public ActionResult Index(
string searchQuery,
bool importGenes,
bool importPartial,
bool filterMinLength,
int minLength,
bool filterMaxLength,
int maxLength)
{
return(CreateTask(() =>
{
string searchResults;
string[] accessions;
List <NuccoreObject> nuccoreObjects;
if (filterMinLength)
{
searchResults = filterMaxLength ?
NcbiHelper.FormatNcbiSearchTerm(searchQuery, minLength, maxLength: maxLength) :
NcbiHelper.FormatNcbiSearchTerm(searchQuery, minLength);
}
else
{
searchResults = filterMaxLength ?
NcbiHelper.FormatNcbiSearchTerm(searchQuery, minLength: 1, maxLength: maxLength) :
NcbiHelper.FormatNcbiSearchTerm(searchQuery);
}
nuccoreObjects = NcbiHelper.ExecuteESummaryRequest(searchResults, importPartial);
accessions = nuccoreObjects.Select(no => no.AccessionVersion.Split('.')[0]).Distinct().ToArray();
var importResults = new List <MatterImportResult>(accessions.Length);
using (var db = new LibiadaWebEntities())
{
var matterRepository = new MatterRepository(db);
var dnaSequenceRepository = new GeneticSequenceRepository(db);
var(existingAccessions, accessionsToImport) = dnaSequenceRepository.SplitAccessionsIntoExistingAndNotImported(accessions);
importResults.AddRange(existingAccessions.ConvertAll(existingAccession => new MatterImportResult
{
MatterName = existingAccession,
Result = "Sequence already exists",
Status = "Exists"
}));
foreach (string accession in accessionsToImport)
{
var importResult = new MatterImportResult()
{
MatterName = accession
};
try
{
ISequence bioSequence = NcbiHelper.DownloadGenBankSequence(accession);
GenBankMetadata metadata = NcbiHelper.GetMetadata(bioSequence);
importResult.MatterName = metadata.Version.CompoundAccession;
Matter matter = matterRepository.CreateMatterFromGenBankMetadata(metadata);
importResult.SequenceType = matter.SequenceType.GetDisplayValue();
importResult.Group = matter.Group.GetDisplayValue();
importResult.MatterName = matter.Name;
importResult.AllNames = $"Common name = {metadata.Source.CommonName}, "
+ $"Species = {metadata.Source.Organism.Species}, "
+ $"Definition = {metadata.Definition}, "
+ $"Saved matter name = {importResult.MatterName}";
var sequence = new CommonSequence
{
Matter = matter,
Notation = Notation.Nucleotides,
RemoteDb = RemoteDb.GenBank,
RemoteId = metadata.Version.CompoundAccession
};
bool partial = metadata.Definition.ToLower().Contains("partial");
dnaSequenceRepository.Create(sequence, bioSequence, partial);
(importResult.Result, importResult.Status) = importGenes ?
ImportFeatures(metadata, sequence) :
("Successfully imported sequence", "Success");
}
catch (Exception exception)
{
importResult.Status = "Error";
importResult.Result = $"Error: {exception.Message}";
while (exception.InnerException != null)
{
exception = exception.InnerException;
importResult.Result += $" {exception.Message}";
}
foreach (var dbEntityEntry in db.ChangeTracker.Entries())
{
if (dbEntityEntry.Entity != null)
{
dbEntityEntry.State = EntityState.Detached;
}
}
}
finally
{
importResults.Add(importResult);
}
}
string[] names = importResults.Select(r => r.MatterName).ToArray();
// removing matters for which adding of sequence failed
Matter[] orphanMatters = db.Matter
.Include(m => m.Sequence)
.Where(m => names.Contains(m.Name) && m.Sequence.Count == 0)
.ToArray();
if (orphanMatters.Length > 0)
{
db.Matter.RemoveRange(orphanMatters);
db.SaveChanges();
}
}
var result = new Dictionary <string, object> {
{ "result", importResults }
};
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
public ActionResult Index(long matterId,
Notation notation,
Language?language,
Translator?translator,
PauseTreatment?pauseTreatment,
bool?sequentialTransfer,
int scrambling)
{
Matter matter = db.Matter.Single(m => m.Id == matterId);
long sequenceId;
switch (matter.Nature)
{
case Nature.Literature:
sequenceId = db.LiteratureSequence.Single(l => l.MatterId == matterId &&
l.Notation == notation &&
l.Language == language &&
l.Translator == translator).Id;
break;
case Nature.Music:
sequenceId = db.MusicSequence.Single(m => m.MatterId == matterId &&
m.Notation == notation &&
m.PauseTreatment == pauseTreatment &&
m.SequentialTransfer == sequentialTransfer).Id;
break;
default:
sequenceId = db.CommonSequence.Single(c => c.MatterId == matterId && c.Notation == notation).Id;
break;
}
BaseChain chain = sequenceRepository.GetLibiadaBaseChain(sequenceId);
for (int i = 0; i < scrambling; i++)
{
int firstIndex = randomGenerator.Next(chain.Length);
int secondIndex = randomGenerator.Next(chain.Length);
IBaseObject firstElement = chain[firstIndex];
IBaseObject secondElement = chain[secondIndex];
chain[firstIndex] = secondElement;
chain[secondIndex] = firstElement;
}
var resultMatter = new Matter
{
Nature = matter.Nature,
Name = $"{matter.Name} {scrambling} mixes"
};
db.Matter.Add(resultMatter);
db.SaveChanges();
var result = new CommonSequence
{
Notation = notation,
MatterId = resultMatter.Id
};
long[] alphabet = elementRepository.ToDbElements(chain.Alphabet, notation, false);
switch (matter.Nature)
{
case Nature.Genetic:
DnaSequence dnaSequence = db.DnaSequence.Single(c => c.Id == sequenceId);
dnaSequenceRepository.Create(result, dnaSequence.Partial, alphabet, chain.Building);
break;
case Nature.Music:
musicSequenceRepository.Create(result, alphabet, chain.Building);
break;
case Nature.Literature:
LiteratureSequence sequence = db.LiteratureSequence.Single(c => c.Id == sequenceId);
literatureSequenceRepository.Create(result, sequence.Original, sequence.Language, sequence.Translator, alphabet, chain.Building);
break;
case Nature.MeasurementData:
dataSequenceRepository.Create(result, alphabet, chain.Building);
break;
default:
throw new InvalidEnumArgumentException(nameof(matter.Nature), (int)matter.Nature, typeof(Nature));
}
return(RedirectToAction("Index", "Matters"));
}
public ActionResult Index(string[] accessions, bool importGenes)
{
return Action(() =>
{
var matterNames = new string[accessions.Length];
var savedMatterNames = new string[accessions.Length];
var results = new string[accessions.Length];
var statuses = new string[accessions.Length];
using (var db = new LibiadaWebEntities())
{
var existingAccessions = db.DnaSequence.Select(d => d.RemoteId).Distinct().ToArray();
var dnaSequenceRepository = new DnaSequenceRepository(db);
var bioSequences = NcbiHelper.GetGenBankSequences(accessions);
for (int i = 0; i < accessions.Length; i++)
{
string accession = accessions[i];
matterNames[i] = accession;
if (existingAccessions.Contains(accession) || existingAccessions.Contains(accession + ".1"))
{
results[i] = "Sequence already exists";
statuses[i] = "Exist";
continue;
}
try
{
var metadata = NcbiHelper.GetMetadata(bioSequences[i]);
if (existingAccessions.Contains(metadata.Version.CompoundAccession))
{
results[i] = "Sequence already exists";
statuses[i] = "Exist";
continue;
}
savedMatterNames[i] = NcbiHelper.ExtractSequenceName(metadata) + " | " + metadata.Version.CompoundAccession;
matterNames[i] = "Common name=" + metadata.Source.CommonName +
", Species=" + metadata.Source.Organism.Species +
", Definition=" + metadata.Definition +
", Saved matter name=" + savedMatterNames[i];
var matter = new Matter
{
Name = savedMatterNames[i],
Nature = Nature.Genetic,
Group = GroupRepository.ExtractSequenceGroup(savedMatterNames[i]),
SequenceType = SequenceTypeRepsitory.ExtractSequenceGroup(savedMatterNames[i])
};
var sequence = new CommonSequence
{
Matter = matter,
NotationId = Aliases.Notation.Nucleotide,
RemoteDbId = Aliases.RemoteDb.RemoteDbNcbi,
RemoteId = metadata.Version.CompoundAccession
};
dnaSequenceRepository.Create(sequence, bioSequences[i], metadata.Definition.ToLower().Contains("partial"));
if (importGenes)
{
try
{
using (var subsequenceImporter = new SubsequenceImporter(metadata.Features.All, sequence.Id))
{
subsequenceImporter.CreateSubsequences();
}
var nonCodingCount = db.Subsequence.Count(s => s.SequenceId == sequence.Id && s.FeatureId == Aliases.Feature.NonCodingSequence);
var featuresCount = db.Subsequence.Count(s => s.SequenceId == sequence.Id && s.FeatureId != Aliases.Feature.NonCodingSequence);
statuses[i] = "Success";
results[i] = "Successfully imported sequence and " + featuresCount + " features and " + nonCodingCount + " non coding subsequences";
}
catch (Exception exception)
{
results[i] = "successfully imported sequence but failed to import genes: " + exception.Message;
statuses[i] = "Error";
if (exception.InnerException != null)
{
results[i] += " " + exception.InnerException.Message;
}
}
}
else
{
results[i] = "successfully imported sequence";
statuses[i] = "Success";
}
}
catch (Exception exception)
{
results[i] = "Error:" + exception.Message + (exception.InnerException == null ? string.Empty : exception.InnerException.Message);
statuses[i] = "Error";
}
}
// removing matters for whitch adding of sequence failed
var orphanMatters = db.Matter.Include(m => m.Sequence).Where(m => savedMatterNames.Contains(m.Name) && m.Sequence.Count == 0).ToArray();
if (orphanMatters.Length > 0)
{
db.Matter.RemoveRange(orphanMatters);
db.SaveChanges();
}
}
return new Dictionary<string, object>
{
{ "matterNames", matterNames },
{ "results", results },
{ "status", statuses }
};
});
}
public ActionResult Create(
[Bind(Include = "Id,Notation,RemoteDb,RemoteId,Description,Matter,MatterId")] CommonSequence commonSequence,
bool localFile,
Language?language,
bool?original,
Translator?translator,
bool?partial,
int?precision)
{
return(CreateTask(() =>
{
var db = new LibiadaWebEntities();
try
{
if (!ModelState.IsValid)
{
throw new Exception("Model state is invalid");
}
Stream sequenceStream;
Nature nature = commonSequence.Notation.GetNature();
if (nature == Nature.Genetic && !localFile)
{
sequenceStream = NcbiHelper.GetFastaFileStream(commonSequence.RemoteId);
}
else
{
sequenceStream = FileHelper.GetFileStream(Request.Files[0]);
}
switch (nature)
{
case Nature.Genetic:
ISequence bioSequence = NcbiHelper.GetFastaSequence(sequenceStream);
var dnaSequenceRepository = new GeneticSequenceRepository(db);
dnaSequenceRepository.Create(commonSequence, bioSequence, partial ?? false);
break;
case Nature.Music:
var musicSequenceRepository = new MusicSequenceRepository(db);
musicSequenceRepository.Create(commonSequence, sequenceStream);
break;
case Nature.Literature:
var literatureSequenceRepository = new LiteratureSequenceRepository(db);
literatureSequenceRepository.Create(commonSequence, sequenceStream, language ?? Language.Russian, original ?? true, translator ?? Translator.NoneOrManual);
break;
case Nature.MeasurementData:
var dataSequenceRepository = new DataSequenceRepository(db);
dataSequenceRepository.Create(commonSequence, sequenceStream, precision ?? 0);
break;
case Nature.Image:
var matterRepository = new MatterRepository(db);
int fileSize = Request.Files[0].ContentLength;
var file = new byte[fileSize];
Request.Files[0].InputStream.Read(file, 0, fileSize);
var matter = new Matter
{
Nature = Nature.Image,
SequenceType = commonSequence.Matter.SequenceType,
Name = commonSequence.Matter.Name,
Source = file,
Group = commonSequence.Matter.Group
};
matterRepository.SaveToDatabase(matter);
break;
default:
throw new InvalidEnumArgumentException(nameof(nature), (int)nature, typeof(Nature));
}
string multisequenceName = db.Multisequence.SingleOrDefault(ms => ms.Id == commonSequence.Matter.MultisequenceId).Name;
var result = new ImportResult(commonSequence, language, original, translator, partial, precision, multisequenceName);
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(result) }
};
}
catch (Exception)
{
long matterId = commonSequence.MatterId;
if (matterId != 0)
{
List <Matter> orphanMatter = db.Matter
.Include(m => m.Sequence)
.Where(m => m.Id == matterId && m.Sequence.Count == 0)
.ToList();
if (orphanMatter.Count > 0)
{
db.Matter.Remove(orphanMatter[0]);
db.SaveChanges();
}
}
throw;
}
finally
{
Dispose(true);
}
}));
}
/// <summary>
/// Starts a new thread with the given task.
/// </summary>
/// <param name="task">
/// The task.
/// </param>
private void ExecuteTaskAction(Task task)
{
try
{
Func <Dictionary <string, object> > actionToCall;
lock (task)
{
actionToCall = task.Action;
task.TaskData.Started = DateTime.Now;
using (var db = new LibiadaWebEntities())
{
CalculationTask databaseTask = db.CalculationTask.Single(t => t.Id == task.TaskData.Id);
databaseTask.Started = DateTime.Now;
databaseTask.Status = TaskState.InProgress;
db.Entry(databaseTask).State = EntityState.Modified;
db.SaveChanges();
}
signalrHub.Send(TaskEvent.ChangeStatus, task.TaskData);
}
// executing action
Dictionary <string, object> result = actionToCall();
lock (task)
{
task.TaskData.Completed = DateTime.Now;
task.TaskData.ExecutionTime = task.TaskData.Completed - task.TaskData.Started;
task.Result = result;
task.TaskData.TaskState = TaskState.Completed;
using (var db = new LibiadaWebEntities())
{
CalculationTask databaseTask = db.CalculationTask.Single(t => (t.Id == task.TaskData.Id));
databaseTask.Completed = DateTime.Now;
databaseTask.Status = TaskState.Completed;
if (result.ContainsKey("data"))
{
databaseTask.Result = result["data"].ToString();
}
if (result.ContainsKey("additionalData"))
{
databaseTask.AdditionalResultData = JsonConvert.SerializeObject(result["additionalData"]);
}
db.Entry(databaseTask).State = EntityState.Modified;
db.SaveChanges();
}
signalrHub.Send(TaskEvent.ChangeStatus, task.TaskData);
}
}
catch (Exception e)
{
string errorMessage = e.Message;
string stackTrace = e.StackTrace;
while (e.InnerException != null)
{
e = e.InnerException;
errorMessage += $"{Environment.NewLine} {e.Message}";
}
lock (task)
{
task.TaskData.Completed = DateTime.Now;
task.TaskData.ExecutionTime = task.TaskData.Completed - task.TaskData.Started;
task.TaskData.TaskState = TaskState.Error;
task.Result = new Dictionary <string, object>
{
{ "Error", true },
{ "ErrorMessage", errorMessage },
{ "StackTrace", stackTrace }
};
using (var db = new LibiadaWebEntities())
{
CalculationTask databaseTask = db.CalculationTask.Single(t => (t.Id == task.TaskData.Id));
databaseTask.Completed = DateTime.Now;
databaseTask.Status = TaskState.Error;
databaseTask.Result = JsonConvert.SerializeObject(task.Result);
db.Entry(databaseTask).State = EntityState.Modified;
db.SaveChanges();
}
signalrHub.Send(TaskEvent.ChangeStatus, task.TaskData);
}
}
ManageTasks();
}
/// <summary>
/// Adds given matter to database.
/// </summary>
/// <param name="matter">
/// The matter.
/// </param>
/// <returns>
/// The <see cref="long"/>.
/// </returns>
public long CreateMatter(Matter matter)
{
db.Matter.Add(matter);
db.SaveChanges();
return(matter.Id);
}