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" <[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 _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
