[BioMart Users] martservice from release candidate for version 0.8

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[BioMart Users] martservice from release candidate for version 0.8

Sean Davis
I have been playing with the release candidate 4 for a day now and really like the clean design and implementation.  After setting up a test local dataset and a couple of URL datasets, I wanted to try martservice.  It may be in the docs, but I didn't find any detail, I guess.  What is the URL for martservice?  Is the release candidate backwards-compatible with calls from the previous martservice implementations?  Perhaps to shortcircuit emails a bit, I tried localhost:9000/martservice?type=registry, for example, and got back a stack trace.

Thanks,
Sean


java.lang.NullPointerException
	at org.biomart.api.rest.MartResource.streamResults(MartResource.java:469)
	at org.biomart.api.rest.MartResource.doGetStreamResults(MartResource.java:461)
	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:597)
	at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:168)
	at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:70)
	at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:279)
	at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
	at com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept(ResourceObjectRule.java:84)
	at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
	at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:74)
	at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1357)
	at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1289)
	at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1239)
	at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1229)
	at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:420)
	at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:497)
	at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:684)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
	at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
	at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:390)
	at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
	at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
	at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
	at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
	at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:327)
	at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:126)
	at org.biomart.api.ProxyServlet.doGet(ProxyServlet.java:17)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
	at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
	at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1166)
	at org.biomart.api.rest.LocationsFilter.doFilter(LocationsFilter.java:28)
	at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
	at org.biomart.api.rest.AuthFilter.doFilter(AuthFilter.java:47)
	at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
	at org.biomart.api.rest.FlashMessageFilter.doFilter(FlashMessageFilter.java:35)
	at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
	at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
	at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
	at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
	at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
	at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
	at org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)
	at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
	at org.mortbay.jetty.Server.handle(Server.java:326)
	at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
	at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:924)
	at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549)
	at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
	at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
	at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409)
	at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)

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Re: [BioMart Users] martservice from release candidate for version 0.8

Jack Hsu
Re: [BioMart Users] martservice from release candidate for version 0.8 Hi Sean,

The 0.8 REST service is will be a little bit different from the 0.7 version. The current rc4 REST service implementation is not exactly what we’ll be using going forward.

We’re currently working on releasing a new version of the 0.8 REST service which will be closer to the 0.7 services. We’re also working on SOAP and Java APIs.

For now, if you want to poke around the rc4 REST services you can fire me an email directly, or reverse engineering it from the web GUI ;) However, please keep in mind that we will not be supporting the rc4 REST services going forward.

-jack


On 11-02-15 4:43 PM, "Sean Davis" <sdavis2@...> wrote:

I have been playing with the release candidate 4 for a day now and really like the clean design and implementation.  After setting up a test local dataset and a couple of URL datasets, I wanted to try martservice.  It may be in the docs, but I didn't find any detail, I guess.  What is the URL for martservice?  Is the release candidate backwards-compatible with calls from the previous martservice implementations?  Perhaps to shortcircuit emails a bit, I tried localhost:9000/martservice?type=registry, for example, and got back a stack trace.

Thanks,
Sean



java.lang.NullPointerException
 at org.biomart.api.rest.MartResource.streamResults(MartResource.java:469)
 at org.biomart.api.rest.MartResource.doGetStreamResults(MartResource.java:461)
 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:597)
 at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:168)
 at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:70)
 at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:279)
 at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
 at com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept(ResourceObjectRule.java:84)
 at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
 at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:74)
 at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1357)
 at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1289)
 at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1239)
 at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1229)
 at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:420)
 at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:497)
 at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:684)
 at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
 at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
 at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:390)
 at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
 at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
 at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
 at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
 at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:327)
 at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:126)
 at org.biomart.api.ProxyServlet.doGet(ProxyServlet.java:17)
 at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
 at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
 at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1166)
 at org.biomart.api.rest.LocationsFilter.doFilter(LocationsFilter.java:28)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
 at org.biomart.api.rest.AuthFilter.doFilter(AuthFilter.java:47)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
 at org.biomart.api.rest.FlashMessageFilter.doFilter(FlashMessageFilter.java:35)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
 at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
 at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
 at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
 at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
 at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
 at org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)
 at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
 at org.mortbay.jetty.Server.handle(Server.java:326)
 at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
 at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:924)
 at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549)
 at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
 at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
 at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409)
 at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)


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Re: [BioMart Users] martservice from release candidate for version 0.8

Sean Davis


On Tue, Feb 15, 2011 at 5:09 PM, Jack Hsu <[hidden email]> wrote:
Hi Sean,

The 0.8 REST service is will be a little bit different from the 0.7 version. The current rc4 REST service implementation is not exactly what we’ll be using going forward.

We’re currently working on releasing a new version of the 0.8 REST service which will be closer to the 0.7 services. We’re also working on SOAP and Java APIs.

For now, if you want to poke around the rc4 REST services you can fire me an email directly, or reverse engineering it from the web GUI ;) However, please keep in mind that we will not be supporting the rc4 REST services going forward.


Thanks, Jack.  What I am after is what is available for web services  and how they might be accessed for version 0.8 and forward.  How much of that will be compatible with existing tools for querying biomart, particularly tools like biomaRt (for R)?

Thanks,
Sean
 
-jack


On 11-02-15 4:43 PM, "Sean Davis" <sdavis2@...> wrote:

I have been playing with the release candidate 4 for a day now and really like the clean design and implementation.  After setting up a test local dataset and a couple of URL datasets, I wanted to try martservice.  It may be in the docs, but I didn't find any detail, I guess.  What is the URL for martservice?  Is the release candidate backwards-compatible with calls from the previous martservice implementations?  Perhaps to shortcircuit emails a bit, I tried localhost:9000/martservice?type=registry, for example, and got back a stack trace.

Thanks,
Sean



java.lang.NullPointerException
 at org.biomart.api.rest.MartResource.streamResults(MartResource.java:469)
 at org.biomart.api.rest.MartResource.doGetStreamResults(MartResource.java:461)
 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:597)
 at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:168)
 at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:70)
 at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:279)
 at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
 at com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept(ResourceObjectRule.java:84)
 at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
 at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:74)
 at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1357)
 at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1289)
 at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1239)
 at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1229)
 at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:420)
 at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:497)
 at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:684)
 at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
 at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
 at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:390)
 at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
 at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
 at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
 at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
 at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:327)
 at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:126)
 at org.biomart.api.ProxyServlet.doGet(ProxyServlet.java:17)
 at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
 at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
 at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1166)
 at org.biomart.api.rest.LocationsFilter.doFilter(LocationsFilter.java:28)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
 at org.biomart.api.rest.AuthFilter.doFilter(AuthFilter.java:47)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
 at org.biomart.api.rest.FlashMessageFilter.doFilter(FlashMessageFilter.java:35)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
 at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
 at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
 at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
 at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
 at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
 at org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)
 at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
 at org.mortbay.jetty.Server.handle(Server.java:326)
 at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
 at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:924)
 at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549)
 at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
 at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
 at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409)
 at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)



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Re: [BioMart Users] martservice from release candidate for version 0.8

Jack Hsu
Re: [BioMart Users] martservice from release candidate for version 0.8 Migration will be needed to go from 0.7 to 0.8. We will be deploying the final version of the 0.8 services in rc5, so we’ll have more details then regarding migrating.

-jack


On 11-02-15 5:22 PM, "Sean Davis" <sdavis2@...> wrote:



On Tue, Feb 15, 2011 at 5:09 PM, Jack Hsu <Jack.Hsu@...> wrote:
Hi Sean,

The 0.8 REST service is will be a little bit different from the 0.7 version. The current rc4 REST service implementation is not exactly what we’ll be using going forward.

We’re currently working on releasing a new version of the 0.8 REST service which will be closer to the 0.7 services. We’re also working on SOAP and Java APIs.

For now, if you want to poke around the rc4 REST services you can fire me an email directly, or reverse engineering it from the web GUI ;) However, please keep in mind that we will not be supporting the rc4 REST services going forward.


Thanks, Jack.  What I am after is what is available for web services  and how they might be accessed for version 0.8 and forward.  How much of that will be compatible with existing tools for querying biomart, particularly tools like biomaRt (for R)?

Thanks,
Sean
 
-jack


On 11-02-15 4:43 PM, "Sean Davis" <sdavis2@... <http://sdavis2@...> > wrote:

I have been playing with the release candidate 4 for a day now and really like the clean design and implementation.  After setting up a test local dataset and a couple of URL datasets, I wanted to try martservice.  It may be in the docs, but I didn't find any detail, I guess.  What is the URL for martservice?  Is the release candidate backwards-compatible with calls from the previous martservice implementations?  Perhaps to shortcircuit emails a bit, I tried localhost:9000/martservice?type=registry, for example, and got back a stack trace.

Thanks,
Sean



java.lang.NullPointerException
 at org.biomart.api.rest.MartResource.streamResults(MartResource.java:469)
 at org.biomart.api.rest.MartResource.doGetStreamResults(MartResource.java:461)
 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:597)
 at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:168)
 at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:70)
 at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:279)
 at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
 at com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept(ResourceObjectRule.java:84)
 at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
 at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:74)
 at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1357)
 at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1289)
 at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1239)
 at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1229)
 at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:420)
 at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:497)
 at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:684)
 at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
 at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
 at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:390)
 at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
 at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
 at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
 at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
 at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:327)
 at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:126)
 at org.biomart.api.ProxyServlet.doGet(ProxyServlet.java:17)
 at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
 at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
 at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1166)
 at org.biomart.api.rest.LocationsFilter.doFilter(LocationsFilter.java:28)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
 at org.biomart.api.rest.AuthFilter.doFilter(AuthFilter.java:47)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
 at org.biomart.api.rest.FlashMessageFilter.doFilter(FlashMessageFilter.java:35)
 at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
 at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
 at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
 at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
 at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
 at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
 at org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)
 at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
 at org.mortbay.jetty.Server.handle(Server.java:326)
 at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
 at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:924)
 at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549)
 at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
 at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
 at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409)
 at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)




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Re: [BioMart Users] martservice from release candidate for version 0.8

Syed Haider
In reply to this post by Sean Davis
Hi Sean,

The new web service would have the same abstractions as in (marts,
datasets, attributes, filters etc).

In the new webservice, the signatures of all metadata requests would be
different. More importantly, the response of metadata requests would
different too (XML based as opposed to tab separated). In addition,
there will be JSON and SOAP end points too, same information but
different response format.
The response of the data queries would be just the same as before.

As far as biomaRt and other clients go, they would need to be adjusted
to communicate using new requests. For this, as Jack mentioned a test
server will ease the transition from rc5 up until official 0.8 release.
However, i see that people who have bioconductor packages installed
already would have problems right away which isnt good. So, a nice
solution would be to keep the current web service end-point running for
a while in addition to the new webservice.  Over to Arek to see what he
thinks about this.

Best,
Syed



On 15/02/2011 21:43, Sean Davis wrote:

> I have been playing with the release candidate 4 for a day now and really like the clean design and implementation.  After setting up a test local dataset and a couple of URL datasets, I wanted to try martservice.  It may be in the docs, but I didn't find any detail, I guess.  What is the URL for martservice?  Is the release candidate backwards-compatible with calls from the previous martservice implementations?  Perhaps to shortcircuit emails a bit, I tried localhost:9000/martservice?type=registry, for example, and got back a stack trace.
>
> Thanks,
> Sean
>
>
>
>
> java.lang.NullPointerException
>          at org.biomart.api.rest.MartResource.streamResults(MartResource.java:469)
>          at org.biomart.api.rest.MartResource.doGetStreamResults(MartResource.java:461)
>          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:597)
>          at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:168)
>          at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:70)
>          at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:279)
>          at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
>          at com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept(ResourceObjectRule.java:84)
>          at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
>          at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:74)
>          at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1357)
>          at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1289)
>          at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1239)
>          at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1229)
>          at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:420)
>          at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:497)
>          at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:684)
>          at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>          at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
>          at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:390)
>          at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
>          at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
>          at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
>          at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
>          at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:327)
>          at org.mortbay.jetty.servlet.Dispatcher.forward(Dispatcher.java:126)
>          at org.biomart.api.ProxyServlet.doGet(ProxyServlet.java:17)
>          at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
>          at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>          at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
>          at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1166)
>          at org.biomart.api.rest.LocationsFilter.doFilter(LocationsFilter.java:28)
>          at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
>          at org.biomart.api.rest.AuthFilter.doFilter(AuthFilter.java:47)
>          at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
>          at org.biomart.api.rest.FlashMessageFilter.doFilter(FlashMessageFilter.java:35)
>          at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
>          at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
>          at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
>          at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
>          at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
>          at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
>          at org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)
>          at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
>          at org.mortbay.jetty.Server.handle(Server.java:326)
>          at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
>          at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:924)
>          at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549)
>          at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
>          at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
>          at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409)
>          at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)
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Re: [BioMart Users] martservice from release candidate for version 0.8

Arek Kasprzyk-2
Hi Sean
Soon after rc5 (ETA march 1st) Jack will be making an announcement  
about the 0.8 web service test server to let people poke around a new  
service and get prepared for the move. After the official release of  
the new 0.8 service we will be maintaing central portal in 0.7 and 0.8  
in parallel for a while to give people extra time to adapt and  
minimize any possible disruptions to the service.


a



On 2011-02-15, at 17:31, "Syed Haider" <[hidden email]> wrote:

> Hi Sean,
>
> The new web service would have the same abstractions as in (marts,
> datasets, attributes, filters etc).
>
> In the new webservice, the signatures of all metadata requests would  
> be
> different. More importantly, the response of metadata requests would
> different too (XML based as opposed to tab separated). In addition,
> there will be JSON and SOAP end points too, same information but
> different response format.
> The response of the data queries would be just the same as before.
>
> As far as biomaRt and other clients go, they would need to be adjusted
> to communicate using new requests. For this, as Jack mentioned a test
> server will ease the transition from rc5 up until official 0.8  
> release.
> However, i see that people who have bioconductor packages installed
> already would have problems right away which isnt good. So, a nice
> solution would be to keep the current web service end-point running  
> for
> a while in addition to the new webservice.  Over to Arek to see what  
> he
> thinks about this.
>
> Best,
> Syed
>
>
>
> On 15/02/2011 21:43, Sean Davis wrote:
>> I have been playing with the release candidate 4 for a day now and  
>> really like the clean design and implementation.  After setting up  
>> a test local dataset and a couple of URL datasets, I wanted to try  
>> martservice.  It may be in the docs, but I didn't find any detail,  
>> I guess.  What is the URL for martservice?  Is the release  
>> candidate backwards-compatible with calls from the previous  
>> martservice implementations?  Perhaps to shortcircuit emails a bit,  
>> I tried localhost:9000/martservice?type=registry, for example, and  
>> got back a stack trace.
>>
>> Thanks,
>> Sean
>>
>>
>>
>>
>> java.lang.NullPointerException
>>         at org.biomart.api.rest.MartResource.streamResults
>> (MartResource.java:469)
>>         at org.biomart.api.rest.MartResource.doGetStreamResults
>> (MartResource.java:461)
>>         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:597)
>>         at  
>> com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$
>> TypeOutInvoker._dispatch
>> (AbstractResourceMethodDispatchProvider.java:168)
>>         at  
>> com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(
>> ResourceJavaMethodDispatcher.java:70)
>>         at  
>> com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept
>> (HttpMethodRule.java:279)
>>         at  
>> com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept
>> (RightHandPathRule.java:136)
>>         at  
>> com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept
>> (ResourceObjectRule.java:84)
>>         at  
>> com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept
>> (RightHandPathRule.java:136)
>>         at  
>> com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept
>> (RootResourceClassesRule.java:74)
>>         at  
>> com.sun.jersey.server.impl.application.WebApplicationImpl.
>> _handleRequest(WebApplicationImpl.java:1357)
>>         at  
>> com.sun.jersey.server.impl.application.WebApplicationImpl.
>> _handleRequest(WebApplicationImpl.java:1289)
>>         at  
>> com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(
>> WebApplicationImpl.java:1239)
>>         at  
>> com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(
>> WebApplicationImpl.java:1229)
>>         at com.sun.jersey.spi.container.servlet.WebComponent.service
>> (WebComponent.java:420)
>>         at  
>> com.sun.jersey.spi.container.servlet.ServletContainer.service
>> (ServletContainer.java:497)
>>         at  
>> com.sun.jersey.spi.container.servlet.ServletContainer.service
>> (ServletContainer.java:684)
>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:
>> 802)
>>         at org.mortbay.jetty.servlet.ServletHolder.handle
>> (ServletHolder.java:511)
>>         at org.mortbay.jetty.servlet.ServletHandler.handle
>> (ServletHandler.java:390)
>>         at org.mortbay.jetty.security.SecurityHandler.handle
>> (SecurityHandler.java:216)
>>         at org.mortbay.jetty.servlet.SessionHandler.handle
>> (SessionHandler.java:182)
>>         at org.mortbay.jetty.handler.ContextHandler.handle
>> (ContextHandler.java:765)
>>         at org.mortbay.jetty.webapp.WebAppContext.handle
>> (WebAppContext.java:418)
>>         at org.mortbay.jetty.servlet.Dispatcher.forward
>> (Dispatcher.java:327)
>>         at org.mortbay.jetty.servlet.Dispatcher.forward
>> (Dispatcher.java:126)
>>         at org.biomart.api.ProxyServlet.doGet(ProxyServlet.java:17)
>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:
>> 689)
>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:
>> 802)
>>         at org.mortbay.jetty.servlet.ServletHolder.handle
>> (ServletHolder.java:511)
>>         at org.mortbay.jetty.servlet.ServletHandler
>> $CachedChain.doFilter(ServletHandler.java:1166)
>>         at org.biomart.api.rest.LocationsFilter.doFilter
>> (LocationsFilter.java:28)
>>         at org.mortbay.jetty.servlet.ServletHandler
>> $CachedChain.doFilter(ServletHandler.java:1157)
>>         at org.biomart.api.rest.AuthFilter.doFilter(AuthFilter.java:
>> 47)
>>         at org.mortbay.jetty.servlet.ServletHandler
>> $CachedChain.doFilter(ServletHandler.java:1157)
>>         at org.biomart.api.rest.FlashMessageFilter.doFilter
>> (FlashMessageFilter.java:35)
>>         at org.mortbay.jetty.servlet.ServletHandler
>> $CachedChain.doFilter(ServletHandler.java:1157)
>>         at org.mortbay.jetty.servlet.ServletHandler.handle
>> (ServletHandler.java:388)
>>         at org.mortbay.jetty.security.SecurityHandler.handle
>> (SecurityHandler.java:216)
>>         at org.mortbay.jetty.servlet.SessionHandler.handle
>> (SessionHandler.java:182)
>>         at org.mortbay.jetty.handler.ContextHandler.handle
>> (ContextHandler.java:765)
>>         at org.mortbay.jetty.webapp.WebAppContext.handle
>> (WebAppContext.java:418)
>>         at org.mortbay.jetty.handler.HandlerCollection.handle
>> (HandlerCollection.java:114)
>>         at org.mortbay.jetty.handler.HandlerWrapper.handle
>> (HandlerWrapper.java:152)
>>         at org.mortbay.jetty.Server.handle(Server.java:326)
>>         at org.mortbay.jetty.HttpConnection.handleRequest
>> (HttpConnection.java:542)
>>         at org.mortbay.jetty.HttpConnection
>> $RequestHandler.headerComplete(HttpConnection.java:924)
>>         at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:
>> 549)
>>         at org.mortbay.jetty.HttpParser.parseAvailable
>> (HttpParser.java:212)
>>         at org.mortbay.jetty.HttpConnection.handle
>> (HttpConnection.java:404)
>>         at org.mortbay.io.nio.SelectChannelEndPoint.run
>> (SelectChannelEndPoint.java:409)
>>         at org.mortbay.thread.QueuedThreadPool$PoolThread.run
>> (QueuedThreadPool.java:582)
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] martservice from release candidate for version 0.8

Sean Davis


On Tue, Feb 15, 2011 at 6:05 PM, Arek Kasprzyk <[hidden email]> wrote:
Hi Sean
Soon after rc5 (ETA march 1st) Jack will be making an announcement
about the 0.8 web service test server to let people poke around a new
service and get prepared for the move. After the official release of
the new 0.8 service we will be maintaing central portal in 0.7 and 0.8
in parallel for a while to give people extra time to adapt and
minimize any possible disruptions to the service.


Great, Arek.  I appreciate the (even approximate) timeframe and plan.  

Thanks,
Sean


 
On 2011-02-15, at 17:31, "Syed Haider" <[hidden email]> wrote:

> Hi Sean,
>
> The new web service would have the same abstractions as in (marts,
> datasets, attributes, filters etc).
>
> In the new webservice, the signatures of all metadata requests would
> be
> different. More importantly, the response of metadata requests would
> different too (XML based as opposed to tab separated). In addition,
> there will be JSON and SOAP end points too, same information but
> different response format.
> The response of the data queries would be just the same as before.
>
> As far as biomaRt and other clients go, they would need to be adjusted
> to communicate using new requests. For this, as Jack mentioned a test
> server will ease the transition from rc5 up until official 0.8
> release.
> However, i see that people who have bioconductor packages installed
> already would have problems right away which isnt good. So, a nice
> solution would be to keep the current web service end-point running
> for
> a while in addition to the new webservice.  Over to Arek to see what
> he
> thinks about this.
>
> Best,
> Syed
>
>
>
> On 15/02/2011 21:43, Sean Davis wrote:
>> I have been playing with the release candidate 4 for a day now and
>> really like the clean design and implementation.  After setting up
>> a test local dataset and a couple of URL datasets, I wanted to try
>> martservice.  It may be in the docs, but I didn't find any detail,
>> I guess.  What is the URL for martservice?  Is the release
>> candidate backwards-compatible with calls from the previous
>> martservice implementations?  Perhaps to shortcircuit emails a bit,
>> I tried localhost:9000/martservice?type=registry, for example, and
>> got back a stack trace.
>>
>> Thanks,
>> Sean
>>
>>
>>
>>
>> java.lang.NullPointerException
>>         at org.biomart.api.rest.MartResource.streamResults
>> (MartResource.java:469)
>>         at org.biomart.api.rest.MartResource.doGetStreamResults
>> (MartResource.java:461)
>>         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:597)
>>         at
>> com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$
>> TypeOutInvoker._dispatch
>> (AbstractResourceMethodDispatchProvider.java:168)
>>         at
>> com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(
>> ResourceJavaMethodDispatcher.java:70)
>>         at
>> com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept
>> (HttpMethodRule.java:279)
>>         at
>> com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept
>> (RightHandPathRule.java:136)
>>         at
>> com.sun.jersey.server.impl.uri.rules.ResourceObjectRule.accept
>> (ResourceObjectRule.java:84)
>>         at
>> com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept
>> (RightHandPathRule.java:136)
>>         at
>> com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept
>> (RootResourceClassesRule.java:74)
>>         at
>> com.sun.jersey.server.impl.application.WebApplicationImpl.
>> _handleRequest(WebApplicationImpl.java:1357)
>>         at
>> com.sun.jersey.server.impl.application.WebApplicationImpl.
>> _handleRequest(WebApplicationImpl.java:1289)
>>         at
>> com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(
>> WebApplicationImpl.java:1239)
>>         at
>> com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(
>> WebApplicationImpl.java:1229)
>>         at com.sun.jersey.spi.container.servlet.WebComponent.service
>> (WebComponent.java:420)
>>         at
>> com.sun.jersey.spi.container.servlet.ServletContainer.service
>> (ServletContainer.java:497)
>>         at
>> com.sun.jersey.spi.container.servlet.ServletContainer.service
>> (ServletContainer.java:684)
>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:
>> 802)
>>         at org.mortbay.jetty.servlet.ServletHolder.handle
>> (ServletHolder.java:511)
>>         at org.mortbay.jetty.servlet.ServletHandler.handle
>> (ServletHandler.java:390)
>>         at org.mortbay.jetty.security.SecurityHandler.handle
>> (SecurityHandler.java:216)
>>         at org.mortbay.jetty.servlet.SessionHandler.handle
>> (SessionHandler.java:182)
>>         at org.mortbay.jetty.handler.ContextHandler.handle
>> (ContextHandler.java:765)
>>         at org.mortbay.jetty.webapp.WebAppContext.handle
>> (WebAppContext.java:418)
>>         at org.mortbay.jetty.servlet.Dispatcher.forward
>> (Dispatcher.java:327)
>>         at org.mortbay.jetty.servlet.Dispatcher.forward
>> (Dispatcher.java:126)
>>         at org.biomart.api.ProxyServlet.doGet(ProxyServlet.java:17)
>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:
>> 689)
>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:
>> 802)
>>         at org.mortbay.jetty.servlet.ServletHolder.handle
>> (ServletHolder.java:511)
>>         at org.mortbay.jetty.servlet.ServletHandler
>> $CachedChain.doFilter(ServletHandler.java:1166)
>>         at org.biomart.api.rest.LocationsFilter.doFilter
>> (LocationsFilter.java:28)
>>         at org.mortbay.jetty.servlet.ServletHandler
>> $CachedChain.doFilter(ServletHandler.java:1157)
>>         at org.biomart.api.rest.AuthFilter.doFilter(AuthFilter.java:
>> 47)
>>         at org.mortbay.jetty.servlet.ServletHandler
>> $CachedChain.doFilter(ServletHandler.java:1157)
>>         at org.biomart.api.rest.FlashMessageFilter.doFilter
>> (FlashMessageFilter.java:35)
>>         at org.mortbay.jetty.servlet.ServletHandler
>> $CachedChain.doFilter(ServletHandler.java:1157)
>>         at org.mortbay.jetty.servlet.ServletHandler.handle
>> (ServletHandler.java:388)
>>         at org.mortbay.jetty.security.SecurityHandler.handle
>> (SecurityHandler.java:216)
>>         at org.mortbay.jetty.servlet.SessionHandler.handle
>> (SessionHandler.java:182)
>>         at org.mortbay.jetty.handler.ContextHandler.handle
>> (ContextHandler.java:765)
>>         at org.mortbay.jetty.webapp.WebAppContext.handle
>> (WebAppContext.java:418)
>>         at org.mortbay.jetty.handler.HandlerCollection.handle
>> (HandlerCollection.java:114)
>>         at org.mortbay.jetty.handler.HandlerWrapper.handle
>> (HandlerWrapper.java:152)
>>         at org.mortbay.jetty.Server.handle(Server.java:326)
>>         at org.mortbay.jetty.HttpConnection.handleRequest
>> (HttpConnection.java:542)
>>         at org.mortbay.jetty.HttpConnection
>> $RequestHandler.headerComplete(HttpConnection.java:924)
>>         at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:
>> 549)
>>         at org.mortbay.jetty.HttpParser.parseAvailable
>> (HttpParser.java:212)
>>         at org.mortbay.jetty.HttpConnection.handle
>> (HttpConnection.java:404)
>>         at org.mortbay.io.nio.SelectChannelEndPoint.run
>> (SelectChannelEndPoint.java:409)
>>         at org.mortbay.thread.QueuedThreadPool$PoolThread.run
>> (QueuedThreadPool.java:582)
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users


_______________________________________________
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