@Override
public void setProtocolStatus(
Protocol protocol,
ProtocolStatusEnum protocolStatusEnum,
User user,
Committee committee,
String note) {
try {
ProtocolStatus protocolStatus = new ProtocolStatus();
protocolStatus.setCauseByUser(user);
protocolStatus.setCausedByCommittee(committee);
protocolStatus.setModified(new Date());
protocolStatus.setNote(note);
protocolStatus.setProtocol(protocol);
protocolStatus.setProtocolStatus(protocolStatusEnum);
protocolStatus.setRetired(Boolean.FALSE);
protocolStatusDao.saveOrUpdate(protocolStatus);
String protocolMetaDataXml = protocol.getMetaDataXml();
protocolMetaDataXml =
xmlProcessor.replaceOrAddNodeValueByPath(
"/protocol/status",
protocolMetaDataXml,
org.apache.commons.lang.StringEscapeUtils.escapeXml(
protocolStatusEnum.getDescription()));
Map<String, String> attributes = Maps.newHashMap();
attributes.put("priority", protocolStatusEnum.getPriorityLevel());
protocolMetaDataXml =
xmlProcessor.addAttributesByPath("/protocol/status", protocolMetaDataXml, attributes);
protocol.setMetaDataXml(protocolMetaDataXml);
protocolDao.saveOrUpdate(protocol);
} catch (Exception e) {
e.printStackTrace();
}
}
@Override
public boolean isPushedToPSC(String protocolMetaData) {
boolean isPushedToPSC = false;
try {
Document assertXml = xmlProcessor.loadXmlStringToDOM(protocolMetaData);
XPath xpathInstance = xmlProcessor.getXPathInstance();
isPushedToPSC =
(Boolean)
(xpathInstance.evaluate(
"boolean(count(/protocol/pushed-to-psc[text()='y'])>0)",
assertXml,
XPathConstants.BOOLEAN));
} catch (Exception e) {
// don't care
}
return isPushedToPSC;
}
@Override
public void addPushedToEpic(Protocol protocol) {
try {
String protocolMetaData = protocol.getMetaDataXml();
protocolMetaData =
xmlProcessor.replaceOrAddNodeValueByPath(
"/protocol/pushed-to-epic", protocolMetaData, "y");
protocolMetaData =
xmlProcessor.replaceOrAddNodeValueByPath(
"/protocol/pushed-to-epic-date",
protocolMetaData,
DateFormatUtil.formateDateToMDY(new Date()));
protocol.setMetaDataXml(protocolMetaData);
protocol = protocolDao.saveOrUpdate(protocol);
} catch (Exception e) {
// don't care
}
}
private boolean isReportableOrNot(ProtocolFormXmlData protocolXmlData) {
boolean isReportableOrNot = false;
try {
List<String> values =
xmlProcessor.listElementStringValuesByPath(
"/reportable-new-information/is-reportable", protocolXmlData.getXmlData());
if (values.size() > 0) {
if (values.get(0).equals("y")) {
isReportableOrNot = true;
} else {
isReportableOrNot = false;
}
}
} catch (Exception e) {
e.printStackTrace();
isReportableOrNot = false;
}
return isReportableOrNot;
}
@Override
public Protocol consolidateProtocol(Protocol protocol, List<String> xPathList) {
String protocolMetaData = protocol.getMetaDataXml();
Map<String, Object> resultMap = Maps.newHashMap();
for (String xPath : xPathList) {
try {
resultMap = xmlProcessor.deleteElementByPath(xPath, protocolMetaData);
} catch (Exception e) {
}
if (resultMap != null && !resultMap.isEmpty())
protocolMetaData = resultMap.get("finalXml").toString();
}
protocol.setMetaDataXml(protocolMetaData);
protocol = protocolDao.saveOrUpdate(protocol);
return protocol;
}
@Override
public Map<String, Boolean> checkStudyCharacteristic(String protocolMetaData) {
Map<String, Boolean> studyCharacteristicMap = Maps.newHashMap();
String isAchStudyXpath =
"boolean(count(/protocol/site-responsible[text()='ach-achri'])>0 or count(/protocol/study-sites/site[@site-id=\"2\" or @site-id=\"1\"])>0)";
String isAchStudyWithDrugXpath =
"boolean((count(/protocol/site-responsible[text()='ach-achri'])>0 or count(/protocol/study-sites/site[@site-id=\"2\" or @site-id=\"1\"])>0) and count(/protocol/drugs/drug)>0)";
String isInvestigatorStudyPath =
"boolean(count(/protocol/study-type[text()='investigator-initiated'])>0)";
String isIndustryOrCoorpStudyPath =
"boolean(count(/protocol/study-type[text()='cooperative-group'])>0 or count(/protocol/study-type[text()='industry-sponsored'])>0)";
String isUamsStudyPath = "boolean(count(/protocol/site-responsible[text()='uams'])>0)";
try {
boolean isAchStudy = false;
boolean isAchStudyWithDrug = false;
boolean isInvestigatorStudy = false;
boolean isIndustryOrCoorpStudy = false;
boolean isUAMSStudy = false;
Document assertXml = xmlProcessor.loadXmlStringToDOM(protocolMetaData);
XPath xpathInstance = xmlProcessor.getXPathInstance();
isAchStudy =
(Boolean) (xpathInstance.evaluate(isAchStudyXpath, assertXml, XPathConstants.BOOLEAN));
studyCharacteristicMap.put("isAchStudy", isAchStudy);
xpathInstance.reset();
isAchStudyWithDrug =
(Boolean)
(xpathInstance.evaluate(isAchStudyWithDrugXpath, assertXml, XPathConstants.BOOLEAN));
studyCharacteristicMap.put("isAchStudyWithDrug", isAchStudyWithDrug);
xpathInstance.reset();
isInvestigatorStudy =
(Boolean)
(xpathInstance.evaluate(isInvestigatorStudyPath, assertXml, XPathConstants.BOOLEAN));
studyCharacteristicMap.put("isInvestigatorStudy", isInvestigatorStudy);
xpathInstance.reset();
isIndustryOrCoorpStudy =
(Boolean)
(xpathInstance.evaluate(
isIndustryOrCoorpStudyPath, assertXml, XPathConstants.BOOLEAN));
studyCharacteristicMap.put("isIndustryOrCoorpStudy", isIndustryOrCoorpStudy);
xpathInstance.reset();
isUAMSStudy =
(Boolean) (xpathInstance.evaluate(isUamsStudyPath, assertXml, XPathConstants.BOOLEAN));
studyCharacteristicMap.put("isUAMSStudy", isUAMSStudy);
} catch (Exception e) {
// don't care
}
return studyCharacteristicMap;
}
@RequestMapping(
value =
"/ajax/protocols/{protocolId}/protocol-forms/{protocolFormId}/reportable-new-information/protocol-form-xml-datas/{protocolFormXmlDataId}/validate",
method = RequestMethod.GET)
public @ResponseBody List<ValidationResponse> validateProtocolReportableNewInformationForm(
@PathVariable("protocolFormXmlDataId") long protocolFormXmlDataId) {
ProtocolFormXmlData protocolXmlData = protocolFormXmlDataDao.findById(protocolFormXmlDataId);
String xmldata = protocolXmlData.getXmlData();
List<ValidationResponse> validationResponses = new ArrayList<ValidationResponse>();
if (StringUtils.hasText(xmldata)) {
List<Rule> reportableNewInformationValidationRules =
getValidationRuleContainer()
.getValidationRules("reportableNewInformationValidationRules");
Assert.notNull(reportableNewInformationValidationRules);
Set<String> valueKeys =
getValidationRuleContainer()
.getCachedValueKeys("reportableNewInformationValidationRules");
Assert.notNull(valueKeys);
Map<String, List<String>> values = null;
// setup values
try {
values = xmlProcessor.listElementStringValuesByPaths(valueKeys, xmldata);
} catch (XPathExpressionException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (SAXException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
validationResponses =
validationRuleHandler.validate(reportableNewInformationValidationRules, values);
}
if (!isReportableOrNot(protocolXmlData)) {
Constraint notReportableConstraint = new Constraint();
Map<String, Object> notReportableAdditionalData = new HashMap<String, Object>();
notReportableConstraint.setConstraintLevel(ConstraintLevel.ERROR);
notReportableConstraint.setErrorMessage(
"This event/information does not meet the criteria for an Unanticipated Problem Involving Risk "
+ "to Subjects or Others (UPIRTSO) and does not require immediate reporting to the IRB."
+ "<br/>"
+ "Please submit the information in summary format at Continuing Review."
+ "<br/>"
+ "A suggested summary format is available at:<a href=\"http://www.uams.edu/irb/Reporting%20Events%20and%20Deviations.asp\" target=\"_blank\">http://www.uams.edu/irb/Reporting%20Events%20and%20Deviations.asp</a>"
+ "<br/>"
+ "The IRB recommends that events be compiled throughout the year."
+ "<br/>"
+ "If you need to update documents now, please do so using a Modification.");
notReportableAdditionalData.put("pagename", "Review");
notReportableAdditionalData.put("pageref", "review");
ValidationResponse budgetVP =
new ValidationResponse(notReportableConstraint, notReportableAdditionalData);
validationResponses.add(budgetVP);
}
return validationResponses;
}