On Tue, Feb 15, 2011 at 6:05 PM, Arek Kasprzyk <[email protected]>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" <[email protected]> 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 > > [email protected] > > https://lists.biomart.org/mailman/listinfo/users >
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