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 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;
}
}
}
