/// <summary>
/// Returns true when the settings of the other study will produce the same output.
/// This function assumes the other settings refer to the same clinical study
/// </summary>
/// <param name="other"></param>
/// <returns></returns>
internal bool IsCompatible(StudySettings other)
{
if (other == null)
{
return(false);
}
return(this.Cumulative == other.Cumulative &&
this.SubjectCTCorrelation == other.SubjectCTCorrelation &&
this.ScatterPlot == other.ScatterPlot &&
this.Demographictable == other.ScatterPlot &&
this.UseEx == other.UseEx &&
this.UseExRef == other.UseExRef &&
this.UseSuppdm == other.UseSuppdm &&
this.DisablePcCleanup == other.DisablePcCleanup &&
this.UseCustomArms == other.UseCustomArms &&
this.UseCustomPcPctptnum == other.UseCustomPcPctptnum &&
this.UseCustomPcVisit == other.UseCustomPcVisit &&
this.UseCustomPpVisit == other.UseCustomPpVisit &&
this.ArmsCompatible(this.ArmMappings, other.ArmMappings) &&
this.ValuesCompatible(this.PcVisitMappings, other.PcVisitMappings) &&
this.ValuesCompatible(this.PpVisitMappings, other.PpVisitMappings) &&
this.ValuesCompatible(this.PcPctptnumMappings, other.PcPctptnumMappings) &&
this.DomainsCompatible(this.StudyMappings, other.StudyMappings) &&
this.CohortsCompatible(this.Cohorts, other.Cohorts));
}
/// <summary>
/// Start initialization of a study in the backend and return the job id
/// </summary>
/// <param name="submissionId"></param>
/// <param name="supplementNumber"></param>
/// <param name="studyCode"></param>
/// <returns></returns>
public string Initialize(string submissionId, string supplementNumber, string studyCode)
{
string studyFolder = getStudyFolder(submissionId, supplementNumber, studyCode).FullName;
int hash = StudySettings.GetFilesHash(studyFolder);
// Run the 'RunMappings' stored procedure in the SAS server. This procedure will extract
// The variables and make the initial mappings for the user to review.
return(SasClientObject.NewJob("RunStudyMappings", new { StudyFolder = studyFolder, NdaHash = hash }).ToString());
}
/// <summary>
/// Poll the server for the results of a study initialization
/// </summary>
/// <param name="submissionId"></param>
/// <param name="supplementNumber"></param>
/// <param name="studyCode"></param>
/// <param name="jobId"></param>
/// <returns></returns>
public JobResponse <StudySettings> GetInitializationResult(string submissionId, string supplementNumber, string studyCode, string jobId)
{
var response = SasClientObject.Getjob(new Guid(jobId));
// If no data was received the process is still running, return an empty list
if (response.Status != SasJobs.Messages.StatusCode.Done)
{
var noDataResponse = new JobResponse <StudySettings>(response, null);
// Give a better response when the process is stuck at 1%
if (response.PercentComplete == 1)
{
noDataResponse.FeedbackMessage =
String.Format(@"Determining file structure and study design for study {0}", studyCode);
}
return(noDataResponse);
}
// If no data was returned
if (response.Data.Tables.Count == 0)
{
return(new JobResponse <StudySettings>(response, null));
}
// Check if an error code was received
var errorTable = response.Data.Tables["errorstudy"];
int errorCode = (errorTable != null && errorTable.Rows.Count > 0) ?
Convert.ToInt32(errorTable.Rows[0]["error_code"]) : 0;
// Retrieve datasets
var rawStudies = response.Data.Tables["design"].AsEnumerable();
var mappings = response.Data.Tables["mapping"].AsEnumerable();
var arms = response.Data.Tables["arms"].AsEnumerable();
var ppvisit = response.Data.Tables["ppvisit"].AsEnumerable();
var pcvisit = response.Data.Tables["pcvisit"].AsEnumerable();
var fileVariables = response.Data.Tables["out"].AsEnumerable();
// Initialize study profile
var study = new StudySettings
{
NDAName = submissionId,
SupplementNumber = supplementNumber,
StudyCode = studyCode,
StudyError = errorCode
};
// Retrieve study mapping information (FIXME simplify sas-C# interface)
var studyRow = rawStudies.FirstOrDefault();
if (studyRow != null)
{
// study type
study.StudyType = Convert.ToInt32(studyRow["Study_Type"]);
// Arms
study.Arms = arms.Where(arow => arow["Study_Code"].ToString().Equals(study.StudyCode))
.Select(arow => arow["arm"].ToString()).ToList();
// PP:Visit
study.PpVisit = ppvisit.Where(pprow => pprow["Study_Code"].ToString().Equals(study.StudyCode))
.Select(pprow => pprow["visit"].ToString()).ToList();
// PC:Visit
study.PcVisit = pcvisit.Where(pcrow => pcrow["Study_Code"].ToString().Equals(study.StudyCode))
.Select(pcrow => pcrow["visit"].ToString()).ToList();
// Mappings
study.StudyMappings = mappings
.Where(mrow => mrow["Study_Code"].ToString().Equals(study.StudyCode))
.GroupBy(mrow => mrow["Source"]).Select(mrows => new Domain
{
Type = mrows.First()["Source"].ToString(),
DomainMappings = mrows.Select(mrow => new Mapping
{
FileVariable = mrow["File_Variable"].ToString(),
SdtmVariable = mrow["SDTM_Variable"].ToString(),
MappingQuality = Convert.ToInt32(mrow["Mapping_Quality"])
}).Where(m => m.MappingQuality >= 0).ToList(), // Filter out mappings with quality -1 (dummy mappings)
// The way sas returns the data, the variables will be listed in the first table of the dataset.
FileVariables = fileVariables.Where(frow =>
frow["study"].ToString().Equals(study.StudyCode) &&
frow["source"].Equals(mrows.First()["Source"]))
.Select(frow => new FileVariable
{
Name = frow["variable"].ToString(),
Description = frow["variableDescription"].ToString(),
Label = String.Format("{0} - {1}", frow["variable"].ToString(), frow["variableDescription"].ToString())
}).ToList(),
FileId = mrows.First()["Path"].ToString()
}).ToList();
}
// If no studies have been retrieved return null
return(new JobResponse <StudySettings>(response, study));
}
