private void mnuRemove_Click(object sender, EventArgs e)
{
BioSeqRemove frm = new BioSeqRemove();
DialogResult rc = frm.ShowDialog();
if (rc == DialogResult.OK) // then the config has the specs
{
Cursor.Current = Cursors.WaitCursor;
//int ret = SeqDBHelper.RemoveSample(); // Parameters are in appsettings.
WSLProxyResponse WSLResponse = ServiceCallHelper.RemoveSample(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()); // Parameters are in appsettings.
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser); // To retrieve StandardOutput and LastError.
Cursor.Current = Cursors.Default;
if (WSLResponse.ExitCode == 0)
{
MessageBox.Show(AppConfigHelper.RemoveSampleID() + " successfully removed.", "Success", MessageBoxButtons.OK);
AppConfigHelper.RemoveSample(string.Empty); // So we don't prompt for it again.
ReloadSampleIDs(); // Reload list without sample ID.
}
else
{
MessageBox.Show("Remove completed with error code " + WSLResponse.ExitCode.ToString() + "." + Environment.NewLine + Environment.NewLine +
AppConfigHelper.StandardOutput + Environment.NewLine + AppConfigHelper.LastError, "Error", MessageBoxButtons.OK);
}
}
}
private string LIMSListKey; // Current LIMSList selection.
public BioSeqLIMSEdit()
{
InitializeComponent();
btnOK.Enabled = false;
btnApply.Enabled = false;
Cursor.Current = Cursors.WaitCursor;
LIMSBaseList = ServiceCallHelper.ReadLIMSData(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
LIMSList = new Dictionary <string, string>();
foreach (string key in LIMSBaseList.Keys)
{
LIMSList.Add(LIMSBaseList[key], key);
}
lstSampleIDs.Items.Clear();
lstSampleIDs.Items.AddRange(ServiceCallHelper.SampleIDs(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()).ToArray());
if (lstSampleIDs.Items.Count > 0)
{
lstSampleIDs.SetSelected(0, true);
lstSampleIDs.ItemCheck -= lstSampleIDs_ItemCheck;
for (int i = 0; i < lstSampleIDs.Items.Count; i++)
{
lstSampleIDs.SetItemChecked(i, LIMSList.ContainsKey(lstSampleIDs.Items[i].ToString()));
}
lstSampleIDs.ItemCheck += lstSampleIDs_ItemCheck;
}
Cursor.Current = Cursors.Default;
}
private bool ValidFastqFiles(string path, bool IsServerPath)
{
int fCount = ServiceCallHelper.TraverseTree(path, IsServerPath, "fastq");
if (fCount == 0)
{
MessageBox.Show("There are no *.fastq files in the " + path + " folder.", "Wrong folder", MessageBoxButtons.OK);
return(false);
}
// Make sure it is not already in the list.
List <string> querySamples = new List <string>();
for (int i = 0; i < lstSamples.Items.Count; i++)
{
querySamples.Add(lstSamples.Items[i].ToString());
}
if (querySamples.Contains(path))
{
MessageBox.Show(path + " has already been selected.", "Duplicate selection", MessageBoxButtons.OK);
return(false);
}
lstSamples.SetItemChecked(lstSamples.Items.Add(path), true);
EnableOK();
return(true);
}
private int ValidFastaFiles(string root, bool IsServerPath)
{
if (!DirectoryHelper.DirectoryExists(root))
{
MessageBox.Show("The " + root + " folder does not exist.", "Wrong folder", MessageBoxButtons.OK);
return(0);
}
string[] subDirs = DirectoryHelper.GetDirectories(root);
int fCount = 0;
foreach (string subfolderName in subDirs)
{
fCount += ServiceCallHelper.TraverseTree(subfolderName, IsServerPath, "fasta");
}
if (fCount == 0)
{
MessageBox.Show("There are no *.fasta files in the sub-folders of the " + root + " folder.", "Wrong folder", MessageBoxButtons.OK);
return(fCount);
}
EnableOK();
return(fCount);
}
private void backgroundWorker_DoWork(object sender, System.ComponentModel.DoWorkEventArgs e)
{
BioSeqTask task = AppConfigHelper.TaskOfID(AppConfigHelper.LastTaskID);
WSLProxyResponse WSLResponse = null;
switch (task.TaskType)
{
case "Centrifuge":
WSLResponse = ServiceCallHelper.Centrifuge(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Salmonella":
WSLResponse = ServiceCallHelper.Salmonella(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "VFabricate":
WSLResponse = ServiceCallHelper.VFabricate(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Search":
WSLResponse = ServiceCallHelper.SearchSample(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Kraken2":
WSLResponse = ServiceCallHelper.Kraken2(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Quast":
WSLResponse = ServiceCallHelper.Quast(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "BBMap":
WSLResponse = ServiceCallHelper.BBMap(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "BuildTree":
WSLResponse = ServiceCallHelper.BuildTree(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Assemble":
WSLResponse = ServiceCallHelper.Assemble(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig(), AppConfigHelper.QuerySampleConfig());
break;
case "InfluenzaA":
WSLResponse = ServiceCallHelper.InfluenzaA(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Nextstrain":
WSLResponse = ServiceCallHelper.Nextstrain(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
}
task.LastError = WSLResponse.StandardError;
task.StandardOutput = WSLResponse.StandardOutput;
e.Result = new List <object>()
{
WSLResponse.ExitCode, task
};
}
private void btnApply_Click(object sender, EventArgs e)
{
// Copy LIMSList to LIMSBaseList and write to <dbname>_LIMS.fasta.
//LIMSBaseList = LIMSList.ToDictionary(entry => entry.Key, entry => entry.Value);
LIMSBaseList = new Dictionary <string, string>();
foreach (string key in LIMSList.Keys)
{
LIMSBaseList.Add(LIMSList[key], key);
}
ServiceCallHelper.WriteLIMSData(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig(), LIMSBaseList);
btnApply.Enabled = btnOK.Enabled = AnyChanges(); // There should not be any.
lstSampleIDs.ItemCheck -= lstSampleIDs_ItemCheck;
lstSampleIDs.SetItemChecked(lstSampleIDs.SelectedIndex, true);
lstSampleIDs.ItemCheck += lstSampleIDs_ItemCheck;
}
private string GetCentrifugeDBName()
{
string lblCentrifugeDBName = "Centrifuge database name: ";
if (!string.IsNullOrEmpty(txtCentrifugePath.Text.Trim()))
{
string centrifugeDBName = ServiceCallHelper.CentrifugeDatabaseName(txtCentrifugePath.Text);
if (!string.IsNullOrEmpty(centrifugeDBName))
{
lblCentrifugeDBName += centrifugeDBName;
}
else
{
lblCentrifugeDBName = txtCentrifugePath.Text + " is not a valid Centrifuge database path.";
}
}
return(lblCentrifugeDBName);
}
private void mnuInsert_Click(object sender, EventArgs e)
{
BioSeqInsert frm = new BioSeqInsert(lstSampleIDs.Items);
DialogResult rc = frm.ShowDialog();
if (rc == DialogResult.OK) // then the config has the specs
{
Cursor.Current = Cursors.WaitCursor;
int ret;
string function = "Replace";
// If the InsertInputPath is local, copy it to UserFolder on the server.
if (AppConfigHelper.InsertInputPath().StartsWith("[L]"))
{
DirectoryHelper.FileCopy(AppConfigHelper.InsertInputPath(), "[S]" + AppConfigHelper.UserFolder(), true);
}
WSLProxyResponse WSLResponse;
if (AppConfigHelper.InsertSampleReplace)
{
WSLResponse = ServiceCallHelper.ReplaceSample(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()); // Parameters are in appsettings.
}
else // Go ahead without prompting.
{
function = "Insert";
WSLResponse = ServiceCallHelper.InsertSample(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()); // Parameters are in appsettings.
}
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser); // To retrieve StandardOutput and LastError.
Cursor.Current = Cursors.Default;
if (WSLResponse.ExitCode == 0)
{
MessageBox.Show(AppConfigHelper.StandardOutput + Environment.NewLine + function + " completed successfully.", "Success", MessageBoxButtons.OK);
ReloadSampleIDs(); // Reload list with new sample ID.
}
else
{
MessageBox.Show(function + " completed with error code " + WSLResponse.ExitCode.ToString() + "." + Environment.NewLine + Environment.NewLine +
AppConfigHelper.StandardOutput + Environment.NewLine + AppConfigHelper.LastError, "Error", MessageBoxButtons.OK);
}
}
}
private static void InitConfig()
{
ServiceCallHelper.LoadConfig(string.Empty); // Loads the global appsettings.json.
//// Start by copying the local copy of <loggedOnUser>_appsettings.json to the server.
//DirectoryHelper.FileCopy("[L]" + AppConfigHelper.executablePath + "\\" + AppConfigHelper.LoggedOnUser + "_appsettings.json",
// "[S]" + AppConfigHelper.PathToServerAppsettings, true);
if (!IsServiceClass.IsService)
{
if (!File.Exists(DirectoryHelper.CleanPath(AppConfigHelper.NormalizePathToWindows(AppConfigHelper.PathToWSL()))))
{
// Learned that wsl.exe cannot run from \Windows\System32 (file not found).
MessageBox.Show(DirectoryHelper.CleanPath(AppConfigHelper.PathToWSL()) + " (" +
DirectoryHelper.CleanPath(AppConfigHelper.NormalizePathToWindows(AppConfigHelper.PathToWSL())) +
") does not exist. Correct PathToWSL in appsettings.json before continuing.", "ERROR", MessageBoxButtons.OK);
}
string path = DirectoryHelper.CleanPath(AppConfigHelper.NormalizePathToWindows(AppConfigHelper.PathToSeqDB()));
if (!File.Exists(path))
{
// Learned that although Ubuntu prefix is \\wsl on my machine, it is \\wsl$ on WIMMER.
MessageBox.Show(DirectoryHelper.CleanPath(AppConfigHelper.PathToSeqDB()) + " (" +
DirectoryHelper.CleanPath(AppConfigHelper.NormalizePathToWindows(AppConfigHelper.PathToSeqDB())) +
") does not exist. " + Environment.NewLine + "Correct PathToSeqDB in appsettings.json before continuing, or" +
Environment.NewLine + "issue 'wsl --shutdown' in PowerShell.", "ERROR", MessageBoxButtons.OK);
}
}
else // IsService
{
try
{
AppConfigHelper.seqdbConfigGlobal.ServerDriveList = ServiceCallHelper.DriveList();
ServiceCallHelper.SaveConfigGlobal();
}
catch (Exception ex)
{
MessageBox.Show("Unable to obtain the drive list from the server." + Environment.NewLine + ex.ToString(), "ERROR", MessageBoxButtons.OK);
}
}
}
private void mnuRestore_Click(object sender, EventArgs e)
{
BioSeqRestore frm = new BioSeqRestore(txtVersions.Text.Trim());
DialogResult rc = frm.ShowDialog();
if (rc == DialogResult.OK) // then the config has the specs
{
Cursor.Current = Cursors.WaitCursor;
WSLProxyResponse WSLResponse = ServiceCallHelper.RestoreDatabase(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()); // Parameters are in appsettings.
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser); // To retrieve StandardOutput and LastError.
Cursor.Current = Cursors.Default;
if (WSLResponse.ExitCode == 0)
{
ReloadSampleIDs(); // Reload list without sample ID.
MessageBox.Show(AppConfigHelper.StandardOutput + Environment.NewLine + "Restore successfully completed.", "Success", MessageBoxButtons.OK);
}
else
{
MessageBox.Show("Restore completed with error code " + WSLResponse.ExitCode.ToString() + "." + Environment.NewLine + Environment.NewLine +
AppConfigHelper.StandardOutput + Environment.NewLine + AppConfigHelper.LastError, "Error", MessageBoxButtons.OK);
}
}
}
private void btnDeleteDB_Click(object sender, EventArgs e)
{
// Delete the currently selected database and associated archive database.
ConfirmDBDelete.MainInstruction = "You are about to completely delete " + txtDB.Text + " in " + txtPath.Text;
if (txtVersions.Text.Length > 0)
{
ConfirmDBDelete.MainInstruction = ConfirmDBDelete.MainInstruction + ", as well as the associated archival database";
}
ConfirmDBDelete.MainInstruction = ConfirmDBDelete.MainInstruction + ". Do you want to continue?";
TaskDialogButton button = ConfirmDBDelete.ShowDialog(this);
if (button == btnDeleteDBNo)
{
return;
}
Cursor.Current = Cursors.WaitCursor;
int rc = ServiceCallHelper.DeleteDB(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
if (rc == 0)
{
MessageBox.Show("Database successfully deleted.", "Success", MessageBoxButtons.OK);
}
else
{
MessageBox.Show("Failed to delete database. Error code " + rc.ToString(), "ERROR", MessageBoxButtons.OK);
}
cmbUser.SelectedIndexChanged -= cmbUser_SelectedIndexChanged;
ServiceCallHelper.LoadConfig(string.Empty);
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser);
AppConfigHelper.seqdbConfig.LastDBSelected = string.Empty;
Initialize();
cmbUser.SelectedIndexChanged += cmbUser_SelectedIndexChanged;
Cursor.Current = Cursors.Default;
}
private void mnuExtract_Click(object sender, EventArgs e)
{
BioSeqExtract frm = new BioSeqExtract();
DialogResult rc = frm.ShowDialog();
if (rc == DialogResult.OK) // then the config has the specs
{
Cursor.Current = Cursors.WaitCursor;
// Parameters are in appsettings.
WSLProxyResponse WSLResponse = ServiceCallHelper.Extract(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()); // Parameters are in appsettings.
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser); // To retrieve StandardOutput and LastError.
Cursor.Current = Cursors.Default;
if (WSLResponse.ExitCode == 0)
{
MessageBox.Show(AppConfigHelper.StandardOutput + Environment.NewLine + "Extract completed successfully. Result is in " +
AppConfigHelper.ExtractOutputPath() + "\\" + AppConfigHelper.ExtractSampleID() + ".fasta", "Success", MessageBoxButtons.OK);
}
else
{
MessageBox.Show("Extract completed with error code " + WSLResponse.ExitCode.ToString() + "." + Environment.NewLine + Environment.NewLine +
AppConfigHelper.StandardOutput + Environment.NewLine + AppConfigHelper.LastError, "Error", MessageBoxButtons.OK);
}
}
}
private void mnuBackup_Click(object sender, EventArgs e)
{
BioSeqBackup frm = new BioSeqBackup();
DialogResult rc = frm.ShowDialog();
if (rc == DialogResult.OK) // then the config has the specs
{
Cursor.Current = Cursors.WaitCursor;
WSLProxyResponse WSLResponse = ServiceCallHelper.BackupDatabase(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()); // Parameters are in appsettings.
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser); // To retrieve StandardOutput and LastError.
Cursor.Current = Cursors.Default;
if (WSLResponse.ExitCode == 0)
{
RefreshVersionInformation(AppConfigHelper.seqdbConfig.seqDBs[AppConfigHelper.seqdbConfig.LastDBSelected]);
MessageBox.Show(AppConfigHelper.StandardOutput + Environment.NewLine + "Backup successfully completed.", "Success", MessageBoxButtons.OK);
// Refresh backup version display.
}
else
{
MessageBox.Show("Backup completed with error code " + WSLResponse.ExitCode.ToString() + "." + Environment.NewLine + Environment.NewLine +
AppConfigHelper.StandardOutput + Environment.NewLine + AppConfigHelper.LastError, "Error", MessageBoxButtons.OK);
}
}
}
private void btnOK_Click(object sender, EventArgs e)
{
// TODO: Should check the validity of the paths here.
AppConfigHelper.OutputPath(analysis, txtOutputPath.Text.Trim());
AppConfigHelper.SampleChecked(analysis, radSample.Checked);
AppConfigHelper.TaskMemo = txtMemo.Text.Trim();
if (analysis == "Kraken2")
{
AppConfigHelper.Kraken2UseFastq = radUseFastq.Checked;
if (radUseFastq.Checked)
{
AppConfigHelper.Kraken2FastqPath = txtInputPath.Text.Trim();
}
}
if (analysis == "BBMap")
{
AppConfigHelper.BBMapFastqPath(analysis, txtFastqPath.Text.Trim());
string fastqPath = txtFastqPath.Text.Trim();
if (IsServiceClass.IsService)
{
if (fastqPath.StartsWith("[L]")) // Not extract sample ID
{
ServiceCallHelper.ResetFastqFolder(AppConfigHelper.LoggedOnUser);
string[] files = Directory.GetFiles(DirectoryHelper.CleanPath(fastqPath), "*.fastq", SearchOption.TopDirectoryOnly);
foreach (string file in files)
{
DirectoryHelper.FileCopy("[L]" + file, "[S]" + AppConfigHelper.UserFolder() + "FastqFiles", true);
}
}
}
}
if (analysis == "VFabricate")
{
AppConfigHelper.VFabricateGeneXref = txtFastqPath.Text.Trim();
}
if (analysis == "Search")
{
if (!float.TryParse(txtCutoff.Text, out float cutoff))
{
MessageBox.Show("A cutoff number between 0 and 1 is required.", "Missing cutoff", MessageBoxButtons.OK);
txtCutoff.Focus();
DialogResult = DialogResult.None;
return;
}
if (cutoff < 0.0 || cutoff > 1.0)
{
MessageBox.Show("A cutoff number between 0 and 1 is required.", "Invalid cutoff", MessageBoxButtons.OK);
txtCutoff.Focus();
DialogResult = DialogResult.None;
return;
}
if (radContig.Checked && !DirectoryHelper.FileExists(AppConfigHelper.NormalizePathToWindows(txtInputPath.Text)))
{
MessageBox.Show(txtInputPath.Text + " does not exist. Choose a valid input file.", "Invalid input file", MessageBoxButtons.OK);
txtInputPath.Focus();
DialogResult = DialogResult.None;
return;
}
if (!DirectoryHelper.DirectoryExists(AppConfigHelper.NormalizePathToWindows(txtOutputPath.Text)))
{
MessageBox.Show(txtOutputPath.Text + " does not exist. Choose a valid output path.", "Invalid output path", MessageBoxButtons.OK);
txtOutputPath.Focus();
DialogResult = DialogResult.None;
return;
}
// Update config to reflect selection.
AppConfigHelper.SearchSample(txtOutputSampleName.Text, txtOutputPath.Text, txtInputPath.Text.Trim(), txtCutoff.Text, txtThreads.Text);
}
if (radSample.Checked)
{
if (lstSampleIDs.SelectedIndex == -1)
{
MessageBox.Show("Select a sample from the sample list", "ERROR", MessageBoxButtons.OK);
return;
}
AppConfigHelper.SampleID(analysis, lstSampleIDs.SelectedItem.ToString().Trim());
}
else // If the txtInputPath is local, send it to the UserFolder() on the server.
{
string inputPath = txtInputPath.Text.Trim();
if (!radSample.Checked && IsServiceClass.IsService)
{
if (inputPath.StartsWith("[L]")) // Not extract sample ID
{
DirectoryHelper.FileCopy(inputPath, AppConfigHelper.UserFolder(), true);
}
}
AppConfigHelper.InputPath(analysis, inputPath);
}
}
private void backgroundWorker_SampleIDs_DoWork(object sender, System.ComponentModel.DoWorkEventArgs e)
{
e.Result = ServiceCallHelper.SampleIDs(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()).ToArray();
}
static void Main()
{
Application.EnableVisualStyles();
Application.SetCompatibleTextRenderingDefault(false);
s_Mutex = new Mutex(true, "BioSeqDB");
if (!s_Mutex.WaitOne(0, false))
{
return;
}
Cursor.Current = Cursors.WaitCursor;
Logger.Initialize(logger);
UserProfileHelper.GetUserProfile(); // From C:\Temp\Remember.json.
Properties.Settings.Default.ModelServer = UserProfileHelper.userProfile.ServerIPAddress;
//MessageBox.Show("ServerIPAddress: " + Properties.Settings.Default.ModelServer, "ERROR", MessageBoxButtons.OK);
Properties.Settings.Default.Save();
// Check if BioSeqService is listening.
string IsClientOnServer = string.Empty;
try
{
IsClientOnServer = ServiceCallHelper.HelloBioSeqDBService();
}
catch (Exception ex)
{
MessageBox.Show("It appears that the BioSeqDB service is not running on the '" + Properties.Settings.Default.ModelServer +
"' server. Check VPN if running remotely?", "ERROR", MessageBoxButtons.OK);
return;
}
// Check if WSLProxy is listening.
try
{
string message = BioSeqDBModel.Instance.WSLVersion();
}
catch (Exception ex)
{
MessageBox.Show("It appears that the WSLProxy service is not running on the '" + Properties.Settings.Default.ModelServer +
"' server.", "ERROR", MessageBoxButtons.OK);
Logger.Log.Debug("It appears that the WSLProxy service is not running on the server. Exception\n" + ex.ToString());
return;
}
try
{
BioSeqDBLogin frmLogin = new BioSeqDBLogin(IsClientOnServer);
if (frmLogin.ShowDialog() == DialogResult.OK)
{
Application.Run(new BioSeqUI());
}
}
catch (Exception ex)
{
Logger.Log.Debug("Fatal error: " + ex.ToString());
MessageBox.Show(ex.ToString(), "ERROR", MessageBoxButtons.OK);
}
}
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);
}
}
}
private void btnFindInputPath_Click(object sender, EventArgs e)
{
DialogResult result;
string samplePath = string.Empty;
List <string> folderList = new List <string>();
items = new Dictionary <string, string>(); // Start from square one with items in this batch.
if (IsServiceClass.IsService)
{
string path = IsSalmonella ? AppConfigHelper.NormalizePathToWindows(AppConfigHelper.SalmonellaSamplesPath) :
AppConfigHelper.NormalizePathToWindows(AppConfigHelper.InfluenzaASamplesPath);
// We want an actual file, so don't append "\\".
// Jan-8-2021 No, we want a folder with fastq files in it.
path += "\\";
Explorer.frmExplorer = new Explorer(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig(), "Input path to folder containing sample fastq files",
DirectoryHelper.IsServerPath(path), DirectoryHelper.CleanPath(path),
"Fastq files (*.fastq)|*.fastq|All files (*.*)|*.*", folderList, AppConfigHelper.UbuntuPrefix());
Explorer.frmExplorer.ServerOnly = true;
result = Explorer.frmExplorer.ShowDialog();
if (result != DialogResult.Cancel)
{
folderList = Explorer.FileNames;
samplePath = Explorer.PresentServerPath + Explorer.PresentLocalPath; // One of these is empty.
}
}
else
{
VistaOpenFileDialog ofn = new VistaOpenFileDialog();
if (IsSalmonella ? Directory.Exists(AppConfigHelper.SalmonellaSamplesPath) : Directory.Exists(AppConfigHelper.InfluenzaASamplesPath))
{
ofn.InitialDirectory = ofn.FileName = IsSalmonella ? AppConfigHelper.FileExists(AppConfigHelper.SalmonellaSamplesPath) :
AppConfigHelper.FileExists(AppConfigHelper.InfluenzaASamplesPath);
}
ofn.Title = "Input path to folder containing sample fastq files";
ofn.CheckFileExists = true;
ofn.Multiselect = false;
ofn.Filter = "Fastq files (*.fastq)|*.fastq|All files (*.*)|*.*";
result = ofn.ShowDialog();
samplePath = ofn.FileName;
}
if (result != DialogResult.Cancel)
{
samplePath = samplePath.Substring(0, samplePath.LastIndexOf("\\") + 1);
// If the selection already exists, boot it out.
string msg = "Folders already selected or having no .fastq files (will be ignored): " + Environment.NewLine;
bool isSelected = false;
if (folderList.Count == 0)
{
foreach (string key in alreadySelected.Keys)
{
if (alreadySelected[key].Substring(1) == samplePath)
{
isSelected = true;
msg += samplePath + Environment.NewLine;
break;
}
}
if (!isSelected)
{
int fCount = ServiceCallHelper.TraverseTree(DirectoryHelper.CleanPath(samplePath), true, "fastq");
if (fCount == 0)
{
isSelected = true;
msg += samplePath + Environment.NewLine;
}
}
if (!isSelected)
{
string path = samplePath.Substring(0, samplePath.Length - 1);
path = path.Substring(path.LastIndexOf("\\") + 1);
//samplePath = samplePath.Substring(0, samplePath.Length - 1 - path.Length); // Chop off last folder name.
currentSampleSelection = path;
items.Add(path, samplePath);
}
}
else
{
foreach (string folder in folderList)
{
isSelected = false;
foreach (string key in alreadySelected.Keys)
{
if (Path.GetDirectoryName(alreadySelected[key].Substring(1)) == Path.GetDirectoryName(samplePath + folder + "\\"))
{
isSelected = true;
msg += samplePath + folder + Environment.NewLine;
break;
}
}
if (!isSelected)
{
int fCount = ServiceCallHelper.TraverseTree(DirectoryHelper.CleanPath(samplePath + folder), true, "fastq");
if (fCount == 0)
{
isSelected = true;
msg += samplePath + folder + Environment.NewLine;
}
}
if (!isSelected)
{
currentSampleSelection = folder;
items.Add(folder, samplePath + folder);
}
}
}
if (msg.Length > 72)
{
MessageBox.Show(msg, "WARNING", MessageBoxButtons.OK);
}
ReloadSampleList();
if (IsSalmonella)
{
AppConfigHelper.SalmonellaSamplesPath = samplePath;
}
else if (IsInfluenzaA)
{
AppConfigHelper.InfluenzaASamplesPath = samplePath;
}
}
}
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 btnPushTask_Click(object sender, EventArgs e)
{
Cursor.Current = Cursors.WaitCursor;
BioSeqTask task = AppConfigHelper.TaskOfIndex(lstTasks.SelectedIndex);
Cursor.Current = Cursors.Default;
if (task == null || task.LastExitCode == -999)
{
MessageBox.Show("Task output is no longer available but may have completed.", "Warning", MessageBoxButtons.OK);
return;
}
AppConfigHelper.LastCommand = task.TaskCommand;
switch (task.TaskType)
{
case "VFabricate":
TaskCompletion(task, "VFabricate", "VFabricate completed.");
Cursor.Current = Cursors.Default;
if (task.LastExitCode == 0)
{
string sampleName = string.Empty;
if (AppConfigHelper.SampleChecked("VFabricate"))
{
sampleName = AppConfigHelper.SampleID("VFabricate");
}
string destination = AppConfigHelper.CopyResultFromServer(AppConfigHelper.OutputPath("VFabricate"),
new string[] { sampleName + ".VFList.tsv" });
MessageBox.Show(task.StandardOutput + Environment.NewLine + "VFabricate completed successfully. Result is in " +
destination + "\\" + sampleName + ".VFList.tsv", "Success", MessageBoxButtons.OK);
destination = DirectoryHelper.CleanPath(destination);
Process.Start(destination + "\\" + sampleName + ".VFList.tsv");
}
break;
case "Quast":
TaskCompletion(task, "Quast", "Quast completed.");
Cursor.Current = Cursors.Default;
if (task.LastExitCode == 0)
{
string sampleName = string.Empty;
if (AppConfigHelper.SampleChecked("Quast"))
{
sampleName = AppConfigHelper.SampleID("Quast");
}
string destination = AppConfigHelper.CopyResultFromServer(AppConfigHelper.OutputPath("Quast"), new string[] { "\\Quast" + sampleName }, false); // folder copy
//destination = DirectoryHelper.CleanPath(destination);
MessageBox.Show(task.StandardOutput + Environment.NewLine + "Quast completed successfully. Result is in the " +
destination + " folder.", "Success", MessageBoxButtons.OK);
}
break;
case "Kraken2":
TaskCompletion(task, "Kraken2", "Kraken2 completed.");
Cursor.Current = Cursors.Default;
if (task.LastExitCode == 0)
{
MessageBox.Show(task.StandardOutput + Environment.NewLine + "Kraken2 completed successfully. Result is in " +
AppConfigHelper.OutputPath("Kraken2") + ".", "Success", MessageBoxButtons.OK);
if (AppConfigHelper.OutputPath("Kraken2").StartsWith("[L]"))
{
string destination = DirectoryHelper.CleanPath(AppConfigHelper.OutputPath("Kraken2")) + "\\";
if (File.Exists(destination + "kraken.aggregates.txt"))
{
File.Delete(destination + "kraken.aggregates.txt");
}
if (File.Exists(destination + "kraken.txt"))
{
File.Delete(destination + "kraken.txt");
}
if (File.Exists(destination + "RefseqIdent.txt"))
{
File.Delete(destination + "RefseqIdent.txt");
}
AppConfigHelper.CopyResultFromServer(AppConfigHelper.OutputPath("Kraken2"),
new string[] { "kraken.aggregates.txt", "kraken.txt", "RefseqIdent.txt" });
if (File.Exists(destination + "kraken.aggregates.txt"))
{
Process.Start(destination + "kraken.aggregates.txt");
}
if (File.Exists(destination + "kraken.txt"))
{
Process.Start(destination + "kraken.txt");
}
if (File.Exists(destination + "RefseqIdent.txt"))
{
Process.Start(destination + "RefseqIdent.txt");
}
}
}
break;
case "BBMap":
TaskCompletion(task, "BBMap", "BBMap completed.");
if (task.LastExitCode == 0)
{
string destination = AppConfigHelper.CopyResultFromServer(AppConfigHelper.OutputPath("BBMap"),
new string[] { "covhist.txt", "covstats.txt", "bincov.txt", "basecov.txt", "RefseqIdent.txt" });
destination = DirectoryHelper.CleanPath(destination);
MessageBox.Show(task.StandardOutput + Environment.NewLine + "BBMap completed successfully. Result is in " +
destination + ".", "Success", MessageBoxButtons.OK);
if (File.Exists(destination + "covhist.txt"))
{
Process.Start(destination + "covhist.txt");
}
if (File.Exists(destination + "covstats.txt"))
{
Process.Start(destination + "covstats.txt");
}
if (File.Exists(destination + "bincov.txt"))
{
Process.Start(destination + "bincov.txt");
}
if (File.Exists(destination + "basecov.txt"))
{
Process.Start(destination + "basecov.txt");
}
if (File.Exists(destination + "RefseqIdent.txt"))
{
Process.Start(destination + "RefseqIdent.txt");
}
}
break;
case "Search":
TaskCompletion(task, "Search", "Search completed.");
Cursor.Current = Cursors.WaitCursor;
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser); // To retrieve StandardOutput and LastError.
Cursor.Current = Cursors.Default;
if (task.LastExitCode == 0)
{
string filename = AppConfigHelper.OutputPath("Search") + "\\" + AppConfigHelper.SearchOutputSampleName() + ".txt";
MessageBox.Show(task.StandardOutput + Environment.NewLine +
"Search completed successfully. Close this dialog to open the result file in " + filename + ".", "Success", MessageBoxButtons.OK);
// If the output path is on the server, we need to copy it to the local Temp folder to display the results.
// If the output path is on the local machine, we need to copy from the user folder on the server to the local destination.
string destination = AppConfigHelper.CopyResultFromServer(AppConfigHelper.OutputPath("Search"),
new string[] { AppConfigHelper.SearchOutputSampleName() + ".txt" });
Process.Start(DirectoryHelper.CleanPath(destination) + AppConfigHelper.SearchOutputSampleName() + ".txt");
}
break;
case "Assemble":
TaskCompletion(task, "Assembly", "Assembly completed. If there are no errors, the results including the contig files are in the E:/data/staging folder on the server.");
break;
case "InfluenzaA":
TaskCompletion(task, "InfluenzaA", "InfluenzaA completed.");
Cursor.Current = Cursors.Default;
if (task.LastExitCode == 0)
{
//MessageBox.Show(task.StandardOutput + Environment.NewLine + "InfluenzaA completed successfully. Result is in the " +
// AppConfigHelper.InfluenzaAOutputPath + " folder.", "Success", MessageBoxButtons.OK);
if (IsServiceClass.IsService)
{
if (AppConfigHelper.InfluenzaAOutputPath.StartsWith("[L]")) // Output was created on server, to be stored on client. [L]
{
// For each sample that was processed, there is a subfolder in the UserFolder on the server named after the sample name.
// That subfolder needs to be copied to the local output folder. Note that we only copy the <sample>\consensus contents.
foreach (string sampleName in AppConfigHelper.InfluenzaASamplesList.Keys)
{
if (AppConfigHelper.InfluenzaASamplesList[sampleName].Substring(0, 1) == "1")
{
string sourceFolderName = "[S]" + AppConfigHelper.UserFolder() + sampleName + "\\consensus\\";
Directory.CreateDirectory(DirectoryHelper.CleanPath(AppConfigHelper.InfluenzaAOutputPath) + "\\" + sampleName + "\\");
//Logger.Log.Debug("Copy from " + sourceFolderName + " to " + AppConfigHelper.InfluenzaAOutputPath + "\\");
DirectoryHelper.FolderCopy(sourceFolderName, AppConfigHelper.InfluenzaAOutputPath + "\\" + sampleName + "\\");
}
}
}
MessageBox.Show(task.StandardOutput + Environment.NewLine + "Influenza A pipeline completed successfully. Results copied to " +
AppConfigHelper.InfluenzaAOutputPath + "\\, including consensus fasta files in sample name subfolder[s].",
"Files copied", MessageBoxButtons.OK);
}
}
break;
case "Centrifuge":
TaskCompletion(task, "Centrifuge", "Centrifuge completed.");
Cursor.Current = Cursors.Default;
if (task.LastExitCode == 0)
{
if (IsServiceClass.IsService)
{
if (AppConfigHelper.CentrifugeOutputPath.StartsWith("[L]")) // Output was created on server, to be stored on client. [L]
{
if (AppConfigHelper.CentrifugeOutputPath.StartsWith("[L]"))
{
string destination = DirectoryHelper.CleanPath(AppConfigHelper.CentrifugeOutputPath) + "\\";
if (File.Exists(destination + "centrifuge_res.tsv"))
{
File.Delete(destination + "centrifuge_res.tsv");
}
if (File.Exists(destination + "centrifuge_report.tsv"))
{
File.Delete(destination + "centrifuge_report.tsv");
}
AppConfigHelper.CopyResultFromServer(AppConfigHelper.CentrifugeOutputPath, new string[] { "centrifuge_res.tsv", "centrifuge_report.tsv" });
if (File.Exists(destination + "centrifuge_report.tsv"))
{
Process.Start(destination + "centrifuge_report.tsv");
}
}
}
MessageBox.Show(task.StandardOutput + Environment.NewLine + "Centrifuge pipeline completed successfully. Results copied to " +
AppConfigHelper.CentrifugeOutputPath + ".", "Files copied", MessageBoxButtons.OK);
}
}
break;
case "Salmonella":
TaskCompletion(task, "Salmonella", "Salmonella serotyping completed.");
Cursor.Current = Cursors.Default;
if (task.LastExitCode == 0)
{
MessageBox.Show(task.StandardOutput + Environment.NewLine + "Salmonella serotyping completed successfully. Result is in " +
AppConfigHelper.SalmonellaOutputPath, "Success", MessageBoxButtons.OK);
if (IsServiceClass.IsService)
{
if (AppConfigHelper.SalmonellaOutputPath.StartsWith("[L]")) // Output was created on server, to be stored on client. [L]
{
string sourceFolderName = "[S]" + AppConfigHelper.UserFolder() + "\\sistr_res_aggregate.csv";
string destinationFolderName = AppConfigHelper.SalmonellaOutputPath;
DirectoryHelper.FileCopy(sourceFolderName, destinationFolderName, true);
File.Move(DirectoryHelper.CleanPath(destinationFolderName) + "\\sistr_res_aggregate.csv",
DirectoryHelper.CleanPath(destinationFolderName) + "\\sistr_res_aggregate" + DateTime.Now.ToString("yyMMddHHmmss") + ".csv"); // Rename
Process.Start(DirectoryHelper.CleanPath(destinationFolderName) + "\\sistr_res_aggregate" + DateTime.Now.ToString("yyMMddHHmmss") + ".csv");
}
else // Rename on server.
{
DirectoryHelper.FileMove(AppConfigHelper.SalmonellaOutputPath + "\\sistr_res_aggregate.csv",
AppConfigHelper.SalmonellaOutputPath + "\\sistr_res_aggregate" + DateTime.Now.ToString("yyMMddHHmmss") + ".csv");
}
}
}
break;
case "Nextstrain":
TaskCompletion(task, "Nextstrain", "Nextstrain phylogenetic processing completed.");
Cursor.Current = Cursors.Default;
if (task.LastExitCode == 0)
{
//NextstrainProfile nextstrainProfile = AppConfigHelper.GetNextstrainProfile(); // for current database.
MessageBox.Show(task.StandardOutput + Environment.NewLine + "Nextstrain completed successfully.", "Success", MessageBoxButtons.OK);
if (IsServiceClass.IsService)
{
//string browser = string.Empty;
//RegistryKey key = null;
//try
//{
// key = Registry.ClassesRoot.OpenSubKey(@"HTTP\shell\open\command");
// if (key != null)
// {
// // Get default Browser
// browser = key.GetValue(null).ToString().ToLower().Trim(new[] { '"' });
// }
// if (!browser.EndsWith("exe"))
// {
// //Remove all after the ".exe"
// browser = browser.Substring(0, browser.LastIndexOf(".exe", StringComparison.InvariantCultureIgnoreCase) + 4);
// }
//}
//finally
//{
// if (key != null)
// {
// key.Close();
// }
//}
// Open the browser.
// See documentation for this approach:
// https://docs.nextstrain.org/en/latest/guides/share/community-builds.html
// The GitHub repository file structure must be:
// nextstrain/auspice/nextstrain.json
// The BioSeqDB service will have already pushed the updated files to Github.
Process proc = Process.Start("https://nextstrain.org/community/ArnieBerg/nextstrain@main");
//if (nextstrainProfile.OuputPath.StartsWith("[L]")) // Output was created on server, to be stored on client. [L]
//{
// string sourceFolderName = "[S]" + AppConfigHelper.UserFolder() + "\\ncov_global.json";
// string destinationFolderName = nextstrainProfile.OuputPath;
// DirectoryHelper.FileCopy(sourceFolderName, destinationFolderName, true);
// File.Move(DirectoryHelper.CleanPath(destinationFolderName) + "\\ncov_global.json",
// DirectoryHelper.CleanPath(destinationFolderName) + "\\sistr_res_aggregate" + DateTime.Now.ToString("yyMMddHHmmss") + ".csv"); // Rename
// Process.Start(DirectoryHelper.CleanPath(destinationFolderName) + "\\sistr_res_aggregate" + DateTime.Now.ToString("yyMMddHHmmss") + ".csv");
//}
//else // Rename on server.
//{
// DirectoryHelper.FileMove(nextstrainProfile.OuputPath + "\\sistr_res_aggregate.csv",
// nextstrainProfile.OuputPath + "\\sistr_res_aggregate" + DateTime.Now.ToString("yyMMddHHmmss") + ".csv");
//}
}
}
break;
case "BuildTree":
TaskCompletion(task, "BuildTree", "BuildTree completed. Close this dialog to open the result file.");
//Logger.Log.Debug("ExitCode=" + task.LastExitCode.ToString() + @" Write to c:\temp\commandline.txt: open file='" +
// AppConfigHelper.BuildTreeOutputPath() + "\\tree.nwk';" + Environment.NewLine);
if (!Directory.Exists("C:\\Temp"))
{
Directory.CreateDirectory("C:\\Temp");
}
string dendroscopePath = @"C:\Temp\";
if (IsServiceClass.IsService)
{
// For service, copy the tree.nwk from wherever it was stored to C:\Temp. If it is on the server, call the service to copy it.
// If it is on the local machine, do a File.Copy.
string sourceFolderName = "[S]" + AppConfigHelper.UserFolder();
string destinationFolderName = AppConfigHelper.BuildTreeOutputPath() + "\\";
Logger.Log.Debug("btnPushTask: FileCopy " + sourceFolderName + "tree.nwk to " + destinationFolderName);
Logger.Log.Debug("btnPushTask: DirectoryHelper destination: " +
AppConfigHelper.GetDirectoryName(DirectoryHelper.CleanPath(destinationFolderName + "\\")) + "\\" +
Path.GetFileName(DirectoryHelper.CleanPath(sourceFolderName)) + "tree.nwk");
if (destinationFolderName.StartsWith("[L]")) // Buildtree output was created on server, to be stored on client. [L]
{
DirectoryHelper.FileCopy(sourceFolderName + "tree.nwk", destinationFolderName, true);
DirectoryHelper.FileCopy(sourceFolderName + "metadata_microreact.csv", destinationFolderName, true);
dendroscopePath = DirectoryHelper.CleanPath(destinationFolderName);
Logger.Log.Debug("btnPushTask: dendroscopePath: " + dendroscopePath);
}
else // Buildtree output was created on server, to be stored on server. [S]
{
DirectoryHelper.FileCopy(sourceFolderName + "tree.nwk", destinationFolderName, true);
DirectoryHelper.FileCopy(sourceFolderName + "metadata_microreact.csv", destinationFolderName, true);
// Also copy to local Temp folder for Dendroscope to pick up.
DirectoryHelper.FileCopy(sourceFolderName + "tree.nwk", @"[L]C:\Temp\", true);
DirectoryHelper.FileCopy(sourceFolderName + "metadata_microreact.csv", @"[L]C:\Temp\", true);
}
}
else
{
if (DirectoryHelper.CleanPath(AppConfigHelper.BuildTreeOutputPath()) != @"C:\Temp")
{
if (File.Exists(@"C:\Temp\tree.nwk"))
{
File.Delete(@"C:\Temp\tree.nwk");
}
File.Copy(DirectoryHelper.CleanPath(AppConfigHelper.BuildTreeOutputPath() + "\\tree.nwk"), @"C:\Temp\tree.nwk", true);
}
if (File.Exists(@"C:\Temp\metadata_microreact.csv"))
{
File.Delete(@"C:\Temp\metadata_microreact.csv");
}
File.Copy(DirectoryHelper.CleanPath(AppConfigHelper.BuildTreeOutputPath() + "\\metadata_microreact.csv"), @"C:\Temp\metadata_microreact.csv", true);
}
File.WriteAllText("C:\\Temp\\commandline.txt", @"open file='" + dendroscopePath + "tree.nwk';" + Environment.NewLine);
if (task.LastExitCode == 0)
{
// Invoke Dendroscope to visualize tree. c:\\Temp\\commandine.txt contains the line:
// open file='C:\Temp\Save\tree.nwk';
try
{
Cursor.Current = Cursors.WaitCursor;
Process.Start(AppConfigHelper.PathToDendroscope(), "-g -c c:\\Temp\\commandline.txt");
Cursor.Current = Cursors.Default;
}
catch (Exception ex)
{
MessageBox.Show("Dendroscope needs to be installed to view the result. Check path " + AppConfigHelper.PathToDendroscope() +
Environment.NewLine + Environment.NewLine + ex.ToString(), "INSTALL DENDROSCOPE", MessageBoxButtons.OK);
}
}
break;
}
UIThreadRefresh(sender, e);
}