private void ReadVersion(ISession session)
{
// do we even have a version? 0th-gen protdb doesn't have this.
if (!SqliteOperations.TableExists(session.Connection, @"ProteomeDbSchemaVersion"))
{
_schemaVersionMajor = SCHEMA_VERSION_MAJOR_0; // an ancient, unversioned file
_schemaVersionMinor = SCHEMA_VERSION_MINOR_0; // an ancient, unversioned file
}
else
{
using (IDbCommand cmd2 = session.Connection.CreateCommand())
{
cmd2.CommandText = @"SELECT SchemaVersionMajor FROM ProteomeDbSchemaVersion";
var obj2 = cmd2.ExecuteScalar();
_schemaVersionMajor = Convert.ToInt32(obj2);
}
using (IDbCommand cmd3 = session.Connection.CreateCommand())
{
cmd3.CommandText = @"SELECT SchemaVersionMinor FROM ProteomeDbSchemaVersion";
var obj3 = cmd3.ExecuteScalar();
_schemaVersionMinor = Convert.ToInt32(obj3);
}
}
_schemaVersionMajorAsRead = _schemaVersionMajor;
_schemaVersionMinorAsRead = _schemaVersionMinor;
}
public void ReadScores(SQLiteConnection connection)
{
if (!SqliteOperations.TableExists(connection, @"peptidescores"))
{
return;
}
using (var cmd = new SQLiteCommand(connection))
{
cmd.CommandText =
@"select PeptideModSeq, PrecursorCharge, SourceFile, QValue, PosteriorErrorProbability from peptidescores";
using (var reader = cmd.ExecuteReader())
{
while (reader.Read())
{
var key = Tuple.Create(reader.GetString(0), Convert.ToInt32(reader.GetValue(1)));
var value = Tuple.Create(reader.GetDouble(3), reader.GetDouble(3));
string filename = reader.GetString(2);
IDictionary <string, Tuple <double, double> > values;
if (!_dictionary.TryGetValue(key, out values))
{
values = new Dictionary <string, Tuple <double, double> >();
_dictionary.Add(key, values);
}
values[filename] = value;
}
}
}
}
public string GetDocumentXml()
{
using (var session = new StatelessSessionWithLock(_sessionFactory.OpenStatelessSession(), _databaseLock,
false, CancellationToken.None))
{
if (!SqliteOperations.TableExists(session.Connection, @"DocumentXml"))
{
return(null);
}
using (var cmd = session.Connection.CreateCommand())
{
cmd.CommandText = @"SELECT Xml FROM DocumentXml";
return(Convert.ToString(cmd.ExecuteScalar()));
}
}
}
private readonly bool _isTmp; // We won't hang onto the global session factory if we know we're temporary
private ProteomeDb(String path, CancellationToken cancellationToken, bool isTmp)
{
_schemaVersionMajor = -1; // unknown
_schemaVersionMinor = -1; // unknown
_schemaVersionMajorAsRead = -1; // unknown
_schemaVersionMinorAsRead = -1; // unknown
_isTmp = isTmp;
if (!File.Exists(path))
{
// Do not try to open the file if it does not exist, because that would create a zero byte file.
throw new FileLoadException(String.Format(Resources.ProteomeDb_ProteomeDb_The_file__0__does_not_exist_, path));
}
_databaseResource = DatabaseResource.GetDbResource(path);
CancellationToken = cancellationToken;
using (var session = OpenSession())
{
// Is this even a proper protDB file? (https://skyline.gs.washington.edu/labkey/announcements/home/issues/exceptions/thread.view?rowId=14893)
if (!SqliteOperations.TableExists(session.Connection, @"ProteomeDbProteinName"))
{
throw new FileLoadException(
String.Format(Resources.ProteomeDb_ProteomeDb__0__does_not_appear_to_be_a_valid___protDB__background_proteome_file_, path));
}
// Do we need to update the db to current version?
ReadVersion(session);
}
if (_schemaVersionMajor != SCHEMA_VERSION_MAJOR_CURRENT)
{
throw new FileLoadException(
String.Format(Resources.SessionFactoryFactory_EnsureVersion_Background_proteome_file__0__has_a_format_which_is_newer_than_the_current_software___Please_update_to_the_latest_software_version_and_try_again_,
Path));
}
else if (_schemaVersionMinor < SCHEMA_VERSION_MINOR_CURRENT)
{
using (var session = OpenWriteSession())
{
UpdateSchema(session);
}
}
}
public void TestTableExists()
{
using (var connection = new SQLiteConnection(new SQLiteConnectionStringBuilder
{
DataSource = ":memory:"
}.ToString()))
{
connection.Open();
using (var cmd = connection.CreateCommand())
{
cmd.CommandText = "CREATE TABLE Table1(Id INTEGER)";
cmd.ExecuteNonQuery();
}
using (var cmd = connection.CreateCommand())
{
cmd.CommandText = "CREATE TABLE \"Table With Space\"(Id INTEGER)";
cmd.ExecuteNonQuery();
}
Assert.IsTrue(SqliteOperations.TableExists(connection, "Table1"));
Assert.IsFalse(SqliteOperations.TableExists(connection, "Table2"));
Assert.IsTrue(SqliteOperations.TableExists(connection, "Table With Space"));
Assert.IsFalse(SqliteOperations.TableExists(connection, "Other Table With Space"));
}
}
internal static bool CheckHasSubsequenceTable(IDbConnection connection)
{
return(SqliteOperations.TableExists(connection, @"ProteomeDbSubsequence"));
}
