Autoconfirm or deny file overwrite prompts

[Pierre Klemmer]

Hi all,

I'm importing and exporting data, mostly node and edge tables, to and from Cytoscape regularly. Most actions are performed using the RCy3 package for R. Is there any way to automatically overwrite exported files like tables? Using

commandsRun('table export options=CSV outputFile=xyz.csv table="Network default node" ')

from within R generates a Cytoscape GUI prompt about whether the file that I am saving to should be overwritten that needs to manually be accepted or declined, which prevents my RCy3 script from being totally hands-off. From using help table export in the command line, I don't think that there is an option to force overwrite. Is there some flag in the Cytoscape preferences I can set to auto-overwrite files for all exports? I know that for exporting networks, RCy3 has a function, exportNetwork(), that has an overwrite argument, but there appears to be no such function for exporting tables.

Kind regards,

Pierre

[Ruth Isserlin]

Hi Pierre, 

I have encountered this a lot. The easiest way to get around it is from R.  I check if the file already exists and modify the name if I want to keep the original file or delete it before calling the RCy3 command.  I don’t think there is an option in RCy3 to suppress the pop ups unfortunately. 

Thanks, 

Ruth 

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