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Added RIN, TotalMass to RNA report and RNA report to sample manifest #397

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Merged
FahimehMirhaj merged 3 commits into from
Mar 23, 2026
Merged

Added RIN, TotalMass to RNA report and RNA report to sample manifest #397

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f9c6e58
Added RIN, TotalMass to RNA report and RNA report to sample manifest
Mar 19, 2026
0c8fc5e
Cleaning
Mar 19, 2026
4aa26b3
checking for empty/null return for samples rna qc report
Mar 19, 2026
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20 changes: 18 additions & 2 deletions src/main/java/org/mskcc/limsrest/model/SampleManifest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -63,20 +63,36 @@ public void addQcReport(QcReport r) {
public static class QcReport {
public QcReport() {}

public QcReport(QcReportType qcReportType,
String IGORecommendation, String comments, String investigatorDecision, String DIN) {
/**
* DNA / Library QC (and RNA when rin/totalMass are not needed): {@code rin} and {@code totalMass} are null.
*/
public QcReport(QcReportType qcReportType,
String IGORecommendation, String comments, String investigatorDecision, String DIN) {
this(qcReportType, IGORecommendation, comments, investigatorDecision, DIN, null, null);
}

/**
* Full QC report; use {@code rin} and {@code totalMass} for {@link QcReportType#RNA}.
*/
public QcReport(QcReportType qcReportType,
String IGORecommendation, String comments, String investigatorDecision, String DIN,
String RIN, Double totalMass) {
this.qcReportType = qcReportType;
this.IGORecommendation = IGORecommendation;
this.comments = comments;
this.investigatorDecision = investigatorDecision;
this.din = DIN;
this.rin = RIN;
this.totalMass = totalMass;
}

public QcReportType qcReportType;
public String IGORecommendation;
public String comments;
public String investigatorDecision;
public String din;
public String rin;
public Double totalMass;
}
@NoArgsConstructor @ToString
@Getter @Setter
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32 changes: 32 additions & 0 deletions src/main/java/org/mskcc/limsrest/service/GetSampleManifestTask.java
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Expand Up @@ -476,6 +476,38 @@ protected void addIGOQcRecommendations(SampleManifest sampleManifest, DataRecord
}
}

log.info("Searching for QcReportRna report");
List<DataRecord> qcRecordsRna = sample.getDescendantsOfType("QcReportRna", user);
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@RTimal RTimal Mar 19, 2026

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@FahimehMirhaj can this return null? If accessing null qcrecordsrna if statement will fill

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@FahimehMirhaj FahimehMirhaj Mar 19, 2026 •
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Addressed.

if (qcRecordsRna != null && !qcRecordsRna.isEmpty()) {
try {
DataRecord qcRecord = qcRecordsRna.get(0);
int i = 1;
while (qcRecord.getBooleanVal("HideFromSampleQC", user) && i < qcRecordsRna.size()) {
qcRecord = qcRecordsRna.get(i++);
}
String igoQcRecommendation = qcRecord.getStringVal("IgoQcRecommendation", user);
String comments = qcRecord.getStringVal("Comments", user);
String id = qcRecord.getStringVal("InvestigatorDecision", user);
String rin = null;
try {
rin = qcRecord.getStringVal("RIN", user);
} catch (Exception rinEx) {
log.warn("Failed to retrieve RIN value: " + rinEx.getMessage());
}
Double totalMass = null;
try {
totalMass = qcRecord.getDoubleVal("TotalMass", user);
} catch (Exception massEx) {
log.warn("Failed to retrieve TotalMass value: " + massEx.getMessage());
}
SampleManifest.QcReport r = new SampleManifest.QcReport(
SampleManifest.QcReportType.RNA, igoQcRecommendation, comments, id, null, rin, totalMass);
sampleManifest.addQcReport(r);
} catch (Exception e) {
log.warn("Failed to retrieve RNA QC Record value: " + e.getMessage());
}
}

log.info("Searching for QcReportLibrary");
List<DataRecord> qcRecordsLib = sample.getDescendantsOfType("QcReportLibrary", user);
if (qcRecordsLib.size() > 0) {
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