Examples with IdentityHashMap java.util.IdentityHashMap used on opensource projects

Example 66 with IdentityHashMap

use of java.util.IdentityHashMap in project vcell by virtualcell.

the class BioCartoonTool method pasteReactionSteps0.

/**
 * pasteReactionSteps0 : does the actual pasting. First called with a cloned model, to track issues. If user still wants to proceed, the paste
 * is performed on the original model.
 *
 * Insert the method's description here.
 * Creation date: (5/10/2003 3:55:25 PM)
 * @param pasteToModel cbit.vcell.model.Model
 * @param pasteToStructure cbit.vcell.model.Structure
 * @param bNew boolean
 */
private static final PasteHelper pasteReactionSteps0(HashMap<String, HashMap<ReactionParticipant, Structure>> rxPartMapStructure, Component parent, IssueContext issueContext, ReactionStep[] copyFromRxSteps, Model pasteToModel, Structure pasteToStructure, boolean bNew, /*boolean bUseDBSpecies,*/
UserResolvedRxElements userResolvedRxElements) throws Exception {
    HashMap<BioModelEntityObject, BioModelEntityObject> reactionsAndSpeciesContexts = new HashMap<>();
    if (copyFromRxSteps == null || copyFromRxSteps.length == 0 || pasteToModel == null || pasteToStructure == null) {
        throw new IllegalArgumentException("CartoonTool.pasteReactionSteps Error " + (copyFromRxSteps == null || copyFromRxSteps.length == 0 ? "reactionStepsArr empty " : "") + (pasteToModel == null ? "model is null " : "") + (pasteToStructure == null ? "struct is null " : ""));
    }
    if (!pasteToModel.contains(pasteToStructure)) {
        throw new IllegalArgumentException("CartoonTool.pasteReactionSteps model " + pasteToModel.getName() + " does not contain structure " + pasteToStructure.getName());
    }
    // Check PasteToModel has preferred targets if set
    if (userResolvedRxElements != null) {
        for (int i = 0; i < userResolvedRxElements.toSpeciesArr.length; i++) {
            if (userResolvedRxElements.toSpeciesArr[i] != null) {
                if (!pasteToModel.contains(userResolvedRxElements.toSpeciesArr[i])) {
                    throw new RuntimeException("PasteToModel does not contain preferred Species " + userResolvedRxElements.toSpeciesArr[i]);
                }
            }
            if (userResolvedRxElements.toStructureArr[i] != null) {
                if (!pasteToModel.contains(userResolvedRxElements.toStructureArr[i])) {
                    throw new RuntimeException("PasteToModel does not contain preferred Structure " + userResolvedRxElements.toStructureArr[i]);
                }
            }
        }
    }
    int counter = 0;
    Structure currentStruct = pasteToStructure;
    String copiedStructName = copyFromRxSteps[counter].getStructure().getName();
    StructureTopology structTopology = (copyFromRxSteps[counter].getModel() == null ? pasteToModel.getStructureTopology() : copyFromRxSteps[counter].getModel().getStructureTopology());
    IdentityHashMap<Species, Species> speciesHash = new IdentityHashMap<Species, Species>();
    IdentityHashMap<SpeciesContext, SpeciesContext> speciesContextHash = new IdentityHashMap<SpeciesContext, SpeciesContext>();
    Vector<Issue> issueVector = new Vector<Issue>();
    do {
        // create a new reaction, instead of cloning the old one; set struc
        ReactionStep copyFromReactionStep = copyFromRxSteps[counter];
        String newName = copyFromReactionStep.getName();
        while (pasteToModel.getReactionStep(newName) != null) {
            newName = org.vcell.util.TokenMangler.getNextEnumeratedToken(newName);
        }
        ReactionStep newReactionStep = null;
        if (copyFromReactionStep instanceof SimpleReaction) {
            newReactionStep = new SimpleReaction(pasteToModel, currentStruct, newName, copyFromReactionStep.isReversible());
        } else if (copyFromReactionStep instanceof FluxReaction && currentStruct instanceof Membrane) {
            newReactionStep = new FluxReaction(pasteToModel, (Membrane) currentStruct, null, newName, copyFromReactionStep.isReversible());
        }
        pasteToModel.addReactionStep(newReactionStep);
        reactionsAndSpeciesContexts.put(newReactionStep, copyFromReactionStep);
        Structure toRxnStruct = newReactionStep.getStructure();
        Structure fromRxnStruct = copyFromReactionStep.getStructure();
        if (!fromRxnStruct.getClass().equals(pasteToStructure.getClass())) {
            throw new Exception("Cannot copy reaction from " + fromRxnStruct.getTypeName() + " to " + pasteToStructure.getTypeName() + ".");
        }
        // add appropriate reactionParticipants to newReactionStep.
        StructureTopology toStructureTopology = pasteToModel.getStructureTopology();
        ReactionParticipant[] copyFromRxParticipantArr = copyFromReactionStep.getReactionParticipants();
        if (rxPartMapStructure == null) {
            // null during 'issues' trial
            rxPartMapStructure = new HashMap<String, HashMap<ReactionParticipant, Structure>>();
        }
        if (rxPartMapStructure.get(copyFromReactionStep.getName()) == null) {
            // Ask user to assign species to compartments for each reaction to be pasted
            rxPartMapStructure.put(copyFromReactionStep.getName(), askUserResolveMembraneConnections(parent, pasteToModel.getStructures(), currentStruct, fromRxnStruct, toRxnStruct, copyFromRxParticipantArr, toStructureTopology, structTopology));
        }
        for (int i = 0; i < copyFromRxParticipantArr.length; i += 1) {
            Structure pasteToStruct = currentStruct;
            // if(toRxnStruct instanceof Membrane){
            pasteToStruct = rxPartMapStructure.get(copyFromReactionStep.getName()).get(copyFromRxParticipantArr[i]);
            // if(pasteToStruct == null){
            // for(ReactionParticipant myRXPart:rxPartMapStructure.get(copyFromReactionStep.getName()).keySet()){
            // if(myRXPart.getSpeciesContext().getName().equals(copyFromRxParticipantArr[i].getSpeciesContext().getName())){
            // pasteToStruct = rxPartMapStructure.get(copyFromReactionStep.getName()).get(myRXPart);
            // break;
            // }
            // }
            // }
            // }
            // this adds the speciesContexts and species (if any) to the model)
            String rootSC = ReactionCartoonTool.speciesContextRootFinder(copyFromRxParticipantArr[i].getSpeciesContext());
            SpeciesContext newSc = null;
            SpeciesContext[] matchSC = pasteToModel.getSpeciesContexts();
            for (int j = 0; matchSC != null && j < matchSC.length; j++) {
                String matchRoot = ReactionCartoonTool.speciesContextRootFinder(matchSC[j]);
                if (matchRoot != null && matchRoot.equals(rootSC) && matchSC[j].getStructure().getName().equals(pasteToStruct.getName())) {
                    newSc = matchSC[j];
                    reactionsAndSpeciesContexts.put(newSc, matchSC[j]);
                    break;
                }
            }
            if (newSc == null) {
                newSc = pasteSpecies(parent, copyFromRxParticipantArr[i].getSpecies(), rootSC, pasteToModel, pasteToStruct, bNew, /*bUseDBSpecies,*/
                speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, copyFromRxParticipantArr[i]));
                reactionsAndSpeciesContexts.put(newSc, copyFromRxParticipantArr[i].getSpeciesContext());
            }
            // record the old-new speciesContexts (reactionparticipants) in the IdHashMap, this is useful, esp for 'Paste new', while replacing proxyparams.
            SpeciesContext oldSc = copyFromRxParticipantArr[i].getSpeciesContext();
            if (speciesContextHash.get(oldSc) == null) {
                speciesContextHash.put(oldSc, newSc);
            }
            if (copyFromRxParticipantArr[i] instanceof Reactant) {
                newReactionStep.addReactionParticipant(new Reactant(null, newReactionStep, newSc, copyFromRxParticipantArr[i].getStoichiometry()));
            } else if (copyFromRxParticipantArr[i] instanceof Product) {
                newReactionStep.addReactionParticipant(new Product(null, newReactionStep, newSc, copyFromRxParticipantArr[i].getStoichiometry()));
            } else if (copyFromRxParticipantArr[i] instanceof Catalyst) {
                newReactionStep.addCatalyst(newSc);
            }
        }
        // // If 'newReactionStep' is a fluxRxn, set its fluxCarrier
        // if (newReactionStep instanceof FluxReaction) {
        // if (fluxCarrierSp != null) {
        // ((FluxReaction)newReactionStep).setFluxCarrier(fluxCarrierSp, pasteToModel);
        // } else {
        // throw new RuntimeException("Could not set FluxCarrier species for the flux reaction to be pasted");
        // }
        // }
        // For each kinetic parameter expression for new kinetics, replace the proxyParams from old kinetics with proxyParams in new kinetics
        // i.e., if the proxyParams are speciesContexts, replace with corresponding speciesContext in newReactionStep;
        // if the proxyParams are structureSizes or MembraneVoltages, replace with corresponding structure quantity in newReactionStep
        Kinetics oldKinetics = copyFromReactionStep.getKinetics();
        KineticsParameter[] oldKps = oldKinetics.getKineticsParameters();
        KineticsProxyParameter[] oldKprps = oldKinetics.getProxyParameters();
        Hashtable<String, Expression> paramExprHash = new Hashtable<String, Expression>();
        for (int i = 0; oldKps != null && i < oldKps.length; i++) {
            Expression newExpression = new Expression(oldKps[i].getExpression());
            for (int j = 0; oldKprps != null && j < oldKprps.length; j++) {
                // check if kinetic proxy parameter is in kinetic parameter expression
                if (newExpression.hasSymbol(oldKprps[j].getName())) {
                    SymbolTableEntry ste = oldKprps[j].getTarget();
                    Model pasteFromModel = copyFromReactionStep.getModel();
                    if (ste instanceof SpeciesContext) {
                        // if newRxnStruct is a feature/membrane, get matching spContexts from old reaction and replace them in new rate expr.
                        SpeciesContext oldSC = (SpeciesContext) ste;
                        SpeciesContext newSC = speciesContextHash.get(oldSC);
                        if (newSC == null) {
                            // check if oldSc is present in paste-model; if not, add it.
                            if (!pasteToModel.equals(pasteFromModel)) {
                                if (pasteToModel.getSpeciesContext(oldSC.getName()) == null) {
                                    // if paste-model has oldSc struct, paste it there,
                                    Structure newSCStruct = pasteToModel.getStructure(oldSC.getStructure().getName());
                                    if (newSCStruct != null) {
                                        newSC = pasteSpecies(parent, oldSC.getSpecies(), null, pasteToModel, newSCStruct, bNew, /*bUseDBSpecies,*/
                                        speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, oldSC));
                                        speciesContextHash.put(oldSC, newSC);
                                    } else {
                                        // oldStruct wasn't found in paste-model, paste it in newRxnStruct and add warning to issues list
                                        newSC = pasteSpecies(parent, oldSC.getSpecies(), null, pasteToModel, toRxnStruct, bNew, /*bUseDBSpecies,*/
                                        speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, oldSC));
                                        speciesContextHash.put(oldSC, newSC);
                                        Issue issue = new Issue(oldSC, issueContext, IssueCategory.CopyPaste, "SpeciesContext '" + oldSC.getSpecies().getCommonName() + "' was not found in compartment '" + oldSC.getStructure().getName() + "' in the model; the species was added to the compartment '" + toRxnStruct.getName() + "' where the reaction was pasted.", Issue.SEVERITY_WARNING);
                                        issueVector.add(issue);
                                    }
                                }
                            }
                        // if models are the same and newSc is null, then oldSc is not a rxnParticipant. Leave it as is in the expr.
                        }
                        if (newSC != null) {
                            reactionsAndSpeciesContexts.put(newSC, oldSC);
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(newSC.getName()));
                        }
                    // SpeciesContext sc = null;
                    // Species newSp = model.getSpecies(oldSc.getSpecies().getCommonName());
                    // if  (oldSc.getStructure() == (oldRxnStruct)) {
                    // sc = model.getSpeciesContext(newSp, newRxnStruct);
                    // } else {
                    // if (newRxnStruct instanceof Membrane) {
                    // // for a membrane, we need to make sure that inside-outside spContexts used are appropriately replaced.
                    // if (oldSc.getStructure() == ((Membrane)oldRxnStruct).getOutsideFeature()) {
                    // // old speciesContext is outside (old) membrane, new spContext should be outside new membrane
                    // sc = model.getSpeciesContext(newSp, ((Membrane)newRxnStruct).getOutsideFeature());
                    // } else if (oldSc.getStructure() == ((Membrane)oldRxnStruct).getInsideFeature()) {
                    // // old speciesContext is inside (old) membrane, new spContext should be inside new membrane
                    // sc = model.getSpeciesContext(newSp, ((Membrane)newRxnStruct).getInsideFeature());
                    // }
                    // }
                    // }
                    // if (sc != null) {
                    // newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(sc.getName()));
                    // }
                    } else if (ste instanceof StructureSize) {
                        Structure str = ((StructureSize) ste).getStructure();
                        // if the structure size used is same as the structure in which the reaction is present, change the structSize to appropriate new struct
                        if (str.compareEqual(fromRxnStruct)) {
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(toRxnStruct.getStructureSize().getName()));
                        } else {
                            if (fromRxnStruct instanceof Membrane) {
                                if (str.equals(structTopology.getOutsideFeature((Membrane) fromRxnStruct))) {
                                    newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(structTopology.getOutsideFeature((Membrane) toRxnStruct).getStructureSize().getName()));
                                } else if (str.equals(structTopology.getInsideFeature((Membrane) fromRxnStruct))) {
                                    newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(structTopology.getInsideFeature((Membrane) toRxnStruct).getStructureSize().getName()));
                                }
                            }
                        }
                    } else if (ste instanceof MembraneVoltage) {
                        Membrane membr = ((MembraneVoltage) ste).getMembrane();
                        // if the MembraneVoltage used is same as that of the membrane in which the reaction is present, change the MemVoltage
                        if ((fromRxnStruct instanceof Membrane) && (membr.compareEqual(fromRxnStruct))) {
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(((Membrane) toRxnStruct).getMembraneVoltage().getName()));
                        }
                    } else if (ste instanceof ModelParameter) {
                        // see if model has this global parameter (if rxn is being pasted into another model, it won't)
                        if (!pasteToModel.equals(pasteFromModel)) {
                            ModelParameter oldMp = (ModelParameter) ste;
                            ModelParameter mp = pasteToModel.getModelParameter(oldMp.getName());
                            boolean bNonNumeric = false;
                            String newMpName = oldMp.getName();
                            if (mp != null) {
                                // new model has a model parameter with same name - are they the same param?
                                if (!mp.getExpression().equals(oldMp.getExpression())) {
                                    // no, they are not the same param, so mangle the 'ste' name and add as global in the other model
                                    while (pasteToModel.getModelParameter(newMpName) != null) {
                                        newMpName = TokenMangler.getNextEnumeratedToken(newMpName);
                                    }
                                    // if expression if numeric, add it as such. If not, set it to 0.0 and add it as global
                                    Expression exp = oldMp.getExpression();
                                    if (!exp.flatten().isNumeric()) {
                                        exp = new Expression(0.0);
                                        bNonNumeric = true;
                                    }
                                    ModelParameter newMp = pasteToModel.new ModelParameter(newMpName, exp, Model.ROLE_UserDefined, oldMp.getUnitDefinition());
                                    String annotation = "Copied from model : " + pasteFromModel.getNameScope();
                                    newMp.setModelParameterAnnotation(annotation);
                                    pasteToModel.addModelParameter(newMp);
                                    // if global param name had to be changed, make sure newExpr is updated as well.
                                    if (!newMpName.equals(oldMp.getName())) {
                                        newExpression.substituteInPlace(new Expression(oldMp.getName()), new Expression(newMpName));
                                    }
                                }
                            } else {
                                // no global param with same name was found in other model, so add it to other model.
                                // if expression if numeric, add it as such. If not, set it to 0.0 and add it as global
                                Expression exp = oldMp.getExpression();
                                if (!exp.flatten().isNumeric()) {
                                    exp = new Expression(0.0);
                                    bNonNumeric = true;
                                }
                                ModelParameter newMp = pasteToModel.new ModelParameter(newMpName, exp, Model.ROLE_UserDefined, oldMp.getUnitDefinition());
                                String annotation = "Copied from model : " + pasteFromModel.getNameScope();
                                newMp.setModelParameterAnnotation(annotation);
                                pasteToModel.addModelParameter(newMp);
                            }
                            // if a non-numeric parameter was encountered in the old model, it was added as a numeric (0.0), warn user of change.
                            if (bNonNumeric) {
                                Issue issue = new Issue(oldMp, issueContext, IssueCategory.CopyPaste, "Global parameter '" + oldMp.getName() + "' was non-numeric; it has been added " + "as global parameter '" + newMpName + "' in the new model with value = 0.0. " + "Please update its value, if required, before using it.", Issue.SEVERITY_WARNING);
                                issueVector.add(issue);
                            }
                        }
                    }
                }
            // end - if newExpr.hasSymbol(ProxyParam)
            }
            // now if store <param names, new expression> in hashTable
            if (paramExprHash.get(oldKps[i].getName()) == null) {
                paramExprHash.put(oldKps[i].getName(), newExpression);
            }
        }
        // end for - oldKps (old kinetic parameters)
        // use this new expression to generate 'vcml' for the (new) kinetics (easier way to transfer all kinetic parameters)
        String newKineticsStr = oldKinetics.writeTokensWithReplacingProxyParams(paramExprHash);
        // convert the kinetics 'vcml' to tokens.
        CommentStringTokenizer kineticsTokens = new CommentStringTokenizer(newKineticsStr);
        // skip the first token;
        kineticsTokens.nextToken();
        // second token is the kinetic type; use this to create a dummy kinetics
        String kineticType = kineticsTokens.nextToken();
        Kinetics newkinetics = KineticsDescription.fromVCMLKineticsName(kineticType).createKinetics(newReactionStep);
        // use the remaining tokens to construct the new kinetics
        newkinetics.fromTokens(newKineticsStr);
        // bind newkinetics to newReactionStep and add it to newReactionStep
        newkinetics.bind(newReactionStep);
        newReactionStep.setKinetics(newkinetics);
        counter += 1;
        if (counter == copyFromRxSteps.length) {
            break;
        }
        if (!copiedStructName.equals(fromRxnStruct.getName())) {
            if (currentStruct instanceof Feature) {
                currentStruct = structTopology.getMembrane((Feature) currentStruct);
            } else if (currentStruct instanceof Membrane) {
                currentStruct = structTopology.getInsideFeature((Membrane) currentStruct);
            }
        }
        copiedStructName = fromRxnStruct.getName();
    } while (true);
    return new PasteHelper(issueVector, rxPartMapStructure, reactionsAndSpeciesContexts);
}

Example 67 with IdentityHashMap

use of java.util.IdentityHashMap in project dubbo by alibaba.

the class JavaBeanSerializeUtil method serializeInternal.

private static void serializeInternal(JavaBeanDescriptor descriptor, Object obj, JavaBeanAccessor accessor, IdentityHashMap<Object, JavaBeanDescriptor> cache) {
    if (obj == null || descriptor == null) {
        return;
    }
    if (obj.getClass().isEnum()) {
        descriptor.setEnumNameProperty(((Enum<?>) obj).name());
    } else if (ReflectUtils.isPrimitive(obj.getClass())) {
        descriptor.setPrimitiveProperty(obj);
    } else if (Class.class.equals(obj.getClass())) {
        descriptor.setClassNameProperty(((Class<?>) obj).getName());
    } else if (obj.getClass().isArray()) {
        int len = Array.getLength(obj);
        for (int i = 0; i < len; i++) {
            Object item = Array.get(obj, i);
            if (item == null) {
                descriptor.setProperty(i, null);
            } else {
                JavaBeanDescriptor itemDescriptor = createDescriptorIfAbsent(item, accessor, cache);
                descriptor.setProperty(i, itemDescriptor);
            }
        }
    } else if (obj instanceof Collection) {
        Collection collection = (Collection) obj;
        int index = 0;
        for (Object item : collection) {
            if (item == null) {
                descriptor.setProperty(index++, null);
            } else {
                JavaBeanDescriptor itemDescriptor = createDescriptorIfAbsent(item, accessor, cache);
                descriptor.setProperty(index++, itemDescriptor);
            }
        }
    } else if (obj instanceof Map) {
        Map map = (Map) obj;
        for (Object key : map.keySet()) {
            Object value = map.get(key);
            Object keyDescriptor = key == null ? null : createDescriptorIfAbsent(key, accessor, cache);
            Object valueDescriptor = value == null ? null : createDescriptorIfAbsent(value, accessor, cache);
            descriptor.setProperty(keyDescriptor, valueDescriptor);
        }
    // ~ end of loop map
    } else {
        if (JavaBeanAccessor.isAccessByMethod(accessor)) {
            Map<String, Method> methods = ReflectUtils.getBeanPropertyReadMethods(obj.getClass());
            for (Map.Entry<String, Method> entry : methods.entrySet()) {
                try {
                    Object value = entry.getValue().invoke(obj);
                    if (value == null) {
                        continue;
                    }
                    JavaBeanDescriptor valueDescriptor = createDescriptorIfAbsent(value, accessor, cache);
                    descriptor.setProperty(entry.getKey(), valueDescriptor);
                } catch (Exception e) {
                    throw new RuntimeException(e.getMessage(), e);
                }
            }
        // ~ end of loop method map
        }
        if (JavaBeanAccessor.isAccessByField(accessor)) {
            Map<String, Field> fields = ReflectUtils.getBeanPropertyFields(obj.getClass());
            for (Map.Entry<String, Field> entry : fields.entrySet()) {
                if (!descriptor.containsProperty(entry.getKey())) {
                    try {
                        Object value = entry.getValue().get(obj);
                        if (value == null) {
                            continue;
                        }
                        JavaBeanDescriptor valueDescriptor = createDescriptorIfAbsent(value, accessor, cache);
                        descriptor.setProperty(entry.getKey(), valueDescriptor);
                    } catch (Exception e) {
                        throw new RuntimeException(e.getMessage(), e);
                    }
                }
            }
        // ~ end of loop field map
        }
    // ~ end of if (JavaBeanAccessor.isAccessByField(accessor))
    }
// ~ end of else
}

Example 68 with IdentityHashMap

use of java.util.IdentityHashMap in project elasticsearch by elastic.

the class ClusterService method submitStateUpdateTasks.

/**
     * Submits a batch of cluster state update tasks; submitted updates are guaranteed to be processed together,
     * potentially with more tasks of the same executor.
     *
     * @param source   the source of the cluster state update task
     * @param tasks    a map of update tasks and their corresponding listeners
     * @param config   the cluster state update task configuration
     * @param executor the cluster state update task executor; tasks
     *                 that share the same executor will be executed
     *                 batches on this executor
     * @param <T>      the type of the cluster state update task state
     *
     */
public <T> void submitStateUpdateTasks(final String source, final Map<T, ClusterStateTaskListener> tasks, final ClusterStateTaskConfig config, final ClusterStateTaskExecutor<T> executor) {
    if (!lifecycle.started()) {
        return;
    }
    if (tasks.isEmpty()) {
        return;
    }
    try {
        @SuppressWarnings("unchecked") ClusterStateTaskExecutor<Object> taskExecutor = (ClusterStateTaskExecutor<Object>) executor;
        // convert to an identity map to check for dups based on update tasks semantics of using identity instead of equal
        final IdentityHashMap<Object, ClusterStateTaskListener> tasksIdentity = new IdentityHashMap<>(tasks);
        final List<UpdateTask> updateTasks = tasksIdentity.entrySet().stream().map(entry -> new UpdateTask(source, entry.getKey(), config.priority(), taskExecutor, safe(entry.getValue(), logger))).collect(Collectors.toList());
        synchronized (updateTasksPerExecutor) {
            LinkedHashSet<UpdateTask> existingTasks = updateTasksPerExecutor.computeIfAbsent(executor, k -> new LinkedHashSet<>(updateTasks.size()));
            for (UpdateTask existing : existingTasks) {
                if (tasksIdentity.containsKey(existing.task)) {
                    throw new IllegalStateException("task [" + taskExecutor.describeTasks(Collections.singletonList(existing.task)) + "] with source [" + source + "] is already queued");
                }
            }
            existingTasks.addAll(updateTasks);
        }
        final UpdateTask firstTask = updateTasks.get(0);
        final TimeValue timeout = config.timeout();
        if (timeout != null) {
            threadPoolExecutor.execute(firstTask, threadPool.scheduler(), timeout, () -> onTimeout(updateTasks, source, timeout));
        } else {
            threadPoolExecutor.execute(firstTask);
        }
    } catch (EsRejectedExecutionException e) {
        // to be done here...
        if (!lifecycle.stoppedOrClosed()) {
            throw e;
        }
    }
}

Example 69 with IdentityHashMap

use of java.util.IdentityHashMap in project jersey by jersey.

the class ApplicationHandler method bindProvidersAndResources.

private void bindProvidersAndResources(final Iterable<ComponentProvider> componentProviders, final ComponentBag componentBag, final Collection<Class<?>> resourceClasses, final Collection<Object> resourceInstances) {
    JerseyResourceContext resourceContext = injectionManager.getInstance(JerseyResourceContext.class);
    Set<Class<?>> registeredClasses = runtimeConfig.getRegisteredClasses();
    /*
         * Check the {@code component} whether it is correctly configured for client or server {@link RuntimeType runtime}.
         */
    java.util.function.Predicate<Class<?>> correctlyConfigured = componentClass -> Providers.checkProviderRuntime(componentClass, componentBag.getModel(componentClass), RuntimeType.SERVER, !registeredClasses.contains(componentClass), resourceClasses.contains(componentClass));
    /*
         * Check the {@code resource class} whether it is correctly configured for client or server {@link RuntimeType runtime}.
         */
    BiPredicate<Class<?>, ContractProvider> correctlyConfiguredResource = (resourceClass, model) -> Providers.checkProviderRuntime(resourceClass, model, RuntimeType.SERVER, !registeredClasses.contains(resourceClass), true);
    Set<Class<?>> componentClassses = componentBag.getClasses(ComponentBag.excludeMetaProviders(injectionManager)).stream().filter(correctlyConfigured).collect(Collectors.toSet());
    // Merge programmatic resource classes with component classes.
    Set<Class<?>> classes = Collections.newSetFromMap(new IdentityHashMap<>());
    classes.addAll(componentClassses);
    classes.addAll(resourceClasses);
    // Bind classes.
    for (final Class<?> componentClass : classes) {
        ContractProvider model = componentBag.getModel(componentClass);
        if (bindWithComponentProvider(componentClass, model, componentProviders)) {
            continue;
        }
        if (resourceClasses.contains(componentClass)) {
            if (!Resource.isAcceptable(componentClass)) {
                LOGGER.warning(LocalizationMessages.NON_INSTANTIABLE_COMPONENT(componentClass));
                continue;
            }
            if (model != null && !correctlyConfiguredResource.test(componentClass, model)) {
                model = null;
            }
            resourceContext.unsafeBindResource(componentClass, model, injectionManager);
        } else {
            ProviderBinder.bindProvider(componentClass, model, injectionManager);
        }
    }
    // Merge programmatic resource instances with other component instances.
    Set<Object> instances = componentBag.getInstances(ComponentBag.excludeMetaProviders(injectionManager)).stream().filter(instance -> correctlyConfigured.test(instance.getClass())).collect(Collectors.toSet());
    instances.addAll(resourceInstances);
    // Bind instances.
    for (Object component : instances) {
        ContractProvider model = componentBag.getModel(component.getClass());
        if (resourceInstances.contains(component)) {
            if (model != null && !correctlyConfiguredResource.test(component.getClass(), model)) {
                model = null;
            }
            resourceContext.unsafeBindResource(component, model, injectionManager);
        } else {
            ProviderBinder.bindProvider(component, model, injectionManager);
        }
    }
}

Example 70 with IdentityHashMap

use of java.util.IdentityHashMap in project jersey by jersey.

the class CommonConfigTest method testProviderOrderDifForContracts.

@Test
@SuppressWarnings("unchecked")
public void testProviderOrderDifForContracts() throws Exception {
    final Map<Class<?>, Integer> contracts = new IdentityHashMap<Class<?>, Integer>();
    contracts.put(WriterInterceptor.class, ContractProvider.NO_PRIORITY);
    contracts.put(ReaderInterceptor.class, 2000);
    config.register(MidPriorityProvider.class, contracts);
    contracts.clear();
    contracts.put(WriterInterceptor.class, ContractProvider.NO_PRIORITY);
    contracts.put(ReaderInterceptor.class, 1000);
    config.register(LowPriorityProvider.class, contracts);
    contracts.clear();
    contracts.put(WriterInterceptor.class, ContractProvider.NO_PRIORITY);
    contracts.put(ReaderInterceptor.class, 3000);
    config.register(HighPriorityProvider.class, contracts);
    contracts.clear();
    final InjectionManager injectionManager = Injections.createInjectionManager();
    ProviderBinder.bindProviders(config.getComponentBag(), injectionManager);
    final Iterable<WriterInterceptor> writerInterceptors = Providers.getAllProviders(injectionManager, WriterInterceptor.class, new RankedComparator<WriterInterceptor>());
    final Iterator<WriterInterceptor> writerIterator = writerInterceptors.iterator();
    assertEquals(HighPriorityProvider.class, writerIterator.next().getClass());
    assertEquals(MidPriorityProvider.class, writerIterator.next().getClass());
    assertEquals(LowPriorityProvider.class, writerIterator.next().getClass());
    assertFalse(writerIterator.hasNext());
    final Iterable<ReaderInterceptor> readerInterceptors = Providers.getAllProviders(injectionManager, ReaderInterceptor.class, new RankedComparator<ReaderInterceptor>());
    final Iterator<ReaderInterceptor> readerIterator = readerInterceptors.iterator();
    assertEquals(LowPriorityProvider.class, readerIterator.next().getClass());
    assertEquals(MidPriorityProvider.class, readerIterator.next().getClass());
    assertEquals(HighPriorityProvider.class, readerIterator.next().getClass());
    assertFalse(readerIterator.hasNext());
}