List of usage examples for org.apache.commons.csv CSVFormat DEFAULT
CSVFormat DEFAULT
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From source file:edu.nyu.vida.data_polygamy.utils.FrameworkUtils.java
/** * String Parsing /* w ww .j a v a2 s. com*/ */ public static String[] splitStr(String val, Integer len) throws IOException { String[] input; try { CSVParser parser = new CSVParser(new StringReader(val), CSVFormat.DEFAULT); CSVRecord record = parser.getRecords().get(0); input = new String[len]; Iterator<String> valuesIt = record.iterator(); int i = 0; while (valuesIt.hasNext()) { input[i] = valuesIt.next().trim(); i++; } parser.close(); } catch (ArrayIndexOutOfBoundsException e) { input = val.split(",", len); for (int i = 0; i < input.length; i++) input[i] = input[i].trim(); } return input; }
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 w w w . j a v a2s. c om .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:com.datascience.cascading.scheme.CsvScheme.java
/** * Creates a new CSV scheme with the given source and sink {@link cascading.tuple.Fields}. * <p>//from ww w. j a va 2s .c o m * The CSV input/output encoding set defaults to {@code UTF-8} * * @param sourceFields The source fields. * @param sinkFields The sink fields. * @param strict Indicates whether to parse records in strict parsing mode. When strict mode is disabled, single record * parse errors will be caught and logged. * @see com.datascience.cascading.scheme.CsvScheme */ public CsvScheme(Fields sourceFields, Fields sinkFields, boolean strict) { this(sourceFields, sinkFields, CSVFormat.DEFAULT, StandardCharsets.UTF_8, strict); }
From source file:edu.nyu.vida.data_polygamy.utils.FrameworkUtils.java
public static String[] splitStr(String val) throws IOException { CSVParser parser = new CSVParser(new StringReader(val), CSVFormat.DEFAULT); CSVRecord record = parser.getRecords().get(0); Iterator<String> valuesIt = record.iterator(); String[] input = new String[record.size()]; int i = 0;/*from w ww . j av a2 s. c o m*/ while (valuesIt.hasNext()) { input[i] = valuesIt.next(); i++; } parser.close(); return input; }
From source file:com.datascience.cascading.scheme.CsvScheme.java
/** * Creates a new CSV scheme with the given source and sink {@link cascading.tuple.Fields}. * * @param sourceFields The source fields. * @param sinkFields The sink fields./* w w w .jav a 2s . com*/ * @param charset The character set with which to read and write CSV files. * @param strict Indicates whether to parse records in strict parsing mode. When strict mode is disabled, single record * parse errors will be caught and logged. * @see com.datascience.cascading.scheme.CsvScheme */ public CsvScheme(Fields sourceFields, Fields sinkFields, Charset charset, boolean strict) { this(sourceFields, sinkFields, CSVFormat.DEFAULT, charset, strict); }
From source file:canreg.client.gui.components.PreviewFilePanel.java
/** * *///from ww w . j a v a2s . c o m @Action public void previewAction() { // show the contents of the file BufferedReader br = null; try { changeFile(); // numberOfRecordsTextField.setText(""+(canreg.common.Tools.numberOfLinesInFile(inFile.getAbsolutePath())-1)); FileInputStream fis = new FileInputStream(inFile); br = new BufferedReader(new InputStreamReader(fis, (Charset) charsetsComboBox.getSelectedItem())); CSVFormat csvFormat = CSVFormat.DEFAULT.withFirstRecordAsHeader().withDelimiter(getSeparator()); CSVParser csvParser = new CSVParser(br, csvFormat); int linesToRead = Globals.NUMBER_OF_LINES_IN_IMPORT_PREVIEW; int numberOfLinesRead = 0; Vector<Vector<String>> data = new Vector<Vector<String>>(); String[] headers = csvParser.getHeaderMap().keySet().toArray(new String[0]); for (CSVRecord csvRecord : csvParser) { csvRecord.toMap(); Vector vec = new Vector(); Iterator<String> iterator = csvRecord.iterator(); while (iterator.hasNext()) { vec.add(iterator.next()); } data.add(vec); numberOfLinesRead++; if (numberOfLinesRead >= linesToRead) { break; } } numberOfRecordsShownTextField.setText(numberOfLinesRead + ""); // previewTextArea.setText(headers + "\n" + dataText); // previewTextArea.setCaretPosition(0); previewPanel.setVisible(true); Vector columnNames = new Vector(Arrays.asList(headers)); previewTable.setModel(new DefaultTableModel(data, columnNames)); } catch (FileNotFoundException fileNotFoundException) { JOptionPane.showInternalMessageDialog(CanRegClientApp.getApplication().getMainFrame().getContentPane(), java.util.ResourceBundle.getBundle("canreg/client/gui/dataentry/resources/ImportView") .getString("COULD_NOT_PREVIEW_FILE:") + " \'" + fileNameTextField.getText().trim() + "\'.", java.util.ResourceBundle.getBundle("canreg/client/gui/dataentry/resources/ImportView") .getString("ERROR"), JOptionPane.ERROR_MESSAGE); Logger.getLogger(PreviewFilePanel.class.getName()).log(Level.SEVERE, null, fileNotFoundException); } catch (IOException ex) { Logger.getLogger(PreviewFilePanel.class.getName()).log(Level.SEVERE, null, ex); } finally { try { if (br != null) { br.close(); } } catch (IOException ex) { Logger.getLogger(PreviewFilePanel.class.getName()).log(Level.SEVERE, null, ex); } } }
From source file:it.sayservice.platform.smartplanner.cache.annotated.AnnotatedReader.java
private List<String[]> readCSV(String fileName) throws IOException { FileInputStream fis = new FileInputStream(new File(fileName)); UnicodeReader ur = new UnicodeReader(fis, "UTF-8"); List<String[]> lines = new ArrayList<String[]>(); try {//from ww w. ja va2 s. c om for (CSVRecord record : CSVFormat.DEFAULT.withDelimiter(';').parse(ur)) { String[] line = Iterables.toArray(record, String.class); lines.add(line); } } catch (Exception e) { e.printStackTrace(); } lines.get(0)[0] = lines.get(0)[0].replaceAll(Constants.UTF8_BOM, ""); return lines; }
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 ww w . j a v a2s . c o m*/ 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:canreg.client.analysis.AgeSpecificCasesTableBuilder.java
@Override public LinkedList<String> buildTable(String registryLabel, String reportFileName, int startYear, int endYear, Object[][] incidenceData, PopulationDataset[] populations, PopulationDataset[] standardPopulations, LinkedList<ConfigFields> configList, String[] engineParameters, FileTypes fileType) throws NotCompatibleDataException { LinkedList<String> generatedFiles = new LinkedList<String>(); String footerString = java.util.ResourceBundle .getBundle("canreg/client/analysis/resources/AgeSpecificCasesTableBuilder") .getString("TABLE BUILT ") + new Date() + java.util.ResourceBundle .getBundle("canreg/client/analysis/resources/AgeSpecificCasesTableBuilder") .getString(" BY CANREG5."); String notesString = ""; if (populations[0].getFilter().length() > 0) { notesString = java.util.ResourceBundle .getBundle("canreg/client/analysis/resources/AgeSpecificCasesTableBuilder") .getString("FILTER USED:") + " " + populations[0].getFilter(); }// www . ja v a 2s . com double tableFontSize = 7.5; String font = "Times"; int[] years = { startYear, endYear }; // double RegPop[][]; double totalCases[][]; String sexLabel[] = null; String tableLabel[] = null; String icdLabel[] = null; LinkedList cancerGroupsLocal[] = null; boolean showSeeNotesNote = true; char Childc[][] = new char[2][3]; double casesPerHundredThousand[][][]; double cumRate64[][]; double cumRate74[][]; tableLabel = ConfigFieldsReader.findConfig("table_label", configList); // sexLabel = ConfigFieldsReader.findConfig("sex_label", configList); sexLabel = new String[] { java.util.ResourceBundle.getBundle("canreg/client/analysis/resources/AbstractEditorialTableBuilder") .getString("MALE"), java.util.ResourceBundle.getBundle("canreg/client/analysis/resources/AbstractEditorialTableBuilder") .getString("FEMALE") }; icdLabel = ConfigFieldsReader.findConfig("ICD_groups_labels", configList); icd10GroupDescriptions = ConfigFieldsReader.findConfig("ICD10_groups", configList); cancerGroupsLocal = EditorialTableTools.generateICD10Groups(icd10GroupDescriptions); allCancerGroupsIndex = EditorialTableTools.getICD10index("ALL", icd10GroupDescriptions); leukemiaNOSCancerGroupIndex = EditorialTableTools.getICD10index(950, cancerGroupsLocal); skinCancerGroupIndex = EditorialTableTools.getICD10index("C44", icd10GroupDescriptions); bladderCancerGroupIndex = EditorialTableTools.getICD10index("C67", icd10GroupDescriptions); mesotheliomaCancerGroupIndex = EditorialTableTools.getICD10index("C45", icd10GroupDescriptions); kaposiSarkomaCancerGroupIndex = EditorialTableTools.getICD10index("C46", icd10GroupDescriptions); myeloproliferativeDisordersCancerGroupIndex = EditorialTableTools.getICD10index("MPD", icd10GroupDescriptions); myelodysplasticSyndromesCancerGroupIndex = EditorialTableTools.getICD10index("MDS", icd10GroupDescriptions); allCancerGroupsButSkinIndex = EditorialTableTools.getICD10index("ALLbC44", icd10GroupDescriptions); leukemiaNOSCancerGroupIndex = EditorialTableTools.getICD10index(950, cancerGroupsLocal); brainAndCentralNervousSystemCancerGroupIndex = EditorialTableTools.getICD10index("C70-72", icd10GroupDescriptions); ovaryCancerGroupIndex = EditorialTableTools.getICD10index(569, cancerGroupsLocal); otherCancerGroupsIndex = EditorialTableTools.getICD10index("O&U", icd10GroupDescriptions); numberOfCancerGroups = cancerGroupsLocal.length; lineBreaks = parseLineBreaks(ConfigFieldsReader.findConfig("line_breaks", configList)); numberOfYears = years[1] - years[0] + 1; minimumCasesLimit = minimumCasesPerYearLimit * numberOfYears; noOldData = true; casesPerHundredThousand = new double[numberOfSexes][numberOfAgeGroups][numberOfCancerGroups]; casesArray = new double[numberOfCancerGroups][numberOfSexes][numberOfAgeGroups]; // cumRate64 = new double[numberOfSexes][numberOfCancerGroups]; // cumRate74 = new double[numberOfSexes][numberOfCancerGroups]; populationArray = new double[numberOfSexes][numberOfAgeGroups]; foundAgeGroups = new boolean[numberOfAgeGroups]; if (areThesePopulationDatasetsCompatible(populations)) { for (PopulationDataset population : populations) { population.addPopulationDataToArrayForTableBuilder(populationArray, foundAgeGroups, new AgeGroupStructure(5, 85, 1)); } } else { throw new NotCompatibleDataException(); } populationString = populations[0].getPopulationDatasetName(); int lastCommaPlace = populationString.lastIndexOf(","); if (lastCommaPlace != -1) { populationString = populationString.substring(0, lastCommaPlace); } if (populations[0].getFilter().length() > 0) { notesString = java.util.ResourceBundle .getBundle("canreg/client/analysis/resources/AgeSpecificCasesTableBuilder") .getString("FILTER USED:") + populations[0].getFilter(); } standardPopulationArray = new double[numberOfSexes][numberOfAgeGroups]; for (PopulationDataset stdPopulation : standardPopulations) { stdPopulation.addPopulationDataToArrayForTableBuilder(standardPopulationArray, null, new AgeGroupStructure(5, 85, 1)); } // standardize population array for (int sexNumber = 0; sexNumber < numberOfSexes; sexNumber++) { for (int ageGroupNumber = 0; ageGroupNumber < numberOfAgeGroups; ageGroupNumber++) { standardPopulationArray[sexNumber][ageGroupNumber] = (standardPopulationArray[sexNumber][ageGroupNumber] / standardPopulationArray[sexNumber][numberOfAgeGroups - 1]) * 100000; } } highestPopulationAgeGroup = findHighestAgeGroup(foundAgeGroups); lowestPopulationAgeGroup = findLowestAgeGroup(foundAgeGroups); int records = 0; // generate statistics String sexString; String icdString; String yearString; String ageString; String basisString; int sex, icdNumber, year, icdIndex, yearIndex, ageGroup, ageInt, basis, cases; if (incidenceData != null) { for (Object[] line : incidenceData) { try { // Set default icdIndex = -1; cases = 0; // Unknown sex group = 3 sex = 3; // Extract data sexString = (String) line[SEX_COLUMN]; sex = Integer.parseInt(sexString.trim()); // sex = 3 is unknown sex if (sex > 2) { sex = 3; } // morphologyString = (String) line[MORPHOLOGY_COLUMN]; /* if (morphologyString.length() > 0) { int morphology = Integer.parseInt(morphologyString); if (morphology == 9140) { String behaviourString = getContentOfField( incidenceFieldDescriptionList, "behaviour", line).trim(); if (behaviourString.equals("3")) { icdIndex = kaposiSarkomaCancerGroupIndex; } } else if ((int)(morphology/10) == 905) { String behaviourString = getContentOfField(incidenceFieldDescriptionList, "behaviour", line).trim(); if (behaviourString.equals("3")) { icdIndex = mesotheliomaCancerGroupIndex; } } } */ if (icdIndex < 0) { icdString = (String) line[ICD10_COLUMN]; if (icdString.length() > 0 && icdString.trim().substring(0, 1).equals("C")) { icdString = icdString.trim().substring(1); icdNumber = Integer.parseInt(icdString); if (icdString.length() < 3) { icdNumber = icdNumber * 10; } icdIndex = EditorialTableTools.getICD10index(icdNumber, cancerGroupsLocal); if (icdIndex == -1) { icdIndex = -1; } } else if (icdString.length() > 0 && icdString.trim().substring(0, 1).equals("D")) { icdIndex = DONT_COUNT; // set don't count as default icdString = icdString.trim().substring(1); icdNumber = Integer.parseInt(icdString); if (icdString.length() < 3) { icdNumber = icdNumber * 10; } if (icdNumber == 90 || icdNumber == 414) { icdIndex = bladderCancerGroupIndex; } else if (((int) (icdNumber / 10)) == 45 || ((int) (icdNumber / 10)) == 47) { icdIndex = myeloproliferativeDisordersCancerGroupIndex; } else if (((int) (icdNumber / 10)) == 46) { icdIndex = myelodysplasticSyndromesCancerGroupIndex; } } } yearString = line[YEAR_COLUMN].toString(); year = Integer.parseInt(yearString); yearIndex = year - years[0]; ageString = line[AGE_COLUMN].toString(); ageInt = Integer.parseInt(ageString); if (ageInt == unknownAgeInt) { ageGroup = unknownAgeGroupIndex; } else { ageGroup = populations[yearIndex].getAgeGroupIndex(ageInt); // Adjust age group if (populations[yearIndex].getAgeGroupStructure().getSizeOfFirstGroup() != 1) { ageGroup += 1; } } // Extract cases cases = (Integer) line[CASES_COLUMN]; if (icdIndex != DONT_COUNT && year <= years[1] && year >= years[0]) { // Basis of diagnosis basisString = line[BASIS_DIAGNOSIS_COLUMN].toString(); if (basisString != null) { basis = Integer.parseInt(basisString.trim()); } else { basis = -1; } if (sex <= numberOfSexes && icdIndex >= 0 && icdIndex <= cancerGroupsLocal.length) { casesArray[icdIndex][sex - 1][ageGroup] += cases; } else if (otherCancerGroupsIndex >= 0) { casesArray[otherCancerGroupsIndex][sex - 1][ageGroup] += cases; } if (allCancerGroupsIndex >= 0) { casesArray[allCancerGroupsIndex][sex - 1][ageGroup] += cases; } if (allCancerGroupsButSkinIndex >= 0 && skinCancerGroupIndex >= 0 && icdIndex != skinCancerGroupIndex) { casesArray[allCancerGroupsButSkinIndex][sex - 1][ageGroup] += cases; } records += cases; if (records % recordsPerFeedback == 0) { System.out.println(java.util.ResourceBundle .getBundle("canreg/client/analysis/resources/AgeSpecificCasesTableBuilder") .getString("PROCESSING RECORD NUMBER: ") + records); } } } catch (NumberFormatException nfe) { Logger.getLogger(AgeSpecificCasesTableBuilder.class.getName()).log(Level.WARNING, null, nfe); } // Read next line } } System.out.println(java.util.ResourceBundle .getBundle("canreg/client/analysis/resources/AgeSpecificCasesTableBuilder").getString("PROCESSED ") + records + java.util.ResourceBundle .getBundle("canreg/client/analysis/resources/AgeSpecificCasesTableBuilder") .getString(" RECORDS.")); // Total casesPerHundredThousand totalCases = new double[numberOfSexes][numberOfCancerGroups]; // Crude rate // crudeRate = new double[numberOfSexes][numberOfCancerGroups]; for (int sexNumber = 0; sexNumber < 2; sexNumber++) { // The age groups ageLabel[lowestPopulationAgeGroup] = "0-"; for (int icdGroup = 0; icdGroup < numberOfCancerGroups; icdGroup++) { if (icdLabel[icdGroup].substring(0 + sexNumber, 1 + sexNumber).equalsIgnoreCase("1")) { // The age groups double previousAgeGroupCases = 0; double previousAgeGroupPopulation = 0; double previousAgeGroupWstdPopulation = 0; double lastAgeGroupCases = 0; double lastAgeGroupPopulation = 0; double lastAgeGroupWstdPopulation = 0; for (int ageGroupNumber = 1; ageGroupNumber < unknownAgeGroupIndex; ageGroupNumber++) { if (ageGroupNumber == 1) { for (int ag = lowestIncidenceAgeGroup; ag < ageGroupNumber; ag++) { previousAgeGroupCases += casesArray[icdGroup][sexNumber][ag]; previousAgeGroupPopulation += populationArray[sexNumber][ag]; previousAgeGroupWstdPopulation += standardPopulationArray[sexNumber][ag]; } } if (foundAgeGroups[ageGroupNumber] && ageGroupNumber < highestPopulationAgeGroup) { casesPerHundredThousand[sexNumber][ageGroupNumber][icdGroup] = 100000 * (casesArray[icdGroup][sexNumber][ageGroupNumber] + previousAgeGroupCases) / (populationArray[sexNumber][ageGroupNumber] + previousAgeGroupPopulation); previousAgeGroupCases = 0; previousAgeGroupPopulation = 0; previousAgeGroupWstdPopulation = 0; } else { previousAgeGroupCases += casesArray[icdGroup][sexNumber][ageGroupNumber]; previousAgeGroupPopulation += populationArray[sexNumber][ageGroupNumber]; previousAgeGroupWstdPopulation += standardPopulationArray[sexNumber][ageGroupNumber]; } } // We calculate the "leftovers" from the last age group if (previousAgeGroupPopulation > 0) { casesPerHundredThousand[sexNumber][highestPopulationAgeGroup][icdGroup] = 100000 * (previousAgeGroupCases) / (previousAgeGroupPopulation); } previousAgeGroupCases = 0; previousAgeGroupPopulation = 0; previousAgeGroupWstdPopulation = 0; } } } // ASR, vASR, MV, MI, DCO for (int sexNumber = 0; sexNumber < numberOfSexes; sexNumber++) { for (int icdGroup = 0; icdGroup < numberOfCancerGroups; icdGroup++) { double previousAgeGroupCases = 0; double previousAgeGroupPopulation = 0; double previousAgeGroupWstdPopulation = 0; double lastAgeGroupCases = 0; double lastAgeGroupPopulation = 0; double lastAgeGroupWstdPopulation = 0; totalCases[sexNumber][icdGroup] += casesArray[icdGroup][sexNumber][0]; for (int ageGroupNumber = 1; ageGroupNumber < unknownAgeGroupIndex; ageGroupNumber++) { if (ageGroupNumber == 1) { for (int ag = lowestIncidenceAgeGroup; ag < ageGroupNumber; ag++) { previousAgeGroupCases += casesArray[icdGroup][sexNumber][ag]; previousAgeGroupPopulation += populationArray[sexNumber][ag]; previousAgeGroupWstdPopulation += standardPopulationArray[sexNumber][ag]; } } if (foundAgeGroups[ageGroupNumber] && ageGroupNumber < highestPopulationAgeGroup && (previousAgeGroupPopulation + populationArray[sexNumber][ageGroupNumber] > 0)) { double asr = calculateASR( (previousAgeGroupCases + casesArray[icdGroup][sexNumber][ageGroupNumber]), (previousAgeGroupPopulation + populationArray[sexNumber][ageGroupNumber]), (previousAgeGroupWstdPopulation + standardPopulationArray[sexNumber][ageGroupNumber])); previousAgeGroupCases = 0; previousAgeGroupPopulation = 0; previousAgeGroupWstdPopulation = 0; } else if (ageGroupNumber < highestPopulationAgeGroup) { previousAgeGroupCases += casesArray[icdGroup][sexNumber][ageGroupNumber]; previousAgeGroupPopulation += populationArray[sexNumber][ageGroupNumber]; previousAgeGroupWstdPopulation += standardPopulationArray[sexNumber][ageGroupNumber]; } else { lastAgeGroupCases += casesArray[icdGroup][sexNumber][ageGroupNumber]; lastAgeGroupPopulation += populationArray[sexNumber][ageGroupNumber]; lastAgeGroupWstdPopulation += standardPopulationArray[sexNumber][ageGroupNumber]; } totalCases[sexNumber][icdGroup] += casesArray[icdGroup][sexNumber][ageGroupNumber]; } // We calculate the "leftovers" from the last age group if (lastAgeGroupPopulation > 0) { double asr = calculateASR(lastAgeGroupCases, lastAgeGroupPopulation, lastAgeGroupWstdPopulation); } // and take the unknown age group into account totalCases[sexNumber][icdGroup] += casesArray[icdGroup][sexNumber][unknownAgeGroupIndex]; if (totalCases[sexNumber][icdGroup] > 0) { /* We don't use confidence intervals so this was removed 16.07.07 double[] asrlul = calculateASRluL(ASR[sex][icdGroup], variL[sex][icdGroup], wstdPop[allAgeGroupsIndex]); ASRluL[sex][icdGroup][0] = asrlul[0]; ASRluL[sex][icdGroup][1] = asrlul[1]; */ // Cum. Rates if (highestPopulationAgeGroup > 13) { for (int k = 1; k <= 13; k++) { // cumRate64[sexNumber][icdGroup] += casesPerHundredThousand[sexNumber][k][icdGroup] * cumPop18[k] / 1000.0; } } if (highestPopulationAgeGroup > 15) { for (int k = 1; k <= 15; k++) { // cumRate74[sexNumber][icdGroup] += casesPerHundredThousand[sexNumber][k][icdGroup] * cumPop18[k] / 1000.0; } } /* if (!isSpecialized) { cumRate64[sex][allCancerGroupsIndex] += cumRate64[sex][icdGroup]; cumRate74[sex][allCancerGroupsIndex] += cumRate74[sex][icdGroup]; if (icdGroup!=skinCancerGroupIndex) { cumRate64[sex][allCancerGroupsIndex] += cumRate64[sex][icdGroup]; cumRate74[sex][allCancerGroupsIndex] += cumRate74[sex][icdGroup]; } } */ } } } // Adjust the age labels ageLabel[1] = "0-"; ageLabel[highestPopulationAgeGroup] = ageLabel[highestPopulationAgeGroup].substring(0, ageLabel[highestPopulationAgeGroup].length() - 1) + "+"; // Write it out NumberFormat nf = NumberFormat.getInstance(); nf.setMaximumFractionDigits(1); nf.setMinimumFractionDigits(1); Writer reportFileWriter; if (fileType.equals(FileTypes.csv)) { // write tab separated stuff here CSVPrinter csvOut; for (int sexNumber = 0; sexNumber < numberOfSexes - 1; sexNumber++) { try { String tabReportFileName = ""; try { tabReportFileName = reportFileName + sexLabel[sexNumber] + ".csv"; System.out.println(java.util.ResourceBundle.getBundle( "canreg/client/analysis/resources/AgeSpecificCasesPerHundredThousandTableBuilder") .getString("WRITING TO ") + tabReportFileName); reportFileWriter = new OutputStreamWriter(new FileOutputStream(tabReportFileName), "UTF-8"); } catch (IOException ioe) { System.out.println(java.util.ResourceBundle.getBundle( "canreg/client/analysis/resources/AgeSpecificCasesPerHundredThousandTableBuilder") .getString("ERROR IN REPORTFILE: ") + tabReportFileName); reportFileWriter = new OutputStreamWriter(System.out); } // reportStream = new PrintStream(tabReportFileName); // write the header line // reportStream = new PrintStream(tabReportFileName); // write the header line LinkedList<String> headers = new LinkedList<String>(); headers.add("SITE"); headers.add("ALL AGES"); headers.add("AGE UNK"); // add age groups for (int age = 1; age <= highestPopulationAgeGroup; age++) { headers.add(ageLabel[age]); } // headers.add("CRUDE RATE"); headers.add("(%)"); // headers.add("CUM 0-64"); // headers.add("CUM 0-74"); // headers.add("ASR"); headers.add("ICD (10th)"); CSVFormat format = CSVFormat.DEFAULT.withDelimiter(',') .withHeader(headers.toArray(new String[0])); csvOut = new CSVPrinter(reportFileWriter, format); LinkedList<String> line = new LinkedList<String>(); // write the data for (int j = 0; j < numberOfCancerGroups; j++) { if (icdLabel[j].charAt(sexNumber) == '1') { line.add(icdLabel[j].substring(3)); line.add(formatNumber(totalCases[sexNumber][j], 0)); line.add(formatNumber(casesArray[j][sexNumber][unknownAgeGroupIndex], 0)); for (int age = 1; age <= highestPopulationAgeGroup; age++) { if (casesArray[j][sexNumber][age] > 0) { line.add(formatNumber(casesArray[j][sexNumber][age], 0)); } else { line.add("0"); } } // line.add(formatNumber(crudeRate[sexNumber][j], 2)); line.add(formatNumber(100 * totalCases[sexNumber][j] / totalCases[sexNumber][allCancerGroupsButSkinIndex])); // line.add(formatNumber(cumRate64[sexNumber][j], 2)); // line.add(formatNumber(cumRate74[sexNumber][j], 2)); // line.add(formatNumber(ASR[sexNumber][j])); line.add(icd10GroupDescriptions[j]); csvOut.printRecord(line); line.clear(); } } try { csvOut.flush(); csvOut.close(); } catch (IOException ex) { Logger.getLogger(AgeSpecificCasesPerHundredThousandTableBuilder.class.getName()) .log(Level.SEVERE, null, ex); } generatedFiles.add(tabReportFileName); } catch (IOException ex) { Logger.getLogger(AgeSpecificCasesTableBuilder.class.getName()).log(Level.SEVERE, null, ex); } } } else { // Make PS-file for (int sexNumber = 0; sexNumber < numberOfSexes - 1; sexNumber++) { String psFileName = reportFileName + "-" + sexLabel[sexNumber] + ".ps"; generatedFiles.add(psFileName); try { Writer fw = new OutputStreamWriter(new FileOutputStream(psFileName), "UTF-8"); nf.setMaximumFractionDigits(1); nf.setMinimumFractionDigits(1); fw.write("/RLT {rlineto} def\n"); fw.write("/LT {lineto} def\n"); fw.write("/MT {moveto} def\n"); fw.write("/SCF {scalefont} def\n"); fw.write("/SF {setfont} def\n"); fw.write("/SG {setgray} def\n"); fw.write("/FF {findfont} def\n"); fw.write("/SLW {setlinewidth} def\n"); fw.write("/CP {closepath} def\n"); fw.write("/Mainfont\n"); fw.write("/Helvetica-Bold FF " + (int) (tableFontSize * 2 - 3) + " SCF def\n"); fw.write("/Titlefont\n"); fw.write("/Helvetica FF " + tableFontSize + " SCF def\n"); fw.write("/Tablefont\n"); fw.write("/" + font + " FF " + tableFontSize + " SCF def\n"); fw.write("/ASRfont\n"); fw.write("/" + font + "-Bold FF " + tableFontSize + " SCF def\n"); fw.write("/ICDfont\n"); fw.write("/" + font + "-Italic FF " + tableFontSize + " SCF def\n"); fw.write("/ASRitalicsfont\n"); fw.write("/" + font + "-Italic-Bold FF " + tableFontSize + " SCF def\n"); fw.write("/col 735 def\n"); fw.write("/RS {dup stringwidth pop col exch sub 0 rmoveto show} def\n"); fw.write("/CS {dup stringwidth pop 810 exch sub 2 div 0 rmoveto show} def\n"); fw.write("/nstr 1 string def\n"); fw.write("/prtchar {nstr 0 3 -1 roll put nstr show} def\n"); fw.write("newpath\n"); fw.write("90 rotate -20 -570 translate\n"); // Landscape fw.write("Mainfont SF\n"); fw.write("0 535 MT (" + registryLabel + ") CS\n"); fw.write("Titlefont SF\n"); fw.write("0 525 MT (" + populationString + ") CS\n"); fw.write("0 513 MT (" + tableLabel[0] + " - " + sexLabel[sexNumber] + ") CS\n"); // draw the grey frame fw.write("0.85 SG 27 510 translate\n"); fw.write("0 -5 MT 785 -5 LT 785 -27 LT 0 -27 LT CP fill\n"); fw.write("0 -510 translate 0.95 SG\n"); double k = 475; for (int icd = 0; icd < numberOfCancerGroups; icd++) { if ((icd + 1) < numberOfCancerGroups && icdLabel[icd + 1].charAt(sexNumber) == '1') { int lines = (isLineBreak(icd)); if (lines > 0) { k -= 2; fw.write("0 " + (k - 2) + " MT 785 " + (k - 2) + " LT 785 " + (k - 2 - (lines * (tableFontSize))) + " LT 0 " + (k - 2 - (lines * (tableFontSize))) + " LT CP fill\n"); } else if (lines < 0) { k -= 2; } k -= tableFontSize; } } /* for (int j = 0; j < numberOfCancerGroups; j++) { if (icdLabel[j].charAt(sex) == '1') { int lines = (isLineBreak(j)); if (lines > 0) { k -= 2; fw.write( "0 " + (k + tableFontSize) + " MT 774 " + (k + tableFontSize) + " LT 774 " + (k - lines * tableFontSize) + " LT 0 " + (k - lines * tableFontSize) + " LT CP fill\n"); } else if (lines > 0) k -= 2; k -= lines * tableFontSize; if (IsLineBreak(j)) { k -= 2; } // draw the grey frames if (j == 8) { fw.write( "0 " + (k + tableFontSize) + " MT 774 " + (k + tableFontSize) + " LT 774 " + (k - 35) + " LT 0 " + (k - 35) + " LT CP fill\n"); } else if (j == 34) { fw.write( "0 " + (k + tableFontSize) + " MT 774 " + (k + tableFontSize) + " LT 774 " + (k - 26) + " LT 0 " + (k - 26) + " LT CP fill\n"); } else if (j == 16 || j == 22 || j == 40) { fw.write( "0 " + (k + tableFontSize) + " MT 774 " + (k + tableFontSize) + " LT 774 " + (k - 18) + " LT 0 " + (k - 18) + " LT CP fill\n"); } else if (j == 27) { fw.write( "0 " + (k + tableFontSize) + " MT 774 " + (k + tableFontSize) + " LT 774 " + (k - 42) + " LT 0 " + (k - 42) + " LT CP fill\n"); } else if (j == 47) { fw.write( "0 " + (k + tableFontSize) + " MT 774 " + (k + tableFontSize) + " LT 774 " + (k - 34) + " LT 0 " + (k - 34) + " LT CP fill\n"); } else if (j == 53) { fw.write( "0 " + (k + tableFontSize) + " MT 774 " + (k + tableFontSize) + " LT 774 " + (k - 12) + " LT 0 " + (k - 12) + " LT CP fill\n"); } k -= (tableFontSize); } } */ fw.write("0 SG\n"); fw.write("ICDfont SF\n"); fw.write(" 740 496 MT (ICD) show\n"); fw.write(" 740 487 MT ((10th)) show\n"); k = 475; for (int j = 0; j < numberOfCancerGroups; j++) { if (icdLabel[j].charAt(sexNumber) == '1') { if (isLineBreak(j - 1) != 0) { k -= 2; } if (j == skinCancerGroupIndex || j == ovaryCancerGroupIndex || j == bladderCancerGroupIndex || j == myelodysplasticSyndromesCancerGroupIndex || j == myeloproliferativeDisordersCancerGroupIndex || j == brainAndCentralNervousSystemCancerGroupIndex) { fw.write("ICDfont SF\n"); } else { fw.write("ICDfont SF\n"); } fw.write("745 " + k + " MT (" + icd10GroupDescriptions[j] + ") show\n"); k -= (tableFontSize); } } fw.write("/col col 20 sub def\n"); fw.write("0 491 MT ((%)) RS\n"); k = 475; for (int j = 0; j < numberOfCancerGroups; j++) { if (icdLabel[j].charAt(sexNumber) == '1') { if (isLineBreak(j - 1) != 0) { k -= 2; } if (j == skinCancerGroupIndex || j == ovaryCancerGroupIndex || j == bladderCancerGroupIndex || j == myelodysplasticSyndromesCancerGroupIndex || j == myeloproliferativeDisordersCancerGroupIndex || j == brainAndCentralNervousSystemCancerGroupIndex) { fw.write("ICDfont SF\n"); } else { fw.write("Tablefont SF\n"); } if (j != allCancerGroupsIndex && allCancerGroupsButSkinIndex >= 0) { fw.write( "0 " + k + " MT (" + formatNumber(100 * totalCases[sexNumber][j] / totalCases[sexNumber][allCancerGroupsButSkinIndex]) + ") RS\n"); } k -= (tableFontSize); } } fw.write("/col 119 def\n"); fw.write("0 496 MT (ALL) RS\n"); fw.write("0 487 MT (AGES) RS\n"); k = 475; for (int j = 0; j < numberOfCancerGroups; j++) { if (icdLabel[j].charAt(sexNumber) == '1') { if (isLineBreak(j - 1) != 0) { k -= 2; } if (j == skinCancerGroupIndex || j == ovaryCancerGroupIndex || j == bladderCancerGroupIndex || j == myelodysplasticSyndromesCancerGroupIndex || j == myeloproliferativeDisordersCancerGroupIndex || j == brainAndCentralNervousSystemCancerGroupIndex) { fw.write("ICDfont SF\n"); } else { fw.write("Tablefont SF\n"); } fw.write("0 " + k + " MT (" + formatNumber(totalCases[sexNumber][j], 0) + ") RS\n"); k -= (tableFontSize); } } fw.write("/col col 20 add def\n"); fw.write("0 496 MT (AGE) RS\n"); fw.write("0 487 MT (UNK) RS\n"); k = 475; for (int j = 0; j < numberOfCancerGroups; j++) { if (icdLabel[j].charAt(sexNumber) == '1') { if (isLineBreak(j - 1) != 0) { k -= 2; } if (j == skinCancerGroupIndex || j == ovaryCancerGroupIndex || j == bladderCancerGroupIndex || j == myelodysplasticSyndromesCancerGroupIndex || j == myeloproliferativeDisordersCancerGroupIndex || j == brainAndCentralNervousSystemCancerGroupIndex) { fw.write("ICDfont SF\n"); } else { fw.write("Tablefont SF\n"); } fw.write("0 " + k + " MT (" + formatNumber(casesArray[j][sexNumber][unknownAgeGroupIndex], 0) + ") RS\n"); k -= (tableFontSize); } } if (highestPopulationAgeGroup == numberOfAgeGroups - 4) { fw.write("/col 145 def\n"); } else if (highestPopulationAgeGroup == numberOfAgeGroups - 5) { fw.write("/col 176 def\n"); } else if (highestPopulationAgeGroup == numberOfAgeGroups - 6) { fw.write("/col 208 def\n"); } else { fw.write("/col 145 def\n"); } for (int age = 1; age <= highestPopulationAgeGroup; age++) { fw.write("/col col 26 add def\n"); fw.write("0 491 MT (" + ageLabel[age] + ") RS\n"); // fw.write("/col col 5 sub def\n"); k = 475; for (int j = 0; j < numberOfCancerGroups; j++) { if (icdLabel[j].charAt(sexNumber) == '1') { if (isLineBreak(j - 1) != 0) { k -= 2; } if (j == skinCancerGroupIndex || j == ovaryCancerGroupIndex || j == bladderCancerGroupIndex || j == myelodysplasticSyndromesCancerGroupIndex || j == myeloproliferativeDisordersCancerGroupIndex || j == brainAndCentralNervousSystemCancerGroupIndex) { fw.write("ICDfont SF\n"); } else { fw.write("Tablefont SF\n"); } if (casesArray[j][sexNumber][age] > 0) { fw.write("0 " + k + " MT (" + formatNumber(casesArray[j][sexNumber][age], 0) + ") RS\n"); } else { fw.write("0 " + k + " MT ( - ) RS\n"); } k -= (tableFontSize); } } } fw.write("3 492 MT ( S I T E) show\n"); k = 475; for (int j = 0; j < numberOfCancerGroups; j++) { if (icdLabel[j].charAt(sexNumber) == '1') { if (isLineBreak(j - 1) != 0) { k -= 2; } if (j == skinCancerGroupIndex || j == ovaryCancerGroupIndex || j == bladderCancerGroupIndex || j == myelodysplasticSyndromesCancerGroupIndex || j == myeloproliferativeDisordersCancerGroupIndex || j == brainAndCentralNervousSystemCancerGroupIndex) { fw.write("ICDfont SF\n"); } else { fw.write("Tablefont SF\n"); } fw.write("3 " + k + " MT (" + icdLabel[j].substring(3) + ") show\n"); k -= (tableFontSize); } } if (showSeeNotesNote) { fw.write("3 0 MT (" + notesString + ") show\n"); } // Write the footer fw.write("0 0 MT (" + footerString + ") CS\n"); fw.write("showpage\n"); System.out.println("Wrote " + psFileName + "."); fw.close(); } catch (IOException ioe) { System.out.println(ioe); } } } if (fileType == FileTypes.pdf) { LinkedList<String> newlyGeneratedFiles = new LinkedList<String>(); for (String fileN : generatedFiles) { PsToPdfConverter pstopdf = new PsToPdfConverter(gspath); newlyGeneratedFiles.add(pstopdf.convert(fileN)); // delete the ps file File file = new File(fileN); file.delete(); } generatedFiles = newlyGeneratedFiles; } System.out.println("Fini!"); return generatedFiles; }
From source file:com.kdmanalytics.toif.ui.common.AdaptorConfiguration.java
/** Export to the specified file * //from w w w . j a va 2 s .com * @param file * @throws IOException */ public void export(File file) throws IOException { OutputStream os = null; CSVPrinter printer = null; try { os = new FileOutputStream(file); // Create the CSVFormat object with "\n" as a record delimiter CSVFormat csvFileFormat = CSVFormat.DEFAULT.withRecordSeparator(NEW_LINE_SEPARATOR); OutputStreamWriter out = new OutputStreamWriter(os); printer = new CSVPrinter(out, csvFileFormat); printer.printRecord(headers); for (List<?> row : data) { printer.printRecord(row); } } finally { if (printer != null) printer.close(); if (os != null) os.close(); } }