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[GLT-4060] require release for stopped cases #172

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Jan 3, 2024
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[GLT-4060] require release for stopped cases #172

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6da593c
[GLT-4060] require release for stopped cases
djcooke Dec 22, 2023
db965db
stopping no longer affects urgency; removed tests for this
djcooke Dec 22, 2023
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1 change: 1 addition & 0 deletions changes/change_stopped_release.md
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@@ -0,0 +1 @@
Release approval and release steps are now required even for stopped cases
1 change: 1 addition & 0 deletions changes/fix_stopped_overdue.md
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@@ -0,0 +1 @@
Steps that were skipped due to the case being stopped could still be shown as overdue
4 changes: 3 additions & 1 deletion src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/CaseFilterKey.java
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Expand Up @@ -20,7 +20,9 @@ public enum CaseFilterKey {
|| kase.getDonor().getExternalName().toLowerCase().contains(string.toLowerCase())),
PENDING(string -> {
PendingState state = getState(string);
Predicate<Case> notStoppedOrPaused = kase -> !kase.getRequisition().isStopped() && !kase.getRequisition().isPaused();
Predicate<Case> notStoppedOrPaused = kase ->
(!state.isStoppable() || !kase.getRequisition().isStopped())
&& !kase.getRequisition().isPaused();
return notStoppedOrPaused.and(state.predicate());
}) {
@Override
Expand Down
38 changes: 21 additions & 17 deletions src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/CaseSort.java
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Expand Up @@ -16,7 +16,7 @@ public enum CaseSort {
@Override
public Comparator<Case> comparator(Map<Long, Assay> assaysById) {
return (a, b) -> {
// If one case is inactive (stopped/paused/complete), the other is more urgent
// If one case is inactive (paused/complete), the other is more urgent
// If both cases are inactive, consider them equal
if (isInactive(a)) {
if (isInactive(b)) {
Expand Down Expand Up @@ -58,8 +58,7 @@ public Comparator<Case> comparator(Map<Long, Assay> assaysById) {
}

private static boolean isInactive(Case kase) {
return kase.isStopped()
|| kase.getRequisition().isPaused()
return kase.getRequisition().isPaused()
|| CompletedGate.RELEASE.qualifyCase(kase);
}

Expand Down Expand Up @@ -93,23 +92,28 @@ private static int calculateStepDaysOverdue(Case kase, AssayTargets targets) {
}

private static boolean isStepBehind(Integer target, Case kase, CompletedGate completedGate) {
return target != null && kase.getCaseDaysSpent() > target && !completedGate.qualifyCase(kase);
return target != null && kase.getCaseDaysSpent() > target
&& (!kase.getRequisition().isStopped() || !completedGate.isStoppable())
&& !completedGate.qualifyCase(kase);
}

private static int calculateStepDaysRemaining(Case kase, AssayTargets targets) {
if (!CompletedGate.RECEIPT.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getReceiptDays());
} else if (!CompletedGate.EXTRACTION.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getExtractionDays());
} else if (!CompletedGate.LIBRARY_PREPARATION.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getLibraryPreparationDays());
} else if (!CompletedGate.LIBRARY_QUALIFICATION.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getLibraryQualificationDays());
} else if (!CompletedGate.FULL_DEPTH_SEQUENCING.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getFullDepthSequencingDays());
} else if (!CompletedGate.ANALYSIS_REVIEW.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getAnalysisReviewDays());
} else if (!CompletedGate.RELEASE_APPROVAL.qualifyCase(kase)) {
if (!kase.getRequisition().isStopped()) {
if (!CompletedGate.RECEIPT.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getReceiptDays());
} else if (!CompletedGate.EXTRACTION.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getExtractionDays());
} else if (!CompletedGate.LIBRARY_PREPARATION.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getLibraryPreparationDays());
} else if (!CompletedGate.LIBRARY_QUALIFICATION.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getLibraryQualificationDays());
} else if (!CompletedGate.FULL_DEPTH_SEQUENCING.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getFullDepthSequencingDays());
} else if (!CompletedGate.ANALYSIS_REVIEW.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getAnalysisReviewDays());
}
}
if (!CompletedGate.RELEASE_APPROVAL.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getReleaseApprovalDays());
} else if (!CompletedGate.RELEASE.qualifyCase(kase)) {
return calculateDaysRemaining(kase, targets.getReleaseDays());
Expand Down
24 changes: 15 additions & 9 deletions src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/CompletedGate.java
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Expand Up @@ -17,7 +17,7 @@

public enum CompletedGate {
// @formatter:off
RECEIPT("Receipt") {
RECEIPT("Receipt", true) {
@Override
public boolean qualifyCase(Case kase) {
return Helpers.isReceiptCompleted(kase);
Expand All @@ -37,7 +37,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
EXTRACTION("Extraction") {
EXTRACTION("Extraction", true) {
@Override
public boolean qualifyTest(Test test) {
return test.isExtractionSkipped() || Helpers.isCompleted(test.getExtractions());
Expand All @@ -53,7 +53,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {

}
},
LIBRARY_PREPARATION("Library Preparation") {
LIBRARY_PREPARATION("Library Preparation", true) {
@Override
public boolean qualifyTest(Test test) {
return test.isLibraryPreparationSkipped()
Expand All @@ -70,7 +70,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}

},
LIBRARY_QUALIFICATION("Library Qualification") {
LIBRARY_QUALIFICATION("Library Qualification", true) {
@Override
public boolean qualifyTest(Test test) {
return Helpers.isCompleted(test.getLibraryQualifications());
Expand All @@ -85,7 +85,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
FULL_DEPTH_SEQUENCING("Full-Depth Sequencing") {
FULL_DEPTH_SEQUENCING("Full-Depth Sequencing", true) {
@Override
public boolean qualifyTest(Test test) {
return Helpers.isCompleted(test.getFullDepthSequencings());
Expand All @@ -100,7 +100,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
ANALYSIS_REVIEW("Analysis Review") {
ANALYSIS_REVIEW("Analysis Review", true) {
@Override
public boolean qualifyCase(Case kase) {
return Helpers.isCompletedRequisitionQc(kase.getRequisition(), Requisition::getAnalysisReviews);
Expand All @@ -113,7 +113,7 @@ public boolean qualifyRequisition(Requisition requisition) {
}

},
RELEASE_APPROVAL("Release Approval") {
RELEASE_APPROVAL("Release Approval", false) {
@Override
public boolean qualifyCase(Case kase) {
return Helpers.isCompletedRequisitionQc(kase.getRequisition(), Requisition::getReleaseApprovals);
Expand All @@ -124,7 +124,7 @@ public boolean qualifyRequisition(Requisition requisition) {
return Helpers.isCompletedRequisitionQc(requisition, Requisition::getReleaseApprovals);
}
},
RELEASE("Release") {
RELEASE("Release", false) {
@Override
public boolean qualifyCase(Case kase) {
return Helpers.isCompletedRequisitionQc(kase.getRequisition(), Requisition::getReleases);
Expand All @@ -145,18 +145,24 @@ public static CompletedGate getByLabel(String label) {
}

private final String label;
private final boolean stoppable;
private final Predicate<Case> casePredicate = this::qualifyCase;
private final Predicate<Test> testPredicate = this::qualifyTest;
private final Predicate<Requisition> requisitionPredicate = this::qualifyRequisition;

private CompletedGate(String label) {
private CompletedGate(String label, boolean stoppable) {
this.label = label;
this.stoppable = stoppable;
}

public String getLabel() {
return label;
}

public boolean isStoppable() {
return stoppable;
}

public Predicate<Case> predicate() {
return casePredicate;
}
Expand Down
38 changes: 22 additions & 16 deletions src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/PendingState.java
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Expand Up @@ -44,7 +44,7 @@
public enum PendingState {

// @formatter:off
RECEIPT_QC("Receipt QC") {
RECEIPT_QC("Receipt QC", true) {
@Override
public boolean qualifyCase(Case kase) {
return Helpers.isPendingReceiptQc(kase);
Expand All @@ -64,7 +64,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
EXTRACTION("Extraction") {
EXTRACTION("Extraction", true) {
@Override
public boolean qualifyCase(Case kase) {
return Helpers.isReceiptPassed
Expand All @@ -86,7 +86,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
EXTRACTION_QC("Extraction QC Sign-Off") {
EXTRACTION_QC("Extraction QC Sign-Off", true) {
@Override
public boolean qualifyTest(Test test) {
return Helpers.hasPendingQc(test.getExtractions());
Expand All @@ -101,7 +101,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
LIBRARY_PREPARATION("Library Preparation") {
LIBRARY_PREPARATION("Library Preparation", true) {
@Override
public boolean qualifyTest(Test test) {
return !test.isLibraryPreparationSkipped()
Expand All @@ -119,7 +119,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
LIBRARY_QC("Library QC Sign-Off") {
LIBRARY_QC("Library QC Sign-Off", true) {
@Override
public boolean qualifyTest(Test test) {
return Helpers.hasPendingQc(test.getLibraryPreparations());
Expand All @@ -134,7 +134,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
LIBRARY_QUALIFICATION("Library Qualification") {
LIBRARY_QUALIFICATION("Library Qualification", true) {
@Override
public boolean qualifyTest(Test test) {
return Helpers.hasPendingWork(test.getLibraryQualifications(), test.getLibraryPreparations());
Expand All @@ -152,7 +152,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
LIBRARY_QUALIFICATION_QC("Library Qualification QC Sign-Off") {
LIBRARY_QUALIFICATION_QC("Library Qualification QC Sign-Off", true) {
@Override
public boolean qualifyTest(Test test) {
return Helpers.hasPendingQc(test.getLibraryQualifications());
Expand All @@ -167,7 +167,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
LIBRARY_QUALIFICATION_DATA_REVIEW("Library Qualification Data Review") {
LIBRARY_QUALIFICATION_DATA_REVIEW("Library Qualification Data Review", true) {
@Override
public boolean qualifyTest(Test test) {
return Helpers.hasPendingDataReview(test.getLibraryQualifications());
Expand All @@ -182,7 +182,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
FULL_DEPTH_SEQUENCING("Full-Depth Sequencing") {
FULL_DEPTH_SEQUENCING("Full-Depth Sequencing", true) {
@Override
public boolean qualifyTest(Test test) {
return Helpers.hasPendingWork(test.getFullDepthSequencings(), test.getLibraryQualifications());
Expand All @@ -201,7 +201,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
FULL_DEPTH_QC("Full-Depth Sequencing QC Sign-Off") {
FULL_DEPTH_QC("Full-Depth Sequencing QC Sign-Off", true) {
@Override
public boolean qualifyTest(Test test) {
return Helpers.hasPendingQc(test.getFullDepthSequencings());
Expand All @@ -216,7 +216,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
FULL_DEPTH_DATA_REVIEW("Full-Depth Sequencing Data Review") {
FULL_DEPTH_DATA_REVIEW("Full-Depth Sequencing Data Review", true) {
@Override
public boolean qualifyTest(Test test) {
return Helpers.hasPendingDataReview(test.getFullDepthSequencings());
Expand All @@ -231,7 +231,7 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
}
}
},
ANALYSIS_REVIEW("Analysis Review") {
ANALYSIS_REVIEW("Analysis Review", true) {
@Override
public boolean qualifyCase(Case kase) {
return kase.getTests().stream().allMatch(Helpers.isCompleted(Test::getFullDepthSequencings))
Expand All @@ -243,11 +243,11 @@ public boolean qualifyRequisition(Requisition requisition) {
return requisition.getAnalysisReviews().isEmpty();
}
},
RELEASE_APPROVAL("Release Approval") {
RELEASE_APPROVAL("Release Approval", false) {

@Override
public boolean qualifyCase(Case kase) {
return Helpers.isCompletedRequisitionQc(kase, Requisition::getAnalysisReviews)
return (kase.isStopped() || Helpers.isCompletedRequisitionQc(kase, Requisition::getAnalysisReviews))
&& this.qualifyRequisition(kase.getRequisition());
}

Expand All @@ -256,7 +256,7 @@ public boolean qualifyRequisition(Requisition requisition) {
return requisition.getReleaseApprovals().isEmpty();
}
},
RELEASE("Release") {
RELEASE("Release", false) {
@Override
public boolean qualifyCase(Case kase) {
return Helpers.isCompletedRequisitionQc(kase, Requisition::getReleaseApprovals)
Expand All @@ -278,18 +278,24 @@ public static PendingState getByLabel(String label) {
}

private final String label;
private final boolean stoppable;
private final Predicate<Case> casePredicate = this::qualifyCase;
private final Predicate<Test> testPredicate = this::qualifyTest;
private final Predicate<Requisition> requisitionPredicate = this::qualifyRequisition;

private PendingState(String label) {
private PendingState(String label, boolean stoppable) {
this.label = label;
this.stoppable = stoppable;
}

public String getLabel() {
return label;
}

public boolean isStoppable() {
return stoppable;
}

public Predicate<Case> predicate() {
return casePredicate;
}
Expand Down
47 changes: 0 additions & 47 deletions src/test/java/ca/on/oicr/gsi/dimsum/service/filtering/CaseSortTest.java
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Expand Up @@ -99,30 +99,6 @@ public void testSortByUrgencyBothCompleted() {
testUrgencyComparator(a, b, true);
}

@org.junit.jupiter.api.Test
public void testSortByUrgencyBothStopped() {
Case a = mockEmptyCase(1L);
when(a.isStopped()).thenReturn(true);

Case b = mockEmptyCase(1L);
when(b.isStopped()).thenReturn(true);

// Both stopped, should be considered equivalent
testUrgencyComparator(a, b, true);
}

@org.junit.jupiter.api.Test
public void testSortByUrgencyOneCompletedOneStopped() {
Case a = mockEmptyCase(1L);
a.getRequisition().getReleases().add(mockRequisitionQc(true, 2023, 1, 1));

Case b = mockEmptyCase(1L);
when(b.isStopped()).thenReturn(true);

// One completed, one stopped. Should be considered equivalent
testUrgencyComparator(a, b, true);
}

@org.junit.jupiter.api.Test
public void testSortByUrgencyOneCompleted() {
Case a = mockEmptyCase(1L);
Expand All @@ -134,17 +110,6 @@ public void testSortByUrgencyOneCompleted() {
testUrgencyComparator(a, b);
}

@org.junit.jupiter.api.Test
public void testSortByUrgencyOneStopped() {
Case a = mockEmptyCase(1L);

Case b = mockEmptyCase(1L);
when(b.isStopped()).thenReturn(true);

// B stopped. A is more urgent
testUrgencyComparator(a, b);
}

@org.junit.jupiter.api.Test
public void testSortByUrgencyBothPaused() {
Case a = mockEmptyCase(1L);
Expand All @@ -168,18 +133,6 @@ public void testSortByUrgencyOnePaused() {
testUrgencyComparator(a, b);
}

@org.junit.jupiter.api.Test
public void testSortByUrgencyOnePausedOneStopped() {
Case a = mockEmptyCase(1L);
when(a.getRequisition().isPaused()).thenReturn(true);

Case b = mockEmptyCase(1L);
when(b.isStopped()).thenReturn(true);

// A paused, B stopped. Should be considered equivalent
testUrgencyComparator(a, b, true);
}

@org.junit.jupiter.api.Test
public void testSortByUrgencyBothOverdue() {
Case a = mockEmptyCase(1L);
Expand Down
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