public IHttpActionResult GetResearchProjects()
{
using (var context = new CCFDataEntities())
{
var researchProjects = context.ResearchProjects
.ToList()
.Select(Mapper.Map <ResearchProject, ResearchProjectDto>);
return(Ok(researchProjects));
}
}
/**
* Author: Zak Zinda
* Updated By:
* Date Updated: 12.6.18
* Description: Return the project information for a selected research project.
* Parameters: int id - The id of the project to query.
*/
// GET /Api/ResearchProjects/1
public IHttpActionResult GetResearchProject(int id)
{
using (var context = new CCFDataEntities())
{
var researchProject = context.ResearchProjects.SingleOrDefault(p => p.ProjectID == id);
if (researchProject == null)
{
return(BadRequest("The selected research project could not be found."));
}
return(Ok(Mapper.Map <ResearchProjectDto>(researchProject)));
}
}
public async Task <IHttpActionResult> Upload(int id)
{
if (!Request.Content.IsMimeMultipartContent())
{
return(BadRequest("File improperly formatted."));
}
string root = HttpContext.Current.Server.MapPath("~/App_Data");
var provider = new MultipartFormDataStreamProvider(root);
try
{
await Request.Content.ReadAsMultipartAsync(provider);
var file = provider.FileData[0];
string fileName = file.LocalFileName;
string hasHeaderFormValue = provider.FormData.GetValues("hasHeader")[0];
bool hasHeader = hasHeaderFormValue.Contains("yes") ? true : false;
FileUploadHelper helper = new FileUploadHelper();
List <string> accessionNumbers = helper.ParseFileToList(fileName, hasHeader);
List <RejectedAccessionDto> rejectedAccessions = new List <RejectedAccessionDto>();
using (var context = new CCFDataEntities())
{
var researchProjectInDb = context.ResearchProjects.Single(p => p.ProjectID == id);
if (researchProjectInDb == null)
{
return(BadRequest("The selected research project does not exist."));
}
rejectedAccessions = ValidateUploadedAccessions(accessionNumbers, context, researchProjectInDb);
}
return(Ok(rejectedAccessions));
}
catch (InvalidCastException e)
{
return(InternalServerError(e));
}
catch (Exception e)
{
return(InternalServerError(e));
}
}
// GET: Dashboard/EditProject/1
public ActionResult EditProject(int id)
{
using (var context = new CCFDataEntities())
{
var researchProject = context.ResearchProjects
.SingleOrDefault(p => p.ProjectID == id);
if (researchProject == null)
{
return(HttpNotFound());
}
var viewModel = new DashboardViewModel
{
ProjectId = researchProject.ProjectID
};
return(View(viewModel));
}
}
public IHttpActionResult CreateResearchProject(ResearchProjectDto researchProjectDto)
{
if (!ModelState.IsValid)
{
return(BadRequest("Invalid form data."));
}
var researchProject = Mapper.Map <ResearchProjectDto, ResearchProject>(researchProjectDto);
researchProject.InsertDate = DateTime.Now;
using (var context = new CCFDataEntities())
{
context.ResearchProjects.Add(researchProject);
context.SaveChanges();
}
researchProjectDto.ProjectID = researchProject.ProjectID;
researchProjectDto.InsertDate = researchProject.InsertDate.ToShortDateString();
return(Created(new Uri(Request.RequestUri + "/" + researchProject.ProjectID), researchProjectDto));
}
public IHttpActionResult Update(int id, ResearchProjectDto researchProjectDto)
{
if (!ModelState.IsValid)
{
return(BadRequest("Invalid form data."));
}
using (var context = new CCFDataEntities())
{
var researchProjectInDb = context.ResearchProjects.SingleOrDefault(p => p.ProjectID == id);
if (researchProjectInDb == null)
{
return(BadRequest("The selected research project could not be found."));
}
Mapper.Map(researchProjectDto, researchProjectInDb);
Mapper.Map(researchProjectInDb, researchProjectDto);
context.SaveChanges();
}
return(Ok(researchProjectDto));
}
public ActionResult DownloadKeyPairs(int projectId, int downloadType)
{
// Create new stringbuilder and empty file name.
var sb = new System.Text.StringBuilder();
var fileName = "KeyPairs.csv";
using (var context = new CCFDataEntities())
{
var researchProjectInDb = context.ResearchProjects.Single(p => p.ProjectID == projectId);
// First check if the associated project exists.
if (researchProjectInDb == null)
{
return(HttpNotFound());
}
// Return all ResearchProjectAccession objects associated with that project.
var keyPairs = context.ResearchProjectAccessions
.Where(p => p.ProjectID == projectId)
.ToList()
.Select(Mapper.Map <ResearchProjectAccession, KeyPairDto>);
// Check if any key pairs exist. If not, skip downloadType check.
if (keyPairs.Count() == 0)
{
sb.Append("This project does not yet have any accession numbers uploaded.\r\n");
}
else
{
// Checks downloadType.
// DownloadType.AccessionOnly = 1
// DownloadType.MRNOnly = 2
// DownloadType.Both = 3
switch (downloadType)
{
case DownloadType.AccessionOnly:
// Set appropriate file name.
fileName = "AccessionKeyPairs.csv";
// Add only accession numbers associated with that project to the file.
sb.Append("Accession,Randomized Accession\r\n");
foreach (var keyPair in keyPairs)
{
sb.AppendFormat("=\"{0}\",", keyPair.Accession.ToString());
sb.AppendFormat("=\"{0}\"\r\n", keyPair.AccessionGuid.ToString());
}
break;
case DownloadType.MRNOnly:
// Set appropriate file name.
fileName = "MRNKeyPairs.csv";
// Add only MRNs associated with that project to the file.
sb.Append("MRN,Randomized MRN\r\n");
foreach (var keyPair in keyPairs)
{
sb.AppendFormat("=\"{0}\",", keyPair.MRN.ToString());
sb.AppendFormat("=\"{0}\"\r\n", keyPair.MRNGuid.ToString());
}
break;
case DownloadType.Both:
// Set appropriate file name.
fileName = "AccessionAndMRNKeyPairs.csv";
// Add both accessions and MRNs to the file.
sb.Append("Accession,Randomized Accession,MRN,Randomized MRN\r\n");
foreach (var keyPair in keyPairs)
{
sb.AppendFormat("=\"{0}\",", keyPair.Accession.ToString());
sb.AppendFormat("=\"{0}\",", keyPair.AccessionGuid.ToString());
sb.AppendFormat("=\"{0}\",", keyPair.MRN.ToString());
sb.AppendFormat("=\"{0}\"\r\n", keyPair.MRNGuid.ToString());
}
break;
default:
break;
}
}
// Convert stringbuilder into a file string.
string file = sb.ToString();
// Return file as a csv.
return(File(new System.Text.UTF8Encoding().GetBytes(file), "text/csv", fileName));
}
}
public List <RejectedAccessionDto> ValidateUploadedAccessions(List <string> accessions, CCFDataEntities context, ResearchProject researchProjectInDb)
{
List <RejectedAccessionDto> rejectedAccessions = new List <RejectedAccessionDto>();
var projectId = researchProjectInDb.ProjectID;
foreach (var accessionNumber in accessions)
{
RejectedAccessionDto rejectedAccession;
// Ensure the accession number is an integer.
if (!accessionNumber.All(char.IsDigit))
{
rejectedAccession = new RejectedAccessionDto
{
Accession = accessionNumber,
Reason = "Accession must be an integer."
};
rejectedAccessions.Add(rejectedAccession);
continue;
}
var convertedAccessionNumber = Convert.ToInt32(accessionNumber.Trim());
var researchAccessionInDb = context.ResearchProjectAccessions
.SingleOrDefault(a => a.ProjectID == projectId && a.Accession == convertedAccessionNumber);
// Ensure the accession number has not already been added.
if (researchAccessionInDb != null)
{
rejectedAccession = new RejectedAccessionDto
{
Accession = accessionNumber,
Reason = "Accession has already been added to the project."
};
rejectedAccessions.Add(rejectedAccession);
continue;
}
var globalAccessionInDb = context.GlobalAccessions
.SingleOrDefault(a => a.Accession == convertedAccessionNumber);
// Ensure the accession number exists globally.
if (globalAccessionInDb == null)
{
rejectedAccession = new RejectedAccessionDto
{
Accession = accessionNumber,
Reason = "Accession does not exist in the global database."
};
rejectedAccessions.Add(rejectedAccession);
continue;
}
//accession passed validation, create an accession object to add to the database
var accession = new ResearchProjectAccession()
{
ResearchProject = researchProjectInDb,
Accession = globalAccessionInDb.Accession,
AccessionGUID = Guid.NewGuid(), //deidentified accession number
MRN = globalAccessionInDb.MRN,
MRNGUID = Guid.NewGuid()
};
context.ResearchProjectAccessions.Add(accession);
context.SaveChanges();
}
return(rejectedAccessions);
}
