public ActionResult Index(long matterId)
{
return Action(() =>
{
string matterName;
Subsequence[] sequenceSubsequences;
using (var db = new LibiadaWebEntities())
{
long parentSequenceId = db.DnaSequence.Single(d => d.MatterId == matterId).Id;
DnaSequence parentSequence = db.DnaSequence.Single(c => c.Id == parentSequenceId);
var features = NcbiHelper.GetFeatures(parentSequence.RemoteId);
using (var subsequenceImporter = new SubsequenceImporter(features, parentSequenceId))
{
subsequenceImporter.CreateSubsequences();
}
matterName = db.Matter.Single(m => m.Id == matterId).Name;
sequenceSubsequences = db.Subsequence.Where(s => s.SequenceId == parentSequenceId)
.Include(s => s.Position)
.Include(s => s.Feature)
.Include(s => s.SequenceAttribute)
.ToArray();
}
return new Dictionary<string, object>
{
{ "matterName", matterName },
{ "genes", sequenceSubsequences }
};
});
}
public ActionResult Index(long[] matterIds)
{
return Action(() =>
{
string[] matterNames;
string[] results = new string[matterIds.Length];
string[] statuses = new string[matterIds.Length];
using (var db = new LibiadaWebEntities())
{
matterNames = db.Matter.Where(m => matterIds.Contains(m.Id)).OrderBy(m => m.Id).Select(m => m.Name).ToArray();
var parentSequences = db.DnaSequence.Where(c => matterIds.Contains(c.MatterId)).OrderBy(c => c.MatterId);
long[] parentSequenceIds = parentSequences.Select(c => c.Id).ToArray();
string[] parentRemoteIds = parentSequences.Select(c => c.RemoteId).ToArray();
var features = NcbiHelper.GetFeatures(parentRemoteIds);
for (int i = 0; i < matterIds.Length; i++)
{
try
{
var parentSequenceId = parentSequenceIds[i];
using (var subsequenceImporter = new SubsequenceImporter(features[i], parentSequenceId))
{
subsequenceImporter.CreateSubsequences();
}
var nonCodingCount = db.Subsequence.Count(s => s.SequenceId == parentSequenceId && s.FeatureId == Aliases.Feature.NonCodingSequence);
var featuresCount = db.Subsequence.Count(s => s.SequenceId == parentSequenceId && s.FeatureId != Aliases.Feature.NonCodingSequence);
statuses[i] = "Success";
results[i] = "Successfully imported " + featuresCount + " features and " + nonCodingCount + " non coding subsequences";
}
catch (Exception exception)
{
statuses[i] = "Error";
results[i] = exception.Message;
if (exception.InnerException != null)
{
results[i] += " " + exception.InnerException.Message;
}
}
}
}
return new Dictionary<string, object>
{
{ "matterNames", matterNames },
{ "results", results },
{ "status", statuses }
};
});
}
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 }
};
});
}
