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);
}
}
