public override void Validate(ValidationMessages messages)
{
var service = new TaxaService(PluginManager.Instance.User);
if (!service.SafeToDeleteTaxon(Taxon.TaxaID.Value)) {
messages.Warn("There are material and or associations that will be orphaned if you delete this taxon.");
}
}
public override DataMatrix ExtractReportData(IProgressObserver progress)
{
var service = new TaxaService(User);
progress.ProgressStart(String.Format("Preparing Darwin Core records for {0} specimens...", _idSet.Count));
DataMatrix result = null;
var idSet = new LinkedList<int>(_idSet);
int chunkSize = 2000;
var helper = new DarwinCoreReportHelper();
var chunk = new List<int>();
var count = 0;
while (idSet.Count > 0) {
chunk.Add(idSet.First.Value);
idSet.RemoveFirst();
count++;
if (chunk.Count >= chunkSize || idSet.Count == 0) {
var percentComplete = ((double) count / (double) _idSet.Count) * 100;
progress.ProgressMessage(String.Format("Preparing Darwin Core records {0} of {1}", count, _idSet.Count), percentComplete);
var where = "tblMaterial.intMaterialID in (" + chunk.Join(",") + ")";
var dataChunk = helper.RunDwcQuery(service, where);
if (result == null) {
result = dataChunk;
} else {
result.AppendMatrix(dataChunk);
}
chunk = new List<int>();
}
}
progress.ProgressEnd(String.Format("{0} Darwin Core records retrieved.", count));
return result;
}
void TaxonTooltipContent_Loaded(object sender, RoutedEventArgs e)
{
var service = new TaxaService(PluginManager.Instance.User);
var Model = service.GetTaxon(TaxonID);
if (Model == null) {
return;
}
var elementRank = service.GetTaxonRank(Model);
var header = Model.TaxaFullName;
if (Model.AvailableName.ValueOrFalse()) {
header += " (Available name)";
} else if (Model.LiteratureName.ValueOrFalse()) {
header += " (Literature name)";
}
lblHeader.Content = header;
var rankName = (elementRank == null ? "Unranked" : elementRank.LongName + (Model.AvailableName.ValueOrFalse() ? " Available Name" : ""));
var kingdom = string.IsNullOrEmpty(Model.KingdomCode) ? "No Kingdom" : Model.KingdomCode;
lblSystem.Content = string.Format("[{0}] {1} <{2}> Last updated: {3:g} by {4}", Model.TaxaID.Value, rankName, kingdom, Model.DateLastUpdated, Model.WhoLastUpdated);
imgIcon.Source = TaxonViewModel.ConstructIcon(Model.AvailableName.ValueOrFalse() || Model.LiteratureName.ValueOrFalse(), Model.ElemType, false);
// Ancestry
var bits = Model.Parentage.Split('\\');
int i = bits.Length - 1;
int j = 0;
var parents = new Stack<Taxon>();
while (--i >= 0 && j++ < 3) {
if (!string.IsNullOrEmpty(bits[i])) {
var parentId = Int32.Parse(bits[i]);
var parent = service.GetTaxon(parentId);
parents.Push(parent);
}
}
i = 0;
grdAncestry.Children.Clear();
foreach (Taxon t in parents) {
var parentPanel = new StackPanel() { Orientation = Orientation.Horizontal, Margin = new Thickness(i * 15, i * 25, 0, 0) };
var parentIcon = new Image() { VerticalAlignment = System.Windows.VerticalAlignment.Top, UseLayoutRounding = true, SnapsToDevicePixels = true, Stretch = Stretch.None, Margin = new Thickness(6, 0, 6, 0) };
parentIcon.Source = TaxonViewModel.ConstructIcon(t.AvailableName.ValueOrFalse() || t.LiteratureName.ValueOrFalse(), t.ElemType, false);
parentPanel.Children.Add(parentIcon);
var rank = service.GetTaxonRank(t);
rankName = (rank == null ? "Unranked" : rank.LongName);
var txt = new TextBlock() {VerticalAlignment = System.Windows.VerticalAlignment.Top, Text = string.Format("{1} ({0})", rankName, t.TaxaFullName) };
parentPanel.Children.Add(txt);
grdAncestry.Children.Add(parentPanel);
i++;
}
}
public SelectRankWindow()
{
InitializeComponent();
var service = new TaxaService(PluginManager.Instance.User);
_map = service.GetTaxonRankMap();
var kingdoms = service.GetKingdomList().Where((kingdom) => {
return !string.IsNullOrWhiteSpace(kingdom.KingdomCode);
});
cmbKingdom.SelectionChanged += new SelectionChangedEventHandler(cmbKingdom_SelectionChanged);
cmbKingdom.ItemsSource = kingdoms;
if (kingdoms.Count() > 0) {
cmbKingdom.SelectedIndex = 0;
}
this.DataContext = this;
}
public XMLExportOptions(User user, List<int> taxonIds)
{
InitializeComponent();
TaxonIDs = taxonIds;
this.User = user;
var lastFile = Config.GetUser(User, "XMLIOExport.LastExportFile", "");
if (!string.IsNullOrEmpty(lastFile)) {
if (taxonIds.Count == 1) {
var service = new TaxaService(user);
var taxon = service.GetTaxon(taxonIds[0]);
if (taxon != null) {
var f = new FileInfo(lastFile);
var directory = f.DirectoryName;
var taxaName = taxon.TaxaFullName == null ? "Unnamed" : taxon.TaxaFullName;
txtFilename.Text = System.IO.Path.Combine(f.DirectoryName, SystemUtils.StripIllegalFilenameChars(taxaName) + ".xml");
}
} else {
txtFilename.Text = lastFile;
}
}
}
public List<HierarchicalViewModelBase> LoadModel(HierarchicalViewModelBase parent)
{
var service = new TaxaService(User);
List<Taxon> model = null;
if (parent == null) {
model = service.GetTopLevelTaxa();
} else {
model = service.GetTaxaForParent((parent as TaxonViewModel).TaxaID.Value);
}
if (model != null) {
var temp = model.Where((taxon) => {
return _options == LookupOptions.TaxonExcludeAvailableNames ? !taxon.AvailableName.ValueOrFalse() : true;
}).Select((m) => {
return new TaxonViewModel(parent, m, _explorer.GenerateTaxonDisplayLabel);
});
var list = new List<HierarchicalViewModelBase>(temp);
return list;
}
return null;
}
public override Data.DataMatrix ExtractReportData(IProgressObserver progress)
{
var service = new TaxaService(User);
return service.TaxaForDistributionRegionReport(DistributionRegion.DistRegionID, TaxonID);
}
public DataMatrix GetTaxaForSites(bool includeLocations, string itemType, int itemID, int biotaID, string criteriaText)
{
var taxonService = new TaxaService(User);
var rtf = new RTFReportBuilder();
// Create the Header inforrmation
rtf.AppendFullHeader();
// Create the title information
rtf.Append(@"\pard\fs36\b Taxa for Site/Region Report\b0\pard\par\fs24 ").Append(criteriaText);
rtf.Append(@"\pard\par\fs24 Produced: ").AppendCurrentDate();
// extract the parentage string from the database.
// Loop through the recordset and build the report output.
int lngLastBiotaID = -1;
int lngLastRegionID = -1;
int lngLastSiteID = -1;
string strOrderRank = "";
string strFamilyRank = "";
StoredProcReaderForEach("spReportTaxaForSites", (reader) => {
// If there is a change in taxa, print the header.
int currentBiotaID = (int) reader["BiotaID"];
if (lngLastBiotaID != currentBiotaID) {
lngLastBiotaID = currentBiotaID;
lngLastRegionID = -1;
lngLastSiteID = -1;
rtf.Par().Par().Append(@"\pard\sb20\fs28\b ");
rtf.Append(AsString(reader["BiotaFullName"])).Append(@"\b0");
// extract the family and order
strOrderRank = taxonService.GetBiotaRankElemType(currentBiotaID, "O");
strFamilyRank = taxonService.GetBiotaRankElemType(currentBiotaID, "F");
if (!string.IsNullOrWhiteSpace(strOrderRank) && string.IsNullOrWhiteSpace(strFamilyRank)) {
rtf.Append(" [").Append(strOrderRank).Append("]");
} else if ((!string.IsNullOrWhiteSpace(strOrderRank) || (!string.IsNullOrWhiteSpace(strFamilyRank)))) {
rtf.Append(" [").Append(strOrderRank).Append(": ").Append(strFamilyRank).Append("]");
}
}
if (includeLocations) {
// Add the region group
int currentRegionID = (int) reader["RegionID"];
if (lngLastRegionID != currentRegionID) {
// Add the region
lngLastRegionID = currentRegionID;
rtf.Par().Append(@"\pard\sb10\fs20\li600 ");
rtf.Append(AsString(reader["FullRegion"]));
}
int currentSiteID = (int) reader["SiteID"];
if (lngLastSiteID != currentSiteID) {
lngLastSiteID = currentSiteID;
// Add the Site
rtf.Par().Append(@"\pard\sb10\fs20\li1200 ");
// Add the locality
int localType = (byte) reader["LocalType"];
switch (localType) {
case 0:
rtf.Append(AsString(reader["Local"]));
break;
case 1:
rtf.Append(AsString(reader["DistanceFromPlace"])).Append(" ");
rtf.Append(AsString(reader["DirFromPlace"])).Append(" of ").Append(AsString(reader["Local"]));
break;
default:
rtf.Append(AsString(reader["Local"]));
break;
}
// Add the long and lat.
int areaType = (int) reader.Get<byte>("AreaType", (byte) 0);
double? lat = reader.Get<double?>("Lat");
double? lon = reader.Get<double?>("Long");
double? lat2 = reader.Get<double?>("Lat2");
double? lon2 = reader.Get<double?>("Long2");
switch (areaType) {
case 1: // Point
if (!lat.HasValue || !lon.HasValue) {
rtf.Append("; No position data");
} else {
rtf.Append("; {0}, {1}", GeoUtils.DecDegToDMS(lat.Value, CoordinateType.Latitude), GeoUtils.DecDegToDMS(lon.Value, CoordinateType.Longitude));
}
break;
case 2: // Box
if (!lat.HasValue || !lon.HasValue || !lat2.HasValue || !lon2.HasValue) {
rtf.Append("; No position data");
} else {
rtf.Append("; Box: {0}, {1}; {2}, {3}",
GeoUtils.DecDegToDMS(lat.Value, CoordinateType.Latitude),
GeoUtils.DecDegToDMS(lon.Value, CoordinateType.Longitude),
GeoUtils.DecDegToDMS(lat2.Value, CoordinateType.Latitude),
GeoUtils.DecDegToDMS(lon2.Value, CoordinateType.Longitude));
}
break;
case 3: // Line
if (!lat.HasValue || !lon.HasValue || !lat2.HasValue || !lon2.HasValue) {
rtf.Append("; No position data");
} else {
rtf.Append("; Line: {0}, {1}; {2}, {3}",
GeoUtils.DecDegToDMS(lat.Value, CoordinateType.Latitude),
GeoUtils.DecDegToDMS(lon.Value, CoordinateType.Longitude),
GeoUtils.DecDegToDMS(lat2.Value, CoordinateType.Latitude),
GeoUtils.DecDegToDMS(lon2.Value, CoordinateType.Longitude));
}
break;
default:
// ignore
break;
}
}
}
}, _P("vchrItemType", itemType), _P("intItemID", itemID), _P("intBiotaID", biotaID));
rtf.Append(" }");
return rtf.GetAsMatrix();
}
public DataMatrix GetDarwinCoreForBiotaID(int biotaID)
{
var taxon = new TaxaService(User).GetTaxon(biotaID);
if (taxon == null) {
return new DataMatrix();
}
return new DarwinCoreReportHelper().RunDwcQuery(this, String.Format("tblBiota.vchrParentage LIKE '{0}\\%'", taxon.Parentage));
}
private void BuildTaxaChildrenViewModel(HierarchicalViewModelBase item, int taxaID)
{
// The model node is a Taxon favorites, so we can get the 'real' taxon children for it...
item.Children.Clear();
var taxaService = new TaxaService(User);
List<Taxon> taxa = taxaService.GetTaxaForParent(taxaID);
foreach (Taxon taxon in taxa) {
TaxonViewModel child = new TaxonViewModel(item, taxon, null);
if (child.NumChildren > 0) {
child.LazyLoadChildren += new HierarchicalViewModelAction(viewModel_LazyLoadChildren);
child.Children.Add(new ViewModelPlaceholder("Loading..."));
}
item.Children.Add(child);
}
}
protected override List<RefLink> SelectReferences(IProgressObserver progress)
{
var service = new SupportService(User);
var taxaService = new TaxaService(User);
if (progress != null) {
progress.ProgressMessage("Retrieving Reference links...");
}
var reflinks = service.GetReferenceLinks(TraitCategoryType.Taxon.ToString(), Taxon.TaxaID.Value);
if (Options.IncludeChildReferences == true) {
var children = taxaService.GetExpandFullTree(Taxon.TaxaID.Value);
var elementCount = 0;
int total = children.Count;
if (progress != null) {
progress.ProgressStart("Extracting references for children...");
}
foreach (Taxon child in children) {
if (progress != null) {
double percent = (((double)elementCount) / ((double)total)) * 100.0;
progress.ProgressMessage(string.Format("Processing {0}", child.TaxaFullName), percent);
}
elementCount++;
var links = service.GetReferenceLinks(TraitCategoryType.Taxon.ToString(), child.TaxaID.Value);
foreach (RefLink link in links) {
reflinks.Add(link);
}
}
if (progress != null) {
progress.ProgressEnd("");
}
}
return reflinks;
}
protected override void ProcessImpl(User user)
{
var service = new TaxaService(user);
service.UpdateTaxon(Taxon);
}
protected override void ProcessImpl(User user)
{
var service = new TaxaService(user);
service.MoveTaxon(Taxon.TaxaID.Value, NewParent.TaxaID.Value);
}
protected override void ProcessImpl(User user)
{
var service = new TaxaService(user);
service.MergeTaxon(Source.TaxaID.Value, Target.TaxaID.Value, CreateNewIDRecord);
service.DeleteTaxon(Source.TaxaID.Value);
}
protected override void ProcessImpl(User user)
{
var service = new TaxaService(user);
service.InsertTaxon(Taxon.Taxon);
// The service will have updated the new taxon with its database identity.
// If this taxon has any children we can update their identity too.
foreach (HierarchicalViewModelBase child in Taxon.Children) {
TaxonViewModel tvm = child as TaxonViewModel;
tvm.TaxaParentID = Taxon.Taxon.TaxaID;
}
}
private void DoFind(string searchTerm)
{
if (String.IsNullOrEmpty(searchTerm)) {
return;
}
_searchModel.Clear();
using (new OverrideCursor(Cursors.Wait)) {
if (Owner == null) {
return;
}
List<TaxonSearchResult> results = new TaxaService(Owner.User).FindTaxa(searchTerm);
if (!PluginManager.Instance.CheckSearchResults(results)) {
return;
}
tvwResults.InvokeIfRequired(() => {
foreach (Taxon t in results) {
var item = new TaxonViewModel(null, t, GenerateTaxonDisplayLabel);
if (item.NumChildren > 0) {
item.LazyLoadChildren += new HierarchicalViewModelAction(item_LazyLoadChildren);
item.Children.Add(new ViewModelPlaceholder(_R("TaxonExplorer.explorer.loading", item.Epithet)));
}
_searchModel.Add(item);
}
});
}
}
private void TreeViewItem_MouseRightButtonDown(object sender, MouseEventArgs e)
{
TreeViewItem item = sender as TreeViewItem;
if (item == null) {
return;
}
item.Focus();
e.Handled = true;
var model = tvwFavorites.SelectedItem as HierarchicalViewModelBase;
Debug.Assert(model != null);
int? favoriteId = null;
TaxonViewModel tvm = null;
bool isGroup = false;
if (model is TaxonFavoriteViewModel) {
var fav = model as TaxonFavoriteViewModel;
favoriteId = fav.FavoriteID;
if (!fav.IsGroup) {
var taxon = new TaxaService(User).GetTaxon(fav.TaxaID);
tvm = new TaxonViewModel(null, taxon, TaxonExplorer.GenerateTaxonDisplayLabel);
} else {
isGroup = true;
}
} else if (model is TaxonViewModel) {
tvm = model as TaxonViewModel;
}
if (tvm != null) {
TaxonMenuFactory f = new TaxonMenuFactory(tvm, TaxonExplorer, TaxonExplorer._R);
tvwFavorites.ContextMenu = f.BuildFavoritesMenu(model);
} else {
var builder = new ContextMenuBuilder(null);
builder.New("Add favorite group").Handler(() => { AddFavoriteGroup(model); }).End();
if (isGroup) {
builder.New("Rename group").Handler(() => { RenameFavoriteGroup(model as TaxonFavoriteViewModel); }).End();
builder.New("Remove favorite group").Handler(() => { DeleteFavoriteGroup(model); }).End();
}
tvwFavorites.ContextMenu = builder.ContextMenu;
}
}
public List<HierarchicalViewModelBase> Search(string searchTerm)
{
var service = new TaxaService(User);
var list = service.FindTaxa(searchTerm).Where((taxon) => {
return _options == LookupOptions.TaxonExcludeAvailableNames ? !taxon.AvailableName.ValueOrFalse() : true;
});
var results = new List<HierarchicalViewModelBase>(list.Select((m) => {
return new TaxonViewModel(null, m, _explorer.GenerateTaxonDisplayLabel);
}));
results.Sort(new TaxonComparer());
//(vm1, vm2) => {
// var t1 = vm1 as TaxonViewModel;
// var t2 = vm2 as TaxonViewModel;
// return StringComparer.CurrentCultureIgnoreCase.Compare(t2.DefaultSortOrder, t1.DefaultSortOrder);
//});
return results;
}
protected override void InitImportImpl()
{
LogMsg("Caching rank data...");
var taxonService = new TaxaService(User);
_ranks = taxonService.GetOrderedRanks();
}
protected override void ProcessImpl(User user)
{
var service = new TaxaService(user);
service.DeleteTaxon(Taxon.TaxaID.Value);
}