SynBioDex/libSBOLj

Issues

• Mystery conversion failure

  #622 opened 3 years ago by jakebeal
  3

• Opaque failure while reading GenBank

  #623 opened 3 years ago by jakebeal
  1

• Invalid reporting of error sbol-11003

  #621 opened 3 years ago by jakebeal
  1

• displayID truncation in LOCUS field of GenBank conversions

  #620 opened 3 years ago by jakebeal
  0

• getRootComponentDefinitions() does not treat the Variants in a Variable Component as a child Component of a Component Definition

  #613 opened 4 years ago by ImperialiGEM2020
  1

• Logout doesn't call logout endpoint

  #612 opened 4 years ago by jvscholz
  1

• A robust Genbank – SBOL converter tool

  #611 opened 5 years ago by cjmyers
  0

• Wrap GenBank, FASTA, GFF3 SynBioHub download options

  #605 opened 5 years ago by cjmyers
  2

• Error converting GenBank files with spaces in feature types

  #607 opened 5 years ago by cjmyers
  0

• Support non-local SBH fetches

  #606 opened 5 years ago by cjmyers
  0

• Several potential ArrayIndexOutOfBounds bugs.

  #603 opened 5 years ago by ITWOI
  1

• Some potential NPE bugs

  #601 opened 5 years ago by JulyChen728
  2

• GenBank/FASTA converters do not work with multiple ranges

  #600 opened 5 years ago by cjmyers
  0

• getImpliedNucleicAcidSequence does not work with multiple ranges

  #599 opened 5 years ago by cjmyers
  0

• Update GenBank converter

  #598 opened 5 years ago by cjmyers
  0

• Copy method for Model and Sequence calling Identified copy rather than TopLevel

  #597 opened 5 years ago by cjmyers
  0

• Converter mangle-merges unrecognized GenBank features

  #594 opened 5 years ago by jakebeal
  9

• Support import/conversion from GFF

  #547 opened 6 years ago by cjmyers
  0

• sbol-10204 does not capture null displayId values

  #596 opened 5 years ago by jakebeal
  2

• displayId rejection should say which ID is the problem

  #595 opened 5 years ago by jakebeal
  2

• FASTA parser should generate unique ids

  #591 opened 5 years ago by cjmyers
  3

• GenBank exports lose names

  #593 opened 5 years ago by jakebeal
  4

• Add a flag to validation to indicate missing parts should be fetched from the web-of-registries

  #550 opened 6 years ago by cjmyers
  0

• URIs for nested annotations must be unique over the entire document

  #585 opened 5 years ago by cjmyers
  2

• Validation for unique URIs should check nested annotation URIs

  #586 opened 5 years ago by cjmyers
  1

• Add Support for REGION Tag to GenBank-to-SBOL Conversion

  #554 opened 5 years ago by nroehner
  3

• Problem with fix URI prefixes with overlapping prefix names

  #561 opened 6 years ago by cjmyers
  0

• Validation of sbol that uses persistentIdentity references may not work completely

  #549 opened 6 years ago by cjmyers
  0

• Certificate errors connecting to SynBioHub instances

  #544 opened 7 years ago by jakebeal
  9

• Parsing of RDF files depends on XML structure

  #551 opened 6 years ago by jamesamcl
  1

• Inverted recursive copy method

  #553 opened 6 years ago by cjmyers
  0

• Add a method to compile a sequence that satisfies the SequenceConstraints

  #555 opened 6 years ago by cjmyers
  0

• Need better provenance construction helper functions

  #556 opened 6 years ago by cjmyers
  0

• Should add methods to count objects and print these counts

  #557 opened 6 years ago by cjmyers
  0

• Should have method to print in XML format a specified TopLevel

  #558 opened 6 years ago by cjmyers
  0

• Flipping orientation with an all caps sequence creates N's.

  #564 opened 5 years ago by SamuelSauce
  2

• libSBOLj serializes Boolean annotations as strings

  #565 opened 6 years ago by jakebeal
  2

• Problems parsing the LOCUS line in GenBank files

  #569 opened 5 years ago by cjmyers
  1

• Add Measure class

  #584 opened 5 years ago by cjmyers
  1

• Add Experiment and Experimental Data Classes

  #583 opened 5 years ago by cjmyers
  1

• Add SBOL type to Activity

  #582 opened 5 years ago by cjmyers
  1

• Add sequence to Location object (SEP 026)

  #572 opened 5 years ago by cjmyers
  2

• getImpliedNucleicAcid should return null if range is out of bounds.

  #570 opened 5 years ago by SamuelSauce
  1

• Check sbol-13506 hasUnit in Measure refers to a Unit

  #581 opened 5 years ago by cjmyers
  0

• getImpliedNucleicAcidSequence needs to be sourceLocation aware

  #575 opened 5 years ago by cjmyers
  1

• org.synbiohub.frontend.SynBioHubFrontend should include timeouts

  #559 opened 6 years ago by jakebeal
  10

• Interaction/Participation only recognize some recommended SBO terms

  #563 opened 6 years ago by jakebeal
  7

• Multiple types for GenericTopLevel getting dropped

  #560 opened 6 years ago by cjmyers
  0

• StringIndexOutOfBoundsException in SBOLValidate

  #545 opened 6 years ago by 3ach
  1

• SequenceConstraints of derived CDs must be consistent with template (sbol-12908)

  #548 opened 6 years ago by cjmyers
  1