/// <summary>
/// Create a new Clinical Data File object loading the data from the server
/// </summary>
/// <param name="path"></param>
public ClinicalDataFile(string path)
{
// Start a new sas job to retrieve the file
var id = SasClientObject.NewJob("RunDatasetTransfer", new
{
filepath = path,
timestamp = DateTime.Now.ToString("yyyyMMddHHmmssffff")
}); // Timestamp added to avoid caching in the backend
// Poll the server until we get a response other than 'running'
JobResponse response;
do
{
Thread.Sleep(500);
response = SasClientObject.Getjob(id);
} while (response.Status == SasJobs.Messages.StatusCode.Running);
// Store the data on success, otherwise throw an exception
if (response.Status == SasJobs.Messages.StatusCode.Done)
{
this.data = response.Data.Tables[0];
}
else
{
throw new Exception("The system was unable to read the specified xpt file.");
}
}
/// <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());
}
public DateTime?GenerateReport([FromBody] StudySettings revisedMappings, int reportId)
{
// Apply Ex setting for reference computation
revisedMappings.UseEx = revisedMappings.UseExRef;
DataSet data = revisedMappings.ToReportGenerationDataSet(reportId);
Report newReport = revisedMappings.Reports[reportId];
JobResponse response;
Guid id;
// Clean up old report files first
DeleteReportFiles(revisedMappings, newReport.Name);
// Use different SAS Api calls for different types of report
switch (newReport.Type)
{
case 1: id = SasClientObject.NewJob(data, "GenerateReport"); break;
case 2: id = SasClientObject.NewJob(data, "GenerateForestPlot"); break;
case 3: id = SasClientObject.NewJob(data, "GenerateNcaAnalysis"); break;
default: return(null);
}
// Wait for job response
do
{
System.Threading.Thread.Sleep(500);
response = SasClientObject.Getjob(id);
} while (response.Status == SasJobs.Messages.StatusCode.Running);
// if done save report and return creation date
if (response.Status == SasJobs.Messages.StatusCode.Done)
{
// Set the creation date
newReport.CreationDate = DateTime.Now;
newReport.Generated = true;
// If success, save the settings and return the creation date
DoSaveReport(revisedMappings.NDAName, revisedMappings.SupplementNumber,
revisedMappings.StudyCode, revisedMappings.ProfileName, newReport);
// If nca, generate script
if (newReport.Type == 3)
{
var scriptBuilder = new NcaBuilder(revisedMappings, newReport);
scriptBuilder.Create();
}
return(newReport.CreationDate);
}
else
{
return(null);
}
}
public string Run([FromBody] StudySettings revisedMappings)
{
// Apply Ex setting used for reference computation
revisedMappings.UseEx = revisedMappings.UseExRef;
DataSet data = revisedMappings.ToMappingDataSet(true);
// Delete old analysis results
DeleteAnalysisResults(revisedMappings);
// Run the analysis code
return(SasClientObject.NewJob(data, "RunStudyAnalysis").ToString());
}
public string Get(string ndaFolderName, string profileName = null)
{
var userName = HttpContext.Current.User.Identity.Name ?? "DEFAULT";
userName = userName.Substring(userName.LastIndexOfAny(new[] { '/', '\\' }) + 1);
// Run the 'CreatePackage' stored procedure in the SAS server. This procedure will create a
// zip files with the results of the individual study analyses
return(SasClientObject.NewJob("CreatePackage", new {
NDAName = ndaFolderName,
userName = userName,
profileName = profileName,
timestamp = DateTime.Now.ToString("yyyyMMddHHmmssffff"), // Timestamp added to avoid caching in the backend
}).ToString());
}
public IDictionary <string, IEnumerable <string> > GetReference([FromBody] StudySettings revisedMappings)
{
// Apply Ex setting for reference computation
revisedMappings.UseEx = revisedMappings.UseExRef;
DataSet data = revisedMappings.ToMappingDataSet();
JobResponse response;
var id = SasClientObject.NewJob(data, "ListReferences");
do
{
System.Threading.Thread.Sleep(500);
response = SasClientObject.Getjob(id);
} while (response.Status == SasJobs.Messages.StatusCode.Running);
// return the potential references
if (response.Status == SasJobs.Messages.StatusCode.Done)
{
var resultsTable = response.Data.Tables[0];
if (resultsTable.Rows.Count > 0)
{
var referenceTable = new Dictionary <string, IEnumerable <string> >();
foreach (var row in resultsTable.AsEnumerable())
{
var cohort = row["CohortDescription"].ToString();
if (!referenceTable.ContainsKey(cohort))
{
referenceTable.Add(cohort, new List <string>());
}
var reference = row["Reference"].ToString().Trim();
if (!String.IsNullOrWhiteSpace(reference))
{
((List <string>)referenceTable[cohort])
.Add(reference);
}
}
return(referenceTable);
}
}
return(null);
}
public int GenerateDemographicSummary([FromBody] StudySettings revisedMappings)
{
// Apply Ex setting for reference computation
revisedMappings.UseEx = revisedMappings.UseExRef;
DataSet data = revisedMappings.ToMappingDataSet(true);
JobResponse response;
Guid id;
id = SasClientObject.NewJob(data, "Reports_DemographicSummary");
// Wait for job response
do
{
System.Threading.Thread.Sleep(500);
response = SasClientObject.Getjob(id);
} while (response.Status == SasJobs.Messages.StatusCode.Running);
// Return the completion code
return(response.Status == SasJobs.Messages.StatusCode.Done ? 0 : -1);
}
public int?DetermineStudyDesign([FromBody] StudySettings revisedMappings)
{
DataSet data = revisedMappings.ToMappingDataSet();
JobResponse response;
var id = SasClientObject.NewJob(data, "DetermineStudyDesign");
//var id = SasClientObject.NewJob(data, "variabilitytest4");
do
{
System.Threading.Thread.Sleep(500);
response = SasClientObject.Getjob(id);
} while (response.Status == SasJobs.Messages.StatusCode.Running);
// return the potential references
if (response.Status == SasJobs.Messages.StatusCode.Done)
{
var resultsTable = response.Data.Tables[0];
if (resultsTable.Rows.Count > 0)
{
var studyDesign = resultsTable.AsEnumerable().First()["StudyDesign"].ToString();
switch (studyDesign.ToLower())
{
case "unknown": return(1);
case "sequential": return(2);
case "parallel": return(3);
case "crossover": return(4);
default: return(0);
}
}
}
return(null);
}
public DateTime?VariabilityMetaAnalysis([FromBody] List <StudySettings> revisedMappingsList, int reportId)
{
// Apply Ex setting for reference computation
//revisedMappings.UseEx = revisedMappings.UseExRef;
Report newReport0 = revisedMappingsList[0].Reports[reportId];
StudySettings revisedMappings = revisedMappingsList[0];
DataSet data = new DataSet();
for (int i = 0; i < revisedMappingsList.Count; i++)
{
DataSet data1 = revisedMappingsList[i].ToVariabilityMetaAnalysisGenerationDataSet(reportId);
if (data1 != null)
{
data.Merge(data1);
}
}
JobResponse response;
Guid id;
//// Clean up old report files first
//DeleteReportFiles(revisedMappings, newReport.Name);
// Use different SAS Api calls for different types of report
id = SasClientObject.NewJob(data, "GenerateMetaVariability");
//id = SasClientObject.NewJob(data, "variabilitytest4");
// Wait for job response
do
{
System.Threading.Thread.Sleep(500);
response = SasClientObject.Getjob(id);
} while (response.Status == SasJobs.Messages.StatusCode.Running);
// if done save report and return creation date
if (response.Status == SasJobs.Messages.StatusCode.Done)
{
// Set the creation date
// If success, save the settings and return the creation date
for (int i = 0; i < revisedMappingsList.Count; i++)
{
Report newReport = revisedMappingsList[i].Reports[reportId];
newReport.CreationDate = DateTime.Now;
newReport.Generated = true;
DoSaveVariabilityMetaAnalysisReport(revisedMappingsList[i].NDAName, revisedMappingsList[i].SupplementNumber, revisedMappingsList[i].StudyCode, revisedMappingsList[i].ProfileName, newReport);
}
//var scriptBuilder = new MetaBuilder(revisedMappings, newReport0);
//scriptBuilder.Create();
return(DateTime.Now);
}
else
{
return(null);
}
}
