private void checkedListBox1_SelectedIndexChanged(object sender, EventArgs e)
{
if (checkedListBox1.CheckedItems.Contains(checkedListBox1.SelectedItem))
{
List<int> descedants = new List<int>();
descedants.Add(proband.relativeID);
proband.owningFHx.GetDescendants(proband.relativeID, ref descedants);
foreach (int i in descedants)
{
Person p = proband.owningFHx.getRelative(i);
if (p != null)
{
Race r = new Race(p.Ethnicity);
r.race = checkedListBox1.SelectedItem.ToString();
p.Ethnicity.AddToList(r, new HraModelChangedEventArgs(this));
}
}
}
else
{
Race doomed = null;
foreach (Race r in proband.Ethnicity)
{
if (string.Compare(checkedListBox1.SelectedItem.ToString(), r.race, true) == 0)
{
doomed = r;
break;
}
}
if (doomed != null)
{
//proband.Ethnicity.RemoveFromList(doomed, SessionManager.Instance.securityContext);
proband.owningFHx.getRelative(1).Ethnicity.RemoveFromList(doomed, SessionManager.Instance.securityContext);
}
}
}
private static void ProcessPersonNode(XPathNavigator personNode, XPathNavigator riskMean_rootNode, ref Person targetPerson, bool isProband, ref int nextRelIdIfNeeded)
{
string dataroot;
if (isProband)
dataroot = "patientPerson";
else
dataroot = "relationshipHolder";
XPathNavigator dataRootNode = personNode.SelectSingleNode(dataroot);
/////////////////////////
//Age
/////////////////////////
string age_val = personNode.Evaluate("string(subjectOf1/livingEstimatedAge/value/@value)").ToString();
if (string.IsNullOrEmpty(age_val) == false)
{
targetPerson.age = age_val;
}
else
{
age_val = personNode.Evaluate("string(subjectOf1/deceasedEstimatedAge/value/@value)").ToString();
if (string.IsNullOrEmpty(age_val) == false)
{
targetPerson.age = age_val;
}
}
if (String.IsNullOrEmpty(age_val))
{
//try to get age from the birthdate
string birthDateRaw = personNode.Evaluate("string(patientPerson/birthTime/@value)").ToString();
if (!string.IsNullOrEmpty(birthDateRaw))
{
//convert the raw birthdate in YYYYMMDD format to the current age
string[] format = { "yyyyMMdd" }; //official HL7 date format
DateTime birthDate;
if (DateTime.TryParseExact(birthDateRaw,
format,
System.Globalization.CultureInfo.InvariantCulture,
System.Globalization.DateTimeStyles.None,
out birthDate))
{
DateTime today = DateTime.Today;
int age = today.Year - birthDate.Year;
if (birthDate > today.AddYears(-age)) age--;
targetPerson.age = age.ToString();
}
}
}
//////////////////////////
// other basics
//////////////////////////
//old way fails when relative Id isn't integer in source xml/hl7
//targetPerson.relativeID = Convert.ToInt32(dataRootNode.Evaluate("string(id/@extension)").ToString());
int number;
bool resultRelId = Int32.TryParse(dataRootNode.Evaluate("string(id/@extension)").ToString(), out number);
if (resultRelId)
{
targetPerson.relativeID = number;
}
else
{
targetPerson.relativeID = nextRelIdIfNeeded++;
}
targetPerson.name = dataRootNode.Evaluate("string(name/@formatted)").ToString();
targetPerson.firstName = dataRootNode.Evaluate("string(name/@first)").ToString();
targetPerson.lastName = dataRootNode.Evaluate("string(name/@last)").ToString();
targetPerson.homephone = dataRootNode.Evaluate("string(telecom[@use='H']/@value)").ToString();
targetPerson.workphone = dataRootNode.Evaluate("string(telecom[@use='WP']/@value)").ToString();
targetPerson.gender = HL7FormatTranslator.GenderFromHL7(dataRootNode.Evaluate("string(administrativeGenderCode/@code)").ToString());
targetPerson.dob = HL7FormatTranslator.DateFromHL7(dataRootNode.Evaluate("string(birthTime/@value)").ToString()); ;
targetPerson.vitalStatus = HL7FormatTranslator.VitalStatusFromHL7(dataRootNode.Evaluate("string(deceasedInd/@value)").ToString());
int temp_mom_id;
int temp_dad_id;
if (int.TryParse(dataRootNode.Evaluate("string(relative[code/@code='NMTH']/relationshipHolder/id/@extension)").ToString(), out temp_mom_id))
{
targetPerson.motherID = temp_mom_id;
}
if (int.TryParse(dataRootNode.Evaluate("string(relative[code/@code='NFTH']/relationshipHolder/id/@extension)").ToString(), out temp_dad_id))
{
targetPerson.fatherID = temp_dad_id;
}
//////////////////////////
// ethnicity
//////////////////////////
XPathNodeIterator raceIter = dataRootNode.Select("raceCode");
foreach (XPathNavigator raceNode in raceIter)
{
string code = raceNode.Evaluate("string(@code)").ToString();
string displayName = raceNode.Evaluate("string(@displayName)").ToString();
string hraRaceText = HL7FormatTranslator.RaceFromHL7(code, displayName);
if (hraRaceText == "Ashkenazi")
{
targetPerson.isAshkenazi = "Yes";
}
else if (hraRaceText == "Hispanic")
{
targetPerson.isHispanic = "Yes";
}
else
{
Race r = new Race();
r.race = hraRaceText;
targetPerson.Ethnicity.Add(r);
}
}
//SG encodes above in ethnicGroupCode rather than raceCode, so we check these too
XPathNodeIterator ethnicIter = dataRootNode.Select("ethnicGroupCode");
foreach (XPathNavigator ethnicNode in ethnicIter)
{
string code = ethnicNode.Evaluate("string(@code)").ToString();
string displayName = ethnicNode.Evaluate("string(@displayName)").ToString();
string hraEthnicityText = HL7FormatTranslator.EthnicityFromHL7(code, displayName);
if (hraEthnicityText == "Ashkenazi")
{
targetPerson.isAshkenazi = "Yes";
}
else if (hraEthnicityText == "Hispanic or Latino")
{
targetPerson.isHispanic = "Yes";
}
else if (hraEthnicityText == "not Hispanic or Latino")
{
targetPerson.isHispanic = "No";
}
else
{
Race r = new Race();
r.race = hraEthnicityText;
targetPerson.Ethnicity.Add(r);
}
}
//////////////////////////
// Clinical Observations
//////////////////////////
//PRB modified XPath in next to *not* include COs that are for cause of death, which SG duplicates from another CO with that same disease
XPathNodeIterator coIter = personNode.Select(@"subjectOf2/clinicalObservation[not(sourceOf/@typeCode='CAUS')]");
foreach (XPathNavigator coNode in coIter)
{
string coText = coNode.Evaluate("string(code/@displayName)").ToString();
string coCode = coNode.Evaluate("string(code/@code)").ToString();
string coCodeSystem = coNode.Evaluate("string(code/@codeSystemName)").ToString();
string ageLowText = coNode.Evaluate("string(subject/dataEstimatedAge/value/low/@value)").ToString();
string ageHighText = coNode.Evaluate("string(subject/dataEstimatedAge/value/high/@value)").ToString();
string statusCode = coNode.Evaluate("string(statusCode/@code)").ToString();
string coValue = coNode.Evaluate("string(code/qualifier/value/@code)").ToString();
string coAgeDx = HL7FormatTranslator.GetIntFromHL7HighLow(ageLowText, ageHighText);
string hra_tag = riskMean_rootNode.Evaluate("string(row[codeSystem/.='" + coCodeSystem + "'][code/.='" + coCode + "']/Mgh/.)").ToString();
if (string.IsNullOrEmpty(hra_tag) == false)
{
if (string.Compare(hra_tag, "Identical twin", true) == 0)
{
int temp;
if (int.TryParse(coValue, out temp))
{
targetPerson.twinID = temp;
}
}
else
{
if (targetPerson is Patient)
{
Patient p = (Patient)targetPerson;
bool result = processAsRiskFactorClinicalObservation(hra_tag, ref p, coAgeDx, statusCode, coValue);
if (!result)
{
ClincalObservation co = new ClincalObservation(targetPerson.PMH);
co.ClinicalObservation_disease = hra_tag;
co.ClinicalObservation_ageDiagnosis = coAgeDx;
targetPerson.PMH.Observations.Add(co);
}
}
else
{
ClincalObservation co = new ClincalObservation(targetPerson.PMH);
co.ClinicalObservation_disease = hra_tag;
co.ClinicalObservation_ageDiagnosis = coAgeDx;
targetPerson.PMH.Observations.Add(co);
}
}
}
else
{
ClincalObservation co = new ClincalObservation(targetPerson.PMH);
co.ClinicalObservation_disease = coText;
co.ClinicalObservation_ageDiagnosis = coAgeDx;
targetPerson.PMH.Observations.Add(co);
}
}
//////////////////////////
// Cause of Death
//////////////////////////
XPathNavigator cdNav = personNode.SelectSingleNode(@"subjectOf2/clinicalObservation[sourceOf[@typeCode='CAUS']/clinicalObservation/code[(@displayName='death') or (@code='419620001')]]/code[1]");
if (cdNav != null) {
string cdText = cdNav.Evaluate("string(@displayName)").ToString();
string cdCode = cdNav.Evaluate("string(@code)").ToString();
string cdCodeSystem = cdNav.Evaluate("string(@codeSystemName)").ToString();
string cd_hra_tag = riskMean_rootNode.Evaluate("string(row[codeSystem/.='" + cdCodeSystem + "'][code/.='" + cdCode + "']/Mgh/.)").ToString();
if (string.IsNullOrEmpty(cd_hra_tag) == false)
{
targetPerson.causeOfDeath = cd_hra_tag;
}
else
{
targetPerson.causeOfDeath = cdText;
}
}
//////////////////////////
// Genetic Testing
//////////////////////////
//Panels first
XPathNodeIterator gtIter = personNode.Select("subjectOf2/geneticLocus");
List<GeneticTest> panels = new List<GeneticTest>();
List<string> panelNames = new List<string>();
foreach (XPathNavigator gtNode in gtIter)
{
string locusText = gtNode.Evaluate("string(text/.)").ToString();
if (string.IsNullOrEmpty(locusText) == false)
{
if (panelNames.Contains(locusText) == false)
{
GeneticTest new_panel = new GeneticTest(targetPerson.PMH);
new_panel.comments = locusText;
new_panel.GeneticTest_panelID = 34;
panels.Add(new_panel);
panelNames.Add(locusText);
}
}
}
//then results
foreach(GeneticTest panel in panels)
{
XPathNodeIterator resultIter = personNode.Select("subjectOf2/geneticLocus[text/.='" + panel.comments + "']");
foreach (XPathNavigator resultNode in resultIter)
{
string geneName = resultNode.Evaluate("string(value/@displayName)").ToString();
if (string.IsNullOrEmpty(geneName) == false)
{
GeneticTestResult result = new GeneticTestResult(panel);
result.geneName = geneName;
string significance = resultNode.Evaluate("string(component3/sequenceVariation/interpretationCode/@code)").ToString();
result.resultSignificance = significance;
panel.GeneticTestResults.Add(result);
}
}
targetPerson.PMH.GeneticTests.Add(panel);
}
}
public bool Equals(Race p)
{
// If parameter is null return false:
if ((object)p == null)
{
return false;
}
// Return true if the fields match:
return (race == p.race);
}
