have the reference to 'default'. Is there another naming convention I need to invoke to get what is displayed on the screen?

[Tim Hull]

The table that should contain the proper data is test_new2.csv(8) default edge - that's very strange that you get an empty table. Do you have a test case that you can share that demonstrates this problem? I don't have the issue when working with an example subnetwork here?  

Also, if you look in the framework-cytoscape.log (under CytoscapeConfiguration/3 in your home directory), do you see any errors related to the export?

Tim

[cov...@mail.nih.gov]

Tim,

Thanks for your reply. I have discovered that the output eventually appears in the target file. The delay is hard
to estimate, but it is certainly greater than 10 minutes.
Per your suggestion, the most recent entries in the log file are below. These begin with setting the current
network to test_new2.csv(8). The silencing/unsilencing comments may be a clue?? However, I have repeated this
more than once, and the delay is significant. Could this be a networking issue, or a file closure issue?

David


2015-06-16 15:18:23,114 [AWT-EventQueue-0] INFO  org.cytoscape.application.internal.CyApplicationManagerImpl - Set current network called: test_new2.csv(8)
2015-06-16 15:27:48,950 [AWT-EventQueue-0] INFO  org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=javax.swing.plaf.basic.BasicBorders$MarginBorder@5f0ca84,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=2,left=2,bottom=2,right=2],paintBorder=false,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Apply to entire column] with gravity: -1.0
2015-06-16 15:27:48,950 [AWT-EventQueue-0] INFO  org.cytoscape.util.swing.PopupMenuGravityTracker - Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=javax.swing.plaf.basic.BasicBorders$MarginBorder@5f0ca84,flags=264,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=2,left=2,bottom=2,right=2],paintBorder=false,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Apply to selected edges] with gravity: -1.0
2015-06-16 15:28:04,785 [AWT-EventQueue-0] INFO  org.cytoscape.event.internal.CyEventHelperImpl - silencing event source: test_new2.csv(8) default node
2015-06-16 15:28:04,785 [AWT-EventQueue-0] INFO  org.cytoscape.event.internal.CyEventHelperImpl - unsilencing event source: test_new2.csv(8) default node
2015-06-16 15:28:04,964 [AWT-EventQueue-0] INFO  org.cytoscape.event.internal.CyEventHelperImpl - silencing event source: test_new2.csv(8) default edge
2015-06-16 15:28:04,964 [AWT-EventQueue-0] INFO  org.cytoscape.event.internal.CyEventHelperImpl - unsilencing event source: test_new2.csv(8) default edge

On Thursday, June 11, 2015 at 1:02:45 PM UTC-4, cov...@mail.nih.gov wrote:

[Tim Hull]

Given that, I suspect you may be running low on free memory. Can you check how much free memory Cytoscape has with the session loaded? To do that, just click the Memory button in the bottom-right corner of the Cytoscape window.

If you are running low on free memory in Cytoscape, one thing to check may be the version of Cytoscape installed. You need 64-bit to address more than 1.1GB of memory - and to run that, you will need to manually download 64-bit Java from Oracle's website (the standard Java version supplied by java.com is 32-bit). This will require a 64-bit version of Windows, which is the most common variant on Windows 7+.

Let me know if you can resolve the issue - if not, could you send a copy of your session file (or any session file that demonstrates the problem). That would help in being able to reproduce this..

Tim