private void btnOK_Click(object sender, EventArgs e)
{
string dbname = txtDBName.Text.Trim();
if (AppConfigHelper.seqdbConfig.seqDBs.ContainsKey(dbname)) // This can only be checked after we know the name of the db.
{
if (MessageBox.Show("There is already a database named " + dbname + ". Do you want to replace it?",
"Replace database?", MessageBoxButtons.OKCancel) != DialogResult.OK)
{
return;
}
SeqDB db = AppConfigHelper.seqdbConfig.seqDBs[dbname];
if (db != null && db.DBPath == txtDBPath.Text + "/" + dbname)
{
if (MessageBox.Show("The database path " + db.DBPath + " already exists. Do you want to replace it?",
"Overwrite database?", MessageBoxButtons.OKCancel) != DialogResult.OK)
{
return;
}
}
}
// Update config to reflect selection.
AppConfigHelper.NewDatabase(dbname, txtDBPath.Text.Trim(), chkImportFasta.Checked, txtInputPath.Text.Trim(), txtStandardReferenceGenome.Text.Trim());
}
// Build a new database. Treat the new database as the selected database if all goes well and update config.
// If there is already a database by the specified name, prompt to overwrite.
public BioSeqNewDB()
{
InitializeComponent();
btnOK.Enabled = false;
string dbPath = AppConfigHelper.NewDBPath;
if (string.IsNullOrEmpty(dbPath))
{
SeqDB db = AppConfigHelper.seqdbConfigGlobal.Current();
if (db != null) // Default the new database path to the same as the current db.
{
txtDBPath.Text = AppConfigHelper.GetDirectoryName(AppConfigHelper.NormalizePathToWindows(DirectoryHelper.UnCleanPath(db.DBPath)));
txtDBPath.Text = AppConfigHelper.NormalizePathToLinux(AppConfigHelper.GetDirectoryName(txtDBPath.Text)); // DB path much be on the server.
if (!txtDBPath.Text.StartsWith("["))
{
txtDBPath.Text = "[S]" + txtDBPath.Text;
}
}
}
else
{
txtDBPath.Text = dbPath;
}
txtDBName.Text = AppConfigHelper.NewDBName;
chkImportFasta.Checked = AppConfigHelper.NewDBImportFasta;
txtInputPath.Text = AppConfigHelper.NewDBInputPath;
txtStandardReferenceGenome.Text = AppConfigHelper.NewDBReference;
EnableOK();
}
private void RefreshVersionInformation(SeqDB db)
{
if (!VersionsBusyFlag)
{
VersionsBusyFlag = true;
backgroundWorker_Versions.RunWorkerAsync(db);
}
}
private void backgroundWorker_Versions_RunWorkerCompleted(object sender, System.ComponentModel.RunWorkerCompletedEventArgs e)
{
// Get version info. Version information comes from the global config.
Cursor.Current = Cursors.WaitCursor;
VersionsBusyFlag = false;
txtVersions.Text = (string)e.Result;
lblKipper.Visible = false;
if (txtVersions.Text.Trim().Length > 0)
{
SeqDB db = AppConfigHelper.seqdbConfigGlobal.seqDBs[AppConfigHelper.seqdbConfig.LastDBSelected];
lblKipper.Text = "This backup is stored at " + db.KipperPath + db.KipperFilenamePrefix + ".";
lblKipper.Visible = true;
}
btnRestore.Enabled = txtVersions.Text.Split(new string[] { "\n" }, StringSplitOptions.RemoveEmptyEntries).Length > 2; // Must have at least two backups before restore is meaningful.
Cursor.Current = Cursors.Default;
}
internal static int DeleteDB()
{
SeqDB db = AppConfigHelper.seqdbConfig.Current();
string filename = AppConfigHelper.NormalizePathToWindows(db.DBPath);
if (File.Exists(filename))
{
string path = AppConfigHelper.GetDirectoryName(filename);
Directory.Delete(path, true);
AppConfigHelper.seqdbConfig.seqDBs.Remove(AppConfigHelper.seqdbConfig.LastDBSelected); // Remove all traces of this database.
AppConfigHelper.SaveConfig();
string dbName = AppConfigHelper.seqdbConfig.LastDBSelected;
AppConfigHelper.seqdbConfig.LastDBSelected = AppConfigHelper.CurrentDBName();
// Also update the global config to remove the database.
db = AppConfigHelper.seqdbConfigGlobal.seqDBs[dbName];
AppConfigHelper.seqdbConfigGlobal.seqDBs.Remove(dbName); // Remove all traces of this database.
AppConfigHelper.seqdbConfigGlobal.LastDBSelected = AppConfigHelper.seqdbConfig.LastDBSelected;
if (db.KipperPath != null) // This should be done first because these files might be in the same folder as the one being deleted below.
{
if (Directory.Exists(AppConfigHelper.NormalizePathToWindows(db.KipperPath))) // it could have been deleted if it was already in the same folder as the database itself.
{
DirectoryInfo dir = new DirectoryInfo(AppConfigHelper.NormalizePathToWindows(db.KipperPath));
foreach (FileInfo file in dir.EnumerateFiles(db.KipperFilenamePrefix + "*.*"))
{
if (File.Exists(file.FullName)) // it could have been deleted if it was already in the same folder as the database itself.
{
file.Delete();
}
}
}
}
AppConfigHelper.SaveConfigGlobal();
}
return(0);
}
public static WSLProxyResponse Build_DB(SeqDB db)
{
// eg. ~/seqdb/seqdb build_db -i /data/amrDBinput/organism -o /data/amrDB/hpsuis/hpsuis.fasta
if (db.BuildTreeWildReference.Length > 0)
{
// Also copy the wild to the database folder so it can be used in the future.
if (File.Exists(db.BuildTreeWildReference))
{
db.BuildTreeDomesticReference = AppConfigHelper.GetDirectoryName(AppConfigHelper.NormalizePathToWindows(db.DBPath)) +
"\\" + Path.GetFileName(AppConfigHelper.NormalizePathToWindows(db.BuildTreeWildReference));
File.Copy(db.BuildTreeWildReference, db.BuildTreeDomesticReference, true);
db.BuildTreeWildReference = string.Empty; // No longer need to overload it, now available for its intended purpose.
}
}
if (!Directory.Exists(db.DBPath))
{
Directory.CreateDirectory(db.DBPath);
}
AppConfigHelper.LastCommand = AppConfigHelper.PathToSeqDB() + " build_db -i " + AppConfigHelper.NormalizePathToLinux(db.Build_DBInput) +
" -o " + AppConfigHelper.NormalizePathToLinux(db.DBPath);
return(StandardCallToWSL());
}
private void backgroundWorker_Versions_DoWork(object sender, System.ComponentModel.DoWorkEventArgs e)
{
SeqDB db = (SeqDB)e.Argument;
e.Result = ServiceCallHelper.GetVersions(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig(), DirectoryHelper.CleanPath(db.DBPath));
}
private void cmbSeqDB_SelectedIndexChanged(object sender, EventArgs e)
{
if (cmbSeqDB.SelectedIndex == 0) // empty = none = reset
{
menuStrip1.Enabled = false;
btnDeleteDB.Enabled = false;
txtDB.Text = txtPath.Text = txtVersions.Text = AppConfigHelper.seqdbConfig.LastDBSelected = string.Empty;
lblKipper.Visible = false;
lstSampleIDs.Items.Clear();
chkDetailSamples.Enabled = false;
lstSampleIDs.Enabled = false;
AppConfigHelper.SaveConfig();
}
else if (cmbSeqDB.SelectedIndex == 1) // New
{
BioSeqNewDB frmNewDB = new BioSeqNewDB();
DialogResult rc = frmNewDB.ShowDialog();
if (rc == DialogResult.OK) // then the config has the specs for the new db to select.
{
Cursor.Current = Cursors.WaitCursor;
// If necessary, copy local files to server.
string fastaPath = AppConfigHelper.Build_DBInput();
if (IsServiceClass.IsService && !string.IsNullOrEmpty(fastaPath))
{
if (fastaPath.StartsWith("[L]") || !fastaPath.StartsWith("["))
{
ServiceCallHelper.ResetFastaFolder(AppConfigHelper.LoggedOnUser);
string[] folders = Directory.GetDirectories(DirectoryHelper.CleanPath(fastaPath));
foreach (string folder in folders)
{
string[] files = Directory.GetFiles(folder, "*.fasta", SearchOption.TopDirectoryOnly);
foreach (string file in files)
{
DirectoryHelper.FileCopy("[L]" + file, "[S]" + AppConfigHelper.UserFolder() + "FastaFiles", true);
}
files = Directory.GetFiles(folder, "*.fna", SearchOption.TopDirectoryOnly);
foreach (string file in files)
{
DirectoryHelper.FileCopy("[L]" + file, "[S]" + AppConfigHelper.UserFolder() + "FastaFiles", true);
}
files = Directory.GetFiles(folder, "*.fa", SearchOption.TopDirectoryOnly);
foreach (string file in files)
{
DirectoryHelper.FileCopy("[L]" + file, "[S]" + AppConfigHelper.UserFolder() + "FastaFiles", true);
}
}
}
}
if (!string.IsNullOrEmpty(AppConfigHelper.BuildTreeWildReference())) // This is the standard genome for the new database.
{
// Wherever it is, store it temporarily in the UserFolder.
DirectoryHelper.FileCopy(AppConfigHelper.BuildTreeWildReference(), "[S]" + AppConfigHelper.UserFolder(), true);
}
/////////// Call Build_DB in SeqDB.
try
{
ServiceCallHelper.Build_DB(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
}
catch (Exception ex)
{
Cursor.Current = Cursors.Default;
MessageBox.Show("Error: " + ex.ToString(), "ERROR", MessageBoxButtons.OK);
return;
}
if (AppConfigHelper.LastError.Length > 0)
{
Cursor.Current = Cursors.Default;
MessageBox.Show("Error: " + AppConfigHelper.LastError, "ERROR", MessageBoxButtons.OK);
return;
}
if (string.IsNullOrEmpty(AppConfigHelper.BuildTreeDomesticReference))
{
AppConfigHelper.BuildTreeDomesticReference = AppConfigHelper.BuildTreeWildReference();
AppConfigHelper.SaveConfig();
}
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser);
PopulateDBDropdownAndSelect();
Cursor.Current = Cursors.Default;
}
}
else // a database is selected.
{
Cursor.Current = Cursors.WaitCursor;
AppConfigHelper.seqdbConfig.LastDBSelected = cmbSeqDB.SelectedItem.ToString();
AppConfigHelper.SaveConfig();
menuStrip1.Enabled = true;
btnDeleteDB.Enabled = true;
chkDetailSamples.Enabled = true;
lstSampleIDs.Enabled = true;
txtVersions.Text = string.Empty;
lstSampleIDs.Items.Clear();
SeqDB db = AppConfigHelper.seqdbConfig.seqDBs[AppConfigHelper.seqdbConfig.LastDBSelected];
txtDB.Text = db.DBName;
txtPath.Text = db.DBPath;
AppConfigHelper.LastError = string.Empty;
if (SampleIDsBusyFlag || VersionsBusyFlag)
{
MessageBox.Show("Version information and sample IDs are being loaded for previous database. Please select " +
db.DBName + " again.", "Warning", MessageBoxButtons.OK);
return;
}
// Version information comes from the global config.
RefreshVersionInformation(AppConfigHelper.seqdbConfigGlobal.seqDBs[AppConfigHelper.seqdbConfig.LastDBSelected]);
// Also get sample IDs into listbox.
ReloadSampleIDs();
Cursor.Current = Cursors.Default;
if (AppConfigHelper.LastError.Length > 0)
{
MessageBox.Show("Error: " + AppConfigHelper.LastError, "ERROR", MessageBoxButtons.OK);
}
}
}
