SBOLDocument. addNamespaceBinding(NamespaceBinding)

[eoberortner]

I'm always running into the exception: sbol-10105: An SBOL document MUST be serialized as a well-formed RDF/XML file that adheres to the grammar defined by: “https://www.w3.org/TR/rdf-syntax-grammar/”

Please, could anybody let me know how to set the namespace properly? Currently, I'm just using the default namespace

[cjmyers]

You should never call addNamespaceBinding. This is a package private method. You should be using addNamespace.

The && is correct. Namely, a namespace is required to end in a delimiter (#, :, or /).

On Aug 28, 2017, at 2:22 PM, eoberortner notifications@github.com wrote:

It appears that the conditions in the if statement should be connected using a logical OR ('||')

I'm always running into the exception: sbol-10105: An SBOL document MUST be serialized as a well-formed RDF/XML file that adheres to the grammar defined by: “https://www.w3.org/TR/rdf-syntax-grammar/” https://www.w3.org/TR/rdf-syntax-grammar/%E2%80%9D — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/487, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWD94Ie8TT83mW81V3JDtCHkbK1tKTpks5scyGYgaJpZM4PFBFc.

[eoberortner]

I do not call the addNamespaceBinding method. I was wrong with the logical OR. it should be logical AND as it is. However, I'm still running into the exception: sbol-10105: An SBOL document MUST be serialized as a well-formed RDF/XML file that adheres to the grammar defined by: “https://www.w3.org/TR/rdf-syntax-grammar/” Reference: SBOL Version 2.1.0 Section 10 on page 58

[cjmyers]

Can you give me the sample code where you call addNamespace?

On Aug 28, 2017, at 2:28 PM, eoberortner notifications@github.com wrote:

I do not call the addNamespaceBinding method. I was wrong with the logical OR. it should be logical AND as it is. However, I'm still running into the exception: sbol-10105: An SBOL document MUST be serialized as a well-formed RDF/XML file that adheres to the grammar defined by: “https://www.w3.org/TR/rdf-syntax-grammar/” https://www.w3.org/TR/rdf-syntax-grammar/%E2%80%9D Reference: SBOL Version 2.1.0 Section 10 on page 58

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[eoberortner]

Attached the code. it's caused when calling the createAnnotation method (line 60)

sbol-issue.txt

[eoberortner]

also, here is my stacktrace: Exception in thread "main" org.sbolstandard.core2.SBOLValidationException: sbol-10105: An SBOL document MUST be serialized as a well-formed RDF/XML file that adheres to the grammar defined by: “https://www.w3.org/TR/rdf-syntax-grammar/” Reference: SBOL Version 2.1.0 Section 10 on page 58 at org.sbolstandard.core2.SBOLDocument.addNamespaceBinding(SBOLDocument.java:2170) at org.sbolstandard.core2.SBOLDocument.addNamespace(SBOLDocument.java:2151) at org.sbolstandard.core2.Identified.addNamespace(Identified.java:463) at org.sbolstandard.core2.Identified.addAnnotation(Identified.java:530) at org.sbolstandard.core2.Identified.createAnnotation(Identified.java:366) at org.sbolstandard.assembly.demo.SBOLTest.main(SBOLTest.java:60)

[cjmyers]

Try adding a delimiter (/, #, : ) at the end of string in URI_PREFIX

On Aug 28, 2017, at 2:33 PM, eoberortner notifications@github.com wrote:

Attached the code. it's caused when calling the createAnnotation method (line 60)

sbol-issue.txt https://github.com/SynBioDex/libSBOLj/files/1258291/sbol-issue.txt — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/487#issuecomment-325472988, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWD9_nIGJIJHn6kF7gwixNWYz78gUxgks5scyQagaJpZM4PFBFc.

[eoberortner]

OK, the following command works: cd.createAnnotation(new QName(URI_PREFIX + "#", "derivation", "derivation"), "purchase");

thanks for your help! interesting behavior though.

[eoberortner]

I'll just add the '#' sign to the URI_PREFIX constants. that should solve the issue.

thanks again!

[cjmyers]

The reason we need to have the delimiter is namespaces without them cause all kinds of problems especially when serialized as anything other than XML.

On Aug 28, 2017, at 2:48 PM, eoberortner notifications@github.com wrote:

OK, the following command works: cd.createAnnotation(new QName(URI_PREFIX + "#", "derivation", "derivation"), "purchase");

thanks for your help! interesting behavior though.

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[eoberortner]

just out of curiosity, could the library add a delimiter if non is provided?

[cjmyers]

Perhaps, but it would not know the correct one. It is often #, but sometimes /.

On Aug 28, 2017, at 2:56 PM, eoberortner notifications@github.com wrote:

just out of curiosity, could the library add a delimiter if non is provided?

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