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");
}
}
public static void AddSampleIDColumnToFileAndExport(string path, string newPath)
{
//Impor a file:
CSVReader reader = new CSVReader();
reader.ReadPath = path;
using (DataTable importTable = reader.Read())
{
IntervalHierarchyNames columnNames = new IntervalHierarchyNames()
{
Expedition = "Exp",
Site = "Site",
Hole = "Hole",
Core = "Core",
Type = "Type",
Section = "Section",
Half = "A/W",
};
IODPDataTable iODPDataTable = new IODPDataTable(importTable, columnNames);
if (iODPDataTable.DataTable.Columns.Contains("Sample") || iODPDataTable.DataTable.Columns.Contains("Label ID"))
{
return;
}
if (!iODPDataTable.DataTable.Columns.Contains("Sample"))
{
iODPDataTable.DataTable.Columns.Add("Sample").SetOrdinal(1);
}
foreach (DataRow row in importTable.Rows)
{
row.BeginEdit();
row["Sample"] = $"{row[iODPDataTable.ExpeditionColumn]}" +
$"-{row[iODPDataTable.SiteColumn]}{row[iODPDataTable.HoleColumn]}" +
$"-{row[iODPDataTable.CoreColumn]}{row[iODPDataTable.TypeColumn]}" +
$"-{row[iODPDataTable.SectionColumn]}" +
$"-{row[columnNames.Half]}";
row.EndEdit();
}
//Export File
Importer.ExportDataTableAsNewFile(newPath, importTable);
}
}
public static async Task <bool> GetMeasurementIDForMeasurementFile(string file, string exportFilePath)
{
ICollection <Measurement> measurements = await MeasurementHandler.GetMeasurementsFromFileAsync(file).ConfigureAwait(true);
using (DescDBContext dBContext = new DescDBContext())
{
foreach (var measurement in measurements)
{
measurement.ID = await DatabaseWorkflowHandler.GetMeasurementIDAsync(dBContext, measurement).ConfigureAwait(true);
}
}
//Column Names
HashSet <string> columns = measurements.First().MeasurementData.Select(x => x.ColumnName).ToHashSet();
//Check if all measurements have the same Columns
foreach (var measurement in measurements)
{
var compareColumns = measurement.MeasurementData.Select(x => x.ColumnName).ToHashSet();
if (!columns.SetEquals(compareColumns))
{
return(false);
}
}
//TODO: Construct new Datatable
using (DataTable dataTable = new DataTable())
{
foreach (var column in columns)
{
dataTable.Columns.Add(column);
}
dataTable.Columns.Add("MeasurementID").SetOrdinal(0);
int currentRow = 0;
foreach (var measurement in measurements)
{
dataTable.ImportRow(measurement.DataRow);
var row = dataTable.Rows[currentRow];
row.BeginEdit();
row["MeasurementID"] = measurement.ID;
row.EndEdit();
currentRow++;
}
//AddID column
//Export measurements to File
Importer.ExportDataTableAsNewFile(exportFilePath, dataTable);
}
return(true);
}
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);
}