protected void setFormObject(Forms forms, XmlObject formObject) {
// Create a cursor from the grants.gov form
XmlCursor formCursor = formObject.newCursor();
formCursor.toStartDoc();
formCursor.toNextToken();
// Create a cursor from the Forms object
XmlCursor metaGrantCursor = forms.newCursor();
metaGrantCursor.toNextToken();
// Add the form to the Forms object.
formCursor.moveXml(metaGrantCursor);
}
public static void fixNamespaceForXsiType(XmlObject content, Map<?, ?> namespaces) {
final XmlCursor cursor = content.newCursor();
while (cursor.hasNextToken()) {
if (cursor.toNextToken().isStart()) {
final String xsiType = cursor.getAttributeText(W3CConstants.QN_XSI_TYPE);
if (xsiType != null) {
final String[] toks = xsiType.split(":");
if (toks.length > 1) {
String prefix = toks[0];
String localName = toks[1];
String namespace = (String) namespaces.get(prefix);
if (Strings.isNullOrEmpty(namespace)) {
namespace = CodingRepository.getInstance().getNamespaceFor(prefix);
}
if (StringHelper.isNotEmpty(namespace)) {
cursor.setAttributeText(
W3CConstants.QN_XSI_TYPE,
Joiner.on(Constants.COLON_CHAR)
.join(
XmlHelper.getPrefixForNamespace(content, (String) namespaces.get(prefix)),
localName));
}
}
}
}
}
cursor.dispose();
}
public static void fixNamespaceForXsiType(final XmlObject object, final QName value) {
final XmlCursor cursor = object.newCursor();
while (cursor.hasNextToken()) {
if (cursor.toNextToken().isStart()) {
final String xsiType = cursor.getAttributeText(W3CConstants.QN_XSI_TYPE);
if (xsiType != null) {
final String[] toks = xsiType.split(":");
String localName;
String prefix;
if (toks.length > 1) {
prefix = toks[0];
localName = toks[1];
} else {
localName = toks[0];
}
if (localName.equals(value.getLocalPart())) {
cursor.setAttributeText(
W3CConstants.QN_XSI_TYPE,
Joiner.on(Constants.COLON_CHAR)
.join(
XmlHelper.getPrefixForNamespace(object, value.getNamespaceURI()),
value.getLocalPart()));
}
}
}
}
cursor.dispose();
}
private void processElement(SchemaParticle sp, XmlCursor xmlc, boolean mixed) {
// cast as schema local element
SchemaLocalElement element = (SchemaLocalElement) sp;
// Add comment about type
addElementTypeAndRestricionsComment(element, xmlc);
// / ^ -> <elemenname></elem>^
if (_soapEnc) xmlc.insertElement(element.getName().getLocalPart()); // soap
// encoded?
// drop
// namespaces.
else xmlc.insertElement(element.getName().getLocalPart(), element.getName().getNamespaceURI());
// / -> <elem>^</elem>
// processAttributes( sp.getType(), xmlc );
xmlc.toPrevToken();
// -> <elem>stuff^</elem>
String[] values = null;
if (multiValues != null) values = multiValues.get(element.getName());
if (values != null) xmlc.insertChars(StringUtils.join(values, ","));
else if (sp.isDefault()) xmlc.insertChars(sp.getDefaultText());
else createSampleForType(element.getType(), xmlc);
// -> <elem>stuff</elem>^
xmlc.toNextToken();
}
/**
* Creates the administrative metadata section of a mets document.
*
* @param id the id of this amdSec
* @param owner the rights owner of the item
* @param logo the logo of the organization
* @param url the url of the organization
* @param reference the items url
*/
public void createAmdSec(String id, String owner, String logo, String url, String reference) {
this.amdSec = this.mets.addNewAmdSec();
this.amdSec.setID(id);
// DVRights
MdSecType rightsMD = this.amdSec.addNewRightsMD();
rightsMD.setID("rights" + id);
MdWrap wrap = rightsMD.addNewMdWrap();
wrap.setMIMETYPE("text/xml");
wrap.setMDTYPE(MdWrap.MDTYPE.OTHER);
wrap.setOTHERMDTYPE("DVRIGHTS");
XmlData xml = wrap.addNewXmlData();
XmlObject dvrights = XmlObject.Factory.newInstance();
XmlCursor cur = dvrights.newCursor();
cur.toNextToken();
cur.beginElement("rights", "http://dfg-viewer.de/");
cur.insertElementWithText("owner", "http://dfg-viewer.de/", owner);
cur.insertElementWithText("ownerLogo", "http://dfg-viewer.de/", logo);
cur.insertElementWithText("ownerSiteURL", "http://dfg-viewer.de/", url);
cur.insertElementWithText("contact", "http://dfg-viewer.de/", "*****@*****.**");
cur.dispose();
xml.set(dvrights);
wrap.setXmlData(xml);
rightsMD.setMdWrap(wrap);
this.amdSec.setRightsMDArray(0, rightsMD);
// DVLinks
MdSecType digiprovMD = this.amdSec.addNewDigiprovMD();
digiprovMD.setID("digiprov" + id);
MdWrap dpWrap = digiprovMD.addNewMdWrap();
dpWrap.setMIMETYPE("text/xml");
dpWrap.setMDTYPE(MdWrap.MDTYPE.OTHER);
dpWrap.setOTHERMDTYPE("DVLINKS");
XmlData dpXml = dpWrap.addNewXmlData();
XmlObject dvdigiprov = XmlObject.Factory.newInstance();
XmlCursor dpCur = dvdigiprov.newCursor();
dpCur.toNextToken();
dpCur.beginElement("links", "http://dfg-viewer.de/");
dpCur.insertElementWithText("reference", "http://dfg-viewer.de/", reference);
dpCur.insertElementWithText(
"presentation", "http://dfg-viewer.de/", "http://vm38.mpdl.mpg.de:8080/dlib-journals/");
dpCur.dispose();
dpXml.set(dvdigiprov);
dpWrap.setXmlData(dpXml);
digiprovMD.setMdWrap(dpWrap);
this.amdSec.setDigiprovMDArray(0, digiprovMD);
}
@SuppressWarnings("unused")
private void moveToken(int numToMove, XmlCursor xmlc) {
for (int i = 0; i < Math.abs(numToMove); i++) {
if (numToMove < 0) {
xmlc.toPrevToken();
} else {
xmlc.toNextToken();
}
}
}
/**
* Remove namespace declarations from an xml fragment (useful for moving all declarations to a
* document root
*
* @param x The fragment to localize
*/
public static void removeNamespaces(final XmlObject x) {
final XmlCursor c = x.newCursor();
while (c.hasNextToken()) {
if (c.isNamespace()) {
c.removeXml();
} else {
c.toNextToken();
}
}
c.dispose();
}
public static String createSampleForElement(SchemaGlobalElement element) {
XmlObject xml = XmlObject.Factory.newInstance();
XmlCursor c = xml.newCursor();
c.toNextToken();
c.beginElement(element.getName());
new SampleXmlUtil(false).createSampleForType(element.getType(), c);
c.dispose();
XmlOptions options = new XmlOptions();
options.put(XmlOptions.SAVE_PRETTY_PRINT);
options.put(XmlOptions.SAVE_PRETTY_PRINT_INDENT, 3);
options.put(XmlOptions.SAVE_AGGRESSIVE_NAMESPACES);
options.setSaveOuter();
String result = xml.xmlText(options);
return result;
}
public static String createSampleForType(SchemaType sType) {
XmlObject object = XmlObject.Factory.newInstance();
XmlCursor cursor = object.newCursor();
// Skip the document node
cursor.toNextToken();
// Using the type and the cursor, call the utility method to get a
// sample XML payload for that Schema element
new SampleXmlUtil(false).createSampleForType(sType, cursor);
// Cursor now contains the sample payload
// Pretty print the result. Note that the cursor is positioned at the
// end of the doc so we use the original xml object that the cursor was
// created upon to do the xmlText() against.
cursor.dispose();
XmlOptions options = new XmlOptions();
options.put(XmlOptions.SAVE_PRETTY_PRINT);
options.put(XmlOptions.SAVE_PRETTY_PRINT_INDENT, 3);
options.put(XmlOptions.SAVE_AGGRESSIVE_NAMESPACES);
options.setSaveOuter();
String result = object.xmlText(options);
return result;
}
static void addStylesheet(InterfaceDocument feed) {
XmlCursor cursor = feed.newCursor();
cursor.toNextToken();
cursor.insertProcInst("xml-stylesheet", "type='text/xsl' href='feed.xsl'");
}
@Override
protected void checkMessageStructure() throws MessageValidationException {
boolean messageStructureFailure = false;
try {
// Create a pseudo XML message
XmlObject pseudoMessage = XmlObject.Factory.newInstance();
XmlCursor pmCursor = pseudoMessage.newCursor();
pmCursor.toNextToken();
pmCursor.beginElement(profile.getMessageStructureID(), "urn:hl7-org:v2xml");
BufferedReader br = new BufferedReader(new StringReader(message.getMessageAsString()));
String line = null;
while ((line = br.readLine()) != null) {
if (!line.matches("\\s*")) {
String fieldSep = ((Er7Message) message).getFieldSeparatorChar();
try {
int idx = line.indexOf(fieldSep);
if (idx == -1 && line.length() <= 3) {
idx = 3;
}
line = line.substring(0, idx);
if (!line.startsWith("Z")) {
pmCursor.beginElement(line, "urn:hl7-org:v2xml");
pmCursor.toNextToken();
}
} catch (StringIndexOutOfBoundsException e) {
if (line.length() > 3) {
System.out.println(line);
}
}
}
}
pmCursor.dispose();
// Create a schema
StreamSource xsltStream =
new StreamSource(
MessageStructureValidationV2Er7.class
.getClassLoader()
.getResourceAsStream(MessageValidationConstants.XSLT_CHECK_STRUCTURE));
Transformer t = TransformerFactory.newInstance().newTransformer(xsltStream);
t.setParameter("groups", "false");
t.setParameter("xml", "false");
StreamSource src = new StreamSource(profile.getDocument().newInputStream());
ByteArrayOutputStream out = new ByteArrayOutputStream();
t.transform(src, new StreamResult(out));
XmlObject schemaDoc =
XmlObject.Factory.parse(
new ByteArrayInputStream(out.toByteArray()), (new XmlOptions()).setLoadLineNumbers());
// pseudoMessage.save(new File("tmp/mu/PseudoMessage.xml"));
// schemaDoc.save(new File("tmp/mu/Schema.xsd"));
// Load the schema
SchemaTypeLoader sLoader = null;
Collection<Object> compErrors = new ArrayList<Object>();
XmlOptions schemaOptions = new XmlOptions();
schemaOptions.setErrorListener(compErrors);
XmlObject[] schemas = new XmlObject[1];
schemas[0] = schemaDoc;
sLoader = XmlBeans.compileXsd(schemas, sLoader, schemaOptions);
// Load the Message
XmlObject xobj =
sLoader.parse(pseudoMessage.toString(), null, (new XmlOptions()).setLoadLineNumbers());
// Validate the Message against the schema
Collection<XmlValidationError> errors = new ArrayList<XmlValidationError>();
xobj.validate(new XmlOptions().setErrorListener(errors));
Iterator<XmlValidationError> it = errors.iterator();
while (it.hasNext()) {
XmlValidationError xve = it.next();
messageFailures.add(interpretSchemaError(xve));
messageStructureFailure = true;
}
} catch (XmlException xmle) {
// This type of exception is thrown when the generated schema is
// ambiguous
MessageFailureV2 mf = new MessageFailureV2(message.getEncoding());
mf.setDescription(
"The message validation can't be performed because the profile is ambiguous."
+ " Possible reasons for this problem include an ambiguous message definition"
+ " specified in the standard or an ambiguous message definition caused by the"
+ " user changing the Usage settings for segments during profile creation."
+ " Remember that a segment with the same name MUST be separated by at least one"
+ " non-optional segment with a different name.");
mf.setFailureSeverity(ErrorSeverityConstants.FATAL);
mf.setFailureType(AssertionTypeV2Constants.AMBIGUOUS_PROFILE);
messageFailures.add(mf);
} catch (Exception e) {
throw new MessageValidationException(e.getMessage());
} finally {
if (!messageStructureFailure) {
MessageFailureV2 mf = new MessageFailureV2(message.getEncoding());
mf.setDescription("The message structure at the segment level is correct.");
mf.setFailureSeverity(ErrorSeverityConstants.NORMAL);
mf.setFailureType(AssertionTypeV2Constants.CHECKED);
messageFailures.add(mf);
}
}
}
