public static Dictionary <int, Measurement> Convert(IODPDataTable dataTable, SectionInfoCollection SectionCollection)
{
_ = SectionCollection ?? throw new ArgumentNullException(nameof(SectionCollection));
_ = dataTable ?? throw new ArgumentNullException(nameof(dataTable));
Dictionary <int, Measurement> _measurements = new Dictionary <int, Measurement>();
int measurementCount = _measurements.Count + 1;
//TODO: Ignore record if error is thrown, ex: offsets with TCON
foreach (DataRow record in dataTable.DataTable.Rows)
{
SectionInfo measurementSectionInfo = new SectionInfo();
try
{
measurementSectionInfo.Expedition = record[dataTable.ExpeditionColumn].ToString();
measurementSectionInfo.Site = record[dataTable.SiteColumn].ToString();
measurementSectionInfo.Hole = record[dataTable.HoleColumn].ToString();
measurementSectionInfo.Core = record[dataTable.CoreColumn].ToString();
measurementSectionInfo.Type = record[dataTable.TypeColumn].ToString();
measurementSectionInfo.Section = record[dataTable.SectionColumn].ToString();
}
catch (Exception)
{
throw new IndexOutOfRangeException(nameof(record));
}
Measurement measurement = new Measurement(measurementSectionInfo);
measurement.SectionInfo = SectionCollection.GetExistingElseAddAndGetCurrentSection(measurement.SectionInfo);
//CARB files throw error here because there isn't an offset field within the file. Ensure there is.
try
{
if (!string.IsNullOrEmpty(dataTable.OffsetColumn))
{
measurement.StartOffset = double.Parse(record[dataTable.OffsetColumn].ToString(), CultureInfo.CurrentCulture);
measurement.EndOffset = double.Parse(record[dataTable.OffsetColumn].ToString(), CultureInfo.CurrentCulture);
}
if (!string.IsNullOrEmpty(dataTable.TopOffsetColumn))
{
measurement.StartOffset = double.Parse(record[dataTable.TopOffsetColumn].ToString(), CultureInfo.CurrentCulture);
}
if (!string.IsNullOrEmpty(dataTable.BottomOffsetColumn))
{
measurement.EndOffset = double.Parse(record[dataTable.BottomOffsetColumn].ToString(), CultureInfo.CurrentCulture);
}
measurement.DataRow = record;
_measurements.Add(measurementCount, measurement);
measurementCount++;
}
catch (Exception)
{
//throw;
}
}
return(_measurements);
}
public static async Task <ICollection <SectionInfo> > GetSectionsFromFileAsync(string fileName, [Optional] IntervalHierarchyNames columnNames)
{
SectionInfoCollection sectionCollection = new SectionInfoCollection();
columnNames = columnNames ?? new IntervalHierarchyNames
{
Expedition = "Exp",
Site = "Site",
Hole = "Hole",
Core = "Core",
Type = "Type",
Section = "Sect",
ParentTextID = "Text ID of section",
ArchiveTextID = "Text ID of archive half",
WorkingTextID = "Text ID of working half"
};
try
{
sectionCollection.ParseSectionInfoFromDataTable(SectionInfoCollection.ImportAllSections(fileName), columnNames);
}
catch (Exception ex)
{
throw new Exception($"{fileName}: Could not parse section info from datatable");
}
return(sectionCollection.Sections);
}
private static void CleanupDescriptionFile(string filePath, string exportFilePath, string errorExportFilePath)
{
var iodpDataTable = Importer.ImportDataTableFromFile(filePath);
string currentFileName = Importer.GetFileName(filePath);
try
{
Importer.CheckFile(iodpDataTable);
AddMissingColumnsToDescriptionTable(iodpDataTable.DataTable);
AddDataToHierarchyColumns(iodpDataTable, Importer.GetFileName(filePath), SectionInfoCollection.ImportAllSections(ConfigurationManager.AppSettings["AllSectionsFile"]));
Log.Information($"{currentFileName}: Processed successfully");
}
catch (Exception ex)
{
Log.Warning($"{currentFileName}: {ex.Message}");
exportFilePath = errorExportFilePath;
}
try
{
Importer.ExportDataTableAsNewFile(exportFilePath, iodpDataTable.DataTable);
}
catch (Exception)
{
throw new Exception($"{currentFileName}: Error exporting to file");
}
}
private static void ProcessData(FileCollection DescriptionFileCollection, FileCollection MeasurementFileCollection)
{
#region ImportDescriptionData
DescriptionFileCollection.Filenames.ForEach(fileName => Console.WriteLine(fileName.ToString()));
var lithologyWorkflowHandler = new CSVLithologyWorkflowHandler();
lithologyWorkflowHandler.FileCollection = DescriptionFileCollection;
lithologyWorkflowHandler.ExportDirectory = DescriptionFileCollection.ExportDirectory;
var SectionCollection = new SectionInfoCollection();
var lithologyCache = lithologyWorkflowHandler.ImportCache(SectionCollection);
if (ProgramSettings.SendDataToDESCDataBase)
{
DatabaseWorkflowHandler.SendLithologiesToDatabase(lithologyCache);
}
if (ProgramSettings.SendDataToLithologyDataBase)
{
//Need to specify which columns to keep, ex is for x375
List <string> acceptableColumns = new List <string>()
{
"LITHOLOGY PREFIX", "Lithology principal name", "Lithology SUFFIX"
};
LithologyDatabaseWorkflowHandler.SendLithologiesToDataBase(lithologyCache, acceptableColumns);
}
var LithCache = CacheReconfigurer.CreateDescriptionSearchHierarchy(lithologyCache);
#endregion
#region ImportMeasurementData
if (ProgramSettings.ProcessMeaurements == false)
{
Console.WriteLine("Finished processing files at: " + DateTime.Now.ToString());
return;
}
var measurementWorkFlowHandler = new CSVMeasurementWorkFlowHandler();
measurementWorkFlowHandler.FileCollection = new FileCollection();
foreach (string path in MeasurementFileCollection.Filenames)
{
Console.WriteLine("Processing measurement file: " + path);
measurementWorkFlowHandler.FileCollection.RemoveFiles();
measurementWorkFlowHandler.FileCollection.Filenames.Add(path);
var measurementCache = measurementWorkFlowHandler.ImportCache(SectionCollection);
Console.WriteLine(string.Format(CultureInfo.CurrentCulture, "Processing {0} measurements", measurementCache.Count.ToString(CultureInfo.CurrentCulture)));
measurementWorkFlowHandler.UpdateMeasurementCacheWithLithologicDescriptions(measurementCache, LithCache);
if (ProgramSettings.SendDataToDESCDataBase)
{
DatabaseWorkflowHandler.SendMeasurementsToDatabase(measurementCache);
}
if (ProgramSettings.ExportCachesToFiles)
{
measurementWorkFlowHandler.ExportDirectory = MeasurementFileCollection.ExportDirectory;
measurementWorkFlowHandler.ExportToFile(measurementCache);
}
measurementCache = null;
GC.Collect();
Console.WriteLine("The total section count is: " + SectionCollection.Sections.Count);
}
#endregion
Console.WriteLine("Finished processing measurement files at: " + DateTime.Now.ToString());
}
public static List <DrillingDisturbanceRecord> FormatDrillingDisturbanceFile(string filename, string exportFilename)
{
Log.Information("--------Parsing a new file--------");
DataTable sections = SectionInfoCollection.ImportAllSections(ConfigurationManager.AppSettings["AllSectionsFile"]);
ICollection <DrillingDisturbanceRecord> descriptions = new HashSet <DrillingDisturbanceRecord>();
List <DrillingDisturbanceRecord> FinalDescriptionsToAdd = new List <DrillingDisturbanceRecord>();
#region ImportDrillingDisturbances
var dataTableReader = new CSVReader();
dataTableReader.ReadPath = filename;
DataTable drillingDisturbances = dataTableReader.Read();
//Correct Column Names:
ChangeColumn(drillingDisturbances, "Drilling disturbance intensity [rank]", "Drilling disturbance intensity rank");
ChangeColumn(drillingDisturbances, "Drilling disturbance intensity rank(read only)", "Drilling disturbance intensity rank");
ChangeColumn(drillingDisturbances, "Drilling disturbance intensity rank (read only)", "Drilling disturbance intensity rank");
ChangeColumn(drillingDisturbances, "Label ID", "Sample");
ChangeColumn(drillingDisturbances, "Top depth [m]", "Top Depth [m]");
ChangeColumn(drillingDisturbances, "Bottom depth [m]", "Bottom Depth [m]");
ChangeColumn(drillingDisturbances, "Disturbance [name]", "Disturbance");
ChangeColumn(drillingDisturbances, "File data", "File Data");
//Add additional columns
if (!drillingDisturbances.Columns.Contains("Drilling disturbance comment"))
{
drillingDisturbances.Columns.Add("Drilling disturbance comment");
}
if (!drillingDisturbances.Columns.Contains("Drilling disturbance type"))
{
drillingDisturbances.Columns.Add("Drilling disturbance type");
}
if (!drillingDisturbances.Columns.Contains("Drilling disturbance intensity"))
{
drillingDisturbances.Columns.Add("Drilling disturbance intensity");
}
if (!drillingDisturbances.Columns.Contains("Drilling disturbance intensity rank"))
{
drillingDisturbances.Columns.Add("Drilling disturbance intensity rank");
}
try
{
//Collection of all drilling disturbances
foreach (DataRow row in drillingDisturbances.Rows)
{
DrillingDisturbanceRecord record = new DrillingDisturbanceRecord()
{
Column1 = row["Column1"].ToString(),
SampleID = row["Sample"].ToString(),
Top_cm = row["Top [cm]"].ToString(),
Bottom_cm = row["Bottom [cm]"].ToString(),
TopDepth_m = row["Top Depth [m]"].ToString(),
BottomDepth_m = row["Bottom Depth [m]"].ToString(),
DrillingDisturbanceType = row["Drilling disturbance type"].ToString(),
DrillingDisturbanceIntensity = row["Drilling disturbance intensity"].ToString(),
DrillingDisturbanceIntensityRank = row["Drilling disturbance intensity rank"].ToString(),
DrillingDisturbanceComment = row["Drilling disturbance comment"].ToString(),
// ShipFileLinks = row["Ship File Links"].ToString(),
// ShoreFileLinks = row["Shore File Links"].ToString(),
FileData = row["File Data"].ToString()
};
descriptions.Add(record);
}
}
catch (Exception ex)
{
Log.Warning(ex.Message);
Log.Warning($"Could not created disturbance records from {filename}");
return(FinalDescriptionsToAdd);
}
#endregion
#region GetTheSectionsInCoreDescription
foreach (var description in descriptions)
{
//Find rows where sample Id doesn't end in A OR W
if (description.SampleID.EndsWith("A") || description.SampleID.EndsWith("W"))
{
FinalDescriptionsToAdd.Add(description);
continue;
}
Log.Information($"{description.SampleID} is a description on the Core");
Log.Information($"{description.SampleID} TOP OFFSET: {description.Top_cm} BOTTOM OFFSET: {description.Bottom_cm} TOPDEPTH: {description.TopDepth_m} BOTTOM DEPTH: {description.BottomDepth_m}");
//At this point the description should be of the entire Core;
//Parse Core information from the Sample:
SectionInfo coreInfo = new SectionInfo(description.SampleID);
//Find all the sections within the AllSectionsTable which overlap with the Top/Bottom offsets of the Core description
var constituentSections = sections.AsEnumerable()
.Where(x => x.Field <string>("Exp") == coreInfo.Expedition)
.Where(x => x.Field <string>("Site") == coreInfo.Site)
.Where(x => x.Field <string>("Hole") == coreInfo.Hole)
.Where(x => x.Field <string>("Core") == coreInfo.Core)
.Where(x => x.Field <string>("Type") == coreInfo.Type)
.Where(x =>
(x.Field <string>("Top depth CSF-A (m)").ToDouble() >= description.TopDepth_m.ToDouble() && x.Field <string>("Top depth CSF-A (m)").ToDouble() < description.BottomDepth_m.ToDouble()) ||
(x.Field <string>("Bottom depth CSF-A (m)").ToDouble() > description.TopDepth_m.ToDouble() && x.Field <string>("Bottom depth CSF-A (m)").ToDouble() <= description.BottomDepth_m.ToDouble())
)
.Select(x => x)
.ToHashSet(); //collection of datarows...
//Create new drilling disturbance records by mashing up data between original Disturbances and sections:
//Need to relook at this: Use only the top and bottom offsets from the Sample
//Find the sections from the allsections table which overlap those intervals
//Create new drilling disturbances with section information
HashSet <DrillingDisturbanceRecord> newDrillingRecords = new HashSet <DrillingDisturbanceRecord>();
foreach (var section in constituentSections)
{
//Create new sampleID, All of them will be on the Archive half
string newSampleID = string.Format("{0}-{1}{2}-{3}{4}-{5}-A",
section["Exp"],
section["Site"],
section["Hole"],
section["Core"],
section["Type"],
section["Sect"]);
//Create a new drilling disturbance record
var record = new DrillingDisturbanceRecord
{
Column1 = description.Column1,
SampleID = newSampleID,
Top_cm = "0", //section["Top Offset (cm)"].ToString(),
Bottom_cm = Math.Round((section["Curated length (m)"].ToString().ToDouble() * 100), 2).ToString(),
TopDepth_m = section["Top depth CSF-A (m)"].ToString(),
BottomDepth_m = section["Bottom depth CSF-A (m)"].ToString(),
DrillingDisturbanceType = description.DrillingDisturbanceType,
DrillingDisturbanceIntensity = description.DrillingDisturbanceIntensityRank,
DrillingDisturbanceComment = description.DrillingDisturbanceComment,
DrillingDisturbanceIntensityRank = description.DrillingDisturbanceIntensityRank,
ShipFileLinks = description.ShipFileLinks,
ShoreFileLinks = description.ShoreFileLinks,
FileData = description.FileData
};
newDrillingRecords.Add(record);
Log.Information($"{newSampleID}: Section Added: TOP OFFSET: {record.Top_cm} BOTTOM OFFSET: {record.Bottom_cm} TOP DEPTH: {record.TopDepth_m} BOTTOM DEPTH: {record.BottomDepth_m}");
}
#endregion region
#region SetTheOffsetsForBorderingSections
//Set the TOP/BOTTOM offsets for core description's first and last sections to be equal to the core descriptions TOP/BOTTOM Offsets
var topSection = newDrillingRecords.OrderBy(x => x.TopDepth_m).First();
var topCorrection = topSection.Top_cm.ToDouble() + (description.TopDepth_m.ToDouble() - topSection.TopDepth_m.ToDouble()) * 100;
topCorrection = Math.Round(topCorrection, 2);
topSection.Top_cm = topCorrection.ToString(); //Need to calculate offsets based on depths
topSection.TopDepth_m = description.TopDepth_m;
Log.Information($"{topSection.SampleID}: Changed TopDepth to {topSection.TopDepth_m} and TopOffset to {topSection.Top_cm}");
var bottomSection = newDrillingRecords.OrderBy(x => x.BottomDepth_m).Last();
var bottomCorrection = bottomSection.Bottom_cm.ToDouble() - (bottomSection.BottomDepth_m.ToDouble() - description.BottomDepth_m.ToDouble()) * 100;
bottomCorrection = Math.Round(bottomCorrection, 2);
bottomSection.Bottom_cm = bottomCorrection.ToString();
bottomSection.BottomDepth_m = description.BottomDepth_m;
#endregion
Log.Information($"{bottomSection.SampleID}: Changed BottomDepth to {bottomSection.BottomDepth_m} and BottomOffset to {bottomSection.Bottom_cm}");
foreach (var newSectionDescription in newDrillingRecords)
{
//Find all descriptions the core describer's made for this SECTION. The sample ID's should be equal
var describedIntervalsOnSection = descriptions.Where(x => x.SampleID == newSectionDescription.SampleID).ToHashSet();
//If they described any intervals, pass those intervals into the algo to correctly process gap intervals
if (describedIntervalsOnSection.Any())
{
ICollection <DrillingDisturbanceRecord> finalRecords = CoreToSectionAlgo(newSectionDescription, describedIntervalsOnSection);
FinalDescriptionsToAdd.AddRange(finalRecords);
foreach (var record in finalRecords)
{
Log.Information($"{newSectionDescription.SampleID}: Adding to final descriptions");
}
}
else if (!describedIntervalsOnSection.Any())
{
FinalDescriptionsToAdd.Add(newSectionDescription);
Log.Information($"{newSectionDescription.SampleID}: Adding to final descriptions");
}
}
}
//These are new descriptions to add to the file
foreach (var record in FinalDescriptionsToAdd)
{
var offsetDifference = Math.Round(record.Bottom_cm.ToDouble() - record.Top_cm.ToDouble(), 2);
var depthDifference = Math.Round((record.BottomDepth_m.ToDouble() - record.TopDepth_m.ToDouble()) * 100, 2);
if (offsetDifference != depthDifference)
{
Log.Warning($"Error in Offsets: {record.SampleID}: TOP OFFSET: {record.Top_cm} BOTTOMOFFSET: {record.Bottom_cm} TOPDEPTH: {record.TopDepth_m} BOTTOMDEPTH: {record.BottomDepth_m}");
}
else
{
Log.Information($"{record.SampleID}: TOP OFFSET: {record.Top_cm} BOTTOMOFFSET: {record.Bottom_cm} TOPDEPTH: {record.TopDepth_m} BOTTOMDEPTH: {record.BottomDepth_m}");
}
}
DataTable dt = new DataTable();
// DataColumn[] columns = new DataColumn[drillingDisturbances.Columns.Count];
// drillingDisturbances.Columns.CopyTo(columns, 0);
// dt.Columns.AddRange(columns);
for (int i = 0; i < drillingDisturbances.Columns.Count; i++)
{
dt.Columns.Add(drillingDisturbances.Columns[i].ColumnName, drillingDisturbances.Columns[i].DataType);
}
//Add in new corrected drilling disturbances
foreach (var item in FinalDescriptionsToAdd)
{
DataRow row = dt.NewRow();
//row.BeginEdit();
row["Column1"] = item.Column1;
row["Sample"] = item.SampleID;
row["Top [cm]"] = item.Top_cm;
row["Bottom [cm]"] = item.Bottom_cm;
row["Top Depth [m]"] = item.TopDepth_m;
row["Bottom Depth [m]"] = item.BottomDepth_m;
row["Drilling disturbance type"] = item.DrillingDisturbanceType;
row["Drilling disturbance intensity"] = item.DrillingDisturbanceIntensity;
row["Drilling disturbance intensity rank"] = item.DrillingDisturbanceIntensityRank;
row["Drilling disturbance comment"] = item.DrillingDisturbanceComment;
//row["Ship File Links"] = item.ShipFileLinks;
//row["Shore File Links"] = item.ShoreFileLinks;
row["File Data"] = item.FileData;
dt.Rows.Add(row);
//row.EndEdit();
}
Importer.ExportDataTableAsNewFile(exportFilename, dt);
return(FinalDescriptionsToAdd);
}
/// <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);
}
