Generate SBOL 2.2 - Githubissues

hicsail / constellation-js

Library for combinatorially specifying, constraining, and exploring genetic design spaces.

http://constellationcad.org

MIT License

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Generate SBOL 2.2 #68

Closed dany-fu closed 5 years ago

dany-fu commented 5 years ago

It would be good if you could enter some random specifications to try to break the SBOL generation. You don't have to worry about the correctness of it, just see if you can break any of the assumptions I'm making (there are lots). The SBOL/errors will get printed to the console.

If you want to take it a step further, you can copy the SBOL into this validator which checks for the correctness of the structure.

This branch also fixes the missing icon bug that we noticed during the Broad demo.

The bulk of the "files changed" are from when Glenn added a bunch of new svg files for new icons. Most of my SBOL changes are in sbol.js and constellation.js

lucyq commented 5 years ago

@dany-fu tests are not passing :S

dany-fu commented 5 years ago

All the test are failing with a is not a valid SBOL part which is a check we put in a while back to that validates the name of the input parts against a list in sbol.js. Its benefit is that it standardizes the inputs and we can readily assign the correct role in SBOL, but at the same time, it might be too restrictive and relies too heavily on how often that list in sbol.js is updated. Let's confer with Nic tomorrow.

dany-fu commented 5 years ago

@lucyq passing now

Glenn did fix the unit tests a while back when he implemented the check, but with all the merging it got lost. Regardless, Nic said he doesn't police the part names in Knox, so we should just mirror that.

coveralls commented 5 years ago

Coverage increased (+6.3%) to 93.827% when pulling 18cb122f7fe0795aba67c97e8531be91c9ac595f on generate_sbol into 82e6b21f9028403e66397c0de5fb1c12cffd09ad on master.