public static void testEnum() throws Exception {
Builder b = new Builder();
b.addClasspath(new File("bin"));
b.setProperty("Export-Package", "test.metatype");
b.setProperty("-metatype", "*");
b.build();
assertEquals(0, b.getErrors().size());
assertEquals(0, b.getWarnings().size());
Resource r = b.getJar().getResource("OSGI-INF/metatype/test.metatype.MetatypeTest$Enums.xml");
IO.copy(r.openInputStream(), System.err);
Document d = db.parse(r.openInputStream());
assertEquals(
"http://www.osgi.org/xmlns/metatype/v1.1.0", d.getDocumentElement().getNamespaceURI());
Properties p = new Properties();
p.setProperty("r", "requireConfiguration");
p.setProperty("i", "ignoreConfiguration");
p.setProperty("o", "optionalConfiguration");
Enums enums = Configurable.createConfigurable(Enums.class, (Map<Object, Object>) p);
assertEquals(Enums.X.requireConfiguration, enums.r());
assertEquals(Enums.X.ignoreConfiguration, enums.i());
assertEquals(Enums.X.optionalConfiguration, enums.o());
}
Document parseDocument(String filename) throws Exception {
FileReader reader = new FileReader(filename);
String firstLine = new BufferedReader(reader).readLine();
reader.close();
Document document = null;
if (firstLine.startsWith("<?xml")) {
System.err.println("XML detected; using default XML parser.");
} else {
try {
Class nekoParserClass = Class.forName("org.cyberneko.html.parsers.DOMParser");
Object parser = nekoParserClass.newInstance();
Method parse = nekoParserClass.getMethod("parse", new Class[] {String.class});
Method getDocument = nekoParserClass.getMethod("getDocument", new Class[0]);
parse.invoke(parser, filename);
document = (Document) getDocument.invoke(parser);
} catch (Exception e) {
System.err.println("NekoHTML HTML parser not found; HTML4 support disabled.");
}
}
if (document == null) {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
try { // http://www.w3.org/blog/systeam/2008/02/08/w3c_s_excessive_dtd_traffic
factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
} catch (ParserConfigurationException e) {
System.err.println("Warning: Could not disable external DTD loading");
}
DocumentBuilder builder = factory.newDocumentBuilder();
document = builder.parse(filename);
}
return document;
}
public ArrayList<String> parseXML() throws Exception {
ArrayList<String> ret = new ArrayList<String>();
handshake();
URL url =
new URL(
"http://mangaonweb.com/page.do?cdn="
+ cdn
+ "&cpn=book.xml&crcod="
+ crcod
+ "&rid="
+ (int) (Math.random() * 10000));
String page = DownloaderUtils.getPage(url.toString(), "UTF-8", cookies);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
InputSource is = new InputSource(new StringReader(page));
Document d = builder.parse(is);
Element doc = d.getDocumentElement();
NodeList pages = doc.getElementsByTagName("page");
total = pages.getLength();
for (int i = 0; i < pages.getLength(); i++) {
Element e = (Element) pages.item(i);
ret.add(e.getAttribute("path"));
}
return (ret);
}
/**
* Performs an XPATH lookup in an xml document whose filename is specified by the first parameter
* (assumed to be in the auxiliary subdirectory) The XPATH expression is supplied as the second
* string parameter The return value is of type string e.g. this is currently used primarily for
* looking up the Company Prefix Index for encoding a GS1 Company Prefix into a 64-bit EPC tag
*/
private String xpathlookup(String xml, String expression) {
try {
// Parse the XML as a W3C document.
DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Document document =
builder.parse(new File(xmldir + File.separator + "auxiliary" + File.separator + xml));
XPath xpath = XPathFactory.newInstance().newXPath();
String rv = (String) xpath.evaluate(expression, document, XPathConstants.STRING);
return rv;
} catch (ParserConfigurationException e) {
System.err.println("ParserConfigurationException caught...");
e.printStackTrace();
return null;
} catch (XPathExpressionException e) {
System.err.println("XPathExpressionException caught...");
e.printStackTrace();
return null;
} catch (SAXException e) {
System.err.println("SAXException caught...");
e.printStackTrace();
return null;
} catch (IOException e) {
System.err.println("IOException caught...");
e.printStackTrace();
return null;
}
}
private void guardaRes(String resu, CliGol cliGol)
throws ParserConfigurationException, SAXException, IOException {
String[] nodos = {"NoHit", "Hit", "Buro"};
DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
InputSource is = new InputSource(new StringReader(resu));
Document xml = db.parse(is);
Element raiz = xml.getDocumentElement();
String nombre = obtenerNombre(raiz);
for (String s : nodos) {
Node nodo =
raiz.getElementsByTagName(s) == null ? null : raiz.getElementsByTagName(s).item(0);
if (nodo != null) {
String informacion = sustraerInformacionNodo(cliGol, nodo);
guardarEnListas(nodo.getNodeName(), nombre + "," + informacion);
}
}
}
public List parsePage(String pageCode) {
List sections = new ArrayList();
List folders = new ArrayList();
List files = new ArrayList();
int start = pageCode.indexOf("<div id=\"list-view\" class=\"view\"");
int end = pageCode.indexOf("<div id=\"gallery-view\" class=\"view\"");
String usefulSection = "";
if (start != -1 && end != -1) {
usefulSection = pageCode.substring(start, end);
} else {
debug("Could not parse page");
}
try {
DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
InputSource is = new InputSource();
is.setCharacterStream(new StringReader(usefulSection));
Document doc = db.parse(is);
NodeList divs = doc.getElementsByTagName("div");
for (int i = 0; i < divs.getLength(); i++) {
Element div = (Element) divs.item(i);
boolean isFolder = false;
if (div.getAttribute("class").equals("filename")) {
NodeList imgs = div.getElementsByTagName("img");
for (int j = 0; j < imgs.getLength(); j++) {
Element img = (Element) imgs.item(j);
if (img.getAttribute("class").indexOf("folder") > 0) {
isFolder = true;
} else {
isFolder = false; // it's a file
}
}
NodeList anchors = div.getElementsByTagName("a");
Element anchor = (Element) anchors.item(0);
String attr = anchor.getAttribute("href");
String fileName = anchor.getAttribute("title");
String fileURL;
if (isFolder && !attr.equals("#")) {
folders.add(attr);
folders.add(fileName);
} else if (!isFolder && !attr.equals("#")) {
// Dropbox uses ajax to get the file for download, so the url isn't enough. We must be
// sneaky here.
fileURL = "https://dl.dropbox.com" + attr.substring(23) + "?dl=1";
files.add(fileURL);
files.add(fileName);
}
}
}
} catch (Exception e) {
debug(e.toString());
}
sections.add(files);
sections.add(folders);
return sections;
}
/** Возвращает объект Document, который является объектным представлением XML документа. */
private static Document getDocument() throws Exception {
try {
DocumentBuilderFactory f = DocumentBuilderFactory.newInstance();
f.setValidating(false);
DocumentBuilder builder = f.newDocumentBuilder();
return builder.parse(new File("app.xml"));
} catch (Exception exception) {
String message = "XML parsing error!";
throw new Exception(message);
}
}
public WikipediaMinerAnnotator(String configFile)
throws ParserConfigurationException, FileNotFoundException, SAXException, IOException,
XPathExpressionException {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(new FileInputStream(configFile));
url = getConfigValue("access", "url", doc);
if (url.equals(""))
throw new AnnotationException(
"Configuration file " + configFile + " has missing value 'url'.");
}
public void load(InputStream is) throws IOException, ParserConfigurationException, SAXException {
doc = db.parse(is);
docElt = doc.getDocumentElement();
if (docElt.getTagName().equals(docElementName)) {
NodeList nl = docElt.getElementsByTagName(trackElementName);
for (int i = 0; i < nl.getLength(); i++) {
Element elt = (Element) nl.item(i);
Track track = new Track(elt);
tracks.add(track);
hash.put(track.getKey(), track);
}
}
}
public static final Skeleton loadSkeleton(File file) {
try {
FileInputStream input_stream = new FileInputStream(file);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setValidating(true);
DocumentBuilder builder = factory.newDocumentBuilder();
builder.setErrorHandler(new GeometryErrorHandler());
Document document = builder.parse(input_stream);
Element root = document.getDocumentElement();
return parseSkeleton(root);
} catch (Exception e) {
throw new RuntimeException(e);
}
}
static {
try {
URL url = SpellCheckActivator.bundleContext.getBundle().getResource(RESOURCE_LOC);
InputStream stream = url.openStream();
if (stream == null) throw new IOException();
// strict parsing options
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setValidating(false);
factory.setIgnoringComments(true);
factory.setIgnoringElementContentWhitespace(true);
// parses configuration xml
/*-
* Warning: Felix is unable to import the com.sun.rowset.internal
* package, meaning this can't use the XmlErrorHandler. This causes
* a warning and a default handler to be attached. Otherwise this
* should have: builder.setErrorHandler(new XmlErrorHandler());
*/
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(stream);
// iterates over nodes, parsing contents
Node root = doc.getChildNodes().item(1);
NodeList categories = root.getChildNodes();
for (int i = 0; i < categories.getLength(); ++i) {
Node node = categories.item(i);
if (node.getNodeName().equals(NODE_DEFAULTS)) {
parseDefaults(node.getChildNodes());
} else if (node.getNodeName().equals(NODE_LOCALES)) {
parseLocales(node.getChildNodes());
} else {
logger.warn("Unrecognized category: " + node.getNodeName());
}
}
} catch (IOException exc) {
logger.error("Unable to load spell checker parameters", exc);
} catch (SAXException exc) {
logger.error("Unable to parse spell checker parameters", exc);
} catch (ParserConfigurationException exc) {
logger.error("Unable to parse spell checker parameters", exc);
}
}
public static void testADWithInheritance() throws Exception {
Builder b = new Builder();
b.addClasspath(new File("bin"));
b.setProperty("Export-Package", "test.metatype");
b.setProperty("-metatype", "*");
b.setProperty("-metatype-inherit", "true");
b.build();
Resource r =
b.getJar()
.getResource(
"OSGI-INF/metatype/test.metatype.MetatypeTest$TestADWithInheritanceChild.xml");
assertEquals(0, b.getErrors().size());
assertEquals(0, b.getWarnings().size());
System.err.println(b.getJar().getResources().keySet());
assertNotNull(r);
IO.copy(r.openInputStream(), System.err);
Document d = db.parse(r.openInputStream());
assertAD(
d, "fromChild", "From child", "fromChild", null, null, null, 0, "String", null, null, null);
assertAD(
d,
"fromSuperOne",
"From super one",
"fromSuperOne",
null,
null,
null,
0,
"String",
null,
null,
null);
assertAD(
d,
"fromSuperTwo",
"From super two",
"fromSuperTwo",
null,
null,
null,
0,
"String",
null,
null,
null);
}
public void CaricamentoFile() {
DocumentBuilderFactory factory;
DocumentBuilder parser;
Document document;
try {
factory = DocumentBuilderFactory.newInstance();
parser = factory.newDocumentBuilder();
InputStream is = getClass().getClassLoader().getResource("text/caselle.xml").openStream();
document = parser.parse(is);
handleDocument(document);
} catch (Exception ex) {
System.out.println("Errore." + ex);
ex.printStackTrace();
}
}
private void processXml(Node operation)
throws ParserConfigurationException, TransformerConfigurationException {
List<Node> targets = getChildNodes(operation, "target");
List<Node> appendOpNodes = getChildNodes(operation, "append");
List<Node> setOpNodes = getChildNodes(operation, "set");
List<Node> replaceOpNodes = getChildNodes(operation, "replace");
List<Node> removeOpNodes = getChildNodes(operation, "remove");
if (targets.isEmpty()) {
return;
}
for (int t = 0; t < targets.size(); t++) {
File target = new File(absolutePath(targets.get(t).getTextContent()));
if (!target.exists()) {
Utils.onError(new Error.FileNotFound(target.getPath()));
return;
}
DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Document doc = null;
try {
doc = db.parse(target);
} catch (Exception ex) {
Utils.onError(new Error.FileParse(target.getPath()));
return;
}
for (int i = 0; i < removeOpNodes.size(); i++) removeXmlEntry(doc, removeOpNodes.get(i));
for (int i = 0; i < replaceOpNodes.size(); i++) replaceXmlEntry(doc, replaceOpNodes.get(i));
for (int i = 0; i < setOpNodes.size(); i++) setXmlEntry(doc, setOpNodes.get(i));
for (int i = 0; i < appendOpNodes.size(); i++) appendXmlEntry(doc, appendOpNodes.get(i));
try {
OutputFormat format = new OutputFormat(doc);
format.setOmitXMLDeclaration(true);
format.setLineWidth(65);
format.setIndenting(true);
format.setIndent(4);
Writer out = new FileWriter(target);
XMLSerializer serializer = new XMLSerializer(out, format);
serializer.serialize(doc);
} catch (IOException e) {
Utils.onError(new Error.WriteXmlConfig(target.getPath()));
}
}
}
/**
* Reads an XML document from an input source and copies its values into the specified object
*
* @param ob The object to receive the values
* @param source The location of the XML document
* @throws IOException If there is an error reading the document
*/
public void readObject(Object ob, InputSource source) throws IOException {
try {
// Create a document builder to read the document
DocumentBuilder builder = factory.newDocumentBuilder();
// Read the document
Document doc = builder.parse(source);
// Get the root element
Element element = doc.getDocumentElement();
// Copy the root element into the bean
readObject(ob, element);
} catch (SAXException exc) {
throw new IOException("Error parsing XML document: " + exc.toString());
} catch (ParserConfigurationException exc) {
throw new IOException("Error parsing XML document: " + exc.toString());
}
}
protected static Document GetXMLDocument(String url, int timeoutMS) {
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
InputStream input = HTMLTools.inputStream_GET(url, timeoutMS);
InputStreamReader reader = new InputStreamReader(input, ENCODING_UTF8);
InputSource inSrc = new InputSource(reader);
inSrc.setEncoding(ENCODING_UTF8);
return db.parse(inSrc);
} catch (ParserConfigurationException pce) {
Print.logError("Parse error: " + pce);
return null;
} catch (SAXException se) {
Print.logError("Parse error: " + se);
return null;
} catch (IOException ioe) {
Print.logError("IO error: " + ioe);
return null;
}
}
public static void testSimple() throws Exception {
Builder b = new Builder();
b.addClasspath(new File("bin"));
b.setProperty("Export-Package", "test.metatype");
b.setProperty("-metatype", "*");
b.build();
Resource r =
b.getJar().getResource("OSGI-INF/metatype/test.metatype.MetatypeTest$TestSimple.xml");
assertEquals(0, b.getErrors().size());
assertEquals(0, b.getWarnings().size());
System.err.println(b.getJar().getResources().keySet());
assertNotNull(r);
IO.copy(r.openInputStream(), System.err);
Document d = db.parse(r.openInputStream());
assertEquals("TestSimple", xpath.evaluate("//OCD/@name", d));
assertEquals("simple", xpath.evaluate("//OCD/@description", d));
assertEquals("test.metatype.MetatypeTest$TestSimple", xpath.evaluate("//OCD/@id", d));
assertEquals("test.metatype.MetatypeTest$TestSimple", xpath.evaluate("//Designate/@pid", d));
assertEquals("test.metatype.MetatypeTest$TestSimple", xpath.evaluate("//Object/@ocdref", d));
assertEquals("simple", xpath.evaluate("//OCD/AD[@id='simple']/@id", d));
assertEquals("Simple", xpath.evaluate("//OCD/AD[@id='simple']/@name", d));
assertEquals("String", xpath.evaluate("//OCD/AD[@id='simple']/@type", d));
assertEquals("true", xpath.evaluate("//OCD/AD[@id='notSoSimple']/@required", d));
/**
* https://github.com/bndtools/bnd/issues/281
*
* <p>Using the Bnd annotations library (1.52.3), the generated metatype file will have
* required='false' for all fields annotated with @Meta.AD(). When this annotation is omitted,
* or when the required property is explicitly set, the field is correctly marked as required.
* Taking a glance at the code, the bug appears to be due to aQute.bnd.osgi.Annotation using
* aQute.bnd.annotation.metatype.Configurable internally for bridging Bnd-annotations to
* Java-annotations. This configurable only obtains the values from the Bnd-annotation, omitting
* the defaults defined in the Java annotation. The workaround is to explicitly mention the
* required property on each field annotated with @Meta.AD.
*/
assertEquals("true", xpath.evaluate("//OCD/AD[@id='simple']/@required", d));
assertEquals(
Integer.MAX_VALUE + "", xpath.evaluate("//OCD/AD[@id='notSoSimple']/@cardinality", d));
}
protected Object exec(Object[] args, Context context) {
int nargs = args.length;
Object schema = null;
Map properties = null;
Object errorHandler;
Object input;
switch (nargs) {
case 4:
schema = args[3];
case 3:
properties = (Map) args[2];
case 2:
errorHandler = args[1];
break;
case 1:
errorHandler = Util.getDefaultErrorHandler(context);
break;
default:
undefined(args, context);
return null;
}
input = args[0];
if (properties == null) {
properties = new LinkedHashMap();
}
if (schema != null) {
properties.put(Util.KEY_SCHEMA, schema);
}
DocumentBuilder builder = Util.getDocumentBuilder(properties, context);
if (errorHandler != null) {
builder.setErrorHandler((ErrorHandler) Util.contentHandler(errorHandler, context));
}
try {
return builder.parse(Util.inputSource(input, context));
} catch (IOException e1) {
throw new PnutsException(e1, context);
} catch (SAXException e2) {
throw new PnutsException(e2, context);
}
}
private void call(String script)
throws ParserConfigurationException, TransformerConfigurationException {
File callerScript = this.currentScript;
Document doc = null;
try {
this.currentScript = new File(script);
DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
doc = db.parse(this.currentScript);
} catch (Exception ex) {
this.currentScript = callerScript;
Utils.onError(new Error.FileParse(script));
return;
}
NodeList operations = doc.getDocumentElement().getChildNodes();
for (int i = 0; i < operations.getLength(); i++) {
Node operation = operations.item(i);
if (operation.getNodeType() != Node.ELEMENT_NODE) continue;
call(operation);
}
this.currentScript = callerScript;
}
public String getFolderName(String pageCode) {
String usefulSection =
pageCode.substring(
pageCode.indexOf("<h3 id=\"breadcrumb\">"),
pageCode.indexOf("<div id=\"list-view\" class=\"view\""));
String folderName;
try {
DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
InputSource is = new InputSource();
is.setCharacterStream(new StringReader(usefulSection));
Document doc = db.parse(is);
NodeList divs = doc.getElementsByTagName("h3");
for (int i = 0; i < divs.getLength(); i++) {
Element div = (Element) divs.item(i);
String a = div.getTextContent();
folderName = a.substring(a.indexOf("/>") + 2).trim();
return folderName;
}
} catch (Exception e) {
debug(e.toString());
}
return "Error!";
}
static void assertOCD(
Builder b,
String cname,
String id,
String name,
String description,
String designate,
boolean factory,
String localization)
throws Exception {
Resource r = b.getJar().getResource("OSGI-INF/metatype/" + cname + ".xml");
assertNotNull(r);
IO.copy(r.openInputStream(), System.err);
Document d = db.parse(r.openInputStream());
assertEquals(id, xpath.evaluate("//OCD/@id", d, XPathConstants.STRING));
assertEquals(name, xpath.evaluate("//OCD/@name", d, XPathConstants.STRING));
assertEquals(
localization == null ? cname : localization,
xpath.evaluate("//OCD/@localization", d, XPathConstants.STRING));
assertEquals(
description == null ? "" : description,
xpath.evaluate("//OCD/@description", d, XPathConstants.STRING));
if (designate == null) {
assertEquals(id, xpath.evaluate("//Designate/@pid", d, XPathConstants.STRING));
if (factory)
assertEquals(id, xpath.evaluate("//Designate/@factoryPid", d, XPathConstants.STRING));
} else {
assertEquals(designate, xpath.evaluate("//Designate/@pid", d, XPathConstants.STRING));
if (factory)
assertEquals(
designate, xpath.evaluate("//Designate/@factoryPid", d, XPathConstants.STRING));
}
assertEquals(id, xpath.evaluate("//Object/@ocdref", d, XPathConstants.STRING));
}
/**
* XML Circuit constructor
*
* @param file the file that contains the XML description of the circuit
* @param g the graphics that will paint the node
* @throws CircuitLoadingException if the internal circuit can not be loaded
*/
public CircuitUI(File file, Graphics g) throws CircuitLoadingException {
this("");
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
Document doc;
Element root;
Hashtable<Integer, Link> linkstable = new Hashtable<Integer, Link>();
try {
builder = factory.newDocumentBuilder();
doc = builder.parse(file);
} catch (SAXException sxe) {
throw new CircuitLoadingException("SAX exception raised, invalid XML file.");
} catch (ParserConfigurationException pce) {
throw new CircuitLoadingException(
"Parser exception raised, parser configuration is invalid.");
} catch (IOException ioe) {
throw new CircuitLoadingException("I/O exception, file cannot be loaded.");
}
root = (Element) doc.getElementsByTagName("Circuit").item(0);
this.setName(root.getAttribute("name"));
NodeList nl = root.getElementsByTagName("Node");
Element e;
Node n;
Class cl;
for (int i = 0; i < nl.getLength(); ++i) {
e = (Element) nl.item(i);
try {
cl = Class.forName(e.getAttribute("class"));
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
try {
n = ((Node) cl.newInstance());
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
this.nodes.add(n);
n.setLocation(new Integer(e.getAttribute("x")), new Integer(e.getAttribute("y")));
if (n instanceof giraffe.ui.Nameable) ((Nameable) n).setNodeName(e.getAttribute("node_name"));
if (n instanceof giraffe.ui.CompositeNode) {
try {
((CompositeNode) n)
.load(new File(file.getParent() + "/" + e.getAttribute("file_name")), g);
} catch (Exception exc) {
/* try to load from the lib */
((CompositeNode) n)
.load(new File(giraffe.Giraffe.PATH + "/lib/" + e.getAttribute("file_name")), g);
}
}
NodeList nlist = e.getElementsByTagName("Anchor");
Element el;
for (int j = 0; j < nlist.getLength(); ++j) {
el = (Element) nlist.item(j);
Anchor a = n.getAnchor(new Integer(el.getAttribute("id")));
NodeList linklist = el.getElementsByTagName("Link");
Element link;
Link l;
for (int k = 0; k < linklist.getLength(); ++k) {
link = (Element) linklist.item(k);
int id = new Integer(link.getAttribute("id"));
int index = new Integer(link.getAttribute("index"));
if (id >= this.linkID) linkID = id + 1;
if (linkstable.containsKey(id)) {
l = linkstable.get(id);
l.addLinkedAnchorAt(a, index);
a.addLink(l);
} else {
l = new Link(id);
l.addLinkedAnchorAt(a, index);
this.links.add(l);
linkstable.put(id, l);
a.addLink(l);
}
}
}
}
}
// ## operation readReactorOutputFile(ReactionModel)
public SystemSnapshot readReactorOutputFile(ReactionModel p_reactionModel) {
// #[ operation readReactorOutputFile(ReactionModel)
try {
// open output file and build the DOM tree
String dir = System.getProperty("RMG.workingDirectory");
String filename = "chemkin/reactorOutput.xml";
File inputFile = new File(filename);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setValidating(true); // validate the document with the DTD
factory.setIgnoringElementContentWhitespace(true); // ignore whitespace
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(inputFile);
// get root element and its children
Element root = doc.getDocumentElement();
NodeList rootchildren = root.getChildNodes();
// header is rootchildren.item(0)
// get return message and check for successful run
Element returnmessageElement = (Element) rootchildren.item(1);
Text returnmessageText = (Text) returnmessageElement.getFirstChild();
String returnmessage = returnmessageText.toString();
returnmessage = returnmessage.trim();
if (!returnmessage.contains("SUCCESSFULLY COMPLETED RUN.")) {
System.out.println("External reactor model failed!");
System.out.println("Reactor model error message: " + returnmessage);
System.exit(0);
}
// get outputvalues element and its children
Element outputvaluesElement = (Element) rootchildren.item(2);
NodeList children = outputvaluesElement.getChildNodes();
// get time
Element timeElement = (Element) children.item(0);
Text timeText = (Text) timeElement.getFirstChild();
double time = Double.parseDouble(timeText.getData());
String timeUnits = timeElement.getAttribute("units");
// get systemstate element and its children
Element systemstateElement = (Element) children.item(1);
NodeList states = systemstateElement.getChildNodes();
// get temperature and its units
Element temperatureElement = (Element) states.item(0);
String tempUnits = temperatureElement.getAttribute("units");
Text temperatureText = (Text) temperatureElement.getFirstChild();
double temp = Double.parseDouble(temperatureText.getData());
Temperature T = new Temperature(temp, tempUnits);
// get pressure and its units
Element pressureElement = (Element) states.item(1);
String presUnits = pressureElement.getAttribute("units");
Text pressureText = (Text) pressureElement.getFirstChild();
double pres = Double.parseDouble(pressureText.getData());
Pressure P = new Pressure(pres, presUnits);
// get species amounts (e.g. concentrations)
ArrayList speciesIDs = new ArrayList();
ArrayList amounts = new ArrayList();
ArrayList fluxes = new ArrayList();
String amountUnits = null;
String fluxUnits = null;
// loop thru all the species
// begin at i=2, since T and P take already the first two position of states
int nSpe = (states.getLength() - 2) / 2;
int index = 0;
LinkedHashMap inertGas = new LinkedHashMap();
for (int i = 2; i < nSpe + 2; i++) {
// get amount element and the units
Element amountElement = (Element) states.item(i);
amountUnits = amountElement.getAttribute("units");
Element fluxElement = (Element) states.item(i + nSpe);
fluxUnits = fluxElement.getAttribute("units");
// get speciesid and store in an array list
String thisSpeciesID = amountElement.getAttribute("speciesid");
// get amount (e.g. concentraion) and store in an array list
Text amountText = (Text) amountElement.getFirstChild();
double thisAmount = Double.parseDouble(amountText.getData());
if (thisAmount < 0) {
double aTol = ReactionModelGenerator.getAtol();
// if (Math.abs(thisAmount) < aTol) thisAmount = 0;
// else throw new NegativeConcentrationException("Negative concentration in
// reactorOutput.xml: " + thisSpeciesID);
if (thisAmount < -100.0 * aTol)
throw new NegativeConcentrationException(
"Species "
+ thisSpeciesID
+ " has negative concentration: "
+ String.valueOf(thisAmount));
}
// get amount (e.g. concentraion) and store in an array list
Text fluxText = (Text) fluxElement.getFirstChild();
double thisFlux = Double.parseDouble(fluxText.getData());
if (thisSpeciesID.compareToIgnoreCase("N2") == 0
|| thisSpeciesID.compareToIgnoreCase("Ne") == 0
|| thisSpeciesID.compareToIgnoreCase("Ar") == 0) {
inertGas.put(thisSpeciesID, new Double(thisAmount));
} else {
speciesIDs.add(index, thisSpeciesID);
amounts.add(index, new Double(thisAmount));
fluxes.add(index, new Double(thisFlux));
index++;
}
}
// print results for debugging purposes
/**
* System.out.println(returnmessage); System.out.println("Temp = " + temp + " " + tempUnits);
* System.out.println("Pres = " + pres + " " + presUnits); for (int i = 0; i < amounts.size();
* i++) { System.out.println(speciesIDs.get(i) + " " + amounts.get(i) + " " + amountUnits); }
*/
ReactionTime rt = new ReactionTime(time, timeUnits);
LinkedHashMap speStatus = generateSpeciesStatus(p_reactionModel, speciesIDs, amounts, fluxes);
SystemSnapshot ss = new SystemSnapshot(rt, speStatus, T, P);
ss.inertGas = inertGas;
return ss;
} catch (Exception e) {
System.out.println("Error reading reactor model output: " + e.getMessage());
System.exit(0);
return null;
}
// #]
}
public static MiningResult importFile(InputStream input) throws IOException {
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
Document doc;
// NodeList netNodes;
dbf.setValidating(false);
dbf.setIgnoringComments(true);
dbf.setIgnoringElementContentWhitespace(true);
// dbf.setExpandEntityReferences(false);
// dbf.setNamespaceAware(false);
DocumentBuilder db = dbf.newDocumentBuilder();
db.setEntityResolver(
new EntityResolver() {
public InputSource resolveEntity(String publicId, String systemId) {
if (systemId.indexOf("ARIS-Export") != -1) {
return new InputSource("file:" + About.EXTLIBLOCATION() + "ARIS-Export101.dtd");
} else {
return null;
}
}
});
InputSource inpStream = new InputSource(input);
inpStream.setSystemId("file:" + System.getProperty("user.dir", ""));
doc = db.parse(inpStream);
// check if root element is a aml tag
Message.add("parsing done" + doc, Message.DEBUG);
if (!(doc.getDocumentElement().getNodeName().equals("AML"))) {
Message.add("aml tag not found", Message.ERROR);
throw new Exception("aml tag not found");
} else {
Message.add("aml root element found");
}
EPCResult result = new EPCResult(null, (EPC) null);
HashMap ObjDef_LinkId = new HashMap();
HashMap modelid_net = new HashMap();
HashMap ObjDef_Name = new HashMap();
HashMap function_LinkId = new HashMap();
HashMap ModelId_ModelType = new HashMap();
traverseAMLforObjectNames(
ObjDef_Name, doc.getDocumentElement(), ObjDef_LinkId, ModelId_ModelType);
Iterator findLinkToEpc = ObjDef_LinkId.keySet().iterator();
while (findLinkToEpc.hasNext()) {
String currentObjDef = (String) findLinkToEpc.next();
String Links = (String) ObjDef_LinkId.get(currentObjDef);
StringTokenizer linkSet = new StringTokenizer(Links);
String realEpcLink = "";
while (linkSet.hasMoreTokens()) {
String currentLink = linkSet.nextToken();
if (ModelId_ModelType.get(currentLink).equals("MT_EEPC")) {
realEpcLink = currentLink;
break;
}
}
if (realEpcLink.equals(" ")) {
ObjDef_LinkId.remove(currentObjDef);
} else {
ObjDef_LinkId.put(currentObjDef, realEpcLink);
}
}
result =
traverseAML(
result,
doc.getDocumentElement(),
null,
ObjDef_Name,
ObjDef_LinkId,
modelid_net,
function_LinkId);
Iterator hierarchicalFunctions = function_LinkId.keySet().iterator();
while (hierarchicalFunctions.hasNext()) {
EPCSubstFunction f = (EPCSubstFunction) hierarchicalFunctions.next();
f.setSubstitutedEPC((EPC) modelid_net.get(function_LinkId.get(f)));
// Message.add(f.getSubstitutedEPC().getName());
}
return result;
} catch (Throwable x) {
Message.add(x.toString());
throw new IOException(x.getMessage());
}
}
/**
* Given a DICOM object encoded as an XML document in a stream convert it to a list of attributes.
*
* @param stream the input stream containing the XML document
* @return the list of DICOM attributes
* @exception IOException
* @exception SAXException
* @exception DicomException
*/
public AttributeList getAttributeList(InputStream stream)
throws IOException, SAXException, DicomException {
Document document = db.parse(stream);
return getAttributeList(document);
}
// -----------------------------------------------------
// Description: Using the specified template, create
// csv records corresponding to the output xml criteria.
// -----------------------------------------------------
void transformWithTemplate(String templateName, String fileName, String destinationDirectory) {
System.out.println("fileName = " + fileName);
String fileName_woext = fileName.substring(0, fileName.lastIndexOf('.'));
try {
File fXmlFile = new File(templateLocation, templateName);
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document doc = dBuilder.parse(fXmlFile);
doc.getDocumentElement().normalize();
System.out.println("Root element :" + doc.getDocumentElement().getNodeName());
NodeList nList = doc.getElementsByTagName("output");
// loop through all the output nodes
for (int temp = 0; temp < nList.getLength(); temp++) {
Node nNode = nList.item(temp);
if (nNode.getNodeType() == Node.ELEMENT_NODE) {
Element eElement = (Element) nNode;
String outputLine = getTagValue("line", eElement);
FileWriter output =
new FileWriter(
destinationDirectory
+ File.separator
+ fileName_woext.substring(0, fileName.lastIndexOf('_'))
+ ".csv",
true);
BufferedWriter bufWrite = new BufferedWriter(output);
System.out.println(
destinationDirectory
+ File.separator
+ fileName_woext.substring(0, fileName.lastIndexOf("_"))
+ ".csv");
if (Settings.optionalIdentifier != null) {
bufWrite.write("\"" + Settings.optionalIdentifier + "\"");
}
String[] outputItems = outputLine.split("#");
for (String outputItem : outputItems) {
if ((temp == 0) && (Settings.optionalIdentifier == null)) {
bufWrite.write(
"\"" + interpretText(destinationDirectory, fileName_woext, outputItem) + "\"");
} else {
bufWrite.write(
",\"" + interpretText(destinationDirectory, fileName_woext, outputItem) + "\"");
}
}
bufWrite.write("\r\n");
bufWrite.close();
output.close();
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
public static void main(String[] args) {
try {
DocumentBuilderFactory db = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = db.newDocumentBuilder();
Document dom = builder.parse("data/geographic-area-data.html");
XPathFactory xpath = XPathFactory.newInstance();
XPath path = xpath.newXPath();
XPathExpression table =
path.compile("//div[@id='mw-content-text']/table[contains(@class,'wikitable')]/tr");
NodeList wikiData = (NodeList) table.evaluate(dom, XPathConstants.NODESET);
NodeList children;
String currentData, cleanData;
/* Open output stream */
FileWriter fstream = new FileWriter("data/parsed.yaml");
BufferedWriter out = new BufferedWriter(fstream);
for (int i = 0; i < wikiData.getLength(); i++) {
if (i == 0) {
continue;
}
out.write(new Integer(i).toString() + ":\n");
children = wikiData.item(i).getChildNodes();
for (int j = 0; j < children.getLength(); j++) {
currentData = (String) children.item(j).getTextContent();
switch (j) {
case 0:
/* Current Data is empty */
break;
case 1:
cleanData = decompose(currentData).trim().replaceAll("[^a-zA-Z\\s]+", "");
out.write("\t\"Geographic entity\": \"" + cleanData + "\"\n");
break;
case 2:
/* Current Data is empty */
break;
case 3:
cleanData = decompose(currentData).trim().replaceAll(",", "");
out.write("\t\"Area\": \"" + cleanData + "\"\n");
break;
case 4:
/* Current Data is empty */
break;
case 5:
cleanData = decompose(currentData).trim();
out.write("\t\"Notes\": \"" + cleanData + "\"\n");
break;
case 6:
/* Current Data is empty */
break;
default:
/* System.out.println("[" + j + "] Hit default case statement. Current Data is: " + currentData); */
break;
}
}
}
/* Close output stream */
out.close();
} catch (Exception e) {
System.out.println(e);
}
}
// -----------------------------------------------------
// Description: Determine if a template exists for the
// given file and return true on success.
// -----------------------------------------------------
boolean templateExistFor(String fileName, String destinationDirectory) {
templateIdentified = false;
// from template
int intOriginX = 0;
int intOriginY = 0;
// from template
int intX = 0;
int intY = 0;
int intWidth = 0;
int intHeight = 0;
// calculated
int viaTemplateX = 0;
int viaTemplateY = 0;
int viaTemplatePlusWidth = 0;
int viaTemplatePlusHeight = 0;
String fileName_woext = fileName.substring(0, fileName.lastIndexOf('.'));
String pathPlusFileName_woext =
destinationDirectory + File.separator + fileName_woext + File.separator + fileName_woext;
try {
File folder = new File(templateLocation);
File[] listOfFiles = folder.listFiles();
long startTime = System.currentTimeMillis();
for (File file : listOfFiles) {
if (file.isFile()) {
templateName = "";
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document doc = dBuilder.parse(file);
doc.getDocumentElement().normalize();
System.out.println("Root element :" + doc.getDocumentElement().getNodeName());
NodeList nList = doc.getElementsByTagName("condition");
for (int temp = 0; temp < nList.getLength(); temp++) {
Node nNode = nList.item(temp);
if (nNode.getNodeType() == Node.ELEMENT_NODE) {
Element eElement = (Element) nNode;
String myX = getTagValue("x", eElement);
String myY = getTagValue("y", eElement);
String myWidth = getTagValue("width", eElement);
String myHeight = getTagValue("height", eElement);
String mySuffix = getTagValue("suffix", eElement);
String myRequirements = getTagValue("required", eElement);
intX = Integer.parseInt(myX);
intY = Integer.parseInt(myY);
intWidth = Integer.parseInt(myWidth);
intHeight = Integer.parseInt(myHeight);
viaTemplateX = intX - (intOriginX - pageX);
viaTemplateY = intY - (intOriginY - pageY);
viaTemplatePlusWidth = viaTemplateX + intWidth;
viaTemplatePlusHeight = viaTemplateY + intHeight;
Spawn.execute(
Settings.Programs.CONVERT.path(),
pathPlusFileName_woext + "_trim.png",
"-crop",
String.format("%dx%d+%d+%d", intWidth, intHeight, viaTemplateX, viaTemplateY),
"+repage",
pathPlusFileName_woext + "_" + mySuffix + ".png");
Spawn.execute(
Settings.Programs.CONVERT.path(),
pathPlusFileName_woext + "_trim.png",
"-fill",
"none",
"-stroke",
"red",
"-strokewidth",
"3",
"-draw",
String.format(
"rectangle %d,%d %d,%d",
viaTemplateX, viaTemplateY, viaTemplatePlusWidth, viaTemplatePlusHeight),
"+repage",
pathPlusFileName_woext + "_draw.png");
Spawn.execute(
Settings.Programs.TESSERACT.path(),
pathPlusFileName_woext + "_" + mySuffix + ".png",
pathPlusFileName_woext + "_" + mySuffix);
String line = ""; // String that holds current file line
String accumulate = "";
try {
FileReader input = new FileReader(pathPlusFileName_woext + "_" + mySuffix + ".txt");
BufferedReader bufRead = new BufferedReader(input);
line = bufRead.readLine();
while (line != null) {
accumulate += line;
line = bufRead.readLine();
}
bufRead.close();
input.close();
} catch (IOException e) {
e.printStackTrace();
}
String[] requirements = myRequirements.split("#");
for (String requirement : requirements) {
if (requirement.equals(accumulate.trim())) {
templateName = file.getName();
templateIdentified = true;
return templateIdentified;
}
}
}
}
}
}
// record end time
long endTime = System.currentTimeMillis();
System.out.println(
"Template Search [" + fileName + "] " + (endTime - startTime) / 1000 + " seconds");
} catch (Exception e) {
e.printStackTrace();
}
return templateIdentified;
}
/** @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);
}
// -----------------------------------------------------
// Description: Using the specified template, extract
// the template sections into PNG and TXT corresponding
// parts.
// -----------------------------------------------------
void extractWithTemplate(String templateName, String fileName, String destinationDirectory) {
// from template
int intOriginX = 0;
int intOriginY = 0;
// from template
int intX = 0;
int intY = 0;
int intWidth = 0;
int intHeight = 0;
// calculated
int viaTemplateX = 0;
int viaTemplateY = 0;
int viaTemplatePlusWidth = 0;
int viaTemplatePlusHeight = 0;
System.out.println("fileName = " + fileName);
String fileName_woext = fileName.substring(0, fileName.lastIndexOf('.'));
String pathPlusFileName_woext =
destinationDirectory + File.separator + fileName_woext + File.separator + fileName_woext;
System.out.println("pathPlusFileName_woext = " + pathPlusFileName_woext);
try {
File fXmlFile = new File(templateLocation, templateName);
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document doc = dBuilder.parse(fXmlFile);
doc.getDocumentElement().normalize();
System.out.println("Root element :" + doc.getDocumentElement().getNodeName());
NodeList nList = doc.getElementsByTagName("section");
Node nNode;
for (int temp = 0; temp < nList.getLength(); temp++) {
nNode = nList.item(temp);
if (nNode.getNodeType() == Node.ELEMENT_NODE) {
Element eElement = (Element) nNode;
String myX = getTagValue("x", eElement);
String myY = getTagValue("y", eElement);
String myWidth = getTagValue("width", eElement);
String myHeight = getTagValue("height", eElement);
String mySuffix = getTagValue("suffix", eElement);
intX = Integer.parseInt(myX);
intY = Integer.parseInt(myY);
intWidth = Integer.parseInt(myWidth);
intHeight = Integer.parseInt(myHeight);
viaTemplateX = intX - (intOriginX - pageX);
viaTemplateY = intY - (intOriginY - pageY);
viaTemplatePlusWidth = viaTemplateX + intWidth;
viaTemplatePlusHeight = viaTemplateY + intHeight;
Spawn.execute(
Settings.Programs.CONVERT.path(),
pathPlusFileName_woext + "_trim.png",
"-crop",
String.format("%dx%d+%d+%d", intWidth, intHeight, viaTemplateX, viaTemplateY),
"+repage",
pathPlusFileName_woext + "_" + mySuffix + ".png");
Spawn.execute(
Settings.Programs.CONVERT.path(),
pathPlusFileName_woext + "_trim.png",
"-fill",
"none",
"-stroke",
"red",
"-strokewidth",
"3",
"-draw",
String.format(
"rectangle %d,%d %d,%d",
viaTemplateX, viaTemplateY, viaTemplatePlusWidth, viaTemplatePlusHeight),
"+repage",
pathPlusFileName_woext + "_draw.png");
Spawn.execute(
Settings.Programs.TESSERACT.path(),
pathPlusFileName_woext + "_" + mySuffix + ".png",
pathPlusFileName_woext + "_" + mySuffix);
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
