Examples of org.odftoolkit.odfdom.doc.table.OdfTableCell

org.odftoolkit.odfdom.doc.table.OdfTableCell
OdfTableCell represents table cell feature in ODF document.
OdfTable provides methods to get/set/modify the cell content and cell properties. @deprecated As of release 0.8.8, replaced by {@link org.odftoolkit.simple.table.Cell} in Simple API.

                    if (row != null) {
                        int lastCell = row.getCellCount();
                        for (int cellIndex = 0; cellIndex <= lastCell; cellIndex++) {
                            Cell cell = null;


                            OdfTableCell sourceCell = row.getCellByIndex(cellIndex);
                            if (sourceCell != null) {
                                cell = extractCell(sourceCell, reconMap);
                            }
                            cells.add(cell);
                        }

View Full Code Here

            public void addRow(List<CellData> cells, boolean isHeader) {
                OdfTableRow r = table.appendRow();
                //rowCount++;
                
                for (int i = 0; i < cells.size(); i++) {
                    OdfTableCell c = r.getCellByIndex(i); // implicitly creates cell
                    CellData cellData = cells.get(i);


                    if (cellData != null && cellData.text != null && cellData.value != null) {
                        Object v = cellData.value;
                        if (v instanceof Number) {
                            c.setDoubleValue(((Number) v).doubleValue());
                        } else if (v instanceof Boolean) {
                            c.setBooleanValue(((Boolean) v).booleanValue());
                        } else if (v instanceof Date) {
                            Calendar cal = Calendar.getInstance();
                            cal.setTime((Date) v);
                            c.setDateValue(cal);
                        } else if (v instanceof Calendar) {
                            c.setDateValue((Calendar) v);
                        } else {
                            c.setStringValue(cellData.text);
                        }


                        if (cellData.link != null) {
                            // TODO: How do we do output hyperlinks?
                        }

View Full Code Here


    List<Sample> samples = new ArrayList<Sample>();
    OdfTable oTable = oDoc.getTableList().get(0);


    //process global headers
    OdfTableCell pairedCell = oTable.getCellByPosition("A2");
    boolean paired = false;
    if (pairedCell.getBooleanValue() != null) {
      paired = pairedCell.getBooleanValue();
      log.info("Got paired: " + paired);
    }


    OdfTableCell platformCell = oTable.getCellByPosition("B2");
    PlatformType pt = null;
    if (!"".equals(platformCell.getStringValue())) {
      pt = PlatformType.get(platformCell.getStringValue());
    }
    if (pt == null) {
      throw new InputFormException("Cannot resolve Platform type from: '" + platformCell.getStringValue() + "'");
    }
    else {
      log.info("Got platform type: " + pt.getKey());
    }


    OdfTableCell typeCell = oTable.getCellByPosition("C2");
    LibraryType lt = null;
    if (!"".equals(typeCell.getStringValue())) {
      String[] split = typeCell.getStringValue().split("-");
      String plat = split[0];
      String type = split[1];
      if (platformCell.getStringValue().equals(plat)) {
        lt = manager.getLibraryTypeByDescriptionAndPlatform(type, pt);
      }
      else {
        throw new InputFormException("Selected library type '" + typeCell.getStringValue() + "' doesn't match platform type: '" + platformCell.getStringValue() + "'");
      }
    }
    if (lt == null) {
      throw new InputFormException("Cannot resolve Library type from: '" + typeCell.getStringValue() + "'");
    }
    else {
      log.info("Got library type: " + lt.getDescription());
    }


    OdfTableCell selectionCell = oTable.getCellByPosition("D2");
    LibrarySelectionType ls = null;
    if (!"".equals(selectionCell.getStringValue())) {
      ls = manager.getLibrarySelectionTypeByName(selectionCell.getStringValue());
    }
    if (ls == null) {
      throw new InputFormException("Cannot resolve Library Selection type from: '" + selectionCell.getStringValue() + "'");
    }
    else {
      log.info("Got library selection type: " + ls.getName());
    }


    OdfTableCell strategyCell = oTable.getCellByPosition("E2");
    LibraryStrategyType lst = null;
    if (!"".equals(strategyCell.getStringValue())) {
      lst = manager.getLibraryStrategyTypeByName(strategyCell.getStringValue());
    }
    if (lst == null) {
      throw new InputFormException("Cannot resolve Library Strategy type from: '" + strategyCell.getStringValue() + "'");
    }
    else {
      log.info("Got library strategy type: " + lst.getName());
    }


    OdfTableCell plateBarcodeCell = oTable.getCellByPosition("F2");
    String plateBarcode = null;
    if (!"".equals(plateBarcodeCell.getStringValue())) {
      plateBarcode = plateBarcodeCell.getStringValue();
    }
    if (plateBarcode == null) {
      throw new InputFormException("Cannot resolve plate barcode from: '" + plateBarcodeCell.getStringValue() + "'");
    }
    else {
      log.info("Got plate parcode: " + plateBarcode);
    }


    //process entries
    Simple384WellPlate libraryPlate = null;
    //Map<String, Pool<Plate<LinkedList<Library>, Library>>> pools = new HashMap<String, Pool<Plate<LinkedList<Library>, Library>>>();
    Map<String, PlatePool> pools = new HashMap<String, PlatePool>();
    for (OdfTableRow row : oTable.getRowList()) {
      int ri = row.getRowIndex();
      if (ri > 3) {
        // Ax - plate position
        OdfTableCell platePosCell = oTable.getCellByPosition(0, ri);
        if (!"".equals(platePosCell.getStringValue()) && libraryPlate == null) {
          //plated libraries - process as plate
          libraryPlate = new Simple384WellPlate();
          libraryPlate.setIdentificationBarcode(plateBarcode);
          libraryPlate.setCreationDate(new Date());
        }


        //cell defs
        OdfTableCell sampleAliasCell = oTable.getCellByPosition(1, ri);


        Sample s = null;
        if (!"".equals(sampleAliasCell.getStringValue())) {
          Collection<Sample> ss = manager.listSamplesByAlias(sampleAliasCell.getStringValue());
          if (!ss.isEmpty()) {
            if (ss.size() == 1) {
              s = ss.iterator().next();
              log.info("Got sample: " + s.getAlias());
            }
            else {
              throw new InputFormException("Multiple samples retrieved with this alias: '" + sampleAliasCell.getStringValue() + "'. Cannot process.");
            }
          }
          else {
            throw new InputFormException("No such sample '" + sampleAliasCell.getStringValue() + "'in database. Samples need to be created before using the form input functionality");
          }
        }
        else {
          log.info("Blank sample row found. Ending import.");
          break;
        }


        //sample OK - good to go
        if (s != null) {
          OdfTableCell entityIDCell = oTable.getCellByPosition(2, ri);
          OdfTableCell poolNumberCell = oTable.getCellByPosition(3, ri);
          OdfTableCell sampleQcCell = oTable.getCellByPosition(4, ri);
          //OdfTableCell sampleAmountCell = oTable.getCellByPosition(5, ri);
          //OdfTableCell sampleWaterAmountCell = oTable.getCellByPosition(6, ri);
          OdfTableCell barcodeKitCell = oTable.getCellByPosition(7, ri);
          OdfTableCell barcodeTagsCell = oTable.getCellByPosition(8, ri);
          OdfTableCell libraryQcCell = oTable.getCellByPosition(9, ri);
          OdfTableCell libraryQcInsertSizeCell = oTable.getCellByPosition(10, ri);
          OdfTableCell libraryQcMolarityCell = oTable.getCellByPosition(11, ri);
          OdfTableCell libraryQcPassFailCell = oTable.getCellByPosition(12, ri);
          //OdfTableCell libraryAmountCell = oTable.getCellByPosition(13, ri);
          //OdfTableCell libraryWaterAmountCell = oTable.getCellByPosition(14, ri);
          //OdfTableCell dilutionQcCell = oTable.getCellByPosition(15, ri);
          OdfTableCell dilutionMolarityCell = oTable.getCellByPosition(16, ri);
          //OdfTableCell dilutionAmountCell = oTable.getCellByPosition(17, ri);
          //OdfTableCell dilutionWaterAmountCell = oTable.getCellByPosition(18, ri);
          OdfTableCell poolQcCell = oTable.getCellByPosition(19, ri);
          //OdfTableCell poolAverageInsertSizeCell = oTable.getCellByPosition(20, ri);
          OdfTableCell poolConvertedMolarityCell = oTable.getCellByPosition(21, ri);


          //add pool, if any
          if (!"".equals(poolNumberCell.getStringValue())) {
            if (!pools.containsKey(poolNumberCell.getStringValue())) {
              PlatePool pool = new PlatePool();
              pool.setAlias(poolNumberCell.getStringValue());
              pool.setPlatformType(pt);
              pool.setReadyToRun(true);
              pool.setCreationDate(new Date());
              pools.put(poolNumberCell.getStringValue(), pool);
              log.info("Added pool: " + poolNumberCell.getStringValue());
            }
          }


          //process sample QC
          if (!"".equals(sampleQcCell.getStringValue())) {
            try {
              SampleQC sqc = new SampleQCImpl();
              sqc.setSample(s);
              sqc.setResults(Double.valueOf(sampleQcCell.getStringValue()));
              sqc.setQcCreator(u.getLoginName());
              sqc.setQcDate(new Date());
              sqc.setQcType(manager.getSampleQcTypeByName("Picogreen"));
              if (!s.getSampleQCs().contains(sqc)) {
                s.addQc(sqc);
                log.info("Added sample QC: " + sqc.toString());
              }
            }
            catch (NumberFormatException nfe) {
              throw new InputFormException("Supplied Sample QC concentration for sample '" + sampleAliasCell.getStringValue() + "' is invalid", nfe);
            }
          }


          //if (!"".equals(libraryQcCell.getStringValue())) {
          if (barcodeKitCell.getStringValue() != null && barcodeTagsCell.getStringValue() != null) {
            //create library
            Library library = new LibraryImpl();
            library.setSample(s);


            Matcher mat = samplePattern.matcher(s.getAlias());
            if (mat.matches()) {
              String libAlias = plateBarcode + "_" + "L" + mat.group(2) + "-" + platePosCell.getStringValue() + "_" + entityIDCell.getStringValue();
              //String libAlias = libraryNamingScheme.generateNameFor("alias", library);
              //library.setAlias(libAlias);


              library.setAlias(libAlias);
              library.setSecurityProfile(s.getSecurityProfile());
              library.setDescription(s.getDescription());
              library.setCreationDate(new Date());
              library.setPlatformName(pt.name());
              library.setLibraryType(lt);
              library.setLibrarySelectionType(ls);
              library.setLibraryStrategyType(lst);
              library.setPaired(paired);


              if (!"".equals(libraryQcMolarityCell.getStringValue())) {
                int insertSize = 0;
                try {
                  String bp = libraryQcInsertSizeCell.getStringValue();
                  Matcher m = digitPattern.matcher(bp);
                  if (m.matches()) {
                    insertSize = Integer.valueOf(m.group(1));
                  }
                  else {
                    throw new InputFormException("Supplied Library insert size for library '" + libAlias + "' (" + s.getAlias() + ") is invalid");
                  }
                }
                catch (NumberFormatException nfe) {
                  throw new InputFormException("Supplied Library insert size for library '" + libAlias + "' (" + s.getAlias() + ") is invalid", nfe);
                }


                try {
                  LibraryQC lqc = new LibraryQCImpl();
                  lqc.setLibrary(library);
                  lqc.setInsertSize(insertSize);
                  lqc.setResults(Double.valueOf(libraryQcMolarityCell.getStringValue()));
                  lqc.setQcCreator(u.getLoginName());
                  lqc.setQcDate(new Date());
                  lqc.setQcType(manager.getLibraryQcTypeByName("Picogreen"));
                  if (!library.getLibraryQCs().contains(lqc)) {
                    library.addQc(lqc);
                    log.info("Added library QC: " + lqc.toString());
                  }


                  if (insertSize == 0 && lqc.getResults() == 0) {
                    library.setQcPassed(false);
                  }
                  else {
                    //TODO check libraryQcPassFailCell?
                    library.setQcPassed(true);
                  }
                }
                catch (NumberFormatException nfe) {
                  throw new InputFormException("Supplied Library QC concentration for library '" + libAlias + "' (" + s.getAlias() + ") is invalid", nfe);
                }
              }


              if (!"".equals(barcodeKitCell.getStringValue())) {
                Collection<TagBarcode> bcs = manager.listAllTagBarcodesByStrategyName(barcodeKitCell.getStringValue());
                if (!bcs.isEmpty()) {
                  String tags = barcodeTagsCell.getStringValue();
                  if (!"".equals(tags)) {
                    HashMap<Integer, TagBarcode> tbs = new HashMap<Integer, TagBarcode>();
                    if (tags.contains("-")) {
                      String[] splits = tags.split("-");
                      int count = 1;
                      for (String tag : splits) {
                        for (TagBarcode tb : bcs) {
                          if (tb.getName().equals(tag)) {
                            //set tag barcodes
                            tbs.put(count, tb);
                            count++;
                          }
                        }
                      }
                    }
                    else {
                      for (TagBarcode tb : bcs) {
                        if (tb.getName().equals(tags)) {
                          //set tag barcode
                          tbs.put(1, tb);
                        }
                      }
                    }


                    library.setTagBarcodes(tbs);
                  }
                  else {
                    throw new InputFormException("Barcode Kit specified but no tag barcodes entered for: '" + sampleAliasCell.getStringValue() + "'.");
                  }
                }
                else {
                  throw new InputFormException("No tag barcodes associated with this kit definition: '" + barcodeKitCell.getStringValue() + "'.");
                }
              }


              /*
              if (!"".equals(dilutionMolarityCell.getStringValue())) {
                try {
                  LibraryDilution ldi = new LibraryDilution();
                  ldi.setLibrary(library);
                  ldi.setSecurityProfile(library.getSecurityProfile());
                  ldi.setConcentration(Double.valueOf(dilutionMolarityCell.getStringValue()));
                  ldi.setCreationDate(new Date());
                  ldi.setDilutionCreator(u.getLoginName());
                  if (!library.getLibraryDilutions().contains(ldi)) {
                    library.addDilution(ldi);
                    log.info("Added library dilution: " + ldi.toString());
                  }


                  Pool<Plate<LinkedList<Library>, Library>> p = pools.get(poolNumberCell.getStringValue());
                  if (p != null) {
                    p.addPoolableElement(ldi);
                    log.info("Added library dilution to pool: " + p.toString());
                  }
                }
                catch (NumberFormatException nfe) {
                  throw new InputFormException("Supplied LibraryDilution concentration for library '"+libAlias+"' ("+s.getAlias()+") is invalid", nfe);
                }
              }
              */


              if (!"".equals(poolConvertedMolarityCell.getStringValue())) {
                Pool<Plate<LinkedList<Library>, Library>> p = pools.get(poolNumberCell.getStringValue());
                if (p != null) {
                  log.debug("Retrieved pool " + poolNumberCell.getStringValue());
                  try {
                    double d = Double.valueOf(poolConvertedMolarityCell.getStringValue());
                    p.setConcentration(d);
                  }
                  catch (NumberFormatException nfe) {
                    throw new InputFormException("Supplied pool concentration for pool '" + poolNumberCell.getStringValue() + "' is invalid", nfe);
                  }

View Full Code Here


    List<Sample> samples = new ArrayList<Sample>();
    OdfTable oTable = oDoc.getTableList().get(0);


    //process global headers
    OdfTableCell pairedCell = oTable.getCellByPosition("A2");
    boolean paired;
    if (pairedCell != null && pairedCell.getBooleanValue() != null) {
      paired = pairedCell.getBooleanValue();
      log.info("Got paired: " + paired);
    }
    else {
      throw new InputFormException("'Paired' cell is empty. Please specify TRUE or FALSE.");
    }


    OdfTableCell platformCell = oTable.getCellByPosition("B2");
    PlatformType pt = null;
    if (!"".equals(platformCell.getStringValue())) {
      pt = PlatformType.get(platformCell.getStringValue());
    }
    if (pt == null) {
      throw new InputFormException("Cannot resolve Platform type from: '" + platformCell.getStringValue() + "'");
    }
    else {
      log.info("Got platform type: " + pt.getKey());
    }


    OdfTableCell typeCell = oTable.getCellByPosition("C2");
    LibraryType lt = null;
    if (!"".equals(typeCell.getStringValue())) {
      String[] split = typeCell.getStringValue().split("-");
      String plat = split[0];
      String type = split[1];
      if (platformCell.getStringValue().equals(plat)) {
        lt = manager.getLibraryTypeByDescriptionAndPlatform(type, pt);
      }
      else {
        throw new InputFormException("Selected library type '" + typeCell.getStringValue() + "' doesn't match platform type: '" + platformCell.getStringValue() + "'");
      }
    }
    if (lt == null) {
      throw new InputFormException("Cannot resolve Library type from: '" + typeCell.getStringValue() + "'");
    }
    else {
      log.info("Got library type: " + lt.getDescription());
    }


    OdfTableCell selectionCell = oTable.getCellByPosition("D2");
    LibrarySelectionType ls = null;
    if (!"".equals(selectionCell.getStringValue())) {
      ls = manager.getLibrarySelectionTypeByName(selectionCell.getStringValue());
    }
    if (ls == null) {
      throw new InputFormException("Cannot resolve Library Selection type from: '" + selectionCell.getStringValue() + "'");
    }
    else {
      log.info("Got library selection type: " + ls.getName());
    }


    OdfTableCell strategyCell = oTable.getCellByPosition("E2");
    LibraryStrategyType lst = null;
    if (!"".equals(strategyCell.getStringValue())) {
      lst = manager.getLibraryStrategyTypeByName(strategyCell.getStringValue());
    }
    if (lst == null) {
      throw new InputFormException("Cannot resolve Library Strategy type from: '" + strategyCell.getStringValue() + "'");
    }
    else {
      log.info("Got library strategy type: " + lst.getName());
    }


    //process entries
    Plate<LinkedList<Sample>, Sample> samplePlate = null;
    Map<String, Pool<Dilution>> pools = new HashMap<String, Pool<Dilution>>();
    for (OdfTableRow row : oTable.getRowList()) {
      int ri = row.getRowIndex();
      if (ri > 3) {
        // Ax - plate position
        OdfTableCell platePosCell = oTable.getCellByPosition(0, ri);
        if (!"".equals(platePosCell.getStringValue())) {
          //plated samples - process as plate
          samplePlate = new PlateImpl<Sample>();
        }


        //cell defs
        OdfTableCell sampleAliasCell = oTable.getCellByPosition(2, ri);


        Sample s = null;
        if (!"".equals(sampleAliasCell.getStringValue())) {
          Collection<Sample> ss = manager.listSamplesByAlias(sampleAliasCell.getStringValue());
          if (!ss.isEmpty()) {
            if (ss.size() == 1) {
              s = ss.iterator().next();
              log.info("Got sample: " + s.getAlias());
            }
            else {
              throw new InputFormException("Multiple samples retrieved with this alias: '" + sampleAliasCell.getStringValue() + "'. Cannot process.");
            }
          }
          else {
            throw new InputFormException("No such sample '" + sampleAliasCell.getStringValue() + "'in database. Samples need to be created before using the form input functionality");
          }
        }
        else {
          log.info("Blank sample row found. Ending import.");
          break;

View Full Code Here

      OdfTable oTable = oDoc.getTableByName("SamplesTable");


      for (Sample s : samples) {
        OdfTableRow row = oTable.appendRow();


        OdfTableCell cell0 = row.getCellByIndex(0);
        OdfTextParagraph cp0 = new OdfTextParagraph(contentDom);
        cp0.setTextContent(s.getAlias());
        cp0.setProperty(StyleTextPropertiesElement.FontSize, "8pt");
        cell0.getOdfElement().appendChild(cp0);


        OdfTableCell cell1 = row.getCellByIndex(1);
        OdfTextParagraph cp1 = new OdfTextParagraph(contentDom);
        cp1.setTextContent(s.getScientificName());
        cp1.setProperty(StyleTextPropertiesElement.FontSize, "8pt");
        cell1.getOdfElement().appendChild(cp1);


        OdfTableCell cell2 = row.getCellByIndex(2);
        OdfTextParagraph cp2 = new OdfTextParagraph(contentDom);
        cp2.setTextContent(s.getIdentificationBarcode());
        cp2.setProperty(StyleTextPropertiesElement.FontSize, "8pt");
        cell2.getOdfElement().appendChild(cp2);


        OdfTableCell cell3 = row.getCellByIndex(3);
        OdfTextParagraph cp3 = new OdfTextParagraph(contentDom);
        cp3.setTextContent(s.getSampleType());
        cp3.setProperty(StyleTextPropertiesElement.FontSize, "8pt");
        cell3.getOdfElement().appendChild(cp3);
      }


      int count = 0;
      for (OdfTableRow row : oTable.getRowList()) {
        if (count % 2 != 0) {

View Full Code Here

TOP

Related Classes of org.odftoolkit.odfdom.doc.table.OdfTableCell

com.google.refine.exporters.OdsExporter

com.google.refine.importers.OdsImporter

org.odftoolkit.odfdom.dom.element.OdfStyleBase

org.odftoolkit.odfdom.dom.element.table.TableTableCellElement

org.odftoolkit.odfdom.dom.element.table.TableTableCellElementBase

org.odftoolkit.odfdom.dom.element.table.TableTableElement

org.odftoolkit.odfdom.dom.element.table.TableTableHeaderRowsElement

org.odftoolkit.odfdom.dom.element.table.TableTableRowElement

org.odftoolkit.odfdom.dom.element.table.TableTableRowGroupElement

org.odftoolkit.odfdom.dom.element.table.TableTableRowsElement

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.