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;
}
}
}
private int GetTaxonNumber()
{
// test to see if an internal taxon id is present in the incoming dataset
var existingTaxonId = Get("Taxon.ExistingTaxonID");
if (!String.IsNullOrEmpty(existingTaxonId))
{
var existingTaxon = TaxaService.GetTaxon(Int32.Parse(existingTaxonId));
if (existingTaxon != null)
{
return(existingTaxon.TaxaID.Value);
}
}
// No existing taxon found? need to create it
var strLowestRank = LowestTaxonLevel();
var taxon = BuildTaxonCacheRecord();
int elementID = -1;
if (!_taxonCache.FindInCache(taxon, out elementID))
{
elementID = 0;
foreach (TaxonRankName name in _ranks)
{
elementID = AddElementID(elementID, name, strLowestRank);
}
taxon.TaxonID = elementID;
taxon.SourceRowID = CurrentRowId;
_taxonCache.AddToCache(taxon);
}
return(elementID);
}
public TaxonNameDetails(int?taxonId, User user, Action <TaxonNameViewModel> successAction) : base(user, "TaxonNameDetails::" + taxonId.Value)
{
_successAction = successAction;
var service = new TaxaService(user);
Taxon taxon = service.GetTaxon(taxonId.Value);
_rank = service.GetTaxonRank(taxon);
_kingdomList = service.GetKingdomList();
Kingdom kingdom = _kingdomList.Find((k) => k.KingdomCode.Equals(taxon.KingdomCode));
_model = new TaxonNameViewModel(taxon, kingdom, _rank);
_model.DataChanged += new DataChangedHandler(_model_DataChanged);
InitializeComponent();
cmbKingdom.ItemsSource = _kingdomList;
this.chkChangedCombination.Visibility = (_rank != null && _rank.Category == "S" ? Visibility.Visible : Visibility.Hidden);
if (taxon.AvailableName.ValueOrFalse() || taxon.LiteratureName.ValueOrFalse())
{
string phraseCategory = "ALN Name Status";
chkChangedCombination.Visibility = System.Windows.Visibility.Hidden;
if (taxon.AvailableName.ValueOrFalse())
{
TaxonRank rank = service.GetTaxonRank(taxon);
if (rank != null)
{
switch (rank.Category.ToLower())
{
case "g": phraseCategory = "GAN Name Status";
break;
case "s": phraseCategory = "SAN Name Status";
break;
}
}
}
txtNameStatus.BindUser(PluginManager.Instance.User, PickListType.Phrase, phraseCategory, TraitCategoryType.Taxon);
}
else
{
txtNameStatus.Visibility = System.Windows.Visibility.Collapsed;
lblNameStatus.Visibility = System.Windows.Visibility.Collapsed;
}
this.DataContext = _model;
this.ChangesCommitted += new PendingChangesCommittedHandler(TaxonNameDetails_ChangesCommitted);
}
public override ViewModelBase CreatePinnableViewModel(PinnableObject pinnable)
{
if (pinnable != null && pinnable.LookupType == LookupType.Taxon)
{
Taxon t = Service.GetTaxon(pinnable.ObjectID);
if (t != null)
{
var m = new TaxonViewModel(null, t, tt => tt.TaxaFullName);
return(m);
}
}
if (pinnable != null && pinnable.LookupType == LookupType.DistributionRegion)
{
var service = new SupportService(User);
var region = service.GetDistributionRegion(pinnable.ObjectID);
if (region != null)
{
return(new DistributionRegionViewModel(region));
}
}
return(null);
}
private DataMatrix AddMediaForTaxon(int taxonId, IProgressObserver progress)
{
var results = new DataMatrix();
results.Columns.Add(new MatrixColumn {
Name = "MultimediaID", IsHidden = true
});
results.Columns.Add(new MatrixColumn {
Name = "TaxonID", IsHidden = true
});
results.Columns.Add(new MatrixColumn {
Name = "MultimediaLink", IsHidden = true
});
results.Columns.Add(new MatrixColumn {
Name = "Taxon name"
});
results.Columns.Add(new MatrixColumn {
Name = "Rank"
});
results.Columns.Add(new MatrixColumn {
Name = "Multimedia Name"
});
results.Columns.Add(new MatrixColumn {
Name = "Extension"
});
results.Columns.Add(new MatrixColumn {
Name = "Multimedia Type"
});
results.Columns.Add(new MatrixColumn {
Name = "Size"
});
results.Columns.Add(new MatrixColumn {
Name = "Attached To"
});
results.Columns.Add(new MatrixColumn {
Name = "MaterialID", IsHidden = true
});
if (progress != null)
{
progress.ProgressMessage("Extracting multimedia details for item...");
}
// First add the multimedia for this item
var links = SupportService.GetMultimediaItems(TraitCategoryType.Taxon.ToString(), taxonId);
var taxon = TaxaService.GetTaxon(taxonId);
foreach (MultimediaLink link in links)
{
AddTaxonRow(results, taxon, link);
}
if (_includeMaterial)
{
AddMaterialRowsForTaxon(results, taxon);
}
if (_recurse)
{
// Now find all the children of this item
if (progress != null)
{
progress.ProgressMessage("Retrieving child items...");
}
var children = TaxaService.GetExpandFullTree(taxonId);
var elementCount = 0;
int total = children.Count;
if (progress != null)
{
progress.ProgressStart("Extracting multimedia 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++;
links = SupportService.GetMultimediaItems(TraitCategoryType.Taxon.ToString(), child.TaxaID.Value);
foreach (MultimediaLink link in links)
{
AddTaxonRow(results, child, link);
}
if (_includeMaterial)
{
AddMaterialRowsForTaxon(results, child);
}
}
}
if (progress != null)
{
progress.ProgressEnd(string.Format("{0} multimedia items found.", results.Rows.Count));
}
return(results);
}
public override DataMatrix ExtractReportData(IProgressObserver progress)
{
var matrix = new DataMatrix();
if (IsGroupedByTaxon)
{
matrix.Columns.Add(new MatrixColumn {
Name = "TaxonName"
});
matrix.Columns.Add(new MatrixColumn {
Name = "BiotaID", IsHidden = true
});
}
matrix.Columns.Add(new MatrixColumn {
Name = "Count"
});
foreach (string colname in SelectedColumns)
{
matrix.Columns.Add(new MatrixColumn {
Name = colname
});
}
// Open the feature layer data
SelectedFeatureLayer.DataSource.Open();
var map = new Dictionary <string, FeatureCountPair>();
if (progress != null)
{
progress.ProgressMessage("Counting points...", 0);
}
int pointCount = 0;
foreach (VectorLayer pointLayer in SelectedPointLayers)
{
var ds = pointLayer.DataSource;
ds.Open();
pointCount += ds.GetFeatureCount();
}
if (progress != null)
{
progress.ProgressStart(String.Format("Processing {0} points...", pointCount));
}
int processed = 0;
int notFoundCount = 0;
var materialService = new MaterialService(User);
var taxaService = new TaxaService(User);
foreach (VectorLayer pointLayer in SelectedPointLayers)
{
var pointProvider = pointLayer.DataSource;
pointProvider.Open();
for (uint i = 0; i < pointProvider.GetFeatureCount(); ++i)
{
var row = pointProvider.GetFeature(i);
Taxon taxon = null;
if (IsGroupedByTaxon)
{
int?materialId = (int?)row["MaterialID"];
if (materialId.HasValue)
{
var m = materialService.GetMaterial(materialId.Value);
if (m.BiotaID > 0)
{
if (_taxonCache.ContainsKey(m.BiotaID))
{
taxon = _taxonCache[m.BiotaID];
}
else
{
taxon = taxaService.GetTaxon(m.BiotaID);
_taxonCache[m.BiotaID] = taxon;
}
}
}
}
SharpMap.Geometries.Point p = row.Geometry as Point;
if (!ProcessPoint(SelectedFeatureLayer.DataSource, pointLayer, p, map, taxon))
{
notFoundCount++;
}
processed++;
if (progress != null)
{
double percent = ((double)processed) / ((double)pointCount) * 100;
progress.ProgressMessage(String.Format("Processing {0} points...", pointCount), percent);
}
}
}
if (progress != null)
{
progress.ProgressMessage("Constructing result set...", 100);
}
int countIndex = matrix.IndexOf("Count");
int taxaIndex = matrix.IndexOf("TaxonName");
int biotaIDIndex = matrix.IndexOf("BiotaID");
foreach (FeatureCountPair pair in map.Values)
{
var matrixRow = matrix.AddRow();
foreach (DataColumn col in pair.First.Table.Columns)
{
if (SelectedColumns.Contains(col.ColumnName))
{
var index = matrix.IndexOf(col.ColumnName);
matrixRow[index] = pair.First[col];
}
}
matrixRow[countIndex] = pair.Second;
if (IsGroupedByTaxon)
{
matrixRow[taxaIndex] = pair.Taxon == null ? "Unidentified" : pair.Taxon.TaxaFullName;
matrixRow[biotaIDIndex] = pair.Taxon == null ? -1 : pair.Taxon.TaxaID.Value;
}
}
if (IncludeUnmatchedPointRow && notFoundCount > 0)
{
var unmatched = matrix.AddRow();
unmatched[countIndex] = notFoundCount;
}
if (progress != null)
{
progress.ProgressEnd(String.Format("{0} points processed.", pointCount));
}
return(matrix);
}
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++;
}
}