import table attribute into cytoscape 3.1 beta 3 -> Error

[Ruth Isserlin]

Hi, 

I am trying to import node attributes to my network, very basic node name + single attribute.  I put it into a tab-delimited text file and followed:

File->import->table->file...

I select the file

In the Import Columns From Table box everything is set ok but I think in the 3.2 snapshot I was using previously there was the capability to select more options (how to map the primary keys, which columns to choose).

I have attached a screen shot of the imput screen I get.

When I click on ok I get the following error - "The primary key column needs to be selected" but there is no place I can select it.  

I went back and tried the same with an excel file instead of text file but I got the same results.

This is on windows 7 machine. (maybe it was working fine yesterday with 3.1 beta 3 on my Mac)

Thanks, 

Ruth 

[Tim Hull]

This dialog looks correct for a single-attribute file (.attrs format) - is that what you have? It's only when you have a table file (xls/csv) that you get the preview pane and extra options.

Also, with the network you are importing into, does "shared name" correspond to the ID in your attrs file? If not, you need to choose that column from the "Key Column for Network" drop down.

If you are still having problems, do you have a file you can send us that demonstrates this? I want to see what is happening (since .attrs file import seems to be working fine here) - perhaps it was fixed post-beta 3....

Let me know...

Tim

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[Ruth]

Hi Tim,

I wasn’t using an attrs file.  I am using a txt file and when the txt file didn’t work I swapped it out for a xlsx file and got the same shortened menu.

I just tried to recreate the issue on my saved session and I couldn’t.  I went back and recreated the same network  using my app and had the same issue as before.  There are no errors coming up in the console or in the karaf log file.  The only thing different about my network is that it has a really long name (129 characters)  Could that be the issue?  Is there something with network/node attribute creation that my app is doing wrong so that it messes up node attribute loading?

Thanks,

Ruth

[Tim Hull]

Hi,

If I understand correctly, the problem only happens when you initially create the network using your app, and not if you save that session and reload it later. Is this correct? Also, could you try renaming the network/network collection to something shorter and see if that helps?

With that said, is there a way I can test the app and create a session which has this problem? If not, you may want to show this to Jason or someone else in the Toronto group who knows more about the Cytoscape core...

Hope this helps...

Tim

[Ruth Isserlin]

Hi Tim, 

On Tue, Feb 4, 2014 at 4:51 PM, Tim Hull <tmh...@eng.ucsd.edu> wrote:

Hi,

If I understand correctly, the problem only happens when you initially create the network using your app, and not if you save that session and reload it later. Is this correct?

Correct. 

 

Also, could you try renaming the network/network collection to something shorter and see if that helps?

I tried that already and it didn't work.  I renamed the network and the network group and it didn't help.  i also created a network with a smaller query and had no issues with loading attributes.  So there is something with the large query that messes with the attribute table loading (that subsequently gets fixed if I save and restore).  

 

With that said, is there a way I can test the app and create a session which has this problem? If not, you may want to show this to Jason or someone else in the Toronto group who knows more about the Cytoscape core...

Thanks for the help, I will badger Jason.

[Alexander Pico]

I ran across this same problem recently. The source of the problem was Excel mangling some special text characters and exporting crazy stuff into the .csv I was trying to import into Cytoscape. Apparently, the Cytoscape table importer half-dies when if fails to parse, i.e., the preview fails and a primary key can not be selected. 

I'll report a bug so that the table readers can give a proper error. In the meantime, the workaround is to carefully check your table file for odd characters.

 - Alex

[Linsey Raaijmakers]

I also had the same problem. In my case it was because for the nodes that I added I didn't fill in the "name" column.

Linsey