internal IndexedHashtable toChemHemSpecimens(string[] response, ref string fromDate, ref string toDate)
{
IndexedHashtable result = new IndexedHashtable(response.Length);
for (int i = 0; i < response.Length; i++)
{
string[] flds = StringUtils.split(response[i], StringUtils.CARET);
LabSpecimen specimen = new LabSpecimen();
specimen.Id = flds[0];
specimen.ReportDate = VistaTimestamp.toUtcString(flds[2]);
specimen.CollectionDate = VistaTimestamp.toUtcString(flds[1]);
if (i == 0)
{
fromDate = specimen.CollectionDate;
}
if (i == response.Length - 1)
{
toDate = specimen.CollectionDate;
}
specimen.Name = flds[3];
specimen.AccessionNumber = flds[4];
if (flds.Length > 6)
{
specimen.Site = flds[5];
}
if (flds.Length > 7)
{
specimen.Facility = new SiteId(flds[7], flds[6]);
}
string key = flds[1] + '^' + flds[4];
result.Add(key, specimen);
}
return(result);
}
private LabTest BuildLabTest(LabSpecimen labSpecimen, LabTestName labTestNameCodedConcept)
{
var labTest = labSpecimen.AddLabTest(new LabTestInfoBuilder().WithLabTestName(labTestNameCodedConcept));
Session.SaveOrUpdate(labTest);
return(labTest);
}
public void CreateLabSpecimen_GivenValidArguments_CreatesLabSpecimen()
{
var activityType = new Mock <ActivityType>();
var lookupValueRepository = new Mock <ILookupValueRepository>();
lookupValueRepository
.Setup(l => l.GetLookupByWellKnownName <ActivityType>(It.IsAny <string>()))
.Returns(activityType.Object);
var labSpecimenRepository = new Mock <ILabSpecimenRepository>();
var labSpecimenFactory = new LabSpecimenFactory(
labSpecimenRepository.Object,
lookupValueRepository.Object);
var visit = new Mock <Visit>();
var clinicalCase = new Mock <ClinicalCase>();
var patient = new Mock <Patient>();
visit.Setup(v => v.ClinicalCase).Returns(clinicalCase.Object);
clinicalCase.Setup(c => c.Patient).Returns(patient.Object);
LabSpecimen labSpecimen = labSpecimenFactory.CreateLabSpecimen(visit.Object);
Assert.IsNotNull(labSpecimen);
}
private LabSpecimen BuildLabSpecimen(Visit visit,
ActivityType activityType)
{
var labSpecimen = new LabSpecimen(visit, activityType);
Session.SaveOrUpdate(labSpecimen);
return(labSpecimen);
}
public LabSpecimenTO(LabSpecimen mdo)
{
this.id = mdo.Id;
this.name = StringUtils.stripInvalidXmlCharacters(mdo.Name);
this.collectionDate = mdo.CollectionDate;
this.accessionNum = mdo.AccessionNumber;
this.site = mdo.Site;
if (mdo.Facility != null)
{
this.facility = new TaggedText(mdo.Facility.Name);
}
}
public LabSpecimenTO(LabSpecimen mdo)
{
this.id = mdo.Id;
this.name = StringUtils.stripInvalidXmlCharacters(mdo.Name);
this.collectionDate = mdo.CollectionDate;
this.accessionNum = mdo.AccessionNumber;
this.site = mdo.Site;
if (mdo.Facility != null)
{
this.facility = new TaggedText(mdo.Facility.Name);
}
}
internal IndexedHashtable toChemHemSpecimens(string[] response, ref string fromDate, ref string toDate)
{
IndexedHashtable result = new IndexedHashtable(response.Length);
for (int i = 0; i < response.Length; i++)
{
string[] flds = StringUtils.split(response[i], StringUtils.CARET);
LabSpecimen specimen = new LabSpecimen();
specimen.Id = flds[0];
specimen.ReportDate = VistaTimestamp.toUtcString(flds[2]);
specimen.CollectionDate = VistaTimestamp.toUtcString(flds[1]);
if (i == 0)
{
fromDate = specimen.CollectionDate;
}
if (i == response.Length-1)
{
toDate = specimen.CollectionDate;
}
specimen.Name = flds[3];
specimen.AccessionNumber = flds[4];
if (flds.Length > 6)
{
specimen.Site = flds[5];
}
if (flds.Length > 7)
{
specimen.Facility = new SiteId(flds[7], flds[6]);
}
string key = flds[1] + '^' + flds[4];
result.Add(key, specimen);
}
return result;
}
internal ChemHemReport buildChemHemReport(IDataReader reader)
{
string patientIcn = DbReaderUtil.getValue(reader, reader.GetOrdinal("PatientICN"));
string testName = DbReaderUtil.getValue(reader, reader.GetOrdinal("LabChemTestName")); // LabResult.LabTest.ShortName
string resultValue = DbReaderUtil.getValue(reader, reader.GetOrdinal("LabChemResultValue")); // LabResult.Value
string refHigh = DbReaderUtil.getValue(reader, reader.GetOrdinal("RefHigh")); // LabResult.LabTest.hiRef
string refLow = DbReaderUtil.getValue(reader, reader.GetOrdinal("RefLow")); // LabResult.LabTest.lowRef
string abnormal = DbReaderUtil.getValue(reader, reader.GetOrdinal("Abnormal")); // LabResult.BoundaryStatus
string loinc = DbReaderUtil.getValue(reader, reader.GetOrdinal("LOINC")); // LabResult.LabTest.Loinc
string component = DbReaderUtil.getValue(reader, reader.GetOrdinal("Component")); // LabResult.LabTest.Name
string labTestType = DbReaderUtil.getValue(reader, reader.GetOrdinal("LabTestType")); //LabResult.LabTest.Category
string labChemTestSid = DbReaderUtil.getInt32Value(reader, reader.GetOrdinal("LabChemTestSID"));
string labChemTestIen = DbReaderUtil.getValue(reader, reader.GetOrdinal("LabChemTestIEN"));
string labChemIen = DbReaderUtil.getValue(reader, reader.GetOrdinal("LabChemIEN")); // LabTest.Id
string labChemSid = DbReaderUtil.getInt64Value(reader, reader.GetOrdinal("LabChemSID"));
string siteCode = DbReaderUtil.getInt16Value(reader, reader.GetOrdinal("Sta3n"));
string labChemCompleteDate = DbReaderUtil.getDateValue(reader, reader.GetOrdinal("LabChemCompleteDateTime"));
SiteId facility = new SiteId()
{
Id = siteCode
};
LabTest labTest = new LabTest()
{
Id = labChemTestIen,
Name = testName,
ShortName = labTestType,
DataId = labChemTestSid,
HiRef = refHigh,
LowRef = refLow,
Loinc = loinc
};
LabResult labResult = new LabResult()
{
Value = resultValue,
BoundaryStatus = abnormal,
Test = labTest
};
LabResult[] labResults = new LabResult[1];
labResults[0] = labResult;
LabSpecimen labSpecimen = new LabSpecimen()
{
Id = labChemIen,
Name = DbReaderUtil.getValue(reader, reader.GetOrdinal("Specimen")),
CollectionDate = labChemCompleteDate,
Site = siteCode
};
ChemHemReport report = new ChemHemReport()
{
Id = labChemSid,
Specimen = labSpecimen,
Facility = facility,
Results = labResults,
Timestamp = labChemCompleteDate
};
return(report);
}
/*
* In order to get the correct results with the correct reports using the DDR calls and RPCs
* available, we are going to use the user specified fromDate but use today as the toDate (like
* CPRS does) and retrieve all the specimens with in that time period. Then, we will find the
* reports, match them up with their specimens and lastly filter those results using our original
* date range
*/
public ChemHemReport[] getChemHemReports(string dfn, string fromDate, string toDate)
{
if (!String.IsNullOrEmpty(toDate) && toDate.IndexOf(".") == -1)
{
toDate += ".235959";
}
IndexedHashtable specimens = getChemHemSpecimens(dfn, fromDate, toDate, "3");
if (specimens == null || specimens.Count == 0)
{
return(null);
}
ArrayList lst = new ArrayList();
//string nextDate = VistaTimestamp.fromUtcString(today);
string nextDate = VistaTimestamp.fromUtcString(toDate);
// Due to comment above, we want to loop through "ORWLRR INTERIMG" RPC until we
// get as many reports as the DDR call above told us we would
// TBD - this while statement screams infinite loop (i.e. what happens if we don't get all the
// reports the DDR call above said we would?) Should we put an arbitrarily large stop in here?
// e.g. if count > 1,000,000 then throw an exception that we didn't get what VistA said we should?
int i = 0;
while (lst.Count < specimens.Count)
{
LabSpecimen specimen = (LabSpecimen)specimens.GetValue(i);
// ORWLRR INTERIMG rpc and function below updates nextDate for subsequent calls so LEAVE REF ALONE
string nextDateBefore = nextDate;
ChemHemReport rpt = getChemHemReport(dfn, ref nextDate);
if (rpt != null)
{
if ((rpt.Specimen != null) && (rpt.Specimen.AccessionNumber == specimen.AccessionNumber))
{
i++;
rpt.Id = specimen.Id;
rpt.Facility = specimen.Facility;
rpt.Specimen = specimen;
rpt.Timestamp = specimen.ReportDate;
lst.Add(rpt);
}
}
// if the next date variable was not changed below, it means we are no longer looping through
// the reports so we should go ahead and break out of this loop - should take care of
// infinite loop concerns
if (nextDate.Equals(nextDateBefore))
{
break;
}
}
// At last, filter the reports based on their timestamps
ArrayList filteredList = new ArrayList();
double startDate = Convert.ToDouble(fromDate);
double stopDate = Convert.ToDouble(toDate);
ChemHemReport[] rpts = (ChemHemReport[])lst.ToArray(typeof(ChemHemReport));
foreach (ChemHemReport report in rpts)
{
// if the report doesn't have a timestamp, we will just add it to our list
if (String.IsNullOrEmpty(report.Timestamp))
{
filteredList.Add(report);
continue;
}
double reportTimeStamp = Convert.ToDouble(report.Timestamp);
if (startDate <= reportTimeStamp && reportTimeStamp <= stopDate)
{
filteredList.Add(report);
}
}
return((ChemHemReport[])filteredList.ToArray(typeof(ChemHemReport)));
}
private bool MapProperties(LabSpecimenDto dto, LabSpecimen entity)
{
var labSpecimenType = _mappingHelper.MapLookupField <LabSpecimenType> (dto.LabSpecimenType);
entity.ReviseLabSpecimenType(labSpecimenType);
entity.ReviseLabReceivedDate(dto.LabReceivedDate);
entity.ReviseCollectedHereIndicator(dto.CollectedHereIndicator);
// TODO: This needs to be rethought when the domain for Lab is redone.
var labTest = entity.LabTests.FirstOrDefault(lt => lt.LabTestInfo.LabTestName.WellKnownName == dto.LabTestName.WellKnownName);
if (labTest == null && entity.LabTests.Count > 0)
{
//right now there is only every one lab test per lab specimen?
entity.RemoveLabTest(entity.LabTests.ElementAt(0));
}
var labTestInfo = new LabTestInfoBuilder()
.WithLabTestName(_mappingHelper.MapLookupField <LabTestName> (dto.LabTestName))
.WithTestReportDate(dto.LabTestDate)
.WithLabTestNote(dto.LabTestNote);
if (labTest == null)
{
labTest = entity.AddLabTest(labTestInfo);
}
else
{
labTest.ReviseLabTestInfo(labTestInfo);
}
var result = new AggregateNodeCollectionMapper <LabResultDto, LabTest, LabResult> (dto.LabResults, labTest, labTest.LabResults)
.MapAddedItem(
(lrdto, lt) =>
{
CodedConcept labTestResultNameCodedConcept = null;
if (lrdto.LabTestResultNameCodedConcept != null)
{
labTestResultNameCodedConcept = new CodedConceptBuilder().WithCodedConceptDto(lrdto.LabTestResultNameCodedConcept);
}
lt.AddLabResult(
new LabResultBuilder()
.WithLabTestResultNameCodedConcept(labTestResultNameCodedConcept)
.WithValue(lrdto.Value)
.WithUnitOfMeasureCode(lrdto.UnitOfMeasureCode));
}
)
.MapChangedItem(
(lrdto, lt, lr) =>
{
lt.RemoveLabResult(lr);
CodedConcept labTestResultNameCodedConcept = null;
if (lrdto.LabTestResultNameCodedConcept != null)
{
labTestResultNameCodedConcept = new CodedConceptBuilder().WithCodedConceptDto(lrdto.LabTestResultNameCodedConcept);
}
lt.AddLabResult(
new LabResultBuilder()
.WithLabTestResultNameCodedConcept(labTestResultNameCodedConcept)
.WithValue(lrdto.Value)
.WithUnitOfMeasureCode(lrdto.UnitOfMeasureCode));
})
.MapRemovedItem((lrdto, lt, lr) => lt.RemoveLabResult(lr))
.Map();
return(result);
}
/// <summary>
/// Processes the single aggregate.
/// </summary>
/// <param name="dto">The dto to process.</param>
/// <param name="entity">The entity.</param>
/// <returns>A <see cref="System.Boolean"/></returns>
protected override bool ProcessSingleAggregate(LabSpecimenDto dto, LabSpecimen entity)
{
_mappingResult &= MapProperties(dto, entity);
return(_mappingResult);
}