public ActionResult AddCodeFileCurationTasks(FileViewModel model)
{
var logger = LogManager.GetLogger("FileController");
using (var db = ApplicationDbContext.Create())
{
var user = db.Users
.Where(x => x.UserName == User.Identity.Name)
.FirstOrDefault();
if (user == null)
{
return(RedirectToAction("Index"));
}
if (!user.IsAdministrator)
{
throw new HttpException(403, "This is only allowed for administrators.");
}
// Fetch the appropriate ManagedFile by ID.
Guid id = model.Id;
var file = GetFile(id, db);
// Add the code file tasks, if needed.
logger.Debug("Updating file tasks");
TaskHelpers.AddProcessingTasksForFile(file, file.CatalogRecord, db, addAllCodeTasks: true);
logger.Debug("Done updating file tasks");
// Log the editing of the file.
var log = new Event()
{
EventType = EventTypes.EditManagedFile,
Timestamp = DateTime.UtcNow,
User = user,
RelatedCatalogRecord = file.CatalogRecord,
Title = "Edit a File",
Details = "Added code file curation tasks"
};
log.RelatedManagedFiles.Add(file);
db.Events.Add(log);
db.SaveChanges();
return(RedirectToAction("General", new { id = file.Id }));
}
}
public void IngestIntoCurator(Group group, HttpRequestBase request, string userName)
{
MefConfig.RegisterMef(string.Empty);
// Load and populate all the StudyUnits in the group.
using (var db = new ApplicationDbContext())
{
var organization = OrganizationHelper.GetOrganizationByHost(request, db);
string storagePath = SettingsHelper.GetProcessingDirectory(organization, db);
var user = db.Users.Where(x => x.UserName == userName)
.Include(x => x.Organizations)
.FirstOrDefault();
// For every StudyUnit
int i = 1;
foreach (StudyUnit study in group.StudyUnits)
{
Console.WriteLine("Study " + i.ToString());
// Create a CatalogRecord and add it to the database.
var record = new CatalogRecord();
record.Id = study.Identifier;
record.Organization = organization;
// See if we can find a user with the contributor name.
// Otherwise just use the current user.
string contributorName = study.DublinCoreMetadata.Contributor.Best;
string[] parts = contributorName.Split(new char[] { ' ' });
if (parts.Length == 2)
{
string first = parts[0];
string last = parts[1];
var contribUser = db.Users.FirstOrDefault(x => x.FirstName == first &&
x.LastName == last);
if (contribUser != null)
{
record.CreatedBy = contribUser;
}
}
if (record.CreatedBy == null)
{
record.CreatedBy = user;
}
record.CreatedDate = DateTime.UtcNow;
record.Version = 1;
record.LastUpdatedDate = DateTime.UtcNow;
record.Status = CatalogRecordStatus.New;
record.DepositAgreement = organization.DepositAgreement;
var log = new Event()
{
EventType = ImportEventType,
Timestamp = DateTime.UtcNow,
User = user,
RelatedCatalogRecord = record,
Title = "Import"
};
record.Title = FixString(study.DublinCoreMetadata.Title.Current);
if (string.IsNullOrWhiteSpace(record.Title))
{
record.Title = "Missing title";
}
Directory.CreateDirectory(Path.Combine(storagePath, record.Id.ToString()));
record.Keywords = study.Coverage.TopicalCoverage.Subjects.Select(x => x.Value).FirstOrDefault();
record.AccessStatement = FixString(study.DublinCoreMetadata.Rights.Current);
record.AuthorsText = study.DublinCoreMetadata.Creator.Current;
record.ResearchDesign = study.DataCollections.First().Methodology.Methodology.First().Description.Best;
record.Location = study.Coverage.SpatialCoverage.Description.Current;
record.InclusionExclusionCriteria = study.DataCollections.First().Methodology.SamplingProcedure.First().Description.Best;
record.UnitOfObservation = study.AnalysisUnit.Value;
record.DataSource = study.DublinCoreMetadata.Source.Current;
record.ArchiveDate = study.DublinCoreMetadata.Date;
record.Number = study.DublinCoreMetadata.Identifiers.First().Identifier;
if (study.Coverage.TemporalCoverage.Dates.Count != 0)
{
var date = study.Coverage.TemporalCoverage.Dates[0];
var dateModel = new DateModel();
dateModel.dateType = "Date";
dateModel.date = date.Date.DateOnly.Value.ToString("yyyy-MM-dd");
dateModel.isRange = false;
record.FieldDates = Newtonsoft.Json.JsonConvert.SerializeObject(dateModel);
}
record.OwnerText = study.DublinCoreMetadata.Publisher.Current;
List <string> kindofdata = new List <string>();
foreach (var data in study.KindsOfData)
{
kindofdata.Add(data.Value);
}
record.DataType = string.Join(",", kindofdata.ToArray());
//record.IspsID = study.DublinCoreMetadata.Identifiers;
//record.DataSourceInformation =
record.DataSourceInformation = GetUserAttribute(study, "DataSourceInformation");
record.SampleSize = GetUserAttribute(study, "SampleSize");
record.RandomizationProcedure = GetUserAttribute(study, "RandomizationProcedure");
record.Treatment = GetUserAttribute(study, "Treatment");
record.TreatmentAdministration = GetUserAttribute(study, "TreatmentAdministration");
record.OutcomeMeasures = GetUserAttribute(study, "OutcomeMeasures");
//record.OwnerContact =
record.RelatedDatabase = GetUserAttribute(study, "RelatedDatabase");
//record.PrincipalInvestigator = enumerator.Current.Value.Value;
//record.AreaOfStudy = GetUserAttribute(study, "AreaOfStudy");
//record.Discipline=
//record.FeatureImage =
//record.FeatureText =
record.LocationDetails = GetUserAttribute(study, "LocationDetails");
//record.DrupalNodeID =
record.RelatedProjects = GetUserAttribute(study, "RelatedProjects");
record.RelatedPublications = GetUserAttribute(study, "RelatedPublications");
db.CatalogRecords.Add(record);
CreateTaskStatuses(record, user, db);
// For every PhysicalInstance in the StudyUnit
foreach (var pi in study.PhysicalInstances)
{
// Create a ManagedFile in the curation system.
var file = new ManagedFile();
file.Id = pi.Identifier;
file.CatalogRecord = record;
file.Number = GetUserAttribute(pi, "DataFileNumber");
file.Version = 1;
//file.Number = ++record.LastFileNumber;
file.CreationDate = DateTime.UtcNow;
file.Status = FileStatus.Accepted;
file.UploadedDate = DateTime.UtcNow;
file.AcceptedDate = DateTime.UtcNow;
// Map the Handle to the PersisentLink
file.PersistentLink = pi.FileIdentifications
.Select(x => x.Uri.ToString())
.Where(x => x.Contains("hdl.handle.net"))
.FirstOrDefault();
file.Name = pi.DublinCoreMetadata.Title.Best;
if (string.IsNullOrWhiteSpace(file.Name))
{
file.Name = "Unnamed file";
}
file.Title = pi.Description.Best;
if (string.IsNullOrWhiteSpace(file.Title))
{
file.Title = "Untitled";
}
file.PublicName = file.Title;
file.FormatName = pi.Format;
file.IsPublicAccess = pi.FileIdentifications
.Select(x => x.IsPublic)
.FirstOrDefault();
file.Owner = user;
var temp = GetSize(pi);
//file.Size = Convert.ToInt64(GetUserAttribute(pi, "FileSize").Split('.')[0]);
file.Size = temp;
file.Type = "Data";
file.Software = MetadataHelpers.GetSoftware(file.Name);
db.Files.Add(file);
TaskHelpers.AddProcessingTasksForFile(file, record, db);
log.RelatedManagedFiles.Add(file);
// TODO Ingest all the files into the processing space.
// For now, write a dummy file.
//string dummyPath = Path.Combine(storagePath, record.Id.ToString(), file.Name);
//File.WriteAllText(dummyPath, "This is a placeholder file without real content.");
}
// For every OtherMaterial in the StudyUnit
foreach (var material in study.OtherMaterials)
{
// Create a ManagedFile in the curation system.
var file = new ManagedFile();
file.CatalogRecord = record;
file.Id = Guid.NewGuid();
file.Status = FileStatus.Accepted;
file.UploadedDate = DateTime.UtcNow; // TODO get the historical date
if (material.UrlReference != null)
{
file.PersistentLink = material.UrlReference.ToString();
}
file.Name = material.DublinCoreMetadata.Title.Best;
if (string.IsNullOrWhiteSpace(file.Name))
{
file.Name = "Unnamed file";
}
file.Title = material.DublinCoreMetadata.Description.Best;
if (string.IsNullOrWhiteSpace(file.Title))
{
file.Title = "Unnamed";
}
file.Owner = user;
//file.Size = GetSize(pi);
file.Type = "Other";
file.Number = material.DublinCoreMetadata.Identifiers.Select(x => x.Identifier).FirstOrDefault();
file.FormatName = material.MimeType;
file.IsPublicAccess = material.DublinCoreMetadata.Rights.Best != "Not Public";
long size = 0;
string sizeStr = material.UserIds
.Where(x => x.Type == "Size")
.Select(x => x.Identifier)
.FirstOrDefault();
if (long.TryParse(sizeStr, out size))
{
file.Size = size;
}
db.Files.Add(file);
TaskHelpers.AddProcessingTasksForFile(file, record, db);
// TODO Ingest all the files into the processing space.
// For now, write a dummy file.
//string dummyPath = Path.Combine(storagePath, record.Id.ToString(), file.Name);
//File.WriteAllText(dummyPath, "This is a placeholder file without real content.");
}
db.Events.Add(log);
try
{
db.SaveChanges();
}
catch (Exception ex)
{
Console.WriteLine(ex.Message);
}
i++;
}
}
}
public ActionResult General(FileViewModel model)
{
var logger = LogManager.GetLogger("FileController");
logger.Debug("Entering FileController.General() POST handler");
if (Request.Form.AllKeys.Contains("RemovePersistentId"))
{
logger.Debug("Removing persistent ID");
return(RemovePersistentId(model));
}
else if (Request.Form.AllKeys.Contains("AddDataFileCurationTasks"))
{
logger.Debug("Adding data file curation tasks");
return(AddDataFileCurationTasks(model));
}
else if (Request.Form.AllKeys.Contains("AddCodeFileCurationTasks"))
{
logger.Debug("Adding code file curation tasks");
return(AddCodeFileCurationTasks(model));
}
using (var db = ApplicationDbContext.Create())
{
logger.Debug("Created database object");
var user = db.Users
.Where(x => x.UserName == User.Identity.Name)
.FirstOrDefault();
if (user == null)
{
logger.Debug("No user. Returning.");
return(RedirectToAction("Index"));
}
// Fetch the appropriate ManagedFile by ID.
Guid id = model.Id;
var file = GetFile(id, db);
EnsureUserIsAllowed(file.CatalogRecord, db);
EnsureUserCanEdit(file.CatalogRecord, db);
logger.Debug("User is allowed");
if (file.CatalogRecord.IsLocked)
{
logger.Debug("Catalog record is locked. Throwing.");
throw new HttpException(400, "This operation cannot be performed while the record is locked");
}
string changeSummary = ManagedFileChangeDetector.GetChangeSummary(file, model);
logger.Debug("Got change summary");
// Copy the information from the POST to the ManagedFile, ignoring read-only properties.
Mapper.Map(model, file);
logger.Debug("Mapped");
// Log the editing of the file.
var log = new Event()
{
EventType = EventTypes.EditManagedFile,
Timestamp = DateTime.UtcNow,
User = user,
RelatedCatalogRecord = file.CatalogRecord,
Title = "Edit a File",
Details = changeSummary
};
log.RelatedManagedFiles.Add(file);
db.Events.Add(log);
logger.Debug("Logged");
// Update any tasks, in case the file type has changed.
logger.Debug("Updating file tasks");
TaskHelpers.AddProcessingTasksForFile(file, file.CatalogRecord, db);
logger.Debug("Done updating file tasks");
// Save the updated record.
db.SaveChanges();
logger.Debug("Wrote to database");
logger.Debug("Returning from FileController.General() POST handler");
return(RedirectToAction("General", new { id = file.Id }));
}
}
