Remove analysis type remnants and require non-null values for analysis method in samplePreview (#394)

* Fix missing value exception.

* Subject line

Description

* log exception

* Refactor analysistype to AnalysisMethod and streamline sample deletion

* Add null check to AnalysisMethod within SamplePreview to avoid tedious debugging

---------

Co-authored-by: Tobias Koch <[email protected]>

Author: Steffengreiner

database-connector/src/main/java/life/qbic/projectmanagement/persistence/SampleRepositoryImpl.java

@@ -68,7 +68,7 @@ public Result<Collection<Sample>, ResponseCode> addAll(Project project,
     } catch (Exception e) {
       log.error("The samples:" + commaSeperatedSampleIds + "could not be stored in openBIS", e);
       log.error("Removing samples from repository, as well.");
-      samples.forEach(sample -> qbicSampleRepository.delete(sample));
+      qbicSampleRepository.deleteAll(samples);
       return Result.fromError(ResponseCode.REGISTRATION_FAILED);
     }
     return Result.fromValue(samples);
@@ -83,7 +83,7 @@ public Result<Collection<Sample>, SampleInformationService.ResponseCode> findSam
       samples = qbicSampleRepository.findAllByExperimentId(experimentId);
     } catch (Exception e) {
       log.error(
-          "Retrieving Samples for experiment with id " + experimentId.value() + " failed: " + e);
+          "Retrieving Samples for experiment with id " + experimentId.value() + " failed: " + e, e);
       return Result.fromError(SampleInformationService.ResponseCode.QUERY_FAILED);
     }
     return Result.fromValue(samples);

projectmanagement/src/main/java/life/qbic/projectmanagement/application/sample/SamplePreview.java

@@ -72,6 +72,7 @@ private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampl
     Objects.requireNonNull(species);
     Objects.requireNonNull(specimen);
     Objects.requireNonNull(analyte);
+    Objects.requireNonNull(analysisMethod);
     this.experimentId = experimentId;
     this.sampleId = sampleId;
     this.sampleCode = sampleCode;
@@ -206,7 +207,7 @@ public String toString() {
         ", species='" + species + '\'' +
         ", specimen='" + specimen + '\'' +
         ", analyte='" + analyte + '\'' +
-        ", analysisType='" + analysisMethod + '\'' +
+        ", analysisMethod='" + analysisMethod + '\'' +
         ", comment='" + comment + '\'' +
         ", conditions=" + experimentalGroup +
         '}';

projectmanagement/src/main/java/life/qbic/projectmanagement/domain/project/sample/AnalysisMethod.java

@@ -14,7 +14,7 @@
 public enum AnalysisMethod {
 
   /*
-  NGS related analysis types
+  NGS related analysis methods
    */
 
   SIXTEEN_S("16S", "16S amplicon sequencing",
@@ -57,7 +57,7 @@ public enum AnalysisMethod {
   SEQ_ONLY("SEQ-ONLY", "Sequencing only", "Processing of ready-to-sequence pools"),
 
   /*
-  Proteomics related analysis types
+  Proteomics related analysis methods
    */
 
   PROTEOMICS("PROTEOMIICS", "Proteomics", ""),
@@ -71,7 +71,7 @@ public enum AnalysisMethod {
   PTMS("PTMS", "Posttransductional mutations", ""),
 
   /*
-  Metabolomics related analysis types
+  Metabolomics related analysis methods
    */
 
   UNTARGETED_MX("UNTARGETED-MX", "Untargeted metabolomics", ""),

vaadinfrontend/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleDetailsComponent.java

@@ -26,6 +26,7 @@
 import java.util.Collection;
 import java.util.List;
 import java.util.stream.Collectors;
+import life.qbic.application.commons.ApplicationException;
 import life.qbic.application.commons.Result;
 import life.qbic.datamanager.views.AppRoutes.Projects;
 import life.qbic.datamanager.views.general.Disclaimer;
@@ -334,7 +335,7 @@ private Grid<SamplePreview> createSampleGrid() {
       sampleGrid.addColumn(SamplePreview::analyte).setHeader("Analyte").setSortProperty("analyte")
           .setTooltipGenerator(SamplePreview::analyte);
       sampleGrid.addColumn(SamplePreview::analysisMethod).setHeader("Analysis to Perform")
-          .setSortProperty("analysisType").setTooltipGenerator(SamplePreview::analysisMethod);
+          .setSortProperty("analysisMethod").setTooltipGenerator(SamplePreview::analysisMethod);
       sampleGrid.addColumn(SamplePreview::comment).setHeader("Comment").setSortProperty("comment")
           .setTooltipGenerator(SamplePreview::comment);
       sampleGrid.addClassName("sample-grid");
@@ -365,7 +366,11 @@ private boolean noExperimentGroupsInExperiment(Experiment experiment) {
 
     private boolean noSamplesRegisteredInExperiment(Experiment experiment) {
       return sampleInformationService.retrieveSamplesForExperiment(experiment.experimentId())
-          .getValue().isEmpty();
+          .map(Collection::isEmpty)
+          .onError(error -> {
+            throw new ApplicationException("Unexpected response code : " + error);
+          })
+          .getValue();
     }
 
     private Disclaimer createNoGroupsDefinedDisclaimer(Experiment experiment) {

vaadinfrontend/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/SampleRegistrationSpreadsheet.java

@@ -398,7 +398,7 @@ private void generateCellValueOptionsMap(
   /**
    * Collects all {@link AnalysisMethod} specific for the genomic {@link MetadataType}
    *
-   * @return List of String labels for all genomic analysis types.
+   * @return List of String labels for all genomic analysis methods.
    */
   private List<String> generateGenomicsAnalysisMethods() {
     return Arrays.stream(AnalysisMethod.values())