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

Example 1 with DataPort

use of org.apache.airavata.workflow.model.graph.DataPort 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 DataPort

use of org.apache.airavata.workflow.model.graph.DataPort 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 3 with DataPort

use of org.apache.airavata.workflow.model.graph.DataPort 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);
}

Example 4 with DataPort

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

the class WorkflowInterpreter method sendOutputsDynamically.

private void sendOutputsDynamically() throws WorkflowException, RegistryException, AiravataException {
    ArrayList<Node> outputNodes = getReadyOutputNodesDynamically();
    if (outputNodes.size() != 0) {
        LinkedList<Object> outputValues = new LinkedList<Object>();
        LinkedList<String> outputKeywords = new LinkedList<String>();
        for (Node node : outputNodes) {
            // Change it to processing state so we will not pic it up in the
            // next run
            // even if the next run runs before the notification arrives
            WorkflowNodeDetails workflowNodeDetails = createWorkflowNodeDetails(node);
            // workflowNodeDetails.setNodeInstanceId((String)getExperimentCatalog().add(ChildDataType.WORKFLOW_NODE_DETAIL, workflowNodeDetails, getExperiment().getExperimentID()));
            node.setState(NodeExecutionState.EXECUTING);
            updateWorkflowNodeStatus(workflowNodeDetails, WorkflowNodeState.EXECUTING);
            publishNodeStatusChange(WorkflowNodeState.EXECUTING, node.getID(), experiment.getExperimentID());
            // OutputNode node = (OutputNode) outputNode;
            List<DataPort> inputPorts = node.getInputPorts();
            for (DataPort dataPort : inputPorts) {
                Object val = InterpreterUtil.findInputFromPort(dataPort);
                if (null == val) {
                    throw new WorkFlowInterpreterException("Unable to find output for the node:" + node.getID());
                }
                // input
                if (val instanceof org.xmlpull.v1.builder.XmlElement) {
                    ((OutputNode) node).setDescription(XMLUtil.xmlElementToString((org.xmlpull.v1.builder.XmlElement) val));
                } else {
                    ((OutputNode) node).setDescription(val.toString());
                }
                // Saving output Node data in to database
                // WorkflowNodeType workflowNodeType = new WorkflowNodeType();
                // workflowNodeType.setNodeType(WorkflowNodeType.WorkflowNode.OUTPUTNODE);
                // WorkflowInstanceNode workflowInstanceNode = new WorkflowInstanceNode(new WorkflowExecution(config.getTopic(), config.getTopic()), node.getID());
                String portname = node.getName();
                String portValue = ((OutputNode) node).getDescription();
                // this.getConfig().getConfiguration().getAiravataAPI().getProvenanceManager().setWorkflowInstanceNodeOutput(workflowInstanceNode, portname + "=" + portValue);
                // this.getConfig().getConfiguration().getAiravataAPI().getProvenanceManager().setWorkflowNodeType(workflowInstanceNode, workflowNodeType);
                OutputDataObjectType elem = new OutputDataObjectType();
                elem.setName(portname);
                elem.setValue(portValue);
                workflowNodeDetails.addToNodeOutputs(elem);
                getExperimentCatalog().update(ExperimentCatalogModelType.WORKFLOW_NODE_DETAIL, workflowNodeDetails, workflowNodeDetails.getNodeInstanceId());
                if (this.config.isActOnProvenance()) {
                // TODO do provanence thing
                // try {
                // if (val instanceof String) {
                // this.getConfig().getConfiguration().getAiravataAPI().getProvenanceManager()
                // .saveWorkflowExecutionOutput(this.config.getTopic(), node.getName(), val.toString());
                // } else if (val instanceof org.xmlpull.v1.builder.XmlElement) {
                // this.getConfig()
                // .getConfiguration()
                // .getAiravataAPI().getProvenanceManager()
                // .saveWorkflowExecutionOutput(this.config.getTopic(), node.getName(),
                // XMLUtil.xmlElementToString((org.xmlpull.v1.builder.XmlElement) val));
                // }
                // outputValues.add(val);
                // outputKeywords.add(dataPort.getID());
                // } catch (AiravataAPIInvocationException e) {
                // e.printStackTrace(); // To change body of catch
                // // statement use File |
                // // Settings | File
                // // Templates.
                // }
                }
            }
            node.setState(NodeExecutionState.FINISHED);
            publishNodeStatusChange(WorkflowNodeState.COMPLETED, node.getID(), experiment.getExperimentID());
            updateWorkflowNodeStatus(workflowNodeDetails, WorkflowNodeState.COMPLETED);
            notifyViaInteractor(WorkflowExecutionMessage.NODE_STATE_CHANGED, null);
        }
    }
}

Example 5 with DataPort

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

the class WorkflowHarvester method getRemainderPorts.

/**
 * @param pair
 * @return
 */
private List<DataPort> getRemainderPorts(Pair<WSNode, DataPort> pair) {
    LinkedList<DataPort> ret = new LinkedList<DataPort>();
    List<DataPort> inputPorts = pair.getLeft().getInputPorts();
    for (DataPort dataPort : inputPorts) {
        if (pair.getRight() != dataPort) {
            ret.add(dataPort);
        }
    }
    return ret;
}