public override void PersistFullList(HraModelChangedEventArgs e)
{
RiskFactors.PersistFullObject(e, OwningPatient.unitnum, OwningPatient.apptid);
int proband_age;
if (int.TryParse(OwningPatient.age, out proband_age))
{
int lifetime_age = proband_age;
foreach (ClausRiskByAge o in this)
{
if (o.age > lifetime_age)
{
lifetime_age = o.age;
}
}
foreach (ClausRiskByAge o in this)
{
if (o.age - proband_age == 5)
{
o.description = "Five Year";
}
if (lifetime_age == o.age)
{
o.description = "Lifetime";
}
o.PersistFullObject(e, OwningPatient.unitnum, OwningPatient.apptid);
}
}
}
public override void PersistFullList(HraModelChangedEventArgs e)
{
foreach (TcRiskByAge o in this)
{
o.PersistFullObject(e, OwningPatient.unitnum, OwningPatient.apptid, RiskFactors.TYRER_CUZICK7_VERSION, OwningPatient.RP.BMRS_EffectiveTime, OwningPatient.RP.BMRS_RequestId);
}
}
//this override passes in the unitnum for the persist of each BrcaProCancerRiskByAge
public override void PersistFullList(HraModelChangedEventArgs e)
{
foreach (BrcaProCancerRiskByAge o in this)
{
o.PersistFullObject(e, OwningPatient.unitnum, OwningPatient.apptid);
}
}
/**************************************************************************************************/
public override void PersistFullList(HraModelChangedEventArgs e)
{
foreach (HraObject o in this)
{
((GUIPreference)o).owningPatient = OwningPatient;
}
base.PersistFullList(e);
}
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("apptID", this.apptID);
DoPersistWithSpAndParams(e, "sp_3_Save_Appointment", ref pc);
}
/**************************************************************************************************/
public override void PersistFullList(HraModelChangedEventArgs e)
{
foreach (HraObject o in this)
{
((ClincalObservation)o).owningPMH = OwningPMH;
}
base.PersistFullList(e);
}
private void NewTask_Click(object sender, EventArgs e)
{
Task t = new Task(proband, "Task", "Pending", SessionManager.Instance.ActiveUser.ToString(), DateTime.Now);
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
args.Persist = true;
proband.Tasks.AddToList(t, args);
}
/**************************************************************************************************/
public override void PersistFullList(HraModelChangedEventArgs e)
{
foreach (HraObject o in this)
{
((ClincalObservation)o).owningPMH = OwningPMH;
}
base.PersistFullList(e);
}
/**************************************************************************************************/
public override void PersistFullList(HraModelChangedEventArgs e)
{
foreach (HraObject o in this)
{
((GeneticTest)o).owningPMH = OwningPMH;
}
base.PersistFullList(e);
}
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
var pc = new ParameterCollection();
pc.Add("unitnum", unitnum);
DoPersistWithSpAndParams(e,
"sp_3_Save_PedigreeAnnotations",
ref pc);
}
private void MammoHxChangedHandler(object sender, HraModelChangedEventArgs e)
{
if (e.sendingView != this)
{
FillControlsByControlName(this._mammoHx);
FillMammoControls();
ToggleDateFields();
}
}
private void BreastBxChangedHander(object sender, HraModelChangedEventArgs e)
{
if (e.sendingView != this)
{
FillControlsByControlName(this._breastBx);
FillBreastBxControls();
ToggleDateFields();
}
}
/*****************************************************/
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("diseaseID", diseaseID);
DoPersistWithSpAndParams(e,
"sp_3_Save_DiseaseObject",
ref pc);
}
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
var pc = new ParameterCollection();
pc.Add("unitnum", unitnum);
DoPersistWithSpAndParams(e,
"sp_3_Save_PedigreeAnnotations",
ref pc);
}
/**************************************************************************************************/
public override void PersistFullList(HraModelChangedEventArgs e)
{
foreach (HraObject o in this)
{
((Race)o).owner = this;
}
base.PersistFullList(e);
}
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("unitnum", theProband.unitnum);
pc.Add("apptid", theProband.apptid);
DoPersistWithSpAndParams(e,
"sp_3_Save_ProcHx",
ref pc);
}
/**************************************************************************************************/
public override void PersistFullList(HraModelChangedEventArgs e)
{
foreach (HraObject o in this)
{
((Nation)o).owner = this;
}
base.PersistFullList(e);
}
public override void PersistFullObject(HraModelChangedEventArgs e)
{
if (Details != null)
{
Details.owningClincalObservation = this;
Details.BackgroundPersistWork(e);
}
base.PersistFullObject(e);
}
private void addNewOrderButton_Click(object sender, EventArgs e)
{
tabControl1.SelectedTab = todaysOrdersTabPage;
Order order = new Order();
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
args.Persist = false;
orders.AddToList(order, args);
}
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("patientUnitnum", patientOwning.unitnum);
pc.Add("apptid", patientOwning.apptid);
DoPersistWithSpAndParams(e,
"sp_3_Save_SocialHistory",
ref pc);
}
private void comboBox3_SelectionChangeCommitted(object sender, EventArgs e)
{
Recommendation r = (Recommendation)ScreeningRecComboBox.SelectedItem;
cdsbo.ScreeningRec = r.recID;
HraModelChangedEventArgs args = new HraModelChangedEventArgs(this);
args.updatedMembers.Add(cdsbo.GetMemberByName("ScreeningRec"));
cdsbo.SignalModelChanged(args);
}
private void SaveASOData()
{
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
args.updatedMembers.Add(geneticTestResult.GetMemberByName("geneName"));
args.updatedMembers.Add(geneticTestResult.GetMemberByName("ASOMutationName"));
args.updatedMembers.Add(geneticTestResult.GetMemberByName("ASOResultSignificance"));
args.updatedMembers.Add(geneticTestResult.GetMemberByName("ASOMutationAA"));
this.geneticTestResult.SignalModelChanged(args);
}
/*******************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("paragraphID", paragraphID);
pc.Add("providerID", providerID);
DoPersistWithSpAndParams(e,
"sp_3_Save_ProviderParagraph",
ref pc);
}
/**************************************************************************************************/
private void TaskChanged(object sender, HraModelChangedEventArgs e)
{
foreach (Control c in flowLayoutPanel1.Controls)
{
if (((PendingTaskSummaryRow)c).GetTask() == sender)
{
((PendingTaskSummaryRow)c).SetTask((Task)sender);
}
}
}
/*******************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("userLogin", userLogin);
DoPersistWithSpAndParams(e,
"sp_3_Save_User",
ref pc);
}
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("unitnum", owner.person.owningFHx.proband.unitnum);
pc.Add("relativeID", owner.person.relativeID);
pc.Add("apptid", owner.person.owningFHx.proband.apptid);
DoPersistWithSpAndParams(e,
"sp_3_Save_Nation",
ref pc);
}
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("unitnum", theProband.unitnum);
pc.Add("apptid", theProband.apptid);
DoPersistWithSpAndParams(e,
"sp_3_Save_ProcHx",
ref pc);
}
private void comboBox2_SelectionChangeCommitted(object sender, EventArgs e)
{
Recommendation r = (Recommendation)MmrTestResultComboBox.SelectedItem;
cdsbo.MmrGenTestResult = r.recID;
HraModelChangedEventArgs args = new HraModelChangedEventArgs(this);
args.updatedMembers.Add(cdsbo.GetMemberByName("MmrGenTestResult"));
cdsbo.SignalModelChanged(args);
}
private void cA125ToolStripMenuItem_Click(object sender, EventArgs e)
{
LabResult lr = new LabResult();
lr.unitnum = proband.unitnum;
lr.date = DateTime.Today;
lr.TestDesc = "CA125";
HraModelChangedEventArgs args = new HraModelChangedEventArgs(this);
proband.labsHx.AddToList(lr, args);
}
/*******************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("paragraphID", paragraphID);
pc.Add("providerID", providerID);
DoPersistWithSpAndParams(e,
"sp_3_Save_ProviderParagraph",
ref pc);
}
private void testYearComboBox_SelectedIndexChanged(object sender, EventArgs e)
{
if (geneticTest.testYear != testYearComboBox.Text)
{
HraModelChangedEventArgs args = new HraModelChangedEventArgs(geneticTestingView);
geneticTest.testYear = testYearComboBox.Text;
args.updatedMembers.Add(geneticTest.GetMemberByName("testYear"));
geneticTest.SignalModelChanged(args);
}
}
/*****************************************************/
public void Set_snomed(string value, HraView sendingView)
{
if (snomed != value)
{
snomed = value;
var args = new HraModelChangedEventArgs(null);
args.sendingView = sendingView;
args.updatedMembers.Add(GetMemberByName("snomed"));
SignalModelChanged(args);
}
}
//a customized persistence method for BrcaProCancerRiskByAge items
public void PersistFullObject(HraModelChangedEventArgs e, string unitnum, int apptid)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("unitnum", unitnum);
pc.Add("apptid", apptid);
DoPersistWithSpAndParams(e,
"sp_3_Save_BrcaProCancerRiskByAge",
ref pc);
}
/*****************************************************/
public void Set_Problem(string value, HraView sendingView)
{
if (Problem != value)
{
Problem = value;
var args = new HraModelChangedEventArgs(null);
args.sendingView = sendingView;
args.updatedMembers.Add(GetMemberByName("Problem"));
SignalModelChanged(args);
}
}
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("unitnum", owner.person.owningFHx.proband.unitnum);
pc.Add("relativeID", owner.person.relativeID);
pc.Add("apptid", owner.person.owningFHx.proband.apptid);
DoPersistWithSpAndParams(e,
"sp_3_Save_Nation",
ref pc);
}
private void allelicStateComboBox_SelectionChangeCommitted(object sender, EventArgs e)
{
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
geneticTestResult.allelicState = allelicStateComboBox.SelectedItem.ToString();
args.updatedMembers.Add(geneticTestResult.GetMemberByName("allelicState"));
geneticTestResult.SignalModelChanged(args);
SignalOwningTestCompleted();
}
/**************************************************************************************************/
private void ClinicalObservationChanged(object sender, HraModelChangedEventArgs e)
{
int senderId = ((ClincalObservation)sender).instanceID;
if (e.Delete)
{
}
else
{
}
}
/*****************************************************/
public void Set_diseaseOrder(string value, HraView sendingView)
{
if (diseaseOrder != value)
{
diseaseOrder = value;
var args = new HraModelChangedEventArgs(null);
args.sendingView = sendingView;
args.updatedMembers.Add(GetMemberByName("diseaseOrder"));
SignalModelChanged(args);
}
}
/**************************************************************************************************/
private void AddDiseaseButton_Click(object sender, EventArgs e)
{
ClincalObservation co = new ClincalObservation(pmh);
//SessionManager.Instance.MetaData.Diseases.SetDataFromDiseaseName(ref co);
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
args.Persist = false;
pmh.Observations.AddToList(co, args);
noLabel.Visible = false;
}
/*****************************************************/
public void Set_comments(string value, HraView sendingView)
{
if (comments != value)
{
comments = value;
var args = new HraModelChangedEventArgs(null);
args.sendingView = sendingView;
args.updatedMembers.Add(GetMemberByName("comments"));
SignalModelChanged(args);
}
}
/*****************************************************/
public void Set_ageDiagnosis(string value, HraView sendingView)
{
if (ageDiagnosis != value)
{
ageDiagnosis = value;
var args = new HraModelChangedEventArgs(null);
args.sendingView = sendingView;
args.updatedMembers.Add(GetMemberByName("ageDiagnosis"));
SignalModelChanged(args);
}
}
//a customized persistence method for TcRiskByAge items
public void PersistFullObject(HraModelChangedEventArgs e, string unitnum, int apptid, string version, DateTime? BMRS_EffectiveTime, Int64? BMRS_RequestId)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("unitnum", unitnum);
pc.Add("apptid", apptid);
pc.Add("version", version);
pc.Add("BMRS_EffectiveTime", BMRS_EffectiveTime);
pc.Add("BMRS_RequestId", BMRS_RequestId);
DoPersistWithSpAndParams(e,
"sp_3_Save_TcRiskByAge",
ref pc);
}
public override void PersistFullList(HraModelChangedEventArgs e)
{
if (proband!= null)
{
if (proband.apptid > 0)
{
foreach (HraObject ho in this)
{
Provider p = (Provider)ho;
p.apptid = proband.apptid;
}
}
}
base.PersistFullList(e);
}
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
try
{
pc.Add("ID", ID);
pc.Add("parameterValue", parameterValue);
SqlDataReader reader = BCDB2.Instance.ExecuteReaderSPWithParams("sp_3_SetQueueParameter", pc);
}
catch (Exception ee)
{
Logger.Instance.WriteToLog("Error saving QueueParameter: \r\n" + ee.InnerException.ToString());
}
}
/**************************************************************************************************/
public override void PersistFullObject(HraModelChangedEventArgs e)
{
base.PersistFullObject(e);
breastBx.PersistFullObject(e);
}
private void processMmrProHL7Scores(XPathNavigator nav)
{
//get MmrPro scores
XPathNavigator mpNode = nav.SelectSingleNode("//pedigreeAnalysisResults[methodCode/@code='MMRPRO'][1]");
if (mpNode != null)
{
RP.MmrPro_Version = mpNode.Evaluate("string(methodCode[@code='MMRPRO']/@codeSystemVersion)").ToString();
XPathNavigator textNode = mpNode.SelectSingleNode("text");
//create XML fragment with messages and hazard rates
XmlDocument myTempDoc = new XmlDocument();
myTempDoc.LoadXml("<text>" + System.Web.HttpUtility.HtmlDecode(textNode.InnerXml) + "</text>");
XPathNavigator n1 = myTempDoc.CreateNavigator();
RP.MmrPro_Messages = n1.Evaluate("string(//messages[1])").ToString().Trim();
XPathNodeIterator xnit = n1.Select("//hazardMMRRates[1]/row"); //gets all the hazard rate rows (one per age)
int ptAge = -1;
Int32.TryParse(this.age, out ptAge);
XPathNodeIterator ptCPRIter = mpNode.Select("component/percentageRisk[typeId/@extension = '" + this.relativeID + "']");
foreach (XPathNavigator cpr in ptCPRIter)
{
switch (cpr.Evaluate("string(code/@displayName)").ToString())
{
case "probCarrier":
RP.MmrPro_1_2_6_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
case "probMLH1Mutation":
RP.MmrPro_MLH1_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
case "probMSH2Mutation":
RP.MmrPro_MSH2_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
case "probMSH6Mutation":
RP.MmrPro_MSH6_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
default:
//do nothing
break;
}
}
foreach (XPathNavigator row in xnit)
{
int id = Convert.ToInt32(row.Evaluate("string(@id)").ToString());
if (id <= ptAge) continue; //no need to save all 0 hazard rate rows in object model or DB
//find an existing MMRproCancerRiskByAge for this age, if any
// else make a new one and add it to the MmrproCancerRiskList
MMRproCancerRiskByAge mpcrba = (MMRproCancerRiskByAge)RP.MmrproCancerRiskList.FirstOrDefault(item => ((MMRproCancerRiskByAge)item).age == id);
if (mpcrba == null)
{
mpcrba = new MMRproCancerRiskByAge();
mpcrba.age = id;
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
RP.MmrproCancerRiskList.AddToList(mpcrba, args);
}
mpcrba.hFX0 = Convert.ToDouble(row.Evaluate("concat(string(@hFX0), string(@hMX0))").ToString());
mpcrba.hFX1 = Convert.ToDouble(row.Evaluate("concat(string(@hFX1), string(@hMX1))").ToString());
mpcrba.hFX2 = Convert.ToDouble(row.Evaluate("concat(string(@hFX2), string(@hMX2))").ToString());
mpcrba.hFX6 = Convert.ToDouble(row.Evaluate("concat(string(@hFX6), string(@hMX6))").ToString());
mpcrba.hFY0 = Convert.ToDouble(row.Evaluate("concat(string(@hFY0), string(@hMY0))").ToString());
mpcrba.hFY1 = Convert.ToDouble(row.Evaluate("concat(string(@hFY1), string(@hMY1))").ToString());
mpcrba.hFY2 = Convert.ToDouble(row.Evaluate("concat(string(@hFY2), string(@hMY2))").ToString());
mpcrba.hFY6 = Convert.ToDouble(row.Evaluate("concat(string(@hFY6), string(@hMY6))").ToString());
mpcrba.ColonCaRisk = ((double)RP.MmrPro_MLH1_Mut_Prob / 100.0 * mpcrba.hFX1) +
((double)RP.MmrPro_MSH2_Mut_Prob / 100.0 * mpcrba.hFX2) +
((double)RP.MmrPro_MSH6_Mut_Prob / 100.0 * mpcrba.hFX6) +
((1 - (double)(RP.MmrPro_MLH1_Mut_Prob / 100.0 + RP.MmrPro_MSH2_Mut_Prob / 100.0 + RP.MmrPro_MSH6_Mut_Prob / 100.0)) * mpcrba.hFX0);
mpcrba.EndometrialCaRisk = ((double)RP.MmrPro_MLH1_Mut_Prob / 100.0 * mpcrba.hFY1) +
((double)RP.MmrPro_MSH2_Mut_Prob / 100.0 * mpcrba.hFY2) +
((double)RP.MmrPro_MSH6_Mut_Prob / 100.0 * mpcrba.hFY6) +
((1 - (double)(RP.MmrPro_MLH1_Mut_Prob / 100.0 + RP.MmrPro_MSH2_Mut_Prob / 100.0 + RP.MmrPro_MSH6_Mut_Prob / 100.0)) * mpcrba.hFY0);
mpcrba.ColonCaRisk = mpcrba.ColonCaRisk * 100;
mpcrba.EndometrialCaRisk = mpcrba.EndometrialCaRisk * 100;
mpcrba.ColonCaRiskWithMLH1 = 100 * mpcrba.hFX1;
mpcrba.EndometrialCaRiskWithMLH1 = 100 * mpcrba.hFY1;
mpcrba.ColonCaRiskWithMSH2 = 100 * mpcrba.hFX2;
mpcrba.EndometrialCaRiskWithMSH2 = 100 * mpcrba.hFY2;
mpcrba.ColonCaRiskWithMSH6 = 100 * mpcrba.hFX6;
mpcrba.EndometrialCaRiskWithMSH6 = 100 * mpcrba.hFY6;
mpcrba.ColonCaRiskNoMut = 100 * mpcrba.hFX0;
mpcrba.EndometrialCaRiskNoMut = 100 * mpcrba.hFY0;
}
XPathNodeIterator ptAgeChunkIter = mpNode.Select("component/age[value/low/@value]");
int five_year_age = 105;
int lifetime_age = 0;
foreach (XPathNavigator ac in ptAgeChunkIter)
{
int age = Convert.ToInt32(ac.Evaluate("string(value/low/@value)").ToString());
if (age < five_year_age) five_year_age = age;
if (age > lifetime_age) lifetime_age = age;
//find an existing MmrProCancerRiskByAge for this age, if any
// else make a new one and add it to the MmrproCancerRiskList
MMRproCancerRiskByAge mpcrba = (MMRproCancerRiskByAge)RP.MmrproCancerRiskList.FirstOrDefault(item => ((MMRproCancerRiskByAge)item).age == age);
if (mpcrba == null)
{
mpcrba = new MMRproCancerRiskByAge();
mpcrba.age = age;
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
RP.MmrproCancerRiskList.AddToList(mpcrba, args);
}
switch (ac.Evaluate("string(pertinentInformation/realmCode/@code)").ToString())
{
case "colorectalCancerRisk":
mpcrba.ColonCaRisk = Math.Round(100.0 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString()), 6);
if (age == five_year_age) RP.MmrPro_5Year_Colon = mpcrba.ColonCaRisk;
if (age == lifetime_age) RP.MmrPro_Lifetime_Colon = mpcrba.ColonCaRisk;
break;
case "endometrialCancerRisk":
mpcrba.EndometrialCaRisk = Math.Round(100.0 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString()), 6);
if (age == five_year_age) RP.MmrPro_5Year_Endometrial = mpcrba.EndometrialCaRisk;
if (age == lifetime_age) RP.MmrPro_Lifetime_Endometrial = mpcrba.EndometrialCaRisk;
break;
default:
//do nothing
break;
}
}
//update risk scores for all non-proband family members
//these are mutation probs only
XPathNodeIterator relCPRIter = mpNode.Select("component/percentageRisk[typeId/@extension != '" + this.relativeID + "']");
foreach (XPathNavigator cpr in relCPRIter)
{
int relId = Convert.ToInt32(cpr.Evaluate("string(typeId/@extension)").ToString());
Person rel = FHx.Relatives.FirstOrDefault(item => ((Person)item).relativeID == relId);
if (rel.RP.BMRS_EffectiveTime == null) rel.RP.BMRS_EffectiveTime = RP.BMRS_EffectiveTime;
if (rel.RP.MmrPro_Version == null) rel.RP.MmrPro_Version = RP.MmrPro_Version;
switch (cpr.Evaluate("string(code/@displayName)").ToString())
{
case "probCarrier":
rel.RP.MmrPro_1_2_6_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
case "probMLH1Mutation":
rel.RP.MmrPro_MLH1_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
case "probMSH2Mutation":
rel.RP.MmrPro_MSH2_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
case "probMSH6Mutation":
rel.RP.MmrPro_MSH6_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
default:
//do nothing
break;
}
}
}
}
/**************************************************************************************************/
public override void PersistFullObject(HraModelChangedEventArgs e)
{
base.PersistFullObject(e);
FHx.proband = this;
FHx.PersistFullList(e);
MedHx.theProband = this;
MedHx.PersistFullObject(e);
SocialHx.patientOwning = this;
SocialHx.PersistFullObject(e);
PhysicalExam.patientOwning = this;
PhysicalExam.PersistFullObject(e);
ObGynHx.patientOwning = this;
ObGynHx.PersistFullObject(e);
procedureHx.theProband = this;
procedureHx.PersistFullObject(e);
breastImagingHx.OwningPatient = this;
breastImagingHx.PersistFullList(e);
labsHx.OwningPatient = this;
labsHx.PersistFullList(e);
if (follupSatus != null)
{
follupSatus.unitnum = this.unitnum;
follupSatus.apptid = this.apptid;
follupSatus.PersistFullObject(e);
}
transvaginalImagingHx.OwningPatient = this;
transvaginalImagingHx.PersistFullList(e);
Tasks.OwningPatient = this;
Tasks.PersistFullList(e);
if (cdsBreastOvary != null)
{
cdsBreastOvary.patientOwning = this;
cdsBreastOvary.PersistFullObject(e);
}
if (Providers != null)
{
Providers.proband = this;
Providers.PersistFullList(e);
}
guiPreferences.OwningPatient = this;
guiPreferences.PersistFullList(e);
PediatricCDS.OwningPatient = this;
PediatricCDS.PersistFullList(e);
SurveyReponses.OwningPatient = this;
foreach (SurveyResponse sr in SurveyReponses)
{
sr.owningPatient = this;
}
SurveyReponses.PersistFullList(e);
}
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("unitnum", patientOwning.unitnum);
pc.Add("apptid", patientOwning.apptid);
DoPersistWithSpAndParams(e,
"sp_3_Save_CDSRecs",
ref pc);
}
private void processCCRATHL7Scores(XPathNavigator nav)
{
//get ccrat scores
XPathNavigator ccNode = nav.SelectSingleNode("//pedigreeAnalysisResults[methodCode/@code='CCRAT'][1]");
if (ccNode != null)
{
RP.CCRATModel.Details.CCRAT_VERSION = ccNode.Evaluate("string(methodCode[@code='CCRAT']/@codeSystemVersion)").ToString();
XPathNavigator textNode = ccNode.SelectSingleNode("text");
if (textNode != null)
{
//create XML fragment with messages
XmlDocument myTempDoc = new XmlDocument();
myTempDoc.LoadXml("<text>" + System.Web.HttpUtility.HtmlDecode(textNode.InnerXml) + "</text>");
XPathNavigator n1 = myTempDoc.CreateNavigator();
RP.CCRATModel.Details.CCRAT_MESSAGES = n1.Evaluate("string(//messages[1])").ToString().Trim();
RP.CCRATModel.Details.CCRAT_NAERRORS = n1.Evaluate("string(//NAError[1])").ToString().Trim();
RP.CCRATModel.Details.CCRAT_ERRORS = n1.Evaluate("string(//Error[1])").ToString().Trim();
}
else
{
RP.CCRATModel.Details.CCRAT_MESSAGES = "";
RP.CCRATModel.Details.CCRAT_NAERRORS = "";
RP.CCRATModel.Details.CCRAT_ERRORS = "";
}
XPathNodeIterator ptAgeChunkIter = ccNode.Select("component/age[value/low/@value]");
int five_year_age = 105;
int lifetime_age = 0;
foreach (XPathNavigator ac in ptAgeChunkIter)
{
int age = Convert.ToInt32(ac.Evaluate("string(value/low/@value)").ToString());
if (age < five_year_age) five_year_age = age;
if (age > lifetime_age) lifetime_age = age;
//find an existing CCRATRiskByAge for this age, if any
// else make a new one and add it to the CCRAT list
CCRATRiskByAge ccrba = (CCRATRiskByAge)RP.CCRATModel.FirstOrDefault(item => ((CCRATRiskByAge)item).age == age);
if (ccrba == null)
{
ccrba = new CCRATRiskByAge();
ccrba.age = age;
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
RP.CCRATModel.AddToList(ccrba, args);
}
switch (ac.Evaluate("string(pertinentInformation/realmCode/@code)").ToString())
{
case "colorectalCancerRisk":
ccrba.ColonCaRisk = 100.0 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString());
if (age == five_year_age) RP.CCRATModel.Details.CCRAT_FiveYear_CRC = ccrba.ColonCaRisk;
if (age == lifetime_age) RP.CCRATModel.Details.CCRAT_Lifetime_CRC = ccrba.ColonCaRisk;
break;
default:
//do nothing
break;
}
}
}
}
public void RecalculateRisk()
{
//Assembly.LoadFrom("C:\\HRA\\Dev\\RiskAppCoreProjects\\RiskClinicApp\\bin\\Debug\\RiskAppCore.dll");
if (Configurator.useAggregatorService())
{
//new way
//Serialize the FH
this.LoadFullObject(); //needed to ensure patient object is complete, including ObGynHx, etc.
RiskApps3.Model.PatientRecord.FHx.FamilyHistory theFH = this.owningFHx;
bool dcis_found = false;
bool dcisAsCancer = true;
foreach (Person p in this.FHx)
{
foreach (ClincalObservation co in p.PMH.Observations)
{
if (string.Compare(co.riskMeaning, "DCIS", true) == 0)
{
dcis_found = true;
}
}
}
if (dcis_found && !bSilent) // added silent mode jdg 9/1/15
{
DialogResult dr = MessageBox.Show("Would you like to consider DCIS a cancer diagnosis for BRCAPRO and Tyrer-Cuzick model calculations? DCIS WILL be considered as cancer for use with the Myriad, Claus and Gail models.", "BRCAPRO Question", MessageBoxButtons.YesNo, MessageBoxIcon.Question);
if (dr == DialogResult.No)
{
dcisAsCancer = false;
}
}
else
{
if (dcis_found && bSilent)
{
// to use or not to use? that is the question.
// And the answer is... YES.
dcisAsCancer = true; // though it defaulted to this anyway, as it turns out
}
}
string fhAsString = TransformUtils.DataContractSerializeObject<RiskApps3.Model.PatientRecord.FHx.FamilyHistory>(theFH);
//transform it
XmlDocument inDOM = new XmlDocument();
inDOM.LoadXml(fhAsString);
if (String.IsNullOrEmpty(toolsPath))
{
toolsPath = RiskApps3.Utilities.Configurator.getNodeValue("Globals", "ToolsPath"); // @"C:\Program Files\riskappsv2\tools\";
}
if (String.IsNullOrEmpty(strServiceBinding))
{
strServiceBinding = "WSHttpBinding_IService1";
}
XmlDocument resultXmlDoc = TransformUtils.performTransform(inDOM, toolsPath, @"hra_to_ccd_remove_namespaces.xsl");
XmlDocument hl7FHData;
if (dcis_found && dcisAsCancer)
{
//only do this when calling the RiskAggravator Service; we don't want to change the actual diseases in the object model
hl7FHData = TransformUtils.performTransformWith2Params(resultXmlDoc, toolsPath, @"hra_serialized_to_hl7.xsl", "dcisAsCancer", "1", "deIdentify", "1");
}
else
{
hl7FHData = TransformUtils.performTransformWithParam(resultXmlDoc, toolsPath, @"hra_serialized_to_hl7.xsl", "deIdentify", "1");
}
//Insert Clinic Name and Institution Name into HL7
//Get the first (and only) text node
XmlNode theFirstTextNode = hl7FHData.SelectSingleNode("(//FamilyHistory/text)[1]");
//and replace its contents with the clinic name and institution names
theFirstTextNode.InnerText = " Current User: ; " + BCDB2.Instance.GetClinicAndInstitutionNames(apptid);
bool dump = Configurator.getConfigBool("WriteAggregatorFiles");
//convert to string
string hl7Request = convertXMLDocToString(hl7FHData);
if (dump)
{
File.WriteAllText("AggregatorRequest.xml", hl7Request);
}
//call the aggregator servicethis is a blocking call, up to 60 seconds
//AggregatorServiceReference2.Service1Client client = new AggregatorServiceReference2.Service1Client();
//next line is for testing locally only
//AggregatorServiceReferenceDev3.Service1Client client = new AggregatorServiceReferenceDev3.Service1Client();
HraRiskAggregator.Service1Client client = new HraRiskAggregator.Service1Client(strServiceBinding);
client.InnerChannel.OperationTimeout = new TimeSpan(0, 1, 0); //set the timeout to 1 minute
string hl7Reply = "";
try
{
// old way:
// hl7Reply = client.GetRiskData(hl7Request);
//
//call the aggregator using the licenseID in the config file
string licID = Configurator.getAggregatorLicenseID();
hl7Reply = client.GetRiskDataWithDetails(hl7Request, licID);
//if we make it here, the synchronous web service call completed successfully
if (dump)
{
File.WriteAllText("AggregatorReply.xml", hl7Reply);
}
RP.ClearRP();
//Use an XPath navigator to retrieve the XML results into the object model
StringReader sr = new StringReader(hl7Reply);
XmlTextReader tx = new XmlTextReader(sr);
XPathDocument docNav = new XPathDocument(tx);
XPathNavigator nav = docNav.CreateNavigator();
//get BMRS requestId, effectiveTime, and top level messages from HL7 reply
XPathNavigator bmrsInfo = nav.SelectSingleNode("//pedigreeAnalysisResults[id/@extension][1]");
if (bmrsInfo != null)
{
RP.BMRS_RequestId = Convert.ToInt64(bmrsInfo.Evaluate("string(id/@extension)").ToString());
string hl7effTime = bmrsInfo.Evaluate("string(effectiveTime/@value)").ToString();
string[] formats = {"yyyyMMddHHmmss", "yyyyMMddHHmm", "yyyyMMddHH", "yyyyMMdd"};
DateTime dateValue;
if (DateTime.TryParseExact(hl7effTime, formats, null, System.Globalization.DateTimeStyles.None, out dateValue))
RP.BMRS_EffectiveTime = dateValue;
else
RP.BMRS_EffectiveTime = null;
RP.BMRS_Messages = bmrsInfo.Evaluate("string(text)").ToString().Trim();
}
processBrcaProHL7Scores(nav);
processMmrProHL7Scores(nav);
processTyrerCuzickHL7Scores(nav);
processTyrerCuzickv7HL7Scores(nav);
processMyriadHL7Score(nav);
processClausHL7Scores(nav);
processGailHL7Scores(nav);
processCCRATHL7Scores(nav);
processPREMMScores(nav);
//invoke sp_RunNCCN if appropriate
BCDB2.Instance.ExecuteNonQuery("EXEC sp_RunNCCN @apptid='" + apptid + "'");
RP.NCCNGuideline.BackgroundListLoad();
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
//since we know we have new risk scores, persist 'em
foreach (Person p in FHx.Relatives)
{
p.RP.PersistFullObject(args);
}
}
catch (Exception e) //exceptioned out on web service call; likely due to timeout
{
if (dump)
{
File.WriteAllText("AggregatorReply.xml", e.Message);
}
//Configurator.aggregatorActive = false;
//updateServiceStatusOnMainForm(false);
//doThisWhenNotUsingAggregator();
}
} //end of if block for using Aggregator Service
else
{
doThisWhenNotUsingAggregator();
}
BCDB2.Instance.ExecuteNonQuery("EXEC sp_3_populateBigQueue @unitnum='"+unitnum+"'");
//RunCdsForm cds = new RunCdsForm();
//cds.apptid = apptid;
//cds.unitnum = unitnum;
//cds.ShowDialog();
//cdsBreastOvary.LoadObject();
}
/**************************************************************************************************/
public override void PersistFullObject(HraModelChangedEventArgs e)
{
base.PersistFullObject(e);
chemoprevention.patientOwning = theProband;
chemoprevention.PersistFullObject(e);
}
public override void PersistFullObject(HraModelChangedEventArgs e)
{
//Azure barked on configurator
//if (Configurator.useAggregatorService())
//{
//base.PersistFullObject(e);
string ptUnitnum = OwningPerson.owningFHx.proband.unitnum;
ParameterCollection pc = new ParameterCollection("unitnum", ptUnitnum);
pc.Add("relId", ((Person)OwningPerson).relativeID);
pc.Add("apptid", OwningPerson.owningFHx.proband.apptid);
if (OwningPerson is Patient)
{
if (OwningPerson.owningFHx.proband.RP.TyrerCuzickModel != null && OwningPerson.owningFHx.proband.RP.TyrerCuzickModel_v7 != null)
{
string tcVersion = OwningPerson.owningFHx.proband.RP.TyrerCuzickModel.RiskFactors.TYRER_CUZICK_VERSION;
string tcMessages = OwningPerson.owningFHx.proband.RP.TyrerCuzickModel.RiskFactors.TYRER_CUZICK_MESSAGES;
string tc7Version = OwningPerson.owningFHx.proband.RP.TyrerCuzickModel_v7.RiskFactors.TYRER_CUZICK7_VERSION;
string tc7Messages = OwningPerson.owningFHx.proband.RP.TyrerCuzickModel_v7.RiskFactors.TYRER_CUZICK7_MESSAGES;
pc.Add("TyrerCuzick_Version", tcVersion);
pc.Add("TyrerCuzick_Messages", tcMessages);
pc.Add("TyrerCuzick_v7_Version", tc7Version);
pc.Add("TyrerCuzick_v7_Messages", tc7Messages);
}
}
DoPersistWithSpAndParams(e,
"sp_3_Save_RiskProfile",
ref pc);
if (OwningPerson is Patient)
{
if (BracproCancerRisk != null)
BracproCancerRisk.PersistFullList(e);
if (MmrproCancerRiskList != null)
MmrproCancerRiskList.PersistFullList(e);
if (TyrerCuzickModel != null)
TyrerCuzickModel.PersistFullList(e);
if (TyrerCuzickModel_v7 != null)
TyrerCuzickModel_v7.PersistFullList(e);
if (GailModel != null)
GailModel.PersistFullList(e);
if (ClausModel != null)
ClausModel.PersistFullList(e);
AuditFullObject();
}
//}
}
/*******************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("providerID", providerID,true);
if (apptid > 0)
{
pc.Add("apptid", apptid, false);
pc.Add("PCP", PCP, false);
pc.Add("refPhys", refPhys, false);
}
DoPersistWithSpAndParams(e,
"sp_3_Save_Provider",
ref pc);
this.providerID = (int)pc["providerID"].obj;
}
private void processTyrerCuzickv7HL7Scores(XPathNavigator nav)
{
//get TC scores
XPathNavigator tcNode = nav.SelectSingleNode("//pedigreeAnalysisResults[methodCode/@code='TYRER-CUZICK7'][1]");
if (tcNode != null)
{
RP.TyrerCuzickModel_v7.RiskFactors.TYRER_CUZICK7_VERSION = tcNode.Evaluate("string(methodCode[@code='TYRER-CUZICK7']/@codeSystemVersion)").ToString();
XPathNavigator textNode = tcNode.SelectSingleNode("text");
//create XML fragment with messages and hazard rates
XmlDocument myTempDoc = new XmlDocument();
myTempDoc.LoadXml("<text>" + (textNode != null ? System.Web.HttpUtility.HtmlDecode(textNode.InnerXml) : "<messages>No TC Messages</messages>") + "</text>");
XPathNavigator n1 = myTempDoc.CreateNavigator();
RP.TyrerCuzickModel_v7.RiskFactors.TYRER_CUZICK7_MESSAGES = n1.Evaluate("string(//messages[1])").ToString().Trim();
XPathNodeIterator ptCPRIter = tcNode.Select("component/percentageRisk[typeId/@extension = '" + this.relativeID + "']");
foreach (XPathNavigator cpr in ptCPRIter)
{
switch (cpr.Evaluate("string(code/@displayName)").ToString())
{
case "probCarrier":
RP.TyrerCuzickModel_v7.RiskFactors.TYRER_CUZICK7_1_2 = (100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString())).ToString();
RP.TyrerCuzick_v7_Brca_1_2 = Convert.ToDouble(RP.TyrerCuzickModel_v7.RiskFactors.TYRER_CUZICK7_1_2);
break;
case "probBRCA1Mutation":
RP.TyrerCuzickModel_v7.RiskFactors.TYRER_CUZICK7_1 = (100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString())).ToString();
break;
case "probBRCA2Mutation":
RP.TyrerCuzickModel_v7.RiskFactors.TYRER_CUZICK7_2 = (100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString())).ToString();
break;
default:
//do nothing
break;
}
}
XPathNodeIterator ptAgeChunkIter = tcNode.Select("component/age[value/low/@value]");
int five_year_age = 105;
int lifetime_age = 0;
int ptAge = -1;
Int32.TryParse(this.age, out ptAge);
foreach (XPathNavigator ac in ptAgeChunkIter)
{
int age = Convert.ToInt32(ac.Evaluate("string(value/low/@value)").ToString());
if (age < five_year_age) five_year_age = age;
if (age > lifetime_age) lifetime_age = age;
//find an existing TcRiskByAge for this age, if any
// else make a new one and add it to the TyrerCuzick_v7 list
TcRiskByAge tcrba = (TcRiskByAge)RP.TyrerCuzickModel_v7.FirstOrDefault(item => ((TcRiskByAge)item).age == age);
if (tcrba == null)
{
tcrba = new TcRiskByAge();
tcrba.age = age;
if (ptAge >= 0)
{
int deltaAge = age - ptAge;
tcrba.description = (deltaAge % 5 == 0) ? deltaAge.ToString() + " Year" : "";
}
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
RP.TyrerCuzickModel_v7.AddToList(tcrba, args);
}
switch (ac.Evaluate("string(pertinentInformation/realmCode/@code)").ToString())
{
case "breastCancerRisk":
tcrba.BreastCaRisk = Math.Round(100.0 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString()), 6);
if (age == five_year_age) RP.TyrerCuzick_v7_5Year_Breast = tcrba.BreastCaRisk;
if (age == lifetime_age) RP.TyrerCuzick_v7_Lifetime_Breast = tcrba.BreastCaRisk;
break;
case "populationBreastCancerRisk":
tcrba.PopulationCaRisk = Math.Round(100.0 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString()), 6);
break;
default:
//do nothing
break;
}
}
TcRiskByAge tcrbaoldest = (TcRiskByAge)RP.TyrerCuzickModel_v7.FirstOrDefault(item => ((TcRiskByAge)item).age == lifetime_age);
if (tcrbaoldest != null)
{
TcRiskByAge tcrbaLifetime = new TcRiskByAge();
tcrbaLifetime.age = tcrbaoldest.age;
tcrbaLifetime.BreastCaRisk = tcrbaoldest.BreastCaRisk;
tcrbaLifetime.PopulationCaRisk = tcrbaoldest.PopulationCaRisk;
tcrbaLifetime.description = "Lifetime";
RP.TyrerCuzickModel_v7.AddToList(tcrbaLifetime, new HraModelChangedEventArgs(null));
}
}
}
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
}
private void processBrcaProHL7Scores(XPathNavigator nav)
{
//get BrcaPro scores
XPathNavigator bpNode = nav.SelectSingleNode("//pedigreeAnalysisResults[methodCode/@code='BRCAPRO'][1]");
if (bpNode != null)
{
RP.BrcaPro_Version = bpNode.Evaluate("string(methodCode[@code='BRCAPRO']/@codeSystemVersion)").ToString();
XPathNavigator textNode = bpNode.SelectSingleNode("text");
//create XML fragment with messages and hazard rates
XmlDocument myTempDoc = new XmlDocument();
myTempDoc.LoadXml("<text>" + System.Web.HttpUtility.HtmlDecode(textNode.InnerXml) + "</text>");
XPathNavigator n1 = myTempDoc.CreateNavigator();
RP.BrcaPro_Messages = n1.Evaluate("string(//messages[1])").ToString().Trim();
XPathNodeIterator xnit = n1.Select("//hazardRates[1]/row"); //gets all the hazard rate rows (one per age)
int ptAge = -1; //handy to have age as an integer for hazard rate zero interest rows
Int32.TryParse(this.age, out ptAge);
foreach (XPathNavigator row in xnit)
{
int id = Convert.ToInt32(row.Evaluate("string(@id)").ToString());
if (id <= ptAge) continue; //no need to save all 0 hazard rate rows in object model or DB
//find an existing BrcaProCancerRiskByAge for this age, if any
// else make a new one and add it to the BracproCancerRiskList
BrcaProCancerRiskByAge bpcrba = (BrcaProCancerRiskByAge)RP.BracproCancerRisk.FirstOrDefault(item => ((BrcaProCancerRiskByAge)item).age == id);
if (bpcrba == null)
{
bpcrba = new BrcaProCancerRiskByAge();
bpcrba.age = id;
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
RP.BracproCancerRisk.AddToList(bpcrba, args);
}
bpcrba.hFX0 = Convert.ToDouble(row.Evaluate("concat(string(@hFX0), string(@hMX0))").ToString());
bpcrba.hFY0 = Convert.ToDouble(row.Evaluate("concat(string(@hFY0), string(@hMY0))").ToString());
bpcrba.hFX1 = Convert.ToDouble(row.Evaluate("concat(string(@hFX1), string(@hMX1))").ToString());
bpcrba.hFY1 = Convert.ToDouble(row.Evaluate("concat(string(@hFY1), string(@hMY1))").ToString());
bpcrba.hFX2 = Convert.ToDouble(row.Evaluate("concat(string(@hFX2), string(@hMX2))").ToString());
bpcrba.hFY2 = Convert.ToDouble(row.Evaluate("concat(string(@hFY2), string(@hMY2))").ToString());
bpcrba.hFX12 = Convert.ToDouble(row.Evaluate("concat(string(@hFX12), string(@hMX12))").ToString());
bpcrba.hFY12 = Convert.ToDouble(row.Evaluate("concat(string(@hFY12), string(@hMY12))").ToString());
}
XPathNodeIterator ptCPRIter = bpNode.Select("component/percentageRisk[typeId/@extension = '" + this.relativeID + "']");
foreach (XPathNavigator cpr in ptCPRIter)
{
switch (cpr.Evaluate("string(code/@displayName)").ToString())
{
case "probCarrier":
RP.BrcaPro_1_2_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
case "probBRCA1Mutation":
RP.BrcaPro_1_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
case "probBRCA2Mutation":
RP.BrcaPro_2_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
default:
//do nothing
break;
}
}
XPathNodeIterator ptAgeChunkIter = bpNode.Select("component/age[value/low/@value]");
int five_year_age = 105;
int lifetime_age = 0;
foreach (XPathNavigator ac in ptAgeChunkIter)
{
int age = Convert.ToInt32(ac.Evaluate("string(value/low/@value)").ToString());
if (age < five_year_age) five_year_age = age;
if (age > lifetime_age) lifetime_age = age;
//find an existing BrcaProCancerRiskByAge for this age, if any
// else make a new one and add it to the BracproCancerRiskList
BrcaProCancerRiskByAge bpcrba = (BrcaProCancerRiskByAge)RP.BracproCancerRisk.FirstOrDefault(item => ((BrcaProCancerRiskByAge)item).age == age);
if (bpcrba == null) //since we already processed hazard rates, list element for every age should already exist, and this code block should never run
{
bpcrba = new BrcaProCancerRiskByAge();
bpcrba.age = age;
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
RP.BracproCancerRisk.AddToList(bpcrba, args);
}
double brca0 = 100 - (double)RP.BrcaPro_1_2_Mut_Prob;
double brca11_and_2 = (double)(RP.BrcaPro_1_2_Mut_Prob - (RP.BrcaPro_1_Mut_Prob + RP.BrcaPro_2_Mut_Prob));
bpcrba.BreastCaRisk = (bpcrba.hFX0 * brca0) +
(bpcrba.hFX1 * (double)RP.BrcaPro_1_Mut_Prob) +
(bpcrba.hFX2 * (double)RP.BrcaPro_2_Mut_Prob) +
(bpcrba.hFX12 * brca11_and_2);
bpcrba.BreastCaRiskWithNoMutation = (bpcrba.hFX0 * 100) +
(bpcrba.hFX1 * 0) +
(bpcrba.hFX2 * 0) +
(bpcrba.hFX12 * 0);
bpcrba.BreastCaRiskWithBrca1Mutation = (bpcrba.hFX0 * 0) +
(bpcrba.hFX1 * 100) +
(bpcrba.hFX2 * 0) +
(bpcrba.hFX12 * 0);
bpcrba.BreastCaRiskWithBrca2Mutation = (bpcrba.hFX0 * 0) +
(bpcrba.hFX1 * 0) +
(bpcrba.hFX2 * 100) +
(bpcrba.hFX12 * 0);
bpcrba.BreastCaRiskWithBrca1And2Mutation = (bpcrba.hFX0 * 0) +
(bpcrba.hFX1 * 0) +
(bpcrba.hFX2 * 0) +
(bpcrba.hFX12 * 100);
bpcrba.OvarianCaRisk = (bpcrba.hFY0 * brca0) +
(bpcrba.hFY1 * (double)RP.BrcaPro_1_Mut_Prob) +
(bpcrba.hFY2 * (double)RP.BrcaPro_2_Mut_Prob) +
(bpcrba.hFY12 * brca11_and_2);
bpcrba.OvarianCaRiskWithNoMutation = (bpcrba.hFY0 * 100) +
(bpcrba.hFY1 * 0) +
(bpcrba.hFY2 * 0) +
(bpcrba.hFY12 * 0);
bpcrba.OvarianCaRiskWithBrca1Mutation = (bpcrba.hFY0 * 0) +
(bpcrba.hFY1 * 100) +
(bpcrba.hFY2 * 0) +
(bpcrba.hFY12 * 0);
bpcrba.OvarianCaRiskWithBrca2Mutation = (bpcrba.hFY0 * 0) +
(bpcrba.hFY1 * 0) +
(bpcrba.hFY2 * 100) +
(bpcrba.hFY12 * 0);
bpcrba.OvarianCaRiskWithBrca1And2Mutation = (bpcrba.hFY0 * 0) +
(bpcrba.hFY1 * 0) +
(bpcrba.hFY2 * 0) +
(bpcrba.hFY12 * 100);
switch (ac.Evaluate("string(pertinentInformation/realmCode/@code)").ToString())
{
case "breastCancerRisk":
bpcrba.BreastCaRisk = Math.Round(100.0 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString()), 6);
if (age == five_year_age) RP.BrcaPro_5Year_Breast = bpcrba.BreastCaRisk;
if (age == lifetime_age) RP.BrcaPro_Lifetime_Breast = bpcrba.BreastCaRisk;
break;
case "ovarianCancerRisk":
bpcrba.OvarianCaRisk = Math.Round(100.0 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString()), 6);
if (age == five_year_age) RP.BrcaPro_5Year_Ovary = bpcrba.OvarianCaRisk;
if (age == lifetime_age) RP.BrcaPro_Lifetime_Ovary = bpcrba.OvarianCaRisk;
break;
default:
//do nothing
break;
}
}
RP.BM_5Year_Age = five_year_age;
RP.BM_Lifetime_Age = lifetime_age;
//update risk scores for all non-proband family members
//these are mutation probs only
XPathNodeIterator relCPRIter = bpNode.Select("component/percentageRisk[typeId/@extension != '" + this.relativeID + "']");
foreach (XPathNavigator cpr in relCPRIter)
{
int relId = Convert.ToInt32(cpr.Evaluate("string(typeId/@extension)").ToString());
Person rel = FHx.Relatives.FirstOrDefault(item => ((Person)item).relativeID == relId);
if (rel.RP.BMRS_EffectiveTime == null) rel.RP.BMRS_EffectiveTime = RP.BMRS_EffectiveTime;
if (rel.RP.BrcaPro_Version == null) rel.RP.BrcaPro_Version = RP.BrcaPro_Version;
switch (cpr.Evaluate("string(code/@displayName)").ToString())
{
case "probCarrier":
rel.RP.BrcaPro_1_2_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
case "probBRCA1Mutation":
rel.RP.BrcaPro_1_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
case "probBRCA2Mutation":
rel.RP.BrcaPro_2_Mut_Prob = Math.Round(100.0 * Convert.ToDouble(cpr.Evaluate("string(value/@value)").ToString()), 6);
break;
default:
//do nothing
break;
}
}
}
}
public void PersistFullObject(HraModelChangedEventArgs e, string unitnum, int apptid)
{
ParameterCollection pc = new ParameterCollection();
pc.Add("unitnum", unitnum);
pc.Add("apptid", apptid);
DoPersistWithSpAndParams(e,
"sp_3_Save_ClausParameters",
ref pc);
}
/**************************************************************************************************/
public override void BackgroundPersistWork(HraModelChangedEventArgs e)
{
ParameterCollection pc = new ParameterCollection();
if (owningPatient != null)
{
pc.Add("unitnum", owningPatient.unitnum);
}
else
{
pc.Add("unitnum", -1);
}
DoPersistWithSpAndParams(e,
"sp_3_Save_GUIPreference",
ref pc);
}
private void processClausHL7Scores(XPathNavigator nav)
{
//get Claus scores
XPathNavigator cNode = nav.SelectSingleNode("//pedigreeAnalysisResults[methodCode/@code='CLAUS'][1]");
if (cNode != null)
{
RP.ClausModel.Clear();
RP.ClausModel.RiskFactors.Claus_Table = "";
RP.ClausModel.RiskFactors.RelOne = "";
RP.ClausModel.RiskFactors.RelTwo = "";
XPathNavigator textNode = cNode.SelectSingleNode("text");
string clausMessages = textNode.Evaluate("string(.)").ToString().Trim().Replace("\r", "");
//extract the three Claus messages that are always present
string pattern = @"^\s*Claus_Table: (?<clausTable>.*)$\s*^\s*Claus_RelOne: (?<clausRel1>.*)$\s*^\s*Claus_RelTwo: (?<clausRel2>.*)$";
Match m = Regex.Match(clausMessages, pattern, RegexOptions.IgnoreCase | RegexOptions.Multiline);
if (m.Success) {
RP.ClausModel.RiskFactors.Claus_Table = m.Result("${clausTable}");
RP.ClausModel.RiskFactors.ClausRiskFactors_RelOne = m.Result("${clausRel1}");
RP.ClausModel.RiskFactors.ClausRiskFactors_RelTwo = m.Result("${clausRel2}");
}
RP.ClausModel.RiskFactors.effectiveTime = cNode.Evaluate("string(effectiveTime/@value)").ToString();
XPathNodeIterator ptAgeChunkIter = cNode.Select("component/age[value/low/@value]");
foreach (XPathNavigator ac in ptAgeChunkIter)
{
int age = Convert.ToInt32(ac.Evaluate("string(value/low/@value)").ToString());
//find an existing ClausRiskByAge for this age, if any
// else make a new one and add it to the Claus list
ClausRiskByAge crba = (ClausRiskByAge)RP.ClausModel.FirstOrDefault(item => ((ClausRiskByAge)item).age == age);
if (crba == null)
{
crba = new ClausRiskByAge();
crba.age = age;
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
RP.ClausModel.AddToList(crba, args);
}
crba.BreastCaRisk = 100 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString());
switch (ac.Evaluate("string(pertinentInformation/realmCode/@code)").ToString())
{
//case "breastCancerRisk":
// crba.BreastCaRisk = Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString());
// break;
case "Claus_FiveYear":
RP.Claus_5Year_Breast = 100 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString());
break;
case "Claus_Lifetime":
RP.Claus_Lifetime_Breast = 100 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString());
break;
default:
//do nothing
break;
}
}
}
}
private void processGailHL7Scores(XPathNavigator nav)
{
//get Gail scores
XPathNavigator gNode = nav.SelectSingleNode("//pedigreeAnalysisResults[methodCode/@code='GAIL'][1]");
if (gNode != null)
{
XPathNavigator textNode = gNode.SelectSingleNode("text");
string gailInputs = textNode.Evaluate("string(.)").ToString().Trim().Replace("\r", "");
//recover Gail Input values
Dictionary<string, string> ptGailInfo = new Dictionary<string, string>();
List<string> names = null;
//Now iterate through the three lines and create the Gail values
//routine works even if headers produced by hraGetGail.xsl change in the future
foreach (var myRow in gailInputs.Split(new char[] { '\n' }, StringSplitOptions.RemoveEmptyEntries))
{
if (myRow.Trim().StartsWith("Gail inputs:"))
{
//do nothing
}
else if (myRow.Trim().StartsWith("currentAge menarcheAge"))
{
//this is the first row which contains the headers
string[] headers = myRow.Split((char[])null, StringSplitOptions.RemoveEmptyEntries);
names = headers.ToList<string>();
}
else //this is the Gail info row
{
string[] gail_inputs = myRow.Trim().Split((char[])null, StringSplitOptions.RemoveEmptyEntries);
for (int i = 0; i < gail_inputs.Length; i++) ptGailInfo.Add(names[i], gail_inputs[i]);
}
}
RP.GailModel.RiskFactors.currentAge = ptGailInfo.ContainsKey("currentAge") ? ptGailInfo["currentAge"] : "UNKNOWN";
RP.GailModel.RiskFactors.menarcheAge = ptGailInfo.ContainsKey("menarcheAge") ? ptGailInfo["menarcheAge"] : "UNKNOWN";
RP.GailModel.RiskFactors.firstLiveBirthAge = ptGailInfo.ContainsKey("firstLiveBirthAge") ? ptGailInfo["firstLiveBirthAge"] : "UNKNOWN";
RP.GailModel.RiskFactors.hadBiopsy = ptGailInfo.ContainsKey("hadBiopsy") ? ptGailInfo["hadBiopsy"] : "UNKNOWN";
RP.GailModel.RiskFactors.numBiopsy = ptGailInfo.ContainsKey("numBiopsy") ? ptGailInfo["numBiopsy"] : "UNKNOWN";
RP.GailModel.RiskFactors.hyperPlasia = ptGailInfo.ContainsKey("hyperPlasia") ? ptGailInfo["hyperPlasia"] : "UNKNOWN";
RP.GailModel.RiskFactors.firstDegreeRel = ptGailInfo.ContainsKey("firstDegreeRel") ? ptGailInfo["firstDegreeRel"] : "UNKNOWN";
RP.GailModel.RiskFactors.race = ptGailInfo.ContainsKey("race") ? ptGailInfo["race"] : "UNKNOWN";
if (string.Compare("white", RP.GailModel.RiskFactors.race, true) == 0)
RP.GailModel.RiskFactors.race = "1";
else if (string.Compare("black", RP.GailModel.RiskFactors.race, true) == 0)
RP.GailModel.RiskFactors.race = "2";
else if (string.Compare("hispanic", RP.GailModel.RiskFactors.race, true) == 0)
RP.GailModel.RiskFactors.race = "3";
else
RP.GailModel.RiskFactors.race = "";
if (string.Compare("UNKNOWN", RP.GailModel.RiskFactors.menarcheAge, true) == 0)
RP.GailModel.RiskFactors.menarcheAge = "99";
if (string.Compare("UNKNOWN", RP.GailModel.RiskFactors.firstLiveBirthAge, true) == 0)
RP.GailModel.RiskFactors.firstLiveBirthAge = "99";
if (string.Compare("UNKNOWN", RP.GailModel.RiskFactors.hadBiopsy, true) == 0)
RP.GailModel.RiskFactors.hadBiopsy = "99";
if (string.Compare("UNKNOWN", RP.GailModel.RiskFactors.numBiopsy, true) == 0)
RP.GailModel.RiskFactors.numBiopsy = "99";
if (string.Compare("UNKNOWN", RP.GailModel.RiskFactors.hyperPlasia, true) == 0)
RP.GailModel.RiskFactors.hyperPlasia = "99";
if (string.Compare("UNKNOWN", RP.GailModel.RiskFactors.firstDegreeRel, true) == 0)
RP.GailModel.RiskFactors.firstDegreeRel = "99";
if (string.Compare("UNKNOWN", RP.GailModel.RiskFactors.race, true) == 0)
RP.GailModel.RiskFactors.race = "99";
RP.GailModel.RiskFactors.effectiveTime = gNode.Evaluate("string(effectiveTime/@value)").ToString();
XPathNodeIterator ptAgeChunkIter = gNode.Select("component/age[value/low/@value]");
foreach (XPathNavigator ac in ptAgeChunkIter)
{
int age = Convert.ToInt32(ac.Evaluate("string(value/low/@value)").ToString());
//find an existing GailRiskByAge for this age, if any
// else make a new one and add it to the Gail list
GailRiskByAge grba = (GailRiskByAge)RP.GailModel.FirstOrDefault(item => ((GailRiskByAge)item).age == age);
if (grba == null)
{
grba = new GailRiskByAge();
grba.age = age;
HraModelChangedEventArgs args = new HraModelChangedEventArgs(null);
RP.GailModel.AddToList(grba, args);
}
switch (ac.Evaluate("string(pertinentInformation/realmCode/@code)").ToString())
{
case "Gail_Proband":
grba.BreastCaRisk = 100.0 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString());
break;
case "Gail_Population":
grba.PopulationCaRisk = 100.0 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString());
break;
case "Gail_Proband_FiveYear":
RP.Gail_5Year_Breast = 100.0 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString());
break;
case "Gail_Proband_Lifetime":
RP.Gail_Lifetime_Breast = 100.0 * Convert.ToDouble(ac.Evaluate("string(pertinentInformation/probability/value/@value)").ToString());
break;
default:
//do nothing
break;
}
}
}
}
