public MemoryStream CreateExcelFile(MatchSettingsViewModel options, List <DyntaxaMatchItem> items, ExcelFileFormat fileFormat)
{
var excelFile = new MatchExcelFile();
var dataTable = GetResultTable(items, options);
return(excelFile.CreateExcelFile(dataTable, fileFormat, true));
}
/// <summary>
/// Method that generate a list och match items based on a single string.
/// </summary>
/// <param name="text">A text string.</param>
/// <param name="options">Options determining the match proces.</param>
/// <returns></returns>
public List <DyntaxaMatchItem> GetDyntaxaMatchItemsFromText(string text, MatchSettingsViewModel options)
{
string[] stringArray = null;
switch (options.RowDelimiter)
{
case MatchTaxonRowDelimiter.ReturnLinefeed:
stringArray = options.ClipBoard.Split('\n');
break;
case MatchTaxonRowDelimiter.Semicolon:
stringArray = options.ClipBoard.Split(';');
break;
case MatchTaxonRowDelimiter.Tab:
stringArray = options.ClipBoard.Split('\t');
break;
case MatchTaxonRowDelimiter.VerticalBar:
stringArray = options.ClipBoard.Split('|');
break;
default:
stringArray = options.ClipBoard.Split('\n');
break;
}
return(GetMatches(stringArray, options));
}
/// <summary>
/// A method that perform matches of taxon identifiers provided in a list.
/// </summary>
/// <param name="items">List of match items or identifiers that should be matched with taxon concepts in Dyntaxa.</param>
/// <param name="options">Options determining the matching process.</param>
/// <returns>A list of matches</returns>
public List <DyntaxaMatchItem> GetMatches(List <DyntaxaMatchItem> items, MatchSettingsViewModel options)
{
var matches = new List <DyntaxaMatchItem>();
int row = 1;
foreach (var item in items)
{
item.RowNumber = row++;
matches.Add(item.Status.Equals(MatchStatus.Undone) ? GetMatch(item, options) : item);
}
return(matches);
}
public void SetTaxon(ITaxon taxon, MatchSettingsViewModel options)
{
IUserContext userContext = CoreData.UserManager.GetCurrentUser();
this.TaxonId = taxon.Id;
this.ScientificName = taxon.ScientificName;
this.GUID = taxon.Guid;
this.Author = taxon.Author;
this.CommonName = taxon.CommonName.IsNotEmpty() ? taxon.CommonName : "";
this.TaxonCategory = taxon.Category.Name;
if (options.OutputRecommendedGUID)
{
this.RecommendedGUID = taxon.GetRecommendedGuid(userContext);
}
if (options.OutputSwedishOccurrence)
{
try
{
//Dictionary<FactorId, SpeciesFact> dicSpeciesFacts = SpeciesFactHelper.GetSpeciesFacts(taxon, new[] { FactorId.SwedishOccurence, FactorId.SwedishHistory });
Dictionary <ArtDatabanken.Data.FactorId, ArtDatabanken.Data.SpeciesFact> dicSpeciesFacts = SpeciesFactHelper.GetCommonDyntaxaSpeciesFacts(userContext, taxon);
this.SwedishOccurrence = SpeciesFactHelper.GetFactorValue(dicSpeciesFacts, ArtDatabanken.Data.FactorId.SwedishOccurrence);
//this.SwedishHistory = SpeciesFactHelper.GetFactorValue(dicSpeciesFacts, FactorId.SwedishHistory);
}
catch (Exception)
{
this.SwedishOccurrence = "";
}
}
//base.SetTaxon(taxon);
//base.Author = taxon.Author;
//base.CommonName = taxon.CommonName;
//base.Id = taxon.Id;
//base.ScientificName = taxon.ScientificName;
//base.TaxonCategory = taxon.TaxonType.Name;
//base.TaxonCategoryId = taxon.TaxonType.Id;
//base.TaxonCategorySortOrder = taxon.TaxonType.SortOrder;
//base.TaxonId = taxon.Id.ToString();
//base.GUID = Resources.DyntaxaSettings.Default.LSIDString.Replace("[TaxonId]", taxon.Id.ToString());
}
public List <DyntaxaMatchItem> GetMatches(List <Int32> taxonIds, MatchSettingsViewModel options)
{
var list = new List <DyntaxaMatchItem>();
// todo - it would be nice if GetTaxaByIds don't throw Exception on non existing taxon ids.
//var taxa = CoreData.TaxonManager.GetTaxaByIds(_user, taxonIds);
int row = 1;
foreach (Int32 id in taxonIds)
{
var matchItem = new DyntaxaMatchItem(id);
matchItem.RowNumber = row++;
ITaxon taxon = null;
try
{
taxon = CoreData.TaxonManager.GetTaxon(_user, id);
}
catch { }
if (taxon != null)
{
matchItem.SetTaxon(taxon, options);
matchItem.Status = MatchStatus.Exact;
}
else
{
matchItem.Status = MatchStatus.NoMatch;
}
list.Add(matchItem);
}
return(list);
}
/// <summary>
/// Procedure that writes match results into a DataTable.
/// </summary>
/// <param name="items"></param>
/// <param name="options"></param>
/// <returns></returns>
public DataTable GetResultTable(List <DyntaxaMatchItem> items, MatchSettingsViewModel options)
{
var table = new DataTable();
//Provided
var column = new DataColumn();
column.Caption = options.LabelForProvidedText;
column.ColumnName = "Provided";
if (options.MatchToType == MatchTaxonToType.TaxonId)
{
column.DataType = typeof(Int32);
}
table.Columns.Add(column);
//Match status
column = new DataColumn();
column.Caption = Resources.DyntaxaResource.MatchOptionsOutputMatchStatusLabel;
column.ColumnName = "MatchStatus";
table.Columns.Add(column);
//Taxon id
if (options.OutputTaxonId)
{
column = new DataColumn();
column.Caption = Resources.DyntaxaResource.MatchOptionsOutputTaxonIdLabel;
column.ColumnName = "TaxonId";
column.DataType = typeof(Int32);
table.Columns.Add(column);
}
//Recommended scientific name
if (options.OutputScientificName)
{
column = new DataColumn();
column.Caption = Resources.DyntaxaResource.MatchOptionsOutputScientificNameLabel;
column.ColumnName = "ScientificName";
table.Columns.Add(column);
}
//Author of recommended scientific name
if (options.OutputAuthor)
{
column = new DataColumn();
column.Caption = Resources.DyntaxaResource.MatchOptionsOutputAuthorLabel;
column.ColumnName = "Author";
table.Columns.Add(column);
}
//Recommended common name
if (options.OutputCommonName)
{
column = new DataColumn();
column.Caption = Resources.DyntaxaResource.MatchOptionsOutputCommonNameLabel;
column.ColumnName = "CommonName";
table.Columns.Add(column);
}
//Taxon category
if (options.OutputTaxonCategory)
{
column = new DataColumn();
column.Caption = Resources.DyntaxaResource.MatchOptionsOutputTaxonCetegoryLabel;
column.ColumnName = "TaxonCategory";
table.Columns.Add(column);
}
//Scientific Synonyms
if (options.OutputScientificSynonyms)
{
column = new DataColumn();
column.Caption = Resources.DyntaxaResource.MatchOptionsOutputScientificSynonymsLabel;
column.ColumnName = "ScientificSynonyms";
table.Columns.Add(column);
}
//Parent taxa
if (options.OutputParentTaxa)
{
column = new DataColumn();
column.Caption = Resources.DyntaxaResource.MatchOptionsOutputParentTaxaLabel;
column.ColumnName = "ParentTaxa";
table.Columns.Add(column);
}
//GUID
if (options.OutputGUID)
{
column = new DataColumn();
column.Caption = Resources.DyntaxaResource.MatchOptionsOutputGUIDLabel;
column.ColumnName = "GUID";
table.Columns.Add(column);
}
// Recommended GUID
if (options.OutputRecommendedGUID)
{
column = new DataColumn();
column.Caption = Resources.DyntaxaResource.ExportStraightColumnRecommendedGUID;
column.ColumnName = "RecommendedGUID";
table.Columns.Add(column);
}
// Swedish occurrence
if (options.OutputSwedishOccurrence)
{
column = new DataColumn();
column.Caption = Resources.DyntaxaResource.ExportStraightSwedishOccurrence;
column.ColumnName = "SwedishOccurrence";
table.Columns.Add(column);
}
foreach (DyntaxaMatchItem item in items)
{
table.Rows.Add();
table.Rows[table.Rows.Count - 1]["Provided"] = item.ProvidedText;
table.Rows[table.Rows.Count - 1]["MatchStatus"] = item.Status;
if (item.Status == MatchStatus.Exact || item.Status == MatchStatus.Fuzzy || item.Status == MatchStatus.ManualSelection)
{
if (options.OutputTaxonId)
{
table.Rows[table.Rows.Count - 1]["TaxonId"] = item.TaxonId;
}
if (options.OutputScientificName)
{
table.Rows[table.Rows.Count - 1]["ScientificName"] = item.ScientificName;
}
if (options.OutputAuthor)
{
table.Rows[table.Rows.Count - 1]["Author"] = item.Author;
}
if (options.OutputCommonName)
{
table.Rows[table.Rows.Count - 1]["CommonName"] = item.CommonName;
}
if (options.OutputTaxonCategory)
{
table.Rows[table.Rows.Count - 1]["TaxonCategory"] = item.TaxonCategory;
}
if (options.OutputScientificSynonyms)
{
table.Rows[table.Rows.Count - 1]["ScientificSynonyms"] = item.ScientificSynonyms;
}
if (options.OutputParentTaxa)
{
table.Rows[table.Rows.Count - 1]["ParentTaxa"] = item.ParentTaxa;
}
if (options.OutputGUID)
{
table.Rows[table.Rows.Count - 1]["GUID"] = item.GUID;
}
if (options.OutputRecommendedGUID)
{
table.Rows[table.Rows.Count - 1]["RecommendedGUID"] = item.RecommendedGUID;
}
if (options.OutputSwedishOccurrence)
{
table.Rows[table.Rows.Count - 1]["SwedishOccurrence"] = item.SwedishOccurrence;
}
}
if (item.Status == MatchStatus.NeedsManualSelection)
{
if (options.OutputScientificName)
{
var alternativeTaxa = new StringBuilder();
foreach (var taxon in item.AlternativeTaxa)
{
if (taxon.Value != "0")
{
alternativeTaxa.Append("; ");
}
alternativeTaxa.Append(taxon.Text);
}
table.Rows[table.Rows.Count - 1]["ScientificName"] = alternativeTaxa.ToString();
}
}
}
return(table);
}
/// <summary>
/// The general matching algorithm.
/// This method is called by all the other methods in order to get the match result.
/// </summary>
/// <param name="item">The match item.</param>
/// <param name="options">Match options.</param>
/// <returns></returns>
private DyntaxaMatchItem GetMatch(DyntaxaMatchItem item, MatchSettingsViewModel options)
{
item.Status = MatchStatus.NoMatch;
if (options.ColumnContentAlternative == MatchColumnContentAlternative.NameAndAuthorCombined)
{
//TODO: split name and author
/*
* StringBuilder name = new StringBuilder();
* StringBuilder author = new StringBuilder();
* bool nameIsCompleted = false;
* string[] stringArray = item.NameString.Split(' ');
* for (int i = 0; i < stringArray.Length; i++)
* {
* if (!nameIsCompleted)
* {
* if (name.Length > 0)
* {
* name.Append(" ");
*
* }
* name.Append(stringArray[i]);
* }
* }
*/
}
//ITaxonSearchCriteria taxonSearchCriteria = new TaxonSearchCriteria();
//taxonSearchCriteria.TaxonName = item.NameString;
////taxonSearchCriteria.TaxonIds =
////taxonSearchCriteria.TaxonCategoryIds =
//CoreData.TaxonManager.GetTaxaBySearchCriteria(_user, taxonSearchCriteria);
//var taxonNameSearchCriteria = new TaxonNameSearchCriteria();
//taxonNameSearchCriteria.NameSearchString = new StringSearchCriteria();
//taxonNameSearchCriteria.NameSearchString.SearchString = item.NameString;
//taxonNameSearchCriteria.NameSearchString.CompareOperators = new List<StringCompareOperator>();
//taxonNameSearchCriteria.NameSearchString.CompareOperators.Add(StringCompareOperator.Iterative);
//if (options.LimitToTaxon && options.LimitToParentTaxonId.HasValue)
//{
// taxonNameSearchCriteria.TaxonIdList = new List<int> { options.LimitToParentTaxonId.Value };
//}
options.SearchOptions.NameSearchString = item.NameString;
TaxonNameSearchCriteria taxonNameSearchCriteria = options.SearchOptions.CreateTaxonNameSearchCriteriaObject();
if (options.MatchToType == MatchTaxonToType.TaxonNameAndAuthor)
{
taxonNameSearchCriteria.IsAuthorIncludedInNameSearchString = true;
}
TaxonNameList taxonNames = CoreData.TaxonManager.GetTaxonNames(_user, taxonNameSearchCriteria);
if (taxonNames.IsNotEmpty())
{
var dicTaxonNames = new Dictionary <int, ITaxonName>();
foreach (ITaxonName taxonName in taxonNames)
{
if (taxonName.Status.Id == (int)TaxonNameStatusId.Removed)
{
continue;
}
if (!dicTaxonNames.ContainsKey(taxonName.Taxon.Id))
{
dicTaxonNames.Add(taxonName.Taxon.Id, taxonName);
}
}
if (dicTaxonNames.Count == 1)
{
ITaxon taxon = CoreData.TaxonManager.GetTaxon(_user, dicTaxonNames.Keys.First());
item.SetTaxon(taxon, options);
item.Status = MatchStatus.Exact;
}
else if (dicTaxonNames.Count > 1)
{
item.Status = MatchStatus.NeedsManualSelection;
item.DropDownListIdentifier = "AlternativeTaxa" + item.RowNumber.ToString();
item.AlternativeTaxa = new TaxonSelectList(taxonNames).GetList(); // todo - den här ska vara med
}
}
else
{
//TODO: Using som fuzzy algorithms to obtain taxon suggestions.
}
return(item);
}
public List <DyntaxaMatchItem> GetMatchResults(List <DyntaxaMatchItem> items, MatchSettingsViewModel options)
{
foreach (DyntaxaMatchItem item in items)
{
if (item.Status == MatchStatus.NeedsManualSelection)
{
if (item.TaxonId != 0)
{
try
{
ITaxon taxon = CoreData.TaxonManager.GetTaxon(_user, item.TaxonId);
item.SetTaxon(taxon, options);
item.Status = MatchStatus.ManualSelection;
if (options.OutputParentTaxa)
{
item.ParentTaxa = GetParenTaxa(taxon);
}
if (options.OutputScientificSynonyms)
{
item.ScientificSynonyms = GetScientificSynonyms(taxon);
}
}
catch (Exception)
{
// int x = 8;
}
}
}
else if (item.Status == MatchStatus.Exact || item.Status == MatchStatus.ManualSelection)
{
ITaxon taxon = CoreData.TaxonManager.GetTaxon(_user, item.TaxonId);
//item.SetTaxon(taxon);
if (options.OutputParentTaxa)
{
item.ParentTaxa = GetParenTaxa(taxon);
}
if (options.OutputScientificSynonyms)
{
item.ScientificSynonyms = GetScientificSynonyms(taxon);
}
}
}
return(items);
}
/// <summary>
/// A method that perform matches of taxon identifiers provided in a list.
/// </summary>
/// <param name="items">Array of strings representing names or identifiers that should be matched with taxon concepts in Dyntaxa.</param>
/// <param name="options">Options determining the matching process.</param>
/// <returns>A list of matches</returns>
public List <DyntaxaMatchItem> GetMatches(string[] items, MatchSettingsViewModel options)
{
var list = new List <DyntaxaMatchItem>();
if (options.MatchToType == MatchTaxonToType.TaxonId)
{
var ids = new List <Int32>();
foreach (var item in items)
{
Int32 id;
if (Int32.TryParse(item, out id))
{
ids.Add(id);
}
}
return(this.GetMatches(ids, options));
}
else
{
for (int i = 0; i < items.Count(); i++)
{
string item = items[i];
if (!((i == items.Count() - 1) && item == ""))
{
DyntaxaMatchItem matchItem;
if (options.ColumnContentAlternative == MatchColumnContentAlternative.NameAndAuthorInSeparateColumns)
{
string[] stringArray = null;
switch (options.ColumnDelimiter)
{
case MatchTaxonColumnDelimiter.Semicolon:
stringArray = item.Split(';');
break;
case MatchTaxonColumnDelimiter.Tab:
stringArray = item.Split('\t');
break;
case MatchTaxonColumnDelimiter.VerticalBar:
stringArray = item.Split('|');
break;
default:
stringArray = item.Split('\t');
break;
}
if (stringArray.Length > 1)
{
matchItem = new DyntaxaMatchItem(stringArray[0], stringArray[1]);
}
else
{
matchItem = new DyntaxaMatchItem(item);
}
}
else
{
matchItem = new DyntaxaMatchItem(item);
}
list.Add(matchItem);
}
}
}
return(GetMatches(list, options));
}
/// <summary>
/// A method that perform matches of taxon identifiers provided in a list.
/// </summary>
/// <param name="filePath">Full file name including its path of an excel file including the provided list of taxon identifiers.</param>
/// <param name="options">Options determining the matching process.</param>
/// <returns>A list of matches.</returns>
public List <DyntaxaMatchItem> GetMatches(string filePath, MatchSettingsViewModel options)
{
string strName;
var list = new List <DyntaxaMatchItem>();
//var file = new ExcelFile(filePath, options.IsFirstRowColumnName);
var file = new XlsxExcelFile(filePath, options.IsFirstRowColumnName);
DataTable table = file.DataTable;
if (table.Rows.Count > 0 && table.Columns.Count > 0)
{
if (options.MatchToType == MatchTaxonToType.TaxonId)
{
var ids = new List <Int32>();
foreach (DataRow row in table.Rows)
{
int id;
if (Int32.TryParse(row[0].ToString(), out id))
{
ids.Add(id);
}
}
list = this.GetMatches(ids, options);
}
else if (options.MatchToType == MatchTaxonToType.TaxonNameAndAuthor)
{
if (table.Columns.Count >= 2)
{
foreach (DataRow row in table.Rows)
{
string strColumn1 = row[0].ToString();
string strColumn2 = row[1].ToString();
if (string.IsNullOrEmpty(strColumn1))
{
strName = strColumn2;
}
else if (string.IsNullOrEmpty(strColumn2))
{
strName = strColumn1;
}
else
{
strName = string.Format("{0} {1}", row[0], row[1]).Trim();
}
if (!string.IsNullOrEmpty(strName))
{
var matchItem = new DyntaxaMatchItem(strName);
list.Add(matchItem);
}
}
}
else
{
foreach (DataRow row in table.Rows)
{
strName = row[0].ToString();
if (!string.IsNullOrEmpty(strName))
{
var matchItem = new DyntaxaMatchItem(strName);
list.Add(matchItem);
}
}
}
}
else
{
foreach (DataRow row in table.Rows)
{
strName = row[0].ToString();
if (!string.IsNullOrEmpty(strName))
{
var matchItem = new DyntaxaMatchItem(strName);
list.Add(matchItem);
}
}
}
}
return(GetMatches(list, options));
}
