/// <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.");
}
}
public JobResponse <AnalysisResults> Get(Guid jobId)
{
var response = SasClientObject.Getjob(jobId);
// If no data was received the process is still running, return an empty list
if (response.Status != SasJobs.Messages.StatusCode.Done)
{
return(new JobResponse <AnalysisResults>(response, null));
}
// no data was returned
if (response.Data.Tables.Count == 0)
{
return(new JobResponse <AnalysisResults>(response, null));
}
// Save analysis results
var resultData = new AnalysisResults(response.Data);
Project project = this.projectRepository.Find(resultData.SubmissionId, resultData.Profile ?? "");
if (project != null)
{
var study = project.Studies.FirstOrDefault(s =>
s.SupplementNumber.Equals(resultData.SupplementId, StringComparison.InvariantCultureIgnoreCase) &&
s.StudyCode.Equals(resultData.StudyId, StringComparison.InvariantCultureIgnoreCase));
if (study != null)
{
var revision = new ProjectRevision
{
RevisionId = project.RevisionHistory.Last().RevisionId + 1,
Name = project.ProjectName,
Date = DateTime.Now,
Owner = Users.GetCurrentUserName(),
Action = ActionTypes.Save
};
project.RevisionHistory.Add(revision);
study.RevisionId = revision.RevisionId;
study.Concentration = resultData.Concentration;
study.Pharmacokinetics = resultData.Pharmacokinetics;
study.Analytes = null; // deprecated
study.Parameters = null; // deprecated
this.projectRepository.CreateOrUpdate(project);
}
}
// Clear individual data before sending the response back
if (resultData.Concentration != null && resultData.Concentration.Sections != null)
{
resultData.Concentration.Sections.ForEach(s => s.SubSections = null);
}
if (resultData.Pharmacokinetics != null && resultData.Pharmacokinetics.Sections != null)
{
resultData.Pharmacokinetics.Sections.ForEach(s => s.SubSections = null);
}
return(new JobResponse <AnalysisResults>(response, resultData));
}
/// <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);
}
}
public JobResponse <int> Get(Guid jobId)
{
var response = SasClientObject.Getjob(jobId);
return(new JobResponse <int>(response));
}
public string Run(string jsonPlot)
{
JavaScriptSerializer jss = new JavaScriptSerializer();
Plot revisedPlot = jss.Deserialize <Plot>(jsonPlot);
// Use the iportal database context
using (OCPSQLEntities db = new OCPSQLEntities())
{
// For each project, update the plot data in the database
//FPTOOLS_PROJECT project = new FPTOOLS_PROJECT();
var plot = new IPORTAL_FP();
// retrieve plot data from the database
plot = db.IPORTAL_FP.SingleOrDefault(p => p.FP_ID == revisedPlot.Id);
// if the plot does not exist return error TODO improve
if (plot == null)
{
throw new Exception();
}
// Update plot setting data into database
plot.DRUGNAME = revisedPlot.Settings.DrugName;
plot.TITLE = revisedPlot.Settings.Title;
plot.RANGE_BOTTOM = (double)revisedPlot.Settings.RangeBottom;
plot.RANGE_TOP = (double)revisedPlot.Settings.RangeTop;
plot.RANGE_STEP = (double)revisedPlot.Settings.RangeStep;
plot.XLABEL = revisedPlot.Settings.Xlabel;
plot.FOOTNOTE = revisedPlot.Settings.FootNote;
plot.SCALE_ID = revisedPlot.Settings.Scale;
plot.FP_STYLE_ID = revisedPlot.Settings.Style;
db.SaveChanges();
}
// Run the analysis code
var filename = "Forest_plot_" + revisedPlot.Id;
try
{
SasClientObject.RunJob("GenForestPlot",
(new { IdName = "FP_ID", IdVal = revisedPlot.Id, PlotId = "Forest_plot" }));
// new SasGenericClient.RunOptions {
// AbortExisting = true, RunId = "GenForestPlot" + revisedPlot.Id
// });
}
catch (Exception ex)
{
return("");
}
// Download the plot as a base64 encoded string
try
{
var result = new HttpResponseMessage(HttpStatusCode.OK);
var stream = new FileStream(ForestPlotConfig.OutputFolder + filename + ".png", FileMode.Open);
byte[] filebytes = new byte[stream.Length];
stream.Read(filebytes, 0, Convert.ToInt32(stream.Length));
var encodedImage = Convert.ToBase64String(filebytes);
return("data:image/png;base64," + encodedImage);
}
catch (Exception ex)
{
return("");
}
}
/// <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));
}
