search

SynBioDex / libSBOLj

Java Library for Synthetic Biology Open Language (SBOL)
Apache License 2.0
37 stars 24 forks source link

Wrap GenBank, FASTA, GFF3 SynBioHub download options #605

Closed cjmyers closed 4 years ago

cjmyers commented 4 years ago

Add GenBank, FASTA, GFF3 SynBioHub download options to the SynBioHubFrontend.

bbartley commented 4 years ago

Hi,

Just noting, when I submit an SBOL2->GFF3 conversion job through the SBOL-Validator's http API, I receive the following response body:

libSBOLj version 2.3.0
Description: validates the contents of an SBOL 2.2.0 document, can compare two documents,
and can convert to/from SBOL 1, GenBank, FASTA, and SnapGene formats.

Usage:
    java --jar libSBOLj.jar [options] <inputFile> [-o <outputFile> -e <compareFile>]

Options:
    -l  <language> specfies language (SBOL1/SBOL2/GenBank/FASTA/SnapGene) for output (default=SBOL2)
    -s  <topLevelURI> select only this object and those it references
    -p  <URIprefix> used for converted objects
    -c  change URI prefix to specified <URIprefix>
    -v  <version> used for converted objects
    -t  uses types in URIs
    -n  allow non-compliant URIs
    -i  allow SBOL document to be incomplete
    -b  check best practices
    -f  fail on first error
    -d  display detailed error trace
    -mf main SBOL file if file diff. option is selected
    -cf second SBOL file if file diff. option is selected
    -no indicate no output file to be generated from validation

I do not receive this error with any other language options

cjmyers commented 4 years ago

Fixed by PR #609