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Adapt proteomics template
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Fixes the edit case and renames instrument to MS device

fixes #786
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@KochTobi
KochTobi committed Sep 16, 2024
1 parent 82f0b1d commit 265accb
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Showing 3 changed files with 176 additions and 167 deletions.
4 changes: 4 additions & 0 deletions .../projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -180,6 +180,10 @@ public static boolean isDigestionMethod(String input) {
public String getName() {
return name;
}

public static List<String> getOptions() {
return Arrays.stream(values()).map(DigestionMethod::getName).toList();
}
}

private class ValidationPolicy {
Expand Down
104 changes: 44 additions & 60 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 @@ -8,7 +8,6 @@
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import java.util.LinkedList;
import java.util.List;
import java.util.Optional;
Expand Down Expand Up @@ -98,27 +97,27 @@ private static void setCellStyle(Cell cell, boolean isReadOnly) {
}

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

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

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

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

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

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

var facilityCol = getOrCreateCell(entry, NGSMeasurementColumns.FACILITY.columnIndex());
facilityCol.setCellValue(ngsMeasurementEntry.facility());
Expand All @@ -128,38 +127,39 @@ private static void writeMeasurementIntoRow(NGSMeasurementEntry ngsMeasurementEn
setCellStyle(instrumentCol, NGSMeasurementColumns.INSTRUMENT.readOnly());

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

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

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

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

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

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

var indexI7Col = getOrCreateCell(entry, NGSMeasurementColumns.INDEXI7.columnIndex());
var indexI7Col = getOrCreateCell(entry, NGSMeasurementColumns.INDEX_I7.columnIndex());
indexI7Col.setCellValue(ngsMeasurementEntry.indexI7());
setCellStyle(indexI7Col, NGSMeasurementColumns.INDEXI7.readOnly());
setCellStyle(indexI7Col, NGSMeasurementColumns.INDEX_I7.readOnly());

var indexI5Col = getOrCreateCell(entry, NGSMeasurementColumns.INDEXI5.columnIndex());
var indexI5Col = getOrCreateCell(entry, NGSMeasurementColumns.INDEX_I5.columnIndex());
indexI5Col.setCellValue(ngsMeasurementEntry.indexI5());
setCellStyle(indexI5Col, NGSMeasurementColumns.INDEXI5.readOnly());
setCellStyle(indexI5Col, NGSMeasurementColumns.INDEX_I5.readOnly());

var commentCol = getOrCreateCell(entry, NGSMeasurementColumns.COMMENT.columnIndex());
commentCol.setCellValue(ngsMeasurementEntry.comment());
Expand Down Expand Up @@ -240,9 +240,9 @@ public byte[] getContent() {
assert generatedRowCount == measurements.size() : "all measurements have a corresponding row";

XLSXTemplateHelper.addDataValidation(sheet,
NGSMeasurementColumns.SEQUENCINGREADTYPE.columnIndex(),
NGSMeasurementColumns.SEQUENCING_READ_TYPE.columnIndex(),
startIndex,
NGSMeasurementColumns.SEQUENCINGREADTYPE.columnIndex(),
NGSMeasurementColumns.SEQUENCING_READ_TYPE.columnIndex(),
DEFAULT_GENERATED_ROW_COUNT - 1,
sequencingReadTypeArea);

Expand Down Expand Up @@ -289,36 +289,36 @@ public String getFileName() {
*/
enum NGSMeasurementColumns {

MEASUREMENTCODE("Measurement ID", 0,
MEASUREMENT_ID("Measurement ID", 0,
true),
SAMPLEID("QBiC Sample Id", 1,
SAMPLE_ID("QBiC Sample Id", 1,
true),
SAMPLENAME(
SAMPLE_NAME(
"Sample Name", 2,
true),
POOLGROUP("Sample Pool Group", 3,
POOL_GROUP("Sample Pool Group", 3,
true),
ORGANISATIONID("Organisation ID", 4,
ORGANISATION_ID("Organisation ID", 4,
false),
ORGANISATIONNAME("Organisation Name", 5,
ORGANISATION_NAME("Organisation Name", 5,
true),
FACILITY("Facility", 6,
false),
INSTRUMENT("Instrument", 7,
false),
INSTRUMENTNAME("Instrument Name", 8,
INSTRUMENT_NAME("Instrument Name", 8,
true),
SEQUENCINGREADTYPE("Sequencing Read Type", 9,
false, List.of("single-end", "paired-end")),
LIBRARYKIT("Library Kit", 10,
SEQUENCING_READ_TYPE("Sequencing Read Type", 9,
false),
FLOWCELL("Flow Cell", 11,
LIBRARY_KIT("Library Kit", 10,
false),
RUNPROTOCOL("Sequencing Run Protocol", 12,
FLOW_CELL("Flow Cell", 11,
false),
INDEXI7("Index i7", 13,
SEQUENCING_RUN_PROTOCOL("Sequencing Run Protocol", 12,
false),
INDEXI5("Index i5", 14,
INDEX_I7("Index i7", 13,
false),
INDEX_I5("Index i5", 14,
false),
COMMENT("Comment", 15,
false),
Expand All @@ -327,7 +327,6 @@ enum NGSMeasurementColumns {
private final String headerName;
private final int columnIndex;
private final boolean readOnly;
private final List<String> allowedValues;

static int maxColumnIndex() {
return Arrays.stream(values())
Expand All @@ -339,23 +338,11 @@ static int maxColumnIndex() {
* @param headerName the name in the header
* @param columnIndex the index of the column this property is in
* @param readOnly is the property read only
* @param allowedValues a list of allowed values; null if not applicable
*/
NGSMeasurementColumns(String headerName, int columnIndex, boolean readOnly,
List<String> allowedValues) {
NGSMeasurementColumns(String headerName, int columnIndex, boolean readOnly) {
this.headerName = headerName;
this.columnIndex = columnIndex;
this.readOnly = readOnly;
this.allowedValues = allowedValues;
}

/**
* @param headerName the name in the header
* @param columnIndex the index of the column this property is in
* @param readOnly is the property read only
*/
NGSMeasurementColumns(String headerName, int columnIndex, boolean readOnly) {
this(headerName, columnIndex, readOnly, null);
}

public String headerName() {
Expand All @@ -370,8 +357,5 @@ public boolean readOnly() {
return readOnly;
}

public List<String> allowedValues() {
return Optional.ofNullable(allowedValues).orElse(Collections.emptyList());
}
}
}
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