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From jeroen vannevel <jer_vanne...@hotmail.com>
Subject RE: Deploying emboss in Opal2
Date Mon, 11 Jul 2011 07:12:01 GMT



> Date: Fri, 8 Jul 2011 10:39:16 -0700
> From: its_toasted@yahoo.com
> Subject: Re: Deploying emboss in Opal2
> To: users@tomcat.apache.org
> 
> ----- Original Message -----
> 
> > From: jeroen vannevel <jer_vannevel@hotmail.com>
> > To: users@tomcat.apache.org
> > Cc: 
> > Sent: Friday, July 8, 2011 6:37 AM
> > Subject: RE: Deploying emboss in Opal2
> > 
> > 
> > 
> > 
> >>  Date: Fri, 8 Jul 2011 15:21:05 +0200
> >>  From: aw@ice-sa.com
> >>  To: users@tomcat.apache.org
> >>  Subject: Re: Deploying emboss in Opal2
> >> 
> >>  jeroen vannevel wrote:
> >>  > 
> >>  > 
> >>  >> Date: Fri, 8 Jul 2011 14:04:37 +0200
> >>  >> From: aw@ice-sa.com
> >>  >> To: users@tomcat.apache.org
> >>  >> Subject: Re: Deploying emboss in Opal2
> >>  >>
> >>  >> jeroen vannevel wrote:
> >>  >>> Hello
> >>  >>>  
> >>  >>> I've installed Opal2 on my Tomcat 5.5.33 server and now 
> > I'd like to make the emboss programs available in this.
> >>  >>> I've been working on this for two days and I just seem to 
> > trample at the same spot.
> >>  >>> Perhaps someone has the required files or could tell me how to

> > deal with this specific case?
> >>  >>> I've tried compiling all the emboss programs and put them 
> > in a .war package but after uploading this to Tomcat I just keep getting 
> > 'The requested r=
> >>  >>> esource () is not available.' error messages.
> >>  >>>  
> >>  >> It is possible that someone here would not the emboss application,

> > but more likely that 
> >>  >> they would not.  This is just a preliminary to ask : does the 
> > emboss program have a 
> >>  >> mailing list, and did you ask there ?
> >>  >>
> >>  >> Other than that, it would help if you provide some additional 
> > details :
> >>  >> - on what platform are you trying this ?
> >>  >> - where (in what directory) is Tomcat installed ?
> >>  >> - what is the path to the Tomcat "webapps" directory ?
> >>  >> - what is the name of your .war file ?
> >>  >> - how are you uploading your .war file to Tomcat ?
> >>  >> - where does the .war file end up when it is uploaded ?
> >>  >> - in the Tomcat configuration file ..(tomcat_dir)/conf/server.xml,

> > there is (at least) one 
> >>  >> <Host> tag.  Can you copy it here ?
> >>  >>
> >>  > 
> >>  > They do, but I've just signed up there and I'm not sure if 
> > it's a very active one. Figured I might as well test my luck and ask here.
> >>  > 
> >>  > As for additional information:
> >>  > 
> >>  > - Ubuntu 11.04
> >>  > - /home/myname/Downloads/apache-tomcat-5.5.33/
> >>  > - /home/myname/Downloads/apache-tomcat-5.5.33/webapps/
> >>  > - emboss.war
> >>  > - using the built-in File-Upload menu in Tomcat's Manager. (so the 
> > 2nd option to deploy an app)
> >>  > - /home/myname/Downloads/apache-tomcat-5.5.33/webapps/emboss.war
> >>  > 
> >>  > <Host name="localhost" appBase="webapps"
> >>  >        unpackWARs="true" autoDeploy="true"
> >>  >        xmlValidation="false" 
> > xmlNamespaceAware="false">
> >>  >        <Alias>10.0.102.165</Alias>
> >>  > </Host>
> >>  > 
> >>  At first sight, that all looks good to me (except a detail irrelevant here)
> >>  Next questions :
> >>  - what is the URL you use, to try to access this application ?
> >>  - what do the Tomcat logfiles say ?
> >> 
> >>  .. and, if the URL you used was not the same, what happens when you try to

> > access :
> >>  http://your-host-name[:port]/emboss
> >> 
> >> 
> >>  And the irrelevant detail is :
> >>  If the above <Host> tag is the only one which is contained in the 
> > server.xml file, then 
> >>  the line
> >>  <Alias>10.0.102.165</Alias>
> >>  is unnecessary.  Tomcat will default to this Host anyway for all accesses.
> >> 
> > The URL I use is http://localhost:8080/emboss, as you said it should be.
> > Perhaps it is of use to know that http://localhost:8080/opal2 does work and 
> > shows me the page I expect there.
> > 
> > The logfiles from catalina.out when restarting the service and browsing to the 
> > emboss location:
> > http://pastebin.com/UUn2dxmD
> > 
> > 
> > I've used that Alias tag to try and get another program in opal2 to use this 
> > IP adress so it would've been accessible from somewhere else in the network.
> > This failed, the application in opal2 (it was called Babel) kept linking to 
> > http://localhost instead of the alias.
> > Not that it really matters, we didn't need that application and it was for 
> > testing purposes.
> 
> 
> The log files show that there is something else running on port 8080:
> 
> SEVERE: Error initializing endpoint
> java.net.BindException: Address already in use:8080
> 
> Are you running both Ubuntu's installation of Tomcat and one downloaded from tomcat.apache.org?
> 
> Just run one copy. You can get everything running in one Tomcat by using the manager
application and installing WAR files. See:
> 
> http://tomcat.apache.org/tomcat-5.5-doc/manager-howto.html
> 
> 
> for how this works.
> 
> Accessing Tomcat at port 8080 from another host should be fairly straightforward. Just
go to:
> 
> http://<ip-address>:8080/opal2
> 
> to get to the Opal 2 application (for example).
> 
> If your hostname / IP address is in DNS (check with your network person), or of the hostname
/ IP address exists in the other machine's host file, then:
> 
> http://<hostname>:8080/opal2
> 
> should work.
> 
> I don't know Ubuntu Linux (I run Fedora), but accessing http://<hostname>:8080/opal2
from a remote machine might also run into some firewall issues. In Fedora, I would add the
following line to /etc/sysconfig/ipatables and restart the firewall.
> 
> -A INPUT -m state --state NEW -m tcp -p tcp --dport 8080 -s 192.168.0.0/24 -j ACCEPT
> 
> Adjust the 192.168.0.0/24 to meet your needs. I suspect it would be something like:
> 
> 10.0.102.0/24
> 
> 
> to grant access to your local subnet.
> 
> When you go to http://localhost, you're probably hitting Ubuntu's installation of an
Apache HTTPD server, and not Apache Tomcat. Without installing and configuring mod_jk (or
mod_proxy_ajp, or mod_proxy_http), an installation of Apache HTTPD won't know anything about
what's running on a Tomcat server.
> 
> To do then:
> 
> 1. Make sure you only have one copy of Tomcat running
> 
> 2. Make sure there's nothing else running on port 8080 by running this on the command

>    line:
> 
> sudo netstat -tlnp | grep 8080
> 
> You'll have to run this as root since netstat won't report on processes you don't own.
> 
> If something shows up, then another process is running on that port. For example:
> 
> tcp     0   0 :::8080                :::*                   LISTEN      12565/java
> 
> 
> The number 12565 is the process that is listening on port 8080. A quick:
> 
> ps -aef | grep 12565 | grep -v grep
> 
> 
> shows the following on my system.
> 
> mdeggers 12565     1  0 10:18 pts/0    00:00:03 /usr/jre/bin/java
>   -Djava.util.logging.config.file=
>     /home/mdeggers/Apache/apache-tomcat-6.0.29/conf/logging.properties
>   -Dlog4j.home=/home/mdeggers/Apache/apache-tomcat-6.0.29/logs
>   -Dderby.system.home=/home/mdeggers/Apache/apache-tomcat-6.0.29/databases
>   -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
>   -Djava.library.path=/home/mdeggers/Apache/apache-tomcat-6.0.29/bin/libs
>   -Dcom.sun.management.jmxremote -Djava.rmi.server.hostname=phoenix
>   -Dcom.sun.management.jmxremote.ssl=false
>   -Dcom.sun.management.jmxremote.authenticate=false
>   -Djava.endorsed.dirs=/home/mdeggers/Apache/apache-tomcat-6.0.29/endorsed
>   -classpath /home/mdeggers/Apache/apache-tomcat-6.0.29/bin/bootstrap.jar
>   -Dcatalina.base=/home/mdeggers/Apache/apache-tomcat-6.0.29
>   -Dcatalina.home=/home/mdeggers/Apache/apache-tomcat-6.0.29
>   -Djava.io.tmpdir=/home/mdeggers/Apache/apache-tomcat-6.0.29/temp
>   org.apache.catalina.startup.Bootstrap start
> 
> 
> In short, Tomcat 6.0.29.
> 
> Another way to discover this is with the ss command.
> 
> ss -anp | grep 8080
> 
> 
> Gives the following information on my system:
> 
> LISTEN     0      100            :::8080          :::*      users:(("java",12565,37))
> 
> 
> Again, the process ID (pid) 12565 is the important piece of information.
> 
> 3. Finally, make sure your firewall allows remote connections to port 8080
> 
> Hope this is useful.
> 
> . . . . just my two cents.
> 
> /mde/
> 

Thanks for the extensive answer!
I've looked at the port, but it only shows my tomcat installation so I assume I got these
errors because I wanted to start tomcat to soon after shutting down. I think the logs show
that it got booted after 2 errors.

As for the networking solutions: thanks! I'll configure these as soon as I can get these programs
running


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