Checkin Progress

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

@@ -1,4 +1,4 @@
-package life.qbic.projectmanagement.application.measurement.validation;
+package life.qbic.projectmanagement.application;
 
 public class ValidationException extends RuntimeException {
 

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

@@ -1,4 +1,4 @@
-package life.qbic.projectmanagement.application.measurement.validation;
+package life.qbic.projectmanagement.application;
 
 import java.util.ArrayList;
 import java.util.Collection;

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

@@ -10,6 +10,8 @@
 import java.util.regex.Pattern;
 import life.qbic.logging.api.Logger;
 import life.qbic.projectmanagement.application.ProjectInformationService;
+import life.qbic.projectmanagement.application.ValidationException;
+import life.qbic.projectmanagement.application.ValidationResult;
 import life.qbic.projectmanagement.application.measurement.MeasurementService;
 import life.qbic.projectmanagement.application.measurement.NGSMeasurementMetadata;
 import life.qbic.projectmanagement.application.ontology.TerminologyService;

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

@@ -9,6 +9,8 @@
 import java.util.regex.Pattern;
 import life.qbic.logging.api.Logger;
 import life.qbic.projectmanagement.application.ProjectInformationService;
+import life.qbic.projectmanagement.application.ValidationException;
+import life.qbic.projectmanagement.application.ValidationResult;
 import life.qbic.projectmanagement.application.measurement.MeasurementService;
 import life.qbic.projectmanagement.application.measurement.ProteomicsMeasurementMetadata;
 import life.qbic.projectmanagement.application.ontology.TerminologyService;

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

@@ -3,6 +3,7 @@
 import java.util.Collection;
 import java.util.Optional;
 import java.util.concurrent.CompletableFuture;
+import life.qbic.projectmanagement.application.ValidationResult;
 import life.qbic.projectmanagement.application.measurement.NGSMeasurementMetadata;
 import life.qbic.projectmanagement.application.measurement.ProteomicsMeasurementMetadata;
 import life.qbic.projectmanagement.domain.model.project.ProjectId;

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

@@ -1,5 +1,6 @@
 package life.qbic.projectmanagement.application.measurement.validation;
 
+import life.qbic.projectmanagement.application.ValidationResult;
 import life.qbic.projectmanagement.application.measurement.MeasurementMetadata;
 import life.qbic.projectmanagement.domain.model.project.ProjectId;
 

user-interface/src/main/java/life/qbic/datamanager/parser/PropertyToString.java → project-management/src/main/java/life/qbic/projectmanagement/application/sample/PropertyConversion.java

@@ -1,4 +1,4 @@
-package life.qbic.datamanager.parser;
+package life.qbic.projectmanagement.application.sample;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -15,7 +15,7 @@
  *
  * @since 1.5.0
  */
-public class PropertyToString {
+public class PropertyConversion {
 
   private static final String CONDITION_VARIABLE_LEVEL_UNIT_TEMPLATE = "%s: %s %s"; // <variable name>: <value> [unit]
 
@@ -28,7 +28,7 @@ public class PropertyToString {
    * <p>
    * In its current implementation, the String representation results into a
    * <code>;</code>-separated concatenation of {@link VariableLevel}. See
-   * {@link PropertyToString#variableLevel(VariableLevel)} for more details.
+   * {@link PropertyConversion#toString(VariableLevel)} for more details.
    * <p>
    * Example: a condition with the two variable levels <code>size: 20 cm</code> and <code>hue:
    * blue</code> will result in:
@@ -43,11 +43,11 @@ public class PropertyToString {
    * @return the String representation
    * @since 1.5.0
    */
-  public static String condition(Condition condition) {
+  public static String toString(Condition condition) {
     Objects.requireNonNull(condition);
     List<String> stringValues = new ArrayList<>();
     condition.getVariableLevels()
-        .forEach(variableLevel -> stringValues.add(variableLevel(variableLevel)));
+        .forEach(variableLevel -> stringValues.add(toString(variableLevel)));
     return String.join("; ", stringValues);
   }
 
@@ -62,7 +62,7 @@ public static String condition(Condition condition) {
    * @return the String representation of the variable level
    * @since 1.5.0
    */
-  public static String variableLevel(VariableLevel variableLevel) {
+  public static String toString(VariableLevel variableLevel) {
     Objects.requireNonNull(variableLevel);
     if (variableLevel.experimentalValue().unit().isPresent()) {
       return CONDITION_VARIABLE_LEVEL_UNIT_TEMPLATE.formatted(variableLevel.variableName().value(),
@@ -89,8 +89,19 @@ public static String variableLevel(VariableLevel variableLevel) {
    * @return the String representation of the ontology term
    * @since 1.5.0
    */
-  public static String ontologyTerm(OntologyTerm ontologyTerm) {
+  public static String toString(OntologyTerm ontologyTerm) {
     Objects.requireNonNull(ontologyTerm);
     return ONTOLOGY_TERM.formatted(ontologyTerm.getLabel(), ontologyTerm.getOboId());
   }
+
+  public static OntologyTerm fromString(String string) throws ParserException {
+
+  }
+
+  public static class ParserException extends RuntimeException {
+    public ParserException(String message) {
+      super(message);
+    }
+  }
+
 }

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

@@ -0,0 +1,35 @@
+package life.qbic.projectmanagement.application.sample;
+
+import java.util.Optional;
+
+/**
+ * <b>Sample Metadata</b>
+ *
+ * <p>A simple sample metadata DTO to pass them within the application</p>
+ *
+ * @since 1.0.0
+ */
+public record SampleMetadata(String sampleId, String analysisToBePerformed, String sampleName,
+                             String biologicalReplicate, String condition, String specimen,
+                             String analyte, String comment) {
+
+  public static SampleMetadata createNew(String analysisToBePerformed, String sampleName,
+      String biologicalReplicate, String condition, String specimen,
+      String analyte, String comment) {
+    return new SampleMetadata("", analysisToBePerformed, sampleName, biologicalReplicate, condition,
+        specimen, analyte, comment);
+  }
+
+  public static SampleMetadata createUpdate(String sampleId, String analysisToBePerformed,
+      String sampleName,
+      String biologicalReplicate, String condition, String specimen,
+      String analyte, String comment) {
+    return new SampleMetadata(sampleId, analysisToBePerformed, sampleName, biologicalReplicate,
+        condition, specimen, analyte, comment);
+  }
+
+  public Optional<String> getSampleId() {
+    return Optional.ofNullable(sampleId.isBlank() ? null : sampleId);
+  }
+
+}

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

@@ -0,0 +1,100 @@
+package life.qbic.projectmanagement.application.sample;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import life.qbic.projectmanagement.application.ValidationResult;
+import life.qbic.projectmanagement.application.experiment.ExperimentInformationService;
+import life.qbic.projectmanagement.application.ontology.SpeciesLookupService;
+import life.qbic.projectmanagement.application.ontology.TerminologyService;
+import life.qbic.projectmanagement.domain.model.experiment.Condition;
+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 org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+/**
+ * <b><class short description - 1 Line!></b>
+ *
+ * <p><More detailed description - When to use, what it solves, etc.></p>
+ *
+ * @since <version tag>
+ */
+@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.
+   * <p>
+   * 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<String, Condition> conditionLookup(List<Condition> conditions) {
+    return conditions.stream()
+        .collect(Collectors.toMap(PropertyConversion::toString, 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.
+   * <p>
+   * If the client wants to validate the sample id as well, please refer to
+   * {@link SampleValidation#validateExistingSample(SampleMetadata, String, String)}
+   *
+   * @param sampleMetadata the sample metadata to validate
+   * @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 ValidationResult validateNewSample(SampleMetadata sampleMetadata, String experimentId,
+      String projectId) {
+    var experimentQuery = experimentInformationService.find(projectId,
+        ExperimentId.parse(experimentId));
+    if (experimentQuery.isPresent()) {
+      return validateWithExperiment(sampleMetadata, experimentQuery.get(), projectId);
+    } else {
+      return ValidationResult.withFailures(1, List.of("Unknown experiment."));
+    }
+  }
+
+  private ValidationResult validateWithExperiment(SampleMetadata sampleMetadata,
+      Experiment experiment, String projectId) {
+    var conditionsLookupTable = conditionLookup(experiment.getExperimentalGroups().stream().map(
+        ExperimentalGroup::condition).toList());
+
+    throw new RuntimeException("Not implemented yet");
+  }
+
+  public ValidationResult validateExistingSample(SampleMetadata sampleMetadata, String experimentId,
+      String projectId) {
+    throw new RuntimeException("Not yet implemented");
+  }
+
+
+}

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

@@ -0,0 +1,31 @@
+package life.qbic.projectmanagement.application.sample;
+
+import java.util.Objects;
+import life.qbic.projectmanagement.application.ValidationResult;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+/**
+ * <b><class short description - 1 Line!></b>
+ *
+ * <p><More detailed description - When to use, what it solves, etc.></p>
+ *
+ * @since <version tag>
+ */
+@Service
+public class SampleValidationService {
+
+  private final SampleValidation sampleValidation;
+
+  @Autowired
+  public SampleValidationService(SampleValidation sampleValidation) {
+    this.sampleValidation = Objects.requireNonNull(sampleValidation);
+  }
+
+  public ValidationResult validateNewSample(SampleMetadata sampleMetadata, String experimentId,
+      String projectId) {
+    return sampleValidation.validateNewSample(sampleMetadata, experimentId, projectId);
+  }
+
+
+}

user-interface/src/main/java/life/qbic/datamanager/templates/SampleBatchTemplate.java

@@ -1,7 +1,7 @@
 package life.qbic.datamanager.templates;
 
 import java.util.List;
-import life.qbic.datamanager.parser.PropertyToString;
+import life.qbic.projectmanagement.application.sample.PropertyConversion;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentalGroup;
 import life.qbic.projectmanagement.domain.model.sample.Sample;
 import org.apache.poi.ss.usermodel.DataValidation;
@@ -254,13 +254,13 @@ private static void fillRowWithSampleMetadata(XSSFRow row, Sample sample,
     row.createCell(COLUMN_INDEX_SAMPLE_NAME).setCellValue(sample.label());
     row.createCell(COLUMN_INDEX_BIOLOGICAL_REPLICATE).setCellValue(sample.biologicalReplicate());
     row.createCell(COLUMN_INDEX_CONDITION)
-        .setCellValue(PropertyToString.condition(experimentalGroup.condition()));
+        .setCellValue(PropertyConversion.toString(experimentalGroup.condition()));
     row.createCell(COLUMN_INDEX_SPECIES)
-        .setCellValue(PropertyToString.ontologyTerm(sample.sampleOrigin().getSpecies()));
+        .setCellValue(PropertyConversion.toString(sample.sampleOrigin().getSpecies()));
     row.createCell(COLUMN_INDEX_SPECIMEN)
-        .setCellValue(PropertyToString.ontologyTerm(sample.sampleOrigin().getSpecimen()));
+        .setCellValue(PropertyConversion.toString(sample.sampleOrigin().getSpecimen()));
     row.createCell(COLUMN_INDEX_ANALYTES)
-        .setCellValue(PropertyToString.ontologyTerm(sample.sampleOrigin().getAnalyte()));
+        .setCellValue(PropertyConversion.toString(sample.sampleOrigin().getAnalyte()));
     row.createCell(COLUMN_INDEX_COMMENT).setCellValue(sample.comment().orElse(""));
     row.createCell(COLUMN_INDEX_SAMPLE_ID).setCellValue(sample.sampleCode().code());
   }

user-interface/src/main/java/life/qbic/datamanager/templates/TemplateService.java

@@ -3,7 +3,7 @@
 import java.util.Arrays;
 import java.util.List;
 import java.util.Objects;
-import life.qbic.datamanager.parser.PropertyToString;
+import life.qbic.projectmanagement.application.sample.PropertyConversion;
 import life.qbic.projectmanagement.application.experiment.ExperimentInformationService;
 import life.qbic.projectmanagement.application.sample.SampleInformationService;
 import life.qbic.projectmanagement.domain.model.experiment.Experiment;
@@ -92,11 +92,11 @@ private XSSFWorkbook createPrefilledWorkbookFromExperiment(Experiment experiment
       List<Sample> samples) {
     var conditions = experiment.getExperimentalGroups().stream().map(ExperimentalGroup::condition)
         .map(
-            PropertyToString::condition).toList();
+            PropertyConversion::toString).toList();
     var experimentalGroups = experiment.getExperimentalGroups();
-    var species = experiment.getSpecies().stream().map(PropertyToString::ontologyTerm).toList();
-    var specimen = experiment.getSpecimens().stream().map(PropertyToString::ontologyTerm).toList();
-    var analytes = experiment.getAnalytes().stream().map(PropertyToString::ontologyTerm).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 SampleBatchTemplate.createUpdateTemplate(samples,
@@ -108,10 +108,10 @@ private XSSFWorkbook createPrefilledWorkbookFromExperiment(Experiment experiment
   private XSSFWorkbook createWorkbookFromExperiment(Experiment experiment) {
     var conditions = experiment.getExperimentalGroups().stream().map(ExperimentalGroup::condition)
         .map(
-            PropertyToString::condition).toList();
-    var species = experiment.getSpecies().stream().map(PropertyToString::ontologyTerm).toList();
-    var specimen = experiment.getSpecimens().stream().map(PropertyToString::ontologyTerm).toList();
-    var analytes = experiment.getAnalytes().stream().map(PropertyToString::ontologyTerm).toList();
+            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 SampleBatchTemplate.createRegistrationTemplate(

user-interface/src/main/java/life/qbic/datamanager/views/navigation/ProjectSideNavigationComponent.java

@@ -73,7 +73,7 @@ public class ProjectSideNavigationComponent extends Div implements
     BeforeEnterObserver {
 
   public static final String PROJECT_ID_ROUTE_PARAMETER = "projectId";
-  public static final StringEXPERIMENT_ID_ROUTE_PARAMETER = "experimentId";
+  public static final String EXPERIMENT_ID_ROUTE_PARAMETER = "experimentId";
   private static final Logger log = LoggerFactory.logger(ProjectSideNavigationComponent.class);
   private final Div content;
   private final transient ProjectInformationService projectInformationService;

user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementMetadataUploadDialog.java

@@ -46,7 +46,7 @@
 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.application.ValidationResult;
 import life.qbic.projectmanagement.domain.model.experiment.Experiment;
 import life.qbic.projectmanagement.domain.model.project.ProjectId;
 import org.springframework.util.StringUtils;

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;

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;

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;
 
 /**