/**
* This method is used to get RRFedNonFedBudget from BudgetSubAwards
*
* @param budgetSubAwards(BudgetSubAwards) budget sub awards entry.
* @return RRFedNonFedBudget corresponding to the BudgetSubAwards object.
*/
private RRFedNonFedBudgetDocument getRRFedNonFedBudget(BudgetSubAwards budgetSubAwards) {
RRFedNonFedBudgetDocument rrBudget = RRFedNonFedBudgetDocument.Factory.newInstance();
String subAwdXML = budgetSubAwards.getSubAwardXmlFileData();
Document subAwdFormsDoc;
try {
subAwdFormsDoc = stringToDom(subAwdXML);
} catch (S2SException e1) {
return rrBudget;
}
Element subAwdFormsElement = subAwdFormsDoc.getDocumentElement();
NodeList subAwdNodeList =
subAwdFormsElement.getElementsByTagNameNS(
RR_FED_NON_FED_BUDGET30_11_NAMESPACE_URI, LOCAL_FED_NON_FED_NAME);
Node subAwdNode = null;
if (subAwdNodeList != null) {
if (subAwdNodeList.getLength() == 0) {
return null;
}
subAwdNode = subAwdNodeList.item(0);
}
byte[] subAwdNodeBytes = null;
try {
subAwdNodeBytes = docToBytes(nodeToDom(subAwdNode));
InputStream bgtIS = new ByteArrayInputStream(subAwdNodeBytes);
rrBudget = (RRFedNonFedBudgetDocument) XmlObject.Factory.parse(bgtIS);
} catch (S2SException e) {
return rrBudget;
} catch (XmlException e) {
return rrBudget;
} catch (IOException e) {
return rrBudget;
}
return rrBudget;
}
/**
* Parse XML document from HTTP-Post request.
*
* @param request HTTP-Post request
* @return XML document
* @throws OwsExceptionReport If an error occurs
*/
public static XmlObject parseXmlSosRequest(final HttpServletRequest request)
throws OwsExceptionReport {
XmlObject doc;
try {
if (request.getParameterMap().isEmpty()) {
final String requestContent =
StringHelper.convertStreamToString(
HTTPUtils.getInputStream(request), request.getCharacterEncoding());
doc = parseXmlString(requestContent);
} else {
doc =
XmlObject.Factory.parse(
SosHelper.parseHttpPostBodyWithParameter(
request.getParameterNames(), request.getParameterMap()));
}
} catch (final XmlException xmle) {
throw new NoApplicableCodeException()
.causedBy(xmle)
.withMessage(
"An xml error occured when parsing the request! Message: %s", xmle.getMessage());
} catch (final IOException ioe) {
throw new NoApplicableCodeException()
.causedBy(ioe)
.withMessage("Error while reading request! Message: %s", ioe.getMessage());
}
// validateDocument(doc);
return doc;
}
public void afterSubmit(Submit submit, SubmitContext context) {
if (submit.getResponse() == null) return;
HttpResponse httpResponse = (HttpResponse) submit.getResponse();
String content = httpResponse.getContentAsXml();
if (content == null || content.equals("<xml/>")) return;
XmlObject xml;
try {
URL url = httpResponse.getURL();
String defaultNamespace = url.getProtocol() + "://" + url.getHost();
XmlOptions options =
new XmlOptions()
.setLoadSubstituteNamespaces(Collections.singletonMap("", defaultNamespace));
xml = XmlObject.Factory.parse(content, options);
} catch (XmlException e) {
e.printStackTrace();
return;
}
if (!submit.getStatus().equals(Status.CANCELED)
&& !InferredSchemaManager.getInferredSchema(service).validate(xml)) {
setTitle("Schema (conflicts)");
if (thread != null && thread.isAlive()) {
handler.kill();
try {
thread.join();
} catch (InterruptedException e) {
e.printStackTrace();
}
}
handler = new Handler(tabs, xml);
thread = new Thread(handler);
thread.start();
}
}
/**
* HAVE message notification handler.
*
* @param message the message
* @ssdd
*/
@Override
public void haveMessageNotificationHandler(Core2CoreMessage message) {
log.debug("haveMessageNotificationHandler: received messagefrom " + message.getFromCore());
// =[" + message.getMessage()+ "]
XmlObject xmlObj;
try {
EDXLDistributionDocument edxlDoc =
EDXLDistributionDocument.Factory.parse(message.getMessage());
if (edxlDoc.getEDXLDistribution().sizeOfExplicitAddressArray() > 0) {
// Find core name for each explicit address.
for (ValueSchemeType type : edxlDoc.getEDXLDistribution().getExplicitAddressArray()) {
if (type.getExplicitAddressScheme()
.equals(CommunicationsService.UICDSExplicitAddressScheme)) {
for (String address : type.getExplicitAddressValueArray()) {
xmlObj = XmlObject.Factory.parse(edxlDoc.toString());
// log.debug("broadcastMessageNotificationHandler: sending notification ["
// + xmlObj.toString() + "] to " + address);
sendMessageNotification(xmlObj, address);
}
}
}
}
} catch (Throwable e) {
log.error(
"resourceMessageNotificationHandler: Error parsing message - not a valid XML string");
throw new IllegalArgumentException("Message is not a valid XML string");
}
}
/**
* 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);
}
/**
* Builds the SRA {@link SpotDescriptorType}, this is taken from the ISATAB "sequencing" protocol
* that has been used for this assay.
*
* <p>Some of these parameters are mandatory in SRA, and/or constrained to certain values, so the
* method raises an exception in case they're not defined.
*/
protected SpotDescriptorType buildExportedSpotDescriptor(Assay assay) {
ProtocolApplication pApp = getProtocol(assay, "sequencing");
if (pApp == null) {
return null;
}
String barcode = getParameterValue(assay, pApp, "barcode", false);
System.out.println("barcode: " + barcode);
String adapterSpec = getParameterValue(assay, pApp, "Adapter Spec", false);
String numOfSpotReads = getParameterValue(assay, pApp, "Number of reads per spot", false);
boolean usesBarcode = (barcode != null);
SRATemplate sraTemplateToInject =
getSRATemplateToInject(SRASection.SPOT_DESCRIPTOR, assay, pApp, usesBarcode);
SpotDescriptorType xspotd = SpotDescriptorType.Factory.newInstance();
Map<SRAAttributes, String> userDefinedAttributes = new HashMap<SRAAttributes, String>();
if (!StringUtils.isEmpty(adapterSpec)) {
userDefinedAttributes.put(SRAAttributes.ADAPTER_SPEC, adapterSpec);
}
if (!StringUtils.isEmpty(numOfSpotReads)) {
userDefinedAttributes.put(SRAAttributes.NUMBER_OF_READS_PER_SPOT, numOfSpotReads);
}
if (!StringUtils.isEmpty(barcode)) {
userDefinedAttributes.put(SRAAttributes.READ_GROUP_TAG, barcode);
}
try {
String sraTemplate =
sraTemplateLoader.getSRAProcessingTemplate(sraTemplateToInject, userDefinedAttributes);
System.out.println(sraTemplate);
XmlOptions xmlOptions = new XmlOptions();
xmlOptions.setDocumentType(SpotDescriptorType.Factory.newInstance().schemaType());
XmlObject parsedAttr = XmlObject.Factory.parse(sraTemplate, xmlOptions);
xspotd.set(parsedAttr);
return xspotd;
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (XmlException e) {
e.printStackTrace();
}
return xspotd;
}
public SchemaTypeSystem getTypeSystem() {
if (typeSystem != null) return typeSystem;
try {
typeSystem = XmlObject.Factory.parse(xml).schemaType().getTypeSystem();
return typeSystem;
} catch (Exception e) {
return XmlBeans.getBuiltinTypeSystem();
}
}
public static XmlObject parseXmlString(final String xmlString) throws OwsExceptionReport {
try {
return XmlObject.Factory.parse(xmlString);
} catch (final XmlException xmle) {
throw new NoApplicableCodeException()
.causedBy(xmle)
.withMessage(
"An xml error occured when parsing the request! Message: %s", xmle.getMessage());
}
}
private QName getResponseBodyElementName(RestMessageExchange messageExchange) {
try {
XmlObject xmlObject = XmlObject.Factory.parse(messageExchange.getResponseContentAsXml());
Element docElement = ((Document) xmlObject.getDomNode()).getDocumentElement();
return new QName(docElement.getNamespaceURI(), docElement.getLocalName());
} catch (XmlException e) {
SoapUI.logError(e);
}
return null;
}
/**
* Uses the XPath text() function to get values from <name> elements in received XML, then
* collects those values as the value of a <names> element created here.
*
* <p>Demonstrates the following characteristics of the selectPath method:
*
* <p>- It supports expressions that include XPath function calls. - selectPath called from an
* XmlCursor instance (instead of an XMLBeans type) places results (if any) into the cursor's
* selection set.
*
* @param empDoc The incoming XML.
* @return <code>true</code> if the XPath expression returned results; otherwise, <code>false
* </code>.
*/
public boolean collectNames(XmlObject empDoc) {
boolean hasResults = false;
// Create a cursor with which to execute query expressions. The cursor
// is inserted at the very beginning of the incoming XML, then moved to
// the first element's START token.
XmlCursor pathCursor = empDoc.newCursor();
pathCursor.toFirstChild();
// Execute the path expression, qualifying it with the namespace
// declaration.
pathCursor.selectPath(m_namespaceDeclaration + "$this//xq:employee/xq:name/text()");
// If there are results, then go ahead and do stuff.
if (pathCursor.getSelectionCount() > 0) {
hasResults = true;
// Create a new <names> element into which names from the XML
// will be copied. Note that this element is in the default
// namespace; it's not part of the schema.
XmlObject namesElement = null;
try {
namesElement = XmlObject.Factory.parse("<names/>");
} catch (XmlException e) {
e.printStackTrace();
}
// Add a cursor the new element and put it between its START and END
// tokens, where new values can be inserted.
XmlCursor namesCursor = namesElement.newCursor();
namesCursor.toFirstContentToken();
namesCursor.toEndToken();
// Loop through the selections, appending the incoming <name> element's
// value to the new <name> element's value. (Of course, this could have
// been done with a StringBuffer, but that wouldn't show the cursor in
// use.)
while (pathCursor.toNextSelection()) {
namesCursor.insertChars(pathCursor.getTextValue());
if (pathCursor.hasNextSelection()) {
namesCursor.insertChars(", ");
}
}
// Dispose of the cursors now that they're not needed.
pathCursor.dispose();
namesCursor.dispose();
// Print the new element.
System.out.println("\nNames collected by collectNames method: \n\n" + namesElement + "\n");
}
return hasResults;
}
/**
* Loads XML files which can be found via the <code>clazz</code>'s {@link ClassLoader}. If not
* found the {@link FileContentLoader}'s {@link ClassLoader} is asked to load the file. If file
* could not be found an exception is thrown.
*
* @param filePath the path to the file to be loaded.
* @param clazz the class which {@link ClassLoader} to be used.
* @return an XmlObject of the loaded file.
* @throws XmlException if file could not be parsed into XML
* @throws IOException if file could not be read.
* @throws IllegalArgumentException if file path is <code>null</code> or empty
* @throws FileNotFoundException if the resource could not be found be the <code>clazz</code>'s
* {@link ClassLoader}
*/
public static XmlObject loadXmlFileViaClassloader(String filePath, Class<?> clazz)
throws XmlException, IOException {
if (filePath == null || filePath.isEmpty()) {
throw new IllegalArgumentException("Check file path: '" + filePath + "'.");
}
InputStream is = clazz.getResourceAsStream(filePath);
if (is == null) {
is = XmlFileLoader.class.getResourceAsStream(filePath);
if (is == null) {
throw new FileNotFoundException("The resource at '" + filePath + "' cannot be found.");
}
}
return XmlObject.Factory.parse(is);
}
@Override
public InputStream generateStream(IData data, String mimeType, String schema) throws IOException {
if (data instanceof GenericXMLDataBinding) {
XmlObject xmlData = ((GenericXMLDataBinding) data).getPayload();
XmlOptions xmlOptions = new XmlOptions();
xmlOptions.setSaveNoXmlDecl();
return xmlData.newInputStream(xmlOptions);
}
return XmlObject.Factory.newInstance().newInputStream();
}
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;
}
/**
* Finds nested XML schema definition and compiles it to a schema type system instance.
*
* @param wsdl
* @return
* @throws MojoExecutionException
*/
private SchemaTypeSystem compileXsd(XmlObject wsdl) throws MojoExecutionException {
// extract namespaces defined on wsdl-level:
String[] namespacesWsdl = extractNamespacesOnWsdlLevel(wsdl);
// calc the namespace-prefix of the schema-tag, default ""
String schemaNsPrefix = extractSchemaNamespacePrefix(wsdl);
// extract each schema-element and add missing namespaces defined on wsdl-level
String[] schemas = getNestedSchemas(wsdl, namespacesWsdl, schemaNsPrefix);
XmlObject[] xsd = new XmlObject[schemas.length];
try {
for (int i = 0; i < schemas.length; i++) {
xsd[i] =
XmlObject.Factory.parse(
schemas[i],
(new XmlOptions())
.setLoadLineNumbers()
.setLoadMessageDigest()
.setCompileDownloadUrls());
}
} catch (Exception e) {
throw new MojoExecutionException("Failed to parse XSD schema", e);
}
SchemaTypeSystem schemaTypeSystem = null;
try {
schemaTypeSystem =
XmlBeans.compileXsd(xsd, XmlBeans.getContextTypeLoader(), new XmlOptions());
} catch (XmlException e) {
for (Object error : e.getErrors()) {
getLog().error("Line " + ((XmlError) error).getLine() + ": " + error.toString());
}
throw new MojoExecutionException("Failed to compile XSD schema", e);
} catch (Exception e) {
throw new MojoExecutionException("Failed to compile XSD schema", e);
}
return schemaTypeSystem;
}
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;
}
/**
* Loads a XML document from File.
*
* @param file File
* @return XML document
* @throws OwsExceptionReport If an error occurs
*/
public static XmlObject loadXmlDocumentFromFile(final File file) throws OwsExceptionReport {
InputStream is = null;
try {
is = FileIOHelper.loadInputStreamFromFile(file);
return XmlObject.Factory.parse(is);
} catch (final XmlException xmle) {
throw new NoApplicableCodeException()
.causedBy(xmle)
.withMessage("Error while parsing file %s!", file.getName());
} catch (final IOException ioe) {
throw new NoApplicableCodeException()
.causedBy(ioe)
.withMessage("Error while parsing file %s!", file.getName());
} finally {
if (is != null) {
try {
is.close();
} catch (final IOException ioe) {
LOGGER.warn("Error while closing the file " + file.getName() + " input stream!", ioe);
}
}
}
}
/**
* Compiles WSDL file resource to a XmlObject.
*
* @return
* @throws MojoExecutionException
* @throws IOException
*/
private XmlObject compileWsdl() throws MojoExecutionException, IOException {
Resource wsdlFile = new PathMatchingResourcePatternResolver().getResource(pathToWsdl);
if (!wsdlFile.exists()) {
throw new MojoExecutionException(
"Unable to read WSDL - does not exist in " + wsdlFile.getFile().getAbsolutePath());
}
if (!wsdlFile.getFile().canRead()) {
throw new MojoExecutionException("Unable to read WSDL - could not open in read mode");
}
try {
return XmlObject.Factory.parse(
wsdlFile.getFile(),
(new XmlOptions()).setLoadLineNumbers().setLoadMessageDigest().setCompileDownloadUrls());
} catch (XmlException e) {
for (Object error : e.getErrors()) {
getLog().error(((XmlError) error).getLine() + "" + error.toString());
}
throw new MojoExecutionException("WSDL could not be parsed", e);
} catch (Exception e) {
throw new MojoExecutionException("WSDL could not be parsed", e);
}
}
@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);
}
}
}
/**
* Builds the SRA {@link PROCESSING}, this is taken from the ISATAB "sequencing" protocol that has
* been used for this assay.
*
* <p>Some of these parameters are mandatory in SRA, and/or constrained to certain values, so the
* method raises an exception in case they're not defined.
*/
protected PROCESSING buildExportedProcessing(final Assay assay) {
ProtocolApplication pApp = getProtocol(assay, "sequencing");
SRATemplate sraTemplateToInject = getSRATemplateToInject(SRASection.PROCESSING, assay, pApp);
String seqSpaceStr = getParameterValue(assay, pApp, "Sequence space", false);
String baseCaller = getParameterValue(assay, pApp, "Base caller", false);
String qualityScorer = getParameterValue(assay, pApp, "Quality scorer", false);
String numberOfLevels = getParameterValue(assay, pApp, "Number of levels", false);
String multiplier = getParameterValue(assay, pApp, "Multiplier", false);
Map<SRAAttributes, String> userDefinedAttributes = new HashMap<SRAAttributes, String>();
if (!StringUtils.isEmpty(seqSpaceStr)) {
userDefinedAttributes.put(SRAAttributes.SEQUENCE_SPACE, seqSpaceStr);
}
if (!StringUtils.isEmpty(baseCaller)) {
userDefinedAttributes.put(SRAAttributes.BASE_CALLER, baseCaller);
}
if (!StringUtils.isEmpty(qualityScorer)) {
userDefinedAttributes.put(SRAAttributes.QUALITY_SCORER, qualityScorer);
}
if (!StringUtils.isEmpty(numberOfLevels)) {
userDefinedAttributes.put(SRAAttributes.NUMBER_OF_LEVELS, numberOfLevels);
}
if (!StringUtils.isEmpty(multiplier)) {
userDefinedAttributes.put(SRAAttributes.MULTIPLIER, multiplier);
}
// TODO: modify to pull out the technology and library using Parameter Value[platform] &
// ParameterValue[library layout] respectively
// TODO: PRS-> according to new configuration for sequencing, Parameter Value[library layout] is
// moved to the library construction protocol
// TODO: PRS-> replace Parameter Value[platform] with Parameter Value[sequencing instrument] and
// checks on values.
// TODO: PRS-> add support for Immunoprecipitation techniques, requires detection of Protocol
// TODO: PRS-> add support for 'Targeted Loci' in SRA experiment and find in ISA-TAB file if
// assay is environmental gene survey
try {
String sraTemplate =
sraTemplateLoader.getSRAProcessingTemplate(sraTemplateToInject, userDefinedAttributes);
XmlOptions xmlOptions = new XmlOptions();
xmlOptions.setDocumentType(PROCESSING.Factory.newInstance().schemaType());
PROCESSING processing = PROCESSING.Factory.newInstance();
XmlObject processingObject = XmlObject.Factory.parse(sraTemplate, xmlOptions);
processing.set(processingObject);
return processing;
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (XmlException e) {
e.printStackTrace();
}
return PROCESSING.Factory.newInstance();
}
/**
* add an input element. sets the data in the xml request
*
* @param parameterID the ID of the input (see process description)
* @param value the actual value (for xml data xml for binary data is should be base64 encoded
* data)
* @param schema schema if applicable otherwise null
* @param encoding encoding if not the default encoding (for default encoding set it to null)
* (i.e. binary data, use base64)
* @param mimeType mimetype of the data, has to be set
* @throws WPSClientException
*/
public void addComplexData(
String parameterID, IData value, String schema, String encoding, String mimeType)
throws WPSClientException {
GeneratorFactory fac = StaticDataHandlerRepository.getGeneratorFactory();
InputDescriptionType inputDesc = getParameterDescription(parameterID);
if (inputDesc == null) {
throw new IllegalArgumentException("inputDesription is null for: " + parameterID);
}
if (inputDesc.getComplexData() == null) {
throw new IllegalArgumentException(
"inputDescription is not of type ComplexData: " + parameterID);
}
LOGGER.debug(
"Looking for matching Generator ..."
+ " schema: "
+ schema
+ " mimeType: "
+ mimeType
+ " encoding: "
+ encoding);
IGenerator generator = fac.getGenerator(schema, mimeType, encoding, value.getClass());
if (generator == null) {
// generator is still null
throw new IllegalArgumentException(
"Could not find an appropriate generator for parameter: " + parameterID);
}
InputStream stream = null;
InputType input = execute.getExecute().getDataInputs().addNewInput();
input.addNewIdentifier().setStringValue(inputDesc.getIdentifier().getStringValue());
// encoding is UTF-8 (or nothing and we default to UTF-8)
// everything that goes to this condition should be inline xml data
try {
if (encoding == null
|| encoding.equals("")
|| encoding.equalsIgnoreCase(IOHandler.DEFAULT_ENCODING)) {
stream = generator.generateStream(value, mimeType, schema);
} else if (encoding.equalsIgnoreCase("base64")) {
stream = generator.generateBase64Stream(value, mimeType, schema);
} else {
throw new WPSClientException("Encoding not supported");
}
ComplexDataType data = input.addNewData().addNewComplexData();
data.set(XmlObject.Factory.parse(stream));
if (schema != null) {
data.setSchema(schema);
}
if (mimeType != null) {
data.setMimeType(mimeType);
}
if (encoding != null) {
data.setEncoding(encoding);
}
} catch (XmlException e) {
throw new IllegalArgumentException("error inserting node into execute request", e);
} catch (IOException e) {
throw new IllegalArgumentException("error reading generator output", e);
}
}
private String readMessage() throws XmlException, IOException {
XmlObject xo = XmlObject.Factory.parse(getClass().getResourceAsStream("NotifyMessage.xml"));
return xo.xmlText(new XmlOptions().setSavePrettyPrint());
}
private boolean validateSensorMLDocument(String s) throws XmlException, IOException {
boolean b = this.validator.validate(XmlObject.Factory.parse(s));
return b;
}
public XmlHolder(Node node) throws XmlException {
xmlObject = XmlObject.Factory.parse(node);
}
public XmlHolder(String xml) throws XmlException {
xmlObject = XmlObject.Factory.parse(xml);
}