[MOBY-dev] Dashboard can't connect to Registries
Michael Gerlich
MichaelGerlich at gmx.de
Thu Feb 28 20:07:24 UTC 2008
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
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