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Edit templates for measurement registration #832

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merged 20 commits into from
Sep 17, 2024
Merged

Edit templates for measurement registration #832

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2b9dc75
WIP
KochTobi Sep 10, 2024
7ca7d72
wip
KochTobi Sep 10, 2024
d45eb87
make it work
KochTobi Sep 13, 2024
f0e073b
Extract behaviour
KochTobi Sep 13, 2024
82f0b1d
remove unused method
KochTobi Sep 13, 2024
265accb
Adapt proteomics template
KochTobi Sep 16, 2024
f278e28
Make ngs row creation simpler
KochTobi Sep 16, 2024
9ce0bc3
remove duplicate row creation for ngs
KochTobi Sep 16, 2024
c5b7496
Rename `Instrument` to `MS Device` in template
KochTobi Sep 16, 2024
eb906f2
Fix column name
KochTobi Sep 16, 2024
ea44f52
Fix sheet locking
KochTobi Sep 16, 2024
5965ca5
replace instrument by ms device for proteomics
KochTobi Sep 16, 2024
19568fc
correct spelling
KochTobi Sep 16, 2024
df82459
fix jpa access
KochTobi Sep 16, 2024
4c5bccd
solves #747 add technical replicate
KochTobi Sep 16, 2024
aec0f86
fix constructors in tests
KochTobi Sep 16, 2024
5cdefa3
use correct methods
KochTobi Sep 17, 2024
4294945
Fix wrong imports
KochTobi Sep 17, 2024
bbdfa72
move test
KochTobi Sep 17, 2024
b81cef4
Add QBIC_SAMPLE_ID
KochTobi Sep 17, 2024
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4 changes: 2 additions & 2 deletions ...jectmanagement/infrastructure/experiment/measurement/MeasurementLookupImplementation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -252,7 +252,7 @@ public static Specification<ProteomicsMeasurement> isOrganisationLabel(String fi
public static Specification<ProteomicsMeasurement> isOntologyTermName(String filter) {
return (root, query, builder) -> {
Expression<String> function = builder.function("JSON_EXTRACT", String.class,
root.get("instrument"),
root.get("msDevice"),
builder.literal("$.name"));
return builder.like(function,
"%" + filter + "%");
Expand All @@ -263,7 +263,7 @@ public static Specification<ProteomicsMeasurement> isOntologyTermLabel(String fi
return (root, query, builder) ->
{
Expression<String> function = builder.function("JSON_EXTRACT", String.class,
root.get("instrument"), builder.literal("$.label"));
root.get("msDevice"), builder.literal("$.label"));
return builder.like(function,
"%" + filter + "%");
};
Expand Down
41 changes: 26 additions & 15 deletions ...src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java
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Expand Up @@ -389,15 +389,20 @@ private Map<ProteomicsMeasurement, Collection<SampleIdCodeEntry>> buildPxP(
throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ORGANISATION_ROR_ID);
}

var instrumentQuery = resolveOntologyCURI(firstMetadataEntry.instrumentCURI());
if (instrumentQuery.isEmpty()) {
var msDeviceQuery = resolveOntologyCURI(firstMetadataEntry.msDeviceCURIE());
if (msDeviceQuery.isEmpty()) {
throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ONTOLOGY_TERM);
}

var method = new ProteomicsMethodMetadata(instrumentQuery.get(), firstMetadataEntry.facility(),
firstMetadataEntry.digestionMethod(), firstMetadataEntry.digestionEnzyme(),
firstMetadataEntry.enrichmentMethod(), firstMetadataEntry.lcColumn(),
firstMetadataEntry.lcmsMethod(), readInjectionVolume(firstMetadataEntry.injectionVolume()),
var method = new ProteomicsMethodMetadata(msDeviceQuery.get(),
firstMetadataEntry.technicalReplicateName(),
firstMetadataEntry.facility(),
firstMetadataEntry.digestionMethod(),
firstMetadataEntry.digestionEnzyme(),
firstMetadataEntry.enrichmentMethod(),
firstMetadataEntry.lcColumn(),
firstMetadataEntry.lcmsMethod(),
readInjectionVolume(firstMetadataEntry.injectionVolume()),
firstMetadataEntry.labeling()
.labelType());

Expand Down Expand Up @@ -611,12 +616,13 @@ private List<Result<MeasurementId, ErrorCode>> updateAllPxP(
throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ORGANISATION_ROR_ID);
}

var instrumentQuery = resolveOntologyCURI(measurementMetadata.instrumentCURI());
if (instrumentQuery.isEmpty()) {
var msDeviceQuery = resolveOntologyCURI(measurementMetadata.msDeviceCURIE());
if (msDeviceQuery.isEmpty()) {
throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ONTOLOGY_TERM);
}

var method = new ProteomicsMethodMetadata(instrumentQuery.get(),
var method = new ProteomicsMethodMetadata(msDeviceQuery.get(),
measurementMetadata.technicalReplicateName(),
measurementMetadata.facility(),
measurementMetadata.digestionMethod(), measurementMetadata.digestionEnzyme(),
measurementMetadata.enrichmentMethod(), measurementMetadata.lcColumn(),
Expand All @@ -642,15 +648,20 @@ private List<Result<MeasurementId, ErrorCode>> updateAllPxP(
throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ORGANISATION_ROR_ID);
}

var instrumentQuery = resolveOntologyCURI(firstEntry.instrumentCURI());
if (instrumentQuery.isEmpty()) {
var msDeviceQuery = resolveOntologyCURI(firstEntry.msDeviceCURIE());
if (msDeviceQuery.isEmpty()) {
throw new MeasurementRegistrationException(ErrorCode.UNKNOWN_ONTOLOGY_TERM);
}

var method = new ProteomicsMethodMetadata(instrumentQuery.get(), firstEntry.facility(),
firstEntry.digestionMethod(), firstEntry.digestionEnzyme(),
firstEntry.enrichmentMethod(), firstEntry.lcColumn(),
firstEntry.lcmsMethod(), readInjectionVolume(firstEntry.injectionVolume()),
var method = new ProteomicsMethodMetadata(msDeviceQuery.get(),
firstEntry.technicalReplicateName(),
firstEntry.facility(),
firstEntry.digestionMethod(),
firstEntry.digestionEnzyme(),
firstEntry.enrichmentMethod(),
firstEntry.lcColumn(),
firstEntry.lcmsMethod(),
readInjectionVolume(firstEntry.injectionVolume()),
firstEntry.labeling()
.labelType());

Expand Down
49 changes: 19 additions & 30 deletions ...va/life/qbic/projectmanagement/application/measurement/ProteomicsMeasurementMetadata.java
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Expand Up @@ -10,38 +10,26 @@
*
* @since 1.0.0
*/
public record ProteomicsMeasurementMetadata(String measurementId,
SampleCode sampleCode,
String organisationId, String instrumentCURI,
String samplePoolGroup, String facility,
String fractionName,
String digestionEnzyme,
String digestionMethod, String enrichmentMethod,
String injectionVolume, String lcColumn,
String lcmsMethod, Labeling labeling,
String comment) implements MeasurementMetadata {
public record ProteomicsMeasurementMetadata(
String measurementId,
SampleCode sampleCode,
String technicalReplicateName,
String organisationId,
String msDeviceCURIE,
String samplePoolGroup,
String facility,
String fractionName,
String digestionEnzyme,
String digestionMethod,
String enrichmentMethod,
String injectionVolume,
String lcColumn,
String lcmsMethod,
Labeling labeling,
String comment
) implements MeasurementMetadata {


public static ProteomicsMeasurementMetadata copyWithNewProperties(SampleCode associatedSample,
Labeling labeling,
ProteomicsMeasurementMetadata metadata) {
return new ProteomicsMeasurementMetadata(metadata.measurementId(),
associatedSample,
metadata.organisationId(),
metadata.instrumentCURI(),
metadata.samplePoolGroup(),
metadata.facility(),
metadata.fractionName(),
metadata.digestionEnzyme(),
metadata.digestionMethod(),
metadata.enrichmentMethod(),
metadata.injectionVolume(),
metadata.lcColumn(),
metadata.lcmsMethod(),
labeling,
metadata.comment());
}

@Override
public Optional<String> assignedSamplePoolGroup() {
return Optional.ofNullable(samplePoolGroup.isBlank() ? null : samplePoolGroup);
Expand Down Expand Up @@ -72,4 +60,5 @@ public boolean equals(Object o) {
public int hashCode() {
return measurementId.hashCode();
}

}
27 changes: 16 additions & 11 deletions .../projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@ public ValidationResult validate(ProteomicsMeasurementMetadata measurementMetada
return validationPolicy.validateSampleId(measurementMetadata.sampleCode())
.combine(validationPolicy.validateMandatoryDataProvided(measurementMetadata))
.combine(validationPolicy.validateOrganisation(measurementMetadata.organisationId())
.combine(validationPolicy.validateInstrument(measurementMetadata.instrumentCURI())));
.combine(validationPolicy.validateMsDevice(measurementMetadata.msDeviceCURIE())));
}

/**
Expand All @@ -121,17 +121,18 @@ public ValidationResult validateUpdate(ProteomicsMeasurementMetadata metadata,
.combine(validationPolicy.validateMeasurementCode(metadata.measurementIdentifier().orElse(""))
.combine(validationPolicy.validateMandatoryDataForUpdate(metadata))
.combine(validationPolicy.validateOrganisation(metadata.organisationId())
.combine(validationPolicy.validateInstrument(metadata.instrumentCURI())
.combine(validationPolicy.validateMsDevice(metadata.msDeviceCURIE())
.combine(
validationPolicy.validateDigestionMethod(metadata.digestionMethod())))));
}

public enum PROTEOMICS_PROPERTY {
QBIC_SAMPLE_ID("qbic sample id"),
SAMPLE_LABEL("sample name"),
TECHNICAL_REPLICATE_NAME("technical replicate"),
ORGANISATION_ID("organisation id"),
FACILITY("facility"),
INSTRUMENT("instrument"),
MS_DEVICE("ms device"),
SAMPLE_POOL_GROUP("sample pool group"),
CYCLE_FRACTION_NAME("cycle/fraction name"),
DIGESTION_METHOD("digestion method"),
Expand Down Expand Up @@ -180,6 +181,10 @@ 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 All @@ -188,7 +193,7 @@ private class ValidationPolicy {

private static final String UNKNOWN_ORGANISATION_ID_MESSAGE = "The organisation ID does not seem to be a ROR ID: \"%s\"";

private static final String UNKNOWN_INSTRUMENT_ID = "Unknown instrument id: \"%s\"";
private static final String UNKNOWN_MS_DEVICE_ID = "Unknown ms device id: \"%s\"";

private static final String UNKNOWN_DIGESTION_METHOD = "Unknown digestion method: \"%s\"";

Expand Down Expand Up @@ -242,13 +247,13 @@ ValidationResult validateMeasurementCode(String measurementCode) {
List.of("Measurement Code: Unknown measurement for id '%s'".formatted(measurementCode))));
}

ValidationResult validateInstrument(String instrument) {
var result = terminologyService.findByCurie(instrument);
ValidationResult validateMsDevice(String msDevice) {
var result = terminologyService.findByCurie(msDevice);
if (result.isPresent()) {
return ValidationResult.successful(1);
}
return ValidationResult.withFailures(1,
List.of(UNKNOWN_INSTRUMENT_ID.formatted(instrument)));
List.of(UNKNOWN_MS_DEVICE_ID.formatted(msDevice)));
}

ValidationResult validateDigestionMethod(String digestionMethod) {
Expand All @@ -273,9 +278,9 @@ ValidationResult validateMandatoryDataForUpdate(ProteomicsMeasurementMetadata me
} else {
validation = validation.combine(ValidationResult.successful(1));
}
if (metadata.instrumentCURI().isBlank()) {
if (metadata.msDeviceCURIE().isBlank()) {
validation = validation.combine(
ValidationResult.withFailures(1, List.of("Instrument: missing mandatory metadata")));
ValidationResult.withFailures(1, List.of("MS Device: missing mandatory metadata")));
} else {
validation = validation.combine(ValidationResult.successful(1));
}
Expand Down Expand Up @@ -323,10 +328,10 @@ ValidationResult validateMandatoryDataProvided(
} else {
validation = validation.combine(ValidationResult.successful(1));
}
if (metadata.instrumentCURI().isBlank()) {
if (metadata.msDeviceCURIE().isBlank()) {
validation = validation.combine(
ValidationResult.withFailures(1,
List.of("Instrument: missing mandatory metadata")));
List.of("MS Device: missing mandatory metadata")));
} else {
validation = validation.combine(ValidationResult.successful(1));
}
Expand Down
6 changes: 3 additions & 3 deletions ...nt/src/main/java/life/qbic/projectmanagement/domain/model/measurement/NGSMeasurement.java
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Expand Up @@ -18,8 +18,8 @@
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import life.qbic.domain.concepts.LocalDomainEventDispatcher;
import java.util.Set;
import life.qbic.domain.concepts.LocalDomainEventDispatcher;
import life.qbic.projectmanagement.domain.Organisation;
import life.qbic.projectmanagement.domain.model.OntologyTerm;
import life.qbic.projectmanagement.domain.model.measurement.event.MeasurementCreatedEvent;
Expand Down Expand Up @@ -93,7 +93,7 @@ private NGSMeasurement(MeasurementId measurementId, ProjectId projectId,
this.measurementId = measurementId;
this.projectId = requireNonNull(projectId, "projectId must not be null");
this.organisation = requireNonNull(organisation, "organisation must not be null");
this.instrument = requireNonNull(method.instrument(), "instrument must not be null");
this.instrument = requireNonNull(method.instrument(), "msDevice must not be null");
this.measurementCode = requireNonNull(measurementCode, "measurement code must not be null");
this.facility = requireNonNull(method.facility(), "facility must not be null");
this.sequencingReadType = requireNonNull(method.sequencingReadType(),
Expand Down Expand Up @@ -136,7 +136,7 @@ public static NGSMeasurement createWithPool(ProjectId projectId, String samplePo
throws IllegalArgumentException {
requireNonNull(measurementCode, "measurement Code must not be null");
requireNonNull(method, "method must not be null");
requireNonNull(method.instrument(), "instrument must not be null");
requireNonNull(method.instrument(), "msDevice must not be null");
if (samplePool.isBlank()) {
throw new IllegalArgumentException("Sample Pool: no value provided");
}
Expand Down
22 changes: 15 additions & 7 deletions ...main/java/life/qbic/projectmanagement/domain/model/measurement/ProteomicsMeasurement.java
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Expand Up @@ -57,7 +57,10 @@ public class ProteomicsMeasurement {
private MeasurementId measurementId;

@Column(name = "instrument", columnDefinition = "longtext CHECK (json_valid(`instrument`))")
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Shouldn't this change also be reflected in the db?

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Yes but this would break all existing measurements. So not sure yet how to go about it.

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Probably best to keep as is right now.

private OntologyTerm instrument;
private OntologyTerm msDevice;

@Column(name = "technicalReplicateName")
private String technicalReplicateName;

@Column(name = "samplePool")
private String samplePool = "";
Expand Down Expand Up @@ -127,8 +130,8 @@ private static void evaluateMandatorySpecificMetadata(

private static void evaluateMandatoryMetadata(ProteomicsMethodMetadata method)
throws IllegalArgumentException {
if (method.instrument() == null) {
throw new IllegalArgumentException("Instrument: Missing metadata.");
if (method.msDevice() == null) {
throw new IllegalArgumentException("MS Device: Missing metadata.");
}
if (method.facility().isBlank()) {
throw new IllegalArgumentException("Facility: Missing metadata");
Expand Down Expand Up @@ -157,7 +160,7 @@ public static ProteomicsMeasurement create(ProjectId projectId,
MeasurementCode measurementCode, Organisation organisation, ProteomicsMethodMetadata method,
Collection<ProteomicsSpecificMeasurementMetadata> proteomicsSpecificMeasurementMetadata)
throws IllegalArgumentException {
requireNonNull(method.instrument());
requireNonNull(method.msDevice());
requireNonNull(measurementCode);
requireNonNull(proteomicsSpecificMeasurementMetadata);
if (!measurementCode.isMSDomain()) {
Expand Down Expand Up @@ -215,8 +218,8 @@ public Collection<SampleId> measuredSamples() {
.toList();
}

public OntologyTerm instrument() {
return instrument;
public OntologyTerm msDevice() {
return msDevice;
}

public Organisation organisation() {
Expand Down Expand Up @@ -257,7 +260,8 @@ public void updateMethod(ProteomicsMethodMetadata method) {
}

private void setMethodMetadata(ProteomicsMethodMetadata methodMetadata) {
this.instrument = methodMetadata.instrument();
this.msDevice = methodMetadata.msDevice();
this.technicalReplicateName = methodMetadata.technicalReplicate();
this.facility = methodMetadata.facility();
this.digestionMethod = methodMetadata.digestionMethod();
this.digestionEnzyme = methodMetadata.digestionEnzyme();
Expand Down Expand Up @@ -319,4 +323,8 @@ public int hashCode() {
public Optional<String> comment() {
return Optional.empty();
}

public Optional<String> technicalReplicateName() {
return Optional.ofNullable(technicalReplicateName);
}
}
17 changes: 12 additions & 5 deletions ...n/java/life/qbic/projectmanagement/domain/model/measurement/ProteomicsMethodMetadata.java
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Expand Up @@ -9,10 +9,17 @@
*
* @since 1.0.0
*/
public record ProteomicsMethodMetadata(OntologyTerm instrument, String facility,
String digestionMethod,
String digestionEnzyme, String enrichmentMethod,
String lcColumn, String lcmsMethod, int injectionVolume,
String labelType) {
public record ProteomicsMethodMetadata(
OntologyTerm msDevice,
String technicalReplicate,
String facility,
String digestionMethod,
String digestionEnzyme,
String enrichmentMethod,
String lcColumn,
String lcmsMethod,
int injectionVolume,
String labelType
) {

}
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