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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