protected void ProgressStart(string message, bool indeterminate = false)
{
if (ProgressObserver != null)
{
ProgressObserver.ProgressStart(message, indeterminate);
}
}
public override Data.DataMatrix ExtractReportData(IProgressObserver progress)
{
var service = new MaterialService(User);
if (progress != null) {
progress.ProgressStart(string.Format("Retrieving Material records for Trap {0}", Trap.DisplayLabel), true);
}
var serviceMessage = new ServiceMessageDelegate((message) => {
progress.ProgressMessage(message, 0);
});
service.ServiceMessage += serviceMessage;
DataMatrix matrix = service.GetMaterialForTrap(Trap.ElemID);
service.ServiceMessage -= serviceMessage;
if (progress != null) {
progress.ProgressEnd(string.Format("{0} rows retreived", matrix.Rows.Count));
}
matrix.Columns.Add(new FormattedLatLongVirtualColumn(matrix));
matrix.Columns.Add(new FormattedDateVirtualColumn(matrix));
return matrix;
}
public override DataMatrix ExtractReportData(IProgressObserver progress)
{
if (progress != null)
{
progress.ProgressStart(string.Format("Retrieving Material records for {0}", Taxon.DisplayLabel), true);
}
var serviceMessage = new ServiceMessageDelegate((message) => {
progress.ProgressMessage(message, 0);
});
Service.ServiceMessage += serviceMessage;
DataMatrix matrix = Service.GetMaterialForTaxon(Taxon.TaxaID.Value);
Service.ServiceMessage -= serviceMessage;
if (progress != null)
{
progress.ProgressEnd(string.Format("{0} rows retreived", matrix.Rows.Count));
}
matrix.Columns.Add(new FormattedLatLongVirtualColumn(matrix));
matrix.Columns.Add(new FormattedDateVirtualColumn(matrix));
return(matrix);
}
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;
}
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);
}
public void ExportXML(List <int> taxonIds, XMLIOExportOptions options, IProgressObserver progress, Func <bool> isCancelledCallback)
{
try {
if (progress != null)
{
progress.ProgressStart("Counting total taxa to export...");
}
var exporter = new XMLIOExporter(User, taxonIds, options, progress, isCancelledCallback);
exporter.Export();
} finally {
if (progress != null)
{
progress.ProgressEnd("Export complete.");
}
}
}
public bool OnProgress(string message, double percentComplete, ProgressEventType progressEventType)
{
if (_observer != null)
{
switch (progressEventType)
{
case ProgressEventType.Start:
_observer.ProgressStart(message);
break;
case ProgressEventType.Update:
_observer.ProgressMessage(message, percentComplete);
break;
case ProgressEventType.End:
_observer.ProgressEnd(message);
break;
}
}
return(true);
}
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);
}
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 UpdateCheckResults CheckForUpdates(IProgressObserver progress)
{
// Get the running apps version to compare...
// We need to use the parent window because its the main application assembly version we want, not this plugin.
var v = PluginManager.Instance.ParentWindow.GetType().Assembly.GetName().Version;
var results = new UpdateCheckResults {
CurrentMajor = v.Major, CurrentMinor = v.Minor, CurrentBuild = v.Revision, UpdateExists = false, UpdateLink = ""
};
if (progress != null)
{
progress.ProgressStart("Checking for updates...");
}
Config.SetGlobal("BioLink.UpdateURL", "http://downloads.ala.org.au/feed/p/biolink");
var updateURL = Config.GetGlobal("BioLink.UpdateURL", "http://downloads.ala.org.au/feed/p/biolink");
try {
if (progress != null)
{
progress.ProgressMessage("Contacting update site...");
}
var reader = XmlReader.Create(updateURL);
var feed = SyndicationFeed.Load(reader);
if (progress != null)
{
progress.ProgressMessage("Checking update site data...");
}
var pattern = new Regex(@"BioLinkInstaller-(\d+)[.](\d+)[.](\d+)[.]exe");
foreach (SyndicationItem item in feed.Items)
{
foreach (var link in item.Links)
{
var m = pattern.Match(link.Uri.AbsoluteUri);
if (m.Success)
{
bool updateExists = false;
var major = Int32.Parse(m.Groups[1].Value);
var minor = Int32.Parse(m.Groups[2].Value);
var build = Int32.Parse(m.Groups[3].Value);
if (major > results.CurrentMajor)
{
updateExists = true;
}
else if (major == results.CurrentMajor)
{
if (minor > results.CurrentMinor)
{
updateExists = true;
}
else if (minor == results.CurrentMinor)
{
updateExists = build > results.CurrentBuild;
}
}
if (updateExists)
{
results.UpdateMajor = major;
results.UpdateMinor = minor;
results.UpdateBuild = build;
results.UpdateExists = true;
results.UpdateLink = link.Uri.AbsoluteUri;
return(results);
}
}
}
}
} catch (Exception ex) {
GlobalExceptionHandler.Handle(ex);
} finally {
if (progress != null)
{
progress.ProgressEnd("Update check complete.");
}
}
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);
}
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)
{
if (progress != null)
{
progress.ProgressMessage("Phase 1: Finding associate relationships...");
}
int[] ids = new int[Taxa.Count];
int i = 0;
foreach (TaxonViewModel vm in Taxa)
{
ids[i++] = vm.TaxaID.Value;
}
var matrix = Service.GetAssociatesForTaxa(RegionID, this.StripRTF, ids);
var index = matrix.IndexOf("AssociateID");
if (index >= 0)
{
if (progress != null)
{
progress.ProgressMessage("Phase 2: Retrieving associates...");
}
var idList = new List <int>();
foreach (MatrixRow row in matrix)
{
var associateId = (int)row[index];
if (!idList.Contains(associateId))
{
idList.Add(associateId);
}
}
if (progress != null)
{
progress.ProgressStart("Phase 3: Building view models...");
}
var viewModels = new List <AssociateReportViewModel>();
if (idList.Count > 0)
{
var service = new SupportService(PluginManager.Instance.User);
var associates = service.GetAssociatesById(idList);
int count = 0;
foreach (Associate m in associates)
{
count++;
if (progress != null)
{
var percentComplete = ((double)count / (double)associates.Count) * 100.0;
progress.ProgressMessage("Phase 3: Building view models...", percentComplete);
}
var vm = new AssociateReportViewModel(m);
if (m.FromCatID == TraitCategoryTypeHelper.GetTraitCategoryTypeID(TraitCategoryType.Material))
{
vm.FromViewModel = GetViewModel(LookupType.Material, m.FromIntraCatID);
}
else if (m.FromCatID == TraitCategoryTypeHelper.GetTraitCategoryTypeID(TraitCategoryType.Taxon))
{
vm.FromViewModel = GetViewModel(LookupType.Taxon, m.FromIntraCatID);
}
else
{
vm.FromViewModel = new ViewModelPlaceholder(m.AssocDescription, "images/Description.png");
}
if (m.ToCatID == TraitCategoryTypeHelper.GetTraitCategoryTypeID(TraitCategoryType.Material))
{
vm.ToViewModel = GetViewModel(LookupType.Material, m.ToIntraCatID);
}
else if (m.ToCatID == TraitCategoryTypeHelper.GetTraitCategoryTypeID(TraitCategoryType.Taxon))
{
vm.ToViewModel = GetViewModel(LookupType.Taxon, m.ToIntraCatID);
}
else
{
vm.ToViewModel = new ViewModelPlaceholder(m.AssocDescription, "images/Description.png");
}
viewModels.Add(vm);
}
progress.ProgressEnd("Complete.");
}
matrix.Tag = viewModels;
}
return(matrix);
}
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;
}
public UpdateCheckResults CheckForUpdates(IProgressObserver progress)
{
// Get the running apps version to compare...
// We need to use the parent window because its the main application assembly version we want, not this plugin.
var v = PluginManager.Instance.ParentWindow.GetType().Assembly.GetName().Version;
var results = new UpdateCheckResults { CurrentMajor = v.Major, CurrentMinor = v.Minor, CurrentBuild = v.Revision, UpdateExists = false, UpdateLink = "" };
if (progress != null) {
progress.ProgressStart("Checking for updates...");
}
Config.SetGlobal("BioLink.UpdateURL", "http://downloads.ala.org.au/feed/p/biolink");
var updateURL = Config.GetGlobal("BioLink.UpdateURL", "http://downloads.ala.org.au/feed/p/biolink");
try {
if (progress != null) {
progress.ProgressMessage("Contacting update site...");
}
var reader = XmlReader.Create(updateURL);
var feed = SyndicationFeed.Load(reader);
if (progress != null) {
progress.ProgressMessage("Checking update site data...");
}
var pattern = new Regex(@"BioLinkInstaller-(\d+)[.](\d+)[.](\d+)[.]exe");
foreach (SyndicationItem item in feed.Items) {
foreach (var link in item.Links) {
var m = pattern.Match(link.Uri.AbsoluteUri);
if (m.Success) {
bool updateExists = false;
var major = Int32.Parse(m.Groups[1].Value);
var minor = Int32.Parse(m.Groups[2].Value);
var build = Int32.Parse(m.Groups[3].Value);
if (major > results.CurrentMajor) {
updateExists = true;
} else if (major == results.CurrentMajor) {
if (minor > results.CurrentMinor) {
updateExists = true;
} else if (minor == results.CurrentMinor) {
updateExists = build > results.CurrentBuild;
}
}
if (updateExists) {
results.UpdateMajor = major;
results.UpdateMinor = minor;
results.UpdateBuild = build;
results.UpdateExists = true;
results.UpdateLink = link.Uri.AbsoluteUri;
return results;
}
}
}
}
} catch (Exception ex) {
GlobalExceptionHandler.Handle(ex);
} finally {
if (progress != null) {
progress.ProgressEnd("Update check complete.");
}
}
return results;
}
