Improve error reporting when parsing RDF

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Certain errors are swallowed silently when Foresite parses RDF XML.  It
appears that certain syntax errors (e.g. illegal/not-well-formed URIs) in
ORE RDF XML are not found eagerly.  They are found at the time Jena
attempts to read that portion of the graph.

For example, calling JenaOREParser.parse(InputStream is) with the attached
ReM returns null, with no errors reported.  If
JenaOREParser.parse(InputStream is) is modified to write out the model
prior to creating the ReM, the error is reported.  It would be nice if
Foresite/Jena could eagerly parse a ReM and report errors without silently
swallowing them.

After modifying JenaOREParser.parse(InputStream is) to write out the model,
I was able to see the error:
ERROR [main]: datapub.mapping.ForesiteOreRemMapper@104 2009-12-14
11:08:11,587 ORE ReM parsing failed: Only well-formed absolute URIrefs can
be included in RDF/XML output: <info://figure:figure1> Code:
0/ILLEGAL_CHARACTER in PORT: The character violates the grammar rules for
URIs/IRIs. 
com.hp.hpl.jena.shared.BadURIException: Only well-formed absolute URIrefs
can be included in RDF/XML output: <info://figure:figure1> Code:
0/ILLEGAL_CHARACTER in PORT: The character violates the grammar rules for
URIs/IRIs.
    at
com.hp.hpl.jena.xmloutput.impl.BaseXMLWriter.checkURI(BaseXMLWriter.java:768)
    at
com.hp.hpl.jena.xmloutput.impl.BaseXMLWriter.relativize(BaseXMLWriter.java:745)
    at com.hp.hpl.jena.xmloutput.impl.Basic.writeResourceReference(Basic.java:154)
    at com.hp.hpl.jena.xmloutput.impl.Basic.writePredicate(Basic.java:101)
    at com.hp.hpl.jena.xmloutput.impl.Basic.writeRDFStatements(Basic.java:77)
    at com.hp.hpl.jena.xmloutput.impl.Basic.writeRDFStatements(Basic.java:66)
    at com.hp.hpl.jena.xmloutput.impl.Basic.writeBody(Basic.java:40)
    at
com.hp.hpl.jena.xmloutput.impl.BaseXMLWriter.writeXMLBody(BaseXMLWriter.java:452
)
    at com.hp.hpl.jena.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:424)
    at com.hp.hpl.jena.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:410)
    at com.hp.hpl.jena.rdf.model.impl.ModelCom.write(ModelCom.java:270)
    at org.dspace.foresite.jena.JenaOREParser.parse(JenaOREParser.java:70)
    at
edu.jhu.library.datapub.mapping.ForesiteOreRemMapper.fromPublisherRem(ForesiteOr
eRemMapper.java:97)
    at
edu.jhu.library.datapub.mapping.MapperTest.testSimplePublisherMapping(MapperTest
.java:78)

Original issue reported on code.google.com by emets...@gmail.com on 14 Dec 2009 at 4:20

Attachments:

• testcase-002.xml