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From Mark Eggers <its_toas...@yahoo.com>
Subject Re: Deploying emboss in Opal2
Date Fri, 08 Jul 2011 17:39:16 GMT
----- 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/

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