/**
* @param bean
* @param progressListener
* @return
* @throws NotEnoughDiskSpaceException
* @throws FileBrokerException
* @throws JMSException
* @throws IOException
* @throws Exception
*/
public boolean uploadToCacheIfNeeded(DataBean bean, CopyProgressListener progressListener)
throws NotEnoughDiskSpaceException, FileBrokerException, JMSException, IOException,
Exception {
try {
bean.getLock().readLock().lock();
// upload only if not already available in cache or storage
if (Session.getSession()
.getServiceAccessor()
.getFileBrokerClient()
.isAvailable(bean.getId(), bean.getSize(), bean.getChecksum(), FileBrokerArea.CACHE)
|| Session.getSession()
.getServiceAccessor()
.getFileBrokerClient()
.isAvailable(
bean.getId(), bean.getSize(), bean.getChecksum(), FileBrokerArea.STORAGE)) {
return false;
}
// need to upload
return upload(bean, FileBrokerArea.CACHE, progressListener);
} finally {
bean.getLock().readLock().unlock();
}
}
private void doImportSequence() {
try {
new SequenceImportDialog(Session.getSession().getApplication());
} catch (Exception me) {
Session.getSession().getApplication().reportException(me);
}
}
private void doCreateFromText() {
try {
new CreateFromTextDialog(Session.getSession().getApplication());
} catch (Exception me) {
Session.getSession().getApplication().reportException(me);
}
}
private boolean upload(
DataBean dataBean, FileBrokerArea area, CopyProgressListener progressListener)
throws Exception {
// check if content is still available
if (dataBean.getContentLocations().size() == 0) {
return false;
}
// try to upload
try {
String checksum =
Session.getSession()
.getServiceAccessor()
.getFileBrokerClient()
.addFile(
dataBean.getId(),
area,
getContentStream(dataBean, DataNotAvailableHandling.EXCEPTION_ON_NA),
getContentLength(dataBean),
progressListener);
setOrVerifyChecksum(dataBean, checksum);
} catch (Exception e) {
logger.warn("could not upload data: " + dataBean.getName(), e);
throw e;
}
return true;
}
public void addContentLocationForDataBean(DataBean bean, StorageMethod method, URL url)
throws ContentLengthException, IOException {
ContentLocation location = new ContentLocation(method, getHandlerFor(method), url);
try {
setOrVerifyContentLength(bean, getContentLength(location));
} catch (IOException e) {
throw new IOException("content length not available: " + e);
} catch (ContentLengthException e) {
try {
DataManager manager = Session.getSession().getDataManager();
String msg;
msg =
"Wrong content length for dataset "
+ bean.getName()
+ ". "
+ " In ContentLocation "
+ location.getUrl()
+ ", length is "
+ getContentLength(location)
+ " bytes. ";
msg += "Content locations: ";
for (ContentLocation loc : manager.getContentLocationsForDataBeanSaving(bean)) {
msg += loc.getUrl() + " " + manager.getContentLength(loc) + " bytes, ";
}
throw new ContentLengthException(msg);
} catch (IOException e1) {
logger.error("another exception while handling " + Exceptions.getStackTrace(e), e);
}
}
bean.addContentLocation(location);
}
public void connectChildren(final List<? extends DataItem> children, final DataFolder parent) {
final ArrayList<AddTypeTagsCallable> callables = new ArrayList<>();
final ArrayList<DataItemCreatedEvent> events = new ArrayList<>();
// edit databeans in EDT
ThreadUtils.runInEDT(
new Runnable() {
@Override
public void run() {
for (DataItem child : children) {
// was it already connected?
boolean wasConnected = child.getParent() != null;
if (!wasConnected) {
// prepare event, but don't send it yet
events.add(new DataItemCreatedEvent(child));
}
// connect to this
child.setParent(parent);
// add
parent.children.add(child);
// prepare type tagging callables
if (child instanceof DataBean) {
callables.add(new AddTypeTagsCallable((DataBean) child));
}
}
}
});
// run type tagging in parallel in background threads
try {
// run callables and wait until all have finished
List<Future<Object>> futures = executor.invokeAll(callables);
for (Future<Object> future : futures) {
// check callable for exception, and throw if found
future.get();
}
// dispatch events in EDT
ThreadUtils.runInEDT(
new Runnable() {
@Override
public void run() {
for (DataItemCreatedEvent event : events) {
dispatchEvent(event);
}
}
});
} catch (InterruptedException | ExecutionException e) {
Session.getSession().getApplication().reportExceptionThreadSafely(e);
}
}
public boolean uploadToStorageIfNeeded(DataBean bean) throws Exception {
// check if already in storage
if (Session.getSession()
.getServiceAccessor()
.getFileBrokerClient()
.isAvailable(bean.getId(), bean.getSize(), bean.getChecksum(), FileBrokerArea.STORAGE)) {
return true;
}
// move from cache if possible
if (Session.getSession()
.getServiceAccessor()
.getFileBrokerClient()
.moveFromCacheToStorage(bean.getId())) {
return true;
}
// upload
return upload(bean, FileBrokerArea.STORAGE, null);
}
/**
* Reset import screen. This can be used while creating totally new instance of import screen or
* just resetting the default.
*
* @param setVisibleAfterReset set import screen frame visible after it has been reseted
*/
public void resetImportScreen(boolean setVisibleAfterReset) {
application = Session.getSession().getApplication();
// If frame exists, set visibility to false while resetting
if (frame != null) {
frame.setVisible(false);
}
// Create new instances of conversion model, column type manager and trimmers
conversionModel = new ConversionModel(this);
columnTypeManager = new ColumnTypeManager(0);
dataTrimmer = new DataTrimmer();
// Ignore first
dataTrimmer.addIgnoreColumnNumber(0);
flagTrimmer = new DataTrimmer();
flagTrimmer.addIgnoreColumnNumber(0);
// Table has to be first to get references right
tableFrame = new TableInternalFrame(this);
toolsFrame = new ToolsInternalFrame(this);
conversionModel.addConversionChangeListener(tableFrame);
columnTypeManager.addColumnTypeChangeListener(tableFrame);
columnTypeManager.addColumnTypeChangeListener(toolsFrame);
frame = new JFrame("Import tool");
mainSplit = new JSplitPane();
frame.setLayout(new BorderLayout());
frame.setSize(IMPORT_SCREEN_SIZE);
mainSplit.setOrientation(JSplitPane.HORIZONTAL_SPLIT);
mainSplit.setDividerLocation(TOOLS_FRAME_WIDTH);
mainSplit.setLeftComponent(toolsFrame);
mainSplit.setRightComponent(tableFrame);
mainSplit.getLeftComponent().setMinimumSize(new Dimension(150, 0));
mainSplit.setResizeWeight(0);
frame.add(mainSplit, BorderLayout.CENTER);
// Reset buttons
changeStepPanel = null;
frame.add(getChangeStepButtonsPanel(), BorderLayout.SOUTH);
if (setVisibleAfterReset) {
frame.setVisible(true);
}
}
/**
* Creates a new instance of AutomatedMovement
*
* @param projection
* @param worker
*/
public AutomatedMovement(Projection projection, Worker worker) {
this.projection = projection;
this.worker = worker;
this.taskQueue = new LinkedList<Task>();
// this.obj = new Object();
Session.getSession()
.getApplication()
.addClientEventListener(
new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent evt) {
if (evt instanceof VisualisationMethodChangedEvent) {
AutomatedMovement.this.kill();
}
}
});
}
private InputStream getBaseContentStream(DataBean bean, DataNotAvailableHandling naHandling)
throws IOException {
// try local content locations first
ContentLocation location = getClosestContentLocation(bean);
if (location != null) {
// local available TODO maybe check if it really is available
return location.getHandler().getInputStream(location);
}
// try from filebroker
Exception remoteException;
try {
return Session.getSession()
.getServiceAccessor()
.getFileBrokerClient()
.getInputStream(bean.getId());
} catch (Exception e) {
remoteException = e;
}
// not available
switch (naHandling) {
case EMPTY_ON_NA:
return new ByteArrayInputStream(new byte[] {});
case INFOTEXT_ON_NA:
return new ByteArrayInputStream(DATA_NA_INFOTEXT.getBytes());
case NULL_ON_NA:
return null;
default:
String message = "data contents not available";
if (remoteException != null) {
message += ": " + remoteException.getMessage();
}
throw new RuntimeException(message, remoteException);
}
}
/**
* Returns content size in bytes. Returns -1 if data is not available.
*
* <p>Size reported by content location is stored in DataBean in read from there when possible.
*/
public Long getContentLength(DataBean bean) {
if (bean.getSize() == null) {
try {
ContentLocation location = getClosestContentLocation(bean);
if (location != null) {
bean.setSize(getContentLength(location));
} else {
Long size =
Session.getSession()
.getServiceAccessor()
.getFileBrokerClient()
.getContentLength(bean.getId());
if (size != null) {
bean.setSize(size);
} else {
return -1l;
}
}
} catch (Exception e) {
throw new RuntimeException(e);
}
}
return bean.getSize();
}
private void createOperations() {
for (OperationType operationType : sessionType.getOperation()) {
String operationSessionId = operationType.getId();
// check for unique id
if (operationRecords.containsKey(operationSessionId)) {
logger.warn("duplicate operation id: " + operationSessionId);
continue;
}
OperationRecord operationRecord = new OperationRecord();
// name id
operationRecord.setNameID(createNameID(operationType.getName()));
// category
operationRecord.setCategoryName(operationType.getCategory());
String colorString = operationType.getCategoryColor();
if (colorString != null) {
operationRecord.setCategoryColor(Color.decode(colorString));
}
// module
operationRecord.setModule(operationType.getModule());
// parameters
for (ParameterType parameterType : operationType.getParameter()) {
operationRecord.addParameter(
parameterType.getName().getId(),
parameterType.getName().getDisplayName(),
parameterType.getName().getDescription(),
parameterType.getValue());
}
// source code
String sourceCodeFileName = operationType.getSourceCodeFile();
if (sourceCodeFileName != null && !sourceCodeFileName.isEmpty()) {
String sourceCode = null;
try {
sourceCode = getSourceCode(sourceCodeFileName);
} catch (Exception e) {
logger.warn("could not load source code from " + sourceCodeFileName);
}
// might be null, is ok
operationRecord.setSourceCode(sourceCode);
}
// update names, category from the current version of the tool
OperationDefinition currentTool;
currentTool =
Session.getSession()
.getApplication()
.getOperationDefinitionBestMatch(
operationRecord.getNameID().getID(),
operationRecord.getModule(),
operationRecord.getCategoryName());
if (currentTool != null) {
operationRecord.getNameID().setDisplayName(currentTool.getDisplayName());
operationRecord.getNameID().setDescription(currentTool.getDescription());
if (currentTool.getCategory().getModule() != null) {
operationRecord.setModule(currentTool.getCategory().getModule().getModuleName());
}
operationRecord.setCategoryName(currentTool.getCategoryName());
operationRecord.setCategoryColor(currentTool.getCategory().getColor());
for (ParameterRecord parameterRecord : operationRecord.getParameters()) {
Parameter currentParameter =
currentTool.getParameter(parameterRecord.getNameID().getID());
if (currentParameter != null) {
parameterRecord.getNameID().setDisplayName(currentParameter.getDisplayName());
parameterRecord.getNameID().setDescription(currentParameter.getDescription());
}
}
}
// store the operation record
operationRecords.put(operationSessionId, operationRecord);
operationTypes.put(operationRecord, operationType);
}
}
@Override
public void taskToDo() {
List<ImportItem> dataItems = new ArrayList<ImportItem>();
boolean hasNext = files.hasNext();
File currentFile = null;
try {
do {
// Write file to disk
conversionModel.writeToFile(informator); // Throws exceptions
// Import files to application and create the DataBeans
if (application != null) {
for (File outputFile : conversionModel.getOutputFiles()) {
ImportItem item = new ImportItem(outputFile);
item.setType(Session.getSession().getDataManager().getContentType("text/tab"));
item.setFilename(outputFile.getName());
dataItems.add(item);
}
}
// Get next file
hasNext = files.hasNext();
if (hasNext) {
currentFile = files.next();
conversionModel.setInputFile(currentFile);
}
if (hasNext) {
informator.setMessage("Writing data to disk from file " + currentFile.getName());
}
} while (hasNext && importSession.getUseSameDescriptions());
application.importGroup(dataItems, importSession.getDestinationFolder());
}
// Catch exceptions
catch (ClosedByInterruptException cbie) {
// Do nothing
} catch (Exception ex) {
if (application != null) {
application.reportException(ex);
} else {
ex.printStackTrace();
}
} finally {
// All files wrote with the same description
if (!hasNext) {
// Reset the import screen and do not show it after resetting
resetImportScreen(false);
resetImportSession();
// Initialize the first step, but do no show it
gotoFirstStep();
} else {
// Reset the import screen and show it again after resetting
resetImportScreen(true);
conversionModel.setInputFile(currentFile);
// Update table and chop the data from input file
updateTable(false);
// Initialize the first step and show it
gotoFirstStep();
}
}
}
