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  1. Jalview
  2. JAL-3988

Cannot connect to JABAWS webservice from Jalview



    • Type: Story
    • Status: Closed
    • Priority: Major
    • Resolution: Not A Bug
    • Affects Version/s:
    • Fix Version/s: None
    • Component/s: Jalview Project
    • Labels:
    • Environment:
      Java version:
      Java Home: /usr/lib/jvm/java-11-openjdk-amd64
      amd64 Linux 5.4.0-107-generic
    • Urgency:


      I cannot connect to the JABAWS web server. I have tried this from home internet and from the office behind the University of Adelaide firewall. Same result for both.

      Started jalview, here is the terminal output:

      a1071750@BxDave:~$ jalview
      Running jalview.bin.Jalview with memory setting -Xmx30108262400
      Java version:
      Java Home: /usr/lib/jvm/java-11-openjdk-amd64
      amd64 Linux 5.4.0-107-generic
      Jalview Version: (Source git-commit:53f3ef526c [releases/Release_2_11_2_Branch])
      WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
      # INFO: Setting default net timeout to 30 seconds.
      Gtk-Message: 17:46:03.438: Failed to load module "appmenu-gtk-module"
      SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
      SLF4J: Defaulting to no-operation (NOP) logger implementation
      SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
      INFO - Loaded Sequence Ontology from so-xp-simple.obo.zip (70ms)
      INFO - Getting messages for lang: en_AU
      WARNING: An illegal reflective access operation has occurred
      WARNING: Illegal reflective access by jalview.gui.Desktop (file:/opt/jalview-all- to field sun.awt.X11.XToolkit.awtAppClassName
      WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
      WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
      WARNING: All illegal access operations will be denied in a future release
      INFO - Setting no proxy settings
      ERROR - Exception when discovering Jws2 services.
      java.lang.NoClassDefFoundError: javax/xml/ws/WebServiceException
      at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:117) [jalview-all-]
      at java.lang.Thread.run(Thread.java:829) [?:?]
      Caused by: java.lang.ClassNotFoundException: javax.xml.ws.WebServiceException
      at jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581) ~[?:?]
      at jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178) ~[?:?]
      at java.lang.ClassLoader.loadClass(ClassLoader.java:522) ~[?:?]
      ... 2 more
      File format identified as Jalview
      Exception in thread "main" java.lang.NoClassDefFoundError: javax/xml/bind/JAXBContext
      at jalview.project.Jalview2XML.loadJalviewAlign(Jalview2XML.java:2886)
      at jalview.project.Jalview2XML.loadJalviewAlign(Jalview2XML.java:2752)
      at jalview.io.FileLoader.run(FileLoader.java:339)
      at jalview.io.FileLoader._LoadFileWaitTillLoaded(FileLoader.java:211)
      at jalview.io.FileLoader.LoadFileWaitTillLoaded(FileLoader.java:164)
      at jalview.bin.Jalview.doMain(Jalview.java:832)
      at jalview.bin.Jalview.main(Jalview.java:216)
      Caused by: java.lang.ClassNotFoundException: javax.xml.bind.JAXBContext
      at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
      at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
      at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
      ... 7 more

      At this point the GUI loads (see attached screenshot).

      Using no proxy server.

      As you can see from the preferences (see image) the web server is shown, but does not connect.

      Finally tried pinging the web server again, still no joy. Pinged the main Dundee web site as well and then Exeter and Glasgow. For some reason Scotland does not respond to pings. See below.

      a1071750@BxDave:~$ ping www.dundee.ac.uk
      PING sky.dundee.ac.uk ( 56(84) bytes of data.
      --- sky.dundee.ac.uk ping statistics ---
      6 packets transmitted, 0 received, 100% packet loss, time 5119ms

      a1071750@BxDave:~$ ping www.compbio.dundee.ac.uk
      PING www-prod.compbio.dundee.ac.uk ( 56(84) bytes of data.
      --- www-prod.compbio.dundee.ac.uk ping statistics ---
      8 packets transmitted, 0 received, 100% packet loss, time 7168ms

      a1071750@BxDave:~$ ping www.gla.ac.uk
      PING www.gla.ac.uk ( 56(84) bytes of data.
      --- www.gla.ac.uk ping statistics ---
      7 packets transmitted, 0 received, 100% packet loss, time 6131ms

      a1071750@BxDave:~$ ping www.exeter.ac.uk
      PING d3k7x9v5al5uiv.cloudfront.net ( 56(84) bytes of data.
      64 bytes from server-65-8-33-58.mel50.r.cloudfront.net ( icmp_seq=1 ttl=245 time=23.0 ms
      64 bytes from server-65-8-33-58.mel50.r.cloudfront.net ( icmp_seq=2 ttl=245 time=24.2 ms
      64 bytes from server-65-8-33-58.mel50.r.cloudfront.net ( icmp_seq=3 ttl=245 time=29.6 ms
      64 bytes from server-65-8-33-58.mel50.r.cloudfront.net ( icmp_seq=4 ttl=245 time=25.0 ms
      64 bytes from server-65-8-33-58.mel50.r.cloudfront.net ( icmp_seq=5 ttl=245 time=28.2 ms
      64 bytes from server-65-8-33-58.mel50.r.cloudfront.net ( icmp_seq=6 ttl=245 time=26.4 ms
      --- d3k7x9v5al5uiv.cloudfront.net ping statistics ---
      6 packets transmitted, 6 received, 0% packet loss, time 5006ms
      rtt min/avg/max/mdev = 22.983/26.059/29.567/2.286 ms


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              jprocter James Procter
              davead David Adelson
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