List of usage examples for org.apache.poi.hssf.usermodel HSSFSheet rowIterator
@Override
public Iterator<Row> rowIterator()
From source file:de.sub.goobi.forms.ProzessverwaltungForm.java
License:Open Source License
/** * Generate result as PDF./* w w w . j a v a 2 s. c o m*/ */ public void generateResultAsPdf() { FacesContext facesContext = FacesContext.getCurrentInstance(); if (!facesContext.getResponseComplete()) { /* * Vorbereiten der Header-Informationen */ HttpServletResponse response = (HttpServletResponse) facesContext.getExternalContext().getResponse(); try { ServletContext servletContext = (ServletContext) facesContext.getExternalContext().getContext(); String contentType = servletContext.getMimeType("search.pdf"); response.setContentType(contentType); response.setHeader("Content-Disposition", "attachment;filename=\"search.pdf\""); ServletOutputStream out = response.getOutputStream(); SearchResultGeneration sr = new SearchResultGeneration(this.filter, this.showClosedProcesses, this.showArchivedProjects); HSSFWorkbook wb = sr.getResult(); List<List<HSSFCell>> rowList = new ArrayList<>(); HSSFSheet mySheet = wb.getSheetAt(0); Iterator<Row> rowIter = mySheet.rowIterator(); while (rowIter.hasNext()) { HSSFRow myRow = (HSSFRow) rowIter.next(); Iterator<Cell> cellIter = myRow.cellIterator(); List<HSSFCell> row = new ArrayList<>(); while (cellIter.hasNext()) { HSSFCell myCell = (HSSFCell) cellIter.next(); row.add(myCell); } rowList.add(row); } Document document = new Document(); Rectangle a4quer = new Rectangle(PageSize.A3.getHeight(), PageSize.A3.getWidth()); PdfWriter.getInstance(document, out); document.setPageSize(a4quer); document.open(); if (rowList.size() > 0) { Paragraph p = new Paragraph(rowList.get(0).get(0).toString()); document.add(p); PdfPTable table = new PdfPTable(9); table.setSpacingBefore(20); for (List<HSSFCell> row : rowList) { for (HSSFCell hssfCell : row) { // TODO aufhbschen und nicht toString() nutzen String stringCellValue = hssfCell.toString(); table.addCell(stringCellValue); } } document.add(table); } document.close(); out.flush(); facesContext.responseComplete(); } catch (Exception e) { logger.error(e); } } }
From source file:domain.Excel.java
public static void leerArchivoSesion(String archivoSesion) { List sheetData = new ArrayList(); FileInputStream fis = null; try {/*from ww w .j av a 2 s .c o m*/ fis = new FileInputStream(archivoSesion); HSSFWorkbook workbook = new HSSFWorkbook(fis); HSSFSheet sheet = workbook.getSheetAt(0); Iterator rows = sheet.rowIterator(); while (rows.hasNext()) { HSSFRow row = (HSSFRow) rows.next(); Iterator cells = row.cellIterator(); List data = new ArrayList(); while (cells.hasNext()) { HSSFCell cell = (HSSFCell) cells.next(); data.add(cell); } sheetData.add(data); } } catch (FileNotFoundException ex) { Logger.getLogger(Excel.class.getName()).log(Level.SEVERE, null, ex); } catch (IOException ex) { Logger.getLogger(Excel.class.getName()).log(Level.SEVERE, null, ex); } finally { if (fis != null) { try { fis.close(); } catch (IOException ex) { Logger.getLogger(Excel.class.getName()).log(Level.SEVERE, null, ex); } } } showExelData(sheetData); }
From source file:edu.duke.cabig.c3pr.web.study.tabs.StudyEligibilityChecklistTab.java
License:BSD License
public void parseCadsrFile(Study study, POIFSFileSystem pfs, String name) { List<InclusionEligibilityCriteria> incList = null; List<ExclusionEligibilityCriteria> excList = null; if (study.getEpochByName(name) != null) { incList = study.getEpochByName(name).getInclusionEligibilityCriteria(); excList = study.getEpochByName(name).getExclusionEligibilityCriteria(); } else {/*from w ww . ja v a2 s . c om*/ return; } try { HSSFWorkbook wb = new HSSFWorkbook(pfs); HSSFSheet sheet = wb.getSheetAt(0); HSSFRow currentRow; HSSFCell currentCell; InclusionEligibilityCriteria inc = null; ExclusionEligibilityCriteria exc = null; Iterator rowIter = sheet.rowIterator(); // iterating over the entire file while (rowIter.hasNext()) { currentRow = (HSSFRow) rowIter.next(); // inclusion section if (currentRow.getCell((short) 0) != null && currentRow.getCell((short) 0).getCellType() == HSSFCell.CELL_TYPE_STRING && currentRow .getCell((short) 0).getRichStringCellValue().toString().startsWith(INCLUSION)) { // iterating over the inclusion rows HSSFRow innerCurrentRow; while (rowIter.hasNext()) { innerCurrentRow = (HSSFRow) rowIter.next(); if (innerCurrentRow.getCell((short) 0) != null && innerCurrentRow.getCell((short) 0).getCellType() == HSSFCell.CELL_TYPE_STRING && innerCurrentRow.getCell((short) 0).getRichStringCellValue().toString() .startsWith(EXCLUSION)) { currentRow = innerCurrentRow; break; } currentCell = innerCurrentRow.getCell((short) 3); if (currentCell != null && currentCell.getCellType() == HSSFCell.CELL_TYPE_STRING && currentCell.getRichStringCellValue().toString().length() > 0) { // create the new inc and populate the list if (inc != null) { incList.add(inc); } inc = new InclusionEligibilityCriteria(); inc.setQuestionText(currentCell.getRichStringCellValue().toString()); } else { // get the answers currentCell = innerCurrentRow.getCell((short) 15); if (currentCell != null && currentCell.getCellType() == HSSFCell.CELL_TYPE_STRING && currentCell.getRichStringCellValue().toString() .equalsIgnoreCase(NOT_APPLICABLE)) { if (inc != null) { inc.setNotApplicableIndicator(true); } } } } // adding the last criteria to the list incList.add(inc); } // end of inclusion if // exclusion section if (currentRow.getCell((short) 0) != null && currentRow.getCell((short) 0).getCellType() == HSSFCell.CELL_TYPE_STRING && currentRow .getCell((short) 0).getRichStringCellValue().toString().startsWith(EXCLUSION)) { // iterating over the exclusion rows HSSFRow innerCurrentRow; while (rowIter.hasNext()) { innerCurrentRow = (HSSFRow) rowIter.next(); // This if loop is not needed as we only have 1 inc section and 1 exc // section // however leaving it in place as it is harmless and will be useful if we // ever have repeated inc/exc sections in the input file if (innerCurrentRow.getCell((short) 0) != null && innerCurrentRow.getCell((short) 0).getCellType() == HSSFCell.CELL_TYPE_STRING && innerCurrentRow.getCell((short) 0).getRichStringCellValue().toString() .startsWith(INCLUSION)) { currentRow = innerCurrentRow; break; } currentCell = innerCurrentRow.getCell((short) 3); if (currentCell != null && currentCell.getCellType() == HSSFCell.CELL_TYPE_STRING && currentCell.getRichStringCellValue().toString().length() > 0) { // create the new exc and populate the list if (exc != null) { excList.add(exc); } exc = new ExclusionEligibilityCriteria(); exc.setQuestionText(currentCell.getRichStringCellValue().toString()); } else { // get the answers currentCell = innerCurrentRow.getCell((short) 15); if (currentCell != null && currentCell.getRichStringCellValue() != null && currentCell.getCellType() == HSSFCell.CELL_TYPE_STRING && currentCell .getRichStringCellValue().toString().equalsIgnoreCase(NOT_APPLICABLE)) { if (exc != null) { exc.setNotApplicableIndicator(true); } } } } // adding the last criteria to the list excList.add(exc); } // end of exclusion if } // end if while loop that iterates over the entire file. } catch (IOException ioe) { log.error(ioe.getMessage()); } }
From source file:edu.ku.brc.specify.tasks.subpane.wb.ConfigureXLS.java
License:Open Source License
/** * Fills badHeads with indexes for columns that contain data but don't have a header or have an non-string header (because it makes things difficult with HSSF). * Fills emptyCols with indexes for columns that are totally empty. * Assumes that badHeads and emptyCols are not null and empty. * /*from w w w . j a va2 s . c om*/ */ public void checkHeadsAndCols(final HSSFSheet sheet, Vector<Integer> badHeads, Vector<Integer> emptyCols) { boolean firstRow = true; Vector<Boolean> firstRowCells = new Vector<Boolean>(); Vector<Boolean> restCells = new Vector<Boolean>(); // Iterate over each row in the sheet Iterator<?> rows = sheet.rowIterator(); while (rows.hasNext()) { HSSFRow row = (HSSFRow) rows.next(); int maxSize = Math.max(row.getPhysicalNumberOfCells(), row.getLastCellNum()); for (int col = 0; col < maxSize; col++) { if (firstRow) { if (row.getCell(col) == null) { firstRowCells.add(false); } else if (row.getCell(col).getCellType() == HSSFCell.CELL_TYPE_STRING) { firstRowCells.add(true); } else { firstRowCells.add(null); } } else { if (col == restCells.size()) { restCells.add(false); } if (!restCells.get(col)) { restCells.set(col, row.getCell(col) != null); } } } firstRow = false; } //pad smaller vector with false if necessary. while (restCells.size() < firstRowCells.size()) { restCells.add(false); } while (firstRowCells.size() < restCells.size()) { firstRowCells.add(false); } for (int c = 0; c < firstRowCells.size(); c++) { if (firstRowCells.get(c) == null || (!firstRowCells.get(c) && restCells.get(c))) { badHeads.add(c); } if (firstRowCells.get(c) != null && !firstRowCells.get(c) && !restCells.get(c)) { emptyCols.add(c); } } }
From source file:edu.ku.brc.specify.tasks.subpane.wb.ConfigureXLS.java
License:Open Source License
@Override protected void nonInteractiveConfig() { try {//from ww w . ja va 2 s. c o m InputStream input = new FileInputStream(externalFile); POIFSFileSystem fs = new POIFSFileSystem(input); HSSFWorkbook workBook = new HSSFWorkbook(fs); HSSFSheet sheet = workBook.getSheetAt(0); // Calculate the number of rows and columns colInfo = new Vector<ImportColumnInfo>(16); Hashtable<Integer, Boolean> colTracker = new Hashtable<Integer, Boolean>(); boolean firstRow = true; int col = 0; colTracker.clear(); Vector<Integer> badHeads = new Vector<Integer>(); Vector<Integer> emptyCols = new Vector<Integer>(); checkHeadsAndCols(sheet, badHeads, emptyCols); if (firstRowHasHeaders && badHeads.size() > 0) { status = ConfigureExternalDataIFace.Status.Error; showBadHeadingsMsg(badHeads, null, getResourceString("Error")); return; } // Iterate over each row in the sheet @SuppressWarnings("unchecked") Iterator<HSSFRow> rows = sheet.rowIterator(); while (rows.hasNext()) { HSSFRow row = rows.next(); if (firstRow || numRows == 1) { // Iterate over each cell in the row and print out the cell's content int colNum = 0; int maxSize = Math.max(row.getPhysicalNumberOfCells(), row.getLastCellNum()); while (colNum < maxSize) { if (emptyCols.indexOf(new Integer(colNum)) == -1) { ImportColumnInfo.ColumnType disciplinee = ImportColumnInfo.ColumnType.Integer; String value = null; boolean skip = false; HSSFCell cell = row.getCell(colNum); if (cell == null) { //assuming numRows == 1 or not firstRowHasHeaders. //the call to checkHeadsAndCols would have already blank headers. value = ""; disciplinee = ImportColumnInfo.ColumnType.String; } else switch (cell.getCellType()) { case HSSFCell.CELL_TYPE_NUMERIC: double numeric = cell.getNumericCellValue(); value = Double.toString(numeric); disciplinee = ImportColumnInfo.ColumnType.Double; break; case HSSFCell.CELL_TYPE_STRING: HSSFRichTextString richVal = cell.getRichStringCellValue(); value = richVal.getString().trim(); disciplinee = ImportColumnInfo.ColumnType.String; break; case HSSFCell.CELL_TYPE_BLANK: value = ""; disciplinee = ImportColumnInfo.ColumnType.String; break; case HSSFCell.CELL_TYPE_BOOLEAN: boolean bool = cell.getBooleanCellValue(); value = Boolean.toString(bool); disciplinee = ImportColumnInfo.ColumnType.Boolean; break; default: skip = true; break; } if (numRows == 1 && !skip) { colInfo.get(col).setData(value); col++; } else if (!skip) { if (firstRowHasHeaders) { colInfo.add(new ImportColumnInfo(colNum, disciplinee, value, value, null, null, null)); colTracker.put(col, true); } else { String colName = getResourceString("DEFAULT_COLUMN_NAME") + " " + (colNum + 1); colInfo.add(new ImportColumnInfo(colNum, disciplinee, colName, colName, null, null, null)); colTracker.put(colNum, true); } numCols++; } } colNum++; } firstRow = false; } numRows++; } Collections.sort(colInfo); readMappings(fs); status = Status.Valid; } catch (IOException ex) { edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(ConfigureXLS.class, ex); status = Status.Error; } }
From source file:edu.ku.brc.specify.tasks.subpane.wb.DataImportDialog.java
License:Open Source License
/** * Parses the given import xls file according to the users selection and creates/updates the * Preview table, showing the user how the import options effect the way the data will be * imported into the spreadsheet.// w w w . j a v a2 s . c o m * * @param table - the table to display the data * @return JTable - the table to display the data */ private JTable setXLSTableData(final JTable table) { int numRows = 0; int numCols = 0; String[] headers = {}; Vector<Vector<String>> tableDataVector = new Vector<Vector<String>>(); Vector<String> rowData = new Vector<String>(); Vector<String> headerVector = new Vector<String>(); DateWrapper scrDateFormat = AppPrefsCache.getDateWrapper("ui", "formatting", "scrdateformat"); try { log.debug("setXLSTableData - file - " + configXLS.getFile().toString()); InputStream input = new FileInputStream(configXLS.getFile()); POIFSFileSystem fs = new POIFSFileSystem(input); HSSFWorkbook workBook = new HSSFWorkbook(fs); HSSFSheet sheet = workBook.getSheetAt(0); Vector<Integer> badHeads = new Vector<Integer>(); Vector<Integer> emptyCols = new Vector<Integer>(); ((ConfigureXLS) config).checkHeadsAndCols(sheet, badHeads, emptyCols); if (badHeads.size() > 0 && doesFirstRowHaveHeaders) { if (table != null) { ((ConfigureXLS) config).showBadHeadingsMsg(badHeads, emptyCols, getTitle()); } this.doesFirstRowHaveHeaders = false; try { ignoreActions = true; this.containsHeaders.setSelected(false); } finally { ignoreActions = false; } if (table != null) { return table; } } boolean firstRow = true; //quick fix to prevent ".0" at end of catalog numbers etc NumberFormat nf = NumberFormat.getInstance(); nf.setMinimumFractionDigits(0); nf.setMaximumFractionDigits(20); nf.setGroupingUsed(false); //gets rid of commas int maxCols = 0; // Iterate over each row in the sheet Iterator<?> rows = sheet.rowIterator(); while (rows.hasNext()) { numCols = 0; rowData = new Vector<String>(); HSSFRow row = (HSSFRow) rows.next(); //log.debug(row.getLastCellNum()+" "+row.getPhysicalNumberOfCells()); int maxSize = Math.max(row.getPhysicalNumberOfCells(), row.getLastCellNum()); if (maxSize > maxCols) { maxCols = maxSize; } while (numCols < maxSize) { if (emptyCols.indexOf(new Integer(numCols)) == -1) { HSSFCell cell = row.getCell(numCols); String value = null; // if cell is blank, set value to "" if (cell == null) { value = ""; } else { int type = cell.getCellType(); switch (type) { case HSSFCell.CELL_TYPE_NUMERIC: // The best I can do at this point in the app is to guess if a // cell is a date. // Handle dates carefully while using HSSF. Excel stores all // dates as numbers, internally. // The only way to distinguish a date is by the formatting of // the cell. (If you // have ever formatted a cell containing a date in Excel, you // will know what I mean.) // Therefore, for a cell containing a date, cell.getCellType() // will return // HSSFCell.CELL_TYPE_NUMERIC. However, you can use a utility // function, // HSSFDateUtil.isCellDateFormatted(cell), to check if the cell // can be a date. // This function checks the format against a few internal // formats to decide the issue, // but by its very nature it is prone to false negatives. if (HSSFDateUtil.isCellDateFormatted(cell)) { value = scrDateFormat.getSimpleDateFormat().format(cell.getDateCellValue()); //value = scrDateFormat.getSimpleDateFormat().format(cell.getDateCellValue()); } else { double numeric = cell.getNumericCellValue(); value = nf.format(numeric); } break; case HSSFCell.CELL_TYPE_STRING: value = cell.getRichStringCellValue().getString(); break; case HSSFCell.CELL_TYPE_BLANK: value = ""; break; case HSSFCell.CELL_TYPE_BOOLEAN: value = Boolean.toString(cell.getBooleanCellValue()); break; case HSSFCell.CELL_TYPE_FORMULA: value = UIRegistry.getResourceString("WB_FORMULA_IMPORT_NO_PREVIEW"); break; default: value = ""; log.error("unsuported cell type"); break; } } if (firstRow && doesFirstRowHaveHeaders) { checkUserColInfo(value, numCols); } if (isUserCol(numCols)) { rowData.add(value.toString()); } } numCols++; } if (doesFirstRowHaveHeaders && firstRow) { headerVector = rowData; headers = new String[rowData.size()]; } else if (!doesFirstRowHaveHeaders && firstRow) { //headers = createDummyHeaders(rowData.size()); tableDataVector.add(rowData); } else { tableDataVector.add(rowData); } firstRow = false; numRows++; } maxCols -= emptyCols.size(); if (!doesFirstRowHaveHeaders) { headerVector = createDummyHeadersAsVector(maxCols); headers = new String[maxCols]; } for (int i = 0; i < headerVector.size(); i++) { headers[i] = headerVector.elementAt(i); } printArray(headers); String[][] tableData = new String[tableDataVector.size()][maxCols]; for (int i = 0; i < tableDataVector.size(); i++) { Vector<String> v = tableDataVector.get(i); for (int j = 0; j < v.size(); j++) { tableData[i][j] = v.get(j).toString(); } } if (checkForErrors(headers, tableData)) { errorPanel.showDataImportStatusPanel(true); } else { errorPanel.showDataImportStatusPanel(false); } if ((doesFirstRowHaveHeaders ? numRows - 1 : numRows) > WorkbenchTask.MAX_ROWS) { hasTooManyRows = true; showTooManyRowsErrorDialog(); } else { hasTooManyRows = false; } log.debug(headers); log.debug(tableData); model = new PreviewTableModel(headers, tableData); JTable result = null; if (table == null) { result = new JTable(); result.setColumnSelectionAllowed(false); result.setRowSelectionAllowed(false); result.setCellSelectionEnabled(false); result.getTableHeader().setReorderingAllowed(false); result.setPreferredScrollableViewportSize(new Dimension(500, 100)); result.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); } else { result = table; } result.setModel(model); result.setDefaultRenderer(String.class, new BiColorTableCellRenderer(false)); model.fireTableDataChanged(); model.fireTableStructureChanged(); return result; } catch (Exception ex) { UIRegistry.displayErrorDlgLocalized(UIRegistry.getResourceString("WB_ERROR_READING_IMPORT_FILE")); if (table != null) { String[] columnNames = {}; String[][] blankData = { {} }; model = new PreviewTableModel(columnNames, blankData); table.setModel(model); table.setColumnSelectionAllowed(false); table.setRowSelectionAllowed(false); table.setCellSelectionEnabled(false); table.getTableHeader().setReorderingAllowed(false); table.setPreferredScrollableViewportSize(new Dimension(500, 100)); table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); table.setDefaultRenderer(String.class, new BiColorTableCellRenderer(false)); model.fireTableDataChanged(); model.fireTableStructureChanged(); return table; } //log.error("Error attempting to parse input xls file:" + ex); //ex.printStackTrace(); } return null; }
From source file:edu.ku.brc.specify.tasks.subpane.wb.XLSImport.java
License:Open Source License
public DataImportIFace.Status getData(final Workbench workbench) { if (config.getStatus() == ConfigureExternalDataIFace.Status.Valid) { DateWrapper scrDateFormat = AppPrefsCache.getDateWrapper("ui", "formatting", "scrdateformat"); try {//w ww . ja va2 s . com InputStream input = new FileInputStream(config.getFile()); POIFSFileSystem fs = new POIFSFileSystem(input); HSSFWorkbook workBook = new HSSFWorkbook(fs); HSSFSheet sheet = workBook.getSheetAt(0); int numRows = 0; // Calculate the number of rows and columns Set<WorkbenchTemplateMappingItem> wbtmiSet = workbench.getWorkbenchTemplate() .getWorkbenchTemplateMappingItems(); Vector<WorkbenchTemplateMappingItem> wbtmiList = new Vector<WorkbenchTemplateMappingItem>(); NumberFormat nf = NumberFormat.getInstance(); nf.setMinimumFractionDigits(0); nf.setMaximumFractionDigits(20); nf.setGroupingUsed(false); //gets rid of commas NumberFormat nfGeoCoord = NumberFormat.getInstance(); nfGeoCoord.setMinimumFractionDigits(0); nfGeoCoord.setMaximumFractionDigits( LatLonConverter.DECIMAL_SIZES[LatLonConverter.FORMAT.DDDDDD.ordinal()]); nfGeoCoord.setGroupingUsed(false); //gets rid of commas char decSep = new DecimalFormatSymbols().getDecimalSeparator(); wbtmiList.addAll(wbtmiSet); Collections.sort(wbtmiList); this.truncations.clear(); Vector<HSSFHyperlink> activeHyperlinks = new Vector<HSSFHyperlink>(); // Iterate over each row in the sheet Iterator<?> rows = sheet.rowIterator(); while (rows.hasNext()) { HSSFRow row = (HSSFRow) rows.next(); if (numRows == 0 && config.getFirstRowHasHeaders()) { numRows++; getSystemCols(row); continue; } WorkbenchRow wbRow = workbench.addRow(); for (WorkbenchTemplateMappingItem wbtmi : wbtmiList) { int cellNum = wbtmi.getOrigImportColumnIndex().intValue(); if (cellNum == -1) { if (wbtmi.getViewOrder() != null) { cellNum = wbtmi.getViewOrder().intValue(); if (cellNum == -1) { continue; } } } HSSFCell cell = row.getCell(cellNum); if (cell == null) { continue; } int type = cell.getCellType(); if (type == HSSFCell.CELL_TYPE_FORMULA) { type = cell.getCachedFormulaResultType(); } String value = ""; boolean skip = false; switch (type) { case HSSFCell.CELL_TYPE_NUMERIC: { if (HSSFDateUtil.isCellDateFormatted(cell)) { //even if WorkbenchTask.getDataType(wbtmi) is not Calendar or Date. Hmmmm. value = scrDateFormat.getSimpleDateFormat().format(cell.getDateCellValue()); } else { Class<?> classObj = WorkbenchTask.getDataType(wbtmi); if (classObj.equals(Integer.class)) { double numeric = cell.getNumericCellValue(); value = Integer.toString((int) numeric); } else if (classObj.equals(Calendar.class) || classObj.equals(Date.class)) { Date d = cell.getDateCellValue(); if (d != null) { value = scrDateFormat.getSimpleDateFormat().format(cell.getDateCellValue()); } else { value = null; } } else { double numeric = cell.getNumericCellValue(); value = nf.format(numeric); if (isGeoCoordinate(wbtmi)) { int sepInx = value.indexOf(decSep); if (sepInx > -1 && value.substring(sepInx).length() > nfGeoCoord .getMaximumFractionDigits()) { String value2 = nfGeoCoord.format(numeric); int maxlen = wbtmi.getFieldName().startsWith("latitude") ? nfGeoCoord.getMaximumFractionDigits() + 3 : nfGeoCoord.getMaximumFractionDigits() + 4; if (numeric < 0) { maxlen++; } //System.out.println(value + " " + trackTrunc(value, numRows, wbtmi.getViewOrder(), wbtmi.getCaption(), // maxlen) + " " + value2); value = value2; } } } } break; } case HSSFCell.CELL_TYPE_STRING: HSSFHyperlink hl = checkHyperlinks(cell, activeHyperlinks); if (hl == null /*|| (hl != null && hl.getType() == HSSFHyperlink.LINK_EMAIL)*/) { value = cell.getRichStringCellValue().getString(); } else { //value = hl.getAddress(); value = hl.getLabel(); } break; case HSSFCell.CELL_TYPE_BLANK: value = ""; type = HSSFCell.CELL_TYPE_STRING; break; case HSSFCell.CELL_TYPE_BOOLEAN: boolean bool = cell.getBooleanCellValue(); value = Boolean.toString(bool); break; default: skip = true; break; } if (!skip && value != null && !value.trim().equals("")) { wbRow.setData(truncateIfNecessary(value, numRows, wbtmi), wbtmi.getViewOrder(), true); } } addImageInfo(row, wbRow); addGeoInfo(row, wbRow); numRows++; } if (activeHyperlinks.size() > 0) { log.warn("Hyperlinks vector not empty after import. Overlapping hyperlink ranges?"); } return status = this.truncations.size() == 0 && this.messages.size() == 0 ? DataImportIFace.Status.Valid : DataImportIFace.Status.Modified; } catch (Exception ex) { edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(XLSImport.class, ex); log.error(ex); } } return status = DataImportIFace.Status.Error; }
From source file:edu.ku.brc.specify.utilapps.BuildSampleDatabase.java
License:Open Source License
/** * @param treeDef//from w ww .jav a2 s.com * @return */ public Geography convertGeographyFromXLS(final GeographyTreeDef treeDef) { frame.setDesc("Building Geography Tree..."); Hashtable<String, Geography> geoHash = new Hashtable<String, Geography>(); geoHash.clear(); String fileName = "Geography.xls"; File file = XMLHelper.getConfigDir("../demo_files/" + fileName); if (!file.exists()) { log.error("Couldn't file[" + file.getAbsolutePath() + "] checking the config dir"); file = XMLHelper.getConfigDir(fileName); if (!file.exists()) { file = new File("Specify/demo_files/" + fileName); } } if (file == null || !file.exists()) { log.error("Couldn't file[" + file.getAbsolutePath() + "]"); return null; } // setup the root Geography record (planet Earth) Geography earth = new Geography(); earth.initialize(); earth.setName(getResourceString("Earth")); earth.setFullName(earth.getName()); earth.setNodeNumber(1); earth.setHighestChildNodeNumber(1); earth.setRankId(0); earth.setDefinition(treeDef); GeographyTreeDefItem defItem = treeDef.getDefItemByRank(0); earth.setDefinitionItem(defItem); int counter = 0; try { startTx(); persist(earth); String[] cells = new String[4]; InputStream input = new FileInputStream(file); POIFSFileSystem fs = new POIFSFileSystem(input); HSSFWorkbook workBook = new HSSFWorkbook(fs); HSSFSheet sheet = workBook.getSheetAt(0); Iterator<?> rows = sheet.rowIterator(); int lastRowNum = sheet.getLastRowNum(); if (frame != null) { final int mx = lastRowNum; SwingUtilities.invokeLater(new Runnable() { public void run() { frame.setProcess(0, mx); } }); } while (rows.hasNext()) { if (counter == 0) { counter = 1; rows.next(); continue; } if (counter % 100 == 0) { if (frame != null) frame.setProcess(counter); log.info("Converted " + counter + " Geography records"); } HSSFRow row = (HSSFRow) rows.next(); Iterator<?> cellsIter = row.cellIterator(); int i = 0; while (cellsIter.hasNext() && i < 4) { HSSFCell cell = (HSSFCell) cellsIter.next(); if (cell != null) { cells[i] = StringUtils.trim(cell.getRichStringCellValue().getString()); i++; } } // Sets nulls to unused cells for (int j = i; j < 4; j++) { cells[j] = null; } //System.out.println(); @SuppressWarnings("unused") Geography newGeo = convertGeographyRecord(cells[0], cells[1], cells[2], cells[3], earth); counter++; } } catch (Exception ex) { ex.printStackTrace(); } if (frame != null) frame.setProcess(counter); log.info("Converted " + counter + " Geography records"); frame.setDesc("Saving Geography Tree..."); frame.getProcessProgress().setIndeterminate(true); TreeHelper.fixFullnameForNodeAndDescendants(earth); earth.setNodeNumber(1); fixNodeNumbersFromRoot(earth); commitTx(); /*startTx(); TreeHelper.fixFullnameForNodeAndDescendants(earth); earth.setNodeNumber(1); fixNodeNumbersFromRoot(earth); printTree(earth, 0); saveTree(earth); commitTx();*/ log.info("Converted " + counter + " Stratigraphy records"); // set up Geography foreign key mapping for locality geoHash.clear(); return earth; }
From source file:edu.ku.brc.specify.utilapps.BuildSampleDatabase.java
License:Open Source License
/** * @param fileName//from ww w .jav a 2 s . c o m * @return */ public HashSet<String> getColumnNamesFromXLS(final String fileName, final boolean doUserProvidedFile) { File file = TaxonLoadSetupPanel.getFileForTaxon(fileName, doUserProvidedFile); if (file == null) { return null; } HashSet<String> nameHash = new HashSet<String>(); try { String[] cells = new String[35]; InputStream input = new FileInputStream(file); POIFSFileSystem fs = new POIFSFileSystem(input); HSSFWorkbook workBook = new HSSFWorkbook(fs); HSSFSheet sheet = workBook.getSheetAt(0); Iterator<?> rows = sheet.rowIterator(); rows = sheet.rowIterator(); if (rows.hasNext()) { for (int i = 0; i < cells.length; i++) { cells[i] = null; } HSSFRow row = (HSSFRow) rows.next(); Iterator<?> cellsIter = row.cellIterator(); while (cellsIter.hasNext()) { HSSFCell cell = (HSSFCell) cellsIter.next(); if (cell != null) { nameHash.add(StringUtils.trim(cell.getRichStringCellValue().getString())); } } } } catch (Exception ex) { ex.printStackTrace(); } return nameHash; }
From source file:edu.ku.brc.specify.utilapps.BuildSampleDatabase.java
License:Open Source License
/** * @param treeDef//from www. j a va2s.c om * @param fileName * @param doUserProvidedFile * @return */ public Taxon convertTaxonFromXLS(final TaxonTreeDef treeDef, final String fileName, final boolean doUserProvidedFile) { Hashtable<String, Taxon> taxonHash = new Hashtable<String, Taxon>(); taxonHash.clear(); File file = TaxonLoadSetupPanel.getFileForTaxon(fileName, doUserProvidedFile); if (file == null) { return null; } Vector<TaxonTreeDefItem> rankedItems = new Vector<TaxonTreeDefItem>(); Hashtable<String, Boolean> colNames = new Hashtable<String, Boolean>(); for (TaxonTreeDefItem item : treeDef.getTreeDefItems()) { colNames.put(item.getName().toLowerCase(), true); rankedItems.add(item); } Collections.sort(rankedItems, new Comparator<TaxonTreeDefItem>() { @Override public int compare(TaxonTreeDefItem o1, TaxonTreeDefItem o2) { return o1.getRankId().compareTo(o2.getRankId()); } }); Connection conn = null; Statement stmt = null; TaxonTreeDefItem rootTreeDefItem = rankedItems.get(0); Set<Taxon> rootKids = rootTreeDefItem.getTreeEntries(); Taxon root = rootKids.iterator().next(); Vector<Pair<String, Integer>> nodeList = new Vector<Pair<String, Integer>>(); Pair<String, Integer> rootNode = new Pair<String, Integer>(root.getName(), root.getId()); nodeList.add(rootNode); int counter = 0; int numDataCols = 0; try { startTx(); for (TaxonTreeDefItem item : treeDef.getTreeDefItems()) { persist(item); } persist(root); commitTx(); String[] cells = new String[35]; String[] header = new String[35]; InputStream input = new FileInputStream(file); POIFSFileSystem fs = new POIFSFileSystem(input); HSSFWorkbook workBook = new HSSFWorkbook(fs); HSSFSheet sheet = workBook.getSheetAt(0); Iterator<?> rows = sheet.rowIterator(); int lastRowNum = sheet.getLastRowNum(); if (frame != null) { final int mx = lastRowNum; SwingUtilities.invokeLater(new Runnable() { public void run() { frame.setProcess(0, mx); } }); } conn = DBConnection.getInstance().createConnection(); //conn.setAutoCommit(false); stmt = conn.createStatement(); rows = sheet.rowIterator(); while (rows.hasNext()) { for (int i = 0; i < cells.length; i++) { cells[i] = null; } if (counter == 0) { HSSFRow row = (HSSFRow) rows.next(); Iterator<?> cellsIter = row.cellIterator(); int i = 0; while (cellsIter.hasNext()) { HSSFCell cell = (HSSFCell) cellsIter.next(); if (cell != null) { cells[i] = getXLSCellValueAsStr(cell); header[i] = cells[i]; i++; } } for (i = 0; i < cells.length; i++) { if (cells[i] == null) break; if (colNames.get(cells[i].toLowerCase()) != null) { numDataCols = i + 1; } else { for (String key : colNames.keySet()) { System.err.println("key[" + key + "]"); } System.err.println("Not Found: [" + cells[i].toLowerCase() + "]"); break; } } loadIndexes(cells); counter = 1; for (String hdr : header) { if (hdr == null) break; int inx = 0; for (TaxonTreeDefItem item : rankedItems) { if (hdr.equalsIgnoreCase(item.getName())) { log.debug("Header: " + hdr + " -> " + inx); taxonIndexes.put(hdr, inx); item.setIsInFullName(item.getRankId() >= TaxonTreeDef.GENUS); } else { log.debug("Header: " + hdr + " -> skipped."); } inx++; } } continue; } if (counter % 100 == 0) { if (frame != null) frame.setProcess(counter); //log.info("Converted " + counter + " of "+lastRowNum+" Taxon records"); } HSSFRow row = (HSSFRow) rows.next(); Iterator<?> cellsIter = row.cellIterator(); int i = 0; while (cellsIter.hasNext() && i < cells.length) { HSSFCell cell = (HSSFCell) cellsIter.next(); if (cell != null) { cells[i] = getXLSCellValueAsStr(cell); i++; } } convertTaxonNodes(conn, stmt, header, cells, numDataCols, rootNode, nodeList, rankedItems, root.getDefinition().getId()); counter++; } stmt.executeUpdate( "UPDATE taxon SET IsAccepted = true WHERE IsAccepted IS NULL and AcceptedID IS NULL AND TaxonTReeDefID = " + treeDef.getId()); // Clear all GUIDs in Taxon. stmt.executeUpdate("UPDATE taxon SET GUID = NULL WHERE TaxonTreeDefID = " + treeDef.getId()); conn.close(); input.close(); if (frame != null) frame.setProcess(lastRowNum); root = (Taxon) session.createQuery("FROM Taxon WHERE id = " + root.getId()).list().get(0); } catch (Exception ex) { ex.printStackTrace(); edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(BackupServiceFactory.class, ex); } finally { try { if (stmt != null) { stmt.close(); } if (conn != null) { conn.close(); } } catch (Exception ex) { ex.printStackTrace(); } } if (frame != null) { frame.setDesc("Saving Taxon Tree..."); frame.getProcessProgress().setIndeterminate(true); } NodeNumberer<Taxon, TaxonTreeDef, TaxonTreeDefItem> nodeNumberer = new NodeNumberer<Taxon, TaxonTreeDef, TaxonTreeDefItem>( root.getDefinition()); nodeNumberer.doInBackground(); //startTx(); //TreeHelper.fixFullnameForNodeAndDescendants(root); //root.setNodeNumber(1); //fixNodeNumbersFromRoot(root); //commitTx(); log.info("Converted " + counter + " Taxon records"); // set up Taxon foreign key mapping for locality taxonHash.clear(); return root; }