static void Main(string[] args)
{
ObjectFactory.Initialize(x =>
{
x.Scan(y =>
{
y.WithDefaultConventions();
y.LookForRegistries();
//y.AssembliesFromPath(Environment.CurrentDirectory, a => a.FullName.StartsWith("Lending"));
y.AssembliesFromPath(Environment.CurrentDirectory, Blah);
});
});
ObjectFactory.AssertConfigurationIsValid();
string blah = ObjectFactory.WhatDoIHave();
SchemaUpdater.UpdateSchema();
//using (var host = new NancyHost(new Uri("http://localhost:8080")))
//{
// host.Start();
// Console.WriteLine("Nancy has started");
// Console.ReadLine();
//}
var host = new AppHost();
host.Init();
host.Start("http://localhost:8085/");
Console.WriteLine("Listening, GO!");
Console.ReadLine();
}
public void Import(MigrationToolOptions settings)
{
var sourceImportFilePath = Path.Combine(settings.SourceDirectory, "localization-resource-translations.sql");
if (!File.Exists(sourceImportFilePath))
{
throw new IOException($"Import source file '{sourceImportFilePath}' not found!");
}
// create DB structures in target database
var updater = new SchemaUpdater();
updater.Execute(new UpdateSchema.Command());
var fileInfo = new FileInfo(sourceImportFilePath);
var script = fileInfo.OpenText().ReadToEnd();
using (var connection = new SqlConnection(settings.ConnectionString))
{
connection.Open();
using (var command = new SqlCommand(script, connection))
{
command.ExecuteNonQuery();
}
}
}
private void InitializeDb(MigrationToolOptions settings)
{
try
{
var updater = new SchemaUpdater();
updater.Execute(new UpdateSchema.Command());
}
catch
{
// it's OK to have exception here
}
}
// This method gets called by the runtime. Use this method to configure the HTTP request pipeline.
public void Configure(IApplicationBuilder app, IHostingEnvironment env, SchemaUpdater schemaUpdater)
{
if (env.IsDevelopment())
{
app.UseDeveloperExceptionPage();
}
app.UseMvc();
schemaUpdater.UpdateSchema(CancellationToken.None).GetAwaiter().GetResult();
}
public void CanRunMigration()
{
using (var connection = GetDbConnection("TestDb"))
{
var schemaUpdater = new SchemaUpdater
{
Assembly = Assembly.GetExecutingAssembly(),
Namespace = "Cheezburger.SchemaManager.Tests",
Mappings = { new SchemaMapping { Name = "Schema.xml" } }
};
connection.Open();
schemaUpdater.Upgrade(connection, true, Log.Write);
connection.Close();
}
AssertTableExists("Category");
}
public void CanRunMigration()
{
using (var connection = GetDbConnection("TestDb"))
{
var schemaUpdater = new SchemaUpdater
{
Assembly = Assembly.GetExecutingAssembly(),
Namespace = "Cheezburger.SchemaManager.Tests",
Mappings = { new SchemaMapping {
Name = "Schema.xml"
} }
};
connection.Open();
schemaUpdater.Upgrade(connection, true, Log.Write);
connection.Close();
}
AssertTableExists("Category");
}
private void btnOk_Click(object sender, EventArgs e)
{
var settings = Properties.Settings.Default;
settings.DefaultMaxFDR = Convert.ToDouble(maxQValueComboBox.Text) / 100;
settings.DefaultMaxImportFDR = Convert.ToDouble(maxImportFdrComboBox.Text) / 100;
settings.DefaultMinSpectraPerDistinctMatch = Convert.ToInt32(minSpectraPerMatchTextBox.Text);
settings.DefaultMinSpectraPerDistinctPeptide = Convert.ToInt32(minSpectraPerPeptideTextBox.Text);
settings.DefaultMaxPrecursorMzError = maxPrecursorMzToleranceTextBox.Text.Length > 0 ? maxPrecursorMzToleranceTextBox.Text + " " + maxPrecursorMzToleranceUnitsComboBox.SelectedItem.ToString() : String.Empty;
settings.DefaultMaxProteinGroupsPerPeptide = Convert.ToInt32(maxProteinGroupsTextBox.Text);
settings.DefaultMinDistinctPeptides = Convert.ToInt32(minDistinctPeptidesTextBox.Text);
settings.DefaultMinSpectra = Convert.ToInt32(minSpectraTextBox.Text);
settings.DefaultMinAdditionalPeptides = Convert.ToInt32(minAdditionalPeptidesTextBox.Text);
settings.DefaultDecoyPrefix = defaultDecoyPrefixTextBox.Text;
settings.DefaultMaxRank = Convert.ToInt32(maxImportRankTextBox.Text);
settings.DefaultIgnoreUnmappedPeptides = ignoreUnmappedPeptidesCheckBox.Checked;
settings.DefaultGeneLevelFiltering = filterByGeneCheckBox.Checked;
settings.DefaultChargeIsDistinct = chargeIsDistinctCheckBox.Checked;
settings.DefaultAnalysisIsDistinct = analysisIsDistinctCheckBox.Checked;
settings.DefaultModificationsAreDistinct = modificationsAreDistinctCheckbox.Checked;
settings.DefaultModificationRoundToNearest = Convert.ToDecimal(modificationRoundToMassTextBox.Text);
settings.FastaPaths.Clear(); settings.FastaPaths.AddRange(lbFastaPaths.Items.OfType <string>().ToArray());
settings.SourcePaths.Clear(); settings.SourcePaths.AddRange(lbSourcePaths.Items.OfType <string>().ToArray());
settings.SourceExtensions = sourceExtensionsTextBox.Text;
settings.GroupConcatSeparator = groupSeparatorTextBox.Text;
SchemaUpdater.SetGroupConcatSeparator(settings.GroupConcatSeparator);
Properties.GUI.Settings.Default.QuantitationRollupMethod = (QuantitationRollupMethod)(quantitationRollupMethodComboBox.SelectedIndex + 1);
Properties.GUI.Settings.Default.WarnAboutNonFixedDrive = nonFixedDriveWarningCheckBox.Checked;
Properties.GUI.Settings.Default.WarnAboutNoGeneMetadata = embedGeneMetadataWarningCheckBox.Checked;
Properties.GUI.Settings.Default.Save();
settings.Save();
}
public static ISessionFactory CreateSessionFactory (string path, SessionFactoryConfig config)
{
string uncCompatiblePath = Util.GetSQLiteUncCompatiblePath(path);
// update the existing database's schema if necessary, and if updated, recreate the indexes
if (path != ":memory:" &&
File.Exists(path) &&
IsValidFile(path) &&
SchemaUpdater.Update(path, null))
{
using (var conn = new SQLiteConnection(String.Format("Data Source={0};Version=3", uncCompatiblePath)))
{
conn.Open();
conn.ExecuteNonQuery(@"PRAGMA journal_mode=DELETE;
PRAGMA synchronous=OFF;
PRAGMA automatic_indexing=OFF;
PRAGMA cache_size=30000;
PRAGMA temp_store=MEMORY;
PRAGMA page_size=32768;
PRAGMA mmap_size=70368744177664; -- 2^46");
DropIndexes(conn);
CreateIndexes(conn);
}
}
bool pooling = path == ":memory:";
var configuration = new Configuration()
.SetProperty("show_sql", config.WriteSqlToConsoleOut ? "true" : "false")
.SetProperty("dialect", typeof(CustomSQLiteDialect).AssemblyQualifiedName)
.SetProperty("hibernate.cache.use_query_cache", "true")
//.SetProperty("adonet.batch_size", batchSize.ToString())
.SetProperty("connection.connection_string", String.Format("Data Source={0};Version=3;{1}", uncCompatiblePath, (pooling ? "Pooling=True;Max Pool Size=1;" : "")))
.SetProperty("connection.driver_class", typeof(NHibernate.Driver.SQLite20Driver).AssemblyQualifiedName)
.SetProperty("connection.provider", typeof(NHibernate.Connection.DriverConnectionProvider).AssemblyQualifiedName)
.SetProperty("connection.release_mode", "on_close")
;
ConfigureMappings(configuration);
if (config.UseUnfilteredTables)
{
configuration.ClassMappings.Single(o => o.Table.Name == "Protein").Table.Name = "UnfilteredProtein";
configuration.ClassMappings.Single(o => o.Table.Name == "Peptide").Table.Name = "UnfilteredPeptide";
configuration.ClassMappings.Single(o => o.Table.Name == "PeptideInstance").Table.Name = "UnfilteredPeptideInstance";
configuration.ClassMappings.Single(o => o.Table.Name == "PeptideSpectrumMatch").Table.Name = "UnfilteredPeptideSpectrumMatch";
configuration.ClassMappings.Single(o => o.Table.Name == "Spectrum").Table.Name = "UnfilteredSpectrum";
}
ISessionFactory sessionFactory = null;
lock(mutex)
sessionFactory = configuration.BuildSessionFactory();
sessionFactory.OpenStatelessSession().CreateSQLQuery(@"PRAGMA cache_size=10000;
PRAGMA temp_store=MEMORY;
PRAGMA page_size=32768;
PRAGMA mmap_size=70368744177664; -- 2^46").ExecuteUpdate();
if (config.CreateSchema)
CreateFile(path);
return sessionFactory;
}
public void CreateTable_ShouldSucceed_ForNonEmptyTableName()
{
using var schemaUpdater = new SchemaUpdater(new NpgsqlConnection(ConnectionString));
Assert.NotEqual(0, schemaUpdater.CreateTable("testTable"));
}
public TestPostgresUsage(string connectionString)
{
schemaUpdater = new SchemaUpdater(new NpgsqlConnection(connectionString));
}
public OtherTestPostgresUsage(NpgsqlConnection connection)
{
schemaUpdater = new SchemaUpdater(connection);
}
