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make it work
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@KochTobi
KochTobi committed Sep 13, 2024
1 parent 7ca7d72 commit d45eb87
Showing 1 changed file with 82 additions and 39 deletions.
121 changes: 82 additions & 39 deletions ...tamanager/views/projects/project/measurements/download/NGSMeasurementContentProvider.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,13 +18,18 @@
import life.qbic.projectmanagement.domain.model.measurement.NGSMeasurement;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.CellStyle;
import org.apache.poi.ss.usermodel.DataValidation;
import org.apache.poi.ss.usermodel.DataValidationConstraint;
import org.apache.poi.ss.usermodel.DataValidationHelper;
import org.apache.poi.ss.usermodel.FillPatternType;
import org.apache.poi.ss.usermodel.Font;
import org.apache.poi.ss.usermodel.Name;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Row.MissingCellPolicy;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.ss.usermodel.Workbook;
import org.apache.poi.ss.util.CellRangeAddress;
import org.apache.poi.ss.util.CellRangeAddressList;
import org.apache.poi.ss.util.CellReference;
import org.apache.poi.xssf.usermodel.DefaultIndexedColorMap;
import org.apache.poi.xssf.usermodel.XSSFColor;
Expand All @@ -50,10 +55,10 @@ public class NGSMeasurementContentProvider implements DownloadContentProvider {
private final List<NGSMeasurementEntry> measurements = new LinkedList<>();
private static final String DEFAULT_FILE_NAME_PREFIX = "QBiC";
private String fileNamePrefix = DEFAULT_FILE_NAME_PREFIX;
private static final int DEFAULT_GENERATED_ROW_COUNT = 2_000;
private static final int DEFAULT_GENERATED_ROW_COUNT = 200;

private enum SequencingReadType {
SINGLE_END("singe-end"),
SINGLE_END("single-end"),
PAIRED_END("paired-end");
private final String presentationString;

Expand All @@ -74,7 +79,7 @@ private static void setAutoWidth(Sheet sheet) {

private static void formatHeader(Row header) {
for (NGSMeasurementColumns value : NGSMeasurementColumns.values()) {
var cell = header.createCell(value.columnNumber());
var cell = header.createCell(value.columnIndex());
cell.setCellValue(value.headerName());
setHeaderStyle(cell, value.readOnly());
}
Expand All @@ -95,70 +100,70 @@ private static void setCellStyle(Cell cell, boolean isReadOnly) {
}

private static void writeMeasurementIntoRow(NGSMeasurementEntry ngsMeasurementEntry, Row entry) {
var measureCol = getCellNeverNull(entry, NGSMeasurementColumns.MEASUREMENTCODE.columnNumber());
var measureCol = getOrCreateCell(entry, NGSMeasurementColumns.MEASUREMENTCODE.columnIndex());
measureCol.setCellValue(ngsMeasurementEntry.measurementCode());
setCellStyle(measureCol, NGSMeasurementColumns.MEASUREMENTCODE.readOnly());

var sampleIdCol = getCellNeverNull(entry, NGSMeasurementColumns.SAMPLEID.columnNumber());
var sampleIdCol = getOrCreateCell(entry, NGSMeasurementColumns.SAMPLEID.columnIndex());
sampleIdCol.setCellValue(ngsMeasurementEntry.sampleInformation().sampleId());
setCellStyle(sampleIdCol, NGSMeasurementColumns.SAMPLEID.readOnly());

var sampleNameCol = getCellNeverNull(entry, NGSMeasurementColumns.SAMPLENAME.columnNumber());
var sampleNameCol = getOrCreateCell(entry, NGSMeasurementColumns.SAMPLENAME.columnIndex());
sampleNameCol.setCellValue(ngsMeasurementEntry.sampleInformation().sampleName());
setCellStyle(sampleNameCol, NGSMeasurementColumns.SAMPLENAME.readOnly());

var orgIdCol = getCellNeverNull(entry, NGSMeasurementColumns.ORGANISATIONID.columnNumber());
var orgIdCol = getOrCreateCell(entry, NGSMeasurementColumns.ORGANISATIONID.columnIndex());
orgIdCol.setCellValue(ngsMeasurementEntry.organisationId());
setCellStyle(orgIdCol, NGSMeasurementColumns.ORGANISATIONID.readOnly());

var organisationNameCol = getCellNeverNull(entry,
NGSMeasurementColumns.ORGANISATIONNAME.columnNumber());
var organisationNameCol = getOrCreateCell(entry,
NGSMeasurementColumns.ORGANISATIONNAME.columnIndex());

organisationNameCol.setCellValue(ngsMeasurementEntry.organisationName());
setCellStyle(organisationNameCol, NGSMeasurementColumns.ORGANISATIONNAME.readOnly());

var facilityCol = getCellNeverNull(entry, NGSMeasurementColumns.FACILITY.columnNumber());
var facilityCol = getOrCreateCell(entry, NGSMeasurementColumns.FACILITY.columnIndex());
facilityCol.setCellValue(ngsMeasurementEntry.facility());
setCellStyle(facilityCol, NGSMeasurementColumns.FACILITY.readOnly);
var instrumentCol = getCellNeverNull(entry, NGSMeasurementColumns.INSTRUMENT.columnNumber());
var instrumentCol = getOrCreateCell(entry, NGSMeasurementColumns.INSTRUMENT.columnIndex());
instrumentCol.setCellValue(ngsMeasurementEntry.instrumentCURI());
setCellStyle(instrumentCol, NGSMeasurementColumns.INSTRUMENT.readOnly());

var instrumentNameCol = getCellNeverNull(entry,
NGSMeasurementColumns.INSTRUMENTNAME.columnNumber());
var instrumentNameCol = getOrCreateCell(entry,
NGSMeasurementColumns.INSTRUMENTNAME.columnIndex());
instrumentNameCol.setCellValue(ngsMeasurementEntry.instrumentName());
setCellStyle(instrumentNameCol, NGSMeasurementColumns.INSTRUMENTNAME.readOnly());

var readTypeCol = getCellNeverNull(entry,
NGSMeasurementColumns.SEQUENCINGREADTYPE.columnNumber());
var readTypeCol = getOrCreateCell(entry,
NGSMeasurementColumns.SEQUENCINGREADTYPE.columnIndex());
readTypeCol.setCellValue(ngsMeasurementEntry.readType());
setCellStyle(readTypeCol, NGSMeasurementColumns.SEQUENCINGREADTYPE.readOnly());

var libraryKitCol = getCellNeverNull(entry, NGSMeasurementColumns.LIBRARYKIT.columnNumber());
var libraryKitCol = getOrCreateCell(entry, NGSMeasurementColumns.LIBRARYKIT.columnIndex());
libraryKitCol.setCellValue(ngsMeasurementEntry.libraryKit());
setCellStyle(libraryKitCol, NGSMeasurementColumns.LIBRARYKIT.readOnly());

var flowCellCol = getCellNeverNull(entry, NGSMeasurementColumns.FLOWCELL.columnNumber());
var flowCellCol = getOrCreateCell(entry, NGSMeasurementColumns.FLOWCELL.columnIndex());
flowCellCol.setCellValue(ngsMeasurementEntry.flowCell());
setCellStyle(flowCellCol, NGSMeasurementColumns.FLOWCELL.readOnly());

var runProtocolCol = getCellNeverNull(entry, NGSMeasurementColumns.RUNPROTOCOL.columnNumber());
var runProtocolCol = getOrCreateCell(entry, NGSMeasurementColumns.RUNPROTOCOL.columnIndex());
runProtocolCol.setCellValue(ngsMeasurementEntry.runProtocol());
setCellStyle(runProtocolCol, NGSMeasurementColumns.RUNPROTOCOL.readOnly());

var poolGroupCol = getCellNeverNull(entry, NGSMeasurementColumns.POOLGROUP.columnNumber());
var poolGroupCol = getOrCreateCell(entry, NGSMeasurementColumns.POOLGROUP.columnIndex());
poolGroupCol.setCellValue(ngsMeasurementEntry.samplePoolGroup());
setCellStyle(poolGroupCol, NGSMeasurementColumns.POOLGROUP.readOnly());

var indexI7Col = getCellNeverNull(entry, NGSMeasurementColumns.INDEXI7.columnNumber());
var indexI7Col = getOrCreateCell(entry, NGSMeasurementColumns.INDEXI7.columnIndex());
indexI7Col.setCellValue(ngsMeasurementEntry.indexI7());
setCellStyle(indexI7Col, NGSMeasurementColumns.INDEXI7.readOnly());

var indexI5Col = getCellNeverNull(entry, NGSMeasurementColumns.INDEXI5.columnNumber());
var indexI5Col = getOrCreateCell(entry, NGSMeasurementColumns.INDEXI5.columnIndex());
indexI5Col.setCellValue(ngsMeasurementEntry.indexI5());
setCellStyle(indexI5Col, NGSMeasurementColumns.INDEXI5.readOnly());

var commentCol = getCellNeverNull(entry, NGSMeasurementColumns.COMMENT.columnNumber());
var commentCol = getOrCreateCell(entry, NGSMeasurementColumns.COMMENT.columnIndex());
commentCol.setCellValue(ngsMeasurementEntry.comment());
setCellStyle(commentCol, NGSMeasurementColumns.COMMENT.readOnly());
}
Expand Down Expand Up @@ -208,7 +213,7 @@ private void defineReadOnlyHeaderStyle(Workbook workbook) {
*/
protected static Name addValueListWithName(String name, Sheet sheet,
PropertyValues propertyValues) {
Row headerRow = getRowNeverNull(sheet, 0);
Row headerRow = getOrCreateRow(sheet, 0);
var columnNumber = Math.max(1,
headerRow.getLastCellNum()); // we want to obtain 1 for the first to come if there are none and not -1 -.-
var columnIndex = columnNumber - 1;
Expand All @@ -219,13 +224,13 @@ protected static Name addValueListWithName(String name, Sheet sheet,

for (int i = 0; i < propertyValues.size(); i++) {
var rowIndex = i + 1; // +1 because of header row
Row valueRow = getRowNeverNull(sheet, rowIndex);
Row valueRow = getOrCreateRow(sheet, rowIndex);
valueRow.createCell(columnIndex).setCellValue(propertyValues.get(i));
}
var reference = "'%s'!$%s$%s:$%s$%s".formatted( //e.g. 'My Sheet'!$A$1:$E$23
var reference = "'%s'!$%s$%s:$%s$%s".formatted( //e.g. 'My Sheet'!$A$2:$E$23
sheet.getSheetName(),
CellReference.convertNumToColString(columnIndex),
1,
2, //ignore the header
CellReference.convertNumToColString(columnIndex),
propertyValues.size() + 1
);
Expand Down Expand Up @@ -271,24 +276,57 @@ public byte[] getContent() {
new PropertyValues("Sequencing read type", SequencingReadType.getOptions()));

Sheet sheet = workbook.createSheet("NGS Measurement Metadata");
workbook.setSheetOrder(sheet.getSheetName(), 0);

Row header = getRowNeverNull(sheet, 0);
Row header = getOrCreateRow(sheet, 0);
for (NGSMeasurementColumns value : NGSMeasurementColumns.values()) {
var cell = header.createCell(value.columnNumber());
var cell = header.createCell(value.columnIndex());
cell.setCellValue(value.headerName());
setHeaderStyle(cell, value.readOnly());
}

for (int i = 0; i < measurements.size(); i++) {
var measurement = measurements.get(i);
var rowIndex = i + 1;
Row row = getRowNeverNull(sheet, rowIndex);
var startIndex = 1; // start in row number 2 with index 1 as the header row has number 1 index 0
int rowIndex = startIndex;
for (NGSMeasurementEntry measurement : measurements) {
Row row = getOrCreateRow(sheet, rowIndex);
writeMeasurementIntoRow(measurement, row);
rowIndex++;
}

var generatedRowCount = rowIndex - startIndex;
assert generatedRowCount == measurements.size() : "all measurements have a corresponding row";

for (int i = generatedRowCount + startIndex; i < DEFAULT_GENERATED_ROW_COUNT; i++) {
Row row = getOrCreateRow(sheet, i);
for (int j = 0; j < NGSMeasurementColumns.maxColumnIndex(); j++) {
getOrCreateCell(row, j); // make sure all cells exist
}
}

//TODO add data validation
CellRangeAddressList sequencingReadTypeValueCells = new CellRangeAddressList(startIndex,
DEFAULT_GENERATED_ROW_COUNT - 1, //need the index
NGSMeasurementColumns.SEQUENCINGREADTYPE.columnIndex(),
NGSMeasurementColumns.SEQUENCINGREADTYPE.columnIndex());
DataValidationHelper dvHelper = sheet.getDataValidationHelper();
DataValidationConstraint dvConstraint = dvHelper.createFormulaListConstraint(
sequencingReadTypeArea.getNameName());
System.out.println("dvConstraint.getFormula1() = " + dvConstraint.getFormula1());
DataValidation sequencingReadTypeValidation = dvHelper.createValidation(dvConstraint,
sequencingReadTypeValueCells);
System.out.println("sequencingReadTypeValidation.getRegions() = "
+ Arrays.stream(sequencingReadTypeValidation.getRegions().getCellRangeAddresses())
.map(CellRangeAddress::formatAsString).toList());
System.out.println("sequencingReadTypeValidation.getSuppressDropDownArrow() = "
+ sequencingReadTypeValidation.getSuppressDropDownArrow());
sequencingReadTypeValidation.setShowErrorBox(true);
sequencingReadTypeValidation.createErrorBox("Invalid entry",
"Please select from " + String.join(", ",
SequencingReadType.getOptions()));
sheet.addValidationData(sequencingReadTypeValidation);

setAutoWidth(sheet);
workbook.setSheetOrder(sheet.getSheetName(), 0);
workbook.setActiveSheet(0);

byteArrayOutputStream = new ByteArrayOutputStream();
workbook.write(byteArrayOutputStream);
Expand All @@ -309,12 +347,12 @@ private static String getCellValue(Cell cell) {
};
}

private static Row getRowNeverNull(Sheet sheet, int index) {
private static Row getOrCreateRow(Sheet sheet, int index) {
return Optional.ofNullable(sheet.getRow(index))
.orElse(sheet.createRow(index));
}

private static Cell getCellNeverNull(Row row, int colIndex) {
private static Cell getOrCreateCell(Row row, int colIndex) {
return Optional.ofNullable(row.getCell(colIndex, MissingCellPolicy.RETURN_BLANK_AS_NULL))
.orElse(row.createCell(colIndex));
}
Expand Down Expand Up @@ -371,10 +409,15 @@ enum NGSMeasurementColumns {
;

private final String headerName;
private final int columnNumber;
private final int columnIndex;
private final boolean readOnly;
private final List<String> allowedValues;

static int maxColumnIndex() {
return Arrays.stream(values())
.mapToInt(NGSMeasurementColumns::columnIndex)
.max().orElse(0);
}

/**
* @param headerName the name in the header
Expand All @@ -385,7 +428,7 @@ enum NGSMeasurementColumns {
NGSMeasurementColumns(String headerName, int columnIndex, boolean readOnly,
List<String> allowedValues) {
this.headerName = headerName;
this.columnNumber = columnIndex;
this.columnIndex = columnIndex;
this.readOnly = readOnly;
this.allowedValues = allowedValues;
}
Expand All @@ -403,8 +446,8 @@ public String headerName() {
return headerName;
}

public int columnNumber() {
return columnNumber;
public int columnIndex() {
return columnIndex;
}

public boolean readOnly() {
Expand Down

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