if ( oboObj.getName() != null && oboObj.getName().length() <= AnnotatedObject.MAX_SHORT_LABEL_LEN ) { return oboObj.getName(); } else if ( oboObj.getName() != null && oboObj.getName().length() > AnnotatedObject.MAX_SHORT_LABEL_LEN ) { if ( log.isDebugEnabled() ) log.debug( "No shortLabel for " + oboObj.getName() ); return oboObj.getName().substring( 0, AnnotatedObject.MAX_SHORT_LABEL_LEN );
trm.setName(safeTrim(obj.getName()));
trm.setName(safeTrim(obj.getName()));
private static void findParents( Collection<OBOObject> parents, OBOObject oboObject, boolean recursive, Set<String> processedIdSet ) { final String id = oboObject.getID(); if( processedIdSet.contains( id ) ) { return; // cuts infinite loop as the ontology can have cycles. } else { processedIdSet.add( id ); } for ( Link parentLink : oboObject.getParents() ) { OBOObject parent = (OBOObject) parentLink.getParent(); parents.add( parent ); if( recursive && !parent.getParents().isEmpty() ) { if ( log.isTraceEnabled() ) { log.trace( "Calling recursively findParent( "+ parent.getID() +" - "+ parent.getName() +" ) ..." ); } findParents( parents, parent, recursive, processedIdSet ); } } }
trm.setName(safeTrim(obj.getName(), true));
private static void findChildren( Collection<OBOObject> children, OBOObject oboObject, boolean recursive, Set<String> processedIdSet ) { final String id = oboObject.getID(); if( processedIdSet.contains( id ) ) { return; // cuts infinite loop as the ontology can have cycles. } else { processedIdSet.add( id ); } for ( Link childLink : oboObject.getChildren() ) { OBOObject child = (OBOObject) childLink.getChild(); children.add( child ); if( recursive && !child.getChildren().isEmpty() ) { if ( log.isTraceEnabled() ) { log.trace( "Calling recursively findChildren( "+ child.getID() +" - "+ child.getName() +" ) ..." ); } findChildren( children, child, recursive, processedIdSet ); } } }
log.debug( " targetTerm ID: " + targetTerm.getID() + " Name: " + targetTerm.getName() + " Children: " + targetTerm.getChildren().size() ); log.debug( " sourceTerm ID: " + sourceTerm.getID() + " Name: " + sourceTerm.getName() + " Children: " + sourceTerm.getChildren().size() ); log.debug( " sourceChildren size: " + children.size() ); log.debug( " targetTermAfter " + targetTermAfter.getID() + " " + targetTermAfter.getName() + " " + targetTermAfter.getChildren().size() );
try { if ( log.isTraceEnabled() ) log.trace( "ID ->" + oboObj.getID() + " Name ->" + oboObj.getName() ); cvObject.setFullName( oboObj.getName() ); if (category.getName().equalsIgnoreCase(oboCat.getName())) { if (log.isTraceEnabled()) { log.trace("Adding child after subset check: " + childObj.getID() + " " + childObj.getName());