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Address data issues that are causing the MSK-IMPACT studies to fail validation #1293

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Address data issues that are causing the MSK-IMPACT studies to fail validation #1293

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8e1aab1
NA for missing cna data
jamesqo Feb 2, 2026
b07fcf5
fix behavior
jamesqo Feb 2, 2026
32e3682
fix gene panel NAs
jamesqo Feb 2, 2026
bfff74a
remove comments
jamesqo Feb 2, 2026
e310dfa
Normalize blank values in clinical data
jamesqo Feb 10, 2026
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7 changes: 5 additions & 2 deletions cvr/src/main/java/org/cbioportal/cmo/pipelines/cvr/cna/CVRCnaDataReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -151,10 +151,13 @@ private void makeRecordsList() {
for (String gene : genes) {
StringBuilder line = new StringBuilder(gene);
for (String sample : samples) {
String cnaValue = "0";
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@jamesqo jamesqo Feb 4, 2026

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note: consider whether "0" or "NA" should be the default value in such cases

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@jamesqo jamesqo Feb 10, 2026

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In both cases (diploid / NA) there isn't a record added to the database, so they're equivalent.

String cnaValue;
Object value = cnaMap.get(gene, sample);
if (value != null) {
cnaValue = value.toString();
cnaValue = value.toString().trim();
cnaValue = cnaValue.isEmpty() ? "NA" : cnaValue;
} else {
cnaValue = "NA";
}
line.append("\t").append(cnaValue);
}
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4 changes: 3 additions & 1 deletion cvr/src/main/java/org/cbioportal/cmo/pipelines/cvr/genepanel/CVRGenePanelProcessor.java
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Expand Up @@ -56,7 +56,9 @@ public String process(CVRGenePanelRecord i) throws Exception {
List<String> record = new ArrayList<>();
record.add(cvrUtilities.convertWhitespace(i.getSAMPLE_ID()));
for (String profile : geneticProfiles) {
record.add(cvrUtilities.convertWhitespace(i.getPanelMap().get(profile)));
String raw = i.getPanelMap().get(profile);
String value = (raw == null || raw.trim().isEmpty()) ? "NA" : raw;
record.add(cvrUtilities.convertWhitespace(value));
}
return String.join("\t", record);
}
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15 changes: 12 additions & 3 deletions cvr/src/main/java/org/cbioportal/cmo/pipelines/cvr/model/staging/CVRClinicalRecord.java
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Expand Up @@ -245,15 +245,21 @@ public void setSO_COMMENTS(String soComments) {
}

public String getSAMPLE_COVERAGE() {
return this.sampleCoverage != null ? this.sampleCoverage : "";
if (Strings.isNullOrEmpty(this.sampleCoverage) || "null".equals(this.sampleCoverage)) {
return "NA";
}
return this.sampleCoverage;
}

public void setSAMPLE_COVERAGE(String sampleCoverage) {
this.sampleCoverage = sampleCoverage;
}

public String getCYCLE_THRESHOLD() {
return this.cycleThreshold != null ? this.cycleThreshold : "";
if (Strings.isNullOrEmpty(this.cycleThreshold) || "null".equals(this.cycleThreshold)) {
return "NA";
}
return this.cycleThreshold;
}

public void setCYCLE_THRESHOLD(String cycleThreshold) {
Expand Down Expand Up @@ -301,7 +307,10 @@ public void setMSI_COMMENT(String msiComment) {
}

public String getMSI_SCORE() {
return this.msiScore != null ? this.msiScore : "";
if (Strings.isNullOrEmpty(this.msiScore) || "Not Available".equals(this.msiScore)) {
return "NA";
}
return this.msiScore;
}

public void setMSI_SCORE(String msiScore) {
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