/// <summary>
/// Adds new task to db and tasks list.
/// </summary>
/// <param name="action">
/// The action.
/// </param>
/// <param name="taskType">
/// The task Type.
/// </param>
public long CreateTask(Func <Dictionary <string, string> > action, TaskType taskType)
{
CalculationTask databaseTask;
Task task;
using (var db = new LibiadaWebEntities())
{
databaseTask = new CalculationTask
{
Created = DateTime.Now,
Description = taskType.GetDisplayValue(),
Status = TaskState.InQueue,
UserId = AccountHelper.GetUserId(),
TaskType = taskType
};
db.CalculationTask.Add(databaseTask);
db.SaveChanges();
}
lock (tasks)
{
task = new Task(databaseTask.Id, action, databaseTask.UserId, taskType);
lock (task)
{
tasks.Add(task);
signalrHub.Send(TaskEvent.AddTask, task.TaskData);
}
}
ManageTasks();
return(task.TaskData.Id);
}
/// <summary>
/// TExtracts alphabet elements ids for given sequence.
/// </summary>
/// <param name="db">
/// Database connection.
/// </param>
/// <param name="sequenceId">
/// The sequence id.
/// </param>
/// <returns>
/// The <see cref="long[]"/>.
/// </returns>
public static long[] GetAlphabetElementIds(this LibiadaWebEntities db, long sequenceId)
{
var dbConnection = (NpgsqlConnection)db.Database.Connection;
const string Query = "SELECT alphabet FROM chain WHERE id = @id";
var id = new NpgsqlParameter <long>("id", NpgsqlDbType.Bigint)
{
TypedValue = sequenceId
};
long[] result;
dbConnection.Open();
using (var command = new NpgsqlCommand(Query, dbConnection))
{
command.Parameters.Add(id);
using (NpgsqlDataReader reader = command.ExecuteReader())
{
if (!reader.Read())
{
dbConnection.Close();
throw new ArgumentException($"sequence id {sequenceId} does not exist", nameof(sequenceId));
}
result = (long[])reader[0];
}
}
dbConnection.Close();
return(result);
}
/// <summary>
/// Initializes a new instance of the <see cref="LocalCalculationController"/> class.
/// </summary>
public LocalCalculationController()
: base("Local calculation")
{
db = new LibiadaWebEntities();
commonSequenceRepository = new CommonSequenceRepository(db);
characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
}
/// <summary>
/// Finds user by it's id.
/// </summary>
/// <param name="id">
/// The user id.
/// </param>
/// <returns>
/// The <see cref="Models.Account.ApplicationUser"/>.
/// </returns>
private static AspNetUser GetUserById(int id)
{
using (var db = new LibiadaWebEntities())
{
return(db.AspNetUsers.Find(id));
}
}
/// <summary>
/// Send push notification to subscribers.
/// </summary>
/// <param name="userId">
/// User id for sending the push notification.
/// </param>
/// <param name="data">
/// Data dictionary containing push notification elements.
/// </param>
public static void Send(int userId, Dictionary <string, string> data)
{
using (var db = new LibiadaWebEntities())
{
var subscribers = db.AspNetPushNotificationSubscribers.Where(s => s.UserId == userId);
if (subscribers.Count() != 0)
{
foreach (var subscriber in subscribers)
{
var endpoint = subscriber.Endpoint;
var p256dh = subscriber.P256dh;
var auth = subscriber.Auth;
var payload = JsonConvert.SerializeObject(data);
var subscription = new PushSubscription(endpoint, p256dh, auth);
var options = new Dictionary <string, object>();
options["TTL"] = 3600;
var publicKey = ConfigurationManager.AppSettings["PublicVapidKey"];
var privateKey = ConfigurationManager.AppSettings["PrivateVapidKey"];
options["vapidDetails"] = new VapidDetails(subject, publicKey, privateKey);
var webPushClient = new WebPushClient();
try
{
webPushClient.SendNotification(subscription, payload, options);
}
catch (WebPushException exception)
{
Debug.WriteLine("Http STATUS code: {0}", exception.StatusCode);
}
}
}
}
}
/// <summary>
/// Deletes the task by id.
/// </summary>
/// <param name="id">
/// The task id.
/// </param>
public void DeleteTask(long id)
{
lock (tasks)
{
Task task = tasks.Single(t => t.TaskData.Id == id);
if (task.TaskData.UserId == AccountHelper.GetUserId() || AccountHelper.IsAdmin())
{
lock (task)
{
if ((task.SystemTask != null) && (!task.SystemTask.IsCompleted))
{
CancellationTokenSource cancellationTokenSource = task.CancellationTokenSource;
cancellationTokenSource.Cancel();
cancellationTokenSource.Dispose();
}
tasks.Remove(task);
using (var db = new LibiadaWebEntities())
{
CalculationTask databaseTask = db.CalculationTask.Find(id);
db.CalculationTask.Remove(databaseTask);
db.SaveChanges();
}
signalrHub.Send(TaskEvent.DeleteTask, task.TaskData);
}
}
}
}
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 }
};
});
}
/// <summary>
/// Initializes a new instance of the <see cref="SequenceTransformerController"/> class.
/// </summary>
public SequenceTransformerController()
{
db = new LibiadaWebEntities();
dnaSequenceRepository = new GeneticSequenceRepository(db);
commonSequenceRepository = new CommonSequenceRepository(db);
elementRepository = new ElementRepository(db);
}
/// <summary>
/// Initializes a new instance of the <see cref="SequenceTransformerController"/> class.
/// </summary>
public SequenceTransformerController()
{
db = new LibiadaWebEntities();
dnaSequenceRepository = new DnaSequenceRepository(db);
commonSequenceRepository = new CommonSequenceRepository(db);
elementRepository = new ElementRepository(db);
}
/// <summary>
/// Deletes the task by id.
/// </summary>
/// <param name="id">
/// The task id.
/// </param>
public void DeleteTask(long id)
{
lock (tasks)
{
Task task = tasks.Single(t => t.TaskData.Id == id);
if (task.TaskData.UserId == AccountHelper.GetUserId() || AccountHelper.IsAdmin())
{
lock (task)
{
if (task.Thread != null && task.Thread.IsAlive)
{
task.Thread.Abort();
}
tasks.Remove(task);
using (var db = new LibiadaWebEntities())
{
CalculationTask databaseTask = db.CalculationTask.Find(id);
db.CalculationTask.Remove(databaseTask);
db.SaveChanges();
}
signalrHub.Send(TaskEvent.DeleteTask, task.TaskData);
}
}
}
}
/// <summary>
/// The edit.
/// </summary>
/// <param name="id">
/// The id.
/// </param>
/// <returns>
/// The <see cref="System.Threading.Tasks.Task"/>.
/// </returns>
public async Task <ActionResult> Edit(long?id)
{
if (id == null)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
using (var db = new LibiadaWebEntities())
{
Matter matter = await db.Matter.FindAsync(id);
if (matter == null)
{
return(HttpNotFound());
}
var groups = EnumExtensions.ToArray <Group>().ToSelectListWithNature();
var sequenceTypes = EnumExtensions.ToArray <SequenceType>().ToSelectListWithNature();
var natures = EnumHelper.GetSelectList(typeof(Nature), matter.Nature);
var data = new Dictionary <string, object>
{
{ "natures", natures },
{ "groups", groups },
{ "sequenceTypes", sequenceTypes },
{ "matter", new StringedMatter(matter, db.CommonSequence.Count(c => c.MatterId == matter.Id)) }
};
ViewBag.data = JsonConvert.SerializeObject(data);
return(View(matter));
}
}
/// <summary>
/// The edit.
/// </summary>
/// <param name="id">
/// The id.
/// </param>
/// <returns>
/// The <see cref="Task"/>.
/// </returns>
public async Task <ActionResult> Edit(int?id)
{
if (id == null)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
SequenceGroup sequenceGroup = await db.SequenceGroup.FindAsync(id);
if (sequenceGroup == null)
{
return(HttpNotFound());
}
using (var db = new LibiadaWebEntities())
{
var viewDataHelper = new ViewDataHelper(db);
var viewData = viewDataHelper.FillViewData(1, int.MaxValue);
var matterRepository = new MatterRepository(db);
var matterIds = sequenceGroup.Matters.Select(m => m.Id);
bool Selected(Matter m) => matterIds.Contains(m.Id);
viewData["matters"] = matterRepository.GetMatterSelectList(db.Matter, Selected);
viewData["sequenceGroupTypes"] = EnumExtensions.ToArray <SequenceGroupType>().ToSelectListWithNature();
ViewBag.data = JsonConvert.SerializeObject(viewData);
}
return(View(sequenceGroup));
}
/// <summary>
/// The edit.
/// </summary>
/// <param name="id">
/// The id.
/// </param>
/// <returns>
/// The <see cref="System.Threading.Tasks.Task"/>.
/// </returns>
public ActionResult Edit(long?id)
{
if (id == null)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
using (var db = new LibiadaWebEntities())
{
Matter matter = db.Matter.Include(m => m.Multisequence).SingleOrDefault(m => m.Id == id);
if (matter == null)
{
return(HttpNotFound());
}
var data = new Dictionary <string, object>
{
{ "natures", EnumHelper.GetSelectList(typeof(Nature), matter.Nature) },
{ "groups", EnumExtensions.ToArray <Group>().ToSelectListWithNature() },
{ "sequenceTypes", EnumExtensions.ToArray <SequenceType>().ToSelectListWithNature() },
{ "sequencesCount", db.CommonSequence.Count(c => c.MatterId == matter.Id) },
{ "matter", matter },
{ "multisequences", db.Multisequence.ToList() },
{ "nature", ((byte)matter.Nature).ToString() },
{ "group", ((byte)matter.Group).ToString() },
{ "sequenceType", ((byte)matter.SequenceType).ToString() }
};
ViewBag.data = JsonConvert.SerializeObject(data, new JsonSerializerSettings()
{
ReferenceLoopHandling = ReferenceLoopHandling.Ignore
});
return(View(matter));
}
}
public async Task <ActionResult> Edit(
[Bind(Include = "Id,Name,Nature,Description,Group,SequenceType,MultisequenceId,MultisequenceNumber,CollectionCountry,CollectionDate")] Matter matter)
{
using (var db = new LibiadaWebEntities())
{
if (ModelState.IsValid)
{
db.Entry(matter).State = EntityState.Modified;
await db.SaveChangesAsync();
return(RedirectToAction("Index"));
}
var data = new Dictionary <string, object>
{
{ "natures", EnumHelper.GetSelectList(typeof(Nature), matter.Nature) },
{ "groups", EnumExtensions.ToArray <Group>().ToSelectListWithNature() },
{ "sequenceTypes", EnumExtensions.ToArray <SequenceType>().ToSelectListWithNature() },
{ "sequencesCount", db.CommonSequence.Count(c => c.MatterId == matter.Id) },
{ "matter", matter },
{ "multisequences", db.Multisequence.ToList() },
{ "nature", ((byte)matter.Nature).ToString() },
{ "group", ((byte)matter.Group).ToString() },
{ "sequenceType", ((byte)matter.SequenceType).ToString() }
};
ViewBag.data = JsonConvert.SerializeObject(data);
return(View(matter));
}
}
/// <summary>
/// Initializes a new instance of the <see cref="SubsequencesSimilarityController"/> class.
/// </summary>
public SubsequencesSimilarityController() : base(TaskType.SubsequencesSimilarity)
{
db = new LibiadaWebEntities();
subsequenceExtractor = new SubsequenceExtractor(db);
characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
sequenceAttributeRepository = new SequenceAttributeRepository(db);
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Index()
{
var db = new LibiadaWebEntities();
var viewDataHelper = new ViewDataHelper(db);
Func<CharacteristicType, bool> filter;
if (UserHelper.IsAdmin())
{
filter = c => c.FullSequenceApplicable;
}
else
{
filter = c => c.FullSequenceApplicable && Aliases.UserAvailableCharacteristics.Contains((Aliases.CharacteristicType)c.Id);
}
var data = new Dictionary<string, object>
{
{ "characteristicTypes", viewDataHelper.GetCharacteristicTypes(filter) }
};
var transformationLinks = new[] { Link.Start, Link.End, Link.CycleStart, Link.CycleEnd };
transformationLinks = transformationLinks.OrderBy(n => (int)n).ToArray();
data.Add("transformationLinks", transformationLinks.ToSelectList());
var operations = new List<SelectListItem> { new SelectListItem { Text = "Dissimilar", Value = 1.ToString() }, new SelectListItem { Text = "Higher order", Value = 2.ToString() } };
data.Add("operations", operations);
ViewBag.data = JsonConvert.SerializeObject(data);
return View();
}
public ActionResult Index(long[] matterIds)
{
return(CreateTask(() =>
{
string[] matterNames;
var results = new string[matterIds.Length];
var 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)
.ToArray();
for (int i = 0; i < parentSequences.Length; i++)
{
try
{
DnaSequence parentSequence = parentSequences[i];
using (var subsequenceImporter = new SubsequenceImporter(parentSequence))
{
subsequenceImporter.CreateSubsequences();
}
int featuresCount = db.Subsequence.Count(s => s.SequenceId == parentSequence.Id &&
s.Feature != Feature.NonCodingSequence);
int nonCodingCount = db.Subsequence.Count(s => s.SequenceId == parentSequence.Id &&
s.Feature == 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;
while (exception.InnerException != null)
{
results[i] += $" {exception.InnerException.Message}";
exception = exception.InnerException;
}
}
}
}
return new Dictionary <string, object>
{
{ "matterNames", matterNames },
{ "results", results },
{ "status", statuses }
};
}));
}
public ActionResult Index(
long matterId,
short characteristicLinkId,
Notation notation,
int step,
int initialLength,
string accuracy)
{
return(CreateTask(() =>
{
string characteristicName;
string matterName;
double[] characteristics;
Chain sequence;
IFullCalculator calculator;
Link link;
using (var db = new LibiadaWebEntities())
{
var commonSequenceRepository = new CommonSequenceRepository(db);
matterName = Cache.GetInstance().Matters.Single(m => matterId == m.Id).Name;
var sequenceId = db.CommonSequence.Single(c => matterId == c.MatterId && c.Notation == notation).Id;
sequence = commonSequenceRepository.GetLibiadaChain(sequenceId);
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
characteristicName = characteristicTypeLinkRepository.GetCharacteristicName(characteristicLinkId, notation);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
calculator = FullCalculatorsFactory.CreateCalculator(characteristic);
link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
}
// characteristics = SequencesCharacteristicsCalculator.Calculate( new[] { sequenceId }, characteristicLinkId);
AverageRemoteness averageRemotenessCalc = new AverageRemoteness();
double averageRemoteness = averageRemotenessCalc.Calculate(sequence, Link.Start);
Alphabet alphabet = sequence.Alphabet;
var doubleAccuracy = double.Parse(accuracy);
List <SequencePredictionData> sequencePredictionResult;
Chain chain;
(sequencePredictionResult, chain) = Predict(averageRemotenessCalc, sequence, initialLength, alphabet, averageRemoteness, doubleAccuracy);
var matching = FindPercentageOfMatching(sequence, chain, initialLength) * 100;
var result = new Dictionary <string, object>
{
{ "result", sequencePredictionResult },
{ "matterName", matterName },
{ "matching", matching }
};
return new Dictionary <string, string>
{
{ "data", JsonConvert.SerializeObject(result) }
};
}));
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="System.Threading.Tasks.Task"/>.
/// </returns>
public async Task <ActionResult> Index()
{
using (var db = new LibiadaWebEntities())
{
var musicSequence = db.MusicSequence.Where(m => m.Notation == Notation.FormalMotifs).Include(m => m.Matter);
return(View(await musicSequence.ToListAsync()));
}
}
/// <summary>
/// Initializes a new instance of the <see cref="SubsequencesSimilarityController"/> class.
/// </summary>
public SubsequencesSimilarityController()
: base("Subsequences similarity")
{
db = new LibiadaWebEntities();
subsequenceExtractor = new SubsequenceExtractor(db);
characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
sequenceAttributeRepository = new SequenceAttributeRepository(db);
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Index()
{
using (var db = new LibiadaWebEntities())
{
ViewBag.matterId = new SelectList(Cache.GetInstance().Matters.ToArray(), "id", "name");
return(View());
}
}
/// <summary>
/// Initializes a new instance of the <see cref="SequencesAlignmentController"/> class.
/// </summary>
public SequencesAlignmentController()
: base("Sequences alignment")
{
db = new LibiadaWebEntities();
subsequenceExtractor = new SubsequenceExtractor(db);
characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
featureRepository = new FeatureRepository(db);
}
/// <summary>
/// Retrieves attributes values of given subsequences from database.
/// </summary>
/// <param name="subsequenceIds">
/// Ids of subsequences which attributes values are to be retrieved.
/// </param>
/// <returns>
/// Dictionary containing subsequences ids as keys and attributes values as values.
/// </returns>
private Dictionary <long, AttributeValue[]> GetSubsequencesAttributesValues(long[] subsequenceIds)
{
using (var db = new LibiadaWebEntities())
{
var sequenceAttributeRepository = new SequenceAttributeRepository(db);
return(sequenceAttributeRepository.GetAttributes(subsequenceIds));
}
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="System.Threading.Tasks.Task"/>.
/// </returns>
public async Task <ActionResult> Index()
{
using (var db = new LibiadaWebEntities())
{
var commonSequence = db.CommonSequence.Include(c => c.Matter);
return(View(await commonSequence.ToListAsync()));
}
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chainCharacteristicsIds">
/// Dictionary with chain ids as a key
/// and characteristicLink ids array as value.
/// </param>
/// <returns>
/// The <see cref="T:double[][]"/>.
/// </returns>
public static Dictionary <long, Dictionary <short, double> > Calculate(Dictionary <long, short[]> chainCharacteristicsIds)
{
var newCharacteristics = new List <CharacteristicValue>();
var allCharacteristics = new Dictionary <long, Dictionary <short, double> >();
using (var db = new LibiadaWebEntities())
{
short[] characteristicLinkIds = chainCharacteristicsIds.SelectMany(c => c.Value).Distinct().ToArray();
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
var calculators = new Dictionary <short, LinkedFullCalculator>();
foreach (short characteristicLinkId in characteristicLinkIds)
{
Link link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
calculators.Add(characteristicLinkId, new LinkedFullCalculator(characteristic, link));
}
var commonSequenceRepository = new CommonSequenceRepository(db);
long[] sequenceIds = chainCharacteristicsIds.Keys.ToArray();
foreach (long sequenceId in sequenceIds)
{
short[] sequenceCharacteristicLinkIds = chainCharacteristicsIds[sequenceId];
Dictionary <short, double> characteristics = db.CharacteristicValue
.Where(c => sequenceId == c.SequenceId && sequenceCharacteristicLinkIds.Contains(c.CharacteristicLinkId))
.ToDictionary(ct => ct.CharacteristicLinkId, ct => ct.Value);
allCharacteristics.Add(sequenceId, characteristics);
if (characteristics.Count < sequenceCharacteristicLinkIds.Length)
{
Chain sequence = commonSequenceRepository.GetLibiadaChain(sequenceId);
foreach (short sequenceCharacteristicLinkId in sequenceCharacteristicLinkIds)
{
if (!characteristics.ContainsKey(sequenceCharacteristicLinkId))
{
LinkedFullCalculator calculator = calculators[sequenceCharacteristicLinkId];
double characteristicValue = calculator.Calculate(sequence);
var characteristic = new CharacteristicValue
{
SequenceId = sequenceId,
CharacteristicLinkId = sequenceCharacteristicLinkId,
Value = characteristicValue
};
characteristics.Add(sequenceCharacteristicLinkId, characteristicValue);
newCharacteristics.Add(characteristic);
}
}
}
}
var characteristicRepository = new CharacteristicRepository(db);
characteristicRepository.TrySaveCharacteristicsToDatabase(newCharacteristics);
return(allCharacteristics);
}
}
/// <summary>
/// Initializes a new instance of the <see cref="ViewDataHelper"/> class.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
public ViewDataHelper(LibiadaWebEntities db)
{
this.db = db;
matterRepository = new MatterRepository(db);
notationRepository = new NotationRepository(db);
featureRepository = new FeatureRepository(db);
characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
remoteDbRepository = new RemoteDbRepository(db);
}
/// <summary>
/// Initializes a new instance of the <see cref="SequencesMattersController"/> class.
/// </summary>
protected SequencesMattersController()
: base("Sequence upload")
{
Db = new LibiadaWebEntities();
dnaSequenceRepository = new DnaSequenceRepository(Db);
literatureSequenceRepository = new LiteratureSequenceRepository(Db);
musicSequenceRepository = new MusicSequenceRepository(Db);
dataSequenceRepository = new DataSequenceRepository(Db);
}
/// <summary>
/// The create.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Create()
{
using (var db = new LibiadaWebEntities())
{
var viewDataHelper = new ViewDataHelper(db);
ViewBag.data = JsonConvert.SerializeObject(viewDataHelper.FillMatterCreationViewData());
}
return(View());
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Index()
{
using (var db = new LibiadaWebEntities())
{
var viewDataHelper = new ViewDataHelper(db);
Dictionary <string, object> viewData = viewDataHelper.GetCharacteristicsData(CharacteristicCategory.Full);
ViewBag.data = JsonConvert.SerializeObject(viewData);
return(View());
}
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Index()
{
using (var db = new LibiadaWebEntities())
{
var viewDataHelper = new ViewDataHelper(db);
ViewBag.data = JsonConvert.SerializeObject(viewDataHelper.FillSubsequencesViewData(1, int.MaxValue, "Calculate"));
}
return(View());
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Index()
{
using (var db = new LibiadaWebEntities())
{
var viewDataHelper = new ViewDataHelper(db);
ViewBag.data = JsonConvert.SerializeObject(viewDataHelper.FillSubsequencesViewData(1, int.MaxValue, "Calculate"));
}
return View();
}
/// <summary>
/// Extracts sequence length from database.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
/// <param name="sequenceId">
/// The sequence id.
/// </param>
/// <returns>
/// The <see cref="int"/>.
/// </returns>
public static int GetSequenceLength(this LibiadaWebEntities db, long sequenceId)
{
const string Query = "SELECT cardinality(building) FROM chain WHERE id = @id";
var id = new NpgsqlParameter <long>("id", NpgsqlDbType.Bigint)
{
TypedValue = sequenceId
};
return(db.Database.SqlQuery <int>(Query, id).First());
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Index()
{
using (var db = new LibiadaWebEntities())
{
var viewDataHelper = new ViewDataHelper(db);
var viewData = viewDataHelper.FillViewData(CharacteristicCategory.Full, 1, int.MaxValue, "Calculate");
ViewBag.data = JsonConvert.SerializeObject(viewData);
return(View());
}
}
/// <summary>
/// Initializes a new instance of the <see cref="SequenceMixerController"/> class.
/// </summary>
public SequenceMixerController()
{
db = new LibiadaWebEntities();
sequenceRepository = new CommonSequenceRepository(db);
dnaSequenceRepository = new GeneticSequenceRepository(db);
musicSequenceRepository = new MusicSequenceRepository(db);
literatureSequenceRepository = new LiteratureSequenceRepository(db);
dataSequenceRepository = new DataSequenceRepository(db);
elementRepository = new ElementRepository(db);
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chains">
/// The chains.
/// </param>
/// <param name="calculators">
/// The calculators.
/// </param>
/// <param name="links">
/// The links.
/// </param>
/// <param name="characteristicTypeLinkIds">
/// The characteristic type link ids.
/// </param>
/// <returns>
/// The <see cref="T:double[][]"/>.
/// </returns>
public static double[][] Calculate(Chain[][] chains, IFullCalculator[] calculators, Link[] links, int[] characteristicTypeLinkIds)
{
var newCharacteristics = new List<Characteristic>();
var characteristics = new double[chains.Length][];
var sequenceIds = chains.SelectMany(c => c).Select(c => c.Id).Distinct();
Dictionary<long, Dictionary<int, double>> dbCharacteristics;
using (var db = new LibiadaWebEntities())
{
dbCharacteristics = db.Characteristic
.Where(c => characteristicTypeLinkIds.Contains(c.CharacteristicTypeLinkId) && sequenceIds.Contains(c.SequenceId))
.ToArray()
.GroupBy(c => c.SequenceId)
.ToDictionary(c => c.Key, c => c.ToDictionary(ct => ct.CharacteristicTypeLinkId, ct => ct.Value));
}
for (int i = 0; i < chains.Length; i++)
{
characteristics[i] = new double[calculators.Length];
for (int j = 0; j < calculators.Length; j++)
{
long sequenceId = chains[i][j].Id;
chains[i][j].FillIntervalManagers();
Dictionary<int, double> sequenceDbCharacteristics;
if (!dbCharacteristics.TryGetValue(sequenceId, out sequenceDbCharacteristics))
{
sequenceDbCharacteristics = new Dictionary<int, double>();
}
if (!sequenceDbCharacteristics.TryGetValue(characteristicTypeLinkIds[j], out characteristics[i][j]))
{
characteristics[i][j] = calculators[j].Calculate(chains[i][j], links[j]);
var currentCharacteristic = new Characteristic
{
SequenceId = sequenceId,
CharacteristicTypeLinkId = characteristicTypeLinkIds[j],
Value = characteristics[i][j]
};
newCharacteristics.Add(currentCharacteristic);
}
}
}
// trying to save calculated characteristics to database
using (var db = new LibiadaWebEntities())
{
var characteristicRepository = new CharacteristicRepository(db);
characteristicRepository.TrySaveCharacteristicsToDatabase(newCharacteristics);
}
return characteristics;
}
/// <summary>
/// The get subsequence characteristic.
/// </summary>
/// <param name="subsequenceId">
/// The subsequence id.
/// </param>
/// <param name="characteristicLinkId">
/// The characteristic type link id.
/// </param>
/// <param name="windowSize">
/// The window size.
/// </param>
/// <param name="step">
/// The step.
/// </param>
/// <returns>
/// The <see cref="string"/>.
/// </returns>
public string GetSubsequenceCharacteristic(
long subsequenceId,
short characteristicLinkId,
int windowSize,
int step)
{
Chain chain;
IFullCalculator calculator;
Link link;
using (var db = new LibiadaWebEntities())
{
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
FullCharacteristic characteristic =
characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkId);
calculator = FullCalculatorsFactory.CreateCalculator(characteristic);
link = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkId);
var subsequenceExtractor = new SubsequenceExtractor(db);
Subsequence subsequence = db.Subsequence.Single(s => s.Id == subsequenceId);
chain = subsequenceExtractor.GetSubsequenceSequence(subsequence);
}
CutRule cutRule = new SimpleCutRule(chain.Length, step, windowSize);
CutRuleIterator iterator = cutRule.GetIterator();
var fragments = new List <Chain>();
while (iterator.Next())
{
int start = iterator.GetStartPosition();
int end = iterator.GetEndPosition();
var fragment = new List <IBaseObject>();
for (int k = 0; start + k < end; k++)
{
fragment.Add(chain[start + k]);
}
fragments.Add(new Chain(fragment));
}
var characteristics = new double[fragments.Count];
for (int k = 0; k < fragments.Count; k++)
{
characteristics[k] = calculator.Calculate(fragments[k], link);
}
return(JsonConvert.SerializeObject(characteristics));
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chainIds">
/// The chains ids.
/// </param>
/// <param name="characteristicLinkIds">
/// The characteristic type link ids.
/// </param>
/// <param name="rotate">
/// The rotate flag.
/// </param>
/// <param name="complementary">
/// The complementary flag.
/// </param>
/// <param name="rotationLength">
/// The rotation length.
/// </param>
/// <returns>
/// The <see cref="T:double[][]"/>.
/// </returns>
public static double[][] Calculate(long[][] chainIds, short[] characteristicLinkIds, bool rotate, bool complementary, uint?rotationLength)
{
var links = new Link[characteristicLinkIds.Length];
var calculators = new IFullCalculator[characteristicLinkIds.Length];
var characteristics = new double[chainIds.Length][];
long[] sequenceIds = chainIds.SelectMany(c => c).Distinct().ToArray();
var sequences = new Dictionary <long, Chain>();
using (var db = new LibiadaWebEntities())
{
var commonSequenceRepository = new CommonSequenceRepository(db);
for (int i = 0; i < sequenceIds.Length; i++)
{
sequences.Add(sequenceIds[i], commonSequenceRepository.GetLibiadaChain(sequenceIds[i]));
}
var characteristicTypeLinkRepository = FullCharacteristicRepository.Instance;
for (int k = 0; k < characteristicLinkIds.Length; k++)
{
links[k] = characteristicTypeLinkRepository.GetLinkForCharacteristic(characteristicLinkIds[k]);
FullCharacteristic characteristic = characteristicTypeLinkRepository.GetCharacteristic(characteristicLinkIds[k]);
calculators[k] = FullCalculatorsFactory.CreateCalculator(characteristic);
}
}
for (int i = 0; i < chainIds.Length; i++)
{
characteristics[i] = new double[calculators.Length];
for (int j = 0; j < calculators.Length; j++)
{
long sequenceId = chainIds[i][j];
var sequence = (Chain)sequences[sequenceId].Clone();
if (complementary)
{
var sourceSequence = new Sequence(Alphabets.DNA, sequence.ToString());
ISequence complementarySequence = sourceSequence.GetReverseComplementedSequence();
sequence = new Chain(complementarySequence.ConvertToString());
}
if (rotate)
{
int[] building = sequence.Building.Rotate(rotationLength ?? 0);
List <IBaseObject> newSequence = building.Select(t => new ValueInt(t)).ToList <IBaseObject>();
sequence = new Chain(newSequence);
}
characteristics[i][j] = calculators[j].Calculate(sequence, links[j]);
}
}
return(characteristics);
}
/// <summary>
/// The create.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Create()
{
using (var db = new LibiadaWebEntities())
{
var viewDataHelper = new ViewDataHelper(db);
var viewData = viewDataHelper.FillViewData(1, int.MaxValue);
viewData["sequenceGroupTypes"] = EnumExtensions.ToArray <SequenceGroupType>().ToSelectListWithNature();
ViewBag.data = JsonConvert.SerializeObject(viewData);
return(View());
}
}
public void Create(ImageSequence sequence, LibiadaWebEntities db)
{
if (sequence.Id == default)
{
sequence.Id = db.GetNewElementId();
}
var parameters = new List <NpgsqlParameter>
{
new NpgsqlParameter <long>("id", NpgsqlDbType.Bigint)
{
TypedValue = sequence.Id
},
new NpgsqlParameter <byte>("notation", NpgsqlDbType.Smallint)
{
TypedValue = (byte)sequence.Notation
},
new NpgsqlParameter <long>("matter_id", NpgsqlDbType.Bigint)
{
TypedValue = sequence.MatterId
},
new NpgsqlParameter <byte[]>("image_transformations", NpgsqlDbType.Array | NpgsqlDbType.Smallint)
{
TypedValue = Array.Empty <byte>()
},
new NpgsqlParameter <byte[]>("matrix_transformations", NpgsqlDbType.Array | NpgsqlDbType.Smallint)
{
TypedValue = Array.Empty <byte>()
},
new NpgsqlParameter <byte>("order_extractor", NpgsqlDbType.Smallint)
{
TypedValue = (byte)sequence.OrderExtractor
},
};
const string Query = @"INSERT INTO image_sequence (
id,
notation,
matter_id,
image_transformations,
matrix_transformations,
order_extractor
) VALUES (
@id,
@notation,
@matter_id,
@image_transformations,
@matrix_transformations,
@order_extractor
);";
db.ExecuteCommand(Query, parameters.ToArray());
}
/// <summary>
/// Removes not finished and not started tasks from database
/// on task manager initialization.
/// </summary>
private void RemoveGarbageFromDb()
{
using (var db = new LibiadaWebEntities())
{
var tasksToDelete = db.CalculationTask
.Where(t => t.Status != TaskState.Completed && t.Status != TaskState.Error)
.ToArray();
db.CalculationTask.RemoveRange(tasksToDelete);
db.SaveChanges();
}
}
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 }
};
});
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Index()
{
var db = new LibiadaWebEntities();
var genesSequenceIds = db.Subsequence.Select(s => s.SequenceId).Distinct();
var matterIds = db.DnaSequence.Include(c => c.Matter).Where(c => !string.IsNullOrEmpty(c.RemoteId) &&
!genesSequenceIds.Contains(c.Id) &&
(c.Matter.SequenceType == SequenceType.CompleteGenome
|| c.Matter.SequenceType == SequenceType.MitochondrionGenome
|| c.Matter.SequenceType == SequenceType.Plasmid)).Select(c => c.MatterId).ToList();
var viewDataHelper = new ViewDataHelper(db);
var data = viewDataHelper.GetMattersData(1, 1, m => matterIds.Contains(m.Id), "Import");
data.Add("nature", (byte)Nature.Genetic);
ViewBag.data = JsonConvert.SerializeObject(data);
return View();
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Index()
{
var db = new LibiadaWebEntities();
var viewDataHelper = new ViewDataHelper(db);
Func<CharacteristicType, bool> filter;
if (UserHelper.IsAdmin())
{
filter = c => c.FullSequenceApplicable;
}
else
{
filter = c => c.FullSequenceApplicable && Aliases.UserAvailableCharacteristics.Contains((Aliases.CharacteristicType)c.Id);
}
ViewBag.data = JsonConvert.SerializeObject(viewDataHelper.FillViewData(filter, 1, int.MaxValue, "Calculate"));
return View();
}
/// <summary>
/// The execute custom sql command with parameters.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
/// <param name="query">
/// The query.
/// </param>
/// <param name="parameters">
/// The parameters.
/// </param>
public static void ExecuteCommand(LibiadaWebEntities db, string query, object[] parameters)
{
db.Database.ExecuteSqlCommand(query, parameters);
}
/// <summary>
/// Initializes a new instance of the <see cref="ElementRepository"/> class.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
public ElementRepository(LibiadaWebEntities db)
{
this.db = db;
}
/// <summary>
/// Gets building of sequence by id..
/// </summary>
/// <param name="db">
/// Database connection.
/// </param>
/// <param name="sequenceId">
/// The sequence id.
/// </param>
/// <returns>
/// The <see cref="T:int[]"/>.
/// </returns>
public static int[] GetBuilding(LibiadaWebEntities db, long sequenceId)
{
const string Query = "SELECT unnest(building) FROM chain WHERE id = @id";
return db.Database.SqlQuery<int>(Query, new NpgsqlParameter("@id", sequenceId)).ToArray();
}
/// <summary>
/// Initializes a new instance of the <see cref="SequenceAttributeRepository"/> class.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
public SequenceAttributeRepository(LibiadaWebEntities db)
{
this.db = db;
attributeRepository = new AttributeRepository();
}
public ActionResult Index(long[] matterIds, int characteristicTypeLinkId, int[] characteristicTypeLinkIds, int[] featureIds)
{
return Action(() =>
{
var matterNames = new string[matterIds.Length];
var remoteIds = new string[matterIds.Length];
var subsequencesCharacteristicsNames = new string[characteristicTypeLinkIds.Length];
var calculators = new IFullCalculator[characteristicTypeLinkIds.Length];
var links = new Link[characteristicTypeLinkIds.Length];
var subsequencesCharacteristicsList = new SelectListItem[characteristicTypeLinkIds.Length];
var attributeValues = new List<AttributeValue>();
IEnumerable<SelectListItem> featuresSelectList;
Chain[] chains;
long[] parentSequenceIds;
string sequenceCharacteristicName;
IFullCalculator calculator;
Link link;
using (var db = new LibiadaWebEntities())
{
var featureRepository = new FeatureRepository(db);
featuresSelectList = featureRepository.GetFeaturesById(featureIds).Select(f => new SelectListItem { Value = f.Id.ToString(), Text = f.Name, Selected = true });
var parentSequences = db.DnaSequence.Include(s => s.Matter)
.Where(s => s.NotationId == Aliases.Notation.Nucleotide && matterIds.Contains(s.MatterId))
.Select(s => new { s.Id, MatterName = s.Matter.Name, s.RemoteId })
.ToDictionary(s => s.Id);
parentSequenceIds = parentSequences.Keys.ToArray();
for (int n = 0; n < parentSequenceIds.Length; n++)
{
matterNames[n] = parentSequences[parentSequenceIds[n]].MatterName;
remoteIds[n] = parentSequences[parentSequenceIds[n]].RemoteId;
}
var commonSequenceRepository = new CommonSequenceRepository(db);
chains = commonSequenceRepository.GetNucleotideChains(matterIds);
var characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
sequenceCharacteristicName = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkId);
calculator = CalculatorsFactory.CreateFullCalculator(characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkId).ClassName);
link = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkId);
for (int k = 0; k < characteristicTypeLinkIds.Length; k++)
{
links[k] = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkIds[k]);
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkIds[k]).ClassName;
calculators[k] = CalculatorsFactory.CreateFullCalculator(className);
subsequencesCharacteristicsNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkIds[k]);
subsequencesCharacteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = subsequencesCharacteristicsNames[k],
Selected = false
};
}
}
var characteristics = SequencesCharacteristicsCalculator.Calculate(chains, calculator, link, characteristicTypeLinkId);
var sequenceData = new SequenceData[parentSequenceIds.Length];
for (int i = 0; i < parentSequenceIds.Length; i++)
{
// all subsequence calculations
var subsequencesData = SubsequencesCharacteristicsCalculator.CalculateSubsequencesCharacteristics(
characteristicTypeLinkIds,
featureIds,
parentSequenceIds[i],
calculators,
links,
attributeValues);
sequenceData[i] = new SequenceData(matterIds[i], matterNames[i], remoteIds[i], characteristics[i], subsequencesData);
}
// sorting organisms by their characteristic
sequenceData = sequenceData.OrderBy(r => r.Characteristic).ToArray();
var resultData = new Dictionary<string, object>
{
{ "result", sequenceData },
{ "subsequencesCharacteristicsNames", subsequencesCharacteristicsNames },
{ "subsequencesCharacteristicsList", subsequencesCharacteristicsList },
{ "sequenceCharacteristicName", sequenceCharacteristicName },
{ "features", featuresSelectList.ToDictionary(f => f.Value) },
{ "attributes", EnumExtensions.ToArray<Attribute>().ToDictionary(a => (byte)a, a => a.GetDisplayValue()) },
{ "attributeValues", attributeValues.Select(sa => new { attribute = sa.AttributeId, value = sa.Value }) }
};
return new Dictionary<string, object>
{
{ "data", JsonConvert.SerializeObject(resultData) }
};
});
}
/// <summary>
/// Initializes a new instance of the <see cref="MatterRepository"/> class.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
public MatterRepository(LibiadaWebEntities db)
{
this.db = db;
}
/// <summary>
/// Initializes a new instance of the <see cref="SequenceElementsController"/> class.
/// </summary>
public SequenceElementsController()
{
db = new LibiadaWebEntities();
elementRepository = new ElementRepository(db);
sequenceRepository = new CommonSequenceRepository(db);
}
/// <summary>
/// Initializes a new instance of the <see cref="BuildingsSimilarityController"/> class.
/// </summary>
public BuildingsSimilarityController()
: base("Buildings comparison")
{
db = new LibiadaWebEntities();
sequenceRepository = new CommonSequenceRepository(db);
}
/// <summary>
/// Initializes a new instance of the <see cref="CharacteristicTypeLinkRepository"/> class.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
public CharacteristicTypeLinkRepository(LibiadaWebEntities db)
{
characteristicTypeLinks = db.CharacteristicTypeLink.Include(ctl => ctl.CharacteristicType).Include(ctl => ctl.Link).ToList();
notations = db.Notation.ToList();
}
/// <summary>
/// Initializes a new instance of the <see cref="DataSequenceRepository"/> class.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
public DataSequenceRepository(LibiadaWebEntities db)
: base(db)
{
}
public ActionResult Index(
int[] transformationLinkIds,
int[] transformationIds,
int iterationsCount,
int[] characteristicTypeLinkIds,
string[] customSequences,
bool localFile,
HttpPostedFileBase[] file)
{
return Action(() =>
{
var db = new LibiadaWebEntities();
var characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
int sequencesCount = localFile ? Request.Files.Count : customSequences.Length;
var sequences = new string[sequencesCount];
var names = new string[sequencesCount];
for (int i = 0; i < sequencesCount; i++)
{
if (localFile)
{
var sequenceStream = FileHelper.GetFileStream(file[i]);
var fastaSequence = NcbiHelper.GetFastaSequence(sequenceStream);
sequences[i] = fastaSequence.ConvertToString();
names[i] = fastaSequence.ID;
}
else
{
sequences[i] = customSequences[i];
names[i] = "Custom sequence " + (i + 1) + ". Length: " + customSequences[i].Length;
}
}
var characteristics = new double[sequences.Length, characteristicTypeLinkIds.Length];
for (int j = 0; j < sequences.Length; j++)
{
for (int k = 0; k < characteristicTypeLinkIds.Length; k++)
{
var sequence = new Chain(sequences[j]);
for (int l = 0; l < iterationsCount; l++)
{
for (int w = 0; w < transformationIds.Length; w++)
{
if (transformationIds[w] == 1)
{
sequence = DissimilarChainFactory.Create(sequence);
}
else
{
sequence = HighOrderFactory.Create(sequence, (Link)transformationLinkIds[w]);
}
}
}
var link = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkIds[k]);
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkIds[k]).ClassName;
var calculator = CalculatorsFactory.CreateFullCalculator(className);
characteristics[j, k] = calculator.Calculate(sequence, link);
}
}
var characteristicNames = characteristicTypeLinkIds.Select(c => characteristicTypeLinkRepository.GetCharacteristicName(c)).ToArray();
var characteristicsList = new SelectListItem[characteristicTypeLinkIds.Length];
for (int i = 0; i < characteristicNames.Length; i++)
{
characteristicsList[i] = new SelectListItem
{
Value = i.ToString(),
Text = characteristicNames[i],
Selected = false
};
}
var transformations = new Dictionary<int, string>();
for (int i = 0; i < transformationIds.Length; i++)
{
var link = ((Link)transformationLinkIds[i]).GetDisplayValue();
transformations.Add(i, transformationIds[i] == 1 ? "dissimilar" : "higher order " + link);
}
var result = new Dictionary<string, object>
{
{ "characteristics", characteristics },
{ "characteristicNames", characteristicNames },
{ "characteristicsList", characteristicsList },
{ "transformationsList", transformations },
{ "iterationsCount", iterationsCount }
};
return new Dictionary<string, object>
{
{ "data", JsonConvert.SerializeObject(result) }
};
});
}
/// <summary>
/// Calculation method.
/// </summary>
/// <param name="chains">
/// The chains.
/// </param>
/// <param name="calculator">
/// The calculator.
/// </param>
/// <param name="link">
/// The link.
/// </param>
/// <param name="characteristicTypeLinkId">
/// The characteristic type link id.
/// </param>
/// <returns>
/// The <see cref="T:double[]"/>.
/// </returns>
public static double[] Calculate(Chain[] chains, IFullCalculator calculator, Link link, int characteristicTypeLinkId)
{
var newCharacteristics = new List<Characteristic>();
var characteristics = new double[chains.Length];
var sequenceIds = chains.Select(c => c.Id);
Dictionary<long, double> dbCharacteristics;
using (var db = new LibiadaWebEntities())
{
dbCharacteristics = db.Characteristic
.Where(c => characteristicTypeLinkId == c.CharacteristicTypeLinkId && sequenceIds.Contains(c.SequenceId))
.ToArray()
.GroupBy(c => c.SequenceId)
.ToDictionary(c => c.Key, c => c.Single().Value);
}
for (int i = 0; i < chains.Length; i++)
{
chains[i].FillIntervalManagers();
long sequenceId = chains[i].Id;
if (!dbCharacteristics.TryGetValue(sequenceId, out characteristics[i]))
{
characteristics[i] = calculator.Calculate(chains[i], link);
var currentCharacteristic = new Characteristic
{
SequenceId = sequenceId,
CharacteristicTypeLinkId = characteristicTypeLinkId,
Value = characteristics[i]
};
newCharacteristics.Add(currentCharacteristic);
}
}
// trying to save calculated characteristics to database
using (var db = new LibiadaWebEntities())
{
var characteristicRepository = new CharacteristicRepository(db);
characteristicRepository.TrySaveCharacteristicsToDatabase(newCharacteristics);
}
return characteristics;
}
/// <summary>
/// Initializes a new instance of the <see cref="SequenceImporter"/> class.
/// </summary>
/// <param name="db">
/// The db.
/// </param>
protected SequenceImporter(LibiadaWebEntities db)
{
Db = db;
MatterRepository = new MatterRepository(db);
ElementRepository = new ElementRepository(db);
}
public ActionResult Index(
long[] matterIds,
int[] characteristicTypeLinkIds,
int[] notationIds,
int[] languageIds,
int?[] translatorIds,
bool rotate,
bool complementary,
uint? rotationLength)
{
return Action(() =>
{
var sequencesCharacteristics = new SequenceCharacteristics[matterIds.Length];
var characteristicNames = new string[characteristicTypeLinkIds.Length];
var characteristicsList = new SelectListItem[characteristicTypeLinkIds.Length];
var links = new Link[characteristicTypeLinkIds.Length];
var calculators = new IFullCalculator[characteristicTypeLinkIds.Length];
Dictionary<long, string> mattersNames;
double[][] characteristics;
Chain[][] chains;
using (var db = new LibiadaWebEntities())
{
mattersNames = db.Matter.Where(m => matterIds.Contains(m.Id)).ToDictionary(m => m.Id, m => m.Name);
var commonSequenceRepository = new CommonSequenceRepository(db);
chains = commonSequenceRepository.GetChains(matterIds, notationIds, languageIds, translatorIds);
var characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
for (int k = 0; k < characteristicTypeLinkIds.Length; k++)
{
links[k] = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkIds[k]);
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkIds[k]).ClassName;
calculators[k] = CalculatorsFactory.CreateFullCalculator(className);
characteristicNames[k] = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkIds[k], notationIds[k]);
characteristicsList[k] = new SelectListItem
{
Value = k.ToString(),
Text = characteristicNames[k],
Selected = false
};
}
}
if (!rotate && !complementary)
{
characteristics = SequencesCharacteristicsCalculator.Calculate(chains, calculators, links, characteristicTypeLinkIds);
}
else
{
characteristics = SequencesCharacteristicsCalculator.Calculate(chains, calculators, links, rotate, complementary, rotationLength);
}
for (int i = 0; i < matterIds.Length; i++)
{
sequencesCharacteristics[i] = new SequenceCharacteristics
{
MatterName = mattersNames[matterIds[i]],
Characteristics = characteristics[i]
};
}
var result = new Dictionary<string, object>
{
{ "characteristics", sequencesCharacteristics },
{ "characteristicNames", characteristicNames },
{ "characteristicsList", characteristicsList }
};
return new Dictionary<string, object>
{
{ "data", JsonConvert.SerializeObject(result) }
};
});
}
/// <summary>
/// Initializes a new instance of the <see cref="OrderTransformerController"/> class.
/// </summary>
public OrderTransformerController()
: base("Order transformation")
{
db = new LibiadaWebEntities();
commonSequenceRepository = new CommonSequenceRepository(db);
}
public ActionResult Index(
long[] matterIds,
int characteristicTypeLinkId,
int[] featureIds,
string maxPercentageDifference,
double characteristicValueFrom,
double characteristicValueTo)
{
return Action(() =>
{
Dictionary<int, string> features;
var attributeValues = new List<AttributeValue>();
var characteristics = new SubsequenceData[matterIds.Length][];
string characteristicName;
long[] parentSequenceIds;
var matterNames = new string[matterIds.Length];
IFullCalculator calculator;
Link link;
int mattersCount = matterIds.Length;
int[] subsequencesCount = new int[mattersCount];
using (var db = new LibiadaWebEntities())
{
var featureRepository = new FeatureRepository(db);
features = featureRepository.Features.ToDictionary(f => f.Id, f => f.Name);
var parentSequences = db.DnaSequence.Include(s => s.Matter)
.Where(s => s.NotationId == Aliases.Notation.Nucleotide && matterIds.Contains(s.MatterId))
.Select(s => new { s.Id, MatterName = s.Matter.Name })
.ToDictionary(s => s.Id);
parentSequenceIds = parentSequences.Keys.ToArray();
for (int n = 0; n < parentSequenceIds.Length; n++)
{
matterNames[n] = parentSequences[parentSequenceIds[n]].MatterName;
}
var characteristicTypeLinkRepository = new CharacteristicTypeLinkRepository(db);
characteristicName = characteristicTypeLinkRepository.GetCharacteristicName(characteristicTypeLinkId);
string className = characteristicTypeLinkRepository.GetCharacteristicType(characteristicTypeLinkId).ClassName;
calculator = CalculatorsFactory.CreateFullCalculator(className);
link = characteristicTypeLinkRepository.GetLibiadaLink(characteristicTypeLinkId);
}
// cycle through matters; first level of characteristics array
for (int i = 0; i < parentSequenceIds.Length; i++)
{
var subsequencesData = SubsequencesCharacteristicsCalculator.CalculateSubsequencesCharacteristics(
new[] { characteristicTypeLinkId },
featureIds,
parentSequenceIds[i],
new[] { calculator },
new[] { link },
attributeValues);
subsequencesCount[i] = subsequencesData.Length;
subsequencesData = subsequencesData.Where(c => (characteristicValueFrom == 0 && characteristicValueTo == 0)
|| (c.CharacteristicsValues[0] >= characteristicValueFrom && c.CharacteristicsValues[0] <= characteristicValueTo)).
OrderBy(c => c.CharacteristicsValues[0]).ToArray();
characteristics[i] = subsequencesData;
}
double decimalDifference = double.Parse(maxPercentageDifference, CultureInfo.InvariantCulture) / 100;
var similarities = new object[mattersCount, mattersCount];
var equalElements = new List<SubsequenceComparisonData>();
int comparisonNumber = 0;
for (int i = 0; i < characteristics.Length; i++)
{
for (int j = 0; j < characteristics.Length; j++)
{
comparisonNumber++;
double similarSequencesCharacteristicValueFirst = 0;
var similarSequencesCharacteristicValueSecond = new Dictionary<int, double>();
double similarFirstSequencesCharacteristicValue = 0;
double similarSecondSequencesCharacteristicValue = 0;
int secondArrayStartPosition = 0;
double differenceSum = 0;
int equalElementsCountFromFirst = 0;
var equalElementsCountFromSecond = new Dictionary<int, int>();
bool equalFound = false;
int equalPairsCount = 0;
for (int k = 0; k < characteristics[i].Length; k++)
{
double first = characteristics[i][k].CharacteristicsValues[0];
for (int l = secondArrayStartPosition; l < characteristics[j].Length; l++)
{
double second = characteristics[j][l].CharacteristicsValues[0];
double difference = calculateAverageDifference(first, second);
bool nextElementInSecondArrayIsEqual = false;
if (l < characteristics[j].Length - 1)
{
nextElementInSecondArrayIsEqual = calculateAverageDifference(second, characteristics[j][l + 1].CharacteristicsValues[0]) <= decimalDifference;
}
if (difference <= decimalDifference)
{
equalFound = true;
equalPairsCount++;
if (!equalElementsCountFromSecond.ContainsKey(l))
{
equalElementsCountFromSecond.Add(l, 1);
differenceSum += difference;
}
if (!similarSequencesCharacteristicValueSecond.ContainsKey(l))
{
similarSequencesCharacteristicValueSecond.Add(l, second);
}
if (i != j)
{
equalElements.Add(new SubsequenceComparisonData
{
Difference = difference,
FirstMatterId = i,
SecondMatterId = j,
FirstSubsequenceId = k,
SecondSubsequenceId = l,
});
}
similarFirstSequencesCharacteristicValue += first;
similarSecondSequencesCharacteristicValue += second;
if (!nextElementInSecondArrayIsEqual)
{
break;
}
}
else if (second < first)
{
secondArrayStartPosition++;
}
}
if (equalFound)
{
equalElementsCountFromFirst++;
similarSequencesCharacteristicValueFirst += first;
}
}
double differenceSecondFinal = equalElementsCountFromSecond.Sum(s => s.Value);
double differenceFinal = equalElementsCountFromFirst < differenceSecondFinal ? equalElementsCountFromFirst * 2d : differenceSecondFinal * 2d;
double formula1 = differenceFinal / (subsequencesCount[i] + subsequencesCount[j]);
double formula2 = 0;
if (equalPairsCount != 0 && formula1 != 0)
{
formula2 = (differenceSum / equalPairsCount) / formula1;
}
double similarSequencesCharacteristicValueSecondFinal = similarSequencesCharacteristicValueSecond.Sum(s => s.Value);
double similarSequencesCharacteristicValue = similarSequencesCharacteristicValueFirst < similarSequencesCharacteristicValueSecondFinal ?
similarSequencesCharacteristicValueFirst * 2d : similarSequencesCharacteristicValueSecondFinal * 2d;
double formula3 = similarSequencesCharacteristicValue * 100d / (characteristics[i].Sum(c => c.CharacteristicsValues[0]) + characteristics[j].Sum(c => c.CharacteristicsValues[0]));
similarities[i, j] = new
{
formula1 = Math.Round(formula1 * 100d, 3),
formula2 = Math.Round(formula2, 3),
formula3 = Math.Round(formula3, 3)
};
}
}
var result = new Dictionary<string, object>
{
{ "mattersNames", matterNames },
{ "characteristicName", characteristicName },
{ "similarities", similarities },
{ "characteristics", characteristics },
{ "equalElements", equalElements.OrderBy(e => e.Difference).ToList() },
{ "features", features },
{ "attributeValues", attributeValues.Select(sa => new { attribute = sa.AttributeId, value = sa.Value }) },
{ "attributes", EnumExtensions.ToArray<LibiadaWeb.Attribute>().ToDictionary(a => (byte)a, a => a.GetDisplayValue()) }
};
return new Dictionary<string, object>
{
{ "data", JsonConvert.SerializeObject(result) }
};
});
}
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 }
};
});
}
