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Unable to import a large file (?) #1841

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Manaswwm opened this issue Nov 14, 2017 · 11 comments
Closed

Unable to import a large file (?) #1841

Manaswwm opened this issue Nov 14, 2017 · 11 comments
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@mbastian
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Fix Committed GraphML Import
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0.9.3

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@Manaswwm
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I have imported a large network in python (1000+ nodes and about 10000+ edges), I have processed it with networkx package and have exported the data in a '.graphml' file (file size ~4 MB). This file also contains information on color of nodes that are present in my network(as it is absolutely essential for me to be able to distinguish between some nodes).

When I try to open this file using Gephi, the screen does not show anything after I select the file i.e File -> Open -> My_Graphml_file.graphml , following which I do not get a thing in all the three tabs.

Surprisingly, even if I try to import some other file which does not have any color information and about the same size as the one I described above, it still does not show a thing in all the three tabs. But, if I try to import file with small size, I get something on my screen to work with.

So is it the size problem and if it is then how do I solve it?
@eduramiba
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Can you share your file (or a minimal example file) for reproducing the problem?

@eduramiba eduramiba self-assigned this Nov 15, 2017
@Manaswwm
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I think the editor does not support uploading file formats .graphml and .gexf (?)

I am sharing the Dropbox links for those files :
https://www.dropbox.com/s/jryrxy9fz4pjl1u/networkx_graphml.graphml?dl=0 -- this would be the file containing no node color information, but still would not open

https://www.dropbox.com/s/lhztjls2o5tusnd/networkx_gexf.gexf?dl=0 -- this would be the file containing the node color information and would not open

Thanks in advance for help!

@eduramiba
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Thanks, I will check them when possible. Uploading the files as zip here
files.zip

@Manaswwm
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If it helps: I get the following exception thrown when I try to upload the large network -

java.lang.IllegalArgumentException: The id can't be empty
at org.gephi.io.importer.impl.ImportContainerImpl.checkId(ImportContainerImpl.java:1035)
at org.gephi.io.importer.impl.ImportContainerImpl.nodeExists(ImportContainerImpl.java:209)
at org.gephi.io.importer.plugin.file.ImporterGEXF.readNode(ImporterGEXF.java:364)
at org.gephi.io.importer.plugin.file.ImporterGEXF.execute(ImporterGEXF.java:153)
at org.gephi.io.importer.impl.ImportControllerImpl.importFile(ImportControllerImpl.java:199)
at org.gephi.io.importer.impl.ImportControllerImpl.importFile(ImportControllerImpl.java:169)
at org.gephi.desktop.importer.DesktopImportControllerUI$4.run(DesktopImportControllerUI.java:341)
Caused: java.lang.RuntimeException
at org.gephi.desktop.importer.DesktopImportControllerUI$4.run(DesktopImportControllerUI.java:349)
[catch] at org.gephi.utils.longtask.api.LongTaskExecutor$RunningLongTask.run(LongTaskExecutor.java:274)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

@Manaswwm
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Short update:
I dropped the idea of coloring nodes, I just wanted to visualize the large network (which has 1226 nodes and 50976 edges). I constructed a .graphml file using python(networkx) for the same and now I try opening it with Gephi (and it does not open). As a control to check whether my network has some error, I try opening the same .graphml file in Cytoscape and it works.
The only reason why I want to open network in Gephi instead of Cytoscape is that the layout options in former are better than the later.

@Manaswwm
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I figured out the solution to this problem:

I opened the .graphml file that I obtained from python in Cytoscape, then without modifying I exported .graphml from Cytoscape to Gephi and now I am able to visualize the network.

@BonnieSchrack
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I don't think the large file size is so much the problem, as the file type. I import CSV files of thousands of nodes and over 100000 edges, not that Gephi is happy about excessive numbers of edges, but CSV seems to be a Gephi-friendly file type.

@Yalaoui-Bilal
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what is the graph size limitations for Gephi ?

@graemediack
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You could try to use networkx.write_gml instead of .write_graphml, this worked for me after I was having a similiar problem!

@Manaswwm
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Manaswwm commented Dec 13, 2018 via email

@mbastian mbastian added this to the 0.9.3 milestone Jan 22, 2022
@mbastian mbastian assigned mbastian and unassigned eduramiba Jan 22, 2022
mbastian added a commit that referenced this issue Jan 22, 2022
@mbastian
Fix bug #1841
f0fd876
@mbastian
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This issue has been fixed and will be included in the upcoming 0.9.3 release. Thank you for the report!

The root cause was because of a node id being a whitespace " " in your file example. As long as the id is not empty it should work but we had a bug that was trimming the id and therefore it would be empty.

@gskarp gskarp mentioned this issue Mar 28, 2022
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Fix Committed GraphML Import
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@eduramiba @mbastian @BonnieSchrack @Manaswwm @graemediack @Yalaoui-Bilal