The following document contains the results of PMD's CPD 5.3.5.
| File | Line |
|---|---|
| edu/columbia/rascal/business/pdfGenerator/irb/IrbClosureDataSheetPDFService.java | 298 |
| edu/columbia/rascal/business/pdfGenerator/irb/IrbProtocolHeaderDatasheetPDFService.java | 1895 |
addNewParagraphToChapter(
chapter,
"Of the number of subjects enrolled, or the number accrued for interventional studies with a screening process:",
INDENT_0, true);
addNewParagraphToChapter(chapter, "How many remain on the study?", INDENT_1, true);
addNewParagraphToChapter(chapter, formatNumber(subjects.getEnrolledRemaining()),
INDENT_1, false);
addNewParagraphToChapter(chapter, "How many are off study?", INDENT_1, true);
addNewParagraphToChapter(chapter, formatNumber(subjects.getEnrolledOffStudy()),
INDENT_1, false);
addNewParagraphToChapter(chapter, "How many completed the study?", INDENT_2, true);
addNewParagraphToChapter(chapter, formatNumber(subjects.getCompletedStudy()),
INDENT_2, false);
addRadioQuestionAnswer(chapter, "Have any withdrawn of their own initiative?",
subjects.getAnyWithdrawn(), INDENT_2);
if (StringUtils.equalsIgnoreCase(subjects.getAnyWithdrawn(), "Y")) {
addNewParagraphToChapter(chapter, "How many?", INDENT_3, true);
addNewParagraphToChapter(chapter, formatNumber(subjects.getNumberWithdrawn()),
INDENT_3, false);
addNewParagraphToChapter(chapter, "Please explain:", INDENT_3, true);
addNewParagraphToChapter(chapter, subjects.getExplainWithdrawn(), INDENT_3,
false);
}
addRadioQuestionAnswer(chapter, "Have any been removed by PI?",
subjects.getRemovedByPi(), INDENT_2);
if (StringUtils.equalsIgnoreCase(subjects.getRemovedByPi(), "Y")) {
addNewParagraphToChapter(chapter, "How many?", INDENT_3, true);
addNewParagraphToChapter(chapter,
formatNumber(subjects.getHowManyRemovedByPi()), INDENT_3, false);
addNewParagraphToChapter(chapter, "Please explain:", INDENT_3, true);
addNewParagraphToChapter(chapter, subjects.getExplainRemovedByPi(), INDENT_3,
false);
}
addRadioQuestionAnswer(chapter, "Have any been lost to follow-up?",
subjects.getLostToFollowup(), INDENT_2);
if (StringUtils.equalsIgnoreCase(subjects.getLostToFollowup(), "Y")) {
addNewParagraphToChapter(chapter, "How many?", INDENT_3, true);
addNewParagraphToChapter(chapter,
formatNumber(subjects.getHowManyLostToFollowup()), INDENT_3, false);
addNewParagraphToChapter(chapter, "Please explain:", INDENT_3, true);
addNewParagraphToChapter(chapter, subjects.getExplainLostToFollowup(),
INDENT_3, false);
}
addRadioQuestionAnswer(chapter, "Have any died while on study?",
subjects.getDiedOnStudy(), INDENT_2);
if (StringUtils.equalsIgnoreCase(subjects.getDiedOnStudy(), "Y")) {
addNewParagraphToChapter(chapter, "How many?", INDENT_3, true);
addNewParagraphToChapter(chapter,
formatNumber(subjects.getHowManyDiedOnStudy()), INDENT_3, false);
addNewParagraphToChapter(chapter, "Please explain:", INDENT_3, true);
addNewParagraphToChapter(chapter, subjects.getExplainDiedOnStudy(), INDENT_3,
false);
}
addRadioQuestionAnswer(chapter, "Have any subject complaints been received?",
subjects.getAnySubjectComplaints(), INDENT_0);
if (StringUtils.equalsIgnoreCase(subjects.getAnySubjectComplaints(), "Y")) {
addNewParagraphToChapter(chapter, "How many?", INDENT_1, true);
addNewParagraphToChapter(chapter,
formatNumber(subjects.getHowManyComplaints()), INDENT_1, false);
addNewParagraphToChapter(chapter, "Please explain:", INDENT_1, true);
addNewParagraphToChapter(chapter, subjects.getExplainComplaints(), INDENT_1,
false);
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 261 |
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 448 |
);
buff.append(" AND ((a.administratorRid = ");
buff.append(adminRid);
buff.append(" OR a.contactRid = ");
buff.append(adminRid);
buff.append(')');
buff.append("OR (ac.tc_courseheader_id= a.oid and ac.rid =");
buff.append(adminRid);
buff.append(") OR (a.isReleased = 'Y')) and a.testLocation = ");
buff.append(aLocation);
buff.append(" ) ");
buff.append(" ORDER BY a.sequenceNumber ASC");
// TCJdbcAccessor acc = new TCJdbcAccessor(null);
// this is to get the unreleased or released headers by Rid of the User
try {
ResultSet res = ServiceLocator.getCURascalJdbcAccessorService().executeQuery(
buff.toString()
);
while (res.next()) {
row = new Vector<Object>(6);
row.addElement(res.getLong(1));
row.addElement(res.getString(2));
if (!useAbbreviated || (res.getString(3) == null) ||
res.getString(3).trim().equals("")
) {
row.addElement(res.getString(4));
} else {
row.addElement(res.getString(3));
}
if (res.getInt(5) > 0) {
row.addElement(String.valueOf(res.getInt(5)));
} else {
row.addElement(String.valueOf(res.getInt(6)));
}
if (res.getDate(7) == null) {
row.addElement("");
} else {
row.addElement(res.getDate(7));
}
if (res.getString(8) == null) {
row.addElement("");
} else {
row.addElement(res.getString(8));
}
results.addElement(row);
} // end while
} catch (Exception e) {
log.error("Exception while retrieving safety courses for location/administrator.", e); | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IacucProtocolDataSheetPDFService.java | 4448 |
| edu/columbia/rascal/business/service/IrbProtocolDataSheetPDFService.java | 162 |
}
private String formatDateWithNull(Date date) {
if (date == null)
return "";
return DATEFORMAT.print(date.getTime());
}
/** Inner class to add a header and a footer. */
static class HeaderFooter extends PdfPageEventHelper {
/** The header text. */
String header;
/** The template with the total number of pages. */
PdfTemplate total;
/**
* Allows us to change the content of the header.
*
* @param header
* The new header String
*/
public void setHeader(String header) {
this.header = header;
}
/**
* Creates the PdfTemplate that will hold the total number of pages.
*
* @see com.itextpdf.text.pdf.PdfPageEventHelper#onOpenDocument(com.itextpdf.text.pdf.PdfWriter,
* com.itextpdf.text.Document)
*/
public void onOpenDocument(PdfWriter writer, Document document) {
total = writer.getDirectContent().createTemplate(30, 16);
}
public void onEndPage(PdfWriter writer, Document document) {
PdfPTable table = new PdfPTable(3);
try {
table.setWidths(new int[] { 24, 24, 2 });
table.setTotalWidth(527);
table.setLockedWidth(true);
table.getDefaultCell().setFixedHeight(20);
table.getDefaultCell().setBorder(Rectangle.TOP);
table.addCell(header);
table.getDefaultCell().setHorizontalAlignment(
Element.ALIGN_RIGHT);
table.addCell(String.format("Page %d of",
writer.getPageNumber()));
PdfPCell cell = new PdfPCell(Image.getInstance(total));
cell.setBorder(Rectangle.TOP);
table.addCell(cell);
table.writeSelectedRows(0, -1, 34, 34,
writer.getDirectContent());
} catch (DocumentException de) {
throw new ExceptionConverter(de);
}
}
/**
* Fills out the total number of pages before the document is closed.
*
* @see com.itextpdf.text.pdf.PdfPageEventHelper#onCloseDocument(com.itextpdf.text.pdf.PdfWriter,
* com.itextpdf.text.Document)
*/
public void onCloseDocument(PdfWriter writer, Document document) {
ColumnText.showTextAligned(total, Element.ALIGN_LEFT, new Phrase(
String.valueOf(writer.getPageNumber() - 1)), 2, 2, 0);
}
}
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 177 |
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 363 |
);
buff.append(" AND testLocation = ");
buff.append(aLocation);
buff.append(" ) ");
buff.append(" ORDER BY sequenceNumber ASC");
try {
ResultSet res = ServiceLocator.getCURascalJdbcAccessorService().executeQuery(
buff.toString()
);
while (res.next()) {
row = new Vector<Object>(6);
row.addElement(res.getLong(1));
row.addElement(res.getString(2));
if (!useAbbreviated || (res.getString(3) == null) ||
res.getString(3).trim().equals("")
) {
row.addElement(res.getString(4));
} else {
row.addElement(res.getString(3));
}
if (res.getInt(5) > 0) {
row.addElement(String.valueOf(res.getInt(5)));
} else {
row.addElement(String.valueOf(res.getInt(6)));
}
if (res.getDate(7) == null) {
row.addElement("");
} else {
row.addElement(res.getDate(7));
}
if (res.getString(8) == null) {
row.addElement("");
} else {
row.addElement(res.getString(8));
}
results.addElement(row);
} // end while
} catch (Exception e) {
log.error("Exception while retrieving safety courses.", e); | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 181 |
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 272 |
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 367 |
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 459 |
buff.append(" ORDER BY sequenceNumber ASC");
try {
ResultSet res = ServiceLocator.getCURascalJdbcAccessorService().executeQuery(
buff.toString()
);
while (res.next()) {
row = new Vector<Object>(6);
row.addElement(res.getLong(1));
row.addElement(res.getString(2));
if (!useAbbreviated || (res.getString(3) == null) ||
res.getString(3).trim().equals("")
) {
row.addElement(res.getString(4));
} else {
row.addElement(res.getString(3));
}
if (res.getInt(5) > 0) {
row.addElement(String.valueOf(res.getInt(5)));
} else {
row.addElement(String.valueOf(res.getInt(6)));
}
if (res.getDate(7) == null) {
row.addElement("");
} else {
row.addElement(res.getDate(7));
}
if (res.getString(8) == null) {
row.addElement("");
} else {
row.addElement(res.getString(8));
}
results.addElement(row);
} // end while
} catch (Exception e) {
log.error("Exception while retrieving safety courses.", e); | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/pdfGenerator/irb/IrbClosureDataSheetPDFService.java | 124 |
| edu/columbia/rascal/business/pdfGenerator/irb/IrbClosureDataSheetPDFService.java | 203 |
addNewParagraphToChapter(chapter,
"Why is this study being closed (check all that apply): "
+ "\n\n",
INDENT_1, true);
addNewParagraphToChapter(chapter, "[" + getCheckboxValue(closure.getDelayedApproval()) + "]"
+ " Delayed grant/contract approval ",
INDENT_1);
addNewParagraphToChapter(chapter, "[" + getCheckboxValue(closure.getLackOfFunding()) + "]"
+ " Lack of funding ",
INDENT_1);
addNewParagraphToChapter(chapter, "[" + getCheckboxValue(closure.getPoorEnrollment()) + "]"
+ " Poor enrollment ",
INDENT_1);
addNewParagraphToChapter(chapter, "[" + getCheckboxValue(closure.getClosedBySponsor()) + "]"
+ " Closed by Sponsor ",
INDENT_1);
addNewParagraphToChapter(chapter, "[" + getCheckboxValue(closure.getDelayedIRBApproval()) + "]"
+ " Delayed IRB approval ",
INDENT_1);
addNewParagraphToChapter(chapter, "[" + getCheckboxValue(closure.getStudyCompleted()) + "]"
+ " Study Completed ",
INDENT_1);
addNewParagraphToChapter(chapter, "[" + getCheckboxValue(closure.getPiLeft()) + "]"
+ " PI left university ",
INDENT_1);
addNewParagraphToChapter(chapter, "[" + getCheckboxValue(closure.getResearcherLeft()) + "]"
+ " Student research/Student left university ",
INDENT_1);
addNewParagraphToChapter(chapter, "[" + getCheckboxValue(closure.getOther()) + "]"
+ " Other ",
INDENT_1);
if (StringUtils.equalsIgnoreCase(closure.getOther(), "Y")) {
addNewParagraphToChapter(chapter,"Provide reason for closure:",
INDENT_2, true);
addNewParagraphToChapter(chapter,closure.getOtherReason(),
INDENT_2);
}
addNewParagraphToChapter(chapter, | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IrbAdverseEventService.java | 127 |
| edu/columbia/rascal/business/service/IrbUnanticipatedProblemService.java | 167 |
IrbNameConstants.ADVERSE_EVENT, "Consultant"
);
int size = revs.size();
for (int i = 0; i < size; i++) {
if (revs.elementAt(i).equals(aUser.getId())) {
return true;
}
}
}
// if Staff
IrbProtocolHeader ph = up.getIrbProtocol().getLastProtocolHeader();
List<IrbStaff> staffs = ph.getIrbStaffs();
for (IrbStaff staff : staffs) {
if (staff.getRid().equals(aUser.getId())) {
return true;
}
}
// if department approvals
Vector<IrbApproval> depApp = ServiceLocator.getIrbApprovalService().getAllApprovalsByType(
ph.getId(),
IrbNameConstants.PROTOCOL_HEADER, "Department"
);
int depAppSize = depApp.size();
for (int i = 0; i < depAppSize; i++) {
if (depApp.elementAt(i).getWhoRid().equals(aUser.getId())) {
return true;
}
}
return false;
}
/**
* TODO: DOCUMENT ME!
*
* @param anOid TODO: DOCUMENT ME!
* @param aUser TODO: DOCUMENT ME!
*
* @return TODO: DOCUMENT ME!
*/
public IrbAdverseEvent getAdverseEventByOid(String anOid, RascalUser aUser) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IrbProtocolHeaderService.java | 426 |
| edu/columbia/rascal/business/service/IrbProtocolHeaderService.java | 613 |
(CURascalGuardian.hasIrbCancerCenterApproval() || CURascalGuardian.hasIrbCancerCenterViewer())
) {
return true;
}
if (currentApproval.isCTSA() && (CURascalGuardian.hasIrbCTSA() || CURascalGuardian.hasIrbCTSAViewer())) {
return true;
}
// If this protocol requires psychiatric institute approval and
// aUser is an authorized psychiatric institute person, grant
// access.
if (currentApproval.isPsychiatricInstitute() &&
CURascalGuardian.hasIrbPsychInstituteApproval()
) {
return true;
}
}
// If radiation safety member and protocol involves radiation and
// protocol is being submitted to Med Center
if ((CURascalGuardian.hasIrbRadiationSafetyMC() || CURascalGuardian.hasIrbRadiationSafetyMS()) &&
(((header.getHazMatRadioIsotopes() != null) &&
header.getHazMatRadioIsotopes().equals("Y")) ||
((header.getHazMatXray() != null) && header.getHazMatXray().equals("Y")))
) {
return true;
}
}
IrbProtocolHeader last = header.getIrbProtocol().getLastProtocolHeader();
// If Staff, grant access.
List<IrbStaff> staffs = last.getIrbStaffs();
for (IrbStaff staff : staffs) {
if (staff.getRid().equals(aUser.getId())) {
return true;
}
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IacucProtocolDataSheetPDFService.java | 259 |
| edu/columbia/rascal/business/service/IrbProtocolDataSheetPDFService.java | 77 |
addDataSignature(document, protocol);
document.close();
return baos;
}
private static void addEmptyLine(final Document document, int number)
throws DocumentException {
for (int i = 0; i < number; i++) {
document.add(new Paragraph(" "));
}
}
private void addSectionName(final Document document, String sectionName)
throws DocumentException {
Font FONT_HELVETICA_12_BOLD = FontFactory.getFont(
Font.FontFamily.HELVETICA.toString(), 12, Font.BOLD);
addEmptyLine(document, 1);
PdfPTable tableSection = createPdfTable(1);
PdfPCell cellTitle = createPdfTableCellWithNull(sectionName,
FONT_HELVETICA_12_BOLD, Element.ALIGN_CENTER);
cellTitle.setHorizontalAlignment(Element.ALIGN_CENTER);
cellTitle.setBorderWidth(1);
cellTitle.setFixedHeight(20f);
tableSection.addCell(cellTitle);
document.add(tableSection);
addEmptyLine(document, 1);
}
private void addDataProtocolHeader1(final Document document, | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IrbUnanticipatedProblemService.java | 234 |
| edu/columbia/rascal/business/service/IrbUnanticipatedProblemService.java | 270 |
Vector row = new Vector(6);
try {
java.sql.ResultSet res = ServiceLocator.getCURascalJdbcAccessorService().executeQuery(
aQuery
);
while (res.next()) {
row.addElement(res.getString(1)); // oid
row.addElement(res.getString(2)); // documentIdentifier
row.addElement(res.getString(3)); // fileName
row.addElement(res.getDate(4)); // dateCreated
row.addElement(res.getString(5)); // archive
row.addElement(res.getString(6)); // internalFlag
results.addElement(row.clone());
row = new Vector(6);
}
} catch (Exception e) {
log.error(e);
}
return results;
}
/**
* @see edu.columbia.rascal.business.service.IrbUnanticipatedProblemService#getAllSortedAttachmentsInternal(edu.columbia.rascal.domain.irb.IrbUnanticipatedProblem)
*/
public Vector getAllSortedAttachmentsInternal(IrbUnanticipatedProblem up) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 130 |
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 191 |
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 284 |
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 379 |
| edu/columbia/rascal/business/service/TccourseHeaderService.java | 471 |
row = new Vector<Object>(6);
row.addElement(res.getLong(1));
row.addElement(res.getString(2));
if (!useAbbreviated || (res.getString(3) == null) || res.getString(3).trim().equals("")
) {
row.addElement(res.getString(4));
} else {
row.addElement(res.getString(3));
}
if (res.getInt(5) > 0) {
row.addElement(String.valueOf(res.getInt(5)));
} else {
row.addElement(String.valueOf(res.getInt(6)));
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/AppendixHService.java | 365 |
| edu/columbia/rascal/business/service/AppendixHService.java | 428 |
tmpActivities = this.historyService
.createHistoricActivityInstanceQuery()
.processInstanceId(processInstanceId).finished()
.orderByHistoricActivityInstanceEndTime().desc().list();
for (final HistoricActivityInstance activity : tmpActivities) {
// Hide activities without and end time, name, or type. Also
// hide exclusive gateways
// and start/end tasks
if (activity.getEndTime() != null
&& StringUtils.isNotBlank(activity.getActivityName())
&& StringUtils.isNotBlank(activity.getActivityType())
&& !StringUtils.equalsIgnoreCase(
activity.getActivityType(), "exclusiveGateway")
&& !StringUtils.equalsIgnoreCase(
activity.getActivityType(), "endEvent")
&& !StringUtils.equalsIgnoreCase(
activity.getActivityType(), "startEvent")) {
activities.add(activity);
}
}
if (!activities.isEmpty()) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/atunes/jaxb/IacucManagementWebServiceSoap_IacucManagementWebServiceSoap12_Client.java | 25 |
| edu/columbia/rascal/business/atunes/jaxb/IacucManagementWebServiceSoap_IacucManagementWebServiceSoap_Client.java | 25 |
private IacucManagementWebServiceSoap_IacucManagementWebServiceSoap12_Client() {
}
public static void main(String args[]) throws java.lang.Exception {
URL wsdlURL = IacucManagementWebService.WSDL_LOCATION;
if (args.length > 0 && args[0] != null && !"".equals(args[0])) {
File wsdlFile = new File(args[0]);
try {
if (wsdlFile.exists()) {
wsdlURL = wsdlFile.toURI().toURL();
} else {
wsdlURL = new URL(args[0]);
}
} catch (MalformedURLException e) {
e.printStackTrace();
}
}
IacucManagementWebService ss = new IacucManagementWebService(wsdlURL, SERVICE_NAME);
IacucManagementWebServiceSoap port = ss.getIacucManagementWebServiceSoap12(); | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/HazMatsDataSheetService.java | 600 |
| edu/columbia/rascal/business/service/HazMatsDataSheetService.java | 656 |
};
document.add(getBulletList(bulletList));
addLine(document,
"Contact the Radiation Safety Office at (212) 305-4095 for additional information.",
HEADER_FONT,
Element.ALIGN_LEFT,
true);
addLine(document,
"Appendix H: " + appendixH.getAppendixNumber(),
HEADER_FONT,
Element.ALIGN_LEFT,
false);
boolean showSubmittedDate = false;
Task task = appendixHProcessService.findTaskByGroup(appendixH, AppendixHProcessService.GROUP_PRE_APPROVE);
if (task != null) {
showSubmittedDate = true;
}
addLine(document, "Created: " + sdf.format(appendixH.getCreateDate()), HEADER_FONT, Element.ALIGN_LEFT, !showSubmittedDate);
// Find all tasks in the APPENDIXH_PRE_APPROVE group which is SUBMITTED record
if (showSubmittedDate)
addLine(document, "Submitted: " + sdf.format(task.getCreateTime()), HEADER_FONT, Element.ALIGN_LEFT, true);
}
private void createJRSCHeader(Document document, AppendixH appendixH) throws DocumentException { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IacucProtocolDataSheetPDFService.java | 2891 |
| edu/columbia/rascal/business/service/IrbProtocolDataSheetPDFService.java | 130 |
document.add(table);
}
private void setPdfTableCellWithBorder(final PdfPTable table,
final Font font, final int alignment, final String cellValue) {
if (table == null || font == null)
throw new IllegalArgumentException(
"Check parameters. All parameters must not be null");
PdfPCell cell = new PdfPCell(new Paragraph(((cellValue == null) ? ""
: cellValue), font));
cell.setHorizontalAlignment(alignment);
cell.setBorderWidth(1);
table.addCell(cell);
}
private void setPdfTableRowWithBorder(final PdfPTable table,
final Font font, final String[] rows) {
if (rows == null || rows.length == 0 || table == null || font == null)
throw new IllegalArgumentException(
"Check parameters. All parameters must not be null");
for (String row : rows) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IacucProtocolHeaderService.java | 1056 |
| edu/columbia/rascal/business/service/PtProposalHeaderService.java | 1380 |
}
/**
* TODO: DOCUMENT ME!
*
* @param oldTracker TODO: DOCUMENT ME!
* @param newTracker TODO: DOCUMENT ME!
* @param copyApprovals TODO: DOCUMENT ME!
*/
private void copyApprovals(AppendixTracking oldTracker,
AppendixTracking newTracker, boolean copyApprovals) {
Set<AppendixApproval> apps = oldTracker.getAppendixApprovals();
if (apps != null) {
for (AppendixApproval oldApp : apps) {
if ((oldApp != null)
&& !oldApp.getApprovalRole().equals("veterinarian")) {
AppendixApproval newApp = new AppendixApproval(newTracker);
newApp.setApprovalRole(oldApp.getApprovalRole());
if (copyApprovals) {
newApp.setApprovalDate(oldApp.getApprovalDate());
newApp.setApprovalType(oldApp.getApprovalType());
newApp.setApproverRid(oldApp.getApproverRid());
}
appendixApprovalService.save(newApp);
}
}
}
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IrbAdverseEventService.java | 243 |
| edu/columbia/rascal/business/service/IrbClosureService.java | 221 |
Vector row = new Vector(5);
try {
ResultSet res = ServiceLocator.getCURascalJdbcAccessorService().executeQuery(aQuery);
while (res.next()) {
row.addElement(res.getString(1)); // oid
row.addElement(res.getString(2)); // documentIdentifier
row.addElement(res.getString(3)); // fileName
row.addElement(res.getDate(4)); // dateCreated
row.addElement(res.getString(5)); // archive
results.addElement(row.clone());
row = new Vector(5);
}
} catch (Exception e) {
log.error(e);
}
return results;
}
/**
* TODO: DOCUMENT ME!
*
* @param event TODO: DOCUMENT ME!
*
* @return TODO: DOCUMENT ME!
*/
public Vector<IrbAdverseEventAttachment> getAllSortedAttachmentsExternal2(IrbAdverseEvent event) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IrbAdverseEventService.java | 243 |
| edu/columbia/rascal/business/service/IrbClosureService.java | 221 |
| edu/columbia/rascal/business/service/IrbClosureService.java | 263 |
Vector row = new Vector(5);
try {
ResultSet res = ServiceLocator.getCURascalJdbcAccessorService().executeQuery(aQuery);
while (res.next()) {
row.addElement(res.getString(1)); // oid
row.addElement(res.getString(2)); // documentIdentifier
row.addElement(res.getString(3)); // fileName
row.addElement(res.getDate(4)); // dateCreated
row.addElement(res.getString(5)); // archive
results.addElement(row.clone());
row = new Vector(5);
}
} catch (Exception e) {
log.error(e);
}
return results;
}
/**
* TODO: DOCUMENT ME!
*
* @param event TODO: DOCUMENT ME!
*
* @return TODO: DOCUMENT ME!
*/
public Vector<IrbAdverseEventAttachment> getAllSortedAttachmentsExternal2(IrbAdverseEvent event) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/pdfGenerator/irb/AbstractIrbDatasheetService.java | 262 |
| edu/columbia/rascal/business/pdfGenerator/irb/AbstractIrbDatasheetService.java | 275 |
protected void renderSubjectPopulation(Chapter chapter, Map<Long, IrbSubjectPopulation> subjectPopulationsSaved, String category, Set<RascalSubjectPopulation> subjectPopulations) {
addNewParagraphToChapter(chapter, "Population " +category, INDENT_0, true);
PdfPTable subPopTable = createPdfTable(subjectPopulations.size(), 10f, 10f);
for (RascalSubjectPopulation population : subjectPopulations) {
subPopTable.addCell(createPdfTableCell(population.getDescription()));
}
for (RascalSubjectPopulation population : subjectPopulations) {
if (subjectPopulationsSaved.get(population.getId()) != null)
subPopTable.addCell(createPdfTableCellWithNull(subjectPopulationsSaved.get(population.getId()).getPercentage().toString()+"%"));
}
chapter.add(subPopTable);
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IrbProtocolHeaderService.java | 390 |
| edu/columbia/rascal/business/service/IrbProtocolHeaderService.java | 575 |
comms.contains(currentone.getCommitteeId().toString())
) {
return true;
}
}
// If status is NOT "Creating" or "Returned"...
if (!(currentStatusName.startsWith(CREATING)) && !(currentStatusName.equals(RETURNED))) { // If consultant and is a reviewer for this protocol, grant access.
if (CURascalGuardian.hasIrbConsultant()) {
Vector revs = ServiceLocator.getIrbReviewerService().getAllCurrentReviewerRids(
header.getId(), IrbNameConstants.PROTOCOL_HEADER, "Consultant"
);
int size = revs.size();
for (int n = 0; n < size; n++) {
if (revs.elementAt(n).equals(aUser.getId())) {
return true;
}
}
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/RascalActivityTypeService.java | 130 |
| edu/columbia/rascal/business/service/RascalAgencyService.java | 131 |
return rascalActivityTypeDAO.findAll();
}
/**
* TODO: DOCUMENT ME!
*
* @param aString TODO: DOCUMENT ME!
*
* @return TODO: DOCUMENT ME!
*/
public String prepText(String aString) {
if ((aString != null) && (aString.contains("'"))) {
StringTokenizer aTokenizer = new StringTokenizer(aString.trim(),
"'\r\n"
);
StringBuilder detokenizedString = new StringBuilder("");
while (aTokenizer.hasMoreTokens()) {
detokenizedString.append(aTokenizer.nextToken());
if (aTokenizer.hasMoreTokens()) {
detokenizedString.append("''");
}
}
return detokenizedString.toString();
} else if (aString != null) {
return aString;
} else {
return "";
}
}
/**
* TODO: DOCUMENT ME!
*
* @param rascalActivityTypeDAO TODO: DOCUMENT ME!
*/
public void setRascalActivityTypeDAO(RascalActivityTypeDAO rascalActivityTypeDAO) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/RascalDepartmentService.java | 388 |
| edu/columbia/rascal/business/service/RascalSchoolService.java | 197 |
return rascalDepartmentDAO.save(entity);
}
/**
* TODO: DOCUMENT ME!
*
* @param aString TODO: DOCUMENT ME!
*
* @return TODO: DOCUMENT ME!
*/
private String prepText(String aString) {
if ((aString != null) && (aString.contains("'"))) {
StringTokenizer aTokenizer = new StringTokenizer(aString.trim(),
"'\r\n"
);
StringBuilder detokenizedString = new StringBuilder("");
while (aTokenizer.hasMoreTokens()) {
detokenizedString.append(aTokenizer.nextToken());
if (aTokenizer.hasMoreTokens()) {
detokenizedString.append("''");
}
}
return detokenizedString.toString();
} else if (aString != null) {
return aString;
} else {
return "";
}
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/AppendixIService.java | 220 |
| edu/columbia/rascal/business/service/IrbProtocolHeaderService.java | 2343 |
String numberString = "000" + Long.toString(id);
numberString = numberString.substring(numberString.length() - 4, numberString.length());
char charPart[] = new char[4];
int letterPart = id / 10000;
charPart[3] = getLetters()[letterPart % 26];
charPart[2] = getLetters()[(letterPart / 26) % 26];
charPart[1] = getLetters()[(letterPart / (26 * 26)) % 26];
charPart[0] = getLetters()[(letterPart / (26 * 26 * 26)) % 26]; | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/RascalAgencyService.java | 141 |
| edu/columbia/rascal/business/service/RascalDepartmentService.java | 398 |
public String prepText(String aString) {
if ((aString != null) && (aString.contains("'"))) {
StringTokenizer aTokenizer = new StringTokenizer(aString.trim(),
"'\r\n"
);
StringBuilder detokenizedString = new StringBuilder("");
while (aTokenizer.hasMoreTokens()) {
detokenizedString.append(aTokenizer.nextToken());
if (aTokenizer.hasMoreTokens()) {
detokenizedString.append("''");
}
}
return detokenizedString.toString();
} else if (aString != null) {
return aString;
} else {
return "";
}
}
/**
*
* @param name search term
* @return List<RascalAgencyDTO> a list of immutable code and name.
* It is particularly useful for the front dojo dev, such as, QueryReadStore + dojox.data.ComboBox
*/
public List<RascalAgencyDTO> getCodeNameByNameLike(String name) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/RascalDepartmentService.java | 389 |
| edu/columbia/rascal/business/service/RascalReportDistributionService.java | 123 |
}
/**
* TODO: DOCUMENT ME!
*
* @param aString TODO: DOCUMENT ME!
*
* @return TODO: DOCUMENT ME!
*/
private String prepText(String aString) {
if ((aString != null) && (aString.contains("'"))) {
StringTokenizer aTokenizer = new StringTokenizer(aString.trim(),
"'\r\n"
);
StringBuilder detokenizedString = new StringBuilder("");
while (aTokenizer.hasMoreTokens()) {
detokenizedString.append(aTokenizer.nextToken());
if (aTokenizer.hasMoreTokens()) {
detokenizedString.append("''");
}
}
return detokenizedString.toString();
} else if (aString != null) {
return aString;
} else {
return "";
}
}
/**
* @param searchTerm
* @param cutoff
* @return
*/
public List<RascalDepartment> findActiveByNameOrCodeLike(String searchTerm, int cutoff) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IacucProcessService.java | 828 |
| edu/columbia/rascal/business/service/IacucProcessService.java | 885 |
Comment comment = taskService.addComment(taskId, task.getProcessInstanceId(), taskDefKey, content);
iacucTaskForm.setCommentId(comment.getId());
}
// attach attribute to this task
Map<String, String> attribute = iacucTaskForm.getProperties();
if (attribute != null && !attribute.isEmpty())
taskService.setVariableLocal(taskId, TASK_FORM_LOOKUP_PREFIX + taskId, attribute);
// attach correspondence to this task
IacucCorrespondence corr = iacucTaskForm.getCorrespondence();
if (corr != null) {
corr.apply();
Map<String, String> corrProperties = corr.getProperties();
if (!corrProperties.isEmpty()) {
taskService.setVariableLocal(taskId, IACUC_COORESPONDENCE + taskId, corrProperties);
}
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IrbStatusService.java | 665 |
| edu/columbia/rascal/business/service/IrbStatusService.java | 736 |
String hostURL = RascalProperties.getProperty("host.name");
model.addAttribute("protocolNumber", header.getIrbProtocol().getProtocolNumber());
model.addAttribute("title", header.getTitle());
model.addAttribute("role", staff.getProtocolRole());
model.addAttribute("coiFileNewAmendUrl", hostURL + "/coi");
model.addAttribute("pi", header.getPI().getNameFirst() + " " + header.getPI().getNameLast());
model.addAttribute("protocolCoiUrl", hostURL + "/irb/protocol/" + lastApprovedProtocol.getIrbProtocol().getProtocolNumber() + "/" + lastApprovedProtocol.getId() + "/disclosures"); | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/RascalActivityTypeService.java | 140 |
| edu/columbia/rascal/business/service/RascalReportDistributionService.java | 132 |
public String prepText(String aString) {
if ((aString != null) && (aString.contains("'"))) {
StringTokenizer aTokenizer = new StringTokenizer(aString.trim(),
"'\r\n"
);
StringBuilder detokenizedString = new StringBuilder("");
while (aTokenizer.hasMoreTokens()) {
detokenizedString.append(aTokenizer.nextToken());
if (aTokenizer.hasMoreTokens()) {
detokenizedString.append("''");
}
}
return detokenizedString.toString();
} else if (aString != null) {
return aString;
} else {
return "";
}
}
/**
* TODO: DOCUMENT ME!
*
* @param rascalActivityTypeDAO TODO: DOCUMENT ME!
*/
public void setRascalActivityTypeDAO(RascalActivityTypeDAO rascalActivityTypeDAO) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/RascalReportDistributionService.java | 123 |
| edu/columbia/rascal/business/service/RascalSchoolService.java | 198 |
}
/**
* TODO: DOCUMENT ME!
*
* @param aString TODO: DOCUMENT ME!
*
* @return TODO: DOCUMENT ME!
*/
private String prepText(String aString) {
if ((aString != null) && (aString.contains("'"))) {
StringTokenizer aTokenizer = new StringTokenizer(aString.trim(),
"'\r\n"
);
StringBuilder detokenizedString = new StringBuilder("");
while (aTokenizer.hasMoreTokens()) {
detokenizedString.append(aTokenizer.nextToken());
if (aTokenizer.hasMoreTokens()) {
detokenizedString.append("''");
}
}
return detokenizedString.toString();
} else if (aString != null) {
return aString;
} else {
return "";
}
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IrbAdverseEventService.java | 114 |
| edu/columbia/rascal/business/service/IrbClosureService.java | 153 |
).getStatusName().equals(IrbStatusConstants.CREATING)) &&
(CURascalGuardian.hasIrbAdmin() || CURascalGuardian.hasIrbCommitteeChair() || CURascalGuardian.hasIrbCancerCenterApproval() ||
CURascalGuardian.hasIrbCPDM() || CURascalGuardian.hasIrbCancerCenterViewer() || CURascalGuardian.hasIrbPsychInstituteApproval() ||
CURascalGuardian.hasIrbCommitteeMember() || CURascalGuardian.hasIrbCTSA() || CURascalGuardian.hasIrbCTSAViewer() ||
CURascalGuardian.hasIrbClinicalTrials())
) {
return true;
}
// if consultant
if (CURascalGuardian.hasIrbConsultant()) {
Vector revs = ServiceLocator.getIrbReviewerService().getAllCurrentReviewerRids(
up.getId(),
IrbNameConstants.ADVERSE_EVENT, "Consultant" | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/RascalActivityTypeService.java | 140 |
| edu/columbia/rascal/business/service/RascalDepartmentService.java | 398 |
public String prepText(String aString) {
if ((aString != null) && (aString.contains("'"))) {
StringTokenizer aTokenizer = new StringTokenizer(aString.trim(),
"'\r\n"
);
StringBuilder detokenizedString = new StringBuilder("");
while (aTokenizer.hasMoreTokens()) {
detokenizedString.append(aTokenizer.nextToken());
if (aTokenizer.hasMoreTokens()) {
detokenizedString.append("''");
}
}
return detokenizedString.toString();
} else if (aString != null) {
return aString;
} else {
return "";
}
}
/**
* TODO: DOCUMENT ME!
*
* @param rascalActivityTypeDAO TODO: DOCUMENT ME!
*/
public void setRascalActivityTypeDAO(RascalActivityTypeDAO rascalActivityTypeDAO) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/RascalAgencyService.java | 141 |
| edu/columbia/rascal/business/service/RascalReportDistributionService.java | 132 |
public String prepText(String aString) {
if ((aString != null) && (aString.contains("'"))) {
StringTokenizer aTokenizer = new StringTokenizer(aString.trim(),
"'\r\n"
);
StringBuilder detokenizedString = new StringBuilder("");
while (aTokenizer.hasMoreTokens()) {
detokenizedString.append(aTokenizer.nextToken());
if (aTokenizer.hasMoreTokens()) {
detokenizedString.append("''");
}
}
return detokenizedString.toString();
} else if (aString != null) {
return aString;
} else {
return "";
}
}
/**
*
* @param name search term
* @return List<RascalAgencyDTO> a list of immutable code and name.
* It is particularly useful for the front dojo dev, such as, QueryReadStore + dojox.data.ComboBox
*/
public List<RascalAgencyDTO> getCodeNameByNameLike(String name) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/RascalActivityTypeService.java | 140 |
| edu/columbia/rascal/business/service/RascalAgencyService.java | 141 |
| edu/columbia/rascal/business/service/RascalSchoolService.java | 207 |
public String prepText(String aString) {
if ((aString != null) && (aString.contains("'"))) {
StringTokenizer aTokenizer = new StringTokenizer(aString.trim(),
"'\r\n"
);
StringBuilder detokenizedString = new StringBuilder("");
while (aTokenizer.hasMoreTokens()) {
detokenizedString.append(aTokenizer.nextToken());
if (aTokenizer.hasMoreTokens()) {
detokenizedString.append("''");
}
}
return detokenizedString.toString();
} else if (aString != null) {
return aString;
} else {
return "";
}
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IacucProcessService.java | 241 |
| edu/columbia/rascal/business/service/IacucProcessService.java | 281 |
form.setTaskName(hs.getName());
form.setEndTime(hs.getEndTime());
form.setAuthor(hs.getAssignee());
form.setTaskId(hs.getId());
//
Map<String, Object> localMap = hs.getTaskLocalVariables();
@SuppressWarnings("unchecked")
Map<String, String> taskMap = (Map<String, String>) localMap.get(TASK_FORM_LOOKUP_PREFIX + hs.getId());
if (taskMap != null) {
form.setProperties(taskMap);
form.setComment(getCommentText(form.getCommentId()));
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IrbAdverseEventService.java | 413 |
| edu/columbia/rascal/business/service/IrbAdverseEventService.java | 485 |
oldOne.getReportedToCode()
).getDescription()
);
}
for (int i = 0; i < oldNameSize; i++) {
if (!newOnes.contains(oldNames.elementAt(i))) {
changed = true;
break;
} else {
for (i = 0; i < newOneSize; i++) {
if (!oldNames.contains(newOnes.elementAt(i))) {
changed = true;
break;
}
}
}
}
} else {
changed = true;
}
if (changed) {
while (!oldOnes.isEmpty()) { | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/CoiBusinessInterestService.java | 241 |
| edu/columbia/rascal/business/service/CoiBusinessInterestService.java | 259 |
subQuestionTypeUnique.add(answer.getSubQuestionType());
if(findIsIdentifiedInSection(businessInterest, CoiConstants.BUSINESS_INTEREST))
result.put("research", "*");
if(disclosureDetail.getCoiDisclosure().getDisclosureType().equals(CoiConstants.RC) && findIsIdentifiedInSection(businessInterest, CoiConstants.CLINICAL_CARE))
result.put("clinical", "*");
if(findIsIdentifiedInSection(businessInterest, CoiConstants.PHS_FUNDED_SECTION))
result.put("phs", "*");
if(findIsIdentifiedInSection(businessInterest, CoiConstants.ADMIN_SECTION))
result.put("admin_other", "*");
results.add(result);
}
} | |
| File | Line |
|---|---|
| edu/columbia/rascal/business/service/IrbProtocolHeaderService.java | 483 |
| edu/columbia/rascal/business/service/IrbProtocolHeaderService.java | 664 |
if (app.getWhoRid().equals(aUser.getId())) {
return true;
}
}
// If safety officer and protocol has been submitted, grant access.
if (CURascalGuardian.hasHmSafetyApprove() &&
(currentStatusName.equals(LOGGED_IN) || currentStatusName.equals(DISTRIBUTED) ||
currentStatusName.equals(ASSIGNED_TO_MEETING) ||
currentStatusName.equals(RETURNED_TO_CHAIR))
) {
return true;
}
// If HIPAA logger, admin or member and protocol has been submitted,
// grant access.
return (CURascalGuardian.hasHipaaRascal() || CURascalGuardian.hasHipaaLogger() || CURascalGuardian.hasHipaaAdministrator() ||
CURascalGuardian.hasHipaaPrivacyBoard()) && !currentStatusName.equals(CREATING);
}
/**
* TODO: DOCUMENT ME!
*
* @param aUser TODO: DOCUMENT ME!
* @param header TODO: DOCUMENT ME!
*
* @return TODO: DOCUMENT ME!
*/
public boolean getAccessibleByUserForDataSheet(RascalUser aUser, IrbProtocolHeader header) { | |
