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(
string searchQuery,
bool importPartial,
bool filterMinLength,
int minLength,
bool filterMaxLength,
int maxLength)
{
return(CreateTask(() =>
{
if (filterMinLength)
{
searchQuery = filterMaxLength ?
NcbiHelper.FormatNcbiSearchTerm(searchQuery, minLength, maxLength: maxLength) :
NcbiHelper.FormatNcbiSearchTerm(searchQuery, minLength);
}
else
{
searchQuery = filterMaxLength ?
NcbiHelper.FormatNcbiSearchTerm(searchQuery, maxLength: maxLength) :
NcbiHelper.FormatNcbiSearchTerm(searchQuery);
}
List <NuccoreObject> searchResults = NcbiHelper.ExecuteESummaryRequest(searchQuery, importPartial);
List <NuccoreObject> unfilteredSearchResults;
List <NuccoreObject> filteresOutSearchResults = searchResults;
string[] accessions;
if (!importPartial)
{
unfilteredSearchResults = NcbiHelper.ExecuteESummaryRequest(searchQuery, true);
filteresOutSearchResults = unfilteredSearchResults.Except(searchResults).ToList();
accessions = unfilteredSearchResults.Select(no => no.AccessionVersion.Split('.')[0]).Distinct().ToArray();
}
else
{
accessions = searchResults.Select(no => no.AccessionVersion.Split('.')[0]).Distinct().ToArray();
}
var results = new List <MatterImportResult>(accessions.Length);
string[] existingAccessions;
using (var db = new LibiadaWebEntities())
{
var dnaSequenceRepository = new GeneticSequenceRepository(db);
(existingAccessions, _) = dnaSequenceRepository.SplitAccessionsIntoExistingAndNotImported(accessions);
}
searchResults = searchResults
.Where(sr => !existingAccessions.Contains(sr.AccessionVersion.Split('.')[0]))
.ToList();
foreach (var searchResult in searchResults)
{
results.Add(new MatterImportResult()
{
MatterName = $"{searchResult.Title} | {searchResult.AccessionVersion}",
Result = "Found new sequence",
Status = "Success"
});
}
results.AddRange(existingAccessions.ConvertAll(existingAccession => new MatterImportResult
{
MatterName = existingAccession,
Result = "Sequence already exists",
Status = "Exists"
}));
if (!importPartial)
{
filteresOutSearchResults = filteresOutSearchResults
.Where(sr => !existingAccessions.Contains(sr.AccessionVersion.Split('.')[0]))
.ToList();
foreach (var filteresOutSearchResult in filteresOutSearchResults)
{
results.Add(new MatterImportResult()
{
MatterName = $"{filteresOutSearchResult.Title} | {filteresOutSearchResult.AccessionVersion}",
Result = "Filtered out",
Status = "Error"
});
}
}
accessions = searchResults.Select(sr => sr.AccessionVersion).ToArray();
var result = new Dictionary <string, object> {
{ "result", results }, { "accessions", accessions }
};
return new Dictionary <string, string> {
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
