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Parse creators from dcterms:creator vCard4 annotations #274

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Parse creators from dcterms:creator vCard4 annotations #274

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e812e48
Parse creators from dcterms:creator vCard4 annotations
dyrpsf Jan 12, 2026
c117f99
Factor vCard element names into constants in SBMLRDFAnnotationParser
dyrpsf Jan 25, 2026
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163 changes: 132 additions & 31 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.parsers.SBMLRDFAnnotationParser.NODE_COLOR;
import org.w3c.util.DateParser;
import org.w3c.util.InvalidDateException;

Expand Down Expand Up @@ -65,6 +66,24 @@ public class SBMLRDFAnnotationParser implements AnnotationReader, AnnotationWrit
*
*/
public static final String CUSTOM_RDF = "jsbml.custom.rdf";
/**
* Namespace for vCard4 RDF (used by some tools such as libSBML).
*/
private static final String VCARD4_NS = "http://www.w3.org/2006/vcard/ns#";
// vCard 3 element names
private static final String VCARD3_ELEMENT_N = "N";
private static final String VCARD3_ELEMENT_EMAIL = "EMAIL";
private static final String VCARD3_ELEMENT_ORG = "ORG";
private static final String VCARD3_ELEMENT_FAMILY = "Family";
private static final String VCARD3_ELEMENT_GIVEN = "Given";
private static final String VCARD3_ELEMENT_ORGNAME = "Orgname";

// vCard 4 element names
private static final String VCARD4_ELEMENT_HAS_NAME = "hasName";
private static final String VCARD4_ELEMENT_FAMILY_NAME = "family-name";
private static final String VCARD4_ELEMENT_GIVEN_NAME = "given-name";
private static final String VCARD4_ELEMENT_HAS_EMAIL = "hasEmail";
private static final String VCARD4_ELEMENT_ORGANIZATION_NAME = "organization-name";

/**
*
Expand Down Expand Up @@ -294,9 +313,9 @@ private NODE_COLOR isValidVCard(XMLNode xmlNode) {
// nothing really mandatory there !!

// vCard:N->vCard:Family|vCard:given vCard:EMAIL vCard:ORG->vCard:Orgname
XMLNode nameNode = xmlNode.getChildElement("N", Creator.URI_RDF_VCARD_NS);
XMLNode emailNode = xmlNode.getChildElement("EMAIL", Creator.URI_RDF_VCARD_NS);
XMLNode orgNode = xmlNode.getChildElement("ORG", Creator.URI_RDF_VCARD_NS);
XMLNode nameNode = xmlNode.getChildElement(VCARD3_ELEMENT_N, Creator.URI_RDF_VCARD_NS);
XMLNode emailNode = xmlNode.getChildElement(VCARD3_ELEMENT_EMAIL, Creator.URI_RDF_VCARD_NS);
XMLNode orgNode = xmlNode.getChildElement(VCARD3_ELEMENT_ORG, Creator.URI_RDF_VCARD_NS);

// at least one of these three nodes is present
if (nameNode != null || emailNode != null || orgNode != null) {
Expand Down Expand Up @@ -527,9 +546,8 @@ private void readRDFHistory(SBase contextSBase, XMLNode descriptionNode)
{
logger.debug("readRDFHistory - called");

// get the dc:creator children
// dc:creator children (old vCard format)
List<XMLNode> creatorNodes = descriptionNode.getChildElements("creator", JSBML.URI_PURL_ELEMENTS);

if (creatorNodes != null && creatorNodes.size() > 0)
{
for (XMLNode creator : creatorNodes)
Expand All @@ -538,6 +556,16 @@ private void readRDFHistory(SBase contextSBase, XMLNode descriptionNode)
}
}

// dcterms:creator children (vCard4 format as written by libSBML)
List<XMLNode> dctermsCreatorNodes = descriptionNode.getChildElements("creator", JSBML.URI_PURL_TERMS);
if (dctermsCreatorNodes != null && dctermsCreatorNodes.size() > 0)
{
for (XMLNode creator : dctermsCreatorNodes)
{
readCreator(contextSBase, creator);
}
}

// getting the dates children
List<XMLNode> createdNodes = descriptionNode.getChildElements("created", JSBML.URI_PURL_TERMS);
List<XMLNode> modifiedNodes = descriptionNode.getChildElements("modified", JSBML.URI_PURL_TERMS);
Expand Down Expand Up @@ -721,21 +749,21 @@ private void readCreatedDate(SBase contextSBase, XMLNode createdNode)
}

/**
* Reads the 'dc:creator' part of the SBML RDF annotation into {@link Creator}s.
* Reads the 'dc:creator' / 'dcterms:creator' part of the SBML RDF annotation into {@link Creator}s.
*
* @param contextSBase the {@link SBase} in which we will add the {@link Creator}s.
* @param creatorNode the 'dc:creator' {@link XMLNode} that contain the definition of the creator vCards.
* @param creatorNode the 'dc:creator' or 'dcterms:creator' {@link XMLNode} that contain the definition of the creator vCards.
*/
private void readCreator(SBase contextSBase, XMLNode creatorNode)
{
logger.debug("readCreator called");

XMLNode bagNode = creatorNode.getChildElement("Bag", Annotation.URI_RDF_SYNTAX_NS);

if (bagNode == null) {
return;
}

List<XMLNode> liNodes = bagNode.getChildElements("li", Annotation.URI_RDF_SYNTAX_NS);

for (XMLNode liNode : liNodes)
Expand All @@ -749,16 +777,16 @@ private void readCreator(SBase contextSBase, XMLNode creatorNode)
contextSBase.getHistory().addCreator(creator);
creator.putUserObject(JSBML.READING_IN_PROGRESS, Boolean.TRUE);

// get name information
List<XMLNode> nameNodes = liNode.getChildElements("N", Creator.URI_RDF_VCARD_NS);
// ---- vCard3 name (N/Family/Given) ----
boolean nameFound = false;
List<XMLNode> nameNodes = liNode.getChildElements(VCARD3_ELEMENT_N, Creator.URI_RDF_VCARD_NS);

if (nameNodes != null && nameNodes.size() == 1)
{
XMLNode nameNode = nameNodes.get(0);

// get family name information
List<XMLNode> famillyNameNodes = nameNode.getChildElements("Family", Creator.URI_RDF_VCARD_NS);

// family name
List<XMLNode> famillyNameNodes = nameNode.getChildElements(VCARD3_ELEMENT_FAMILY, Creator.URI_RDF_VCARD_NS);
if (famillyNameNodes != null & famillyNameNodes.size() == 1)
{
XMLNode famillyNode = famillyNameNodes.get(0);
Expand All @@ -781,9 +809,8 @@ private void readCreator(SBase contextSBase, XMLNode creatorNode)
logger.debug("readCreator - did not found one and only one 'Family' node: " + famillyNameNodes);
}

// get first name information
List<XMLNode> firstNameNodes = nameNode.getChildElements("Given", Creator.URI_RDF_VCARD_NS);

// given name
List<XMLNode> firstNameNodes = nameNode.getChildElements(VCARD3_ELEMENT_GIVEN, Creator.URI_RDF_VCARD_NS);
if (firstNameNodes != null & firstNameNodes.size() == 1)
{
XMLNode firstNameNode = firstNameNodes.get(0);
Expand All @@ -808,14 +835,51 @@ private void readCreator(SBase contextSBase, XMLNode creatorNode)

nameNode.removeAttr("parseType");
removeXmlNodeIfEmpty(nameNode);
nameFound = true;
}
else
{
logger.debug("readCreator - did not found one and only one 'N' node: " + nameNodes);
}

// get email information
List<XMLNode> emailNodes = liNode.getChildElements("EMAIL", Creator.URI_RDF_VCARD_NS);
// ---- vCard4 name (hasName/family-name/given-name) ----
if (!nameFound)
{
List<XMLNode> v4NameNodes = liNode.getChildElements(VCARD4_ELEMENT_HAS_NAME, VCARD4_NS);
if (v4NameNodes != null && v4NameNodes.size() == 1)
{
XMLNode hasNameNode = v4NameNodes.get(0);

List<XMLNode> familyNodes = hasNameNode.getChildElements(VCARD4_ELEMENT_FAMILY_NAME, VCARD4_NS);
if (familyNodes != null && familyNodes.size() == 1)
{
XMLNode familyNode = familyNodes.get(0);
int textNodeIndex = findFirstNonEmptyTextElementIndex(familyNode);
if (textNodeIndex != -1)
{
String familyName = familyNode.getChildAt(textNodeIndex).getCharacters().trim();
logger.debug("readCreator (vCard4) - family name = " + familyName);
creator.setFamilyName(familyName);
}
}

List<XMLNode> givenNodes = hasNameNode.getChildElements(VCARD4_ELEMENT_GIVEN_NAME, VCARD4_NS);
if (givenNodes != null && givenNodes.size() == 1)
{
XMLNode givenNode = givenNodes.get(0);
int textNodeIndex = findFirstNonEmptyTextElementIndex(givenNode);
if (textNodeIndex != -1)
{
String givenName = givenNode.getChildAt(textNodeIndex).getCharacters().trim();
logger.debug("readCreator (vCard4) - given name = " + givenName);
creator.setGivenName(givenName);
}
}
}
}

// ---- email (vCard3: EMAIL) ----
List<XMLNode> emailNodes = liNode.getChildElements(VCARD3_ELEMENT_EMAIL, Creator.URI_RDF_VCARD_NS);

if (emailNodes != null && emailNodes.size() == 1)
{
Expand All @@ -839,15 +903,34 @@ private void readCreator(SBase contextSBase, XMLNode creatorNode)
logger.debug("readCreator - did not found one and only one 'EMAIL' node : " + emailNodes);
}

// get organization information
List<XMLNode> orgNodes = liNode.getChildElements("ORG", Creator.URI_RDF_VCARD_NS);
// ---- email (vCard4: hasEmail) ----
if (!creator.isSetEmail())
{
List<XMLNode> v4EmailNodes = liNode.getChildElements(VCARD4_ELEMENT_HAS_EMAIL, VCARD4_NS);

if (v4EmailNodes != null && v4EmailNodes.size() == 1)
{
XMLNode emailNode = v4EmailNodes.get(0);
int textNodeIndex = findFirstNonEmptyTextElementIndex(emailNode);

if (textNodeIndex != -1)
{
String email = emailNode.getChildAt(textNodeIndex).getCharacters().trim();
logger.debug("readCreator (vCard4) - email = " + email);
creator.setEmail(email);
}
}
}

// ---- organisation (vCard3: ORG/Orgname) ----
List<XMLNode> orgNodes = liNode.getChildElements(VCARD3_ELEMENT_ORG, Creator.URI_RDF_VCARD_NS);

if (orgNodes != null && orgNodes.size() == 1)
{
XMLNode firstNode = orgNodes.get(0);

// get Organization name information
List<XMLNode> orgNameNodes = firstNode.getChildElements("Orgname", Creator.URI_RDF_VCARD_NS);
List<XMLNode> orgNameNodes = firstNode.getChildElements(VCARD3_ELEMENT_ORGNAME, Creator.URI_RDF_VCARD_NS);


if (orgNameNodes != null & orgNameNodes.size() == 1)
{
Expand Down Expand Up @@ -879,12 +962,30 @@ private void readCreator(SBase contextSBase, XMLNode creatorNode)
logger.debug("readCreator - did not found one and only one 'ORG' node : " + orgNodes);
}

// ---- organisation (vCard4: organization-name) ----
if (!creator.isSetOrganisation())
{
List<XMLNode> v4OrgNodes = liNode.getChildElements(VCARD4_ELEMENT_ORGANIZATION_NAME, VCARD4_NS);

if (v4OrgNodes != null && v4OrgNodes.size() == 1)
{
XMLNode orgNode = v4OrgNodes.get(0);
int textNodeIndex = findFirstNonEmptyTextElementIndex(orgNode);

if (textNodeIndex != -1)
{
String orgName = orgNode.getChildAt(textNodeIndex).getCharacters().trim();
logger.debug("readCreator (vCard4) - organization-name = " + orgName);
creator.setOrganisation(orgName);
}
}
}

liNode.removeAttr("parseType");
boolean nodeRemoved = removeXmlNodeIfEmpty(liNode);

if (!nodeRemoved)
{
// remove and store the 'li' XMLNode to be able to keep any additional information part of the SBML specifications or not.
liNode.removeFromParent();
creator.putUserObject(CUSTOM_RDF, liNode);
}
Expand Down Expand Up @@ -1653,34 +1754,34 @@ private void writeCreators(History history, XMLNode descriptionNode)

if (creator.isSetFamilyName() || creator.isSetGivenName())
{
XMLNode vCardNNode = getOrCreate(liNode, "N", Creator.URI_RDF_VCARD_NS, "vCard");
XMLNode vCardNNode = getOrCreate(liNode, VCARD3_ELEMENT_N, Creator.URI_RDF_VCARD_NS, "vCard");
vCardNNode.addAttr("parseType", "Resource", Annotation.URI_RDF_SYNTAX_NS, "rdf");

if (creator.isSetFamilyName())
{
XMLNode vCardFamilyNode = getOrCreate(vCardNNode, "Family", Creator.URI_RDF_VCARD_NS, "vCard");
vCardFamilyNode.insertChild(0, new XMLNode(creator.getFamilyName()));
XMLNode vCardFamilyNode = getOrCreate(vCardNNode, VCARD3_ELEMENT_FAMILY, Creator.URI_RDF_VCARD_NS, "vCard");
vCardFamilyNode.insertChild(0, new XMLNode(creator.getFamilyName()));
}

if (creator.isSetGivenName())
{
XMLNode vCardGivenNode = getOrCreate(vCardNNode, "Given", Creator.URI_RDF_VCARD_NS, "vCard");
XMLNode vCardGivenNode = getOrCreate(vCardNNode, VCARD3_ELEMENT_GIVEN, Creator.URI_RDF_VCARD_NS, "vCard");
vCardGivenNode.insertChild(0, new XMLNode(creator.getGivenName()));
}
}

if (creator.isSetEmail())
{
XMLNode vCardEmailNode = getOrCreate(liNode, "EMAIL", Creator.URI_RDF_VCARD_NS, "vCard");
XMLNode vCardEmailNode = getOrCreate(liNode, VCARD3_ELEMENT_EMAIL, Creator.URI_RDF_VCARD_NS, "vCard");
vCardEmailNode.insertChild(0, new XMLNode(creator.getEmail()));
}

if (creator.isSetOrganisation())
{
XMLNode vCardOrgNode = getOrCreate(liNode, "ORG", Creator.URI_RDF_VCARD_NS, "vCard");
XMLNode vCardOrgNode = getOrCreate(liNode, VCARD3_ELEMENT_ORG, Creator.URI_RDF_VCARD_NS, "vCard");
vCardOrgNode.addAttr("parseType", "Resource", Annotation.URI_RDF_SYNTAX_NS, "rdf");

XMLNode vCardOrgNameNode = getOrCreate(vCardOrgNode, "Orgname", Creator.URI_RDF_VCARD_NS, "vCard");
XMLNode vCardOrgNameNode = getOrCreate(vCardOrgNode, VCARD3_ELEMENT_ORGNAME, Creator.URI_RDF_VCARD_NS, "vCard");
vCardOrgNameNode.insertChild(0, new XMLNode(creator.getOrganisation()));
}

Expand Down