Error Importing node table

[giovanni scardoni]

Hi all,

I cannot import  node tables. The error says that the data type is not correctly selected even if it is.

The same if I export the node table and then try to re-import the same file.

What is the right format and the right extension to correctly import a table?

[Barry Demchak]

Hi –

 

Can you attach a copy of a file that is giving you trouble??

 

Thanks.

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[Scooter Morris]

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Hi Giovanni,

    You should be able to import either .txt, .xlsx, or .csv files without any problems.  Can you send me a sample of the file you're having problems importing?

-- scooter

[Giovanni Scardoni]

Hi,

attached you find the network, the table and the screenshot of the error.

It always happens if I export the table and then I import it. 

2017-04-21 17:35 GMT+02:00 Scooter Morris <sco...@cgl.ucsf.edu>:

On 04/21/2017 03:29 AM, giovanni scardoni wrote:

Hi all,

I cannot import  node tables. The error says that the data type is not correctly selected even if it is.

The same if I export the node table and then try to re-import the same file.

What is the right format and the right extension to correctly import a table?

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Hi Giovanni,

    You should be able to import either .txt, .xlsx, or .csv files without any problems.  Can you send me a sample of the file you're having problems importing?

-- scooter

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Giovanni Scardoni
The Center for BioMedical Computing (CBMC)
www.cbmc.it/~scardonig/
University of Verona
Strada le Grazie, 15 -37134
Verona -Italy

Try these Cytoscape apps!
CentiScaPe: http://www.cbmc.it/~scardonig/centiscape/centiscape.php
Interference: http://www.cbmc.it/~scardonig/interference/Interference.php

[Barry Demchak]

Hi, Giovanni –

 

I see the issue.

 

Looking at the CSV, I see a number of columns, including SUID, name, shared name, selected and a couple of value columns.

 

A table load attempts to merge the file contents with the existing (node) table. The merge is performed by matching key values coming from the existing table with values coming from the file.

 

From the existing table, the default key is shared name. From the file, the default key is the first column, which in your case is SUID. However, SUID isn’t a valid merge key (… happy to explain why if you’re interested). Instead, name or shared name would work.

 

So, to get this to work, I chose shared name as the file’s merge key. I then disabled SUID, name, and selected, as they’re already present in the existing table. The net result was a key of shared name and only your two data columns.

 

With that configuration, the merge went fine.

 

See below:

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Giovanni Scardoni
Sent: Friday, April 21, 2017 10:35 AM
To: cytoscape...@googlegroups.com
Subject: Re: [cytoscape-helpdesk] Error Importing node table

 

 

Hi,

attached you find the network, the table and the screenshot of the error.

 

It always happens if I export the table and then I import it. 

 

 

2017-04-21 17:35 GMT+02:00 Scooter Morris <sco...@cgl.ucsf.edu>:

On 04/21/2017 03:29 AM, giovanni scardoni wrote:

Hi all,

I cannot import  node tables. The error says that the data type is not correctly selected even if it is.

The same if I export the node table and then try to re-import the same file.

What is the right format and the right extension to correctly import a table?

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Hi Giovanni,

    You should be able to import either .txt, .xlsx, or .csv files without any problems.  Can you send me a sample of the file you're having problems importing?

-- scooter

 

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Giovanni Scardoni
The Center for BioMedical Computing (CBMC)
www.cbmc.it/~scardonig/
University of Verona
Strada le Grazie, 15 -37134
Verona -Italy

Try these Cytoscape apps!
CentiScaPe: http://www.cbmc.it/~scardonig/centiscape/centiscape.php
Interference: http://www.cbmc.it/~scardonig/interference/Interference.php

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[Giovanni Scardoni]

Great!

It works.

But all the column are automatically exported. Maybe in the next released it will be good if they can be selected. 

Anyway, SUID seemed to be the best choice for the key, if my DataBase knowledge is not wrong. You arouse my curiosity. Why not?

Thanks!

Giovanni

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Hi Giovanni,

    You should be able to import either .txt, .xlsx, or .csv files without any problems.  Can you send me a sample of the file you're having problems importing?

-- scooter

 

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Giovanni Scardoni
The Center for BioMedical Computing (CBMC)
www.cbmc.it/~scardonig/
University of Verona
Strada le Grazie, 15 -37134
Verona -Italy

Try these Cytoscape apps!
CentiScaPe: http://www.cbmc.it/~scardonig/centiscape/centiscape.php
Interference: http://www.cbmc.it/~scardonig/interference/Interference.php

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[Scooter Morris]

On 04/21/2017 11:21 AM, Giovanni Scardoni wrote:

Great!

It works.

But all the column are automatically exported. Maybe in the next released it will be good if they can be selected. 

Anyway, SUID seemed to be the best choice for the key, if my DataBase knowledge is not wrong. You arouse my curiosity. Why not?

Thanks!

Giovanni

SUID is automatically generated when the session is opened, so it can (and almost always does) change each time you load the session.

-- scooter

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[Giovanni Scardoni]

Ok thanks!

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Hi Giovanni,

    You should be able to import either .txt, .xlsx, or .csv files without any problems.  Can you send me a sample of the file you're having problems importing?

-- scooter

 

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Giovanni Scardoni
The Center for BioMedical Computing (CBMC)
www.cbmc.it/~scardonig/
University of Verona
Strada le Grazie, 15 -37134
Verona -Italy

Try these Cytoscape apps!
CentiScaPe: http://www.cbmc.it/~scardonig/centiscape/centiscape.php
Interference: http://www.cbmc.it/~scardonig/interference/Interference.php

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