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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From: Hufeng Zhou <zhouhuf...@gmail.com>
Date: Thu, 19 May 2011 20:41:34 +0800
Message-ID: <BANLkTinjJ8=62wGEXnL+O+v0Wefon90...@mail.gmail.com>
Subject: Re: [wp-discuss] Bad links found, on mouse biopax downloadable file.
To: wikipathways-discuss@googlegroups.com
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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
Phone:  +65 81522501



On Thu, May 19, 2011 at 8:14 PM, Martijn van Iersel <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>
>>  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.
>>>
>>> --
>>> You received this message because you are subscribed to the Google Groups
>>> "wikipathways-discuss" group.
>>> To post to this group, send email to
>>> wikipathways-discuss@googlegroups.com.
>>> To unsubscribe from this group, send email to
>>> wikipathways-discuss+unsubscribe@googlegroups.com.
>>> For more options, visit this group at
>>> http://groups.google.com/group/wikipathways-discuss?hl=en.
>>>
>>>
>>
> --
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>

--0016e6d9765112656204a3a055c9
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear=A0<span class=3D"Apple-style-span" style=3D"border-collapse: collapse;=
 font-family: arial, sans-serif; font-size: 13px; ">Martijn:</span><div><fo=
nt class=3D"Apple-style-span" face=3D"arial, sans-serif"><span class=3D"App=
le-style-span" style=3D"border-collapse: collapse;">Thanks very much for yo=
ur help, I am very grateful.</span></font></div>

<div><font class=3D"Apple-style-span" face=3D"arial, sans-serif"><span clas=
s=3D"Apple-style-span" style=3D"border-collapse: collapse;">Another additio=
al problem is, when I try to convert the wikipathway biopax files into SIF(=
simple interaction format) files using the paxtools, it failed.=A0</span></=
font></div>

<div><font class=3D"Apple-style-span" face=3D"arial, sans-serif"><span clas=
s=3D"Apple-style-span" style=3D"border-collapse: collapse; ">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 SI=
F?</span></font></div>

<div><font class=3D"Apple-style-span" face=3D"arial, sans-serif"><span clas=
s=3D"Apple-style-span" style=3D"border-collapse: collapse; ">Thanks again f=
or your help.</span></font></div><div><font class=3D"Apple-style-span" face=
=3D"arial, sans-serif"><span class=3D"Apple-style-span" style=3D"border-col=
lapse: collapse; ">Have a nice day.<br clear=3D"all">

</span></font><div><br></div><div>Best Regards,</div><div>Hufeng Zhou, Ph.D=
 Candidate</div><div>School of Computing</div><div>NUS Graduate School for =
Integrative Sciences and Engineering</div><div>National University of Singa=
pore</div>

<div>Email: <a href=3D"mailto:zhouhuf...@nus.edu.sg" target=3D"_blank">zhou=
huf...@nus.edu.sg</a></div><div>Phone: =A0+65 81522501</div><br>
<br><br><div class=3D"gmail_quote">On Thu, May 19, 2011 at 8:14 PM, Martijn=
 van Iersel <span dir=3D"ltr">&lt;<a href=3D"mailto:mvanier...@gmail.com">m=
vanier...@gmail.com</a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quo=
te" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;=
">

Dear Hufeng Zhou<br>
<br>
Please try again to download the pathways. I&#39;ve made a small fix to wor=
k around this problem.<br>
<br>
regards,<br><font color=3D"#888888">
Martijn</font><div><div></div><div class=3D"h5"><br>
<br>
On 05/19/2011 01:05 PM, Thomas Kelder wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">
Seems to be a bug in the BioPAX converter:<br>
<br>
Exception in thread &quot;main&quot; java.lang.ClassCastException:<br>
org.biopax.paxtools.impl.level3.ProteinImpl cannot be cast to<br>
org.biopax.paxtools.model.level3.PublicationXref<br>
 =A0 =A0 =A0 =A0at org.pathvisio.biopax3.exporter.ExportHelper.transferPubl=
icationXref(ExportHelper.java:106)<br>
 =A0 =A0 =A0 =A0at org.pathvisio.biopax3.exporter.ExportHelper.createOrGetP=
hysicalEntity(ExportHelper.java:419)<br>
 =A0 =A0 =A0 =A0at org.pathvisio.biopax3.exporter.ExportHelper.mapPathway(E=
xportHelper.java:518)<br>
 =A0 =A0 =A0 =A0at org.pathvisio.biopax3.exporter.ExportHelper.&lt;init&gt;=
(ExportHelper.java:135)<br>
 =A0 =A0 =A0 =A0at org.pathvisio.biopax3.BiopaxFormat.doExport(BiopaxFormat=
.java:36)<br>
 =A0 =A0 =A0 =A0at org.pathvisio.Engine.exportPathway(Engine.java:116)<br>
 =A0 =A0 =A0 =A0at org.pathvisio.util.Converter.main(Converter.java:148)<br=
>
<br>
&lt;BR&gt;Command:java -Xmx1024M -jar<br>
/var/www/wikipathways/wpi/bin/pathvisio_core.jar<br>
&quot;/var/www/wikipathways/images/4/41/WP339_41371.gpml&quot;<br>
&quot;/var/www/wikipathways/images/d/d5/WP339_41371.owl&quot; 2&gt;&amp;1&l=
t;BR&gt;<br>
<br>
I added a ticket to trac and added you to the CC:<br>
<a href=3D"http://www.pathvisio.org/ticket/1408" target=3D"_blank">http://w=
ww.pathvisio.org/ticket/1408</a>. You&#39;ll receive an update when<br>
it&#39;s fixed. Sorry for the inconvenience.<br>
<br>
Martijn, you worked on the BioPAX converter most recently. Any idea<br>
what&#39;s wrong?<br>
<br>
Best wishes,<br>
Thomas<br>
<br>
On Thu, May 19, 2011 at 12:58 PM, Hufeng Zhou&lt;<a href=3D"mailto:zhouhufe=
n...@gmail.com" target=3D"_blank">zhouhuf...@gmail.com</a>&gt; =A0wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">
Dear All:<br>
I try to download the mouse pathway biopax format and find it is a broken<b=
r>
link;<br>
I am wondering if anyone is able to fix it.<br>
Thank you so much for your help.<br>
<br>
--<br>
You received this message because you are subscribed to the Google Groups<b=
r>
&quot;wikipathways-discuss&quot; group.<br>
To post to this group, send email to <a href=3D"mailto:wikipathways-discuss=
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/a>.<br>
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For more options, visit this group at<br>
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get=3D"_blank">http://groups.google.com/group/wikipathways-discuss?hl=3Den<=
/a>.<br>
<br>
</blockquote>
<br>
</blockquote>
<br>
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</div></div></blockquote></div><br></div>

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