public static CQLQuery checkDefaultPredicates(CQLQuery original) throws Exception {
LOG.debug("Checking query for Attributes with no predicate defined");
StringWriter originalWriter = new StringWriter();
Utils.serializeObject(original, DataServiceConstants.CQL_QUERY_QNAME, originalWriter);
Element root =
XMLUtilities.stringToDocument(originalWriter.getBuffer().toString()).getRootElement();
Filter attributeNoPredicateFilter =
new Filter() {
public boolean matches(Object o) {
if (o instanceof Element) {
Element e = (Element) o;
if (e.getName().equals("Attribute") && e.getAttribute("predicate") == null) {
return true;
}
}
return false;
}
};
List<?> attributesWithNoPredicate = root.getContent(attributeNoPredicateFilter);
Iterator<?> attribIter = attributesWithNoPredicate.iterator();
while (attribIter.hasNext()) {
LOG.debug("Adding default predicate to an attribute");
Element elem = (Element) attribIter.next();
elem.setAttribute("predicate", "EQUAL_TO");
}
String xml = XMLUtilities.elementToString(root);
CQLQuery edited = Utils.deserializeObject(new StringReader(xml), CQLQuery.class);
return edited;
}
@Override
protected void storyTearDown() throws Throwable {
super.storyTearDown();
if (TEST_DIR.exists()) {
Utils.deleteDir(TEST_DIR);
}
}
protected void writeOutAuditorConfiguration(Data extData, ServiceInformation serviceInfo)
throws CodegenExtensionException {
if (CommonTools.servicePropertyExists(
serviceInfo.getServiceDescriptor(),
DataServiceConstants.DATA_SERVICE_AUDITORS_CONFIG_FILE_PROPERTY)) {
try {
// get the name of the auditor config file
String filename =
CommonTools.getServicePropertyValue(
serviceInfo.getServiceDescriptor(),
DataServiceConstants.DATA_SERVICE_AUDITORS_CONFIG_FILE_PROPERTY);
if (extData.getDataServiceAuditors() != null) {
File outFile =
new File(
serviceInfo.getBaseDirectory().getAbsolutePath()
+ File.separator
+ "etc"
+ File.separator
+ filename);
FileWriter writer = new FileWriter(outFile);
Utils.serializeObject(
extData.getDataServiceAuditors(),
DataServiceConstants.DATA_SERVICE_AUDITORS_QNAME,
writer);
writer.flush();
writer.close();
}
} catch (Exception ex) {
ex.printStackTrace();
throw new CodegenExtensionException(
"Error writing auditor configuration: " + ex.getMessage(), ex);
}
}
}
public void storyTearDown() throws Throwable {
List<Throwable> errors = new LinkedList<Throwable>();
try {
new StopContainerStep(container).runStep();
} catch (Throwable th) {
errors.add(th);
}
try {
new DestroyContainerStep(container).runStep();
} catch (Throwable th) {
errors.add(th);
}
try {
// System.out.println("Data Service in " + testInfo.getDir());
Utils.deleteDir(new File(testInfo.getDir()));
} catch (Throwable th) {
errors.add(th);
}
if (errors.size() != 0) {
System.err.println("EXCEPTION(S) OCCURED DURING TEAR DOWN:");
for (Throwable t : errors) {
System.err.println("----------------");
t.printStackTrace();
}
throw new Exception("EXCEPTION(S) OCCURED DURING TEAR DOWN. SEE LOGS");
}
}
private void addUpdatePrivileges() {
try {
String id = Utils.clean(getIdentity().getText());
if (id == null) {
ErrorDialog.showError("Please enter a valid identity!!!");
}
boolean reload = false;
StringBuffer sb = new StringBuffer();
sb.append("Updating the privileges resulted in the following:\n");
String s1 = addUpdateCreate();
if (s1 != null) {
reload = true;
sb.append(s1 + "\n");
}
String s2 = addUpdateStem();
if (s2 != null) {
reload = true;
sb.append(s2);
}
dispose();
if (reload) {
browser.loadPrivileges();
}
GridApplication.getContext().showMessage(sb.toString());
} catch (Exception e) {
ErrorDialog.showError(e);
FaultUtil.logFault(log, e);
}
}
private void createGallery() {
String name = this.getGalleryNane().getText();
if (Utils.clean(name) == null) {
ErrorDialog.showError("You must specify a gallery name.");
return;
}
try {
getProgress().showProgress("Creating gallery...");
PhotoSharingHandle handle = this.root.getServiceHandle();
handle.createGallery(name);
this.root.refresh();
getProgress().stopProgress();
dispose();
} catch (Exception e) {
ErrorDialog.showError(Utils.getExceptionMessage(e), e);
}
}
public void setAssertingCredentialsEncryptionPassword(
String assertingCredentialsEncryptionPassword) throws DorianInternalFault {
if (Utils.clean(assertingCredentialsEncryptionPassword) == null) {
DorianInternalFault f = new DorianInternalFault();
f.setFaultString("Invalid asserting credentials password specified.");
throw f;
}
this.assertingCredentialsEncryptionPassword = assertingCredentialsEncryptionPassword;
}
public void setAssertingCredentialsEncryptionPassword(
String assertingCredentialsEncryptionPassword) throws DorianInternalException {
if (Utils.clean(assertingCredentialsEncryptionPassword) == null) {
DorianInternalException f =
FaultHelper.createFaultException(
DorianInternalException.class, "Invalid asserting credentials password specified.");
throw f;
}
this.assertingCredentialsEncryptionPassword = assertingCredentialsEncryptionPassword;
}
private void addInstanceCountResourceProperty() throws UpgradeException {
// get the schemas dir so we can copy in the new XSD
File dataSchemasDir = getDataSchemaDir();
File instanceCountXsd = new File(dataSchemasDir, MetadataConstants.DATA_INSTANCE_XSD);
// get the service's schema dir where the wsdl files live
ServiceType baseService = getServiceInformation().getServices().getService(0);
String serviceName = baseService.getName();
File serviceSchemasDir = new File(getServicePath(), "schema" + File.separator + serviceName);
// copy the schema
File instanceCountXsdOut = new File(serviceSchemasDir, instanceCountXsd.getName());
try {
Utils.copyFile(instanceCountXsd, instanceCountXsdOut);
} catch (Exception ex) {
throw new UpgradeException(
"Error copying data instance counts schema: " + ex.getMessage(), ex);
}
// add the schema to the service descriptor
NamespaceType countNamespace = null;
try {
countNamespace =
CommonTools.createNamespaceType(instanceCountXsdOut.getAbsolutePath(), serviceSchemasDir);
} catch (Exception ex) {
throw new UpgradeException(
"Error creating data instance counts namespace: " + ex.getMessage(), ex);
}
countNamespace.setPackageName(MetadataConstants.DATA_INSTANCE_PACKAGE);
countNamespace.setGenerateStubs(Boolean.FALSE);
CommonTools.addNamespace(getServiceInformation().getServiceDescriptor(), countNamespace);
if (CommonTools.getResourcePropertiesOfType(baseService, MetadataConstants.DATA_INSTANCE_QNAME)
.length
== 0) {
// no resource property found, so we have to create and add it
ResourcePropertyType countRp = new ResourcePropertyType();
countRp.setRegister(true);
countRp.setDescription(MetadataConstants.DATA_INSTANCE_DESCRIPTION);
countRp.setQName(MetadataConstants.DATA_INSTANCE_QNAME);
CommonTools.addResourcePropety(baseService, countRp);
}
// instance count frequency property
if (!CommonTools.servicePropertyExists(
getServiceInformation().getServiceDescriptor(),
InstanceCountConstants.COUNT_UPDATE_FREQUENCY)) {
CommonTools.setServiceProperty(
getServiceInformation().getServiceDescriptor(),
InstanceCountConstants.COUNT_UPDATE_FREQUENCY,
InstanceCountConstants.COUNT_UPDATE_FREQUENCY_DEFAULT,
false,
InstanceCountConstants.COUNT_UPDATE_FREQUENCY_DESCRIPTION);
}
}
private void storeExtensionDataElement(Element elem) throws UpgradeException {
MessageElement[] anys = getExtensionType().getExtensionData().get_any();
for (int i = 0; (anys != null) && (i < anys.length); i++) {
if (anys[i].getQName().equals(Data.getTypeDesc().getXmlType())) {
// remove the old extension data
anys = (MessageElement[]) Utils.removeFromArray(anys, anys[i]);
break;
}
}
// create a message element from the JDom element
MessageElement data = null;
try {
data = AxisJdomUtils.fromElement(elem);
} catch (JDOMException ex) {
throw new UpgradeException(
"Error converting extension data to Axis message element: " + ex.getMessage(), ex);
}
anys = (MessageElement[]) Utils.appendToArray(anys, data);
getExtensionType().getExtensionData().set_any(anys);
}
private CQLQuery loadQuery(String queryFilename) {
CQLQuery query = null;
File queryFile = new File(TEST_QUERIES_DIR, queryFilename);
try {
FileReader reader = new FileReader(queryFile);
query = (CQLQuery) Utils.deserializeObject(reader, CQLQuery.class);
} catch (Exception ex) {
ex.printStackTrace();
fail("Error loading query " + queryFilename + ": " + ex.getMessage());
}
return query;
}
/**
* getRegistration reads the XML file and creates a registration object from it for testing
*
* <p>
*
* @return
* @throws DeserializationException
* @throws SAXException
*/
private Registration getRegistration()
throws DeserializationException, SAXException, IOException {
// InputStream sampleIs = getClass().getResourceAsStream(sampleFile);
InputStream sampleIs = new FileInputStream(sampleFile);
InputStreamReader reader = new InputStreamReader(sampleIs);
InputStream wsddIs =
getClass().getResourceAsStream("/gov/nih/nci/ccts/grid/client/client-config.wsdd");
Registration reg =
(gov.nih.nci.cabig.ccts.domain.Registration)
Utils.deserializeObject(
reader, gov.nih.nci.cabig.ccts.domain.Registration.class, wsddIs);
return reg;
}
private void loadServiceMetadataFromFile() {
try {
File dataFile =
new File(
ContainerConfig.getBaseDirectory()
+ File.separator
+ getConfiguration().getServiceMetadataFile());
this.serviceMetadataMD =
(gov.nih.nci.cagrid.metadata.ServiceMetadata)
Utils.deserializeDocument(
dataFile.getAbsolutePath(), gov.nih.nci.cagrid.metadata.ServiceMetadata.class);
} catch (Exception e) {
logger.error("ERROR: problem populating metadata from file: " + e.getMessage(), e);
}
}
private void findCertificates() {
try {
showProgess("Searching...");
getUserCertificates().clearTable();
UserCertificateFilter f = new UserCertificateFilter();
f.setGridIdentity(Utils.clean(getGridIdentity().getText()));
if (Utils.clean(getUserCertificateSerialNumber().getText()) != null) {
try {
f.setSerialNumber(Long.valueOf(Utils.clean(getUserCertificateSerialNumber().getText())));
} catch (NumberFormatException e) {
stopProgess("Error");
enableButtons();
ErrorDialog.showError("The serial number must be an integer.");
return;
}
}
if ((searchStartDate != null) && (searchEndDate != null)) {
if (searchStartDate.after(searchEndDate)) {
stopProgess("Error");
enableButtons();
ErrorDialog.showError("The start date cannot be after the end date.");
return;
} else {
DateRange r = new DateRange();
r.setStartDate(searchStartDate);
r.setEndDate(searchEndDate);
f.setDateRange(r);
}
} else if ((searchStartDate == null) && (searchEndDate != null)) {
stopProgess("Error");
enableButtons();
ErrorDialog.showError("You must specify a start date!!!");
return;
} else if ((searchStartDate != null) && (searchEndDate == null)) {
stopProgess("Error");
enableButtons();
ErrorDialog.showError("You must specify an end date!!!");
return;
}
f.setNotes(Utils.clean(getNotes().getText()));
if (getStatus().getSelectedUserStatus() != null) {
f.setStatus(getStatus().getSelectedUserStatus());
}
GridAdministrationClient client = this.session.getAdminClient();
List<UserCertificateRecord> records = client.findUserCertificateRecords(f);
getUserCertificates().addUserCertificates(records);
stopProgess(records.size() + " user certificate(s) found.");
} catch (Exception e) {
stopProgess("Error");
ErrorDialog.showError(Utils.getExceptionMessage(e), e);
log.error(Utils.getExceptionMessage(e), e);
}
enableButtons();
}
protected static String loadResource(String resourceName) throws IOException {
String resource = null;
synchronized (resourceMap) {
if (resourceMap.containsKey(resourceName)) {
resource = resourceMap.get(resourceName);
} else {
InputStream stream = ClassUtils.getResourceAsStream(SDK44EncodingUtils.class, resourceName);
if (stream != null) {
StringBuffer buffer = Utils.inputStreamToStringBuffer(stream);
resource = buffer.toString();
resourceMap.put(resourceName, resource);
stream.close();
}
}
}
return resource;
}
public static void main(String[] args) throws Exception {
args =
new String[] {
"-gsh", "http://ccis1716.duhs.duke.edu/wsrf/services/cagrid/RPData",
// "-gsh", "http://localhost:8080/wsrf/services/cagrid/RPData",
// "-gsh", "http://140.254.80.99:8080/wsrf/services/cagrid/RPData",
"-query", "queries\\scanFeatures_query3.xml",
"-printXml"
};
Options options = getOptions();
CommandLine cmd = null;
try {
cmd = new BasicParser().parse(options, args);
} catch (ParseException e) {
System.out.println("Error parsing arguments: " + e.getMessage());
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("RPDataClient", options);
System.exit(-1);
return;
}
RPDataClient client = new RPDataClient(cmd.getOptionValue("gsh"));
CQLQueryType query =
(CQLQueryType) Utils.deserializeDocument(cmd.getOptionValue("query"), CQLQueryType.class);
gov.nih.nci.cagrid.cql.CQLQueryResultsType results = client.query(query);
gov.nih.nci.cagrid.cql.CQLQueryResultType[] resultsArray = results.getCQLQueryResult();
if (resultsArray != null) {
System.out.println("Got " + resultsArray.length + " result(s)");
for (int i = 0; i < resultsArray.length; i++) {
gov.nih.nci.cagrid.cql.CQLQueryResultType result = resultsArray[i];
// Deserialize and print out each element........
MessageElement[] msgs = result.get_any();
for (int j = 0; j < msgs.length; j++) {
StringWriter output = new StringWriter();
TransformerFactory.newInstance()
.newTransformer()
.transform(new DOMSource(msgs[j]), new StreamResult(output));
if (cmd.hasOption("printXml")) System.out.println(output.toString());
}
}
}
}
private void upgradeWsdls() throws UpgradeException {
// get the service's schema dir where the wsdl files live
String serviceName =
getServiceInformation().getServiceDescriptor().getServices().getService(0).getName();
File serviceSchemasDir = new File(getServicePath(), "schema" + File.separator + serviceName);
// get the data service schemas dir
File dataSchemasDir = getDataSchemaDir();
// find data wsdls
Map<String, File> dataWsdlsByName = new HashMap<String, File>();
for (File file : dataSchemasDir.listFiles()) {
String name = file.getName();
if (name.endsWith(".wsdl")) {
dataWsdlsByName.put(name, file);
}
}
// list wsdls in service schemas dir. If any match one from data, replace it with the new
// version
File[] serviceWsdls =
serviceSchemasDir.listFiles(
new FileFilter() {
public boolean accept(File path) {
return path.getName().endsWith(".wsdl");
}
});
for (File serviceWsdl : serviceWsdls) {
if (dataWsdlsByName.containsKey(serviceWsdl.getName())) {
// overwrite the service wsdl with the new one
try {
Utils.copyFile(dataWsdlsByName.get(serviceWsdl.getName()), serviceWsdl);
getStatus()
.addDescriptionLine(
"Replaced WSDL "
+ serviceWsdl.getName()
+ " with new version "
+ UpgraderConstants.DATA_CURRENT_VERSION);
} catch (Exception ex) {
throw new UpgradeException("Error replacing wsdl: " + ex.getMessage(), ex);
}
}
}
}
@Override
public void runStep() throws Throwable {
assertNotNull(this.credential);
assertNotNull(this.credential.getGridCredential());
assertNotNull(this.delegatedCredential);
assertNotNull(this.delegatedCredential.getDelegatedCredentialReference());
assertNotNull(this.expectedError);
DelegatedCredentialUserClient client =
new DelegatedCredentialUserClient(
this.delegatedCredential.getDelegatedCredentialReference(),
this.credential.getGridCredential());
try {
client.getDelegatedCredential();
fail("Should not be able to get delegated credential.");
} catch (Exception e) {
String error = Utils.getExceptionMessage(e);
if (error.indexOf(expectedError) == -1) {
fail("Unexpected error encountered:\nEXPECTED:" + expectedError + "\n RECEIVED:" + error);
}
}
}
private String addUpdatePrivilege(boolean wasSelected, boolean selectedNow, Privilege priv)
throws Exception {
String id = Utils.clean(getIdentity().getText());
Subject subj = SubjectUtils.getSubject(id);
if (update) {
if (!wasSelected && selectedNow) {
try {
targetStem.grantPriv(subj, priv);
return "GRANTED " + priv.getName() + " privilege.";
} catch (Exception e) {
FaultUtil.logFault(log, e);
throw new Exception("ERROR granting " + priv.getName() + " privilege: " + e.getMessage());
}
} else if (wasSelected && !selectedNow) {
try {
targetStem.revokePriv(subj, priv);
return "REVOKED " + priv.getName() + " privilege.";
} catch (Exception e) {
FaultUtil.logFault(log, e);
throw new Exception("ERROR revoking " + priv.getName() + " privilege: " + e.getMessage());
}
}
} else {
if (selectedNow) {
try {
targetStem.grantPriv(subj, priv);
return "GRANTED " + priv.getName() + " privilege.";
} catch (Exception e) {
FaultUtil.logFault(log, e);
throw new Exception("ERROR granting " + priv.getName() + " privilege: " + e.getMessage());
}
}
}
return null;
}
private void updateDataLibraries() throws UpgradeException {
FileFilter oldDataLibFilter =
new FileFilter() {
public boolean accept(File pathname) {
String name = pathname.getName();
return name.endsWith(".jar")
&& (name.startsWith("caGrid-data-")
|| name.startsWith("caGrid-core-")
|| name.startsWith("caGrid-CQL-")
|| name.startsWith("caGrid-caDSR-")
|| name.startsWith("caGrid-metadata-"));
}
};
FileFilter newDataLibFilter =
new FileFilter() {
public boolean accept(File pathname) {
String name = pathname.getName();
return name.endsWith(".jar")
&& (name.startsWith("caGrid-data-")
|| name.startsWith("caGrid-core-")
|| name.startsWith("caGrid-CQL-")
|| name.startsWith("caGrid-caDSR-")
|| name.startsWith("caGrid-metadata-")
|| name.startsWith("caGrid-mms-")
|| name.startsWith("castor-1.0.2"));
}
};
// locate the old data service libs in the service
File serviceLibDir = new File(getServicePath() + File.separator + "lib");
File[] serviceDataLibs = serviceLibDir.listFiles(oldDataLibFilter);
// delete the old libraries
for (File oldLib : serviceDataLibs) {
oldLib.delete();
getStatus().addDescriptionLine("caGrid 1.5 library " + oldLib.getName() + " removed");
}
// copy new libraries in
File extLibDir = new File(ExtensionsLoader.EXTENSIONS_DIRECTORY + File.separator + "lib");
File[] dataLibs = extLibDir.listFiles(newDataLibFilter);
List<File> outLibs = new ArrayList<File>(dataLibs.length);
for (File newLib : dataLibs) {
File out = new File(serviceLibDir.getAbsolutePath() + File.separator + newLib.getName());
try {
Utils.copyFile(newLib, out);
getStatus()
.addDescriptionLine(
"caGrid "
+ UpgraderConstants.DATA_CURRENT_VERSION
+ " library "
+ newLib.getName()
+ " added");
} catch (IOException ex) {
throw new UpgradeException(
"Error copying new data service library: " + ex.getMessage(), ex);
}
outLibs.add(out);
}
// update the Eclipse .classpath file
File classpathFile = new File(getServicePath() + File.separator + ".classpath");
File[] outLibArray = new File[dataLibs.length];
outLibs.toArray(outLibArray);
try {
ExtensionUtilities.syncEclipseClasspath(classpathFile, outLibArray);
getStatus().addDescriptionLine("Eclipse .classpath file updated");
} catch (Exception ex) {
throw new UpgradeException("Error updating Eclipse .classpath file: " + ex.getMessage(), ex);
}
}
protected void generateClassToQnameMapping(Data extData, ServiceInformation info)
throws CodegenExtensionException {
try {
Mappings mappings = new Mappings();
List<ClassToQname> classMappings = new LinkedList<ClassToQname>();
// the first place to look for mappings is in the model information, which
// is derived from the data service Domain Model. If no domain model is to be used,
// the mappings are still required to do anything with caCORE SDK beans.
ModelInformation modelInfo = extData.getModelInformation();
if (modelInfo != null
&& !ModelSourceType.none.equals(modelInfo.getSource())
&& modelInfo.getModelPackage() != null) {
logger.debug("Model information / domain model found in service model.");
logger.debug("Generating class to qname mapping from the information");
logger.debug("stored in the service model");
// walk packages in the model
for (ModelPackage pack : modelInfo.getModelPackage()) {
// locate a NamsepaceType in the service model mapped to this package
NamespaceType mappedNamespace = null;
for (NamespaceType nsType : info.getServiceDescriptor().getNamespaces().getNamespace()) {
if (pack.getPackageName().equals(nsType.getPackageName())) {
mappedNamespace = nsType;
break;
}
}
if (mappedNamespace != null && pack.getModelClass() != null) {
// walk classes in this package, if any exist
for (ModelClass clazz : pack.getModelClass()) {
if (clazz.isTargetable()) {
// find a schema element type mapped to this class
for (SchemaElementType element : mappedNamespace.getSchemaElement()) {
if (clazz.getShortClassName().equals(element.getClassName())) {
// found it! Create a mapping
QName qname = new QName(mappedNamespace.getNamespace(), element.getType());
String fullClassname = pack.getPackageName() + "." + clazz.getShortClassName();
ClassToQname map = new ClassToQname(fullClassname, qname.toString());
classMappings.add(map);
break;
}
}
}
}
} else {
logger.warn(
"Model package " + pack.getPackageName() + " is not mapped to any namespace!");
}
}
ClassToQname[] mapArray = new ClassToQname[classMappings.size()];
classMappings.toArray(mapArray);
mappings.setMapping(mapArray);
} else {
logger.warn("No model information / domain model found in service model.");
logger.warn("Falling back to schema information for class to qname mapping.");
NamespaceType[] namespaces = info.getNamespaces().getNamespace();
// a set of namespaces to ignore
Set<String> nsIgnores = new HashSet<String>();
nsIgnores.add(IntroduceConstants.W3CNAMESPACE);
nsIgnores.add(info.getServices().getService(0).getNamespace());
nsIgnores.add(DataServiceConstants.ENUMERATION_DATA_SERVICE_NAMESPACE);
nsIgnores.add(DataServiceConstants.DATA_SERVICE_NAMESPACE);
nsIgnores.add(DataServiceConstants.CQL_QUERY_URI);
nsIgnores.add(DataServiceConstants.CQL_RESULT_SET_URI);
for (int nsIndex = 0; nsIndex < namespaces.length; nsIndex++) {
NamespaceType currentNs = namespaces[nsIndex];
// ignore any unneeded namespaces
if (!nsIgnores.contains(currentNs.getNamespace())) {
SchemaElementType[] schemaElements = currentNs.getSchemaElement();
for (int elemIndex = 0;
schemaElements != null && elemIndex < schemaElements.length;
elemIndex++) {
SchemaElementType currentElement = schemaElements[elemIndex];
ClassToQname toQname = new ClassToQname();
QName qname = new QName(currentNs.getNamespace(), currentElement.getType());
String shortClassName = currentElement.getClassName();
if (shortClassName == null) {
shortClassName = currentElement.getType();
}
String fullClassName = currentNs.getPackageName() + "." + shortClassName;
toQname.setQname(qname.toString());
toQname.setClassName(fullClassName);
classMappings.add(toQname);
}
}
}
}
ClassToQname[] mapArray = new ClassToQname[classMappings.size()];
classMappings.toArray(mapArray);
mappings.setMapping(mapArray);
// create the filename where the mapping will be stored
String mappingFilename =
new File(
info.getBaseDirectory(),
"etc" + File.separator + DataServiceConstants.CLASS_TO_QNAME_XML)
.getAbsolutePath();
// serialize the mapping to that file
Utils.serializeDocument(mappingFilename, mappings, DataServiceConstants.MAPPING_QNAME);
} catch (Exception ex) {
ex.printStackTrace();
throw new CodegenExtensionException(
"Error generating class to QName mapping: " + ex.getMessage(), ex);
}
}
private Credential getBasicCredential(String userName, String password) {
BasicAuthentication basicAuthentication = new BasicAuthentication();
basicAuthentication.setUserId(Utils.clean(userName));
basicAuthentication.setPassword(Utils.clean(password));
return basicAuthentication;
}
private Credential getOnetimePasswordCredential(String userName, String onetimepassword) {
OneTimePassword onetimePassword = new OneTimePassword();
onetimePassword.setUserId(Utils.clean(userName));
onetimePassword.setOneTimePassword(Utils.clean(onetimepassword));
return onetimePassword;
}
public void applyConfiguration() throws Exception {
LOG.debug("Applying configuration");
// just in case...
validateSdkDirectory();
// new data service's lib directory
File libOutDir = new File(getServiceInformation().getBaseDirectory(), "lib");
File tempLibDir = new File(getServiceInformation().getBaseDirectory(), "temp");
tempLibDir.mkdir();
String projectName =
getDeployPropertiesFromSdkDir()
.getProperty(SDK41StyleConstants.DeployProperties.PROJECT_NAME);
File remoteClientDir =
new File(
sdkDirectory,
"output"
+ File.separator
+ projectName
+ File.separator
+ "package"
+ File.separator
+ "remote-client");
File localClientDir =
new File(
sdkDirectory,
"output"
+ File.separator
+ projectName
+ File.separator
+ "package"
+ File.separator
+ "local-client");
// wrap up the remote-client config files as a jar file so it'll be on the classpath
// local client stuff might be added by the API Type configuration step
LOG.debug("Creating a jar to contain the remote configuration of the caCORE SDK system");
File remoteConfigDir = new File(remoteClientDir, "conf");
String remoteConfigJarName = projectName + "-remote-config.jar";
File remoteConfigJar = new File(tempLibDir, remoteConfigJarName);
JarUtilities.jarDirectory(remoteConfigDir, remoteConfigJar);
// also jar up the local-client config files
LOG.debug("Creating a jar to contain the local configuration of the caCORE SDK system");
File localConfigDir = new File(localClientDir, "conf");
String localConfigJarName = projectName + "-local-config.jar";
File localConfigJar = new File(tempLibDir, localConfigJarName);
JarUtilities.jarDirectory(localConfigDir, localConfigJar);
// set the config jar in the shared configuration
SharedConfiguration.getInstance().setRemoteConfigJarFile(remoteConfigJar);
SharedConfiguration.getInstance().setLocalConfigJarFile(localConfigJar);
// get a list of jars found in GLOBUS_LOCATION/lib
File globusLocation = new File(System.getenv(GLOBUS_LOCATION_ENV));
File globusLib = new File(globusLocation, "lib");
File[] globusJars = globusLib.listFiles(new FileFilters.JarFileFilter());
Set<String> globusJarNames = new HashSet<String>();
for (File jar : globusJars) {
globusJarNames.add(jar.getName());
}
Set<String> serviceJarNames = new HashSet<String>();
for (File jar : libOutDir.listFiles(new FileFilters.JarFileFilter())) {
serviceJarNames.add(jar.getName());
}
// get the application name
final String applicationName =
getDeployPropertiesFromSdkDir()
.getProperty(SDK41StyleConstants.DeployProperties.PROJECT_NAME);
// copy in libraries from the remote lib dir that DON'T collide with Globus's
LOG.debug("Copying libraries from remote client directory");
File[] remoteLibs = new File(remoteClientDir, "lib").listFiles(new FileFilters.JarFileFilter());
for (File lib : remoteLibs) {
String libName = lib.getName();
if (!globusJarNames.contains(libName) && !libName.startsWith("caGrid-CQL-cql.1.0-")) {
File libOutput = new File(libOutDir, libName);
Utils.copyFile(lib, libOutput);
LOG.debug(libName + " copied to the service");
}
}
LOG.debug("Copying libraries from the local client directory");
File localLibDir = new File(localClientDir, "lib");
File[] localLibs = localLibDir.listFiles();
for (File lib : localLibs) {
String name = lib.getName();
boolean ok = true;
// is the jar one that is known to conflict with caGrid or Globus?
ok =
!(name.equals("axis.jar")
|| name.startsWith("commons-collections")
|| name.startsWith("commons-logging")
|| name.startsWith("commons-discovery")
|| name.startsWith("log4j"));
// is the jar already copied into the service
if (ok && serviceJarNames.contains(name)) {
ok = false;
}
// is the jar one of the caGrid 1.2 jars?
if (ok && name.startsWith("caGrid-") && name.endsWith("-1.2.jar")) {
if (!name.startsWith("caGrid-sdkQuery4-")) {
ok = false;
}
}
// is the jar in the globus lib dir?
if (ok && !globusJarNames.contains(name)) {
File libOutput = new File(libOutDir, name);
Utils.copyFile(lib, libOutput);
LOG.debug(name + " copied to the service");
}
}
// set the application name service property
setCql1ProcessorProperty(SDK41QueryProcessor.PROPERTY_APPLICATION_NAME, applicationName, false);
setCql2ProcessorProperty(
SDK41CQL2QueryProcessor.PROPERTY_APPLICATION_NAME, applicationName, false);
// grab the castor marshalling and unmarshalling xml mapping files
// from the config dir and copy them into the service's package structure
try {
LOG.debug("Copying castor marshalling and unmarshalling files");
File marshallingMappingFile =
new File(remoteConfigDir, CastorMappingUtil.CASTOR_MARSHALLING_MAPPING_FILE);
File unmarshallingMappingFile =
new File(remoteConfigDir, CastorMappingUtil.CASTOR_UNMARSHALLING_MAPPING_FILE);
// copy the mapping files to the service's source dir + base package name
String marshallOut =
CastorMappingUtil.getMarshallingCastorMappingFileName(getServiceInformation());
String unmarshallOut =
CastorMappingUtil.getUnmarshallingCastorMappingFileName(getServiceInformation());
Utils.copyFile(marshallingMappingFile, new File(marshallOut));
Utils.copyFile(unmarshallingMappingFile, new File(unmarshallOut));
} catch (IOException ex) {
ex.printStackTrace();
CompositeErrorDialog.showErrorDialog(
"Error copying castor mapping files", ex.getMessage(), ex);
}
// set up the shared configuration
SharedConfiguration.getInstance().setSdkDirectory(getSdkDirectory());
SharedConfiguration.getInstance().setServiceInfo(getServiceInformation());
SharedConfiguration.getInstance().setSdkDeployProperties(getDeployPropertiesFromSdkDir());
}
private void editWsddForCastorMappings(ServiceInformation info) throws Exception {
// change out the domain model validator class
CommonTools.setServiceProperty(
info.getServiceDescriptor(),
DataServiceConstants.DOMAIN_MODEL_VALIDATOR_CLASS,
ISODomainModelValidator.class.getName(),
false);
String mainServiceName =
info.getIntroduceServiceProperties()
.getProperty(IntroduceConstants.INTRODUCE_SKELETON_SERVICE_NAME);
ServiceType mainService = CommonTools.getService(info.getServices(), mainServiceName);
String servicePackageName = mainService.getPackageName();
String packageDir = servicePackageName.replace('.', File.separatorChar);
// find the client source directory, where the client-config will be located
File clientConfigFile =
new File(
info.getBaseDirectory(),
"src"
+ File.separator
+ packageDir
+ File.separator
+ "client"
+ File.separator
+ "client-config.wsdd");
LOG.debug("Editing client config wsdd at " + clientConfigFile.getAbsolutePath());
if (!clientConfigFile.exists()) {
throw new CodegenExtensionException(
"Client config file " + clientConfigFile.getAbsolutePath() + " not found!");
}
// find the server-config.wsdd, located in the service's root directory
File serverConfigFile = new File(info.getBaseDirectory(), "server-config.wsdd");
LOG.debug("Editing server config wsdd at " + serverConfigFile.getAbsolutePath());
if (!serverConfigFile.exists()) {
throw new CodegenExtensionException(
"Server config file " + serverConfigFile.getAbsolutePath() + " not found!");
}
// edit the marshaling castor mapping to avoid serializing associations
File castorMappingFile = new File(CastorMappingUtil.getMarshallingCastorMappingFileName(info));
if (castorMappingFile.exists()) {
String marshallingXmlText = Utils.fileToStringBuffer(castorMappingFile).toString();
String editedMarshallingText =
CastorMappingUtil.removeAssociationMappings(marshallingXmlText);
String editedMarshallingFileName =
CastorMappingUtil.getEditedMarshallingCastorMappingFileName(info);
Utils.stringBufferToFile(new StringBuffer(editedMarshallingText), editedMarshallingFileName);
// edit the unmarshaling castor mapping to avoid deserializing associations
String unmarshallingXmlText =
Utils.fileToStringBuffer(
new File(CastorMappingUtil.getUnmarshallingCastorMappingFileName(info)))
.toString();
String editedUnmarshallingText =
CastorMappingUtil.removeAssociationMappings(unmarshallingXmlText);
String editedUnmarshallingFileName =
CastorMappingUtil.getEditedUnmarshallingCastorMappingFileName(info);
Utils.stringBufferToFile(
new StringBuffer(editedUnmarshallingText), editedUnmarshallingFileName);
// set properties in the client to use the edited marshaler
WsddUtil.setGlobalClientParameter(
clientConfigFile.getAbsolutePath(),
SDK43EncodingUtils.CASTOR_MARSHALLER_PROPERTY,
CastorMappingUtil.getEditedMarshallingCastorMappingName(info));
// and the edited unmarshaler
WsddUtil.setGlobalClientParameter(
clientConfigFile.getAbsolutePath(),
SDK43EncodingUtils.CASTOR_UNMARSHALLER_PROPERTY,
CastorMappingUtil.getEditedUnmarshallingCastorMappingName(info));
// set properties in the server to use the edited marshaler
WsddUtil.setServiceParameter(
serverConfigFile.getAbsolutePath(),
info.getServices().getService(0).getName(),
SDK43EncodingUtils.CASTOR_MARSHALLER_PROPERTY,
CastorMappingUtil.getEditedMarshallingCastorMappingName(info));
// and the edited unmarshaler
WsddUtil.setServiceParameter(
serverConfigFile.getAbsolutePath(),
info.getServices().getService(0).getName(),
SDK43EncodingUtils.CASTOR_UNMARSHALLER_PROPERTY,
CastorMappingUtil.getEditedUnmarshallingCastorMappingName(info));
} else {
LOG.debug(
"Castor mapping file "
+ castorMappingFile.getAbsolutePath()
+ " not found... this is OK if you're using JaxB serialization");
}
}
public static void main(String[] args) {
System.out.println("Running the Grid Service Client");
try {
if (!(args.length < 2)) {
if (args[0].equals("-url")) {
IntroduceTestPersistentServiceClient client =
new IntroduceTestPersistentServiceClient(args[1]);
// place client calls here if you want to use this main as a
// test....
java.io.FileReader fr1 = new java.io.FileReader("persistenceTestEPR1.xml");
org.apache.axis.message.addressing.EndpointReferenceType epr1 =
(org.apache.axis.message.addressing.EndpointReferenceType)
gov.nih.nci.cagrid.common.Utils.deserializeObject(
fr1, org.apache.axis.message.addressing.EndpointReferenceType.class);
org.test.persistent.resource.client.IntroduceTestPersistentResourceServiceClient
resourceClient1 =
new org.test.persistent.resource.client
.IntroduceTestPersistentResourceServiceClient(epr1);
projectmobius.org.BookType book1 = resourceClient1.getBook();
if (book1 != null && book1.getAuthor().equals("Shannon Hastings")) {
System.out.println("Got recovered persistence resource and is correct");
new java.io.File("persistenceTestEPR1.xml").delete();
} else {
new java.io.File("persistenceTestEPR1.xml").delete();
System.err.println("Could not retrieve the persistent resource");
System.exit(1);
}
resourceClient1.destroy();
book1 = null;
try {
book1 = resourceClient1.getBook();
} catch (Exception e) {
System.out.println("Destroy and remove of persistence file worked.");
}
if (book1 != null) {
System.err.println("Destroy and remove of persistence file error.");
System.exit(1);
}
java.io.FileReader fr2 = new java.io.FileReader("persistenceTestEPR2.xml");
org.apache.axis.message.addressing.EndpointReferenceType epr2 =
(org.apache.axis.message.addressing.EndpointReferenceType)
gov.nih.nci.cagrid.common.Utils.deserializeObject(
fr2, org.apache.axis.message.addressing.EndpointReferenceType.class);
org.test.persistent.resource.client.IntroduceTestPersistentResourceServiceClient
resourceClient2 =
new org.test.persistent.resource.client
.IntroduceTestPersistentResourceServiceClient(epr2);
projectmobius.org.BookType book2 = resourceClient2.getBook();
if (book2 != null && book2.getAuthor().equals("Bozo The Clown")) {
System.out.println("Got recovered persistence resource and is correct");
new java.io.File("persistenceTestEPR2.xml").delete();
} else {
new java.io.File("persistenceTestEPR2.xml").delete();
System.err.println("Could not retrieve the persistent resource");
System.exit(1);
}
} else {
usage();
System.exit(1);
}
} else {
usage();
System.exit(1);
}
} catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}