Examples of uk.ac.bbsrc.tgac.miso.core.exception.InputFormException

Package uk.ac.bbsrc.tgac.miso.core.exception

Examples of uk.ac.bbsrc.tgac.miso.core.exception.InputFormException

uk.ac.bbsrc.tgac.miso.core.exception.InputFormException
uk.ac.bbsrc.tgac.miso.core.exception
Info @author Rob Davey @date 03-Sep-2010 @since 0.0.2

    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);
                  }
                }
              }


              log.info("Added library: " + library.toString());

View Full Code Here

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


    XSSFCell typeCell = glrow.getCell(2);
    LibraryType lt = null;
    if (getCellValueAsString(typeCell) != null) {
      String[] split = getCellValueAsString(typeCell).split("-");
      String plat = split[0];
      String type = split[1];
      if (getCellValueAsString(platformCell).equals(plat)) {
        lt = manager.getLibraryTypeByDescriptionAndPlatform(type, pt);
      }
      else {
        throw new InputFormException("Selected library type '" + getCellValueAsString(typeCell) + "' doesn't match platform type: '" + getCellValueAsString(platformCell) + "'");
      }
    }
    if (lt == null) {
      throw new InputFormException("Cannot resolve Library type from: '" + getCellValueAsString(typeCell) + "'");
    }
    else {
      log.info("Got library type: " + lt.getDescription());
    }


    XSSFCell selectionCell = glrow.getCell(3);
    LibrarySelectionType ls = null;
    if (getCellValueAsString(selectionCell) != null) {
      ls = manager.getLibrarySelectionTypeByName(getCellValueAsString(selectionCell));
    }
    if (ls == null) {
      throw new InputFormException("Cannot resolve Library Selection type from: '" + getCellValueAsString(selectionCell) + "'");
    }
    else {
      log.info("Got library selection type: " + ls.getName());
    }


    XSSFCell strategyCell = glrow.getCell(4);
    LibraryStrategyType lst = null;
    if (getCellValueAsString(strategyCell) != null) {
      lst = manager.getLibraryStrategyTypeByName(getCellValueAsString(strategyCell));
    }
    if (lst == null) {
      throw new InputFormException("Cannot resolve Library Strategy type from: '" + getCellValueAsString(strategyCell) + "'");
    }
    else {
      log.info("Got library strategy type: " + lst.getName());
    }


    XSSFCell plateBarcodeCell = glrow.getCell(5);
    String plateBarcode = null;
    if (getCellValueAsString(plateBarcodeCell) != null) {
      plateBarcode = getCellValueAsString(plateBarcodeCell);
    }
    if (plateBarcode == null) {
      throw new InputFormException("Cannot resolve plate barcode from: '" + getCellValueAsString(plateBarcodeCell) + "'");
    }
    else {
      log.info("Got plate barcode: " + 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 (int ri = 4; ri < rows; ri++) {
      XSSFRow row = sheet.getRow(ri);


      // Ax - plate position
      XSSFCell platePosCell = row.getCell(0);
      String platePos = getCellValueAsString(platePosCell);
      if (platePos != null && libraryPlate == null) {
        //plated libraries - process as plate
        libraryPlate = new Simple384WellPlate();
        libraryPlate.setIdentificationBarcode(plateBarcode);
        libraryPlate.setCreationDate(new Date());
      }


      //cell defs
      XSSFCell sampleAliasCell = row.getCell(2);


      Sample s = null;
      if (getCellValueAsString(sampleAliasCell) != null) {
        String salias = getCellValueAsString(sampleAliasCell);
        Collection<Sample> ss = manager.listSamplesByAlias(salias);
        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: '" + salias + "'. Cannot process.");
          }
        }
        else {
          throw new InputFormException("No such sample '" + salias + "'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) {
        XSSFCell entityIDCell = row.getCell(2);
        XSSFCell poolNumberCell = row.getCell(3);
        XSSFCell sampleQcCell = row.getCell(4);
        //XSSFCell sampleAmountCell = row.getCell(5);
        //XSSFCell sampleWaterAmountCell = row.getCell(6);
        XSSFCell libraryDescriptionCell = row.getCell(7);
        XSSFCell barcodeKitCell = row.getCell(8);
        XSSFCell barcodeTagsCell = row.getCell(9);
        XSSFCell libraryQcCell = row.getCell(10);
        XSSFCell libraryQcInsertSizeCell = row.getCell(11);
        XSSFCell libraryQcMolarityCell = row.getCell(12);
        XSSFCell libraryQcPassFailCell = row.getCell(13);
        //XSSFCell libraryAmountCell = row.getCell(14);
        //XSSFCell libraryWaterAmountCell = row.getCell(15);
        //XSSFCell dilutionQcCell = row.getCell(16);
        XSSFCell dilutionMolarityCell = row.getCell(17);
        //XSSFCell dilutionAmountCell = row.getCell(18);
        //XSSFCell dilutionWaterAmountCell = row.getCell(19);
        XSSFCell poolQcCell = row.getCell(20);
        //XSSFCell poolAverageInsertSizeCell = row.getCell(21);
        XSSFCell poolConvertedMolarityCell = row.getCell(22);


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


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


        //if (getCellValueAsString(libraryQcCell) != null) {


        if (getCellValueAsString(barcodeKitCell) != null && getCellValueAsString(barcodeTagsCell) != 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) + "-" + platePos + "_" + getCellValueAsString(entityIDCell);
            //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 (getCellValueAsString(libraryQcMolarityCell) != null) {
              int insertSize = 0;
              try {
                String bp = getCellValueAsString(libraryQcInsertSizeCell);
                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(getCellValueAsString(libraryQcMolarityCell)));
                lqc.setQcCreator(u.getLoginName());
                lqc.setQcDate(new Date());
                lqc.setQcType(manager.getLibraryQcTypeByName("Bioanalyzer"));
                if (!library.getLibraryQCs().contains(lqc)) {
                  library.addQc(lqc);
                  manager.saveLibraryQC(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 (getCellValueAsString(barcodeKitCell) != null) {
              Collection<TagBarcode> bcs = manager.listAllTagBarcodesByStrategyName(getCellValueAsString(barcodeKitCell));
              if (!bcs.isEmpty()) {
                String tags = getCellValueAsString(barcodeTagsCell);
                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) || tb.getSequence().equals(tags)) {
                        //set tag barcode
                        tbs.put(1, tb);
                        log.info("Got tag barcode: " + tb.getName());
                        break;
                      }
                    }
                  }


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


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


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


            log.info("Added library: " + library.toString());

View Full Code Here

    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

    if (getCellValueAsString(pairedCell) != null) {
      paired = pairedCell.getBooleanCellValue();
      log.info("Got paired: " + paired);
    }
    else {
      throw new InputFormException("'Paired' cell is empty. Please specify TRUE or FALSE.");
    }


    XSSFCell platformCell = glrow.getCell(1);
    PlatformType pt = null;
    if (getCellValueAsString(platformCell) != null) {
      pt = PlatformType.get(getCellValueAsString(platformCell));
    }
    if (pt == null) {
      throw new InputFormException("Cannot resolve Platform type from: '" + getCellValueAsString(platformCell) + "'");
    }
    else {
      log.info("Got platform type: " + pt.getKey());
    }


    XSSFCell typeCell = glrow.getCell(2);
    LibraryType lt = null;
    if (getCellValueAsString(typeCell) != null) {
      String[] split = getCellValueAsString(typeCell).split("-");
      String plat = split[0];
      String type = split[1];
      if (getCellValueAsString(platformCell).equals(plat)) {
        lt = manager.getLibraryTypeByDescriptionAndPlatform(type, pt);
      }
      else {
        throw new InputFormException("Selected library type '" + getCellValueAsString(typeCell) + "' doesn't match platform type: '" + getCellValueAsString(platformCell) + "'");
      }
    }
    if (lt == null) {
      throw new InputFormException("Cannot resolve Library type from: '" + getCellValueAsString(typeCell) + "'");
    }
    else {
      log.info("Got library type: " + lt.getDescription());
    }


    XSSFCell selectionCell = glrow.getCell(3);
    LibrarySelectionType ls = null;
    if (getCellValueAsString(selectionCell) != null) {
      ls = manager.getLibrarySelectionTypeByName(getCellValueAsString(selectionCell));
    }
    if (ls == null) {
      throw new InputFormException("Cannot resolve Library Selection type from: '" + getCellValueAsString(selectionCell) + "'");
    }
    else {
      log.info("Got library selection type: " + ls.getName());
    }


    XSSFCell strategyCell = glrow.getCell(4);
    LibraryStrategyType lst = null;
    if (getCellValueAsString(strategyCell) != null) {
      lst = manager.getLibraryStrategyTypeByName(getCellValueAsString(strategyCell));
    }
    if (lst == null) {
      throw new InputFormException("Cannot resolve Library Strategy type from: '" + getCellValueAsString(strategyCell) + "'");
    }
    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 (int ri = 4; ri < rows; ri++) {
      XSSFRow row = sheet.getRow(ri);


      // Ax - plate position
      XSSFCell platePosCell = row.getCell(0);
      if (getCellValueAsString(platePosCell) != null && samplePlate == null) {
        //plated samples - process as plate
        samplePlate = new PlateImpl<Sample>();
      }


      //cell defs
      XSSFCell sampleAliasCell = row.getCell(2);


      Sample s = null;
      if (getCellValueAsString(sampleAliasCell) != null) {
        String salias = getCellValueAsString(sampleAliasCell);
        Collection<Sample> ss = manager.listSamplesByAlias(salias);
        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: '" + salias + "'. Cannot process.");
          }
        }
        else {
          throw new InputFormException("No such sample '" + salias + "'in database. Samples need to be created before using the form input functionality");
        }
      }
      else {
        log.info("Blank sample row found. Ending import.");
        break;

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            double d = Double.valueOf(poolConvertedMolarity);
            log.info("Got conc " + d);
            p.setConcentration(d);
          }
          catch (NumberFormatException nfe) {
            throw new InputFormException("Supplied pool concentration for pool '" + poolAlias + "' is invalid", nfe);
          }
        }
      }
    }
  }

View Full Code Here

          s.addQc(sqc);
          log.info("Added sample QC: " + sqc.toString());
        }
      }
      catch (NumberFormatException nfe) {
        throw new InputFormException("Supplied Sample QC concentration for sample '" + sampleQc + "' is invalid", nfe);
      }
    }
  }

View Full Code Here

        Matcher m = digitPattern.matcher(libraryQcInsertSize);
        if (m.matches()) {
          insertSize = Integer.valueOf(m.group(1));
        }
        else {
          throw new InputFormException("Supplied Library insert size for library '" + library.getAlias() + "' (" + library.getSample().getAlias() + ") is invalid");
        }
      }
      catch (NumberFormatException nfe) {
        throw new InputFormException("Supplied Library insert size for library '" + library.getAlias() + "' (" + library.getSample().getAlias() + ") is invalid", nfe);
      }


      try {
        LibraryQC lqc = new LibraryQCImpl();
        lqc.setLibrary(library);
        lqc.setInsertSize(insertSize);
        lqc.setResults(Double.valueOf(libraryQcMolarity));
        lqc.setQcCreator(u.getLoginName());
        lqc.setQcDate(new Date());
        QcType lqct = manager.getLibraryQcTypeByName(libraryQc);
        if (lqct != null) {
          lqc.setQcType(manager.getLibraryQcTypeByName(libraryQc));
          if (!library.getLibraryQCs().contains(lqc)) {
            library.addQc(lqc);
            log.info("Added library QC: " + lqc.toString());
          }
        }
        else {
          throw new InputFormException("No such Library QC type '" + libraryQc + "'");
        }


        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 '" + library.getAlias() + "' (" + library.getSample().getAlias() + ") is invalid", nfe);
      }
    }
  }

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          }


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

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          p.addPoolableElement(ldi);
          log.info("Added library dilution to pool: " + p.toString());
        }
      }
      catch (NumberFormatException nfe) {
        throw new InputFormException("Supplied LibraryDilution concentration for library '" + library.getAlias() + "' (" + library.getSample().getAlias() + ") is invalid", nfe);
      }
    }
  }

View Full Code Here

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Related Classes of uk.ac.bbsrc.tgac.miso.core.exception.InputFormException

uk.ac.bbsrc.tgac.miso.core.util.FormUtils

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