public Collection<IdentifiedObject> getObsoleteOBOObjects() { Collection<IdentifiedObject> ObsoloteOboObjects = new ArrayList<IdentifiedObject>(); Collection<IdentifiedObject> allOBOObjects = oboSession.getObjects(); for ( IdentifiedObject identifiedObject : allOBOObjects ) { if ( identifiedObject.getID().startsWith( "MI:" ) ) { if ( identifiedObject instanceof OBOObject ) { OBOObject obj = ( OBOObject ) identifiedObject; String defText = obj.getDefinition(); if ( obj.isObsolete() || defText.contains( "\nOBSOLETE" ) ) { ObsoloteOboObjects.add( identifiedObject ); } } } } return ObsoloteOboObjects; }
if ( oboObj.getDefinition() != null ) { String definition = oboObj.getDefinition(); if ( log.isDebugEnabled() ) log.debug( " Line Break in Definition--special case MI: " +oboObj.getID()+" Defintion: " +oboObj.getDefinition() ); CvTopic definitionTopic = CvObjectUtils.createCvObject( institution, CvTopic.class, null, CvTopic.DEFINITION ); cvObject.addAnnotation( new Annotation( institution, definitionTopic, oboObj.getDefinition() ) ); cvObject.addAnnotation( new Annotation( institution, definitionTopic, oboObj.getDefinition() ) );
trm.setDefinition(safeTrim(obj.getDefinition())); if (trm.getDefinition() != null && trm.getDefinition().length() > 4000) { logger.warn("term definition longer than allowed database column length - truncating" + trm.getIdentifier());
trm.setDefinition(safeTrim(obj.getDefinition())); if (trm.getDefinition() != null && trm.getDefinition().length() > 4000) { logger.warn("term definition longer than allowed database column length - truncating" + trm.getIdentifier());
trm.setDefinition(safeTrim(obj.getDefinition(), true)); if (trm.getDefinition() != null && trm.getDefinition().length() > 4000) { logger.warn("term definition longer than allowed database column length - truncating" + trm.getIdentifier());