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CIDARLAB / cello

Genetic circuit design automation
http://www.cellocad.org/
BSD 2-Clause "Simplified" License
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SBOL output invalid #28

Open rkrishnasanka opened 6 years ago

rkrishnasanka commented 6 years ago

So I've been playing around with the SBOL reader and it turns out that the SBOL output for Cello is invalid.

Currently the main issue is that the output has no URI Prefix which is expected by the SBOL reading library.

tim-tx commented 6 years ago

What are you using to read the files exactly? Is there any additional context of URI Prefix?

I recently updated the LCP repo version of cello to use libsbolj-2.2.1, an upgrade from 2.0.0 which came out in 2015. Cello was always using setDefaultURIprefix from libsbolj on the SBOLDocument, and it seems that all URI's in the output xml are prefixed with the URI provided (http://cellocad.org/) so I'm not sure what might be causing your issue.

You can try the attached sbol (just rename the file with an .sbol extension if you need to) that was generated after the libsbolj version bump. I do see two validation exceptions when this sbol is produced, but nothing about a uri prefix. test.txt