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Merged
AdamW78 merged 1 commit into from
Apr 8, 2025
Merged

Finish debugging #7

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4 changes: 4 additions & 0 deletions src/main/java/org/awdevelopment/smithlab/io/input/XlsxHeaderReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,10 @@ public static Headers readHeaders(LoggerHelper LOGGER, XSSFSheet sheet) throws I
int rowZeroWidth = sheet.getRow(0).getLastCellNum();
for (int i = 0; i < rowZeroWidth; i++) {
XSSFCell cell = sheet.getRow(0).getCell(i);
if (cell == null) {
LOGGER.atWarn("Cell in header row at zero-indexed column "+i+" is null, skipping...");
continue;
}
CellType cellType = cell.getCellType();
if (cellType == CellType._NONE || cellType == CellType.BLANK || cellType == CellType.ERROR) {
LOGGER.atWarn("Cell in header row at zero-indexed column "+i
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22 changes: 20 additions & 2 deletions src/main/java/org/awdevelopment/smithlab/io/input/XlsxInputReader.java
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Expand Up @@ -253,7 +253,27 @@ private Condition readCondition(XSSFCell cell) throws InvalidConditionValueExcep
}
}

private boolean isCellInMergedRegion(XSSFCell cell) {
XSSFSheet sheet = cell.getSheet();
int rowIndex = cell.getRowIndex();
int colIndex = cell.getColumnIndex();
return sheet.getMergedRegions().stream().anyMatch(region -> region.isInRange(rowIndex, colIndex));
}

private Strain readStrain(XSSFCell cell, Condition condition) throws InvalidStrainValueException {
int rowIndex = cell.getRowIndex();
int colIndex = cell.getColumnIndex();
// Check if the cell is in a merged region
if (cell == null || isCellInMergedRegion(cell)) {
while (cell == null || cell.getCellType() == CellType.BLANK || cell.getCellType() == CellType.ERROR) {
if (rowIndex == 0) break;
rowIndex--;
cell = cell.getSheet().getRow(rowIndex).getCell(colIndex);
rowIndex = cell.getRowIndex();
colIndex = cell.getColumnIndex();
}
}

CellType cellType = cell.getCellType();
if (cellType == CellType.STRING) {
String cellContent = cell.getStringCellValue();
Expand All @@ -265,8 +285,6 @@ private Strain readStrain(XSSFCell cell, Condition condition) throws InvalidStra
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, condition);
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