Tmp

.gitignore

@@ -2545,4 +2545,4 @@ bin/
 /javafx/src/javafx.web/javafx/scene/web/WebView.java
 /javafx/src/javafx.web/module-info.java
 /javafx/src.zip
-/test_output/ynb.xlsx
+/test_output/ynb.xlsx

src/main/java/module-info.java

@@ -7,6 +7,7 @@
     requires javafx.graphics;
     requires javafx.controls;
     requires org.apache.commons.compress;
+    requires java.logging;
     exports org.awdevelopment.smithlab;
     exports org.awdevelopment.smithlab.gui;
     exports org.awdevelopment.smithlab.gui.controllers;

src/main/java/org/awdevelopment/smithlab/MainApplication.java

@@ -19,7 +19,10 @@ public class MainApplication extends javafx.application.Application {
     private static final FXMLResourceType DEFAULT_FXML_RESOURCE = FXMLResourceType.APPLICATION;
 
     public static void main(String[] args) {
-        if (args.length == 0) launch();
+        if (args.length == 0) {
+            launch();
+
+        }
         else {
             Arguments arguments = new Arguments(args, LOGGER);
             try {

src/main/java/org/awdevelopment/smithlab/io/Headers.java

@@ -50,6 +50,11 @@ public void addHeader(String header, int index) {
         }
     }
 
+    public Optional<Header> getConditionColumn() {
+        if (!conditionColumn) return Optional.empty();
+        return headers.stream().filter(header -> header.type() == HeaderType.CONDITION).findFirst();
+    }
+
     public void addDay(short dayNumber, int index) {
         for (short i = 0; i < 3; i++) {
             days.add(new Day(dayNumber, index + i, i));

src/main/java/org/awdevelopment/smithlab/io/input/XlsxInputReader.java

@@ -27,6 +27,7 @@ public class XlsxInputReader {
     private final HashSet<Strain> strains;
     private final HashSet<Condition> conditions;
     private final LoggerHelper LOGGER;
+    private static final Condition DEFAULT_CONDITION = new Condition("Unknown");
 
     public XlsxInputReader(File xlsxFile, LoggerHelper logger) {
         this.xlsxFile = xlsxFile;
@@ -75,7 +76,13 @@ private Optional<Sample> readSampleFromRow(Headers headers, XSSFRow row) {
                     }
                     case HeaderType.STRAIN -> {
                         try {
-                            strainOptional = Optional.of(readStrain(curCell));
+                            Condition condition;
+                            if (conditionOptional.isEmpty()) {
+                                LOGGER.atWarn("Strain cell \"" + curCell.getRawValue() + "\" is missing a condition label! Labeling with \"Unknown\"");
+                                condition = DEFAULT_CONDITION;
+                            }
+                            else condition = conditionOptional.get();
+                            strainOptional = Optional.of(readStrain(curCell, condition));
                         } catch (InvalidStrainValueException e) {
                             LOGGER.atWarn(e + ": " + e.getMessage());
                             strainOptional = Optional.empty();
@@ -190,8 +197,29 @@ private int getInteger(XSSFCell cell) {
     }
 
     private Dilution readDilution(XSSFCell cell) throws InvalidDilutionValueException {
-        if (cell.getCellType() != CellType.NUMERIC) throw new InvalidDilutionValueException(cell.getRawValue(), cell.getRowIndex(), cell.getColumnIndex());
-        double cellValue = cell.getNumericCellValue();
+        double cellValue = -1.0;
+        LOGGER.atFatal("Reading dilution from cell with raw content: \""+cell.getRawValue()+"\"");
+        LOGGER.atFatal("Cell string value: \""+cell.getStringCellValue()+"\"");
+        LOGGER.atFatal("Cell address: "+cell.getAddress());
+        LOGGER.atFatal("Cell type: "+cell.getCellType());
+        if (cell.getCellType() == CellType.NUMERIC) {
+            cellValue = cell.getNumericCellValue();
+        } else if (cell.getCellType() == CellType.STRING) {
+            String cellContent = cell.getStringCellValue();
+            if (cellContent.equalsIgnoreCase("x1000")) {
+                return Dilution.x1000;
+            } else if (cellContent.equalsIgnoreCase("x100")) {
+                return Dilution.x100;
+            } else if (cellContent.equalsIgnoreCase("x10")) {
+                return Dilution.x10;
+            } else if (cellContent.equalsIgnoreCase("1")) {
+                return Dilution.x1000;
+            } else if (cellContent.equalsIgnoreCase("0.1")) {
+                return Dilution.x100;
+            } else if (cellContent.equalsIgnoreCase("0.01")) {
+                return Dilution.x10;
+            }
+        }
         if (Math.abs(cellValue - 1) < DELTA) {
             return Dilution.x1000;
         } else if (Math.abs(cellValue - 0.1) < DELTA) {
@@ -225,22 +253,23 @@ private Condition readCondition(XSSFCell cell) throws InvalidConditionValueExcep
         }
     }
 
-    private Strain readStrain(XSSFCell cell) throws InvalidStrainValueException {
+    private Strain readStrain(XSSFCell cell, Condition condition) throws InvalidStrainValueException {
         CellType cellType = cell.getCellType();
         if (cellType == CellType.STRING) {
             String cellContent = cell.getStringCellValue();
             for (Strain strain : strains) {
                 if (strain.getName().equalsIgnoreCase(cellContent)) return strain;
             }
             Strain newStrain = new Strain(cellContent);
+            newStrain.setCondition(condition);
             strains.add(newStrain);
             return newStrain;
         } else if (cellType == CellType.BLANK || cellType == CellType._NONE) {
             int rowIndex = cell.getRowIndex();
             int colIndex = cell.getColumnIndex();
             for (int i = rowIndex - 1; i > 1; i--) {
                 XSSFCell nextCell = cell.getSheet().getRow(i).getCell(colIndex);
-                if (nextCell.getCellType() == CellType.STRING) return readStrain(nextCell);
+                if (nextCell.getCellType() == CellType.STRING) return readStrain(nextCell, condition);
             }
         throw new InvalidStrainValueException(cell.getRawValue(), cell.getRowIndex(), cell.getColumnIndex());
         } else {

src/main/java/org/awdevelopment/smithlab/io/output/formats/PrismOutputStyle.java

@@ -5,11 +5,14 @@
 import org.apache.poi.xssf.usermodel.XSSFCell;
 import org.apache.poi.xssf.usermodel.XSSFRow;
 import org.awdevelopment.smithlab.config.SortOption;
+import org.awdevelopment.smithlab.data.DayOutOfBoundsException;
 import org.awdevelopment.smithlab.data.experiment.Experiment;
 import org.apache.poi.xssf.usermodel.XSSFSheet;
 import org.awdevelopment.smithlab.data.Sample;
 import org.awdevelopment.smithlab.io.exceptions.NoStrainsOrConditionsException;
 
+import java.util.logging.Logger;
+
 public class PrismOutputStyle extends OutputStyle {
 
     public PrismOutputStyle(SortOption sortOption) {
@@ -43,9 +46,16 @@ private void generateData(XSSFSheet sheet, Experiment experiment) {
                 XSSFCell cell = row.createCell(j + 1);
                 String sheetName = sample.getBaselineCell().getSheet().getSheetName();
                 String baselineCellAddress = getStringCellAddress(sample.getBaselineCell());
-                String timepointCellAddress = getStringCellAddress(sample.getTimepointByDay(dayNumber).originalCell());
-                String dilutionCellAddress = getStringCellAddress(sample.getTimepointByDay(dayNumber).dilutionCell());
-                String cellFormula = "'" + sheetName + "'!" + timepointCellAddress + "*" + "'" + sheetName + "'!" + dilutionCellAddress + "/'" + sheetName + "'!" + baselineCellAddress;
+                String timepointCellAddress, dilutionCellAddress;
+                try {
+                    timepointCellAddress = getStringCellAddress(sample.getTimepointByDay(dayNumber).originalCell());
+                    dilutionCellAddress = getStringCellAddress(sample.getTimepointByDay(dayNumber).dilutionCell());
+                } catch (DayOutOfBoundsException d) {
+                    Logger.getLogger(PrismOutputStyle.class.getName()).warning("Day " + dayNumber + " is out of bounds for sample " + sample.getOutputName() + ". Skipping...");
+                    continue;
+                }
+                String dilutionMultiplierFormula = "IF('" + sheetName + "'!" + dilutionCellAddress + "=\"x1000\",1,IF('" + sheetName + "'!" + dilutionCellAddress + "=\"x100\",0.1,IF('" + sheetName + "'!" + dilutionCellAddress + "=\"x10\",0.01," + dilutionCellAddress + ")))";
+                String cellFormula = "'" + sheetName + "'!" + timepointCellAddress + "*" + dilutionMultiplierFormula + "/'" + sheetName + "'!" + baselineCellAddress;
                 cell.setCellFormula(cellFormula);
                 cell.setCellStyle(sheet.getWorkbook().createCellStyle());
                 cell.getCellStyle().setDataFormat(sheet.getWorkbook().createDataFormat().getFormat("0.000"));

src/main/java/org/awdevelopment/smithlab/io/output/formats/StatisticalTestsOutputStyle.java

@@ -4,11 +4,14 @@
 import org.apache.poi.xssf.usermodel.XSSFCell;
 import org.apache.poi.xssf.usermodel.XSSFRow;
 import org.awdevelopment.smithlab.config.SortOption;
+import org.awdevelopment.smithlab.data.DayOutOfBoundsException;
 import org.awdevelopment.smithlab.data.experiment.Experiment;
 import org.apache.poi.xssf.usermodel.XSSFSheet;
 import org.awdevelopment.smithlab.data.Sample;
 import org.awdevelopment.smithlab.io.exceptions.NoStrainsOrConditionsException;
 
+import java.util.logging.Logger;
+
 public class StatisticalTestsOutputStyle extends OutputStyle {
 
     private final short numberOfReplicates;
@@ -125,9 +128,16 @@ private void generatePrimaryData(XSSFSheet sheet, Experiment experiment) {
                         case SAMPLE_NUMBER -> experiment.getSampleNumber(sampleCounter + 1);
                     };
                     String sheetName = sample.getBaselineCell().getSheet().getSheetName();
-                    String timepointCellAddress = getStringCellAddress(sample.getTimepointByDay(experiment.getDayNumbers()[j]).originalCell());
-                    String dilutionCellAddress = getStringCellAddress(sample.getTimepointByDay(experiment.getDayNumbers()[j]).dilutionCell());
-                    String cellFormula = "'" + sheetName + "'!" + timepointCellAddress + "*" + "'" + sheetName + "'!" + dilutionCellAddress;
+                    String timepointCellAddress, dilutionCellAddress;
+                    try {
+                        timepointCellAddress = getStringCellAddress(sample.getTimepointByDay(experiment.getDayNumbers()[j]).originalCell());
+                        dilutionCellAddress = getStringCellAddress(sample.getTimepointByDay(experiment.getDayNumbers()[j]).dilutionCell());
+                    } catch (DayOutOfBoundsException d) {
+                        Logger.getLogger(StatisticalTestsOutputStyle.class.getName()).warning("Day " + experiment.getDayNumbers()[j] + " is out of bounds for sample " + sample.getOutputName() + ". Skipping...");
+                        continue;
+                    }
+                    String dilutionMultiplierFormula = "IF('" + sheetName + "'!" + dilutionCellAddress + "=\"x1000\",1,IF('" + sheetName + "'!" + dilutionCellAddress + "=\"x100\",0.1,IF('" + sheetName + "'!" + dilutionCellAddress + "=\"x10\",0.01," + dilutionCellAddress + ")))";
+                    String cellFormula = "'" + sheetName + "'!" + timepointCellAddress + "*" + dilutionMultiplierFormula;
                     cell.setCellFormula(cellFormula);
                 }
                 cell.setCellStyle(sheet.getWorkbook().createCellStyle());