void CSVConverter::convertColon(const QString& filename)
{
CSVFile file;
if (!file.read(filename))
{
return;
}
// skip header line
file.parseNextLine();
while (!file.atEnd())
{
QList<QVariant> data = file.parseNextLine();
if (data.size() < 10 || data.first().toString().isEmpty())
continue;
Patient pat;
pat.surname = data[0].toString();
pat.firstName = data[1].toString();
pat.dateOfBirth = data[2].toDate();
pat.gender = (data[3].toInt() == 1) ? Patient::Male : Patient::Female;
QList<Patient::Ptr> ps = PatientManager::instance()->findPatients(pat);
if (!ps.isEmpty())
{
continue;
}
}
}
void CSVConverter::readTNM(const QString& filename)
{
CSVFile file;
if (!file.read(filename))
{
return;
}
while (!file.atEnd())
{
QList<QVariant> data = file.parseNextLine();
if (data.size() < 4 || data.first().toString().isEmpty())
{
qDebug() << "TNM Reader: Invalid line" << data;
continue;
}
Patient pat;
pat.surname = data[0].toString();
pat.firstName = data[1].toString();
pat.dateOfBirth = data[2].toDate();
pat.gender = Patient::UnknownGender;
QList<Patient::Ptr> ps = PatientManager::instance()->findPatients(pat);
if (ps.isEmpty())
{
qDebug() << "TNM Reader: Patient not found" << pat.surname << pat.firstName << pat.dateOfBirth;
continue;
}
Patient::Ptr p = ps.first();
if (p->diseases.isEmpty())
{
qDebug() << "TNM Reader: Patient"<< pat.surname << pat.firstName << pat.dateOfBirth << "has no disease";
}
if (p->diseases.size() > 1)
{
qDebug() << "TNM Reader: Patient"<< pat.surname << pat.firstName << pat.dateOfBirth << "has multiple diseases, taking first";
}
Disease& dis = p->firstDisease();
dis.initialTNM.setTNM(data[3].toString());
//PatientManager::instance()->updateData(p, PatientManager::ChangedDiseaseMetadata);
}
}
void CSVConverter::convertBestRx(const QString& filename)
{
CSVFile file;
if (!file.read(filename))
{
return;
}
// skip header line
file.parseNextLine();
while (!file.atEnd())
{
QList<QVariant> data = file.parseNextLine();
if (data.size() < 40 || data.first().toString().isEmpty())
continue;
Patient pat;
QStringList names = data[0].toString().split(',', QString::SkipEmptyParts);
if (names.size() != 2)
{
qDebug() << "Failed to parse" << data[0];
continue;
}
pat.surname = names.first().trimmed();
pat.firstName = names.last().trimmed();
pat.dateOfBirth = data[5].toDate();
pat.gender = (data[10].toString() == "M") ? Patient::Male : Patient::Female;
if (!pat.isValid())
{
qDebug() << "invalid patient" << pat.surname;
continue;
}
QString entity = data[7].toString();
Pathology path;
path.context = PathologyContextInfo(PathologyContextInfo::BestRx).id;
path.entity = Pathology::Breast;
QDate date;
QList<int> fields;
fields << 17 << 21 << 25;
foreach (int f, fields)
{
if (data[f].isValid() && data[f].type() == QVariant::Date)
{
path.date = data[f].toDate();
break;
}
}
if (!path.date.isValid())
{
qDebug() << "Pathology date not available" << pat.surname;
//continue;
}
QString sampleOrigin = data[35].toString();
if (sampleOrigin.contains("Primär") || sampleOrigin.contains("Zytologie"))
{
path.sampleOrigin = Pathology::Primary;
}
else if (sampleOrigin == "LK")
{
path.sampleOrigin = Pathology::LocalLymphNode;
}
else if (sampleOrigin.contains("Metastase"))
{
path.sampleOrigin = Pathology::Metastasis;
}
else
{
qDebug() << "Unhandled sampleOrigin" << sampleOrigin;
}
// FGFR1
if (data[23].toString().contains("amplified", Qt::CaseInsensitive))
{
bool fgfr1Amplified = data[18].toString() == "Amplified";
path.properties << toProperty(PathologyPropertyInfo::Fish_FGFR1, fgfr1Amplified);
}
// PIK3Ca mut.
if (data[22].toString().contains("Wild Type") || data[22].toString().contains("Mutant"))
{
bool pik3mutant = data[22].toString().contains("Mutant");
QString mutation;
if (pik3mutant)
{
mutation = data[22].toString().remove("Mutant").trimmed();
}
path.properties << toProperty(PathologyPropertyInfo::Mut_PIK3CA_10_21, pik3mutant, mutation);
}
// PIK3ca Ampl.
if (data[23].toString().contains("Amplified", Qt::CaseInsensitive))
{
bool pik3Amplified = data[23].toString() == "Amplified";
path.properties << toProperty(PathologyPropertyInfo::Fish_PIK3CA, pik3Amplified);
}
// PTEN
if (data[29].toString().contains("PTEN staining", Qt::CaseInsensitive))
{
bool ptenLoss = data[29].toString().contains("PTEN loss");
path.properties << toProperty(PathologyPropertyInfo::IHC_PTEN, !ptenLoss);
}
// ER, PR, Her2
if (data[36].toString() == "+" || data[36].toString() == "-")
{
bool er = data[36].toString() == "+";
path.properties << toProperty(PathologyPropertyInfo::IHC_ER, er);
}
if (data[37].toString() == "+" || data[37].toString() == "-")
{
bool pr = data[37].toString() == "+";
path.properties << toProperty(PathologyPropertyInfo::IHC_PR, pr);
}
if (data[38].toString().contains("+") || data[38].toString() == "0")
{
int her2ihc = data[38].toString().remove("+").toInt();
path.properties << toProperty(PathologyPropertyInfo::IHC_HER2_DAKO, her2ihc);
}
if (data[39].toString().contains("amplified", Qt::CaseInsensitive))
{
bool her2fish = data[39].toString() == "amplified";
path.properties << toProperty(PathologyPropertyInfo::Fish_HER2, her2fish);
}
/*qDebug() << pat.surname << pat.firstName;
foreach (const Property& prop, path.properties)
{
PathologyPropertyInfo info = PathologyPropertyInfo::info(prop.property);
ValueTypeCategoryInfo catInfo(info);
qDebug() << info.label << catInfo.toString(catInfo.toValue(prop.value)) << prop.detail;
}*/
QList<Patient::Ptr> ps = PatientManager::instance()->findPatients(pat);
Patient::Ptr p;
if (ps.isEmpty())
{
p = PatientManager::instance()->addPatient(pat);
}
else
{
p = ps.first();
}
if (!p->hasDisease())
{
p->diseases << Disease();
}
p->diseases.first().pathologies << path;
if (!p->diseases.first().initialDiagnosis.isValid())
{
bool ok;
int year = data[31].toInt(&ok);
if (ok)
{
p->diseases.first().initialDiagnosis = QDate(year, 1, 1);
}
}
PatientManager::instance()->updateData(p,
PatientManager::ChangedPathologyData |
PatientManager::ChangedDiseaseMetadata |
PatientManager::ChangedPatientProperties);
}
}
void CSVConverter::convertBGJ389(const QString& filename)
{
CSVFile file;
if (!file.read(filename))
{
return;
}
// skip header line
file.parseNextLine();
while (!file.atEnd())
{
QList<QVariant> data = file.parseNextLine();
if (data.size() < 10 || data.first().type() != QVariant::Int)
continue;
Patient pat;
pat.surname = data[2].toString();
pat.firstName = data[3].toString();
pat.dateOfBirth = data[5].toDate();
pat.gender = (data[4].toString() == "m") ? Patient::Male : Patient::Female;
if (!pat.isValid())
{
qDebug() << "invalid patient" << pat.surname;
continue;
}
QString entity = data[7].toString();
Pathology path;
path.context = PathologyContextInfo(PathologyContextInfo::ScreeningBGJ398).id;
if (entity == "NSCLC")
path.entity = Pathology::PulmonarySquamous;
else if (entity == "Mamma")
path.entity = Pathology::Breast;
else if (entity == "Bladder")
path.entity = Pathology::TransitionalCell;
else
{
qDebug() << "Unhandled entity" << entity;
continue;
}
QString sampleOrigin = data[10].toString();
if (sampleOrigin == "Primär")
{
path.sampleOrigin = Pathology::Primary;
}
else if (sampleOrigin == "LK")
{
path.sampleOrigin = Pathology::LocalLymphNode;
}
else if (sampleOrigin.contains("Metastase"))
{
path.sampleOrigin = Pathology::Metastasis;
}
else
{
qDebug() << "Unhandled sampleOrigin" << sampleOrigin;
continue;
}
QString result = data[15].toString();
bool hasAmplification;
if (result.contains("neg"))
{
hasAmplification = false;
}
else if (result.contains("pos"))
{
hasAmplification = true;
}
else // "NA"
{
qDebug() << "invalid result" << result;
continue;
}
Property prop;
PathologyPropertyInfo info(PathologyPropertyInfo::Fish_FGFR1);
ValueTypeCategoryInfo catInfo(info.valueType);
prop.property = info.id;
prop.value = catInfo.toPropertyValue(hasAmplification);
path.properties << prop;
//qDebug() << pat.surname << path.entity << path.sampleOrigin << hasAmplification;
QList<Patient::Ptr> ps = PatientManager::instance()->findPatients(pat);
Patient::Ptr p;
if (ps.isEmpty())
{
p = PatientManager::instance()->addPatient(pat);
}
else
{
p = ps.first();
}
if (!p->hasDisease())
{
p->diseases << Disease();
}
p->diseases.first().pathologies << path;
PatientManager::instance()->updateData(p,
PatientManager::ChangedPathologyData |
PatientManager::ChangedDiseaseMetadata |
PatientManager::ChangedPatientProperties);
}
}