List of usage examples for java.lang InterruptedException InterruptedException
public InterruptedException()
InterruptedException with no detail message. From source file:edu.mit.mobile.android.locast.sync.SyncEngine.java
/** * Uploads any unpublished casts./*w ww .ja v a 2 s . c om*/ * * This is the method that does all the hard work. * * @param toSync * @param provider * @param syncMap * @param syncResult * @return the number of casts uploaded. * @throws JSONException * @throws NetworkProtocolException * @throws IOException * @throws NoPublicPath * @throws RemoteException * @throws OperationApplicationException * @throws SyncException * @throws InterruptedException */ private int uploadUnpublished(Uri toSync, Account account, ContentProviderClient provider, SyncMap syncMap, HashMap<String, SyncEngine.SyncStatus> syncStatuses, SyncResult syncResult) throws JSONException, NetworkProtocolException, IOException, NoPublicPath, RemoteException, OperationApplicationException, SyncException, InterruptedException { int count = 0; final String type = provider.getType(toSync); final boolean isDir = type.startsWith(CONTENT_TYPE_PREFIX_DIR); final Cursor uploadMe = provider.query(toSync, null, SELECTION_UNPUBLISHED, null, null); if (uploadMe == null) { throw new SyncException("could not query " + toSync); } final int idCol = uploadMe.getColumnIndex(JsonSyncableItem._ID); try { for (uploadMe.moveToFirst(); !uploadMe.isAfterLast(); uploadMe.moveToNext()) { if (Thread.interrupted()) { throw new InterruptedException(); } final long id = uploadMe.getLong(idCol); final Uri localUri = isDir ? ContentUris.withAppendedId(toSync, id) : toSync; final String postUri = MediaProvider.getPostPath(mContext, localUri); Intent intent = new Intent(SYNC_STATUS_CHANGED); intent.putExtra(EXTRA_SYNC_STATUS, "castBegin"); intent.putExtra(EXTRA_SYNC_ID, id); mContext.sendStickyBroadcast(intent); try { final JSONObject jo = JsonSyncableItem.toJSON(mContext, localUri, uploadMe, syncMap); if (DEBUG) { Log.d(TAG, "uploading " + localUri + " to " + postUri); } // Upload! Any non-successful responses are handled by // exceptions. final HttpResponse res = mNetworkClient.post(postUri, jo.toString()); long serverTime; try { serverTime = getServerTime(res); // We should never get a corrupted date from the server, // but if it does happen, // using the local time is a sane fallback. } catch (final DateParseException e) { serverTime = System.currentTimeMillis(); } // newly-created items return the JSON serialization of the // object as the server // knows it, so the local database needs to be updated to // reflect that. final JSONObject newJo = NetworkClient.toJsonObject(res); try { final SyncStatus ss = loadItemFromJsonObject(newJo, syncMap, serverTime); // update immediately, so that any cancellation or // interruption of the sync // keeps the local state in sync with what's on the // server final int updates = provider.update(localUri, ss.remoteCVs, null, null); final String locUriString = localUri.toString(); if (updates == 1) { ss.state = SyncState.NOW_UP_TO_DATE; ss.local = localUri; // ensure that it's findable by local URI too syncStatuses.put(locUriString, ss); syncMap.onPostSyncItem(mContext, account, ss.local, ss.remoteJson, true); count++; syncResult.stats.numUpdates++; } else { Log.e(TAG, "error updating " + locUriString); syncResult.stats.numSkippedEntries++; } syncResult.stats.numEntries++; } catch (final JSONException e) { if (DEBUG) { Log.e(TAG, "result was " + newJo.toString()); } throw e; } } finally { intent = new Intent(SYNC_STATUS_CHANGED); intent.putExtra(EXTRA_SYNC_STATUS, "castEnd"); intent.putExtra(EXTRA_SYNC_ID, id); mContext.sendStickyBroadcast(intent); } } } finally { uploadMe.close(); } return count; }
From source file:org.micromanager.plugins.magellan.imagedisplay.DisplayOverlayer.java
private void addSurfaceInterpolation(Overlay overlay, SingleResolutionInterpolation interp, int displayPixPerInterpTile) throws InterruptedException { int width = display_.getImagePlus().getWidth(); int height = display_.getImagePlus().getHeight(); ZoomableVirtualStack zStack = (ZoomableVirtualStack) display_.virtualStack_; double sliceZ = zStack.getZCoordinateOfDisplayedSlice(display_.getVisibleSliceIndex()); double zStep = acq_.getZStep(); //Make numTestPoints a factor of image size for clean display of surface int numTestPointsX = width / displayPixPerInterpTile; int numTestPointsY = height / displayPixPerInterpTile; double roiWidth = width / (double) numTestPointsX; double roiHeight = height / (double) numTestPointsY; for (int x = 0; x < numTestPointsX; x++) { for (int y = 0; y < numTestPointsY; y++) { if (Thread.interrupted()) { throw new InterruptedException(); }//w w w. j ava 2 s . c o m Point2D.Double stageCoord = display_.stageCoordFromImageCoords((int) ((x + 0.5) * roiWidth), (int) ((y + 0.5) * roiHeight)); if (!interp.isInterpDefined(stageCoord.x, stageCoord.y)) { continue; } float interpZ = interp.getInterpolatedValue(stageCoord.x, stageCoord.y); if (Math.abs(sliceZ - interpZ) < zStep / 2) { double roiX = roiWidth * x; double roiY = roiHeight * y; //calculate distance from last ROI for uninterrupted coverage of image int displayWidth = (int) (roiWidth * (x + 1)) - (int) (roiX); int displayHeight = (int) (roiHeight * (y + 1)) - (int) (roiY); Roi rect = new Roi(roiX, roiY, displayWidth, displayHeight); //make ROI int[] lutRed = VIRIDIS_RED; int[] lutBlue = VIRIDIS_BLUE; int[] lutGreen = VIRIDIS_GREEN; double colorScale = ((sliceZ - interpZ) / (zStep / 2) + 1) / 2; //between 0 and 1 rect.setFillColor(new Color(lutRed[(int) (colorScale * lutRed.length)], lutGreen[(int) (colorScale * lutGreen.length)], lutBlue[(int) (colorScale * lutBlue.length)], 175)); overlay.add(rect); } } } }
From source file:com.cloudbees.jenkins.plugins.bitbucket.client.BitbucketCloudApiClient.java
private CloseableHttpResponse executeMethod(HttpRequestBase httpMethod) throws InterruptedException, IOException { if (authenticator != null) { authenticator.configureRequest(httpMethod); }/*from w ww . j a v a 2 s . c o m*/ RequestConfig.Builder requestConfig = RequestConfig.custom(); requestConfig.setConnectTimeout(10 * 1000); requestConfig.setConnectionRequestTimeout(60 * 1000); requestConfig.setSocketTimeout(60 * 1000); httpMethod.setConfig(requestConfig.build()); CloseableHttpResponse response = client.execute(API_HOST, httpMethod, context); while (response.getStatusLine().getStatusCode() == API_RATE_LIMIT_CODE) { release(httpMethod); if (Thread.interrupted()) { throw new InterruptedException(); } /* TODO: When bitbucket starts supporting rate limit expiration time, remove 5 sec wait and put code to wait till expiration time is over. It should also fix the wait for ever loop. */ LOGGER.fine("Bitbucket Cloud API rate limit reached, sleeping for 5 sec then retry..."); Thread.sleep(5000); response = client.execute(API_HOST, httpMethod, context); } return response; }
From source file:org.micromanager.plugins.magellan.surfacesandregions.SurfaceInterpolator.java
private synchronized void updateConvexHullAndInterpolate() { //duplicate points for use on caluclation thread final LinkedList<Point3d> points = new LinkedList<Point3d>(points_); if (currentInterpolationTask_ != null && !currentInterpolationTask_.isDone()) { //cancel current interpolation because interpolation points have changed, call does not block currentInterpolationTask_.cancel(true); }// w ww. ja va 2s.co m //don't want one of the get methods returning a null object thinking it has a value synchronized (convexHullLock_) { convexHullVertices_ = null; convexHullRegion_ = null; } synchronized (interpolationLock_) { currentInterpolation_ = null; } synchronized (xyPositionLock_) { xyPositions_ = null; } numRows_ = 0; numCols_ = 0; currentInterpolationTask_ = executor_.submit(new Runnable() { @Override public void run() { if (points.size() > 2) { try { //convert xyPoints to a vector2d for convex hull calculation LinkedList<Vector2D> xyPoints = new LinkedList<Vector2D>(); for (Point3d p : points) { xyPoints.add(new Vector2D(p.x, p.y)); } ConvexHull2D hull = null; hull = mChain_.generate(xyPoints); if (Thread.interrupted()) { throw new InterruptedException(); } synchronized (convexHullLock_) { convexHullVertices_ = hull.getVertices(); convexHullLock_.notifyAll(); } if (Thread.interrupted()) { throw new InterruptedException(); } convexHullRegion_ = hull.createRegion(); if (Thread.interrupted()) { throw new InterruptedException(); } calculateConvexHullBounds(); if (Thread.interrupted()) { throw new InterruptedException(); } //use the most recently set overlap value for display purposes. When it comes time to calc the real thing, //get it from the acquisition settings fitXYPositionsToConvexHull(FixedAreaAcquisitionSettings.getStoredTileOverlapPercentage()); //Interpolate surface as specified by the subclass method interpolateSurface(points); //let manager handle event firing to acquisitions using surface manager_.surfaceUpdated(SurfaceInterpolator.this); } catch (InterruptedException e) { return; } } } }); }
From source file:de.blizzy.backup.restore.RestoreDialog.java
private void restoreEntry(Entry entry, File parentFolder, String outputFolder, int backupId, IProgressMonitor monitor, Shell shell) throws IOException, InterruptedException { if (monitor.isCanceled()) { throw new InterruptedException(); }//from w w w. j a va 2 s. com boolean isFolder = entry.type == EntryType.FOLDER; if (entry.type == EntryType.FAILED_FILE) { if (alwaysRestoreFromOlderBackups == null) { alwaysRestoreFromOlderBackups = Boolean.valueOf(promptRestoreFromOlderBackups(shell)); } if (alwaysRestoreFromOlderBackups.booleanValue()) { entry = findInOlderBackups(entry); } } if ((entry != null) && (entry.type != EntryType.FAILED_FILE)) { Path outputPath; if (entry.type == EntryType.FOLDER) { File newFolder = new File(parentFolder, escapeFileName(entry.name)); FileUtils.forceMkdir(newFolder); Cursor<Record> cursor = getEntriesCursor(backupId, entry.id, null, -1); try { for (Entry e : getEntries(cursor, false)) { restoreEntry(e, newFolder, outputFolder, backupId, monitor, shell); } } finally { database.closeQuietly(cursor); } outputPath = newFolder.toPath(); } else { File inputFile = Utils.toBackupFile(entry.backupPath, outputFolder); File outputFile = new File(parentFolder, escapeFileName(entry.name)); outputPath = outputFile.toPath(); InputStream in = null; try { InputStream fileIn = new BufferedInputStream(new FileInputStream(inputFile)); InputStream interceptIn = fileIn; for (IStorageInterceptor interceptor : storageInterceptors) { interceptIn = interceptor.interceptInputStream(interceptIn, entry.length); } InputStream compressIn = entry.compression.getInputStream(interceptIn); in = compressIn; Files.copy(in, outputPath); } finally { IOUtils.closeQuietly(in); } } FileAttributes fileAttributes = FileAttributes.get(outputPath); if (entry.hidden) { fileAttributes.setHidden(entry.hidden); } FileTime createTime = (entry.creationTime != null) ? FileTime.fromMillis(entry.creationTime.getTime()) : null; FileTime modTime = (entry.modificationTime != null) ? FileTime.fromMillis(entry.modificationTime.getTime()) : null; fileAttributes.setTimes(createTime, modTime); } if (!isFolder) { monitor.worked(1); } }
From source file:canreg.client.dataentry.Import.java
public static boolean importFiles(Task<Object, Void> task, Document doc, List<canreg.client.dataentry.Relation> map, File[] files, CanRegServerInterface server, ImportOptions io) throws SQLException, RemoteException, SecurityException, RecordLockedException { int numberOfLinesRead = 0; Writer reportWriter = new BufferedWriter(new OutputStreamWriter(System.out)); if (io.getReportFileName() != null && io.getReportFileName().trim().length() > 0) { try {/*from w w w. j ava 2 s. c om*/ reportWriter = new BufferedWriter(new FileWriter(io.getReportFileName())); } catch (IOException ex) { Logger.getLogger(Import.class.getName()).log(Level.WARNING, null, ex); } } boolean success = false; Set<String> noNeedToLookAtPatientVariables = new TreeSet<String>(); noNeedToLookAtPatientVariables .add(canreg.common.Tools.toLowerCaseStandardized(io.getPatientIDVariableName())); noNeedToLookAtPatientVariables .add(canreg.common.Tools.toLowerCaseStandardized(io.getPatientRecordIDVariableName())); String[] lineElements; ResultCode worstResultCodeFound; // CSVReader reader = null; CSVParser parser = null; CSVFormat format = CSVFormat.DEFAULT.withFirstRecordAsHeader().withDelimiter(io.getSeparators()[0]); int linesToRead = io.getMaxLines(); try { // first we get the patients if (task != null) { task.firePropertyChange(PROGRESS, 0, 0); task.firePropertyChange(PATIENTS, 0, 0); } if (files[0] != null) { reportWriter .write("Starting to import patients from " + files[0].getAbsolutePath() + Globals.newline); FileInputStream patientFIS = new FileInputStream(files[0]); InputStreamReader patientISR = new InputStreamReader(patientFIS, io.getFileCharsets()[0]); Logger.getLogger(Import.class.getName()).log(Level.CONFIG, "Name of the character encoding {0}", patientISR.getEncoding()); int numberOfRecordsInFile = canreg.common.Tools.numberOfLinesInFile(files[0].getAbsolutePath()); numberOfLinesRead = 0; if (linesToRead > 0) { linesToRead = Math.min(numberOfRecordsInFile, linesToRead); } else { linesToRead = numberOfRecordsInFile; } parser = CSVParser.parse(files[0], io.getFileCharsets()[0], format); for (CSVRecord csvRecord : parser) { // We allow for null tasks... boolean savePatient = true; boolean deletePatient = false; int oldPatientDatabaseRecordID = -1; if (task != null) { task.firePropertyChange(PROGRESS, ((numberOfLinesRead - 1) * 100 / linesToRead) / 3, ((numberOfLinesRead) * 100 / linesToRead) / 3); task.firePropertyChange(PATIENTS, ((numberOfLinesRead - 1) * 100 / linesToRead), ((numberOfLinesRead) * 100 / linesToRead)); } // Build patient part Patient patient = new Patient(); for (int i = 0; i < map.size(); i++) { Relation rel = map.get(i); if (rel.getDatabaseTableVariableID() >= 0 && rel.getDatabaseTableName().equalsIgnoreCase("patient")) { if (rel.getVariableType().equalsIgnoreCase("Number")) { if (csvRecord.get(rel.getFileColumnNumber()).length() > 0) { try { patient.setVariable(rel.getDatabaseVariableName(), Integer.parseInt(csvRecord.get(rel.getFileColumnNumber()))); } catch (NumberFormatException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "Number format error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } } } else { patient.setVariable(rel.getDatabaseVariableName(), csvRecord.get(rel.getFileColumnNumber())); } } if (task != null) { task.firePropertyChange(RECORD, i - 1 / map.size() * 50, i / map.size() * 50); } } // debugOut(patient.toString()); // debugOut(tumour.toString()); // add patient to the database Object patientID = patient.getVariable(io.getPatientRecordIDVariableName()); Patient oldPatientRecord = null; try { oldPatientRecord = CanRegClientApp.getApplication().getPatientRecord((String) patientID, false); } catch (DistributedTableDescriptionException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (RecordLockedException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (RemoteException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (SQLException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (SecurityException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (UnknownTableException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } if (oldPatientRecord != null) { // deal with discrepancies switch (io.getDiscrepancies()) { case ImportOptions.REJECT: savePatient = false; break; case ImportOptions.UPDATE: String updateReport = updateRecord(oldPatientRecord, patient); if (updateReport.length() > 0) { reportWriter.write(patient.getVariable(io.getTumourIDVariablename()) + Globals.newline + updateReport); } oldPatientDatabaseRecordID = (Integer) oldPatientRecord .getVariable(Globals.PATIENT_TABLE_RECORD_ID_VARIABLE_NAME); patient = oldPatientRecord; savePatient = true; break; case ImportOptions.OVERWRITE: // deleteTumour; oldPatientDatabaseRecordID = (Integer) oldPatientRecord .getVariable(Globals.PATIENT_TABLE_RECORD_ID_VARIABLE_NAME); String overWriteReport = overwriteRecord(oldPatientRecord, patient); if (overWriteReport.length() > 0) { reportWriter.write(patient.getVariable(io.getTumourIDVariablename()) + Globals.newline + overWriteReport); } patient = oldPatientRecord; savePatient = true; break; } // reportWriter.write(tumour.getVariable(io.getTumourIDVariablename()) + "Tumour already exists.\n"); } if (task != null) { task.firePropertyChange(RECORD, 50, 75); } if ((!io.isTestOnly())) { if (deletePatient) { server.deleteRecord(oldPatientDatabaseRecordID, Globals.PATIENT_TABLE_NAME); } if (savePatient) { if (patient.getVariable(Globals.PATIENT_TABLE_RECORD_ID_VARIABLE_NAME) != null) { server.editPatient(patient); } else { server.savePatient(patient); } } } if (task != null) { task.firePropertyChange(RECORD, 100, 75); } numberOfLinesRead++; if (Thread.interrupted()) { //We've been interrupted: no more importing. reportWriter.flush(); throw new InterruptedException(); } } parser.close(); reportWriter.write("Finished reading patients." + Globals.newline + Globals.newline); reportWriter.flush(); } if (task != null) { task.firePropertyChange(PATIENTS, 100, 100); task.firePropertyChange("progress", 33, 34); } // then we get the tumours if (task != null) { task.firePropertyChange(TUMOURS, 0, 0); } if (files[1] != null) { reportWriter .write("Starting to import tumours from " + files[1].getAbsolutePath() + Globals.newline); FileInputStream tumourFIS = new FileInputStream(files[1]); InputStreamReader tumourISR = new InputStreamReader(tumourFIS, io.getFileCharsets()[1]); Logger.getLogger(Import.class.getName()).log(Level.CONFIG, "Name of the character encoding {0}", tumourISR.getEncoding()); numberOfLinesRead = 0; int numberOfRecordsInFile = canreg.common.Tools.numberOfLinesInFile(files[1].getAbsolutePath()); if (linesToRead > 0) { linesToRead = Math.min(numberOfRecordsInFile, linesToRead); } else { linesToRead = numberOfRecordsInFile; } format = CSVFormat.DEFAULT.withFirstRecordAsHeader().withDelimiter(io.getSeparators()[1]); parser = CSVParser.parse(files[1], io.getFileCharsets()[1], format); for (CSVRecord csvRecord : parser) { // We allow for null tasks... boolean saveTumour = true; boolean deleteTumour = false; if (task != null) { task.firePropertyChange(PROGRESS, 33 + ((numberOfLinesRead - 1) * 100 / linesToRead) / 3, 33 + ((numberOfLinesRead) * 100 / linesToRead) / 3); task.firePropertyChange(TUMOURS, ((numberOfLinesRead - 1) * 100 / linesToRead), ((numberOfLinesRead) * 100 / linesToRead)); } // Build tumour part Tumour tumour = new Tumour(); for (int i = 0; i < map.size(); i++) { Relation rel = map.get(i); if (rel.getDatabaseTableVariableID() >= 0 && rel.getDatabaseTableName().equalsIgnoreCase("tumour")) { if (rel.getVariableType().equalsIgnoreCase("Number")) { if (csvRecord.get(rel.getFileColumnNumber()).length() > 0) { try { tumour.setVariable(rel.getDatabaseVariableName(), Integer.parseInt(csvRecord.get(rel.getFileColumnNumber()))); } catch (NumberFormatException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "Number format error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } } } else { tumour.setVariable(rel.getDatabaseVariableName(), csvRecord.get(rel.getFileColumnNumber())); } } if (task != null) { task.firePropertyChange(RECORD, i - 1 / map.size() * 50, i / map.size() * 50); } } // see if this tumour exists in the database already // TODO: Implement this using arrays and getTumourRexords instead Tumour tumour2 = null; try { tumour2 = CanRegClientApp.getApplication().getTumourRecordBasedOnTumourID( (String) tumour.getVariable(io.getTumourIDVariablename()), false); } catch (DistributedTableDescriptionException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (RecordLockedException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (RemoteException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (SQLException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (SecurityException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (UnknownTableException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } if (tumour2 != null) { // deal with discrepancies switch (io.getDiscrepancies()) { case ImportOptions.REJECT: saveTumour = false; break; case ImportOptions.UPDATE: String updateReport = updateRecord(tumour2, tumour); if (updateReport.length() > 0) { reportWriter.write(tumour.getVariable(io.getTumourIDVariablename()) + Globals.newline + updateReport); } tumour = tumour2; saveTumour = true; break; case ImportOptions.OVERWRITE: // deleteTumour; deleteTumour = true; saveTumour = true; break; } // reportWriter.write(tumour.getVariable(io.getTumourIDVariablename()) + "Tumour already exists.\n"); } Patient patient = null; try { patient = CanRegClientApp.getApplication().getPatientRecord( (String) tumour.getVariable(io.getPatientRecordIDTumourTableVariableName()), false); } catch (DistributedTableDescriptionException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (RecordLockedException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (RemoteException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (SQLException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (SecurityException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (UnknownTableException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } if (patient != null) { if (io.isDoChecks() && saveTumour) { // run the edits... String message = ""; LinkedList<CheckResult> checkResults = canreg.client.CanRegClientApp.getApplication() .performChecks(patient, tumour); Map<Globals.StandardVariableNames, CheckResult.ResultCode> mapOfVariablesAndWorstResultCodes = new EnumMap<Globals.StandardVariableNames, CheckResult.ResultCode>( Globals.StandardVariableNames.class); worstResultCodeFound = CheckResult.ResultCode.OK; for (CheckResult result : checkResults) { if (result.getResultCode() != CheckResult.ResultCode.OK && result.getResultCode() != CheckResult.ResultCode.NotDone) { if (!result.getResultCode().equals(CheckResult.ResultCode.Missing)) { message += result + "\t"; worstResultCodeFound = CheckResult.decideWorstResultCode( result.getResultCode(), worstResultCodeFound); for (Globals.StandardVariableNames standardVariableName : result .getVariablesInvolved()) { CheckResult.ResultCode worstResultCodeFoundForThisVariable = mapOfVariablesAndWorstResultCodes .get(standardVariableName); if (worstResultCodeFoundForThisVariable == null) { mapOfVariablesAndWorstResultCodes.put(standardVariableName, result.getResultCode()); } else if (CheckResult.compareResultSets(result.getResultCode(), worstResultCodeFoundForThisVariable) > 0) { mapOfVariablesAndWorstResultCodes.put(standardVariableName, result.getResultCode()); } } } } // Logger.getLogger(Import.class.getName()).log(Level.INFO, result.toString()); } // always generate ICD10... // ConversionResult[] conversionResult = canreg.client.CanRegClientApp.getApplication().performConversions(Converter.ConversionName.ICDO3toICD10, patient, tumour); // tumour.setVariable(io.getICD10VariableName(), conversionResult[0].getValue()); if (worstResultCodeFound != CheckResult.ResultCode.Invalid && worstResultCodeFound != CheckResult.ResultCode.Missing) { // generate ICD10 codes ConversionResult[] conversionResult = canreg.client.CanRegClientApp.getApplication() .performConversions(Converter.ConversionName.ICDO3toICD10, patient, tumour); tumour.setVariable(io.getICD10VariableName(), conversionResult[0].getValue()); // generate ICCC codes ConversionResult[] conversionResultICCC = canreg.client.CanRegClientApp .getApplication() .performConversions(Converter.ConversionName.ICDO3toICCC3, patient, tumour); tumour.setVariable(io.getICCCVariableName(), conversionResultICCC[0].getValue()); } else { tumour.setVariable(io.getTumourRecordStatus(), "0"); } if (worstResultCodeFound == CheckResult.ResultCode.OK) { // message += "Cross-check conclusion: Valid"; } else { reportWriter.write(tumour.getVariable(io.getTumourIDVariablename()) + "\t" + message + Globals.newline); // System.out.println(tumour.getVariable(io.getTumourIDVariablename()) + " " + message); } tumour.setVariable(io.getTumourCheckStatus(), CheckResult.toDatabaseVariable(worstResultCodeFound)); } else { // try to generate ICD10, if missing, anyway String icd10 = (String) tumour.getVariable(io.getICD10VariableName()); if (icd10 == null || icd10.trim().length() == 0) { ConversionResult[] conversionResult = canreg.client.CanRegClientApp.getApplication() .performConversions(Converter.ConversionName.ICDO3toICD10, patient, tumour); tumour.setVariable(io.getICD10VariableName(), conversionResult[0].getValue()); } // try to generate ICCC3, if missing, anyway String iccc = (String) tumour.getVariable(io.getICCCVariableName()); if (iccc == null || iccc.trim().length() == 0) { ConversionResult[] conversionResult = canreg.client.CanRegClientApp.getApplication() .performConversions(Converter.ConversionName.ICDO3toICCC3, patient, tumour); tumour.setVariable(io.getICCCVariableName(), conversionResult[0].getValue()); } } } else { reportWriter.write(tumour.getVariable(io.getTumourIDVariablename()) + "\t" + "No patient matches this Tumour." + Globals.newline); tumour.setVariable(io.getTumourRecordStatus(), "0"); tumour.setVariable(io.getTumourCheckStatus(), CheckResult.toDatabaseVariable(ResultCode.Missing)); } if (task != null) { task.firePropertyChange(RECORD, 50, 75); } if (!io.isTestOnly()) { if (deleteTumour) { server.deleteRecord( (Integer) tumour2.getVariable(Globals.TUMOUR_TABLE_RECORD_ID_VARIABLE_NAME), Globals.TUMOUR_TABLE_NAME); } if (saveTumour) { // if tumour has no record ID we save it if (tumour.getVariable(Globals.TUMOUR_TABLE_RECORD_ID_VARIABLE_NAME) == null) { server.saveTumour(tumour); } // if not we edit it else { server.editTumour(tumour); } } } if (task != null) { task.firePropertyChange(RECORD, 75, 100); } //Read next line of data numberOfLinesRead++; if (Thread.interrupted()) { //We've been interrupted: no more importing. reportWriter.flush(); throw new InterruptedException(); } } parser.close(); reportWriter.write("Finished reading tumours." + Globals.newline + Globals.newline); reportWriter.flush(); } if (task != null) { task.firePropertyChange(TUMOURS, 100, 100); } // then at last we get the sources if (task != null) { task.firePropertyChange(SOURCES, 0, 0); task.firePropertyChange(PROGRESS, 66, 66); } if (files[2] != null) { reportWriter .write("Starting to import sources from " + files[2].getAbsolutePath() + Globals.newline); FileInputStream sourceFIS = new FileInputStream(files[2]); InputStreamReader sourceISR = new InputStreamReader(sourceFIS, io.getFileCharsets()[2]); Logger.getLogger(Import.class.getName()).log(Level.CONFIG, "Name of the character encoding {0}", sourceISR.getEncoding()); numberOfLinesRead = 0; int numberOfRecordsInFile = canreg.common.Tools.numberOfLinesInFile(files[2].getAbsolutePath()); if (linesToRead > 0) { linesToRead = Math.min(numberOfRecordsInFile, linesToRead); } else { linesToRead = numberOfRecordsInFile; } format = CSVFormat.DEFAULT.withFirstRecordAsHeader().withDelimiter(io.getSeparators()[2]); parser = CSVParser.parse(files[2], io.getFileCharsets()[2], format); for (CSVRecord csvRecord : parser) { // We allow for null tasks... if (task != null) { task.firePropertyChange(PROGRESS, 67 + ((numberOfLinesRead - 1) * 100 / linesToRead) / 3, 67 + ((numberOfLinesRead) * 100 / linesToRead) / 3); task.firePropertyChange(SOURCES, ((numberOfLinesRead - 1) * 100 / linesToRead), ((numberOfLinesRead) * 100 / linesToRead)); } // Build source part Source source = new Source(); for (int i = 0; i < map.size(); i++) { Relation rel = map.get(i); if (rel.getDatabaseTableVariableID() >= 0 && rel.getDatabaseTableName().equalsIgnoreCase(Globals.SOURCE_TABLE_NAME)) { if (rel.getVariableType().equalsIgnoreCase("Number")) { if (csvRecord.get(rel.getFileColumnNumber()).length() > 0) { try { source.setVariable(rel.getDatabaseVariableName(), Integer.parseInt(csvRecord.get(rel.getFileColumnNumber()))); } catch (NumberFormatException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "Number format error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } } } else { source.setVariable(rel.getDatabaseVariableName(), csvRecord.get(rel.getFileColumnNumber())); } } if (task != null) { task.firePropertyChange(RECORD, i - 1 / map.size() * 50, i / map.size() * 50); } } Tumour tumour = null; try { tumour = CanRegClientApp.getApplication().getTumourRecordBasedOnTumourID( (String) source.getVariable(io.getTumourIDSourceTableVariableName()), false); } catch (DistributedTableDescriptionException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (RecordLockedException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (RemoteException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (SQLException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (SecurityException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (UnknownTableException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } if (task != null) { task.firePropertyChange(RECORD, 50, 75); } boolean addSource = true; if (tumour != null) { Set<Source> sources = tumour.getSources(); Object sourceRecordID = source.getVariable(io.getSourceIDVariablename()); // look for source in sources for (Source oldSource : sources) { if (oldSource.getVariable(io.getSourceIDVariablename()).equals(sourceRecordID)) { // deal with discrepancies switch (io.getDiscrepancies()) { case ImportOptions.REJECT: addSource = false; break; case ImportOptions.UPDATE: String updateReport = updateRecord(oldSource, source); if (updateReport.length() > 0) { reportWriter.write(tumour.getVariable(io.getTumourIDVariablename()) + Globals.newline + updateReport); } source = oldSource; addSource = false; break; case ImportOptions.OVERWRITE: // deleteTumour; sources.remove(oldSource); addSource = true; break; } } } if (addSource) { sources.add(source); } tumour.setSources(sources); if (!io.isTestOnly()) { server.editTumour(tumour); } } else { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, "No tumour for source record."); } if (task != null) { task.firePropertyChange(RECORD, 75, 100); } //Read next line of data numberOfLinesRead++; if (Thread.interrupted()) { //We've been interrupted: no more importing. reportWriter.flush(); throw new InterruptedException(); } } reportWriter.write("Finished reading sources." + Globals.newline + Globals.newline); reportWriter.flush(); parser.close(); } if (task != null) { task.firePropertyChange(SOURCES, 100, 100); task.firePropertyChange(PROGRESS, 100, 100); while (!task.isProgressPropertyValid()) { // wait untill progress has been updated... } } reportWriter.write("Finished" + Globals.newline); reportWriter.flush(); success = true; } catch (IOException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "Error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } catch (InterruptedException ex) { Logger.getLogger(Import.class.getName()).log(Level.INFO, "Interupted on line: " + (numberOfLinesRead + 1) + ". ", ex); success = true; } catch (IndexOutOfBoundsException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "String too short error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } finally { if (parser != null) { try { parser.close(); } catch (IOException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } } try { reportWriter.flush(); reportWriter.close(); } catch (IOException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } } if (task != null) { task.firePropertyChange(PROGRESS, 100, 100); task.firePropertyChange("finished", null, null); } return success; }
From source file:edu.unc.lib.dl.fedora.ManagementClient.java
/** * Poll Fedora until the PID is found or timeout. This method will blocking until at most the specified timeout plus * the timeout of the underlying HTTP connection. * * @param pid/*from ww w . j a va 2 s. c o m*/ * the PID to look for * @param delay * the delay between Fedora requests in seconds * @param timeout * the total polling time in seconds * @return true when the object is found within timeout, false on timeout */ public boolean pollForObject(PID pid, int delay, int timeout) throws InterruptedException { long startTime = System.currentTimeMillis(); while (System.currentTimeMillis() - startTime < timeout * 1000) { if (Thread.interrupted()) throw new InterruptedException(); try { ObjectProfile doc = this.getAccessClient().getObjectProfile(pid, null); if (doc != null) return true; } catch (ServiceException e) { if (log.isDebugEnabled()) log.debug("Expected service exception while polling fedora", e); } catch (FedoraException e) { // fedora responded, but object not found log.debug("got exception from fedora", e); } if (Thread.interrupted()) throw new InterruptedException(); log.info(pid + " not found, waiting " + delay + " seconds.."); Thread.sleep(delay * 1000); } return false; }
From source file:canreg.client.dataentry.Convert.java
public static boolean importFile(canreg.client.gui.management.CanReg4MigrationInternalFrame.MigrationTask task, Document doc, List<canreg.client.dataentry.Relation> map, File file, CanRegServerInterface server, ImportOptions io) throws SQLException, RemoteException, SecurityException, RecordLockedException { boolean success = false; Set<String> noNeedToLookAtPatientVariables = new TreeSet<String>(); noNeedToLookAtPatientVariables//from ww w . j a va2 s. c o m .add(canreg.common.Tools.toLowerCaseStandardized(io.getPatientIDVariableName())); noNeedToLookAtPatientVariables .add(canreg.common.Tools.toLowerCaseStandardized(io.getPatientRecordIDVariableName())); String firstNameVariableName = io.getFirstNameVariableName(); String sexVariableName = io.getSexVariableName(); CSVParser parser = null; HashMap mpCodes = new HashMap(); int numberOfLinesRead = 0; Map<String, Integer> nameSexTable = server.getNameSexTables(); try { // Logger.getLogger(Import.class.getName()).log(Level.CONFIG, "Name of the character encoding {0}"); int numberOfRecordsInFile = canreg.common.Tools.numberOfLinesInFile(file.getAbsolutePath()); debugOut("Importing data from " + file); CSVFormat format = CSVFormat.DEFAULT.withFirstRecordAsHeader().withDelimiter(io.getSeparator()); parser = CSVParser.parse(file, io.getFileCharset(), format); int linesToRead = io.getMaxLines(); if (linesToRead == -1 || linesToRead > numberOfRecordsInFile) { linesToRead = numberOfRecordsInFile; } for (CSVRecord csvRecord : parser) { numberOfLinesRead++; // We allow for null tasks... boolean needToSavePatientAgain = true; int patientDatabaseRecordID = -1; if (task != null) { if (canreg.client.gui.management.CanReg4MigrationInternalFrame.isPaused) { task.firePropertyChange("paused", false, true); } if (!canreg.client.gui.management.CanReg4MigrationInternalFrame.isPaused) { task.firePropertyChange("paused", true, false); task.firePropertyChange("progress", (numberOfLinesRead - 1) * 100 / linesToRead, (numberOfLinesRead) * 100 / linesToRead); } } // Build patient part Patient patient = new Patient(); for (int i = 0; i < map.size(); i++) { Relation rel = map.get(i); if (rel.getDatabaseTableVariableID() >= 0 && rel.getDatabaseTableName().equalsIgnoreCase("patient")) { if (rel.getFileColumnNumber() < csvRecord.size()) { if (rel.getVariableType().equalsIgnoreCase("Number")) { if (csvRecord.get(rel.getFileColumnNumber()).length() > 0) { try { patient.setVariable(rel.getDatabaseVariableName(), Integer.parseInt(csvRecord.get(rel.getFileColumnNumber()))); } catch (NumberFormatException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "Number format error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } } } else { patient.setVariable(rel.getDatabaseVariableName(), StringEscapeUtils.unescapeCsv(csvRecord.get(rel.getFileColumnNumber()))); } } else { Logger.getLogger(Import.class.getName()).log(Level.INFO, "Something wrong with patient part of line " + numberOfLinesRead + ".", new Exception("Error in line: " + numberOfLinesRead + ". Can't find field: " + rel.getDatabaseVariableName())); } } } // debugOut(patient.toString()); // Build tumour part Tumour tumour = new Tumour(); for (int i = 0; i < map.size(); i++) { Relation rel = map.get(i); if (rel.getDatabaseTableVariableID() >= 0 && rel.getDatabaseTableName().equalsIgnoreCase("tumour") && rel.getFileColumnNumber() < csvRecord.size()) { if (rel.getFileColumnNumber() < csvRecord.size()) { if (rel.getVariableType().equalsIgnoreCase("Number")) { if (csvRecord.get(rel.getFileColumnNumber()).length() > 0) { try { tumour.setVariable(rel.getDatabaseVariableName(), Integer.parseInt(csvRecord.get(rel.getFileColumnNumber()))); } catch (NumberFormatException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "Number format error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } } } else { tumour.setVariable(rel.getDatabaseVariableName(), StringEscapeUtils.unescapeCsv(csvRecord.get(rel.getFileColumnNumber()))); } } else { Logger.getLogger(Import.class.getName()).log(Level.INFO, "Something wrong with tumour part of line " + numberOfLinesRead + ".", new Exception("Error in line: " + numberOfLinesRead + ". Can't find field: " + rel.getDatabaseVariableName())); } } } // Build source part Set<Source> sources = Collections.synchronizedSet(new LinkedHashSet<Source>()); Source source = new Source(); for (int i = 0; i < map.size(); i++) { Relation rel = map.get(i); if (rel.getDatabaseTableVariableID() >= 0 && rel.getDatabaseTableName().equalsIgnoreCase(Globals.SOURCE_TABLE_NAME) && rel.getFileColumnNumber() < csvRecord.size()) { if (rel.getFileColumnNumber() < csvRecord.size()) { if (rel.getVariableType().equalsIgnoreCase("Number")) { if (csvRecord.get(rel.getFileColumnNumber()).length() > 0) { try { source.setVariable(rel.getDatabaseVariableName(), Integer.parseInt(csvRecord.get(rel.getFileColumnNumber()))); } catch (NumberFormatException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "Number format error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } } } else { source.setVariable(rel.getDatabaseVariableName(), StringEscapeUtils.unescapeCsv(csvRecord.get(rel.getFileColumnNumber()))); } } else { Logger.getLogger(Import.class.getName()).log(Level.INFO, "Something wrong with source part of line " + numberOfLinesRead + ".", new Exception("Error in line: " + numberOfLinesRead + ". Can't find field: " + rel.getDatabaseVariableName())); } } } sources.add(source); tumour.setSources(sources); // debugOut(tumour.toString()); // add patient to the database Object patientID = patient.getVariable(io.getPatientIDVariableName()); Object patientRecordID = patient.getVariable(io.getPatientRecordIDVariableName()); if (patientID == null) { // save the record to get the new patientID; patientDatabaseRecordID = server.savePatient(patient); patient = (Patient) server.getRecord(patientDatabaseRecordID, Globals.PATIENT_TABLE_NAME, false); patientID = patient.getVariable(io.getPatientIDVariableName()); patientRecordID = patient.getVariable(io.getPatientRecordIDVariableName()); } if (io.isDataFromPreviousCanReg()) { // set update date for the patient the same as for the tumour Object updateDate = tumour.getVariable(io.getTumourUpdateDateVariableName()); patient.setVariable(io.getPatientUpdateDateVariableName(), updateDate); // Set the patientID the same as the tumourID initially // Object tumourSequence = tumour.getVariable(io.getTumourSequenceVariableName()); Object tumourSequence = "1"; String tumourSequenceString = tumourSequence + ""; while (tumourSequenceString.length() < Globals.ADDITIONAL_DIGITS_FOR_PATIENT_RECORD) { tumourSequenceString = "0" + tumourSequenceString; } patientRecordID = patientID + "" + tumourSequenceString; // If this is a multiple primary tumour... String mpCodeString = (String) tumour.getVariable(io.getMultiplePrimaryVariableName()); if (mpCodeString != null && mpCodeString.length() > 0) { patientID = lookUpPatientID(mpCodeString, patientID, mpCodes); // rebuild sequenceNumber Tumour[] tumours = new Tumour[0]; try { tumours = CanRegClientApp.getApplication() .getTumourRecordsBasedOnPatientID(patientID + "", false); } catch (DistributedTableDescriptionException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (UnknownTableException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } tumourSequenceString = (tumours.length + 1) + ""; while (tumourSequenceString.length() < Globals.ADDITIONAL_DIGITS_FOR_PATIENT_RECORD) { tumourSequenceString = "0" + tumourSequenceString; } patientRecordID = patientID + "" + tumourSequenceString; Patient[] oldPatients = null; try { oldPatients = CanRegClientApp.getApplication().getPatientRecordsByID((String) patientID, false); } catch (RemoteException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (SecurityException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (DistributedTableDescriptionException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (RecordLockedException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (SQLException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } catch (UnknownTableException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } for (Patient oldPatient : oldPatients) { if (!Tools.newRecordContainsNewInfo(patient, oldPatient, noNeedToLookAtPatientVariables)) { needToSavePatientAgain = false; patient = oldPatient; patientRecordID = oldPatient.getVariable(io.getPatientRecordIDVariableName()); } } } Object tumourID = patientRecordID + "" + tumourSequenceString; // patient.setVariable(io.getPatientIDVariableName(), patientID); tumour.setVariable(io.getTumourIDVariablename(), tumourID); // And store the record ID patient.setVariable(io.getPatientRecordIDVariableName(), patientRecordID); // Set the patient ID number on the tumour tumour.setVariable(io.getPatientIDTumourTableVariableName(), patientID); tumour.setVariable(io.getPatientRecordIDTumourTableVariableName(), patientRecordID); // Set the deprecated flag to 0 - no obsolete records from CR4 tumour.setVariable(io.getObsoleteTumourFlagVariableName(), "0"); patient.setVariable(io.getObsoletePatientFlagVariableName(), "0"); } // Set the name in the firstName database String sex = (String) patient.getVariable(sexVariableName); if (sex != null && sex.length() > 0) { Integer sexCode = Integer.parseInt(sex); String firstNames = (String) patient.getVariable(firstNameVariableName); if (firstNames != null) { String[] firstNamesArray = firstNames.split(" "); for (String firstName : firstNamesArray) { if (firstName != null && firstName.trim().length() > 0) { // here we use the locale specific toUpperCase Integer registeredSexCode = nameSexTable.get(firstName); if (registeredSexCode == null) { NameSexRecord nsr = new NameSexRecord(); nsr.setName(firstName); nsr.setSex(sexCode); server.saveNameSexRecord(nsr, false); nameSexTable.put(firstName, sexCode); } else if (registeredSexCode != sexCode) { if (registeredSexCode != 9) { sexCode = 9; NameSexRecord nsr = new NameSexRecord(); nsr.setName(firstName); nsr.setSex(sexCode); server.saveNameSexRecord(nsr, true); nameSexTable.remove(firstName); nameSexTable.put(firstName, sexCode); } } } } } } if (needToSavePatientAgain) { if (patientDatabaseRecordID > 0) { server.editPatient(patient); } else { patientDatabaseRecordID = server.savePatient(patient); } } if (patient != null && tumour != null) { String icd10 = (String) tumour.getVariable(io.getICD10VariableName()); if (icd10 == null || icd10.trim().length() == 0) { ConversionResult[] conversionResult = canreg.client.CanRegClientApp.getApplication() .performConversions(Converter.ConversionName.ICDO3toICD10, patient, tumour); tumour.setVariable(io.getICD10VariableName(), conversionResult[0].getValue()); } } if (tumour.getVariable(io.getPatientIDTumourTableVariableName()) == null) { tumour.setVariable(io.getPatientIDTumourTableVariableName(), patientID); } if (tumour.getVariable(io.getPatientRecordIDTumourTableVariableName()) == null) { tumour.setVariable(io.getPatientRecordIDTumourTableVariableName(), patientRecordID); } int tumourDatabaseIDNumber = server.saveTumour(tumour); if (Thread.interrupted()) { //We've been interrupted: no more importing. throw new InterruptedException(); } } task.firePropertyChange("finished", null, null); success = true; } catch (IOException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "Error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } catch (NumberFormatException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "Error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } catch (InterruptedException ex) { Logger.getLogger(Import.class.getName()).log(Level.INFO, "Interupted on line: " + (numberOfLinesRead + 1) + ". ", ex); success = true; } catch (IndexOutOfBoundsException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "Error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } catch (SQLException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, "Error in line: " + (numberOfLinesRead + 1 + 1) + ". ", ex); success = false; } finally { if (parser != null) { try { parser.close(); } catch (IOException ex) { Logger.getLogger(Import.class.getName()).log(Level.SEVERE, null, ex); } } } return success; }
From source file:org.eclipse.jubula.client.core.persistence.Persistor.java
/** * @param s// w ww. j av a 2s. c o m * session, which contain the current persistent object * @param po * object to delete * @throws PMException * in case of failed rollback * @throws PMAlreadyLockedException * in case of locked object * @throws PMDirtyVersionException * in case of version conflict * @throws ProjectDeletedException * if the project was deleted in another instance * @throws InterruptedException * if the oepration was canceled */ public void deletePO(EntityManager s, IPersistentObject po) throws PMException, PMAlreadyLockedException, PMDirtyVersionException, ProjectDeletedException, InterruptedException { Validate.notNull(s); try { s.remove(po); } catch (PersistenceException e) { if (e.getCause() instanceof InterruptedException) { // Operation was canceled. throw new InterruptedException(); } PersistenceManager.handleDBExceptionForMasterSession(po, e); } }
From source file:org.eclipse.jubula.client.core.persistence.ProjectPM.java
/** * //ww w. j a v a2s .co m * @param proj * ProjectPO to be attached and saved. * @param newProjectName * name part of the ProjectNamePO. If there is no new name, this * parameter must be null (same project, different version) * @param mapperList mapper to resolve Parameter Names * @param compNameBindingList mapper to resolve Component Names * @param monitor The progress monitor for this potentially long-running * operation. * @throws PMException * in case of any db error * @throws ProjectDeletedException if project is already deleted * @throws InterruptedException if the operation was canceled. */ public static void attachProjectToROSession(IProjectPO proj, String newProjectName, List<INameMapper> mapperList, List<IWritableComponentNameMapper> compNameBindingList, IProgressMonitor monitor) throws PMException, ProjectDeletedException, InterruptedException { monitor.beginTask(NLS.bind(Messages.ProjectWizardCreatingProject, newProjectName), getTotalWorkForSave(proj)); // Register Persistence progress listeners setHbmProgressMonitor(monitor); GeneralStorage.getInstance().reset(); EntityManager s = GeneralStorage.getInstance().getMasterSession(); EntityTransaction tx = null; try { tx = Persistor.instance().getTransaction(s); s.persist(proj); proj.setParentProjectId(proj.getId()); if (newProjectName != null) { ProjectNameBP.getInstance().setName(s, proj.getGuid(), newProjectName); } ProjectNameBP.getInstance().storeTransientNames(s); for (INameMapper mapper : mapperList) { mapper.persist(s, proj.getId()); } for (IWritableComponentNameMapper compNameBinding : compNameBindingList) { CompNamePM.flushCompNames(s, proj.getId(), compNameBinding); } if (!monitor.isCanceled()) { Persistor.instance().commitTransaction(s, tx); GeneralStorage.getInstance().setProject(proj); for (INameMapper mapper : mapperList) { mapper.updateStandardMapperAndCleanup(proj.getId()); } for (IComponentNameMapper compNameBinding : compNameBindingList) { compNameBinding.getCompNameCache().updateStandardMapperAndCleanup(proj.getId()); } } else { Persistor.instance().rollbackTransaction(s, tx); GeneralStorage.getInstance().reset(); for (INameMapper mapper : mapperList) { mapper.clearAllNames(); } for (IComponentNameMapper compNameBinding : compNameBindingList) { compNameBinding.getCompNameCache().clear(); } throw new InterruptedException(); } } catch (PMException pme) { handleAlreadyLockedException(mapperList, s, tx); } catch (OperationCanceledException oce) { handleOperationCanceled(mapperList, s, tx); } catch (PersistenceException e) { handlePersistenceException(mapperList, s, tx, e); } catch (IncompatibleTypeException ite) { handleIncompatibleTypeException(mapperList, s, tx, ite); } finally { // Remove Persistence progress listeners setHbmProgressMonitor(null); } initBPs(proj); }