private void masterClose(OutputFile outputFile)
{
outputFile.Append("</ClinicalData>");
outputFile.Append("</ODM>");
}
private void masterHeader(OutputFile outputFile)
{
String timeStamp = DateTime.Now.ToString("yyyy-MM-ddTHH:mm:ss");
outputFile.Append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
outputFile.Append("<ODM xmlns=\"http://www.cdisc.org/ns/odm/v1.3\"");
outputFile.Append("xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"");
outputFile.Append("xsi:schemaLocation=\"http://www.cdisc.org/ns/odm/v1.3 ODM1-3.xsd\"");
outputFile.Append("ODMVersion=\"1.3\" FileOID=\"1D20080412202420\" FileType=\"Snapshot\"");
outputFile.Append("Description=\"Dataset ODM\" CreationDateTime=\"" + timeStamp + "\" >");
outputFile.Append("<ClinicalData StudyOID=\"" + conversionSettings.studyOID + "\" MetaDataVersionOID=\"v1.0.0\">");
}
public void DoWork(DataGrid dataGrid)
{
Insert2s.Clear();
Insert3s.Clear();
string theDate = DateTime.Now.ToString("yyyy-MM-dd");
string theWrittenSE = "";
string theWrittenGR = "";
string[] theHeaders;
int event_index_row = -1;
int group_index_row = -1;
int site_index_row = -1;
string usedStudyOID = conversionSettings.studyOID;
if (dataGrid.isValid() == false)
{
return;
}
int DGIndexOfOCItem = DataGrid.DGIndexOfOCItem;
int DGIndexOfDataItem = DataGrid.DGIndexOfDataItem;
// initialize files
int maximalNumberOfLinesOutputFile = conversionSettings.outFMaxLines;
if (maximalNumberOfLinesOutputFile == 0)
{
maximalNumberOfLinesOutputFile = 99999;
}
int numberOfLinesOutputFile = 0;
String outputFileBaseName = conversionSettings.workdir + "\\DataImport_";
numberOfOutputFiles = 1;
String outputFilePath = outputFileBaseName + numberOfOutputFiles + ".xml";
OutputFile odmOutputFile = new OutputFile(outputFilePath);
masterHeader(odmOutputFile);
String fileNameINSF = conversionSettings.workdir + "\\Inserts.sql";
OutputFile insertsSQLFile = new OutputFile(fileNameINSF);
String fileNameINSFR = conversionSettings.workdir + "\\Inserts_ONLY_STUDY_EVENTS.sql";
OutputFile insertsOnlyEventsSQLFile = new OutputFile(fileNameINSFR);
String fileNameDELF = conversionSettings.workdir + "\\Deletes.sql";
OutputFile deletesSQLFile = new OutputFile(fileNameDELF);
String fileNameDELFR = conversionSettings.workdir + "\\Deletes_ONLY_STUDY_EVENTS.sql";
OutputFile deletesOnlyEventsSQLFile = new OutputFile(fileNameDELFR);
List<String> subjectIDList = new List<String>();
subjectIDList.Clear();
try
{
String[] linesArray = File.ReadAllLines(conversionSettings.pathToInputFile);
int linecount = 0;
foreach (String line in linesArray)
{
// line = line.Trim(); // 1.1b
if (line.Length == 0) continue;
if (line.Trim().Length == 0) continue; // 4.4.2
studyMetaDataValidator.reset();
linecount++;
if (linecount == 1)
{
theHeaders = line.Split(dataGrid.delimiter); // get row event and group indexes, if defined that way.
for (int i = 0; i < theHeaders.Length; i++)
{
if (theHeaders[i].ToUpper() == "EVENT_INDEX") event_index_row = i; // 2.2 Input file format allows EVENT_INDEX and GROUP_INDEX to define repeating items in rows
if (theHeaders[i].ToUpper() == "GROUP_INDEX") group_index_row = i;
if (theHeaders[i].ToUpper() == "SITE_OID") site_index_row = i;
}
continue; // skip first line; contains only headers
}
int mySepCount = 1;
viewUpdater.updateProgressbarStep(line.Length);
for (int i = 0; i < line.Length; i++) if (line[i] == dataGrid.delimiter) mySepCount++;
if (dataGrid.sepcount != mySepCount)
{
string errtext = "Input data file format incorrect at line = " + linecount.ToString() + " Expecting: " + conversionSettings.sepCount.ToString() + "; found: " + mySepCount.ToString() + " items; this is the faulty line: " + line;
warningLog.appendMessage(errtext);
continue;
}
string[] split = line.Split(dataGrid.delimiter);
String subjectID = split[dataGrid.subjectIDIndex];
subjectID = subjectID.Trim();
if (conversionSettings.checkForDuplicateSubjects)
{
if (subjectIDList.Contains(subjectID))
{
string errtext = "Duplicate subjectID " + subjectID + " at line = " + linecount.ToString();
warningLog.appendMessage(errtext);
}
}
subjectIDList.Add(subjectID);
viewUpdater.performProgressbarStep();
// Handle first DG line
int DGFirstLine = 0;
String lineToSplit = dataGrid.dataGridView.Rows[DGFirstLine].Cells[DGIndexOfOCItem].Value.ToString();
string[] ocparts = dataGrid.dataGridView.Rows[DGFirstLine].Cells[DGIndexOfOCItem].Value.ToString().Split('.');
String TheStudyEventOID = ocparts[0];
String TheFormOID = "";
String TheItemGroupDef = "";
String TheItemId = "";
string theSERK = "1";
string theGRRK = "NOT";
string theStudyDataColumn = "";
if (TheStudyEventOID == "none")
{
DGFirstLine++;
try // fix 2.0.3 -> If no items are matched; can't increase DGFirstLine, causes index out of range
{
ocparts = dataGrid.dataGridView.Rows[DGFirstLine].Cells[DGIndexOfOCItem].Value.ToString().Split('.');
TheFormOID = ocparts[1];
TheItemGroupDef = ocparts[2];
TheItemId = ocparts[3];
if (TheItemGroupDef.IndexOf('-') > 0) TheItemGroupDef = TheItemGroupDef.Substring(0, TheItemGroupDef.IndexOf('-'));
TheStudyEventOID = ocparts[0];
theStudyDataColumn = dataGrid.dataGridView.Rows[DGFirstLine].Cells[DGIndexOfDataItem].Value.ToString();
}
catch (Exception ex)
{
TheFormOID = "none";
TheItemGroupDef = "none";
TheStudyEventOID = "none";
theStudyDataColumn = "none";
TheItemId = "none";
}
}
else // 2.1 fix on above fix
{
TheFormOID = ocparts[1];
TheItemGroupDef = ocparts[2];
if (TheItemGroupDef.IndexOf('-') > 0) TheItemGroupDef = TheItemGroupDef.Substring(0, TheItemGroupDef.IndexOf('-'));
TheItemId = ocparts[3];
theStudyDataColumn = dataGrid.dataGridView.Rows[DGFirstLine].Cells[DGIndexOfDataItem].Value.ToString();
}
if (TheStudyEventOID.Contains("*"))
{
string[] pp = TheStudyEventOID.Split('*');
theWrittenSE = pp[0];
theSERK = pp[1];
}
else
{
theWrittenSE = TheStudyEventOID;
theSERK = "1";
// 2.0.5 use the SE selected item to get the SE repeating index
if (dataGrid.startDateItem.Contains("_E"))
{
theSERK = dataGrid.startDateItem.Substring(dataGrid.startDateItem.IndexOf("_E") + 2);
}
}
if (TheItemGroupDef.Contains("*"))
{
string[] pp = TheItemGroupDef.Split('*');
theWrittenGR = pp[0];
theGRRK = pp[1];
}
else
{
theGRRK = "NOT";
theWrittenGR = TheItemGroupDef.Substring(1); // get rid of the added A to get this above in grid
}
// 2.0.5 Do NOT print formdata with no items
string theXMLEvent = "";
if (event_index_row != -1) theSERK = split[event_index_row];
if (group_index_row != -1) theGRRK = split[group_index_row];
if (site_index_row != -1 && split[site_index_row].Trim() != "")
{
bool found = false;
foreach (string one in Sites)
{
if (one.Trim() == split[site_index_row].Trim())
{
found = true;
}
}
if (!found)
{
string errtext = "Specified site not found in meta file: " + split[site_index_row] + " at line = " + linecount.ToString();
warningLog.appendMessage(errtext);
}
usedStudyOID = split[site_index_row];
}
else usedStudyOID = conversionSettings.studyOID;
if (site_index_row != -1 && split[site_index_row].Trim() == "")
{
string errtext = "No site specified under SITE_OID; assuming STUDY_OID, at line: " + linecount.ToString();
warningLog.appendMessage(errtext);
}
string SStheKEY = "SS_" + subjectID;
if (labelOCoidExists) // 2.1.1 there is a conversion file from label to oid; get the SSid from that file.
{
foreach (string one in labelOID)
{
if (one.StartsWith(subjectID + "^")) SStheKEY = one.Substring(one.IndexOf('^') + 1);
}
}
string theXMLForm = "";
odmOutputFile.Append(" <SubjectData SubjectKey=\"" + SStheKEY + "\">");
theXMLEvent += " <StudyEventData StudyEventOID=\"" + theWrittenSE + "\" StudyEventRepeatKey=\"" + CheckRepeatKey(theSERK, linecount) + "\">" + LINE_SEPARATOR;
theXMLForm += " <FormData FormOID=\"" + TheFormOID + "\">" + LINE_SEPARATOR;
if (theGRRK == "NOT") theXMLForm += " <ItemGroupData ItemGroupOID=\"" + theWrittenGR + "\" TransactionType=\"Insert\" >" + LINE_SEPARATOR;
else theXMLForm += " <ItemGroupData ItemGroupOID=\"" + theWrittenGR + "\" ItemGroupRepeatKey=\"" + CheckRepeatKey(theGRRK, linecount) + "\" TransactionType=\"Insert\" >" + LINE_SEPARATOR;
int indexOfItem = 0;
string itemval = "";
bool datapresentform = false;
bool datapresentevent = false;
if (TheItemId != "none")
{
indexOfItem = dataGrid.GetIndexOfItem(dataGrid.dataGridView.Rows[DGFirstLine].Cells[DGIndexOfOCItem].Value.ToString());
check_index_of_item(linecount, indexOfItem);
itemval = split[indexOfItem];
itemval = studyMetaDataValidator.ValidateItem(subjectID, TheFormOID, TheItemId, itemval, linecount, conversionSettings.dateFormat);
if (itemval != "")
{
theXMLForm += " <ItemData ItemOID=\"" + TheItemId + "\" Value=\"" + SecurityElement.Escape(itemval) + "\" />" + LINE_SEPARATOR;
datapresentform = true;
}
}
// Now handle the rest of the DG
for (int i = DGFirstLine + 1; i < dataGrid.dataGridView.RowCount; i++)
{
if (dataGrid.dataGridView.Rows[i].IsNewRow == false)
{
string[] nwdingen = dataGrid.dataGridView.Rows[i].Cells[DGIndexOfOCItem].Value.ToString().Split('.');
theStudyDataColumn = dataGrid.dataGridView.Rows[i].Cells[DGIndexOfDataItem].Value.ToString();
if (TheStudyEventOID == nwdingen[0] && TheFormOID == nwdingen[1] && TheItemGroupDef == nwdingen[2])
{
if (nwdingen[3] != "none")
{
indexOfItem = dataGrid.GetIndexOfItem(dataGrid.dataGridView.Rows[i].Cells[DGIndexOfOCItem].Value.ToString());
check_index_of_item(linecount, indexOfItem);
itemval = split[indexOfItem];
itemval = studyMetaDataValidator.ValidateItem(subjectID, TheFormOID, nwdingen[3], itemval, linecount, conversionSettings.dateFormat);
if (itemval != "")
{
theXMLForm += " <ItemData ItemOID=\"" + nwdingen[3] + "\" Value=\"" + SecurityElement.Escape(itemval) + "\" />" + LINE_SEPARATOR;
datapresentform = true;
}
}
}
else if (TheStudyEventOID == nwdingen[0] && TheFormOID == nwdingen[1])
{
TheItemGroupDef = nwdingen[2];
theXMLForm += " </ItemGroupData>" + LINE_SEPARATOR;
if (TheItemGroupDef.Contains("*"))
{
string[] pp = TheItemGroupDef.Split('*');
theWrittenGR = pp[0];
theGRRK = pp[1];
}
else
{
theGRRK = "NOT";
theWrittenGR = TheItemGroupDef.Substring(1);
}
if (group_index_row != -1) theGRRK = split[group_index_row];
if (theGRRK == "NOT") theXMLForm += " <ItemGroupData ItemGroupOID=\"" + theWrittenGR + "\" TransactionType=\"Insert\" >" + LINE_SEPARATOR;
else theXMLForm += " <ItemGroupData ItemGroupOID=\"" + theWrittenGR + "\" ItemGroupRepeatKey=\"" + CheckRepeatKey(theGRRK, linecount) + "\" TransactionType=\"Insert\" >" + LINE_SEPARATOR;
if (nwdingen[3] != "none")
{
indexOfItem = dataGrid.GetIndexOfItem(dataGrid.dataGridView.Rows[i].Cells[DGIndexOfOCItem].Value.ToString());
check_index_of_item(linecount, indexOfItem);
itemval = split[indexOfItem];
itemval = studyMetaDataValidator.ValidateItem(subjectID, TheFormOID, nwdingen[3], itemval, linecount, conversionSettings.dateFormat);
if (itemval != "")
{
theXMLForm += " <ItemData ItemOID=\"" + nwdingen[3] + "\" Value=\"" + SecurityElement.Escape(itemval) + "\" />" + LINE_SEPARATOR;
datapresentform = true;
}
}
}
else if (TheStudyEventOID == nwdingen[0])
{
TheFormOID = nwdingen[1];
TheItemGroupDef = nwdingen[2];
theXMLForm += " </ItemGroupData>" + LINE_SEPARATOR;
theXMLForm += " </FormData>" + LINE_SEPARATOR;
if (datapresentform)
{
datapresentevent = true;
theXMLEvent += theXMLForm;
datapresentform = false;
}
theXMLForm = "";
theXMLForm += " <FormData FormOID=\"" + TheFormOID + "\">" + LINE_SEPARATOR;
if (TheItemGroupDef.Contains("*"))
{
string[] pp = TheItemGroupDef.Split('*');
theWrittenGR = pp[0];
theGRRK = pp[1];
}
else
{
theGRRK = "NOT";
theWrittenGR = TheItemGroupDef.Substring(1);
}
if (group_index_row != -1) theGRRK = split[group_index_row];
// fix 2.1.2 -> if (theGRRK == "NOT") was not there and ItemGroupRepeatKey="NOT" was generated!
if (theGRRK == "NOT") theXMLForm += " <ItemGroupData ItemGroupOID=\"" + theWrittenGR + "\" TransactionType=\"Insert\" >" + LINE_SEPARATOR;
else theXMLForm += " <ItemGroupData ItemGroupOID=\"" + theWrittenGR + "\" ItemGroupRepeatKey=\"" + CheckRepeatKey(theGRRK, linecount) + "\" TransactionType=\"Insert\" >" + LINE_SEPARATOR;
if (nwdingen[3] != "none")
{
indexOfItem = dataGrid.GetIndexOfItem(dataGrid.dataGridView.Rows[i].Cells[DGIndexOfOCItem].Value.ToString());
check_index_of_item(linecount, indexOfItem);
itemval = split[indexOfItem];
itemval = studyMetaDataValidator.ValidateItem(subjectID, TheFormOID, nwdingen[3], itemval, linecount, conversionSettings.dateFormat);
if (itemval != "")
{
theXMLForm += " <ItemData ItemOID=\"" + nwdingen[3] + "\" Value=\"" + SecurityElement.Escape(itemval) + "\" />" + LINE_SEPARATOR;
datapresentform = true;
}
}
}
else
{
TheStudyEventOID = nwdingen[0];
if (TheStudyEventOID.Contains("*"))
{
string[] pp = TheStudyEventOID.Split('*');
theWrittenSE = pp[0];
theSERK = pp[1];
}
else
{
theSERK = "1";
theWrittenSE = TheStudyEventOID;
}
if (event_index_row != -1) theSERK = split[event_index_row];
theXMLForm += " </ItemGroupData>" + LINE_SEPARATOR;
theXMLForm += " </FormData>" + LINE_SEPARATOR;
if (datapresentform)
{
datapresentevent = true;
theXMLEvent += theXMLForm;
datapresentform = false;
}
theXMLForm = "";
theXMLEvent += " </StudyEventData>";
if (datapresentevent)
{
odmOutputFile.Append(theXMLEvent);
datapresentevent = false;
}
theXMLEvent = "";
if (conversionSettings.selectedEventRepeating == "Yes")
{
if (event_index_row != -1) theSERK = split[event_index_row];
else theSERK = Utilities.Get_SE_RepeatingKey_FromStudyDataColumn(theStudyDataColumn);
}
theXMLEvent += " <StudyEventData StudyEventOID=\"" + theWrittenSE + "\" StudyEventRepeatKey=\"" + CheckRepeatKey(theSERK, linecount) + "\">" + LINE_SEPARATOR;
TheFormOID = nwdingen[1];
theXMLForm += " <FormData FormOID=\"" + TheFormOID + "\">" + LINE_SEPARATOR;
TheItemGroupDef = nwdingen[2];
if (TheItemGroupDef.Contains("*"))
{
string[] pp = TheItemGroupDef.Split('*');
theWrittenGR = pp[0];
theGRRK = pp[1];
}
else
{
theGRRK = "NOT";
theWrittenGR = TheItemGroupDef.Substring(1);
}
if (group_index_row != -1) theGRRK = split[group_index_row];
if (theGRRK == "NOT") theXMLForm += " <ItemGroupData ItemGroupOID=\"" + theWrittenGR + "\" TransactionType=\"Insert\" >" + LINE_SEPARATOR;
else theXMLForm += " <ItemGroupData ItemGroupOID=\"" + theWrittenGR + "\" ItemGroupRepeatKey=\"" + CheckRepeatKey(theGRRK, linecount) + "\" TransactionType=\"Insert\" >" + LINE_SEPARATOR;
if (nwdingen[3] != "none")
{
indexOfItem = dataGrid.GetIndexOfItem(dataGrid.dataGridView.Rows[i].Cells[DGIndexOfOCItem].Value.ToString());
check_index_of_item(linecount, indexOfItem);
itemval = split[indexOfItem];
itemval = studyMetaDataValidator.ValidateItem(subjectID, TheFormOID, nwdingen[3], itemval, linecount, conversionSettings.dateFormat);
if (itemval != "")
{
theXMLForm += " <ItemData ItemOID=\"" + nwdingen[3] + "\" Value=\"" + SecurityElement.Escape(itemval) + "\" />" + LINE_SEPARATOR;
datapresentform = true;
}
}
}
}
}
string SubSex = conversionSettings.defaultSubjectSex;
if (dataGrid.sexIndex >= 0)
{
SubSex = split[dataGrid.sexIndex];
SubSex = SubSex.Trim();
}
if (SubSex == conversionSettings.SUBJECTSEX_M) SubSex = "m"; // 1.0f
if (SubSex == conversionSettings.SUBJECTSEX_F) SubSex = "f";
if (SubSex != "f" && SubSex != "m" && SubSex != "") // 1.1e Allow nothing to be entered for sex; it is not always mandatory.
{
string errtext = "Subject sex can be only 'f' or 'm'. You have '" + SubSex + "' at line " + linecount.ToString() + ". Index: " + dataGrid.sexIndex + ".";
warningLog.appendMessage(errtext);
}
theXMLForm += " </ItemGroupData>" + LINE_SEPARATOR;
theXMLForm += " </FormData>" + LINE_SEPARATOR;
if (datapresentform)
{
datapresentevent = true;
theXMLEvent += theXMLForm;
datapresentform = false;
}
theXMLForm = "";
theXMLEvent += " </StudyEventData>";
if (datapresentevent)
{
odmOutputFile.Append(theXMLEvent);
datapresentevent = false;
}
theXMLEvent = "";
odmOutputFile.Append(" </SubjectData>");
numberOfLinesOutputFile = numberOfLinesOutputFile + 1;
if (numberOfLinesOutputFile >= maximalNumberOfLinesOutputFile) // 1.0f
{
masterClose(odmOutputFile);
numberOfLinesOutputFile = 0;
numberOfOutputFiles = numberOfOutputFiles + 1;
outputFilePath = outputFileBaseName + numberOfOutputFiles + ".xml";
odmOutputFile.Close();
odmOutputFile = new OutputFile(outputFilePath);
masterHeader(odmOutputFile);
}
// generate insert statements
int theSERKInt = 0;
try
{
theSERKInt = System.Convert.ToInt16(theSERK);
}
catch
{
string errtext = "EVENT_INDEX can't be determined at line " + linecount.ToString() + ". Index: " + theSERK + ". (must be an integer)";
warningLog.appendMessage(errtext);
}
string theDOB = "";
//if (DOBIndex >= 0)
//{
// if (DOY && split[DOBIndex].Trim().Length == 4) theDOB = split[DOBIndex].Trim();
// else theDOB = ConvertToODMFormat(split[DOBIndex]);
//}
if (dataGrid.DOBIndex >= 0)
{
if (DOY && split[dataGrid.DOBIndex].Trim().Length == 4) theDOB = split[dataGrid.DOBIndex].Trim() + "-01-01";
else theDOB = theDOB = Utilities.ConvertToODMFormat(split[dataGrid.DOBIndex], conversionSettings.dateFormat);
}
string theSTD = "";
if (dataGrid.STDIndex >= 0)
{
theSTD = Utilities.ConvertToODMFormat(split[dataGrid.STDIndex], conversionSettings.dateFormat); // This is needed for non repeating events
}
string thePID = "";
if (dataGrid.PIDIndex < 0)
{
thePID = subjectID;
}
else
{
thePID = split[dataGrid.PIDIndex];
}
if (theDOB.StartsWith("Error") || theDOB == "" || dataGrid.DOBIndex < 0)
{
if (theDOB == "" || dataGrid.DOBIndex < 0)
{
if (!IsDuplicatePID(thePID))
{
insertsSQLFile.Append(INSERT_1);
insertsSQLFile.Append(" VALUES (1, '" + SubSex + "', '" + thePID + "', '" + theDate + "', 1, '1');");
}
}
else
{
string errtext = "Invalid subject birth date '" + theDOB + "' at line " + linecount.ToString() + ". Index: " + dataGrid.DOBIndex + ". ";
warningLog.appendMessage(errtext);
}
}
else
{
if (!IsDuplicatePID(thePID))
{
insertsSQLFile.Append(INSERT_1A);
insertsSQLFile.Append(" VALUES (1, '" + SubSex + "', '" + thePID + "', '" + theDate + "', 1, '1', '" + theDOB + "');");
}
}
if (!IsDuplicateInsert2s(subjectID + "^" + usedStudyOID + "^" + theDate + "^" + SStheKEY + "^" + thePID))
{
insertsSQLFile.Append(INSERT_2);
// if there is no PID, use the key (unique_identifier) to fill the field label of study_subject.
insertsSQLFile.Append(" VALUES ('" + subjectID + "', (SELECT study_id FROM study WHERE oc_oid = '" + usedStudyOID + "'),");
insertsSQLFile.Append(" 1, '" + theDate + "', '" + theDate + "', '" + theDate + "', 1, '" + SStheKEY + "', (SELECT subject_id FROM subject where unique_identifier = '" + thePID + "'));");
}
if (theWrittenSE == "none" && conversionSettings.selectedStudyEvent != "-- select --") // 4.1 eliminate -- select --
{
theWrittenSE = Utilities.GetOID(conversionSettings.selectedStudyEvent); // 2.0.5 Use the selected SE to determine current SE, as there is no CRF data
}
if (theWrittenSE != "none")
{
int startindex = 1;
// 2.0.7
for (int say = startindex; say <= theSERKInt; say++)
{
// date_start of study event -> get it from file. If blank, don't create the event. OC will reject any data reletad to an event without a start date.
string part1 = "";
string part2 = "_E" + say.ToString();
if (dataGrid.eventStartDates.Contains(part2)) // there is a date; get it
{
part1 = dataGrid.eventStartDates.Substring(dataGrid.eventStartDates.IndexOf(part2) + 1);
part1 = part1.Substring(part1.IndexOf("^") + 1);
part1 = part1.Substring(0, part1.IndexOf("$")); // part1 is the index of date
theSTD = Utilities.ConvertToODMFormat(split[System.Convert.ToInt16(part1)], conversionSettings.dateFormat);
if (theSTD.StartsWith("Error"))
{
string errtext = "Invalid start date '" + theSTD + "' at line " + linecount.ToString() + ". Index: " + dataGrid.STDIndex + ". ";
warningLog.appendMessage(errtext);
}
else
{
if (theSTD != "")
{
if (!IsDuplicateInsert3s(theWrittenSE + "^" + SStheKEY + "^" + say.ToString() + "^" + theSTD + "^" + theDate))
{
insertsSQLFile.Append(INSERT_3);
insertsSQLFile.Append(" VALUES ((SELECT study_event_definition_id FROM study_event_definition WHERE oc_oid = '" + theWrittenSE + "'),");
insertsOnlyEventsSQLFile.Append(INSERT_3);
insertsOnlyEventsSQLFile.Append(" VALUES ((SELECT study_event_definition_id FROM study_event_definition WHERE oc_oid = '" + theWrittenSE + "'),");
insertsSQLFile.Append(" (SELECT study_subject_id FROM study_subject WHERE oc_oid = '" + SStheKEY + "'),'" + conversionSettings.defaultLocation + "', " + say.ToString() + ", '" + theSTD + " 12:00:00', 1, 1, '" + theDate + "', 1, '0', '0');");
insertsOnlyEventsSQLFile.Append(" (SELECT study_subject_id FROM study_subject WHERE oc_oid = '" + SStheKEY + "'),'" + conversionSettings.defaultLocation + "', " + say.ToString() + ", '" + theSTD + " 12:00:00', 1, 1, '" + theDate + "', 1, '0', '0');");
}
}
}
}
else // no repeating Events; use either todays date as STD or pick it from data file 2.0.9
{
if (!IsDuplicateInsert3s(theWrittenSE + "^" + SStheKEY + "^" + say.ToString() + "^" + theSTD + "^" + theDate))
{
if (theSTD != "") // there is a date specified in the data file
{
insertsSQLFile.Append(INSERT_3);
insertsSQLFile.Append(" VALUES ((SELECT study_event_definition_id FROM study_event_definition WHERE oc_oid = '" + theWrittenSE + "'),");
insertsOnlyEventsSQLFile.Append(INSERT_3);
insertsOnlyEventsSQLFile.Append(" VALUES ((SELECT study_event_definition_id FROM study_event_definition WHERE oc_oid = '" + theWrittenSE + "'),");
insertsSQLFile.Append(" (SELECT study_subject_id FROM study_subject WHERE oc_oid = '" + SStheKEY + "'),'" + conversionSettings.defaultLocation + "', " + say.ToString() + ", '" + theSTD + " 12:00:00', 1, 1, '" + theDate + "', 1, '0', '0');");
insertsOnlyEventsSQLFile.Append(" (SELECT study_subject_id FROM study_subject WHERE oc_oid = '" + SStheKEY + "'),'" + conversionSettings.defaultLocation + "', " + say.ToString() + ", '" + theSTD + " 12:00:00', 1, 1, '" + theDate + "', 1, '0', '0');");
}
else // no date specified in data file
{
if (conversionSettings.useTodaysDateIfNoEventDate) // 2.1.3 Generate inserts for events without dates using todays date, only if user wants to, otherwise
// TODO ask Cuneyt what otherwise
{
insertsSQLFile.Append(INSERT_3);
insertsSQLFile.Append(" VALUES ((SELECT study_event_definition_id FROM study_event_definition WHERE oc_oid = '" + theWrittenSE + "'),");
insertsOnlyEventsSQLFile.Append(INSERT_3);
insertsOnlyEventsSQLFile.Append(" VALUES ((SELECT study_event_definition_id FROM study_event_definition WHERE oc_oid = '" + theWrittenSE + "'),");
insertsSQLFile.Append(" (SELECT study_subject_id FROM study_subject WHERE oc_oid = '" + SStheKEY + "'),'" + conversionSettings.defaultLocation + "', " + say.ToString() + ", '" + theDate + " 12:00:00', 1, 1, '" + theDate + "', 1, '0', '0');");
insertsOnlyEventsSQLFile.Append(" (SELECT study_subject_id FROM study_subject WHERE oc_oid = '" + SStheKEY + "'),'" + conversionSettings.defaultLocation + "', " + say.ToString() + ", '" + theDate + " 12:00:00', 1, 1, '" + theDate + "', 1, '0', '0');");
}
}
}
}
}
deletesOnlyEventsSQLFile.Append("DELETE FROM study_event where study_subject_id = (SELECT study_subject_id FROM study_subject WHERE oc_oid = '" + SStheKEY + "');");
}
deletesSQLFile.Append("DELETE FROM study_event where study_subject_id = (SELECT study_subject_id FROM study_subject WHERE oc_oid = '" + SStheKEY + "');");
deletesSQLFile.Append("DELETE FROM study_subject where oc_oid = '" + SStheKEY + "';");
deletesSQLFile.Append("DELETE FROM subject where unique_identifier = '" + thePID + "';");
// Control hidden values and mandatory values
studyMetaDataValidator.validateHiddens(TheFormOID, linecount, SStheKEY);
}
masterClose(odmOutputFile);
}
catch (Exception ex)
{
string errtext = "Exception while reading data file: " + ex;
if (errtext.Contains("ThreadAbortException") == false)
{
throw new OCDataImporterException(errtext, ex);
}
}
finally
{
deletesOnlyEventsSQLFile.Close();
deletesSQLFile.Close();
insertsOnlyEventsSQLFile.Close();
insertsSQLFile.Close();
odmOutputFile.Close();
}
}
