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Fix measurement registration #854

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merged 7 commits into from
Oct 17, 2024
Merged

Fix measurement registration #854

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79f8764
Fix measurement registration
KochTobi Oct 17, 2024
247f2b8
Fix mandatory property for ngs measurements
KochTobi Oct 17, 2024
3b2ee4c
fix column header names
KochTobi Oct 17, 2024
d80258f
Separate register from edit case
KochTobi Oct 17, 2024
91b7c63
Fix analysisMethod storage to use the enum name again
KochTobi Oct 17, 2024
34f2904
fix wrong method call
KochTobi Oct 17, 2024
3c3feab
fix inverted boolean flag
KochTobi Oct 17, 2024
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7 changes: 4 additions & 3 deletions user-interface/src/main/java/life/qbic/datamanager/parser/MeasurementMetadataConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,17 +25,18 @@ public interface MeasurementMetadataConverter {
* </ul>
*
* @param parsingResult the parsing result to take as input for the conversion.
* @param ignoreMeasurementId weather to ignore the measurement identifier or not
* @return a list of converted implementations of {@link MeasurementMetadata}.
* @throws UnknownMetadataTypeException if no matching implementation of
* {@link MeasurementMetadata} can be associated from the
* provided {@link ParsingResult#columnMap()}.
* @since 1.4.0
*/
List<? extends MeasurementMetadata> convert(ParsingResult parsingResult,
boolean ignoreMeasurementId)
List<? extends MeasurementMetadata> convertRegister(ParsingResult parsingResult)
throws UnknownMetadataTypeException;

List<MeasurementMetadata> convertEdit(ParsingResult parsingResult)
throws UnknownMetadataTypeException, MissingSampleIdException;

class UnknownMetadataTypeException extends RuntimeException {

public UnknownMetadataTypeException(String message) {
Expand Down
172 changes: 151 additions & 21 deletions user-interface/src/main/java/life/qbic/datamanager/parser/MetadataConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,9 @@
import java.util.function.Function;
import java.util.stream.Collectors;
import life.qbic.datamanager.parser.measurement.NGSMeasurementEditColumn;
import life.qbic.datamanager.parser.measurement.NGSMeasurementRegisterColumn;
import life.qbic.datamanager.parser.measurement.ProteomicsMeasurementEditColumn;
import life.qbic.datamanager.parser.measurement.ProteomicsMeasurementRegisterColumn;
import life.qbic.logging.api.Logger;
import life.qbic.projectmanagement.application.measurement.Labeling;
import life.qbic.projectmanagement.application.measurement.MeasurementMetadata;
Expand Down Expand Up @@ -82,14 +84,30 @@ private static Map<String, Integer> countHits(Collection<String> target, Set<Str
}

@Override
public List<MeasurementMetadata> convert(ParsingResult parsingResult, boolean ignoreMeasurementId)
public List<MeasurementMetadata> convertRegister(ParsingResult parsingResult)
throws UnknownMetadataTypeException, MissingSampleIdException {
Objects.requireNonNull(parsingResult);
var properties = parsingResult.columnMap().keySet();
if (looksLikeNgsMeasurement(properties, ignoreMeasurementId)) {
return tryConversion(this::convertNGSMeasurement, parsingResult);
} else if (looksLikeProteomicsMeasurement(properties, ignoreMeasurementId)) {
return tryConversion(this::convertProteomicsMeasurement, parsingResult);
if (looksLikeNgsMeasurement(properties, false)) {
return tryConversion(this::convertExistingNGSMeasurement, parsingResult);
} else if (looksLikeProteomicsMeasurement(properties, false)) {
return tryConversion(this::convertNewProteomicsMeasurement, parsingResult);
} else {
throw new UnknownMetadataTypeException(
"Unknown metadata type: cannot match properties to any known metadata type. Provided [%s]".formatted(
String.join(", ", properties)));
}
}

@Override
public List<MeasurementMetadata> convertEdit(ParsingResult parsingResult)
throws UnknownMetadataTypeException, MissingSampleIdException {
Objects.requireNonNull(parsingResult);
var properties = parsingResult.columnMap().keySet();
if (looksLikeNgsMeasurement(properties, true)) {
return tryConversion(this::convertExistingNGSMeasurement, parsingResult);
} else if (looksLikeProteomicsMeasurement(properties, true)) {
return tryConversion(this::convertExistingProteomicsMeasurement, parsingResult);
} else {
throw new UnknownMetadataTypeException(
"Unknown metadata type: cannot match properties to any known metadata type. Provided [%s]".formatted(
Expand All @@ -106,7 +124,65 @@ private List<MeasurementMetadata> tryConversion(
}
}

private List<MeasurementMetadata> convertProteomicsMeasurement(ParsingResult parsingResult) {
private List<MeasurementMetadata> convertNewProteomicsMeasurement(ParsingResult parsingResult) {
var result = new ArrayList<MeasurementMetadata>();
for (int i = 0; i < parsingResult.rows().size(); i++) {
var sampleCode = SampleCode.create(parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.SAMPLE_ID.headerName(), ""));
var technicalReplicateName = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.TECHNICAL_REPLICATE_NAME.headerName(), "");
var organisationId = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.ORGANISATION_ID.headerName(), "");
var msDevice = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.MS_DEVICE.headerName(), "");
var samplePoolGroup = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.POOL_GROUP.headerName(), "");
var facility = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.FACILITY.headerName(), "");
var fractionName = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.CYCLE_FRACTION_NAME.headerName(), "");
var digestionEnzyme = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.DIGESTION_ENZYME.headerName(), "");
var digestionMethod = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.DIGESTION_METHOD.headerName(), "");
var enrichmentMethod = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.ENRICHMENT_METHOD.headerName(), "");
var injectionVolume = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.INJECTION_VOLUME.headerName(), "");
var lcColumn = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.LC_COLUMN.headerName(), "");
var lcmsMethod = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.LCMS_METHOD.headerName(), "");
var labelingType = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.LABELING_TYPE.headerName(), "");
var label = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.LABEL.headerName(), "");
var comment = parsingResult.getValueOrDefault(i,
ProteomicsMeasurementRegisterColumn.COMMENT.headerName(), "");
var pxpMetaDaturm = new ProteomicsMeasurementMetadata(
"",
sampleCode,
technicalReplicateName,
organisationId,
msDevice,
samplePoolGroup,
facility,
fractionName,
digestionEnzyme,
digestionMethod,
enrichmentMethod,
injectionVolume,
lcColumn,
lcmsMethod,
new Labeling(labelingType, label),
comment);
result.add(pxpMetaDaturm);
}
return result;
}

private List<MeasurementMetadata> convertExistingProteomicsMeasurement(
ParsingResult parsingResult) {
var result = new ArrayList<MeasurementMetadata>();
for (int i = 0; i < parsingResult.rows().size(); i++) {
var measurementId = parsingResult.getValueOrDefault(i,
Expand Down Expand Up @@ -164,7 +240,7 @@ private List<MeasurementMetadata> convertProteomicsMeasurement(ParsingResult par
return result;
}

private List<MeasurementMetadata> convertNGSMeasurement(ParsingResult parsingResult) {
private List<MeasurementMetadata> convertExistingNGSMeasurement(ParsingResult parsingResult) {
var result = new ArrayList<MeasurementMetadata>();

for (int i = 0; i < parsingResult.rows().size(); i++) {
Expand All @@ -182,7 +258,7 @@ private List<MeasurementMetadata> convertNGSMeasurement(ParsingResult parsingRes
var facility = parsingResult.getValueOrDefault(i,
NGSMeasurementEditColumn.FACILITY.headerName(), "");
var sequencingReadType = parsingResult.getValueOrDefault(i,
NGSMeasurementEditColumn.SEQUENCING_RUN_PROTOCOL.headerName(), "");
NGSMeasurementEditColumn.SEQUENCING_READ_TYPE.headerName(), "");
var libraryKit = parsingResult.getValueOrDefault(i,
NGSMeasurementEditColumn.LIBRARY_KIT.headerName(), "");
var flowCell = parsingResult.getValueOrDefault(i,
Expand Down Expand Up @@ -217,22 +293,74 @@ private List<MeasurementMetadata> convertNGSMeasurement(ParsingResult parsingRes
return result;
}

private List<MeasurementMetadata> convertNewNGSMeasurement(ParsingResult parsingResult) {
var result = new ArrayList<MeasurementMetadata>();

for (int i = 0; i < parsingResult.rows().size(); i++) {
var sampleCodes = List.of(
SampleCode.create(
parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.SAMPLE_ID.headerName(),
""))
);
var organisationId = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.ORGANISATION_ID.headerName(), "");
var instrument = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.INSTRUMENT.headerName(), "");
var facility = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.FACILITY.headerName(), "");
var sequencingReadType = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.SEQUENCING_READ_TYPE.headerName(), "");
var libraryKit = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.LIBRARY_KIT.headerName(), "");
var flowCell = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.FLOW_CELL.headerName(), "");
var runProtocol = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.SEQUENCING_RUN_PROTOCOL.headerName(), "");
var poolGroup = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.POOL_GROUP.headerName(), "");
var indexI7 = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.INDEX_I7.headerName(), "");
var indexI5 = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.INDEX_I5.headerName(), "");
var comment = parsingResult.getValueOrDefault(i,
NGSMeasurementRegisterColumn.COMMENT.headerName(), "");
var metadatum = new NGSMeasurementMetadata(
"",
sampleCodes,
organisationId,
instrument,
facility,
sequencingReadType,
libraryKit,
flowCell,
runProtocol,
poolGroup,
indexI7,
indexI5,
comment
);
result.add(metadatum);
}
return result;
}

private boolean looksLikeNgsMeasurement(Collection<String> properties, boolean ignoreID) {
var formattedProperties = properties.stream().map(String::toLowerCase)
.collect(Collectors.toList());
Map<String, Integer> hitMap;
if (ignoreID) {
formattedProperties.remove(NGSMeasurementEditColumn.MEASUREMENT_ID.headerName());
hitMap = countHits(formattedProperties,
Arrays.stream(NGSMeasurementEditColumn.values())
.map(NGSMeasurementEditColumn::headerName)
.collect(
Collectors.toSet()), NGSMeasurementEditColumn.MEASUREMENT_ID.headerName());
Arrays.stream(NGSMeasurementRegisterColumn.values())
.map(NGSMeasurementRegisterColumn::headerName)
.map(Sanitizer::headerEncoder)
.collect(Collectors.toSet()), NGSMeasurementEditColumn.MEASUREMENT_ID.headerName());
} else {
hitMap = countHits(formattedProperties,
Arrays.stream(NGSMeasurementEditColumn.values())
.map(NGSMeasurementEditColumn::headerName).collect(
Collectors.toSet()));
.map(NGSMeasurementEditColumn::headerName)
.map(Sanitizer::headerEncoder)
.collect(Collectors.toSet()));
}
var missingProperties = new ArrayList<>();
for (Entry<String, Integer> entry : hitMap.entrySet()) {
Expand All @@ -253,16 +381,18 @@ private boolean looksLikeProteomicsMeasurement(Collection<String> properties, bo
.collect(Collectors.toList());
Map<String, Integer> hitMap;
if (ignoreID) {
formattedProperties.remove(ProteomicsMeasurementEditColumn.MEASUREMENT_ID.headerName());
hitMap = countHits(formattedProperties,
Arrays.stream(ProteomicsMeasurementEditColumn.values())
.map(ProteomicsMeasurementEditColumn::headerName).collect(
Collectors.toSet()), ProteomicsMeasurementEditColumn.MEASUREMENT_ID.headerName());
Arrays.stream(ProteomicsMeasurementRegisterColumn.values())
.map(ProteomicsMeasurementRegisterColumn::headerName)
.map(Sanitizer::headerEncoder)
.collect(Collectors.toSet()),
ProteomicsMeasurementEditColumn.MEASUREMENT_ID.headerName());
} else {
hitMap = countHits(formattedProperties,
Arrays.stream(ProteomicsMeasurementEditColumn.values())
.map(ProteomicsMeasurementEditColumn::headerName).collect(
Collectors.toSet()));
.map(ProteomicsMeasurementEditColumn::headerName)
.map(Sanitizer::headerEncoder)
.collect(Collectors.toSet()));
}
var missingProperties = new ArrayList<>();
for (Entry<String, Integer> entry : hitMap.entrySet()) {
Expand Down
46 changes: 27 additions & 19 deletions ...face/src/main/java/life/qbic/datamanager/parser/measurement/NGSMeasurementEditColumn.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,34 +5,35 @@
/**
* <b>NGS Measurement Columns</b>
*
* <p>Enumeration of the columns shown in the file used for NGS measurement registration and edit
* <p>Enumeration of the columns shown in the file used for NGS measurement edit
* in the context of measurement file based upload. Provides the name of the header column, the
* column index and if the column should be set to readOnly in the generated sheet
* </p>
*/
public enum NGSMeasurementEditColumn {

MEASUREMENT_ID("Measurement ID", 0, true),
SAMPLE_ID("QBiC Sample Id", 1, true),
SAMPLE_NAME("Sample Name", 2, true),
POOL_GROUP("Sample Pool Group", 3, true),
ORGANISATION_ID("Organisation ID", 4, false),
ORGANISATION_NAME("Organisation Name", 5, true),
FACILITY("Facility", 6, false),
INSTRUMENT("Instrument", 7, false),
INSTRUMENT_NAME("Instrument Name", 8, true),
SEQUENCING_READ_TYPE("Sequencing Read Type", 9, false),
LIBRARY_KIT("Library Kit", 10, false),
FLOW_CELL("Flow Cell", 11, false),
SEQUENCING_RUN_PROTOCOL("Sequencing Run Protocol", 12, false),
INDEX_I7("Index i7", 13, false),
INDEX_I5("Index i5", 14, false),
COMMENT("Comment", 15, false),
MEASUREMENT_ID("Measurement ID", 0, true, true),
SAMPLE_ID("QBiC Sample Id", 1, true, true),
SAMPLE_NAME("Sample Name", 2, true, false),
POOL_GROUP("Sample Pool Group", 3, true, false),
ORGANISATION_ID("Organisation ID", 4, false, true),
ORGANISATION_NAME("Organisation Name", 5, true, false),
FACILITY("Facility", 6, false, true),
INSTRUMENT("Instrument", 7, false, true),
INSTRUMENT_NAME("Instrument Name", 8, true, false),
SEQUENCING_READ_TYPE("Sequencing Read Type", 9, false, true),
LIBRARY_KIT("Library Kit", 10, false, false),
FLOW_CELL("Flow Cell", 11, false, false),
SEQUENCING_RUN_PROTOCOL("Sequencing Run Protocol", 12, false, false),
INDEX_I7("Index i7", 13, false, false),
INDEX_I5("Index i5", 14, false, false),
COMMENT("Comment", 15, false, false),
;

private final String headerName;
private final int columnIndex;
private final boolean readOnly;
private final boolean mandatory;

static int maxColumnIndex() {
return Arrays.stream(values())
Expand All @@ -44,11 +45,14 @@ 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 mandatory
*/
NGSMeasurementEditColumn(String headerName, int columnIndex, boolean readOnly) {
NGSMeasurementEditColumn(String headerName, int columnIndex, boolean readOnly,
boolean mandatory) {
this.headerName = headerName;
this.columnIndex = columnIndex;
this.readOnly = readOnly;
this.mandatory = mandatory;
}

public String headerName() {
Expand All @@ -59,8 +63,12 @@ public int columnIndex() {
return columnIndex;
}

public boolean readOnly() {
public boolean isReadOnly() {
return readOnly;
}

public boolean isMandatory() {
return mandatory;
}

}
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