Skip to content

Commit

Permalink
Fix measurement registration (#854)
Browse files Browse the repository at this point in the history 
* Fix measurement registration

* Fix mandatory property for ngs measurements

* fix column header names

* Separate register from edit case

* Fix analysisMethod storage to use the enum name again

* fix wrong method call

Co-authored-by: steffengreiner <[email protected]>

* fix inverted boolean flag

---------

Co-authored-by: steffengreiner <[email protected]>
  • Loading branch information
@KochTobi @Steffengreiner
KochTobi and Steffengreiner authored Oct 17, 2024
1 parent f9393aa commit 4a5aabc
Show file tree
Hide file tree
Showing 14 changed files with 355 additions and 88 deletions.
4 changes: 2 additions & 2 deletions ...src/main/java/life/qbic/projectmanagement/application/sample/AnalysisMethodConverter.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,15 +12,15 @@ public String convertToDatabaseColumn(AnalysisMethod attribute) {
if (attribute == null) {
return null;
}
return attribute.abbreviation();
return attribute.name();
}

@Override
public AnalysisMethod convertToEntityAttribute(String dbData) {
if (dbData == null) {
return null;
}
return AnalysisMethod.forAbbreviation(dbData).orElse(null);
return AnalysisMethod.valueOf(dbData);
}

}
3 changes: 3 additions & 0 deletions project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/Sample.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -178,6 +178,9 @@ static class AnalysisMethodConverter implements AttributeConverter<AnalysisMetho

@Override
public String convertToDatabaseColumn(AnalysisMethod analysisMethod) {
if (analysisMethod == null) {
return null;
}
return analysisMethod.name();
}

Expand Down
7 changes: 4 additions & 3 deletions user-interface/src/main/java/life/qbic/datamanager/parser/MeasurementMetadataConverter.java
View file
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
View file
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, true)) {
return tryConversion(this::convertNewNGSMeasurement, parsingResult);
} else if (looksLikeProteomicsMeasurement(properties, true)) {
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, false)) {
return tryConversion(this::convertExistingNGSMeasurement, parsingResult);
} else if (looksLikeProteomicsMeasurement(properties, false)) {
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
View file
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;
}

}
Loading

0 comments on commit 4a5aabc

Please sign in to comment.