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  1. Jalview
  2. JAL-1585

Problem connecting to Jabaws

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: web service bug
    • Labels:
      None
    • Environment:
      OXS Yosemite 10.10
    • Urgency:
      Urgent

      Description

      Jalview 2.8.1 can't connect to Jabaws upon launch. I can however connect to Jabaws in an internet browser.

      The output of the Java console is below.

      Many thanks for your help and apologies if this has been reported already.

      Luca

      ***
      Jalview Desktop 2.8.1
      Build Date: 04 June 2014
      Java version: 1.8.0_25
      x86_64 Mac OS X 10.10
      Exception whilst trying to get at registry:
      com.sun.xml.internal.ws.client.ClientTransportException: HTTP transport error: java.net.UnknownHostException: gjb-www-4.cluster.lifesci.dundee.ac.uk
      at com.sun.xml.internal.ws.transport.http.client.HttpClientTransport.getOutput(HttpClientTransport.java:117)
      at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.process(HttpTransportPipe.java:208)
      at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.processRequest(HttpTransportPipe.java:130)
      at com.sun.xml.internal.ws.transport.DeferredTransportPipe.processRequest(DeferredTransportPipe.java:95)
      at com.sun.xml.internal.ws.api.pipe.Fiber.__doRun(Fiber.java:1121)
      at com.sun.xml.internal.ws.api.pipe.Fiber._doRun(Fiber.java:1035)
      at com.sun.xml.internal.ws.api.pipe.Fiber.doRun(Fiber.java:1004)
      at com.sun.xml.internal.ws.api.pipe.Fiber.runSync(Fiber.java:862)
      at com.sun.xml.internal.ws.client.Stub.process(Stub.java:448)
      at com.sun.xml.internal.ws.client.sei.SEIStub.doProcess(SEIStub.java:178)
      at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:93)
      at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:77)
      at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(SEIStub.java:147)
      at com.sun.proxy.$Proxy24.getSupportedServices(Unknown Source)
      at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:119)
      at java.lang.Thread.run(Thread.java:745)
      Caused by: java.net.UnknownHostException: gjb-www-4.cluster.lifesci.dundee.ac.uk
      at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
      at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
      at java.net.Socket.connect(Socket.java:589)
      at java.net.Socket.connect(Socket.java:538)
      at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
      at sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
      at sun.net.www.http.HttpClient.openServer(HttpClient.java:527)
      at sun.net.www.http.HttpClient.<init>(HttpClient.java:211)
      at sun.net.www.http.HttpClient.New(HttpClient.java:308)
      at sun.net.www.http.HttpClient.New(HttpClient.java:326)
      at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1167)
      at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1103)
      at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:987)
      at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:985)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessController.doPrivileged(AccessController.java:713)
      at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:984)
      at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:931)
      at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(HttpURLConnection.java:1281)
      at sun.net.www.protocol.http.HttpURLConnection.access$100(HttpURLConnection.java:90)
      at sun.net.www.protocol.http.HttpURLConnection$8.run(HttpURLConnection.java:1248)
      at sun.net.www.protocol.http.HttpURLConnection$8.run(HttpURLConnection.java:1246)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessController.doPrivileged(AccessController.java:713)
      at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLConnection.java:1245)
      at com.sun.xml.internal.ws.transport.http.client.HttpClientTransport.getOutput(HttpClientTransport.java:104)
      ... 15 more
      JWS2 Discoverer: http://www.compbio.dundee.ac.uk/jabaws is a JABAWS1 server. Using hardwired list.
      Attempting to connect with MafftWS...
      com.sun.xml.internal.ws.client.ClientTransportException: HTTP transport error: java.net.UnknownHostException: gjb-www-4.cluster.lifesci.dundee.ac.uk
      at com.sun.xml.internal.ws.transport.http.client.HttpClientTransport.getOutput(HttpClientTransport.java:117)
      at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.process(HttpTransportPipe.java:208)
      at com.sun.xml.internal.ws.transport.http.client.HttpTransportPipe.processRequest(HttpTransportPipe.java:130)
      at com.sun.xml.internal.ws.transport.DeferredTransportPipe.processRequest(DeferredTransportPipe.java:95)
      at com.sun.xml.internal.ws.api.pipe.Fiber.__doRun(Fiber.java:1121)
      at com.sun.xml.internal.ws.api.pipe.Fiber._doRun(Fiber.java:1035)
      at com.sun.xml.internal.ws.api.pipe.Fiber.doRun(Fiber.java:1004)
      at com.sun.xml.internal.ws.api.pipe.Fiber.runSync(Fiber.java:862)
      at com.sun.xml.internal.ws.client.Stub.process(Stub.java:448)
      at com.sun.xml.internal.ws.client.sei.SEIStub.doProcess(SEIStub.java:178)
      at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:93)
      at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:77)
      at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(SEIStub.java:147)
      at com.sun.proxy.$Proxy24.getServiceDescription(Unknown Source)
      at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:180)
      at java.lang.Thread.run(Thread.java:745)
      Caused by: java.net.UnknownHostException: gjb-www-4.cluster.lifesci.dundee.ac.uk
      at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
      at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
      at java.net.Socket.connect(Socket.java:589)
      at java.net.Socket.connect(Socket.java:538)
      at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
      at sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
      at sun.net.www.http.HttpClient.openServer(HttpClient.java:527)
      at sun.net.www.http.HttpClient.<init>(HttpClient.java:211)
      at sun.net.www.http.HttpClient.New(HttpClient.java:308)
      at sun.net.www.http.HttpClient.New(HttpClient.java:326)
      at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1167)
      at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1103)
      at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:987)
      at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:985)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessController.doPrivileged(AccessController.java:713)
      at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:984)
      at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:931)
      at sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(HttpURLConnection.java:1281)
      at sun.net.www.protocol.http.HttpURLConnection.access$100(HttpURLConnection.java:90)
      at sun.net.www.protocol.http.HttpURLConnection$8.run(HttpURLConnection.java:1248)
      at sun.net.www.protocol.http.HttpURLConnection$8.run(HttINFO - Not enabling Google Tracking.
      INFO - Constructing news reader.
      INFO - Completed construction of reader.
      WARN - Exception when discovering Jws2 services.
      pURLConnection.java:1246)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessController.doPrivileged(AccessController.java:713)
      at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLConnection.java:1245)
      at com.sun.xml.internal.ws.transport.http.client.HttpClientTransport.getOutput(HttpClientTransport.java:104)
      ... 15 more
      INFO - Saved last read date as 09-Nov-2014 14:09:29
      INFO - Saved last read date as 09-Nov-2014 14:09:29
      INFO - Saved last read date as 09-Nov-2014 14:09:29

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              Assignee:
              jprocter Jim Procter
              Reporter:
              lucap Luca
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                Dates

                Created:
                Updated:
                Resolved: