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‎project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/ValidationException.java renamed to ‎project-management/src/main/java/life/qbic/projectmanagement/application/ValidationException.java

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package life.qbic.projectmanagement.application.measurement.validation;
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package life.qbic.projectmanagement.application;
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public class ValidationException extends RuntimeException {
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‎project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/ValidationResult.java renamed to ‎project-management/src/main/java/life/qbic/projectmanagement/application/ValidationResult.java

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package life.qbic.projectmanagement.application.measurement.validation;
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package life.qbic.projectmanagement.application;
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import java.util.ArrayList;
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import java.util.Collection;

‎project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementNGSValidator.java

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import java.util.regex.Pattern;
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import life.qbic.logging.api.Logger;
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import life.qbic.projectmanagement.application.ProjectInformationService;
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import life.qbic.projectmanagement.application.ValidationException;
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import life.qbic.projectmanagement.application.ValidationResult;
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import life.qbic.projectmanagement.application.measurement.MeasurementService;
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import life.qbic.projectmanagement.application.measurement.NGSMeasurementMetadata;
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import life.qbic.projectmanagement.application.ontology.TerminologyService;

‎project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java

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import java.util.regex.Pattern;
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import life.qbic.logging.api.Logger;
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import life.qbic.projectmanagement.application.ProjectInformationService;
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import life.qbic.projectmanagement.application.ValidationException;
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import life.qbic.projectmanagement.application.ValidationResult;
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import life.qbic.projectmanagement.application.measurement.MeasurementService;
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import life.qbic.projectmanagement.application.measurement.ProteomicsMeasurementMetadata;
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import life.qbic.projectmanagement.application.ontology.TerminologyService;

‎project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementValidationService.java

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import java.util.Collection;
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import java.util.Optional;
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import java.util.concurrent.CompletableFuture;
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import life.qbic.projectmanagement.application.ValidationResult;
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import life.qbic.projectmanagement.application.measurement.NGSMeasurementMetadata;
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import life.qbic.projectmanagement.application.measurement.ProteomicsMeasurementMetadata;
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import life.qbic.projectmanagement.domain.model.project.ProjectId;

‎project-management/src/main/java/life/qbic/projectmanagement/application/measurement/validation/MeasurementValidator.java

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package life.qbic.projectmanagement.application.measurement.validation;
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import life.qbic.projectmanagement.application.ValidationResult;
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import life.qbic.projectmanagement.application.measurement.MeasurementMetadata;
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import life.qbic.projectmanagement.domain.model.project.ProjectId;
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‎user-interface/src/main/java/life/qbic/datamanager/parser/PropertyToString.java renamed to ‎project-management/src/main/java/life/qbic/projectmanagement/application/sample/PropertyConversion.java

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package life.qbic.datamanager.parser;
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package life.qbic.projectmanagement.application.sample;
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import java.util.ArrayList;
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import java.util.List;
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*
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* @since 1.5.0
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*/
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public class PropertyToString {
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public class PropertyConversion {
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private static final String CONDITION_VARIABLE_LEVEL_UNIT_TEMPLATE = "%s: %s %s"; // <variable name>: <value> [unit]
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* <p>
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* In its current implementation, the String representation results into a
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* <code>;</code>-separated concatenation of {@link VariableLevel}. See
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* {@link PropertyToString#variableLevel(VariableLevel)} for more details.
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* {@link PropertyConversion#toString(VariableLevel)} for more details.
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* <p>
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* Example: a condition with the two variable levels <code>size: 20 cm</code> and <code>hue:
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* blue</code> will result in:
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* @return the String representation
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* @since 1.5.0
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*/
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public static String condition(Condition condition) {
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public static String toString(Condition condition) {
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Objects.requireNonNull(condition);
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List<String> stringValues = new ArrayList<>();
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condition.getVariableLevels()
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.forEach(variableLevel -> stringValues.add(variableLevel(variableLevel)));
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.forEach(variableLevel -> stringValues.add(toString(variableLevel)));
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return String.join("; ", stringValues);
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}
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* @return the String representation of the variable level
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* @since 1.5.0
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*/
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public static String variableLevel(VariableLevel variableLevel) {
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public static String toString(VariableLevel variableLevel) {
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Objects.requireNonNull(variableLevel);
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if (variableLevel.experimentalValue().unit().isPresent()) {
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return CONDITION_VARIABLE_LEVEL_UNIT_TEMPLATE.formatted(variableLevel.variableName().value(),
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* @return the String representation of the ontology term
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* @since 1.5.0
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*/
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public static String ontologyTerm(OntologyTerm ontologyTerm) {
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public static String toString(OntologyTerm ontologyTerm) {
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Objects.requireNonNull(ontologyTerm);
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return ONTOLOGY_TERM.formatted(ontologyTerm.getLabel(), ontologyTerm.getOboId());
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}
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public static OntologyTerm fromString(String string) throws ParserException {
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}
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public static class ParserException extends RuntimeException {
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public ParserException(String message) {
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super(message);
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}
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}
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}

‎project-management/src/main/java/life/qbic/projectmanagement/application/sample/SampleMetadata.java

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package life.qbic.projectmanagement.application.sample;
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import java.util.Optional;
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/**
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* <b>Sample Metadata</b>
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*
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* <p>A simple sample metadata DTO to pass them within the application</p>
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*
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* @since 1.0.0
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*/
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public record SampleMetadata(String sampleId, String analysisToBePerformed, String sampleName,
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String biologicalReplicate, String condition, String specimen,
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String analyte, String comment) {
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public static SampleMetadata createNew(String analysisToBePerformed, String sampleName,
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String biologicalReplicate, String condition, String specimen,
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String analyte, String comment) {
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return new SampleMetadata("", analysisToBePerformed, sampleName, biologicalReplicate, condition,
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specimen, analyte, comment);
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}
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public static SampleMetadata createUpdate(String sampleId, String analysisToBePerformed,
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String sampleName,
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String biologicalReplicate, String condition, String specimen,
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String analyte, String comment) {
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return new SampleMetadata(sampleId, analysisToBePerformed, sampleName, biologicalReplicate,
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condition, specimen, analyte, comment);
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}
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public Optional<String> getSampleId() {
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return Optional.ofNullable(sampleId.isBlank() ? null : sampleId);
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}
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}

‎project-management/src/main/java/life/qbic/projectmanagement/application/sample/SampleValidation.java

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package life.qbic.projectmanagement.application.sample;
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import java.util.List;
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import java.util.Map;
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import java.util.Objects;
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import java.util.function.Function;
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import java.util.stream.Collectors;
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import life.qbic.projectmanagement.application.ValidationResult;
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import life.qbic.projectmanagement.application.experiment.ExperimentInformationService;
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import life.qbic.projectmanagement.application.ontology.SpeciesLookupService;
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import life.qbic.projectmanagement.application.ontology.TerminologyService;
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import life.qbic.projectmanagement.domain.model.experiment.Condition;
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import life.qbic.projectmanagement.domain.model.experiment.Experiment;
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import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
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import life.qbic.projectmanagement.domain.model.experiment.ExperimentalGroup;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Component;
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/**
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* <b><class short description - 1 Line!></b>
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*
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* <p><More detailed description - When to use, what it solves, etc.></p>
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*
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* @since <version tag>
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*/
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@Component
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public class SampleValidation {
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private final SampleInformationService sampleInformationService;
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private final ExperimentInformationService experimentInformationService;
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private final TerminologyService terminologyService;
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private final SpeciesLookupService speciesLookupService;
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@Autowired
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public SampleValidation(SampleInformationService sampleInformationService,
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ExperimentInformationService experimentInformationService,
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TerminologyService terminologyService, SpeciesLookupService speciesLookupService) {
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this.sampleInformationService = Objects.requireNonNull(sampleInformationService);
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this.experimentInformationService = Objects.requireNonNull(experimentInformationService);
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this.terminologyService = Objects.requireNonNull(terminologyService);
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this.speciesLookupService = Objects.requireNonNull(speciesLookupService);
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}
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/**
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* Creates a lookup table for conditions having their String representation as key.
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* <p>
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* The String representation is done with the {@link PropertyConversion#toString(Condition)}
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* method.
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*
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* @param conditions the conditions to take for the lookup table build
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* @return the lookup table
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* @since 1.5.0
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*/
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private static Map<String, Condition> conditionLookup(List<Condition> conditions) {
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return conditions.stream()
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.collect(Collectors.toMap(PropertyConversion::toString, Function.identity()));
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}
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/**
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* Validates metadata for a not yet registered sample. The validation does not look for any sample
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* id and no sample information lookups are done in this case.
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* <p>
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* If the client wants to validate the sample id as well, please refer to
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* {@link SampleValidation#validateExistingSample(SampleMetadata, String, String)}
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*
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* @param sampleMetadata the sample metadata to validate
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* @param experimentId the experiment id of the experiment the sample belongs to
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* @param projectId the project id of project the experiment belongs to
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* @return the report of the validation
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* @since 1.5.0
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*/
75+
public ValidationResult validateNewSample(SampleMetadata sampleMetadata, String experimentId,
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String projectId) {
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var experimentQuery = experimentInformationService.find(projectId,
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ExperimentId.parse(experimentId));
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if (experimentQuery.isPresent()) {
80+
return validateWithExperiment(sampleMetadata, experimentQuery.get(), projectId);
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} else {
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return ValidationResult.withFailures(1, List.of("Unknown experiment."));
83+
}
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}
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private ValidationResult validateWithExperiment(SampleMetadata sampleMetadata,
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Experiment experiment, String projectId) {
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var conditionsLookupTable = conditionLookup(experiment.getExperimentalGroups().stream().map(
89+
ExperimentalGroup::condition).toList());
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throw new RuntimeException("Not implemented yet");
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}
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public ValidationResult validateExistingSample(SampleMetadata sampleMetadata, String experimentId,
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String projectId) {
96+
throw new RuntimeException("Not yet implemented");
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}
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}

‎project-management/src/main/java/life/qbic/projectmanagement/application/sample/SampleValidationService.java

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package life.qbic.projectmanagement.application.sample;
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import java.util.Objects;
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import life.qbic.projectmanagement.application.ValidationResult;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Service;
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/**
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* <b><class short description - 1 Line!></b>
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*
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* <p><More detailed description - When to use, what it solves, etc.></p>
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*
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* @since <version tag>
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*/
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@Service
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public class SampleValidationService {
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private final SampleValidation sampleValidation;
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@Autowired
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public SampleValidationService(SampleValidation sampleValidation) {
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this.sampleValidation = Objects.requireNonNull(sampleValidation);
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}
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public ValidationResult validateNewSample(SampleMetadata sampleMetadata, String experimentId,
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String projectId) {
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return sampleValidation.validateNewSample(sampleMetadata, experimentId, projectId);
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}
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}

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