Examples with Workflow org.apache.airavata.workflow.model.wf.Workflow used on opensource projects

Example 1 with Workflow

use of org.apache.airavata.workflow.model.wf.Workflow 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 Workflow

use of org.apache.airavata.workflow.model.wf.Workflow in project airavata by apache.

the class WorkflowEngineImpl method launchExperiment.

@Override
public void launchExperiment(String experimentId, String token) throws WorkflowEngineException {
    try {
        ExperimentCatalog experimentCatalog = RegistryFactory.getDefaultExpCatalog();
        Experiment experiment = (Experiment) experimentCatalog.get(ExperimentCatalogModelType.EXPERIMENT, experimentId);
        WorkflowCatalog workflowCatalog = WorkflowCatalogFactory.getWorkflowCatalog();
        WorkflowInterpreterConfiguration config = new WorkflowInterpreterConfiguration(new Workflow(workflowCatalog.getWorkflow(experiment.getApplicationId()).getGraph()));
        final WorkflowInterpreter workflowInterpreter = new WorkflowInterpreter(experiment, token, config, getOrchestratorClient(), rabbitMQPublisher);
        new Thread() {

            public void run() {
                try {
                    workflowInterpreter.scheduleDynamically();
                } catch (WorkflowException e) {
                    logger.error(e.getMessage(), e);
                } catch (RegistryException e) {
                    logger.error(e.getMessage(), e);
                } catch (AiravataException e) {
                    logger.error(e.getMessage(), e);
                }
            }
        }.start();
    } catch (Exception e) {
        logger.error("Error while retrieving the experiment", e);
        WorkflowEngineException exception = new WorkflowEngineException("Error while launching the workflow experiment. More info : " + e.getMessage());
        throw exception;
    }
}

Example 3 with Workflow

use of org.apache.airavata.workflow.model.wf.Workflow in project airavata by apache.

the class ODEScriptFiler method save.

/**
 */
public void save() {
    Workflow wf = this.engine.getGUI().getWorkflow();
    if (0 == wf.getGraph().getNodes().size()) {
        this.engine.getGUI().getErrorWindow().warning("Workflow is Empty");
        return;
    }
    GpelProcess process;
    try {
        int returnVal = this.bpelFileChooser.showSaveDialog(this.engine.getGUI().getFrame());
        if (returnVal == JFileChooser.APPROVE_OPTION) {
            File file = this.bpelFileChooser.getSelectedFile();
            String path = file.getPath();
            // Remove ".bpel" at the end if any
            if (path.endsWith(XBayaConstants.BPEL_SUFFIX)) {
                path = path.substring(0, path.length() - XBayaConstants.BPEL_SUFFIX.length());
            }
            // Add ".bpel" at the end of the file name
            File bpelFile = new File(path + XBayaConstants.BPEL_SUFFIX);
            // Add ".wsdl" at the end of the file name
            File wsdlFile = new File(path + XBayaConstants.WSDL_SUFFIX);
            // todo this has to fix, for compilation purpose passing dummy value instead of xregistry url
            URI temp = null;
            try {
                temp = new URI("temp");
            } catch (URISyntaxException e) {
                log.error(e.getMessage(), e);
            }
        // process = wf.getOdeProcess(WSDLUtil.appendWSDLQuary(temp), this.engine.getConfiguration().getODEURL());
        // String processString = process.xmlStringPretty();
        // FileWriter writer = new FileWriter(bpelFile);
        // writer.write(processString);
        // writer.close();
        // 
        // WsdlDefinitions workflowWSDL = wf.getOdeWorkflowWSDL(this.engine.getConfiguration().getDSCURL(),
        // this.engine.getConfiguration().getODEURL());
        // String workflowWsdlStr = XmlConstants.BUILDER.serializeToStringPretty(workflowWSDL.xml());
        // writer = new FileWriter(wsdlFile);
        // writer.write(workflowWsdlStr);
        // 
        // Map<String, WsdlDefinitions> wsdlMap = wf.getOdeServiceWSDLs(
        // this.engine.getConfiguration().getDSCURL(), this.engine.getConfiguration().getODEURL());
        // Set<String> keySet = wsdlMap.keySet();
        // for (String string : keySet) {
        // writer = new FileWriter(new File(wsdlFile.getParent(), QName.valueOf(string).getLocalPart()));
        // writer.write(XmlConstants.BUILDER.serializeToStringPretty(wsdlMap.get(string).xml()));
        // writer.close();
        // }
        // 
        // XmlElement deployDescriptor = wf.getODEDeploymentDescriptor(this.engine.getConfiguration().getDSCURL(),
        // this.engine.getConfiguration().getODEURL());
        // writer = new FileWriter(new File(wsdlFile.getParent(), "deploy.xml"));
        // writer.write(XmlConstants.BUILDER.serializeToString(deployDescriptor));
        // writer.close();
        // 
        }
    // 
    // } catch (IOException e) {
    // this.engine.getGUI().getErrorWindow().error(ErrorMessages.WRITE_FILE_ERROR, e);
    // } catch (GraphException e) {
    // this.engine.getGUI().getErrorWindow().error(ErrorMessages.GRAPH_FORMAT_ERROR, e);
    } catch (RuntimeException e) {
        this.engine.getGUI().getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e);
    } catch (Error e) {
        this.engine.getGUI().getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e);
    // } catch (ComponentException e) {
    // this.engine.getGUI().getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e);
    }
}

Example 4 with Workflow

use of org.apache.airavata.workflow.model.wf.Workflow in project airavata by apache.

the class WorkflowFiler method getWorkflow.

/**
 * @param workflow
 * @return
 */
public Workflow getWorkflow() {
    Workflow workflow = null;
    int returnVal = this.graphFileChooser.showOpenDialog(this.engine.getGUI().getFrame());
    if (returnVal == JFileChooser.APPROVE_OPTION) {
        File file = this.graphFileChooser.getSelectedFile();
        logger.debug(file.getPath());
        try {
            String path = file.getPath();
            if (path.endsWith(XBayaConstants.GRAPH_FILE_SUFFIX)) {
                WSGraph graph = WSGraphFactory.createGraph(file);
                workflow = Workflow.graphToWorkflow(graph);
            } else {
                XmlElement workflowElement = XMLUtil.loadXML(file);
                workflow = new Workflow(workflowElement);
            }
        } catch (IOException e) {
            this.engine.getGUI().getErrorWindow().error(ErrorMessages.OPEN_FILE_ERROR, e);
        } catch (GraphException e) {
            this.engine.getGUI().getErrorWindow().error(ErrorMessages.GRAPH_FORMAT_ERROR, e);
        } catch (ComponentException e) {
            this.engine.getGUI().getErrorWindow().error(ErrorMessages.GRAPH_FORMAT_ERROR, e);
        } catch (RuntimeException e) {
            this.engine.getGUI().getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e);
        } catch (Error e) {
            this.engine.getGUI().getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e);
        }
    }
    return workflow;
}

Example 5 with Workflow

use of org.apache.airavata.workflow.model.wf.Workflow in project airavata by apache.

the class WorkflowFiler method importWorkflow.

/**
 * Imports a workflow from the local file to the current workflow.
 */
public void importWorkflow() {
    int returnVal = this.graphFileChooser.showOpenDialog(this.engine.getGUI().getFrame());
    if (returnVal == JFileChooser.APPROVE_OPTION) {
        File file = this.graphFileChooser.getSelectedFile();
        try {
            String path = file.getPath();
            Workflow importedWorkflow;
            if (path.endsWith(XBayaConstants.GRAPH_FILE_SUFFIX)) {
                WSGraph importedGraph = WSGraphFactory.createGraph(file);
                importedWorkflow = Workflow.graphToWorkflow(importedGraph);
            } else {
                XmlElement importedWorkflowElement = XMLUtil.loadXML(file);
                importedWorkflow = new Workflow(importedWorkflowElement);
            }
            GraphCanvas newGraphCanvas = engine.getGUI().newGraphCanvas(true);
            newGraphCanvas.setWorkflow(importedWorkflow);
            this.engine.getGUI().setWorkflow(importedWorkflow);
            engine.getGUI().getGraphCanvas().setWorkflowFile(file);
        } catch (IOException e) {
            this.engine.getGUI().getErrorWindow().error(ErrorMessages.OPEN_FILE_ERROR, e);
        } catch (GraphException e) {
            this.engine.getGUI().getErrorWindow().error(ErrorMessages.GRAPH_FORMAT_ERROR, e);
        } catch (ComponentException e) {
            this.engine.getGUI().getErrorWindow().error(ErrorMessages.GRAPH_FORMAT_ERROR, e);
        } catch (RuntimeException e) {
            this.engine.getGUI().getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e);
        } catch (Error e) {
            this.engine.getGUI().getErrorWindow().error(ErrorMessages.UNEXPECTED_ERROR, e);
        }
    }
}