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[GLT-4053] extracted interfaces from Case and related classes #43

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merged 1 commit into from
Feb 28, 2024
Merged

[GLT-4053] extracted interfaces from Case and related classes #43

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302 changes: 25 additions & 277 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
@@ -1,309 +1,57 @@
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;

import java.time.LocalDate;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import java.util.function.Function;
import java.util.stream.Stream;

import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;

/**
* Immutable case
*/
@JsonDeserialize(builder = Case.Builder.class)
public class Case {

private final long assayId;
private final String assayName;
private final String assayDescription;
private final Donor donor;
private final String id;
private final LocalDate latestActivityDate;
private final Set<Project> projects;
private final List<Sample> receipts;
private final Requisition requisition;
private final LocalDate startDate;
private final List<Test> tests;
private final List<AnalysisQcGroup> qcGroups;
private final List<CaseDeliverable> deliverables;
private final String timepoint;
private final String tissueOrigin;
private final String tissueType;
private final int receiptDaysSpent;
private final int analysisReviewDaysSpent;
private final int releaseApprovalDaysSpent;
private final int releaseDaysSpent;
private final int caseDaysSpent;
private final int pauseDays;

private Case(Builder builder) {
this.id = requireNonNull(builder.id);
this.donor = requireNonNull(builder.donor);
this.projects = unmodifiableSet(builder.projects);
this.assayId = builder.assayId;
// fields needed for Dimsum sorting/filtering
this.assayName = builder.assayName;
this.assayDescription = builder.assayDescription;

this.tissueOrigin = requireNonNull(builder.tissueOrigin);
this.tissueType = requireNonNull(builder.tissueType);
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 ? emptyList() : unmodifiableList(builder.deliverables);
this.requisition = requireNonNull(builder.requisition);
this.startDate = requireNonNull(builder.startDate);

this.latestActivityDate = Stream
.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;
this.releaseApprovalDaysSpent = builder.releaseApprovalDaysSpent;
this.releaseDaysSpent = builder.releaseDaysSpent;
this.caseDaysSpent = builder.caseDaysSpent;
this.pauseDays = builder.pauseDays;
}

public long getAssayId() {
return assayId;
}

public String getAssayName() {
return assayName;
}

public String getAssayDescription() {
return assayDescription;
}

public Donor getDonor() {
return donor;
}

public String getId() {
return id;
}

public LocalDate getLatestActivityDate() {
return latestActivityDate;
}

public Set<Project> getProjects() {
return projects;
}

public List<Sample> getReceipts() {
return receipts;
}

public Requisition getRequisition() {
return requisition;
}

public LocalDate getStartDate() {
return startDate;
}

public List<Test> getTests() {
return tests;
}

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

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

public String getTimepoint() {
return timepoint;
}

public String getTissueOrigin() {
return tissueOrigin;
}

public String getTissueType() {
return tissueType;
}

public int getReceiptDaysSpent() {
return receiptDaysSpent;
}

public int getAnalysisReviewDaysSpent() {
return analysisReviewDaysSpent;
}

public int getReleaseApprovalDaysSpent() {
return releaseApprovalDaysSpent;
}

public int getReleaseDaysSpent() {
return releaseDaysSpent;
}

public int getCaseDaysSpent() {
return caseDaysSpent;
}

public int getPauseDays() {
return pauseDays;
}

public boolean isStopped() {
return requisition.isStopped();
}
@JsonDeserialize(as = CaseImpl.class)
public interface Case {

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

private long assayId;
private String assayName;
private String assayDescription;
private Donor donor;
private String id;
private Set<Project> projects;
private List<Sample> receipts;
private Requisition requisition;
private List<Test> tests;
private List<AnalysisQcGroup> qcGroups;
private List<CaseDeliverable> deliverables;
private String timepoint;
private String tissueOrigin;
private String tissueType;
private LocalDate startDate;
private int receiptDaysSpent;
private int analysisReviewDaysSpent;
private int releaseApprovalDaysSpent;
private int releaseDaysSpent;
private int caseDaysSpent;
private int pauseDays;
String getAssayName();

public Case build() {
return new Case(this);
}
String getAssayDescription();

public Builder assayId(long assayId) {
this.assayId = assayId;
return this;
}
Donor getDonor();

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

public Builder assayDescription(String assayDescription) {
this.assayDescription = assayDescription;
return this;
}
LocalDate getLatestActivityDate();

public Builder donor(Donor donor) {
this.donor = donor;
return this;
}
Set<Project> getProjects();

public Builder startDate(LocalDate starDate) {
this.startDate = starDate;
return this;
}
List<Sample> getReceipts();

public Builder id(String id) {
this.id = id;
return this;
}
Requisition getRequisition();

public Builder projects(Set<Project> projects) {
this.projects = projects;
return this;
}
LocalDate getStartDate();

public Builder receipts(List<Sample> receipts) {
this.receipts = receipts;
return this;
}
List<Test> getTests();

public Builder requisition(Requisition requisition) {
this.requisition = requisition;
return this;
}
List<AnalysisQcGroup> getQcGroups();

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

public Builder deliverables(List<CaseDeliverable> deliverables) {
this.deliverables = deliverables;
return this;
}
String getTimepoint();

public Builder tests(List<Test> tests) {
this.tests = tests;
return this;
}
String getTissueOrigin();

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

public Builder tissueOrigin(String tissueOrigin) {
this.tissueOrigin = tissueOrigin;
return this;
}
int getReceiptDaysSpent();

public Builder tissueType(String tissueType) {
this.tissueType = tissueType;
return this;
}
int getAnalysisReviewDaysSpent();

public Builder receiptDaysSpent(int days) {
this.receiptDaysSpent = days;
return this;
}
int getReleaseApprovalDaysSpent();

public Builder analysisReviewDaysSpent(int days) {
this.analysisReviewDaysSpent = days;
return this;
}
int getReleaseDaysSpent();

public Builder releaseApprovalDaysSpent(int days) {
this.releaseApprovalDaysSpent = days;
return this;
}
int getCaseDaysSpent();

public Builder releaseDaysSpent(int days) {
this.releaseDaysSpent = days;
return this;
}
int getPauseDays();

public Builder caseDaysSpent(int days) {
this.caseDaysSpent = days;
return this;
}
boolean isStopped();

public Builder pauseDays(int days) {
this.pauseDays = days;
return this;
}
}
}
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