[MOBY-l] [moby] Re: error when do make test

[Mark Wilkinson]

It sounds to me like what you are trying to do is wrap your web page
with a BioMoby service.

This isn't a particularly stable configuration to be aiming for (for all
of the same reasons that screen-scraping has never been able to
successfully build a semantic web!).  You should probably re-think your
plan and make myfile.cgi into a MOBY service directly...  Nevertheless,
if this is what you are committed to, here's how you would go about it:

1)  set up a MOBY daemon, exactly as in the tutorial
2)  set up a MOBY service exactly as in the tutorial
	- the service consumes an input (apparently SQL string)
	- the service consumes secondary parameters (e.g. BioCyc)
	- the service makes a Perl(?) LWP call to myfile.cgi
	- the service captures the HTML output from myfile.cgi
	- the service parses that HTML to extract the data of interest
	- the service re-packages that data into a MOBY object
	- the service returns the MOBY object to the requester
3)  register that service in MOBY Central

If you have not read the tutorial, I suggest you do that before you ask
more questions, since I think my answers are just re-iterating what is
said in those tutorials...

M







On Thu, 2006-02-16 at 13:35 -0500, Nicholas Sutanto wrote:
> Here is actually what I'm planning to do.
> 
> I have this website: http://www.cs.purdue.edu/homes/nsutanto/bio.html. 
> And when we do submit query, it will call "myfile.cgi".
> 
> I want to make a simple client that can access "myfile.cgi" and query 
> and have a result back to me. And I want to put "myfile.cgi" to the 
> biomoby, and my client can call my functions from myfile.cgi through 
> biomoby.
> So, how do I put "myfile.cgi" to the biomoby?
> 
> Sorry if my previous question confused you all.
> Let me know if you guys still confuse about my goal.
> 
> Thanks a lot for any help.
> Nicholas Sutanto.
> 
> Frank Gibbons wrote:
> > Nicholas,
> >
> > My suggestion is to ignore these errors - it's clear that you do not 
> > have the modules "DBD::mysql" or XML::DOM installed. Unless you are 
> > planning to set up your own MOBY Central database, you do not need 
> > this. But you definitely need XML::DOM, so get it from CPAN, and while 
> > you're there, you might want to just install DBD::mysql as well.
> >
> > As Eddie mentioned earlier, it would help us a lot if you explain a 
> > little about what your interest and ultimate goals are: set up your 
> > own database, set up a service, etc. I'll try to fix the code so that 
> > the tests pass for users like you, who don't have DBD::mysql. In the 
> > meantime, you should just continue to installation and then playing 
> > around with the dispatcher and echo-service.
> >
> > -Frank
> >
> >
> 
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Mark Wilkinson
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University of British Columbia
PI in Bioinformatics
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