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

Example 1 with WSNode

use of org.apache.airavata.workflow.model.graph.ws.WSNode 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 WSNode

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

the class WorkflowHarvester method getCandidates.

/**
 * @param workflow
 * @param dataType
 * @return pair of nodeid and portid
 */
private LinkedList<Pair<String, String>> getCandidates(Workflow workflow, QName dataType) {
    LinkedList<Pair<String, String>> candidates = new LinkedList<Pair<String, String>>();
    List<NodeImpl> nodes = workflow.getGraph().getNodes();
    for (NodeImpl node : nodes) {
        if (node instanceof WSNode) {
            List<DataPort> inputPorts = ((WSNode) node).getInputPorts();
            for (DataPort dataPort : inputPorts) {
                if (dataType.equals(dataPort.getType())) {
                    candidates.add(new Pair<String, String>(node.getID(), dataPort.getID()));
                }
            }
        }
    }
    return candidates;
}

Example 3 with WSNode

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

the class WorkflowHarvester method getCandidates.

/**
 * @param workflow
 * @param dataType
 * @return pair of nodeid and portid
 */
private LinkedList<Pair<String, String>> getCandidates(Workflow workflow, QName dataType) {
    LinkedList<Pair<String, String>> candidates = new LinkedList<Pair<String, String>>();
    List<NodeImpl> nodes = workflow.getGraph().getNodes();
    for (NodeImpl node : nodes) {
        if (node instanceof WSNode) {
            List<DataPort> inputPorts = ((WSNode) node).getInputPorts();
            for (DataPort dataPort : inputPorts) {
                if (dataType.equals(dataPort.getType())) {
                    candidates.add(new Pair<String, String>(node.getID(), dataPort.getID()));
                }
            }
        }
    }
    return candidates;
}

Example 4 with WSNode

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

the class JythonScript method writeInvocation.

/**
 * @param node
 * @param thread
 * @param pw
 */
private void writeInvocation(WSNode node, boolean thread, PrintWriter pw) {
    String id = node.getID();
    String wsdlID = getWSDLID(node);
    WSComponent component = node.getComponent();
    QName portTypeQName = component.getPortTypeQName();
    String operation = component.getOperationName();
    pw.println(TAB + "# Invoke " + id + ".");
    pw.println(TAB + id + QNAME_SUFFIX + " = QName('" + portTypeQName.getNamespaceURI() + "', '" + portTypeQName.getLocalPart() + "')");
    pw.println(TAB + wsdlID + " = " + PROPERTIES_VARIABLE + "." + GET_PROPERTY_METHOD + "('" + wsdlID + "')");
    pw.println(TAB + id + INVOKER_SUFFIX + " = " + "(" + id + QNAME_SUFFIX + ", " + wsdlID + ", '" + id + "',");
    pw.println(TAB + TAB + MESSAGE_BOX_URL_VARIABLE + ", " + GFAC_VARIABLE + ", " + NOTIFICATION_VARIABLE + ")");
    pw.println(TAB + "def " + INVOKE_METHOD + id + "():");
    pw.println(TAB + TAB + id + INVOKER_SUFFIX + "." + SETUP_METHOD + "()");
    pw.println(TAB + TAB + id + INVOKER_SUFFIX + "." + SET_OPERATION_METHOD + "('" + operation + "')");
    // Ports
    for (Port port : node.getInputPorts()) {
        String portName = port.getName();
        String value;
        Node fromNode = port.getFromNode();
        if (fromNode instanceof InputNode) {
            value = PROPERTIES_VARIABLE + "." + GET_PROPERTY_METHOD + "('" + fromNode.getID() + "')";
        } else {
            Port fromPort = port.getFromPort();
            value = "" + fromNode.getID() + INVOKER_SUFFIX + "." + GET_OUTPUT_METHOD + "('" + fromPort.getName() + "')";
            // This might try to remove a node that has been removed
            // already, but it's OK.
            this.executingNodes.remove(fromNode);
        }
        pw.println(TAB + TAB + portName + VALUE_SUFFIX + " = " + value);
        pw.println(TAB + TAB + id + INVOKER_SUFFIX + "." + SET_INPUT_METHOD + "('" + portName + "', " + portName + VALUE_SUFFIX + ")");
    }
    pw.println(TAB + TAB + "print 'Invoking " + id + ".'");
    pw.println(TAB + TAB + id + INVOKER_SUFFIX + "." + INVOKE_METHOD + "()");
    if (thread) {
        pw.println(TAB + "thread.start_new_thread(" + INVOKE_METHOD + id + ", ())");
    } else {
        pw.println(TAB + INVOKE_METHOD + id + "()");
    }
    pw.println();
    this.executingNodes.add(node);
}

Example 5 with WSNode

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

the class JythonScript method writeWSDLLocations.

/**
 * @param pw
 */
private void writeWSDLLocations(PrintWriter pw) {
    pw.println("# Set up default WSDL URLs.");
    for (WSNode node : GraphUtil.getWSNodes(this.graph)) {
        writeWSDLLocation(node, pw);
    }
    pw.println();
}