[GLT-4307] Added donor assay report

changes/add_GLT-4307

@@ -0,0 +1 @@
+Donor Assay Report Download from the Cases table

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

@@ -19,6 +19,7 @@
 import ca.on.oicr.gsi.dimsum.util.reporting.ReportFormat;
 import ca.on.oicr.gsi.dimsum.util.reporting.reports.CaseTatReport;
 import ca.on.oicr.gsi.dimsum.util.reporting.reports.DareInputSheet;
+import ca.on.oicr.gsi.dimsum.util.reporting.reports.DonorAssayReport;
 import ca.on.oicr.gsi.dimsum.util.reporting.reports.FullDepthSummary;
 import ca.on.oicr.gsi.dimsum.util.reporting.reports.TglTrackingReport;
 
@@ -65,6 +66,8 @@ private static Report getReport(String reportName) {
         return DareInputSheet.INSTANCE;
       case "case-tat-report":
         return CaseTatReport.INSTANCE;
+      case "donor-assay-report":
+        return DonorAssayReport.INSTANCE;
       default:
         throw new BadRequestException("Invalid report name");
     }

src/main/java/ca/on/oicr/gsi/dimsum/util/reporting/reports/DonorAssayReport.java

@@ -0,0 +1,89 @@
+package ca.on.oicr.gsi.dimsum.util.reporting.reports;
+
+import java.time.LocalDate;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+import java.util.stream.Collectors;
+import com.fasterxml.jackson.databind.JsonNode;
+import ca.on.oicr.gsi.cardea.data.Case;
+import ca.on.oicr.gsi.cardea.data.Project;
+import ca.on.oicr.gsi.dimsum.controller.BadRequestException;
+import ca.on.oicr.gsi.dimsum.service.CaseService;
+import ca.on.oicr.gsi.dimsum.service.filtering.CompletedGate;
+import ca.on.oicr.gsi.dimsum.util.reporting.Column;
+import ca.on.oicr.gsi.dimsum.util.reporting.Report;
+import ca.on.oicr.gsi.dimsum.util.reporting.ReportSection;
+import ca.on.oicr.gsi.dimsum.util.reporting.ReportSection.TableReportSection;
+import ca.on.oicr.gsi.dimsum.util.reporting.reports.shared.CaseSampleRowData;
+
+public class DonorAssayReport extends Report {
+
+  private static final ReportSection<CaseSampleRowData> mainSection =
+      new TableReportSection<CaseSampleRowData>("Donor Assay Report", Arrays.asList(
+          Column.forString("Project", x -> x.getSample().getProject()),
+          Column.forString("Pipeline", x -> getProjectPipelines(x.getCase())),
+          Column.forString("Donor", x -> x.getCase().getDonor().getName()),
+          Column.forString("External Name", x -> x.getCase().getDonor().getExternalName()),
+          Column.forString("Assay", x -> x.getCase().getAssayName()),
+          Column.forString("Start Date", x -> getStartDate(x.getCase()).toString()),
+          Column.forString("Latest Activity", x -> getLatestActivityDate(x.getCase()).toString()),
+          Column.forString("Status", x -> getCaseStatus(x.getCase())),
+          Column.forString("Stop/Pause Reason", x -> getStopPauseReason(x.getCase())))) {
+        @Override
+        public List<CaseSampleRowData> getData(CaseService caseService, JsonNode parameters) {
+          Set<String> caseIds = getParameterStringSet(parameters, "caseIds");
+          if (caseIds == null) {
+            throw new BadRequestException("caseIds parameter missing");
+          }
+          return CaseSampleRowData.listByCaseIds(caseService, caseIds);
+        }
+      };
+
+  public static final DonorAssayReport INSTANCE = new DonorAssayReport();
+
+  private DonorAssayReport() {
+    super("Donor Assay Report", mainSection);
+  }
+
+  private static String getProjectPipelines(Case kase) {
+    return kase.getProjects().stream()
+        .map(Project::getPipeline)
+        .filter(Objects::nonNull)
+        .collect(Collectors.joining(", "));
+  }
+
+  private static LocalDate getStartDate(Case kase) {
+    return kase.getStartDate();
+  }
+
+  private static LocalDate getLatestActivityDate(Case kase) {
+    return kase.getLatestActivityDate();
+  }
+
+  private static String getCaseStatus(Case kase) {
+    if (CompletedGate.RELEASE.qualifyCase(kase)) {
+      return "Completed";
+    } else if (kase.isStopped()) {
+      return "Failed";
+    } else if (kase.getRequisition().isPaused()) {
+      return "Paused";
+    } else {
+      return "In Progress";
+    }
+  }
+
+  private static String getStopPauseReason(Case kase) {
+    if (kase.isStopped()) {
+      return kase.getRequisition().getStopReason() != null
+          ? kase.getRequisition().getStopReason()
+          : "Reason Unspecified";
+    } else if (kase.getRequisition().isPaused()) {
+      return kase.getRequisition().getPauseReason() != null
+          ? kase.getRequisition().getPauseReason()
+          : "Reason Unspecified";
+    }
+    return "";
+  }
+}

ts/data/case.ts

@@ -1898,11 +1898,13 @@ function hasDeliverable(kase: Case, deliverable: string) {
 
 const REPORT_FULL_DEPTH_SUMMARY = "full-depth-summary";
 const REPORT_DARE_INPUT_SHEET = "dare-input-sheet";
+const DONOR_ASSAY_REPORT = "donor-assay-report";
 
 function showDownloadDialog(items: Case[]) {
   const reportOptions = new Map<string, string>([
     ["Full-Depth Summary", REPORT_FULL_DEPTH_SUMMARY],
     ["DARE Input Sheet", REPORT_DARE_INPUT_SHEET],
+    ["Donor Assay Report", DONOR_ASSAY_REPORT],
   ]);
 
   const reportSelect = new DropdownField(
@@ -1915,6 +1917,7 @@ function showDownloadDialog(items: Case[]) {
     switch (result.report) {
       case REPORT_FULL_DEPTH_SUMMARY:
       case REPORT_DARE_INPUT_SHEET:
+      case DONOR_ASSAY_REPORT:
         showDownloadOptionsDialog(result.report, items);
         break;
       default: