OWL API removes empty lines from a multiline comment

Question

I tried to codify the following comment using OWL API:

<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
CRECK Modeling Group (Politecnico di Milano)
http://creckmodeling.chem.polimi.it/

Primary Reference Fuels (PRF) + PAH Mechanism
Version 1311, November 2013
Detailed and semidetailed (lumped) mechanism of the pyrolysis,
partial oxidation and combustion Primary Reference Fuels,
including PAH (Polycyclic Aromatic Hydrocarbons) formation up to C20.

Kinetic scheme (Low and High temperature): 276 species and 8476 reactions

References

E. Ranzi, A. Frassoldati, S. Granata, T. Faravelli,
Ind. Eng. Chem. Res. 44(14), 5170-5183 (2005), doi: 10.1021/ie049318g

T. Bieleveld, A. Frassoldati, A. Cuoci, T. Faravelli, E. Ranzi, U. Niemann K. Seshadri,
Proceedings of the Combustion Institute 32 I, pp. 493-500 (2009), doi:10.116/j.proci.2008.06.214

Saggese C., Frassoldati, Cuoci A., Faravelli T., Ranzi,
Combustion and Flame (2013), DOI: 10.1016/j.combustflame.2013.02.013

CRECK Modeling Group (Politecnico di Milano)http://creckmodeling.chem.polimi.it/
Version 1311, November 2013

</rdfs:comment>

Unfortunately, it ends up showing me the following comment with empty lines removed:

<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
CRECK Modeling Group (Politecnico di Milano)http://creckmodeling.chem.polimi.it/
Primary Reference Fuels (PRF) + PAH Mechanism
Version 1311, November 2013
Detailed and semidetailed (lumped) mechanism of the pyrolysis,
partial oxidation and combustion Primary Reference Fuels,
including PAH (Polycyclic Aromatic Hydrocarbons) formation up to C20.
Kinetic scheme (Low and High temperature): 276 species and 8476 reactionsReferences
E. Ranzi, A. Frassoldati, S. Granata, T. Faravelli,
Ind. Eng. Chem. Res. 44(14), 5170-5183 (2005), doi: 10.1021/ie049318g
T. Bieleveld, A. Frassoldati, A. Cuoci, T. Faravelli, E. Ranzi, U. Niemann, K. Seshadri,
Proceedings of the Combustion Institute 32 I, pp. 493-500 (2009), doi:10.1016/j.proci.2008.06.214
Saggese C., Frassoldati, Cuoci A., Faravelli T., Ranzi,
Combustion and Flame (2013), DOI: 10.1016/j.combustflame.2013.02.013
CRECK Modeling Group (Politecnico di Milano)
http://creckmodeling.chem.polimi.it/Version 1311, November 2013
</rdfs:comment>

For encoding the above comment in OWL, I'm using the following method: org.semanticweb.owlapi.model.OWLDataFactory.getOWLLiteral(comment);

The code snippet which is relevant to the problem description is as follows:

/**
* Creates an OWL literal with one of the following data types:</br>
* 1. String.
* 2. Integer, and
* 3. Float.
* 
* @param ontoFactory
* @param propertyName
* @param literal
* @return
* @throws OntoException
*/


private OWLLiteral createOWLLiteral(OWLDataFactory ontoFactory, String propertyName, String literal) throws OntoException{
if(propertyName.startsWith(basePathTBox.concat(HASH))){
propertyName = propertyName.replace(basePathTBox.concat(HASH), EMPTY);
}
if(dataPropertyNameVsTypeMap.containsKey(propertyName.toLowerCase())){
if(dataPropertyNameVsTypeMap.get(propertyName.toLowerCase()).equals("string")){
return ontoFactory.getOWLLiteral(literal);
} else if(dataPropertyNameVsTypeMap.get(propertyName.toLowerCase()).equals("integer")){
try{
return ontoFactory.getOWLLiteral(Integer.parseInt(literal));
}catch(NumberFormatException e){
throw new OntoException("The following value is not an integer:"+literal);
}
} else if(dataPropertyNameVsTypeMap.get(propertyName.toLowerCase()).equals("float")){
try{
return ontoFactory.getOWLLiteral(Float.parseFloat(literal));
}catch(NumberFormatException e){
throw new OntoException("The following value is not a float:"+literal);
}
}
}
throw new OntoException("The following data type could not be recognised:"+dataPropertyNameVsTypeMap.get(propertyName.toLowerCase()));
}

I would highly appreciate your help in getting this resolved.

It seems to me that getOWLLiteral(String literal) compresses the literal by removing the empty lines. I'm referring to the following method, which is available in the class uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryInternalsImplNoCache. `@Override public OWLLiteral getOWLLiteral(String value) { if (useCompression) { return new OWLLiteralImpl(value, "", XSDSTRING); } return new OWLLiteralImplString(value); }` — Feroz Farazi, Oct 08 '18 at 23:00
The literal compression does not modify the string. It zips the string bytes. It cannot be the root of this issue. — Ignazio, Oct 18 '18 at 18:31

score 1 · Answer 1 · answered Oct 18 '18 at 18:38

The problem is not the factory. The following code produces a correctly spaced comment annotation. The issue must be on the format used to save or in a bug.

    OWLAnnotation a = df.getRDFSComment("\n" + "CRECK Modeling Group (Politecnico di Milano)\n"
        + "http://creckmodeling.chem.polimi.it/\n" + "\n" + "\n"
        + "Primary Reference Fuels (PRF) + PAH Mechanism\n" + "Version 1311, November 2013\n"
        + "Detailed and semidetailed (lumped) mechanism of the pyrolysis,\n"
        + "partial oxidation and combustion Primary Reference Fuels,\n"
        + "including PAH (Polycyclic Aromatic Hydrocarbons) formation up to C20.\n" + "\n"
        + "Kinetic scheme (Low and High temperature): 276 species and 8476 reactions\n" + "\n"
        + "References\n" + "\n" + "E. Ranzi, A. Frassoldati, S. Granata, T. Faravelli,\n"
        + "Ind. Eng. Chem. Res. 44(14), 5170-5183 (2005), doi: 10.1021/ie049318g\n" + "\n"
        + "T. Bieleveld, A. Frassoldati, A. Cuoci, T. Faravelli, E. Ranzi, U. Niemann K. Seshadri,\n"
        + "Proceedings of the Combustion Institute 32 I, pp. 493-500 (2009), doi:10.116/j.proci.2008.06.214\n"
        + "\n" + "Saggese C., Frassoldati, Cuoci A., Faravelli T., Ranzi,\n"
        + "Combustion and Flame (2013), DOI: 10.1016/j.combustflame.2013.02.013\n" + "\n"
        + "CRECK Modeling Group (Politecnico di Milano)http://creckmodeling.chem.polimi.it/\n"
        + "Version 1311, November 2013\n" + "\n" + "\n");
    System.out.println(a);

Annotation(rdfs:comment "
CRECK Modeling Group (Politecnico di Milano)
http://creckmodeling.chem.polimi.it/


Primary Reference Fuels (PRF) + PAH Mechanism
Version 1311, November 2013
Detailed and semidetailed (lumped) mechanism of the pyrolysis,
partial oxidation and combustion Primary Reference Fuels,
including PAH (Polycyclic Aromatic Hydrocarbons) formation up to C20.

Kinetic scheme (Low and High temperature): 276 species and 8476 reactions

References

E. Ranzi, A. Frassoldati, S. Granata, T. Faravelli,
Ind. Eng. Chem. Res. 44(14), 5170-5183 (2005), doi: 10.1021/ie049318g

T. Bieleveld, A. Frassoldati, A. Cuoci, T. Faravelli, E. Ranzi, U. Niemann K. Seshadri,
Proceedings of the Combustion Institute 32 I, pp. 493-500 (2009), doi:10.116/j.proci.2008.06.214

Saggese C., Frassoldati, Cuoci A., Faravelli T., Ranzi,
Combustion and Flame (2013), DOI: 10.1016/j.combustflame.2013.02.013

CRECK Modeling Group (Politecnico di Milano)http://creckmodeling.chem.polimi.it/
Version 1311, November 2013


"^^xsd:string)

OWL API removes empty lines from a multiline comment

1 Answers1