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Size bp and calibrated concentration added for gDNA QC records #83

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Size bp and calibrated concentration added for gDNA QC records #83

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84b1778
Size bp and calibrated concentration added for gDNA QC records
Nov 27, 2023
491a9ab
QC type name updated.
Dec 5, 2023
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2 changes: 1 addition & 1 deletion src/main/java/com/velox/sloan/cmo/workflows/IgoLimsPluginUtils/IgoLimsPluginUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -638,7 +638,7 @@ public List<Long> getRecordIds(List<DataRecord> records) {

/**
* Method to remove 1000 separator from CSV files. Such values in CSV files are enclosed with double quotes ("123,100")
* This method can be used to fined such values and remove comma (",") to split the lines more efficiently and
* This method can be used to find such values and remove comma (",") to split the lines more efficiently and
* extract column values.
*
* @param line
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64 changes: 64 additions & 0 deletions src/main/java/com/velox/sloan/cmo/workflows/qualitycontrol/QcReportGenerator.java
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Expand Up @@ -31,6 +31,7 @@ public class QcReportGenerator extends DefaultGenericPlugin {
private final String QC_TYPE_FOR_RIN = "bioanalyzer rna pico, bioanalyzer rna nano, tapestation rna screentape hisense sample table, tapestation rna screentape sample table";
private final String QC_TYPE_FOR_A260280 = "nanodrop nano";
private final String QC_TYPE_FOR_A260230 = "nanodrop nano";
private final String QC_TYPE_FOR_CALBRATED_CONCENTRATION = "quant-it";
private final String QC_TYPE_FOR_AVERAGE_BP_SIZE = "TapeStation Compact Peak Table, TapeStation Compact Pico Region Table, " +
"TapeStation D1000 Compact Region Table, TapeStation D1000 HiSense Compact Region Table, Bioanalyzer DNA High Sens Region Table";
private final String TAPESTATION_QC_FOR_AVERAGE_BP_SIZE = "TapeStation Compact Peak Table, TapeStation Compact Pico Region Table, " +
Expand Down Expand Up @@ -688,6 +689,61 @@ private Double getAverageLibrarySizeValue(String sampleId, List<DataRecord> qcRe
return averageBasePairSize;
}

private Double getBpSizeValue(String sampleId, List<DataRecord> qcRecords) {
List<DataRecord> qcRecordsWithBpSizeForSample;
qcRecordsWithBpSizeForSample = getQcRecordsByQcType(sampleId, qcRecords, QC_TYPE_FOR_AVERAGE_BP_SIZE);

double basePairSize = 0.0;
try {
if (!qcRecordsWithBpSizeForSample.isEmpty()) {
for (DataRecord qcRecord : qcRecordsWithBpSizeForSample) {
if (qcRecord.getValue("sizeBp", user) != null && qcRecord.getValue("SampleId", user).equals(sampleId)) {
basePairSize = qcRecord.getDoubleVal("sizeBp", user);
}
}
}
if (qcRecordsWithBpSizeForSample.isEmpty() || basePairSize <= 0) {
clientCallback.displayWarning(String.format("BP Size value not found for '%s'.", sampleId));
logInfo(String.format("WARNING: BP Size value not found for '%s'.", sampleId));
return 0.0;
}
} catch (RemoteException e) {
logError(String.format("RemoteException while getting 'sizeBp' Value for sample with Sample ID %s:\n%s", sampleId, ExceptionUtils.getStackTrace(e)));
} catch (NotFound notFound) {
logError(String.format("NotFound -> Missing 'sizeBp' Value for sample with Sample ID %s:\n%s", sampleId, ExceptionUtils.getStackTrace(notFound)));
} catch (ServerException se) {
logError(String.format("ServerException while getting 'sizeBp' Value for sample with Sample ID %s:\n%s", sampleId, ExceptionUtils.getStackTrace(se)));
}
return basePairSize;
}

private double getCalibConc(String sampleId, List<DataRecord> qcRecords) {
List<DataRecord> qcRecordsWithCalibConceForSample = getQcRecordsByQcType(sampleId, qcRecords, QC_TYPE_FOR_CALBRATED_CONCENTRATION);

double calibratedConcentration = 0.0;
try {
if (!qcRecordsWithCalibConceForSample.isEmpty()) {
for (DataRecord qcRecord : qcRecordsWithCalibConceForSample) {
if (qcRecord.getValue("calibratedConcentration", user) != null && qcRecord.getValue("SampleId", user).equals(sampleId)) {
calibratedConcentration = qcRecord.getDoubleVal("calibratedConcentration", user);
}
}
}
if (qcRecordsWithCalibConceForSample.isEmpty() || calibratedConcentration <= 0) {
clientCallback.displayWarning(String.format("Calibrated concentration value not found for '%s'.", sampleId));
logInfo(String.format("WARNING: Calibrated concentration value not found for '%s'.", sampleId));
return 0.0;
}
} catch (RemoteException e) {
logError(String.format("RemoteException while getting 'calibrated concentration' Value for sample with Sample ID %s:\n%s", sampleId, ExceptionUtils.getStackTrace(e)));
} catch (NotFound notFound) {
logError(String.format("NotFound -> Missing 'calibrated concentration' Value for sample with Sample ID %s:\n%s", sampleId, ExceptionUtils.getStackTrace(notFound)));
} catch (ServerException se) {
logError(String.format("ServerException while getting 'calibrated concentration' Value for sample with Sample ID %s:\n%s", sampleId, ExceptionUtils.getStackTrace(se)));
}
return calibratedConcentration;
}

/**
* Create DNA QC REPORT DataRecords for Samples.
*
Expand Down Expand Up @@ -725,6 +781,8 @@ private List<DataRecord> generateDnaQcReportFieldValuesMap(List<DataRecord> samp
Double dinValue = getDinValueFromQcRecord(sampleId, qcDataRecords);
Double A260280 = getA260280FromQcRecord(sampleId, qcDataRecords);
Double A260230 = getA260230FromQcRecord(sampleId, qcDataRecords);
Double sizeBp = getBpSizeValue(sampleId, qcDataRecords);
Double calibratedConcentration = getCalibConc(sampleId, qcDataRecords);
String igoRecommendation = getIgoRecommendationValue(sampleId, qcProtocolRecords);
String comments = getQcCommentsValue(sampleId, qcProtocolRecords);
if (dinValue > 0) {
Expand All @@ -738,6 +796,12 @@ private List<DataRecord> generateDnaQcReportFieldValuesMap(List<DataRecord> samp
qcRecord.put("A260280", A260280);
logInfo("A260280 is assigned to " + A260280);
}
if (sizeBp > 0) {
qcRecord.put("sizeBp", sizeBp);
}
if (calibratedConcentration > 0) {
qcRecord.put("calibratedConcentration", calibratedConcentration);
}
if (!StringUtils.isBlank(igoRecommendation)) {
qcRecord.put("IgoQcRecommendation", igoRecommendation);
}
Expand Down