[GLT-4050] switched over from requisition QCs to deliverables

.vscode/launch.json

@@ -9,7 +9,7 @@
       "name": "Debug local Dimsum",
       "request": "attach",
       "hostName": "localhost",
-      "port": 8083
+      "port": 8000
     }
   ]
 }

changes/add_deliverableTypeFilters.md

@@ -0,0 +1 @@
+Separate options for Data Release and Clinical Report in Pending, Completed, and Incomplete filters

changes/add_nabuSignoff.md

@@ -0,0 +1 @@
+Ability to sign off cases for Analysis Review, Release Approval, and Release directly from Dimsum

changes/change_deliverable_types.md

@@ -0,0 +1,3 @@
+Analysis review and release approval sign-offs are now tied to a deliverable type - Clinical Report
+or Data Release. Separate sign-offs are required for each deliverable type that is configured for
+the project

changes/change_deliverables.md

@@ -0,0 +1,2 @@
+Release sign-offs are now tied to a deliverable such as a clinical report or fastQs. Separate
+sign-offs are required for each deliverable that is configured for the project

changes/fix_pendingWork_previousSkipped.md

@@ -0,0 +1 @@
+The pending work icon was not appearing when the previous step was "N/A"

changes/fix_projectPendingCount_stoppedRelease.md

@@ -0,0 +1 @@
+Pending Release Approvals and Releases were not counted for stopped cases in the project summary

example-application.properties

@@ -20,6 +20,7 @@ saml.idpmetadataurl=
 saml.ssourl=
 saml.spkey=
 saml.spcert=
+saml.usernameattribute=
 
 ## JIRA integration
 ## if baseurl is set, all other jira properties are also required

package.json

@@ -15,7 +15,7 @@
   "devDependencies": {
     "tailwindcss": "^3.0.24",
     "ts-loader": "^9.3.0",
-    "typescript": "^4.6.4",
+    "typescript": "^5.3.3",
     "webpack": "^5.76.0",
     "webpack-cli": "^4.9.2"
   }

pom.xml

@@ -138,7 +138,7 @@
     <dependency>
       <groupId>ca.on.oicr.gsi.cardea</groupId>
       <artifactId>cardea-data</artifactId>
-      <version>1.7.0</version>
+      <version>1.8.0</version>
     </dependency>
   </dependencies>
 

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

@@ -1,9 +1,9 @@
 package ca.on.oicr.gsi.dimsum;
 
 import java.io.IOException;
+import java.time.LocalDate;
 import java.time.ZonedDateTime;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -22,14 +22,12 @@
 import ca.on.oicr.gsi.cardea.data.Case;
 import ca.on.oicr.gsi.cardea.data.OmittedSample;
 import ca.on.oicr.gsi.cardea.data.Project;
-import ca.on.oicr.gsi.cardea.data.RequisitionQc;
 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.service.filtering.CompletedGate;
-import ca.on.oicr.gsi.dimsum.service.filtering.DateFilter;
 import ca.on.oicr.gsi.dimsum.service.filtering.PendingState;
 import io.micrometer.core.instrument.MeterRegistry;
 import io.micrometer.core.instrument.Timer;
@@ -81,7 +79,7 @@ public CaseData load(ZonedDateTime previousTimestamp) throws IOException {
     Set<String> donorNames = loadDonorNames(cardeaCaseData.getCases());
     Set<String> testNames = getTestNames(cardeaCaseData.getCases());
     Map<String, ProjectSummary> projectSummariesByName =
-        calculateProjectSummaries(cardeaCaseData.getCases(), null);
+        calculateProjectSummaries(cardeaCaseData.getCases(), null, null);
     ZonedDateTime afterTimestamp = cardeaCaseData.getTimestamp();
 
     CaseData caseData =
@@ -181,29 +179,29 @@ private static interface ParseFunction<T, R> {
   }
 
   public static Map<String, ProjectSummary> calculateProjectSummaries(List<Case> cases,
-      Collection<DateFilter> dateFilters) {
+      LocalDate afterDate, LocalDate beforeDate) {
     Map<String, ProjectSummary.Builder> tempProjectSummariesByName = new HashMap<>();
     for (Case kase : cases) {
-      addCounts(kase, kase.getTests(), tempProjectSummariesByName, dateFilters);
+      addCounts(kase, kase.getTests(), tempProjectSummariesByName, afterDate, beforeDate);
     }
 
     return buildProjectSummaries(tempProjectSummariesByName);
   }
 
   public static Map<String, ProjectSummary> calculateFilteredProjectSummaries(
-      Map<Case, List<Test>> map, Collection<DateFilter> dateFilters) {
+      Map<Case, List<Test>> map, LocalDate afterDate, LocalDate beforeDate) {
     Map<String, ProjectSummary.Builder> tempProjectSummariesByName = new HashMap<>();
     List<Case> cases = new ArrayList<>(map.keySet());
     for (Case kase : cases) {
-      addCounts(kase, map.get(kase), tempProjectSummariesByName, dateFilters);
+      addCounts(kase, map.get(kase), tempProjectSummariesByName, afterDate, beforeDate);
     }
     return buildProjectSummaries(tempProjectSummariesByName);
 
   }
 
   private static void addCounts(Case kase, List<Test> tests,
-      Map<String, ProjectSummary.Builder> tempProjectSummariesByName,
-      Collection<DateFilter> dateFilters) {
+      Map<String, ProjectSummary.Builder> tempProjectSummariesByName, LocalDate afterDate,
+      LocalDate beforeDate) {
     ProjectSummary.Builder caseSummary =
         new ProjectSummary.Builder();
     int testSize = tests != null ? tests.size() : 0;
@@ -212,13 +210,13 @@ private static void addCounts(Case kase, List<Test> tests,
       caseSummary.receiptPendingQcCount(testSize);
     }
     if (CompletedGate.RECEIPT.qualifyCase(kase)
-        && anySamplesMatch(kase.getReceipts(), dateFilters)) {
+        && anySamplesMatch(kase.getReceipts(), afterDate, beforeDate)) {
       caseSummary.receiptCompletedCount(testSize);
     }
     for (Test test : tests) {
-      if ((test.isExtractionSkipped() && emptyOrNull(dateFilters))
+      if ((test.isExtractionSkipped() && afterDate == null && beforeDate == null)
           || (CompletedGate.EXTRACTION.qualifyTest(test)
-              && anySamplesMatch(test.getExtractions(), dateFilters))) {
+              && anySamplesMatch(test.getExtractions(), afterDate, beforeDate))) {
         caseSummary.incrementExtractionCompletedCount();
       } else if (PendingState.EXTRACTION_QC.qualifyTest(test) && !kase.isStopped()) {
         caseSummary.incrementExtractionPendingQcCount();
@@ -227,9 +225,9 @@ && anySamplesMatch(test.getExtractions(), dateFilters))) {
       }
 
       // library Preparation
-      if ((test.isLibraryPreparationSkipped() && emptyOrNull(dateFilters))
+      if ((test.isLibraryPreparationSkipped() && afterDate == null && beforeDate == null)
           || (CompletedGate.LIBRARY_PREPARATION.qualifyTest(test)
-              && anySamplesMatch(test.getLibraryPreparations(), dateFilters))) {
+              && anySamplesMatch(test.getLibraryPreparations(), afterDate, beforeDate))) {
         caseSummary.incrementLibraryPrepCompletedCount();
       } else if (PendingState.LIBRARY_QC.qualifyTest(test) && !kase.isStopped()) {
         caseSummary.incrementLibraryPrepPendingQcCount();
@@ -239,7 +237,7 @@ && anySamplesMatch(test.getLibraryPreparations(), dateFilters))) {
 
       // Library Qualification
       if (CompletedGate.LIBRARY_QUALIFICATION.qualifyTest(test)
-          && anySamplesMatch(test.getLibraryQualifications(), dateFilters)) {
+          && anySamplesMatch(test.getLibraryQualifications(), afterDate, beforeDate)) {
         caseSummary.incrementLibraryQualCompletedCount();
       } else if ((PendingState.LIBRARY_QUALIFICATION_QC.qualifyTest(test)
           || PendingState.LIBRARY_QUALIFICATION_DATA_REVIEW.qualifyTest(test))
@@ -251,7 +249,7 @@ && anySamplesMatch(test.getLibraryQualifications(), dateFilters)) {
 
       // Full depth sequncing
       if (CompletedGate.FULL_DEPTH_SEQUENCING.qualifyTest(test)
-          && anySamplesMatch(test.getFullDepthSequencings(), dateFilters)) {
+          && anySamplesMatch(test.getFullDepthSequencings(), afterDate, beforeDate)) {
         caseSummary.incrementFullDepthSeqCompletedCount();
       } else if ((PendingState.FULL_DEPTH_QC.qualifyTest(test)
           || PendingState.FULL_DEPTH_DATA_REVIEW.qualifyTest(test)) && !kase.isStopped()) {
@@ -263,7 +261,8 @@ && anySamplesMatch(test.getFullDepthSequencings(), dateFilters)) {
 
     // analysis review
     if (CompletedGate.ANALYSIS_REVIEW.qualifyCase(kase)
-        && anyRequisitionQcsMatch(kase.getRequisition().getAnalysisReviews(), dateFilters)) {
+        && kase.getDeliverables().stream()
+            .anyMatch(x -> dateBetween(x.getAnalysisReviewQcDate(), afterDate, beforeDate))) {
       caseSummary.analysisReviewCompletedCount(testSize);
     }
     if (PendingState.ANALYSIS_REVIEW.qualifyCase(kase) && !kase.isStopped()) {
@@ -272,19 +271,22 @@ && anyRequisitionQcsMatch(kase.getRequisition().getAnalysisReviews(), dateFilter
 
     // release approval
     if (CompletedGate.RELEASE_APPROVAL.qualifyCase(kase)
-        && anyRequisitionQcsMatch(kase.getRequisition().getReleaseApprovals(), dateFilters)) {
+        && kase.getDeliverables().stream()
+            .anyMatch(x -> Boolean.TRUE.equals(x.getReleaseApprovalQcPassed()))) {
       caseSummary.releaseApprovalCompletedCount(testSize);
     }
-    if (PendingState.RELEASE_APPROVAL.qualifyCase(kase) && !kase.isStopped()) {
+    if (PendingState.RELEASE_APPROVAL.qualifyCase(kase)) {
       caseSummary.releaseApprovalPendingCount(testSize);
     }
 
     // release
     if (CompletedGate.RELEASE.qualifyCase(kase)
-        && anyRequisitionQcsMatch(kase.getRequisition().getReleases(), dateFilters)) {
+        && kase.getDeliverables().stream()
+            .anyMatch(d -> d.getReleases() != null && d.getReleases().stream()
+                .anyMatch(r -> dateBetween(r.getQcDate(), afterDate, beforeDate)))) {
       caseSummary.releaseCompletedCount(testSize);
     }
-    if (PendingState.RELEASE.qualifyCase(kase) && !kase.isStopped()) {
+    if (PendingState.RELEASE.qualifyCase(kase)) {
       caseSummary.releasePendingCount(testSize);
     }
 
@@ -303,6 +305,20 @@ && anyRequisitionQcsMatch(kase.getRequisition().getReleases(), dateFilters)) {
     }
   }
 
+  protected static boolean dateBetween(LocalDate date, LocalDate afterDate, LocalDate beforeDate) {
+    // Note: afterDate is inclusive, but beforeDate is exclusive
+    if (date == null) {
+      return false;
+    }
+    if (afterDate != null && date.isBefore(afterDate)) {
+      return false;
+    }
+    if (beforeDate != null && !beforeDate.isAfter(date)) {
+      return false;
+    }
+    return true;
+  }
+
   private static Map<String, ProjectSummary> buildProjectSummaries(
       Map<String, ProjectSummary.Builder> tempProjectSummariesByName) {
     Map<String, ProjectSummary> projectSummariesByName = new HashMap<>();
@@ -313,27 +329,20 @@ private static Map<String, ProjectSummary> buildProjectSummaries(
     return projectSummariesByName;
   }
 
-  private static boolean anySamplesMatch(List<Sample> samples, Collection<DateFilter> filters) {
-    if (filters == null || filters.isEmpty()) {
-      return !samples.isEmpty();
-    }
-    return samples.stream()
-        .anyMatch(sample -> filters.stream()
-            .allMatch(filter -> filter.samplePredicate().test(sample)));
-  }
-
-  private static boolean anyRequisitionQcsMatch(List<RequisitionQc> requisitionQcs,
-      Collection<DateFilter> filters) {
-    if (filters == null || filters.isEmpty()) {
-      return !requisitionQcs.isEmpty();
+  private static boolean anySamplesMatch(List<Sample> samples, LocalDate afterDate,
+      LocalDate beforeDate) {
+    if (samples.isEmpty()) {
+      return false;
+    } else if (afterDate == null && beforeDate == null) {
+      return true;
     }
-    return requisitionQcs.stream()
-        .anyMatch(qc -> filters.stream()
-            .allMatch(filter -> filter.requisitionQcPredicate().test(qc)));
-  }
-
-  private static boolean emptyOrNull(Collection<?> collection) {
-    return collection == null || collection.isEmpty();
+    return samples.stream().anyMatch(sample -> {
+      LocalDate qcDate = sample.getRun() == null ? sample.getQcDate() : sample.getDataReviewDate();
+      if (qcDate == null) {
+        return false;
+      }
+      return dateBetween(qcDate, afterDate, beforeDate);
+    });
   }
 
 }

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

@@ -1,15 +1,13 @@
 package ca.on.oicr.gsi.dimsum.controller.mvc;
 
+import java.time.LocalDate;
 import java.util.List;
 import java.util.function.Function;
-import java.util.stream.Stream;
 import ca.on.oicr.gsi.dimsum.controller.BadRequestException;
 import ca.on.oicr.gsi.dimsum.controller.rest.request.DataQuery;
 import ca.on.oicr.gsi.dimsum.controller.rest.request.KeyValuePair;
 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.DateFilter;
-import ca.on.oicr.gsi.dimsum.service.filtering.DateFilterKey;
 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.ProjectSummaryFilter;
@@ -18,8 +16,9 @@
 import ca.on.oicr.gsi.dimsum.service.filtering.RunFilterKey;
 
 public class MvcUtils {
-  private final static List<String> dateFilterKeys =
-      Stream.of(DateFilterKey.values()).map(DateFilterKey::name).toList();
+
+  private static final String BEFORE_DATE_KEY = "BEFORE_DATE";
+  private static final String AFTER_DATE_KEY = "AFTER_DATE";
 
 
   public static void validateDataQuery(DataQuery query) {
@@ -67,7 +66,8 @@ public static List<CaseFilter> parseCaseFiltersForProject(DataQuery query) {
     // exclude Date Range Filters before validating each filter KVP
     List<KeyValuePair> queryFilters =
         query.getFilters().stream()
-            .filter(x -> !dateFilterKeys.contains(x.getKey())).toList();
+            .filter(x -> !BEFORE_DATE_KEY.equals(x.getKey()) && !AFTER_DATE_KEY.equals(x.getKey()))
+            .toList();
     if (queryFilters == null || queryFilters.isEmpty()) {
       return null;
     }
@@ -118,25 +118,20 @@ private static OmittedSampleFilter parseOmittedSampleFilter(KeyValuePair pair) {
     }
   }
 
-  public static List<DateFilter> parseDateFilters(DataQuery query) {
-    // exclude Date Range Filters before validating each filter KVP
-    List<KeyValuePair> queryFilters =
-        query.getFilters().stream()
-            .filter(x -> dateFilterKeys.contains(x.getKey())).toList();
-    if (queryFilters == null || queryFilters.isEmpty()) {
-      return null;
-    }
-    return queryFilters.stream()
-        .map(MvcUtils::parseDateFilter).toList();
+  public static LocalDate parseAfterDate(DataQuery query) {
+    return parseDateFilterValue(query, AFTER_DATE_KEY);
   }
 
-  private static DateFilter parseDateFilter(KeyValuePair pair) {
-    try {
-      DateFilterKey key = DateFilterKey.valueOf(pair.getKey());
-      return new DateFilter(key, pair.getValue());
-    } catch (IllegalArgumentException e) {
-      throw new BadRequestException(String.format("Invalid filter key: %s", pair.getKey()));
-    }
+  public static LocalDate parseBeforeDate(DataQuery query) {
+    return parseDateFilterValue(query, BEFORE_DATE_KEY);
+  }
+
+  private static LocalDate parseDateFilterValue(DataQuery query, String key) {
+    String value = query.getFilters().stream()
+        .filter(x -> key.equals(x.getKey()))
+        .map(KeyValuePair::getValue)
+        .findFirst().orElse(null);
+    return value == null ? null : LocalDate.parse(value);
   }
 
   public static List<ProjectSummaryFilter> parseProjectSummaryFilters(DataQuery query) {