[GLT-4120] skip analysis review based on deliverables

oicr-gsi · Apr 10, 2024 · 076f918 · 076f918
1 parent 4dd6b1d
commit 076f918
Show file tree

Hide file tree

Showing 9 changed files with 176 additions and 93 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,30 +1,31 @@
 {
-    "java.configuration.updateBuildConfiguration": "automatic",
-    "java.format.settings.url": ".vscode/eclipse-java-google-style.xml",
-    "[java]": {
-        "editor.defaultFormatter": "redhat.java",
-        "editor.formatOnSaveMode": "file",
-        "editor.formatOnSave": true
-    },
-    "[javascript]": {
-        "editor.defaultFormatter": "esbenp.prettier-vscode",
-        "editor.formatOnSave": true,
-        "editor.formatOnSaveMode": "file"
-    },
-    "[html]": {
-        "editor.defaultFormatter": "vscode.html-language-features",
-        "editor.formatOnSaveMode": "file",
-        "editor.formatOnSave": true
-    },
-    "[typescript]": {
-        "editor.formatOnSave": true,
-        "editor.formatOnSaveMode": "file",
-        "editor.defaultFormatter": "esbenp.prettier-vscode"
-    },
-    "[markdown]": {
-        "editor.formatOnSave": false // Formatting breaks multi-level lists and doesn't respect config
-    },
-    "editor.tabSize": 2,
-    "java.saveActions.organizeImports": true,
-    "java.sources.organizeImports.staticStarThreshold": 2
+  "java.configuration.updateBuildConfiguration": "automatic",
+  "java.format.settings.url": ".vscode/eclipse-java-google-style.xml",
+  "[java]": {
+    "editor.defaultFormatter": "redhat.java",
+    "editor.formatOnSaveMode": "file",
+    "editor.formatOnSave": true
+  },
+  "[javascript]": {
+    "editor.defaultFormatter": "esbenp.prettier-vscode",
+    "editor.formatOnSave": true,
+    "editor.formatOnSaveMode": "file"
+  },
+  "[html]": {
+    "editor.defaultFormatter": "vscode.html-language-features",
+    "editor.formatOnSaveMode": "file",
+    "editor.formatOnSave": true
+  },
+  "[typescript]": {
+    "editor.formatOnSave": true,
+    "editor.formatOnSaveMode": "file",
+    "editor.defaultFormatter": "esbenp.prettier-vscode"
+  },
+  "[markdown]": {
+    "editor.formatOnSave": false // Formatting breaks multi-level lists and doesn't respect config
+  },
+  "editor.tabSize": 2,
+  "java.saveActions.organizeImports": true,
+  "java.sources.organizeImports.staticStarThreshold": 2,
+  "java.compile.nullAnalysis.mode": "automatic"
 }
diff --git a/changes/change_analysisReviewSkip.md b/changes/change_analysisReviewSkip.md
@@ -0,0 +1 @@
+Analysis review will be marked 'N/A' for cases where none of the deliverables require analysis review
diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/CaseFilterKey.java b/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/CaseFilterKey.java
@@ -52,7 +52,8 @@ public Function<String, Predicate<Test>> testPredicate() {
   PAUSED(string -> kase -> ("Yes".equals(string)) ? kase.getRequisition().isPaused() : !kase.getRequisition().isPaused()),
   COMPLETED(string -> {
     CompletedGate gate = getGate(string);
-    return gate.predicate();
+    Predicate<Case> applicable = x -> gate.isApplicable(x);
+    return applicable.and(gate.predicate());
   }) {
     @Override
     public Function<String, Predicate<Test>> testPredicate() {

diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/CompletedGate.java b/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/CompletedGate.java
@@ -104,21 +104,33 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
   ANALYSIS_REVIEW("Analysis Review", true) {
     @Override
     public boolean qualifyCase(Case kase) {
-      return qualifyCaseForDeliverableType(kase, null, CaseDeliverable::getAnalysisReviewQcPassed);
+      if (SampleUtils.isAnalysisReviewSkipped(kase)) {
+        return FULL_DEPTH_SEQUENCING.qualifyCase(kase);
+      } else {
+        return qualifyCaseForDeliverableType(kase, null, CaseDeliverable::getAnalysisReviewQcPassed);
+      }
     }
   },
   ANALYSIS_REVIEW_DATA_RELEASE("Analysis Review - Data Release", true, DeliverableType.DATA_RELEASE) {
     @Override
     public boolean qualifyCase(Case kase) {
-      return qualifyCaseForDeliverableType(kase, DeliverableType.DATA_RELEASE,
-          CaseDeliverable::getAnalysisReviewQcPassed);
+      if (SampleUtils.isAnalysisReviewSkipped(kase)) {
+        return FULL_DEPTH_SEQUENCING.qualifyCase(kase);
+      } else {
+        return qualifyCaseForDeliverableType(kase, DeliverableType.DATA_RELEASE,
+            CaseDeliverable::getAnalysisReviewQcPassed);
+      }
     }
   },
   ANALYSIS_REVIEW_CLINICAL_REPORT("Analysis Review - Clinical Report", true, DeliverableType.CLINICAL_REPORT) {
     @Override
     public boolean qualifyCase(Case kase) {
-      return qualifyCaseForDeliverableType(kase, DeliverableType.CLINICAL_REPORT,
-          CaseDeliverable::getAnalysisReviewQcPassed);
+      if (SampleUtils.isAnalysisReviewSkipped(kase)) {
+        return FULL_DEPTH_SEQUENCING.qualifyCase(kase);
+      } else {
+        return qualifyCaseForDeliverableType(kase, DeliverableType.CLINICAL_REPORT,
+            CaseDeliverable::getAnalysisReviewQcPassed);
+      }
     }
   },
   RELEASE_APPROVAL("Release Approval", false) {

diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/PendingState.java b/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/PendingState.java
@@ -234,22 +234,25 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
   ANALYSIS_REVIEW("Analysis Review", true) {
     @Override
     public boolean qualifyCase(Case kase) {
-      return CompletedGate.FULL_DEPTH_SEQUENCING.qualifyCase(kase)
+      return !SampleUtils.isAnalysisReviewSkipped(kase)
+          && CompletedGate.FULL_DEPTH_SEQUENCING.qualifyCase(kase)
           && !CompletedGate.ANALYSIS_REVIEW.qualifyCase(kase);
     }
   },
   ANALYSIS_REVIEW_DATA_RELEASE("Analysis Review - Data Release", true) {
     @Override
     public boolean qualifyCase(Case kase) {
-      return CompletedGate.FULL_DEPTH_SEQUENCING.qualifyCase(kase)
+      return !SampleUtils.isAnalysisReviewSkipped(kase)
+          && CompletedGate.FULL_DEPTH_SEQUENCING.qualifyCase(kase)
           && CompletedGate.ANALYSIS_REVIEW_DATA_RELEASE.isApplicable(kase)
           && !CompletedGate.ANALYSIS_REVIEW_DATA_RELEASE.qualifyCase(kase);
     }
   },
   ANALYSIS_REVIEW_CLINICAL_REPORT("Analysis Review - Clinical Report", true) {
     @Override
     public boolean qualifyCase(Case kase) {
-      return CompletedGate.FULL_DEPTH_SEQUENCING.qualifyCase(kase)
+      return !SampleUtils.isAnalysisReviewSkipped(kase)
+          && CompletedGate.FULL_DEPTH_SEQUENCING.qualifyCase(kase)
           && CompletedGate.ANALYSIS_REVIEW_CLINICAL_REPORT.isApplicable(kase)
           && !CompletedGate.ANALYSIS_REVIEW_CLINICAL_REPORT.qualifyCase(kase);
     }
@@ -266,17 +269,15 @@ public boolean qualifyCase(Case kase) {
   RELEASE_APPROVAL_DATA_RELEASE("Release Approval - Data Release", false) {
     @Override
     public boolean qualifyCase(Case kase) {
-      return (kase.isStopped() || CompletedGate.ANALYSIS_REVIEW_DATA_RELEASE.qualifyCase(kase))
-          && CompletedGate.RELEASE_APPROVAL_DATA_RELEASE.isApplicable(kase)
-          && !CompletedGate.RELEASE_APPROVAL_DATA_RELEASE.qualifyCase(kase);
+      return Helpers.isPendingReleaseApproval(kase, CompletedGate.ANALYSIS_REVIEW_DATA_RELEASE,
+          CompletedGate.RELEASE_APPROVAL_DATA_RELEASE);
     }
   },
   RELEASE_APPROVAL_CLINICAL_REPORT("Release Approval - Clinical Report", false) {
     @Override
     public boolean qualifyCase(Case kase) {
-      return (kase.isStopped() || CompletedGate.ANALYSIS_REVIEW_CLINICAL_REPORT.qualifyCase(kase))
-          && CompletedGate.RELEASE_APPROVAL_CLINICAL_REPORT.isApplicable(kase)
-          && !CompletedGate.RELEASE_APPROVAL_CLINICAL_REPORT.qualifyCase(kase);
+      return Helpers.isPendingReleaseApproval(kase, CompletedGate.ANALYSIS_REVIEW_CLINICAL_REPORT,
+          CompletedGate.RELEASE_APPROVAL_CLINICAL_REPORT);
     }
   },
   RELEASE("Release", false) {
@@ -395,6 +396,14 @@ public static boolean hasPendingQc(List<Sample> samples) {
     public static boolean hasPendingDataReview(List<Sample> samples) {
       return samples.stream().anyMatch(pendingDataReview);
     }
+
+    public static boolean isPendingReleaseApproval(Case kase, CompletedGate previousGate,
+        CompletedGate gate) {
+      if (!kase.isStopped() && !previousGate.qualifyCase(kase)) {
+        return false;
+      }
+      return gate.isApplicable(kase) && !gate.qualifyCase(kase);
+    }
   }
 
 }
diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/util/SampleUtils.java b/src/main/java/ca/on/oicr/gsi/dimsum/util/SampleUtils.java
@@ -1,6 +1,7 @@
 package ca.on.oicr.gsi.dimsum.util;
 
 import java.util.function.Predicate;
+import ca.on.oicr.gsi.cardea.data.Case;
 import ca.on.oicr.gsi.cardea.data.Sample;
 
 public class SampleUtils {
@@ -44,4 +45,8 @@ public static boolean isPendingDataReview(Sample sample) {
   public static boolean isTopUpRequired(Sample sample) {
     return TOP_UP_REASON.equals(sample.getQcReason());
   }
+
+  public static boolean isAnalysisReviewSkipped(Case kase) {
+    return kase.getProjects().stream().allMatch(project -> project.isAnalysisReviewSkipped());
+  }
 }
diff --git a/src/test/java/ca/on/oicr/gsi/dimsum/MockCase.java b/src/test/java/ca/on/oicr/gsi/dimsum/MockCase.java
@@ -32,7 +32,7 @@ public static List<Case> getCases() {
           makeCase12(), makeCase13(), makeCase14(), makeCase15(), makeCase16(), makeCase17(),
           makeCase18(), makeCase19(), makeCase20(), makeCase21(), makeCase22(), makeCase23(),
           makeCase24(), makeCase25(), makeCase26(), makeCase27(), makeCase28(), makeCase29(),
-          makeCase30(), makeCase31());
+          makeCase30(), makeCase31(), makeCase32(), makeCase33());
 
   private static Case makeCase0() {
     final int caseNumber = 0;
@@ -398,6 +398,28 @@ private static Case makeCase31() {
     return kase;
   }
 
+  private static Case makeCase32() {
+    // Analysis review skipped, but case is not there yet anyway
+    final int caseNumber = 32;
+    Case kase = makeCase("PRO32_0001", "Single Test", "PRO32", "REQ32", caseNumber);
+    addTest(kase, caseNumber, 1, "test", "WG", false, false, false, false);
+    addDeliverable(kase, DeliverableType.DATA_RELEASE, "FastQ");
+    Project project = kase.getProjects().iterator().next();
+    when(project.isAnalysisReviewSkipped()).thenReturn(true);
+    return kase;
+  }
+
+  private static Case makeCase33() {
+    // Full-depth completed, analysis review skipped
+    final int caseNumber = 33;
+    Case kase = makeCase("PRO33_0001", "Single Test", "PRO33", "REQ33", caseNumber);
+    addTest(kase, caseNumber, 1, "test", "WG", true, true, true, true);
+    addDeliverable(kase, DeliverableType.DATA_RELEASE, "FastQ");
+    Project project = kase.getProjects().iterator().next();
+    when(project.isAnalysisReviewSkipped()).thenReturn(true);
+    return kase;
+  }
+
   private static Case makeCase(String donorName, String assayName, String projectName,
       String requisitionName, int caseNumber) {
     Case kase = mock(Case.class);
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Analysis review will be marked 'N/A' for cases where none of the deliverables require analysis review