public GetSupportedTypesRequest(Document doc) throws ExceptionReport {
try {
XmlOptions option = new XmlOptions();
option.setLoadTrimTextBuffer();
this.supportedTypesDoc = GetSupportedTypesDocument.Factory.parse(doc, option);
if (supportedTypesDoc == null) {
LOGGER.error("GetSupportedTypesDocument is null");
throw new ExceptionReport(
"Error while parsing post data", ExceptionReport.MISSING_PARAMETER_VALUE);
}
} catch (XmlException e) {
throw new ExceptionReport(
"Error while parsing post data", ExceptionReport.MISSING_PARAMETER_VALUE, e);
}
this.complexTypesOnly = supportedTypesDoc.getGetSupportedTypes().getComplexTypesOnly();
if (this.complexTypesOnly) {
LOGGER.info("GetSupportedTypes for complex types only.");
} else {
LOGGER.info("GetSupportedTypes for all available types.");
}
responseBuilder = new GetSupportedTypesResponseBuilder(this);
responseBuilder.updateSupportedTypes();
}
private List<Resultado> validarEstructura() {
final List<Resultado> resultados = new ArrayList<Resultado>();
if (docto == null) {
try {
docto = ComprobanteDocument.Factory.parse(xmlFile);
} catch (Exception e) {
throw new RuntimeException(
"Error procesando el archivo XML " + ExceptionUtils.getRootCauseMessage(e), e);
}
}
final XmlOptions options = new XmlOptions();
final List<XmlValidationError> errors = new ArrayList<XmlValidationError>();
options.setErrorListener(errors);
boolean valid = docto.validate(options);
if (valid) {
Resultado res = new Resultado("Estructura");
res.setDescripcion("Estructura del CFD segun la versión 2 del schema del SAT");
res.setResultado("CORRECTO");
resultados.add(res);
} else {
for (XmlValidationError e : errors) {
// buff.append(e.getMessage()+"\n");
Resultado res = new Resultado("Estructura");
res.setDescripcion(e.getMessage());
res.setResultado("ERROR");
resultados.add(res);
}
}
return resultados;
}
public final String modelToXmlString() {
TiersInformationsType object = (TiersInformationsType) this.modelToXml();
XmlOptions opts = new XmlOptions();
opts.setSavePrettyPrint();
opts.setSavePrettyPrintIndent(4);
opts.setUseDefaultNamespace();
opts.setCharacterEncoding("UTF-8");
return object.xmlText(opts);
}
/**
* 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 static OMElement xmlObjectToOMElement(XmlObject responseXmlObj) throws XMLStreamException {
String responseXml;
XmlOptions opts = new XmlOptions();
opts.setSaveOuter();
responseXml = responseXmlObj.xmlText(opts);
OMElement outgoingMsg =
org.apache.airavata.commons.WorkFlowUtils.reader2OMElement(new StringReader(responseXml));
return outgoingMsg;
}
@Override
public final String modelToXmlString() {
TechnicalInterventionRequestDocument object = this.modelToXml();
XmlOptions opts = new XmlOptions();
opts.setSavePrettyPrint();
opts.setSavePrettyPrintIndent(4);
opts.setUseDefaultNamespace();
opts.setCharacterEncoding("UTF-8");
return object.xmlText(opts);
}
@Override
protected void commit() throws IOException {
XmlOptions xmlOptions = new XmlOptions(DEFAULT_XML_OPTIONS);
Map<String, String> map = new HashMap<String, String>();
map.put(STRelationshipId.type.getName().getNamespaceURI(), "r");
xmlOptions.setSaveSuggestedPrefixes(map);
PackagePart part = getPackagePart();
OutputStream out = part.getOutputStream();
_presentation.save(out, xmlOptions);
out.close();
}
private AssertionError[] assertResponse(
RestMessageExchange messageExchange, RestRepresentation.Type type) {
List<AssertionError> result = new ArrayList<AssertionError>();
QName responseBodyElementName = getResponseBodyElementName(messageExchange);
RestRequestInterface restRequest = messageExchange.getRestRequest();
boolean asserted = false;
for (RestRepresentation representation :
restRequest.getRepresentations(type, messageExchange.getResponseContentType())) {
if (representation.getStatus().isEmpty()
|| representation.getStatus().contains(messageExchange.getResponseStatusCode())) {
SchemaType schemaType = representation.getSchemaType();
if (schemaType != null && representation.getElement().equals(responseBodyElementName)) {
try {
XmlObject xmlObject =
schemaType
.getTypeSystem()
.parse(messageExchange.getResponseContentAsXml(), schemaType, new XmlOptions());
// create internal error list
List<?> list = new ArrayList<Object>();
XmlOptions xmlOptions = new XmlOptions();
xmlOptions.setErrorListener(list);
xmlOptions.setValidateTreatLaxAsSkip();
xmlObject.validate(xmlOptions);
for (Object o : list) {
if (o instanceof XmlError) result.add(new AssertionError((XmlError) o));
else result.add(new AssertionError(o.toString()));
}
asserted = true;
} catch (XmlException e) {
SoapUI.logError(e);
}
} else {
asserted = true;
}
}
}
if (!asserted && result.isEmpty()) {
result.add(
new AssertionError(
"Missing matching representation for request with contentType ["
+ messageExchange.getResponseContentType()
+ "]"));
}
return result.toArray(new AssertionError[result.size()]);
}
private void createConfigFile(
String issuer,
String nameQualifier,
String ksType,
String ksFile,
String ksPassword,
String privKeyAlias,
String privKeyPassword,
String certAlias)
throws IOException {
String SSO_CONFIG_FILE = "/WEB-INF/guanxi_idp/config/idp.xml";
String KEYSTORE_KEY_TYPE = "dsa";
IdpDocument idpDoc = null;
try {
idpDoc = IdpDocument.Factory.parse(new File(servletContext.getRealPath(SSO_CONFIG_FILE)));
} catch (XmlException xe) {
logger.error("Can't create config file", xe);
return;
}
IdpDocument.Idp idp = idpDoc.getIdp();
idp.getServiceProviderArray(0).setIdentity("exampleIdentity");
idp.getServiceProviderArray(0).setCreds("exampleCreds");
idp.getServiceProviderArray(0).setName("REPLACE_WITH_PROVIDER_ID_OF_SERVICE_PROVIDER");
idp.getIdentityArray(0).setName("exampleIdentity");
idp.getIdentityArray(0).setNameQualifier(nameQualifier);
idp.getIdentityArray(0).setIssuer(issuer);
idp.getCredsArray(0).setName("exampleCreds");
idp.getCredsArray(0).setKeystoreType("jks");
idp.getCredsArray(0).setKeyType(ksType);
idp.getCredsArray(0).setKeystoreFile(ksFile);
idp.getCredsArray(0).setKeystorePassword(ksPassword);
idp.getCredsArray(0).setPrivateKeyAlias(privKeyAlias);
idp.getCredsArray(0).setPrivateKeyPassword(privKeyPassword);
idp.getCredsArray(0).setCertificateAlias(certAlias);
idp.getCredsArray(0).setKeyType(KEYSTORE_KEY_TYPE);
XmlOptions xmlOptions = new XmlOptions();
xmlOptions.setSavePrettyPrint();
xmlOptions.setSavePrettyPrintIndent(2);
xmlOptions.setUseDefaultNamespace();
idpDoc.save(new File(servletContext.getRealPath(SSO_CONFIG_FILE)), xmlOptions);
servletContext.setAttribute(Guanxi.CONTEXT_ATTR_IDP_CONFIG_DOC, idpDoc);
servletContext.setAttribute(Guanxi.CONTEXT_ATTR_IDP_CONFIG, idpDoc.getIdp());
}
public void saveConfiguration() {
File file = getDefaultConfigurationFile();
log.info("Storing current configuration in file: " + file.getAbsolutePath());
try {
XmlOptions opts = new XmlOptions();
opts.setSavePrettyPrint();
opts.setSavePrettyPrintIndent(4);
configuration.save(file, opts);
} catch (IOException e) {
log.error("Unable to save the updated configuration in file: " + file.getAbsolutePath());
throw new RuntimeException("Unable to save the updated configuration: " + e.getMessage());
}
}
@Test
public void validFullResponse() {
XmlOptions opt = (new XmlOptions()).setSavePrettyPrint();
opt.setSaveSuggestedPrefixes(Utilities.SuggestedNamespaces());
opt.setSaveNamespacesFirst();
opt.setSaveAggressiveNamespaces();
opt.setUseDefaultNamespace();
XmlObject co = completeResponse();
ArrayList errorList = new ArrayList();
boolean validXml = Utilities.validateXml(opt, co, errorList);
assertTrue(errorList.toString(), validXml);
}
private File createXMLMetadata(HashMap<String, Object> inputs) {
ArrayList<?> validationErrors = new ArrayList<Object>();
XmlOptions options;
options = new XmlOptions();
options.setSavePrettyPrint();
options.setSaveAggressiveNamespaces();
HashMap<String, String> suggestedPrefixes = new HashMap<String, String>();
suggestedPrefixes.put("http://www.geoviqua.org/QualityInformationModel/4.0", "gvq");
options.setSaveSuggestedPrefixes(suggestedPrefixes);
options.setErrorListener(validationErrors);
GVQMetadataDocument doc = GVQMetadataDocument.Factory.newInstance();
GVQMetadataType gvqMetadata = doc.addNewGVQMetadata();
gvqMetadata.addNewLanguage().setCharacterString("en");
gvqMetadata.addNewMetadataStandardName().setCharacterString("GVQ");
gvqMetadata.addNewMetadataStandardVersion().setCharacterString("1.0.0");
gvqMetadata.addNewDateStamp().setDate(Calendar.getInstance());
DQDataQualityType quality = gvqMetadata.addNewDataQualityInfo2().addNewDQDataQuality();
GVQDataQualityType gvqQuality =
(GVQDataQualityType)
quality.substitute(
new QName("http://www.geoviqua.org/QualityInformationModel/4.0", "GVQ_DataQuality"),
GVQDataQualityType.type);
GVQDiscoveredIssueType issue = gvqQuality.addNewDiscoveredIssue().addNewGVQDiscoveredIssue();
issue.addNewKnownProblem().setCharacterString(inputs.get("element").toString());
issue.addNewWorkAround().setCharacterString("solution");
// validate schema conformity
boolean isValid = doc.validate();
if (!isValid) System.out.println(Arrays.toString(validationErrors.toArray()));
// print out as XML
System.out.println(doc.xmlText(options));
try {
File tempFile = File.createTempFile("wpsMetdataTempFile", "xml");
doc.save(tempFile);
return tempFile;
} catch (Exception e) {
LOGGER.error("createXMLMetadataError " + e);
}
return null;
}
/**
* Returns an XMLBeans document as a String with full Fedora/RDF namespace support
*
* @param doc The document to parse to a String
* @return String version of the document. This will contain prefixes for rdf and myns
*/
public static String xmlToString(XmlObject doc) {
HashMap<String, String> namespaces = new HashMap<String, String>();
namespaces.put("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
namespaces.put("http://www.nsdl.org/ontologies/relationships#", "myns");
XmlOptions xmlOptions = new XmlOptions();
xmlOptions.setSaveSuggestedPrefixes(namespaces);
xmlOptions.setSaveAggressiveNamespaces();
StringWriter out = new StringWriter();
try {
doc.save(out, xmlOptions);
return out.toString();
} catch (Exception e) {
return null;
}
}
@Override
protected void commit() throws IOException {
XmlOptions xmlOptions = new XmlOptions(DEFAULT_XML_OPTIONS);
xmlOptions.setSaveSyntheticDocumentElement(
new QName(CTSettings.type.getName().getNamespaceURI(), "settings"));
Map<String, String> map = new HashMap<String, String>();
map.put("http://schemas.openxmlformats.org/wordprocessingml/2006/main", "w");
xmlOptions.setSaveSuggestedPrefixes(map);
PackagePart part = getPackagePart();
OutputStream out = part.getOutputStream();
ctSettings.save(out, xmlOptions);
out.close();
}
@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();
}
/**
* Dumps an XML document to disk.
*
* @param doc The document to dump to disk
* @param filePath The full path and name of the file
*/
public static void dumpXML(XmlObject doc, String filePath) {
HashMap<String, String> namespaces = new HashMap<String, String>();
namespaces.put("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
namespaces.put("http://www.nsdl.org/ontologies/relationships#", "myns");
XmlOptions xmlOptions = new XmlOptions();
xmlOptions.setSavePrettyPrint();
xmlOptions.setSavePrettyPrintIndent(2);
// xmlOptions.setUseDefaultNamespace();
// xmlOptions.setSaveAggressiveNamespaces();
xmlOptions.setSaveSuggestedPrefixes(namespaces);
// xmlOptions.setSaveNamespacesFirst();
try {
doc.save(new File(filePath), xmlOptions);
} catch (Exception e) {
}
}
private void validateConfiguration(MpiConfigDocument configuration) {
// Set up the validation error listener.
ArrayList<XmlError> validationErrors = new ArrayList<XmlError>();
XmlOptions validationOptions = new XmlOptions();
validationOptions.setErrorListener(validationErrors);
// During validation, errors are added to the ArrayList for
// retrieval and printing by the printErrors method.
boolean isValid = configuration.validate(validationOptions);
// Print the errors if the XML is invalid.
if (!isValid) {
java.util.Iterator<XmlError> iter = validationErrors.iterator();
StringBuffer sb = new StringBuffer("MPI Configuration validation errors:\n");
while (iter.hasNext()) {
sb.append(">> ").append(iter.next()).append("\n");
}
}
}
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;
}
/** save and commit numbering */
@Override
protected void commit() throws IOException {
XmlOptions xmlOptions = new XmlOptions(DEFAULT_XML_OPTIONS);
xmlOptions.setSaveSyntheticDocumentElement(
new QName(CTNumbering.type.getName().getNamespaceURI(), "numbering"));
Map map = new HashMap();
map.put("http://schemas.openxmlformats.org/markup-compatibility/2006", "ve");
map.put("urn:schemas-microsoft-com:office:office", "o");
map.put("http://schemas.openxmlformats.org/officeDocument/2006/relationships", "r");
map.put("http://schemas.openxmlformats.org/officeDocument/2006/math", "m");
map.put("urn:schemas-microsoft-com:vml", "v");
map.put("http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing", "wp");
map.put("urn:schemas-microsoft-com:office:word", "w10");
map.put("http://schemas.openxmlformats.org/wordprocessingml/2006/main", "w");
map.put("http://schemas.microsoft.com/office/word/2006/wordml", "wne");
xmlOptions.setSaveSuggestedPrefixes(map);
PackagePart part = getPackagePart();
OutputStream out = part.getOutputStream();
ctNumbering.save(out, xmlOptions);
out.close();
}
public String AsXml() {
XmlOptions opt = (new XmlOptions()).setSavePrettyPrint();
opt.setSaveSuggestedPrefixes(Utilities.SuggestedNamespaces());
opt.setSaveNamespacesFirst();
opt.setSaveAggressiveNamespaces();
opt.setUseDefaultNamespace();
DescribeSRSResponseDocument document = completeResponse();
ArrayList errorList = new ArrayList();
opt.setErrorListener(errorList);
boolean isValid = document.validate(opt);
// If the XML isn't valid, loop through the listener's contents,
// printing contained messages.
if (!isValid) {
for (int i = 0; i < errorList.size(); i++) {
XmlError error = (XmlError) errorList.get(i);
System.out.println("\n");
System.out.println("Message: " + error.getMessage() + "\n");
System.out.println(
"Location of invalid XML: " + error.getCursorLocation().xmlText() + "\n");
}
}
return document.xmlText(opt);
}
private SoapVersion11() {
try {
XmlOptions options = new XmlOptions();
options.setCompileNoValidation();
options.setCompileNoPvrRule();
options.setCompileDownloadUrls();
options.setCompileNoUpaRule();
options.setValidateTreatLaxAsSkip();
URL soapSchemaXmlResource =
ResourceUtils.getResourceWithAbsolutePackagePath(
getClass(), "/xsds/", "soapEnvelope.xsd");
soapSchemaXml = XmlUtils.createXmlObject(soapSchemaXmlResource, options);
soapSchema = XmlBeans.loadXsd(new XmlObject[] {soapSchemaXml});
soapEnvelopeType = soapSchema.findDocumentType(envelopeQName);
soapFaultType = soapSchema.findDocumentType(faultQName);
URL soapEncodingXmlResource =
ResourceUtils.getResourceWithAbsolutePackagePath(
getClass(), "/xsds/", "soapEncoding.xsd");
soapEncodingXml = XmlUtils.createXmlObject(soapEncodingXmlResource, options);
} catch (XmlException ex) {
throw new SoapBuilderException(ex);
}
}
private byte[] generateXml(
Integer demographicNo, Integer rourkeFdid, Integer nddsFdid, Integer report18mFdid) {
HashMap<String, String> suggestedPrefixes = new HashMap<String, String>();
suggestedPrefixes.put("http://www.w3.org/2001/XMLSchema-instance", "xsi");
XmlOptions opts = new XmlOptions();
opts.setSaveSuggestedPrefixes(suggestedPrefixes);
opts.setSavePrettyPrint();
opts.setSaveNoXmlDecl();
opts.setUseDefaultNamespace();
opts.setSaveNamespacesFirst();
ByteArrayOutputStream os = null;
PrintWriter pw = null;
boolean xmlCreated = false;
BORN18MFormToXML xml = new BORN18MFormToXML(demographicNo);
try {
os = new ByteArrayOutputStream();
pw = new PrintWriter(os, true);
pw.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
xmlCreated = xml.addXmlToStream(pw, opts, rourkeFdid, nddsFdid, report18mFdid);
pw.close();
if (xmlCreated) return os.toByteArray();
} catch (Exception e) {
logger.warn("Unable to add record", e);
}
return null;
}
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;
}
protected void validateXmlDocument(XmlObject xmlDocument) {
ArrayList<XmlError> validationErrors = new ArrayList<XmlError>();
XmlOptions validationOptions = new XmlOptions();
validationOptions.setErrorListener(validationErrors);
xmlDocument.validate(validationOptions);
List<String> excludeErrors = new ArrayList<String>();
excludeErrors.add("Expected element '_Feature@http://www.opengis.net/gml' instead of");
excludeErrors.add("Expected element 'InsertionMetadata@http://www.opengis.net/swes/2.0'");
excludeErrors.add(
"Expected element 'AbstractFeature@http://www.opengis.net/gml/3.2' instead of 'SF_SpatialSamplingFeature@http://www.opengis.net/samplingSpatial/2.0'");
for (XmlError validationError : validationErrors) {
boolean skip = false;
for (String excludeError : excludeErrors) {
if (validationError.getMessage().startsWith(excludeError)) {
skip = true;
}
}
if (!skip) {
fail(validationError.getMessage());
}
}
}
/**
* Generate the ExceptionReport as an XML string.
*
* @return the ExceptionReport as an XML string
*/
public String getXMLExceptionReport() {
Map<String, String> suggestedPrefixes = new HashMap<String, String>();
suggestedPrefixes.put("http://www.opengis.net/ows/2.0", "ows");
XmlOptions opts = new XmlOptions();
opts.setSavePrettyPrint();
opts.setSaveSuggestedPrefixes(suggestedPrefixes);
opts.setSaveNamespacesFirst();
opts.setSaveAggressiveNamespaces();
opts.setUseDefaultNamespace();
return exceptionReportDoc.xmlText(opts);
}
@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);
}
}
}
public ReginfoHandler() {
_xmlOptions = new XmlOptions();
_xmlOptions.setUseDefaultNamespace();
_xmlOptions.setSavePrettyPrint();
}
public static void main(String[] args) throws Exception {
EntityManagerFactory emf = Persistence.createEntityManagerFactory("DownloadContraArticlesJPA");
em = emf.createEntityManager();
SimpleDateFormat dtf = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
String outfolder = "import-stories-arch-1";
opt = new XmlOptions();
opt.setUseCDataBookmarks();
opt.setSaveCDataLengthThreshold(0);
opt.setSaveCDataEntityCountThreshold(-1);
int i = 0;
int maxResults = 1000;
competitions = em.createQuery(" SELECT c FROM Competition c ").getResultList();
sports = em.createQuery(" SELECT c FROM Sport c ").getResultList();
Query q = em.createQuery(queryString).setFirstResult(i * maxResults).setMaxResults(maxResults);
List<Articles_Archives100_130000> results = q.getResultList();
while (!results.isEmpty()) {
EscenicDocument escenicDocument = EscenicDocument.Factory.newInstance(opt);
initializeEscenic(escenicDocument);
for (Articles_Archives100_130000 article : results) {
Content content = escenicDocument.getEscenic().addNewContent();
content.addNewSource().setStringValue("ContraNews");
content.addNewSourceid().setStringValue(Integer.toString(article.getArticleID()));
content.addNewType().setStringValue("news");
content.setState(State.PUBLISHED);
content.addNewPublishdate().setStringValue(dtf.format(article.getArticleDate()));
content.addNewCreationdate().setStringValue(dtf.format(article.getArticleDate()));
SectionRef sectionRef = content.addNewSectionRef();
try {
if (article.getCompetition().getCompetitionID() != 0) {
sectionRef
.addNewUniqueName()
.setStringValue(article.getCompetition().getCompetitionName_url());
} else if (article.getCompetition().getCompetitionID() == 0
&& article.getPlace().getPlaceID() != 0
&& article.getSport().getSportID() != 0
&& existCompetition(article.getSport(), article.getPlace())) {
sectionRef
.addNewUniqueName()
.setStringValue(
article.getPlace().getPlaceName_url()
+ "_"
+ article.getSport().getSportName_url());
} else if (article.getSport().getSportID() != 0) {
sectionRef.addNewUniqueName().setStringValue(article.getSport().getSportName_url());
} else {
sectionRef.addNewUniqueName().setStringValue("ece_incoming");
}
} catch (Exception e) {
System.out.println("No section found for article" + article.getArticleID());
throw new Exception(e.getMessage());
}
if (article.getSubSection().getSubSectionID() != 1) {
sectionRef = content.addNewSectionRef();
sectionRef
.addNewUniqueName()
.setStringValue(article.getSubSection().getSubSectionName_url());
}
sectionRef.setHomeSection(true);
// List<Image> images = em.createQuery(" SELECT i FROM Image i WHERE i.articleId = " +
// article.getId()).getResultList();
//
// for (Image image : images) {
// // picture relation
// if(article.getArticlePhoto() !=null && !article.getArticlePhoto().trim().isEmpty()){
// String fullPath = "/home/vassilis/Pictures/contra/"+article.getArticlePhoto().trim();
//
// //check if file
// if(new File(fullPath).exists()){
// Relation relation = content.addNewRelation();
// relation.addNewType().setStringValue("PICTUREREL");
// relation.addNewSource().setStringValue("ContraImages");
// relation.addNewSourceid().setStringValue(article.getArticlePhoto().trim());
// }
// }
if (article.getLinks() != null) {
for (String articleId : article.getLinks().split(",")) {
articleId = articleId.trim();
if (articleId.isEmpty()) continue;
if (articleId.startsWith("ph")) {
// try {
// em.createQuery("SELECT p.photoStoryID FROM PhotoStory p WHERE p.photoStoryID
// = :thePhotoStoryID ")
// .setParameter("thePhotoStoryID",
// Integer.valueOf(articleId.toLowerCase().replaceAll("ph", "")))
// .getSingleResult();
// Relation relationStory = content.addNewRelation();
// relationStory.addNewType().setStringValue("PHOTOSTORYREL");
// relationStory.addNewSource().setStringValue("ContraPhotostory");
// relationStory.addNewSourceid().setStringValue(articleId.replaceAll("ph",
// ""));
// } catch (Exception e) {
// e.printStackTrace();
// System.out.println("No PhotoStory found with id " +
// articleId.replaceAll("ph", ""));
// }
} else if (!articleId.matches("[0-9]*")) {
continue;
} else {
Relation relationStory = content.addNewRelation();
relationStory.addNewType().setStringValue("STORYREL");
relationStory.addNewSource().setStringValue("ContraNews");
relationStory.addNewSourceid().setStringValue(articleId);
}
}
}
if (article.getTeam1() != null
&& article.getTeam1().getTeamID() > 0
&& article.getTeam1().getTeamName_url() != null) {
Relation relationTag = content.addNewRelation();
relationTag.addNewType().setStringValue("TAGREL");
relationTag.addNewSource().setStringValue("ContraTags");
relationTag
.addNewSourceid()
.setStringValue(Integer.toString(article.getTeam1().getTeamID()));
}
if (article.getTeam2() != null
&& article.getTeam2().getTeamID() > 0
&& article.getTeam2().getTeamName_url() != null) {
Relation relationTag = content.addNewRelation();
relationTag.addNewType().setStringValue("TAGREL");
relationTag.addNewSource().setStringValue("ContraTags");
relationTag
.addNewSourceid()
.setStringValue(Integer.toString(article.getTeam2().getTeamID()));
}
// Field titlePictureField = relation.addNewField();
// titlePictureField.addNewName().setStringValue("title");
// titlePictureField.newCursor().setTextValue(image.getCaption());
//
// Field captionTitlePictureField = relation.addNewField();
// captionTitlePictureField.addNewName().setStringValue("captiontitle");
// Field captionPictureField = relation.addNewField();
// captionPictureField.addNewName().setStringValue("caption");
// captionPictureField.newCursor().setTextValue(image.getCaption());
// }
Priority priority = content.addNewPriority();
priority.setValue(0);
Field titleField = content.addNewField();
titleField.addNewName().setStringValue("title");
titleField.newCursor().setTextValue(article.getArticleTitle());
//// Field superTitleField = content.addNewField();
//// superTitleField.addNewName().setStringValue("supertitle");
//// superTitleField.newCursor().setTextValue(article.getTitle());
//
Field leadtextField = content.addNewField();
leadtextField.addNewName().setStringValue("leadtext");
leadtextField
.newCursor()
.setTextValue(
article.getArticleSummary() == null
? ""
: article.getArticleSummary().replaceAll("\\<.*?\\>", ""));
// Field quoteField = content.addNewField();
// quoteField.addNewName().setStringValue("quote");
if (article.getArticleBody() != null && !article.getArticleBody().trim().isEmpty()) {
Field bodyField = content.addNewField();
bodyField.addNewName().setStringValue("body");
// //body
XmlCursor bodyCursor = bodyField.newCursor();
bodyCursor.xmlText(opt);
String fixedBody = article.getArticleBody().trim();
fixedBody = HTMLFilter.fixHtml(fixedBody);
bodyCursor.setTextValue(fixedBody);
}
//
Field bylineField = content.addNewField();
bylineField.addNewName().setStringValue("byline");
bylineField
.newCursor()
.setTextValue(
article.getArticleAuthor() == null ? "" : article.getArticleAuthor().trim());
String tagFieldString = "";
if (article.getTeam1() != null
&& article.getTeam1().getTeamID() > 0
&& article.getTeam1().getTeamName_url() != null) {
tagFieldString = "tagppo" + article.getTeam1().getTeamName_url().toLowerCase();
}
if (article.getTeam2() != null
&& article.getTeam2().getTeamID() > 0
&& article.getTeam2().getTeamName_url() != null) {
tagFieldString =
tagFieldString + " tagppo" + article.getTeam2().getTeamName_url().toLowerCase();
}
if (!tagFieldString.isEmpty()) {
Field tagField = content.addNewField();
tagField.addNewName().setStringValue("tag");
tagField.newCursor().setTextValue(tagFieldString);
}
//
//
// if(article.getTeam1()!=null && article.getTeam1().getTeamID()!=0){
// Tag tag = content.addNewTag();
// tag.newCursor().setTextValue(article.getTeam1().getTeamName_url());
// }
//
// if(article.getTeam2()!=null && article.getTeam2().getTeamID()!=0){
// Tag tag = content.addNewTag();
// tag.newCursor().setTextValue(article.getTeam2().getTeamName_url());
// }
// Field bylineprefixField = content.addNewField();
// bylineprefixField.addNewName().setStringValue("bylineprefix");
//
// Field notesField = content.addNewField();
// notesField.addNewName().setStringValue("notes");
//
// Field geocodeField = content.addNewField();
// geocodeField.addNewName().setStringValue("com.escenic.geocode");
}
String counterString = "";
++i;
if (i < 10) {
counterString = "000";
} else if (i < 100) {
counterString = "00";
} else if (i < 1000) {
counterString = "0";
} else if (i < 10000) {
counterString = "";
}
counterString = counterString + i;
String outFileName = outfolder + "/stories1-arch" + (counterString) + ".xml";
File f = new File(outFileName);
escenicDocument.save(f);
q = em.createQuery(queryString).setFirstResult(i * maxResults).setMaxResults(maxResults);
results = q.getResultList();
}
ReplaceCDATA.replace(outfolder);
}
@Override
public void process(ProcessletInputs in, ProcessletOutputs out, ProcessletExecutionInfo info)
throws ProcessletException {
try {
// validate against allowed values in process definition file
URL processDefinitionUrl =
this.getClass().getResource("/" + this.getClass().getSimpleName() + ".xml");
// get validated data inputs or default values
DataInputHandler dataInputHandler =
new DataInputHandler(new File(processDefinitionUrl.toURI()));
String srsName = dataInputHandler.getValidatedStringValue(in, "srsName");
String filter = dataInputHandler.getValidatedStringValue(in, "filter");
double x = DataInputHandler.getDoubleInputValue(in, "x");
double y = DataInputHandler.getDoubleInputValue(in, "y");
double z = DataInputHandler.getDoubleInputValue(in, "z");
LOG.debug(
String.format(
"DataInputs: srsName: %s, poi: (%f, %f, %f), filter: %s", srsName, x, y, z, filter));
responseValues = new ResponseValues();
responseValues.clientSrsName = srsName;
// transform non-AGEA coordinates to AGEA
if (!srsName.equals("Mouse_AGEA_1.0")) {
ABAServiceVO vo = getTransformPOI(srsName, x, y, z);
if (vo.getTransformationXMLResponseString().startsWith("Error:")) {
throw new OWSException(
"Transformation Coordinates Error: ", vo.getTransformationXMLResponseString());
}
x = Double.parseDouble(vo.getTransformedCoordinateX());
y = Double.parseDouble(vo.getTransformedCoordinateY());
z = Double.parseDouble(vo.getTransformedCoordinateZ());
}
LOG.debug("X from Transformation Method: " + x);
LOG.debug("Y from Transformation Method: " + y);
LOG.debug("Z from Transformation Method: " + z);
String srsFromClient = srsName;
Point3d poiFromClient = new Point3d(x, y, z);
// get plane; defaults to sagittal
ImageSeriesPlane desiredPlane =
filter.equals("maptype:coronal") ? ImageSeriesPlane.CORONAL : ImageSeriesPlane.SAGITTAL;
// 1. get strong gene(s) at POI
List<ABAGene> strongGenes = ABAUtil.retrieveStrongGenesAtAGEAPOI(x, y, z, NBR_STRONG_GENES);
// make sure we have something
if (strongGenes.size() == 0) {
throw new OWSException(
"No 'strong genes' found at " + "coordinates, hence no images to return.",
ControllerException.NO_APPLICABLE_CODE);
}
if (LOG.isDebugEnabled()) {
StringBuilder buf = new StringBuilder();
for (ABAGene gene : strongGenes) {
buf.append(gene.getGenesymbol()).append(", ");
}
LOG.debug("Strong genes: {}", buf.toString());
}
// 2. get image series'es for strong genes and desired plane
List<ImageSeries> imageSerieses = new ArrayList<ImageSeries>();
for (ABAGene gene : strongGenes) {
ImageSeries imageSeries = retrieveImagesSeriesForGene(gene.getGenesymbol(), desiredPlane);
if (imageSeries != null) {
imageSerieses.add(imageSeries);
}
}
// make sure we have something
if (imageSerieses.size() == 0) {
throw new OWSException(
"No image series found for 'strong "
+ "genes' and desired plane, hence no images to "
+ "return.",
ControllerException.NO_APPLICABLE_CODE);
}
if (LOG.isDebugEnabled()) {
StringBuilder buf = new StringBuilder();
for (ImageSeries is : imageSerieses) {
buf.append(is.imageSeriesId).append(':');
buf.append(is.imageSeriesPlane).append(", ");
}
LOG.debug("Image Serieses id:plane: {}", buf.toString());
}
Point3d poiForProximity = new Point3d(poiFromClient);
// divide POI coords by 100
Point3d poi100 = new Point3d();
poi100.scale(0.01, poiForProximity);
LOG.debug("POI for closest position (srs, xyz): {}, {}", srsFromClient, poi100.toString());
// 3. get ......... for each image series
for (ImageSeries imageSeries : imageSerieses) {
// begin to add values to image
Image image = new Image(imageSeries.imageSeriesId);
// get atlas map
// find closest point, get other values including position
// add more (atlas map) values to image
getClosestPosition(imageSeries, poi100, image);
LOG.debug("Position: {}", image.abaImagePosition);
// get best image id in image series based on position
// add more (image elements) values to image
// match position to find image in series, get imageid
// /image-series/images/image/position
// /image-series/images/image/imageid
retrieveImageForPosition(imageSeries.imageSeriesId, image.abaImagePosition, image);
LOG.debug("Image id: {}", image.imageId);
// zoom level not applicable
// image.zoomLevel = zoomLevel;
// assemble aba view image uri
image.imageURI = assembleImageURI(image.downloadImagePath, HI_RES, MIME);
image.thumbnailurl = assembleImageURI(image.downloadImagePath, THUMB, MIME);
LOG.debug("Image URI: {}", image.imageURI.toString());
responseValues.images.add(image);
} // for
// ImagesResponseDocument 'is a' org.apache.xmlbeans.XmlObject
// 'is a' org.apache.xmlbeans.XmlTokenSource
ImagesResponseDocument document = completeResponse();
if (LOG.isDebugEnabled()) {
XmlOptions opt = (new XmlOptions()).setSavePrettyPrint();
opt.setSaveSuggestedPrefixes(Utilities.SuggestedNamespaces());
opt.setSaveNamespacesFirst();
opt.setSaveAggressiveNamespaces();
opt.setUseDefaultNamespace();
LOG.debug("Xml:\n{}", document.xmlText(opt));
}
// 4. Send it
// get reader on document
XMLStreamReader reader = document.newXMLStreamReader();
// get ComplexOutput object from ProcessletOutput...
ComplexOutput complexOutput = (ComplexOutput) out.getParameter("Get2DImagesByPOIOutput");
LOG.debug("Setting complex output (requested=" + complexOutput.isRequested() + ")");
// ComplexOutput objects can be huge so stream it
XMLStreamWriter writer = complexOutput.getXMLStreamWriter();
XMLAdapter.writeElement(writer, reader);
// transform any exceptions into ProcessletException wrapping
// OWSException
} catch (MissingParameterException e) {
LOG.error(e.getMessage(), e);
throw new ProcessletException(new OWSException(e));
} catch (InvalidParameterValueException e) {
LOG.error(e.getMessage(), e);
throw new ProcessletException(new OWSException(e));
} catch (InvalidDataInputValueException e) {
LOG.error(e.getMessage(), e);
throw new ProcessletException(e); // is already OWSException
} catch (OWSException e) {
LOG.error(e.getMessage(), e);
throw new ProcessletException(e); // is already OWSException
} catch (Throwable e) {
String message = "Unexpected exception occurred: " + e.getMessage();
LOG.error(message, e);
throw new ProcessletException(
new OWSException(message, e, ControllerException.NO_APPLICABLE_CODE));
}
}
/**
* 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();
}