Error importing node/edge table files with Cytoscape command line

[THL]

Originally, I imported our network.sif file through GUI Menu. I then used “Command Line Dialog” to import node and edge table files. They were all loaded successfully.

 

Now, I also use “Command Line Dialog” to import our network.sif file, as the following:

 

network import file indexColumnSourceInteraction=1 indexColumnTargetInteraction=3 firstRowAsColumnNames=false file="C:\Users\Project\network.sif"

 

It was loaded successfully.

 

I then use the same command line as before to load the node table, which is:

 

table import file TargetNetworkCollection="network.sif" WhereImportTable="To a Network Collection" caseSensitiveNetworCollectionKeys=true caseSensitiveNetworkKeys=true DataTypeTargetForNetworkCollection="Node Table Columns" DataTypeTargetForNetworkList="Node Table Columns" firstRowAsColumnNames=true KeyColumnForMapping="shared name" KeyColumnForMappingNetworkList="shared name" keyColumnIndex=1 startLoadRow=1 file="C:\Users\Project\nodeattributes.tsv"

 

However, I got the following error message:

 

Error executing task: Error processing arguments: Couldn't parse value from: org.cytoscape.work.util.ListSingleSelection@a377267 for setting: TargetNetworkCollection

 

I thought maybe we need to give full-path name for TargetNetworkCollection this time since the network.sif file is loaded by command line and a full-path name is displayed at the bottom of the graph. So I changed the command to the following:

 

table import file TargetNetworkCollection=" C:\Users\Project\network.sif" WhereImportTable="To a Network Collection" caseSensitiveNetworCollectionKeys=true caseSensitiveNetworkKeys=true DataTypeTargetForNetworkCollection="Node Table Columns" DataTypeTargetForNetworkList="Node Table Columns" firstRowAsColumnNames=true KeyColumnForMapping="shared name" KeyColumnForMappingNetworkList="shared name" keyColumnIndex=1 startLoadRow=1 file="C:\Users\Project\nodeattributes.tsv"

 

But I still got the same error message.

 

I got exactly the same error message when importing the edge file as well.

 

Any ideas?

 

Another thing I noticed is that the layouts look different between loading network.sif through GUI Menu and loading network.sif by command line. I checked the edges connections, and both layouts seem correct, but the nodes placements are different in two layouts.

 

So does the command line use a different algorithm from the GUI Menu for loading network.sif?

 

Thank you very much for your help!

 

 

[Barry Demchak]

Hi –

 

Would you be able to share your SIF file with us??

 

The Command Line Dialog parameter documentation is very sparse and sketchy. For mastering them, it really helps to have the Cytoscape on hand, as the parameters match directly to the corresponding Java function parameters. I’ll be glad to take a look for you if you can send the file.

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