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Re: LSID lookup details: help? [was: All about the LSID URI/URN]

From: Benjamin H Szekely <bhszekel@us.ibm.com>
Date: Mon, 31 Jul 2006 15:15:31 -0400
To: Dan Connolly <connolly@w3.org>
Cc: Alan Ruttenberg <alanruttenberg@gmail.com>, "Henry S. Thompson" <ht@inf.ed.ac.uk>, Noah Mendelsohn <noah_mendelsohn@us.ibm.com>, public-semweb-lifesci@w3.org, public-semweb-lifesci-request@w3.org, Sean Martin <sjmm@us.ibm.com>
Message-ID: <OFD1ABC606.B792E33F-ON852571BC.0069BB47-852571BC.0069CB83@us.ibm.com>
Perhaps try one of the following LSIDs

urn:lsid:gdb.org:GenomicSegment:GDB132938
urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed:12441807

- Ben

Ben Szekely
IBM Software Engineer
Advanced Internet Technology, Cambridge, MA
bhszekel@us.ibm.com

public-semweb-lifesci-request@w3.org wrote on 07/31/2006 01:34:31 PM:

> 
> In today's call, I learned a bit about how LSID lookup
> works:
> 
>  (1) try to find an SRV record using the domain in the LSID
>  (2) fall back to a DDDS lookup and NAPTR and such
> 
> Option (2) depends on some NAPTR stuff in the "arpa" parts
> of DNS space that OMG is expected to install but hasn't
> gotten around to, largely for lack of urgent need, I gather.
> 
> I'm trying to verify my understanding from some code.
> I found some perl code[2], and I got it installed
> with "All tests successful." But when I run it,
> using an example from the LSID spec[1]:
> 
>   URN:LSID:rcsb.org:PDB:1D4X:22
> 
> I get "Unable to resolve authority to SRV record: NXDOMAIN".
> 
> 
> Any clues? A full trace is below:
> 
> > ~/src/lsid-perl-1.1.4$ perl examples/client/lsid_client.pl
> > URN:LSID:rcsb.org:PDB:1D4X:22
> Client settings:
> Cleaning cache:
>         no
> 
> LSID Given:
>         URN:LSID:rcsb.org:PDB:1D4X:22
> 
> Canonicalized LSID:
>         urn:lsid:rcsb.org:PDB:1D4X:22
> 
> Unable to resolve authority.
>  -> Unable to resolve authority to SRV record: NXDOMAIN
> 
> Stack trace at LS/Locator.pm line 230
>         LS::Locator::resolveAuthority('LS::Locator=HASH(0x824e900)',
> 'LS::ID=SCALAR(0x823f7cc)') called at LS/Client/BasicResolver.pm line
> 138
> 
> LS::Client::BasicResolver::resolve('LS::Client::
> BasicResolver=HASH(0x824e4b0)', 'lsid', 'LS::ID=SCALAR(0x823f7cc)') 
> called at examples/client/lsid_client.pl line 165
>         main::resolveLSID('LS::ID=SCALAR(0x823f7cc)', 'undef', 'undef')
> called at examples/client/lsid_client.pl line 125
> 
> 
> Stack trace at LS/Client/BasicResolver.pm line 143
> 
> LS::Client::BasicResolver::resolve('LS::Client::
> BasicResolver=HASH(0x824e4b0)', 'lsid', 'LS::ID=SCALAR(0x823f7cc)') 
> called at examples/client/lsid_client.pl line 165
>         main::resolveLSID('LS::ID=SCALAR(0x823f7cc)', 'undef', 'undef')
> called at examples/client/lsid_client.pl line 125
> 
> > 
> [1] http://www.omg.org/cgi-bin/doc?dtc/04-05-01
> [2] 
> 
http://easynews.dl.sourceforge.net/sourceforge/lsid/lsid-perl-1.1.4.tar.gz
>  <- http://lsid.sourceforge.net/
> 
> -- 
> Dan Connolly, W3C http://www.w3.org/People/Connolly/
> D3C2 887B 0F92 6005 C541  0875 0F91 96DE 6E52 C29E
> 
> 
Received on Monday, 31 July 2006 19:16:57 GMT

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