/// <summary>
/// Prepare HATEOAS links for a identifier based collection resource
/// </summary>
/// <param name="wrapper">The linked dto wrapper that will host each link</param>
/// <param name="workFlowGuid">The unique identifier of the work flow that we are generating analysis for</param>
/// <param name="termId">The unique id of the meddra term</param>
/// <param name="analyserTermSetResourceParameters">Standard parameters for representing resource</param>
/// <param name="hasNext">Are there additional pages</param>
/// <param name="hasPrevious">Are there previous pages</param>
/// <returns></returns>
private LinkedResourceBaseDto CreateLinksForAnalyserPatients(
LinkedResourceBaseDto wrapper,
Guid workFlowGuid,
int termId,
AnalyserTermSetResourceParameters analyserTermSetResourceParameters,
bool hasNext, bool hasPrevious)
{
wrapper.Links.Add(
new LinkDto(
_linkGeneratorService.CreateAnalyserTermPatientsResourceUri(workFlowGuid, termId, ResourceUriType.Current, analyserTermSetResourceParameters),
"self", "GET"));
if (hasNext)
{
wrapper.Links.Add(
new LinkDto(
_linkGeneratorService.CreateAnalyserTermPatientsResourceUri(workFlowGuid, termId, ResourceUriType.NextPage, analyserTermSetResourceParameters),
"nextPage", "GET"));
}
if (hasPrevious)
{
wrapper.Links.Add(
new LinkDto(
_linkGeneratorService.CreateAnalyserTermPatientsResourceUri(workFlowGuid, termId, ResourceUriType.PreviousPage, analyserTermSetResourceParameters),
"previousPage", "GET"));
}
return(wrapper);
}
public string CreateAnalyserTermPatientsResourceUri(Guid workFlowGuid,
int termId,
ResourceUriType type,
AnalyserTermSetResourceParameters analyserTermSetResourceParameters)
{
switch (type)
{
case ResourceUriType.PreviousPage:
return(_linkGenerator.GetPathByName(_accessor.HttpContext, "GetAnalyserTermPatients",
new
{
workFlowGuid,
id = termId,
conditionId = analyserTermSetResourceParameters.ConditionId,
cohortGroupId = analyserTermSetResourceParameters.CohortGroupId,
searchFrom = analyserTermSetResourceParameters.SearchFrom,
searchTo = analyserTermSetResourceParameters.SearchTo,
riskFactorOptionNames = analyserTermSetResourceParameters.RiskFactorOptionNames,
pageNumber = analyserTermSetResourceParameters.PageNumber - 1,
pageSize = analyserTermSetResourceParameters.PageSize
}));
case ResourceUriType.NextPage:
return(_linkGenerator.GetPathByName(_accessor.HttpContext, "GetAnalyserTermPatients",
new
{
workFlowGuid,
id = termId,
conditionId = analyserTermSetResourceParameters.ConditionId,
cohortGroupId = analyserTermSetResourceParameters.CohortGroupId,
searchFrom = analyserTermSetResourceParameters.SearchFrom,
searchTo = analyserTermSetResourceParameters.SearchTo,
riskFactorOptionNames = analyserTermSetResourceParameters.RiskFactorOptionNames,
pageNumber = analyserTermSetResourceParameters.PageNumber + 1,
pageSize = analyserTermSetResourceParameters.PageSize
}));
case ResourceUriType.Current:
default:
return(_linkGenerator.GetPathByName(_accessor.HttpContext, "GetAnalyserTermPatients",
new
{
workFlowGuid,
id = termId,
conditionId = analyserTermSetResourceParameters.ConditionId,
cohortGroupId = analyserTermSetResourceParameters.CohortGroupId,
searchFrom = analyserTermSetResourceParameters.SearchFrom,
searchTo = analyserTermSetResourceParameters.SearchTo,
riskFactorOptionNames = analyserTermSetResourceParameters.RiskFactorOptionNames,
pageNumber = analyserTermSetResourceParameters.PageNumber,
pageSize = analyserTermSetResourceParameters.PageSize
}));
}
}
/// <summary>
/// Map additional dto detail elements not handled through automapper
/// </summary>
/// <param name="dto">The dto that the link has been added to</param>
/// <param name="analyserTermSetResourceParameters">Standard parameters for representing resource</param>
/// <returns></returns>
private AnalyserTermDetailDto CustomResultMap(AnalyserTermDetailDto dto, AnalyserTermSetResourceParameters analyserTermSetResourceParameters)
{
dto.Results = GetAnalyserResultSets <AnalyserResultDto>(dto.TerminologyMeddraId, analyserTermSetResourceParameters);
// Generate series for exposed cases
var exposedSeriesValueArray = new List <SeriesValueList>();
var exposedSeriesValueList = new SeriesValueList()
{
Name = "Exposed Cases"
};
var exposedValues = new List <SeriesValueListItem>();
var riskSeriesValueArray = new List <SeriesValueList>();
var riskSeriesValueList = new SeriesValueList()
{
Name = "Unadjused Relative Risks"
};
var riskValues = new List <SeriesValueListItem>();
foreach (var result in dto.Results)
{
var exposedModelItem = new SeriesValueListItem()
{
Value = result.ExposedIncidenceRate.Cases,
//Min = intValue - ((intValue * 20) / 100),
//Max = intValue + ((intValue * 20) / 100),
Name = result.Medication
};
exposedValues.Add(exposedModelItem);
var riskModelItem = new SeriesValueListItem()
{
Value = result.UnadjustedRelativeRisk,
//Min = intValue - ((intValue * 20) / 100),
//Max = intValue + ((intValue * 20) / 100),
Name = result.Medication
};
riskValues.Add(riskModelItem);
}
exposedSeriesValueList.Series = exposedValues;
exposedSeriesValueArray.Add(exposedSeriesValueList);
riskSeriesValueList.Series = riskValues;
riskSeriesValueArray.Add(riskSeriesValueList);
dto.ExposedCaseSeries = exposedSeriesValueArray.ToArray();
dto.RelativeRiskSeries = riskSeriesValueArray.ToArray();
return(dto);
}
public ActionResult <LinkedCollectionResourceWrapperDto <AnalyserTermIdentifierDto> > GetAnalyserTermsByIdentifier(Guid workFlowGuid,
[FromQuery] AnalyserTermSetResourceParameters analyserTermSetResourceParameters)
{
if (analyserTermSetResourceParameters == null)
{
ModelState.AddModelError("Message", "Unable to locate filter parameters payload");
return(BadRequest(ModelState));
}
var mappedResults = GetAnalyserTermSets <AnalyserTermIdentifierDto>(analyserTermSetResourceParameters);
var wrapper = new LinkedCollectionResourceWrapperDto <AnalyserTermIdentifierDto>(mappedResults.TotalCount, mappedResults);
var wrapperWithLinks = CreateLinksForAnalyserTermSets(wrapper, workFlowGuid, analyserTermSetResourceParameters,
mappedResults.HasNext, mappedResults.HasPrevious);
return(Ok(wrapperWithLinks));
}
/// <summary>
/// Get patient results from repository and auto map to Dto
/// </summary>
/// <typeparam name="T">Identifier, detail or expanded Dto</typeparam>
/// <param name="termId">The unique id of the MedDRA term that we are getting results for</param>
/// <param name="analyserTermSetResourceParameters">Standard parameters for representing resource</param>
/// <returns></returns>
private PagedCollection <T> GetAnalyserPatientSets <T>(int termId, AnalyserTermSetResourceParameters analyserTermSetResourceParameters) where T : class
{
var pagingInfo = new PagingInfo()
{
PageNumber = analyserTermSetResourceParameters.PageNumber,
PageSize = analyserTermSetResourceParameters.PageSize
};
// prepare risk factor xml
var riskFactorXml = "";
var includeRiskFactor = "False";
XmlDocument xmlDoc = new XmlDocument();
if (analyserTermSetResourceParameters.RiskFactorOptionNames?.Count > 0)
{
XmlNode rootNode = xmlDoc.CreateElement("Factors", "");
foreach (var display in analyserTermSetResourceParameters.RiskFactorOptionNames)
{
var riskFactor = _riskFactorRepository.Get(r => r.Options.Any(ro => ro.Display == display));
if (riskFactor != null)
{
XmlNode factorNode = xmlDoc.CreateElement("Factor", "");
XmlNode factorChildNode = xmlDoc.CreateElement("Name", "");
factorChildNode.InnerText = riskFactor.FactorName;
factorNode.AppendChild(factorChildNode);
factorChildNode = xmlDoc.CreateElement("Option", "");
factorChildNode.InnerText = riskFactor.Options.Single(ro => ro.Display == display)?.Display;
factorNode.AppendChild(factorChildNode);
rootNode.AppendChild(factorNode);
includeRiskFactor = "True";
}
}
xmlDoc.AppendChild(rootNode);
riskFactorXml = xmlDoc.InnerXml;
}
List <SqlParameter> parameters = new List <SqlParameter>();
parameters.Add(new SqlParameter("@ConditionId", analyserTermSetResourceParameters.ConditionId.ToString()));
parameters.Add(new SqlParameter("@CohortId", analyserTermSetResourceParameters.CohortGroupId.ToString()));
parameters.Add(new SqlParameter("@StartDate", analyserTermSetResourceParameters.SearchFrom.ToString()));
parameters.Add(new SqlParameter("@FinishDate", analyserTermSetResourceParameters.SearchTo.ToString()));
parameters.Add(new SqlParameter("@TermID", termId.ToString()));
parameters.Add(new SqlParameter("@IncludeRiskFactor", includeRiskFactor));
parameters.Add(new SqlParameter("@RateByCount", "True"));
parameters.Add(new SqlParameter("@DebugPatientList", "True"));
parameters.Add(new SqlParameter("@RiskFactorXml", riskFactorXml));
parameters.Add(new SqlParameter("@DebugMode", "False"));
var resultsFromService = PagedCollection <ContingencyAnalysisPatient> .Create(
_context.ContingencyAnalysisPatients
.FromSqlRaw($"Exec spGenerateAnalysis @ConditionId, @CohortId, @StartDate, @FinishDate, @TermID, @IncludeRiskFactor, @RateByCount, @DebugPatientList, @RiskFactorXml, @DebugMode",
parameters.ToArray()).ToList(), pagingInfo.PageNumber, pagingInfo.PageSize);
if (resultsFromService != null)
{
// Map results to Dto
var mappedResults = PagedCollection <T> .Create(_mapper.Map <PagedCollection <T> >(resultsFromService),
pagingInfo.PageNumber,
pagingInfo.PageSize,
resultsFromService.TotalCount);
// Prepare pagination data for response
var paginationMetadata = new
{
totalCount = mappedResults.TotalCount,
pageSize = mappedResults.PageSize,
currentPage = mappedResults.CurrentPage,
totalPages = mappedResults.TotalPages,
};
Response.Headers.Add("X-Pagination",
JsonConvert.SerializeObject(paginationMetadata));
return(mappedResults);
}
return(null);
}
/// <summary>
/// Get results from repository and auto map to Dto
/// </summary>
/// <typeparam name="T">Identifier, detail or expanded Dto</typeparam>
/// <param name="termId">The unique id of the MedDRA term that we are getting results for</param>
/// <param name="analyserTermSetResourceParameters">Standard parameters for representing resource</param>
/// <returns></returns>
private ICollection <T> GetAnalyserResultSets <T>(int termId, AnalyserTermSetResourceParameters analyserTermSetResourceParameters) where T : class
{
// prepare risk factor xml
var riskFactorXml = "";
var includeRiskFactor = "False";
XmlDocument xmlDoc = new XmlDocument();
if (analyserTermSetResourceParameters.RiskFactorOptionNames?.Count > 0)
{
XmlNode rootNode = xmlDoc.CreateElement("Factors", "");
foreach (var display in analyserTermSetResourceParameters.RiskFactorOptionNames)
{
var riskFactor = _riskFactorRepository.Get(r => r.Options.Any(ro => ro.Display == display));
if (riskFactor != null)
{
XmlNode factorNode = xmlDoc.CreateElement("Factor", "");
XmlNode factorChildNode = xmlDoc.CreateElement("Name", "");
factorChildNode.InnerText = riskFactor.FactorName;
factorNode.AppendChild(factorChildNode);
factorChildNode = xmlDoc.CreateElement("Option", "");
factorChildNode.InnerText = riskFactor.Options.Single(ro => ro.Display == display)?.Display;
factorNode.AppendChild(factorChildNode);
rootNode.AppendChild(factorNode);
includeRiskFactor = "True";
}
}
xmlDoc.AppendChild(rootNode);
riskFactorXml = xmlDoc.InnerXml;
}
List <SqlParameter> parameters = new List <SqlParameter>();
parameters.Add(new SqlParameter("@ConditionId", analyserTermSetResourceParameters.ConditionId.ToString()));
parameters.Add(new SqlParameter("@CohortId", analyserTermSetResourceParameters.CohortGroupId.ToString()));
parameters.Add(new SqlParameter("@StartDate", analyserTermSetResourceParameters.SearchFrom.ToString()));
parameters.Add(new SqlParameter("@FinishDate", analyserTermSetResourceParameters.SearchTo.ToString()));
parameters.Add(new SqlParameter("@TermID", termId.ToString()));
parameters.Add(new SqlParameter("@IncludeRiskFactor", includeRiskFactor));
parameters.Add(new SqlParameter("@RateByCount", "True"));
parameters.Add(new SqlParameter("@DebugPatientList", "False"));
parameters.Add(new SqlParameter("@RiskFactorXml", riskFactorXml));
parameters.Add(new SqlParameter("@DebugMode", "False"));
var resultsFromService = _context.ContingencyAnalysisItems
.FromSqlRaw($"Exec spGenerateAnalysis @ConditionId, @CohortId, @StartDate, @FinishDate, @TermID, @IncludeRiskFactor, @RateByCount, @DebugPatientList, @RiskFactorXml, @DebugMode",
parameters.ToArray()).ToList();
if (resultsFromService != null)
{
// Map results to Dto
return(_mapper.Map <ICollection <T> >(resultsFromService));
}
return(null);
}
public ActionResult <LinkedCollectionResourceWrapperDto <AnalyserPatientDto> > GetAnalyserTermPatients(Guid workFlowGuid, int id,
[FromQuery] AnalyserTermSetResourceParameters analyserTermSetResourceParameters)
{
var workFlowFromRepo = _workFlowRepository.Get(r => r.WorkFlowGuid == workFlowGuid);
if (workFlowFromRepo == null)
{
return(BadRequest());
}
if (analyserTermSetResourceParameters == null)
{
ModelState.AddModelError("Message", "Unable to locate filter parameters payload");
return(BadRequest(ModelState));
}
var mappedResults = GetAnalyserPatientSets <AnalyserPatientDto>(id, analyserTermSetResourceParameters);
var wrapper = new LinkedCollectionResourceWrapperDto <AnalyserPatientDto>(mappedResults.TotalCount, mappedResults);
var wrapperWithLinks = CreateLinksForAnalyserPatients(wrapper, workFlowGuid, id, analyserTermSetResourceParameters,
mappedResults.HasNext, mappedResults.HasPrevious);
return(Ok(wrapperWithLinks));
}
public async Task <ActionResult <AnalyserTermDetailDto> > GetAnalyserTermByDetail(Guid workFlowGuid, int id,
[FromQuery] AnalyserTermSetResourceParameters analyserTermSetResourceParameters)
{
var workFlowFromRepo = _workFlowRepository.Get(r => r.WorkFlowGuid == workFlowGuid);
if (workFlowFromRepo == null)
{
return(BadRequest());
}
var mappedMeddraTerm = await GetMeddraTermAsync <AnalyserTermDetailDto>(id);
if (mappedMeddraTerm == null)
{
return(NotFound());
}
return(Ok(CreateLinksForMeddraTerm <AnalyserTermDetailDto>(CustomResultMap(mappedMeddraTerm, analyserTermSetResourceParameters))));
}
