Problem Using The Kgml Reader Plugin In Cytoscape.

Question

[Blenderous]

I downloaded the jar file of this plugin and tried to open the xml file of a pathway in micobacterium tuberculosis (mtb00061.xml). I then get the following error: Unable to load network

And in the error details i get:

Caused by: Java.lang.RuntimeException: java.io.IOException: Could not unmarshall KGML file

What is causing this error and how can it be corrected? Thanks in advance!

Answer 1

[Giovanni M Dall'Olio]

Maybe you should better address this question to the plugin's authors. If you don't alert them that you have found an error in their software, they won't never be able to fix it, and this will affect other users apart from you.

Send them an error report here: http://code.google.com/p/kgmlreader/issues/list

[Blenderous]

cool, I posted this issue there :)

Answer 2

[Pierre Lindenbaum]

is your software/data up-to-date ? This kind of exception occurs when the XML schema (that is not only used to describe the data but also used to convert a XML node to a java object) is not synchronized to the XML data (the schema has changed, the xml data don't follow their own schema, the xml schema describing those data is too old, etc...).

[Blenderous]

The cytoscape version I am using is 2.7.0 and I had downloaded this path file about a month ago from the kgml ftp.

[Blenderous]

The KGML version of the file is 0.7.1 and I found on the site of KGML reader that it is compatible with this version.

[Pierre Lindenbaum]

is it the only message you got or do you have the full stack trace ?

[Blenderous]

I don't know what you mean by a stack trace, but this error message is a folder in the Root Error folder and this folder also has many more folders in it like cytoscape.Cytopscape.createNetwork(Cytoscape.java:1431)

[Pierre Lindenbaum]

http://en.wikipedia.org/wiki/Stack_trace is a report of the active stack frames at a certain point in time during the execution of a program. I asked this because your XML error could have been caused by something else deeper in the stack (e.g. I/O , memory problem).

Answer 3

[Kozo2]

Hi blenderous

Sorry for the inconvenience. For now, please use following combination. This works well.

• Cytoscape 2.7
• kgmlreader 0.06 from plugin manager

[Blenderous]

i dont knw if i'm doing something wrong...but this is the combination that i'm using...still i get the error message :(