KGML Reader

[Mona Razaghi]

I am using Cytoscape 3.0.2 and I want to install KGML reader for it. First of all it is not shown in the app manager. I download the JAR file and try to install it through "Install from file". but then it causes this error " org.cytoscape.app.internal.exception.AppParsingException: Error parsing given file as a jar file: error in opening zip file ".

 Could any one please let me know what should I do?

[Tim Hull]

Hi,

KGMLReader is not currently available for Cytoscape 3 - you probably downloaded the version for Cytoscape 2.8, which does not work on the 3.0.x series. To use KGMLReader, you will have to use Cytoscape 2.8.3 for the time being...

Tim

On Fri, Aug 2, 2013 at 1:59 AM, Mona Razaghi <mona.r...@gmail.com> wrote:

I am using Cytoscape 3.0.2 and I want to install KGML reader for it. First of all it is not shown in the app manager. I download the JAR file and try to install it through "Install from file". but then it causes this error " org.cytoscape.app.internal.exception.AppParsingException: Error parsing given file as a jar file: error in opening zip file ".

 Could any one please let me know what should I do?

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[Mona Razaghi]

Hi,

Thanks for your reply. I did so. now I have problem in importing .xml files to Cytoscape. This error message "Unable to open...". Could you please help me?

On Saturday, August 3, 2013 12:24:49 AM UTC+4:30, Tim Hull wrote:

Hi,

KGMLReader is not currently available for Cytoscape 3 - you probably downloaded the version for Cytoscape 2.8, which does not work on the 3.0.x series. To use KGMLReader, you will have to use Cytoscape 2.8.3 for the time being...

Tim

On Fri, Aug 2, 2013 at 1:59 AM, Mona Razaghi <mona.r...@gmail.com> wrote:

I am using Cytoscape 3.0.2 and I want to install KGML reader for it. First of all it is not shown in the app manager. I download the JAR file and try to install it through "Install from file". but then it causes this error " org.cytoscape.app.internal.exception.AppParsingException: Error parsing given file as a jar file: error in opening zip file ".

 Could any one please let me know what should I do?

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[Kristian Unger]

Same thing for me - XML import does not work with KGML reader installed in 2.8.2....

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[Tim Hull]

What kind of XML file are you trying to import? Is this on 2.8 or 3.0?

Tim

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[Kristian Unger]

I tried with Download KGML .

[Keiichiro Ono]

Hi.

Looks like it's a KGMLReader's bug. I'll look into it.

Thanks,
Kei


2013/8/5 Kristian Unger <kristi...@googlemail.com>:

--
Keiichiro Ono http://www.keiono.net/

[Keiichiro Ono]

Hi.
I found a problem, and here is a workaround.

On the top of XML file, you can see the line:

<!DOCTYPE pathway SYSTEM "http://www.kegg.jp/kegg/xml/KGML_v0.7.1_.dtd">

Please modify it to:

<!DOCTYPE pathway SYSTEM "http://www.genome.jp/kegg/xml/KGML_v0.7.1_.dtd">

Then the file can be loaded to Cytoscape.
By the way, even if you load this file, you cannot see any edges in
the view. This is a known issue (those edge types are not supported
in current version). We will fix this in the next release.

Thanks,
Kei



2013/8/5 Kristian Unger <kristi...@googlemail.com>:

[Mona Razaghi]

Hi Kei,

Thank you for your consideration and useful reply. I did as you said. finally It opens the file, but just the nodes with no edges. Could you please continue helping me?

Thanks again