Bad links found, on mouse biopax downloadable file. - wikipathways-discuss

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Message from discussion Bad links found, on mouse biopax downloadable file.
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Date: Thu, 19 May 2011 15:01:21 +0200
From: Martijn van Iersel <mvanier...@gmail.com>
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To: wikipathways-discuss@googlegroups.com
Subject: Re: [wp-discuss] Bad links found, on mouse biopax downloadable file.
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I'm not sure, I haven't attempted to convert to SIF myself. Do you get 
an error message when you attempt this?

regards,
Martijn

On 05/19/2011 02:41 PM, Hufeng Zhou wrote:
> Dear Martijn:
> Thanks very much for your help, I am very grateful.
> Another additioal problem is, when I try to convert the wikipathway
> biopax files into SIF(simple interaction format) files using the
> paxtools, it failed.
> While the same approach works in orther Biocyc, BioPax files, so I am
> wondering where can I figure out this problem and convert the
> wikipathways information into SIF?
> Thanks again for your help.
> Have a nice day.
>
> Best Regards,
> Hufeng Zhou, Ph.D Candidate
> School of Computing
> NUS Graduate School for Integrative Sciences and Engineering
> National University of Singapore
> Email: zhouhuf...@nus.edu.sg <mailto:zhouhuf...@nus.edu.sg>
> Phone:  +65 81522501
>
>
>
> On Thu, May 19, 2011 at 8:14 PM, Martijn van Iersel
> <mvanier...@gmail.com <mailto:mvanier...@gmail.com>> wrote:
>
>     Dear Hufeng Zhou
>
>     Please try again to download the pathways. I've made a small fix to
>     work around this problem.
>
>     regards,
>     Martijn
>
>
>     On 05/19/2011 01:05 PM, Thomas Kelder wrote:
>
>         Seems to be a bug in the BioPAX converter:
>
>         Exception in thread "main" java.lang.ClassCastException:
>         org.biopax.paxtools.impl.level3.ProteinImpl cannot be cast to
>         org.biopax.paxtools.model.level3.PublicationXref
>                 at
>         org.pathvisio.biopax3.exporter.ExportHelper.transferPublicationXref(ExportHelper.java:106)
>                 at
>         org.pathvisio.biopax3.exporter.ExportHelper.createOrGetPhysicalEntity(ExportHelper.java:419)
>                 at
>         org.pathvisio.biopax3.exporter.ExportHelper.mapPathway(ExportHelper.java:518)
>                 at
>         org.pathvisio.biopax3.exporter.ExportHelper.<init>(ExportHelper.java:135)
>                 at
>         org.pathvisio.biopax3.BiopaxFormat.doExport(BiopaxFormat.java:36)
>                 at org.pathvisio.Engine.exportPathway(Engine.java:116)
>                 at org.pathvisio.util.Converter.main(Converter.java:148)
>
>         <BR>Command:java -Xmx1024M -jar
>         /var/www/wikipathways/wpi/bin/pathvisio_core.jar
>         "/var/www/wikipathways/images/4/41/WP339_41371.gpml"
>         "/var/www/wikipathways/images/d/d5/WP339_41371.owl" 2>&1<BR>
>
>         I added a ticket to trac and added you to the CC:
>         http://www.pathvisio.org/ticket/1408. You'll receive an update when
>         it's fixed. Sorry for the inconvenience.
>
>         Martijn, you worked on the BioPAX converter most recently. Any idea
>         what's wrong?
>
>         Best wishes,
>         Thomas
>
>         On Thu, May 19, 2011 at 12:58 PM, Hufeng
>         Zhou<zhouhuf...@gmail.com <mailto:zhouhuf...@gmail.com>>  wrote:
>
>             Dear All:
>             I try to download the mouse pathway biopax format and find
>             it is a broken
>             link;
>             I am wondering if anyone is able to fix it.
>             Thank you so much for your help.
>
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