private Plankton IdentifyPlankton(string searchText)
{
Plankton plankton = new Plankton();
TaxonNameList result = this.DyntaxaSession.searchTaxa(searchText);
if (result.IsNotEmpty())
{
if (result.Count == 1)
{
List <Plankton> resultList = this.DyntaxaSession.MakePlanktonList(result);
try
{
plankton = resultList[0];
}
catch (IndexOutOfRangeException e)
{
Console.WriteLine(e);
}
}
else
{
plankton = this.GetUserSelectedPlankton(searchText, result);
}
}
else
{
plankton = this.GetUserSelectedPlankton(searchText, result);
}
return(plankton);
}
private Plankton GetUserSelectedPlankton(string taxonSearch, TaxonNameList matchingResult)
{
var viewModel = new DyntaxaMatchingDialogViewModel($"Found {matchingResult.Count} matches when searching for species: {taxonSearch}", taxonSearch, matchingResult);
Plankton plankton = null;
bool? result = dialogService.ShowDialog(viewModel);
if (result.HasValue)
{
if (result.Value)
{
plankton = viewModel.SelectedPlankton;
}
else
{
plankton = new Plankton(taxonSearch);
// Cancelled
}
}
return(plankton);
}
public List <Plankton> MakePlanktonList(TaxonNameList search)
{
List <Plankton> planktonList = new List <Plankton>();
foreach (TaxonName match in search)
{
Plankton plankton = new Plankton();
ITaxonTreeNode taxonTreeNode = match.Taxon.GetParentTaxonTree(this.getUserContext(), true);
while (taxonTreeNode != null)
{
string categoryName = taxonTreeNode.Taxon.Category.Name;
if (!(plankton.TaxonDyntaxaIDIsInitialized))
{
plankton.TaxonDyntaxaID = taxonTreeNode.Taxon.Id;
}
switch (categoryName)
{
case "Variety":
plankton.TaxonVariety = taxonTreeNode.Taxon.ScientificName;
break;
case "Species":
plankton.TaxonSpecies = taxonTreeNode.Taxon.ScientificName;
break;
case "Genus":
plankton.TaxonGenus = taxonTreeNode.Taxon.ScientificName;
break;
case "Class":
plankton.TaxonClass = taxonTreeNode.Taxon.ScientificName;
break;
case "Family":
plankton.TaxonFamily = taxonTreeNode.Taxon.ScientificName;
break;
case "Order":
plankton.TaxonOrder = taxonTreeNode.Taxon.ScientificName;
break;
case "Phylum":
plankton.TaxonPhylum = taxonTreeNode.Taxon.ScientificName;
break;
case "Superphylum":
plankton.TaxonSuperPhylum = taxonTreeNode.Taxon.ScientificName;
break;
case "Organism group":
plankton.TaxonOrganismGroup = taxonTreeNode.Taxon.ScientificName;
break;
default: break;
}
if (taxonTreeNode.Parents == null)
{
break;
}
taxonTreeNode = taxonTreeNode.Parents[0];
}
planktonList.Add(plankton);
}
return(planktonList);
}
public void ExportSamples()
{
List <string> flags = new List <string> {
"cf", "sp", "spp"
};
List <string> comments = new List <string> {
"avl", "rund", "enstaka", "oval", "runda", "koloni",
"i", "gele", "ovala", "filament", "gelé", "med", "flagell",
"stjärnformad", "bandkoloni", "klyftform", "långsmal",
"gissel", "copepodit", "adult", "naupliuslarv", "hanne",
"bentisk"
};
List <string> ignores = new List <string> {
"um"
};
List <Sample> exportedSamples = new List <Sample>();
foreach (var inputSample in this.Samples)
{
using (var stream = File.Open(inputSample.FilePath, FileMode.Open, FileAccess.Read))
{
// Auto-detect format, supports:
// - Binary Excel files (2.0-2003 format; *.xls)
// - OpenXml Excel files (2007 format; *.xlsx)
using (var reader = ExcelReaderFactory.CreateReader(stream))
{
do
{
int rowNum = 0;
while (reader.Read())
{
// Start of species declarations
if (rowNum >= 13)
{
// End of species declarations
if (reader.GetString(0) == null)
{
break;
}
// Species was counted
if (reader.GetDouble(9) > 0)
{
string taxonSpecies = reader.GetString(0);
Double concentration = reader.GetDouble(12);
Double biovolume = reader.GetDouble(13);
Double freshweight = reader.GetDouble(14);
Plankton plankton = new Plankton(taxonSpecies, concentration, biovolume, freshweight);
plankton.CleanTaxonSpecies(flags, comments, ignores);
Plankton newPlankton = this.IdentifyPlankton(plankton.TaxonSpecies);
newPlankton.TaxonConcentration = plankton.TaxonConcentration;
newPlankton.TaxonBiovolume = plankton.TaxonBiovolume;
newPlankton.ConvertBiovolume(1e-9);
newPlankton.TaxonFreshweight = plankton.TaxonFreshweight;
newPlankton.TaxonMinSize = plankton.TaxonMinSize;
newPlankton.TaxonMaxSize = plankton.TaxonMaxSize;
newPlankton.TaxonSpeciesFlags = plankton.TaxonSpeciesFlags;
newPlankton.TaxonSpeciesComments = plankton.TaxonSpeciesComments;
newPlankton.TaxonSpeciesIgnores = plankton.TaxonSpeciesIgnores;
newPlankton.TaxonSpeciesMinAndMax = plankton.TaxonSpeciesMinAndMax;
inputSample.AddPlankton(newPlankton);
}
}
rowNum++;
}
} while (reader.NextResult());
}
exportedSamples.Add(inputSample);
}
}
foreach (Sample sample in exportedSamples)
{
string FileDir = Path.GetDirectoryName(sample.FilePath);
string FileName = Path.GetFileNameWithoutExtension(sample.FileName);
string FileExt = Path.GetExtension(sample.FileName);
string ExportedFullFileName = $"{FileName}_Exported{FileExt}";
string ExportedFilePath = Path.Combine(FileDir, ExportedFullFileName);
var newFile = new FileInfo(ExportedFilePath);
if (newFile.Exists)
{
newFile.Delete(); // ensures we create a new workbook
newFile = new FileInfo(ExportedFilePath);
}
using (var package = new ExcelPackage(newFile))
{
// Add a new worksheet to the empty workbook
ExcelWorksheet worksheet = package.Workbook.Worksheets.Add("Compilation");
//Add the headers
worksheet.Cells[1, 1].Value = "Origin";
worksheet.Cells[1, 2].Value = "Date";
worksheet.Cells[1, 3].Value = "Sample Number";
worksheet.Cells[1, 4].Value = "Phylum";
worksheet.Cells[1, 5].Value = "Class";
worksheet.Cells[1, 6].Value = "Order";
worksheet.Cells[1, 7].Value = "Species";
worksheet.Cells[1, 8].Value = "Flags";
if (this.phytoSampleIsChecked)
{
worksheet.Cells[1, 9].Value = "Min Size";
worksheet.Cells[1, 10].Value = "Max Size";
worksheet.Cells[1, 11].Value = "Comments";
worksheet.Cells[1, 12].Value = "Dyntaxa ID";
worksheet.Cells[1, 13].Value = "Concentration";
worksheet.Cells[1, 14].Value = "Biovolume";
worksheet.Cells[1, 15].Value = "Analysis Method";
worksheet.Cells[1, 16].Value = "Analysis Laboratory";
}
else if (this.zooSampleIsChecked)
{
worksheet.Cells[1, 9].Value = "Comments";
worksheet.Cells[1, 10].Value = "Dyntaxa ID";
worksheet.Cells[1, 11].Value = "Concentration";
worksheet.Cells[1, 12].Value = "Biovolume";
worksheet.Cells[1, 13].Value = "Analysis Method";
worksheet.Cells[1, 14].Value = "Analysis Laboratory";
}
for (int i = 0; i < sample.exportedSamples.Count; i++)
{
Plankton plankton = sample.exportedSamples[i];
if (string.IsNullOrEmpty(plankton.TaxonPhylum))
{
if (string.IsNullOrEmpty(plankton.TaxonSuperPhylum))
{
if (string.IsNullOrEmpty(plankton.TaxonOrganismGroup) == false)
{
plankton.TaxonPhylum = plankton.TaxonOrganismGroup;
}
}
else
{
plankton.TaxonPhylum = plankton.TaxonSuperPhylum;
}
}
if (string.IsNullOrEmpty(plankton.TaxonSpecies))
{
if (string.IsNullOrEmpty(plankton.TaxonGenus))
{
if (string.IsNullOrEmpty(plankton.TaxonFamily))
{
if (string.IsNullOrEmpty(plankton.TaxonOrder))
{
if (string.IsNullOrEmpty(plankton.TaxonClass))
{
if (string.IsNullOrEmpty(plankton.TaxonPhylum) == false)
{
plankton.TaxonSpecies = plankton.TaxonPhylum;
}
}
else
{
plankton.TaxonSpecies = plankton.TaxonClass;
}
}
else
{
plankton.TaxonSpecies = plankton.TaxonOrder;
}
}
else
{
plankton.TaxonSpecies = plankton.TaxonFamily;
}
}
else
{
plankton.TaxonSpecies = plankton.TaxonGenus;
}
}
else
{
if (string.IsNullOrEmpty(plankton.TaxonVariety) == false)
{
plankton.TaxonSpecies = plankton.TaxonVariety;
}
}
int row = i + 2;
worksheet.Cells[row, 1].Value = sample.Origin;
worksheet.Cells[row, 2].Style.Numberformat.Format = "yyyy-mm-dd";
worksheet.Cells[row, 2].Formula = $"=DATE({sample.Date.Year},{sample.Date.Month},{sample.Date.Day})";
worksheet.Cells[row, 3].Value = sample.SampleNumber;
worksheet.Cells[row, 4].Value = plankton.TaxonPhylum;
worksheet.Cells[row, 5].Value = plankton.TaxonClass;
worksheet.Cells[row, 6].Value = plankton.TaxonOrder;
worksheet.Cells[row, 7].Value = plankton.TaxonSpecies;
worksheet.Cells[row, 8].Value = plankton.GetTaxonSpeciesFlagsAsString();
if (this.phytoSampleIsChecked)
{
if (plankton.TaxonMinSize == 0)
{
worksheet.Cells[row, 9].Value = "";
}
else
{
worksheet.Cells[row, 9].Value = plankton.TaxonMinSize;
}
if (plankton.TaxonMaxSize == 0)
{
worksheet.Cells[row, 10].Value = "";
}
else
{
worksheet.Cells[row, 10].Value = plankton.TaxonMaxSize;
}
worksheet.Cells[row, 11].Value = plankton.GetTaxonSpeciesCommentsAsString();
worksheet.Cells[row, 12].Value = plankton.TaxonDyntaxaID;
worksheet.Cells[row, 13].Value = plankton.TaxonConcentration;
worksheet.Cells[row, 14].Value = plankton.TaxonBiovolume;
worksheet.Cells[row, 15].Value = "SS-EN 15204:2006";
worksheet.Cells[row, 16].Value = "Erkenlaboratoriet";
}
else if (this.zooSampleIsChecked)
{
worksheet.Cells[row, 9].Value = plankton.GetTaxonSpeciesCommentsAsString();
worksheet.Cells[row, 10].Value = plankton.TaxonDyntaxaID;
worksheet.Cells[row, 11].Value = plankton.TaxonConcentration;
worksheet.Cells[row, 12].Value = plankton.TaxonBiovolume;
worksheet.Cells[row, 13].Value = "Naturvårdsverkets Djurplankton i sjöar 2003-05-27";
worksheet.Cells[row, 14].Value = "Erkenlaboratoriet";
}
}
sample.exportedSamples.Clear();
package.Save();
}
}
}
public void AddPlankton(Plankton plankton)
{
this.exportedSamples.Add(plankton);
}