private void addReferencesToDataset(DataSet data, StudySettings study)
{
if (this.Settings.References == null || study.Cohorts == null)
{
return;
}
var references = new DataTable("references");
references.Columns.Add("Cohort", typeof(string));
references.Columns.Add("Number", typeof(int));
references.Columns.Add("Reference", typeof(string));
// Merge with study cohorts list to obtain the cohort number
var cohortReferences = this.Settings.References.Join(study.Cohorts, c1 => c1.Cohort, c2 => c2.Name,
(c1, c2) => new Cohort {
Name = c2.Name, Number = c2.Number, Reference = c1.Reference
});
foreach (var cohort in cohortReferences)
{
references.Rows.Add(
cohort.Name,
cohort.Number,
cohort.Reference);
}
if (data.Tables.Contains("references"))
{
data.Tables.Remove("references");
}
data.Tables.Add(references);
}
private void DeleteAnalysisResults(StudySettings studyMetadata)
{
// Delete report settings
var study = new MappingController().LoadStudy(studyMetadata.NDAName, studyMetadata.ProfileName,
studyMetadata.SupplementNumber, studyMetadata.StudyCode);
// Delete reports
study.Reports = new List <Report>();
study.Analytes = null;
study.Parameters = null;
study.Concentration = null;
study.Pharmacokinetics = null;
new MappingController().SaveStudy(study, study.NDAName, study.ProfileName, study.SupplementNumber, study.StudyCode);
// Delete the output files
var userName = Users.GetCurrentUserName();
var studyPath = string.Format(@"\\{0}\Output Files\PKView\{1}\{2}\{3}\{4}\{5}",
iPortalApp.AppServerName, userName, study.ProfileName, study.NDAName, study.SupplementNumber, study.StudyCode);
var studyFolder = new DirectoryInfo(studyPath);
if (studyFolder.Exists)
{
studyFolder.Delete(true);
}
}
/// <summary>
/// Add report settings to the dataset to be sent to SAS
/// </summary>
/// <param name="data">dataset where the tables will be added</param>
/// <param name="study">study this repor relates to</param>
internal void AddMetaSettingsToDataset(DataSet data, StudySettings study, string StudyCode)
{
// Report name
var reportConfig = new DataTable("reportConfig");
reportConfig.Columns.Add("Name", typeof(string));
reportConfig.Columns.Add("Value", typeof(string));
reportConfig.Columns.Add("StudyCode", typeof(string));
reportConfig.Rows.Add("Name", this.Name, StudyCode);
data.Tables.Add(reportConfig);
// exclude subject information
var excludesubjectinfo = new DataTable("excludesubject");
excludesubjectinfo.Columns.Add("BigthanExcludeSD", typeof(float));
excludesubjectinfo.Columns.Add("SmallthanExcludeSD", typeof(float));
excludesubjectinfo.Columns.Add("ExcludeParameters1", typeof(string));
excludesubjectinfo.Columns.Add("ExcludeParameters2", typeof(string));
excludesubjectinfo.Columns.Add("percent", typeof(int));
excludesubjectinfo.Rows.Add(
this.BigthanExcludeSD,
this.SmallthanExcludeSD,
this.ExcludeParameters1,
this.ExcludeParameters2,
this.percent);
data.Tables.Add(excludesubjectinfo);
// exclude edited subject data
//this.excludedatatable = null;
//data.Tables.Add(this.excludedatatable);
// Add different data tables depending on the type of report
this.Type = 2;
switch (this.Type)
{
case 1: // Pk tables
addReferencesToDataset(data, study);
addAnalytesToDataset(data);
addParametersToDataset(data);
addStatisticalMethodToDataset(data);
addPkSortingOptionsToDataset(data);
break;
case 2: // Forest plots
addMetaReferencesToDataset(data, study, StudyCode);
addMetaAnalytesToDataset(data, StudyCode);
addMetaParametersToDataset(data, StudyCode);
addMetaStatisticalMethodToDataset(data, StudyCode);
addMetaPkSortingOptionsToDataset(data, StudyCode);
break;
case 3: // NCA Analysis
addConcentrationToDataset(data, study);
addPharmacokineticsToDataset(data, study);
break;
}
}
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);
}
}
private void DeleteReportFiles(StudySettings study, string reportName)
{
var userName = Users.GetCurrentUserName();
var reportPath = string.Format(@"\\{0}\Output Files\PKView\{1}\{2}\{3}\{4}\{5}\{6}",
iPortalApp.AppServerName, userName, study.ProfileName, study.NDAName, study.SupplementNumber, study.StudyCode, reportName);
var reportFolder = new DirectoryInfo(reportPath);
if (reportFolder.Exists)
{
reportFolder.Delete(true);
}
}
public int SaveReport([FromBody] StudySettings revisedMappings, int reportId)
{
var newReport = revisedMappings.Reports[reportId];
newReport.Generated = false;
// Save report settings into the user study profile (FIXME: Improve profile management)
DoSaveReport(revisedMappings.NDAName, revisedMappings.SupplementNumber,
revisedMappings.StudyCode, revisedMappings.ProfileName, newReport);
return(0);
}
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 override bool Equals(object obj)
{
if (obj == null || GetType() != obj.GetType())
{
return(false);
}
StudySettings s = (StudySettings)obj;
m_startingGain = s.m_startingGain;
m_increaseFactor = s.m_increaseFactor;
m_decreaseFactor = s.m_decreaseFactor;
m_fixedNumberOfReversalPoints = s.m_fixedNumberOfReversalPoints;
m_usedNumberOfReversalPoints = s.m_usedNumberOfReversalPoints;
return((m_startingGain == s.m_startingGain) && (m_increaseFactor == s.m_increaseFactor) && (m_decreaseFactor == s.m_decreaseFactor) &&
(m_fixedNumberOfReversalPoints == s.m_fixedNumberOfReversalPoints) && (m_usedNumberOfReversalPoints == s.m_usedNumberOfReversalPoints));
}
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 DeleteReport([FromBody] StudySettings revisedMappings, int reportId)
{
// Save report settings into the user study profile (FIXME: Improve profile management)
var study = new MappingController().LoadStudy(revisedMappings.NDAName, revisedMappings.ProfileName,
revisedMappings.SupplementNumber, revisedMappings.StudyCode, null, true);
var reportName = revisedMappings.Reports[reportId].Name;
// Add or replace report
var reportList = study.Reports.Where(report => report.Name != reportName).ToList();
study.Reports = reportList;
new MappingController().SaveStudy(study, study.NDAName, study.ProfileName, study.SupplementNumber, study.StudyCode);
// Delete report files
DeleteReportFiles(study, reportName);
return(0);
}
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);
}
/// <summary>
/// Add Excluded data to the dataset to be sent to SAS
/// </summary>
/// <param name="data">dataset where the tables will be added</param>
/// <param name="study">study this repor relates to</param>
internal void AddExcludedataToDataset(DataSet data, StudySettings study)
{
// exclude data
var excludedata = new DataTable("Excludedata");
excludedata = study.excludedatatable;
excludedata.TableName = "Excludedata";
for (int i = excludedata.Rows.Count - 1; i >= 0; i--)
{
DataRow dr = excludedata.Rows[i];
if (study.ExcludeIndex[i] == "False")
{
dr.Delete();
}
}
excludedata.AcceptChanges();
data.Tables.Add(excludedata);
}
public MetaBuilder(StudySettings study, Report report)
{
this.template = new TemplateEngine();
// Location of the template
this.templateFolder = HostingEnvironment.MapPath(@"~\Content\templates\PkView");
this.template.TemplatePath = Path.Combine(this.templateFolder, "MetaForestPlot.sas");
// Location where the script will be created
this.outputFolder = string.Format(
@"\\{0}\Output Files\PKView\{1}\{2}\{3}\{4}\{5}\{6}",
iPortalApp.AppServerName,
Users.GetCurrentUserName(),
study.ProfileName,
study.NDAName,
study.SupplementNumber,
"Meta",
"Package");
string scriptName = String.Format("MetaForestPlot.sas");
this.template.OutputPath = Path.Combine(this.outputFolder, scriptName);
}
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);
}
/// <summary>
/// Add the pk data to the SAS input, already subset by the UI options
/// </summary>
/// <param name="data"></param>
private void addPharmacokineticsToDataset(DataSet data, StudySettings study)
{
var pharmacokinetics = new DataTable("pharmacokinetics");
pharmacokinetics.Columns.Add("Selected", typeof(string));
pharmacokinetics.Columns.Add("Result", typeof(double));
pharmacokinetics.Columns.Add("Parameter", typeof(string));
pharmacokinetics.Columns.Add("Treatment", typeof(string));
pharmacokinetics.Columns.Add("Specimen", typeof(string));
pharmacokinetics.Columns.Add("Analyte", typeof(string));
pharmacokinetics.Columns.Add("Period", typeof(string));
pharmacokinetics.Columns.Add("Arm", typeof(string));
pharmacokinetics.Columns.Add("Cohort", typeof(string));
pharmacokinetics.Columns.Add("Subject", typeof(string));
// Load individual concentration from xml file
var fullStudy = new MappingController().LoadStudy(study.NDAName, study.ProfileName,
study.SupplementNumber, study.StudyCode, null, true);
// Find the subset of selected pk
string period = this.Settings.SelectedPeriod;
string specimen = this.Settings.SelectedPpSpecimen;
if (period == "noPeriod")
{
period = null;
}
if (specimen == "noSpecimen")
{
specimen = null;
}
var selectedSections = fullStudy.Pharmacokinetics.Sections.Where(s =>
s.Cohort == this.Settings.SelectedCohort &&
s.Analyte == this.Settings.SelectedPpAnalyte &&
s.Period == period && s.Specimen == specimen);
// Create a dictionary of pk parameter mappings
var pkParameterMappings = new Dictionary <string, List <string> >();
addParameterSelectionToTable(pkParameterMappings, this.Settings.SelectedAuct, "AUCT");
addParameterSelectionToTable(pkParameterMappings, this.Settings.SelectedAucInfinity, "AUCI");
addParameterSelectionToTable(pkParameterMappings, this.Settings.SelectedCmax, "CMAX");
addParameterSelectionToTable(pkParameterMappings, this.Settings.SelectedThalf, "THALF");
addParameterSelectionToTable(pkParameterMappings, this.Settings.SelectedTmax, "TMAX");
// Add the pk data to the table
foreach (PkDataSection section in selectedSections)
{
foreach (PkDataSubSection subsection in section.SubSections)
{
foreach (IndividualPk individual in subsection.Individual)
{
// Add each value to the dataset
foreach (var pkValue in individual.PkValues)
{
// Add one row for each selection of the pk parameter or one row with empty selection
List <string> selections;
if (!pkParameterMappings.TryGetValue(pkValue.Parameter, out selections))
{
selections = new List <string> {
""
}
}
;
string suffix = ""; int i = 1;
foreach (var selection in selections)
{
pharmacokinetics.Rows.Add(
selection,
pkValue.Value.HasValue ? (object)pkValue.Value.Value : DBNull.Value,
pkValue.Parameter + suffix,
section.TreatmentOrGroup,
section.Specimen ?? "",
section.Analyte,
subsection.Period ?? section.Period ?? "",
subsection.Arm ?? "",
section.Cohort,
individual.Subject);
suffix = "__" + i++;
}
}
}
}
}
data.Tables.Add(pharmacokinetics);
}
/// <summary>
/// Add the concentration data table to the SAS input, already subset by the UI options
/// </summary>
/// <param name="data"></param>
/// <param name="study"></param>
private void addConcentrationToDataset(DataSet data, StudySettings study)
{
var concentration = new DataTable("concentration");
concentration.Columns.Add("Result", typeof(double));
concentration.Columns.Add("NominalTime", typeof(double));
concentration.Columns.Add("Treatment", typeof(string));
concentration.Columns.Add("Specimen", typeof(string));
concentration.Columns.Add("Analyte", typeof(string));
concentration.Columns.Add("Period", typeof(string));
concentration.Columns.Add("Arm", typeof(string));
concentration.Columns.Add("Cohort", typeof(string));
concentration.Columns.Add("Subject", typeof(string));
// Load individual concentration from xml file (FIXME)
var fullStudy = new MappingController().LoadStudy(study.NDAName, study.ProfileName,
study.SupplementNumber, study.StudyCode, null, true);
// Find the subset of selected curves
string period = this.Settings.SelectedPeriod;
string specimen = this.Settings.SelectedPcSpecimen;
if (period == "noPeriod")
{
period = null;
}
if (specimen == "noSpecimen")
{
specimen = null;
}
var selectedSections = fullStudy.Concentration.Sections.Where(s =>
s.Cohort == this.Settings.SelectedCohort &&
s.Analyte == this.Settings.SelectedPcAnalyte &&
s.Period == period && s.Specimen == specimen);
// Add the concentration curves to the table
foreach (ConcentrationDataSection section in selectedSections)
{
foreach (ConcentrationDataSubSection subsection in section.SubSections)
{
foreach (IndividualConcentration individual in subsection.Individual)
{
var curvePoints = individual.Concentration;
// trim the curve to the selected range if a range is found
if (this.Settings.StartTime.HasValue && this.Settings.EndTime.HasValue)
{
curvePoints = curvePoints.Where(p =>
p.NominalTime >= this.Settings.StartTime.Value &&
p.NominalTime <= this.Settings.EndTime.Value).ToList();
}
// Add each point in the curve to the dataset
foreach (var point in curvePoints)
{
concentration.Rows.Add(
point.Value.HasValue ? (object)point.Value.Value : DBNull.Value,
point.NominalTime.HasValue ? (object)point.NominalTime.Value : DBNull.Value,
section.TreatmentOrGroup,
section.Specimen ?? "",
section.Analyte,
subsection.Period ?? section.Period ?? "",
subsection.Arm ?? "",
section.Cohort,
individual.Subject);
}
}
}
}
data.Tables.Add(concentration);
}
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 NcaBuilder(StudySettings study, Report report)
{
this.template = new TemplateEngine();
// Location of the template
this.templateFolder = HostingEnvironment.MapPath(@"~\Content\templates\PkView");
this.template.TemplatePath = Path.Combine(this.templateFolder, "NcaAnalysisTemplate.sas.tpl");
// Location where the script will be created
this.outputFolder = string.Format(
@"\\{0}\Output Files\PKView\{1}\{2}\{3}\{4}\{5}\{6}",
iPortalApp.AppServerName,
Users.GetCurrentUserName(),
study.ProfileName,
study.NDAName,
study.SupplementNumber,
study.StudyCode,
report.Name);
string scriptName = String.Format("ncaRun_{0}_{1}.sas",
report.Settings.SelectedPcSpecimen ?? report.Settings.SelectedPpSpecimen ?? "BLOOD",
report.Settings.SelectedPcAnalyte);
this.template.OutputPath = Path.Combine(this.outputFolder, scriptName);
// Parameters for the template to customize the script
this.template.LoadParameters(new
{
SCRIPT_NAME = scriptName,
GENERATION_DATE = DateTime.Now.ToShortDateString(),
SUBMISSION = study.NDAName,
STUDY = study.StudyCode,
LEVEL = report.Settings.SelectedPcAnalyte,
});
// Load pk parameters adding a suffix when they are repeated
var pkct = new Dictionary <string, int>();
this.template.LoadParameter("FIRMAUCI", report.Settings.SelectedAucInfinity);
pkct[report.Settings.SelectedAucInfinity] = 1;
var pkMap = new Dictionary <string, string>
{
{ "FIRMAUCT", report.Settings.SelectedAuct },
{ "FIRMCMAX", report.Settings.SelectedCmax },
{ "FIRMTHALF", report.Settings.SelectedThalf },
{ "FIRMTMAX", report.Settings.SelectedTmax }
};
// Load each parameter
foreach (var mapping in pkMap)
{
string firmPk = mapping.Value;
if (!String.IsNullOrWhiteSpace(firmPk) && pkct.ContainsKey(firmPk))
{
firmPk += "__" + pkct[firmPk]++;
}
else
{
pkct[firmPk] = 1;
}
this.template.LoadParameter(mapping.Key, firmPk);
}
}
public string SaveStudy([FromBody] StudySettings revisedMappings, string SubmissionId, string profileName, string SupplementNumber, string StudyCode)
{
return(this.Save(new List <StudySettings> {
revisedMappings
}, profileName));
}
