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 backgroundWorker_RunWorkerCompleted(object sender, System.ComponentModel.RunWorkerCompletedEventArgs e)
{
// Parse the return from the background task.
try
{
//AppConfigHelper.LoadConfig(AppConfigHelper.LoggedOnUser); // Reload user's config (gets at least the LastCommand)
List <object> arguments = (List <object>)e.Result;
int ret = (int)arguments[0];
BioSeqTask task = (BioSeqTask)arguments[1];
switch (task.TaskType)
{
case "Search":
case "Kraken2":
case "Quast":
case "VFabricate":
ReportExtractError(ret, task.TaskType);
break;
case "BBMap":
ReportExtractError(ret, task.TaskType);
if (ret == -3)
{
MessageBox.Show("There are no .fastq files in " + AppConfigHelper.BBMapFastqPath() + ".", "Error", MessageBoxButtons.OK);
}
else if (ret == -2)
{
MessageBox.Show(task.LastError, "Error", MessageBoxButtons.OK);
}
else if (ret == -4)
{
MessageBox.Show("The seqtk step failed in BBMap.", "Error", MessageBoxButtons.OK);
}
else if (ret != 0)
{
MessageBox.Show("BBMap failed with error code " + ret.ToString() + ".", "Error", MessageBoxButtons.OK);
}
break;
case "BuildTree":
case "Assemble":
case "InfluenzaA":
case "Salmonella":
case "Nextstrain":
break;
}
}
catch (Exception ex)
{
}
}
private void RefreshTaskList(int index)
{
lstTasks.Items.Clear();
btnDeleteTask.Enabled = false;
if (AppConfigHelper.TaskList.Count == 0)
{
return;
}
Cursor.Current = Cursors.WaitCursor;
foreach (BioSeqTask task in AppConfigHelper.TaskList.Values)
{
if (string.IsNullOrEmpty(TaskFilter) || TaskFilter == "All" || TaskFilter == task.TaskStatus)
{
if (IsServiceClass.IsService)
{
// If the task has completed, this brings back the task details and deletes the task file on the server.
string taskCompleted = BioSeqDBModel.Instance.TaskComplete(AppConfigHelper.LoggedOnUser, task.TaskID);
if (!string.IsNullOrEmpty(taskCompleted))
{
BioSeqTask taskFromService = JsonSerializer.Deserialize <BioSeqTask>(taskCompleted);
task.LastError = taskFromService.LastError;
task.LastExitCode = taskFromService.LastExitCode;
task.StandardOutput = taskFromService.StandardOutput;
task.TaskComplete = taskFromService.TaskComplete;
task.TaskCommand = taskFromService.TaskCommand;
AppConfigHelper.BackgroundTaskComplete(task); // Mark task Ready and save config.
}
}
task.TaskIndexInList = lstTasks.Items.Add(task.TaskType + ": " + task.TaskStatus + " " + task.TaskDB + " " + task.TaskUser);
}
}
if (index < 0)
{
index = 0;
}
if (index >= lstTasks.Items.Count)
{
index = lstTasks.Items.Count - 1;
}
lstTasks.SelectedIndex = index;
btnDeleteTask.Enabled = lstTasks.Items.Count > 0;
StatusChangeEvent?.Invoke(this, null); // Notify parent we have a potential status change.
Cursor.Current = Cursors.Default;
}
private void CreateNewTask(string taskType, string taskMemo, string DB)
{
int taskid = AppConfigHelper.MaxTaskID() + 1;
BioSeqTask task = new BioSeqTask()
{
TaskMemo = taskMemo,
TaskDB = DB, // AppConfigHelper.CurrentDBName(),
TaskID = taskid.ToString(),
TaskStatus = "Pending",
TaskTime = DateTime.Now,
TaskComplete = DateTime.MinValue,
TaskType = taskType,
TaskUser = AppConfigHelper.LoggedOnUser,
StandardOutput = string.Empty,
LastError = string.Empty,
LastExitCode = -999
};
AppConfigHelper.AddTask(task);
}
private void lstTasks_SelectedIndexChanged(object sender, EventArgs e)
{
// Show the details of the selected task and set enable status of push button.
BioSeqTask task = AppConfigHelper.TaskOfIndex(lstTasks.SelectedIndex);
//lblData.Text = task.TaskData;
lblDatabase.Text = task.TaskDB;
lblStatus.Text = task.TaskStatus;
lblTime.Text = task.TaskTime.ToString("MMM d, yyyy H:mm");
lblType.Text = task.TaskType;
lblUser.Text = task.TaskUser;
lblMemo.Text = task.TaskMemo;
if (task.TaskComplete != DateTime.MinValue)
{
lblCompleted.Text = task.TaskComplete.ToString("MMM d, yyyy H:mm");
}
btnPushTask.Enabled = task.TaskStatus == "Ready";
btnPushTask.BackgroundImage = btnPushTask.Enabled ? Properties.Resources.push : Properties.Resources.pushdull;
lblStatus.BackColor = btnPushTask.Enabled ? Color.OrangeRed : lblType.BackColor;
}
private void TaskCompletion(BioSeqTask task, string taskName, string successMsg)
{
// Called by the user from the Push button when task status is Ready.
Cursor.Current = Cursors.WaitCursor;
TimeSpan duration = task.TaskComplete - task.TaskTime;
string db = string.IsNullOrEmpty(task.TaskDB) ? string.Empty : "Sequence database: " + task.TaskDB;
string memo = string.IsNullOrEmpty(task.TaskMemo) ? string.Empty : "Memo: " + task.TaskMemo;
string subject = "Task completed: " + taskName + " at " + task.TaskComplete.ToString("MMM d, yyyy HH:mm") + " after " +
duration.TotalMinutes.ToString("#.0") + " minutes." + Environment.NewLine + (db + " " + Environment.NewLine + memo).Trim();
string message = subject + Environment.NewLine + AppConfigHelper.LastCommand + Environment.NewLine;
subject = subject.Replace(Environment.NewLine, " ");
List <string> attachments = new List <string>();
string output = task.StandardOutput + Environment.NewLine + task.LastError;
message += "Standard output: " + output + Environment.NewLine;
// Read and delete the output file from the command.
string linuxCapture = string.Empty;
string filename = AppConfigHelper.NormalizePathToWindows(AppConfigHelper.LinuxHomeDirectory + "/output" + task.TaskID);
if (DirectoryHelper.FileExists("[S]" + filename))
{
linuxCapture = BioSeqDBModel.Instance.ReadAllText(filename, AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()); // We know it is on the server.
int residual = 6000;
if (linuxCapture.Length > residual)
{
// Write the whole thing to a log file that can be opened separately.
string tasklog = "C:\\Temp\\TaskLog.txt";
File.WriteAllText(tasklog, linuxCapture);
linuxCapture = "[Full text truncated; see saved log file " + tasklog + "]" + Environment.NewLine + Environment.NewLine +
linuxCapture.Substring(linuxCapture.Length - residual); // Display the last residual chars.
Process.Start(tasklog);
attachments.Add(tasklog);
}
}
SuccessDialog.MainInstruction = successMsg;
SuccessDialog.Content = output;
if (linuxCapture.Length > 0 && output.IndexOf(linuxCapture) == -1)
{
SuccessDialog.Content += (output.Length > 0 ? Environment.NewLine : string.Empty) + linuxCapture;
}
if (task.LastExitCode != 0 && task.LastExitCode != -999) // We handle -999 elsewhere (lost task status after completion, likely because BioSeqDB was restarted).
{
SuccessDialog.WindowTitle = "ERROR";
SuccessDialog.MainInstruction = taskName + " completed with error code " + task.LastExitCode.ToString() + ".";
message += SuccessDialog.MainInstruction + Environment.NewLine;
}
SuccessDialog.ShowDialog(this);
RemoveTask(false); // Do this as soon as possible to reflect the user's closing of the dialog.
StatusChangeEvent?.Invoke(this, null); // Notify parent we have a potential status change.
message += linuxCapture;
User user = AppConfigHelper.seqdbConfigGlobal.Users[AppConfigHelper.LoggedOnUser];
if (user.EmailNotifications)
{
string s1 = Emailer.SendEmail(AppConfigHelper.LoggedOnUser + "@mail.usask.ca", "BioSeqDB User: "******" " + subject, message, attachments, null);
if (!string.IsNullOrEmpty(s1))
{
Logger.Log.Debug("Email error: " + s1);
//MessageBox.Show(s1, "ERROR", MessageBoxButtons.OK);
}
}
if (File.Exists(filename)) // Must do after email since it might be attached.
{
File.Delete(filename);
}
Cursor.Current = Cursors.Default;
}
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);
}
