Parsing of RDF files depends on XML structure

[jamesamcl]

While testing some things with GenericTopLevels I found that this file validates:

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF xmlns:cheese="http://wiki.synbiohub.org/Terms/cheese#"
   xmlns:dcterms="http://purl.org/dc/terms/"
   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
   xmlns:sbol="http://sbols.org/v2#">
  <cheese:Cheese rdf:about="http://cheese/camembert/1">
    <dcterms:description>Camembert is a moist, soft, creamy, surface-ripened cow's milk cheese. It was first made in the late 18th century at Camembert, Normandy, in northern France.</dcterms:description>
    <dcterms:title>Camembert</dcterms:title>
    <sbol:displayId>camembert</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://cheese/camembert"/>
    <sbol:version>1</sbol:version>
  </cheese:Cheese>
</rdf:RDF>

While this file throws an error:

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF xmlns:cheese="http://wiki.synbiohub.org/Terms/cheese#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:sbol="http://sbols.org/v2#">
  <rdf:Description rdf:about="http://cheese/camembert/1">
    <rdf:type rdf:resource="http://wiki.synbiohub.org/Terms/cheese#Cheese"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://cheese/camembert/1">
    <sbol:persistentIdentity rdf:resource="http://cheese/camembert"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://cheese/camembert/1">
    <sbol:displayId>camembert</sbol:displayId>
  </rdf:Description>
  <rdf:Description rdf:about="http://cheese/camembert/1">
    <sbol:version>1</sbol:version>
  </rdf:Description>
  <rdf:Description rdf:about="http://cheese/camembert/1">
    <dcterms:title>Camembert</dcterms:title>
  </rdf:Description>
  <rdf:Description rdf:about="http://cheese/camembert/1">
    <dcterms:description>Camembert is a moist, soft, creamy, surface-ripened cow's milk cheese. It was first made in the late 18th century at Camembert, Normandy, in northern France.</dcterms:description>
  </rdf:Description>
</rdf:RDF>

The error is:

[/tmp/UnGkrJiMDSKL2wpsu-NWZkfY.xml] sbol-12302: The rdfType property of a GenericTopLevel object is REQUIRED and MUST contain a QName.
Reference: SBOL Version 2.2.0 Section 7.14.2 on page 55
: http://cheese/camembert/1

sbol-12302: The rdfType property of a GenericTopLevel object is REQUIRED and MUST contain a QName.
Reference: SBOL Version 2.2.0 Section 7.14.2 on page 55
: http://cheese/camembert/1

sbol-12302: The rdfType property of a GenericTopLevel object is REQUIRED and MUST contain a QName.
Reference: SBOL Version 2.2.0 Section 7.14.2 on page 55
: http://cheese/camembert/1

sbol-12302: The rdfType property of a GenericTopLevel object is REQUIRED and MUST contain a QName.
Reference: SBOL Version 2.2.0 Section 7.14.2 on page 55
: http://cheese/camembert/1

sbol-12302: The rdfType property of a GenericTopLevel object is REQUIRED and MUST contain a QName.
Reference: SBOL Version 2.2.0 Section 7.14.2 on page 55
: http://cheese/camembert/1

Validation failed.

The two files are different representations of exactly the same RDF.

[cjmyers]

This would be a fairly substantial rewrite to support individual triples. It also would be rather inefficient I think.

…

On Jun 19, 2018, at 4:23 PM, James Alastair McLaughlin ***@***.***> wrote: While testing some things with GenericTopLevels I found that this file validates: <?xml version="1.0" encoding="utf-8"?> <rdf:RDF xmlns:cheese="http://wiki.synbiohub.org/Terms/cheese#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:sbol="http://sbols.org/v2#"> <cheese:Cheese rdf:about="http://cheese/camembert/1"> <dcterms:description>Camembert is a moist, soft, creamy, surface-ripened cow's milk cheese. It was first made in the late 18th century at Camembert, Normandy, in northern France.</dcterms:description> <dcterms:title>Camembert</dcterms:title> <sbol:displayId>camembert</sbol:displayId> <sbol:persistentIdentity rdf:resource="http://cheese/camembert"/> <sbol:version>1</sbol:version> </cheese:Cheese> </rdf:RDF> While this file throws an error: <?xml version="1.0" encoding="utf-8"?> <rdf:RDF xmlns:cheese="http://wiki.synbiohub.org/Terms/cheese#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:sbol="http://sbols.org/v2#"> <rdf:Description rdf:about="http://cheese/camembert/1"> <rdf:type rdf:resource="http://wiki.synbiohub.org/Terms/cheese#Cheese"/> </rdf:Description> <rdf:Description rdf:about="http://cheese/camembert/1"> <sbol:persistentIdentity rdf:resource="http://cheese/camembert"/> </rdf:Description> <rdf:Description rdf:about="http://cheese/camembert/1"> <sbol:displayId>camembert</sbol:displayId> </rdf:Description> <rdf:Description rdf:about="http://cheese/camembert/1"> <sbol:version>1</sbol:version> </rdf:Description> <rdf:Description rdf:about="http://cheese/camembert/1"> <dcterms:title>Camembert</dcterms:title> </rdf:Description> <rdf:Description rdf:about="http://cheese/camembert/1"> <dcterms:description>Camembert is a moist, soft, creamy, surface-ripened cow's milk cheese. It was first made in the late 18th century at Camembert, Normandy, in northern France.</dcterms:description> </rdf:Description> </rdf:RDF> The error is: [/tmp/UnGkrJiMDSKL2wpsu-NWZkfY.xml] sbol-12302: The rdfType property of a GenericTopLevel object is REQUIRED and MUST contain a QName. Reference: SBOL Version 2.2.0 Section 7.14.2 on page 55 : http://cheese/camembert/1 sbol-12302: The rdfType property of a GenericTopLevel object is REQUIRED and MUST contain a QName. Reference: SBOL Version 2.2.0 Section 7.14.2 on page 55 : http://cheese/camembert/1 sbol-12302: The rdfType property of a GenericTopLevel object is REQUIRED and MUST contain a QName. Reference: SBOL Version 2.2.0 Section 7.14.2 on page 55 : http://cheese/camembert/1 sbol-12302: The rdfType property of a GenericTopLevel object is REQUIRED and MUST contain a QName. Reference: SBOL Version 2.2.0 Section 7.14.2 on page 55 : http://cheese/camembert/1 sbol-12302: The rdfType property of a GenericTopLevel object is REQUIRED and MUST contain a QName. Reference: SBOL Version 2.2.0 Section 7.14.2 on page 55 : http://cheese/camembert/1 Validation failed. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#551>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADWD97SW8k3e_XDFQ3rEL4hsqHfBLQF6ks5t-ReDgaJpZM4Utul5>.