related pathways - cytoscape - superpathways - wikipathways

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mezhoud

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Jul 6, 2010, 9:26:51 AM7/6/10
to wikipathwa...@googlegroups.com
Dear user,

Goal: Find related pathways using cytoscape and superpathways
problem: I can't replay the example cited in
:http://www.pathvisio.org/wiki/SuperPathways?version=22
I did not find any related pathways for WP565.
Putative source: Built the superpathways file using code source.


Tools:
Ubuntu 9.10
Intallation using : ./Cytoscape.sh
I add the superpathways.jer file in plugins directory
/opt/cytoscape/plugins
the Import networks from the web service using wikipathways and
superpathways are working.


Any idea?
Thank you for your time
Best regards

--
Karim Mezhoud, PhD. ir.
https://wiki.edubuntu.org/kmezhoud/Bioinformatics |
Molecular biology Lab Tel: 25909901
National Center of Nuclear Sciences and Technologies
Technopole Sidi thabet, 2020, Ariana, Tunisia
FRE 3206 CNRS-USM 0505 Mol�cules de communication et adaptation des micro-organismes, Museum national d'Histoire naturelle, http://www.mnhn.fr/mcam/
12 rue Buffon, F-75231 Paris cedex 05, France. Tel: 0140793212

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Alexander Pico

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Jul 6, 2010, 5:05:59 PM7/6/10
to wikipathwa...@googlegroups.com
One minor point that would make a big difference in running through the
example: The example uses WP656, not WP565.

- Alex

Thomas Kelder

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Jul 7, 2010, 5:14:31 AM7/7/10
to wikipathwa...@googlegroups.com
That might indeed make a difference, but the nullpointer exception
shouldn't happen anyway. Karim, I see you already created a trac
ticket for this problem, I added a reference to this thread and I'll
try to replicate the issue. What might help is if you could attach the
console output (what you see in the console after you run
./cytoscape.sh and try to use the plugin) to the ticket as well.

Thanks,
Thomas

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karim mezhoud

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Jul 7, 2010, 6:06:44 AM7/7/10
to wikipathways-discuss
Dear Thomas,
I installed the superpathway plugin via the Cytoscape.

The consol output after using superpathway plugin with WP656:

mezhoud@sunny-deb:~$ Cytoscape
cytoscape.CytoscapeInit[INFO]: CytoscapeInit static initialization
cytoscape.CytoscapeInit[INFO]: Log information can now be found in the
Help->Error Console menu
CommonAttributesPlugin constructor v1
[ 37,469] Info: Searching
org.pathvisio.cytoscape.superpathways.SuperpathwaysClient
$FindPathwaysByTextParameters@7ae165
Superpathways!
Superpathways-run!
After clicking 'Find Related Pathways' button!
[ 47,154] Trace: Build JDOM tree
[ 47,185] Info: Recognized format [Namespace: prefix "" is mapped
to URI "http://genmapp.org/GPML/2008a"]
[ 47,186] Trace: Start Validation
[ 47,346] Info: Document is valid according to the xml schema
definition 'GPML.xsd'
[ 47,346] Trace: Copy map elements
[ 47,368] Trace: Refreshing biopax
[ 47,368] Trace: Biopax element found
[ 47,377] Trace: End copying map elements

#################################### Now I selected WP656 and
specify the nomber of sharing nodes between 3 and 20
Nodes################


Error: Unable to find the candidate pathways due to the
RemoteException
exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}: exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Receiver
faultSubcode:
faultString: exception 'Exception' with message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
faultActor:
faultNode:
faultDetail:
{http://xml.apache.org/axis/}stackTrace:exception 'Exception' with
message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)

{http://xml.apache.org/axis/}hostname:sunny-deb

exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)
S:Q80ZG6
Error: Unable to find the candidate pathways due to the
RemoteException
exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}: exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Receiver
faultSubcode:
faultString: exception 'Exception' with message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
faultActor:
faultNode:
faultDetail:
{http://xml.apache.org/axis/}stackTrace:exception 'Exception' with
message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)

{http://xml.apache.org/axis/}hostname:sunny-deb

exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)
Error: Error while searching candidate pathways
java.lang.NullPointerException: null
java.lang.NullPointerException
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:667)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)





















































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)

{http://xml.apache.org/axis/}hostname:sunny-deb

exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)
EnRn:ENSRNOG00000018770
Error: Unable to find the candidate pathways due to the
RemoteException
exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}: exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Receiver
faultSubcode:
faultString: exception 'Exception' with message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
faultActor:
faultNode:
faultDetail:
{http://xml.apache.org/axis/}stackTrace:exception 'Exception' with
message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)

{http://xml.apache.org/axis/}hostname:sunny-deb

exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)
S:Q80ZG6
Error: Unable to find the candidate pathways due to the
RemoteException
exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}: exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Receiver
faultSubcode:
faultString: exception 'Exception' with message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
faultActor:
faultNode:
faultDetail:
{http://xml.apache.org/axis/}stackTrace:exception 'Exception' with
message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)

{http://xml.apache.org/axis/}hostname:sunny-deb

exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)







































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)

{http://xml.apache.org/axis/}hostname:sunny-deb

exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)
EnRn:ENSRNOG00000018770
Error: Unable to find the candidate pathways due to the
RemoteException
exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}: exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Receiver
faultSubcode:
faultString: exception 'Exception' with message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
faultActor:
faultNode:
faultDetail:
{http://xml.apache.org/axis/}stackTrace:exception 'Exception' with
message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)

{http://xml.apache.org/axis/}hostname:sunny-deb

exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)
S:Q80ZG6
Error: Unable to find the candidate pathways due to the
RemoteException
exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}: exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Receiver
faultSubcode:
faultString: exception 'Exception' with message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
faultActor:
faultNode:
faultDetail:
{http://xml.apache.org/axis/}stackTrace:exception 'Exception' with
message '&lt;html&gt;
&lt;head&gt;
&lt;title&gt;Status page&lt;/title&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;h3&gt;The server encountered an unexpected condition which
prevented it from fulfilling the request&lt;/h3&gt;&lt;p&gt;You can
get technical details &lt;a href=&quot;http://www.w3.org/Protocols/
rfc2616/rfc2616-sec10.html#sec10.5.1&quot;&gt;here&lt;/
a&gt;.&lt;br&gt;
Please continue your visit at our &lt;a href=&quot;/&quot;&gt;home
page&lt;/a&gt;.
&lt;/p&gt;
&lt;/body&gt;
&lt;/html&gt;
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
&gt;reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)

{http://xml.apache.org/axis/}hostname:sunny-deb

exception 'Exception' with message '<html>
<head>
<title>Status page</title>
</head>
<body>
<h3>The server encountered an unexpected condition which prevented it
from fulfilling the request</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-
sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
' in /var/www/wikipathways/wpi/search.php:47
Stack trace:
#0 /var/www/wikipathways/wpi/search.php(116):
IndexClient::doQuery('http://137.120....')
#1 /var/www/wikipathways/wpi/search.php(215):
IndexClient::queryXrefs(Array, Array)
#2 /var/www/wikipathways/wpi/webservice/webservice.php(451):
PathwayIndex::searchByXref(Array, true)
#3 [internal function]: findPathwaysByXref()
#4 /usr/lib/php5/20060613+lfs/wsf_c/scripts/dynamic_invocation/
wsf_wsdl_service.php(226): call_user_func_array('findPathwaysByX...',
Array)
#5 wsf_wsdl.php(702): wsf_serivce_invoke_function(Object(DOMElement),
'findPathwaysByX...', NULL, NULL, Object(DOMElement), NULL, Array,
false, Array, Array)
#6 [internal function]: wsf_wsdl_process_in_msg(Array)
#7 /var/www/wikipathways/wpi/webservice/webservice.php(140): WSService-
>reply()
#8 {main}
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:
601)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:
1782)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl
$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:
227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:
62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.pathvisio.wikipathways.webservice.WikiPathwaysSOAPBindingStub.findPathwaysByXref(WikiPathwaysSOAPBindingStub.java:
523)
at
org.pathvisio.wikipathways.WikiPathwaysClient.findPathwaysByXref(WikiPathwaysClient.java:
308)
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:634)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)
Error: Error while searching candidate pathways
java.lang.NullPointerException: null
java.lang.NullPointerException
at org.pathvisio.cytoscape.superpathways.FindRelatedPwsDialog
$searchSharingNodePwsTask.run(FindRelatedPwsDialog.java:667)
at cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)




On Jul 7, 11:14 am, Thomas Kelder <thomaskel...@gmail.com> wrote:
> That might indeed make a difference, but the nullpointer exception
> shouldn't happen anyway. Karim, I see you already created a trac
> ticket for this problem, I added a reference to this thread and I'll
> try to replicate the issue. What might help is if you could attach the
> console output (what you see in the console after you run
> ./cytoscape.sh and try to use the plugin) to the ticket as well.
>
> Thanks,
> Thomas
>
> On Tue, Jul 6, 2010 at 11:05 PM, Alexander Pico
>
> <ap...@gladstone.ucsf.edu> wrote:
> > One minor point that would make a big difference in running through the
> > example:  The example uses WP656, not WP565.
>
> >  - Alex
>

Thomas Kelder

unread,
Jul 7, 2010, 9:55:20 AM7/7/10
to wikipathwa...@googlegroups.com, mezhoud
There were multiple regressions causing the nullpointerexception and
web service call error. I compiled a new jar that should resolve your
problems (I tested it in Cytoscape 2.6.3):

http://ftp.bigcat.unimaas.nl/shared_folder/thomas/superpathways.jar

Please try it out to see if it works for you (remove previously installed
superpathways plugin and put this jar in the cytoscape/plugins
directory).

I'll do some extra testing tomorrow and then submit this new version
to the Cytoscape plugin repository.

Best wishes,
Thomas

karim mezhoud

unread,
Jul 7, 2010, 10:46:44 AM7/7/10
to wikipathways-discuss
It works!!
Many many Thanks.
I'm trying common node option.

Best regards

On Jul 7, 3:55 pm, Thomas Kelder <thomaskel...@gmail.com> wrote:
> There were multiple regressions causing the nullpointerexception and
> web service call error. I compiled a new jar that should resolve your
> problems (I tested it in Cytoscape 2.6.3):
>
> http://ftp.bigcat.unimaas.nl/shared_folder/thomas/superpathways.jar
>
> Please try it out to see if it works for you (remove previously installed
> superpathways plugin and put this jar in the cytoscape/plugins
> directory).
>
> I'll do some extra testing tomorrow and then submit this new version
> to the Cytoscape plugin repository.
>
> Best wishes,
> Thomas
>
> ...
>
> read more »

karim mezhoud

unread,
Jul 7, 2010, 10:48:51 AM7/7/10
to wikipathways-discuss
It works!!
Many many thanks!
I'm trying the common nodes option.
Best regards

On Jul 7, 3:55 pm, Thomas Kelder <thomaskel...@gmail.com> wrote:
> There were multiple regressions causing the nullpointerexception and
> web service call error. I compiled a new jar that should resolve your
> problems (I tested it in Cytoscape 2.6.3):
>
> http://ftp.bigcat.unimaas.nl/shared_folder/thomas/superpathways.jar
>
> Please try it out to see if it works for you (remove previously installed
> superpathways plugin and put this jar in the cytoscape/plugins
> directory).
>
> I'll do some extra testing tomorrow and then submit this new version
> to the Cytoscape plugin repository.
>
> Best wishes,
> Thomas
>
> ...
>
> read more »
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