[MOBY-dev] Dashboard can't connect to Registries
Andreas Groscurth
groscurt at mpiz-koeln.mpg.de
Sat Mar 1 08:12:14 UTC 2008
Hi Michael,
sorry thats my fault - I offer for Eclipse user the .classpath file, but
unfortunatley I had some problems with the plone software and it didnt
update the file. Please download the .classpath file from the tutorial
again and refresh your project - this should remove your first problem.
For the second... I cant check that now - but this should work when you
copy the build.properties.template to build.properties and change their
the proxy settings in that file (there should be poperties for that)
Best
andreas
Michael Gerlich wrote:
> 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.<init>(Socket.java:367)
> [Dashboard] at java.net.Socket.<init>(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.<init>(Socket.java:367)
> [Dashboard] at java.net.Socket.<init>(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
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
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