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[GLT-4050] switched over from requisition QCs to deliverables (#42)
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@djcooke
djcooke authored Feb 27, 2024
1 parent c60c681 commit c5f0b61
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Showing 18 changed files with 358 additions and 354 deletions.
22 changes: 5 additions & 17 deletions ...r/gsi/cardea/data/RequisitionQcGroup.java → ...oicr/gsi/cardea/data/AnalysisQcGroup.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,20 +9,18 @@
/**
* Immutable RequisitionQcGroup
*/
@JsonDeserialize(builder = RequisitionQcGroup.Builder.class)
public class RequisitionQcGroup {
@JsonDeserialize(builder = AnalysisQcGroup.Builder.class)
public class AnalysisQcGroup {

private final BigDecimal callability;
private final BigDecimal collapsedCoverage;
private final Donor donor;
private final String groupId;
private final String libraryDesignCode;
private final BigDecimal purity;
private final String tissueOrigin;
private final String tissueType;

private RequisitionQcGroup(Builder builder) {
this.donor = requireNonNull(builder.donor);
private AnalysisQcGroup(Builder builder) {
this.tissueOrigin = requireNonNull(builder.tissueOrigin);
this.tissueType = requireNonNull(builder.tissueType);
this.libraryDesignCode = requireNonNull(builder.libraryDesignCode);
Expand All @@ -40,10 +38,6 @@ public BigDecimal getCollapsedCoverage() {
return collapsedCoverage;
}

public Donor getDonor() {
return donor;
}

public String getGroupId() {
return groupId;
}
Expand All @@ -69,15 +63,14 @@ public static class Builder {

private BigDecimal callability;
private BigDecimal collapsedCoverage;
private Donor donor;
private String groupId;
private String libraryDesignCode;
private BigDecimal purity;
private String tissueOrigin;
private String tissueType;

public RequisitionQcGroup build() {
return new RequisitionQcGroup(this);
public AnalysisQcGroup build() {
return new AnalysisQcGroup(this);
}

public Builder callability(BigDecimal callability) {
Expand All @@ -90,11 +83,6 @@ public Builder collapsedCoverage(BigDecimal collapsedCoverage) {
return this;
}

public Builder donor(Donor donor) {
this.donor = donor;
return this;
}

public Builder groupId(String groupId) {
this.groupId = groupId;
return this;
Expand Down
34 changes: 25 additions & 9 deletions cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Case.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package ca.on.oicr.gsi.cardea.data;

import static java.util.Collections.emptyList;
import static java.util.Collections.unmodifiableList;
import static java.util.Collections.unmodifiableSet;
import static java.util.Objects.requireNonNull;
Expand Down Expand Up @@ -31,7 +32,8 @@ public class Case {
private final Requisition requisition;
private final LocalDate startDate;
private final List<Test> tests;
private final List<Deliverable> deliverables;
private final List<AnalysisQcGroup> qcGroups;
private final List<CaseDeliverable> deliverables;
private final String timepoint;
private final String tissueOrigin;
private final String tissueType;
Expand All @@ -56,15 +58,19 @@ private Case(Builder builder) {
this.timepoint = builder.timepoint;
this.receipts = unmodifiableList(builder.receipts);
this.tests = unmodifiableList(builder.tests);
this.qcGroups = builder.qcGroups == null ? emptyList() : unmodifiableList(builder.qcGroups);
this.deliverables =
builder.deliverables == null ? null : unmodifiableList(builder.deliverables);
builder.deliverables == null ? emptyList() : unmodifiableList(builder.deliverables);
this.requisition = requireNonNull(builder.requisition);
this.startDate = requireNonNull(builder.startDate);

this.latestActivityDate = Stream
.of(receipts.stream().map(Sample::getLatestActivityDate),
tests.stream().map(Test::getLatestActivityDate),
Stream.of(requisition.getLatestActivityDate()))
.flatMap(Function.identity()).filter(Objects::nonNull).max(LocalDate::compareTo)
.concat(Stream.of(receipts.stream().map(Sample::getLatestActivityDate),
tests.stream().map(Test::getLatestActivityDate))
.flatMap(Function.identity()),
deliverables == null ? Stream.empty()
: deliverables.stream().map(CaseDeliverable::getLatestActivityDate))
.filter(Objects::nonNull).max(LocalDate::compareTo)
.orElse(null);
this.receiptDaysSpent = builder.receiptDaysSpent;
this.analysisReviewDaysSpent = builder.analysisReviewDaysSpent;
Expand Down Expand Up @@ -118,7 +124,11 @@ public List<Test> getTests() {
return tests;
}

public List<Deliverable> getDeliverables() {
public List<AnalysisQcGroup> getQcGroups() {
return qcGroups;
}

public List<CaseDeliverable> getDeliverables() {
return deliverables;
}

Expand Down Expand Up @@ -174,7 +184,8 @@ public static class Builder {
private List<Sample> receipts;
private Requisition requisition;
private List<Test> tests;
private List<Deliverable> deliverables;
private List<AnalysisQcGroup> qcGroups;
private List<CaseDeliverable> deliverables;
private String timepoint;
private String tissueOrigin;
private String tissueType;
Expand Down Expand Up @@ -235,7 +246,12 @@ public Builder requisition(Requisition requisition) {
return this;
}

public Builder deliverables(List<Deliverable> deliverables) {
public Builder qcGroups(List<AnalysisQcGroup> qcGroups) {
this.qcGroups = qcGroups;
return this;
}

public Builder deliverables(List<CaseDeliverable> deliverables) {
this.deliverables = deliverables;
return this;
}
Expand Down
71 changes: 26 additions & 45 deletions .../on/oicr/gsi/cardea/data/Deliverable.java → ...oicr/gsi/cardea/data/CaseDeliverable.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,15 @@
import static java.util.Objects.requireNonNull;

import java.time.LocalDate;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
import java.util.stream.Stream;
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;

@JsonDeserialize(builder = Deliverable.Builder.class)
public class Deliverable {
@JsonDeserialize(builder = CaseDeliverable.Builder.class)
public class CaseDeliverable {

private final DeliverableType deliverableType;
private final LocalDate analysisReviewQcDate;
Expand All @@ -18,12 +22,10 @@ public class Deliverable {
private final Boolean releaseApprovalQcPassed;
private final String releaseApprovalQcUser;
private final String releaseApprovalQcNote;
private final LocalDate releaseQcDate;
private final Boolean releaseQcPassed;
private final String releaseQcUser;
private final String releaseQcNote;
private final List<CaseRelease> releases;
private final LocalDate latestActivityDate;

private Deliverable(Builder builder) {
private CaseDeliverable(Builder builder) {
this.deliverableType = requireNonNull(builder.deliverableType);
this.analysisReviewQcDate = builder.analysisReviewQcDate;
this.analysisReviewQcPassed = builder.analysisReviewQcPassed;
Expand All @@ -33,10 +35,14 @@ private Deliverable(Builder builder) {
this.releaseApprovalQcPassed = builder.releaseApprovalQcPassed;
this.releaseApprovalQcUser = builder.releaseApprovalQcUser;
this.releaseApprovalQcNote = builder.releaseApprovalQcNote;
this.releaseQcDate = builder.releaseQcDate;
this.releaseQcPassed = builder.releaseQcPassed;
this.releaseQcUser = builder.releaseQcUser;
this.releaseQcNote = builder.releaseQcNote;
this.releases = builder.releases == null ? Collections.emptyList()
: Collections.unmodifiableList(builder.releases);
this.latestActivityDate = Stream
.concat(releases == null ? Stream.empty() : releases.stream().map(CaseRelease::getQcDate),
Stream.of(analysisReviewQcDate, releaseApprovalQcDate))
.filter(Objects::nonNull)
.max(LocalDate::compareTo)
.orElse(null);
}

public DeliverableType getDeliverableType() {
Expand Down Expand Up @@ -75,21 +81,14 @@ public String getReleaseApprovalQcNote() {
return releaseApprovalQcNote;
}

public LocalDate getReleaseQcDate() {
return releaseQcDate;
public List<CaseRelease> getReleases() {
return releases;
}

public Boolean getReleaseQcPassed() {
return releaseQcPassed;
public LocalDate getLatestActivityDate() {
return latestActivityDate;
}

public String getReleaseQcUser() {
return releaseQcUser;
}

public String getReleaseQcNote() {
return releaseQcNote;
}

@JsonPOJOBuilder(withPrefix = "")
public static class Builder {
Expand All @@ -103,10 +102,7 @@ public static class Builder {
private Boolean releaseApprovalQcPassed;
private String releaseApprovalQcUser;
private String releaseApprovalQcNote;
private LocalDate releaseQcDate;
private Boolean releaseQcPassed;
private String releaseQcUser;
private String releaseQcNote;
private List<CaseRelease> releases;

public Builder deliverableType(DeliverableType deliverableType) {
this.deliverableType = deliverableType;
Expand Down Expand Up @@ -153,28 +149,13 @@ public Builder releaseApprovalQcNote(String releaseApprovalQcNote) {
return this;
}

public Builder releaseQcDate(LocalDate releaseQcDate) {
this.releaseQcDate = releaseQcDate;
return this;
}

public Builder releaseQcPassed(Boolean releaseQcPassed) {
this.releaseQcPassed = releaseQcPassed;
return this;
}

public Builder releaseQcUser(String releaseQcUser) {
this.releaseQcUser = releaseQcUser;
return this;
}

public Builder releaseQcNote(String releaseQcNote) {
this.releaseQcNote = releaseQcNote;
public Builder releases(List<CaseRelease> releases) {
this.releases = releases;
return this;
}

public Deliverable build() {
return new Deliverable(this);
public CaseDeliverable build() {
return new CaseDeliverable(this);
}

}
Expand Down
84 changes: 84 additions & 0 deletions cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/CaseRelease.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,84 @@
package ca.on.oicr.gsi.cardea.data;

import java.time.LocalDate;
import java.util.Objects;
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;

@JsonDeserialize(builder = CaseRelease.Builder.class)
public class CaseRelease {

private final String deliverable;
private final LocalDate qcDate;
private final Boolean qcPassed;
private final String qcUser;
private final String qcNote;

private CaseRelease(Builder builder) {
this.deliverable = Objects.requireNonNull(builder.deliverable);
this.qcDate = builder.qcDate;
this.qcPassed = builder.qcPassed;
this.qcUser = builder.qcUser;
this.qcNote = builder.qcNote;
}

public String getDeliverable() {
return deliverable;
}

public LocalDate getQcDate() {
return qcDate;
}

public Boolean getQcPassed() {
return qcPassed;
}

public String getQcUser() {
return qcUser;
}

public String getQcNote() {
return qcNote;
}

@JsonPOJOBuilder(withPrefix = "")
public static class Builder {

private String deliverable;
private LocalDate qcDate;
private Boolean qcPassed;
private String qcUser;
private String qcNote;

public Builder deliverable(String deliverable) {
this.deliverable = deliverable;
return this;
}

public Builder qcDate(LocalDate qcDate) {
this.qcDate = qcDate;
return this;
}

public Builder qcPassed(Boolean qcPassed) {
this.qcPassed = qcPassed;
return this;
}

public Builder qcUser(String qcUser) {
this.qcUser = qcUser;
return this;
}

public Builder qcNote(String qcNote) {
this.qcNote = qcNote;
return this;
}

public CaseRelease build() {
return new CaseRelease(this);
}

}
}
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