[GLT-4068] added case TAT report

changes/add_GLT-4068.md

@@ -0,0 +1 @@
+Case TAT report generated from the Cases list and uses the same filters that are applied to the list

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

@@ -3,7 +3,6 @@
 import java.io.IOException;
 import java.time.ZonedDateTime;
 import java.time.format.DateTimeFormatter;
-import java.util.Map;
 import javax.servlet.http.HttpServletResponse;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpEntity;
@@ -13,10 +12,12 @@
 import org.springframework.web.bind.annotation.RequestBody;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
+import com.fasterxml.jackson.databind.JsonNode;
 import ca.on.oicr.gsi.dimsum.controller.BadRequestException;
 import ca.on.oicr.gsi.dimsum.service.CaseService;
 import ca.on.oicr.gsi.dimsum.util.reporting.Report;
 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.FullDepthSummary;
 import ca.on.oicr.gsi.dimsum.util.reporting.reports.TglTrackingReport;
@@ -30,7 +31,7 @@ public class DownloadRestController {
 
   @PostMapping("/reports/{reportName}")
   public HttpEntity<byte[]> generateReport(@PathVariable String reportName,
-      @RequestBody Map<String, String> parameters, HttpServletResponse response)
+      @RequestBody JsonNode parameters, HttpServletResponse response)
       throws IOException {
 
     ReportFormat format = Report.getFormat(parameters);
@@ -55,6 +56,8 @@ private static Report getReport(String reportName) {
         return FullDepthSummary.INSTANCE;
       case "dare-input-sheet":
         return DareInputSheet.INSTANCE;
+      case "case-tat-report":
+        return CaseTatReport.INSTANCE;
       default:
         throw new BadRequestException("Invalid report name");
     }

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

@@ -51,6 +51,25 @@ public String getDelimitedColumnString(String delimiter, T object) {
     };
   }
 
+  public static <T> Column<T> forInteger(String title, Function<T, Integer> getter) {
+    return new Column<T>(title) {
+
+      @Override
+      public void writeExcelCell(Cell cell, T object) {
+        Integer value = getter.apply(object);
+        if (value != null) {
+          cell.setCellValue(value.doubleValue());
+        }
+      }
+
+      @Override
+      public String getDelimitedColumnString(String delimiter, T object) {
+        Integer value = getter.apply(object);
+        return value != null ? value.toString() : "";
+      }
+    };
+  }
+
   private final String title;
 
   public Column(String title) {

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

@@ -5,9 +5,8 @@
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
-import java.util.Map;
-import java.util.Objects;
 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import com.fasterxml.jackson.databind.JsonNode;
 import ca.on.oicr.gsi.dimsum.controller.BadRequestException;
 import ca.on.oicr.gsi.dimsum.service.CaseService;
 
@@ -28,8 +27,8 @@ public String getTitle() {
     return title;
   }
 
-  public static ReportFormat getFormat(Map<String, String> parameters) {
-    String format = parameters.get(PARAM_FORMAT);
+  public static ReportFormat getFormat(JsonNode parameters) {
+    String format = parameters.has(PARAM_FORMAT) ? parameters.get(PARAM_FORMAT).asText() : null;
     if (format == null) {
       return ReportFormat.EXCEL;
     }
@@ -45,7 +44,7 @@ public static ReportFormat getFormat(Map<String, String> parameters) {
     }
   }
 
-  public byte[] writeFile(CaseService caseService, Map<String, String> parameters)
+  public byte[] writeFile(CaseService caseService, JsonNode parameters)
       throws IOException {
     ReportFormat format = getFormat(parameters);
 
@@ -61,7 +60,7 @@ public byte[] writeFile(CaseService caseService, Map<String, String> parameters)
     }
   }
 
-  private byte[] writeExcelFile(CaseService caseService, Map<String, String> parameters)
+  private byte[] writeExcelFile(CaseService caseService, JsonNode parameters)
       throws IOException {
     XSSFWorkbook workbook = new XSSFWorkbook();
     for (ReportSection<?> section : sections) {
@@ -74,9 +73,10 @@ private byte[] writeExcelFile(CaseService caseService, Map<String, String> param
   }
 
   private byte[] writeDelimitedFile(CaseService caseService, String delimiter,
-      Map<String, String> parameters) {
+      JsonNode parameters) {
     StringBuilder sb = new StringBuilder();
-    boolean includeHeadings = Objects.equals("true", parameters.get(PARAM_HEADINGS));
+    boolean includeHeadings =
+        parameters.has(PARAM_HEADINGS) && "true".equals(parameters.get(PARAM_HEADINGS).asText());
     // This does not support multiple sections
     sections.get(0).createDelimitedText(sb, caseService, delimiter, includeHeadings, parameters);
     return sb.toString().getBytes();

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

@@ -2,14 +2,14 @@
 
 import java.util.Collections;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 import org.apache.poi.ss.usermodel.Cell;
 import org.apache.poi.ss.usermodel.Row;
 import org.apache.poi.xssf.usermodel.XSSFSheet;
 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import com.fasterxml.jackson.databind.JsonNode;
 import ca.on.oicr.gsi.dimsum.controller.BadRequestException;
 import ca.on.oicr.gsi.dimsum.service.CaseService;
 
@@ -84,7 +84,7 @@ public List<Column<T>> getColumns() {
   }
 
   public void createExcelSheet(XSSFWorkbook workbook, CaseService caseService,
-      Map<String, String> parameters) {
+      JsonNode parameters) {
     List<T> objects = getData(caseService, parameters);
     XSSFSheet worksheet = workbook.createSheet(getTitle());
     writeExcelSheet(worksheet, objects);
@@ -93,7 +93,7 @@ public void createExcelSheet(XSSFWorkbook workbook, CaseService caseService,
   protected abstract void writeExcelSheet(XSSFSheet worksheet, List<T> objects);
 
   public void createDelimitedText(StringBuilder sb, CaseService caseService,
-      String delimiter, boolean includeHeadings, Map<String, String> parameters) {
+      String delimiter, boolean includeHeadings, JsonNode parameters) {
     List<T> objects = getData(caseService, parameters);
     writeDelimitedText(sb, objects, delimiter, includeHeadings);
   }
@@ -110,10 +110,11 @@ protected abstract void writeDelimitedText(StringBuilder sb, List<T> objects, St
    * 
    * @throws BadRequestException if there are invalid parameters
    */
-  public abstract List<T> getData(CaseService caseService, Map<String, String> parameters);
+  public abstract List<T> getData(CaseService caseService, JsonNode parameters);
 
-  protected static Set<String> getParameterStringSet(Map<String, String> parameters, String name) {
-    String value = parameters.get(name);
+  protected static Set<String> getParameterStringSet(JsonNode parameters, String name) {
+    JsonNode valueNode = parameters.get(name);
+    String value = (valueNode != null) ? valueNode.asText() : null;
     if (value == null || value.isEmpty()) {
       return null;
     }

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

@@ -0,0 +1,226 @@
+package ca.on.oicr.gsi.dimsum.util.reporting.reports;
+
+import java.time.LocalDate;
+import java.time.format.DateTimeFormatter;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.function.Function;
+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.CaseDeliverable;
+import ca.on.oicr.gsi.cardea.data.CaseRelease;
+import ca.on.oicr.gsi.cardea.data.Project;
+import ca.on.oicr.gsi.cardea.data.Requisition;
+import ca.on.oicr.gsi.cardea.data.Sample;
+import ca.on.oicr.gsi.cardea.data.Test;
+import ca.on.oicr.gsi.dimsum.controller.BadRequestException;
+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.CaseFilterKey;
+import ca.on.oicr.gsi.dimsum.util.SampleUtils;
+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;
+
+public class CaseTatReport extends Report {
+
+  private static class RowData {
+
+    private final Case kase;
+    private final Test test;
+
+    public RowData(Case kase, Test test) {
+      this.kase = kase;
+      this.test = test;
+    }
+
+    public Case getCase() {
+      return kase;
+    }
+
+    public Test getTest() {
+      return test;
+    }
+  }
+
+  private static final ReportSection<RowData> caseSection =
+      new TableReportSection<>("Case Report",
+          Arrays.asList(
+              Column.forString("Case ID", x -> x.getCase().getId()),
+              Column.forString("Projects",
+                  x -> getSortedProjectNameOrPipeline(x.getCase(), Project::getName)),
+              Column.forString("Pipeline",
+                  x -> getSortedProjectNameOrPipeline(x.getCase(), Project::getPipeline)),
+              Column.forString("Requisition", x -> x.getCase().getRequisition().getName()),
+              Column.forString("Assay", x -> x.getCase().getAssayName()),
+              Column.forString("Start Date",
+                  x -> x.getCase().getStartDate().format(DateTimeFormatter.ISO_LOCAL_DATE)),
+              Column.forString("Receipt Completed",
+                  x -> findLatestCompletionDate(x.getCase().getReceipts())),
+              Column.forInteger("Receipt Days", x -> x.getCase().getReceiptDaysSpent()),
+              Column.forString("Test", x -> x.getTest().getName()),
+              Column.forString("Supplemental Only",
+                  x -> isSupplementalOnly(x.getTest(), x.getCase().getRequisition()) ? "Yes"
+                      : "No"),
+              Column.forString("Extraction Completed",
+                  x -> findLatestCompletionDate(x.getTest().getExtractions())),
+              Column.forInteger("Extraction Days", x -> x.getTest().getExtractionDaysSpent()),
+              Column.forString("Library Prep Completed",
+                  x -> findLatestCompletionDate(x.getTest().getLibraryPreparations())),
+              Column.forInteger("Library Prep. Days",
+                  x -> x.getTest().getLibraryPreparationDaysSpent()),
+              Column.forString("Library Qual Completed",
+                  x -> findLatestCompletionDate(x.getTest().getLibraryQualifications())),
+              Column.forInteger("Library Qual. Days",
+                  x -> x.getTest().getLibraryQualificationDaysSpent()),
+              Column.forString("Full-Depth Completed",
+                  x -> findLatestCompletionDate(x.getTest().getFullDepthSequencings())),
+              Column.forInteger("Full-Depth Days",
+                  x -> x.getTest().getFullDepthSequencingDaysSpent()),
+              Column.forString("Analysis Review Completed",
+                  x -> getMaxDateFromDeliverables(x.getCase(),
+                      CaseDeliverable::getAnalysisReviewQcDate)),
+              Column.forInteger("Analysis Review Days",
+                  x -> x.getCase().getAnalysisReviewDaysSpent()),
+              Column.forString("Release Approval Completed",
+                  x -> getMaxDateFromDeliverables(x.getCase(),
+                      CaseDeliverable::getReleaseApprovalQcDate)),
+              Column.forString("Release Completed", x -> {
+                if (!x.getCase().isStopped()) {
+                  return getCompletionDate(x.getCase());
+                }
+                List<LocalDate> dates = x.getCase().getDeliverables().stream()
+                    .flatMap(deliverable -> deliverable.getReleases().stream())
+                    .map(CaseRelease::getQcDate)
+                    .collect(Collectors.toList());
+                if (dates.contains(null)) {
+                  return null;
+                }
+                return dates.stream().max(LocalDate::compareTo)
+                    .map(date -> date.format(DateTimeFormatter.ISO_LOCAL_DATE)).orElse(null);
+              }),
+              Column.forInteger("Release Days", x -> x.getCase().getReleaseDaysSpent()),
+              Column.forString("Completion Date", x -> getCompletionDate(x.getCase())),
+              Column.forInteger("Total Days", x -> x.getCase().getCaseDaysSpent()))) {
+
+        @Override
+        public List<RowData> getData(CaseService caseService, JsonNode parameters) {
+          List<CaseFilter> filters = convertParametersToFilters(parameters);
+          return caseService.getCaseStream(filters)
+              .flatMap(kase -> kase.getTests().stream().map(test -> new RowData(kase, test)))
+              .collect(Collectors.toList());
+        }
+      };
+
+  public static final CaseTatReport INSTANCE = new CaseTatReport();
+
+  private CaseTatReport() {
+    super("Case TAT Report", caseSection);
+  }
+
+  private static String getSortedProjectNameOrPipeline(Case kase,
+      Function<Project, String> function) {
+    return kase.getProjects().stream()
+        .map(function)
+        .sorted()
+        .collect(Collectors.joining(", "));
+  }
+
+  private static List<CaseFilter> convertParametersToFilters(JsonNode parameters) {
+    List<CaseFilter> filters = new ArrayList<>();
+    parameters.fields().forEachRemaining(entry -> {
+      try {
+        CaseFilterKey filterKey = CaseFilterKey.valueOf(entry.getKey().toUpperCase());
+        String[] values = entry.getValue().asText().split(",");
+        for (String value : values) {
+          CaseFilter filter = new CaseFilter(filterKey, value.trim());
+          filters.add(filter);
+        }
+      } catch (IllegalArgumentException e) {
+        throw new BadRequestException(
+            "Invalid filter key: " + entry.getKey() + ". " + e.getMessage());
+      }
+    });
+    return filters;
+  }
+
+  private static boolean isSupplementalOnly(Test test, Requisition requisition) {
+    if (test.getExtractions().isEmpty()
+        || test.getLibraryPreparations().isEmpty()
+        || test.getLibraryQualifications().isEmpty()
+        || test.getFullDepthSequencings().isEmpty()) {
+      return false;
+    }
+    return test.getExtractions().stream()
+        .allMatch(sample -> !sample.getRequisitionId().equals(requisition.getId()))
+        && test.getLibraryPreparations().stream()
+            .allMatch(sample -> !sample.getRequisitionId().equals(requisition.getId()))
+        && test.getLibraryQualifications().stream()
+            .allMatch(sample -> !sample.getRequisitionId().equals(requisition.getId()))
+        && test.getFullDepthSequencings().stream()
+            .allMatch(sample -> !sample.getRequisitionId().equals(requisition.getId()));
+  }
+
+  private static String findLatestCompletionDate(List<Sample> samples) {
+    LocalDate latestDate = null;
+    for (Sample sample : samples) {
+      if (SampleUtils.isPassed(sample)) {
+        LocalDate dateToCompare = null;
+        if (sample.getRun() != null) {
+          LocalDate sampleReviewDate = sample.getDataReviewDate();
+          LocalDate runReviewDate = sample.getRun().getDataReviewDate();
+          if (sampleReviewDate != null && runReviewDate != null) {
+            dateToCompare =
+                runReviewDate.isAfter(sampleReviewDate) ? runReviewDate : sampleReviewDate;
+          }
+        } else {
+          dateToCompare = sample.getQcDate();
+        }
+        if (dateToCompare != null && (latestDate == null || dateToCompare.isAfter(latestDate))) {
+          latestDate = dateToCompare;
+        }
+      }
+    }
+    return latestDate != null ? latestDate.format(DateTimeFormatter.ISO_LOCAL_DATE) : null;
+  }
+
+  private static String getMaxDateFromDeliverables(Case x,
+      Function<CaseDeliverable, LocalDate> dateExtractor) {
+    List<LocalDate> dates = x.getDeliverables().stream()
+        .map(dateExtractor)
+        .collect(Collectors.toList());
+    if (dates.contains(null)) {
+      return null;
+    }
+    return dates.stream().max(LocalDate::compareTo)
+        .map(date -> date.format(DateTimeFormatter.ISO_LOCAL_DATE)).orElse(null);
+  }
+
+  private static String getCompletionDate(Case x) {
+    if (x.isStopped()) {
+      return "STOPPED";
+    }
+    List<CaseDeliverable> deliverables = x.getDeliverables();
+    if (deliverables.isEmpty()) {
+      return null;
+    }
+    List<CaseRelease> releases = deliverables.stream()
+        .flatMap(deliverable -> deliverable.getReleases().stream())
+        .collect(Collectors.toList());
+    if (releases.isEmpty()) {
+      return null;
+    }
+    if (releases.stream()
+        .anyMatch(release -> release.getQcPassed() == null || !release.getQcPassed())) {
+      return null;
+    }
+    LocalDate latestQcDate = releases.stream()
+        .map(CaseRelease::getQcDate)
+        .max(LocalDate::compareTo)
+        .orElse(null);
+    return latestQcDate != null ? latestQcDate.toString() : null;
+  }
+}