From legnitto at ucsc.edu  Thu May  8 16:21:49 2003
From: legnitto at ucsc.edu (Christian Legnitto)
Date: Thu, 08 May 2003 16:21:49 -0700
Subject: Problems with Monarch (possible bug?)
Message-ID: <3EBAE68D.6030804@ucsc.edu>

Hey all, Christian Legnitto here in Santa Cruz. Rex is having me setup 
monarch and metacat here at UCSC.  I am having very odd issues and was 
wondering if anyone has seen/fixed the same problems.

Version Information:
-------------------------------------------------------
Metacat Version: 1.2.1
* Checked out from CVS on May 8th using
   'cvs co -r CHANGES_FOR_MONARCH_01062003 metacat'
Monarch Version: 0.0.0 Alpha1
* Checked out from CVS on May 6th using
   'cvs co monarch'
Java Version: Sun 1.4.1_02

*Using standard pipelines that came with Monarch

Everything built properly with no errors.
-------------------------------------------------------

I have two problems actually...

1) I access monarch through metacat 
(http://<server>/catalog/monarch-index.html), select a dataset (via 
checkbox), then select the desired pipeline (via radio button).  At the 
next screen (selecting databindings) the selection boxes are not 
populated with choices.  You can not run pipelines because they do not 
know what the inputs are if you cannot select them at the selection 
page.  The error happens every time.  Restarting tomcat, rebuilding 
monarch/metacat, and reloading the page does not fix anything.

It can be fixed though, but it requires a little voodoo.  On the main 
menu I have to click on the graphIcon.jpg (which runs the simple 
scatterplot).  Then I get an internal server error:

   javax.servlet.ServletException:
   edu.ucsb.nceas.monarch.MonarchMetacatInterfaceServlet
   Error processing servlet action.
   Server returned HTTP response code: 500 for URL:
   http://<server>/monarch/servlet/monarch
   java.io.IOException: Server returned HTTP response code: 500 for URL:
   http://<server>/monarch/servlet/monarch

(which I assume is monarch dying on the pipeline because it could not 
get the inputs)

Then if I go back and select a dataset and the desired pipeline again 
the selection boxes are magically populated.

The selection boxes will be populated for a bit, but if I leave monarch 
alone for an hour and try it again they will not be populated again.

This leads me to believe it is a cache problem.  My data directory has 
the right permissions and the data is in there.  The cache directory has 
the right permissions as well.  The data is NOT in the cache until I 
click on the icon (but it *should* be in the cache when I run a 
pipeline...it isn't)

This is a really weird error, and I do not know if it is metacat, 
monarch, or my setup. It could also be incompatible versions of 
metacat/monarch. Anyone have any ideas?

Then the next problem.....

2) When the selection boxes ARE populated, if I try to run a pipeline 
SAS terminates with errors.  The error files have a bunch of ^M's all 
over the place. SAS has errors on the lines with ^M's. Both the code in 
the steps and the generated runfile.sas have no ^M's in them (looked 
with vi), so I cannot figure out where they are generated.  SAS works 
fine with other programs.


So far setting up metacat and monarch has been trivial, but getting them 
to work together correctly has not.  Does anyone have a working 
Metacat+Monarch install right now?  If so, which sources were they built 
from?  Could you send them to me :^) ?

Thanks for listening to my longwinded plea for help :^)

- Christian Legnitto



From berkley at nceas.ucsb.edu  Sat May 10 11:18:00 2003
From: berkley at nceas.ucsb.edu (Chad Berkley)
Date: Sat, 10 May 2003 11:18:00 -0700
Subject: Problems with Monarch (possible bug?)
In-Reply-To: <3EBAE68D.6030804@ucsc.edu>
References: <3EBAE68D.6030804@ucsc.edu>
Message-ID: <1052590680.3ebd4258d5430@hyperion.nceas.ucsb.edu>

Hey Christian,

It sounds like you may have a windows/linux compatibility problem.  Are you 
running monarch and metacat on the same machine?  Is it a linux box or 
windows?  What version of java and tomcat do you have?  You may have noticed 
that at the top of monarch's build.xml file, there are two targets aptly 
named "rich" and "chad".  They should actually be called "windows" and "linux" 
respectively.  You can choose which one intializes by changing the depends on 
the init target. 

I have metacat and monarch working together on my machine.  I use the head of 
CVS for metacat though.  I haven't tested monarch with the release 1.2.1, 
though I probably should.  we had some early incompatibilities with the apache 
jar files in metacat and monarch.  this may also be a problem.  

If you want to be a guinea pig for a new product, you could check out the cvs 
module called "overlay" and try to use it.  It is an attempt to get metacat 
and monarch to install together in a simple way.  It works on my linux box at 
least so you might try it out.  The build file is pretty self explanatory.  If 
you need any help interpreting it let me know. 

I'm at a meeting all this week so I won't be able to do much for you until I 
get back to nceas, but if you want to chat, I'm on IRC.  I think the most 
major thing you can do to try to fix your problem(s) is to upgrade metacat to 
the head of CVS.

chad

Chad Berkley
Metadata Systems Developer
National Center for Ecological Analysis and Synthesis
735 State St. Suite 300
Santa Barbara, CA 93117


Quoting Christian Legnitto <legnitto at ucsc.edu>:

> Hey all, Christian Legnitto here in Santa Cruz. Rex is having me setup 
> monarch and metacat here at UCSC.  I am having very odd issues and was 
> wondering if anyone has seen/fixed the same problems.
> 
> Version Information:
> -------------------------------------------------------
> Metacat Version: 1.2.1
> * Checked out from CVS on May 8th using
>    'cvs co -r CHANGES_FOR_MONARCH_01062003 metacat'
> Monarch Version: 0.0.0 Alpha1
> * Checked out from CVS on May 6th using
>    'cvs co monarch'
> Java Version: Sun 1.4.1_02
> 
> *Using standard pipelines that came with Monarch
> 
> Everything built properly with no errors.
> -------------------------------------------------------
> 
> I have two problems actually...
> 
> 1) I access monarch through metacat 
> (http://<server>/catalog/monarch-index.html), select a dataset (via 
> checkbox), then select the desired pipeline (via radio button).  At the 
> next screen (selecting databindings) the selection boxes are not 
> populated with choices.  You can not run pipelines because they do not 
> know what the inputs are if you cannot select them at the selection 
> page.  The error happens every time.  Restarting tomcat, rebuilding 
> monarch/metacat, and reloading the page does not fix anything.
> 
> It can be fixed though, but it requires a little voodoo.  On the main 
> menu I have to click on the graphIcon.jpg (which runs the simple 
> scatterplot).  Then I get an internal server error:
> 
>    javax.servlet.ServletException:
>    edu.ucsb.nceas.monarch.MonarchMetacatInterfaceServlet
>    Error processing servlet action.
>    Server returned HTTP response code: 500 for URL:
>    http://<server>/monarch/servlet/monarch
>    java.io.IOException: Server returned HTTP response code: 500 for URL:
>    http://<server>/monarch/servlet/monarch
> 
> (which I assume is monarch dying on the pipeline because it could not 
> get the inputs)
> 
> Then if I go back and select a dataset and the desired pipeline again 
> the selection boxes are magically populated.
> 
> The selection boxes will be populated for a bit, but if I leave monarch 
> alone for an hour and try it again they will not be populated again.
> 
> This leads me to believe it is a cache problem.  My data directory has 
> the right permissions and the data is in there.  The cache directory has 
> the right permissions as well.  The data is NOT in the cache until I 
> click on the icon (but it *should* be in the cache when I run a 
> pipeline...it isn't)
> 
> This is a really weird error, and I do not know if it is metacat, 
> monarch, or my setup. It could also be incompatible versions of 
> metacat/monarch. Anyone have any ideas?
> 
> Then the next problem.....
> 
> 2) When the selection boxes ARE populated, if I try to run a pipeline 
> SAS terminates with errors.  The error files have a bunch of ^M's all 
> over the place. SAS has errors on the lines with ^M's. Both the code in 
> the steps and the generated runfile.sas have no ^M's in them (looked 
> with vi), so I cannot figure out where they are generated.  SAS works 
> fine with other programs.
> 
> 
> So far setting up metacat and monarch has been trivial, but getting them 
> to work together correctly has not.  Does anyone have a working 
> Metacat+Monarch install right now?  If so, which sources were they built 
> from?  Could you send them to me :^) ?
> 
> Thanks for listening to my longwinded plea for help :^)
> 
> - Christian Legnitto
> 
> _______________________________________________
> monarch-dev mailing list
> monarch-dev at ecoinformatics.org
> http://www.ecoinformatics.org/mailman/listinfo/monarch-dev
> 


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