public void UpdateAvailableImages()
{
DateTime ts_Start = DateTime.Now;
UpdateAvailableImagesRec();
int count = 0;
ParseNodeDesc((d) => { if (d.HasImage)
{
count++;
}
});
Loggers.WriteInformation(LogTags.Image, string.Format("Update available images took {0} ms\n {1} taxon have images", (DateTime.Now - ts_Start).Milliseconds, count));
}
public static CommentFileDesc CreateOnlyIfFileExists(CommentsCollection _collection, string _name)
{
try
{
string path = Path.Combine(_collection.Path, _name + ".html");
if (File.Exists(path))
{
return(new CommentFileDesc(_collection, _name));
}
}
catch (Exception e)
{
Loggers.WriteError(LogTags.Data, "Loading comment for " + _name + " raise an exception:\n" + e.Message);
}
return(null);
}
//=========================================================================================
// generic function to load
//
public static TaxonTreeNode Load(string _fileName)
{
if (_fileName == string.Empty)
{
return(null);
}
DateTime ts_Start = DateTime.Now;
if (!File.Exists(_fileName))
{
return(null);
}
Cursor.Current = Cursors.WaitCursor;
string extension = Path.GetExtension(_fileName).ToLower();
if (extension == ".tol")
{
FormAbout.SetSplashScreenMessage(".. Loading data ...", false, new Action(() => CancelLoad()));
}
else
{
FormAbout.SetSplashScreenMessage(".. Loading data ...");
}
TaxonTreeNode result = null;
if (extension == ".xml")
{
result = LoadXML(_fileName);
}
if (extension == ".tol")
{
result = LoadBin(_fileName);
}
if (extension == ".txt")
{
result = LoadTxt(_fileName);
}
Loggers.WriteInformation(LogTags.Data, string.Format("Loading {0} took {1} ms ", _fileName, (int)((DateTime.Now - ts_Start).TotalMilliseconds)));
if (result != null)
{
result.AfterLoad();
}
Cursor.Current = Cursors.Default;
return(result);
}
//-----------------------------------------------------------------------------------------
// Save infos
public void SaveInfos()
{
string filename = System.IO.Path.Combine(Path, "_infos.xml");
TreeOfLife.Helpers.FileSystem.EnsureReadOnlyFlagIsOff(filename);
try
{
XmlSerializer serializer = new XmlSerializer(typeof(ImageCollection));
using (TextWriter writer = new StreamWriter(filename))
{
serializer.Serialize(writer, this);
}
}
catch (Exception e)
{
Loggers.WriteWarning(LogTags.Collection, "Exception while saving file : \n " + filename + "\n" + e.Message);
}
}
public bool Save(bool chooseFile = false, FileFilterIndexEnum _preferredFileExt = FileFilterIndexEnum.Xml)
{
if (!HasFile)
{
string message = "Cannot save that list in a file, it has not the HasFile flag set !";
MessageBox.Show(message, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return(false);
}
if (chooseFile || String.IsNullOrWhiteSpace(FileName))
{
SaveFileDialog sfd = new SaveFileDialog
{
FileName = FileName,
InitialDirectory = GetFolder(),
FilterIndex = 2 * (int)_preferredFileExt,
Filter = FileFilters,
AddExtension = true
};
if (sfd.ShowDialog() != DialogResult.OK)
{
return(false);
}
FileName = sfd.FileName;
}
try
{
XmlSerializer serializer = new XmlSerializer(typeof(TaxonList));
using (TextWriter writer = new StreamWriter(FileName))
{
serializer.Serialize(writer, this);
}
}
catch (Exception e)
{
Loggers.WriteError(LogTags.Data, "Exception while saving file : \n " + FileName + "\n" + e.Message);
return(false);
}
return(true);
}
public static TaxonTreeNode LoadXMLFromMemory(MemoryStream ms)
{
try
{
XmlSerializer deserializer = new XmlSerializer(typeof(TaxonTreeNode));
object obj = deserializer.Deserialize(ms);
(obj as TaxonTreeNode).UpdateFather();
(obj as TaxonTreeNode).Visible = true;
return(obj as TaxonTreeNode);
}
catch (Exception e)
{
string message = "Exception while loading from memory : \n\n";
message += e.Message;
if (e.InnerException != null)
{
message += "\n" + e.InnerException.Message;
}
Loggers.WriteError(LogTags.Data, message);
}
return(null);
}
//---------------------------------------------------------------------------------
private void ButtonCreateComment_Click(object sender, EventArgs e)
{
if (Edited == null)
{
return;
}
if (TaxonComments.CommentFile(Edited) != null)
{
return;
}
TaxonComments.CommentFileCreateResult result = TaxonComments.CommentFileCreate(Edited);
if (result == TaxonComments.CommentFileCreateResult.Success)
{
splitContainerComments.Visible = false;
Comments.RefreshContent(true);
return;
}
string message = "Creation failed:\n ";
if (result == TaxonComments.CommentFileCreateResult.ExistsAlready)
{
message += "a comment file already exists";
}
else if (result == TaxonComments.CommentFileCreateResult.NoNameAndID)
{
message += "taxon as no name or id, click on ID button to create a new TOL ID";
}
else if (result == TaxonComments.CommentFileCreateResult.NoCollection)
{
message += "No available collection, edit collections before creating comments";
}
else
{
message += "unknown reason";
}
Loggers.WriteError(LogTags.Comment, message);
}
public void Save(string _filename, string _exeRef = null)
{
BeforeSave(_exeRef);
string filepath = Path.GetDirectoryName(_filename);
try
{
if (!Directory.Exists(filepath))
{
Directory.CreateDirectory(filepath);
}
XmlSerializer serializer = new XmlSerializer(typeof(Config));
using (TextWriter writer = new StreamWriter(_filename))
{
serializer.Serialize(writer, this);
}
}
catch (Exception e)
{
Loggers.WriteError(LogTags.Congif, "Exception while saving config file : \n " + _filename + "\n" + e.Message);
}
}
//=========================================================================================
// txt file
//
static TaxonTreeNode LoadTxt(string _filename)
{
try
{
int ch = 0;
using (StreamReader sr = new StreamReader(_filename))
{
ch = (int)sr.Read();
while (ch != -1)
{
if (ch == '(')
{
break;
}
if (ch == (int)Keys.Return || ch == '>')
{
break;
}
ch = (int)sr.Read();
}
}
if (ch == '(')
{
return(LoadNewick(_filename));
}
if (ch == (int)Keys.Return || ch == '>')
{
return(LoadJacFile(_filename));
}
Loggers.WriteError(LogTags.Data, "Cannot recognize file forma : \n " + _filename);
return(null);
}
catch
{
return(null);
}
}
public void SaveBin(string _fileName)
{
TaxonUtils.LockMainWindow();
try
{
using (ProgressDialog progressDlg = new ProgressDialog())
{
progressDlg.StartPosition = FormStartPosition.CenterScreen;
progressDlg.Show();
ProgressItem piSave = progressDlg.Add("Saving ...", null, 0, Count());
using (FileStream fs = File.Create(_fileName, 65536, FileOptions.None))
{
using (DeflateStream deflateStream = new DeflateStream(fs, CompressionMode.Compress))
{
using (BinaryWriter w = new BinaryWriter(deflateStream))
//using (BinaryWriter w = new BinaryWriter(fs))
{
w.Write(SaveBinVersion);
SaveBin(w, new SaveBinProgress(piSave));
w.Close();
deflateStream.Close();
fs.Close();
}
}
}
}
}
catch (Exception e)
{
Loggers.WriteError(LogTags.Data, "Exception while saving config file : \n " + _fileName + "\n" + e.Message);
}
finally
{
TaxonUtils.UnlockMainWindow();
}
}
//méthode load
public static TaxonTreeNode LoadXML(string _fileName)
{
try
{
XmlSerializer deserializer = new XmlSerializer(typeof(TaxonTreeNode));
TextReader reader = new StreamReader(_fileName);
object obj = deserializer.Deserialize(reader);
reader.Close();
(obj as TaxonTreeNode).UpdateFather();
(obj as TaxonTreeNode).Visible = true;
return(obj as TaxonTreeNode);
}
catch (Exception e)
{
string message = "Exception while loading " + _fileName + " : \n\n";
message += e.Message;
if (e.InnerException != null)
{
message += "\n" + e.InnerException.Message;
}
Loggers.WriteError(LogTags.Data, message);
}
return(null);
}
//=========================================================================================
// Jac File load
//
static TaxonTreeNode LoadJacFile(string _filename)
{
try
{
using (StreamReader sr = new StreamReader(_filename))
{
TaxonTreeNode root = new TaxonTreeNode(new TaxonDesc("__ignore__"));
TaxonTreeNode currentNode = root;
int currentTab = 0;
int currentLine = 0;
string line;
// read header line
while ((line = sr.ReadLine()) != null)
{
currentLine++;
int tab = 0;
while (line.StartsWith("\t"))
{
tab++; line = line.Substring(1);
}
if (tab > currentTab)
{
if (tab - currentTab > 1 || currentNode.Children.Count == 0)
{
Loggers.WriteError(LogTags.Data, _filename + "(" + currentLine.ToString() + ") too many tabs");
return(null);
}
currentTab = tab;
currentNode = currentNode.Children[currentNode.Children.Count - 1];
}
else if (tab < currentTab)
{
while (currentTab != tab)
{
if (currentNode == root)
{
Loggers.WriteError(LogTags.Data, _filename + "(" + currentLine.ToString() + ") tabulation error");
return(null);
}
currentTab--;
currentNode = currentNode.Father;
}
}
string[] parts = line.Split('>');
TaxonTreeNode newNode = new TaxonTreeNode(new TaxonDesc()
{
RefMultiName = new Helpers.MultiName(parts[0]),
FrenchMultiName = parts.Length < 2 || String.IsNullOrWhiteSpace(parts[1]) ? null : new Helpers.MultiName(parts[1]),
ClassicRank = parts.Length < 3 || String.IsNullOrWhiteSpace(parts[2]) ? ClassicRankEnum.None : ClassicRankEnumExt.FromString(parts[2]),
Flags = (parts.Length < 4 || String.IsNullOrWhiteSpace(parts[3])) ? 0 : FlagsEnumExt.FromString(parts[3]),
RedListCategory = (parts.Length < 5 || String.IsNullOrWhiteSpace(parts[4])) ? RedListCategoryEnum.NotEvaluated : RedListCategoryExt.FromString(parts[4]),
}
);
currentNode.AddChild(newNode);
}
return(root);
}
}
catch (Exception e)
{
Loggers.WriteError(LogTags.Data, "Exception raised while reading file " + _filename + "\n " + e.Message);
return(null);
}
}
static void Main(string[] args)
{
System.Globalization.CultureInfo cultureInfo = new System.Globalization.CultureInfo("fr-FR");
Application.CurrentCulture = cultureInfo;
Application.EnableVisualStyles();
Application.SetCompatibleTextRenderingDefault(false);
// Init system
Loggers.Register(new LogFile(null, true));
LogMessageBox logMessageBox = new LogMessageBox();
logMessageBox.SetVerboseMode(VerboseModeEnum.OnlyErrors);
Loggers.Register(logMessageBox);
SystemConfig.OnRunningModeChanged += Loggers_OnRunningModeChanged;
Loggers.WriteInformation("Starting TreeOfLife : " + DateTime.Now.ToLongDateString());
#if USER
SystemConfig.RunningMode = SystemConfig.RunningModeEnum.User;
#else
SystemConfig.RunningMode = SystemConfig.RunningModeEnum.Admin;
#endif
TaxonUtils.MyConfig = Config.Load("auto");
// TaxonUtils.MyConfig.ToData();
//Console.WriteLine(TaxonUtils.);
if (!TaxonUtils.MyConfig.offline)
{
bool ok = TaxonUtils.CheckConnection();
if (!ok)
{
TaxonUtils.MyConfig.dataInitialized = false;
Console.WriteLine(TaxonUtils.MyConfig.dataInitialized);
}
}
InitForm initForm = new InitForm();
if (!TaxonUtils.MyConfig.dataInitialized)
{
initForm.ShowDialog();
TaxonUtils.MyConfig.rootDirectory = TOLData.AppDataDirectory();
Console.WriteLine(TaxonUtils.MyConfig.rootDirectory);
}
else
{
TOLData.offline = TaxonUtils.MyConfig.offline;
}
if (!initForm.quit)
{
TOLData.initSounds();
FormAbout.DoSplashScreen();
//----- config
FormAbout.SetSplashScreenMessage(".. Loading config ...");
TaxonUtils.initCollections();
Application.Run(new Form1(args));
}
}
private void ButtonImport_Click(object sender, EventArgs e)
{
string logFile = Path.Combine(TaxonUtils.GetLogPath(), "TagBatchImport.log");
using (StreamWriter log = new StreamWriter(logFile))
{
string[] srcFiles = null;
bool error = false;
if (!Directory.Exists(textBoxSource.Text))
{
log.WriteLine("Folder " + textBoxSource.Text + " does not exists");
error = true;
}
else
{
try
{
srcFiles = Directory.GetFiles(textBoxSource.Text, "*.txt");
if (srcFiles.Length == 0)
{
log.WriteLine("Folder " + textBoxSource.Text + " contains no txt files");
error = true;
}
}
catch (Exception ex)
{
log.WriteLine("Exception while getting list of txt file in folder " + textBoxSource.Text);
log.WriteLine(" " + ex.Message);
error = true;
}
}
if (!Directory.Exists(textBoxDestination.Text))
{
log.WriteLine("Folder " + textBoxDestination.Text + " does not exists");
error = true;
}
if (error)
{
log.WriteLine("Initialization error, stop batch import");
return;
}
bool overwriteAlways = radioButtonOverwrite.Checked;
bool overwriteNever = radioButtonLeaveIt.Checked;
int skippedFiles = 0;
int errorFiles = 0;
foreach (string file in srcFiles)
{
log.WriteLine();
log.WriteLine("--------------------------------------------------");
log.WriteLine("---> Import " + file);
string destinationFile = Path.Combine(textBoxDestination.Text, Path.GetFileNameWithoutExtension(file));
destinationFile = Path.ChangeExtension(destinationFile, ".lot");
if (File.Exists(destinationFile))
{
if (overwriteNever)
{
log.WriteLine("Import skipped, file " + destinationFile + " already exists");
skippedFiles++;
continue;
}
else if (!overwriteAlways)
{
DateTime datedest = File.GetLastWriteTime(destinationFile);
DateTime datesrc = File.GetLastWriteTime(file);
if (datedest >= datesrc)
{
log.WriteLine("Import skipped, file " + destinationFile + " already exists and is newer than source file");
skippedFiles++;
continue;
}
}
try
{
File.Delete(destinationFile);
}
catch
{
log.WriteLine("Import skipped, file " + destinationFile + " already exists");
log.WriteLine("And got an error while trying to delete it");
errorFiles++;
continue;
}
}
while (_Searchtool == null)
{
Console.WriteLine("Wait search tool");
Thread.Sleep(100);
}
TaxonList.ImportFileResult result = TaxonList.ImportFile(file, _Searchtool, false);
TaxonList list = new TaxonList {
HasFile = true, FileName = destinationFile
};
list.FromTaxonTreeNodeList(result.List);
try
{
list.Save(false, TaxonList.FileFilterIndexEnum.ListOfTaxons);
}
catch (Exception ex)
{
log.WriteLine("Exception while saving list to " + destinationFile);
log.WriteLine(" " + ex.Message);
errorFiles++;
continue;
}
log.WriteLine(string.Format(" taxons found: {0}", result.TaxonsFound));
log.WriteLine(string.Format(" taxons not found: {0}", result.TaxonNotFound));
log.WriteLine(string.Format("for more details, look at " + result.LogFilename + " file"));
log.WriteLine(string.Format("==> Saved in " + destinationFile));
}
string message = "Batch import done,\n";
message += string.Format("{0} total files scanned\n", srcFiles.Length);
message += string.Format("{0} files skipped\n", skippedFiles);
message += string.Format("{0} files not imported due to an error\n", errorFiles);
message += string.Format("{0} files imported\n", srcFiles.Length - skippedFiles - errorFiles);
message += string.Format("for more details, look at {0}", logFile);
Loggers.WriteInformation(LogTags.Data, message);
log.WriteLine("");
log.WriteLine("==================================================");
log.Write(message);
}
}
