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SynBioDex / SBOL-utilities

Command-line utilities and scripts for manipulating SBOL data
MIT License
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Remove dependency on online validator/converter #102

Closed jakebeal closed 2 years ago

jakebeal commented 2 years ago

pySBOL2 uses the SBOL online validator/converter at https://validator.sbolstandard.org/ for validation; we also use it for conversion to GenBank. Although this was stable for a long time, it has recently gone down, which is breaking lots of applications. Even if it goes up quickly again, this outage is painful.

Use of the online validator/converter also means SBOL utilities cannot be used offline and cannot convert confidential data to GenBank format.

jakebeal commented 2 years ago

The longer-term solution to this is going to be having native converters (see: https://github.com/nrnb/GoogleSummerOfCode/issues/183). The near-term patch is to include a jar from https://github.com/SynBioDex/libSBOLj

jakebeal commented 2 years ago

First part of fix in progress at https://github.com/SynBioDex/pySBOL2/tree/offline-validation-conversion Once this is updated, we can proceed to configuring sbol-utilities to use pySBOL2 in offline mode.