Open jakebeal opened 2 years ago
Consider the attached SBOL2 file: lycopene.xml.txt
The following sequence has namespace remapping behavior that is either incorrect or incorrectly used due to lack of documentation:
import sbol2 doc1 = sbol2.Document() doc1.read('lycopene.xml') print(doc1.componentDefinitions[0].identity) # http://liverpool.ac.uk/ComponentDefinition/P21684_10000_gene/1 doc2 = sbol2.Document() doc1.copy(target_doc=doc2) # no namespace activity, no problems print(doc2.componentDefinitions[0].identity) # http://liverpool.ac.uk/ComponentDefinition/P21684_10000_gene/1 doc3 = sbol2.Document() doc1.copy('http://liverpool.ac.uk', doc3) # should be a no-op for materials already in this namespace print(doc3.componentDefinitions[0].identity) # http://examples.org/ComponentDefinition/P21684_10000_gene/1 doc4 = sbol2.Document() doc1.copy('http://somethingelse.org', doc4) print(doc4.componentDefinitions[0].identity) # http://liverpool.ac.uk/ComponentDefinition/P21684_10000_gene/1
Links to sequences get broken with namespaces too. Presumably other links are being broken as well, but these were the ones that appeared:
print(doc1.componentDefinitions[0].sequence.identity) # http://examples.org/Sequence/P21684_10000_gene_seq/1 print(doc2.componentDefinitions[0].sequence) # http://examples.org/Sequence/P21684_10000_gene_seq/1 print(doc3.componentDefinitions[0].sequence) # None print(doc4.componentDefinitions[0].sequence) # None
Consider the attached SBOL2 file: lycopene.xml.txt
The following sequence has namespace remapping behavior that is either incorrect or incorrectly used due to lack of documentation:
Links to sequences get broken with namespaces too. Presumably other links are being broken as well, but these were the ones that appeared: