/// <summary>
/// The fill parameters.
/// </summary>
/// <param name="fmotif">
/// The Fmotif.
/// </param>
/// <param name="alphabet">
/// The alphabet.
/// </param>
/// <param name="building">
/// The building.
/// </param>
/// <returns>
/// The <see cref="List{Object}"/>.
/// </returns>
protected List <NpgsqlParameter> FillParams(Fmotif fmotif, long[] alphabet, int[] building)
{
fmotif.Id = db.GetNewElementId();
var fmotivValue = fmotif.GetHashCode().ToString();
var parameters = new List <NpgsqlParameter>
{
new NpgsqlParameter <long>("id", NpgsqlDbType.Bigint)
{
TypedValue = fmotif.Id
},
new NpgsqlParameter <string>("value", NpgsqlDbType.Varchar)
{
TypedValue = fmotivValue
},
new NpgsqlParameter <byte>("notation", NpgsqlDbType.Smallint)
{
TypedValue = (byte)Notation.FormalMotifs
},
new NpgsqlParameter <long[]>("alphabet", NpgsqlDbType.Array | NpgsqlDbType.Bigint)
{
TypedValue = alphabet
},
new NpgsqlParameter <int[]>("building", NpgsqlDbType.Array | NpgsqlDbType.Integer)
{
TypedValue = building
},
new NpgsqlParameter <byte>("fmotif_type", NpgsqlDbType.Smallint)
{
TypedValue = (byte)fmotif.Type
}
};
return(parameters);
}
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>
/// The fill parameters.
/// </summary>
/// <param name="measure">
/// The measure.
/// </param>
/// <param name="alphabet">
/// The alphabet.
/// </param>
/// <param name="building">
/// The building.
/// </param>
/// <returns>
/// The <see cref="List{Object}"/>.
/// </returns>
protected List <NpgsqlParameter> FillParams(Measure measure, long[] alphabet, int[] building)
{
measure.Id = db.GetNewElementId();
var measureValue = measure.GetHashCode().ToString();
var mode = measure.Attributes.Key.Mode;
var parameters = new List <NpgsqlParameter>
{
new NpgsqlParameter <long>("id", NpgsqlDbType.Bigint)
{
TypedValue = measure.Id
},
new NpgsqlParameter <string>("value", NpgsqlDbType.Varchar)
{
TypedValue = measureValue
},
new NpgsqlParameter <byte>("notation", NpgsqlDbType.Smallint)
{
TypedValue = (byte)Notation.Measures
},
new NpgsqlParameter <long[]>("alphabet", NpgsqlDbType.Array | NpgsqlDbType.Bigint)
{
TypedValue = alphabet
},
new NpgsqlParameter <int[]>("building", NpgsqlDbType.Array | NpgsqlDbType.Integer)
{
TypedValue = building
},
new NpgsqlParameter <int>("beats", NpgsqlDbType.Integer)
{
TypedValue = measure.Attributes.Size.Beats
},
new NpgsqlParameter <int>("beatbase", NpgsqlDbType.Integer)
{
TypedValue = measure.Attributes.Size.BeatBase
},
new NpgsqlParameter <int>("fifths", NpgsqlDbType.Integer)
{
TypedValue = measure.Attributes.Key.Fifths
},
new NpgsqlParameter <bool>("major", NpgsqlDbType.Boolean)
{
TypedValue = (mode.Equals("major") || mode.Equals(null))
}
};
return(parameters);
}
/// <summary>
/// The fill parameters.
/// </summary>
/// <param name="commonSequence">
/// The sequence.
/// </param>
/// <param name="alphabet">
/// The alphabet.
/// </param>
/// <param name="building">
/// The building.
/// </param>
/// <returns>
/// The <see cref="List{Object}"/>.
/// </returns>
protected List <NpgsqlParameter> FillParams(CommonSequence commonSequence, long[] alphabet, int[] building)
{
if (commonSequence.Id == default)
{
commonSequence.Id = Db.GetNewElementId();
}
var parameters = new List <NpgsqlParameter>
{
new NpgsqlParameter <long>("id", NpgsqlDbType.Bigint)
{
TypedValue = commonSequence.Id
},
new NpgsqlParameter <byte>("notation", NpgsqlDbType.Smallint)
{
TypedValue = (byte)commonSequence.Notation
},
new NpgsqlParameter <long>("matter_id", NpgsqlDbType.Bigint)
{
TypedValue = commonSequence.MatterId
},
new NpgsqlParameter <long[]>("alphabet", NpgsqlDbType.Array | NpgsqlDbType.Bigint)
{
TypedValue = alphabet
},
new NpgsqlParameter <int[]>("building", NpgsqlDbType.Array | NpgsqlDbType.Integer)
{
TypedValue = building
},
new NpgsqlParameter <string>("remote_id", NpgsqlDbType.Varchar)
{
TypedValue = commonSequence.RemoteId
},
new NpgsqlParameter("remote_db", NpgsqlDbType.Smallint)
{
Value = (object)((byte?)commonSequence.RemoteDb) ?? DBNull.Value
},
};
return(parameters);
}
/// <summary>
/// The index.
/// </summary>
/// <returns>
/// The <see cref="ActionResult"/>.
/// </returns>
public ActionResult Index()
{
using (var db = new LibiadaWebEntities())
{
var matterRepository = new MatterRepository(db);
var dnaSequenceRepository = new GeneticSequenceRepository(db);
var commonSequenceRepository = new CommonSequenceRepository(db);
var elementRepository = new ElementRepository(db);
var matterIds = new long[] { 1332, 1333, 1339, 1330, 1337, 1342, 1331, 1338, 1340, 1943, 1945, 1334 };
DnaSequence[] sequences = db.DnaSequence.Include(d => d.Matter).Where(d => matterIds.Contains(d.MatterId)).ToArray();
for (int i = 0; i < sequences.Length; i++)
{
var newMatter = new Matter
{
Name = $"{sequences[i].Matter.Name} Cleaned of IS110",
Description = sequences[i].Matter.Description,
Nature = sequences[i].Matter.Nature,
Group = sequences[i].Matter.Group,
SequenceType = sequences[i].Matter.SequenceType
};
var newSequence = new CommonSequence
{
Notation = sequences[i].Notation,
Matter = newMatter,
Description = sequences[i].Description,
RemoteDb = sequences[i].RemoteDb,
RemoteId = sequences[i].RemoteId
};
var chain = commonSequenceRepository.GetLibiadaChain(sequences[i].Id);
matterRepository.CreateOrExtractExistingMatterForSequence(newSequence);
dnaSequenceRepository.Create(newSequence, false, elementRepository.ToDbElements(chain.Alphabet, Notation.Nucleotides, false), chain.Building);
var sequenceId = sequences[i].Id;
var subsequences = db.Subsequence.Include(s => s.Position).Include(s => s.SequenceAttribute).Where(s => s.SequenceId == sequenceId).ToList();
var subsequenceIds = subsequences.Select(s => s.Id);
var subsequencesIdsToRemove = db.SequenceAttribute
.Where(sa => subsequenceIds.Contains(sa.SequenceId) && sa.Value.Contains("IS110"))
.Select(sa => sa.SequenceId)
.Distinct()
.ToArray();
subsequences.RemoveAll(s => subsequencesIdsToRemove.Contains(s.Id));
var newSubsequences = new Subsequence[subsequences.Count];
var newSequenceAttributes = new List <SequenceAttribute>();
var newPositions = new List <Position>();
for (int j = 0; j < subsequences.Count; j++)
{
newSubsequences[j] = new Subsequence
{
Id = db.GetNewElementId(),
Feature = subsequences[j].Feature,
SequenceId = newSequence.Id,
Start = subsequences[j].Start,
Length = subsequences[j].Length,
RemoteId = subsequences[j].RemoteId,
Partial = subsequences[j].Partial
};
foreach (SequenceAttribute subsequenceAttribute in subsequences[j].SequenceAttribute.ToArray())
{
newSequenceAttributes.Add(new SequenceAttribute
{
SequenceId = newSubsequences[j].Id,
Attribute = subsequenceAttribute.Attribute,
Value = subsequenceAttribute.Value
});
}
foreach (Position position in subsequences[j].Position.ToArray())
{
newPositions.Add(new Position
{
SubsequenceId = newSubsequences[j].Id,
Length = position.Length,
Start = position.Start
});
}
}
db.Subsequence.AddRange(newSubsequences);
db.SequenceAttribute.AddRange(newSequenceAttributes);
db.Position.AddRange(newPositions);
db.SaveChanges();
}
}
return(View());
}