[GLT-4274] show omissions on the Run Details page

changes/add_run_omissions.md

@@ -0,0 +1,2 @@
+Omissions table on the Run Details page, showing libraries that are included in the run but not a
+part of any case

pom.xml

@@ -138,7 +138,7 @@
     <dependency>
       <groupId>ca.on.oicr.gsi.cardea</groupId>
       <artifactId>cardea-data</artifactId>
-      <version>1.14.0</version>
+      <version>1.15.1-SNAPSHOT</version>
     </dependency>
   </dependencies>
 
@@ -184,4 +184,4 @@
     </plugins>
   </build>
 
-</project>
+</project>

src/main/java/ca/on/oicr/gsi/dimsum/CaseLoader.java

@@ -20,13 +20,14 @@
 import org.springframework.web.reactive.function.client.WebClient;
 import ca.on.oicr.gsi.cardea.data.Assay;
 import ca.on.oicr.gsi.cardea.data.Case;
+import ca.on.oicr.gsi.cardea.data.OmittedRunSample;
 import ca.on.oicr.gsi.cardea.data.OmittedSample;
 import ca.on.oicr.gsi.cardea.data.Project;
-import ca.on.oicr.gsi.cardea.data.RunAndLibraries;
 import ca.on.oicr.gsi.cardea.data.Sample;
 import ca.on.oicr.gsi.cardea.data.Test;
 import ca.on.oicr.gsi.dimsum.data.CaseData;
 import ca.on.oicr.gsi.dimsum.data.ProjectSummary;
+import ca.on.oicr.gsi.dimsum.data.RunAndLibraries;
 import ca.on.oicr.gsi.dimsum.service.filtering.CompletedGate;
 import ca.on.oicr.gsi.dimsum.service.filtering.PendingState;
 import io.micrometer.core.instrument.MeterRegistry;
@@ -72,7 +73,8 @@ public CaseData load(ZonedDateTime previousTimestamp) throws IOException {
     ca.on.oicr.gsi.cardea.data.CaseData cardeaCaseData = loadCardeaData(builder);
 
     Map<Long, Assay> assaysById = cardeaCaseData.getAssaysById();
-    Map<String, RunAndLibraries> runsByName = sortRuns(cardeaCaseData.getCases());
+    Map<String, RunAndLibraries> runsByName =
+        sortRuns(cardeaCaseData.getCases(), cardeaCaseData.getOmittedRunSamples());
     List<OmittedSample> omittedSamples = cardeaCaseData.getOmittedSamples();
     Set<String> requisitionNames = loadRequisitionNames(cardeaCaseData.getCases());
     Set<String> projectsNames = loadProjectsNames(cardeaCaseData.getCases());
@@ -97,7 +99,7 @@ requisitionNames, projectsNames, donorNames, getRunNames(runsByName), testNames,
    * 
    * @param builder WebClient builder state used to fetch data from Cardea API `/dimsum` endpoint
    */
-  public ca.on.oicr.gsi.cardea.data.CaseData loadCardeaData(WebClient.Builder builder)
+  private ca.on.oicr.gsi.cardea.data.CaseData loadCardeaData(WebClient.Builder builder)
       throws IOException {
     ca.on.oicr.gsi.cardea.data.CaseData data = builder
         .codecs(configurer -> configurer.defaultCodecs().maxInMemorySize(LIMIT_FOR_DATA_LOAD))
@@ -145,8 +147,9 @@ private static Set<String> getRunNames(Map<String, RunAndLibraries> runsByName)
     return runsByName.keySet();
   }
 
-  private Map<String, RunAndLibraries> sortRuns(List<Case> cases) {
-    Map<String, RunAndLibraries.Builder> map = new HashMap<>();
+  private Map<String, RunAndLibraries> sortRuns(List<Case> cases,
+      List<OmittedRunSample> omittedRunSamples) {
+    Map<Long, RunAndLibraries.Builder> map = new HashMap<>();
     for (Case kase : cases) {
       for (Test test : kase.getTests()) {
         for (Sample sample : test.getLibraryQualifications()) {
@@ -159,18 +162,25 @@ private Map<String, RunAndLibraries> sortRuns(List<Case> cases) {
         }
       }
     }
+    for (OmittedRunSample sample : omittedRunSamples) {
+      if (map.containsKey(sample.getRunId())) {
+        map.get(sample.getRunId()).addOmittedSample(sample);
+      } else {
+        log.warn("OmittedRunSample found for missing run ID: {}", sample.getRunId());
+      }
+    }
     return map.values().stream()
         .map(RunAndLibraries.Builder::build)
         .collect(Collectors.toMap(x -> x.getRun().getName(), Function.identity()));
   }
 
-  private void addRunLibrary(Map<String, RunAndLibraries.Builder> map, Sample sample,
+  private void addRunLibrary(Map<Long, RunAndLibraries.Builder> map, Sample sample,
       BiConsumer<RunAndLibraries.Builder, Sample> addSample) {
-    String runName = sample.getRun().getName();
-    if (!map.containsKey(runName)) {
-      map.put(runName, new RunAndLibraries.Builder().run(sample.getRun()));
+    long runId = sample.getRun().getId();
+    if (!map.containsKey(runId)) {
+      map.put(runId, new RunAndLibraries.Builder().run(sample.getRun()));
     }
-    addSample.accept(map.get(runName), sample);
+    addSample.accept(map.get(runId), sample);
   }
 
   @FunctionalInterface

src/main/java/ca/on/oicr/gsi/dimsum/controller/mvc/RunController.java

@@ -9,9 +9,9 @@
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
 import ca.on.oicr.gsi.cardea.data.Run;
-import ca.on.oicr.gsi.cardea.data.RunAndLibraries;
 import ca.on.oicr.gsi.cardea.data.Sample;
 import ca.on.oicr.gsi.dimsum.controller.NotFoundException;
+import ca.on.oicr.gsi.dimsum.data.RunAndLibraries;
 import ca.on.oicr.gsi.dimsum.service.CaseService;
 
 @Controller
@@ -40,7 +40,8 @@ public String getRunPage(@PathVariable String runName, ModelMap model) {
             .collect(Collectors.joining(",")));
     model.put("showLibraryQualifications", !runAndLibraries.getLibraryQualifications().isEmpty());
     model.put("showFullDepthSequencings", !runAndLibraries.getFullDepthSequencings().isEmpty());
-    return "run";
+    model.put("showOmitted", !runAndLibraries.getOmittedSamples().isEmpty());
+    return "run-detail";
   }
 
   private static String getRunStatus(Run run) {

src/main/java/ca/on/oicr/gsi/dimsum/controller/rest/RunRestController.java

@@ -8,13 +8,15 @@
 import org.springframework.web.bind.annotation.RequestBody;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
+import ca.on.oicr.gsi.cardea.data.OmittedRunSample;
 import ca.on.oicr.gsi.cardea.data.Run;
-import ca.on.oicr.gsi.cardea.data.RunAndLibraries;
 import ca.on.oicr.gsi.cardea.data.Sample;
 import ca.on.oicr.gsi.dimsum.controller.NotFoundException;
 import ca.on.oicr.gsi.dimsum.controller.rest.request.DataQuery;
+import ca.on.oicr.gsi.dimsum.data.RunAndLibraries;
 import ca.on.oicr.gsi.dimsum.service.CaseService;
 import ca.on.oicr.gsi.dimsum.service.filtering.CaseFilter;
+import ca.on.oicr.gsi.dimsum.service.filtering.OmittedRunSampleSort;
 import ca.on.oicr.gsi.dimsum.service.filtering.RunFilter;
 import ca.on.oicr.gsi.dimsum.service.filtering.RunSort;
 import ca.on.oicr.gsi.dimsum.service.filtering.SampleSort;
@@ -59,6 +61,16 @@ public TableData<Sample> getFullDepthSequencings(@PathVariable String runName,
         query.getPageNumber(), sort, descending, filters);
   }
 
+  @PostMapping("/{runName}/omissions")
+  public TableData<OmittedRunSample> getOmitted(@PathVariable String runName,
+      @RequestBody DataQuery query) {
+    checkRunExists(runName);
+    OmittedRunSampleSort sort = parseSort(query, OmittedRunSampleSort::getByLabel);
+    boolean descending = parseDescending(query);
+    return caseService.getOmittedSamplesForRun(runName, query.getPageSize(),
+        query.getPageNumber(), sort, descending);
+  }
+
   private void checkRunExists(String runName) {
     RunAndLibraries runAndLibraries = caseService.getRunAndLibraries(runName);
     if (runAndLibraries == null) {

src/main/java/ca/on/oicr/gsi/dimsum/data/CaseData.java

@@ -13,7 +13,6 @@
 import ca.on.oicr.gsi.cardea.data.Assay;
 import ca.on.oicr.gsi.cardea.data.Case;
 import ca.on.oicr.gsi.cardea.data.OmittedSample;
-import ca.on.oicr.gsi.cardea.data.RunAndLibraries;
 
 @Immutable
 public class CaseData {

src/main/java/ca/on/oicr/gsi/dimsum/data/RunAndLibraries.java

@@ -0,0 +1,77 @@
+package ca.on.oicr.gsi.dimsum.data;
+
+import static java.util.Objects.requireNonNull;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+import ca.on.oicr.gsi.cardea.data.OmittedRunSample;
+import ca.on.oicr.gsi.cardea.data.Run;
+import ca.on.oicr.gsi.cardea.data.Sample;
+
+/**
+ * Immutable RunAndLibraries
+ */
+public class RunAndLibraries {
+
+  private final Set<Sample> fullDepthSequencings;
+  private final Set<Sample> libraryQualifications;
+  private final Set<OmittedRunSample> omittedSamples;
+  private final Run run;
+
+  private RunAndLibraries(Builder builder) {
+    this.run = requireNonNull(builder.run);
+    this.libraryQualifications = Collections.unmodifiableSet(builder.libraryQualifications);
+    this.fullDepthSequencings = Collections.unmodifiableSet(builder.fullDepthSequencings);
+    this.omittedSamples = Collections.unmodifiableSet(builder.omittedSamples);
+  }
+
+  public Set<Sample> getFullDepthSequencings() {
+    return fullDepthSequencings;
+  }
+
+  public Set<Sample> getLibraryQualifications() {
+    return libraryQualifications;
+  }
+
+  public Set<OmittedRunSample> getOmittedSamples() {
+    return omittedSamples;
+  }
+
+  public Run getRun() {
+    return run;
+  }
+
+  public static class Builder {
+
+    private Set<Sample> fullDepthSequencings = new HashSet<>();
+    private Set<Sample> libraryQualifications = new HashSet<>();
+    private Set<OmittedRunSample> omittedSamples = new HashSet<>();
+    private Run run;
+
+    public Builder addFullDepthSequencing(Sample sample) {
+      fullDepthSequencings.add(sample);
+      return this;
+    }
+
+    public Builder addLibraryQualification(Sample sample) {
+      libraryQualifications.add(sample);
+      return this;
+    }
+
+    public Builder addOmittedSample(OmittedRunSample sample) {
+      omittedSamples.add(sample);
+      return this;
+    }
+
+    public RunAndLibraries build() {
+      return new RunAndLibraries(this);
+    }
+
+    public Builder run(Run run) {
+      this.run = run;
+      return this;
+    }
+
+  }
+
+}

src/main/java/ca/on/oicr/gsi/dimsum/service/CaseService.java

@@ -28,10 +28,10 @@
 import ca.on.oicr.gsi.cardea.data.Case;
 import ca.on.oicr.gsi.cardea.data.CaseRelease;
 import ca.on.oicr.gsi.cardea.data.MetricCategory;
+import ca.on.oicr.gsi.cardea.data.OmittedRunSample;
 import ca.on.oicr.gsi.cardea.data.OmittedSample;
 import ca.on.oicr.gsi.cardea.data.Project;
 import ca.on.oicr.gsi.cardea.data.Run;
-import ca.on.oicr.gsi.cardea.data.RunAndLibraries;
 import ca.on.oicr.gsi.cardea.data.Sample;
 import ca.on.oicr.gsi.cardea.data.Test;
 import ca.on.oicr.gsi.dimsum.CaseLoader;
@@ -42,11 +42,13 @@
 import ca.on.oicr.gsi.dimsum.data.ProjectSummary;
 import ca.on.oicr.gsi.dimsum.data.ProjectSummaryField;
 import ca.on.oicr.gsi.dimsum.data.ProjectSummaryRow;
+import ca.on.oicr.gsi.dimsum.data.RunAndLibraries;
 import ca.on.oicr.gsi.dimsum.data.TestTableView;
 import ca.on.oicr.gsi.dimsum.service.filtering.CaseFilter;
 import ca.on.oicr.gsi.dimsum.service.filtering.CaseFilterKey;
 import ca.on.oicr.gsi.dimsum.service.filtering.CaseSort;
 import ca.on.oicr.gsi.dimsum.service.filtering.CompletedGate;
+import ca.on.oicr.gsi.dimsum.service.filtering.OmittedRunSampleSort;
 import ca.on.oicr.gsi.dimsum.service.filtering.OmittedSampleFilter;
 import ca.on.oicr.gsi.dimsum.service.filtering.OmittedSampleFilterKey;
 import ca.on.oicr.gsi.dimsum.service.filtering.OmittedSampleSort;
@@ -558,6 +560,23 @@ public TableData<Sample> getFullDepthSequencingsForRun(String runName, int pageS
         RunAndLibraries::getFullDepthSequencings, MetricCategory.FULL_DEPTH_SEQUENCING);
   }
 
+  public TableData<OmittedRunSample> getOmittedSamplesForRun(String runName, int pageSize,
+      int pageNumber, OmittedRunSampleSort sort, boolean descending) {
+    RunAndLibraries runAndLibraries = caseData.getRunAndLibraries(runName);
+    Set<OmittedRunSample> samples =
+        runAndLibraries == null ? Collections.emptySet() : runAndLibraries.getOmittedSamples();
+
+    TableData<OmittedRunSample> data = new TableData<>();
+    data.setTotalCount(samples.size());
+    data.setFilteredCount(samples.size());
+    data.setItems(samples.stream()
+        .sorted(descending ? sort.comparator().reversed() : sort.comparator())
+        .skip(pageSize * (pageNumber - 1))
+        .limit(pageSize)
+        .toList());
+    return data;
+  }
+
   private TableData<Sample> getRunLibraries(String runName, int pageSize,
       int pageNumber, SampleSort sort, boolean descending, Collection<CaseFilter> filters,
       Function<RunAndLibraries, Set<Sample>> getSamples, MetricCategory requestCategory) {

src/main/java/ca/on/oicr/gsi/dimsum/service/NotificationManager.java

@@ -19,10 +19,10 @@
 import ca.on.oicr.gsi.cardea.data.MetricCategory;
 import ca.on.oicr.gsi.cardea.data.MetricSubcategory;
 import ca.on.oicr.gsi.cardea.data.Run;
-import ca.on.oicr.gsi.cardea.data.RunAndLibraries;
 import ca.on.oicr.gsi.cardea.data.Sample;
 import ca.on.oicr.gsi.dimsum.data.IssueState;
 import ca.on.oicr.gsi.dimsum.data.Notification;
+import ca.on.oicr.gsi.dimsum.data.RunAndLibraries;
 import ca.on.oicr.gsi.dimsum.data.RunQcCommentSummary;
 import ca.on.oicr.gsi.dimsum.service.filtering.NotificationSort;
 import ca.on.oicr.gsi.dimsum.service.filtering.TableData;

src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/OmittedRunSampleSort.java

@@ -0,0 +1,55 @@
+package ca.on.oicr.gsi.dimsum.service.filtering;
+
+import java.util.Comparator;
+import java.util.Map;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+import ca.on.oicr.gsi.cardea.data.OmittedRunSample;
+import ca.on.oicr.gsi.dimsum.util.DataUtils;
+
+public enum OmittedRunSampleSort {
+
+  // @formatter:off
+  NAME("Name", Comparator.comparing(OmittedRunSample::getName)),
+  QC_STATUS("QC Status", Comparator.comparing(OmittedRunSampleSort::getQcStatusSortPriority));
+  // @formatter:on
+
+  private static final Map<String, OmittedRunSampleSort> map =
+      Stream.of(OmittedRunSampleSort.values())
+          .collect(Collectors.toMap(OmittedRunSampleSort::getLabel, Function.identity()));
+
+  public static OmittedRunSampleSort getByLabel(String label) {
+    return map.get(label);
+  }
+
+  private final String label;
+  private final Comparator<OmittedRunSample> comparator;
+
+  private OmittedRunSampleSort(String label, Comparator<OmittedRunSample> comparator) {
+    this.label = label;
+    this.comparator = comparator;
+  }
+
+  public String getLabel() {
+    return label;
+  }
+
+  public Comparator<OmittedRunSample> comparator() {
+    return comparator;
+  }
+
+  protected static int getQcStatusSortPriority(OmittedRunSample sample) {
+    if (sample.getQcDate() == null) {
+      return 1;
+    } else if (sample.getDataReviewDate() == null) {
+      return 2;
+    } else if (DataUtils.isTopUpRequired(sample)) {
+      return 3;
+    } else if (Boolean.TRUE.equals(sample.getQcPassed())) {
+      return 4;
+    } else {
+      return 5;
+    }
+  }
+}

src/main/java/ca/on/oicr/gsi/dimsum/util/DataUtils.java

@@ -7,6 +7,7 @@
 import ca.on.oicr.gsi.cardea.data.Case;
 import ca.on.oicr.gsi.cardea.data.CaseDeliverable;
 import ca.on.oicr.gsi.cardea.data.CaseRelease;
+import ca.on.oicr.gsi.cardea.data.OmittedRunSample;
 import ca.on.oicr.gsi.cardea.data.Sample;
 
 public class DataUtils {
@@ -64,6 +65,10 @@ public static boolean isTopUpRequired(Sample sample) {
     return TOP_UP_REASON.equals(sample.getQcReason());
   }
 
+  public static boolean isTopUpRequired(OmittedRunSample sample) {
+    return TOP_UP_REASON.equals(sample.getQcReason());
+  }
+
   public static boolean isAnalysisReviewSkipped(Case kase) {
     return kase.getProjects().stream().allMatch(project -> project.isAnalysisReviewSkipped());
   }

src/main/resources/templates/run.html → src/main/resources/templates/run-detail.html

@@ -51,7 +51,12 @@ <h1 class="text-green-200 font-sarabun font-light font text-32" th:text="${title
         text-24 mt-8">Full Depth Sequencings</h2>
     <div th:if="${showFullDepthSequencings}" id="fullDepthSequencingsTableContainer"></div>
 
-    <script src="/js/run.js"></script>
+    <h2 th:if="${showOmitted}" class="text-green-200 font-sarabun font-light font text-24 mt-8">
+      Omissions <i id="omissionsInfo" class="fa-solid fa-circle-question text-black"></i>
+    </h2>
+    <div th:if="${showOmitted}" id="omissionsTableContainer"></div>
+
+    <script src="/js/runDetails.js"></script>
 
   </div>
 </body>

src/test/java/ca/on/oicr/gsi/dimsum/service/NotificationManagerTest.java

@@ -24,9 +24,9 @@
 import ca.on.oicr.gsi.cardea.data.MetricCategory;
 import ca.on.oicr.gsi.cardea.data.MetricSubcategory;
 import ca.on.oicr.gsi.cardea.data.Run;
-import ca.on.oicr.gsi.cardea.data.RunAndLibraries;
 import ca.on.oicr.gsi.cardea.data.Sample;
 import ca.on.oicr.gsi.dimsum.data.IssueState;
+import ca.on.oicr.gsi.dimsum.data.RunAndLibraries;
 
 public class NotificationManagerTest {