opaltoolkit-users — Users mailing-list for Opal Toolkit

[Opaltoolkit-users] Opal job scheduler benefits

[Guillermo M. P. <gui...@si...>]

Hello,

I would like to know what are the benefits/extras of using Condor 
job.scheduler with Opal.
What's the difference between job scheduler and submitting jobs to 
Condor straight with condor_submit?


Thank you.

Best regards,
Guillermo.

Re: [Opaltoolkit-users] Opal 2.6 Tomcat7 Deploy error

[Luca C. <luc...@gm...>]

Hey Guillermo,
did you succeed running the latest opal 2.6?

Did you find anymore problem?

Luca




On Tue, Feb 19, 2013 at 9:22 AM, Luca Clementi <luc...@gm...> wrote:
> On Tue, Feb 19, 2013 at 5:00 AM, Guillermo Marco Puche
> <gui...@si...> wrote:
>> Ok fixed it,
>>
>> wsdd folder is missing in 2.6 release, had to copy it from 2.4
>>
>
> Marco,
> you don't need that (those file are now under
> webapps/opal2/WEB-INF/wsdd/opal_*).
>
> Version 2.6 uses a new deployment methodology.
> You can simply copy config.xml files into the $CATALINA_HOME/deply floder.
>
>
> So no more:
>
>>
>> cd /opt/web/opal
>> sudo ant deploy -DserviceName=DateService
>> -DappConfig=/opt/web/opal/configs/date_config.xml
>>
>
> But now you can simply
> cp /opt/web/opal/configs/date_config.xml $CATALINA_HOME/deploy
>
> That's one of the main changes with opal 2.4/2.6.
>
>
> You can find the documentation inside the docs folder.
>
> Luca

Re: [Opaltoolkit-users] Opal 2.6 Tomcat7 Deploy error

[Luca C. <luc...@gm...>]

On Tue, Feb 19, 2013 at 5:00 AM, Guillermo Marco Puche
<gui...@si...> wrote:
> Ok fixed it,
>
> wsdd folder is missing in 2.6 release, had to copy it from 2.4
>

Marco,
you don't need that (those file are now under
webapps/opal2/WEB-INF/wsdd/opal_*).

Version 2.6 uses a new deployment methodology.
You can simply copy config.xml files into the $CATALINA_HOME/deply floder.


So no more:

>
> cd /opt/web/opal
> sudo ant deploy -DserviceName=DateService
> -DappConfig=/opt/web/opal/configs/date_config.xml
>

But now you can simply
cp /opt/web/opal/configs/date_config.xml $CATALINA_HOME/deploy

That's one of the main changes with opal 2.4/2.6.


You can find the documentation inside the docs folder.

Luca

Re: [Opaltoolkit-users] Opal 2.6 Tomcat7 Deploy error

[Guillermo M. P. <gui...@si...>]

Ok fixed it,

wsdd folder is missing in 2.6 release, had to copy it from 2.4

On 02/19/2013 01:09 PM, Guillermo Marco Puche wrote:
> Hello,
>
> I'm trying to deploy an app as described on manual. (DateTime) with no 
> success.
> Dashboard not showing the app.
>
> Thank you.
>
> Best regards,
> Guillermo.
>
> Here's the Deploy log:
>
> cd /opt/web/opal
> sudo ant deploy -DserviceName=DateService -DappConfig=/opt/web/opal/configs/date_config.xml
> Buildfile: build.xml
> setenv:
> compile:
> setenv:
> generateStubs:
> jar:
> install:
>       [copy] Copying 1 file to /opt/web/opal/etc
>       [copy] Copying 1 file to /opt/web/opal/etc
>       [move] Moving 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/classes
> deploy:
>       [echo] Deploying service: DateService
>       [java] 2013-02-19 06:08:01,937 INFO  edu.sdsc.nbcr.opal.util.Deploy.main(Deploy.java:49) - Property appConfig set to: /opt/web/opal/configs/date_config.xml
>       [java] 2013-02-19 06:08:01,941 INFO  edu.sdsc.nbcr.opal.util.Deploy.main(Deploy.java:58) - Property serviceName set to: DateService
>       [java] 2013-02-19 06:08:01,941 INFO  edu.sdsc.nbcr.opal.util.Deploy.main(Deploy.java:68) - Version number not supplied by user
>       [java] 2013-02-19 06:08:01,941 INFO  edu.sdsc.nbcr.opal.util.Deploy.main(Deploy.java:79) - Property wsddTemplate set to: /opt/web/opal/wsdd/opal_deploy.wsdd
>       [java] 2013-02-19 06:08:01,942 ERROR edu.sdsc.nbcr.opal.util.Deploy.main(Deploy.java:85) - WSDD template file /opt/web/opal/wsdd/opal_deploy.wsdd does not exist
>       [java] Java Result: 1
>       [java] Processing file /opt/web/opal/build/gen/DateService_deploy.wsdd
>       [java] Exception: /opt/web/opal/build/gen/DateService_deploy.wsdd (No such file or directory)
>       [java] Java Result: 1
> generateTypedWSDL:
> BUILD SUCCESSFUL
> Total time: 1 second
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
>
>
> _______________________________________________
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> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

[Opaltoolkit-users] Opal 2.6 Tomcat7 Deploy error

[Guillermo M. P. <gui...@si...>]

Hello,

I'm trying to deploy an app as described on manual. (DateTime) with no 
success.
Dashboard not showing the app.

Thank you.

Best regards,
Guillermo.

Here's the Deploy log:

cd /opt/web/opal
sudo ant deploy -DserviceName=DateService -DappConfig=/opt/web/opal/configs/date_config.xml

Buildfile: build.xml

setenv:

compile:

setenv:

generateStubs:

jar:

install:

      [copy] Copying 1 file to /opt/web/opal/etc

      [copy] Copying 1 file to /opt/web/opal/etc

      [move] Moving 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/classes

deploy:

      [echo] Deploying service: DateService

      [java] 2013-02-19 06:08:01,937 INFO  edu.sdsc.nbcr.opal.util.Deploy.main(Deploy.java:49) - Property appConfig set to: /opt/web/opal/configs/date_config.xml

      [java] 2013-02-19 06:08:01,941 INFO  edu.sdsc.nbcr.opal.util.Deploy.main(Deploy.java:58) - Property serviceName set to: DateService

      [java] 2013-02-19 06:08:01,941 INFO  edu.sdsc.nbcr.opal.util.Deploy.main(Deploy.java:68) - Version number not supplied by user

      [java] 2013-02-19 06:08:01,941 INFO  edu.sdsc.nbcr.opal.util.Deploy.main(Deploy.java:79) - Property wsddTemplate set to: /opt/web/opal/wsdd/opal_deploy.wsdd

      [java] 2013-02-19 06:08:01,942 ERROR edu.sdsc.nbcr.opal.util.Deploy.main(Deploy.java:85) - WSDD template file /opt/web/opal/wsdd/opal_deploy.wsdd does not exist

      [java] Java Result: 1

      [java] Processing file /opt/web/opal/build/gen/DateService_deploy.wsdd

      [java] Exception: /opt/web/opal/build/gen/DateService_deploy.wsdd (No such file or directory)

      [java] Java Result: 1

generateTypedWSDL:

BUILD SUCCESSFUL

Total time: 1 second

Re: [Opaltoolkit-users] Opal Dashboard Error

[Guillermo M. P. <gui...@si...>]

Hello,

I managed to fix the problem. It was an issue with *.jar inside tomcat's 
lib folder.
Opal 2.6 working with tomcat7. Gonna try to setup a first service 
wrapper and GSI security.


On 02/19/2013 09:32 AM, Guillermo Marco Puche wrote:
> Hello,
>
> I deleted previous opal version, filled in config files 
> opal/etc/opal.properties and build.properties
> Stopped tomcat7 server. Built new opal version with: sudo ant install:
>
> $ sudo ant install
> Buildfile: build.xml
> setenv:
>      [mkdir] Created dir: /opt/web/opal/build
>      [mkdir] Created dir: /opt/web/opal/build/classes
> compile:
> Trying to override old definition of task wsdl2java
> setenv:
> generateStubs:
>      [mkdir] Created dir: /opt/web/opal/build/gen
> [wsdl2java] WSDL2Java /opt/web/opal/wsdl/opal.wsdl
>      [javac] Compiling 31 source files to /opt/web/opal/build/classes
>      [javac] Note: Some input files use unchecked or unsafe operations.
>      [javac] Note: Recompile with -Xlint:unchecked for details.
>      [javac] Compiling 99 source files to /opt/web/opal/build/classes
>      [javac] Note: Some input files use or override a deprecated API.
>      [javac] Note: Recompile with -Xlint:deprecation for details.
>      [javac] Note: Some input files use unchecked or unsafe operations.
>      [javac] Note: Recompile with -Xlint:unchecked for details.
>       [copy] Copying 2 files to /opt/web/opal/build/classes
> jar:
>      [mkdir] Created dir: /opt/web/opal/build/jar
>        [jar] Building jar: /opt/web/opal/build/jar/opal-ws-2.5.jar
> install:
>       [copy] Copying 339 files to /usr/tomcat7/webapps
>       [copy] Copying 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/lib
>       [copy] Copying 13 files to /usr/tomcat7/webapps/opal2/WEB-INF/lib
>       [copy] Copying 1 file to /opt/web/opal/etc
>       [copy] Copying 1 file to /opt/web/opal/etc
>       [move] Moving 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/classes
>       [copy] Copying 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/classes
>       [copy] Copying 13 files to /usr/tomcat7/webapps/opal2/WEB-INF/lib
>       [copy] Copying 11 files to /usr/tomcat7/webapps/opal2/WEB-INF/lib
>       [copy] Copying 9 files to /usr/tomcat7/lib
>       [copy] Copying 1 file to /usr/tomcat7/lib
>       [copy] Copying 1 file to /usr/tomcat7/lib
>       [copy] Copying 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/classes
>       [copy] Copying 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/classes
> BUILD SUCCESSFUL
> Total time: 4 seconds
>
> Started tomat7 server, home page works (172.19.0.12:8080).
> When I try to access http://172.19.0.12:8080/opal2/happyaxis.jsp I get 
> 404 error from tomcat.
> I've no idea what'she problem. Maybe a permission issue?
>
> My tomcat7 install is located on /usr/tomcat7:
>
> $ ls -l /usr/tomcat7/
> total 124
> drwxr-xr-x. 2 tomcat tomcat  4096 Feb 18 11:00 bin
> drwxr-xr-x. 4 tomcat tomcat  4096 Feb 18 05:11 common
> drwxr-xr-x. 3 tomcat tomcat  4096 Feb 18 10:58 conf
> drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:20 lib
> -rw-r--r--. 1 tomcat tomcat 56812 Jan 10 23:55 LICENSE
> drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:21 logs
> -rw-r--r--. 1 tomcat tomcat  1192 Jan 10 23:55 NOTICE
> -rw-r--r--. 1 tomcat tomcat  8826 Jan 10 23:55 RELEASE-NOTES
> -rw-r--r--. 1 tomcat tomcat 16163 Jan 10 23:55 RUNNING.txt
> drwxr-xr-x. 3 tomcat tomcat  4096 Feb 18 05:11 server
> drwxr-xr-x. 2 tomcat tomcat  4096 Feb 18 02:45 temp
> drwxr-xr-x. 8 tomcat tomcat  4096 Feb 18 11:28 webapps
> drwxr-xr-x. 3 tomcat tomcat  4096 Feb 18 02:48 work
>
> webapps dir:
>
> $ ls -l /usr/tomcat7/webapps/opal2/
> total 72
> drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:20 css
> drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:20 dashboard-jsp
> -rw-r--r--. 1 tomcat tomcat  9912 Feb 19 02:20 fingerprint.jsp
> -rw-r--r--. 1 tomcat tomcat 15524 Feb 19 02:20 happyaxis.jsp
> -rw-r--r--. 1 tomcat tomcat  7335 Feb 19 02:20 i18nLib.jsp
> drwxr-xr-x. 4 tomcat tomcat  4096 Feb 19 02:20 images
> -rw-r--r--. 1 tomcat tomcat   582 Feb 19 02:20 index.html
> -rw-r--r--. 1 tomcat tomcat  2282 Feb 19 02:20 index.jsp
> drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:20 opalGUI-jsp
> drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:20 scripts
> drwxr-xr-x. 3 tomcat tomcat  4096 Feb 19 02:20 viewer
> drwxr-xr-x. 5 tomcat tomcat  4096 Feb 19 02:20 WEB-INF
>
> And opal installation is located under /opt/web/opal/:
>
> $ ls -l /opt/web/opal/
> total 80
> drwxr-xr-x. 5 gmarco users  4096 Feb 19 02:20 build
> -rw-r--r--. 1 gmarco users   350 Feb 19 02:18 build.properties
> -rw-r--r--. 1 gmarco users 17873 Feb 19 00:47 build.xml
> -rw-r--r--. 1 gmarco users  8924 Feb 19 00:47 CHANGELOG
> drwxr-xr-x. 2 gmarco users  4096 Feb 19 02:12 configs
> drwxr-xr-x. 3 gmarco users  4096 Feb 19 02:12 docs
> drwxr-xr-x. 2 gmarco users  4096 Feb 19 02:20 etc
> drwxr-xr-x. 3 gmarco users  4096 Feb 19 02:12 lib
> -rw-r--r--. 1 gmarco users  1786 Feb 19 00:47 LICENSE
> -rw-r--r--. 1 gmarco users   511 Feb 19 00:47 README
> drwxr-xr-x. 2 gmarco users  4096 Feb 19 02:12 samples
> drwxr-xr-x. 5 gmarco users  4096 Feb 19 00:47 src
> drwxr-xr-x. 3 gmarco users  4096 Feb 19 00:47 webapps
> drwxr-xr-x. 2 gmarco users  4096 Feb 19 02:12 wsdl
>
> Tomcat7 install guide I've followed is this one: 
> http://www.server-world.info/en/note?os=CentOS_6&p=tomcat7
>
> Thanks.
>
> Best regards,
> Guillermo.
>
>
> On 02/19/2013 01:03 AM, Luca Clementi wrote:
>> On Mon, Feb 18, 2013 at 4:48 AM, Guillermo Marco Puche
>> <gui...@si...>  wrote:
>>> Hello,
>>>
>>> I just installed Opal over my tomcat 7 server.
>>>
>>> My happyaxis.jsp test page is showing the following error:
>> Hey,
>> The current version of opal 2.4 does not support tomcat 7 or tomcat 6,
>> but only tomcat 5.
>> See the doc:http://www.nbcr.net/data/docs/opal/docs/2.X/serverprerequisites.html
>>
>> In the source code we have a new version which works with tomcat 7. I
>> haven't pushed it out as a new release yet though.
>>
>> I sent you a link from which you can download the source code of opal 2.6
>> In case you haven't received here is the link:
>> http://we.tl/7O6ZoGVLEE
>>
>> Could you test it and let me know if you have any problem?
>>
>> Luca
>>
>> PS: Guillermo sorry for the duplicate emails...
>
>
> -- 
> <http://i.imgur.com/1MjpCpe.png> *g.marco*: Informatician at Sistemas 
> Genómicos S.L <#>
> phone: 0034635197460 <callto:0034635197460>
> web: www.sistemasgenomicos.com <http://www.sistemasgenomicos.com>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
>
>
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users


-- 
<http://i.imgur.com/1MjpCpe.png> *g.marco*: Informatician at Sistemas 
Genómicos S.L <#>
phone: 0034635197460 <callto:0034635197460>
web: www.sistemasgenomicos.com <http://www.sistemasgenomicos.com>

Re: [Opaltoolkit-users] Opal Dashboard Error

[Guillermo M. P. <gui...@si...>]

Hello,

I deleted previous opal version, filled in config files 
opal/etc/opal.properties and build.properties
Stopped tomcat7 server. Built new opal version with: sudo ant install:

$ sudo ant install

Buildfile: build.xml

setenv:

     [mkdir] Created dir: /opt/web/opal/build

     [mkdir] Created dir: /opt/web/opal/build/classes

compile:

Trying to override old definition of task wsdl2java

setenv:

generateStubs:

     [mkdir] Created dir: /opt/web/opal/build/gen

[wsdl2java] WSDL2Java /opt/web/opal/wsdl/opal.wsdl

     [javac] Compiling 31 source files to /opt/web/opal/build/classes

     [javac] Note: Some input files use unchecked or unsafe operations.

     [javac] Note: Recompile with -Xlint:unchecked for details.

     [javac] Compiling 99 source files to /opt/web/opal/build/classes

     [javac] Note: Some input files use or override a deprecated API.

     [javac] Note: Recompile with -Xlint:deprecation for details.

     [javac] Note: Some input files use unchecked or unsafe operations.

     [javac] Note: Recompile with -Xlint:unchecked for details.

      [copy] Copying 2 files to /opt/web/opal/build/classes

jar:

     [mkdir] Created dir: /opt/web/opal/build/jar

       [jar] Building jar: /opt/web/opal/build/jar/opal-ws-2.5.jar

install:

      [copy] Copying 339 files to /usr/tomcat7/webapps

      [copy] Copying 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/lib

      [copy] Copying 13 files to /usr/tomcat7/webapps/opal2/WEB-INF/lib

      [copy] Copying 1 file to /opt/web/opal/etc

      [copy] Copying 1 file to /opt/web/opal/etc

      [move] Moving 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/classes

      [copy] Copying 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/classes

      [copy] Copying 13 files to /usr/tomcat7/webapps/opal2/WEB-INF/lib

      [copy] Copying 11 files to /usr/tomcat7/webapps/opal2/WEB-INF/lib

      [copy] Copying 9 files to /usr/tomcat7/lib

      [copy] Copying 1 file to /usr/tomcat7/lib

      [copy] Copying 1 file to /usr/tomcat7/lib

      [copy] Copying 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/classes

      [copy] Copying 1 file to /usr/tomcat7/webapps/opal2/WEB-INF/classes

BUILD SUCCESSFUL

Total time: 4 seconds

Started tomat7 server, home page works (172.19.0.12:8080).
When I try to access http://172.19.0.12:8080/opal2/happyaxis.jsp I get 
404 error from tomcat.
I've no idea what'she problem. Maybe a permission issue?

My tomcat7 install is located on /usr/tomcat7:

$ ls -l /usr/tomcat7/

total 124

drwxr-xr-x. 2 tomcat tomcat  4096 Feb 18 11:00 bin

drwxr-xr-x. 4 tomcat tomcat  4096 Feb 18 05:11 common

drwxr-xr-x. 3 tomcat tomcat  4096 Feb 18 10:58 conf

drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:20 lib

-rw-r--r--. 1 tomcat tomcat 56812 Jan 10 23:55 LICENSE

drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:21 logs

-rw-r--r--. 1 tomcat tomcat  1192 Jan 10 23:55 NOTICE

-rw-r--r--. 1 tomcat tomcat  8826 Jan 10 23:55 RELEASE-NOTES

-rw-r--r--. 1 tomcat tomcat 16163 Jan 10 23:55 RUNNING.txt

drwxr-xr-x. 3 tomcat tomcat  4096 Feb 18 05:11 server

drwxr-xr-x. 2 tomcat tomcat  4096 Feb 18 02:45 temp

drwxr-xr-x. 8 tomcat tomcat  4096 Feb 18 11:28 webapps

drwxr-xr-x. 3 tomcat tomcat  4096 Feb 18 02:48 work


webapps dir:

$ ls -l /usr/tomcat7/webapps/opal2/

total 72

drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:20 css

drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:20 dashboard-jsp

-rw-r--r--. 1 tomcat tomcat  9912 Feb 19 02:20 fingerprint.jsp

-rw-r--r--. 1 tomcat tomcat 15524 Feb 19 02:20 happyaxis.jsp

-rw-r--r--. 1 tomcat tomcat  7335 Feb 19 02:20 i18nLib.jsp

drwxr-xr-x. 4 tomcat tomcat  4096 Feb 19 02:20 images

-rw-r--r--. 1 tomcat tomcat   582 Feb 19 02:20 index.html

-rw-r--r--. 1 tomcat tomcat  2282 Feb 19 02:20 index.jsp

drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:20 opalGUI-jsp

drwxr-xr-x. 2 tomcat tomcat  4096 Feb 19 02:20 scripts

drwxr-xr-x. 3 tomcat tomcat  4096 Feb 19 02:20 viewer

drwxr-xr-x. 5 tomcat tomcat  4096 Feb 19 02:20 WEB-INF


And opal installation is located under /opt/web/opal/:

$ ls -l /opt/web/opal/

total 80

drwxr-xr-x. 5 gmarco users  4096 Feb 19 02:20 build

-rw-r--r--. 1 gmarco users   350 Feb 19 02:18 build.properties

-rw-r--r--. 1 gmarco users 17873 Feb 19 00:47 build.xml

-rw-r--r--. 1 gmarco users  8924 Feb 19 00:47 CHANGELOG

drwxr-xr-x. 2 gmarco users  4096 Feb 19 02:12 configs

drwxr-xr-x. 3 gmarco users  4096 Feb 19 02:12 docs

drwxr-xr-x. 2 gmarco users  4096 Feb 19 02:20 etc

drwxr-xr-x. 3 gmarco users  4096 Feb 19 02:12 lib

-rw-r--r--. 1 gmarco users  1786 Feb 19 00:47 LICENSE

-rw-r--r--. 1 gmarco users   511 Feb 19 00:47 README

drwxr-xr-x. 2 gmarco users  4096 Feb 19 02:12 samples

drwxr-xr-x. 5 gmarco users  4096 Feb 19 00:47 src

drwxr-xr-x. 3 gmarco users  4096 Feb 19 00:47 webapps

drwxr-xr-x. 2 gmarco users  4096 Feb 19 02:12 wsdl


Tomcat7 install guide I've followed is this one: 
http://www.server-world.info/en/note?os=CentOS_6&p=tomcat7

Thanks.

Best regards,
Guillermo.


On 02/19/2013 01:03 AM, Luca Clementi wrote:
> On Mon, Feb 18, 2013 at 4:48 AM, Guillermo Marco Puche
> <gui...@si...> wrote:
>> Hello,
>>
>> I just installed Opal over my tomcat 7 server.
>>
>> My happyaxis.jsp test page is showing the following error:
> Hey,
> The current version of opal 2.4 does not support tomcat 7 or tomcat 6,
> but only tomcat 5.
> See the doc: http://www.nbcr.net/data/docs/opal/docs/2.X/serverprerequisites.html
>
> In the source code we have a new version which works with tomcat 7. I
> haven't pushed it out as a new release yet though.
>
> I sent you a link from which you can download the source code of opal 2.6
> In case you haven't received here is the link:
> http://we.tl/7O6ZoGVLEE
>
> Could you test it and let me know if you have any problem?
>
> Luca
>
> PS: Guillermo sorry for the duplicate emails...


-- 
<http://i.imgur.com/1MjpCpe.png> *g.marco*: Informatician at Sistemas 
Genómicos S.L <#>
phone: 0034635197460 <callto:0034635197460>
web: www.sistemasgenomicos.com <http://www.sistemasgenomicos.com>

Re: [Opaltoolkit-users] Opal Dashboard Error

[Luca C. <luc...@gm...>]

On Mon, Feb 18, 2013 at 4:48 AM, Guillermo Marco Puche
<gui...@si...> wrote:
> Hello,
>
> I just installed Opal over my tomcat 7 server.
>
> My happyaxis.jsp test page is showing the following error:

Hey,
The current version of opal 2.4 does not support tomcat 7 or tomcat 6,
but only tomcat 5.
See the doc: http://www.nbcr.net/data/docs/opal/docs/2.X/serverprerequisites.html

In the source code we have a new version which works with tomcat 7. I
haven't pushed it out as a new release yet though.

I sent you a link from which you can download the source code of opal 2.6
In case you haven't received here is the link:
http://we.tl/7O6ZoGVLEE

Could you test it and let me know if you have any problem?

Luca

PS: Guillermo sorry for the duplicate emails...

[Opaltoolkit-users] Opal Dashboard Error

[Guillermo M. P. <gui...@si...>]

Hello,

I just installed Opal over my tomcat 7 server.

My happyaxis.jsp test page is showing the following error:

*Error*: could not find class org.apache.log4j.Layout from 
file*log4j-1.2.8.jar*
Axis may not work.
Seehttp://jakarta.apache.org/log4j

And this warning:

*Warning*: could not find class org.apache.xml.security.Init from 
file*xmlsec.jar*
XML Security is not supported.
Seehttp://xml.apache.org/security/

When i try to access my dashboard page a get an error 500 code from 
tomcat. I've no idea how to fix that. Any help would be appreciated.


  HTTP Status 500 - Servlet.init() for servlet dashboard threw exception

------------------------------------------------------------------------

*type*Exception report

*message*_Servlet.init() for servlet dashboard threw exception_

*description*_The server encountered an internal error that prevented it 
from fulfilling this request._

*exception*

javax.servlet.ServletException: Servlet.init() for servlet dashboard threw exception
	org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
	org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
	org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:936)
	org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
	org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1004)
	org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589)
	org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:312)
	java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
	java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	java.lang.Thread.run(Thread.java:679)

*root cause*

java.lang.NoClassDefFoundError: Could not initialize class edu.sdsc.nbcr.opal.state.HibernateUtil
	edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:73)
	edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java:109)
	org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
	org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
	org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:936)
	org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
	org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1004)
	org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589)
	org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:312)
	java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
	java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	java.lang.Thread.run(Thread.java:679)

Thank you.

Best regards,
Guillermo.

[Opaltoolkit-users] Opal Python 2.4.1

[Luca C. <luc...@gm...>]

We are pleased to announce the release of the Opal Python client library
version 2.4.1.

This new release has:

 - Upgraded stubs to the new Opal 2.4 wsdl
 - Created a OpalClient class which wrapps python autogenerated code and
   provides simpler API to launching jobs
 - Updated the documentation accordingly
 - Updated ApbsClient and the GenericServiceClient with the new OpalClient
   interface
 - Created a set of UnitTest routines

Opal-py 2.4.1 can be downloaded from here:
https://sourceforge.net/projects/opaltoolkit/files/

Re: [Opaltoolkit-users] Sequential Execution

[nadya w. <na...@sd...>]

Hello Jeff,


On Apr 9, 2012, at 10:29 AM, Jeffrey Allen wrote:

> Hello,
>
>
> My group has been working on developing an execution pipeline for  
> Bioinformatics programs. We’ve been considering using SOAP to  
> handle the input parameters for the individual programs; it seems  
> that Opal could be a good foundation for us to use if we go this  
> direction.
>
this is exactly how we use opal for individual programs.
>
> My question, however, is whether or not there are any built-in or  
> external projects that offer some control of the “flow” of  
> execution of submitted commands. For instance, a user may submit  
> requests A, B, and C, but would like to specify that B and C depend  
> on the output of A. Thus, the proper execution would be to begin A  
> immediately, then begin B and C once A has completed.
>
There are a few that might fit here. There are a few workflow engines  
and all have their pros and cons.
Take a look at
	kepler https://kepler-project.org/
	vision (part of mgltools) http://mgltools.scripps.edu/
	CADD - our first experimental workflows pipeline, http:// 
www2.nbcr.net/wordpress2/?page_id=1175
We had some experience with both. Both a are mainly gui-driven and  
provide one with the
capability to build  'individual nodes' and chain them into the  
pipeline. An individual node then
can be a SOPA call to a specific opal service.  The mgltools 1.5.6 r2  
distro has our experimental first cut
pipeline  with a few workflows.

In all these as far as opal is concerned, opal executes the job once  
it receives it  and it has no "knowledge"
of the jobs dependencies. What we did in situations like this, was to  
build an opal web service that takes
all the needed input  from the user and on the back end runs a script  
that runs certain portions in whatever order is
needed.  In this scenario one is building on top of opal. Each  
scripted pipeline then need to be carefully
crafted. Take a look at http://kryptonite.nbcr.net/opal2/dashboard? 
command=serviceList for AutoDock Vina Screening service,
it does exactly that. The SMAP services are another example.

Another option is to use condor DAG capability. One will need to use  
condor as a job scheduling platform and write
submit scripts that tell condor when and what to execute. This is  
outside opal.

>
> I’d be interested to hear any advice this group has on how to  
> proceed with a project like this. Is this something which could be  
> built on top of Opal, should I consider trying to incorporate this  
> directly into Opal, or is there another platform which I should  
> consider using?
>
to incorporate directly into opal means re-writing opal. Opal was not  
conceived as a scheduling manager. It prepares
the job for the execution and submits it to a real job scheduler like  
condor, pbs, sge. The submission script has to handle
creating all the right dependencies in a syntax that a real job  
scheduler understands.

Nadya

>
> Thanks,
>
>
> Jeff Allen
>
> Computational Biologist
>
> Quantitative Biomedical Research Center
>
> UT Southwestern Medical Center
>
> 214.648.4171 - NC8.512B
>
> Jef...@UT...
>
>
>
>
> UT Southwestern Medical Center
> The future of medicine, today.
> ---------------------------------------------------------------------- 
> --------
> Better than sec? Nothing is better than sec when it comes to
> monitoring Big Data applications. Try Boundary one-second
> resolution app monitoring today. Free.
> http://p.sf.net/sfu/Boundary- 
> dev2dev_______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

Nadya Williams                 University of California, San Diego
na...@sd...             9500 Gilman Dr. MC 0446
+1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
+1 858 822 1619 (fax)      USA

Re: [Opaltoolkit-users] Sequential Execution

[Luca C. <luc...@gm...>]

Dear Jeffry,
please see below...

On Mon, Apr 9, 2012 at 10:29 AM, Jeffrey Allen
<Jef...@ut...> wrote:
> Hello,
>
>
>
> My group has been working on developing an execution pipeline for
> Bioinformatics programs. We’ve been considering using SOAP to handle the
> input parameters for the individual programs; it seems that Opal could be a
> good foundation for us to use if we go this direction.
>
>
>
> My question, however, is whether or not there are any built-in or external
> projects that offer some control of the “flow” of execution of submitted
> commands. For instance, a user may submit requests A, B, and C, but would
> like to specify that B and C depend on the output of A. Thus, the proper
> execution would be to begin A immediately, then begin B and C once A has
> completed.
>
>
>
> I’d be interested to hear any advice this group has on how to proceed with a
> project like this. Is this something which could be built on top of Opal,
> should I consider trying to incorporate this directly into Opal, or is there
> another platform which I should consider using?

It really depends what do you have to do...

If you workflow is as simple as you said above and you need to
integrate this calls into your "client" (some customized GUI) I would
use one of the Opal client side library and simply invoke A, B, C
sequentially in the code.
We have Opal client side libraries for perl java and python (Im
currently writing a higher level python API for Opal).

You can chain A B C in the script that gets invoked by Opal service D
(we also do that to hide a lot of complexity, e.g. file conversion,
directory creation, preprocessing, etc.). We like to create high level
service (screen receptor X against library Z) and this generally
requires a lot of preparation on the server side.

If you like we also have embedded client for some workflow tools,
Vision (from mgltools), and Kepler.

I hope that helps.

Sincerely,
Luca


> Thanks,
>
>
>
> Jeff Allen
>
> Computational Biologist
>
> Quantitative Biomedical Research Center
>
> UT Southwestern Medical Center
>
> 214.648.4171 - NC8.512B
>
> Jef...@UT...
>
>
>
>
> ________________________________
>
> UT Southwestern Medical Center
> The future of medicine, today.
>
> ------------------------------------------------------------------------------
> Better than sec? Nothing is better than sec when it comes to
> monitoring Big Data applications. Try Boundary one-second
> resolution app monitoring today. Free.
> http://p.sf.net/sfu/Boundary-dev2dev
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>

[Opaltoolkit-users] Sequential Execution

[Jeffrey A. <Jef...@UT...>]

Hello,

My group has been working on developing an execution pipeline for Bioinformatics programs. We've been considering using SOAP to handle the input parameters for the individual programs; it seems that Opal could be a good foundation for us to use if we go this direction.

My question, however, is whether or not there are any built-in or external projects that offer some control of the "flow" of execution of submitted commands. For instance, a user may submit requests A, B, and C, but would like to specify that B and C depend on the output of A. Thus, the proper execution would be to begin A immediately, then begin B and C once A has completed.

I'd be interested to hear any advice this group has on how to proceed with a project like this. Is this something which could be built on top of Opal, should I consider trying to incorporate this directly into Opal, or is there another platform which I should consider using?

Thanks,

Jeff Allen
Computational Biologist
Quantitative Biomedical Research Center
UT Southwestern Medical Center
214.648.4171 - NC8.512B
Jef...@UT...<mailto:Jef...@UT...>


________________________________

UT Southwestern Medical Center
The future of medicine, today.

Re: [Opaltoolkit-users] Special characters in file names causing problem

[Conrad H. <co...@cg...>]

Thank you for the quick answer.  I will fix Chimera not to send unsafe 
characters.

Conrad

On 1/17/12 2:43 PM, Luca Clementi wrote:
> Dear Conrad,
> see below...
>
> On Tue, Jan 17, 2012 at 2:04 PM, Conrad Huang<co...@cg...>  wrote:
>> Hi,
>>
>> We are using Opal 2.2 on our RedHat Linux 6.2 cluster as a service
>> provider for UCSF Chimera, our molecular modeling application written in
>> Python.  Things are working quite well with one exception.
>>
>> Background:
>>
>> We provide an interface to Modeller, a structure prediction program from
>> the Sali group.  Chimera sends a few input files and expects to retrieve
>> some output files after the computation is complete.  The names of the
>> output file are derived from names of protein or nucleic acid sequences.
>>
>> The problem:
>>
>> When the output file names contain a '|' character, the retrieval of the
>> output file fails.  The files are generated properly (I can see them in
>> the tomcat directory) but I see these errors in catalina.out:
>>
>> 2012-01-17 10:18:13,440 INFO
>> edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs(HibernateUtil.java:419) -
>> called
>> 2012-01-17 10:18:13,442 ERROR
>> edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs(HibernateUtil.java:435) -
>> Can't get job outputs for job: app1326824032862
>> 2012-01-17 10:18:13,442 ERROR
>> edu.sdsc.nbcr.opal.AppServiceImpl.getOutputs(AppServiceImpl.java:421) -
>> Can't get job outputs for job: app1326824032862
>>
>> The error does not occur if the file names are "normal", i.e., without
>> odd characters.
>>
>> My question:
>>
>> Is this an error in Opal, or should Chimera avoid these characters?  If
>> the former, is it fixed in 2.4?  If the latter, is there a guideline as
>> to which characters are allowed or disallowed?
>
> If you look at the URL rfc:
> http://www.ietf.org/rfc/rfc1738.txt
>
> Find the "Unsafe:" section for a list of character that "should" be avoided.
>
>
> Luca
>
>>
>> Thanks.  (And thanks for the great software.)
>>
>> Conrad
>>
>> ------------------------------------------------------------------------------
>> Keep Your Developer Skills Current with LearnDevNow!
>> The most comprehensive online learning library for Microsoft developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
>> http://p.sf.net/sfu/learndevnow-d2d
>> _______________________________________________
>> Opaltoolkit-users mailing list
>> Opa...@li...
>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>

Re: [Opaltoolkit-users] Special characters in file names causing problem

[Luca C. <luc...@gm...>]

Dear Conrad,
see below...

On Tue, Jan 17, 2012 at 2:04 PM, Conrad Huang <co...@cg...> wrote:
> Hi,
>
> We are using Opal 2.2 on our RedHat Linux 6.2 cluster as a service
> provider for UCSF Chimera, our molecular modeling application written in
> Python.  Things are working quite well with one exception.
>
> Background:
>
> We provide an interface to Modeller, a structure prediction program from
> the Sali group.  Chimera sends a few input files and expects to retrieve
> some output files after the computation is complete.  The names of the
> output file are derived from names of protein or nucleic acid sequences.
>
> The problem:
>
> When the output file names contain a '|' character, the retrieval of the
> output file fails.  The files are generated properly (I can see them in
> the tomcat directory) but I see these errors in catalina.out:
>
> 2012-01-17 10:18:13,440 INFO
> edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs(HibernateUtil.java:419) -
> called
> 2012-01-17 10:18:13,442 ERROR
> edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs(HibernateUtil.java:435) -
> Can't get job outputs for job: app1326824032862
> 2012-01-17 10:18:13,442 ERROR
> edu.sdsc.nbcr.opal.AppServiceImpl.getOutputs(AppServiceImpl.java:421) -
> Can't get job outputs for job: app1326824032862
>
> The error does not occur if the file names are "normal", i.e., without
> odd characters.
>
> My question:
>
> Is this an error in Opal, or should Chimera avoid these characters?  If
> the former, is it fixed in 2.4?  If the latter, is there a guideline as
> to which characters are allowed or disallowed?

If you look at the URL rfc:
http://www.ietf.org/rfc/rfc1738.txt

Find the "Unsafe:" section for a list of character that "should" be avoided.


Luca

>
> Thanks.  (And thanks for the great software.)
>
> Conrad
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

Re: [Opaltoolkit-users] Special characters in file names causing problem

[nadya w. <na...@sd...>]

Hi Conrad,
On Jan 17, 2012, at 2:04 PM, Conrad Huang wrote:

> Hi,
>
> We are using Opal 2.2 on our RedHat Linux 6.2 cluster as a service
> provider for UCSF Chimera, our molecular modeling application  
> written in
> Python.  Things are working quite well with one exception.
>
> Background:
>
> We provide an interface to Modeller, a structure prediction program  
> from
> the Sali group.  Chimera sends a few input files and expects to  
> retrieve
> some output files after the computation is complete.  The names of the
> output file are derived from names of protein or nucleic acid  
> sequences.
>
> The problem:
what database are you using with opal: hibernate, mysql, or postgres?

>
> When the output file names contain a '|' character, the retrieval  
> of the
illegal character. The files may be generated but the databases do  
not except this character as a legal
in files names.
> output file fails.  The files are generated properly (I can see  
> them in
> the tomcat directory) but I see these errors in catalina.out:
>
> 2012-01-17 10:18:13,440 INFO
> edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs 
> (HibernateUtil.java:419) -
> called
> 2012-01-17 10:18:13,442 ERROR
> edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs 
> (HibernateUtil.java:435) -
> Can't get job outputs for job: app1326824032862
> 2012-01-17 10:18:13,442 ERROR
> edu.sdsc.nbcr.opal.AppServiceImpl.getOutputs(AppServiceImpl.java: 
> 421) -
> Can't get job outputs for job: app1326824032862
>
> The error does not occur if the file names are "normal", i.e., without
> odd characters.
>
> My question:
>
> Is this an error in Opal, or should Chimera avoid these  
> characters?  If
it is not opal error. We are using postgres or mysql DB with our opal  
installs on linux OS
the "|" is not a legal character in a file name under UNIX, so the  
best way is to avoid it.

> the former, is it fixed in 2.4?  If the latter, is there a  
> guideline as
> to which characters are allowed or disallowed?
if you are using mysql or postgres I would advise to create a DB for  
opal that has UTF8 encoding.
By default opal generated LATIN9 which will fail sometimes when users  
form other countries use some
characters for which there is no  encoding translation between LATIN9  
and UTF8.

If you are running on any unix flavor OS, then any charaacters that  
are allowed under unixwill be ok
for the db.


Nadya
>
> Thanks.  (And thanks for the great software.)
>
> Conrad
>
> ---------------------------------------------------------------------- 
> --------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft  
> developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3,  
> MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

Nadya Williams                 University of California, San Diego
na...@sd...             9500 Gilman Dr. MC 0446
+1 858 534 1820 (ofc)      La Jolla, CA 92093-0446
+1 858 822 1619 (fax)      USA

[Opaltoolkit-users] Special characters in file names causing problem

[Conrad H. <co...@cg...>]

Hi,

We are using Opal 2.2 on our RedHat Linux 6.2 cluster as a service 
provider for UCSF Chimera, our molecular modeling application written in 
Python.  Things are working quite well with one exception.

Background:

We provide an interface to Modeller, a structure prediction program from 
the Sali group.  Chimera sends a few input files and expects to retrieve 
some output files after the computation is complete.  The names of the 
output file are derived from names of protein or nucleic acid sequences.

The problem:

When the output file names contain a '|' character, the retrieval of the 
output file fails.  The files are generated properly (I can see them in 
the tomcat directory) but I see these errors in catalina.out:

2012-01-17 10:18:13,440 INFO 
edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs(HibernateUtil.java:419) - 
called
2012-01-17 10:18:13,442 ERROR 
edu.sdsc.nbcr.opal.state.HibernateUtil.getOutputs(HibernateUtil.java:435) - 
Can't get job outputs for job: app1326824032862
2012-01-17 10:18:13,442 ERROR 
edu.sdsc.nbcr.opal.AppServiceImpl.getOutputs(AppServiceImpl.java:421) - 
Can't get job outputs for job: app1326824032862

The error does not occur if the file names are "normal", i.e., without 
odd characters.

My question:

Is this an error in Opal, or should Chimera avoid these characters?  If 
the former, is it fixed in 2.4?  If the latter, is there a guideline as 
to which characters are allowed or disallowed?

Thanks.  (And thanks for the great software.)

Conrad

Re: [Opaltoolkit-users] Making Opal return port 80 URLs

[Conrad H. <co...@cg...>]

Thank you very much.  Everything worked as advertised and our web 
service works fine now.

Conrad

On 8/31/11 4:20 PM, Wilfred Li wrote:
> Hi, Conrad,
>
> Please let us know if this helps.
>
> Here is a link that may help.
> http://rocce.ucsd.edu/roll-documentation/opal/5.0/remove-portnum.html
>
> The instruction below is rocks specific,
>
>
>     Removing Port 8080 from Opal URL
>
>  1. Go to opal installation dir, in etc/opal.properties, remove 8080
>     from url, then "ant install"
>  2. In /etc/httpd/conf/httpd.conf, comment out "AddHandler type-map var"
>  3. Modify worker.properties, like below
>  4. Modify /etc/httpd/conf.d/rocks.conf, like below
>  5. service httpd restart
>  6. restart tomcat
>
>
> [root@rocce conf]# cat workers.properties
> #workers.java_home=/usr/java/jdk1.5
> #ps=/
>
> # Define 1 real worker using ajp13
> worker.list=worker1
> # Set properties for worker1 (ajp13)
> worker.worker1.type=ajp13
> worker.worker1.host=localhost
> worker.worker1.port=8009
>
>
> #rocks.conf, add these two lines right above<Directory...
> JkMount /opal* worker1
> JkMount /app* worker1
>
>
> Best regards,
>
> Wilfred
>
>
> 2011/8/31 Conrad Huang <co...@cg... <mailto:co...@cg...>>
>
>     Thank you for the information.
>
>     We do use our apache server to serve up other data as well, so I'd like
>     to configure the Opal server to return an opal-specific URL.  Is
>     changing "tomcat.url" in etc/opal.properties and updating the
>     installation sufficient to do that?  I was always a little wary of
>     changing that URL because I do not know whether it will affect just the
>     returned URLs (pointing to results) or will also require changes to the
>     Tomcat/Apache configuration files to match.  Right now, we use the
>     default configuration where the returned URLs look like
>     http://_server_:8080/appXXXXXXXXXX and the request URLs look like
>     http://_server_/opal2/services/_service_.  I'd really like to keep the
>     request URLs unchanged because we distribute an application that has
>     those URLs hard-wired into code.
>
>     Thanks.
>
>     Conrad
>
>     On 8/30/11 11:52 PM, Olivier Sallou wrote:
>      >
>      >
>      > ----- Mail original -----
>      >> De: "Conrad Huang"<co...@cg... <mailto:co...@cg...>>
>      >> À: opa...@li...
>     <mailto:opa...@li...>
>      >> Envoyé: Mardi 30 Août 2011 21:31:47
>      >> Objet: [Opaltoolkit-users] Making Opal return port 80 URLs
>      >> Hi,
>      >>
>      >> We have been using Opal 2.2 for a while and everything is
>     working fine
>      >> with Apache 2 and Tomcat 5.0.30. Our Opal installation currently
>      >> returns URLs that look like
>      >> "http://_server_name_:8080/app1314720091064/". Recently, we
>     found that
>      >> one of our users had a problem because his firewall blocked port
>     8080.
>      >> Is there some way we can configure Opal and Apache to use port 80
>      >> URLs?
>      >
>      >
>      > hi,
>      > you can configure Apache as a proxy (using module mod_proxy)
>      > There is directive proxy_pass (and reverse).
>      > However if your apache is used for other usages than opal, you
>     should configure your Opal server to be something like
>     "http://_server_name_:8080/opal/..." and on apache apply the proxy
>     to /opal.
>      >
>      > Olivier
>      >
>      >> Thanks.
>      >>
>      >> Conrad
>      >>
>      >>
>     ------------------------------------------------------------------------------
>      >> Special Offer -- Download ArcSight Logger for FREE!
>      >> Finally, a world-class log management solution at an even better
>      >> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>      >> download Logger. Secure your free ArcSight Logger TODAY!
>      >> http://p.sf.net/sfu/arcsisghtdev2dev
>      >> _______________________________________________
>      >> Opaltoolkit-users mailing list
>      >> Opa...@li...
>     <mailto:Opa...@li...>
>      >> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>      >
>
>
>     ------------------------------------------------------------------------------
>     Special Offer -- Download ArcSight Logger for FREE!
>     Finally, a world-class log management solution at an even better
>     price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>     download Logger. Secure your free ArcSight Logger TODAY!
>     http://p.sf.net/sfu/arcsisghtdev2dev
>     _______________________________________________
>     Opaltoolkit-users mailing list
>     Opa...@li...
>     <mailto:Opa...@li...>
>     https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>
>

Re: [Opaltoolkit-users] Making Opal return port 80 URLs

[Wilfred Li <wil...@gm...>]

Hi, Conrad,

Please let us know if this helps.

Here is a link that may help.
http://rocce.ucsd.edu/roll-documentation/opal/5.0/remove-portnum.html

The instruction below is rocks specific,

Removing Port 8080 from Opal URL

   1. Go to opal installation dir, in etc/opal.properties, remove 8080 from
   url, then "ant install"
   2. In /etc/httpd/conf/httpd.conf, comment out "AddHandler type-map var"
   3. Modify worker.properties, like below
   4. Modify /etc/httpd/conf.d/rocks.conf, like below
   5. service httpd restart
   6. restart tomcat


[root@rocce conf]# cat workers.properties
#workers.java_home=/usr/java/jdk1.5
#ps=/

# Define 1 real worker using ajp13
worker.list=worker1
# Set properties for worker1 (ajp13)
worker.worker1.type=ajp13
worker.worker1.host=localhost
worker.worker1.port=8009


#rocks.conf, add these two lines right above <Directory...
JkMount /opal* worker1
JkMount /app* worker1


Best regards,

Wilfred


2011/8/31 Conrad Huang <co...@cg...>

> Thank you for the information.
>
> We do use our apache server to serve up other data as well, so I'd like
> to configure the Opal server to return an opal-specific URL.  Is
> changing "tomcat.url" in etc/opal.properties and updating the
> installation sufficient to do that?  I was always a little wary of
> changing that URL because I do not know whether it will affect just the
> returned URLs (pointing to results) or will also require changes to the
> Tomcat/Apache configuration files to match.  Right now, we use the
> default configuration where the returned URLs look like
> http://_server_:8080/appXXXXXXXXXX and the request URLs look like
> http://_server_/opal2/services/_service_.  I'd really like to keep the
> request URLs unchanged because we distribute an application that has
> those URLs hard-wired into code.
>
> Thanks.
>
> Conrad
>
> On 8/30/11 11:52 PM, Olivier Sallou wrote:
> >
> >
> > ----- Mail original -----
> >> De: "Conrad Huang"<co...@cg...>
> >> À: opa...@li...
> >> Envoyé: Mardi 30 Août 2011 21:31:47
> >> Objet: [Opaltoolkit-users] Making Opal return port 80 URLs
> >> Hi,
> >>
> >> We have been using Opal 2.2 for a while and everything is working fine
> >> with Apache 2 and Tomcat 5.0.30. Our Opal installation currently
> >> returns URLs that look like
> >> "http://_server_name_:8080/app1314720091064/". Recently, we found that
> >> one of our users had a problem because his firewall blocked port 8080.
> >> Is there some way we can configure Opal and Apache to use port 80
> >> URLs?
> >
> >
> > hi,
> > you can configure Apache as a proxy (using module mod_proxy)
> > There is directive proxy_pass (and reverse).
> > However if your apache is used for other usages than opal, you should
> configure your Opal server to be something like "http://_server_name_:8080/opal/..."
> and on apache apply the proxy to /opal.
> >
> > Olivier
> >
> >> Thanks.
> >>
> >> Conrad
> >>
> >>
> ------------------------------------------------------------------------------
> >> Special Offer -- Download ArcSight Logger for FREE!
> >> Finally, a world-class log management solution at an even better
> >> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> >> download Logger. Secure your free ArcSight Logger TODAY!
> >> http://p.sf.net/sfu/arcsisghtdev2dev
> >> _______________________________________________
> >> Opaltoolkit-users mailing list
> >> Opa...@li...
> >> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
> >
>
>
>
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>

Re: [Opaltoolkit-users] Making Opal return port 80 URLs

[Conrad H. <co...@cg...>]

Thank you for the information.

We do use our apache server to serve up other data as well, so I'd like 
to configure the Opal server to return an opal-specific URL.  Is 
changing "tomcat.url" in etc/opal.properties and updating the 
installation sufficient to do that?  I was always a little wary of 
changing that URL because I do not know whether it will affect just the 
returned URLs (pointing to results) or will also require changes to the 
Tomcat/Apache configuration files to match.  Right now, we use the 
default configuration where the returned URLs look like 
http://_server_:8080/appXXXXXXXXXX and the request URLs look like 
http://_server_/opal2/services/_service_.  I'd really like to keep the 
request URLs unchanged because we distribute an application that has 
those URLs hard-wired into code.

Thanks.

Conrad

On 8/30/11 11:52 PM, Olivier Sallou wrote:
>
>
> ----- Mail original -----
>> De: "Conrad Huang"<co...@cg...>
>> À: opa...@li...
>> Envoyé: Mardi 30 Août 2011 21:31:47
>> Objet: [Opaltoolkit-users] Making Opal return port 80 URLs
>> Hi,
>>
>> We have been using Opal 2.2 for a while and everything is working fine
>> with Apache 2 and Tomcat 5.0.30. Our Opal installation currently
>> returns URLs that look like
>> "http://_server_name_:8080/app1314720091064/". Recently, we found that
>> one of our users had a problem because his firewall blocked port 8080.
>> Is there some way we can configure Opal and Apache to use port 80
>> URLs?
>
>
> hi,
> you can configure Apache as a proxy (using module mod_proxy)
> There is directive proxy_pass (and reverse).
> However if your apache is used for other usages than opal, you should configure your Opal server to be something like "http://_server_name_:8080/opal/..." and on apache apply the proxy to /opal.
>
> Olivier
>
>> Thanks.
>>
>> Conrad
>>
>> ------------------------------------------------------------------------------
>> Special Offer -- Download ArcSight Logger for FREE!
>> Finally, a world-class log management solution at an even better
>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>> download Logger. Secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsisghtdev2dev
>> _______________________________________________
>> Opaltoolkit-users mailing list
>> Opa...@li...
>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users
>

Re: [Opaltoolkit-users] Making Opal return port 80 URLs

[Olivier S. <oli...@ir...>]

----- Mail original -----
> De: "Conrad Huang" <co...@cg...>
> À: opa...@li...
> Envoyé: Mardi 30 Août 2011 21:31:47
> Objet: [Opaltoolkit-users] Making Opal return port 80 URLs
> Hi,
> 
> We have been using Opal 2.2 for a while and everything is working fine
> with Apache 2 and Tomcat 5.0.30. Our Opal installation currently
> returns URLs that look like
> "http://_server_name_:8080/app1314720091064/". Recently, we found that
> one of our users had a problem because his firewall blocked port 8080.
> Is there some way we can configure Opal and Apache to use port 80
> URLs?


hi,
you can configure Apache as a proxy (using module mod_proxy)
There is directive proxy_pass (and reverse).
However if your apache is used for other usages than opal, you should configure your Opal server to be something like "http://_server_name_:8080/opal/..." and on apache apply the proxy to /opal.

Olivier

> Thanks.
> 
> Conrad
> 
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

[Opaltoolkit-users] Making Opal return port 80 URLs

[Conrad H. <co...@cg...>]

Hi,

We have been using Opal 2.2 for a while and everything is working fine 
with Apache 2 and Tomcat 5.0.30.  Our Opal installation currently 
returns URLs that look like 
"http://_server_name_:8080/app1314720091064/".  Recently, we found that 
one of our users had a problem because his firewall blocked port 8080. 
Is there some way we can configure Opal and Apache to use port 80 URLs? 
  Thanks.

Conrad

Re: [Opaltoolkit-users] Deploying Emboss in Opal2

[Sriram K. <sr...@sd...>]

Hi Jeroen,

Just to make Jane's question a bit more specific:

1) How did you deploy your Emboss components (what command)?

2) When you say "open the emboss files I've added" - what does that  
mean? How do you open them? Is there a stack trace? Your error  
typically happens if a resource (usually a WAR, or even an html file)  
is not in its right place within Tomcat.

3) What URL are you trying to go to, in order to access your Emboss  
web services? Also if you can be a bit more specific about the java  
exceptions you are seeing (i.e. cut and paste stack trace), that would  
be most useful to help debug this.

Thanks,
Sriram

On Jul 11, 2011, at 11:23 AM, Jane Ren wrote:

> Jeroen,
>
> I'm sorry but I am kind of confused.  You did write an XML config  
> file for Emboss and deployed it, right?
>
> jane
> ________________________________________
> From: jeroen vannevel [jer...@ho...]
> Sent: Monday, July 11, 2011 12:02 AM
> To: opa...@li...
> Subject: Re: [Opaltoolkit-users] Deploying Emboss in Opal2
>
> Emboss itself can't be run, but I've tested with some of its  
> components and they do.
>
> The error 'the requested resource() is not availabe' is shown when I  
> try to open the emboss files I've added to Tomcat.
> I've tried to put them in opal2 directly, but I can't seem to get it  
> working there.
> It doesn't show any program I've put in, not even the one I followed  
> a guide for (
>
> http://www.nbcr.net/software/opal/tutorials/opal-tutorial.ppt).
>
> At first this guide worked, but suddenly from one day on another it  
> stopped showing in the application list from opal2.
> However, when I browse to http://localhost:8080/opal2/services/BabelServicePort 
> , it does say there is an AXIS service.
> But besides that I can't see the interface of the application itself.
> When I use the commando to run the service, I get a big amount of  
> java exceptions concerning my connection.
>
>
>> From: j2...@uc...
>> To: jer...@ho...; opa...@li...
>> Date: Fri, 8 Jul 2011 09:47:47 -0700
>> Subject: RE: [Opaltoolkit-users] Deploying Emboss in Opal2
>>
>> Hi Jeroen,
>>
>> First of all, can you run emboss from the command line directly?
>>
>> Also, did you see "the quested resource () is not available" after  
>> you clicked on "submit" from the opal web form?
>>
>> Jane
>>
>>
>> ________________________________________
>> From: jeroen vannevel [jer...@ho...]
>> Sent: Friday, July 08, 2011 5:02 AM
>> To: opa...@li...
>> Subject: [Opaltoolkit-users] Deploying Emboss in Opal2
>>
>> 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 resource () is not available.' error messages.
>>
>> Yours
>> Jeroen V.
>>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously  
> valuable.
> Why? It contains a definitive record of application performance,  
> security
> threats, fraudulent activity, and more. Splunk takes this data and  
> makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> Opaltoolkit-users mailing list
> Opa...@li...
> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users

Re: [Opaltoolkit-users] Deploying Emboss in Opal2

[Jane R. <j2...@uc...>]

Jeroen,

I'm sorry but I am kind of confused.  You did write an XML config file for Emboss and deployed it, right?

jane
________________________________________
From: jeroen vannevel [jer...@ho...]
Sent: Monday, July 11, 2011 12:02 AM
To: opa...@li...
Subject: Re: [Opaltoolkit-users] Deploying Emboss in Opal2

Emboss itself can't be run, but I've tested with some of its components and they do.

The error 'the requested resource() is not availabe' is shown when I try to open the emboss files I've added to Tomcat.
I've tried to put them in opal2 directly, but I can't seem to get it working there.
It doesn't show any program I've put in, not even the one I followed a guide for (

http://www.nbcr.net/software/opal/tutorials/opal-tutorial.ppt).

At first this guide worked, but suddenly from one day on another it stopped showing in the application list from opal2.
However, when I browse to http://localhost:8080/opal2/services/BabelServicePort, it does say there is an AXIS service.
But besides that I can't see the interface of the application itself.
When I use the commando to run the service, I get a big amount of java exceptions concerning my connection.


> From: j2...@uc...
> To: jer...@ho...; opa...@li...
> Date: Fri, 8 Jul 2011 09:47:47 -0700
> Subject: RE: [Opaltoolkit-users] Deploying Emboss in Opal2
>
> Hi Jeroen,
>
> First of all, can you run emboss from the command line directly?
>
> Also, did you see "the quested resource () is not available" after you clicked on "submit" from the opal web form?
>
> Jane
>
>
> ________________________________________
> From: jeroen vannevel [jer...@ho...]
> Sent: Friday, July 08, 2011 5:02 AM
> To: opa...@li...
> Subject: [Opaltoolkit-users] Deploying Emboss in Opal2
>
> 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 resource () is not available.' error messages.
>
> Yours
> Jeroen V.
>

Re: [Opaltoolkit-users] Deploying Emboss in Opal2

[jeroen v. <jer...@ho...>]

Emboss itself can't be run, but I've tested with some of its components and they do.

The error 'the requested resource() is not availabe' is shown when I try to open the emboss files I've added to Tomcat.
I've tried to put them in opal2 directly, but I can't seem to get it working there.
It doesn't show any program I've put in, not even the one I followed a guide for (
http://www.nbcr.net/software/opal/tutorials/opal-tutorial.ppt).

At first this guide worked, but suddenly from one day on another it stopped showing in the application list from opal2.
However, when I browse to http://localhost:8080/opal2/services/BabelServicePort, it does say there is an AXIS service.
But besides that I can't see the interface of the application itself.
When I use the commando to run the service, I get a big amount of java exceptions concerning my connection.


> From: j2...@uc...
> To: jer...@ho...; opa...@li...
> Date: Fri, 8 Jul 2011 09:47:47 -0700
> Subject: RE: [Opaltoolkit-users] Deploying Emboss in Opal2
> 
> Hi Jeroen,
> 
> First of all, can you run emboss from the command line directly?
> 
> Also, did you see "the quested resource () is not available" after you clicked on "submit" from the opal web form?
> 
> Jane
> 
> 
> ________________________________________
> From: jeroen vannevel [jer...@ho...]
> Sent: Friday, July 08, 2011 5:02 AM
> To: opa...@li...
> Subject: [Opaltoolkit-users] Deploying Emboss in Opal2
> 
> 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 resource () is not available.' error messages.
> 
> Yours
> Jeroen V.
>