On Tue, Feb 15, 2011 at 5:09 PM, Jack Hsu <[email protected]> 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" <[email protected]> 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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