From maliha.aziz at yahoo.com Mon Feb 4 17:19:03 2008 From: maliha.aziz at yahoo.com (maliha aziz) Date: Mon, 4 Feb 2008 14:19:03 -0800 (PST) Subject: [MOBY-l] get lineage function Message-ID: <229377.86275.qm@web57403.mail.re1.yahoo.com> Hi I am trying to use the getlineage function to retrieve the lineage of a few data types but its giving me the following error MobyDataType[] dt_typ=dttyp[counter].getLineage(); ERORR is as follows Cannot parse MOBY Object Ontology: java.lang.NullPointerException hmmmm.... i used the getlineage function for the service types and it worked perfectly fine... :S so what am i going wrong here One more question ... the function getAllChildren()... MobyRelationship[] dt=dttyp[countz].getAllChildren(); does it return children of all relation types or just HAS HASA... i know itz written tht itz only HAS HASA types are returned but just wanted to confirm and if I want to obtain children with ISA relationships which function shud i use??? maliha p.s. and yea ive configured the registry to point to the new address... --------------------------------- Never miss a thing. Make Yahoo your homepage. From edward.kawas at gmail.com Mon Feb 4 18:47:43 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 15:47:43 -0800 Subject: [MOBY-l] get lineage function In-Reply-To: <229377.86275.qm@web57403.mail.re1.yahoo.com> References: <229377.86275.qm@web57403.mail.re1.yahoo.com> Message-ID: <47a7a425.0e578c0a.0282.ffffcd8e@mx.google.com> Hi Maliha, Can you post all of your code? Also, some datatypes in the ontology are unrooted (I know that this is illegal, but they somehow made it in!). This could be why you are getting the error that you are seeing. Eddie -----Original Message----- From: moby-l-bounces at lists.open-bio.org [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of maliha aziz Sent: February-04-08 2:19 PM To: moby-l at lists.open-bio.org Subject: [MOBY-l] get lineage function Hi I am trying to use the getlineage function to retrieve the lineage of a few data types but its giving me the following error MobyDataType[] dt_typ=dttyp[counter].getLineage(); ERORR is as follows Cannot parse MOBY Object Ontology: java.lang.NullPointerException hmmmm.... i used the getlineage function for the service types and it worked perfectly fine... :S so what am i going wrong here One more question ... the function getAllChildren()... MobyRelationship[] dt=dttyp[countz].getAllChildren(); does it return children of all relation types or just HAS HASA... i know itz written tht itz only HAS HASA types are returned but just wanted to confirm and if I want to obtain children with ISA relationships which function shud i use??? maliha p.s. and yea ive configured the registry to point to the new address... --------------------------------- Never miss a thing. Make Yahoo your homepage. _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l From edward.kawas at gmail.com Mon Feb 4 18:54:55 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 15:54:55 -0800 Subject: [MOBY-l] one more question In-Reply-To: <152541.47291.qm@web57414.mail.re1.yahoo.com> References: <152541.47291.qm@web57414.mail.re1.yahoo.com> Message-ID: <47a7a5d2.22b38c0a.1e8f.ffffe382@mx.google.com> getAllChildren() gets only HAS/HASA relationships. To get ISA relationships, you may have to recursively call getParent() on the datatype until you hit Object. Eddie -----Original Message----- From: moby-l-bounces at lists.open-bio.org [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of maliha aziz Sent: January-31-08 4:47 PM To: moby-l at biomoby.org Subject: [MOBY-l] one more question sorry for bombarding you with questions but i really need to find out the answers the function getAllChildren()... MobyRelationship[] dt=dttyp[countz].getAllChildren(); does it return children of all relation types or just HAS HASA... i know itz written tht itz only HAS HASA types are returned but just wanted to confirm and if I want to obtain children with ISA relationships which function shud i use??? thnks maliha --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search. _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l From jeedward at yahoo.com Tue Feb 5 14:58:42 2008 From: jeedward at yahoo.com (John Edward) Date: Tue, 5 Feb 2008 11:58:42 -0800 (PST) Subject: [MOBY-l] Draft paper submission deadline is extended: BCBGC-08 Message-ID: <683247.89005.qm@web45914.mail.sp1.yahoo.com> Dear Colleagues and Friends Kindly share the announcement below with those who may be interested: thank you in advance. Sincerely John Edward BCBGC-08 Draft paper submission deadline is extended. The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. The draft paper submission deadline is extended until February 19 2008 due to several requests from the authors. The conference will be held at the same time and location where several major events (see below) will be taking place. BCBGC brings together both academic and industrial scientists and developers from a diverse range of disciplines including bioinformatics, computer science, computational biology, genomics, proteomics and chemoinformatics. One of the main goals of the conference is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers in different fields. Papers that demonstrate applications of existing techniques or developments of new methods are equally welcomed to the conference. Sincerely John Edward ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-08) ? International Conference on Automation, Robotics and Control Systems (ARCS-08) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-08) ? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-08) ? International Conference on Software Engineering Theory and Practice (SETP-08) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-08) --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. From jeedward at yahoo.com Fri Feb 8 08:55:17 2008 From: jeedward at yahoo.com (John Edward) Date: Fri, 8 Feb 2008 05:55:17 -0800 (PST) Subject: [MOBY-l] Draft paper submission deadline is extended : MULTICONF-08 Message-ID: <303064.98970.qm@web45906.mail.sp1.yahoo.com> Dear Colleagues, Professors and Friends Kindly share the announcement below with those who may be interested: thank you in advance. Sincerely John Edward MULTICONF-08 Draft paper submission deadline is extended The MULTICONF-08 (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. We invite draft paper submissions and the deadline for submission is extended until February 19 2008 due to several requests from the authors. The event consists of the following conferences: ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-08) ? International Conference on Automation, Robotics and Control Systems (ARCS-08) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-08) ? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-08) ? International Conference on Software Engineering Theory and Practice (SETP-08) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-08) Sincerely John Edward --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. From jeedward at yahoo.com Mon Feb 11 22:05:35 2008 From: jeedward at yahoo.com (John Edward) Date: Mon, 11 Feb 2008 19:05:35 -0800 (PST) Subject: [MOBY-l] BCBGC-08 Draft paper submission deadline is just few days from now Message-ID: <708139.38326.qm@web45908.mail.sp1.yahoo.com> Dear Professors, Colleagues and Friends Kindly share the announcement below with those who may be interested: thank you in advance. Sincerely John Edward BCBGC-08 Draft paper submission deadline is just few days from now The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. The draft paper submission deadline is extended until February 19 2008 due to several requests from the authors. The conference will be held at the same time and location where several major events (see below) will be taking place. BCBGC brings together both academic and industrial scientists and developers from a diverse range of disciplines including bioinformatics, computer science, computational biology, genomics, proteomics and chemoinformatics. One of the main goals of the conference is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers in different fields. Papers that demonstrate applications of existing techniques or developments of new methods are equally welcomed to the conference. Sincerely John Edward ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-08) ? International Conference on Automation, Robotics and Control Systems (ARCS-08) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-08) ? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-08) ? International Conference on Software Engineering Theory and Practice (SETP-08) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-08) --------------------------------- Never miss a thing. Make Yahoo your homepage. From alexgutteridge at gmail.com Wed Feb 13 20:21:22 2008 From: alexgutteridge at gmail.com (Alex Gutteridge) Date: Thu, 14 Feb 2008 10:21:22 +0900 Subject: [MOBY-l] A couple of bug fixes Message-ID: <1AD377F7-E0F0-474C-84CC-14D9EE6E29F8@ruggedtextile.com> Hi, There are a couple of (tiny) bugs in the Perl example on the biomoby website here: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/ExecuteSyncService.html I've pasted a diff to fix them below: --- orig.pl 2008-02-12 14:01:06.000000000 +0900 +++ new.pl 2008-02-12 14:02:45.000000000 +0900 @@ -2,7 +2,7 @@ use MOBY::Client::Service; # this is what we use to interact with a service my $m = MOBY::Client::Central->new; -my ($serv_instances, $reg) = $findService->( +my ($serv_instances, $reg) = $m->findService( authURI => "mydomain.mycompany.org", serviceName => "getGoTerm"); @@ -20,7 +20,7 @@ # here we'll just set it explicitly... my $articleName = "my_input_parameter"; -my $wsdl = $M->retrieveService($SI); +my $wsdl = $m->retrieveService($SI); # we now have the WSDL description of the Service # we use this to create a MOBY::Client::Service object @@ -33,7 +33,7 @@ my $inputdata2 = ">Object namespace='GO' id='0050789'>"; @single_invocation = ([$articleName, $inputdata1]); - at multiple_invocation = ([$articleName, $inputdata1], [$articleName, $inputdata2]) + at multiple_invocation = ([$articleName, $inputdata1], [$articleName, $inputdata2]); my $result1 = $SERV->execute(XMLinputlist => \@single_invocation); my $result2 = $SERV->execute(XMLinputlist => \@multiple_invocation); AlexG From MichaelGerlich at gmx.de Fri Feb 29 07:47:30 2008 From: MichaelGerlich at gmx.de (Michael Gerlich) Date: Fri, 29 Feb 2008 13:47:30 +0100 Subject: [MOBY-l] Dashboard can't connect to Registries Message-ID: <000001c87ad1$3f176330$bd462990$@de> Hi there, First of all thanks for your tutorials about setting up Biomoby with Eclipse and for the newly created Known errors site at http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/jmoby-step-by-step /writing-biomoby-web-services/known-errors-and-problems, they helped me a lot and I finally have successful Builds with the Ant Scripts (using JDK 1.5). But there are some things I still have problems with. 1) Eclipse keeps reporting that it misses required libraries, even though the initeclipse script says Build successful. Are these errors some kind of artifacts or should I check the ant scripts or checkout JMoby again? micge at linux-vm:~/eclipse> ./eclipse -vmargs -Djava.home=/usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/ ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) Severity and Description Project 'moby' is missing required library: 'lib/activation.jar' Project 'moby' is missing required library: 'lib/adenine.jar' Project 'moby' is missing required library: 'lib/alltools2.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-antlr.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-bcel.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-bsf.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-log4j.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-oro.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-regexp.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-resolver.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-commons-logging.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-commons-net.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-contrib.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-icontract.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jai.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-javamail.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jdepend.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jmf.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jsch.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-junit.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-launcher.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-netrexx.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-nodeps.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-starteam.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-stylebook.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-swing.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-trax.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-vaj.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-weblogic.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-xalan1.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-xslp.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/xercesImpl.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/xml-apis.jar' Project 'moby' is missing required library: 'lib/axis-ant.jar' Project 'moby' is missing required library: 'lib/axis.jar' Project 'moby' is missing required library: 'lib/castor-0.9.5.jar' Project 'moby' is missing required library: 'lib/commons-codec-1.3.jar' Project 'moby' is missing required library: 'lib/commons-collections-2.1.jar' Project 'moby' is missing required library: 'lib/commons-dbcp-1.1.jar' Project 'moby' is missing required library: 'lib/commons-discovery-0.2.jar' Project 'moby' is missing required library: 'lib/commons-httpclient-3.0-rc2.jar' Project 'moby' is missing required library: 'lib/commons-io-1.0.jar' Project 'moby' is missing required library: 'lib/commons-lang-2.1.jar' Project 'moby' is missing required library: 'lib/commons-logging-1.0.4.jar' Project 'moby' is missing required library: 'lib/commons-pool-1.1.jar' Project 'moby' is missing required library: 'lib/concurrent.jar' Project 'moby' is missing required library: 'lib/dnsjava-1.3.2.jar' Project 'moby' is missing required library: 'lib/icis-pedigree.jar' Project 'moby' is missing required library: 'lib/icu4j.jar' Project 'moby' is missing required library: 'lib/jakarta-oro-2.0.5.jar' Project 'moby' is missing required library: 'lib/jaxen-core.jar' Project 'moby' is missing required library: 'lib/jaxen-jdom.jar' Project 'moby' is missing required library: 'lib/jaxrpc.jar' Project 'moby' is missing required library: 'lib/jcalendar.jar' Project 'moby' is missing required library: 'lib/jdom.jar' Project 'moby' is missing required library: 'lib/jena.jar' Project 'moby' is missing required library: 'lib/jfcunit.jar' Project 'moby' is missing required library: 'lib/jodconverter-2.2.0.jar' Project 'moby' is missing required library: 'lib/junit.jar' Project 'moby' is missing required library: 'lib/log4j-1.2.12.jar' Project 'moby' is missing required library: 'lib/lsid-client-1.1.2.jar' Project 'moby' is missing required library: 'lib/lsid-server-1.1.2.jar' Project 'moby' is missing required library: 'lib/mail.jar' Project 'moby' is missing required library: 'lib/mailapi_1_3_1.jar' Project 'moby' is missing required library: 'lib/mysql-connector-java-3.1.7-bin.jar' Project 'moby' is missing required library: 'lib/rdf-api-2001-01-19.jar' Project 'moby' is missing required library: 'lib/saaj.jar' Project 'moby' is missing required library: 'lib/saxpath.jar' Project 'moby' is missing required library: 'lib/servlet.jar' Project 'moby' is missing required library: 'lib/taverna.jar' Project 'moby' is missing required library: 'lib/wsdl4j-1.5.1.jar' Project 'moby' is missing required library: 'lib/xalan.jar' Project 'moby' is missing required library: 'lib/xercesImpl.jar' Project 'moby' is missing required library: 'lib/xercesSamples.jar' Project 'moby' is missing required library: 'lib/xml-apis.jar' Project 'moby' is missing required library: 'lib/xmlParserAPIs.jar' Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-core:jar:1.0.0 moby/src/main pom.xml line 1 1204224268317 133440 Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-plugins:jar:1.0.0 moby/src/samples pom.xml line 1 1204224267905 133439 The project cannot be built until build path errors are resolved moby 2) I'am behind a proxy server, so I had to edit proxy settings in net.properties of JDK 1.5 (http_proxy environment variable is set, but without effect to Java). With this, all the ant scripts work without any problems, but when I run Dashboard, all I got are empty lists and the following messages: Inside Eclipse: --------------- Buildfile: /home/micge/workspace/moby/build.xml checkmaven: initmaven: init: config: compile: moses-init: samples-init: dashboard-init: dashboard-config: dashboard: [Dashboard] libxcb: WARNING! Program tries to unlock a connection without having acquired [Dashboard] a lock first, which indicates a programming error. [Dashboard] There will be no further warnings about this issue. [Dashboard] libxcb: WARNING! Program tries to lock an already locked connection, [Dashboard] which indicates a programming error. [Dashboard] There will be no further warnings about this issue. [Dashboard] 192616 [Thread-6] WARN CentralDigestCachedImpl - Error with Services RDF [Dashboard] org.biomoby.shared.MobyException: ===ERROR=== [Dashboard] Fault details: [Dashboard] Fault string: java.net.ConnectException: Connection timed out [Dashboard] Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException [Dashboard] Fault actor: null [Dashboard] When calling: [Dashboard] http://moby.ucalgary.ca/moby/MOBY-Central.pl [Dashboard] =========== [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) [Dashboard] at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1772) [Dashboard] at org.biomoby.client.CentralImpl.getResource(CentralImpl.java:1807) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getResourceAsString(CentralDigest CachedImpl.java:216) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.fillServicesCache(CentralDigestCa chedImpl.java:243) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getServices(CentralDigestCachedIm pl.java:709) [Dashboard] at org.biomoby.service.dashboard.RegistryModel.getServices(RegistryModel.java:5 61) [Dashboard] at org.biomoby.service.dashboard.ServicesTree$4.construct(ServicesTree.java:121 ) [Dashboard] at org.biomoby.service.dashboard.SwingWorker$2.run(SwingWorker.java:117) [Dashboard] at java.lang.Thread.run(Thread.java:595) [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154) [Dashboard] at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java: 32) [Dashboard] at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) [Dashboard] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) [Dashboard] at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) [Dashboard] at org.apache.axis.client.Call.invokeEngine(Call.java:2784) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2767) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2443) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2366) [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:226) [Dashboard] ... 9 more [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at java.net.PlainSocketImpl.socketConnect(Native Method) [Dashboard] at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) [Dashboard] at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) [Dashboard] at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) [Dashboard] at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) [Dashboard] at java.net.Socket.connect(Socket.java:520) [Dashboard] at java.net.Socket.connect(Socket.java:470) [Dashboard] at java.net.Socket.(Socket.java:367) [Dashboard] at java.net.Socket.(Socket.java:180) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:149) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:120) [Dashboard] at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191) [Dashboard] at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138) [Dashboard] ... 18 more [Dashboard] 193461 [Thread-7] WARN CentralDigestCachedImpl - Error with Services RDF [Dashboard] org.biomoby.shared.MobyException: ===ERROR=== [Dashboard] Fault details: [Dashboard] Fault string: java.net.ConnectException: Connection timed out [Dashboard] Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException [Dashboard] Fault actor: null [Dashboard] When calling: [Dashboard] http://moby.ucalgary.ca/moby/MOBY-Central.pl [Dashboard] =========== [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) [Dashboard] at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1772) [Dashboard] at org.biomoby.client.CentralImpl.getResource(CentralImpl.java:1807) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getResourceAsString(CentralDigest CachedImpl.java:216) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.fillServicesCache(CentralDigestCa chedImpl.java:243) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getServices(CentralDigestCachedIm pl.java:709) [Dashboard] at org.biomoby.service.dashboard.RegistryModel.getServices(RegistryModel.java:5 61) [Dashboard] at org.biomoby.service.dashboard.ServicesTree$4.construct(ServicesTree.java:121 ) [Dashboard] at org.biomoby.service.dashboard.SwingWorker$2.run(SwingWorker.java:117) [Dashboard] at java.lang.Thread.run(Thread.java:595) [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154) [Dashboard] at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java: 32) [Dashboard] at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) [Dashboard] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) [Dashboard] at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) [Dashboard] at org.apache.axis.client.Call.invokeEngine(Call.java:2784) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2767) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2443) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2366) [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:226) [Dashboard] ... 9 more [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at java.net.PlainSocketImpl.socketConnect(Native Method) [Dashboard] at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) [Dashboard] at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) [Dashboard] at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) [Dashboard] at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) [Dashboard] at java.net.Socket.connect(Socket.java:520) [Dashboard] at java.net.Socket.connect(Socket.java:470) [Dashboard] at java.net.Socket.(Socket.java:367) [Dashboard] at java.net.Socket.(Socket.java:180) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:149) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:120) [Dashboard] at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191) [Dashboard] at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138) [Dashboard] ... 18 more BUILD SUCCESSFUL >From Dashboard (after one minute) -------------- ===Error=== Fault details: Fault string: java.net.ConnectException: Connection timed out Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null when calling: http://moby.uralgary.ca/moby/MOBY-Central.pl Is this a problem with the proxy settings I made in net.properties or is it inside Dashboard? Regards, Michael