command line --network import ignored?

[Jason Trenouth]

Hi,

cytoscape.bat --network foo.sif

or

cytoscape.bat --network foo.xgmml

seem to import the network files in Cytoscape 2.8.3, but not in Cytoscape 3.2.1.

Cytoscape 3.2.1 just starts, but with no network imported.

I can import those files via the GUI afterwards.

So am I missing a trick from the command line?

__Jason

[Tim Hull]

This seems to work fine here on Windows - do you see a dialog box after Cytoscape has started up? One should be displayed to select the network collection and node identifier column - you can leave these as defaults, though the network will not import until OK is pressed. 

Also, are the files in question located in your current directory when you run cytoscape.bat? If not, you will need to specify their path (either relative or absolute).

If those ideas don't resolve the issue, can you describe in greater details what happens when you use the --network option? Does any console or GUI error message appear, and does anything related to the file import appear in framework-cytoscape.log (which is located in CytoscapeConfiguration\3 under your home directory in \Users\<username>)...

Hope this helps...

Tim

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[Jason Trenouth]

Hi,

So I did some more experimenting and it looks like the problem is that Cytoscape v3.2.1 expects the pathname separator to be either forward slash or escaped backslash (ie double backslash). This is different from Cytoscape 2.8.3 which allows unescaped backslash on Windows.

Is that a bug or by design?

__Jason

[Tim Hull]

This is a bug - you should be able to use backslashes in paths with command-line options, and in fact you can with some other command line options. 

I went ahead and opened a bug ticket for this:

https://code.cytoscape.org/redmine/issues/3089

Tim