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Re: [Lsid-developer] Question about running the lsid toolkit TestClient.java
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From: Benjamin H S. <bhs...@us...> - 2006-09-21 18:23:26
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Hi Allyson
I'm a little confused by this last bit of your message
"Initially this was a classnotfound error, and I realized that I hadn't
copied my TestAuthority.class into LSIDJars/ and therefore it wasn't
getting put into authority.war . However, there is no longer a
classnotfound error, but it does seem to be having a problem with
default-services.xml. This file is in the location it is looking in above,
and I have copied it into this email"
Is the stack trace you copied the latest you are getting? If so, it still
cannot find you your authority implementation. I would start by manually
copying the class file in the right package/folder in
/var/lib/tomcat5/webapps/authority/WEB-INF/classes/
com/ibm/lsid/server/impl/test/. See if that helps. Also, you might as
well remove the ncbi-services.xml from your services directory. The
current version of the NCBI example resolution service is not compliant
with NCBI's web services. If you later want to get this working, I can
provide you with updated code.
- Ben
Ben Szekely
IBM Software Engineer
Advanced Internet Technology, Cambridge, MA
bhs...@us...
lsi...@li... wrote on 09/21/2006 06:00:46
AM:
>
> Hi Ben and everyone on the list,
>
> I've just sent a question about the LSID tutorial to Ben Szekely,
> who mentioned this mailing list, so for the benefit of others here,
> I'm posting my original question, Ben's response, and my response to
> him in turn. This is still unresolved, at the moment. Here we go, my
> most recent response first, and then back in time as you go down the
page :)
>
> I am running TestClient.java in IntelliJ by the simple expedient of
> "shift-f10", which runs the .java file you currently have selected
> (within JUnit in this case). this means that it runs through the
> main() method, running all four tests in turn. There are errors
> associated with each test at the moment, but I just sent the first
> error (for testLSIDMetadata) as I suspect they might all be related
> to the same error.
>
> As you requested, my default-services.xml is as follows:
>
> <deployment-descriptor xmlns=" http://www.ibm.com/LSID/Standard/rsdl">
> <component-handlers>
> <!-- These handlers (along with "class" and
> "caching") are added by default, we include these as examples -->
> <component-handler type="asdl" classname=" com.ibm.
> lsid.server.conf.ASDLComponentHandler" />
> <component-handler type="msdl" classname="com.ibm.
> lsid.server.conf.MSDLComponentHandler" />
> </component-handlers>
> <maps>
> <map name="all">
> <pattern auth="*" ns="*" />
> </map>
> <map name="ibmtest">
> <pattern auth="test.lsid.ibm.com" ns="*" />
> </map>
> </maps>
> <services>
> <service name="ReallySimpleAssigningService" >
> <components>
> <assn type="class">com.ibm.lsid.
> server.impl.ReallySimpleAssigningService </assn>
> </components>
> </service>
> <service name="CachingProxyResolutionService" >
> <components>
> <auth map="all" type="class">com.
> ibm.lsid.server.impl.CachingProxyAuthority</auth>
> <meta map="all" type="class"> com.
> ibm.lsid.server.impl.CachingProxyAuthority</meta>
> <data map="all" type="class">com.
> ibm.lsid.server.impl.CachingProxyAuthority</data>
> </components>
> </service>
> <service name="ibmdefault" >
> <components>
> <auth map="ibmtest" type="class">
> com.ibm.lsid.server.impl.test.TestAuthority</auth>
> <meta map="ibmtest"
> type="class">com.ibm.lsid.server.impl.test.TestAuthority</meta>
> <data map="ibmtest" type="class">
> com.ibm.lsid.server.impl.test.TestAuthority</data>
> <authentication map="ibmtest"
>
type="class">com.ibm.lsid.server.impl.test.TestAuthority</authentication>
> </components>
> </service>
> </services>
> </deployment-descriptor>
>
> I think you're definitely on to something about a class failing
> loading during startup: I've just looked at the catalina log. There
> seem to be one problem. Here is the logfile from the moment the
> authority.war is deployed, and I've bolded the error:
>
> 21-Sep-2006 10:49:11 org.apache.catalina.core.StandardHostDeployer
install
> INFO: Installing web application at context path /authority from URL
> jar:file:/var/lib/tomcat5/webapps/authority.war!/
> Loading authentication components from
> /var/lib/tomcat5/webapps/authority/services/default-services.xml
> LSID config file:
> /var/lib/tomcat5/webapps/authority/services/default-services.xml
> could not be loaded
> com.ibm.lsid.server.conf.LSIDConfigurationException: 521 : Error
> loading service Root Cause: java.lang.ClassNotFoundException com.
> ibm.lsid.server.impl.test.TestAuthority
> at com.ibm.lsid.server.conf.LSIDServiceComponentHandler.
> loadComponent(LSIDServiceComponentHandler.java:62)
> at com.ibm.lsid.server.conf.ServiceRegistry.
> loadComponents(ServiceRegistry.java:391)
> at com.ibm.lsid.server.conf.ServiceRegistry.
> loadSingle(ServiceRegistry.java:288)
> at com.ibm.lsid.server.conf.ServiceRegistry.
> load(ServiceRegistry.java:251)
> at com.ibm.lsid.server.conf.ServiceRegistry.
> getAuthenticationServiceRegistry (ServiceRegistry.java:160)
> at
com.ibm.lsid.server.servlet.BaseServlet.init(BaseServlet.java:95)
> at com.ibm.lsid.server.servlet.AuthorityServlet.
> init(AuthorityServlet.java:50)
> at javax.servlet.GenericServlet.init (GenericServlet.java:211)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.
> invoke(NativeMethodAccessorImpl.java:39)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke
> (DelegatingMethodAccessorImpl.java:25)
>
>
> Initially this was a classnotfound error, and I realized that I
> hadn't copied my TestAuthority.class into LSIDJars/ and therefore it
> wasn't getting put into authority.war . However, there is no longer
> a classnotfound error, but it does seem to be having a problem with
> default-services.xml. This file is in the location it is looking in
> above, and I have copied it into this email.
>
> Any ideas?
>
> Thanks very much for your help!
>
> :) Allyson
>
> p.s. You asked for all other xml files in the services directory, so
> here they are:
>
> ensembl-services.xml:
> <deployment-descriptor xmlns="http://www.ibm.com/LSID/Standard/rsdl ">
> <maps>
> <map name="ensembl-main">
> <pattern auth="ensembl.org.lsid.biopathways.org
> " ns="*" />
> </map>
> <map name="ensembl-rdf">
> <pattern auth="ensembl.org.lsid.biopathways.org
> " ns="predicates" />
> <pattern auth=" ensembl.org.lsid.biopathways.org
> " ns="types" />
> </map>
> </maps>
> <services>
> <service name="ensembl">
> <components>
> <auth map="ensembl-main"
> type="caching">com.ibm.lsid.server.impl.ensembl.EnsemblAuthority</auth>
> <meta map="ensembl-main"
> type="caching"> com.ibm.lsid.server.impl.ensembl.EnsemblAuthority</meta>
> <data map="ensembl-main"
> type="caching">com.ibm.lsid.server.impl.ensembl.EnsemblAuthority</data>
> <auth map="ensembl-rdf" type="asdl"
>
location="java-resource">/com/ibm/lsid/server/impl/ensembl/mdasdl.xml</auth>
> <meta map="ensembl-rdf" type="msdl"
>
location="java-resource">/com/ibm/lsid/server/impl/ensembl/preds.xml</meta>
> </components>
> </service>
> </services>
> </deployment-descriptor>
>
>
> ncbi-services.xml:
>
> <deployment-descriptor xmlns=" http://www.ibm.com/LSID/Standard/rsdl">
> <maps>
> <map name="ncbi-main">
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="nucleotide" />
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="genbank" />
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="protein" />
> <pattern
auth="ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="pubmed" />
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="omim" />
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="entrezgene" />
> </map>
> <map name="ncbi-ontology">
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="gbseq-predicates" />
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="gbseq-classes" />
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="mim-predicates" />
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="mim-classes" />
> <pattern
auth="ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="pubmed-predicates" />
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="pubmed-classes" />
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="entrezgene-predicates" />
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="entrezgene-classes" />
> <pattern auth="
ncbi.nlm.nih.gov.lsid.biopathways.org
> " ns="ontologies" />
> </map>
> </maps>
> <services>
> <service name="NCBI">
> <params>
> <param name="gdblinkservice"> http://lsid.
> biopathways.org:9090/gdblink/link</param>
> </params>
> <components>
> <auth map="ncbi-main"
> type="caching">
com.ibm.lsid.server.impl.ncbi.NCBIResolutionService</auth>
> <meta map="ncbi-main"
>
type="caching">com.ibm.lsid.server.impl.ncbi.NCBIResolutionService</meta>
> <data map="ncbi-main"
>
type="caching">com.ibm.lsid.server.impl.ncbi.NCBIResolutionService</data>
>
> <auth map="ncbi-ontology"
> type="caching"> com.ibm.lsid.server.impl.ncbi.
> NCBIOntologyResolutionService</auth>
> <meta map="ncbi-ontology"
> type="caching">com.ibm.lsid.server.impl.ncbi.
> NCBIOntologyResolutionService </meta>
> <data map="ncbi-ontology"
> type="caching">com.ibm.lsid.server.impl.ncbi.
> NCBIOntologyResolutionService</data>
> </components>
> </service>
> </services>
> </deployment-descriptor>
>
>
> And
> Which particular method in TestClient.java are you running? Can you
> show me the default-services.xml file that you have in your
> services/ folder in the webapp? Whenever you see an exception
> involving the CachingProxyAuthority, it means that the LSID your
> server is trying to handle is not a recognized authority and/or
> namespace and so it falls back to a caching service that tries to
> resolve the LSID in the big world. The particular LSID you are
> resolving, is just a tester (obviously) and only works against a
> locally running authority. The code in TestClient is setup to
> resolve directly to the local authority. It looks like you are
> almost there Allyson. One more error log that would be useful
> would be the entire catalina.out starting from when the server
> starts up. If a particular set of services fails to load, for
> reasons such as NoClassDefFound, then the service will just not
> load, and when you try to resolve your LSID, it will act as if no
> service is registered and fall back to the CachingProxyAuthority
> which is as you can see, failing correctly. Again, just show me
> your complete tomcat output, as well as default-services.xml (and
> any other xml files in the serivces/ folder) and I should be able to
> pinpoint the problem
>
> - Ben
>
> Ben Szekely
> IBM Software Engineer
> Advanced Internet Technology, Cambridge, MA
> bhs...@us...
>
> allyson wrote on 09/20/2006 09:27:03 AM:
> > Hi Ben,
> >
> > Sorry to bug you with what I am sure will be a simple question, but
> > I am running TestClient.java, and am getting the following error:
> >
> > Retrieving document at 'localhost'.
> > Retrieving document at 'LSIDAuthorityServiceHTTPBindings.wsdl ',
> > relative to 'localhost'.
> > Retrieving document at 'LSIDPortTypes.wsdl', relative to
> > 'LSIDAuthorityServiceHTTPBindings.wsdl'.
> > Retrieving document at 'LSIDAuthorityServiceSOAPBindings.wsdl',
> > relative to 'localhost'.
> > Retrieving document at 'LSIDPortTypes.wsdl', relative to
> > 'LSIDAuthorityServiceSOAPBindings.wsdl'.
> > 500 : Proxy Error in getAvailableOperations(urn:lsid:test.lsid.ibm.
> > com:test:default):
> > com.ibm.lsid.server.LSIDServerException : 500 : Proxy Error in
> > getAvailableOperations(urn:lsid:test.lsid.ibm.com:test:default):
> > Root Cause: com.ibm.lsid.LSIDException 500 : Root Cause: org.
> > apache.axis.AxisFault ; nested exception is:
> > java.net.UnknownHostException : test.lsid.ibm.com
> > at com.ibm.lsid.server.impl.CachingProxyAuthority.
> > getAvailableServices(CachingProxyAuthority.java:116)
> > at com.ibm.lsid.server.servlet.AuthorityServlet.processGet
> > (AuthorityServlet.java:98)
> > at
com.ibm.lsid.server.servlet.BaseServlet.doGet(BaseServlet.java:175)
> > at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
> > at javax.servlet.http.HttpServlet.service (HttpServlet.java:802)
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > at sun.reflect.NativeMethodAccessorImpl.
> > invoke(NativeMethodAccessorImpl.java:39)
> > at sun.reflect.DelegatingMethodAccessorImpl.invoke
> > (DelegatingMethodAccessorImpl.java:25)
> > at java.lang.reflect.Method.invoke(Method.java:585)
> > at org.apache.catalina.security.SecurityUtil$1.
> run(SecurityUtil.java:243)
> > at java.security.AccessController.doPrivileged (Native Method)
> > at javax.security.auth.Subject.doAsPrivileged(Subject.java:517)
> > at org.apache.catalina.security.SecurityUtil.
> > execute(SecurityUtil.java:272)
> >
> > I am behind a proxy server here at newcastle ( wwwcache.ncl.ac.uk:8080
> > ). Do you think this message has something to do with that? Does the
> > TestClient try to access something in the big wide world? :)
> >
> > While I've used tomcat before, I've never used it as an admin, and
> > wouldn't know if this error has anything to do with it, and google
> > hasn't been the font of information I had hoped. Do you have any
> > ideas? (By the way, if there is a forum/mailing list I should post
> > this to instead, please let me know and I'll post there).
> >
> > Thanks :) Allyson
>
>
> --
> Allyson Lister
> Research Associate
> Centre for Integrated Systems Biology in Ageing and Nutrition
> Newcastle University
> http://www.cisban.ac.uk
> School of Computing Science
> Newcastle University
> Newcastle upon Tyne, NE1 7RU
>
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