iGEM-Engineering / iGEM-distribution

Repository for collective design of an iGEM DNA distribution
https://igem-distribution.readthedocs.io
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Parentheses in part names cause an error during create vector build step #151

Open ethanj801 opened 2 years ago

ethanj801 commented 2 years ago

Ok. So the issue was in fact with the "(" not with the ".". This is actually preferable because for these particular parts it was not too big of a deal to remove the "(".

Originally posted by @ethanj801 in https://github.com/iGEM-Engineering/iGEM-distribution/issues/148#issuecomment-1013400923

Using a name containing a parenthesis causes an error during the create vector build step of the build and validate packages workflow. There is no clear error message associated with the failure.

ethanj801 commented 2 years ago

Example failed log run attached. logs_14.zip

To replicate, push a branch containing the attached CRISPR-Cas directory to the repository and run the build and validate packages workflow. The error is resolved when the names ABE8e(TadA-8e V106W) andSaABE8e(TadA-8e V106W) are changed to ABE8e TadA-8e V106W and SaABE8e TadA-8e V106W.

CRISPR-Cas.zip

nickdelkis commented 2 years ago

To pin it down a tad bit more, SBOL translation makes the parentheses look like this:

https://github.com/iGEM-Engineering/iGEM-distribution/CRISPR-Cas/SaABE8e_LEFT_PARENTHESISTadA_V106W_RIGHT_PARENTHESIS

So maybe replace actual parentheses ( ) with LEFT_PARENTHESIS and RIGHT_PARENTHESIS, respectively, during the inventory naming process?

noahsprent commented 2 years ago

I've followed Ethan's instructions to reproduce the bug, and can confirm that this is still an issue as of now: https://github.com/iGEM-Engineering/iGEM-distribution/runs/7846006038?check_suite_focus=true