Examples with Node org.apache.airavata.workflow.model.graph.Node used on opensource projects

Example 1 with Node

use of org.apache.airavata.workflow.model.graph.Node in project airavata by apache.

the class WorkflowInterpreter method handleForEach.

private void handleForEach(Node node) throws WorkflowException {
    final ForEachNode forEachNode = (ForEachNode) node;
    EndForEachNode endForEachNode = null;
    Collection<Node> repeatNodes = node.getOutputPort(0).getToNodes();
    // we will support only one for now
    if (repeatNodes.size() != 1) {
        throw new WorkFlowInterpreterException("Only one node allowed inside foreach");
    }
    Iterator<Node> iterator = repeatNodes.iterator();
    if (iterator.hasNext()) {
        Node middleNode = iterator.next();
        // output
        if ((!(middleNode instanceof WSNode)) && (!(middleNode instanceof SubWorkflowNode))) {
            throw new WorkFlowInterpreterException("Encountered Node inside foreach that is not a WSNode" + middleNode);
        } else if (middleNode instanceof SubWorkflowNode) {
            /* Get the EndforEach Node of the Subworkflow */
            Iterator<Node> subWorkflowOut = middleNode.getOutputPort(0).getToNodes().iterator();
            while (subWorkflowOut.hasNext()) {
                Node node2 = subWorkflowOut.next();
                if (node2 instanceof EndForEachNode) {
                    endForEachNode = (EndForEachNode) node2;
                }
            }
            final LinkedList<String> listOfValues = new LinkedList<String>();
            InterpreterUtil.getInputsForForEachNode(forEachNode, listOfValues, this.invokerMap);
            final Integer[] inputNumbers = InterpreterUtil.getNumberOfInputsForForEachNode(forEachNode, this.invokerMap);
            Workflow workflow1 = ((SubWorkflowNode) middleNode).getWorkflow();
            List<NodeImpl> nodes = workflow1.getGraph().getNodes();
            List<Node> wsNodes = new ArrayList<Node>();
            /* Take the List of WSNodes in the subworkflow */
            for (NodeImpl subWorkflowNode : nodes) {
                if (subWorkflowNode instanceof WSNode) {
                    wsNodes.add(subWorkflowNode);
                }
            }
            for (int i = 0; i < wsNodes.size(); i++) {
                final WSNode node1 = (WSNode) wsNodes.get(i);
                SystemComponentInvoker systemInvoker = null;
                List<DataPort> outputPorts1 = node1.getOutputPorts();
                List<Node> endForEachNodes = new ArrayList<Node>();
                for (DataPort port : outputPorts1) {
                    Iterator<Node> endForEachNodeItr1 = port.getToNodes().iterator();
                    while (endForEachNodeItr1.hasNext()) {
                        Node node2 = endForEachNodeItr1.next();
                        if (node2 instanceof EndForEachNode) {
                            endForEachNodes.add(node2);
                        } else if (node2 instanceof OutputNode) {
                        // intentionally left noop
                        } else {
                            throw new WorkFlowInterpreterException("Found More than one node inside foreach");
                        }
                    }
                }
                final List<Node> finalEndForEachNodes = endForEachNodes;
                Iterator<Node> endForEachNodeItr1 = node1.getOutputPort(0).getToNodes().iterator();
                while (endForEachNodeItr1.hasNext()) {
                    Node node2 = endForEachNodeItr1.next();
                    // Start reading input came for foreach node
                    int parallelRuns = listOfValues.size() * node1.getOutputPorts().size();
                    if (listOfValues.size() > 0) {
                        forEachNode.setState(NodeExecutionState.EXECUTING);
                        node1.setState(NodeExecutionState.EXECUTING);
                        List<DataPort> outputPorts = node1.getOutputPorts();
                        final AtomicInteger counter = new AtomicInteger();
                        for (Node endFor : endForEachNodes) {
                            systemInvoker = new SystemComponentInvoker();
                            this.invokerMap.put(endFor, systemInvoker);
                        }
                        final Map<Node, Invoker> finalMap = this.invokerMap;
                        new Thread() {

                            @Override
                            public void run() {
                                try {
                                    runInThread(listOfValues, forEachNode, node1, finalEndForEachNodes, finalMap, counter, inputNumbers);
                                } catch (WorkflowException e) {
                                    log.error(e.getLocalizedMessage(), e);
                                } catch (RegistryException e) {
                                    log.error(e.getMessage(), e);
                                } catch (TException e) {
                                    log.error(e.getMessage(), e);
                                }
                            }
                        }.start();
                        while (counter.intValue() < parallelRuns) {
                            try {
                                Thread.sleep(100);
                            } catch (InterruptedException e) {
                                Thread.currentThread().interrupt();
                            }
                        }
                    // if (!(node2 instanceof OutputNode)) {
                    // listOfValues.removeAll(listOfValues);
                    // String output = (String) systemInvoker.getOutput(node1.getOutputPort(0).getName());
                    // XmlElement xmlElement = XMLUtil.stringToXmlElement("<result>" + output + "</result>");
                    // Iterator iterator1 = xmlElement.children().iterator();
                    // while (iterator1.hasNext()) {
                    // Object next1 = iterator1.next();
                    // if (next1 instanceof XmlElement) {
                    // listOfValues.add((String) ((XmlElement) next1).children().iterator().next());
                    // }
                    // }
                    // }
                    }
                }
            }
            // we have finished execution so end foreach is finished
            // todo this has to be done in a separate thread
            endForEachNode.setState(NodeExecutionState.FINISHED);
            middleNode.setState(NodeExecutionState.FINISHED);
            node.setState(NodeExecutionState.FINISHED);
        } else {
            // First node after foreach should end with EndForEachNode
            List<DataPort> outputPorts1 = middleNode.getOutputPorts();
            List<Node> endForEachNodes = new ArrayList<Node>();
            for (DataPort port : outputPorts1) {
                Iterator<Node> endForEachNodeItr1 = port.getToNodes().iterator();
                while (endForEachNodeItr1.hasNext()) {
                    Node node2 = endForEachNodeItr1.next();
                    if (node2 instanceof EndForEachNode) {
                        endForEachNodes.add(node2);
                    } else if (node2 instanceof OutputNode) {
                    // intentionally left noop
                    } else {
                        throw new WorkFlowInterpreterException("Found More than one node inside foreach");
                    }
                }
            }
            final List<Node> finalEndForEachNodes = endForEachNodes;
            final Node foreachWSNode = middleNode;
            final LinkedList<String> listOfValues = new LinkedList<String>();
            // Start reading input came for foreach node
            InterpreterUtil.getInputsForForEachNode(forEachNode, listOfValues, this.invokerMap);
            final Integer[] inputNumbers = InterpreterUtil.getNumberOfInputsForForEachNode(forEachNode, this.invokerMap);
            int parallelRuns = createInputValues(listOfValues, inputNumbers).size() * outputPorts1.size();
            if (listOfValues.size() > 0) {
                forEachNode.setState(NodeExecutionState.EXECUTING);
                foreachWSNode.setState(NodeExecutionState.EXECUTING);
                List<DataPort> outputPorts = middleNode.getOutputPorts();
                final AtomicInteger counter = new AtomicInteger();
                for (Node endFor : endForEachNodes) {
                    final SystemComponentInvoker systemInvoker = new SystemComponentInvoker();
                    this.invokerMap.put(endFor, systemInvoker);
                }
                final Map<Node, Invoker> finalInvokerMap = this.invokerMap;
                new Thread() {

                    @Override
                    public void run() {
                        try {
                            runInThread(listOfValues, forEachNode, foreachWSNode, finalEndForEachNodes, finalInvokerMap, counter, inputNumbers);
                        } catch (WorkflowException e) {
                            log.error(e.getLocalizedMessage(), e);
                        } catch (RegistryException e) {
                            // TODO Auto-generated catch block
                            e.printStackTrace();
                        } catch (TException e) {
                            // TODO Auto-generated catch block
                            e.printStackTrace();
                        }
                    }
                }.start();
                while (counter.intValue() < parallelRuns) {
                    try {
                        Thread.sleep(100);
                    } catch (InterruptedException e) {
                        Thread.currentThread().interrupt();
                    }
                }
                // we have finished execution so end foreach is finished
                // todo this has to be done in a separate thread
                middleNode.setState(NodeExecutionState.FINISHED);
                for (Node endForEach : endForEachNodes) {
                    endForEach.setState(NodeExecutionState.FINISHED);
                }
            } else {
                throw new WorkFlowInterpreterException("No array values found for foreach");
            }
        }
    }
}

Example 2 with Node

use of org.apache.airavata.workflow.model.graph.Node in project airavata by apache.

the class WorkflowInterpreter method taskStatusChanged.

@Subscribe
public void taskStatusChanged(TaskStatusChangeEvent taskStatus) {
    String taskId = taskStatus.getTaskIdentity().getTaskId();
    if (isTaskAwaiting(taskId)) {
        WorkflowNodeState state = WorkflowNodeState.UNKNOWN;
        Node node = getAwaitingNodeForTask(taskId);
        switch(taskStatus.getState()) {
            case CANCELED:
                ;
                break;
            case COMPLETED:
                // but we'll wait for outputdata
                break;
            case CONFIGURING_WORKSPACE:
                break;
            case FAILED:
                state = WorkflowNodeState.FAILED;
                node.setState(NodeExecutionState.FAILED);
                break;
            case EXECUTING:
            case WAITING:
            case PRE_PROCESSING:
            case POST_PROCESSING:
            case OUTPUT_DATA_STAGING:
            case INPUT_DATA_STAGING:
                state = WorkflowNodeState.EXECUTING;
                node.setState(NodeExecutionState.EXECUTING);
                break;
            case STARTED:
                break;
            case CANCELING:
                state = WorkflowNodeState.CANCELING;
                break;
            default:
                break;
        }
        try {
            if (state != WorkflowNodeState.UNKNOWN) {
                updateWorkflowNodeStatus(nodeInstanceList.get(node), state);
            }
        } catch (RegistryException e) {
            log.error(e.getMessage(), e);
        }
    }
}

Example 3 with Node

use of org.apache.airavata.workflow.model.graph.Node in project airavata by apache.

the class WorkflowInterpreter method getReadyNodesDynamically.

private ArrayList<Node> getReadyNodesDynamically() {
    ArrayList<Node> list = new ArrayList<Node>();
    ArrayList<Node> waiting = InterpreterUtil.getWaitingNodesDynamically(this.getGraph());
    // ArrayList<Node> finishedNodes = InterpreterUtil.getFinishedNodesDynamically(this.getGraph());
    // This is to support repeat the same application in the workflow.
    List<String> finishedNodeIds = InterpreterUtil.getFinishedNodesIds(this.getGraph());
    for (Node node : waiting) {
        Component component = node.getComponent();
        if (component instanceof WSComponent || component instanceof DynamicComponent || component instanceof SubWorkflowComponent || component instanceof ForEachComponent || component instanceof EndForEachComponent || component instanceof IfComponent || component instanceof InstanceComponent) {
            /*
				 * Check for control ports from other node
				 */
            ControlPort control = node.getControlInPort();
            boolean controlDone = true;
            if (control != null) {
                for (EdgeImpl edge : control.getEdges()) {
                    controlDone = controlDone && (finishedNodeIds.contains(edge.getFromPort().getNode().getID()) || // that makes sense and if anyone found a scenario it should be otherwise pls fix
                    ((ControlPort) edge.getFromPort()).isConditionMet());
                }
            }
            /*
				 * Check for input ports
				 */
            List<DataPort> inputPorts = node.getInputPorts();
            boolean inputsDone = true;
            for (DataPort dataPort : inputPorts) {
                inputsDone = inputsDone && finishedNodeIds.contains(dataPort.getFromNode().getID());
            }
            if (inputsDone && controlDone) {
                list.add(node);
            }
        } else if (component instanceof EndifComponent) {
            /*
				 * EndIfComponent can run if number of input equals to number of
				 * output that it expects
				 */
            int expectedOutput = node.getOutputPorts().size();
            int actualInput = 0;
            List<DataPort> inputPorts = node.getInputPorts();
            for (DataPort dataPort : inputPorts) {
                if (finishedNodeIds.contains(dataPort.getFromNode().getID()))
                    actualInput++;
            }
            if (expectedOutput == actualInput) {
                list.add(node);
            }
        } else if (component instanceof TerminateInstanceComponent) {
            /*
				 * All node connected to controlIn port must be done
				 */
            ControlPort control = node.getControlInPort();
            boolean controlDone = true;
            if (control != null) {
                for (EdgeImpl edge : control.getEdges()) {
                    controlDone = controlDone && finishedNodeIds.contains(edge.getFromPort().getFromNode().getID());
                }
            }
            /*
				 * Check for input ports
				 */
            List<DataPort> inputPorts = node.getInputPorts();
            boolean inputsDone = true;
            for (DataPort dataPort : inputPorts) {
                inputsDone = inputsDone && finishedNodeIds.contains(dataPort.getFromNode().getID());
            }
            if (inputsDone && controlDone) {
                list.add(node);
            }
        } else if (InputComponent.NAME.equals(component.getName()) || DifferedInputComponent.NAME.equals(component.getName()) || S3InputComponent.NAME.equals(component.getName()) || OutputComponent.NAME.equals(component.getName()) || MemoComponent.NAME.equals(component.getName()) || component instanceof EndDoWhileComponent) {
        // no op
        } else if (component instanceof DoWhileComponent) {
            ControlPort control = node.getControlInPort();
            boolean controlDone = true;
            if (control != null) {
                for (EdgeImpl edge : control.getEdges()) {
                    controlDone = controlDone && finishedNodeIds.contains(edge.getFromPort().getFromNode().getID());
                }
            }
            if (controlDone) {
                list.add(node);
            }
        } else {
            throw new WorkFlowInterpreterException("Component Not handled :" + component.getName());
        }
    }
    notifyViaInteractor(WorkflowExecutionMessage.HANDLE_DEPENDENT_NODES_DIFFERED_INPUTS, this.getGraph());
    return list;
}

Example 4 with Node

use of org.apache.airavata.workflow.model.graph.Node in project airavata by apache.

the class WorkflowInterpreter method getInputNodes.

private ArrayList<Node> getInputNodes(Workflow wf) {
    ArrayList<Node> list = new ArrayList<Node>();
    List<NodeImpl> nodes = wf.getGraph().getNodes();
    for (Node node : nodes) {
        String name = node.getComponent().getName();
        if (InputComponent.NAME.equals(name) || ConstantComponent.NAME.equals(name) || S3InputComponent.NAME.equals(name)) {
            list.add(node);
        }
    }
    return list;
}

Example 5 with Node

use of org.apache.airavata.workflow.model.graph.Node in project airavata by apache.

the class WorkflowInterpreter method handleDynamicComponent.

private void handleDynamicComponent(Node node) throws WorkflowException {
    DynamicComponent dynamicComponent = (DynamicComponent) node.getComponent();
    String className = dynamicComponent.getClassName();
    String operationName = dynamicComponent.getOperationName();
    URL implJarLocation = dynamicComponent.getImplJarLocation();
    DynamicNode dynamicNode = (DynamicNode) node;
    LinkedList<Object> inputs = new LinkedList<Object>();
    List<DataPort> inputPorts = dynamicNode.getInputPorts();
    for (DataPort dataPort : inputPorts) {
        Object inputVal = InterpreterUtil.findInputFromPort(dataPort, this.invokerMap);
        /*
			 * Set type after get input value, and override inputValue if output
			 * type is array
			 */
        Node fromNode = dataPort.getFromNode();
        DataType type = null;
        if (fromNode instanceof InputNode) {
            type = DataType.STRING;
        } else if (fromNode instanceof ConstantNode) {
            type = ((ConstantNode) fromNode).getType();
        } else if ((dataPort.getFromPort() instanceof WSPort) && BasicTypeMapping.isArrayType(((WSPort) dataPort.getFromPort()).getComponentPort().getElement())) {
            Invoker fromInvoker = this.invokerMap.get(fromNode);
            // inputVal = BasicTypeMapping.getOutputArray(XmlConstants.BUILDER.parseFragmentFromString(fromInvoker.getOutputs().toString()), dataPort
            // .getFromPort().getName(), BasicTypeMapping.getSimpleTypeIndex(((DataPort) dataPort.getFromPort()).getType()));
            type = ((DataPort) dataPort.getFromPort()).getType();
        } else {
            type = ((DataPort) dataPort.getFromPort()).getType();
        }
        if (null == inputVal) {
            throw new WorkFlowInterpreterException("Unable to find inputs for the node:" + node.getID());
        }
    // inputs.add(BasicTypeMapping.getObjectOfType(type, inputVal));
    }
    DynamicInvoker dynamicInvoker = new DynamicInvoker(className, implJarLocation, operationName, inputs.toArray());
    this.invokerMap.put(node, dynamicInvoker);
    dynamicInvoker.setup();
    dynamicInvoker.invoke();
    node.setState(NodeExecutionState.FINISHED);
}