/// <summary>
/// Creates a new Lithologic Subinterval
/// </summary>
public LithologicSubinterval(int subID, LithologicDescription Description) : this()
{
_ = Description ?? throw new ArgumentNullException(nameof(Description));
LithologicSubID = subID;
SectionInfo = Description.SectionInfo;
}
/// <summary>
/// Returns a string ID based off the hierarchal information of a lithologic description
/// </summary>
/// <param name="description">The lithologic description to identify</param>
/// <returns>A string representing a LithologicID</returns>
public string GenerateID(LithologicDescription description)
{
try
{
string LithologicID = GenerateExpedition(description.SectionInfo.Expedition).ToString() +
GenerateExpeditionModifier(description.SectionInfo.Expedition).ToString() +
GenerateSite(description.SectionInfo.Site).ToString() +
GenerateHole(description.SectionInfo.Hole).ToString() +
GenerateCore(description.SectionInfo.Core).ToString() +
GenerateType(description.SectionInfo.Type).ToString() +
GenerateSection(description.SectionInfo.Section).ToString() +
GenerateSectionHalf(description.SectionInfo.Half) +
GenerateOffset(description.StartOffset.ToString()).ToString() +
GenerateOffset(description.EndOffset.ToString()).ToString();
description.LithologicID = LithologicID;
return LithologicID;
}
catch (Exception)
{
throw;
}
}
public static void CheckFile(IODPDataTable IODPDataTable)
{
int rowNumber = 1;
foreach (DataRow row in IODPDataTable.DataTable.Rows)
{
if (!DataRowContainsDescription(row, IODPDataTable))
{
throw new Exception(string.Format("Row {0}: Does not contain description", rowNumber));
}
if (!DataRowContainsSampleIDColumn(row, IODPDataTable))
{
throw new Exception(string.Format("Row {0}: Does not contain SampleID column", rowNumber));
}
if (!DataRowContainsOffsetColumns(row, IODPDataTable))
{
throw new Exception(string.Format("Row {0}: Data row does not contain Offset columns", rowNumber));
}
if (!StartOffsetValuesAreValid(row, IODPDataTable))
{
throw new Exception(string.Format("Row {0}: Does not contain correct Start Offset values", rowNumber));
}
if (!EndOffsetValuesAreValid(row, IODPDataTable))
{
throw new Exception(string.Format("Row {0}: Does not contain correct End Offset values", rowNumber));
}
LithologicDescription Description = new LithologicDescription();
try
{
Description = new LithologicDescription(row[IODPDataTable.SampleIDColumn].ToString());
}
catch (Exception ex)
{
throw new Exception(string.Format("Row {0}: Could not parse SampleID. Error Message: {1}", rowNumber, ex.Message));
}
if (!DescriptionContainsSectionInfo(Description))
{
throw new Exception(string.Format("Row {0}: Description does not contain section information", rowNumber));
}
rowNumber++;
}
}
/// <summary>
/// Gets a collection of LithologicDescriptions from a corrected file.
/// </summary>
/// <param name="filename"></param>
/// <param name="columnIdentifiers"></param>
/// <returns></returns>
public static async Task <ICollection <LithologicDescription> > GetDescriptionsFromFileAsync(string filename, [Optional] IntervalHierarchyNames columnIdentifiers)
{
columnIdentifiers = columnIdentifiers ?? new IntervalHierarchyNames()
{
Expedition = "Expedition_VP",
Site = "Site_VP",
Hole = "Hole_VP",
Core = "Core_VP",
Type = "Type_VP",
Section = "Section_VP",
Half = "SectionHalf_VP",
TopOffset = "TopOffset_VP",
BottomOffset = "BottomOffset_VP",
ArchiveTextID = "ArchiveSectionTextID_VP",
WorkingTextID = "WorkingSectionTextID_VP",
ParentTextID = "ParentSectionTextID_VP"
};
IODPDataTable iODPDataTable = Importer.ImportDataTableFromFile(filename, columnIdentifiers);
ICollection <LithologicDescription> descriptions = new HashSet <LithologicDescription>();
using (DescDBContext dbContext = new DescDBContext())
{
try
{
foreach (DataRow row in iODPDataTable.DataTable.Rows)
{
SectionInfo section = new SectionInfo(Importer.GetHierarchyValuesFromDataRow(row, columnIdentifiers));
LithologicDescription description = new LithologicDescription();
// description.SectionInfo = section;
description.SectionInfo = await DatabaseWorkflowHandler.GetSectionInfoFromDatabaseForIntervalAsync(dbContext, section).ConfigureAwait(true);
description.LithologicID = row["LithologicID_VP"].ToString();
description.DataRow = row;
description.DescriptionReport = row["Filename_VP"].ToString();;
description.StartOffset = double.TryParse(row[columnIdentifiers.TopOffset].ToString(), out double startOffset) ? startOffset : -1;
description.EndOffset = double.TryParse(row[columnIdentifiers.BottomOffset].ToString(), out double endOffset) ? endOffset : -1;
descriptions.Add(description);
}
}
catch (Exception)
{
throw new Exception("Error creating lithologic description from data row");
}
}
return(descriptions);
}
private static void AddDataToHierarchyColumns(IODPDataTable IODPDataTable, string fileName, DataTable allSectionsDataTable)
{
int rowNumber = 1;
IntervalHierarchyNames sectionTableColumnNames = new IntervalHierarchyNames()
{
Expedition = "Exp",
Site = "Site",
Hole = "Hole",
Core = "Core",
Type = "Type",
Section = "Sect"
};
foreach (DataRow row in IODPDataTable.DataTable.Rows)
{
LithologicDescription description = new LithologicDescription(row[IODPDataTable.SampleIDColumn].ToString());
double parsedOffset = 0;
Importer.StartOffsetValuesAreValid(row, IODPDataTable, ref parsedOffset);
description.StartOffset = parsedOffset;
Importer.EndOffsetValuesAreValid(row, IODPDataTable, ref parsedOffset);
description.EndOffset = parsedOffset;
LithologicIDGenerator idGenerator = new LithologicIDGenerator();
var textids = GetSectionTextIDsForDescription(allSectionsDataTable, description, sectionTableColumnNames);
try
{
var descriptionID = idGenerator.GenerateID(description);
row.BeginEdit();
row["Filename_VP"] = fileName;
row["LithologicID_VP"] = descriptionID;
row["ArchiveSectionTextID_VP"] = textids.Archive;
row["WorkingSectionTextID_VP"] = textids.Working;
row["ParentSectionTextID_VP"] = textids.Parent;
row["Expedition_VP"] = description.SectionInfo.Expedition;
row["Site_VP"] = description.SectionInfo.Site;
row["Hole_VP"] = description.SectionInfo.Hole;
row["Core_VP"] = description.SectionInfo.Core;
row["Type_VP"] = description.SectionInfo.Type;
row["Section_VP"] = description.SectionInfo.Section;
row["SectionHalf_VP"] = description.SectionInfo.Half;
row["TopOffset_VP"] = description.StartOffset.ToString();
row["BottomOffset_VP"] = description.EndOffset.ToString();
row.EndEdit();
}
catch (Exception)
{
Log.Warning(string.Format("Row {0}: Unable to populate data for description", rowNumber.ToString()));
}
rowNumber++;
}
}
private static (string Archive, string Working, string Parent) GetSectionTextIDsForDescription(DataTable allSections, LithologicDescription description, IntervalHierarchyNames columnNames)
{
var matchingTextID = allSections.AsEnumerable().Where(x => x.Field <string>(columnNames.Expedition) == description.SectionInfo.Expedition &&
x.Field <string>(columnNames.Site) == description.SectionInfo.Site &&
x.Field <string>(columnNames.Hole) == description.SectionInfo.Hole &&
x.Field <string>(columnNames.Core) == description.SectionInfo.Core &&
x.Field <string>(columnNames.Type) == description.SectionInfo.Type &&
x.Field <string>(columnNames.Section) == description.SectionInfo.Section).FirstOrDefault();
if (matchingTextID == null)
{
return(Archive : "-1", Working : "-1", Parent : "-1");
}
(string Archive, string Working, string Parent)textids = (matchingTextID["Text ID of archive half"].ToString(), matchingTextID["Text ID of working half"].ToString(), matchingTextID["Text ID of section"].ToString());
return(textids);
}
public static bool DescriptionContainsSectionInfo(LithologicDescription description)
{
return(description.SectionInfo.Section != null ? true : false);
}
public static void PrintDescriptionToConsole(LithologicDescription description)
{
Console.WriteLine(string.Format("ID:{0}, LithologicSubID:{1}, StartOffset:{2}, EndOffset:{3}", description.ID, description.LithologicID, description.StartOffset, description.EndOffset));
}
public static async Task <bool> CheckForDescriptionAsync(DescDBContext dBContext, LithologicDescription description)
{
bool recordExists = await dBContext.LithologicDescriptions
.Where(x => x.SectionInfo.ID == description.SectionInfo.ID)
.Where(x => x.DescriptionReport == description.DescriptionReport) //Report names may change depending on how we name the files,
.Where(x => x.StartOffset == description.StartOffset && x.EndOffset == description.EndOffset)
.AnyAsync().ConfigureAwait(true);
return(recordExists);
}
/// <summary>
/// Converts an IODPDataTable object into a collection of Lithologic Descriptions
/// </summary>
/// <param name="dataTable">The datatable to convert</param>
/// <returns></returns>
public static Dictionary <string, LithologicDescription> ConvertDatatableToDictionary(IODPDataTable dataTable, SectionInfoCollection SectionCollection)
{
_ = SectionCollection ?? throw new ArgumentNullException(nameof(SectionCollection));
var LithologyCache = new Dictionary <string, LithologicDescription>();
if (dataTable == null)
{
return(LithologyCache);
}
//Add a column in the datatable to ensure consistency between files with and without descriptions:
dataTable.DataTable.Columns.Add("LithologicID_VP", typeof(string)).SetOrdinal(0);
foreach (DataRow dataTableRow in dataTable.DataTable.Rows)
{
dataTableRow["LithologicID_VP"] = "-1";
if (!Importer.DataRowContainsDescription(dataTableRow, dataTable))
{
return(LithologyCache);
}
if (!Importer.DataRowContainsSampleIDColumn(dataTableRow, dataTable))
{
return(LithologyCache);
}
LithologicDescription description = new LithologicDescription(dataTableRow[dataTable.SampleIDColumn].ToString());
description.SectionInfo = SectionCollection.GetExistingElseAddAndGetCurrentSection(description.SectionInfo);
if (!Importer.DescriptionContainsSectionInfo(description))
{
return(LithologyCache);
}
description.DataRow = dataTableRow;
double parsedOffset = 0;
if (!Importer.DataRowContainsOffsetColumns(dataTableRow, dataTable))
{
return(LithologyCache);
}
if (!Importer.StartOffsetValuesAreValid(dataTableRow, dataTable, ref parsedOffset))
{
return(LithologyCache);
}
description.StartOffset = parsedOffset;
if (!Importer.EndOffsetValuesAreValid(dataTableRow, dataTable, ref parsedOffset))
{
return(LithologyCache);
}
description.EndOffset = parsedOffset;
LithologicIDGenerator IDGenerator = new LithologicIDGenerator();
IDGenerator.GenerateID(description);
if (description.OffsetsSet())
{
description.GenerateSubintervals();
}
description.DataRow["LithologicID_VP"] = description.LithologicID;
//Some descriptions are split in two rows. It's very uncommon, but throws an error
//Only selecting the first row, despite the loss of data
if (!LithologyCache.ContainsKey(description.LithologicID))
{
LithologyCache.Add(description.LithologicID, description);
}
}
return(LithologyCache);
}
