List of usage examples for java.util Collection clear
void clear();
From source file:org.openmrs.web.dwr.DWRPatientService.java
/** * Returns a map of results with the values as count of matches and a partial list of the * matching patients (depending on values of start and length parameters) while the keys are are * 'count' and 'objectList' respectively, if the length parameter is not specified, then all * matches will be returned from the start index if specified. * * @param searchValue patient name or identifier * @param includeVoided true/false whether or not to included voided patients * @param start the beginning index//from www . j a va 2s .c om * @param length the number of matching patients to return * @param getMatchCount Specifies if the count of matches should be included in the returned map * @return a map of results * @throws APIException */ public Map<String, Object> findCountAndPatientsWithVoided(String searchValue, Integer start, Integer length, boolean getMatchCount, Boolean includeVoided) throws APIException { //Map to return Map<String, Object> resultsMap = new HashMap<String, Object>(); Collection<Object> objectList = new Vector<Object>(); if (includeVoided == null) { includeVoided = false; } try { PatientService ps = Context.getPatientService(); int patientCount = 0; //if this is the first call if (getMatchCount) { patientCount += ps.getCountOfPatients(searchValue, includeVoided); // if there are no results found and a number was not in the // search and this is the first call, then do a decapitated search: //trim each word down to the first three characters and search again if (patientCount == 0 && start == 0 && !searchValue.matches(".*\\d+.*")) { String[] names = searchValue.split(" "); StringBuilder newSearch = new StringBuilder(""); for (String name : names) { if (name.length() > 3) { name = name.substring(0, 3); } newSearch.append(" ").append(name); } String newSearchStr = newSearch.toString().trim(); if (!newSearchStr.equals(searchValue)) { int newPatientCount = ps.getCountOfPatients(newSearchStr); if (newPatientCount > 0) { // Send a signal to the core search widget to search again against newSearch resultsMap.put("searchAgain", newSearchStr); resultsMap.put("notification", Context.getMessageSourceService().getMessage("searchWidget.noResultsFoundFor", new Object[] { searchValue, newSearchStr }, Context.getLocale())); } } } //no results found and a number was in the search -- //should check whether the check digit is correct. else if (patientCount == 0 && searchValue.matches(".*\\d+.*")) { //Looks through all the patient identifier validators to see if this type of identifier //is supported for any of them. If it isn't, then no need to warn about a bad check //digit. If it does match, then if any of the validators validates the check digit //successfully, then the user is notified that the identifier has been entered correctly. //Otherwise, the user is notified that the identifier was entered incorrectly. Collection<IdentifierValidator> pivs = ps.getAllIdentifierValidators(); boolean shouldWarnUser = true; boolean validCheckDigit = false; boolean identifierMatchesValidationScheme = false; for (IdentifierValidator piv : pivs) { try { if (piv.isValid(searchValue)) { shouldWarnUser = false; validCheckDigit = true; } identifierMatchesValidationScheme = true; } catch (UnallowedIdentifierException e) { } } if (identifierMatchesValidationScheme) { if (shouldWarnUser) { resultsMap.put("notification", "<b>" + Context.getMessageSourceService() .getMessage("Patient.warning.inValidIdentifier") + "<b/>"); } else if (validCheckDigit) { resultsMap.put("notification", "<b style=\"color:green;\">" + Context.getMessageSourceService() .getMessage("Patient.message.validIdentifier") + "<b/>"); } } } else { //ensure that count never exceeds this value because the API's service layer would never //return more than it since it is limited in the DAO layer if (maximumResults == null) { setMaximumResults(getMaximumSearchResults()); } if (length != null && length > maximumResults) { length = maximumResults; } if (patientCount > maximumResults) { patientCount = maximumResults; if (log.isDebugEnabled()) { log.debug("Limitng the size of matching patients to " + maximumResults); } } } } //if we have any matches or this isn't the first ajax call when the caller //requests for the count if (patientCount > 0 || !getMatchCount) { objectList = findBatchOfPatients(searchValue, includeVoided, start, length); } resultsMap.put("count", patientCount); resultsMap.put("objectList", objectList); } catch (Exception e) { log.error("Error while searching for patients", e); objectList.clear(); objectList.add( Context.getMessageSourceService().getMessage("Patient.search.error") + " - " + e.getMessage()); resultsMap.put("count", 0); resultsMap.put("objectList", objectList); } return resultsMap; }
From source file:org.apache.tomee.embedded.TomEEEmbeddedApplicationRunner.java
public synchronized void start(final Class<?> marker, final Properties config, final String... args) throws Exception { if (started) { return;/* w w w . ja v a2 s.c o m*/ } ensureAppInit(marker); started = true; final Class<?> appClass = app.getClass(); final AnnotationFinder finder = new AnnotationFinder(new ClassesArchive(ancestors(appClass))); // setup the container config reading class annotation, using a randome http port and deploying the classpath final Configuration configuration = new Configuration(); final ContainerProperties props = appClass.getAnnotation(ContainerProperties.class); if (props != null) { final Properties runnerProperties = new Properties(); for (final ContainerProperties.Property p : props.value()) { final String name = p.name(); if (name.startsWith("tomee.embedded.application.runner.")) { // allow to tune the Configuration // no need to filter there since it is done in loadFromProperties() runnerProperties.setProperty(name.substring("tomee.embedded.application.runner.".length()), p.value()); } else { configuration.property(name, StrSubstitutor.replaceSystemProperties(p.value())); } } if (!runnerProperties.isEmpty()) { configuration.loadFromProperties(runnerProperties); } } configuration.loadFromProperties(System.getProperties()); // overrides, note that some config are additive by design final List<Method> annotatedMethods = finder .findAnnotatedMethods(org.apache.openejb.testing.Configuration.class); if (annotatedMethods.size() > 1) { throw new IllegalArgumentException("Only one @Configuration is supported: " + annotatedMethods); } for (final Method m : annotatedMethods) { final Object o = m.invoke(app); if (Properties.class.isInstance(o)) { final Properties properties = Properties.class.cast(o); if (configuration.getProperties() == null) { configuration.setProperties(new Properties()); } configuration.getProperties().putAll(properties); } else { throw new IllegalArgumentException("Unsupported " + o + " for @Configuration"); } } final Collection<org.apache.tomee.embedded.LifecycleTask> lifecycleTasks = new ArrayList<>(); final Collection<Closeable> postTasks = new ArrayList<>(); final LifecycleTasks tasks = appClass.getAnnotation(LifecycleTasks.class); if (tasks != null) { for (final Class<? extends org.apache.tomee.embedded.LifecycleTask> type : tasks.value()) { final org.apache.tomee.embedded.LifecycleTask lifecycleTask = type.newInstance(); lifecycleTasks.add(lifecycleTask); postTasks.add(lifecycleTask.beforeContainerStartup()); } } final Map<String, Field> ports = new HashMap<>(); { Class<?> type = appClass; while (type != null && type != Object.class) { for (final Field f : type.getDeclaredFields()) { final RandomPort annotation = f.getAnnotation(RandomPort.class); final String value = annotation == null ? null : annotation.value(); if (value != null && value.startsWith("http")) { f.setAccessible(true); ports.put(value, f); } } type = type.getSuperclass(); } } if (ports.containsKey("http")) { configuration.randomHttpPort(); } // at least after LifecycleTasks to inherit from potential states (system properties to get a port etc...) final Configurers configurers = appClass.getAnnotation(Configurers.class); if (configurers != null) { for (final Class<? extends Configurer> type : configurers.value()) { type.newInstance().configure(configuration); } } final Classes classes = appClass.getAnnotation(Classes.class); String context = classes != null ? classes.context() : ""; context = !context.isEmpty() && context.startsWith("/") ? context.substring(1) : context; Archive archive = null; if (classes != null && classes.value().length > 0) { archive = new ClassesArchive(classes.value()); } final Jars jars = appClass.getAnnotation(Jars.class); final List<URL> urls; if (jars != null) { final Collection<File> files = ApplicationComposers.findFiles(jars); urls = new ArrayList<>(files.size()); for (final File f : files) { urls.add(f.toURI().toURL()); } } else { urls = null; } final WebResource resources = appClass.getAnnotation(WebResource.class); if (resources != null && resources.value().length > 1) { throw new IllegalArgumentException("Only one docBase is supported for now using @WebResource"); } String webResource = null; if (resources != null && resources.value().length > 0) { webResource = resources.value()[0]; } else { final File webapp = new File("src/main/webapp"); if (webapp.isDirectory()) { webResource = "src/main/webapp"; } } if (config != null) { // override other config from annotations configuration.loadFromProperties(config); } final Container container = new Container(configuration); SystemInstance.get().setComponent(TomEEEmbeddedArgs.class, new TomEEEmbeddedArgs(args, null)); SystemInstance.get().setComponent(LifecycleTaskAccessor.class, new LifecycleTaskAccessor(lifecycleTasks)); container.deploy(new Container.DeploymentRequest(context, // call ClasspathSearcher that lazily since container needs to be started to not preload logging urls == null ? new DeploymentsResolver.ClasspathSearcher() .loadUrls(Thread.currentThread().getContextClassLoader()).getUrls() : urls, webResource != null ? new File(webResource) : null, true, null, archive)); for (final Map.Entry<String, Field> f : ports.entrySet()) { switch (f.getKey()) { case "http": setPortField(f.getKey(), f.getValue(), configuration, context, app); break; case "https": break; default: throw new IllegalArgumentException("port " + f.getKey() + " not yet supported"); } } SystemInstance.get().addObserver(app); composerInject(app); final AnnotationFinder appFinder = new AnnotationFinder(new ClassesArchive(appClass)); for (final Method mtd : appFinder.findAnnotatedMethods(PostConstruct.class)) { if (mtd.getParameterTypes().length == 0) { if (!mtd.isAccessible()) { mtd.setAccessible(true); } mtd.invoke(app); } } hook = new Thread() { @Override public void run() { // ensure to log errors but not fail there for (final Method mtd : appFinder.findAnnotatedMethods(PreDestroy.class)) { if (mtd.getParameterTypes().length == 0) { if (!mtd.isAccessible()) { mtd.setAccessible(true); } try { mtd.invoke(app); } catch (final IllegalAccessException e) { throw new IllegalStateException(e); } catch (final InvocationTargetException e) { throw new IllegalStateException(e.getCause()); } } } try { container.close(); } catch (final Exception e) { e.printStackTrace(); } for (final Closeable c : postTasks) { try { c.close(); } catch (final IOException e) { e.printStackTrace(); } } postTasks.clear(); app = null; try { SHUTDOWN_TASKS.remove(this); } catch (final Exception e) { // no-op: that's ok at that moment if not called manually } } }; SHUTDOWN_TASKS.put(hook, hook); }
From source file:com.gst.portfolio.loanaccount.domain.Loan.java
private Collection<LoanDisbursementDetails> fetchUndisbursedDetail() { Collection<LoanDisbursementDetails> disbursementDetails = new ArrayList<>(); Date date = null;//from www . j a v a 2 s . c om for (LoanDisbursementDetails disbursementDetail : this.disbursementDetails) { if (disbursementDetail.actualDisbursementDate() == null) { if (date == null || disbursementDetail.expectedDisbursementDate().equals(date)) { disbursementDetails.add(disbursementDetail); date = disbursementDetail.expectedDisbursementDate(); } else if (disbursementDetail.expectedDisbursementDate().before(date)) { disbursementDetails.clear(); disbursementDetails.add(disbursementDetail); date = disbursementDetail.expectedDisbursementDate(); } } } return disbursementDetails; }
From source file:org.alfresco.module.org_alfresco_module_rm.capability.RMAfterInvocationProvider.java
@SuppressWarnings({ "unchecked", "rawtypes" })
private Collection decide(Authentication authentication, Object object, ConfigAttributeDefinition config,
Collection returnedObject) {
if (returnedObject == null) {
return null;
}//w w w . java2 s .c om
List<ConfigAttributeDefintion> supportedDefinitions = extractSupportedDefinitions(config);
if (logger.isDebugEnabled()) {
logger.debug("Entries are " + supportedDefinitions);
}
if (supportedDefinitions.size() == 0) {
return returnedObject;
}
// Default to the system-wide values and we'll see if they need to be reduced
long targetResultCount = returnedObject.size();
int maxPermissionChecks = Integer.MAX_VALUE;
long maxPermissionCheckTimeMillis = this.maxPermissionCheckTimeMillis;
if (returnedObject instanceof PermissionCheckCollection<?>) {
PermissionCheckCollection permissionCheckCollection = (PermissionCheckCollection) returnedObject;
// Get values
targetResultCount = permissionCheckCollection.getTargetResultCount();
if (permissionCheckCollection.getCutOffAfterCount() > 0) {
maxPermissionChecks = permissionCheckCollection.getCutOffAfterCount();
}
if (permissionCheckCollection.getCutOffAfterTimeMs() > 0) {
maxPermissionCheckTimeMillis = permissionCheckCollection.getCutOffAfterTimeMs();
}
}
// Start timer and counter for cut-off
boolean cutoff = false;
long startTimeMillis = System.currentTimeMillis();
int count = 0;
// Keep values explicitly
List<Object> keepValues = new ArrayList<Object>(returnedObject.size());
for (Object nextObject : returnedObject) {
// if the maximum result size or time has been exceeded, then we have to remove only
long currentTimeMillis = System.currentTimeMillis();
// NOTE: for reference - the "maxPermissionChecks" has never been honoured by this loop (since previously the count was not being incremented)
if (count >= targetResultCount) {
// We have enough results. We stop without cutoff.
break;
} else if (count >= maxPermissionChecks) {
// We have been cut off by count
cutoff = true;
if (logger.isDebugEnabled()) {
logger.debug("decide (collection) cut-off: " + count + " checks exceeded " + maxPermissionChecks
+ " checks");
}
break;
} else if ((currentTimeMillis - startTimeMillis) > maxPermissionCheckTimeMillis) {
// We have been cut off by time
cutoff = true;
if (logger.isDebugEnabled()) {
logger.debug("decide (collection) cut-off: " + (currentTimeMillis - startTimeMillis)
+ "ms exceeded " + maxPermissionCheckTimeMillis + "ms");
}
break;
}
boolean allowed = true;
for (ConfigAttributeDefintion cad : supportedDefinitions) {
if (cad.mode.equalsIgnoreCase("FilterNode")) {
NodeRef testNodeRef = null;
if (cad.parent) {
if (StoreRef.class.isAssignableFrom(nextObject.getClass())) {
// Will be allowed
testNodeRef = null;
} else if (NodeRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = nodeService.getPrimaryParent((NodeRef) nextObject).getParentRef();
} else if (ChildAssociationRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = ((ChildAssociationRef) nextObject).getParentRef();
} else if (AssociationRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = ((AssociationRef) nextObject).getSourceRef();
} else if (PermissionCheckValue.class.isAssignableFrom(nextObject.getClass())) {
NodeRef nodeRef = ((PermissionCheckValue) nextObject).getNodeRef();
testNodeRef = nodeService.getPrimaryParent(nodeRef).getParentRef();
} else {
throw new ACLEntryVoterException(
"The specified parameter is recognized: " + nextObject.getClass());
}
} else {
if (StoreRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = nodeService.getRootNode((StoreRef) nextObject);
} else if (NodeRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = (NodeRef) nextObject;
} else if (ChildAssociationRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = ((ChildAssociationRef) nextObject).getChildRef();
} else if (AssociationRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = ((AssociationRef) nextObject).getTargetRef();
} else if (PermissionCheckValue.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = ((PermissionCheckValue) nextObject).getNodeRef();
} else {
throw new ACLEntryVoterException(
"The specified parameter is recognized: " + nextObject.getClass());
}
}
if (logger.isDebugEnabled()) {
logger.debug("\t" + cad.typeString + " test on " + testNodeRef + " from "
+ nextObject.getClass().getName());
}
// Null allows
if (isUnfiltered(testNodeRef)) {
// Continue to next ConfigAttributeDefintion
continue;
}
if (allowed && testNodeRef != null
&& checkRead(testNodeRef) != AccessDecisionVoter.ACCESS_GRANTED) {
allowed = false;
// No point evaluating more ConfigAttributeDefintions
break;
}
}
}
// Failure or success, increase the count
count++;
if (allowed) {
keepValues.add(nextObject);
}
}
// Work out how many were left unchecked (for whatever reason)
int sizeOriginal = returnedObject.size();
int checksRemaining = sizeOriginal - count;
// Note: There are use-cases where unmodifiable collections are passing through.
// So make sure that the collection needs modification at all
if (keepValues.size() < sizeOriginal) {
// There are values that need to be removed. We have to modify the collection.
try {
returnedObject.clear();
returnedObject.addAll(keepValues);
} catch (UnsupportedOperationException e) {
throw new AccessDeniedException("Permission-checked list must be modifiable", e);
}
}
// Attach the extra permission-check data to the collection
return PermissionCheckedCollectionMixin.create(returnedObject, cutoff, checksRemaining, sizeOriginal);
}
From source file:org.alfresco.repo.security.permissions.impl.acegi.ACLEntryAfterInvocationProvider.java
@SuppressWarnings({ "rawtypes", "unchecked" })
private Collection decide(Authentication authentication, Object object, ConfigAttributeDefinition config,
Collection returnedObject) throws AccessDeniedException {
if (returnedObject == null) {
return null;
}//from ww w.j av a 2 s.c o m
List<ConfigAttributeDefintion> supportedDefinitions = extractSupportedDefinitions(config);
if (log.isDebugEnabled()) {
log.debug("Entries are " + supportedDefinitions);
}
if (supportedDefinitions.size() == 0) {
return returnedObject;
}
// Default to the system-wide values and we'll see if they need to be reduced
long targetResultCount = returnedObject.size();
int maxPermissionChecks = Integer.MAX_VALUE;
long maxPermissionCheckTimeMillis = this.maxPermissionCheckTimeMillis;
if (returnedObject instanceof PermissionCheckCollection<?>) {
PermissionCheckCollection permissionCheckCollection = (PermissionCheckCollection) returnedObject;
// Get values
targetResultCount = permissionCheckCollection.getTargetResultCount();
if (permissionCheckCollection.getCutOffAfterCount() > 0) {
maxPermissionChecks = permissionCheckCollection.getCutOffAfterCount();
}
if (permissionCheckCollection.getCutOffAfterTimeMs() > 0) {
maxPermissionCheckTimeMillis = permissionCheckCollection.getCutOffAfterTimeMs();
}
}
// Start timer and counter for cut-off
boolean cutoff = false;
long startTimeMillis = System.currentTimeMillis();
int count = 0;
// Keep values explicitly
List<Object> keepValues = new ArrayList<Object>(returnedObject.size());
for (Object nextObject : returnedObject) {
// if the maximum result size or time has been exceeded, then we have to remove only
long currentTimeMillis = System.currentTimeMillis();
if (keepValues.size() >= targetResultCount) {
// We have enough results. We stop without cutoff.
break;
} else if (count >= maxPermissionChecks) {
// We have been cut off by count
cutoff = true;
if (log.isDebugEnabled()) {
log.debug("decide (collection) cut-off: " + count + " checks exceeded " + maxPermissionChecks
+ " checks");
}
break;
} else if ((currentTimeMillis - startTimeMillis) > maxPermissionCheckTimeMillis) {
// We have been cut off by time
cutoff = true;
if (log.isDebugEnabled()) {
log.debug("decide (collection) cut-off: " + (currentTimeMillis - startTimeMillis)
+ "ms exceeded " + maxPermissionCheckTimeMillis + "ms");
}
break;
}
boolean allowed = true;
for (ConfigAttributeDefintion cad : supportedDefinitions) {
NodeRef testNodeRef = null;
if (cad.typeString.equals(AFTER_ACL_NODE)) {
if (StoreRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = nodeService.getRootNode((StoreRef) nextObject);
} else if (NodeRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = (NodeRef) nextObject;
} else if (ChildAssociationRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = ((ChildAssociationRef) nextObject).getChildRef();
} else if (Pair.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = (NodeRef) ((Pair) nextObject).getSecond();
} else if (PermissionCheckValue.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = ((PermissionCheckValue) nextObject).getNodeRef();
} else if (AssociationRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = ((AssociationRef) nextObject).getTargetRef();
} else {
throw new ACLEntryVoterException(
"The specified parameter is not recognized: " + nextObject.getClass());
}
} else if (cad.typeString.equals(AFTER_ACL_PARENT)) {
if (StoreRef.class.isAssignableFrom(nextObject.getClass())) {
// Will be allowed
testNodeRef = null;
} else if (NodeRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = nodeService.getPrimaryParent((NodeRef) nextObject).getParentRef();
} else if (ChildAssociationRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = ((ChildAssociationRef) nextObject).getParentRef();
} else if (AssociationRef.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = ((AssociationRef) nextObject).getSourceRef();
} else if (Pair.class.isAssignableFrom(nextObject.getClass())) {
testNodeRef = (NodeRef) ((Pair) nextObject).getSecond();
} else if (PermissionCheckValue.class.isAssignableFrom(nextObject.getClass())) {
NodeRef nodeRef = ((PermissionCheckValue) nextObject).getNodeRef();
testNodeRef = nodeService.getPrimaryParent(nodeRef).getParentRef();
} else {
throw new ACLEntryVoterException(
"The specified parameter is recognized: " + nextObject.getClass());
}
}
if (log.isDebugEnabled()) {
log.debug("\t" + cad.typeString + " test on " + testNodeRef + " from "
+ nextObject.getClass().getName());
}
if (isUnfiltered(testNodeRef)) // Null allows
{
continue; // Continue to next ConfigAttributeDefintion
}
if (allowed && (testNodeRef != null) && (permissionService.hasPermission(testNodeRef,
cad.required.toString()) == AccessStatus.DENIED)) {
allowed = false;
break; // No point evaluating more ConfigAttributeDefintions
}
}
// Failure or success, increase the count
count++;
if (allowed) {
keepValues.add(nextObject);
}
}
// Work out how many were left unchecked (for whatever reason)
int sizeOriginal = returnedObject.size();
int checksRemaining = sizeOriginal - count;
// Note: There are use-cases where unmodifiable collections are passing through.
// So make sure that the collection needs modification at all
if (keepValues.size() < sizeOriginal) {
// There are values that need to be removed. We have to modify the collection.
try {
returnedObject.clear();
returnedObject.addAll(keepValues);
} catch (UnsupportedOperationException e) {
throw new AccessDeniedException("Permission-checked list must be modifiable", e);
}
}
// Attach the extra permission-check data to the collection
return PermissionCheckedCollectionMixin.create(returnedObject, cutoff, checksRemaining, sizeOriginal);
}
From source file:org.hyperledger.fabric.sdkintegration.End2endIT.java
void runChannel(HFClient client, Channel channel, boolean installChaincode, SampleOrg sampleOrg, int delta) { class ChaincodeEventCapture { //A test class to capture chaincode events final String handle; final BlockEvent blockEvent; final ChaincodeEvent chaincodeEvent; ChaincodeEventCapture(String handle, BlockEvent blockEvent, ChaincodeEvent chaincodeEvent) { this.handle = handle; this.blockEvent = blockEvent; this.chaincodeEvent = chaincodeEvent; }//from w w w . j av a2 s . c o m } // The following is just a test to see if peers and orderers can be added and removed. // not pertinent to the code flow. testRemovingAddingPeersOrderers(client, channel); Vector<ChaincodeEventCapture> chaincodeEvents = new Vector<>(); // Test list to capture chaincode events. try { final String channelName = channel.getName(); boolean isFooChain = FOO_CHANNEL_NAME.equals(channelName); out("Running channel %s", channelName); Collection<Orderer> orderers = channel.getOrderers(); final ChaincodeID chaincodeID; Collection<ProposalResponse> responses; Collection<ProposalResponse> successful = new LinkedList<>(); Collection<ProposalResponse> failed = new LinkedList<>(); // Register a chaincode event listener that will trigger for any chaincode id and only for EXPECTED_EVENT_NAME event. String chaincodeEventListenerHandle = channel.registerChaincodeEventListener(Pattern.compile(".*"), Pattern.compile(Pattern.quote(EXPECTED_EVENT_NAME)), (handle, blockEvent, chaincodeEvent) -> { chaincodeEvents.add(new ChaincodeEventCapture(handle, blockEvent, chaincodeEvent)); String es = blockEvent.getPeer() != null ? blockEvent.getPeer().getName() : blockEvent.getEventHub().getName(); out("RECEIVED Chaincode event with handle: %s, chaincode Id: %s, chaincode event name: %s, " + "transaction id: %s, event payload: \"%s\", from eventhub: %s", handle, chaincodeEvent.getChaincodeId(), chaincodeEvent.getEventName(), chaincodeEvent.getTxId(), new String(chaincodeEvent.getPayload()), es); }); //For non foo channel unregister event listener to test events are not called. if (!isFooChain) { channel.unregisterChaincodeEventListener(chaincodeEventListenerHandle); chaincodeEventListenerHandle = null; } ChaincodeID.Builder chaincodeIDBuilder = ChaincodeID.newBuilder().setName(CHAIN_CODE_NAME) .setVersion(CHAIN_CODE_VERSION); if (null != CHAIN_CODE_PATH) { chaincodeIDBuilder.setPath(CHAIN_CODE_PATH); } chaincodeID = chaincodeIDBuilder.build(); if (installChaincode) { //////////////////////////// // Install Proposal Request // client.setUserContext(sampleOrg.getPeerAdmin()); out("Creating install proposal"); InstallProposalRequest installProposalRequest = client.newInstallProposalRequest(); installProposalRequest.setChaincodeID(chaincodeID); if (isFooChain) { // on foo chain install from directory. ////For GO language and serving just a single user, chaincodeSource is mostly likely the users GOPATH installProposalRequest.setChaincodeSourceLocation( Paths.get(TEST_FIXTURES_PATH, CHAIN_CODE_FILEPATH).toFile()); if (testConfig.isFabricVersionAtOrAfter("1.1")) { // Fabric 1.1 added support for META-INF in the chaincode image. //This sets an index on the variable a in the chaincode // see http://hyperledger-fabric.readthedocs.io/en/master/couchdb_as_state_database.html#using-couchdb-from-chaincode // The file IndexA.json as part of the META-INF will be packaged with the source to create the index. installProposalRequest .setChaincodeMetaInfLocation(new File("src/test/fixture/meta-infs/end2endit")); } } else { // On bar chain install from an input stream. // For inputstream if indicies are desired the application needs to make sure the META-INF is provided in the stream. // The SDK does not change anything in the stream. if (CHAIN_CODE_LANG.equals(Type.GO_LANG)) { installProposalRequest .setChaincodeInputStream( Util.generateTarGzInputStream( (Paths.get(TEST_FIXTURES_PATH, CHAIN_CODE_FILEPATH, "src", CHAIN_CODE_PATH).toFile()), Paths.get("src", CHAIN_CODE_PATH).toString())); } else { installProposalRequest.setChaincodeInputStream(Util.generateTarGzInputStream( (Paths.get(TEST_FIXTURES_PATH, CHAIN_CODE_FILEPATH).toFile()), "src")); } } installProposalRequest.setChaincodeVersion(CHAIN_CODE_VERSION); installProposalRequest.setChaincodeLanguage(CHAIN_CODE_LANG); out("Sending install proposal"); //////////////////////////// // only a client from the same org as the peer can issue an install request int numInstallProposal = 0; // Set<String> orgs = orgPeers.keySet(); // for (SampleOrg org : testSampleOrgs) { Collection<Peer> peers = channel.getPeers(); numInstallProposal = numInstallProposal + peers.size(); responses = client.sendInstallProposal(installProposalRequest, peers); for (ProposalResponse response : responses) { if (response.getStatus() == ProposalResponse.Status.SUCCESS) { out("Successful install proposal response Txid: %s from peer %s", response.getTransactionID(), response.getPeer().getName()); successful.add(response); } else { failed.add(response); } } // } out("Received %d install proposal responses. Successful+verified: %d . Failed: %d", numInstallProposal, successful.size(), failed.size()); if (failed.size() > 0) { ProposalResponse first = failed.iterator().next(); fail("Not enough endorsers for install :" + successful.size() + ". " + first.getMessage()); } } // client.setUserContext(sampleOrg.getUser(TEST_ADMIN_NAME)); // final ChaincodeID chaincodeID = firstInstallProposalResponse.getChaincodeID(); // Note installing chaincode does not require transaction no need to // send to Orderers /////////////// //// Instantiate chaincode. InstantiateProposalRequest instantiateProposalRequest = client.newInstantiationProposalRequest(); instantiateProposalRequest.setProposalWaitTime(DEPLOYWAITTIME); instantiateProposalRequest.setChaincodeID(chaincodeID); instantiateProposalRequest.setChaincodeLanguage(CHAIN_CODE_LANG); instantiateProposalRequest.setFcn("init"); instantiateProposalRequest.setArgs(new String[] { "a", "500", "b", "" + (200 + delta) }); Map<String, byte[]> tm = new HashMap<>(); tm.put("HyperLedgerFabric", "InstantiateProposalRequest:JavaSDK".getBytes(UTF_8)); tm.put("method", "InstantiateProposalRequest".getBytes(UTF_8)); instantiateProposalRequest.setTransientMap(tm); /* policy OR(Org1MSP.member, Org2MSP.member) meaning 1 signature from someone in either Org1 or Org2 See README.md Chaincode endorsement policies section for more details. */ ChaincodeEndorsementPolicy chaincodeEndorsementPolicy = new ChaincodeEndorsementPolicy(); chaincodeEndorsementPolicy .fromYamlFile(new File(TEST_FIXTURES_PATH + "/sdkintegration/chaincodeendorsementpolicy.yaml")); instantiateProposalRequest.setChaincodeEndorsementPolicy(chaincodeEndorsementPolicy); out("Sending instantiateProposalRequest to all peers with arguments: a and b set to 100 and %s respectively", "" + (200 + delta)); successful.clear(); failed.clear(); if (isFooChain) { //Send responses both ways with specifying peers and by using those on the channel. responses = channel.sendInstantiationProposal(instantiateProposalRequest, channel.getPeers()); } else { responses = channel.sendInstantiationProposal(instantiateProposalRequest); } for (ProposalResponse response : responses) { if (response.isVerified() && response.getStatus() == ProposalResponse.Status.SUCCESS) { successful.add(response); out("Succesful instantiate proposal response Txid: %s from peer %s", response.getTransactionID(), response.getPeer().getName()); } else { failed.add(response); } } out("Received %d instantiate proposal responses. Successful+verified: %d . Failed: %d", responses.size(), successful.size(), failed.size()); if (failed.size() > 0) { for (ProposalResponse fail : failed) { out("Not enough endorsers for instantiate :" + successful.size() + "endorser failed with " + fail.getMessage() + ", on peer" + fail.getPeer()); } ProposalResponse first = failed.iterator().next(); fail("Not enough endorsers for instantiate :" + successful.size() + "endorser failed with " + first.getMessage() + ". Was verified:" + first.isVerified()); } /////////////// /// Send instantiate transaction to orderer out("Sending instantiateTransaction to orderer with a and b set to 100 and %s respectively", "" + (200 + delta)); //Specify what events should complete the interest in this transaction. This is the default // for all to complete. It's possible to specify many different combinations like //any from a group, all from one group and just one from another or even None(NOfEvents.createNoEvents). // See. Channel.NOfEvents Channel.NOfEvents nOfEvents = createNofEvents(); if (!channel.getPeers(EnumSet.of(PeerRole.EVENT_SOURCE)).isEmpty()) { nOfEvents.addPeers(channel.getPeers(EnumSet.of(PeerRole.EVENT_SOURCE))); } if (!channel.getEventHubs().isEmpty()) { nOfEvents.addEventHubs(channel.getEventHubs()); } channel.sendTransaction(successful, createTransactionOptions() //Basically the default options but shows it's usage. .userContext(client.getUserContext()) //could be a different user context. this is the default. .shuffleOrders(false) // don't shuffle any orderers the default is true. .orderers(channel.getOrderers()) // specify the orderers we want to try this transaction. Fails once all Orderers are tried. .nOfEvents(nOfEvents) // The events to signal the completion of the interest in the transaction ).thenApply(transactionEvent -> { waitOnFabric(0); assertTrue(transactionEvent.isValid()); // must be valid to be here. assertNotNull(transactionEvent.getSignature()); //musth have a signature. BlockEvent blockEvent = transactionEvent.getBlockEvent(); // This is the blockevent that has this transaction. assertNotNull(blockEvent.getBlock()); // Make sure the RAW Fabric block is returned. out("Finished instantiate transaction with transaction id %s", transactionEvent.getTransactionID()); try { assertEquals(blockEvent.getChannelId(), channel.getName()); successful.clear(); failed.clear(); client.setUserContext(sampleOrg.getUser(testUser1)); /////////////// /// Send transaction proposal to all peers TransactionProposalRequest transactionProposalRequest = client.newTransactionProposalRequest(); transactionProposalRequest.setChaincodeID(chaincodeID); transactionProposalRequest.setChaincodeLanguage(CHAIN_CODE_LANG); //transactionProposalRequest.setFcn("invoke"); transactionProposalRequest.setFcn("move"); transactionProposalRequest.setProposalWaitTime(testConfig.getProposalWaitTime()); transactionProposalRequest.setArgs("a", "b", "100"); Map<String, byte[]> tm2 = new HashMap<>(); tm2.put("HyperLedgerFabric", "TransactionProposalRequest:JavaSDK".getBytes(UTF_8)); //Just some extra junk in transient map tm2.put("method", "TransactionProposalRequest".getBytes(UTF_8)); // ditto tm2.put("result", ":)".getBytes(UTF_8)); // This should be returned in the payload see chaincode why. if (Type.GO_LANG.equals(CHAIN_CODE_LANG) && testConfig.isFabricVersionAtOrAfter("1.2")) { expectedMoveRCMap.put(channelName, random.nextInt(300) + 100L); // the chaincode will return this as status see chaincode why. tm2.put("rc", (expectedMoveRCMap.get(channelName) + "").getBytes(UTF_8)); // This should be returned see chaincode why. // 400 and above results in the peer not endorsing! } else { expectedMoveRCMap.put(channelName, 200L); // not really supported for Java or Node. } tm2.put(EXPECTED_EVENT_NAME, EXPECTED_EVENT_DATA); //This should trigger an event see chaincode why. transactionProposalRequest.setTransientMap(tm2); out("sending transactionProposal to all peers with arguments: move(a,b,100)"); // Collection<ProposalResponse> transactionPropResp = channel.sendTransactionProposalToEndorsers(transactionProposalRequest); Collection<ProposalResponse> transactionPropResp = channel .sendTransactionProposal(transactionProposalRequest, channel.getPeers()); for (ProposalResponse response : transactionPropResp) { if (response.getStatus() == ProposalResponse.Status.SUCCESS) { out("Successful transaction proposal response Txid: %s from peer %s", response.getTransactionID(), response.getPeer().getName()); successful.add(response); } else { failed.add(response); } } out("Received %d transaction proposal responses. Successful+verified: %d . Failed: %d", transactionPropResp.size(), successful.size(), failed.size()); if (failed.size() > 0) { ProposalResponse firstTransactionProposalResponse = failed.iterator().next(); fail("Not enough endorsers for invoke(move a,b,100):" + failed.size() + " endorser error: " + firstTransactionProposalResponse.getMessage() + ". Was verified: " + firstTransactionProposalResponse.isVerified()); } // Check that all the proposals are consistent with each other. We should have only one set // where all the proposals above are consistent. Note the when sending to Orderer this is done automatically. // Shown here as an example that applications can invoke and select. // See org.hyperledger.fabric.sdk.proposal.consistency_validation config property. Collection<Set<ProposalResponse>> proposalConsistencySets = SDKUtils .getProposalConsistencySets(transactionPropResp); if (proposalConsistencySets.size() != 1) { fail(format("Expected only one set of consistent proposal responses but got %d", proposalConsistencySets.size())); } out("Successfully received transaction proposal responses."); // System.exit(10); ProposalResponse resp = successful.iterator().next(); byte[] x = resp.getChaincodeActionResponsePayload(); // This is the data returned by the chaincode. String resultAsString = null; if (x != null) { resultAsString = new String(x, UTF_8); } assertEquals(":)", resultAsString); assertEquals(expectedMoveRCMap.get(channelName).longValue(), resp.getChaincodeActionResponseStatus()); //Chaincode's status. TxReadWriteSetInfo readWriteSetInfo = resp.getChaincodeActionResponseReadWriteSetInfo(); //See blockwalker below how to transverse this assertNotNull(readWriteSetInfo); assertTrue(readWriteSetInfo.getNsRwsetCount() > 0); ChaincodeID cid = resp.getChaincodeID(); assertNotNull(cid); final String path = cid.getPath(); if (null == CHAIN_CODE_PATH) { assertTrue(path == null || "".equals(path)); } else { assertEquals(CHAIN_CODE_PATH, path); } assertEquals(CHAIN_CODE_NAME, cid.getName()); assertEquals(CHAIN_CODE_VERSION, cid.getVersion()); //////////////////////////// // Send Transaction Transaction to orderer out("Sending chaincode transaction(move a,b,100) to orderer."); return channel.sendTransaction(successful).get(testConfig.getTransactionWaitTime(), TimeUnit.SECONDS); } catch (Exception e) { out("Caught an exception while invoking chaincode"); e.printStackTrace(); fail("Failed invoking chaincode with error : " + e.getMessage()); } return null; }).thenApply(transactionEvent -> { try { waitOnFabric(0); assertTrue(transactionEvent.isValid()); // must be valid to be here. out("Finished transaction with transaction id %s", transactionEvent.getTransactionID()); testTxID = transactionEvent.getTransactionID(); // used in the channel queries later //////////////////////////// // Send Query Proposal to all peers // String expect = "" + (300 + delta); out("Now query chaincode for the value of b."); QueryByChaincodeRequest queryByChaincodeRequest = client.newQueryProposalRequest(); queryByChaincodeRequest.setArgs(new String[] { "b" }); queryByChaincodeRequest.setFcn("query"); queryByChaincodeRequest.setChaincodeID(chaincodeID); Map<String, byte[]> tm2 = new HashMap<>(); tm2.put("HyperLedgerFabric", "QueryByChaincodeRequest:JavaSDK".getBytes(UTF_8)); tm2.put("method", "QueryByChaincodeRequest".getBytes(UTF_8)); queryByChaincodeRequest.setTransientMap(tm2); Collection<ProposalResponse> queryProposals = channel.queryByChaincode(queryByChaincodeRequest, channel.getPeers()); for (ProposalResponse proposalResponse : queryProposals) { if (!proposalResponse.isVerified() || proposalResponse.getStatus() != ProposalResponse.Status.SUCCESS) { fail("Failed query proposal from peer " + proposalResponse.getPeer().getName() + " status: " + proposalResponse.getStatus() + ". Messages: " + proposalResponse.getMessage() + ". Was verified : " + proposalResponse.isVerified()); } else { String payload = proposalResponse.getProposalResponse().getResponse().getPayload() .toStringUtf8(); out("Query payload of b from peer %s returned %s", proposalResponse.getPeer().getName(), payload); assertEquals(payload, expect); } } return null; } catch (Exception e) { out("Caught exception while running query"); e.printStackTrace(); fail("Failed during chaincode query with error : " + e.getMessage()); } return null; }).exceptionally(e -> { if (e instanceof TransactionEventException) { BlockEvent.TransactionEvent te = ((TransactionEventException) e).getTransactionEvent(); if (te != null) { throw new AssertionError(format("Transaction with txid %s failed. %s", te.getTransactionID(), e.getMessage()), e); } } throw new AssertionError( format("Test failed with %s exception %s", e.getClass().getName(), e.getMessage()), e); }).get(testConfig.getTransactionWaitTime(), TimeUnit.SECONDS); // Channel queries // We can only send channel queries to peers that are in the same org as the SDK user context // Get the peers from the current org being used and pick one randomly to send the queries to. // Set<Peer> peerSet = sampleOrg.getPeers(); // Peer queryPeer = peerSet.iterator().next(); // out("Using peer %s for channel queries", queryPeer.getName()); BlockchainInfo channelInfo = channel.queryBlockchainInfo(); out("Channel info for : " + channelName); out("Channel height: " + channelInfo.getHeight()); String chainCurrentHash = Hex.encodeHexString(channelInfo.getCurrentBlockHash()); String chainPreviousHash = Hex.encodeHexString(channelInfo.getPreviousBlockHash()); out("Chain current block hash: " + chainCurrentHash); out("Chainl previous block hash: " + chainPreviousHash); // Query by block number. Should return latest block, i.e. block number 2 BlockInfo returnedBlock = channel.queryBlockByNumber(channelInfo.getHeight() - 1); String previousHash = Hex.encodeHexString(returnedBlock.getPreviousHash()); out("queryBlockByNumber returned correct block with blockNumber " + returnedBlock.getBlockNumber() + " \n previous_hash " + previousHash); assertEquals(channelInfo.getHeight() - 1, returnedBlock.getBlockNumber()); assertEquals(chainPreviousHash, previousHash); // Query by block hash. Using latest block's previous hash so should return block number 1 byte[] hashQuery = returnedBlock.getPreviousHash(); returnedBlock = channel.queryBlockByHash(hashQuery); out("queryBlockByHash returned block with blockNumber " + returnedBlock.getBlockNumber()); assertEquals(channelInfo.getHeight() - 2, returnedBlock.getBlockNumber()); // Query block by TxID. Since it's the last TxID, should be block 2 returnedBlock = channel.queryBlockByTransactionID(testTxID); out("queryBlockByTxID returned block with blockNumber " + returnedBlock.getBlockNumber()); assertEquals(channelInfo.getHeight() - 1, returnedBlock.getBlockNumber()); // query transaction by ID TransactionInfo txInfo = channel.queryTransactionByID(testTxID); out("QueryTransactionByID returned TransactionInfo: txID " + txInfo.getTransactionID() + "\n validation code " + txInfo.getValidationCode().getNumber()); if (chaincodeEventListenerHandle != null) { channel.unregisterChaincodeEventListener(chaincodeEventListenerHandle); //Should be two. One event in chaincode and two notification for each of the two event hubs final int numberEventsExpected = channel.getEventHubs().size() + channel.getPeers(EnumSet.of(PeerRole.EVENT_SOURCE)).size(); //just make sure we get the notifications. for (int i = 15; i > 0; --i) { if (chaincodeEvents.size() == numberEventsExpected) { break; } else { Thread.sleep(90); // wait for the events. } } assertEquals(numberEventsExpected, chaincodeEvents.size()); for (ChaincodeEventCapture chaincodeEventCapture : chaincodeEvents) { assertEquals(chaincodeEventListenerHandle, chaincodeEventCapture.handle); assertEquals(testTxID, chaincodeEventCapture.chaincodeEvent.getTxId()); assertEquals(EXPECTED_EVENT_NAME, chaincodeEventCapture.chaincodeEvent.getEventName()); assertTrue( Arrays.equals(EXPECTED_EVENT_DATA, chaincodeEventCapture.chaincodeEvent.getPayload())); assertEquals(CHAIN_CODE_NAME, chaincodeEventCapture.chaincodeEvent.getChaincodeId()); BlockEvent blockEvent = chaincodeEventCapture.blockEvent; assertEquals(channelName, blockEvent.getChannelId()); // assertTrue(channel.getEventHubs().contains(blockEvent.getEventHub())); } } else { assertTrue(chaincodeEvents.isEmpty()); } out("Running for Channel %s done", channelName); } catch (Exception e) { out("Caught an exception running channel %s", channel.getName()); e.printStackTrace(); fail("Test failed with error : " + e.getMessage()); } }
From source file:org.sakaiproject.tool.messageforums.DiscussionForumTool.java
/** * Takes groups defined and sorts them alphabetically by title * so will be in some order when displayed on permission widget. * //from ww w. ja v a 2 s. c o m * @param groups * Collection of groups to be sorted * * @return * Collection of groups in sorted order */ private Collection sortGroups(Collection groups) { List sortGroupsList = new ArrayList(); sortGroupsList.addAll(groups); final GroupComparator groupComparator = new GroupComparator("title", true); Collections.sort(sortGroupsList, groupComparator); groups.clear(); groups.addAll(sortGroupsList); return groups; }
From source file:dendroscope.autumn.hybridnetwork.ComputeHybridizationNetwork.java
/** * recursively compute the hybrid number * * @param root1//w w w . j ava 2s . c o m * @param root2 * @param isReduced @return hybrid number * @param k * @param totalResults */ private int computeRec(Root root1, Root root2, boolean isReduced, BitSet candidateHybridsOriginal, int k, Collection<Root> totalResults, String depth) throws IOException, CanceledException { if (verbose) { System.err.println(depth + "---------- ComputeRec:"); System.err.println(depth + "Tree1: " + root1.toStringFullTreeX()); System.err.println(depth + "Tree2: " + root2.toStringFullTreeX()); } if (System.currentTimeMillis() > nextTime) { progressListener.incrementProgress(); nextTime += waitTime; waitTime *= 1.5; } else progressListener.checkForCancel(); // root1.reorderSubTree(); // root2.reorderSubTree(); if (checking) { root1.checkTree(); root2.checkTree(); if (!root2.getTaxa().equals(root1.getTaxa())) throw new RuntimeException("Unequal taxon sets: X=" + Basic.toString(root1.getTaxa()) + " vs " + Basic.toString(root2.getTaxa())); } if (!isReduced) { // 1. try to perform a subtree reduction: { final Single<Integer> placeHolderTaxon = new Single<Integer>(); List<Pair<Root, Root>> reducedSubtreePairs = new LinkedList<Pair<Root, Root>>(); switch (SubtreeReduction.apply(root1, root2, reducedSubtreePairs, placeHolderTaxon)) { case ISOMORPHIC: Root isomorphicTree = MergeIsomorphicInducedTrees.apply(root1, root2); if (verbose) { System.err.println(depth + "Trees are isomorphic"); System.err.println(depth + "Isomorphic tree: " + isomorphicTree.toStringFullTreeX()); } totalResults.add(isomorphicTree); return 0; // two trees are isomorphic, no hybrid node needed case REDUCED: // a reduction was performed, cannot maintain lexicographical ordering in removal loop below List<Root> subTrees = new LinkedList<Root>(); for (Pair<Root, Root> pair : reducedSubtreePairs) { subTrees.add(MergeIsomorphicInducedTrees.apply(pair.getFirst(), pair.getSecond())); } if (verbose) { System.err.println(depth + "Trees are reducible:"); System.err.println(depth + "Tree1-reduced: " + root1.toStringFullTreeX()); System.err.println(depth + "Tree2-reduced: " + root2.toStringFullTreeX()); for (Root root : subTrees) { System.err.println(depth + "Merged reduced subtree: " + root.toStringFullTreeX()); } } BitSet candidateHybrids; if (false) candidateHybrids = getAllAliveTaxa(root1, root2); // need to reconsider all possible hybrids else { candidateHybrids = (BitSet) candidateHybridsOriginal.clone(); candidateHybrids.set(placeHolderTaxon.get(), true); } Collection<Root> currentResults = new TreeSet<Root>(new NetworkComparator()); int h = cacheComputeRec(root1, root2, false, candidateHybrids, k, currentResults, depth + " >"); List<Root> merged = MergeNetworks.apply(currentResults, subTrees); if (verbose) { for (Root r : merged) { System.err.println(depth + "Result-merged: " + r.toStringNetworkFull()); } } totalResults.addAll(fixOrdering(merged)); return h; case IRREDUCIBLE: if (verbose) System.err.println(depth + "Trees are subtree-irreducible"); break; } } // 2. try to perform a cluster reduction: { final Single<Integer> placeHolderTaxon = new Single<Integer>(); Pair<Root, Root> clusterTrees = ClusterReduction.apply(root1, root2, placeHolderTaxon); if (clusterTrees != null) { Set<Root> resultBottomPair = new TreeSet<Root>(new NetworkComparator()); int h = cacheComputeRec(clusterTrees.getFirst(), clusterTrees.getSecond(), true, candidateHybridsOriginal, k, resultBottomPair, depth + " >"); // for the top pair, we should reconsider the place holder in the top pair as a possible place holder BitSet candidateHybrids = (BitSet) candidateHybridsOriginal.clone(); candidateHybrids.set(placeHolderTaxon.get(), true); Set<Root> resultTopPair = new TreeSet<Root>(new NetworkComparator()); h += cacheComputeRec(root1, root2, false, candidateHybrids, k - h, resultTopPair, depth + " >"); Set<Root> currentResults = new TreeSet<Root>(new NetworkComparator()); for (Root r : resultBottomPair) { currentResults.addAll(MergeNetworks.apply(resultTopPair, Arrays.asList(r))); } if (verbose) { System.err.println(depth + "Cluster reduction applied::"); System.err.println(depth + "Tree1-reduced: " + root1.toStringFullTreeX()); System.err.println(depth + "Tree2-reduced: " + root2.toStringFullTreeX()); System.err.println(depth + "Subtree-1: " + clusterTrees.getFirst().toStringFullTreeX()); System.err .println(depth + "Subtree-2: " + clusterTrees.getSecond().toStringFullTreeX()); for (Root r : resultBottomPair) { System.err.println(depth + "Results for reduced-trees: " + r.toStringNetworkFull()); } for (Root r : resultTopPair) { System.err.println(depth + "Results for sub-trees: " + r.toStringNetworkFull()); } for (Root r : currentResults) { System.err .println(depth + "Merged cluster-reduced networks: " + r.toStringNetworkFull()); } } totalResults.addAll(currentResults); clusterTrees.getFirst().deleteSubTree(); clusterTrees.getSecond().deleteSubTree(); return h; } } } else { if (verbose) System.err.println(depth + "Trees are already reduced"); } if (k <= 0) // 1, if only interested in number or in finding only one network, 0 else return LARGE; int hBest = LARGE; List<Root> leaves1 = getAllAliveLeaves(root1); /* if (leaves1.size() <= 2) // try 2 rather than one... { totalResults.add(MergeNetworks.apply(root1,root2)); // todo: this needs to be fixed return 0; } */ for (Root leaf2remove : leaves1) { BitSet taxa2remove = leaf2remove.getTaxa(); if (taxa2remove.cardinality() != 1) throw new IOException(depth + "Leaf taxa cardinality: " + taxa2remove.cardinality()); int hybridTaxon = taxa2remove.nextSetBit(0); if (candidateHybridsOriginal.get(hybridTaxon)) { if (verbose) { System.err.println(depth + "Removing: " + hybridTaxon); System.err.println(depth + "candidateHybrids: " + Basic.toString(candidateHybridsOriginal)); System.err.println(depth + "Tree1: " + root1.toStringFullTreeX()); System.err.println(depth + "Tree2: " + root2.toStringFullTreeX()); } Root root1x = root1.copySubNetwork(); Root root2x = root2.copySubNetwork(); RemoveTaxon.apply(root1x, 1, hybridTaxon); RemoveTaxon.apply(root2x, 2, hybridTaxon); // now we keep removed taxa as separate sets if (verbose) { System.err.println(depth + "Tree1-x: " + root1x.toStringFullTreeX()); System.err.println(depth + "Tree2-x: " + root2x.toStringFullTreeX()); } Refine.apply(root1x, root2x); if (verbose) { System.err.println(depth + "Tree1-x-refined: " + root1x.toStringFullTreeX()); System.err.println(depth + "Tree2-x-refined: " + root2x.toStringFullTreeX()); } Collection<Root> currentResults = new TreeSet<Root>(new NetworkComparator()); candidateHybridsOriginal.set(hybridTaxon, false); int h = cacheComputeRec(root1x, root2x, false, candidateHybridsOriginal, k - 1, currentResults, depth + " >") + 1; candidateHybridsOriginal.set(hybridTaxon, true); if (h < k) k = h; // System.err.println("Subproblem with " + Basic.toString(taxa2remove) + " removed, h=" + h); if (h < hBest && h <= k) { hBest = h; totalResults.clear(); } if (h == hBest && h <= k) { if (verbose) { for (Root r : currentResults) { System.err.println(depth + "Result: " + r.toStringNetworkFull()); } } // add the hybrid node: currentResults = copyAll(currentResults); AddHybridNode.apply(currentResults, hybridTaxon); totalResults.addAll(fixOrdering(currentResults)); } root1x.deleteSubTree(); root2x.deleteSubTree(); } } return hBest; }
From source file:org.masukomi.aspirin.core.RemoteDelivery.java
/** * We can assume that the recipients of this message are all going to the * same mail server. We will now rely on the JNDI to do DNS MX record lookup * and try to deliver to the multiple mail servers. If it fails, it should * throw an exception.//from w w w . j a v a 2 s. co m * * Creation date: (2/24/00 11:25:00 PM) * * @param mail * org.apache.james.core.MailImpl * @param session * javax.mail.Session * @return boolean Whether the delivery was successful and the message can * be deleted */ private boolean deliver(QuedItem qi, Session session) { MailAddress rcpt = null; try { if (log.isDebugEnabled()) { log.debug("entering RemoteDelivery.deliver(QuedItem qi, Session session)"); } MailImpl mail = (MailImpl) qi.getMail(); MimeMessage message = mail.getMessage(); // Create an array of the recipients as InternetAddress objects Collection recipients = mail.getRecipients(); InternetAddress addr[] = new InternetAddress[recipients.size()]; int j = 0; // funky ass look because you can't getElementAt() in a Collection for (Iterator i = recipients.iterator(); i.hasNext(); j++) { MailAddress currentRcpt = (MailAddress) i.next(); addr[j] = currentRcpt.toInternetAddress(); } if (addr.length <= 0) { if (log.isDebugEnabled()) { log.debug("No recipients specified... returning"); } return true; } // Figure out which servers to try to send to. This collection // will hold all the possible target servers Collection targetServers = null; Iterator it = recipients.iterator(); while (it.hasNext()) { rcpt = (MailAddress) recipients.iterator().next(); if (!qi.recepientHasBeenHandled(rcpt)) { break; } } // theoretically it is possible to not hav eone that hasn't been // handled // however that's only if something has gone really wrong. if (rcpt != null) { String host = rcpt.getHost(); // Lookup the possible targets try { // targetServers = MXLookup.urlsForHost(host); // farking // unreliable jndi bs targetServers = getMXRecordsForHost(host); } catch (Exception e) { log.error(e); } if (targetServers == null || targetServers.size() == 0) { log.warn("No mail server found for: " + host); StringBuffer exceptionBuffer = new StringBuffer(128) .append("I found no MX record entries for the hostname ").append(host) .append(". I cannot determine where to send this message."); return failMessage(qi, rcpt, new MessagingException(exceptionBuffer.toString()), true); } else if (log.isTraceEnabled()) { log.trace(targetServers.size() + " servers found for " + host); } MessagingException lastError = null; Iterator i = targetServers.iterator(); while (i.hasNext()) { try { URLName outgoingMailServer = (URLName) i.next(); StringBuffer logMessageBuffer = new StringBuffer(256).append("Attempting delivery of ") .append(mail.getName()).append(" to host ").append(outgoingMailServer.toString()) .append(" to addresses ").append(Arrays.asList(addr)); if (log.isDebugEnabled()) { log.debug(logMessageBuffer.toString()); } ; // URLName urlname = new URLName("smtp://" // + outgoingMailServer); Properties props = session.getProperties(); if (mail.getSender() == null) { props.put("mail.smtp.from", "<>"); } else { String sender = mail.getSender().toString(); props.put("mail.smtp.from", sender); } // Many of these properties are only in later JavaMail // versions // "mail.smtp.ehlo" //default true // "mail.smtp.auth" //default false // "mail.smtp.dsn.ret" //default to nothing... appended // as // RET= after MAIL FROM line. // "mail.smtp.dsn.notify" //default to // nothing...appended as // NOTIFY= after RCPT TO line. Transport transport = null; try { transport = session.getTransport(outgoingMailServer); try { transport.connect(); } catch (MessagingException me) { log.error(me); // Any error on connect should cause the mailet // to // attempt // to connect to the next SMTP server associated // with this MX record, // assuming the number of retries hasn't been // exceeded. if (failMessage(qi, rcpt, me, false)) { return true; } else { continue; } } transport.sendMessage(message, addr); // log.debug("message sent to " +addr); /*TODO: catch failures that should result * in failure with no retries } catch (SendFailedException sfe){ qi.failForRecipient(que, ); */ } finally { if (transport != null) { transport.close(); transport = null; } } logMessageBuffer = new StringBuffer(256).append("Mail (").append(mail.getName()) .append(") sent successfully to ").append(outgoingMailServer); log.debug(logMessageBuffer.toString()); qi.succeededForRecipient(que, rcpt); return true; } catch (MessagingException me) { log.error(me); // MessagingException are horribly difficult to figure // out // what actually happened. StringBuffer exceptionBuffer = new StringBuffer(256) .append("Exception delivering message (").append(mail.getName()).append(") - ") .append(me.getMessage()); log.warn(exceptionBuffer.toString()); if ((me.getNextException() != null) && (me.getNextException() instanceof java.io.IOException)) { // This is more than likely a temporary failure // If it's an IO exception with no nested exception, // it's probably // some socket or weird I/O related problem. lastError = me; continue; } // This was not a connection or I/O error particular to // one // SMTP server of an MX set. Instead, it is almost // certainly // a protocol level error. In this case we assume that // this // is an error we'd encounter with any of the SMTP // servers // associated with this MX record, and we pass the // exception // to the code in the outer block that determines its // severity. throw me; } // end catch } // end while // If we encountered an exception while looping through, // throw the last MessagingException we caught. We only // do this if we were unable to send the message to any // server. If sending eventually succeeded, we exit // deliver() though the return at the end of the try // block. if (lastError != null) { throw lastError; } } // END if (rcpt != null) else { log.error("unable to find recipient that handn't already been handled"); } } catch (SendFailedException sfe) { log.error(sfe); boolean deleteMessage = false; Collection recipients = qi.getMail().getRecipients(); // Would like to log all the types of email addresses if (log.isDebugEnabled()) { log.debug("Recipients: " + recipients); } /* * The rest of the recipients failed for one reason or another. * * SendFailedException actually handles this for us. For example, if * you send a message that has multiple invalid addresses, you'll * get a top-level SendFailedException that that has the valid, * valid-unsent, and invalid address lists, with all of the server * response messages will be contained within the nested exceptions. * [Note: the content of the nested exceptions is implementation * dependent.] * * sfe.getInvalidAddresses() should be considered permanent. * sfe.getValidUnsentAddresses() should be considered temporary. * * JavaMail v1.3 properly populates those collections based upon the * 4xx and 5xx response codes. * */ if (sfe.getInvalidAddresses() != null) { Address[] address = sfe.getInvalidAddresses(); if (address.length > 0) { recipients.clear(); for (int i = 0; i < address.length; i++) { try { recipients.add(new MailAddress(address[i].toString())); } catch (ParseException pe) { // this should never happen ... we should have // caught malformed addresses long before we // got to this code. if (log.isDebugEnabled()) { log.debug("Can't parse invalid address: " + pe.getMessage()); } } } if (log.isDebugEnabled()) { log.debug("Invalid recipients: " + recipients); } deleteMessage = failMessage(qi, rcpt, sfe, true); } } if (sfe.getValidUnsentAddresses() != null) { Address[] address = sfe.getValidUnsentAddresses(); if (address.length > 0) { recipients.clear(); for (int i = 0; i < address.length; i++) { try { recipients.add(new MailAddress(address[i].toString())); } catch (ParseException pe) { // this should never happen ... we should have // caught malformed addresses long before we // got to this code. if (log.isDebugEnabled()) { log.debug("Can't parse unsent address: " + pe.getMessage()); } pe.printStackTrace(); } } if (log.isDebugEnabled()) { log.debug("Unsent recipients: " + recipients); } deleteMessage = failMessage(qi, rcpt, sfe, false); } } return deleteMessage; } catch (MessagingException ex) { log.error(ex); // We should do a better job checking this... if the failure is a // general // connect exception, this is less descriptive than more specific // SMTP command // failure... have to lookup and see what are the various Exception // possibilities // Unable to deliver message after numerous tries... fail // accordingly // We check whether this is a 5xx error message, which // indicates a permanent failure (like account doesn't exist // or mailbox is full or domain is setup wrong). // We fail permanently if this was a 5xx error return failMessage(qi, rcpt, ex, ('5' == ex.getMessage().charAt(0))); } catch (Throwable t) { log.error(t); } /* * If we get here, we've exhausted the loop of servers without sending * the message or throwing an exception. One case where this might * happen is if we get a MessagingException on each transport.connect(), * e.g., if there is only one server and we get a connect exception. * Return FALSE to keep run() from deleting the message. */ return false; }
From source file:org.sakaiproject.content.impl.BaseContentService.java
/** * Eliminate from the collection any duplicates as well as any items that are contained within another item whose resource-id is in the collection. * /*from w w w . j av a 2 s. co m*/ * @param resourceIds * A collection of strings (possibly empty) identifying items and/or collections. */ public void eliminateDuplicates(Collection resourceIds) { // eliminate exact duplicates Set others = new TreeSet(resourceIds); // eliminate items contained in other items Iterator itemIt = resourceIds.iterator(); while (itemIt.hasNext()) { String item = (String) itemIt.next(); Iterator otherIt = others.iterator(); while (otherIt.hasNext()) { String other = (String) otherIt.next(); if (other.startsWith(item)) { if (item.equals(other)) { continue; } // item contains other otherIt.remove(); } } } // if any items have been removed, update the original collection if (resourceIds.size() > others.size()) { resourceIds.clear(); resourceIds.addAll(others); } }