/** * Copyright (C) 2012-2013 Selventa, Inc. * * This file is part of the OpenBEL Framework. * * This program 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, either version 3 of the License, or * (at your option) any later version. * * The OpenBEL Framework is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public * License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>. * * Additional Terms under LGPL v3: * * This license does not authorize you and you are prohibited from using the * name, trademarks, service marks, logos or similar indicia of Selventa, Inc., * or, in the discretion of other licensors or authors of the program, the * name, trademarks, service marks, logos or similar indicia of such authors or * licensors, in any marketing or advertising materials relating to your * distribution of the program or any covered product. This restriction does * not waive or limit your obligation to keep intact all copyright notices set * forth in the program as delivered to you. * * If you distribute the program in whole or in part, or any modified version * of the program, and you assume contractual liability to the recipient with * respect to the program or modified version, then you will indemnify the * authors and licensors of the program for any liabilities that these * contractual assumptions directly impose on those licensors and authors. */ package org.openbel.framework.core.annotation; import static java.lang.String.format; import static org.openbel.framework.common.Strings.INVALID_ANNOTATIONS; import static org.openbel.framework.common.util.ValidationUtilities.*; import java.util.ArrayList; import java.util.List; import java.util.regex.PatternSyntaxException; import org.openbel.framework.common.model.Annotation; import org.openbel.framework.common.model.AnnotationDefinition; import org.openbel.framework.common.model.Document; import org.openbel.framework.common.model.Statement; import org.openbel.framework.core.compiler.SymbolWarning; /** * Default implementation of {@link AnnotationService} * * @author Steve Ungerer */ public class DefaultAnnotationService implements AnnotationService { /** * {@inheritDoc} */ @Override public void verify(Annotation annotation) throws AnnotationSyntaxWarning { try { if (isValid(annotation)) return; } catch (PatternSyntaxException e) { // ignore it } // Pattern syntax is bad or annotation is not valid // The annotation is defined by its annotation definition. AnnotationDefinition annodef = annotation.getDefinition(); String annodefID = annodef.getId(); String url = annodef.getURL(); String annoval = annotation.getValue(); if (url == null) { throw new AnnotationSyntaxWarning(annodefID, annoval); } throw new AnnotationSyntaxWarning(url, annodefID, annoval); } /** * {@inheritDoc} */ @Override public void verify(Statement statement) throws SymbolWarning { if (statement.getAnnotationGroup() == null) { return; } List<AnnotationSyntaxWarning> l = new ArrayList<AnnotationSyntaxWarning>(); for (Annotation annotation : statement.getAnnotationGroup() .getAnnotations()) { try { verify(annotation); } catch (AnnotationSyntaxWarning asw) { l.add(asw); } } if (!l.isEmpty()) { final String name = statement.toBELLongForm(); final String fmt = INVALID_ANNOTATIONS; final String msg = format(fmt, l.size()); throw new SymbolWarning(name, msg, l); } } /** * {@inheritDoc} */ @Override public void verify(Document document) throws SymbolWarning { List<AnnotationSyntaxWarning> l = new ArrayList<AnnotationSyntaxWarning>(); for (Annotation annotation : document.getAllAnnotations()) { try { verify(annotation); } catch (AnnotationSyntaxWarning asw) { l.add(asw); } } if (!l.isEmpty()) { final String name = document.getName(); final String fmt = INVALID_ANNOTATIONS; final String msg = format(fmt, l.size()); throw new SymbolWarning(name, msg, l); } } }