private Document checkSubUniprot(String substrateuni) {
String UniprotURL = "http://www.uniprot.org/uniprot/" + substrateuni + ".xml";
System.out.println(UniprotURL + "bbbbb");
ParseUniprotPep parser = new ParseUniprotPep();
Document xml = null;
String xmlstring = parser.getXMLasstring(UniprotURL);
xml = parser.getXML(UniprotURL);
xml.getXmlVersion();
return xml;
}
/**
* Copy the AndroidManifest.xml from sourceManifestFile to androidManifestFile
*
* @throws MojoExecutionException
*/
protected void copyManifest() throws MojoExecutionException {
getLog().debug("copyManifest: " + sourceManifestFile + " -> " + androidManifestFile);
if (sourceManifestFile == null) {
getLog().debug("Manifest copying disabled. Using default manifest only");
return;
}
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc = db.parse(sourceManifestFile);
Source source = new DOMSource(doc);
TransformerFactory xfactory = TransformerFactory.newInstance();
Transformer xformer = xfactory.newTransformer();
xformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
FileWriter writer = null;
try {
androidManifestFile.getParentFile().mkdirs();
writer = new FileWriter(androidManifestFile, false);
if (doc.getXmlEncoding() != null && doc.getXmlVersion() != null) {
String xmldecl =
String.format(
"<?xml version=\"%s\" encoding=\"%s\"?>%n",
doc.getXmlVersion(), doc.getXmlEncoding());
writer.write(xmldecl);
}
Result result = new StreamResult(writer);
xformer.transform(source, result);
getLog().info("Manifest copied from " + sourceManifestFile + " to " + androidManifestFile);
} finally {
IOUtils.closeQuietly(writer);
}
} catch (Exception e) {
getLog().error("Error during copyManifest");
throw new MojoExecutionException("Error during copyManifest", e);
}
}
public boolean enter(Document document) {
if (!noDecl) {
buffer.append("<?xml version=\"");
buffer.append(document.getXmlVersion());
buffer.append("\"");
if (encoding != null) {
buffer.append(" encoding=\"");
buffer.append(encoding);
buffer.append("\"");
}
buffer.append("?>\n");
}
return true;
}
private Document parseUniprot(String url) {
ParseUniprot parser = new ParseUniprot();
Document xml = parser.getXML(url);
xml.getXmlVersion();
return xml;
}
/* */ private void setDocumentInfo(Document document) /* */ {
/* 377 */ if (!document.getXmlStandalone())
/* 378 */ this._handler.setStandalone(Boolean.toString(document.getXmlStandalone()));
/* 379 */ setXMLVersion(document.getXmlVersion());
/* 380 */ setEncoding(document.getXmlEncoding());
/* */ }
public boolean validate() {
boolean retval = false;
FileObject xmlfile = null;
FileObject DTDfile = null;
ByteArrayInputStream ba = null;
try {
if (xmlfilename != null
&& ((getDTDFilename() != null && !isInternDTD()) || (isInternDTD()))) {
xmlfile = KettleVFS.getFileObject(getXMLFilename());
if (xmlfile.exists()) {
URL xmlFile = new File(KettleVFS.getFilename(xmlfile)).toURI().toURL();
StringBuffer xmlStringbuffer = new StringBuffer("");
BufferedReader xmlBufferedReader = null;
InputStreamReader is = null;
try {
// open XML File
is = new InputStreamReader(xmlFile.openStream());
xmlBufferedReader = new BufferedReader(is);
char[] buffertXML = new char[1024];
int LenXML = -1;
while ((LenXML = xmlBufferedReader.read(buffertXML)) != -1) {
xmlStringbuffer.append(buffertXML, 0, LenXML);
}
} finally {
if (is != null) {
is.close();
}
if (xmlBufferedReader != null) {
xmlBufferedReader.close();
}
}
// Prepare parsing ...
DocumentBuilderFactory DocBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder DocBuilder = DocBuilderFactory.newDocumentBuilder();
// Let's try to get XML document encoding
DocBuilderFactory.setValidating(false);
ba = new ByteArrayInputStream(xmlStringbuffer.toString().getBytes("UTF-8"));
Document xmlDocDTD = DocBuilder.parse(ba);
if (ba != null) {
ba.close();
}
String encoding = null;
if (xmlDocDTD.getXmlEncoding() == null) {
encoding = "UTF-8";
} else {
encoding = xmlDocDTD.getXmlEncoding();
}
int xmlStartDTD = xmlStringbuffer.indexOf("<!DOCTYPE");
if (isInternDTD()) {
// DTD find in the XML document
if (xmlStartDTD != -1) {
log.logBasic(
BaseMessages.getString(
PKG, "JobEntryDTDValidator.ERRORDTDFound.Label", getXMLFilename()));
} else {
setErrorMessage(
BaseMessages.getString(
PKG, "JobEntryDTDValidator.ERRORDTDNotFound.Label", getXMLFilename()));
}
} else {
// DTD in external document
// If we find an intern declaration, we remove it
DTDfile = KettleVFS.getFileObject(getDTDFilename());
if (DTDfile.exists()) {
if (xmlStartDTD != -1) {
int EndDTD = xmlStringbuffer.indexOf(">", xmlStartDTD);
// String DocTypeDTD = xmlStringbuffer.substring(xmlStartDTD, EndDTD + 1);
xmlStringbuffer.replace(xmlStartDTD, EndDTD + 1, "");
}
String xmlRootnodeDTD = xmlDocDTD.getDocumentElement().getNodeName();
String RefDTD =
"<?xml version='"
+ xmlDocDTD.getXmlVersion()
+ "' encoding='"
+ encoding
+ "'?>\n<!DOCTYPE "
+ xmlRootnodeDTD
+ " SYSTEM '"
+ KettleVFS.getFilename(DTDfile)
+ "'>\n";
int xmloffsetDTD = xmlStringbuffer.indexOf("<" + xmlRootnodeDTD);
xmlStringbuffer.replace(0, xmloffsetDTD, RefDTD);
} else {
log.logError(
BaseMessages.getString(PKG, "JobEntryDTDValidator.ERRORDTDFileNotExists.Subject"),
BaseMessages.getString(
PKG, "JobEntryDTDValidator.ERRORDTDFileNotExists.Msg", getDTDFilename()));
}
}
if (!(isInternDTD() && xmlStartDTD == -1 || (!isInternDTD() && !DTDfile.exists()))) {
// Let's parse now ...
MyErrorHandler error = new MyErrorHandler();
DocBuilderFactory.setValidating(true);
DocBuilder = DocBuilderFactory.newDocumentBuilder();
DocBuilder.setErrorHandler(error);
ba = new ByteArrayInputStream(xmlStringbuffer.toString().getBytes(encoding));
xmlDocDTD = DocBuilder.parse(ba);
if (error.errorMessage == null) {
log.logBasic(
BaseMessages.getString(PKG, "JobEntryDTDValidator.DTDValidatorOK.Subject"),
BaseMessages.getString(
PKG, "JobEntryDTDValidator.DTDValidatorOK.Label", getXMLFilename()));
// Everything is OK
retval = true;
} else {
// Invalid DTD
setNrErrors(error.nrErrors);
setErrorMessage(
BaseMessages.getString(
PKG,
"JobEntryDTDValidator.DTDValidatorKO",
getXMLFilename(),
error.nrErrors,
error.errorMessage));
}
}
} else {
if (!xmlfile.exists()) {
setErrorMessage(
BaseMessages.getString(
PKG, "JobEntryDTDValidator.FileDoesNotExist.Label", getXMLFilename()));
}
}
} else {
setErrorMessage(BaseMessages.getString(PKG, "JobEntryDTDValidator.AllFilesNotNull.Label"));
}
} catch (Exception e) {
setErrorMessage(
BaseMessages.getString(
PKG,
"JobEntryDTDValidator.ErrorDTDValidator.Label",
getXMLFilename(),
getDTDFilename(),
e.getMessage()));
} finally {
try {
if (xmlfile != null) {
xmlfile.close();
}
if (DTDfile != null) {
DTDfile.close();
}
if (ba != null) {
ba.close();
}
} catch (IOException e) {
// Ignore close errors
}
}
return retval;
}
