Bioperl: Possibly Off-topic: BoulderIO fails with CGI.pm

[Ewan Birney]

On Mon, 21 Jun 1999, Lincoln Stein wrote:

> Hi Sara,
> 
> Is something missing from the second example?  I don't see a place
> where you create the Boulder stream.
> 
> You should address your response directly to me.  Boulder isn't part
> of the bioperl mainstream, even though I wish it were!

We would *love* to see Boulder as part of the bioperl mainstream lincoln!
Please get an account on bioperl and help us integrate into the system
and/or help us switch to XML streams (what you said last time we talked
about boulder/bioperl you said we should focus our effort on XML). We (I
at least) are working on figuring out how to get extendable data dumping
into the bioperl objects in a sensible manner. This should be doable, and
if we get enough people working on it, possible to get into the 0.06
stream. If you can figure out a good way of retrofitting extendable data
dumping onto objects then please let us know.

I look forward to your input! 

> 
> Best,
> 
> Lincoln
> 
> sara yurman writes:
>  > I saw a BoulderIO announcement posted here, and so hope that it's okay
>  > to post a question about it.  If not, please forgive the post.  I have
>  > tried comp.lang.perl.misc and can't even get flamed.
>  > 
>  > I'd like to use Boulder.pm with input from CGI.pm.  Each works fine
>  > separately, but a call to new Boulder::Store gets ignored in a script
>  > with CGI.pm. 
>  >                      
>  > When I run it in my localhost
>  > (http://localhost/cgi-bin/[scriptname].cgi), my error_log file returns
>  > the following message:
>  > Can't call method "write_record" on an undefined value at
>  > /home/httpd/cgi-bin/[scriptname].cgi line [whereever I tried to write
>  > the record].
>  >                      
>  >                     
>  > TIA,
>  >                      
>  > Sara
>  >                      
>  > *********************This works!******************************
>  > #!/usr/bin/perl
>  >                      
>  > use Stone;
>  > use Boulder::Store;
>  >              
>  > my $stone = new Stone;
>  > $stone->insert(name=>'Sara');
>  > my $store=new Boulder::Store("boulder",true);
>  > print "\$store=".$store."\n";
>  > $store->write_record($stone);
>  > 
>  >               
>  > It prints the results nicely, and obediently writes out boulder.data and
>  > boulder.index.
>  > 
>  > **************This gives the hated error message******************* 
>  >       
>  > #!/usr/bin/perl
>  >                      
>  > use CGI qw(:standard);
>  > use Stone;
>  > use Boulder::Store;
>  >                      
>  > print header;
>  > print start_html('A Simple Example'),
>  > h1('A Simple Example'),
>  > start_form,
>  > "What's your name? ",textfield('name'),
>  > submit,
>  > end_form,
>  > hr;
>  >                      
>  > print end_html;
>  >                      
>  > $stone prints nicely, but the attempt to print $store gives only
>  > "$store =".  I was expecting something like HASH0x..... No
>  > boulder.data or boulder.index.  And the httpd log complains
>  > as noted above.
>  >                      
>  > -- 
>  > 
>  > Sara W. Yurman
>  > Spatial Focus, Inc.
>  > 
>  > email: syurman@spatialfocus.com
>  > voice: (404) 378-0989
>  > fax:   (209) 254-9531
>  > =========== Bioperl Project Mailing List Message Footer =======
>  > Project URL: http://bio.perl.org/
>  > For info about how to (un)subscribe, where messages are archived, etc:
>  > http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
>  > ====================================================================
> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein@cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
> =========== Bioperl Project Mailing List Message Footer =======
> Project URL: http://bio.perl.org/
> For info about how to (un)subscribe, where messages are archived, etc:
> http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
> ====================================================================
> 

Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

=========== Bioperl Project Mailing List Message Footer =======
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
====================================================================