Examples with WorkflowObject org.vcell.workflow.WorkflowObject used on opensource projects

Example 1 with WorkflowObject

use of org.vcell.workflow.WorkflowObject in project vcell by virtualcell.

the class WorkflowJGraphProxy method addCells.

private void addCells(mxEventObject event) {
    try {
        // remove an existing connection
        Object[] cells = (Object[]) event.getProperty("cells");
        // add tasks first
        for (Object cellObject : cells) {
            if (cellObject instanceof WorkflowObjectCell) {
                WorkflowObjectCell cell = (WorkflowObjectCell) cellObject;
                if (!cell.isEdge()) {
                    // don't know how to add an object through an event yet ...
                    WorkflowObject addedTask = cell.workflowObject;
                    if (cell.workflowObject instanceof Task) {
                        Task task = (Task) cell.workflowObject;
                        task.setName(context.getWorkflow().getNextAvailableTaskName(task.getName()));
                        context.getWorkflow().addTask((Task) cell.workflowObject);
                        cell.setId(cell.workflowObject.getName());
                        cell.setGraph(graph);
                    } else {
                        // not a task, not an edge, and not already added ... can't handle this now
                        System.err.println("can't handle this now ... non-edge cell (id=" + cell.getId() + ") added to jGraphX but not already added to workflow");
                    }
                }
            }
        }
        // add edges next
        for (Object cellObject : cells) {
            if (cellObject instanceof mxCell) {
                mxCell cell = (mxCell) cellObject;
                if (cell.isEdge()) {
                    mxICell source = cell.getSource();
                    mxICell target = cell.getTarget();
                    if ((source instanceof WorkflowObjectCell) && (target instanceof WorkflowObjectCell)) {
                        String validationError = validateConnection(source, target);
                        if (validationError == null) {
                            WorkflowObject workflowSourceObject = ((WorkflowObjectCell) source).workflowObject;
                            WorkflowObject workflowTargetObject = ((WorkflowObjectCell) target).workflowObject;
                            if (workflowSourceObject instanceof DataOutput && workflowTargetObject instanceof DataInput) {
                                DataInput input = (DataInput) workflowTargetObject;
                                if (context.getWorkflow().getConnectorSource(input) != null) {
                                    System.out.println("don't add this connection, a connection already exists");
                                } else {
                                    DataOutput output = (DataOutput) workflowSourceObject;
                                    context.getWorkflow().connect2(output, input);
                                    System.out.println("added edge from " + workflowSourceObject.getPath() + " to " + workflowTargetObject.getPath());
                                }
                            }
                        } else {
                            System.out.println("didn't connect, " + validationError);
                        }
                    }
                }
            }
        }
    } finally {
        context.getWorkflow().refreshStatus();
    }
}

Example 2 with WorkflowObject

use of org.vcell.workflow.WorkflowObject in project vcell by virtualcell.

the class WorkflowJGraphProxy method validateConnection.

private String validateConnection(mxICell source, mxICell target) {
    try {
        if (!(source instanceof WorkflowObjectCell) || !(target instanceof WorkflowObjectCell)) {
            return "source or target is null";
        }
        WorkflowObject workflowSourceObject = ((WorkflowObjectCell) source).workflowObject;
        WorkflowObject workflowTargetObject = ((WorkflowObjectCell) target).workflowObject;
        if (workflowSourceObject instanceof DataOutput && workflowTargetObject instanceof DataInput) {
            DataInput input = (DataInput) workflowTargetObject;
            Type inputClass = input.getType();
            if (context.getWorkflow().getConnectorSource(input) != null) {
                return "don't add this connection, a connection already exists";
            } else {
                DataOutput output = (DataOutput) workflowSourceObject;
                Type outputClass = output.getType();
                if (outputClass.getClass().isAssignableFrom(inputClass.getClass())) {
                    return null;
                } else {
                    return "can't connect " + workflowSourceObject.getPath() + " of type " + outputClass + "\n to " + workflowTargetObject.getPath() + " of type " + inputClass;
                }
            }
        } else {
            return "unknown source or desintation type";
        }
    } catch (Exception e) {
        e.printStackTrace();
        return "error validating edge: exception: " + e.getMessage();
    } finally {
        context.getWorkflow().refreshStatus();
    }
}

Example 3 with WorkflowObject

use of org.vcell.workflow.WorkflowObject in project vcell by virtualcell.

the class WorkflowObjectsPanel method hasDisplayData.

private boolean hasDisplayData(TaskContext taskContext, WorkflowObject workflowObject) {
    if (workflowObject instanceof DataInput || workflowObject instanceof DataOutput) {
        String title = parametersFunctionsTableModel.getName(workflowObject);
        WindowListener listener = new WindowAdapter() {
        };
        Object data = null;
        if (workflowObject instanceof WorkflowDataSource) {
            WorkflowDataSource dataHolder = (WorkflowDataSource) workflowObject;
            data = taskContext.getRepository().getData(dataHolder);
        } else if (workflowObject instanceof DataInput) {
            DataInput dataInput = (DataInput) workflowObject;
            data = taskContext.getData(dataInput);
        }
        if (data instanceof RowColumnResultSet || data instanceof ROI || data instanceof ProfileData[] || data instanceof Image || data instanceof ImageTimeSeries) {
            return true;
        }
    }
    return false;
}

Example 4 with WorkflowObject

use of org.vcell.workflow.WorkflowObject in project vcell by virtualcell.

the class WorkflowObjectsPanel method displayData.

private void displayData(TaskContext taskContext, WorkflowObject workflowObject) {
    if (workflowObject instanceof DataInput || workflowObject instanceof DataOutput) {
        String title = parametersFunctionsTableModel.getName(workflowObject);
        WindowListener listener = new WindowAdapter() {
        };
        Object data = null;
        if (workflowObject instanceof WorkflowDataSource) {
            WorkflowDataSource dataHolder = (WorkflowDataSource) workflowObject;
            data = taskContext.getRepository().getData(dataHolder);
        } else if (workflowObject instanceof DataInput) {
            DataInput dataInput = (DataInput) workflowObject;
            data = taskContext.getData(dataInput);
        }
        if (data instanceof RowColumnResultSet) {
            RowColumnResultSet rc = (RowColumnResultSet) data;
            try {
                new DisplayPlotOp().displayPlot(rc, title, listener);
            } catch (ExpressionException e) {
                e.printStackTrace();
            }
        } else if (data instanceof ROI) {
            ROI roi = (ROI) data;
            Image image = roi.getRoiImages()[0];
            new DisplayImageOp().displayImage(image, title, listener);
        } else if (data instanceof ProfileData[]) {
            ProfileData[] profileData = (ProfileData[]) data;
            new DisplayProfileLikelihoodPlotsOp().displayProfileLikelihoodPlots(profileData, title, listener);
        } else if (data instanceof Image) {
            Image image = (Image) data;
            new DisplayImageOp().displayImage(image, title, listener);
        } else if (data instanceof ImageTimeSeries) {
            ImageTimeSeries imageTimeSeries = (ImageTimeSeries) data;
            try {
                DisplayTimeSeries.displayImageTimeSeries(imageTimeSeries, title, listener);
            } catch (ImageException | IOException e) {
                e.printStackTrace();
            }
        }
    }
}

Example 5 with WorkflowObject

use of org.vcell.workflow.WorkflowObject in project vcell by virtualcell.

the class WorkflowObjectsTableModel method computeData.

/**
 * Insert the method's description here.
 * Creation date: (9/23/2003 1:24:52 PM)
 * @return cbit.vcell.model.Parameter
 * @param row int
 */
protected List<WorkflowObject> computeData() {
    ArrayList<WorkflowObject> allWorkflowObjectList = new ArrayList<WorkflowObject>();
    if (taskContext == null) {
        return null;
    }
    Workflow workflow = taskContext.getWorkflow();
    if (bTasks) {
        allWorkflowObjectList.addAll(workflow.getTasks());
    }
    if (bParameters) {
        allWorkflowObjectList.addAll(workflow.getParameters());
    }
    if (bTaskInputs) {
        for (Task task : workflow.getTasks()) {
            allWorkflowObjectList.addAll(task.getInputs());
        }
    }
    if (bTaskOutputs) {
        for (Task task : workflow.getTasks()) {
            allWorkflowObjectList.addAll(task.getOutputs());
        }
    }
    boolean bSearchInactive = searchText == null || searchText.length() == 0;
    String lowerCaseSearchText = bSearchInactive ? null : searchText.toLowerCase();
    ArrayList<WorkflowObject> workflowObjectList = new ArrayList<WorkflowObject>();
    for (WorkflowObject workflowObject : allWorkflowObjectList) {
        if (bSearchInactive || getValue(workflowObject).toLowerCase().contains(lowerCaseSearchText) || getName(workflowObject).toLowerCase().contains(lowerCaseSearchText) || getType(workflowObject).toLowerCase().contains(lowerCaseSearchText) || getStatus(taskContext, workflowObject).toLowerCase().contains(lowerCaseSearchText)) {
            workflowObjectList.add(workflowObject);
        }
    }
    return workflowObjectList;
}