private static Transformer getTransformer() throws TransformerException {
if (_transformer == null) {
TransformerFactory factory = TransformerFactory.newInstance();
_transformer = factory.newTransformer();
}
return _transformer;
}
protected void doGet(HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException {
try {
DateFormat df = DateFormat.getDateTimeInstance();
String titleStr = "C3P0 Status - " + df.format(new Date());
DocumentBuilderFactory fact = DocumentBuilderFactory.newInstance();
DocumentBuilder db = fact.newDocumentBuilder();
Document doc = db.newDocument();
Element htmlElem = doc.createElement("html");
Element headElem = doc.createElement("head");
Element titleElem = doc.createElement("title");
titleElem.appendChild(doc.createTextNode(titleStr));
Element bodyElem = doc.createElement("body");
Element h1Elem = doc.createElement("h1");
h1Elem.appendChild(doc.createTextNode(titleStr));
Element h3Elem = doc.createElement("h3");
h3Elem.appendChild(doc.createTextNode("PooledDataSources"));
Element pdsDlElem = doc.createElement("dl");
pdsDlElem.setAttribute("class", "PooledDataSources");
for (Iterator ii = C3P0Registry.getPooledDataSources().iterator(); ii.hasNext(); ) {
PooledDataSource pds = (PooledDataSource) ii.next();
StatusReporter sr = findStatusReporter(pds, doc);
pdsDlElem.appendChild(sr.reportDtElem());
pdsDlElem.appendChild(sr.reportDdElem());
}
headElem.appendChild(titleElem);
htmlElem.appendChild(headElem);
bodyElem.appendChild(h1Elem);
bodyElem.appendChild(h3Elem);
bodyElem.appendChild(pdsDlElem);
htmlElem.appendChild(bodyElem);
res.setContentType("application/xhtml+xml");
TransformerFactory tf = TransformerFactory.newInstance();
Transformer transformer = tf.newTransformer();
Source src = new DOMSource(doc);
Result result = new StreamResult(res.getOutputStream());
transformer.transform(src, result);
} catch (IOException e) {
throw e;
} catch (Exception e) {
throw new ServletException(e);
}
}
void outputDocument(Writer out) throws Exception {
// Set up the output transformer
TransformerFactory transfac = TransformerFactory.newInstance();
Transformer trans = transfac.newTransformer();
// trans.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
trans.setOutputProperty(OutputKeys.INDENT, "yes");
trans.setOutputProperty(OutputKeys.METHOD, "html");
// Print the DOM node
StreamResult result = new StreamResult(out);
DOMSource source = new DOMSource(this.document);
trans.transform(source, result);
}
/**
* http://www.atmarkit.co.jp/fxml/rensai2/xmltool04/02.html
*
* @return
*/
private static Transformer getTransformer() {
if (s_transformer == null) {
TransformerFactory transFactory = TransformerFactory.newInstance();
try {
s_transformer = transFactory.newTransformer();
} catch (TransformerConfigurationException e) {
}
s_transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
s_transformer.setOutputProperty(OutputKeys.INDENT, "yes");
} // if
return s_transformer;
}
/** Check for required facilities. If not available, an exception will be thrown. */
public TemplatesPool(boolean templateCaching) throws Exception {
final TransformerFactory tFactory = TransformerFactory.newInstance();
final String processorClass = tFactory.getClass().getName();
/*
* Only report XSLT processor class once.
*/
if (!reportedProcessors.contains(processorClass)) {
logger.info("XSLT transformer factory: " + processorClass);
reportedProcessors.add(processorClass);
}
if (!tFactory.getFeature(SAXSource.FEATURE) || !tFactory.getFeature(SAXResult.FEATURE)) {
throw new Exception("Required source types not supported by the transformer factory.");
}
if (!tFactory.getFeature(SAXResult.FEATURE) || !tFactory.getFeature(StreamResult.FEATURE)) {
throw new Exception("Required result types not supported by the transformer factory.");
}
if (!(tFactory instanceof SAXTransformerFactory)) {
throw new Exception(
"TransformerFactory not an instance of SAXTransformerFactory: "
+ tFactory.getClass().getName());
}
this.tFactory = ((SAXTransformerFactory) tFactory);
this.tFactory.setErrorListener(new StylesheetErrorListener());
this.templateCaching = templateCaching;
}
/**
* Loads nested schema type definitions from wsdl.
*
* @throws IOException
* @throws WSDLException
* @throws TransformerFactoryConfigurationError
* @throws TransformerException
* @throws TransformerConfigurationException
*/
private void loadSchemas()
throws WSDLException, IOException, TransformerConfigurationException, TransformerException,
TransformerFactoryConfigurationError {
Definition definition =
WSDLFactory.newInstance().newWSDLReader().readWSDL(wsdl.getFile().getAbsolutePath());
Types types = definition.getTypes();
List<?> schemaTypes = types.getExtensibilityElements();
for (Object schemaObject : schemaTypes) {
if (schemaObject instanceof SchemaImpl) {
SchemaImpl schema = (SchemaImpl) schemaObject;
inheritNamespaces(schema, definition);
ByteArrayOutputStream bos = new ByteArrayOutputStream();
Source source = new DOMSource(schema.getElement());
Result result = new StreamResult(bos);
TransformerFactory.newInstance().newTransformer().transform(source, result);
Resource schemaResource = new ByteArrayResource(bos.toByteArray());
schemas.add(schemaResource);
if (definition
.getTargetNamespace()
.equals(schema.getElement().getAttribute("targetNamespace"))) {
setXsd(schemaResource);
}
} else {
log.warn("Found unsupported schema type implementation " + schemaObject.getClass());
}
}
}
/**
* Method removes a Spring bean definition from the XML application context file. Bean definition
* is identified by its id or bean name.
*
* @param project
* @param id
*/
public void removeBeanDefinition(File configFile, Project project, String id) {
Source xsltSource;
Source xmlSource;
try {
xsltSource =
new StreamSource(new ClassPathResource("transform/delete-bean.xsl").getInputStream());
xsltSource.setSystemId("delete-bean");
List<File> configFiles = new ArrayList<>();
configFiles.add(configFile);
configFiles.addAll(getConfigImports(configFile, project));
for (File file : configFiles) {
xmlSource = new StringSource(FileUtils.readToString(new FileInputStream(configFile)));
// create transformer
Transformer transformer = transformerFactory.newTransformer(xsltSource);
transformer.setParameter("bean_id", id);
// transform
StringResult result = new StringResult();
transformer.transform(xmlSource, result);
FileUtils.writeToFile(format(result.toString(), project.getSettings().getTabSize()), file);
return;
}
} catch (IOException e) {
throw new ApplicationRuntimeException(UNABLE_TO_READ_TRANSFORMATION_SOURCE, e);
} catch (TransformerException e) {
throw new ApplicationRuntimeException(FAILED_TO_UPDATE_BEAN_DEFINITION, e);
}
}
/**
* Marshal jaxb element and try to perform basic formatting like namespace clean up and attribute
* formatting with xsl transformation.
*
* @param jaxbElement
* @return
*/
private String getXmlContent(Object jaxbElement) {
StringResult jaxbContent = new StringResult();
springBeanMarshaller.marshal(jaxbElement, jaxbContent);
Source xsltSource;
try {
xsltSource =
new StreamSource(new ClassPathResource("transform/format-bean.xsl").getInputStream());
Transformer transformer = transformerFactory.newTransformer(xsltSource);
// transform
StringResult result = new StringResult();
transformer.transform(new StringSource(jaxbContent.toString()), result);
if (log.isDebugEnabled()) {
log.debug("Created bean definition:\n" + result.toString());
}
return result.toString();
} catch (IOException e) {
throw new ApplicationRuntimeException(UNABLE_TO_READ_TRANSFORMATION_SOURCE, e);
} catch (TransformerException e) {
throw new ApplicationRuntimeException(FAILED_TO_UPDATE_BEAN_DEFINITION, e);
}
}
/**
* Method adds a new Spring bean definition to the XML application context file.
*
* @param project
* @param jaxbElement
*/
public void addBeanDefinition(File configFile, Project project, Object jaxbElement) {
Source xsltSource;
Source xmlSource;
try {
xsltSource =
new StreamSource(new ClassPathResource("transform/add-bean.xsl").getInputStream());
xsltSource.setSystemId("add-bean");
xmlSource = new StringSource(FileUtils.readToString(new FileInputStream(configFile)));
// create transformer
Transformer transformer = transformerFactory.newTransformer(xsltSource);
transformer.setParameter(
"bean_content",
getXmlContent(jaxbElement)
.replaceAll("(?m)^(.)", getTabs(1, project.getSettings().getTabSize()) + "$1"));
// transform
StringResult result = new StringResult();
transformer.transform(xmlSource, result);
FileUtils.writeToFile(
format(result.toString(), project.getSettings().getTabSize()), configFile);
return;
} catch (IOException e) {
throw new ApplicationRuntimeException(UNABLE_TO_READ_TRANSFORMATION_SOURCE, e);
} catch (TransformerException e) {
throw new ApplicationRuntimeException(FAILED_TO_UPDATE_BEAN_DEFINITION, e);
}
}
/**
* Writes an XML file from a Document object.
*
* @param doc the Document object to be written to file
* @param file the file to be written
* @throws IOException
* @author Klaus Meffert
* @since 2.0
*/
public static void writeFile(Document doc, File file) throws IOException {
// Use a Transformer for output
TransformerFactory tFactory = TransformerFactory.newInstance();
Transformer transformer;
try {
transformer = tFactory.newTransformer();
} catch (TransformerConfigurationException tex) {
throw new IOException(tex.getMessage());
}
DOMSource source = new DOMSource(doc);
FileOutputStream fos = new FileOutputStream(file);
StreamResult result = new StreamResult(fos);
try {
transformer.transform(source, result);
fos.close();
} catch (TransformerException tex) {
throw new IOException(tex.getMessage());
}
}
/**
* Save the XML description of the circuit
*
* @param output an output stream to write in
* @return true if the dump was successful, false either
*/
public boolean dumpToXml(OutputStream output) {
Document doc;
Element root;
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
try {
builder = factory.newDocumentBuilder();
doc = builder.newDocument();
} catch (ParserConfigurationException pce) {
System.err.println("dumpToXmlFile: unable to write XML save file.");
return false;
}
root = doc.createElement("Circuit");
root.setAttribute("name", this.getName());
for (iterNodes = this.nodes.iterator(); iterNodes.hasNext(); )
iterNodes.next().dumpToXml(doc, root);
root.normalize();
doc.appendChild(root);
try {
TransformerFactory tffactory = TransformerFactory.newInstance();
Transformer transformer = tffactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(output);
transformer.transform(source, result);
} catch (TransformerConfigurationException tce) {
System.err.println("dumpToXmlFile: Configuration Transformer exception.");
return false;
} catch (TransformerException te) {
System.err.println("dumpToXmlFile: Transformer exception.");
return false;
}
return true;
}
private Transformer buildTransformer(String name, File xslDir, TransformerFactory tf)
throws Exception {
Transformer tr =
tf.newTransformer(
new StreamSource(
new FileReader(xslDir.getAbsolutePath() + File.separatorChar + name + ".xsl")));
tr.setOutputProperty(OutputKeys.INDENT, "yes");
tr.setOutputProperty(OutputKeys.METHOD, "html");
tr.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
return tr;
}
@PostConstruct
protected void init() {
transformerFactory.setURIResolver(
new URIResolver() {
@Override
public Source resolve(String href, String base) throws TransformerException {
try {
return new StreamSource(new ClassPathResource("transform/" + href).getInputStream());
} catch (IOException e) {
throw new TransformerException("Failed to resolve uri: " + href, e);
}
}
});
}
/**
* Method updates existing Spring bean definitions in a XML application context file. Bean
* definition is identified by its type defining class.
*
* @param project
* @param type
* @param jaxbElement
*/
public void updateBeanDefinitions(
File configFile, Project project, Class<?> type, Object jaxbElement) {
Source xsltSource;
Source xmlSource;
try {
xsltSource =
new StreamSource(
new ClassPathResource("transform/update-bean-type.xsl").getInputStream());
xsltSource.setSystemId("update-bean");
List<File> configFiles = new ArrayList<>();
configFiles.add(configFile);
configFiles.addAll(getConfigImports(configFile, project));
LSParser parser = XMLUtils.createLSParser();
GetSpringBeansFilter getBeanFilter = new GetSpringBeansFilter(type, null);
parser.setFilter(getBeanFilter);
for (File file : configFiles) {
parser.parseURI(file.toURI().toString());
if (!CollectionUtils.isEmpty(getBeanFilter.getBeanDefinitions())) {
xmlSource = new StringSource(FileUtils.readToString(new FileInputStream(file)));
String beanElement = type.getAnnotation(XmlRootElement.class).name();
String beanNamespace = type.getPackage().getAnnotation(XmlSchema.class).namespace();
// create transformer
Transformer transformer = transformerFactory.newTransformer(xsltSource);
transformer.setParameter("bean_element", beanElement);
transformer.setParameter("bean_namespace", beanNamespace);
transformer.setParameter(
"bean_content",
getXmlContent(jaxbElement)
.replaceAll("(?m)^(\\s<)", getTabs(1, project.getSettings().getTabSize()) + "$1")
.replaceAll("(?m)^(</)", getTabs(1, project.getSettings().getTabSize()) + "$1"));
// transform
StringResult result = new StringResult();
transformer.transform(xmlSource, result);
FileUtils.writeToFile(
format(result.toString(), project.getSettings().getTabSize()), file);
return;
}
}
} catch (IOException e) {
throw new ApplicationRuntimeException(UNABLE_TO_READ_TRANSFORMATION_SOURCE, e);
} catch (TransformerException e) {
throw new ApplicationRuntimeException(FAILED_TO_UPDATE_BEAN_DEFINITION, e);
}
}
public static boolean writeXML(File file, Document document) {
javax.xml.transform.Transformer transformer = null;
try {
transformer = TransformerFactory.newInstance().newTransformer();
} catch (TransformerConfigurationException e) {
e.printStackTrace();
return false;
}
transformer.setOutputProperty("indent", "yes");
transformer.setOutputProperty(OutputPropertiesFactory.S_KEY_INDENT_AMOUNT, "2");
transformer.setOutputProperty("encoding", "UTF-8");
try {
transformer.transform(new DOMSource(document), new StreamResult(file));
} catch (TransformerException e) {
e.printStackTrace();
return false;
}
return true;
}
public void init(ServletConfig config) throws ServletException {
super.init(config);
context = config.getServletContext();
TextProcessor tp = new CaseFolder();
try {
wikipedia =
new Wikipedia(
context.getInitParameter("mysql_server"),
context.getInitParameter("mysql_database"),
context.getInitParameter("mysql_user"),
context.getInitParameter("mysql_password"));
} catch (Exception e) {
throw new ServletException("Could not connect to wikipedia database.");
}
// Escaper escaper = new Escaper() ;
definer = new Definer(this);
comparer = new Comparer(this);
searcher = new Searcher(this);
try {
wikifier = new Wikifier(this, tp);
} catch (Exception e) {
System.err.println("Could not initialize wikifier");
}
try {
File dataDirectory = new File(context.getInitParameter("data_directory"));
if (!dataDirectory.exists() || !dataDirectory.isDirectory()) {
throw new Exception();
}
cachingThread = new CacherThread(dataDirectory, tp);
cachingThread.start();
} catch (Exception e) {
throw new ServletException("Could not locate wikipedia data directory.");
}
try {
TransformerFactory tf = TransformerFactory.newInstance();
transformersByName = new HashMap<String, Transformer>();
transformersByName.put(
"help", buildTransformer("help", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"loading", buildTransformer("loading", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"search", buildTransformer("search", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"compare", buildTransformer("compare", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"wikify", buildTransformer("wikify", new File("/research/wikipediaminer/web/xsl"), tf));
Transformer serializer = TransformerFactory.newInstance().newTransformer();
serializer.setOutputProperty(OutputKeys.INDENT, "yes");
serializer.setOutputProperty(OutputKeys.METHOD, "xml");
serializer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
transformersByName.put("serializer", serializer);
} catch (Exception e) {
throw new ServletException("Could not load xslt library.");
}
}
/** @author Christoph Deppisch */
@Service
public class SpringBeanService {
public static final String FAILED_TO_UPDATE_BEAN_DEFINITION = "Failed to update bean definition";
public static final String UNABLE_TO_READ_TRANSFORMATION_SOURCE =
"Unable to read update bean definition transformation source";
@Autowired private SpringBeanMarshaller springBeanMarshaller;
/** XSLT transformer factory */
private TransformerFactory transformerFactory = TransformerFactory.newInstance();
/** Logger */
private static Logger log = LoggerFactory.getLogger(SpringBeanService.class);
@PostConstruct
protected void init() {
transformerFactory.setURIResolver(
new URIResolver() {
@Override
public Source resolve(String href, String base) throws TransformerException {
try {
return new StreamSource(new ClassPathResource("transform/" + href).getInputStream());
} catch (IOException e) {
throw new TransformerException("Failed to resolve uri: " + href, e);
}
}
});
}
/**
* Reads file import locations from Spring bean application context.
*
* @param project
* @return
*/
public List<File> getConfigImports(File configFile, Project project) {
LSParser parser = XMLUtils.createLSParser();
GetSpringImportsFilter filter = new GetSpringImportsFilter(configFile);
parser.setFilter(filter);
parser.parseURI(configFile.toURI().toString());
return filter.getImportedFiles();
}
/**
* Finds bean definition element by id and type in Spring application context and performs
* unmarshalling in order to return JaxB object.
*
* @param project
* @param id
* @param type
* @return
*/
public <T> T getBeanDefinition(File configFile, Project project, String id, Class<T> type) {
LSParser parser = XMLUtils.createLSParser();
GetSpringBeanFilter filter = new GetSpringBeanFilter(id, type);
parser.setFilter(filter);
List<File> configFiles = new ArrayList<>();
configFiles.add(configFile);
configFiles.addAll(getConfigImports(configFile, project));
for (File file : configFiles) {
parser.parseURI(file.toURI().toString());
if (filter.getBeanDefinition() != null) {
return createJaxbObjectFromElement(filter.getBeanDefinition());
}
}
return null;
}
/**
* Finds all bean definition elements by type in Spring application context and performs
* unmarshalling in order to return a list of JaxB object.
*
* @param project
* @param type
* @return
*/
public <T> List<T> getBeanDefinitions(File configFile, Project project, Class<T> type) {
return getBeanDefinitions(configFile, project, type, null);
}
/**
* Finds all bean definition elements by type and attribute values in Spring application context
* and performs unmarshalling in order to return a list of JaxB object.
*
* @param project
* @param type
* @param attributes
* @return
*/
public <T> List<T> getBeanDefinitions(
File configFile, Project project, Class<T> type, Map<String, String> attributes) {
List<T> beanDefinitions = new ArrayList<T>();
List<File> importedFiles = getConfigImports(configFile, project);
for (File importLocation : importedFiles) {
beanDefinitions.addAll(getBeanDefinitions(importLocation, project, type, attributes));
}
LSParser parser = XMLUtils.createLSParser();
GetSpringBeansFilter filter = new GetSpringBeansFilter(type, attributes);
parser.setFilter(filter);
parser.parseURI(configFile.toURI().toString());
for (Element element : filter.getBeanDefinitions()) {
beanDefinitions.add(createJaxbObjectFromElement(element));
}
return beanDefinitions;
}
/**
* Find all Spring bean definitions in application context for given bean type.
*
* @param project
* @param beanType
* @return
*/
public List<String> getBeanNames(File configFile, Project project, String beanType) {
List<SpringBean> beanDefinitions =
getBeanDefinitions(
configFile, project, SpringBean.class, Collections.singletonMap("class", beanType));
List<String> beanNames = new ArrayList<String>();
for (SpringBean beanDefinition : beanDefinitions) {
beanNames.add(beanDefinition.getId());
}
return beanNames;
}
/**
* Method adds a new Spring bean definition to the XML application context file.
*
* @param project
* @param jaxbElement
*/
public void addBeanDefinition(File configFile, Project project, Object jaxbElement) {
Source xsltSource;
Source xmlSource;
try {
xsltSource =
new StreamSource(new ClassPathResource("transform/add-bean.xsl").getInputStream());
xsltSource.setSystemId("add-bean");
xmlSource = new StringSource(FileUtils.readToString(new FileInputStream(configFile)));
// create transformer
Transformer transformer = transformerFactory.newTransformer(xsltSource);
transformer.setParameter(
"bean_content",
getXmlContent(jaxbElement)
.replaceAll("(?m)^(.)", getTabs(1, project.getSettings().getTabSize()) + "$1"));
// transform
StringResult result = new StringResult();
transformer.transform(xmlSource, result);
FileUtils.writeToFile(
format(result.toString(), project.getSettings().getTabSize()), configFile);
return;
} catch (IOException e) {
throw new ApplicationRuntimeException(UNABLE_TO_READ_TRANSFORMATION_SOURCE, e);
} catch (TransformerException e) {
throw new ApplicationRuntimeException(FAILED_TO_UPDATE_BEAN_DEFINITION, e);
}
}
/**
* Method removes a Spring bean definition from the XML application context file. Bean definition
* is identified by its id or bean name.
*
* @param project
* @param id
*/
public void removeBeanDefinition(File configFile, Project project, String id) {
Source xsltSource;
Source xmlSource;
try {
xsltSource =
new StreamSource(new ClassPathResource("transform/delete-bean.xsl").getInputStream());
xsltSource.setSystemId("delete-bean");
List<File> configFiles = new ArrayList<>();
configFiles.add(configFile);
configFiles.addAll(getConfigImports(configFile, project));
for (File file : configFiles) {
xmlSource = new StringSource(FileUtils.readToString(new FileInputStream(configFile)));
// create transformer
Transformer transformer = transformerFactory.newTransformer(xsltSource);
transformer.setParameter("bean_id", id);
// transform
StringResult result = new StringResult();
transformer.transform(xmlSource, result);
FileUtils.writeToFile(format(result.toString(), project.getSettings().getTabSize()), file);
return;
}
} catch (IOException e) {
throw new ApplicationRuntimeException(UNABLE_TO_READ_TRANSFORMATION_SOURCE, e);
} catch (TransformerException e) {
throw new ApplicationRuntimeException(FAILED_TO_UPDATE_BEAN_DEFINITION, e);
}
}
/**
* Method removes all Spring bean definitions of given type from the XML application context file.
*
* @param project
* @param type
*/
public void removeBeanDefinitions(File configFile, Project project, Class<?> type) {
Source xsltSource;
Source xmlSource;
try {
xsltSource =
new StreamSource(
new ClassPathResource("transform/delete-bean-type.xsl").getInputStream());
xsltSource.setSystemId("delete-bean");
List<File> configFiles = new ArrayList<>();
configFiles.add(configFile);
configFiles.addAll(getConfigImports(configFile, project));
for (File file : configFiles) {
xmlSource = new StringSource(FileUtils.readToString(new FileInputStream(configFile)));
String beanElement = type.getAnnotation(XmlRootElement.class).name();
String beanNamespace = type.getPackage().getAnnotation(XmlSchema.class).namespace();
// create transformer
Transformer transformer = transformerFactory.newTransformer(xsltSource);
transformer.setParameter("bean_element", beanElement);
transformer.setParameter("bean_namespace", beanNamespace);
// transform
StringResult result = new StringResult();
transformer.transform(xmlSource, result);
FileUtils.writeToFile(format(result.toString(), project.getSettings().getTabSize()), file);
return;
}
} catch (IOException e) {
throw new ApplicationRuntimeException(UNABLE_TO_READ_TRANSFORMATION_SOURCE, e);
} catch (TransformerException e) {
throw new ApplicationRuntimeException(FAILED_TO_UPDATE_BEAN_DEFINITION, e);
}
}
/**
* Method updates an existing Spring bean definition in a XML application context file. Bean
* definition is identified by its id or bean name.
*
* @param project
* @param id
* @param jaxbElement
*/
public void updateBeanDefinition(
File configFile, Project project, String id, Object jaxbElement) {
Source xsltSource;
Source xmlSource;
try {
xsltSource =
new StreamSource(new ClassPathResource("transform/update-bean.xsl").getInputStream());
xsltSource.setSystemId("update-bean");
List<File> configFiles = new ArrayList<>();
configFiles.add(configFile);
configFiles.addAll(getConfigImports(configFile, project));
LSParser parser = XMLUtils.createLSParser();
GetSpringBeanFilter getBeanFilter = new GetSpringBeanFilter(id, jaxbElement.getClass());
parser.setFilter(getBeanFilter);
for (File file : configFiles) {
parser.parseURI(file.toURI().toString());
if (getBeanFilter.getBeanDefinition() != null) {
xmlSource = new StringSource(FileUtils.readToString(new FileInputStream(file)));
// create transformer
Transformer transformer = transformerFactory.newTransformer(xsltSource);
transformer.setParameter("bean_id", id);
transformer.setParameter(
"bean_content",
getXmlContent(jaxbElement)
.replaceAll("(?m)^(\\s<)", getTabs(1, project.getSettings().getTabSize()) + "$1")
.replaceAll("(?m)^(</)", getTabs(1, project.getSettings().getTabSize()) + "$1"));
// transform
StringResult result = new StringResult();
transformer.transform(xmlSource, result);
FileUtils.writeToFile(
format(result.toString(), project.getSettings().getTabSize()), file);
return;
}
}
} catch (IOException e) {
throw new ApplicationRuntimeException(UNABLE_TO_READ_TRANSFORMATION_SOURCE, e);
} catch (TransformerException e) {
throw new ApplicationRuntimeException(FAILED_TO_UPDATE_BEAN_DEFINITION, e);
}
}
/**
* Method updates existing Spring bean definitions in a XML application context file. Bean
* definition is identified by its type defining class.
*
* @param project
* @param type
* @param jaxbElement
*/
public void updateBeanDefinitions(
File configFile, Project project, Class<?> type, Object jaxbElement) {
Source xsltSource;
Source xmlSource;
try {
xsltSource =
new StreamSource(
new ClassPathResource("transform/update-bean-type.xsl").getInputStream());
xsltSource.setSystemId("update-bean");
List<File> configFiles = new ArrayList<>();
configFiles.add(configFile);
configFiles.addAll(getConfigImports(configFile, project));
LSParser parser = XMLUtils.createLSParser();
GetSpringBeansFilter getBeanFilter = new GetSpringBeansFilter(type, null);
parser.setFilter(getBeanFilter);
for (File file : configFiles) {
parser.parseURI(file.toURI().toString());
if (!CollectionUtils.isEmpty(getBeanFilter.getBeanDefinitions())) {
xmlSource = new StringSource(FileUtils.readToString(new FileInputStream(file)));
String beanElement = type.getAnnotation(XmlRootElement.class).name();
String beanNamespace = type.getPackage().getAnnotation(XmlSchema.class).namespace();
// create transformer
Transformer transformer = transformerFactory.newTransformer(xsltSource);
transformer.setParameter("bean_element", beanElement);
transformer.setParameter("bean_namespace", beanNamespace);
transformer.setParameter(
"bean_content",
getXmlContent(jaxbElement)
.replaceAll("(?m)^(\\s<)", getTabs(1, project.getSettings().getTabSize()) + "$1")
.replaceAll("(?m)^(</)", getTabs(1, project.getSettings().getTabSize()) + "$1"));
// transform
StringResult result = new StringResult();
transformer.transform(xmlSource, result);
FileUtils.writeToFile(
format(result.toString(), project.getSettings().getTabSize()), file);
return;
}
}
} catch (IOException e) {
throw new ApplicationRuntimeException(UNABLE_TO_READ_TRANSFORMATION_SOURCE, e);
} catch (TransformerException e) {
throw new ApplicationRuntimeException(FAILED_TO_UPDATE_BEAN_DEFINITION, e);
}
}
/**
* Marshal jaxb element and try to perform basic formatting like namespace clean up and attribute
* formatting with xsl transformation.
*
* @param jaxbElement
* @return
*/
private String getXmlContent(Object jaxbElement) {
StringResult jaxbContent = new StringResult();
springBeanMarshaller.marshal(jaxbElement, jaxbContent);
Source xsltSource;
try {
xsltSource =
new StreamSource(new ClassPathResource("transform/format-bean.xsl").getInputStream());
Transformer transformer = transformerFactory.newTransformer(xsltSource);
// transform
StringResult result = new StringResult();
transformer.transform(new StringSource(jaxbContent.toString()), result);
if (log.isDebugEnabled()) {
log.debug("Created bean definition:\n" + result.toString());
}
return result.toString();
} catch (IOException e) {
throw new ApplicationRuntimeException(UNABLE_TO_READ_TRANSFORMATION_SOURCE, e);
} catch (TransformerException e) {
throw new ApplicationRuntimeException(FAILED_TO_UPDATE_BEAN_DEFINITION, e);
}
}
/**
* Do final formatting with Spring bean XML configuration content. Removes empty double lines and
* formats schemaLocation attribute value with new lines.
*
* @param content
* @param tabSize
* @return
*/
private String format(String content, int tabSize) {
return content
.replaceAll("(?m)(^\\s*$)+", "")
.replaceAll("\\.xsd\\s", ".xsd\n" + getTabs(3, tabSize));
}
/**
* Construct tabs according to project settings.
*
* @param amount
* @param tabSize
* @return
*/
private String getTabs(int amount, int tabSize) {
StringBuilder tabs = new StringBuilder();
for (int i = 1; i <= amount; i++) {
for (int k = 1; k <= tabSize; k++) {
tabs.append(" ");
}
}
return tabs.toString();
}
/**
* Creates a DOM element node from JAXB element.
*
* @param element
* @return
*/
private <T> T createJaxbObjectFromElement(Element element) {
LSSerializer serializer = XMLUtils.createLSSerializer();
return (T)
springBeanMarshaller.unmarshal(
new StreamSource(new StringReader(serializer.writeToString(element))));
}
/**
* Sets the springBeanMarshaller property.
*
* @param springBeanMarshaller
*/
public void setSpringBeanMarshaller(SpringBeanMarshaller springBeanMarshaller) {
this.springBeanMarshaller = springBeanMarshaller;
}
}
public void CollectData(String link) {
try {
// Creating an empty XML Document
DocumentBuilderFactory dbfac = DocumentBuilderFactory.newInstance();
DocumentBuilder docBuilder = dbfac.newDocumentBuilder();
Document doc = docBuilder.newDocument();
int flag = 0;
// create the root element and add it to the document
Element movie = doc.createElement("movie");
doc.appendChild(movie);
movie.setAttribute("id", String.valueOf(n));
n++;
// create sub elements
Element genres = doc.createElement("genres");
Element actors = doc.createElement("actors");
Element reviews = doc.createElement("reviews");
URL movieUrl = new URL(link);
URL reviewsURL = new URL(link + "reviews/#type=top_critics");
BufferedWriter bw3 = new BufferedWriter(new FileWriter("movies.xml", true));
int count = -1;
String auth = "";
BufferedReader br3 = new BufferedReader(new InputStreamReader(movieUrl.openStream()));
String str2 = "";
String info = "";
while (null != (str2 = br3.readLine())) {
// start reading the html document
if (str2.isEmpty()) continue;
if (count == 14) break;
if (count == 12) {
if (!str2.contains("<h3>Cast</h3>")) continue;
else count++;
}
if (count == 13) {
if (str2.contains(">ADVERTISEMENT</p>")) {
count++;
movie.appendChild(actors);
continue;
} else {
if (str2.contains("itemprop=\"name\">")) {
Element actor = doc.createElement("actor");
actors.appendChild(actor);
Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
actor.appendChild(text);
} else continue;
}
}
if (count <= 11) {
switch (count) {
case -1:
{
if (!str2.contains("property=\"og:image\"")) continue;
else {
Pattern image =
Pattern.compile("http://.*.jpg", Pattern.CASE_INSENSITIVE | Pattern.DOTALL);
Matcher match = image.matcher(str2);
while (match.find()) {
Element imageLink = doc.createElement("imageLink");
movie.appendChild(imageLink);
Text text = doc.createTextNode(match.group());
imageLink.appendChild(text);
count++;
}
}
break;
}
case 0:
{
if (str2.contains("<title>")) {
Element name = doc.createElement("name");
movie.appendChild(name);
Text text =
doc.createTextNode(
Jsoup.parse(str2.toString().replace(" - Rotten Tomatoes", "")).text());
name.appendChild(text);
count++;
}
break;
}
case 1:
{
if (!str2.contains("itemprop=\"ratingValue\"")) break;
else {
Element score = doc.createElement("score");
movie.appendChild(score);
Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
score.appendChild(text);
count++;
}
break;
}
case 2:
{
if (!str2.contains("itemprop=\"description\">")) continue;
else count++;
break;
}
case 3:
{
if (!str2.contains("itemprop=\"duration\"")) info = info.concat(str2);
else {
Element MovieInfo = doc.createElement("MovieInfo");
movie.appendChild(MovieInfo);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
MovieInfo.appendChild(text);
info = str2;
count++;
}
break;
}
case 4:
{
if (!str2.contains("itemprop=\"genre\"")) info = info.concat(str2);
else {
Element duration = doc.createElement("duration");
movie.appendChild(duration);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
duration.appendChild(text);
info = str2;
count++;
}
break;
}
case 5:
{
if (info.contains("itemprop=\"genre\"")) {
Element genre = doc.createElement("genre");
genres.appendChild(genre);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
genre.appendChild(text);
info = "";
}
if (str2.contains(">Directed By:<")) {
count++;
movie.appendChild(genres);
continue;
} else {
if (str2.contains("itemprop=\"genre\"")) {
Element genre = doc.createElement("genre");
genres.appendChild(genre);
Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
genre.appendChild(text);
} else continue;
}
break;
}
case 6:
{
if (!str2.contains(">Written By:<")) {
if (str2.contains(">In Theaters:<")) {
Element director = doc.createElement("director");
movie.appendChild(director);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("Directed By: ", "")).text());
director.appendChild(text);
info = str2;
count += 2;
break;
}
info = info.concat(str2);
} else {
Element director = doc.createElement("director");
movie.appendChild(director);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("Directed By: ", "")).text());
director.appendChild(text);
info = "";
count++;
}
break;
}
case 7:
{
if (!str2.contains(">In Theaters:<")) {
if (str2.contains(">On DVD:<")) {
Element writer = doc.createElement("writer");
movie.appendChild(writer);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
writer.appendChild(text);
info = str2;
count += 2;
break;
}
info = info.concat(str2);
} else {
Element writer = doc.createElement("writer");
movie.appendChild(writer);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
writer.appendChild(text);
info = str2;
count++;
}
break;
}
case 8:
{
if (!str2.contains(">On DVD:<")) info = info.concat(str2);
else {
Element TheatreRelease = doc.createElement("TheatreRelease");
movie.appendChild(TheatreRelease);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("In Theaters:", "")).text());
TheatreRelease.appendChild(text);
info = str2;
count++;
}
break;
}
case 9:
{
if (!str2.contains(">US Box Office:<")) {
if (str2.contains("itemprop=\"productionCompany\"")) {
Element DvdRelease = doc.createElement("DvdRelease");
movie.appendChild(DvdRelease);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("On DVD:", "")).text());
DvdRelease.appendChild(text);
info = str2;
count += 2;
break;
}
info = info.concat(str2);
} else {
Element DvdRelease = doc.createElement("DvdRelease");
movie.appendChild(DvdRelease);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("On DVD:", "")).text());
DvdRelease.appendChild(text);
info = str2;
count++;
}
break;
}
case 10:
{
if (!str2.contains("itemprop=\"productionCompany\"")) info = info.concat(str2);
else {
Element BOCollection = doc.createElement("BOCollection");
movie.appendChild(BOCollection);
Text text =
doc.createTextNode(
Jsoup.parse(info.toString().replace("US Box Office:", "")).text());
BOCollection.appendChild(text);
info = str2;
count++;
}
break;
}
case 11:
{
if (!str2.contains(">Official Site")) info = info.concat(str2);
else {
Element Production = doc.createElement("Production");
movie.appendChild(Production);
Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
Production.appendChild(text);
info = str2;
count++;
}
break;
}
default:
break;
}
}
}
BufferedReader br4 = new BufferedReader(new InputStreamReader(reviewsURL.openStream()));
String str3 = "";
String info2 = "";
int count2 = 0;
while (null != (str3 = br4.readLine())) {
if (count2 == 0) {
if (!str3.contains("<div class=\"reviewsnippet\">")) continue;
else count2++;
}
if (count2 == 1) {
if (!str3.contains("<p class=\"small subtle\">")) info2 = info2.concat(str3);
else {
Element review = doc.createElement("review");
reviews.appendChild(review);
Text text = doc.createTextNode(Jsoup.parse(info2.toString()).text());
review.appendChild(text);
info2 = "";
count2 = 0;
}
}
}
movie.appendChild(reviews);
TransformerFactory transfac = TransformerFactory.newInstance();
Transformer trans = transfac.newTransformer();
trans.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
trans.setOutputProperty(OutputKeys.INDENT, "yes");
// create string from xml tree
StringWriter sw = new StringWriter();
StreamResult result = new StreamResult(sw);
DOMSource source = new DOMSource(doc);
trans.transform(source, result);
String xmlString = sw.toString();
bw3.write(xmlString);
br3.close();
br4.close();
bw3.close();
} catch (Exception ex) {
ex.printStackTrace();
}
}
/** @param args the command line arguments */
public static void main(String[] args) {
// TODO code application logic here
Model model;
String insertstmt;
String insertmodel = "",
insertspecies = "",
insertcompartment = "",
insertfunction = "",
insertunitdef = "",
insertunits = "",
insertreaction = "",
insertreactant = "",
insertproduct = "";
String insertmodifier = "",
insertklaw = "",
insertrules = "",
insertconstraint = "",
insertdelay = "",
inserttrigger = "",
insertevent = "",
inserteventassign = "",
insertparameter = "";
String insertstatement = "";
String server, user, password, dbname, filepath;
String Filedata = "";
String cwd = System.getProperty("user.dir");
if (args.length == 0) {
server = "localhost";
user = "******";
password = "******";
dbname = "sbmldb2";
/**
* Path to extract the SBML files from database, where cwd is
* "github\db2sbml\dbtosbml_standalone_Project\dbtosbml" so add a folder in this directory and
* mention folder name instead of extractedbm folder
*/
filepath = cwd + "\\extractedbm\\";
} else {
server = args[0];
user = args[1];
password = args[2];
dbname = args[3];
filepath = args[4];
}
try {
Filedata = readFileAsString(cwd + "\\sbmldbschema.sql");
} catch (Exception e) {
e.printStackTrace();
}
Mysqlconn sql = new Mysqlconn(server, user, password, dbname);
// String modelids.getId() = "MorrisonAllegra" ;
ASTNode math = null;
int level = 0, version = 0;
ArrayList<modellist> modelidlist = sql.getmodels();
insertstatement =
"LOCK TABLES `model` WRITE,`species` WRITE,`compartment` WRITE,`functiondefinition` WRITE,";
insertstatement =
insertstatement
+ "`listofunitdefinitions` WRITE,`listofunits` WRITE,`reaction` WRITE,`simplespeciesreference` WRITE,";
insertstatement =
insertstatement
+ "`modifierspeciesreference` WRITE,`kineticlaw` WRITE,`parameter` WRITE,`sbmlconstraint` WRITE,";
insertstatement =
insertstatement
+ "`event` WRITE,`sbmltrigger` WRITE,`delay` WRITE,`eventassignment` WRITE,`rules` WRITE"
+ ";";
for (modellist modelids : modelidlist) {
ArrayList<modellist> modellevel = sql.getmodeldetails(modelids.getId());
for (modellist modellv : modellevel) {
level = modellv.getlevel();
version = modellv.getversion();
}
SBMLDocument doc = new SBMLDocument(level, version);
ArrayList<modellist> modellists = sql.getmodeldetails(modelids.getId());
if (!modellists.isEmpty())
insertmodel =
insertmodel
+ "\nInsert Into model (id, name,SBML_level,version,notes,annotation) Values";
for (modellist models : modellists) {
insertmodel =
insertmodel
+ "(\'"
+ models.getId()
+ "\',\'"
+ models.getName()
+ "\',"
+ models.getlevel()
+ ","
+ models.getversion()
+ ",\'"
+ models.getnotes()
+ "\',\'"
+ models.getannotation().toString()
+ "\'),";
model = doc.createModel(models.getId());
model.setName(models.getName());
// System.out.println("model : " + models.getId());
// model.setNotes(models.getnotes()); // there is some null exception is command line run
// but run perfectly from netbeans so ommented out
if (!models.getannotation().equals("")) {
Annotation annot = new Annotation(models.getannotation().toString());
model.setAnnotation(annot);
}
doc.setModel(model);
}
if (!modellists.isEmpty()) {
insertmodel = insertmodel.substring(0, insertmodel.length() - 1);
insertmodel = insertmodel + ';';
}
// insertmodel = insertmodel + "\nUNLOCK TABLES;";
// System.out.println(insertmodel);
ArrayList<SpeciesList> specieslist = sql.getspecies(modelids.getId());
if (!specieslist.isEmpty())
insertspecies =
insertspecies
+ "\nInsert Into species (id, name, compartment, initialAmount, initialConcentration,substanceUnits,hasOnlySubstanceUnits,boundaryCondition,constant,conversionFactor,model_id,annotation) Values";
for (SpeciesList species : specieslist) {
insertspecies =
insertspecies
+ "(\'"
+ species.getId()
+ "\',\'"
+ species.getName()
+ "\',\'"
+ species.getcompartment()
+ "\',"
+ species.getia()
+ ","
+ species.getic()
+ ",\'"
+ species.getsu()
+ "\',"
+ species.gethosu()
+ ","
+ species.getbc()
+ ","
+ species.getconstant()
+ ","
+ species.getcf()
+ ",\'"
+ modelids.getId()
+ "\',\'"
+ species.getannotation()
+ "\'),";
Species sp = doc.getModel().createSpecies(species.getId());
sp.setName(species.getName());
sp.setCompartment(species.getcompartment());
sp.setConstant(species.getconstant());
sp.setInitialAmount(species.getia());
sp.setInitialConcentration(species.getic());
sp.setHasOnlySubstanceUnits(species.gethosu());
if (doc.getModel().getLevel() == 3) sp.setConversionFactor(species.getcf());
sp.setBoundaryCondition(species.getbc());
sp.setSubstanceUnits(species.getsu());
if (!species.getannotation().equals("")) {
Annotation annot = new Annotation(species.getannotation().toString());
sp.setAnnotation(annot);
}
// doc.getModel().addSpecies(sp) ;
}
if (!specieslist.isEmpty()) {
insertspecies = insertspecies.substring(0, insertspecies.length() - 1);
insertspecies = insertspecies + ';';
}
ArrayList<CompartmentList> complist = sql.getcompartments(modelids.getId());
if (!complist.isEmpty())
insertcompartment =
insertcompartment
+ "\nInsert Into compartment (id, name,constant,model_id,spacialDimensions,size,units) Values";
for (CompartmentList comp : complist) {
insertcompartment =
insertcompartment
+ "(\'"
+ comp.getId()
+ "\',\'"
+ comp.getName()
+ "\',"
+ comp.getconstant()
+ ",\'"
+ modelids.getId()
+ "\',"
+ comp.getspatialdimensions()
+ ","
+ comp.getsize()
+ ","
+ comp.getunits()
+ "\'),";
Compartment c = doc.getModel().createCompartment(comp.getId());
c.setName(comp.getName());
c.setConstant(comp.getconstant());
c.setSize(comp.getsize());
c.setSpatialDimensions(comp.getspatialdimensions());
if (comp.getspatialdimensions() != 0) c.setUnits(comp.getunits());
// doc.getModel().addSpecies(sp) ;
}
if (!complist.isEmpty()) {
insertcompartment = insertcompartment.substring(0, insertcompartment.length() - 1);
insertcompartment = insertcompartment + ';';
}
ArrayList<functionList> funclist = sql.getfunctions(modelids.getId());
if (!funclist.isEmpty())
insertfunction =
insertfunction + "\nInsert Into functiondefinition (id, xmlns,model_id) Values";
for (functionList func : funclist) {
insertfunction =
insertfunction
+ "(\'"
+ func.getId()
+ "\',\'"
+ func.getxmlns()
+ "\',\'"
+ modelids.getId()
+ "\'),";
FunctionDefinition fd = doc.getModel().createFunctionDefinition(func.getId());
try {
math = ASTNode.parseFormula(func.getxmlns());
fd.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!funclist.isEmpty()) {
insertfunction = insertfunction.substring(0, insertfunction.length() - 1);
insertfunction = insertfunction + ';';
}
ArrayList<unitList> unitlist = sql.getunitlist(modelids.getId());
if (!unitlist.isEmpty())
insertunitdef =
insertunitdef + "\nInsert Into listofunitdefinitions (id,name,model_id) Values";
for (unitList units : unitlist) {
insertunitdef =
insertunitdef
+ "(\'"
+ units.getId()
+ "\',\'"
+ units.getName()
+ "\',\'"
+ modelids.getId()
+ "\'),";
UnitDefinition ud = doc.getModel().createUnitDefinition(units.getId());
ud.setName(units.getName());
ArrayList<unitList> unitdeflist = sql.getunitdef(units.getId());
if (!unitdeflist.isEmpty())
insertunits =
insertunits
+ "\nInsert Into listofunits (listofunitdefinitions_id,kind, scale,exponent,multiplier) Values";
for (unitList unitdef : unitdeflist) {
insertunits =
insertunits
+ "(\'"
+ units.getId()
+ "\',\'"
+ unitdef.getkind()
+ "\',"
+ unitdef.getscale()
+ ","
+ unitdef.getexponent()
+ ","
+ unitdef.getmultiplier()
+ "),";
Unit u = ud.createUnit(Unit.Kind.valueOf(unitdef.getkind()));
u.setScale(unitdef.getscale());
u.setExponent(unitdef.getexponent());
u.setMultiplier(unitdef.getmultiplier());
}
// doc.getModel().addSpecies(sp) ;
if (!unitdeflist.isEmpty()) {
insertunits = insertunits.substring(0, insertunits.length() - 1);
insertunits = insertunits + ';';
}
}
if (!unitlist.isEmpty()) {
insertunitdef = insertunitdef.substring(0, insertunitdef.length() - 1);
insertunitdef = insertunitdef + ';';
}
ArrayList<reactionList> reactionlist = sql.getreactons(modelids.getId());
if (!reactionlist.isEmpty())
insertreaction =
insertreaction
+ "\nInsert Into reaction (id,name, reversible,fast,model_id,compartment,annotation) Values";
for (reactionList reaction : reactionlist) {
insertreaction =
insertreaction
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ reaction.getName()
+ "\',"
+ reaction.getreversible()
+ ","
+ reaction.getfast()
+ ",\'"
+ modelids.getId()
+ "\',\'"
+ reaction.getcompartment()
+ "\',\'"
+ reaction.getannotation()
+ "\'),";
Reaction rn = doc.getModel().createReaction(reaction.getId());
rn.setName(reaction.getName());
if (doc.getModel().getLevel() == 3) rn.setCompartment(reaction.getcompartment());
rn.setFast(reaction.getfast());
rn.setReversible(reaction.getreversible());
if (!reaction.getannotation().equals("")) {
Annotation annot = new Annotation(reaction.getannotation().toString());
rn.setAnnotation(annot);
}
ArrayList<reactionList> reactantlist = sql.getreactants(reaction.getId());
if (!reactantlist.isEmpty())
insertreactant =
insertreactant
+ "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,speciestype,constant) Values";
for (reactionList reactant : reactantlist) {
insertreactant =
insertreactant
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ reactant.getspecies()
+ "\',\'"
+ reactant.getsboTerm()
+ "\',"
+ reactant.getstoichometry()
+ ","
+ reactant.getconstant()
+ ",\'reactants\'),";
SpeciesReference rt = new SpeciesReference();
rt.setName(reactant.getspecies());
rt.setSpecies(reactant.getspecies());
// rt.setSBOTerm(reactant.getsboTerm());
rt.setStoichiometry(reactant.getstoichometry());
// rt.setConstant(reactant.getconstant());
rn.addReactant(rt);
}
if (!reactantlist.isEmpty()) {
insertreactant = insertreactant.substring(0, insertreactant.length() - 1);
insertreactant = insertreactant + ';';
}
ArrayList<reactionList> productlist = sql.getproducts(reaction.getId());
if (!productlist.isEmpty())
insertproduct =
insertproduct
+ "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,constant,speciestype) Values";
for (reactionList product : productlist) {
insertproduct =
insertproduct
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ product.getspecies()
+ "\',\'"
+ product.getsboTerm()
+ "\',"
+ product.getstoichometry()
+ ","
+ product.getconstant()
+ ",\'products\'),";
SpeciesReference pr = new SpeciesReference();
pr.setName(product.getspecies());
pr.setSpecies(product.getspecies());
// pr.setSBOTerm(product.getsboTerm());
pr.setStoichiometry(product.getstoichometry());
// pr.setConstant(product.getconstant());
rn.addProduct(pr);
}
if (!productlist.isEmpty()) {
insertproduct = insertproduct.substring(0, insertproduct.length() - 1);
insertproduct = insertproduct + ';';
}
ArrayList<reactionList> modifierlist = sql.getmodifiers(reaction.getId());
if (!modifierlist.isEmpty())
insertmodifier =
insertmodifier
+ "\nInsert Into modifierspeciesreference (reaction_id,species, sboTerm,speciestype) Values";
for (reactionList modifier : modifierlist) {
insertmodifier =
insertmodifier
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ modifier.getspecies()
+ "\',\'"
+ modifier.getsboTerm()
+ "\',\'modifiers\'),";
ModifierSpeciesReference m = new ModifierSpeciesReference();
m.setName(modifier.getspecies());
m.setSpecies(modifier.getspecies());
// m.setSBOTerm(modifier.getsboTerm());
rn.addModifier(m);
}
if (!modifierlist.isEmpty()) {
insertmodifier = insertmodifier.substring(0, insertmodifier.length() - 1);
insertmodifier = insertmodifier + ';';
}
ArrayList<reactionList> klawlist = sql.getkineticlaws(reaction.getId());
if (!klawlist.isEmpty())
insertklaw =
insertklaw + "\nInsert Into kineticlaw (reaction_id,kid, math,annotation) Values";
for (reactionList klaw : klawlist) {
insertklaw =
insertklaw
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ klaw.getId()
+ "\',\'"
+ klaw.getmath()
+ "\',\'"
+ klaw.getannotation()
+ "\'),";
KineticLaw kl = rn.createKineticLaw();
try {
math = ASTNode.parseFormula(klaw.getmath());
kl.setMath(math);
if (!klaw.getannotation().equals("")) {
Annotation annot = new Annotation(klaw.getannotation().toString());
kl.setAnnotation(annot);
}
} catch (Exception e) {
e.printStackTrace();
}
}
if (!klawlist.isEmpty()) {
insertklaw = insertklaw.substring(0, insertklaw.length() - 1);
insertklaw = insertklaw + ';';
}
}
if (!reactionlist.isEmpty()) {
insertreaction = insertreaction.substring(0, insertreaction.length() - 1);
insertreaction = insertreaction + ';';
}
ArrayList<parameterList> paralist = sql.getparameters(modelids.getId());
if (!paralist.isEmpty())
insertparameter =
insertparameter
+ "\nInsert Into parameter (id,name,value,units,constant,model_id) Values";
for (parameterList para : paralist) {
insertparameter =
insertparameter
+ "(\'"
+ para.getId()
+ "\',\'"
+ para.getName()
+ "\',"
+ para.getvalue()
+ ","
+ para.getunits()
+ ","
+ para.getconstant()
+ ",\'"
+ modelids.getId()
+ "\'),";
Parameter par = doc.getModel().createParameter(para.getId());
par.setName(para.getId());
par.setConstant(para.getconstant());
par.setUnits(para.getunits());
par.setValue(para.getvalue());
}
if (!paralist.isEmpty()) {
insertparameter = insertparameter.substring(0, insertparameter.length() - 1);
insertparameter = insertparameter + ';';
}
ArrayList<constraintList> conslist = sql.getconstraints(modelids.getId());
if (!conslist.isEmpty())
insertconstraint =
insertconstraint + "\nInsert Into sbmlconstraint (math,message,model_id) Values";
for (constraintList constraint : conslist) {
insertconstraint =
insertconstraint
+ "(\'"
+ constraint.getmath()
+ "\',\'"
+ constraint.getmessage()
+ "\',\'"
+ modelids.getId()
+ "\'),";
Constraint cons = doc.getModel().createConstraint();
try {
math = ASTNode.parseFormula(constraint.getmath());
cons.setMath(math);
cons.setMessage(constraint.getmessage());
} catch (Exception e) {
e.printStackTrace();
}
}
if (!conslist.isEmpty()) {
insertconstraint = insertconstraint.substring(0, insertconstraint.length() - 1);
insertconstraint = insertconstraint + ';';
}
ArrayList<eventsList> eventlist = sql.getevents(modelids.getId());
if (!eventlist.isEmpty())
insertevent =
insertevent + "\nInsert Into event (id,name,UseValuesFromTriggerTime,model_id) Values";
for (eventsList events : eventlist) {
insertevent =
insertevent
+ "(\'"
+ events.getId()
+ "\',\'"
+ events.getName()
+ "\',"
+ events.getuservalues()
+ ",\'"
+ modelids.getId()
+ "\'),";
Event ev = doc.getModel().createEvent(events.getId());
ev.setName(events.getName());
// ev.setUseValuesFromTriggerTime(events.getuservalues());
ArrayList<eventsList> triggerlist = sql.gettriggers(events.getId());
if (!triggerlist.isEmpty())
inserttrigger =
inserttrigger
+ "\nInsert Into sbmltrigger (event_id,initialvalue,persisent,math) Values";
for (eventsList triggers : triggerlist) {
Trigger tr = doc.getModel().createTrigger();
try {
math = ASTNode.parseFormula(triggers.getmath());
tr.setMath(math);
tr.setInitialValue(triggers.getinitialval());
tr.setPersistent(triggers.getpersistent());
} catch (Exception e) {
e.printStackTrace();
}
}
if (!triggerlist.isEmpty()) {
inserttrigger = inserttrigger.substring(0, insertmodel.length() - 1);
inserttrigger = inserttrigger + ';';
}
ArrayList<eventsList> delaylist = sql.getdelays(events.getId());
if (!delaylist.isEmpty())
insertdelay = insertdelay + "\nInsert Into delay (event_id,math) Values";
for (eventsList delays : delaylist) {
Delay d = doc.getModel().createDelay();
try {
math = ASTNode.parseFormula(delays.getmath());
d.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!delaylist.isEmpty()) {
insertdelay = insertdelay.substring(0, insertdelay.length() - 1);
insertdelay = insertdelay + ';';
}
ArrayList<eventsList> evasslist = sql.geteventassignments(events.getId());
if (!evasslist.isEmpty())
inserteventassign =
inserteventassign + "\nInsert Into eventassignment (event_id,variable,math) Values";
for (eventsList evassign : evasslist) {
EventAssignment ea = doc.getModel().createEventAssignment();
try {
math = ASTNode.parseFormula(evassign.getmath());
ea.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!evasslist.isEmpty()) {
inserteventassign = inserteventassign.substring(0, inserteventassign.length() - 1);
inserteventassign = inserteventassign + ';';
}
}
if (!eventlist.isEmpty()) {
insertevent = insertevent.substring(0, insertevent.length() - 1);
insertevent = insertevent + ';';
}
ArrayList<ruleslist> rulelist = sql.getrules(modelids.getId());
if (!rulelist.isEmpty())
insertrules = insertrules + "\nInsert Into rules (id,math,ruletype,model_id) Values";
for (ruleslist rules : rulelist) {
insertrules =
insertrules
+ "(\'"
+ rules.getId()
+ "\',\'"
+ rules.getmath()
+ "\',\'"
+ rules.getruletype()
+ "\',\'"
+ modelids.getId()
+ "\'),";
if (rules.getruletype().equals("assignmentrule")) {
Rule r = doc.getModel().createAssignmentRule();
r.setMetaId(rules.getId());
try {
math = ASTNode.parseFormula(rules.getmath());
r.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
}
if (!rulelist.isEmpty()) {
insertrules = insertrules.substring(0, insertrules.length() - 1);
insertrules = insertrules + ';';
}
SBMLWriter writer = new SBMLWriter();
try {
String Path = filepath + modelids.getId() + ".xml";
writer.write(doc, Path);
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(Path);
Element root = document.getDocumentElement();
Element newdataset = document.createElement("dataset");
root.appendChild(newdataset);
ArrayList<dataset> datasetlist = sql.getdataset(modelids.getId());
for (dataset ds : datasetlist) {
// System.out.println(ds.getexpcond());
Element name = document.createElement("experimentalcondition");
name.setAttribute("bioelement", ds.getbioel());
name.setAttribute("name", ds.getName());
name.setAttribute("descr", ds.getdescr());
name.setAttribute("expcond", ds.getexpcond());
name.setAttribute("value", String.valueOf(ds.getvalue()));
name.setAttribute("type", ds.gettype());
name.setAttribute("uri", ds.geturi());
newdataset.appendChild(name);
}
root.appendChild(newdataset);
DOMSource source = new DOMSource(document);
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
StreamResult result = new StreamResult(filepath + modelids.getId() + "d.xml");
transformer.transform(source, result);
System.out.println(
"Files : "
+ modelids.getId()
+ ".xml and "
+ modelids.getId()
+ "d.xml have been generated successfully !!!");
} catch (Exception e) {
e.printStackTrace();
}
insertstatement =
insertstatement
+ "\n\n"
+ insertmodel
+ "\n"
+ insertspecies
+ "\n"
+ insertcompartment
+ "\n"
+ insertfunction;
insertstatement =
insertstatement
+ "\n"
+ insertparameter
+ "\n"
+ insertreaction
+ "\n"
+ insertreactant
+ "\n"
+ insertproduct;
insertstatement =
insertstatement
+ "\n"
+ insertmodifier
+ "\n"
+ insertklaw
+ "\n"
+ insertunitdef
+ "\n"
+ insertunits;
insertstatement =
insertstatement
+ "\n"
+ insertrules
+ "\n"
+ insertconstraint
+ "\n"
+ insertevent
+ "\n"
+ inserttrigger
+ "\n"
+ insertdelay
+ "\n"
+ inserteventassign;
insertcompartment = "";
insertmodel = "";
insertspecies = "";
// System.out.println("document : " + doc);
}
insertstatement = insertstatement + "\nUNLOCK TABLES;";
Filedata = Filedata + "\n\n\n" + insertstatement;
try {
wrtireStringToFile(Filedata, filepath + "sbmldb.sql");
} catch (IOException e) {
e.printStackTrace();
}
// System.out.println(insertstatement);
}
public String toXMLString() {
Document doc;
try { // Create an Empty Dom
DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
doc = builder.newDocument();
} catch (ParserConfigurationException e) {
System.err.println("error when create empty Dom: " + e);
return null;
}
if (doc == null) {
System.err.println("null dom");
return null;
}
try {
Element root = doc.createElement("PathwayLayout");
doc.appendChild(root);
Element nodeslayout = doc.createElement("Nodes");
root.appendChild(nodeslayout);
Element edgeslayout = doc.createElement("Edges");
root.appendChild(edgeslayout);
for (NodeLayout nl : nodes) {
Element ne = doc.createElement("NodeLayout");
ne.setAttribute("ID", nl.nodeID);
ne.setAttribute("NeighboringProcessId", nl.processID);
String co = "false";
if (nl.cofactor.equalsIgnoreCase("true")) {
co = "true";
}
ne.setAttribute("cofactor", co);
ne.setAttribute("X", Double.toString(nl.x));
ne.setAttribute("Y", Double.toString(nl.y));
nodeslayout.appendChild(ne);
}
for (EdgeLayout el : edges) {
Element ee = doc.createElement("EdgeLayout");
ee.setAttribute("SourceID", el.sourceNode);
ee.setAttribute("SourceNeighboringProcessId", el.sourcepid);
String sco = "false";
if (el.scofactor.equalsIgnoreCase("true")) {
sco = "true";
}
ee.setAttribute("SourceCofactor", sco);
ee.setAttribute("TargetID", el.targetNode);
ee.setAttribute("TargetNeighboringProcessId", el.targetpid);
String tco = "false";
if (el.tcofactor.equalsIgnoreCase("true")) {
sco = "true";
}
ee.setAttribute("TargetCofactor", tco);
for (LayoutPoint lp : el.bends) {
Element lpe = doc.createElement("BendPoint");
lpe.setAttribute("X", Double.toString(lp.x));
lpe.setAttribute("Y", Double.toString(lp.y));
ee.appendChild(lpe);
}
edgeslayout.appendChild(ee);
}
// Transform Dom to XML String
Transformer transformer = TransformerFactory.newInstance().newTransformer();
// additional whitespace when outputting the result tree
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
StreamResult result = new StreamResult(new StringWriter());
DOMSource source = new DOMSource(doc);
transformer.transform(source, result);
String xmlString = result.getWriter().toString();
return xmlString;
} catch (Exception e) {
System.err.println("error when fill the Dom: " + e);
return null;
}
}
