Centralises logic to control the String representation of properties for the parsing
+ * context.
+ *
+ * @since 1.5.0
+ */
+public class PropertyConversion {
+
+ private static final String CONDITION_VARIABLE_LEVEL_UNIT_TEMPLATE = "%s: %s %s"; // : [unit]
+
+ private static final String CONDITION_VARIABLE_LEVEL_NO_UNIT_TEMPLATE = "%s: %s"; // :
+
+ private static final String ONTOLOGY_TERM = "%s [%s]"; // [CURIE]
+
+ private static final Pattern CURIE_PATTERN = Pattern.compile("\\[.*\\]");
+
+ /**
+ * Takes a {@link Condition} and transforms it into a String representation.
+ *
+ * In its current implementation, the String representation results into a
+ * ;-separated concatenation of {@link VariableLevel}. See
+ * {@link PropertyConversion#toString(VariableLevel)} for more details.
+ *
+ * Example: a condition with the two variable levels size: 20 cm and hue:
+ * blue will result in:
+ *
+ * size: 20cm; hue: blue
+ *
+ * The generalised form is:
+ * [var name 1]: [level value 1] [unit 1];...; [var name N]: [level value N] [unit N];
+ *
+ *
+ * @param condition the condition object to transform
+ * @return the String representation
+ * @since 1.5.0
+ */
+ public static String toString(Condition condition) {
+ Objects.requireNonNull(condition);
+ List stringValues = new ArrayList<>();
+ condition.getVariableLevels()
+ .forEach(variableLevel -> stringValues.add(toString(variableLevel)));
+ return String.join("; ", stringValues);
+ }
+
+ /**
+ * Takes a {@link VariableLevel} and transforms it into a String representation.
+ *
+ * The generalised form of the output can be described with:
+ *
+ * [name]: [value] [unit]
+ *
+ * @param variableLevel the variable level to transform
+ * @return the String representation of the variable level
+ * @since 1.5.0
+ */
+ public static String toString(VariableLevel variableLevel) {
+ Objects.requireNonNull(variableLevel);
+ if (variableLevel.experimentalValue().unit().isPresent()) {
+ return CONDITION_VARIABLE_LEVEL_UNIT_TEMPLATE.formatted(variableLevel.variableName().value(),
+ variableLevel.experimentalValue().value(),
+ variableLevel.experimentalValue().unit().get());
+ } else {
+ return CONDITION_VARIABLE_LEVEL_NO_UNIT_TEMPLATE.formatted(
+ variableLevel.variableName().value(), variableLevel.experimentalValue().value());
+ }
+ }
+
+ /**
+ * Transforms an {@link OntologyTerm} to its String representation.
+ *
+ * The String representation currently contains the term label and the OBO ID.
+ *
+ * The generalised form can be described as:
+ *
+ * [label] [[obo ID]]
+ *
+ * So e.g. 'Homo sapiens [NCBITaxon:9606]'
+ *
+ * @param ontologyTerm the ontology term to transform
+ * @return the String representation of the ontology term
+ * @since 1.5.0
+ */
+ public static String toString(OntologyTerm ontologyTerm) {
+ Objects.requireNonNull(ontologyTerm);
+ return ONTOLOGY_TERM.formatted(ontologyTerm.getLabel(), ontologyTerm.getOboId());
+ }
+
+ /**
+ * Expects a String that has been created with {@link #toString(OntologyTerm)} and tries to
+ * extract the CURIE of the ontology term.
+ *
+ * The CURIE is expected to be surrounded with [...] squared brackets.
+ *
+ * @param term the term that might contain the CURIE (e.g. OBO ID)
+ * @return an Optional that contains the found CURIE, or is empty else if none was found
+ * @since 1.5.0
+ */
+ public static Optional extractCURIE(String term) {
+ return CURIE_PATTERN.matcher(term).results().map(MatchResult::group).findFirst()
+ .map(PropertyConversion::sanitizeOntologyTerm);
+ }
+
+ private static String removeBrackets(String value) {
+ return value.replace("[", "").replace("]", "");
+ }
+
+ private static String sanitizeOntologyTerm(String term) {
+ return removeBrackets(term).trim();
+ }
+
+}
diff --git a/project-management/src/main/java/life/qbic/projectmanagement/application/sample/SampleMetadata.java b/project-management/src/main/java/life/qbic/projectmanagement/application/sample/SampleMetadata.java
new file mode 100644
index 000000000..9cd1cde34
--- /dev/null
+++ b/project-management/src/main/java/life/qbic/projectmanagement/application/sample/SampleMetadata.java
@@ -0,0 +1,67 @@
+package life.qbic.projectmanagement.application.sample;
+
+import java.util.Optional;
+import life.qbic.projectmanagement.domain.model.OntologyTerm;
+import life.qbic.projectmanagement.domain.model.sample.AnalysisMethod;
+import life.qbic.projectmanagement.domain.model.sample.SampleId;
+
+/**
+ * Sample Metadata
+ *
+ *
A simple sample metadata DTO to pass them within the application
+ *
+ * @since
+ */
+@Component
+public class SampleValidation {
+
+ private final SampleInformationService sampleInformationService;
+
+ private final ExperimentInformationService experimentInformationService;
+
+ private final TerminologyService terminologyService;
+
+ private final SpeciesLookupService speciesLookupService;
+
+ @Autowired
+ public SampleValidation(SampleInformationService sampleInformationService,
+ ExperimentInformationService experimentInformationService,
+ TerminologyService terminologyService, SpeciesLookupService speciesLookupService) {
+ this.sampleInformationService = Objects.requireNonNull(sampleInformationService);
+ this.experimentInformationService = Objects.requireNonNull(experimentInformationService);
+ this.terminologyService = Objects.requireNonNull(terminologyService);
+ this.speciesLookupService = Objects.requireNonNull(speciesLookupService);
+ }
+
+ /**
+ * Creates a lookup table for conditions having their String representation as key.
+ *
+ * The String representation is done with the {@link PropertyConversion#toString(Condition)}
+ * method.
+ *
+ * @param conditions the conditions to take for the lookup table build
+ * @return the lookup table
+ * @since 1.5.0
+ */
+ private static Map conditionLookup(
+ List conditions) {
+ return conditions.stream()
+ .collect(Collectors.toMap(group -> PropertyConversion.toString(group.condition()),
+ Function.identity()));
+ }
+
+ /**
+ * Validates metadata for a not yet registered sample. The validation does not look for any sample
+ * id and no sample information lookups are done in this case.
+ *
+ * If the client wants to validate the sample id as well, please refer to
+ * {@link SampleValidation#validateExistingSample(String, String, String, String, String, String,
+ * String, String, String, String, String)}
+ *
+ * @param sampleName the name of the sample
+ * @param biologicalReplicate the biological replicate
+ * @param condition the condition the sample was collected from
+ * @param species the species the sample was taken from
+ * @param specimen the specimen of the sample
+ * @param analyte the analyte that was extracted from the specimen
+ * @param analysisMethod the method applied on the analyte
+ * @param comment the comment associated with the sample
+ * @param experimentId the experiment id of the experiment the sample belongs to
+ * @param projectId the project id of project the experiment belongs to
+ * @return the report of the validation
+ * @since 1.5.0
+ */
+ public ValidationResultWithPayload validateNewSample(String sampleName,
+ String biologicalReplicate,
+ String condition,
+ String species,
+ String specimen,
+ String analyte,
+ String analysisMethod,
+ String comment,
+ String experimentId,
+ String projectId) {
+
+ var experimentQuery = experimentInformationService.find(projectId,
+ ExperimentId.parse(experimentId));
+ if (experimentQuery.isEmpty()) {
+ return new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Unknown experiment.")), null);
+ }
+ var experiment = experimentQuery.orElseThrow();
+ var experimentalGroupLookupTable = conditionLookup(experiment.getExperimentalGroups());
+
+ return validateForNewSample(sampleName,
+ biologicalReplicate,
+ condition,
+ species,
+ specimen,
+ analyte,
+ analysisMethod,
+ comment,
+ experimentId,
+ experimentalGroupLookupTable);
+ }
+
+ private ValidationResultWithPayload validateForNewSample(
+ String sampleName,
+ String biologicalReplicate,
+ String condition,
+ String species,
+ String specimen,
+ String analyte,
+ String analysisMethod,
+ String comment,
+ String experimentId,
+ Map experimentalGroupLookupTable) {
+
+ var sampleNameValidation = validateSampleName(sampleName);
+ var experimentalGroupValidation = validateExperimentalGroupForCondition(condition,
+ experimentalGroupLookupTable);
+ var analysisMethodValidation = validateAnalysisMethod(analysisMethod);
+ var speciesValidation = validateSpecies(species);
+ var specimenValidation = validateSpecimen(specimen);
+ var analyteValidation = validateAnalyte(analyte);
+
+ ValidationResult combinedValidationResult = ValidationResult.successful()
+ .combine(sampleNameValidation.validationResult())
+ .combine(experimentalGroupValidation.validationResult())
+ .combine(analysisMethodValidation.validationResult())
+ .combine(speciesValidation.validationResult())
+ .combine(specimenValidation.validationResult())
+ .combine(analyteValidation.validationResult());
+ var metadata = combinedValidationResult.containsFailures()
+ ? null
+ : SampleMetadata.createNew(
+ sampleNameValidation.payload(),
+ analysisMethodValidation.payload(),
+ biologicalReplicate,
+ experimentalGroupValidation.payload(),
+ speciesValidation.payload(),
+ specimenValidation.payload(),
+ analyteValidation.payload(),
+ comment,
+ experimentId);
+ return new ValidationResultWithPayload<>(combinedValidationResult, metadata);
+ }
+
+ private ValidationResultWithPayload validateSampleName(String sampleName) {
+ if (isNull(sampleName) || sampleName.isBlank()) {
+ return new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Missing sample name.")), null);
+ }
+ return new ValidationResultWithPayload<>(ValidationResult.successful(), sampleName);
+ }
+
+ private ValidationResultWithPayload validateExperimentalGroupForCondition(String condition,
+ Map conditionsLookupTable) {
+ if (isNull(condition) || condition.isBlank()) {
+ return new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Missing condition")), null);
+ }
+ if (conditionsLookupTable.containsKey(condition)) {
+ return new ValidationResultWithPayload<>(ValidationResult.successful(),
+ conditionsLookupTable.get(condition).id());
+ } else {
+ return new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Unknown condition: " + condition)), null);
+ }
+ }
+
+ private ValidationResultWithPayload validateAnalysisMethod(
+ String analysisMethod) {
+ if (analysisMethod == null || analysisMethod.isBlank()) {
+ return new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("No analysis method provided.")), null);
+ }
+ return AnalysisMethod.forAbbreviation(analysisMethod)
+ .map(it -> new ValidationResultWithPayload<>(ValidationResult.successful(), it))
+ .orElse(new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Unknown analysis: " + analysisMethod)), null));
+ }
+
+ private ValidationResultWithPayload validateSpecies(String species) {
+ var extractedTerm = PropertyConversion.extractCURIE(species);
+ if (extractedTerm.isEmpty()) {
+ return new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Missing CURIE in species: " + species)), null);
+ }
+ var speciesLookup = speciesLookupService.findByCURI(extractedTerm.get());
+ return speciesLookup
+ .map(OntologyTerm::from)
+ .map(it ->
+ new ValidationResultWithPayload<>(ValidationResult.successful(), it))
+ .orElse(new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Unknown species: " + species)), null));
+ }
+
+ private ValidationResultWithPayload validateSpecimen(String specimen) {
+ var extractedTerm = PropertyConversion.extractCURIE(specimen);
+ if (extractedTerm.isEmpty()) {
+ return new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Missing CURIE in specimen: " + specimen)), null);
+ }
+ var speciesLookup = terminologyService.findByCurie(extractedTerm.get());
+ return speciesLookup
+ .map(it ->
+ new ValidationResultWithPayload<>(ValidationResult.successful(), it))
+ .orElse(new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Unknown specimen: " + specimen)), null));
+ }
+
+ private ValidationResultWithPayload validateAnalyte(String analyte) {
+ var extractedTerm = PropertyConversion.extractCURIE(analyte);
+ if (extractedTerm.isEmpty()) {
+ return new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Missing CURIE in analyte: " + analyte)), null);
+ }
+ var speciesLookup = terminologyService.findByCurie(extractedTerm.get());
+ return speciesLookup
+ .map(it ->
+ new ValidationResultWithPayload<>(ValidationResult.successful(), it))
+ .orElse(new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Unknown analyte: " + analyte)), null));
+ }
+
+ private ValidationResultWithPayload validateSampleIdForSampleCode(String sampleCode) {
+ if (sampleCode.isBlank()) {
+ return new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Missing sample id.")),
+ null
+ );
+ }
+ var sampleIdQuery = sampleInformationService.findSampleId(SampleCode.create(sampleCode));
+ if (sampleIdQuery.isEmpty()) {
+ return new ValidationResultWithPayload<>(ValidationResult.withFailures(List.of(
+ "Unknown sample id: " + sampleCode)), null);
+ }
+ var sampleId = sampleIdQuery.orElseThrow().sampleId();
+ return new ValidationResultWithPayload<>(ValidationResult.successful(), sampleId);
+ }
+
+ /**
+ * Validates the metadata for a sample that has previously been registered. A registered sample
+ * has a sample code (sample id to the user) and an internal technical sample id.
+ *
+ * The method verifies the existence of a sample with the provided sample code and resolves it to
+ * the matching internal sample id.
+ *
+ * All other validation steps are equal to a
+ * {@link SampleValidation#validateNewSample(String, String, String, String, String, String,
+ * String, String, String, String)} call.
+ *
+ * @param sampleCode the sample code of the sample, known as sample id to the user
+ * @param condition the condition the sample was collected from
+ * @param species the species the sample was taken from
+ * @param specimen the specimen of the sample
+ * @param analyte the analyte that was extracted from the specimen
+ * @param analysisMethod the method applied on the analyte
+ * @param experimentId the experiment the sample belongs to
+ * @param projectId the project the sample belongs to
+ * @return a {@link ValidationResult} with detailed information about the validation
+ * @since 1.5.0
+ */
+ public ValidationResultWithPayload validateExistingSample(String sampleCode,
+ String sampleName,
+ String biologicalReplicate,
+ String condition,
+ String species,
+ String specimen,
+ String analyte,
+ String analysisMethod,
+ String comment,
+ String experimentId,
+ String projectId) {
+
+ var experimentQuery = experimentInformationService.find(projectId,
+ ExperimentId.parse(experimentId));
+ if (experimentQuery.isEmpty()) {
+ return new ValidationResultWithPayload<>(
+ ValidationResult.withFailures(List.of("Unknown experiment.")), null);
+ }
+
+ var experiment = experimentQuery.orElseThrow();
+ var experimentalGroupLookupTable = conditionLookup(experiment.getExperimentalGroups());
+
+ var sampleIdValidation = validateSampleIdForSampleCode(sampleCode);
+ var sampleNameValidation = validateSampleName(sampleName);
+ var experimentalGroupValidation = validateExperimentalGroupForCondition(condition,
+ experimentalGroupLookupTable);
+ var analysisMethodValidation = validateAnalysisMethod(analysisMethod);
+ var speciesValidation = validateSpecies(species);
+ var specimenValidation = validateSpecimen(specimen);
+ var analyteValidation = validateAnalyte(analyte);
+
+ ValidationResult combinedValidationResult = ValidationResult.successful()
+ .combine(sampleIdValidation.validationResult())
+ .combine(sampleNameValidation.validationResult())
+ .combine(experimentalGroupValidation.validationResult())
+ .combine(analysisMethodValidation.validationResult())
+ .combine(speciesValidation.validationResult())
+ .combine(specimenValidation.validationResult())
+ .combine(analyteValidation.validationResult());
+ var metadata = combinedValidationResult.containsFailures()
+ ? null
+ : SampleMetadata.createUpdate(
+ sampleIdValidation.payload(),
+ sampleCode,
+ sampleNameValidation.payload(),
+ analysisMethodValidation.payload(),
+ biologicalReplicate,
+ experimentalGroupValidation.payload(),
+ speciesValidation.payload(),
+ specimenValidation.payload(),
+ analyteValidation.payload(),
+ comment,
+ experimentId);
+ return new ValidationResultWithPayload<>(combinedValidationResult, metadata);
+ }
+
+}
diff --git a/project-management/src/main/java/life/qbic/projectmanagement/application/sample/SampleValidationService.java b/project-management/src/main/java/life/qbic/projectmanagement/application/sample/SampleValidationService.java
new file mode 100644
index 000000000..2fc8ba172
--- /dev/null
+++ b/project-management/src/main/java/life/qbic/projectmanagement/application/sample/SampleValidationService.java
@@ -0,0 +1,132 @@
+package life.qbic.projectmanagement.application.sample;
+
+import java.util.Objects;
+import java.util.concurrent.CompletableFuture;
+import life.qbic.projectmanagement.application.ValidationResultWithPayload;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.scheduling.annotation.Async;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.stereotype.Service;
+
+/**
+ *
+ *
+ *
*
* @since 1.4.0
@@ -81,19 +83,31 @@ private static Map countHits(Collection target, Set convertRegister(ParsingResult parsingResult)
+ throws UnknownMetadataTypeException, MissingSampleIdException {
+ Objects.requireNonNull(parsingResult);
+ var properties = parsingResult.columnMap().keySet();
+ 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 convert(ParsingResult parsingResult, boolean ignoreMeasurementId)
+ public List convertEdit(ParsingResult parsingResult)
throws UnknownMetadataTypeException, MissingSampleIdException {
Objects.requireNonNull(parsingResult);
- var properties = parsingResult.keys().keySet();
- if (looksLikeNgsMeasurement(properties, ignoreMeasurementId)) {
- return tryConversion(this::convertNGSMeasurement, parsingResult);
- } else if (looksLikeProteomicsMeasurement(properties, ignoreMeasurementId)) {
- return tryConversion(this::convertProteomicsMeasurement, 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(
@@ -110,127 +124,223 @@ private List tryConversion(
}
}
- private List convertProteomicsMeasurement(ParsingResult parsingResult) {
+ private List convertNewProteomicsMeasurement(ParsingResult parsingResult) {
var result = new ArrayList();
- var keyIndices = parsingResult.keys();
- for (ParsingResult.Row row : parsingResult.rows()) {
- // we us -1 as default value if a property cannot be accessed, thus ending up in an empty String
- var pxpMetaDatum = new ProteomicsMeasurementMetadata(
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.MEASUREMENT_ID.propertyName(),
- -1),
- ""),
- SampleCode.create(
- safeListAccess(row.values(),
- keyIndices.getOrDefault(
- ProteomicsMeasurementProperty.QBIC_SAMPLE_ID.propertyName(), -1),
- "")),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(
- ProteomicsMeasurementProperty.TECHNICAL_REPLICATE_NAME.propertyName(), -1), ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.ORGANISATION_ID.propertyName(),
- -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.MS_DEVICE.propertyName(), -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(
- ProteomicsMeasurementProperty.SAMPLE_POOL_GROUP.propertyName(), -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.FACILITY.propertyName(), -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.CYCLE.propertyName(), -1), ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.DIGESTION_ENZYME.propertyName(),
- -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.DIGESTION_METHOD.propertyName(),
- -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(
- ProteomicsMeasurementProperty.ENRICHMENT_METHOD.propertyName(), -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.INJECTION_VOLUME.propertyName(),
- -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.LC_COLUMN.propertyName(), -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.LCMS_METHOD.propertyName(), -1),
- ""),
- new Labeling(
- safeListAccess(row.values(),
- keyIndices.getOrDefault(
- ProteomicsMeasurementProperty.LABELING_TYPE.propertyName(), -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.LABEL.propertyName(), -1),
- "")),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(ProteomicsMeasurementProperty.COMMENT.propertyName(), -1), "")
- );
- result.add(pxpMetaDatum);
+ 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 convertExistingProteomicsMeasurement(
+ ParsingResult parsingResult) {
+ var result = new ArrayList();
+ for (int i = 0; i < parsingResult.rows().size(); i++) {
+ var measurementId = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.MEASUREMENT_ID.headerName(), "");
+ var sampleCode = SampleCode.create(parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.SAMPLE_ID.headerName(), ""));
+ var technicalReplicateName = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.TECHNICAL_REPLICATE_NAME.headerName(), "");
+ var organisationId = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.ORGANISATION_ID.headerName(), "");
+ var msDevice = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.MS_DEVICE.headerName(), "");
+ var samplePoolGroup = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.POOL_GROUP.headerName(), "");
+ var facility = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.FACILITY.headerName(), "");
+ var fractionName = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.CYCLE_FRACTION_NAME.headerName(), "");
+ var digestionEnzyme = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.DIGESTION_ENZYME.headerName(), "");
+ var digestionMethod = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.DIGESTION_METHOD.headerName(), "");
+ var enrichmentMethod = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.ENRICHMENT_METHOD.headerName(), "");
+ var injectionVolume = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.INJECTION_VOLUME.headerName(), "");
+ var lcColumn = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.LC_COLUMN.headerName(), "");
+ var lcmsMethod = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.LCMS_METHOD.headerName(), "");
+ var labelingType = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.LABELING_TYPE.headerName(), "");
+ var label = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.LABEL.headerName(), "");
+ var comment = parsingResult.getValueOrDefault(i,
+ ProteomicsMeasurementEditColumn.COMMENT.headerName(), "");
+ var pxpMetaDaturm = new ProteomicsMeasurementMetadata(measurementId,
+ sampleCode,
+ technicalReplicateName,
+ organisationId,
+ msDevice,
+ samplePoolGroup,
+ facility,
+ fractionName,
+ digestionEnzyme,
+ digestionMethod,
+ enrichmentMethod,
+ injectionVolume,
+ lcColumn,
+ lcmsMethod,
+ new Labeling(labelingType, label),
+ comment);
+ result.add(pxpMetaDaturm);
}
return result;
}
- private String safeListAccess(List list, Integer index, String defaultValue) {
- if (index >= list.size() || index < 0) {
- return defaultValue;
+ private List convertExistingNGSMeasurement(ParsingResult parsingResult) {
+ var result = new ArrayList();
+
+ for (int i = 0; i < parsingResult.rows().size(); i++) {
+ var measurementId = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.MEASUREMENT_ID.headerName(), "");
+ var sampleCodes = List.of(
+ SampleCode.create(
+ parsingResult.getValueOrDefault(i, NGSMeasurementEditColumn.SAMPLE_ID.headerName(),
+ ""))
+ );
+ var organisationId = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.ORGANISATION_ID.headerName(), "");
+ var instrument = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.INSTRUMENT.headerName(), "");
+ var facility = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.FACILITY.headerName(), "");
+ var sequencingReadType = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.SEQUENCING_READ_TYPE.headerName(), "");
+ var libraryKit = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.LIBRARY_KIT.headerName(), "");
+ var flowCell = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.FLOW_CELL.headerName(), "");
+ var runProtocol = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.SEQUENCING_RUN_PROTOCOL.headerName(), "");
+ var poolGroup = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.POOL_GROUP.headerName(), "");
+ var indexI7 = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.INDEX_I7.headerName(), "");
+ var indexI5 = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.INDEX_I5.headerName(), "");
+ var comment = parsingResult.getValueOrDefault(i,
+ NGSMeasurementEditColumn.COMMENT.headerName(), "");
+ var metadatum = new NGSMeasurementMetadata(
+ measurementId,
+ sampleCodes,
+ organisationId,
+ instrument,
+ facility,
+ sequencingReadType,
+ libraryKit,
+ flowCell,
+ runProtocol,
+ poolGroup,
+ indexI7,
+ indexI5,
+ comment
+ );
+ result.add(metadatum);
}
- return list.get(index);
+ return result;
}
- private List convertNGSMeasurement(ParsingResult parsingResult) {
+ private List convertNewNGSMeasurement(ParsingResult parsingResult) {
var result = new ArrayList();
- var keyIndices = parsingResult.keys();
- for (Row row : parsingResult.rows()) {
- var ngsMeasurementMetadata = new NGSMeasurementMetadata(
- safeListAccess(row.values(),
- keyIndices.getOrDefault(NGSMeasurementProperty.MEASUREMENT_ID.propertyName(), -1),
- ""),
- List.of(SampleCode.create(
- safeListAccess(row.values(),
- keyIndices.getOrDefault(NGSMeasurementProperty.QBIC_SAMPLE_ID.propertyName(), -1),
- ""))),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(NGSMeasurementProperty.ORGANISATION_ID.propertyName(), -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(NGSMeasurementProperty.INSTRUMENT.propertyName(), -1), ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(NGSMeasurementProperty.FACILITY.propertyName(), -1), ""),
- safeListAccess(row.values(), keyIndices.getOrDefault(
- NGSMeasurementProperty.SEQUENCING_READ_TYPE.propertyName(), -1), ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(NGSMeasurementProperty.LIBRARY_KIT.propertyName(), -1), ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(NGSMeasurementProperty.FLOW_CELL.propertyName(), -1),
- ""),
- safeListAccess(row.values(), keyIndices.getOrDefault(
- NGSMeasurementProperty.SEQUENCING_RUN_PROTOCOL.propertyName(), -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(NGSMeasurementProperty.SAMPLE_POOL_GROUP.propertyName(), -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(NGSMeasurementProperty.INDEX_I7.propertyName(), -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(NGSMeasurementProperty.INDEX_I5.propertyName(), -1),
- ""),
- safeListAccess(row.values(),
- keyIndices.getOrDefault(NGSMeasurementProperty.COMMENT.propertyName(), -1), "")
+
+ 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(ngsMeasurementMetadata);
+ result.add(metadatum);
}
return result;
}
@@ -240,16 +350,17 @@ private boolean looksLikeNgsMeasurement(Collection properties, boolean i
.collect(Collectors.toList());
Map hitMap;
if (ignoreID) {
- formattedProperties.remove(NGSMeasurementProperty.MEASUREMENT_ID.propertyName());
hitMap = countHits(formattedProperties,
- Arrays.stream(NGSMeasurementProperty.values())
- .map(NGSMeasurementProperty::propertyName).collect(
- Collectors.toSet()), NGSMeasurementProperty.MEASUREMENT_ID.propertyName());
+ Arrays.stream(NGSMeasurementRegisterColumn.values())
+ .map(NGSMeasurementRegisterColumn::headerName)
+ .map(Sanitizer::headerEncoder)
+ .collect(Collectors.toSet()), NGSMeasurementEditColumn.MEASUREMENT_ID.headerName());
} else {
hitMap = countHits(formattedProperties,
- Arrays.stream(NGSMeasurementProperty.values())
- .map(NGSMeasurementProperty::propertyName).collect(
- Collectors.toSet()));
+ Arrays.stream(NGSMeasurementEditColumn.values())
+ .map(NGSMeasurementEditColumn::headerName)
+ .map(Sanitizer::headerEncoder)
+ .collect(Collectors.toSet()));
}
var missingProperties = new ArrayList<>();
for (Entry entry : hitMap.entrySet()) {
@@ -270,16 +381,18 @@ private boolean looksLikeProteomicsMeasurement(Collection properties, bo
.collect(Collectors.toList());
Map hitMap;
if (ignoreID) {
- formattedProperties.remove(ProteomicsMeasurementProperty.MEASUREMENT_ID.propertyName());
hitMap = countHits(formattedProperties,
- Arrays.stream(ProteomicsMeasurementProperty.values())
- .map(ProteomicsMeasurementProperty::propertyName).collect(
- Collectors.toSet()), ProteomicsMeasurementProperty.MEASUREMENT_ID.propertyName());
+ Arrays.stream(ProteomicsMeasurementRegisterColumn.values())
+ .map(ProteomicsMeasurementRegisterColumn::headerName)
+ .map(Sanitizer::headerEncoder)
+ .collect(Collectors.toSet()),
+ ProteomicsMeasurementEditColumn.MEASUREMENT_ID.headerName());
} else {
hitMap = countHits(formattedProperties,
- Arrays.stream(ProteomicsMeasurementProperty.values())
- .map(ProteomicsMeasurementProperty::propertyName).collect(
- Collectors.toSet()));
+ Arrays.stream(ProteomicsMeasurementEditColumn.values())
+ .map(ProteomicsMeasurementEditColumn::headerName)
+ .map(Sanitizer::headerEncoder)
+ .collect(Collectors.toSet()));
}
var missingProperties = new ArrayList<>();
for (Entry entry : hitMap.entrySet()) {
@@ -294,96 +407,4 @@ private boolean looksLikeProteomicsMeasurement(Collection properties, bo
}
return false;
}
-
-
- enum ProteomicsMeasurementProperty {
- MEASUREMENT_ID("measurement id"),
- TECHNICAL_REPLICATE_NAME("technical replicate"),
- QBIC_SAMPLE_ID("qbic sample id"),
- SAMPLE_POOL_GROUP("sample pool group"),
- ORGANISATION_ID("organisation id"),
- FACILITY("facility"),
- MS_DEVICE("ms device"),
- CYCLE("cycle/fraction name"),
- DIGESTION_METHOD("digestion method"),
- DIGESTION_ENZYME("digestion enzyme"),
- ENRICHMENT_METHOD("enrichment method"),
- INJECTION_VOLUME("injection volume (µl)"),
- LC_COLUMN("lc column"),
- LCMS_METHOD("lcms method"),
- LABELING_TYPE("labeling type"),
- LABEL("label"),
- COMMENT("comment");
-
- private final String name;
-
- ProteomicsMeasurementProperty(String value) {
- this.name = value;
- }
-
- static Optional fromString(String value) {
- var sanitizedValue = sanitizeValue(value);
- return Arrays.stream(ProteomicsMeasurementProperty.values())
- .filter(property -> property.propertyName().equals(sanitizedValue)).findFirst();
- }
-
- static boolean valueMatchesAnyProperty(String value) {
- var sanitizedValue = sanitizeValue(value);
- return Arrays.stream(ProteomicsMeasurementProperty.values())
- .map(ProteomicsMeasurementProperty::name)
- .anyMatch(sanitizedValue::equalsIgnoreCase);
- }
-
- public String propertyName() {
- return name;
- }
-
- }
-
- enum NGSMeasurementProperty {
- MEASUREMENT_ID("measurement id"),
- QBIC_SAMPLE_ID("qbic sample id"),
- ORGANISATION_ID("organisation id"),
- SAMPLE_POOL_GROUP("sample pool group"),
- FACILITY("facility"),
- INSTRUMENT("instrument"),
- SEQUENCING_READ_TYPE("sequencing read type"),
- LIBRARY_KIT("library kit"),
- FLOW_CELL("flow cell"),
- SEQUENCING_RUN_PROTOCOL("sequencing run protocol"),
- INDEX_I7("index i7"),
- INDEX_I5("index i5"),
- COMMENT("comment");
-
- private final String name;
-
- NGSMeasurementProperty(String value) {
- this.name = value;
- }
-
- /**
- * Tries to convert an input property value to a known {@link NGSMeasurementProperty}.
- *
- * Trailing whitespace will be ignored.
- *
- * @param value the presumed value to convert to a known {@link NGSMeasurementProperty}
- * @return the matching property, or {@link Optional#empty()}.
- * @since 1.4.0
- */
- static Optional fromStringTrimmed(String value) {
- var sanitizedValue = sanitizeValue(value);
- return Arrays.stream(NGSMeasurementProperty.values())
- .filter(property -> property.propertyName().equalsIgnoreCase(sanitizedValue)).findFirst();
- }
-
- static boolean valueMatchesAnyProperty(String value) {
- var sanitizedValue = sanitizeValue(value);
- return Arrays.stream(NGSMeasurementProperty.values()).map(NGSMeasurementProperty::name)
- .anyMatch(sanitizedValue::equalsIgnoreCase);
- }
-
- String propertyName() {
- return name;
- }
- }
}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/parser/ParsingResult.java b/user-interface/src/main/java/life/qbic/datamanager/parser/ParsingResult.java
index 95281917d..fe1e8992e 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/parser/ParsingResult.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/parser/ParsingResult.java
@@ -1,9 +1,7 @@
package life.qbic.datamanager.parser;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
-import java.util.stream.Stream;
/**
* Parsing Result
@@ -39,7 +37,7 @@
*
*
*
- * So the resulting stored positions of every key in a row can be accessed via {@link #keys()} and would look like:
+ * So the resulting stored positions of every key in a row can be accessed via {@link #columnMap()} and would look like:
*
*
*
A - 0
@@ -57,35 +55,34 @@
*
* @since 1.4.0
*/
-public record ParsingResult(Map keys, List rows) {
+public record ParsingResult(Map columnMap, List rows) {
- public ParsingResult(Map keys, List rows) {
- this.keys = Map.copyOf(keys);
+ public ParsingResult(Map columnMap, List rows) {
+ this.columnMap = Map.copyOf(columnMap);
this.rows = List.copyOf(rows);
}
- public Stream rowsStream() {
- return rows.stream();
- }
-
- public Iterator iterator() {
- return rows.iterator();
- }
-
- public List getRow(int rowIndex) {
+ public Row getRow(int rowIndex) {
if (rowIndex < 0 || rowIndex >= rows.size()) {
throw new IndexOutOfBoundsException(
"Row index out of bounds: %s but size is %s".formatted(rowIndex, rows.size()));
}
- return rows.get(rowIndex).values;
+ return rows.get(rowIndex);
}
- public record Row(List values) {
+ public String getValueOrDefault(int rowIndex, String columnHeader, String defaultValue) {
+ var key = Sanitizer.headerEncoder(columnHeader);
+ if (!columnMap().containsKey(key)) {
+ return defaultValue;
+ }
+ Row row = getRow(rowIndex);
+ return row.values().get(columnMap().get(key));
+ }
+ public record Row(List values) {
public Row(List values) {
this.values = List.copyOf(values);
}
-
}
}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/parser/measurement/NGSMeasurementEditColumn.java b/user-interface/src/main/java/life/qbic/datamanager/parser/measurement/NGSMeasurementEditColumn.java
new file mode 100644
index 000000000..5fef50044
--- /dev/null
+++ b/user-interface/src/main/java/life/qbic/datamanager/parser/measurement/NGSMeasurementEditColumn.java
@@ -0,0 +1,74 @@
+package life.qbic.datamanager.parser.measurement;
+
+import java.util.Arrays;
+
+/**
+ * NGS Measurement Columns
+ *
+ *
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
+ *
+ */
+public enum NGSMeasurementEditColumn {
+
+ 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())
+ .mapToInt(NGSMeasurementEditColumn::columnIndex)
+ .max().orElse(0);
+ }
+
+ /**
+ * @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,
+ boolean mandatory) {
+ this.headerName = headerName;
+ this.columnIndex = columnIndex;
+ this.readOnly = readOnly;
+ this.mandatory = mandatory;
+ }
+
+ public String headerName() {
+ return headerName;
+ }
+
+ public int columnIndex() {
+ return columnIndex;
+ }
+
+ public boolean isReadOnly() {
+ return readOnly;
+ }
+
+ public boolean isMandatory() {
+ return mandatory;
+ }
+
+}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/parser/measurement/NGSMeasurementRegisterColumn.java b/user-interface/src/main/java/life/qbic/datamanager/parser/measurement/NGSMeasurementRegisterColumn.java
new file mode 100644
index 000000000..283e91f3a
--- /dev/null
+++ b/user-interface/src/main/java/life/qbic/datamanager/parser/measurement/NGSMeasurementRegisterColumn.java
@@ -0,0 +1,70 @@
+package life.qbic.datamanager.parser.measurement;
+
+import java.util.Arrays;
+
+/**
+ * NGS Measurement Columns
+ *
+ *
Enumeration of the columns shown in the file used for NGS measurement registration
+ * 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
+ *
+ */
+public enum NGSMeasurementRegisterColumn {
+
+ SAMPLE_ID("QBiC Sample Id", 0, false, true),
+ SAMPLE_NAME("Sample Name", 1, false, false),
+ POOL_GROUP("Sample Pool Group", 2, false, false),
+ ORGANISATION_ID("Organisation ID", 3, false, true),
+ FACILITY("Facility", 4, false, true),
+ INSTRUMENT("Instrument", 5, false, true),
+ SEQUENCING_READ_TYPE("Sequencing Read Type", 6, false, true),
+ LIBRARY_KIT("Library Kit", 7, false, false),
+ FLOW_CELL("Flow Cell", 8, false, false),
+ SEQUENCING_RUN_PROTOCOL("Sequencing Run Protocol", 11, false, false),
+ INDEX_I7("Index i7", 9, false, false),
+ INDEX_I5("Index i5", 10, false, false),
+ COMMENT("Comment", 11, 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())
+ .mapToInt(NGSMeasurementRegisterColumn::columnIndex)
+ .max().orElse(0);
+ }
+
+ /**
+ * @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
+ */
+ NGSMeasurementRegisterColumn(String headerName, int columnIndex, boolean readOnly,
+ boolean mandatory) {
+ this.headerName = headerName;
+ this.columnIndex = columnIndex;
+ this.readOnly = readOnly;
+ this.mandatory = mandatory;
+ }
+
+ public String headerName() {
+ return headerName;
+ }
+
+ public int columnIndex() {
+ return columnIndex;
+ }
+
+ public boolean readOnly() {
+ return readOnly;
+ }
+
+ public boolean isMandatory() {
+ return mandatory;
+ }
+}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/parser/measurement/ProteomicsMeasurementEditColumn.java b/user-interface/src/main/java/life/qbic/datamanager/parser/measurement/ProteomicsMeasurementEditColumn.java
new file mode 100644
index 000000000..db45d76b8
--- /dev/null
+++ b/user-interface/src/main/java/life/qbic/datamanager/parser/measurement/ProteomicsMeasurementEditColumn.java
@@ -0,0 +1,63 @@
+package life.qbic.datamanager.parser.measurement;
+
+/**
+ * NGS Measurement Columns
+ *
+ *
Enumeration of the columns shown in the file used for NGS measurement registration and 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
+ *
Enumeration of the columns shown in the file used for sample edit
+ * in the context of sample batch 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
+ *
+ */
+public enum EditColumn {
+ SAMPLE_ID("QBiC Sample Id", 0, true, true),
+ SAMPLE_NAME("Sample Name", 1, false, true),
+ ANALYSIS("Analysis to be performed", 2, false, true),
+ BIOLOGICAL_REPLICATE("Biological Replicate", 3, false, false),
+ CONDITION("Condition", 4, false, true),
+ SPECIES("Species", 5, false, true),
+ ANALYTE("Analyte", 6, false, true),
+ SPECIMEN("Specimen", 7, false, true),
+ COMMENT("Comment", 8, false, false);
+
+ private final String headerName;
+ private final int columnIndex;
+ private final boolean readOnly;
+ private final boolean mandatory;
+
+ public static int maxColumnIndex() {
+ return Arrays.stream(values())
+ .mapToInt(EditColumn::columnIndex)
+ .max().orElse(0);
+ }
+
+ /**
+ * @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
+ */
+ EditColumn(String headerName, int columnIndex, boolean readOnly, boolean mandatory) {
+ this.headerName = headerName;
+ this.columnIndex = columnIndex;
+ this.readOnly = readOnly;
+ this.mandatory = mandatory;
+ }
+
+ public String headerName() {
+ return headerName;
+ }
+
+ public int columnIndex() {
+ return columnIndex;
+ }
+
+ public boolean isReadOnly() {
+ return readOnly;
+ }
+
+ public boolean isMandatory() {
+ return mandatory;
+ }
+
+}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/parser/sample/RegisterColumn.java b/user-interface/src/main/java/life/qbic/datamanager/parser/sample/RegisterColumn.java
new file mode 100644
index 000000000..ec7c400d2
--- /dev/null
+++ b/user-interface/src/main/java/life/qbic/datamanager/parser/sample/RegisterColumn.java
@@ -0,0 +1,63 @@
+package life.qbic.datamanager.parser.sample;
+
+import java.util.Arrays;
+
+/**
+ * Sample Register Columns
+ *
+ *
Enumeration of the columns shown in the file used for sample registration
+ * in the context of sample batch 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
+ *
+ */
+public enum RegisterColumn {
+
+ SAMPLE_NAME("Sample Name", 0, false, true),
+ ANALYSIS("Analysis to be performed", 1, false, true),
+ BIOLOGICAL_REPLICATE("Biological Replicate", 2, false, false),
+ CONDITION("Condition", 3, false, true),
+ SPECIES("Species", 4, false, true),
+ ANALYTE("Analyte", 5, false, true),
+ SPECIMEN("Specimen", 6, false, true),
+ COMMENT("Comment", 7, false, false);
+
+ private final String headerName;
+ private final int columnIndex;
+ private final boolean readOnly;
+ private final boolean mandatory;
+
+ public static int maxColumnIndex() {
+ return Arrays.stream(values())
+ .mapToInt(RegisterColumn::columnIndex)
+ .max().orElse(0);
+ }
+
+ /**
+ * @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
+ */
+ RegisterColumn(String headerName, int columnIndex, boolean readOnly, boolean mandatory) {
+ this.headerName = headerName;
+ this.columnIndex = columnIndex;
+ this.readOnly = readOnly;
+ this.mandatory = mandatory;
+ }
+
+ public String headerName() {
+ return headerName;
+ }
+
+ public int columnIndex() {
+ return columnIndex;
+ }
+
+ public boolean isReadOnly() {
+ return readOnly;
+ }
+
+ public boolean isMandatory() {
+ return mandatory;
+ }
+}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/parser/sample/SampleInformationExtractor.java b/user-interface/src/main/java/life/qbic/datamanager/parser/sample/SampleInformationExtractor.java
new file mode 100644
index 000000000..104230d7c
--- /dev/null
+++ b/user-interface/src/main/java/life/qbic/datamanager/parser/sample/SampleInformationExtractor.java
@@ -0,0 +1,132 @@
+package life.qbic.datamanager.parser.sample;
+
+import java.util.ArrayList;
+import java.util.List;
+import life.qbic.datamanager.parser.ParsingResult;
+
+/**
+ * Extracts sample information from a parsing result.
+ *
+ * This class does not perform any validation and missing entries will be provided with empty
+ * strings.
+ *
+ * @since 1.5.0
+ */
+public class SampleInformationExtractor {
+
+ /**
+ * Extract information for new samples from a parsing result.
+ *
+ * @param parsingResult the result of parsing user provided information.
+ * @return a record of extracted sample information. Missing entries are provided as empty
+ * strings.
+ */
+ public List extractInformationForNewSamples(
+ ParsingResult parsingResult) {
+ var result = new ArrayList();
+ for (int i = 0; i < parsingResult.rows().size(); i++) {
+ var sampleName = parsingResult.getValueOrDefault(i, RegisterColumn.SAMPLE_NAME.headerName(),
+ "");
+ var analysisMethod = parsingResult.getValueOrDefault(i, RegisterColumn.ANALYSIS.headerName(),
+ "");
+ var biologicalReplicate = parsingResult.getValueOrDefault(i,
+ RegisterColumn.BIOLOGICAL_REPLICATE.headerName(), "");
+ var condition = parsingResult.getValueOrDefault(i, RegisterColumn.CONDITION.headerName(), "");
+ var species = parsingResult.getValueOrDefault(i, RegisterColumn.SPECIES.headerName(), "");
+ var analyte = parsingResult.getValueOrDefault(i, RegisterColumn.ANALYTE.headerName(), "");
+ var specimen = parsingResult.getValueOrDefault(i, RegisterColumn.SPECIMEN.headerName(), "");
+ var comment = parsingResult.getValueOrDefault(i, RegisterColumn.COMMENT.headerName(), "");
+ result.add(new SampleInformationForNewSample(
+ sampleName,
+ analysisMethod,
+ biologicalReplicate,
+ condition,
+ species,
+ analyte,
+ specimen,
+ comment));
+ }
+ return result;
+ }
+
+ /**
+ * Extract information for existing samples from a parsing result.
+ *
+ * @param parsingResult the result of parsing user provided information.
+ * @return a record of extracted sample information. Missing entries are provided as empty
+ * strings.
+ */
+ public List extractInformationForExistingSamples(
+ ParsingResult parsingResult) {
+ var result = new ArrayList();
+ for (int i = 0; i < parsingResult.rows().size(); i++) {
+ var sampleCode = parsingResult.getValueOrDefault(i, EditColumn.SAMPLE_ID.headerName(), "");
+ var sampleName = parsingResult.getValueOrDefault(i, EditColumn.SAMPLE_NAME.headerName(), "");
+ var analysisMethod = parsingResult.getValueOrDefault(i, EditColumn.ANALYSIS.headerName(),
+ "");
+ var biologicalReplicate = parsingResult.getValueOrDefault(i,
+ RegisterColumn.BIOLOGICAL_REPLICATE.headerName(), "");
+ var condition = parsingResult.getValueOrDefault(i, EditColumn.CONDITION.headerName(), "");
+ var species = parsingResult.getValueOrDefault(i, EditColumn.SPECIES.headerName(), "");
+ var analyte = parsingResult.getValueOrDefault(i, EditColumn.ANALYTE.headerName(), "");
+ var specimen = parsingResult.getValueOrDefault(i, EditColumn.SPECIMEN.headerName(), "");
+ var comment = parsingResult.getValueOrDefault(i, EditColumn.COMMENT.headerName(), "");
+ result.add(new SampleInformationForExistingSample(sampleCode,
+ sampleName,
+ analysisMethod,
+ biologicalReplicate,
+ condition,
+ species,
+ specimen,
+ analyte,
+ comment
+ ));
+ }
+ return result;
+ }
+
+ /**
+ * Information expected for registering new samples
+ *
+ * @param condition
+ * @param species
+ * @param specimen
+ * @param analyte
+ * @param analysisMethod
+ */
+ public record SampleInformationForNewSample(
+ String sampleName,
+ String analysisMethod,
+ String biologicalReplicate,
+ String condition,
+ String species,
+ String analyte,
+ String specimen,
+ String comment
+ ) {
+
+ }
+
+ /**
+ * Information expected for editing existing samples
+ *
+ * @param sampleCode
+ * @param condition
+ * @param species
+ * @param specimen
+ * @param analyte
+ * @param analysisMethod
+ */
+ public record SampleInformationForExistingSample(
+ String sampleCode,
+ String sampleName,
+ String analysisMethod,
+ String biologicalReplicate,
+ String condition,
+ String species,
+ String specimen,
+ String analyte,
+ String comment) {
+
+ }
+}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/parser/tsv/TSVParser.java b/user-interface/src/main/java/life/qbic/datamanager/parser/tsv/TSVParser.java
index 43e818e6a..8c60d27bd 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/parser/tsv/TSVParser.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/parser/tsv/TSVParser.java
@@ -24,7 +24,7 @@
* Support for UTF-16 encoding available.
*
* This implementation always considers the first line as the header, and will use its information
- * to create the {@link ParsingResult#keys()} in the returned {@link ParsingResult} object
+ * to create the {@link ParsingResult#columnMap()} in the returned {@link ParsingResult} object
* instance.
*
* @since 1.4.0
diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/Template.java b/user-interface/src/main/java/life/qbic/datamanager/templates/Template.java
index fffbd4d1f..972bc918b 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/templates/Template.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/templates/Template.java
@@ -1,6 +1,6 @@
package life.qbic.datamanager.templates;
-import life.qbic.datamanager.views.general.download.DownloadContentProvider;
+import life.qbic.datamanager.download.DownloadContentProvider;
/**
*
diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/TemplateDownloadFactory.java b/user-interface/src/main/java/life/qbic/datamanager/templates/TemplateDownloadFactory.java
index 859f6fd54..84491cdf6 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/templates/TemplateDownloadFactory.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/templates/TemplateDownloadFactory.java
@@ -1,6 +1,8 @@
package life.qbic.datamanager.templates;
-import life.qbic.datamanager.views.general.download.DownloadContentProvider;
+import life.qbic.datamanager.download.DownloadContentProvider;
+import life.qbic.datamanager.templates.measurement.NGSMeasurementTemplate;
+import life.qbic.datamanager.templates.measurement.ProteomicsMeasurementTemplate;
/**
* Template Download Factory
@@ -15,7 +17,7 @@ public class TemplateDownloadFactory {
public static Template provider(TemplateType templateType) {
return
switch (templateType) {
- case MS_MEASUREMENT -> new MSMeasurementTemplate();
+ case MS_MEASUREMENT -> new ProteomicsMeasurementTemplate();
case NGS_MEASUREMENT -> new NGSMeasurementTemplate();
};
}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/TemplateService.java b/user-interface/src/main/java/life/qbic/datamanager/templates/TemplateService.java
new file mode 100644
index 000000000..2b3f5ac7d
--- /dev/null
+++ b/user-interface/src/main/java/life/qbic/datamanager/templates/TemplateService.java
@@ -0,0 +1,138 @@
+package life.qbic.datamanager.templates;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+import life.qbic.datamanager.templates.sample.SampleBatchRegistrationTemplate;
+import life.qbic.datamanager.templates.sample.SampleBatchUpdateTemplate;
+import life.qbic.projectmanagement.application.experiment.ExperimentInformationService;
+import life.qbic.projectmanagement.application.sample.PropertyConversion;
+import life.qbic.projectmanagement.application.sample.SampleInformationService;
+import life.qbic.projectmanagement.domain.model.batch.BatchId;
+import life.qbic.projectmanagement.domain.model.experiment.Experiment;
+import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
+import life.qbic.projectmanagement.domain.model.experiment.ExperimentalGroup;
+import life.qbic.projectmanagement.domain.model.sample.AnalysisMethod;
+import life.qbic.projectmanagement.domain.model.sample.Sample;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.stereotype.Service;
+
+/**
+ * Template Service
+ *
+ * Service that enables access to various template generation methods to support tasks such as
+ * sample batch registration and sample batch update.
+ *
+ * @since 1.5.0
+ */
+@Service
+public class TemplateService {
+
+ private final ExperimentInformationService experimentInfoService;
+
+ private final SampleInformationService sampleInformationService;
+
+ @Autowired
+ public TemplateService(ExperimentInformationService experimentInfoService,
+ SampleInformationService sampleInformationService) {
+ this.experimentInfoService = Objects.requireNonNull(experimentInfoService);
+ this.sampleInformationService = Objects.requireNonNull(sampleInformationService);
+ }
+
+ /**
+ * Creates a {@link XSSFWorkbook} that contains a template
+ * {@link org.apache.poi.xssf.usermodel.XSSFSheet} that can be used to register one or more sample
+ * batches for an experiment.
+ *
+ * The workbook contains two sheets. The first one is for the user input and contains cell with
+ * data-validation, e.g. a list of available conditions in the experiment.
+ *
+ * In total, the template provides data validation for the properties:
+ *
+ *
+ *
Species
+ *
Specimen
+ *
Analyte
+ *
Condition
+ *
Analysis to perform
+ *
+ *
+ * @param projectId the project id of the project that contains the experiment for which the
+ * template shall be generated
+ * @param experimentId the experiment id of the experiment to create the template for
+ * @return a pre-configured template workbook
+ * @throws NoSuchExperimentException if no experiment with the provided id can be found.
+ * @since 1.5.0
+ */
+ @PreAuthorize(
+ "hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'READ') ")
+ public XSSFWorkbook sampleBatchRegistrationXLSXTemplate(String projectId, String experimentId)
+ throws NoSuchExperimentException {
+ var experiment = experimentInfoService.find(projectId, ExperimentId.parse(experimentId))
+ .orElseThrow(
+ NoSuchExperimentException::new);
+ return createWorkbookFromExperiment(experiment);
+ }
+
+ @PreAuthorize(
+ "hasPermission(#projectId, 'life.qbic.projectmanagement.domain.model.project.Project', 'READ') ")
+ public XSSFWorkbook sampleBatchUpdateXLSXTemplate(BatchId batchId, String projectId,
+ String experimentId)
+ throws NoSuchExperimentException, SampleSearchException {
+ var experiment = experimentInfoService.find(projectId, ExperimentId.parse(experimentId))
+ .orElseThrow(
+ NoSuchExperimentException::new);
+ var samples = sampleInformationService.retrieveSamplesForExperiment(
+ ExperimentId.parse(experimentId));
+ samples.onError(responseCode -> {
+ throw new SampleSearchException();
+ });
+ var samplesInBatch = samples.getValue().stream()
+ .filter(sample -> sample.assignedBatch().equals(batchId))
+ .toList();
+ return createPrefilledWorkbookFromExperiment(experiment, samplesInBatch);
+ }
+
+ private XSSFWorkbook createPrefilledWorkbookFromExperiment(Experiment experiment,
+ List samples) {
+ var conditions = experiment.getExperimentalGroups().stream().map(ExperimentalGroup::condition)
+ .map(
+ PropertyConversion::toString).toList();
+ var experimentalGroups = experiment.getExperimentalGroups();
+ var species = experiment.getSpecies().stream().map(PropertyConversion::toString).toList();
+ var specimen = experiment.getSpecimens().stream().map(PropertyConversion::toString).toList();
+ var analytes = experiment.getAnalytes().stream().map(PropertyConversion::toString).toList();
+ var analysisMethods = Arrays.stream(AnalysisMethod.values()).map(AnalysisMethod::abbreviation)
+ .toList();
+ return SampleBatchUpdateTemplate.createUpdateTemplate(samples,
+ conditions, species,
+ specimen, analytes,
+ analysisMethods, experimentalGroups);
+ }
+
+ private XSSFWorkbook createWorkbookFromExperiment(Experiment experiment) {
+ var conditions = experiment.getExperimentalGroups().stream().map(ExperimentalGroup::condition)
+ .map(
+ PropertyConversion::toString).toList();
+ var species = experiment.getSpecies().stream().map(PropertyConversion::toString).toList();
+ var specimen = experiment.getSpecimens().stream().map(PropertyConversion::toString).toList();
+ var analytes = experiment.getAnalytes().stream().map(PropertyConversion::toString).toList();
+ var analysisMethods = Arrays.stream(AnalysisMethod.values()).map(AnalysisMethod::abbreviation)
+ .toList();
+ return SampleBatchRegistrationTemplate.createRegistrationTemplate(
+ conditions, species,
+ specimen, analytes,
+ analysisMethods);
+ }
+
+ public static class NoSuchExperimentException extends RuntimeException {
+
+ }
+
+ public static class SampleSearchException extends RuntimeException {
+
+ }
+
+}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/spreadsheet/XLSXTemplateHelper.java b/user-interface/src/main/java/life/qbic/datamanager/templates/XLSXTemplateHelper.java
similarity index 63%
rename from user-interface/src/main/java/life/qbic/datamanager/spreadsheet/XLSXTemplateHelper.java
rename to user-interface/src/main/java/life/qbic/datamanager/templates/XLSXTemplateHelper.java
index 1ddec66fe..b57e1eee2 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/spreadsheet/XLSXTemplateHelper.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/templates/XLSXTemplateHelper.java
@@ -1,16 +1,21 @@
-package life.qbic.datamanager.spreadsheet;
+package life.qbic.datamanager.templates;
import static java.util.Objects.isNull;
import static java.util.Objects.nonNull;
import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
import java.util.Random;
import java.util.function.Predicate;
import java.util.stream.Collectors;
import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.CellStyle;
import org.apache.poi.ss.usermodel.DataValidation;
import org.apache.poi.ss.usermodel.DataValidationConstraint;
import org.apache.poi.ss.usermodel.DataValidationHelper;
+import org.apache.poi.ss.usermodel.FillPatternType;
+import org.apache.poi.ss.usermodel.Font;
import org.apache.poi.ss.usermodel.Name;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
@@ -18,6 +23,9 @@
import org.apache.poi.ss.usermodel.Workbook;
import org.apache.poi.ss.util.CellRangeAddressList;
import org.apache.poi.ss.util.CellReference;
+import org.apache.poi.xssf.usermodel.DefaultIndexedColorMap;
+import org.apache.poi.xssf.usermodel.XSSFColor;
+import org.apache.poi.xssf.usermodel.XSSFFont;
/**
* Helps to create excel template sheets.
@@ -30,6 +38,9 @@
public class XLSXTemplateHelper {
private static final Random RANDOM = new Random();
+ private static final byte[] DARK_GREY = {(byte) 119, (byte) 119, (byte) 119};
+ private static final byte[] LIGHT_GREY = {(byte) 220, (byte) 220, (byte) 220};
+ private static final int COLUMN_MAX_WIDTH = 255;
protected XLSXTemplateHelper() {
//hide constructor as static methods only are used
@@ -89,6 +100,90 @@ public static String getCellValueAsString(Cell cell) {
};
}
+ static Optional findBoldCellStyle(Sheet sheet) {
+ for (int i = 0; i < sheet.getWorkbook().getNumCellStyles(); i++) {
+ CellStyle cellStyleAt = sheet.getWorkbook().getCellStyleAt(i);
+ int fontIndex = cellStyleAt.getFontIndex();
+ Font fontAt = sheet.getWorkbook().getFontAt(fontIndex);
+ if (fontAt.getBold()) {
+ return Optional.of(cellStyleAt);
+ }
+ }
+ return Optional.empty();
+ }
+
+ /**
+ * Sets a range of columns via {@link Sheet#autoSizeColumn(int)} to set the width automatically to
+ * the maximum cell value length observed in a column.
+ *
+ * @param sheet the sheet for which the columns shall be adjusted
+ * @param columnIndexStart the first column index to start the formatting
+ * @param columnIndexEnd the last column (inclusive) to have to formatting included
+ * @since 1.5.0
+ */
+ public static void setColumnAutoWidth(Sheet sheet, int columnIndexStart,
+ int columnIndexEnd) {
+ for (int currentColumn = columnIndexStart; currentColumn <= columnIndexEnd;
+ currentColumn++) {
+ sheet.autoSizeColumn(currentColumn);
+ }
+ }
+
+ /**
+ * Sets the width of a column explicitly. The width is expected to be the number in characters to
+ * show.
+ *
+ * Disclaimer: The current maximal value for the width is 255, since we inherit this restraint
+ * from the underlying framework. See {@link Sheet#setColumnWidth(int, int)} for more.
+ *
+ * @param sheet the sheet for which the column shall be adjusted
+ * @param columnIndex the index of the column to adjust
+ * @param widthInCharacters the designated width of the column in number of characters
+ * @throws IllegalArgumentException if the number of characters > 255
+ * @since 1.5.0
+ */
+ public static void setColumnWidth(Sheet sheet, int columnIndex, int widthInCharacters)
+ throws IllegalArgumentException {
+ Objects.requireNonNull(sheet);
+ if (widthInCharacters > COLUMN_MAX_WIDTH) {
+ throw new IllegalArgumentException(
+ "Column width must be less than %s characters. Provided: %s".formatted(COLUMN_MAX_WIDTH, widthInCharacters));
+ }
+ sheet.setColumnWidth(columnIndex, widthInCharacters * 256);
+ }
+
+
+ public static CellStyle createBoldCellStyle(Workbook workbook) {
+ CellStyle boldStyle = workbook.createCellStyle();
+ Font fontBold = workbook.createFont();
+ fontBold.setBold(true);
+ boldStyle.setFont(fontBold);
+
+ return boldStyle;
+ }
+
+ public static CellStyle createReadOnlyCellStyle(Workbook workbook) {
+ CellStyle readOnlyStyle = workbook.createCellStyle();
+ readOnlyStyle.setFillForegroundColor(new XSSFColor(LIGHT_GREY, new DefaultIndexedColorMap()));
+ readOnlyStyle.setFillPattern(FillPatternType.SOLID_FOREGROUND);
+ XSSFFont font = (XSSFFont) workbook.createFont();
+ font.setColor(new XSSFColor(DARK_GREY, new DefaultIndexedColorMap()));
+ readOnlyStyle.setFont(font);
+ return readOnlyStyle;
+ }
+
+ public static CellStyle createReadOnlyHeaderCellStyle(Workbook workbook) {
+ CellStyle readOnlyHeaderStyle = workbook.createCellStyle();
+ readOnlyHeaderStyle.setFillForegroundColor(
+ new XSSFColor(LIGHT_GREY, new DefaultIndexedColorMap()));
+ readOnlyHeaderStyle.setFillPattern(FillPatternType.SOLID_FOREGROUND);
+ XSSFFont fontHeader = (XSSFFont) workbook.createFont();
+ fontHeader.setBold(true);
+ fontHeader.setColor(new XSSFColor(DARK_GREY, new DefaultIndexedColorMap()));
+ readOnlyHeaderStyle.setFont(fontHeader);
+ return readOnlyHeaderStyle;
+ }
+
/**
* Adds values to the sheet and returns the named area where they were added.
*
@@ -103,13 +198,16 @@ public static Name createOptionArea(Sheet sheet, String propertyName,
List options) {
Row headerRow = getOrCreateRow(sheet, 0);
var columnNumber = Math.max(1,
- headerRow.getLastCellNum()); // we want to obtain 1 for the first to come if there are none and not -1 -.-
+ headerRow.getLastCellNum() + 1); // the column to use for the property. Starts with 1
var columnIndex = columnNumber - 1;
// create header cell
Cell headerRowCell = headerRow.createCell(columnIndex);
headerRowCell.setCellValue(propertyName);
+ //if a bold cell style exists, use it
+ findBoldCellStyle(sheet).ifPresent(headerRowCell::setCellStyle);
+
var startIndex = 1; // ignore the header at 0
var rowIndex = startIndex;
for (String option : options) {
diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementEditTemplate.java b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementEditTemplate.java
new file mode 100644
index 000000000..b75de213e
--- /dev/null
+++ b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementEditTemplate.java
@@ -0,0 +1,179 @@
+package life.qbic.datamanager.templates.measurement;
+
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.createBoldCellStyle;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.createOptionArea;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.createReadOnlyCellStyle;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.createReadOnlyHeaderCellStyle;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.getOrCreateCell;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.getOrCreateRow;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.hideSheet;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.lockSheet;
+import static life.qbic.logging.service.LoggerFactory.logger;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+import life.qbic.application.commons.ApplicationException;
+import life.qbic.application.commons.ApplicationException.ErrorCode;
+import life.qbic.datamanager.download.DownloadContentProvider;
+import life.qbic.datamanager.parser.measurement.NGSMeasurementEditColumn;
+import life.qbic.datamanager.templates.XLSXTemplateHelper;
+import life.qbic.datamanager.views.projects.project.measurements.NGSMeasurementEntry;
+import life.qbic.logging.api.Logger;
+import life.qbic.projectmanagement.application.measurement.NGSMeasurementMetadata;
+import life.qbic.projectmanagement.domain.model.measurement.NGSMeasurement;
+import org.apache.poi.ss.usermodel.CellStyle;
+import org.apache.poi.ss.usermodel.Name;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.ss.usermodel.Workbook;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+
+/**
+ * NGS Measurement Content Provider
+ *
+ * Implementation of the {@link DownloadContentProvider} providing the content and file name for any
+ * files created from {@link NGSMeasurement} and {@link NGSMeasurementMetadata}
+ *
+ */
+public class NGSMeasurementEditTemplate implements DownloadContentProvider {
+
+ private static final String FILE_NAME_SUFFIX = "ngs_measurements.xlsx";
+ private static final Logger log = logger(NGSMeasurementEditTemplate.class);
+ private final List measurements = new LinkedList<>();
+ private static final String DEFAULT_FILE_NAME_PREFIX = "QBiC";
+ private String fileNamePrefix = DEFAULT_FILE_NAME_PREFIX;
+ private static final int DEFAULT_GENERATED_ROW_COUNT = 200;
+
+ private enum SequencingReadType {
+ SINGLE_END("single-end"),
+ PAIRED_END("paired-end");
+ private final String presentationString;
+
+ SequencingReadType(String presentationString) {
+ this.presentationString = presentationString;
+ }
+
+ static List getOptions() {
+ return Arrays.stream(values()).map(it -> it.presentationString).toList();
+ }
+ }
+
+ private static void setAutoWidth(Sheet sheet) {
+ for (int col = 0; col <= NGSMeasurementEditColumn.values().length; col++) {
+ sheet.autoSizeColumn(col);
+ }
+ }
+
+ private static void writeMeasurementIntoRow(NGSMeasurementEntry ngsMeasurementEntry,
+ Row entryRow, CellStyle readOnlyCellStyle) {
+
+ for (NGSMeasurementEditColumn measurementColumn : NGSMeasurementEditColumn.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.isReadOnly()) {
+ cell.setCellStyle(readOnlyCellStyle);
+ }
+ }
+
+
+ }
+
+ public void setMeasurements(List measurements, String fileNamePrefix) {
+ this.measurements.clear();
+ this.measurements.addAll(measurements);
+ this.fileNamePrefix = fileNamePrefix.trim();
+ }
+
+
+ @Override
+ public byte[] getContent() {
+ if (measurements.isEmpty()) {
+ return new byte[0];
+ }
+
+ try (Workbook workbook = new XSSFWorkbook();
+ ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream()) {
+ CellStyle readOnlyCellStyle = createReadOnlyCellStyle(workbook);
+ CellStyle readOnlyHeaderStyle = createReadOnlyHeaderCellStyle(workbook);
+ CellStyle boldStyle = createBoldCellStyle(workbook);
+
+ Sheet sheet = workbook.createSheet("NGS Measurement Metadata");
+
+ Row header = getOrCreateRow(sheet, 0);
+ for (NGSMeasurementEditColumn value : NGSMeasurementEditColumn.values()) {
+ var cell = getOrCreateCell(header, value.columnIndex());
+ if (value.isMandatory()) {
+ cell.setCellValue(value.headerName() + "*");
+ } else {
+ cell.setCellValue(value.headerName());
+ }
+ cell.setCellStyle(boldStyle);
+ if (value.isReadOnly()) {
+ cell.setCellStyle(readOnlyHeaderStyle);
+ }
+ }
+
+ var startIndex = 1; // start in row number 2 with index 1 as the header row has number 1 index 0
+ int rowIndex = startIndex;
+ for (NGSMeasurementEntry measurement : measurements) {
+ Row row = getOrCreateRow(sheet, rowIndex);
+ writeMeasurementIntoRow(measurement, row, readOnlyCellStyle);
+ rowIndex++;
+ }
+
+ var generatedRowCount = rowIndex - startIndex;
+ assert generatedRowCount == measurements.size() : "all measurements have a corresponding row";
+
+ // make sure to create the visible sheet first
+ Sheet hiddenSheet = workbook.createSheet("hidden");
+ Name sequencingReadTypeArea = createOptionArea(hiddenSheet,
+ "Sequencing read type", SequencingReadType.getOptions());
+
+ XLSXTemplateHelper.addDataValidation(sheet,
+ NGSMeasurementEditColumn.SEQUENCING_READ_TYPE.columnIndex(),
+ startIndex,
+ NGSMeasurementEditColumn.SEQUENCING_READ_TYPE.columnIndex(),
+ DEFAULT_GENERATED_ROW_COUNT - 1,
+ sequencingReadTypeArea);
+
+ setAutoWidth(sheet);
+ workbook.setActiveSheet(0);
+
+ lockSheet(hiddenSheet);
+ hideSheet(workbook, hiddenSheet);
+
+ workbook.write(byteArrayOutputStream);
+ return byteArrayOutputStream.toByteArray();
+ } catch (IOException e) {
+ log.error(e.getMessage(), e);
+ throw new ApplicationException(ErrorCode.GENERAL, null);
+ }
+ }
+
+ @Override
+ public String getFileName() {
+ return String.join("_", fileNamePrefix, FILE_NAME_SUFFIX);
+ }
+
+}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/NGSMeasurementTemplate.java b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementTemplate.java
similarity index 91%
rename from user-interface/src/main/java/life/qbic/datamanager/templates/NGSMeasurementTemplate.java
rename to user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementTemplate.java
index 2f7abd28b..3e74ab6cf 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/templates/NGSMeasurementTemplate.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementTemplate.java
@@ -1,7 +1,8 @@
-package life.qbic.datamanager.templates;
+package life.qbic.datamanager.templates.measurement;
import java.io.IOException;
import java.util.Objects;
+import life.qbic.datamanager.templates.Template;
/**
* NGS measurement template
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/ProteomicsMeasurementContentProvider.java b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementEditTemplate.java
similarity index 54%
rename from user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/ProteomicsMeasurementContentProvider.java
rename to user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementEditTemplate.java
index 05de7d2b4..7fce85779 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/ProteomicsMeasurementContentProvider.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementEditTemplate.java
@@ -1,11 +1,13 @@
-package life.qbic.datamanager.views.projects.project.measurements.download;
-
-import static life.qbic.datamanager.spreadsheet.XLSXTemplateHelper.addDataValidation;
-import static life.qbic.datamanager.spreadsheet.XLSXTemplateHelper.createOptionArea;
-import static life.qbic.datamanager.spreadsheet.XLSXTemplateHelper.getOrCreateCell;
-import static life.qbic.datamanager.spreadsheet.XLSXTemplateHelper.getOrCreateRow;
-import static life.qbic.datamanager.spreadsheet.XLSXTemplateHelper.hideSheet;
-import static life.qbic.datamanager.spreadsheet.XLSXTemplateHelper.lockSheet;
+package life.qbic.datamanager.templates.measurement;
+
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.addDataValidation;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.createBoldCellStyle;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.createOptionArea;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.createReadOnlyCellStyle;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.getOrCreateCell;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.getOrCreateRow;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.hideSheet;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.lockSheet;
import static life.qbic.logging.service.LoggerFactory.logger;
import java.io.ByteArrayOutputStream;
@@ -14,22 +16,19 @@
import java.util.List;
import life.qbic.application.commons.ApplicationException;
import life.qbic.application.commons.ApplicationException.ErrorCode;
-import life.qbic.datamanager.views.general.download.DownloadContentProvider;
+import life.qbic.datamanager.download.DownloadContentProvider;
+import life.qbic.datamanager.parser.measurement.ProteomicsMeasurementEditColumn;
+import life.qbic.datamanager.templates.XLSXTemplateHelper;
import life.qbic.datamanager.views.projects.project.measurements.ProteomicsMeasurementEntry;
import life.qbic.logging.api.Logger;
import life.qbic.projectmanagement.application.measurement.ProteomicsMeasurementMetadata;
import life.qbic.projectmanagement.application.measurement.validation.MeasurementProteomicsValidator.DigestionMethod;
import life.qbic.projectmanagement.domain.model.measurement.ProteomicsMeasurement;
import org.apache.poi.ss.usermodel.CellStyle;
-import org.apache.poi.ss.usermodel.FillPatternType;
-import org.apache.poi.ss.usermodel.Font;
import org.apache.poi.ss.usermodel.Name;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.ss.usermodel.Workbook;
-import org.apache.poi.xssf.usermodel.DefaultIndexedColorMap;
-import org.apache.poi.xssf.usermodel.XSSFColor;
-import org.apache.poi.xssf.usermodel.XSSFFont;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;
/** Proteomics Measurement Content Provider
@@ -39,12 +38,10 @@
* and {@link ProteomicsMeasurementMetadata}
*
+ *
+ * @since
+ */
+public class SampleBatchRegistrationTemplate {
+
+ public static final int MAX_ROW_INDEX_TO = 2000;
+
+ /**
+ * Creates a template {@link XSSFWorkbook} for sample batch registration.
+ *
+ * The client currently can expect that the workbook contains two {@link XSSFSheet}, accessible
+ * via {@link XSSFWorkbook#getSheetAt(int)}.
+ *
+ * At position 0, the sheet contains the actual template with column headers for the properties
+ * expected for registration. If provided, some properties will also contain field validation
+ * based on enumeration of selection choices.
+ *
+ * This currently is true for the following properties:
+ *
+ *
+ *
Species
+ *
Specimen
+ *
Analyte
+ *
Condition
+ *
Analysis to perform
+ *
+ *
+ * At position 1, the sheet is hidden and protected, containing fixed values for the field validation
+ * in sheet 0. We don't want users to manually change them. They are given via the experimental
+ * design. This is a compromise of using technical identifiers vs ease of use for property values.
+ *
+ * @param conditions all conditions available in the experiment to select from
+ * @param species all the species available in the experiment to select from
+ * @param specimen all the specimen available in the experiment to select from
+ * @param analytes all the analytes available in the experiment to select from
+ * @return a pre-configured template workbook
+ * @since 1.5.0
+ */
+ public static XSSFWorkbook createRegistrationTemplate(List conditions,
+ List species, List specimen, List analytes,
+ List analysisToPerform) {
+ XSSFWorkbook workbook = new XSSFWorkbook();
+ var readOnlyHeaderStyle = createReadOnlyHeaderCellStyle(workbook);
+ var boldCellStyle = createBoldCellStyle(workbook);
+
+ var sheet = workbook.createSheet("Sample Metadata");
+
+ Row header = getOrCreateRow(sheet, 0);
+ for (RegisterColumn column : RegisterColumn.values()) {
+ var cell = getOrCreateCell(header, column.columnIndex());
+
+ cell.setCellStyle(boldCellStyle);
+ if (column.isMandatory()) {
+ cell.setCellValue(column.headerName() + "*");
+ } else {
+ cell.setCellValue(column.headerName());
+ }
+ if (column.isReadOnly()) {
+ cell.setCellStyle(readOnlyHeaderStyle);
+ }
+ }
+ var startIndex = 1; //start in the second row with index 1.
+
+ var hiddenSheet = workbook.createSheet("hidden");
+ Name analysisToBePerformedOptions = createOptionArea(hiddenSheet, "Analysis to be performed",
+ analysisToPerform);
+ Name conditionOptions = createOptionArea(hiddenSheet, "Condition", conditions);
+ Name analyteOptions = createOptionArea(hiddenSheet, "Analyte", analytes);
+ Name speciesOptions = createOptionArea(hiddenSheet, "Species", species);
+ Name specimenOptions = createOptionArea(hiddenSheet, "Specimen", specimen);
+
+ addDataValidation(sheet,
+ RegisterColumn.ANALYSIS.columnIndex(),
+ startIndex,
+ RegisterColumn.ANALYSIS.columnIndex(),
+ MAX_ROW_INDEX_TO,
+ analysisToBePerformedOptions);
+ addDataValidation(sheet,
+ RegisterColumn.CONDITION.columnIndex(),
+ startIndex,
+ RegisterColumn.CONDITION.columnIndex(),
+ MAX_ROW_INDEX_TO,
+ conditionOptions);
+ addDataValidation(sheet,
+ RegisterColumn.ANALYTE.columnIndex(),
+ startIndex,
+ RegisterColumn.ANALYTE.columnIndex(),
+ MAX_ROW_INDEX_TO,
+ analyteOptions);
+ addDataValidation(sheet,
+ RegisterColumn.SPECIES.columnIndex(),
+ startIndex,
+ RegisterColumn.SPECIES.columnIndex(),
+ MAX_ROW_INDEX_TO,
+ speciesOptions);
+ addDataValidation(sheet,
+ RegisterColumn.SPECIMEN.columnIndex(),
+ startIndex,
+ RegisterColumn.SPECIMEN.columnIndex(),
+ MAX_ROW_INDEX_TO,
+ specimenOptions);
+
+ setColumnAutoWidth(sheet, 0, RegisterColumn.maxColumnIndex());
+ // Auto width ignores cell validation values (e.g. a list of valid entries). So we need
+ // to set them explicit
+ setColumnWidth(sheet, RegisterColumn.CONDITION.columnIndex(), maxLength(conditions));
+ setColumnWidth(sheet, RegisterColumn.SPECIES.columnIndex(), maxLength(species));
+ setColumnWidth(sheet, RegisterColumn.SPECIMEN.columnIndex(), maxLength(specimen));
+ setColumnWidth(sheet, RegisterColumn.ANALYTE.columnIndex(), maxLength(analytes));
+ setColumnWidth(sheet, RegisterColumn.ANALYSIS.columnIndex(), maxLength(analysisToPerform));
+ setColumnAutoWidth(hiddenSheet, 0, 4);
+ workbook.setActiveSheet(0);
+ lockSheet(hiddenSheet);
+ hideSheet(workbook, hiddenSheet);
+
+ return workbook;
+ }
+
+ static int maxLength(Collection collection) {
+ return collection.stream().mapToInt(String::length).max().orElse(0);
+ }
+}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchUpdateTemplate.java b/user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchUpdateTemplate.java
new file mode 100644
index 000000000..0fb98dc01
--- /dev/null
+++ b/user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchUpdateTemplate.java
@@ -0,0 +1,154 @@
+package life.qbic.datamanager.templates.sample;
+
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.addDataValidation;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.createOptionArea;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.createReadOnlyCellStyle;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.getOrCreateCell;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.getOrCreateRow;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.hideSheet;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.lockSheet;
+import static life.qbic.datamanager.templates.XLSXTemplateHelper.setColumnAutoWidth;
+
+import java.util.List;
+import life.qbic.datamanager.parser.sample.EditColumn;
+import life.qbic.datamanager.templates.XLSXTemplateHelper;
+import life.qbic.projectmanagement.application.sample.PropertyConversion;
+import life.qbic.projectmanagement.domain.model.experiment.Condition;
+import life.qbic.projectmanagement.domain.model.experiment.ExperimentalGroup;
+import life.qbic.projectmanagement.domain.model.sample.Sample;
+import org.apache.poi.ss.usermodel.CellStyle;
+import org.apache.poi.ss.usermodel.Name;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+
+/**
+ * Sample Batch Template
+ *
+ *
Offers an API to create pre-configured workbooks for sample batch metadata use cases.
+ *
+ * @since 1.5.0
+ */
+public class SampleBatchUpdateTemplate {
+
+ public static final int MAX_ROW_INDEX_TO = 2000;
+
+
+
+ /**
+ * Creates a {@link XSSFWorkbook} that contains a prefilled sheet of sample metadata based on the
+ * provided list of {@link Sample}.
+ *
+ * @param samples a list of samples with metadata that will be used to fill the
+ * spreadsheet
+ * @param conditions a list of conditions that are available for selection
+ * @param species a list of species that are available for selection
+ * @param specimen a list of specimen that are available for selection
+ * @param analytes a list of analytes that are available for selection
+ * @param analysisToPerform a list of analysis types available for the sample measurement
+ * @param experimentalGroups a list of experimental groups the samples belong to
+ * @return a workbook with a prefilled sheet at tab index 0 that contains the sample metadata
+ * @since 1.5.0
+ */
+ public static XSSFWorkbook createUpdateTemplate(List samples, List conditions,
+ List species, List specimen, List analytes,
+ List analysisToPerform, List experimentalGroups) {
+
+ XSSFWorkbook workbook = new XSSFWorkbook();
+ var readOnlyCellStyle = createReadOnlyCellStyle(workbook);
+ var readOnlyHeaderStyle = XLSXTemplateHelper.createReadOnlyHeaderCellStyle(workbook);
+ var boldCellStyle = XLSXTemplateHelper.createBoldCellStyle(workbook);
+
+ var sheet = workbook.createSheet("Sample Metadata");
+
+ Row header = getOrCreateRow(sheet, 0);
+ for (EditColumn column : EditColumn.values()) {
+ var cell = XLSXTemplateHelper.getOrCreateCell(header, column.columnIndex());
+ if (column.isMandatory()) {
+ cell.setCellValue(column.headerName() + "*");
+ } else {
+ cell.setCellValue(column.headerName());
+ }
+ cell.setCellStyle(boldCellStyle);
+ if (column.isReadOnly()) {
+ cell.setCellStyle(readOnlyHeaderStyle);
+ }
+ }
+ var startIndex = 1; //start in the second row with index 1.
+ int rowIndex = startIndex;
+ for (Sample sample : samples) {
+ Row row = getOrCreateRow(sheet, rowIndex);
+ var experimentalGroup = experimentalGroups.stream()
+ .filter(group -> group.id() == sample.experimentalGroupId()).findFirst().orElseThrow();
+ fillRowWithSampleMetadata(row, sample, experimentalGroup.condition(), readOnlyCellStyle);
+ rowIndex++;
+ }
+
+ var hiddenSheet = workbook.createSheet("hidden");
+ Name analysisToBePerformedOptions = createOptionArea(hiddenSheet, "Analysis to be performed",
+ analysisToPerform);
+ Name conditionOptions = createOptionArea(hiddenSheet, "Condition", conditions);
+ Name analyteOptions = createOptionArea(hiddenSheet, "Analyte", analytes);
+ Name speciesOptions = createOptionArea(hiddenSheet, "Species", species);
+ Name specimenOptions = createOptionArea(hiddenSheet, "Specimen", specimen);
+
+ addDataValidation(sheet,
+ EditColumn.ANALYSIS.columnIndex(),
+ startIndex,
+ EditColumn.ANALYSIS.columnIndex(),
+ MAX_ROW_INDEX_TO,
+ analysisToBePerformedOptions);
+ addDataValidation(sheet,
+ EditColumn.CONDITION.columnIndex(),
+ startIndex,
+ EditColumn.CONDITION.columnIndex(),
+ MAX_ROW_INDEX_TO,
+ conditionOptions);
+ addDataValidation(sheet,
+ EditColumn.ANALYTE.columnIndex(),
+ startIndex,
+ EditColumn.ANALYTE.columnIndex(),
+ MAX_ROW_INDEX_TO,
+ analyteOptions);
+ addDataValidation(sheet,
+ EditColumn.SPECIES.columnIndex(),
+ startIndex,
+ EditColumn.SPECIES.columnIndex(),
+ MAX_ROW_INDEX_TO,
+ speciesOptions);
+ addDataValidation(sheet,
+ EditColumn.SPECIMEN.columnIndex(),
+ startIndex,
+ EditColumn.SPECIMEN.columnIndex(),
+ MAX_ROW_INDEX_TO,
+ specimenOptions);
+
+ setColumnAutoWidth(sheet, 0, EditColumn.maxColumnIndex());
+ workbook.setActiveSheet(0);
+ lockSheet(hiddenSheet);
+ hideSheet(workbook, hiddenSheet);
+
+ return workbook;
+ }
+
+ private static void fillRowWithSampleMetadata(Row row, Sample sample,
+ Condition condition, CellStyle readOnlyCellStyle) {
+ for (EditColumn column : EditColumn.values()) {
+ var value = switch (column) {
+ case SAMPLE_ID -> sample.sampleCode().code();
+ case ANALYSIS -> sample.analysisMethod().abbreviation();
+ case SAMPLE_NAME -> sample.label();
+ case BIOLOGICAL_REPLICATE -> sample.biologicalReplicate();
+ case CONDITION -> PropertyConversion.toString(condition);
+ case SPECIES -> PropertyConversion.toString(sample.sampleOrigin().getSpecies());
+ case ANALYTE -> PropertyConversion.toString(sample.sampleOrigin().getAnalyte());
+ case SPECIMEN -> PropertyConversion.toString(sample.sampleOrigin().getSpecimen());
+ case COMMENT -> sample.comment().orElse("");
+ };
+ var cell = getOrCreateCell(row, column.columnIndex());
+ cell.setCellValue(value);
+ if (column.isReadOnly()) {
+ cell.setCellStyle(readOnlyCellStyle);
+ }
+ }
+ }
+}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/account/PersonalAccessTokenComponent.java b/user-interface/src/main/java/life/qbic/datamanager/views/account/PersonalAccessTokenComponent.java
index 610fcf262..b5fa3dc57 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/account/PersonalAccessTokenComponent.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/account/PersonalAccessTokenComponent.java
@@ -358,12 +358,10 @@ public void setToken(String token) {
ui.access(() -> {
addClassName("success-background-hue");
copyDisclaimerText.setText("Token successfully copied.");
- ui.push();
}));
copyToClipBoardComponent.addSwitchToCopyIconListener(event ->
ui.access(() -> {
removeClassName("success-background-hue");
- ui.push();
}));
}
}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/general/CopyToClipBoardComponent.java b/user-interface/src/main/java/life/qbic/datamanager/views/general/CopyToClipBoardComponent.java
index 84b2ad39d..e00499daa 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/general/CopyToClipBoardComponent.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/general/CopyToClipBoardComponent.java
@@ -70,7 +70,6 @@ private void handleCopyClicked(ComponentEvent componentEvent) {
CompletableFuture.runAsync(() -> ui.access(() -> {
copyIcon.setVisible(true);
copySuccessIcon.setVisible(false);
- ui.push();
}), delayedExecutor).thenRun(() ->
fireEvent(new SwitchToCopyIconEvent(this, componentEvent.isFromClient())));
}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/general/download/DownloadContentProvider.java b/user-interface/src/main/java/life/qbic/datamanager/views/general/download/DownloadContentProvider.java
deleted file mode 100644
index 39e886f08..000000000
--- a/user-interface/src/main/java/life/qbic/datamanager/views/general/download/DownloadContentProvider.java
+++ /dev/null
@@ -1,10 +0,0 @@
-package life.qbic.datamanager.views.general.download;
-
-/**
- * Provides content and file name for any files created from data and metadata.
- */
-public interface DownloadContentProvider {
-
- public byte[] getContent();
- public String getFileName();
-}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/EditableMultiFileMemoryBuffer.java b/user-interface/src/main/java/life/qbic/datamanager/views/general/upload/EditableMultiFileMemoryBuffer.java
similarity index 97%
rename from user-interface/src/main/java/life/qbic/datamanager/views/projects/EditableMultiFileMemoryBuffer.java
rename to user-interface/src/main/java/life/qbic/datamanager/views/general/upload/EditableMultiFileMemoryBuffer.java
index 862a1854a..29fbb8e3c 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/EditableMultiFileMemoryBuffer.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/general/upload/EditableMultiFileMemoryBuffer.java
@@ -1,4 +1,4 @@
-package life.qbic.datamanager.views.projects;
+package life.qbic.datamanager.views.general.upload;
import com.vaadin.flow.component.upload.MultiFileReceiver;
import com.vaadin.flow.component.upload.receivers.FileData;
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/general/upload/FileMemoryBuffer.java b/user-interface/src/main/java/life/qbic/datamanager/views/general/upload/FileMemoryBuffer.java
new file mode 100644
index 000000000..2da584110
--- /dev/null
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/general/upload/FileMemoryBuffer.java
@@ -0,0 +1,57 @@
+package life.qbic.datamanager.views.general.upload;
+
+import static java.util.Objects.nonNull;
+
+import com.vaadin.flow.component.upload.Receiver;
+import com.vaadin.flow.component.upload.receivers.FileData;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.Optional;
+
+/**
+ * TODO!
+ * short description
+ *
+ *
+ * Only supports uploading one file at a time, decreasing complexity of display behaviour and data.
+ *
+ * @since 1.4.0
+ */
+public class UploadWithDisplay extends Div {
+
+ private final Upload upload;
+ private final Div errorArea;
+ private final Div displayContainer;
+ private final Span displayContainerTitle;
+ private final FileMemoryBuffer fileMemoryBuffer;
+
+ public UploadWithDisplay(int maxFileSize) {
+ this(maxFileSize, new FileType[]{});
+ }
+
+ public record FileType(String extension, String mimeType) {
+ }
+
+ public UploadWithDisplay(int maxFileSize, FileType[] fileTypes) {
+ errorArea = new Div();
+ displayContainer = new Div();
+ fileMemoryBuffer = new FileMemoryBuffer();
+ upload = new Upload();
+ var restrictions = new Div();
+
+ errorArea.addClassName("error-message-box");
+ displayContainer.addClassName("uploaded-items-section");
+ displayContainer.setVisible(false);
+
+ displayContainerTitle = new Span("Uploaded file");
+ displayContainerTitle.addClassName("section-title");
+ displayContainerTitle.setVisible(false);
+
+ restrictions.addClassName("restrictions");
+ var allowedExtensions = Arrays.stream(fileTypes)
+ .map(FileType::extension)
+ .map(it -> it.startsWith(".") ? it : "." + it)
+ .distinct()
+ .toList();
+ if (fileTypes.length > 0) {
+ restrictions.add(new Div("Supported file formats: " + String.join(", ", allowedExtensions)));
+ restrictions.add(new Div("Maximum file size: " + formatFileSize(maxFileSize)));
+ }
+
+ upload.setAcceptedFileTypes(
+ fileTypes.length > 0 ? Arrays.stream(fileTypes)
+ .map(FileType::mimeType)
+ .filter(it -> !it.isBlank())
+ .toArray(String[]::new) : null);
+
+ upload.setMaxFileSize(maxFileSize);
+ upload.setMaxFiles(1); // we only allow one file
+ upload.setReceiver(fileMemoryBuffer);
+ upload.addFileRemovedListener(fileRemovedEvent -> {
+ fileMemoryBuffer.clear();
+ displayContainer.removeAll();
+ displayContainerTitle.setVisible(false);
+ displayContainer.setVisible(false);
+ fireEvent(new UploadRemovedEvent(this, fileRemovedEvent.isFromClient()));
+ });
+
+ Error errorTranslation = new Error();
+ errorTranslation.setFileIsTooBig(
+ "The provided file is too big. Please make sure your file is smaller than "
+ + formatFileSize(maxFileSize));
+ errorTranslation.setTooManyFiles("Please upload one file at a time.");
+ errorTranslation.setIncorrectFileType(
+ "Unsupported file type. Supported file types are " + String.join(", ", allowedExtensions));
+ UploadI18N uploadI18N = new UploadI18N();
+ uploadI18N.setError(errorTranslation);
+ upload.setI18n(uploadI18N);
+
+ upload.addSucceededListener(it -> fireEvent(new SucceededEvent(this, it.isFromClient())));
+ upload.addFailedListener(it -> fireEvent(new FailedEvent(this, it.isFromClient())));
+ upload.addFileRejectedListener(fileRejected -> {
+ errorArea.setVisible(true);
+ errorArea.setText(fileRejected.getErrorMessage());
+ });
+ upload.addFinishedListener(it -> errorArea.setVisible(false));
+ add(errorArea, upload, restrictions, displayContainerTitle, displayContainer);
+ }
+
+ private static String formatFileSize(int bytes) {
+ if (bytes > Math.pow(1024, 2)) {
+ return bytes / Math.pow(1024, 2) + " MB";
+ }
+ if (bytes > 1024) {
+ return bytes / 1024d + " KB";
+ }
+ return bytes + " B";
+ }
+
+ public Registration addSuccessListener(ComponentEventListener listener) {
+ return addListener(SucceededEvent.class, listener);
+ }
+
+ public Registration addFailureListener(ComponentEventListener listener) {
+ return addListener(FailedEvent.class, listener);
+ }
+
+ public Registration addRemovedListener(ComponentEventListener listener) {
+ return addListener(UploadRemovedEvent.class, listener);
+ }
+
+ /**
+ * Sets component to display the currently available file. This component will be cleared when the
+ * file is removed from the upload component.
+ *
+ * @param uploadProgressDisplay a component to display
+ * @param the type of component to display
+ */
+ public void setDisplay(T uploadProgressDisplay) {
+ displayContainer.removeAll();
+ if (uploadProgressDisplay == null) {
+ displayContainerTitle.setVisible(false);
+ displayContainer.setVisible(false);
+ return;
+ }
+ uploadProgressDisplay.addClassName("uploaded-item");
+ displayContainer.add(uploadProgressDisplay);
+ displayContainerTitle.setVisible(true);
+ displayContainer.setVisible(true);
+ }
+
+ /**
+ * Removes component from display.
+ *
+ * If the component is not displayed, does nothing.
+ * @param display
+ * @param
+ */
+ public void removeDisplay(T display) {
+ displayContainer.remove(display);
+ displayContainerTitle.setVisible(false);
+ displayContainer.setVisible(false);
+ fireEvent(new UploadRemovedEvent(this, false));
+ }
+
+ /**
+ * Clears the upload as well as resets the display.
+ */
+ public void clear() {
+ upload.clearFileList();
+ displayContainer.removeAll();
+ displayContainerTitle.setVisible(false);
+ displayContainer.setVisible(false);
+ errorArea.removeAll();
+ fileMemoryBuffer.clear();
+ }
+
+ /**
+ * @return the uploaded data or {@link Optional#empty()} is nothing was uploaded yet.
+ */
+ public Optional getUploadedData() {
+ if (fileMemoryBuffer.hasUploadedData()) {
+ var fileName = fileMemoryBuffer.getFileName().orElseThrow();
+ var inputStream = fileMemoryBuffer.getInputStream().orElseThrow();
+ var mimeType = fileMemoryBuffer.getMimeType().orElseThrow();
+ return Optional.of(new UploadedData(fileName, inputStream, mimeType));
+ }
+ return Optional.empty();
+ }
+
+ /**
+ * A representation of uploaded data
+ * @param fileName the name of the uploaded file
+ * @param inputStream the contents of the file
+ * @param mimeType the type of file
+ */
+ public record UploadedData(String fileName, InputStream inputStream, String mimeType) {
+
+ /**
+ * {@inheritDoc}
+ *
+ * This method ignores the file content and only compares filename and mime tpye.
+ * @param o the reference object with which to compare.
+ * @return {@inheritDoc}
+ */
+ @Override
+ public boolean equals(Object o) {
+ if (this == o) {
+ return true;
+ }
+ if (!(o instanceof UploadedData that)) {
+ return false;
+ }
+
+ return Objects.equals(fileName, that.fileName) && Objects.equals(mimeType,
+ that.mimeType);
+ }
+
+ @Override
+ public int hashCode() {
+ int result = Objects.hashCode(fileName);
+ result = 31 * result + Objects.hashCode(mimeType);
+ return result;
+ }
+ }
+
+ public static class SucceededEvent extends ComponentEvent {
+
+ /**
+ * Creates a new event using the given source and indicator whether the event originated from
+ * the client side or the server side.
+ *
+ * @param source the source component
+ * @param fromClient true if the event originated from the client
+ * side, false otherwise
+ */
+ public SucceededEvent(UploadWithDisplay source, boolean fromClient) {
+ super(source, fromClient);
+ }
+ }
+
+ public static class FailedEvent extends ComponentEvent {
+
+ /**
+ * Creates a new event using the given source and indicator whether the event originated from
+ * the client side or the server side.
+ *
+ * @param source the source component
+ * @param fromClient true if the event originated from the client
+ * side, false otherwise
+ */
+ public FailedEvent(UploadWithDisplay source, boolean fromClient) {
+ super(source, fromClient);
+ }
+ }
+
+ /**
+ * Indicates that the upload was removed.
+ */
+ public static class UploadRemovedEvent extends ComponentEvent {
+
+ /**
+ * Creates a new event using the given source and indicator whether the event originated from
+ * the client side or the server side.
+ *
+ * @param source the source component
+ * @param fromClient true if the event originated from the client
+ * side, false otherwise
+ */
+ public UploadRemovedEvent(UploadWithDisplay source, boolean fromClient) {
+ super(source, fromClient);
+ }
+ }
+
+}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/navigation/ProjectSideNavigationComponent.java b/user-interface/src/main/java/life/qbic/datamanager/views/navigation/ProjectSideNavigationComponent.java
index 6ae718252..4e25f025e 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/navigation/ProjectSideNavigationComponent.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/navigation/ProjectSideNavigationComponent.java
@@ -239,7 +239,7 @@ private static void routeToProjectOverview() {
log.debug("Routing to ProjectOverview page");
}
- private static void routeToProject(ProjectId projectId) {
+private static void routeToProject(ProjectId projectId) {
RouteParameters routeParameters = new RouteParameters(
new RouteParam(PROJECT_ID_ROUTE_PARAMETER, projectId.value()));
//getUI is not possible on the ProjectSideNavigationComponent directly in a static context
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/notifications/CancelConfirmationDialogFactory.java b/user-interface/src/main/java/life/qbic/datamanager/views/notifications/CancelConfirmationDialogFactory.java
index b85938a5a..1e6285f23 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/notifications/CancelConfirmationDialogFactory.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/notifications/CancelConfirmationDialogFactory.java
@@ -86,7 +86,7 @@ private MessageType parseMessageType(String key, Locale locale) {
EMPTY_PARAMETERS, locale).strip().toUpperCase();
return MessageType.valueOf(messageType);
} catch (NoSuchMessageException e) {
- log.error("No message type specified for %s." + key, e);
+ log.warn("No message type specified for %s." + key);
return DEFAULT_MESSAGE_TYPE;
}
}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMain.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMain.java
index a487b13b0..78b8b15e5 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMain.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMain.java
@@ -28,12 +28,14 @@
import life.qbic.application.commons.ApplicationException;
import life.qbic.application.commons.ApplicationException.ErrorCode;
import life.qbic.application.commons.Result;
+import life.qbic.datamanager.download.DownloadProvider;
+import life.qbic.datamanager.templates.measurement.NGSMeasurementEditTemplate;
+import life.qbic.datamanager.templates.measurement.ProteomicsMeasurementEditTemplate;
import life.qbic.datamanager.views.AppRoutes.Projects;
import life.qbic.datamanager.views.Context;
import life.qbic.datamanager.views.general.Disclaimer;
import life.qbic.datamanager.views.general.InfoBox;
import life.qbic.datamanager.views.general.Main;
-import life.qbic.datamanager.views.general.download.DownloadProvider;
import life.qbic.datamanager.views.general.download.MeasurementTemplateDownload;
import life.qbic.datamanager.views.notifications.CancelConfirmationDialogFactory;
import life.qbic.datamanager.views.notifications.ErrorMessage;
@@ -42,8 +44,6 @@
import life.qbic.datamanager.views.projects.project.measurements.MeasurementMetadataUploadDialog.MODE;
import life.qbic.datamanager.views.projects.project.measurements.MeasurementMetadataUploadDialog.MeasurementMetadataUpload;
import life.qbic.datamanager.views.projects.project.measurements.MeasurementTemplateListComponent.DownloadMeasurementTemplateEvent;
-import life.qbic.datamanager.views.projects.project.measurements.download.NGSMeasurementContentProvider;
-import life.qbic.datamanager.views.projects.project.measurements.download.ProteomicsMeasurementContentProvider;
import life.qbic.logging.api.Logger;
import life.qbic.logging.service.LoggerFactory;
import life.qbic.projectmanagement.application.ProjectInformationService;
@@ -95,8 +95,8 @@ public class MeasurementMain extends Main implements BeforeEnterObserver {
private final Div content = new Div();
private final InfoBox rawDataAvailableInfo = new InfoBox();
private final Div noMeasurementDisclaimer;
- private final ProteomicsMeasurementContentProvider proteomicsMeasurementContentProvider;
- private final NGSMeasurementContentProvider ngsMeasurementContentProvider;
+ private final ProteomicsMeasurementEditTemplate proteomicsMeasurementEditTemplate;
+ private final NGSMeasurementEditTemplate ngsMeasurementEditTemplate;
private final DownloadProvider ngsDownloadProvider;
private final DownloadProvider proteomicsDownloadProvider;
private final ProjectInformationService projectInformationService;
@@ -120,10 +120,10 @@ public MeasurementMain(
this.measurementTemplateListComponent = measurementTemplateListComponent;
this.measurementService = measurementService;
this.measurementPresenter = measurementPresenter;
- this.proteomicsMeasurementContentProvider = new ProteomicsMeasurementContentProvider();
- this.ngsMeasurementContentProvider = new NGSMeasurementContentProvider();
- this.ngsDownloadProvider = new DownloadProvider(ngsMeasurementContentProvider);
- this.proteomicsDownloadProvider = new DownloadProvider(proteomicsMeasurementContentProvider);
+ this.proteomicsMeasurementEditTemplate = new ProteomicsMeasurementEditTemplate();
+ this.ngsMeasurementEditTemplate = new NGSMeasurementEditTemplate();
+ this.ngsDownloadProvider = new DownloadProvider(ngsMeasurementEditTemplate);
+ this.proteomicsDownloadProvider = new DownloadProvider(proteomicsMeasurementEditTemplate);
this.measurementValidationService = measurementValidationService;
this.sampleInformationService = Objects.requireNonNull(sampleInformationService);
this.projectInformationService = projectInformationService;
@@ -371,7 +371,7 @@ private void downloadProteomicsMetadata() {
.flatMap(Collection::stream)
.sorted(Comparator.comparing(ProteomicsMeasurementEntry::measurementCode, natOrder)
.thenComparing(ptx -> ptx.sampleInformation().sampleId(), natOrder)).toList();
- proteomicsMeasurementContentProvider.setMeasurements(result,
+ proteomicsMeasurementEditTemplate.setMeasurements(result,
projectInformationService.find(context.projectId().orElseThrow()).orElseThrow()
.getProjectCode().value());
proteomicsDownloadProvider.trigger();
@@ -390,7 +390,7 @@ private void downloadNGSMetadata() {
// sort by measurement codes first, then by sample codes
.sorted(Comparator.comparing(NGSMeasurementEntry::measurementCode, natOrder)
.thenComparing(ngs -> ngs.sampleInformation().sampleId(), natOrder)).toList();
- ngsMeasurementContentProvider.setMeasurements(result,
+ ngsMeasurementEditTemplate.setMeasurements(result,
projectInformationService.find(context.projectId().orElseThrow()).orElseThrow()
.getProjectCode().value());
ngsDownloadProvider.trigger();
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMetadataUploadDialog.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMetadataUploadDialog.java
index b902de2bb..6a17c423b 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMetadataUploadDialog.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMetadataUploadDialog.java
@@ -9,27 +9,29 @@
import com.vaadin.flow.component.html.Div;
import com.vaadin.flow.component.html.ListItem;
import com.vaadin.flow.component.html.OrderedList;
+import com.vaadin.flow.component.html.OrderedList.NumberingType;
import com.vaadin.flow.component.html.Span;
import com.vaadin.flow.component.icon.Icon;
import com.vaadin.flow.component.icon.VaadinIcon;
import com.vaadin.flow.component.progressbar.ProgressBar;
import com.vaadin.flow.component.upload.FailedEvent;
import com.vaadin.flow.component.upload.FileRejectedEvent;
+import com.vaadin.flow.component.upload.FileRemovedEvent;
import com.vaadin.flow.component.upload.SucceededEvent;
import com.vaadin.flow.component.upload.Upload;
-import com.vaadin.flow.dom.DomEvent;
import com.vaadin.flow.shared.Registration;
-import elemental.json.JsonObject;
import java.io.InputStream;
import java.io.Serial;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
-import java.util.Objects;
import java.util.Optional;
+import java.util.Set;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.ConcurrentLinkedDeque;
+import java.util.stream.Collectors;
import life.qbic.datamanager.parser.MeasurementMetadataConverter.MissingSampleIdException;
import life.qbic.datamanager.parser.MeasurementMetadataConverter.UnknownMetadataTypeException;
import life.qbic.datamanager.parser.MetadataConverter;
@@ -38,15 +40,15 @@
import life.qbic.datamanager.parser.xlsx.XLSXParser;
import life.qbic.datamanager.views.general.InfoBox;
import life.qbic.datamanager.views.general.WizardDialogWindow;
+import life.qbic.datamanager.views.general.upload.EditableMultiFileMemoryBuffer;
import life.qbic.datamanager.views.notifications.CancelConfirmationDialogFactory;
import life.qbic.datamanager.views.notifications.ErrorMessage;
import life.qbic.datamanager.views.notifications.StyledNotification;
-import life.qbic.datamanager.views.projects.EditableMultiFileMemoryBuffer;
+import life.qbic.projectmanagement.application.ValidationResult;
import life.qbic.projectmanagement.application.measurement.MeasurementMetadata;
import life.qbic.projectmanagement.application.measurement.NGSMeasurementMetadata;
import life.qbic.projectmanagement.application.measurement.ProteomicsMeasurementMetadata;
import life.qbic.projectmanagement.application.measurement.validation.MeasurementValidationService;
-import life.qbic.projectmanagement.application.measurement.validation.ValidationResult;
import life.qbic.projectmanagement.domain.model.experiment.Experiment;
import life.qbic.projectmanagement.domain.model.project.ProjectId;
import org.springframework.util.StringUtils;
@@ -66,7 +68,6 @@ public class MeasurementMetadataUploadDialog extends WizardDialogWindow {
public static final int MAX_FILE_SIZE_BYTES = (int) (Math.pow(1024, 2) * 16);
@Serial
private static final long serialVersionUID = -8253078073427291947L;
- private static final String VAADIN_FILENAME_EVENT = "event.detail.file.name";
private final MeasurementValidationService measurementValidationService;
private final CancelConfirmationDialogFactory cancelConfirmationDialogFactory;
@@ -78,6 +79,27 @@ public class MeasurementMetadataUploadDialog extends WizardDialogWindow {
private final UploadProgressDisplay uploadProgressDisplay;
private final UploadItemsDisplay uploadItemsDisplay;
+ private enum AcceptedFileType {
+ EXCEL("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"),
+ TSV("text/tab-separated-values", "text/plain");
+ private final List mimeTypes;
+
+ AcceptedFileType(String... mimeTypes) {
+ this.mimeTypes = List.of(mimeTypes);
+ }
+
+ static Optional forMimeType(String mimeType) {
+ return Arrays.stream(values())
+ .filter(it -> it.mimeTypes.contains(mimeType))
+ .findFirst();
+ }
+
+ static Set allMimeTypes() {
+ return Arrays.stream(values()).flatMap(it -> it.mimeTypes.stream())
+ .collect(Collectors.toUnmodifiableSet());
+ }
+ }
+
public MeasurementMetadataUploadDialog(MeasurementValidationService measurementValidationService,
CancelConfirmationDialogFactory cancelConfirmationDialogFactory,
MODE mode, ProjectId projectId) {
@@ -92,8 +114,7 @@ public MeasurementMetadataUploadDialog(MeasurementValidationService measurementV
this.measurementMetadataUploads = new ArrayList<>();
this.measurementFileItems = new ArrayList<>();
Upload upload = new Upload(uploadBuffer);
- upload.setAcceptedFileTypes("text/tab-separated-values", "text/plain",
- "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
+ upload.setAcceptedFileTypes(AcceptedFileType.allMimeTypes().toArray(String[]::new));
upload.setMaxFileSize(MAX_FILE_SIZE_BYTES);
setModeBasedLabels();
uploadItemsDisplay = new UploadItemsDisplay(upload);
@@ -105,12 +126,8 @@ public MeasurementMetadataUploadDialog(MeasurementValidationService measurementV
upload.addSucceededListener(this::onUploadSucceeded);
upload.addFileRejectedListener(this::onFileRejected);
upload.addFailedListener(this::onUploadFailed);
+ upload.addFileRemovedListener(this::onFileRemoved);
setEscAction(this::onCanceled);
- // Synchronise the Vaadin upload component with the purchase list display
- // When a file is removed from the upload component, we also want to remove it properly from memory
- // and from any additional display
- upload.getElement().addEventListener("file-remove", this::onFileRemoved)
- .addEventData(VAADIN_FILENAME_EVENT);
addClassName("measurement-upload-dialog");
}
@@ -135,11 +152,8 @@ public MODE getMode() {
return mode;
}
- private void onFileRemoved(DomEvent domEvent) {
- JsonObject jsonObject = domEvent.getEventData();
- var fileName = jsonObject.getString(VAADIN_FILENAME_EVENT);
- removeFile(fileName);
-
+ private void onFileRemoved(FileRemovedEvent fileRemovedEvent) {
+ removeFile(fileRemovedEvent.getFileName());
}
private void showFile(MeasurementFileItem measurementFileItem) {
@@ -166,7 +180,7 @@ private void onUploadFailed(FailedEvent failedEvent) {
private MeasurementValidationReport validate(List metadata) {
if (metadata == null || metadata.isEmpty()) {
return new MeasurementValidationReport(0,
- ValidationResult.withFailures(0, List.of("The metadata sheet seems to be empty")));
+ ValidationResult.withFailures(List.of("The metadata sheet seems to be empty")));
}
if (metadata.get(0) instanceof NGSMeasurementMetadata) {
return validateNGS((List) metadata);
@@ -184,20 +198,25 @@ private ParsingResult parseTSV(InputStream inputStream) {
private void onUploadSucceeded(SucceededEvent succeededEvent) {
var fileName = succeededEvent.getFileName();
- ParsingResult parsingResult;
- if (fileName.endsWith(".xlsx")) {
- parsingResult = parseXLSX(uploadBuffer.inputStream(fileName).orElseThrow());
- } else if (fileName.endsWith(".tsv") || fileName.endsWith(".txt")) {
- parsingResult = parseTSV(uploadBuffer.inputStream(fileName).orElseThrow());
- } else {
+ Optional knownFileType = AcceptedFileType.forMimeType(
+ succeededEvent.getMIMEType());
+ if (knownFileType.isEmpty()) {
displayError(succeededEvent.getFileName(),
"Unsupported file type. Please make sure to upload a TSV or XLSX file.");
return;
}
+ var parsingResult = switch (knownFileType.get()) {
+ case EXCEL -> parseXLSX(uploadBuffer.inputStream(fileName).orElseThrow());
+ case TSV -> parseTSV(uploadBuffer.inputStream(fileName).orElseThrow());
+ };
List result;
try {
- result = MetadataConverter.measurementConverter()
- .convert(parsingResult, mode.equals(MODE.ADD));
+ result = switch (mode) {
+ case ADD -> MetadataConverter.measurementConverter()
+ .convertRegister(parsingResult);
+ case EDIT -> MetadataConverter.measurementConverter()
+ .convertEdit(parsingResult);
+ };
} catch (
UnknownMetadataTypeException e) { // we want to display this in the dialog, not via the notification system
displayError(succeededEvent.getFileName(),
@@ -229,7 +248,7 @@ private void displayError(String fileName, String reason) {
fileName, Collections.emptyList());
MeasurementFileItem measurementFileItem = new MeasurementFileItem(
fileName,
- new MeasurementValidationReport(1, ValidationResult.withFailures(1, List.of(
+ new MeasurementValidationReport(1, ValidationResult.withFailures(List.of(
reason))));
addFile(measurementFileItem, metadataUpload);
}
@@ -242,7 +261,7 @@ private void addFile(MeasurementFileItem measurementFileItem,
}
private MeasurementValidationReport validateNGS(List content) {
- var validationResult = ValidationResult.successful(0);
+ var validationResult = ValidationResult.successful();
ConcurrentLinkedDeque concurrentLinkedDeque = new ConcurrentLinkedDeque<>();
List> tasks = new ArrayList<>();
for (NGSMeasurementMetadata metaDatum : content) {
@@ -257,7 +276,7 @@ private MeasurementValidationReport validateNGS(List con
private MeasurementValidationReport validatePxP(List content) {
- var validationResult = ValidationResult.successful(0);
+ var validationResult = ValidationResult.successful();
ConcurrentLinkedDeque concurrentLinkedDeque = new ConcurrentLinkedDeque<>();
List> tasks = new ArrayList<>();
for (ProteomicsMeasurementMetadata metaDatum : content) {
@@ -463,7 +482,7 @@ private Div createInvalidDisplayBox(Collection invalidMeasurements) {
OrderedList invalidMeasurementsList = new OrderedList(
invalidMeasurements.stream().map(ListItem::new).toArray(ListItem[]::new));
invalidMeasurementsList.addClassName("invalid-measurement-list");
- invalidMeasurementsList.setType(OrderedList.NumberingType.NUMBER);
+ invalidMeasurementsList.setType(NumberingType.NUMBER);
validationDetails.add(invalidMeasurementsList);
box.add(header, validationDetails, instruction);
return box;
@@ -579,7 +598,7 @@ private static class UploadProgressDisplay extends Div {
public UploadProgressDisplay(MODE mode) {
- Objects.requireNonNull(mode, "Mode cannot be null");
+ requireNonNull(mode, "Mode cannot be null");
String modeBasedTask = (mode == MODE.ADD ? "register" : "update");
Span title = new Span(
String.format("%s" + " the measurement data", StringUtils.capitalize(modeBasedTask)));
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementNGSValidationExecutor.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementNGSValidationExecutor.java
index 6c030ec11..8f4727d07 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementNGSValidationExecutor.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementNGSValidationExecutor.java
@@ -4,7 +4,7 @@
import java.util.concurrent.CompletableFuture;
import life.qbic.projectmanagement.application.measurement.NGSMeasurementMetadata;
import life.qbic.projectmanagement.application.measurement.validation.MeasurementValidationService;
-import life.qbic.projectmanagement.application.measurement.validation.ValidationResult;
+import life.qbic.projectmanagement.application.ValidationResult;
import life.qbic.projectmanagement.domain.model.project.ProjectId;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementProteomicsValidationExecutor.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementProteomicsValidationExecutor.java
index 2d95b27ff..25b03a604 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementProteomicsValidationExecutor.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementProteomicsValidationExecutor.java
@@ -4,9 +4,8 @@
import java.util.concurrent.CompletableFuture;
import life.qbic.projectmanagement.application.measurement.ProteomicsMeasurementMetadata;
import life.qbic.projectmanagement.application.measurement.validation.MeasurementValidationService;
-import life.qbic.projectmanagement.application.measurement.validation.ValidationResult;
+import life.qbic.projectmanagement.application.ValidationResult;
import life.qbic.projectmanagement.domain.model.project.ProjectId;
-import org.apache.poi.ss.formula.functions.T;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.stereotype.Component;
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementValidationExecutor.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementValidationExecutor.java
index ff17bab52..97ea93249 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementValidationExecutor.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementValidationExecutor.java
@@ -3,7 +3,7 @@
import java.util.concurrent.CompletableFuture;
import life.qbic.projectmanagement.application.measurement.MeasurementMetadata;
import life.qbic.projectmanagement.application.measurement.validation.MeasurementValidationService;
-import life.qbic.projectmanagement.application.measurement.validation.ValidationResult;
+import life.qbic.projectmanagement.application.ValidationResult;
import life.qbic.projectmanagement.domain.model.project.ProjectId;
/**
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/NGSMeasurementContentProvider.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/NGSMeasurementContentProvider.java
deleted file mode 100644
index 6254294d5..000000000
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/download/NGSMeasurementContentProvider.java
+++ /dev/null
@@ -1,312 +0,0 @@
-package life.qbic.datamanager.views.projects.project.measurements.download;
-
-import static life.qbic.datamanager.spreadsheet.XLSXTemplateHelper.createOptionArea;
-import static life.qbic.datamanager.spreadsheet.XLSXTemplateHelper.getOrCreateCell;
-import static life.qbic.datamanager.spreadsheet.XLSXTemplateHelper.getOrCreateRow;
-import static life.qbic.datamanager.spreadsheet.XLSXTemplateHelper.hideSheet;
-import static life.qbic.datamanager.spreadsheet.XLSXTemplateHelper.lockSheet;
-import static life.qbic.logging.service.LoggerFactory.logger;
-
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.LinkedList;
-import java.util.List;
-import life.qbic.application.commons.ApplicationException;
-import life.qbic.application.commons.ApplicationException.ErrorCode;
-import life.qbic.datamanager.spreadsheet.XLSXTemplateHelper;
-import life.qbic.datamanager.views.general.download.DownloadContentProvider;
-import life.qbic.datamanager.views.projects.project.measurements.NGSMeasurementEntry;
-import life.qbic.logging.api.Logger;
-import life.qbic.projectmanagement.application.measurement.NGSMeasurementMetadata;
-import life.qbic.projectmanagement.domain.model.measurement.NGSMeasurement;
-import org.apache.poi.ss.usermodel.Cell;
-import org.apache.poi.ss.usermodel.CellStyle;
-import org.apache.poi.ss.usermodel.FillPatternType;
-import org.apache.poi.ss.usermodel.Font;
-import org.apache.poi.ss.usermodel.Name;
-import org.apache.poi.ss.usermodel.Row;
-import org.apache.poi.ss.usermodel.Sheet;
-import org.apache.poi.ss.usermodel.Workbook;
-import org.apache.poi.xssf.usermodel.DefaultIndexedColorMap;
-import org.apache.poi.xssf.usermodel.XSSFColor;
-import org.apache.poi.xssf.usermodel.XSSFFont;
-import org.apache.poi.xssf.usermodel.XSSFWorkbook;
-
-/**
- * NGS Measurement Content Provider
- *
- * Implementation of the {@link DownloadContentProvider} providing the content and file name for any
- * files created from {@link NGSMeasurement} and {@link NGSMeasurementMetadata}
- *
- */
-public class NGSMeasurementContentProvider implements DownloadContentProvider {
-
- private static final String FILE_NAME_SUFFIX = "ngs_measurements.xlsx";
- private static final Logger log = logger(NGSMeasurementContentProvider.class);
- private static final byte[] DARK_GREY = {119, 119, 119};
- private static final byte[] LIGHT_GREY = {(byte) 220, (byte) 220, (byte) 220};
- private static CellStyle readOnlyCellStyle;
- private static CellStyle readOnlyHeaderStyle;
- private static CellStyle boldStyle;
- private final List measurements = new LinkedList<>();
- private static final String DEFAULT_FILE_NAME_PREFIX = "QBiC";
- private String fileNamePrefix = DEFAULT_FILE_NAME_PREFIX;
- private static final int DEFAULT_GENERATED_ROW_COUNT = 200;
-
- private enum SequencingReadType {
- SINGLE_END("single-end"),
- PAIRED_END("paired-end");
- private final String presentationString;
-
- SequencingReadType(String presentationString) {
- this.presentationString = presentationString;
- }
-
- static List getOptions() {
- return Arrays.stream(values()).map(it -> it.presentationString).toList();
- }
- }
-
- private static void setAutoWidth(Sheet sheet) {
- for (int col = 0; col <= NGSMeasurementColumns.values().length; col++) {
- sheet.autoSizeColumn(col);
- }
- }
-
- private static void formatHeader(Row header) {
- for (NGSMeasurementColumns value : NGSMeasurementColumns.values()) {
- var cell = header.createCell(value.columnIndex());
- cell.setCellValue(value.headerName());
- setHeaderStyle(cell, value.readOnly());
- }
- }
-
- private static void setHeaderStyle(Cell cell, boolean isReadOnly) {
- if (isReadOnly) {
- cell.setCellStyle(readOnlyHeaderStyle);
- } else {
- cell.setCellStyle(boldStyle);
- }
- }
-
- private static void setCellStyle(Cell cell, boolean isReadOnly) {
- if (isReadOnly) {
- cell.setCellStyle(readOnlyCellStyle);
- }
- }
-
- private static void writeMeasurementIntoRow(NGSMeasurementEntry ngsMeasurementEntry,
- Row entryRow) {
-
- 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 measurements, String fileNamePrefix) {
- this.measurements.clear();
- this.measurements.addAll(measurements);
- this.fileNamePrefix = fileNamePrefix.trim();
- }
-
- private void defineBoldStyle(Workbook workbook) {
- boldStyle = workbook.createCellStyle();
- Font fontBold = workbook.createFont();
- fontBold.setBold(true);
- boldStyle.setFont(fontBold);
- }
-
- private void defineReadOnlyCellStyle(Workbook workbook) {
- readOnlyCellStyle = workbook.createCellStyle();
- readOnlyCellStyle.setFillForegroundColor(
- new XSSFColor(LIGHT_GREY, new DefaultIndexedColorMap()));
- readOnlyCellStyle.setFillPattern(FillPatternType.SOLID_FOREGROUND);
- XSSFFont font = (XSSFFont) workbook.createFont();
- font.setColor(new XSSFColor(DARK_GREY, new DefaultIndexedColorMap()));
- readOnlyCellStyle.setFont(font);
- }
-
- private void defineReadOnlyHeaderStyle(Workbook workbook) {
- readOnlyHeaderStyle = workbook.createCellStyle();
- readOnlyHeaderStyle.setFillForegroundColor(
- new XSSFColor(LIGHT_GREY, new DefaultIndexedColorMap()));
- readOnlyHeaderStyle.setFillPattern(FillPatternType.SOLID_FOREGROUND);
- XSSFFont fontHeader = (XSSFFont) workbook.createFont();
- fontHeader.setBold(true);
- fontHeader.setColor(new XSSFColor(DARK_GREY, new DefaultIndexedColorMap()));
- readOnlyHeaderStyle.setFont(fontHeader);
- }
-
-
- @Override
- public byte[] getContent() {
- if (measurements.isEmpty()) {
- return new byte[0];
- }
-
- ByteArrayOutputStream byteArrayOutputStream;
-
- try (Workbook workbook = new XSSFWorkbook()) {
- defineReadOnlyHeaderStyle(workbook);
- defineReadOnlyCellStyle(workbook);
- defineBoldStyle(workbook);
-
- Sheet sheet = workbook.createSheet("NGS Measurement Metadata");
-
- Row header = getOrCreateRow(sheet, 0);
- for (NGSMeasurementColumns value : NGSMeasurementColumns.values()) {
- var cell = getOrCreateCell(header, value.columnIndex());
- cell.setCellValue(value.headerName());
- setHeaderStyle(cell, value.readOnly());
- }
-
- var startIndex = 1; // start in row number 2 with index 1 as the header row has number 1 index 0
- int rowIndex = startIndex;
- for (NGSMeasurementEntry measurement : measurements) {
- Row row = getOrCreateRow(sheet, rowIndex);
- writeMeasurementIntoRow(measurement, row);
- rowIndex++;
- }
-
- var generatedRowCount = rowIndex - startIndex;
- assert generatedRowCount == measurements.size() : "all measurements have a corresponding row";
-
- // make sure to create the visible sheet first
- Sheet hiddenSheet = workbook.createSheet("hidden");
- Name sequencingReadTypeArea = createOptionArea(hiddenSheet,
- "Sequencing read type", SequencingReadType.getOptions());
-
- XLSXTemplateHelper.addDataValidation(sheet,
- NGSMeasurementColumns.SEQUENCING_READ_TYPE.columnIndex(),
- startIndex,
- NGSMeasurementColumns.SEQUENCING_READ_TYPE.columnIndex(),
- DEFAULT_GENERATED_ROW_COUNT - 1,
- sequencingReadTypeArea);
-
- setAutoWidth(sheet);
- workbook.setActiveSheet(0);
-
- lockSheet(hiddenSheet);
- hideSheet(workbook, hiddenSheet);
-
- byteArrayOutputStream = new ByteArrayOutputStream();
- workbook.write(byteArrayOutputStream);
- } catch (IOException e) {
- log.error(e.getMessage(), e);
- throw new ApplicationException(ErrorCode.GENERAL, null);
- }
-
- return byteArrayOutputStream.toByteArray();
- }
-
- @Override
- public String getFileName() {
- return String.join("_", fileNamePrefix, FILE_NAME_SUFFIX);
- }
-
- /**
- * NGS Measurement Columns
- *
- *
Enumeration of the columns shown in the file used for NGS measurement registration and 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
- *
- */
- enum NGSMeasurementColumns {
-
- 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),
- ;
-
- private final String headerName;
- private final int columnIndex;
- private final boolean readOnly;
-
- static int maxColumnIndex() {
- return Arrays.stream(values())
- .mapToInt(NGSMeasurementColumns::columnIndex)
- .max().orElse(0);
- }
-
- /**
- * @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 = headerName;
- this.columnIndex = columnIndex;
- this.readOnly = readOnly;
- }
-
- public String headerName() {
- return headerName;
- }
-
- public int columnIndex() {
- return columnIndex;
- }
-
- public boolean readOnly() {
- return readOnly;
- }
-
- }
-}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/ontology/OntologyLookupComponent.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/ontology/OntologyLookupComponent.java
index aa9b3096a..327a50b2e 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/ontology/OntologyLookupComponent.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/ontology/OntologyLookupComponent.java
@@ -194,11 +194,9 @@ private Span createHeader(String label, String curieText) {
ui.getPushConfiguration().setPushMode(PushMode.MANUAL);
copyToClipBoardComponent.addSwitchToSuccessfulCopyIconListener(event -> ui.access(() -> {
addClassName("success-background-hue");
- ui.push();
}));
copyToClipBoardComponent.addSwitchToCopyIconListener(event -> ui.access(() -> {
removeClassName("success-background-hue");
- ui.push();
}));
header.addClassName("header");
return header;
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/rawdata/RawDataMain.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/rawdata/RawDataMain.java
index 64ca228ce..4c5a79dfc 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/rawdata/RawDataMain.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/rawdata/RawDataMain.java
@@ -19,12 +19,12 @@
import java.util.List;
import java.util.Objects;
import life.qbic.application.commons.ApplicationException;
+import life.qbic.datamanager.download.DownloadProvider;
import life.qbic.datamanager.views.AppRoutes.Projects;
import life.qbic.datamanager.views.Context;
import life.qbic.datamanager.views.account.PersonalAccessTokenMain;
import life.qbic.datamanager.views.general.Disclaimer;
import life.qbic.datamanager.views.general.Main;
-import life.qbic.datamanager.views.general.download.DownloadProvider;
import life.qbic.datamanager.views.notifications.ErrorMessage;
import life.qbic.datamanager.views.notifications.StyledNotification;
import life.qbic.datamanager.views.projects.project.experiments.ExperimentMainLayout;
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/rawdata/RawDataURLContentProvider.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/rawdata/RawDataURLContentProvider.java
index 53dda15ba..0a44dddd3 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/rawdata/RawDataURLContentProvider.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/rawdata/RawDataURLContentProvider.java
@@ -1,10 +1,8 @@
package life.qbic.datamanager.views.projects.project.rawdata;
import java.nio.charset.StandardCharsets;
-import java.time.LocalDateTime;
-import java.time.format.DateTimeFormatter;
import java.util.List;
-import life.qbic.datamanager.views.general.download.DownloadContentProvider;
+import life.qbic.datamanager.download.DownloadContentProvider;
import life.qbic.datamanager.views.general.download.TextFileBuilder;
import life.qbic.datamanager.views.projects.project.rawdata.RawDataMain.RawDataURL;
import life.qbic.projectmanagement.domain.model.experiment.Experiment;
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/BatchDetailsComponent.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/BatchDetailsComponent.java
index 4ab44471c..31201eb70 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/BatchDetailsComponent.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/BatchDetailsComponent.java
@@ -78,7 +78,8 @@ public BatchDetailsComponent(@Autowired BatchInformationService batchInformation
private void createTitleAndControls() {
title.addClassName("title");
titleAndControls.addClassName("title-and-controls");
- Button registerButton = new Button("Register");
+ Button registerButton = new Button("Register sample batch");
+ registerButton.setClassName("primary");
registerButton.addClickListener(event -> fireEvent(new CreateBatchEvent(this,
event.isFromClient())));
titleAndControls.add(title, registerButton);
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java
index 3be5cd306..891e2aadf 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java
@@ -138,10 +138,10 @@ private static Grid createSampleGrid() {
.setTooltipGenerator(preview -> preview.analyte().formatted())
.setAutoWidth(true)
.setResizable(true);
- sampleGrid.addColumn(SamplePreview::analysisMethod)
+ sampleGrid.addColumn(preview -> preview.analysisMethod().label())
.setHeader("Analysis to Perform")
.setSortProperty("analysisMethod")
- .setTooltipGenerator(SamplePreview::analysisMethod)
+ .setTooltipGenerator(samplePreview -> samplePreview.analysisMethod().label())
.setAutoWidth(true)
.setResizable(true);
sampleGrid.addColumn(SamplePreview::comment)
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleInformationMain.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleInformationMain.java
index 2c1a92d76..ffa78404a 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleInformationMain.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleInformationMain.java
@@ -3,6 +3,7 @@
import static java.util.Objects.requireNonNull;
import com.vaadin.flow.component.ComponentEvent;
+import com.vaadin.flow.component.UI;
import com.vaadin.flow.component.button.Button;
import com.vaadin.flow.component.html.Div;
import com.vaadin.flow.component.html.Span;
@@ -16,34 +17,33 @@
import com.vaadin.flow.spring.annotation.UIScope;
import jakarta.annotation.security.PermitAll;
import java.io.Serial;
-import java.util.ArrayList;
import java.util.Collection;
import java.util.Comparator;
import java.util.List;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.TimeUnit;
import life.qbic.application.commons.ApplicationException;
+import life.qbic.datamanager.download.DownloadProvider;
+import life.qbic.datamanager.templates.TemplateService;
import life.qbic.datamanager.views.AppRoutes.Projects;
import life.qbic.datamanager.views.Context;
import life.qbic.datamanager.views.general.Disclaimer;
import life.qbic.datamanager.views.general.DisclaimerConfirmedEvent;
import life.qbic.datamanager.views.general.Main;
-import life.qbic.datamanager.views.general.download.DownloadProvider;
import life.qbic.datamanager.views.notifications.CancelConfirmationDialogFactory;
import life.qbic.datamanager.views.notifications.MessageSourceNotificationFactory;
-import life.qbic.datamanager.views.notifications.StyledNotification;
-import life.qbic.datamanager.views.notifications.SuccessMessage;
import life.qbic.datamanager.views.projects.project.experiments.ExperimentMainLayout;
import life.qbic.datamanager.views.projects.project.samples.BatchDetailsComponent.DeleteBatchEvent;
import life.qbic.datamanager.views.projects.project.samples.BatchDetailsComponent.EditBatchEvent;
import life.qbic.datamanager.views.projects.project.samples.download.SampleInformationXLSXProvider;
-import life.qbic.datamanager.views.projects.project.samples.registration.batch.BatchRegistrationDialog;
-import life.qbic.datamanager.views.projects.project.samples.registration.batch.BatchRegistrationDialog.ConfirmEvent;
-import life.qbic.datamanager.views.projects.project.samples.registration.batch.EditBatchDialog;
-import life.qbic.datamanager.views.projects.project.samples.registration.batch.SampleBatchInformationSpreadsheet;
+import life.qbic.datamanager.views.projects.project.samples.registration.batch.EditSampleBatchDialog;
+import life.qbic.datamanager.views.projects.project.samples.registration.batch.RegisterSampleBatchDialog;
import life.qbic.datamanager.views.projects.project.samples.registration.batch.SampleBatchInformationSpreadsheet.SampleInfo;
import life.qbic.logging.api.Logger;
import life.qbic.logging.service.LoggerFactory;
import life.qbic.projectmanagement.application.DeletionService;
import life.qbic.projectmanagement.application.ProjectInformationService;
+import life.qbic.projectmanagement.application.ProjectOverview;
import life.qbic.projectmanagement.application.batch.BatchRegistrationService;
import life.qbic.projectmanagement.application.batch.SampleUpdateRequest;
import life.qbic.projectmanagement.application.batch.SampleUpdateRequest.SampleInformation;
@@ -51,14 +51,14 @@
import life.qbic.projectmanagement.application.sample.SampleInformationService;
import life.qbic.projectmanagement.application.sample.SamplePreview;
import life.qbic.projectmanagement.application.sample.SampleRegistrationService;
+import life.qbic.projectmanagement.application.sample.SampleRegistrationServiceV2;
+import life.qbic.projectmanagement.application.sample.SampleValidationService;
import life.qbic.projectmanagement.domain.model.batch.BatchId;
import life.qbic.projectmanagement.domain.model.experiment.Experiment;
import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
-import life.qbic.projectmanagement.domain.model.experiment.ExperimentalGroup;
import life.qbic.projectmanagement.domain.model.project.Project;
import life.qbic.projectmanagement.domain.model.project.ProjectId;
import life.qbic.projectmanagement.domain.model.sample.Sample;
-import life.qbic.projectmanagement.domain.model.sample.SampleId;
import life.qbic.projectmanagement.domain.model.sample.SampleOrigin;
import life.qbic.projectmanagement.domain.model.sample.SampleRegistrationRequest;
import org.springframework.beans.factory.annotation.Autowired;
@@ -83,8 +83,6 @@ public class SampleInformationMain extends Main implements BeforeEnterObserver {
private static final long serialVersionUID = 3778218989387044758L;
private static final Logger log = LoggerFactory.logger(SampleInformationMain.class);
private final transient ExperimentInformationService experimentInformationService;
- private final transient BatchRegistrationService batchRegistrationService;
- private final transient SampleRegistrationService sampleRegistrationService;
private final transient SampleInformationService sampleInformationService;
private final transient DeletionService deletionService;
private final transient SampleDetailsComponent sampleDetailsComponent;
@@ -100,6 +98,9 @@ public class SampleInformationMain extends Main implements BeforeEnterObserver {
private final ProjectInformationService projectInformationService;
private final CancelConfirmationDialogFactory cancelConfirmationDialogFactory;
private final MessageSourceNotificationFactory messageSourceNotificationFactory;
+ private final SampleValidationService sampleValidationService;
+ private final TemplateService templateService;
+ private final SampleRegistrationServiceV2 sampleRegistrationServiceV2;
private transient Context context;
public SampleInformationMain(@Autowired ExperimentInformationService experimentInformationService,
@@ -111,13 +112,11 @@ public SampleInformationMain(@Autowired ExperimentInformationService experimentI
@Autowired BatchDetailsComponent batchDetailsComponent,
ProjectInformationService projectInformationService,
CancelConfirmationDialogFactory cancelConfirmationDialogFactory,
- MessageSourceNotificationFactory messageSourceNotificationFactory) {
+ MessageSourceNotificationFactory messageSourceNotificationFactory,
+ SampleValidationService sampleValidationService,
+ TemplateService templateService, SampleRegistrationServiceV2 sampleRegistrationServiceV2) {
this.experimentInformationService = requireNonNull(experimentInformationService,
"ExperimentInformationService cannot be null");
- this.batchRegistrationService = requireNonNull(batchRegistrationService,
- "BatchRegistrationService cannot be null");
- this.sampleRegistrationService = requireNonNull(sampleRegistrationService,
- "SampleRegistrationService cannot be null");
this.sampleInformationService = requireNonNull(sampleInformationService,
"SampleInformationService cannot be null");
this.deletionService = requireNonNull(deletionService,
@@ -131,6 +130,8 @@ public SampleInformationMain(@Autowired ExperimentInformationService experimentI
"cancelConfirmationDialogFactory must not be null");
this.messageSourceNotificationFactory = requireNonNull(messageSourceNotificationFactory,
"messageSourceNotificationFactory must not be null");
+ this.sampleValidationService = sampleValidationService;
+ this.templateService = templateService;
noGroupsDefinedDisclaimer = createNoGroupsDefinedDisclaimer();
noGroupsDefinedDisclaimer.setVisible(false);
@@ -157,6 +158,7 @@ public SampleInformationMain(@Autowired ExperimentInformationService experimentI
System.identityHashCode(batchDetailsComponent),
sampleDetailsComponent.getClass().getSimpleName(),
System.identityHashCode(sampleDetailsComponent)));
+ this.sampleRegistrationServiceV2 = sampleRegistrationServiceV2;
}
private static boolean noExperimentGroupsInExperiment(Experiment experiment) {
@@ -181,7 +183,7 @@ private void initSearchFieldAndButtonBar() {
searchField.setValueChangeMode(ValueChangeMode.LAZY);
searchField.addValueChangeListener(
event -> sampleDetailsComponent.onSearchFieldValueChanged((event.getValue())));
- Button metadataDownloadButton = new Button("Download Sample Metadata",
+ Button metadataDownloadButton = new Button("Download sample metadata",
event -> downloadSampleMetadata());
Span buttonBar = new Span(metadataDownloadButton);
buttonBar.addClassName("button-bar");
@@ -207,48 +209,71 @@ private void downloadSampleMetadata() {
metadataDownload.trigger();
}
+ private static class HandledException extends RuntimeException {
+
+ public HandledException(Throwable cause) {
+ super(cause);
+ }
+ }
+
private void onRegisterBatchClicked() {
- Experiment experiment = context.experimentId()
- .flatMap(
- id -> experimentInformationService.find(context.projectId().orElseThrow().value(), id))
+ ProjectId projectId = context.projectId().orElseThrow();
+ ExperimentId experimentId = context.experimentId().orElseThrow();
+
+ Experiment experiment = experimentInformationService.find(projectId.value(), experimentId)
.orElseThrow();
+
if (experiment.getExperimentalGroups().isEmpty()) {
return;
}
- BatchRegistrationDialog dialog = new BatchRegistrationDialog(
- experiment.getName(), new ArrayList<>(experiment.getSpecies()),
- new ArrayList<>(experiment.getSpecimens()), new ArrayList<>(experiment.getAnalytes()),
- experiment.getExperimentalGroups());
- dialog.addCancelListener(cancelEvent -> showCancelConfirmationDialog(dialog));
- dialog.setEscAction(() -> showCancelConfirmationDialog(dialog));
- dialog.addConfirmListener(this::registerBatch);
- dialog.open();
+ ProjectOverview projectOverview = projectInformationService.findOverview(projectId)
+ .orElseThrow();
+ RegisterSampleBatchDialog registerSampleBatchDialog = new RegisterSampleBatchDialog(
+ sampleValidationService, templateService, experimentId.value(),
+ projectId.value(), projectOverview.projectCode());
+ registerSampleBatchDialog.addConfirmListener(event -> {
+ event.getSource().taskInProgress("Register the sample batch metadata",
+ "It may take some time for the registration task to complete.");
+ UI ui = event.getSource().getUI().orElseThrow();
+ CompletableFuture registrationTask = sampleRegistrationServiceV2.registerSamples(
+ event.validatedSampleMetadata(),
+ projectId, event.batchName(), false)
+ .orTimeout(5, TimeUnit.MINUTES);
+ try {
+ registrationTask
+ .exceptionally(e -> {
+ ui.access(() -> {
+ //this needs to come before all the success events
+ event.getSource().taskFailed("", ""); //todo label and description s
+ displayRegistrationFailure();
+ });
+ throw new HandledException(e);
+ })
+ .thenRun(() -> ui.access(this::setBatchAndSampleInformation))
+ .thenRun(() -> ui.access(() -> event.getSource().taskSucceeded("", "")))
+ .thenRun(() -> displayRegistrationSuccess(event.batchName()))
+ .exceptionally(e -> {
+ //we need to make sure we do not swallow exceptions but still stay in the exceptional state.
+ throw new HandledException(e); //we need the future to complete exceptionally
+ });
+ } catch (HandledException e) {
+ // we only log the exception as the user was presented with the error already and nothing we can do here.
+ log.error(e.getMessage(), e);
+ }
+ });
+ registerSampleBatchDialog.addCancelListener(
+ event -> showCancelConfirmationDialog(event.getSource()));
+ registerSampleBatchDialog.setEscAction(
+ () -> showCancelConfirmationDialog(registerSampleBatchDialog));
+ registerSampleBatchDialog.open();
}
- private void showCancelConfirmationDialog(BatchRegistrationDialog dialog) {
+ private void showCancelConfirmationDialog(RegisterSampleBatchDialog dialog) {
cancelConfirmationDialogFactory.cancelConfirmationDialog(it -> dialog.close(),
"sample-batch.register", getLocale())
.open();
}
- private void registerBatch(ConfirmEvent confirmEvent) {
- String batchLabel = confirmEvent.getData().batchName();
- List samples = confirmEvent.getData().samples();
- List sampleRegistrationRequests = batchRegistrationService.registerBatch(
- batchLabel, false,
- context.projectId().orElseThrow())
- .map(batchId -> generateSampleRequestsFromSampleInfo(batchId, samples))
- .onError(responseCode -> displayRegistrationFailure())
- .valueOrElseThrow(() ->
- new ApplicationException("Could not create sample registration requests"));
- sampleRegistrationService.registerSamples(sampleRegistrationRequests,
- context.projectId().orElseThrow())
- .onError(responseCode -> displayRegistrationFailure())
- .onValue(ignored -> fireEvent(new BatchRegisteredEvent(this, false)))
- .onValue(ignored -> confirmEvent.getSource().close())
- .onValue(batchId -> displayRegistrationSuccess(batchLabel))
- .onValue(ignored -> setBatchAndSampleInformation());
- }
private List generateSampleRequestsFromSampleInfo(BatchId batchId,
List sampleInfos) {
@@ -313,10 +338,9 @@ private void routeToExperimentalGroupCreation(ComponentEvent componentEvent,
}
}
- private void displayUpdateSuccess() {
- SuccessMessage successMessage = new SuccessMessage("Batch update succeeded.", "");
- StyledNotification notification = new StyledNotification(successMessage);
- notification.open();
+ private void displayUpdateSuccess(String batchName) {
+ messageSourceNotificationFactory.toast("sample-batch.", new String[]{batchName}, getLocale())
+ .open();
}
private void displayDeletionSuccess(String batchLabel) {
@@ -333,6 +357,13 @@ private void displayRegistrationSuccess(String batchLabel) {
}
+ private void displayUpdateFailure() {
+ messageSourceNotificationFactory.dialog("sample-batch.update.failure",
+ MessageSourceNotificationFactory.EMPTY_PARAMETERS,
+ getLocale())
+ .open();
+ }
+
private void displayRegistrationFailure() {
messageSourceNotificationFactory.dialog(
"sample-batch.register.failure",
@@ -341,75 +372,72 @@ MessageSourceNotificationFactory.EMPTY_PARAMETERS, getLocale())
}
private void onEditBatchClicked(EditBatchEvent editBatchEvent) {
- Experiment experiment = context.experimentId()
- .flatMap(
- id -> experimentInformationService.find(context.projectId().orElseThrow().value(), id))
+ ProjectId projectId = context.projectId().orElseThrow();
+ ExperimentId experimentId = context.experimentId().orElseThrow();
+
+ Experiment experiment = experimentInformationService.find(projectId.value(), experimentId)
.orElseThrow();
- List samples = sampleInformationService.retrieveSamplesForBatch(
- editBatchEvent.batchPreview().batchId()).stream().toList();
- var experimentalGroups = experimentInformationService.experimentalGroupsFor(
- context.projectId().orElseThrow().value(),
- context.experimentId().orElseThrow());
- // need to create mutable list to order samples
- List sampleInfos = new ArrayList<>(
- samples.stream()
- .map(sample -> convertSampleToSampleInfo(sample, experimentalGroups)).toList());
- sampleInfos.sort(Comparator.comparing(o -> o.getSampleCode().code()));
- EditBatchDialog editBatchDialog = new EditBatchDialog(experiment.getName(),
- experiment.getSpecies().stream().toList(), experiment.getSpecimens().stream().toList(),
- experiment.getAnalytes().stream().toList(), experiment.getExperimentalGroups(),
- editBatchEvent.batchPreview()
- .batchId(), editBatchEvent.batchPreview().batchLabel(), sampleInfos,
- this::isSampleRemovable);
- editBatchDialog.addCancelListener(
- cancelEvent -> showCancelConfirmationDialog(editBatchDialog));
- editBatchDialog.setEscAction(escEvent -> showCancelConfirmationDialog(editBatchDialog));
- editBatchDialog.addConfirmListener(this::editBatch);
- editBatchDialog.open();
+
+ if (experiment.getExperimentalGroups().isEmpty()) {
+ return;
+ }
+ ProjectOverview projectOverview = projectInformationService.findOverview(projectId)
+ .orElseThrow();
+ BatchId batchId = editBatchEvent.batchPreview().batchId();
+ String batchLabel = editBatchEvent.batchPreview().batchLabel();
+ var editSampleBatchDialog = new EditSampleBatchDialog(
+ sampleValidationService, templateService, batchId, batchLabel, experimentId.value(),
+ projectId.value(), projectOverview.projectCode());
+ editSampleBatchDialog.addConfirmListener(event -> {
+ event.getSource().taskInProgress("Edit the sample batch metadata",
+ "It may take some time for the editing to complete.");
+ UI ui = event.getSource().getUI().orElseThrow();
+ CompletableFuture editTask = sampleRegistrationServiceV2.updateSamples(
+ event.validatedSampleMetadata(),
+ projectId,
+ batchId,
+ event.batchName(),
+ false)
+ .orTimeout(5, TimeUnit.MINUTES);
+ try {
+ editTask
+ .exceptionally(e -> {
+ ui.access(() -> {
+ //this needs to come before all the success events
+ event.getSource().taskFailed("", ""); //todo label and description s
+ displayUpdateFailure();
+ });
+ throw new HandledException(e);
+ })
+ .thenRun(() -> ui.access(this::setBatchAndSampleInformation))
+ .thenRun(() -> ui.access(
+ () -> event.getSource().taskSucceeded("", ""))) //todo label and description
+ .thenRun(() -> displayUpdateSuccess(event.batchName()))
+ .exceptionally(e -> {
+ //we need to make sure we do not swallow exceptions but still stay in the exceptional state.
+ throw new HandledException(e); //we need the future to complete exceptionally
+ });
+ } catch (HandledException e) {
+ // we only log the exception as the user was presented with the error already and nothing we can do here.
+ log.error(e.getMessage(), e);
+ }
+ });
+ editSampleBatchDialog.addCancelListener(
+ event -> showCancelConfirmationDialog(event.getSource()));
+ editSampleBatchDialog.setEscAction(
+ () -> showCancelConfirmationDialog(editSampleBatchDialog));
+ editSampleBatchDialog.open();
}
- private void showCancelConfirmationDialog(EditBatchDialog editBatchDialog) {
+ private void showCancelConfirmationDialog(EditSampleBatchDialog editBatchDialog) {
cancelConfirmationDialogFactory
.cancelConfirmationDialog(
- it2 -> editBatchDialog.close(),
+ it -> editBatchDialog.close(),
"sample-batch.edit",
getLocale())
.open();
}
- private boolean isSampleRemovable(SampleId sampleId) {
- return deletionService.isSampleRemovable(sampleId);
- }
-
- private SampleBatchInformationSpreadsheet.SampleInfo convertSampleToSampleInfo(Sample sample,
- Collection experimentalGroups) {
- ExperimentalGroup experimentalGroup = experimentalGroups.stream()
- .filter(expGrp -> expGrp.id() == sample.experimentalGroupId())
- .findFirst().orElseThrow();
- /*We currently allow replicates independent of experimental groups which is why we have to parse all replicates */
- return SampleBatchInformationSpreadsheet.SampleInfo.create(sample.sampleId(),
- sample.sampleCode(), sample.analysisMethod(),
- sample.label(), sample.biologicalReplicate(), experimentalGroup, sample.sampleOrigin()
- .getSpecies(), sample.sampleOrigin().getSpecimen(), sample.sampleOrigin().getAnalyte(),
- sample.comment().orElse(""));
- }
-
- private void editBatch(EditBatchDialog.ConfirmEvent confirmEvent) {
- boolean isPilot = false;
- Collection createdSamples = generateSampleRequestsFromSampleInfo(
- confirmEvent.getData().batchId(), confirmEvent.getData().addedSamples());
- Collection editedSamples = confirmEvent.getData().changedSamples().stream()
- .map(this::generateSampleUpdateRequestFromSampleInfo).toList();
- Collection deletedSamples = confirmEvent.getData().removedSamples().stream()
- .map(SampleInfo::getSampleId).toList();
- var result = batchRegistrationService.editBatch(confirmEvent.getData().batchId(),
- confirmEvent.getData().batchName(), isPilot, createdSamples, editedSamples,
- deletedSamples, context.projectId().orElseThrow());
- result.onValue(ignored -> confirmEvent.getSource().close());
- result.onValue(batchId -> displayUpdateSuccess());
- result.onValue(ignored -> setBatchAndSampleInformation());
- }
-
private void deleteBatch(DeleteBatchEvent deleteBatchEvent) {
deletionService.deleteBatch(context.projectId().orElseThrow(),
deleteBatchEvent.batchId());
@@ -510,19 +538,4 @@ private void reloadBatchInformation() {
private void reloadSampleInformation() {
sampleDetailsComponent.setContext(context);
}
-
- public static class BatchRegisteredEvent extends ComponentEvent {
-
- /**
- * Creates a new event using the given source and indicator whether the event originated from
- * the client side or the server side.
- *
- * @param source the source component
- * @param fromClient true if the event originated from the client
- * side, false otherwise
- */
- public BatchRegisteredEvent(SampleInformationMain source, boolean fromClient) {
- super(source, fromClient);
- }
- }
}
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java
index 10ca48ced..e04933bec 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleMetadataContentProvider.java
@@ -5,7 +5,7 @@
import java.util.Comparator;
import java.util.List;
import java.util.Optional;
-import life.qbic.datamanager.views.general.download.DownloadContentProvider;
+import life.qbic.datamanager.download.DownloadContentProvider;
import life.qbic.datamanager.views.general.download.TSVBuilder;
import life.qbic.projectmanagement.application.sample.SamplePreview;
import life.qbic.projectmanagement.domain.model.experiment.Condition;
@@ -37,7 +37,8 @@ public byte[] getContent() {
tsvBuilder.addColumn("Species", sample -> sample.species().getLabel());
tsvBuilder.addColumn("Specimen", sample -> sample.specimen().getLabel());
tsvBuilder.addColumn("Analyte", sample -> sample.analyte().getLabel());
- tsvBuilder.addColumn("Analysis to Perform", SamplePreview::analysisMethod);
+ tsvBuilder.addColumn("Analysis to Perform",
+ samplePreview -> samplePreview.analysisMethod().abbreviation());
tsvBuilder.addColumn("Comment", SamplePreview::comment);
SamplePreview firstSample = samples.stream().findFirst().get();
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java
index f65f46d74..76235be51 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/download/SampleInformationXLSXProvider.java
@@ -14,7 +14,7 @@
import java.util.Set;
import life.qbic.application.commons.ApplicationException;
import life.qbic.application.commons.ApplicationException.ErrorCode;
-import life.qbic.datamanager.views.general.download.DownloadContentProvider;
+import life.qbic.datamanager.download.DownloadContentProvider;
import life.qbic.logging.api.Logger;
import life.qbic.projectmanagement.application.sample.SamplePreview;
import life.qbic.projectmanagement.domain.model.experiment.VariableLevel;
@@ -137,7 +137,7 @@ private void createSampleInfoEntry(SamplePreview sample, Row sampleRow,
analyteCol.setCellValue(sample.analyte().getLabel());
var analysisCol = sampleRow.createCell(SamplePreviewColumn.ANALYSIS.column());
- analysisCol.setCellValue(sample.analysisMethod());
+ analysisCol.setCellValue(sample.analysisMethod().abbreviation());
var commentCol = sampleRow.createCell(SamplePreviewColumn.COMMENT.column());
commentCol.setCellValue(sample.comment());
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/BatchRegistrationDialog.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/BatchRegistrationDialog.java
index 126fe71c1..c032b76d9 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/BatchRegistrationDialog.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/BatchRegistrationDialog.java
@@ -19,7 +19,9 @@
/**
* A dialog used for sample batch registration.
+ * @deprecated this is replaced by {@link RegisterSampleBatchDialog}
*/
+@Deprecated(forRemoval = true, since = "1.4.0")
public class BatchRegistrationDialog extends DialogWindow {
private final TextField batchNameField;
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/EditBatchDialog.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/EditBatchDialog.java
index a21f037c0..e7cc3308a 100644
--- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/EditBatchDialog.java
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/EditBatchDialog.java
@@ -25,7 +25,9 @@
/**
* A dialog used for editing sample and batch information within an experiment
+ * @Deprecated replaced by {@link EditSampleBatchDialog}
*/
+@Deprecated(forRemoval = true, since = "1.4.0")
public class EditBatchDialog extends DialogWindow {
private final SampleBatchInformationSpreadsheet spreadsheet;
diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/EditSampleBatchDialog.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/EditSampleBatchDialog.java
new file mode 100644
index 000000000..0bbfaf5d9
--- /dev/null
+++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/EditSampleBatchDialog.java
@@ -0,0 +1,489 @@
+package life.qbic.datamanager.views.projects.project.samples.registration.batch;
+
+
+import com.vaadin.flow.component.ClickEvent;
+import com.vaadin.flow.component.ComponentEvent;
+import com.vaadin.flow.component.ComponentEventListener;
+import com.vaadin.flow.component.UI;
+import com.vaadin.flow.component.button.Button;
+import com.vaadin.flow.component.html.Div;
+import com.vaadin.flow.component.html.Span;
+import com.vaadin.flow.component.icon.Icon;
+import com.vaadin.flow.component.icon.VaadinIcon;
+import com.vaadin.flow.component.progressbar.ProgressBar;
+import com.vaadin.flow.component.textfield.TextField;
+import com.vaadin.flow.shared.Registration;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.TimeUnit;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import life.qbic.datamanager.download.DownloadContentProvider.XLSXDownloadContentProvider;
+import life.qbic.datamanager.download.DownloadProvider;
+import life.qbic.datamanager.parser.ParsingResult;
+import life.qbic.datamanager.parser.sample.SampleInformationExtractor;
+import life.qbic.datamanager.parser.sample.SampleInformationExtractor.SampleInformationForExistingSample;
+import life.qbic.datamanager.parser.xlsx.XLSXParser;
+import life.qbic.datamanager.templates.TemplateService;
+import life.qbic.datamanager.views.general.WizardDialogWindow;
+import life.qbic.datamanager.views.general.upload.UploadWithDisplay;
+import life.qbic.datamanager.views.general.upload.UploadWithDisplay.FileType;
+import life.qbic.datamanager.views.general.upload.UploadWithDisplay.SucceededEvent;
+import life.qbic.datamanager.views.general.upload.UploadWithDisplay.UploadedData;
+import life.qbic.logging.api.Logger;
+import life.qbic.logging.service.LoggerFactory;
+import life.qbic.projectmanagement.application.ValidationResult;
+import life.qbic.projectmanagement.application.ValidationResultWithPayload;
+import life.qbic.projectmanagement.application.sample.SampleMetadata;
+import life.qbic.projectmanagement.application.sample.SampleValidationService;
+import life.qbic.projectmanagement.domain.model.batch.BatchId;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+
+/**
+ * A dialog used for editing sample and batch information.
+ *
+ * @since 1.4.0
+ */
+public class EditSampleBatchDialog extends WizardDialogWindow {
+
+ private static final Logger log = LoggerFactory.logger(EditSampleBatchDialog.class);
+
+ private final List validatedSampleMetadata;
+ private final TextField batchNameField;
+ private final Div initialView;
+ private final Div inProgressView;
+ private final Div failedView;
+ private final Div succeededView;
+ private static final int MAX_FILE_SIZE = 25 * 1024 * 1024;
+
+
+ public EditSampleBatchDialog(SampleValidationService sampleValidationService,
+ TemplateService templateService,
+ BatchId batchId,
+ String batchName,
+ String experimentId,
+ String projectId,
+ String projectCode) {
+
+ setHeaderTitle("Edit Sample Batch");
+ setConfirmButtonLabel("Edit Batch");
+ initialView = new Div();
+ initialView.addClassName("initial-view");
+ inProgressView = new Div();
+ inProgressView.addClassName("in-progress-view");
+ failedView = new Div();
+ failedView.addClassName("failed-view");
+ succeededView = new Div();
+ succeededView.addClassName("succeeded-view");
+
+ addClassName("edit-samples-dialog");
+ batchNameField = new TextField("Batch name");
+ batchNameField.setRequired(true);
+ batchNameField.setValue(batchName);
+ batchNameField.setPlaceholder("Please enter a name for your batch");
+ batchNameField.addClassName("batch-name-field");
+
+ Div downloadMetadataSection = setupDownloadMetadataSection(templateService, batchId,
+ experimentId,
+ projectId, projectCode);
+
+
+
+ setHeaderTitle("Edit Sample Batch");
+ validatedSampleMetadata = new ArrayList<>();
+
+ UploadWithDisplay uploadWithDisplay = new UploadWithDisplay(
+ MAX_FILE_SIZE, new FileType[]{
+ new FileType(".xlsx", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet")
+ });
+ uploadWithDisplay.addFailureListener(uploadFailed -> {
+ /* display of the error is handled by the uploadWithDisplay component. So nothing to do here.*/
+ });
+ uploadWithDisplay.addSuccessListener(
+ uploadSucceeded -> onUploadSucceeded(sampleValidationService, experimentId, projectId,
+ uploadSucceeded)
+ );
+ uploadWithDisplay.addRemovedListener(it -> setValidatedSampleMetadata(List.of()));
+
+ initialView.add(batchNameField, downloadMetadataSection, uploadWithDisplay);
+ initialView.setVisible(true);
+ inProgressView.setVisible(false);
+ failedView.setVisible(false);
+ succeededView.setVisible(false);
+ add(initialView, inProgressView, failedView, succeededView);
+ }
+
+ static class InvalidUploadDisplay extends Div {
+
+ public InvalidUploadDisplay(String fileName, List failureReasons) {
+ addClassName("uploaded-item");
+ var fileIcon = VaadinIcon.FILE.create();
+ fileIcon.addClassName("file-icon");
+ Span fileNameLabel = new Span(fileIcon, new Span(fileName));
+ fileNameLabel.addClassName("file-name");
+ Div validationBox = new Div();
+ validationBox.addClassName("validation-display-box");
+ var box = new Div();
+ var failuresTitle = new Span("Invalid sample metadata");
+ var errorIcon = VaadinIcon.CLOSE_CIRCLE.create();
+ errorIcon.addClassName("error");
+ var header = new Span(errorIcon, failuresTitle);
+ header.addClassName("header");
+ var instruction = new Span(
+ "Please correct the entries in the uploaded file and re-upload the file.");
+ instruction.addClassName("secondary");
+ Div validationDetails = new Div();
+ Map frequencyMap = failureReasons.stream()
+ .distinct()
+ .collect(Collectors.toMap(
+ Function.identity(),
+ v -> Collections.frequency(failureReasons, v)
+ ));
+ frequencyMap.forEach(
+ (key, frequency) -> validationDetails.add(new Div(frequency + " times: " + key)));
+ box.add(header, validationDetails, instruction);
+ validationBox.add(box);
+ add(fileNameLabel, validationBox);
+ }
+ }
+
+ static class ValidUploadDisplay extends Div {
+
+ private ValidUploadDisplay(String fileName, int count) {
+ addClassName("uploaded-item");
+ var fileIcon = VaadinIcon.FILE.create();
+ fileIcon.addClassName("file-icon");
+ Span fileNameLabel = new Span(fileIcon, new Span(fileName));
+ fileNameLabel.addClassName("file-name");
+ Div validationBox = new Div();
+ validationBox.addClassName("validation-display-box");
+ var box = new Div();
+ var approvedTitle = new Span("Your data has been approved");
+ var validIcon = VaadinIcon.CHECK_CIRCLE_O.create();
+ validIcon.addClassName("success");
+ var header = new Span(validIcon, approvedTitle);
+ header.addClassName("header");
+ var instruction = new Span("Please click Register to register your samples");
+ instruction.addClassName("secondary");
+ Div validationDetails = new Div();
+ var approvedSamples = new Span("%d samples".formatted(count));
+ approvedSamples.addClassName("bold");
+ validationDetails.add(new Span("Sample data for "), approvedSamples,
+ new Span(" is now ready to be registered."));
+ box.add(header, validationDetails, instruction);
+ validationBox.add(box);
+ add(fileNameLabel, validationBox);
+ }
+ }
+
+ private static class InProgressDisplay extends Div {
+
+ private InProgressDisplay(String fileName) {
+ addClassName("uploaded-item");
+ var fileIcon = VaadinIcon.FILE.create();
+ fileIcon.addClassName("file-icon");
+ Span fileNameLabel = new Span(fileIcon, new Span(fileName));
+ fileNameLabel.addClassName("file-name");
+ ProgressBar progressBar = new ProgressBar();
+ progressBar.setIndeterminate(true);
+ add(fileNameLabel, new Div("Validating file..."), progressBar);
+ }
+ }
+
+ private static InvalidUploadDisplay invalidDisplay(String fileName,
+ List validationResults) {
+ List failureReasons = validationResults.stream()
+ .flatMap(res -> res.failures().stream()).toList();
+ return new InvalidUploadDisplay(fileName, failureReasons);
+ }
+
+
+ private void onUploadSucceeded(SampleValidationService sampleValidationService,
+ String experimentId, String projectId, SucceededEvent uploadSucceeded) {
+ UploadWithDisplay component = uploadSucceeded.getSource();
+ UI ui = component.getUI().orElseThrow();
+ UploadedData uploadedData = component.getUploadedData().orElseThrow();
+
+ InProgressDisplay uploadProgressDisplay = new InProgressDisplay(uploadedData.fileName());
+ component.setDisplay(uploadProgressDisplay);
+
+ List sampleInformationForExistingSamples = extractSampleInformationForExistingSamples(
+ uploadedData);
+
+ List>> validations = new ArrayList<>();
+ for (SampleInformationForExistingSample sampleInformationForExistingSample : sampleInformationForExistingSamples) {
+ CompletableFuture> validation = sampleValidationService.validateExistingSampleAsync(
+ sampleInformationForExistingSample.sampleCode(),
+ sampleInformationForExistingSample.sampleName(),
+ sampleInformationForExistingSample.biologicalReplicate(),
+ sampleInformationForExistingSample.condition(),
+ sampleInformationForExistingSample.species(),
+ sampleInformationForExistingSample.specimen(),
+ sampleInformationForExistingSample.analyte(),
+ sampleInformationForExistingSample.analysisMethod(),
+ sampleInformationForExistingSample.comment(),
+ experimentId,
+ projectId
+ ).orTimeout(1, TimeUnit.MINUTES);
+ validations.add(validation);
+ }
+ var validationTasks = CompletableFuture
+ //allOf makes sure exceptional state is transferred to outer completable future.
+ .allOf(validations.toArray(new CompletableFuture[0]))
+ .thenApply(v -> validations.stream()
+ .map(CompletableFuture::join)
+ .toList())
+ .orTimeout(5, TimeUnit.MINUTES);
+
+ validationTasks
+ .thenAccept(validationResults -> {
+
+ List> failedValidations = validationResults.stream()
+ .filter(validation -> validation.validationResult().containsFailures())
+ .toList();
+ List> succeededValidations = validationResults.stream()
+ .filter(validation -> validation.validationResult().allPassed())
+ .toList();
+
+ if (!failedValidations.isEmpty()) {
+ ui.access(() -> component.setDisplay(invalidDisplay(uploadedData.fileName(),
+ failedValidations.stream().map(ValidationResultWithPayload::validationResult)
+ .toList())));
+ setValidatedSampleMetadata(List.of());
+ return;
+ }
+ if (!succeededValidations.isEmpty()) {
+ ui.access(() -> component
+ .setDisplay(new ValidUploadDisplay(uploadedData.fileName(),
+ succeededValidations.size())));
+ setValidatedSampleMetadata(
+ succeededValidations.stream().map(ValidationResultWithPayload::payload).toList());
+ }
+ })
+ .exceptionally(e -> {
+ RuntimeException runtimeException = new RuntimeException(
+ "At least one validation task could not complete.", e);
+ log.error("Could not complete validation. Please try again.", runtimeException);
+ InvalidUploadDisplay invalidUploadDisplay = invalidDisplay(uploadedData.fileName(),
+ List.of(
+ ValidationResult.withFailures(
+ List.of("Could not complete validation. Please try again."))));
+ ui.access(() -> component.setDisplay(invalidUploadDisplay));
+ throw runtimeException;
+ }
+ );
+ }
+
+ private void setValidatedSampleMetadata(List metadata) {
+ this.validatedSampleMetadata.clear();
+ this.validatedSampleMetadata.addAll(metadata);
+ }
+
+ private List extractSampleInformationForExistingSamples(
+ UploadedData uploadedData) {
+ ParsingResult parsingResult = XLSXParser.create().parse(uploadedData.inputStream());
+ return new SampleInformationExtractor()
+ .extractInformationForExistingSamples(parsingResult);
+
+ }
+
+ private Div setupDownloadMetadataSection(TemplateService templateService,
+ BatchId batchId,
+ String experimentId,
+ String projectId, String projectCode) {
+ Button downloadTemplate = new Button("Download metadata template");
+ downloadTemplate.addClassName("download-metadata-button");
+ downloadTemplate.addClickListener(buttonClickEvent -> {
+ try (XSSFWorkbook workbook = templateService.sampleBatchUpdateXLSXTemplate(
+ batchId,
+ projectId,
+ experimentId)) {
+ var downloadProvider = new DownloadProvider(
+ new XLSXDownloadContentProvider(projectCode + "_edit_batch_template.xlsx", workbook));
+ add(downloadProvider);
+ downloadProvider.trigger();
+ } catch (IOException e) {
+ throw new RuntimeException(e);
+ }
+ });
+ Div text = new Div();
+ text.addClassName("download-metadata-text");
+ text.setText(
+ "Please download the metadata template, adapt the sample properties and upload the metadata sheet below to edit the sample batch.");
+ Div downloadMetadataSection = new Div();
+ downloadMetadataSection.addClassName("download-metadata");
+ Span sectionTitle = new Span("Download metadata template");
+ sectionTitle.addClassName("section-title");
+ sectionTitle.addClassName("download-metadata-section-title");
+ Div sectionContent = new Div();
+ sectionContent.addClassName("download-metadata-section-content");
+ sectionContent.add(text, downloadTemplate);
+ downloadMetadataSection.add(sectionTitle, sectionContent);
+ return downloadMetadataSection;
+ }
+
+ public Registration addConfirmListener(ComponentEventListener listener) {
+ return addListener(ConfirmEvent.class, listener);
+ }
+
+ public Registration addCancelListener(ComponentEventListener listener) {
+ return addListener(CancelEvent.class, listener);
+ }
+
+ @Override
+ public void close() {
+ validatedSampleMetadata.clear();
+ super.close();
+ }
+
+ @Override
+ protected void onConfirmClicked(ClickEvent