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Centralize RDF and XHTML keywords into RDFConstants (#288) #289

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71 changes: 71 additions & 0 deletions core/src/org/sbml/jsbml/xml/RDFConstants.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,71 @@
/*
* ----------------------------------------------------------------------------
* This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
* for the latest version of JSBML and more information about SBML.
*
* Copyright (C) 2009-2022 jointly by the following organizations:
* 1. The University of Tuebingen, Germany
* 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 3. The California Institute of Technology, Pasadena, CA, USA
* 4. The University of California, San Diego, La Jolla, CA, USA
* 5. The Babraham Institute, Cambridge, UK
* * This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation. A copy of the license agreement is provided
* in the file named "LICENSE.txt" included with this software distribution
* and also available online as <http://sbml.org/Software/JSBML/License>.
* ----------------------------------------------------------------------------
*/

package org.sbml.jsbml.xml;

/**
* Centralized constants for RDF and XHTML keywords used in SBML annotations.
* * @author Deepak Yadav
* @since 1.7
*/
public final class RDFConstants {

/** The RDF namespace prefix. */
public static final String PREFIX_RDF = "rdf";

/** The Dublin Core namespace prefix. */
public static final String PREFIX_DC = "dc";

/** The Dublin Core Terms namespace prefix. */
public static final String PREFIX_DCTERMS = "dcterms";

/** The vCard namespace prefix. */
public static final String PREFIX_VCARD = "vCard";

/** The Biology Qualifiers namespace prefix. */
public static final String PREFIX_BQBIOL = "bqbiol";

/** The Model Qualifiers namespace prefix. */
public static final String PREFIX_BQMODEL = "bqmodel";

/** The RDF 'RDF' element name. */
public static final String RDF = "RDF";

/** The RDF 'Description' element name. */
public static final String DESCRIPTION = "Description";

/** The RDF 'Bag' element name. */
public static final String BAG = "Bag";

/** The RDF 'li' element name. */
public static final String LI = "li";

/** The RDF 'about' attribute name. */
public static final String ABOUT = "about";

/** The RDF 'resource' attribute name. */
public static final String RESOURCE = "resource";

/** The RDF 'parseType' attribute name. */
public static final String PARSE_TYPE = "parseType";

/** Private constructor to prevent instantiation. */
private RDFConstants() {
}
}
25 changes: 13 additions & 12 deletions core/src/org/sbml/jsbml/xml/parsers/SBMLRDFAnnotationParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@
import org.sbml.jsbml.xml.XMLAttributes;
import org.sbml.jsbml.xml.XMLNode;
import org.sbml.jsbml.xml.XMLTriple;
import org.sbml.jsbml.xml.RDFConstants;
import org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser.NODE_COLOR;
import org.w3c.util.DateParser;
import org.w3c.util.InvalidDateException;
Expand Down Expand Up @@ -169,7 +170,7 @@ private NODE_COLOR isValidRDF(XMLNode annotationXMLNode) {
return NODE_COLOR.WHITE;
}

XMLNode rdfNode = annotationXMLNode.getChildElement("RDF", Annotation.URI_RDF_SYNTAX_NS);
XMLNode rdfNode = annotationXMLNode.getChildElement(RDFConstants.RDF, Annotation.URI_RDF_SYNTAX_NS);

return isValidRDFDescription(rdfNode);
}
Expand All @@ -189,7 +190,7 @@ private NODE_COLOR isValidRDFDescription(XMLNode rdfNode) {
}

NODE_COLOR rdfNodeColor = null;
List<XMLNode> descriptionNodes = rdfNode.getChildElements("Description", Annotation.URI_RDF_SYNTAX_NS);
List<XMLNode> descriptionNodes = rdfNode.getChildElements(RDFConstants.DESCRIPTION, Annotation.URI_RDF_SYNTAX_NS);

if (descriptionNodes == null || descriptionNodes.size() == 0) {
rdfNodeColor = NODE_COLOR.WHITE;
Expand Down Expand Up @@ -274,10 +275,10 @@ private NODE_COLOR isValidCreator(XMLNode creatorNode) {

// dc:creator->rdf:Bag->rdf:li*->VCard:stuff*
NODE_COLOR wholeColor = NODE_COLOR.GREEN;
XMLNode bagNode = creatorNode.getChildElement("Bag", Annotation.URI_RDF_SYNTAX_NS);
XMLNode bagNode = creatorNode.getChildElement(RDFConstants.BAG, Annotation.URI_RDF_SYNTAX_NS);

if (bagNode != null) {
List<XMLNode> liNodes = bagNode.getChildElements("li", Annotation.URI_RDF_SYNTAX_NS);
List<XMLNode> liNodes = bagNode.getChildElements(RDFConstants.LI, Annotation.URI_RDF_SYNTAX_NS);

if (liNodes != null && liNodes.size() > 0) {

Expand Down Expand Up @@ -509,7 +510,7 @@ private void readSBMLRDF(SBase contextObject)
readRDFURIs(contextObject, descriptionNode);
readRDFHistory(contextObject, descriptionNode);

contextObject.getAnnotation().setAbout(descriptionNode.getAttrValue("about", Annotation.URI_RDF_SYNTAX_NS));
contextObject.getAnnotation().setAbout(descriptionNode.getAttrValue(RDFConstants.ABOUT, Annotation.URI_RDF_SYNTAX_NS));

descriptionNode.removeAttr("about", Annotation.URI_RDF_SYNTAX_NS);
boolean removed = removeXmlNodeIfEmpty(descriptionNode);
Expand All @@ -520,9 +521,9 @@ private void readSBMLRDF(SBase contextObject)

if (nbChildElements > 0 || nbAttributes > 0) {
// removing the usual namespace declarations if the node is empty
rdfNode.removeNamespace("rdf");
rdfNode.removeNamespace("dc");
rdfNode.removeNamespace("dcterms");
rdfNode.removeNamespace(RDFConstants.PREFIX_RDF);
rdfNode.removeNamespace(RDFConstants.PREFIX_DC);
rdfNode.removeNamespace(RDFConstants.PREFIX_DCTERMS);
rdfNode.removeNamespace("vcard");
rdfNode.removeNamespace("vCard");
rdfNode.removeNamespace("bqbiol");
Expand Down Expand Up @@ -1268,7 +1269,7 @@ private XMLNode writeSBMLRDF(SBase contextObject, XMLNode annotationXMLNode)
annotationXMLNode = new XMLNode(new XMLTriple("annotation"), new XMLAttributes());
}

XMLNode rdfNode = getOrCreate(annotationXMLNode, "RDF", Annotation.URI_RDF_SYNTAX_NS, "rdf");
XMLNode rdfNode = getOrCreate(annotationXMLNode, RDFConstants.RDF, Annotation.URI_RDF_SYNTAX_NS, RDFConstants.PREFIX_RDF);
rdfNode.addNamespace(Annotation.URI_RDF_SYNTAX_NS, "rdf");

// writing only the needed namespaces
Expand All @@ -1279,7 +1280,7 @@ private XMLNode writeSBMLRDF(SBase contextObject, XMLNode annotationXMLNode)
if (contextObject.isSetHistory() &&
(contextObject.getHistory().isSetCreatedDate() || contextObject.getHistory().isSetModifiedDate()))
{
rdfNode.addNamespace(JSBML.URI_PURL_TERMS, "dcterms");
rdfNode.addNamespace(JSBML.URI_PURL_TERMS, RDFConstants.PREFIX_DCTERMS);
}
if (contextObject.getCVTermCount() > 0) {
boolean needBqModel = false;
Expand Down Expand Up @@ -1307,7 +1308,7 @@ private XMLNode writeSBMLRDF(SBase contextObject, XMLNode annotationXMLNode)

// check if the rdf:about value is correct
checkAbout(contextObject);
descriptionNode.addAttr("about", contextObject.getAnnotation().getAbout(), Annotation.URI_RDF_SYNTAX_NS, "rdf");
descriptionNode.addAttr(RDFConstants.ABOUT, contextObject.getAnnotation().getAbout(), Annotation.URI_RDF_SYNTAX_NS, RDFConstants.PREFIX_RDF);

writeHistory(contextObject, descriptionNode);
writeURIs(contextObject, descriptionNode);
Expand Down Expand Up @@ -1932,4 +1933,4 @@ private void writeCVTerm(CVTerm cvterm, XMLNode parentNode,
writeURIs(cvterm, bagNode);
}

}
}