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Make ngs row creation simpler
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Uses the enum and enhanced switch to make sure all columns are covered and removes complexity.
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@KochTobi
KochTobi committed Sep 16, 2024
1 parent 265accb commit f278e28
Showing 1 changed file with 46 additions and 17 deletions.
63 changes: 46 additions & 17 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 @@ -96,74 +96,103 @@ private static void setCellStyle(Cell cell, boolean isReadOnly) {
}
}

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

var sampleIdCol = getOrCreateCell(entry, NGSMeasurementColumns.SAMPLE_ID.columnIndex());
var sampleIdCol = getOrCreateCell(entryRow, NGSMeasurementColumns.SAMPLE_ID.columnIndex());
sampleIdCol.setCellValue(ngsMeasurementEntry.sampleInformation().sampleId());
setCellStyle(sampleIdCol, NGSMeasurementColumns.SAMPLE_ID.readOnly());

var sampleNameCol = getOrCreateCell(entry, NGSMeasurementColumns.SAMPLE_NAME.columnIndex());
var sampleNameCol = getOrCreateCell(entryRow, NGSMeasurementColumns.SAMPLE_NAME.columnIndex());
sampleNameCol.setCellValue(ngsMeasurementEntry.sampleInformation().sampleName());
setCellStyle(sampleNameCol, NGSMeasurementColumns.SAMPLE_NAME.readOnly());

var orgIdCol = getOrCreateCell(entry, NGSMeasurementColumns.ORGANISATION_ID.columnIndex());
var orgIdCol = getOrCreateCell(entryRow, NGSMeasurementColumns.ORGANISATION_ID.columnIndex());
orgIdCol.setCellValue(ngsMeasurementEntry.organisationId());
setCellStyle(orgIdCol, NGSMeasurementColumns.ORGANISATION_ID.readOnly());

var organisationNameCol = getOrCreateCell(entry,
var organisationNameCol = getOrCreateCell(entryRow,
NGSMeasurementColumns.ORGANISATION_NAME.columnIndex());

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

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

var instrumentNameCol = getOrCreateCell(entry,
var instrumentNameCol = getOrCreateCell(entryRow,
NGSMeasurementColumns.INSTRUMENT_NAME.columnIndex());
instrumentNameCol.setCellValue(ngsMeasurementEntry.instrumentName());
setCellStyle(instrumentNameCol, NGSMeasurementColumns.INSTRUMENT_NAME.readOnly());

var readTypeCol = getOrCreateCell(entry,
var readTypeCol = getOrCreateCell(entryRow,
NGSMeasurementColumns.SEQUENCING_READ_TYPE.columnIndex());
readTypeCol.setCellValue(ngsMeasurementEntry.readType());
setCellStyle(readTypeCol, NGSMeasurementColumns.SEQUENCING_READ_TYPE.readOnly());

var libraryKitCol = getOrCreateCell(entry, NGSMeasurementColumns.LIBRARY_KIT.columnIndex());
var libraryKitCol = getOrCreateCell(entryRow, NGSMeasurementColumns.LIBRARY_KIT.columnIndex());
libraryKitCol.setCellValue(ngsMeasurementEntry.libraryKit());
setCellStyle(libraryKitCol, NGSMeasurementColumns.LIBRARY_KIT.readOnly());

var flowCellCol = getOrCreateCell(entry, NGSMeasurementColumns.FLOW_CELL.columnIndex());
var flowCellCol = getOrCreateCell(entryRow, NGSMeasurementColumns.FLOW_CELL.columnIndex());
flowCellCol.setCellValue(ngsMeasurementEntry.flowCell());
setCellStyle(flowCellCol, NGSMeasurementColumns.FLOW_CELL.readOnly());

var runProtocolCol = getOrCreateCell(entry,
var runProtocolCol = getOrCreateCell(entryRow,
NGSMeasurementColumns.SEQUENCING_RUN_PROTOCOL.columnIndex());
runProtocolCol.setCellValue(ngsMeasurementEntry.runProtocol());
setCellStyle(runProtocolCol, NGSMeasurementColumns.SEQUENCING_RUN_PROTOCOL.readOnly());

var poolGroupCol = getOrCreateCell(entry, NGSMeasurementColumns.POOL_GROUP.columnIndex());
var poolGroupCol = getOrCreateCell(entryRow, NGSMeasurementColumns.POOL_GROUP.columnIndex());
poolGroupCol.setCellValue(ngsMeasurementEntry.samplePoolGroup());
setCellStyle(poolGroupCol, NGSMeasurementColumns.POOL_GROUP.readOnly());

var indexI7Col = getOrCreateCell(entry, NGSMeasurementColumns.INDEX_I7.columnIndex());
var indexI7Col = getOrCreateCell(entryRow, NGSMeasurementColumns.INDEX_I7.columnIndex());
indexI7Col.setCellValue(ngsMeasurementEntry.indexI7());
setCellStyle(indexI7Col, NGSMeasurementColumns.INDEX_I7.readOnly());

var indexI5Col = getOrCreateCell(entry, NGSMeasurementColumns.INDEX_I5.columnIndex());
var indexI5Col = getOrCreateCell(entryRow, NGSMeasurementColumns.INDEX_I5.columnIndex());
indexI5Col.setCellValue(ngsMeasurementEntry.indexI5());
setCellStyle(indexI5Col, NGSMeasurementColumns.INDEX_I5.readOnly());

var commentCol = getOrCreateCell(entry, NGSMeasurementColumns.COMMENT.columnIndex());
var commentCol = getOrCreateCell(entryRow, NGSMeasurementColumns.COMMENT.columnIndex());
commentCol.setCellValue(ngsMeasurementEntry.comment());
setCellStyle(commentCol, NGSMeasurementColumns.COMMENT.readOnly());

for (NGSMeasurementColumns measurementColumn : NGSMeasurementColumns.values()) {
var value = switch (measurementColumn) {
case MEASUREMENT_ID -> ngsMeasurementEntry.measurementCode();
case SAMPLE_ID -> ngsMeasurementEntry.sampleInformation().sampleId();
case SAMPLE_NAME -> ngsMeasurementEntry.sampleInformation().sampleName();
case POOL_GROUP -> ngsMeasurementEntry.samplePoolGroup();
case ORGANISATION_ID -> ngsMeasurementEntry.organisationId();
case ORGANISATION_NAME -> ngsMeasurementEntry.organisationName();
case FACILITY -> ngsMeasurementEntry.facility();
case INSTRUMENT -> ngsMeasurementEntry.instrumentCURI();
case INSTRUMENT_NAME -> ngsMeasurementEntry.instrumentName();
case SEQUENCING_READ_TYPE -> ngsMeasurementEntry.readType();
case LIBRARY_KIT -> ngsMeasurementEntry.libraryKit();
case FLOW_CELL -> ngsMeasurementEntry.flowCell();
case SEQUENCING_RUN_PROTOCOL -> ngsMeasurementEntry.runProtocol();
case INDEX_I7 -> ngsMeasurementEntry.indexI7();
case INDEX_I5 -> ngsMeasurementEntry.indexI5();
case COMMENT -> ngsMeasurementEntry.comment();
};
var cell = getOrCreateCell(entryRow, measurementColumn.columnIndex());
cell.setCellValue(value);
if (measurementColumn.readOnly()) {
cell.setCellStyle(readOnlyCellStyle);
}
}


}

public void setMeasurements(List<NGSMeasurementEntry> measurements, String fileNamePrefix) {
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