public static void TestConnection(AppWorking f, bool alertUser, bool addToServers)
{
var server = f.textBox4.Text;// "localhost";
var db = (string)(f.comboBoxDatabases.SelectedItem);
var uid = f.textBoxUsername.Text;
var pwd = f.textBoxPassword.Text;
AppWorking.TestConnection(f, server, db, uid, pwd, alertUser, addToServers);
}
private void bgw_RunWorkerCompleted_SQLBlast(object sender, RunWorkerCompletedEventArgs e)
{
var backgroundWorker = (BackgroundWorker)sender;
if (this._loadingForm == null)
return;
this._loadingForm.Close();
if (!this._loadingForm.IsProgressComplete())
{
this._loadingForm = null;
return;
}
this._loadingForm = null;
if (!backgroundWorker.CancellationPending)
this.LocalBlast(true);
}
//Background Blast Worker
void bgw_RunWorkerCompleted_LocalBlast(object sender, RunWorkerCompletedEventArgs e)
{
var backgroundWorker = (BackgroundWorker)sender;
if (backgroundWorker.CancellationPending)
return;
if (this._loadingForm == null)
return;
this._loadingForm.Close();
if (this._loadingForm == null)
return;
if (!this._loadingForm.IsProgressComplete())
{
this._loadingForm = null;
return;
}
this._loadingForm = null;
var dbp = Program.LocalDatabaseDirectory;// this.textBoxLBDWD.Text;
var outBlastFilePath = dbp + @"~tempBlast.txt";
var b = File.Exists(outBlastFilePath);
var tt = Management.GetTextFromFile(outBlastFilePath);
this.richTextBoxLocalBlast.Lines = tt;
this.BlastSplitContainer.Panel2.Enabled = true;
//this.Show();
//this.Invalidate();
}
//Setters
public void ClearLoadingForm()
{
this._loadingForm = null;
}
private void toolStripButton1_Click(object sender, EventArgs e)
{
var bgw = new BackgroundWorker();
//if (tt == "Local")
// bgw.DoWork += bgw_DoWork_LocalBlast;
//else if (tt == "URL")
// bgw.DoWork += bgw_DoWork_LocalBlast;
//else
//{
// MessageBox.Show("Invalid blast source.", "Error");
// return;
//}
//bgw.RunWorkerCompleted += bgw_RunWorkerCompleted_LocalBlast;
this._loadingForm = new AppWorking(AppWorking.Type.LoadMySQLDatabase, "Provide the information below to connect to a SQL database.", this, bgw);
this.Enabled = false;
return;
/*SqlConnection myConnection = new SqlConnection("user id=root;" +
"password=rjw30181;server=localhost:3306;" +
"Trusted_Connection=yes;" +
"database=main; " +
"connection timeout=3");*/
var cs = "uid = admin;" +
"pwd = bios455;" +
"server = 127.0.0.1;" +
"database = localhost; " +
"connection timeout = 3";
//Server=myServerAddress;Port=1234;Database=myDataBase;Uid=myUsername;
//Pwd = myPassword;
var server = "localhost";// "localhost";
var database = "arcogs";
var uid = "admin";
var password = "******";
var connectionString = "server=" + server + ";" + "database=" +
database + ";" + "userid=" + uid + ";" + "password="******";" +
"Connection Timeout=3";
var sc = new MySqlConnection(connectionString);
while (true)
{
var os = "";
try
{
using (sc)
{
sc.Open();
os += "ServerVersion: " + sc.ServerVersion + "\n";
os += "Database: " + sc.Database;
}
}
catch (Exception ex)
{
MessageBox.Show("The connection to the database has timed out with the given parameters.\n\n" + ex.ToString(), this.Text);
break;
}
MessageBox.Show("User " + uid + " successfully connected to databse " + database + " on server " + server + ".\n\n" + os, this.Text);
this.AppSQL.AddDatabase(uid, password, server, database);
break;
}
try
{
sc.Close();
}
catch (Exception ex)
{
MessageBox.Show("The connection to the database was unable to succesfully close.\n\n" + ex.ToString(), this.Text);
}
return;
}
private bool SQLBlast(bool perform)
{
var db = (string)this.listBoxBlastSQLDB.SelectedItem;
var table = (string)this.listBoxBlastSQLTable.SelectedItem;
if (db == null || db == "" || table == null || table == "")
{
if (this.listBoxBlastSQLDB.Items.Count == 0)
MessageBox.Show("A database containing a fasta table is required.", this.TitleText + " - Error");
else
MessageBox.Show("Invalid database query parameters.", this.TitleText + " - Error");
return false;
}
if (!this.LocalBlast(false))
return false;
if (!perform)
return true;
//Create the loading form, which runs the blast in the background.
var bgw = new BackgroundWorker();
Program.SelectedDatabase = db;
Program.SelectedTable = table;
bgw.DoWork += bgw_DoWork_SQLBlast;
bgw.RunWorkerCompleted += bgw_RunWorkerCompleted_SQLBlast;
this._loadingForm = new AppWorking("Downloading SQL database for local blast...", this, bgw);
this._loadingForm.RunWorker();
this.Enabled = false;
return true;
//var cols = this.AppSQL.GetColumnsInTable
}
private bool LocalBlast(bool perform)
{
var filePath = this.textBoxLBDFP.Text;
var databasePath = this.textBoxLBDWD.Text;
var exePath = this.textBoxLBEXED.Text;
var outBlastFilePath = databasePath + @"~tempLocalBlast.txt";
this.pictureBox1.Image = null;
this.pictureBox2.Image = null;
this.pictureBox3.Image = null;
this.pictureBox4.Image = null;
this.richTextBoxLocalBlast.Text = "";
this.BlastSplitContainer.Panel2.Enabled = false;
if (!File.Exists(filePath))
{
this.pictureBox1.Image = ((System.Drawing.Image)
(new System.ComponentModel.ComponentResourceManager(typeof(AppForm)).GetObject("pictureBox2.Image")));
MessageBox.Show("Invalid sequence file path for database construction.", this.TitleText + " - Error");
return false;
}
else
this.pictureBox1.Image = ((System.Drawing.Image)
(new System.ComponentModel.ComponentResourceManager(typeof(AppForm)).GetObject("pictureBox1.Image")));
if (!Directory.Exists(databasePath))
{
this.pictureBox2.Image = ((System.Drawing.Image)
(new System.ComponentModel.ComponentResourceManager(typeof(AppForm)).GetObject("pictureBox2.Image")));
MessageBox.Show("Invalid path for local blast database.", this.TitleText + " - Error");
return false;
}
else
this.pictureBox2.Image = ((System.Drawing.Image)
(new System.ComponentModel.ComponentResourceManager(typeof(AppForm)).GetObject("pictureBox1.Image")));
if (!Directory.Exists(exePath) || !File.Exists(exePath + @"\makeblastdb.exe"))
{
this.pictureBox4.Image = ((System.Drawing.Image)
(new System.ComponentModel.ComponentResourceManager(typeof(AppForm)).GetObject("pictureBox2.Image")));
MessageBox.Show("Invalid path for NCBI executables.", this.TitleText + " - Error");
return false;
}
else
this.pictureBox4.Image = ((System.Drawing.Image)
(new System.ComponentModel.ComponentResourceManager(typeof(AppForm)).GetObject("pictureBox1.Image")));
if (this.textBoxBlastSeq.Text == "")
{
this.pictureBox3.Image = ((System.Drawing.Image)
(new System.ComponentModel.ComponentResourceManager(typeof(AppForm)).GetObject("pictureBox2.Image")));
MessageBox.Show("Invalid sequence for blast.", this.TitleText + " - Error");
return false;
}
else
this.pictureBox3.Image = ((System.Drawing.Image)
(new System.ComponentModel.ComponentResourceManager(typeof(AppForm)).GetObject("pictureBox1.Image")));
if (File.Exists(outBlastFilePath))
File.Delete(outBlastFilePath);
var t = this.toolStripBlastButton.Text.Split(' ');
var tt = t[t.Length - 1];
/*if (tt == "Local")
else if (tt == "URL")
bgw.DoWork += bgw_DoWork_LocalBlast;
else
{
MessageBox.Show("Invalid blast source.", "Error");
return false;
}*/
if (!perform)
return true;
//Create the loading form, which runs the blast in the background.
if (tt == "SQL")
tt = "local " + tt;
tt = tt.Replace("Local", "local");
var bgw = new BackgroundWorker();
bgw.DoWork += bgw_DoWork_LocalBlast;
bgw.RunWorkerCompleted += bgw_RunWorkerCompleted_LocalBlast;
this._loadingForm = new AppWorking("Performing " + tt + " blast...", this, bgw);
this._loadingForm.RunWorker();
this.Enabled = false;
return true;
}
public List<List<string>> GetRowsInTable(string dbName, string tableName, string queryField, string queryValue, AppWorking appW)
{
//SELECT * FROM pet WHERE species = 'snake' OR species = 'bird';
var tr = -1.0;
if (appW != null)
tr = this.GetTotalRowsInTable(dbName, tableName) - 1;
//Get SQL Columns and verify a fasta and sequence columne exist for blasting
string connection = this._dbStringMap[dbName].GetConnectionString();
List<List<string>> t = new List<List<string>>();
t.Add(new List<string>());
using (var con = new MySqlConnection(connection))
{
var x = "";
if (queryField != null && queryValue != null)
x = " WHERE \"" + queryField + "\" = " + queryValue;
string com = "SELECT * FROM " + tableName + x + ";";
using (var schemaCommand = new MySqlCommand(com, con))
{
con.Open();
using (var reader = schemaCommand.ExecuteReader())
{
var tc = 0;
while (reader.Read())
{
tc++;
for (int i = 0; i < reader.FieldCount; i++)
{
var ti = reader.GetValue(i);
var s = ti.ToString();
if (s.ToLower().Contains("system.byte[]"))
{
var tb = (byte[])ti;
s = "";
for (int j = 0; j < tb.Length; j++)
s += Convert.ToChar(tb[j]);
}
bool newLine = false;
if (s.Length > 0 && s.Substring(s.Length - 1, 1) == "\r")
{
newLine = true;
s = s.Substring(0, s.Length - 1);
}
t[t.Count - 1].Add(s);
if (newLine)
t.Add(new List<string>());
}
if (appW != null)
appW.AddProgressPercent(null, 1.0 / tr);
}
}
}
}
//var r = new List<string>();
//if (nameOnly)
//for (int i = 0; i < Columnnames.Count; i += 6)
// r.Add(Columnnames[i]);
//else
// for (int i = 0; i < t.Count; i++)
// r.Add(t[i]);
for (int i = 0; i < t.Count; i++)
{
if (t[i].Count == 0)
{
t.RemoveAt(i);
i--;
}
}
return t;
}
public List<List<string>> GetRowsInTable(string dbName, string tableName, AppWorking appW)
{
return this.GetRowsInTable(dbName, tableName, null, null, appW);
}
private static void TestConnection(AppWorking f, string server, string db, string uid, string pwd, bool alertUser, bool addToServers)
{
var outpt = f.parent.AppSQL.TestConnection(server, db, uid, pwd, addToServers);
if (outpt == null && alertUser)
{
MessageBox.Show("The connection to the database could not be made with given parameters.\n\n",
f.parent.TitleText + " - Test Connection Fail");
return;
}
if (alertUser)
MessageBox.Show(outpt, f.parent.TitleText + " - Test Connection Success");
return;
/*
var connectionString = "server=" + server + ";" + "database=" +
db + ";" + "userid=" + uid + ";" + "password="******";" +
"Connection Timeout=3";
var sqlConnection = new MySqlConnection(connectionString);
while (true)
{
var os = "";
try
{
using (sqlConnection)
{
sqlConnection.Open();
os += "User:\t\t" + uid + "\n";
if (sqlConnection.Database == "")
db = "(none selected)";
os += "Database:\t\t" + db + "\n";
os += "Server:\t\t" + server + "\n";
os += "ServerVersion:\t" + sqlConnection.ServerVersion + "\n";
}
}
catch (Exception ex)
{
if (alertUser)
MessageBox.Show("The connection to the database could not be made.\n\n" + ex.ToString(),
f.parent.TitleText + " - Test Connection Fail");
break;
}
f.tempConnectString = connectionString;
if (addToServers)
{
if (db != "(none selected)")
{
if (addToServers)
f.parent.AppSQL.AddDatabase(uid, pwd, server, db);
if (alertUser)
MessageBox.Show("Database added successfully.\n\n" + os, f.parent.TitleText + " - Database Added");
f.Close();
}
else
{
if (alertUser)
MessageBox.Show("Select database to add",f.parent.TitleText);
}
}
else
{
if (alertUser)
MessageBox.Show("User " + uid + " successfully connected to database " + db + " on server " + server + ".\n\n" + os,
f.parent.TitleText + " - Test Connection Success");
}
break;
}
try
{
sqlConnection.Close();
}
catch (Exception ex)
{
if (alertUser)
MessageBox.Show("The connection to the database was unable to succesfully close.\n\n" + ex.ToString(), f.Text);
}
return;*/
}
