Problem Using The Kgml Reader Plugin In Cytoscape.
3
2
Entering edit mode
10.7 years ago
Blenderous ▴ 180

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!

cytoscape • 3.7k views
ADD COMMENT
3
Entering edit mode
10.7 years ago

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

ADD COMMENT
0
Entering edit mode

cool, I posted this issue there :)

ADD REPLY
2
Entering edit mode
10.7 years ago

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...).

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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)

ADD REPLY
0
Entering edit mode

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).

ADD REPLY
2
Entering edit mode
10.7 years ago
Kozo2 ▴ 20

Hi blenderous

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

  • Cytoscape 2.7
  • kgmlreader 0.06 from plugin manager
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1013 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6