internal List <AssayGroupTestResult> GetDuplicateResult(Dictionary <Guid, AssayGroupTest> assayGroups, Guid sampleID, Guid assayGroupTestID)
{
using (var entityObj = new NKDC(BaseImportTools.XSTRING, null))
{
List <AssayGroupTestResult> resultData = new List <AssayGroupTestResult>();
AssayGroupTest xx = assayGroups[assayGroupTestID];
string testName = xx.AssayTestName;
Guid testParamID = (Guid)xx.ParameterID;
IQueryable <AssayGroupTestResult> res = entityObj.AssayGroupTestResults.Where(c => c.SampleID == sampleID);
bool foundDupe = false;
foreach (AssayGroupTestResult xx2 in res)
{
IQueryable <AssayGroupTest> res2 = entityObj.AssayGroupTests.Where(c => c.AssayGroupID == xx2.AssayGroupTestID);
foreach (AssayGroupTest agt in res2)
{
if (agt.ParameterID == testParamID)
{
foundDupe = true;
break;
}
}
if (foundDupe)
{
resultData.Add(xx2);
break;
}
}
return(resultData);
}
}
private AssayGroupTest FindExistingAssayGroupTest(string p)
{
using (var entityObj = new NKDC(BaseImportTools.XSTRING, null))
{
AssayGroupTest resAssGroup = null;
IQueryable <AssayGroupTest> res = entityObj.AssayGroupTests.Where(c => c.AssayTestName.Trim().Equals(p.Trim()));
foreach (AssayGroupTest xx in res)
{
resAssGroup = xx;
}
return(resAssGroup);
}
}
internal void AddAssayData(ModelImportStatus mos, Stream fileStream, FormatSpecification.ImportDataMap importMap,
int batchSize, Action<string, double> UpdateStatus, int approxNumLines,
string connectionString, Guid XODBProjectID, bool checkForDuplicates, bool doImportOverwrite)
{
bool commitToDB = true;
DateTime currentUpdateTimestamp = DateTime.UtcNow;
// first set up an assay group object - we can do this through the edm
using (var entityObj = new XODBC(connectionString, null))
{
//entityObj.Configuration.AutoDetectChangesEnabled = false;
Guid agGuid = Guid.NewGuid();
AssayGroup ag = new AssayGroup();
ag.AssayGroupID = agGuid;
ag.ProjectID = XODBProjectID;
ag.AssayGroupName = "Manual import";
ag.Comment = "From file " + importMap.mapOriginalDataFile;
ag.Entered = currentUpdateTimestamp;
ag.VersionUpdated = currentUpdateTimestamp;
entityObj.AssayGroups.AddObject(ag);
if (commitToDB)
{
entityObj.SaveChanges();
}
// set up the assay test columns - one of these for each test type
Dictionary<ColumnMap, Guid> resultsColumns = new Dictionary<ColumnMap, Guid>();
Dictionary<Guid, AssayGroupTest> assayGroups = new Dictionary<Guid, AssayGroupTest>();
foreach (ColumnMap cim in importMap.columnMap)
{
if (cim.targetColumnName.Trim().StartsWith("[ASSAY"))
{
// this is a test category
resultsColumns.Add(cim, Guid.NewGuid());
}
}
UpdateStatus("Setting up assay tests ", 2);
foreach (KeyValuePair<ColumnMap, Guid> kvp in resultsColumns)
{
ColumnMap cm = kvp.Key;
Guid g = kvp.Value;
AssayGroupTest xt = new AssayGroupTest();
string ss1 = "";
if (cm.sourceColumnName != null && cm.sourceColumnName.Length > 15)
{
ss1 = cm.sourceColumnName.Substring(0, 16);
}
else
{
ss1 = cm.sourceColumnName;
}
Guid pid = FindParameterForAssayTypeName(cm.sourceColumnName);
xt.ParameterID = pid;
xt.AssayTestName = ss1;
xt.AssayGroupID = agGuid;
xt.AssayGroupTestID = g;
xt.VersionUpdated = currentUpdateTimestamp;
entityObj.AssayGroupTests.AddObject(xt);
assayGroups.Add(g, xt);
if (commitToDB)
{
entityObj.SaveChanges();
}
}
// iterate through the data lines
int ct = 1;
int linesRead = 0;
SqlConnection connection = null;
SqlConnection secondaryConnection = null;
//List<string> uniqueDomains = new List<string>();
// get a connection to the database
try
{
int domainColIDX = -1;
connection = new SqlConnection(connectionString);
connection.Open();
secondaryConnection = new SqlConnection(connectionString);
secondaryConnection.Open();
bool hasDuplicateIntervals = false;
int numCommits = 0;
SqlTransaction trans;
trans = connection.BeginTransaction();
List<SqlCommand> commands = new List<SqlCommand>();
int tb = 0;
int transactionBatchLimit = batchSize;
// open the filestream and read the first line
StreamReader sr = null;
FileStream fs = null;
try
{
//fs = new FileStream(textInputDataFile, FileMode.Open, FileAccess.Read, FileShare.Read);
sr = new StreamReader(fileStream);
}
catch (Exception ex)
{
mos.AddErrorMessage("Error getting data stream for input data:\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_LOADING_FILE;
}
string line = null;
float pct = 0;
float bct = 1;
// report every X blocks
int repCount = 0;
//int reportOnBlock = 1000;
float fNumLines = (float)approxNumLines;
Dictionary<string, Guid> holeIDLookups = new Dictionary<string, Guid>();
Dictionary<string, int> columnIDX = new Dictionary<string, int>();
int fkLookupCount = 0;
PopulateCMapShortcut("HeaderID", importMap, columnIDX);
PopulateCMapShortcut("FromDepth", importMap, columnIDX);
PopulateCMapShortcut("ToDepth", importMap, columnIDX);
PopulateCMapShortcut("SampleNumber", importMap, columnIDX);
PopulateCMapShortcut("LabSampleNumber", importMap, columnIDX);
PopulateCMapShortcut("LabBatchNumber", importMap, columnIDX);
ColumnMap headerCmap = importMap.FindItemsByTargetName("HeaderID");
AssayQueries assayQueries = new AssayQueries();
if (sr != null)
{
while ((line = sr.ReadLine()) != null)
{
repCount++;
pct = ((float)linesRead / (float)approxNumLines) * 100.0f;
bct++;
linesRead++;
if (ct >= importMap.dataStartLine)
{
// digest a row of input data
List<string> items = parseTestLine(line, importMap.inputDelimiter);
Guid holeID = new Guid();
Decimal fromDepth = new Decimal(-9999999999);
Decimal toDepth = new Decimal(-9999999999);
string sampleNumber = null;
string labBatchNumber = null;
string labsampleNumber = null;
// find mapped values by name
//ColumnMap cmap = importMap.FindItemsByTargetName("HeaderID");
int idxVal = 0;
bool foundEntry = columnIDX.TryGetValue("HeaderID", out idxVal);
bool foundHole = false;
string holeName = "";
if (foundEntry)
{
string lookupByName = "HoleName";
string lookupValue = items[idxVal];
holeName = lookupValue;
bool lv = holeIDLookups.ContainsKey(lookupValue);
if (!lv)
{
string headerGUID = ForeignKeyUtils.FindFKValueInOther(lookupValue, headerCmap, secondaryConnection, false, lookupByName, XODBProjectID);
if (headerGUID == null)
{
// this means we have not found the specified records in the header table
// Report on issue and skip line
}
else
{
foundHole = true;
holeID = new Guid(headerGUID);
holeIDLookups.Add(lookupValue, holeID);
fkLookupCount++;
}
}
else
{
holeIDLookups.TryGetValue(lookupValue, out holeID);
foundHole = true;
}
}
if (!foundHole)
{
mos.AddErrorMessage("Failed to find hole " + holeName + ". Skipping record at line " + linesRead + ".");
mos.finalErrorCode = ModelImportStatus.DATA_CONSISTENCY_ERROR;
mos.recordsFailed++;
continue;
}
else
{
bool hasFrom = false;
idxVal = 0;
foundEntry = columnIDX.TryGetValue("FromDepth", out idxVal);
if (foundEntry)
//cmap = importMap.FindItemsByTargetName();
//if (cmap != null)
{
string ii = items[idxVal];
Decimal val = 0;
bool isOk = Decimal.TryParse(ii, out val);
if (isOk)
{
fromDepth = val;
hasFrom = true;
}
}
bool hasTo = false;
idxVal = 0;
foundEntry = columnIDX.TryGetValue("ToDepth", out idxVal);
if (foundEntry)
//cmap = importMap.FindItemsByTargetName("ToDepth");
//if (cmap != null)
{
string ii = items[idxVal];
Decimal val = 0;
bool isOk = Decimal.TryParse(ii, out val);
if (isOk)
{
toDepth = val;
hasTo = true;
}
}
List<Sample> duplicateList = null;
bool isDuplicateInterval = false;
if (checkForDuplicates)
{
if (hasFrom && hasTo)
{
// here we need to check that the hole is not duplicated
duplicateList = assayQueries.CheckForDuplicate(holeID, fromDepth, toDepth);
if (duplicateList.Count > 0)
{
isDuplicateInterval = true;
}
}
if (isDuplicateInterval)
{
hasDuplicateIntervals = true;
mos.AddWarningMessage("Duplicate interval for hole " + holeName + " at depth " + fromDepth + " to " + toDepth);
UpdateStatus("Duplicate interval at " + holeName + " " + fromDepth + ", " + toDepth, pct);
if (!doImportOverwrite)
{
mos.recordsFailed++;
continue;
}
}
}
//cmap = importMap.FindItemsByTargetName("SampleNumber");
idxVal = 0;
foundEntry = columnIDX.TryGetValue("SampleNumber", out idxVal);
if (foundEntry)
// if (cmap != null)
{
string ii = items[idxVal];
sampleNumber = ii;
}
//cmap = importMap.FindItemsByTargetName("LabSampleNumber");
//if (cmap != null)
idxVal = 0;
foundEntry = columnIDX.TryGetValue("SampleNumber", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
labsampleNumber = ii;
}
//cmap = importMap.FindItemsByTargetName("LabBatchNumber");
idxVal = 0;
foundEntry = columnIDX.TryGetValue("SampleNumber", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
labBatchNumber = ii;
}
Sample xs = new Sample();
if (isDuplicateInterval == true)
{
xs = duplicateList.First();
}
else
{
xs.SampleID = Guid.NewGuid();
xs.FromDepth = fromDepth;
xs.ToDepth = toDepth;
xs.HeaderID = holeID;
xs.VersionUpdated = currentUpdateTimestamp;
entityObj.Samples.AddObject(xs);
}
// now pick out all the mapped values
// iterate over all [ASSAY RESULT] columns
bool assayUpdated = false;
bool assayAdded = false;
foreach (KeyValuePair<ColumnMap, Guid> kvp in resultsColumns)
{
ColumnMap cm = kvp.Key;
Guid g = kvp.Value; // this is the AssayGroupTestID
AssayGroupTestResult testResult = new AssayGroupTestResult();
/*bool assayResFound = false;
if (isDuplicateInterval)
{
List<AssayGroupTestResult> testResults = assayQueries.GetDuplicateResult(xs.SampleID, cm.sourceColumnName);
if (testResults.Count > 0)
{
testResult = testResults.First();
assayResFound = true;
}
}*/
//if(!assayResFound)
// {
testResult.AssayGroupTestResultID = Guid.NewGuid();
testResult.AssayGroupTestID = g;
testResult.SampleID = xs.SampleID;
testResult.VersionUpdated = currentUpdateTimestamp;
//}
testResult.LabBatchNumber = labBatchNumber;
// testResult.LabSampleName = labsampleNumber;
Decimal result = new Decimal();
if (items.Count >= cm.sourceColumnNumber)
{
bool parsedOK = Decimal.TryParse(items[cm.sourceColumnNumber], out result);
if (parsedOK)
{
testResult.LabResult = result;
}
else
{
testResult.LabResultText = items[cm.sourceColumnNumber];
}
}
else
{
mos.AddWarningMessage("Line " + linesRead + " contains too few columns to read " + cm.sourceColumnName);
}
//if (isDuplicateInterval == false)
//{
entityObj.AssayGroupTestResults.AddObject(testResult);
assayAdded = true;
//}else{
// if (!assayResFound)
// {
// entityObj.AssayGroupTestResult.Add(testResult);
// assayAdded = true;
// }
// else {
// assayUpdated = true;
// }
//}
}
if (assayAdded == true)
{
mos.recordsAdded++;
}
if (assayUpdated)
{
mos.recordsUpdated++;
}
tb++;
}
}
if (commitToDB)
{
if (tb == transactionBatchLimit)
{
entityObj.SaveChanges();
UpdateStatus("Writing assays to DB (" + ct + " entries)", pct);
tb = 0;
}
}
ct++;
//Console.WriteLine("Processing line "+ct);
}
entityObj.SaveChanges();
}
if (hasDuplicateIntervals)
{
mos.finalErrorCode = ModelImportStatus.DATA_CONSISTENCY_ERROR;
}
string numFKLookups = "FK lookups " + fkLookupCount;
mos.linesReadFromSource = ct - 1;
UpdateStatus("Finished writing assays to database.", 0);
}
catch (Exception ex)
{
UpdateStatus("Error writing assays to database ", 0);
mos.AddErrorMessage("Error writing assay data at line " + linesRead + ":\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_WRITING_TO_DB;
}
finally
{
try
{
connection.Close();
secondaryConnection.Close();
fileStream.Close();
}
catch (Exception ex)
{
mos.AddErrorMessage("Error closing conenction to database:\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_WRITING_TO_DB;
}
}
mos.linesReadFromSource = linesRead;
}
}
internal void AddCoalQualityData(ModelImportStatus mos, Stream fileStream, FormatSpecification.ImportDataMap importMap,
int batchSize, Action <string, double> UpdateStatus, int approxNumLines,
string connectionString, Guid NKDProjectID, bool checkForDuplicates, bool doImportOverwrite)
{
WorkflowProcedureSequenceNumber = 1;
Guid? lastHoleID = new Guid();
string lastStage = "";
decimal lastFromDepth = -999999;
decimal lastToDepth = -999999;
bool commitToDB = true;
DateTime currentUpdateTimestamp = DateTime.UtcNow;
// first set up an assay group object - we can do this through the edm
using (var entityObj = new NKDC(connectionString, null))
{
Guid agGuid = Guid.NewGuid();
AssayGroup ag = new AssayGroup();
ag.AssayGroupID = agGuid;
ag.ProjectID = NKDProjectID;
ag.AssayGroupName = "Manual import";
ag.Comment = "From file " + importMap.mapOriginalDataFile;
ag.Entered = currentUpdateTimestamp;
ag.VersionUpdated = currentUpdateTimestamp;
entityObj.AssayGroups.AddObject(ag);
if (commitToDB)
{
entityObj.SaveChanges();
}
// set up the assay test columns - one of these for each test type
Dictionary <ColumnMap, Guid> resultsColumns = new Dictionary <ColumnMap, Guid>();
Dictionary <Guid, AssayGroupTest> assayGroups = new Dictionary <Guid, AssayGroupTest>();
ColumnMap cmProgram = null;
ColumnMap cmStage = null;
ColumnMap cmSizeFraction = null;
ColumnMap cmWashFraction = null;
foreach (ColumnMap cim in importMap.columnMap)
{
if (cim.targetColumnName.Trim().StartsWith("[RESULT"))
{
// this is a test category
resultsColumns.Add(cim, Guid.NewGuid());
}
else if (cim.targetColumnName.Trim().StartsWith("[PROGRAM"))
{
cmProgram = cim;
}
else if (cim.targetColumnName.Trim().StartsWith("[STAGE"))
{
cmStage = cim;
}
else if (cim.targetColumnName.Trim().StartsWith("[SIZE FRACTION"))
{
cmSizeFraction = cim;
}
else if (cim.targetColumnName.Trim().StartsWith("[WASH FRACTION"))
{
cmWashFraction = cim;
}
}
UpdateStatus("Setting up assay tests ", 2);
foreach (KeyValuePair <ColumnMap, Guid> kvp in resultsColumns)
{
ColumnMap cm = kvp.Key;
Guid g = kvp.Value;
AssayGroupTest xt = new AssayGroupTest();
string ss1 = "";
if (cm.sourceColumnName != null && cm.sourceColumnName.Length > 15)
{
ss1 = cm.sourceColumnName.Substring(0, 16);
}
else
{
ss1 = cm.sourceColumnName;
}
Guid pid = FindParameter("AssayTypeName", cm.sourceColumnName);
xt.ParameterID = pid;
xt.AssayTestName = ss1;
xt.AssayGroupID = agGuid;
xt.AssayGroupTestID = g;
xt.VersionUpdated = currentUpdateTimestamp;
entityObj.AssayGroupTests.AddObject(xt);
assayGroups.Add(g, xt);
if (commitToDB)
{
entityObj.SaveChanges();
}
}
// iterate through the data lines
int ct = 1;
int linesRead = 0;
SqlConnection connection = null;
SqlConnection secondaryConnection = null;
//List<string> uniqueDomains = new List<string>();
// get a connection to the database
try
{
connection = new SqlConnection(connectionString);
connection.Open();
secondaryConnection = new SqlConnection(connectionString);
secondaryConnection.Open();
bool hasDuplicateIntervals = false;
SqlTransaction trans;
trans = connection.BeginTransaction();
List <SqlCommand> commands = new List <SqlCommand>();
int tb = 0;
int transactionBatchLimit = batchSize;
// open the filestream and read the first line
StreamReader sr = null;
try
{
sr = new StreamReader(fileStream);
}
catch (Exception ex)
{
mos.AddErrorMessage("Error getting data stream for input data:\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_LOADING_FILE;
}
string line = null;
float pct = 0;
float bct = 1;
// report every X records
int repCount = 0;
float fNumLines = (float)approxNumLines;
Dictionary <string, Guid> holeIDLookups = new Dictionary <string, Guid>();
Dictionary <string, int> columnIDX = new Dictionary <string, int>();
int fkLookupCount = 0;
BaseImportTools.PopulateCMapShortcut(importMap, columnIDX);
ColumnMap headerCmap = importMap.FindItemsByTargetName("HeaderID");
int seqNum = 1;
if (sr != null)
{
while ((line = sr.ReadLine()) != null)
{
repCount++;
pct = ((float)linesRead / (float)approxNumLines) * 100.0f;
bct++;
linesRead++;
if (ct >= importMap.dataStartLine)
{
// digest a row of input data
List <string> items = BaseImportTools.ParseTestLine(line, importMap.inputDelimiter);
Guid holeID = new Guid();
Decimal fromDepth = new Decimal(-9999999999);
Decimal toDepth = new Decimal(-9999999999);
string sampleNumber = null;
string sampleName = null;
string labBatchNumber = null;
string labsampleNumber = null;
// find mapped values by name
int idxVal = 0;
// -- Get the hole ID foreign key relation
bool foundEntry = columnIDX.TryGetValue("HeaderID", out idxVal);
bool foundHole = false;
string holeName = "";
if (foundEntry)
{
string lookupByName = "HoleName";
string lookupValue = items[idxVal];
holeName = lookupValue;
bool lv = holeIDLookups.ContainsKey(lookupValue);
if (!lv)
{
string headerGUID = ForeignKeyUtils.FindFKValueInOther(lookupValue, headerCmap, secondaryConnection, false, lookupByName, NKDProjectID);
if (headerGUID == null)
{
// this means we have not found the specified records in the header table
// Report on issue and skip line
}
else
{
foundHole = true;
holeID = new Guid(headerGUID);
holeIDLookups.Add(lookupValue, holeID);
fkLookupCount++;
}
}
else
{
holeIDLookups.TryGetValue(lookupValue, out holeID);
foundHole = true;
}
}
if (!foundHole)
{
mos.AddErrorMessage("Failed to find hole " + holeName + ". Skipping record at line " + linesRead + ".");
mos.finalErrorCode = ModelImportStatus.DATA_CONSISTENCY_ERROR;
mos.recordsFailed++;
continue;
}
else
{
bool hasFrom = false;
idxVal = 0;
foundEntry = columnIDX.TryGetValue("FromDepth", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
Decimal val = 0;
bool isOk = Decimal.TryParse(ii, out val);
if (isOk)
{
fromDepth = val;
hasFrom = true;
}
}
bool hasTo = false;
idxVal = 0;
foundEntry = columnIDX.TryGetValue("ToDepth", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
Decimal val = 0;
bool isOk = Decimal.TryParse(ii, out val);
if (isOk)
{
toDepth = val;
hasTo = true;
}
}
idxVal = 0;
foundEntry = columnIDX.TryGetValue("SampleID", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
sampleNumber = ii;
}
idxVal = 0;
foundEntry = columnIDX.TryGetValue("SampleName", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
sampleName = ii;
}
idxVal = 0;
foundEntry = columnIDX.TryGetValue("LabSampleName", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
labsampleNumber = ii;
}
idxVal = 0;
foundEntry = columnIDX.TryGetValue("LabBatchNumber", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
labBatchNumber = ii;
}
// Now iddentify the program, Stage, Size fraction and wash fraction
// get the program text
string programType = null;
if (cmProgram != null)
{
programType = items[cmProgram.sourceColumnNumber];
}
string stage = null;
if (cmStage != null)
{
stage = items[cmStage.sourceColumnNumber];
}
string sizeFraction = null;
if (cmSizeFraction != null)
{
sizeFraction = items[cmSizeFraction.sourceColumnNumber];
}
string washFraction = null;
if (cmWashFraction != null)
{
washFraction = items[cmWashFraction.sourceColumnNumber];
}
IQueryable <AssayGroupSubsample> toUpdate = null;
bool isDuplicate = false;
var washID = (from o in entityObj.Parameters where o.ParameterType == "AssayPrecondition" && o.ParameterName == "Wash fraction" select o.ParameterID).FirstOrDefault();
var sizeID = (from o in entityObj.Parameters where o.ParameterType == "AssayPrecondition" && o.ParameterName == "Size fraction" select o.ParameterID).FirstOrDefault();
if (checkForDuplicates)
{
if (hasFrom && hasTo)
{
// here we need to check that not duplicated
toUpdate =
(from o in entityObj.AssayGroupSubsamples
where
o.OriginalSample.HeaderID == holeID &&
o.OriginalSample.FromDepth == fromDepth &&
o.OriginalSample.ToDepth == toDepth &&
o.AssayGroupWorkflowProcedure.WorkflowStateName == stage &&
o.AssayGroupWorkflowProcedure.AssayGroupWorkflow.WorkflowName == programType &&
(sizeFraction.Trim() == "" || o.AssayGroupSubsamplePrecondition.Any(f => f.PreconditionName == sizeFraction && f.PreconditionParameterID == sizeID)) &&
(washFraction.Trim() == "" || o.AssayGroupSubsamplePrecondition.Any(f => f.PreconditionName == washFraction && f.PreconditionParameterID == washID))
select o);
if (toUpdate.Any())
{
isDuplicate = true;
}
}
if (isDuplicate)
{
hasDuplicateIntervals = true;
mos.AddWarningMessage("Duplicate interval for hole " + holeName + " at depth " + fromDepth + " to " + toDepth);
UpdateStatus("Duplicate interval at " + holeName + " " + fromDepth + ", " + toDepth, pct);
if (!doImportOverwrite)
{
mos.recordsFailed++;
continue;
}
else
{
foreach (var upd in toUpdate)
{
upd.Sequence = seqNum;
}
}
}
}
Sample xs = null;
if (isDuplicate == true)
{
xs = toUpdate.First().OriginalSample;
}
else
{
xs = (from o in entityObj.Samples where o.HeaderID == holeID && o.FromDepth == fromDepth && o.ToDepth == toDepth select o).FirstOrDefault();
if (xs == null)
{
xs = new Sample();
xs.SampleID = Guid.NewGuid();
xs.SampleName = sampleName;
xs.SampleNumber = sampleNumber;
xs.FromDepth = fromDepth;
xs.ToDepth = toDepth;
xs.HeaderID = holeID;
xs.VersionUpdated = currentUpdateTimestamp;
entityObj.Samples.AddObject(xs);
}
}
// see if the interfal has changed, wherby we will need to reset the sequence ID
if (holeID != lastHoleID)
{
if (fromDepth != lastFromDepth && toDepth != lastToDepth)
{
// new interval
WorkflowProcedureSequenceNumber = 1;
}
}
if (!stage.Trim().Equals(lastStage))
{
WorkflowProcedureSequenceNumber = 1;
}
lastHoleID = holeID;
lastFromDepth = fromDepth;
lastToDepth = toDepth;
lastStage = stage;
if (!isDuplicate)
{
AssayGroupWorkflow agWorkflowProgram = GetAssayGroupWorkflow(entityObj, programType, agGuid);
AssayGroupWorkflowProcedure agWorkflowStage = GetAssayGroupWorkflowProcedure(entityObj, stage, agWorkflowProgram);
AssayGroupSubsample agSS = new AssayGroupSubsample();
agSS.AssayGroupID = agGuid;
agSS.FromDepth = fromDepth;
agSS.ToDepth = toDepth;
agSS.Sequence = seqNum;
agSS.AssayGroupSubsampleID = Guid.NewGuid();
agSS.SampleAntecedentID = xs.SampleID;
agSS.OriginalSample = xs;
agSS.AssayGroupWorkflowProcedureID = agWorkflowStage.AssayGroupWorkflowProcedureID;
agSS.AssayGroupWorkflowProcedure = agWorkflowStage;
entityObj.AssayGroupSubsamples.AddObject(agSS);
entityObj.SaveChanges();
AssayGroupSubsamplePrecondition agSizeFraction = GetAssayGroupPrecondition(entityObj, sizeFraction, "Size fraction", agSS.AssayGroupSubsampleID);
AssayGroupSubsamplePrecondition agWashFraction = GetAssayGroupPrecondition(entityObj, washFraction, "Wash fraction", agSS.AssayGroupSubsampleID);
toUpdate = (new[] { agSS }).AsQueryable();
}
if (isDuplicate)
{
entityObj.SaveChanges();
}
foreach (var upd in toUpdate.ToList())
{
// now pick out all the mapped values
// iterate over all [ASSAY RESULT] columns
foreach (KeyValuePair <ColumnMap, Guid> kvp in resultsColumns)
{
ColumnMap cm = kvp.Key;
Guid g = kvp.Value; // this is the AssayGroupTestID
AssayGroupTestResult testResult = null;
Decimal result = default(decimal);
string resultText = null;
bool parsedOK = false;
if (items.Count >= cm.sourceColumnNumber)
{
parsedOK = Decimal.TryParse(items[cm.sourceColumnNumber], out result);
resultText = items[cm.sourceColumnNumber];
}
else
{
mos.AddWarningMessage("Line " + linesRead + " contains too few columns to read " + cm.sourceColumnName);
}
if (string.IsNullOrWhiteSpace(resultText))
{
continue;
}
if (!isDuplicate)
{
testResult = new AssayGroupTestResult();
testResult.AssayGroupSubsampleID = upd.AssayGroupSubsampleID;
testResult.AssayGroupTestResultID = Guid.NewGuid();
testResult.AssayGroupTestID = g;
testResult.SampleID = xs.SampleID;
testResult.LabBatchNumber = labBatchNumber;
entityObj.AssayGroupTestResults.AddObject(testResult);
testResult.VersionUpdated = currentUpdateTimestamp;
if (parsedOK)
{
testResult.LabResult = result;
}
testResult.LabResultText = resultText;
//testResult.LabSampleNumber = labsampleNumber;
mos.recordsAdded++;
}
else
{
var tempRes = (parsedOK) ? result : default(decimal?);
entityObj.AssayGroupTestResults.Where(f =>
f.AssayGroupSubsampleID == upd.AssayGroupSubsampleID &&
f.AssayGroupTest.Parameter.ParameterName == cm.sourceColumnName
)
.Update((f) => new AssayGroupTestResult
{
LabResult = tempRes,
LabResultText = resultText,
VersionUpdated = currentUpdateTimestamp
});
mos.recordsUpdated++;
}
}
}
seqNum++;
tb++;
}
}
if (commitToDB)
{
if (tb == transactionBatchLimit)
{
entityObj.SaveChanges();
UpdateStatus("Writing assays to DB (" + ct + " entries)", pct);
tb = 0;
}
}
ct++;
}
entityObj.SaveChanges();
}
if (hasDuplicateIntervals)
{
mos.finalErrorCode = ModelImportStatus.DATA_CONSISTENCY_ERROR;
}
string numFKLookups = "FK lookups " + fkLookupCount;
mos.linesReadFromSource = ct - 1;
UpdateStatus("Finished writing coal quality data to database.", 0);
}
catch (Exception ex)
{
UpdateStatus("Error writing qualities to database ", 0);
mos.AddErrorMessage("Error writing data at line " + linesRead + ":\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_WRITING_TO_DB;
}
finally
{
try
{
connection.Close();
secondaryConnection.Close();
fileStream.Close();
}
catch (Exception ex)
{
mos.AddErrorMessage("Error closing conenction to database:\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_WRITING_TO_DB;
}
}
mos.linesReadFromSource = linesRead;
}
}
internal void AddCoalQualityData(ModelImportStatus mos, Stream fileStream, FormatSpecification.ImportDataMap importMap,
int batchSize, Action<string, double> UpdateStatus, int approxNumLines,
string connectionString, Guid XODBProjectID, bool checkForDuplicates, bool doImportOverwrite)
{
WorkflowProcedureSequenceNumber = 1;
Guid? lastHoleID = new Guid();
string lastStage = "";
decimal lastFromDepth = -999999;
decimal lastToDepth = -999999;
bool commitToDB = true;
DateTime currentUpdateTimestamp = DateTime.UtcNow;
// first set up an assay group object - we can do this through the edm
using (var entityObj = new XODBC(connectionString, null))
{
Guid agGuid = Guid.NewGuid();
AssayGroup ag = new AssayGroup();
ag.AssayGroupID = agGuid;
ag.ProjectID = XODBProjectID;
ag.AssayGroupName = "Manual import";
ag.Comment = "From file " + importMap.mapOriginalDataFile;
ag.Entered = currentUpdateTimestamp;
ag.VersionUpdated = currentUpdateTimestamp;
entityObj.AssayGroups.AddObject(ag);
if (commitToDB)
{
entityObj.SaveChanges();
}
// set up the assay test columns - one of these for each test type
Dictionary<ColumnMap, Guid> resultsColumns = new Dictionary<ColumnMap, Guid>();
Dictionary<Guid, AssayGroupTest> assayGroups = new Dictionary<Guid, AssayGroupTest>();
ColumnMap cmProgram = null;
ColumnMap cmStage = null;
ColumnMap cmSizeFraction = null;
ColumnMap cmWashFraction = null;
foreach (ColumnMap cim in importMap.columnMap)
{
if (cim.targetColumnName.Trim().StartsWith("[RESULT"))
{
// this is a test category
resultsColumns.Add(cim, Guid.NewGuid());
}
else if (cim.targetColumnName.Trim().StartsWith("[PROGRAM"))
{
cmProgram = cim;
}
else if (cim.targetColumnName.Trim().StartsWith("[STAGE"))
{
cmStage = cim;
}
else if (cim.targetColumnName.Trim().StartsWith("[SIZE FRACTION"))
{
cmSizeFraction = cim;
}
else if (cim.targetColumnName.Trim().StartsWith("[WASH FRACTION"))
{
cmWashFraction = cim;
}
}
UpdateStatus("Setting up assay tests ", 2);
foreach (KeyValuePair<ColumnMap, Guid> kvp in resultsColumns)
{
ColumnMap cm = kvp.Key;
Guid g = kvp.Value;
AssayGroupTest xt = new AssayGroupTest();
string ss1 = "";
if (cm.sourceColumnName != null && cm.sourceColumnName.Length > 15)
{
ss1 = cm.sourceColumnName.Substring(0, 16);
}
else
{
ss1 = cm.sourceColumnName;
}
Guid pid = FindParameter("AssayTypeName", cm.sourceColumnName);
xt.ParameterID = pid;
xt.AssayTestName = ss1;
xt.AssayGroupID = agGuid;
xt.AssayGroupTestID = g;
xt.VersionUpdated = currentUpdateTimestamp;
entityObj.AssayGroupTests.AddObject(xt);
assayGroups.Add(g, xt);
if (commitToDB)
{
entityObj.SaveChanges();
}
}
// iterate through the data lines
int ct = 1;
int linesRead = 0;
SqlConnection connection = null;
SqlConnection secondaryConnection = null;
//List<string> uniqueDomains = new List<string>();
// get a connection to the database
try
{
connection = new SqlConnection(connectionString);
connection.Open();
secondaryConnection = new SqlConnection(connectionString);
secondaryConnection.Open();
bool hasDuplicateIntervals = false;
SqlTransaction trans;
trans = connection.BeginTransaction();
List<SqlCommand> commands = new List<SqlCommand>();
int tb = 0;
int transactionBatchLimit = batchSize;
// open the filestream and read the first line
StreamReader sr = null;
try
{
sr = new StreamReader(fileStream);
}
catch (Exception ex)
{
mos.AddErrorMessage("Error getting data stream for input data:\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_LOADING_FILE;
}
string line = null;
float pct = 0;
float bct = 1;
// report every X records
int repCount = 0;
float fNumLines = (float)approxNumLines;
Dictionary<string, Guid> holeIDLookups = new Dictionary<string, Guid>();
Dictionary<string, int> columnIDX = new Dictionary<string, int>();
int fkLookupCount = 0;
PopulateCMapShortcut("HeaderID", importMap, columnIDX);
PopulateCMapShortcut("FromDepth", importMap, columnIDX);
PopulateCMapShortcut("ToDepth", importMap, columnIDX);
PopulateCMapShortcut("SampleNumber", importMap, columnIDX);
PopulateCMapShortcut("SampleName", importMap, columnIDX);
PopulateCMapShortcut("LabSampleNumber", importMap, columnIDX);
PopulateCMapShortcut("LabBatchNumber", importMap, columnIDX);
ColumnMap headerCmap = importMap.FindItemsByTargetName("HeaderID");
AssayQueries assayQueries = new AssayQueries();
int seqNum = 1;
if (sr != null)
{
while ((line = sr.ReadLine()) != null)
{
repCount++;
pct = ((float)linesRead / (float)approxNumLines) * 100.0f;
bct++;
linesRead++;
if (ct >= importMap.dataStartLine)
{
// digest a row of input data
List<string> items = parseTestLine(line, importMap.inputDelimiter);
Guid holeID = new Guid();
Decimal fromDepth = new Decimal(-9999999999);
Decimal toDepth = new Decimal(-9999999999);
string sampleNumber = null;
string sampleName = null;
string labBatchNumber = null;
string labsampleNumber = null;
// find mapped values by name
int idxVal = 0;
// -- Get the hole ID foreign key relation
bool foundEntry = columnIDX.TryGetValue("HeaderID", out idxVal);
bool foundHole = false;
string holeName = "";
if (foundEntry)
{
string lookupByName = "HoleName";
string lookupValue = items[idxVal];
holeName = lookupValue;
bool lv = holeIDLookups.ContainsKey(lookupValue);
if (!lv)
{
string headerGUID = ForeignKeyUtils.FindFKValueInOther(lookupValue, headerCmap, secondaryConnection, false, lookupByName, XODBProjectID);
if (headerGUID == null)
{
// this means we have not found the specified records in the header table
// Report on issue and skip line
}
else
{
foundHole = true;
holeID = new Guid(headerGUID);
holeIDLookups.Add(lookupValue, holeID);
fkLookupCount++;
}
}
else
{
holeIDLookups.TryGetValue(lookupValue, out holeID);
foundHole = true;
}
}
if (!foundHole)
{
mos.AddErrorMessage("Failed to find hole " + holeName + ". Skipping record at line " + linesRead + ".");
mos.finalErrorCode = ModelImportStatus.DATA_CONSISTENCY_ERROR;
mos.recordsFailed++;
continue;
}
else
{
bool hasFrom = false;
idxVal = 0;
foundEntry = columnIDX.TryGetValue("FromDepth", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
Decimal val = 0;
bool isOk = Decimal.TryParse(ii, out val);
if (isOk)
{
fromDepth = val;
hasFrom = true;
}
}
bool hasTo = false;
idxVal = 0;
foundEntry = columnIDX.TryGetValue("ToDepth", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
Decimal val = 0;
bool isOk = Decimal.TryParse(ii, out val);
if (isOk)
{
toDepth = val;
hasTo = true;
}
}
List<Sample> duplicateList = null;
bool isDuplicateInterval = false;
//if (checkForDuplicates)
//{
// if (hasFrom && hasTo)
// {
// // here we need to check that the hole is not duplicated
// duplicateList = assayQueries.CheckForDuplicate(holeID, fromDepth, toDepth);
// if (duplicateList.Count > 0)
// {
// isDuplicateInterval = true;
// }
// }
// if (isDuplicateInterval)
// {
// hasDuplicateIntervals = true;
// mos.AddWarningMessage("Duplicate interval for hole " + holeName + " at depth " + fromDepth + " to " + toDepth);
// UpdateStatus("Duplicate interval at " + holeName + " " + fromDepth + ", " + toDepth, pct);
// if (!doImportOverwrite)
// {
// mos.recordsFailed++;
// continue;
// }
// }
//}
idxVal = 0;
foundEntry = columnIDX.TryGetValue("SampleNumber", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
sampleNumber = ii;
}
idxVal = 0;
foundEntry = columnIDX.TryGetValue("SampleName", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
sampleName = ii;
}
idxVal = 0;
foundEntry = columnIDX.TryGetValue("SampleNumber", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
labsampleNumber = ii;
}
idxVal = 0;
foundEntry = columnIDX.TryGetValue("SampleNumber", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
labBatchNumber = ii;
}
Sample xs = new Sample();
if (isDuplicateInterval == true)
{
xs = duplicateList.First();
}
else
{
xs.SampleID = Guid.NewGuid();
xs.SampleName = sampleName;
xs.SampleNumber = sampleNumber;
xs.FromDepth = fromDepth;
xs.ToDepth = toDepth;
xs.HeaderID = holeID;
xs.VersionUpdated = currentUpdateTimestamp;
entityObj.Samples.AddObject(xs);
}
// Now iddentify the program, Stage, Size fraction and wash fraction
// get the program text
string programType = null;
if (cmProgram != null) {
programType = items[cmProgram.sourceColumnNumber];
}
string stage = null;
if (cmStage != null)
{
stage = items[cmStage.sourceColumnNumber];
}
string sizeFraction = null;
if (cmSizeFraction != null)
{
sizeFraction = items[cmSizeFraction.sourceColumnNumber];
}
string washFraction = null;
if (cmWashFraction != null)
{
washFraction = items[cmWashFraction.sourceColumnNumber];
}
// see if the interfal has changed, wherby we will need to reset the sequence ID
if (holeID != lastHoleID)
{
if (fromDepth != lastFromDepth && toDepth != lastToDepth)
{
// new interval
WorkflowProcedureSequenceNumber = 1;
}
}
if (!stage.Trim().Equals(lastStage))
{
WorkflowProcedureSequenceNumber = 1;
}
lastHoleID = holeID;
lastFromDepth = fromDepth;
lastToDepth = toDepth;
lastStage = stage;
AssayGroupWorkflow agWorkflowProgram = GetAssayGroupWorkflow(entityObj, programType, agGuid);
AssayGroupWorkflowProcedure agWorkflowStage = GetAssayGroupWorkflowProcedure(entityObj, stage, agWorkflowProgram);
AssayGroupSubsample agSS = new AssayGroupSubsample();
agSS.AssayGroupID = agGuid;
agSS.Sequence = seqNum;
agSS.AssayGroupSubsampleID = Guid.NewGuid();
agSS.SampleAntecedentID = xs.SampleID;
agSS.OriginalSample = xs;
agSS.AssayGroupWorkflowProcedureID = agWorkflowStage.AssayGroupWorkflowProcedureID;
agSS.AssayGroupWorkflowProcedure = agWorkflowStage;
entityObj.AssayGroupSubsamples.AddObject(agSS);
entityObj.SaveChanges();
seqNum++;
AssayGroupSubsamplePrecondition agSizeFraction = GetAssayGroupPrecondition(entityObj, sizeFraction, "Size fraction", agSS.AssayGroupSubsampleID);
AssayGroupSubsamplePrecondition agWashFraction = GetAssayGroupPrecondition(entityObj, washFraction, "Wash fraction", agSS.AssayGroupSubsampleID);
// now pick out all the mapped values
// iterate over all [ASSAY RESULT] columns
bool assayUpdated = false;
bool assayAdded = false;
foreach (KeyValuePair<ColumnMap, Guid> kvp in resultsColumns)
{
ColumnMap cm = kvp.Key;
Guid g = kvp.Value; // this is the AssayGroupTestID
AssayGroupTestResult testResult = new AssayGroupTestResult();
testResult.AssayGroupSubsampleID = agSS.AssayGroupSubsampleID;
testResult.AssayGroupTestResultID = Guid.NewGuid();
testResult.AssayGroupTestID = g;
testResult.SampleID = xs.SampleID;
testResult.VersionUpdated = currentUpdateTimestamp;
testResult.LabBatchNumber = labBatchNumber;
//testResult.LabSampleNumber = labsampleNumber;
Decimal result = new Decimal();
if (items.Count >= cm.sourceColumnNumber)
{
bool parsedOK = Decimal.TryParse(items[cm.sourceColumnNumber], out result);
if (parsedOK)
{
testResult.LabResult = result;
}
else
{
testResult.LabResultText = items[cm.sourceColumnNumber];
}
}
else
{
mos.AddWarningMessage("Line " + linesRead + " contains too few columns to read " + cm.sourceColumnName);
}
entityObj.AssayGroupTestResults.AddObject(testResult);
assayAdded = true;
}
if (assayAdded == true)
{
mos.recordsAdded++;
}
if (assayUpdated)
{
mos.recordsUpdated++;
}
tb++;
}
}
if (commitToDB)
{
if (tb == transactionBatchLimit)
{
entityObj.SaveChanges();
UpdateStatus("Writing assays to DB (" + ct + " entries)", pct);
tb = 0;
}
}
ct++;
}
entityObj.SaveChanges();
}
if (hasDuplicateIntervals)
{
mos.finalErrorCode = ModelImportStatus.DATA_CONSISTENCY_ERROR;
}
string numFKLookups = "FK lookups " + fkLookupCount;
mos.linesReadFromSource = ct - 1;
UpdateStatus("Finished writing coal quality data to database.", 0);
}
catch (Exception ex)
{
UpdateStatus("Error writing qualities to database ", 0);
mos.AddErrorMessage("Error writing data at line " + linesRead + ":\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_WRITING_TO_DB;
}
finally
{
try
{
connection.Close();
secondaryConnection.Close();
fileStream.Close();
}
catch (Exception ex)
{
mos.AddErrorMessage("Error closing conenction to database:\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_WRITING_TO_DB;
}
}
mos.linesReadFromSource = linesRead;
}
}
internal void AddAssayData(ModelImportStatus mos, Stream fileStream, FormatSpecification.ImportDataMap importMap,
int batchSize, Action <string, double> UpdateStatus, int approxNumLines,
string connectionString, Guid NKDProjectID, bool checkForDuplicates, bool doImportOverwrite)
{
bool commitToDB = true;
DateTime currentUpdateTimestamp = DateTime.UtcNow;
// first set up an assay group object - we can do this through the edm
using (var entityObj = new NKDC(connectionString, null))
{
//entityObj.Configuration.AutoDetectChangesEnabled = false;
Guid agGuid = Guid.NewGuid();
AssayGroup ag = new AssayGroup();
ag.AssayGroupID = agGuid;
ag.ProjectID = NKDProjectID;
ag.AssayGroupName = "Manual import";
ag.Comment = "From file " + importMap.mapOriginalDataFile;
ag.Entered = currentUpdateTimestamp;
ag.VersionUpdated = currentUpdateTimestamp;
entityObj.AssayGroups.AddObject(ag);
if (commitToDB)
{
entityObj.SaveChanges();
}
// set up the assay test columns - one of these for each test type
Dictionary <ColumnMap, Guid> resultsColumns = new Dictionary <ColumnMap, Guid>();
Dictionary <Guid, AssayGroupTest> assayGroups = new Dictionary <Guid, AssayGroupTest>();
foreach (ColumnMap cim in importMap.columnMap)
{
if (cim.targetColumnName.Trim().StartsWith("[ASSAY"))
{
// this is a test category
resultsColumns.Add(cim, Guid.NewGuid());
}
}
UpdateStatus("Setting up assay tests ", 2);
foreach (KeyValuePair <ColumnMap, Guid> kvp in resultsColumns)
{
ColumnMap cm = kvp.Key;
Guid g = kvp.Value;
AssayGroupTest xt = new AssayGroupTest();
string ss1 = "";
if (cm.sourceColumnName != null && cm.sourceColumnName.Length > 15)
{
ss1 = cm.sourceColumnName.Substring(0, 16);
}
else
{
ss1 = cm.sourceColumnName;
}
Guid pid = FindParameterForAssayTypeName(cm.sourceColumnName);
xt.ParameterID = pid;
xt.AssayTestName = ss1;
xt.AssayGroupID = agGuid;
xt.AssayGroupTestID = g;
xt.VersionUpdated = currentUpdateTimestamp;
entityObj.AssayGroupTests.AddObject(xt);
assayGroups.Add(g, xt);
if (commitToDB)
{
entityObj.SaveChanges();
}
}
// iterate through the data lines
int ct = 1;
int linesRead = 0;
SqlConnection connection = null;
SqlConnection secondaryConnection = null;
//List<string> uniqueDomains = new List<string>();
// get a connection to the database
string line = null;
try
{
int domainColIDX = -1;
connection = new SqlConnection(connectionString);
connection.Open();
secondaryConnection = new SqlConnection(connectionString);
secondaryConnection.Open();
bool hasDuplicateIntervals = false;
int numCommits = 0;
SqlTransaction trans;
trans = connection.BeginTransaction();
List <SqlCommand> commands = new List <SqlCommand>();
int tb = 0;
int transactionBatchLimit = batchSize;
// open the filestream and read the first line
StreamReader sr = null;
FileStream fs = null;
try
{
//fs = new FileStream(textInputDataFile, FileMode.Open, FileAccess.Read, FileShare.Read);
sr = new StreamReader(fileStream);
}
catch (Exception ex)
{
mos.AddErrorMessage("Error getting data stream for input data:\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_LOADING_FILE;
}
line = null;
float pct = 0;
float bct = 1;
// report every X blocks
int repCount = 0;
//int reportOnBlock = 1000;
float fNumLines = (float)approxNumLines;
Dictionary <string, Guid> holeIDLookups = new Dictionary <string, Guid>();
Dictionary <string, int> columnIDX = new Dictionary <string, int>();
int fkLookupCount = 0;
BaseImportTools.PopulateCMapShortcut(importMap, columnIDX);
ColumnMap headerCmap = importMap.FindItemsByTargetName("HeaderID");
AssayQueries assayQueries = new AssayQueries();
List <string> items = new List <string>();
if (sr != null)
{
while ((line = sr.ReadLine()) != null)
{
repCount++;
pct = ((float)linesRead / (float)approxNumLines) * 100.0f;
bct++;
linesRead++;
if (ct >= importMap.dataStartLine)
{
var append = BaseImportTools.ParseTestLine(line, importMap.inputDelimiter);
if (items.Count == 0 || append.Count == importMap.MaxColumns)
{
items = append;
}
else if (items.Count < importMap.MaxColumns)
{
items[items.Count - 1] = items[items.Count - 1] + append[0];
items.AddRange(append.Skip(1));
}
if (items.Count < importMap.MaxColumns)
{
mos.AddWarningMessage(string.Format("Bad CSV file, attempted to join....{0}", linesRead));
continue;
}
else if (items.Count > importMap.MaxColumns)
{
mos.AddWarningMessage(string.Format("FAILED! Line {0}. Bad CSV file, attempted to join.", linesRead));
items.Clear();
continue;
}
// digest a row of input data
Guid holeID = new Guid();
Decimal?fromDepth = null;
Decimal?toDepth = null;
string sampleNumber = null;
string labBatchNumber = null;
string labsampleNumber = null;
Decimal?sampleMassKg = null;
Decimal?dryMassKg = null;
string standardSampleTypeName = null;
// find mapped values by name
//ColumnMap cmap = importMap.FindItemsByTargetName("HeaderID");
int idxVal = 0;
bool foundEntry = columnIDX.TryGetValue("HeaderID", out idxVal);
bool foundHole = false;
string holeName = "";
if (foundEntry)
{
string lookupByName = "HoleName";
string lookupValue = items[idxVal];
holeName = lookupValue;
bool lv = holeIDLookups.ContainsKey(lookupValue);
if (!lv)
{
string headerGUID = ForeignKeyUtils.FindFKValueInOther(lookupValue, headerCmap, secondaryConnection, false, lookupByName, NKDProjectID);
if (headerGUID == null)
{
// this means we have not found the specified records in the header table
// Report on issue and skip line
}
else
{
foundHole = true;
holeID = new Guid(headerGUID);
holeIDLookups.Add(lookupValue, holeID);
fkLookupCount++;
}
}
else
{
holeIDLookups.TryGetValue(lookupValue, out holeID);
foundHole = true;
}
}
if (!foundHole)
{
mos.AddErrorMessage("Failed to find hole " + holeName + ". Skipping record at line " + linesRead + ".");
mos.finalErrorCode = ModelImportStatus.DATA_CONSISTENCY_ERROR;
mos.recordsFailed++;
continue;
}
else
{
bool hasFrom = false;
idxVal = 0;
foundEntry = columnIDX.TryGetValue("FromDepth", out idxVal);
if (foundEntry)
//cmap = importMap.FindItemsByTargetName();
//if (cmap != null)
{
string ii = items[idxVal];
Decimal val = 0;
bool isOk = Decimal.TryParse(ii, out val);
if (isOk)
{
fromDepth = val;
hasFrom = true;
}
}
bool hasTo = false;
idxVal = 0;
foundEntry = columnIDX.TryGetValue("ToDepth", out idxVal);
if (foundEntry)
//cmap = importMap.FindItemsByTargetName("ToDepth");
//if (cmap != null)
{
string ii = items[idxVal];
Decimal val = 0;
bool isOk = Decimal.TryParse(ii, out val);
if (isOk)
{
toDepth = val;
hasTo = true;
}
}
List <Sample> duplicateList = null;
bool isDuplicateInterval = false;
if (checkForDuplicates)
{
if (hasFrom && hasTo)
{
// here we need to check that the hole is not duplicated
duplicateList = assayQueries.CheckForDuplicate(holeID, fromDepth, toDepth);
if (duplicateList.Count > 0)
{
isDuplicateInterval = true;
}
}
if (isDuplicateInterval)
{
hasDuplicateIntervals = true;
mos.AddWarningMessage("Duplicate interval for hole " + holeName + " at depth " + fromDepth + " to " + toDepth);
UpdateStatus("Duplicate interval at " + holeName + " " + fromDepth + ", " + toDepth, pct);
if (!doImportOverwrite)
{
mos.recordsFailed++;
continue;
}
}
}
//cmap = importMap.FindItemsByTargetName("SampleNumber");
idxVal = 0;
foundEntry = columnIDX.TryGetValue("SampleNumber", out idxVal);
if (foundEntry)
// if (cmap != null)
{
string ii = items[idxVal];
sampleNumber = ii;
}
//cmap = importMap.FindItemsByTargetName("LabSampleNumber");
//if (cmap != null)
idxVal = 0;
foundEntry = columnIDX.TryGetValue("LabSampleName", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
labsampleNumber = ii;
}
//cmap = importMap.FindItemsByTargetName("LabBatchNumber");
idxVal = 0;
foundEntry = columnIDX.TryGetValue("LabBatchNumber", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
labBatchNumber = ii;
}
idxVal = 0;
foundEntry = columnIDX.TryGetValue("SampleMassKg", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
Decimal val = 0;
bool isOk = Decimal.TryParse(ii, out val);
if (isOk)
{
sampleMassKg = val;
}
}
idxVal = 0;
foundEntry = columnIDX.TryGetValue("DryMassKg", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
Decimal val = 0;
bool isOk = Decimal.TryParse(ii, out val);
if (isOk)
{
dryMassKg = val;
}
}
idxVal = 0;
foundEntry = columnIDX.TryGetValue("StandardSampleTypeName", out idxVal);
if (foundEntry)
{
string ii = items[idxVal];
standardSampleTypeName = ii;
}
Sample xs = new Sample();
if (isDuplicateInterval == true)
{
xs = duplicateList.First();
}
else
{
xs.SampleID = Guid.NewGuid();
xs.FromDepth = fromDepth;
xs.ToDepth = toDepth;
xs.HeaderID = holeID;
xs.VersionUpdated = currentUpdateTimestamp;
xs.SampleNumber = sampleNumber;
xs.SampleMassKg = sampleMassKg;
if (!string.IsNullOrWhiteSpace(standardSampleTypeName))
{
var t = entityObj.DictionarySampleTypes.Select(f => new { f.SampleTypeID, f.StandardSampleTypeName }).FirstOrDefault(f => f.StandardSampleTypeName == standardSampleTypeName);
if (t != null)
{
xs.SampleTypeID = t.SampleTypeID;
}
}
xs.DryMassKg = dryMassKg;
}
// now pick out all the mapped values
// iterate over all [ASSAY RESULT] columns
bool assayUpdated = false;
bool assayAdded = false;
var results = new List <AssayGroupTestResult>();
foreach (KeyValuePair <ColumnMap, Guid> kvp in resultsColumns)
{
ColumnMap cm = kvp.Key;
Guid g = kvp.Value; // this is the AssayGroupTestID
AssayGroupTestResult testResult = new AssayGroupTestResult();
/*bool assayResFound = false;
*
* if (isDuplicateInterval)
* {
* List<AssayGroupTestResult> testResults = assayQueries.GetDuplicateResult(xs.SampleID, cm.sourceColumnName);
* if (testResults.Count > 0)
* {
* testResult = testResults.First();
* assayResFound = true;
* }
* }*/
//if(!assayResFound)
// {
testResult.AssayGroupTestResultID = Guid.NewGuid();
testResult.AssayGroupTestID = g;
testResult.SampleID = xs.SampleID;
testResult.VersionUpdated = currentUpdateTimestamp;
//}
testResult.LabBatchNumber = labBatchNumber;
testResult.LabSampleName = labsampleNumber;
Decimal result = new Decimal();
if (items.Count >= cm.sourceColumnNumber)
{
bool parsedOK = Decimal.TryParse(items[cm.sourceColumnNumber], out result);
if (parsedOK)
{
testResult.LabResult = result;
}
testResult.LabResultText = items[cm.sourceColumnNumber];
}
else
{
mos.AddWarningMessage("Line " + linesRead + " contains too few columns to read " + cm.sourceColumnName);
}
results.Add(testResult);
//if (isDuplicateInterval == false)
//{
assayAdded = true;
//}else{
// if (!assayResFound)
// {
// entityObj.AssayGroupTestResult.Add(testResult);
// assayAdded = true;
// }
// else {
// assayUpdated = true;
// }
//}
}
var resultsToSave = (from o in results where !string.IsNullOrWhiteSpace(o.LabResultText) select o);
if (!resultsToSave.Any())
{
continue;
}
if (!isDuplicateInterval)
{
entityObj.Samples.AddObject(xs);
}
foreach (var save in resultsToSave)
{
entityObj.AssayGroupTestResults.AddObject(save);
}
if (assayAdded == true)
{
mos.recordsAdded++;
}
if (assayUpdated)
{
mos.recordsUpdated++;
}
tb++;
}
}
if (commitToDB)
{
if (tb == transactionBatchLimit)
{
entityObj.SaveChanges();
UpdateStatus("Writing assays to DB (" + ct + " entries)", pct);
tb = 0;
}
}
ct++;
//Console.WriteLine("Processing line "+ct);
items.Clear();
}
entityObj.SaveChanges();
}
if (hasDuplicateIntervals)
{
mos.finalErrorCode = ModelImportStatus.DATA_CONSISTENCY_ERROR;
}
string numFKLookups = "FK lookups " + fkLookupCount;
mos.linesReadFromSource = ct - 1;
UpdateStatus("Finished writing assays to database.", 0);
}
catch (Exception ex)
{
UpdateStatus("Error writing assays to database ", 0);
mos.AddErrorMessage("Error writing assay data at line " + linesRead + ":\n" + line + "\n\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_WRITING_TO_DB;
}
finally
{
try
{
connection.Close();
secondaryConnection.Close();
fileStream.Close();
}
catch (Exception ex)
{
mos.AddErrorMessage("Error closing connection to database:\n" + ex.ToString());
mos.finalErrorCode = ModelImportStatus.ERROR_WRITING_TO_DB;
}
}
mos.linesReadFromSource = linesRead;
}
}
