use of org.akaza.openclinica.dao.service.StudyParameterValueDAO in project OpenClinica by OpenClinica.
the class DefineStudyEventServlet method confirmWholeDefinition.
/**
* Validates the entire definition
*
* @throws Exception
*/
private void confirmWholeDefinition() throws Exception {
Validator v = new Validator(request);
FormProcessor fp = new FormProcessor(request);
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) session.getAttribute("definition");
ArrayList eventDefinitionCRFs = new ArrayList();
FormLayoutDAO fldao = new FormLayoutDAO(sm.getDataSource());
for (int i = 0; i < sed.getCrfs().size(); i++) {
EventDefinitionCRFBean edcBean = new EventDefinitionCRFBean();
int crfId = fp.getInt("crfId" + i);
int defaultVersionId = fp.getInt("defaultVersionId" + i);
edcBean.setCrfId(crfId);
edcBean.setDefaultVersionId(defaultVersionId);
FormLayoutBean defaultVersion = (FormLayoutBean) fldao.findByPK(edcBean.getDefaultVersionId());
edcBean.setDefaultVersionName(defaultVersion.getName());
String crfName = fp.getString("crfName" + i);
edcBean.setCrfName(crfName);
String requiredCRF = fp.getString("requiredCRF" + i);
String doubleEntry = fp.getString("doubleEntry" + i);
String decisionCondition = fp.getString("decisionCondition" + i);
String electronicSignature = fp.getString("electronicSignature" + i);
String participantForm = fp.getString("participantForm" + i);
String allowAnonymousSubmission = fp.getString("allowAnonymousSubmission" + i);
String submissionUrl = fp.getString("submissionUrl" + i);
String offline = fp.getString("offline" + i);
// issue 312 BWP<<
String hiddenCrf = fp.getString("hiddenCrf" + i);
// hideCRF is false by default in the bean
if (!StringUtil.isBlank(hiddenCrf) && "yes".equalsIgnoreCase(hiddenCrf.trim())) {
edcBean.setHideCrf(true);
} else {
edcBean.setHideCrf(false);
}
// >>
String sdvOption = fp.getString("sdvOption" + i);
if (!StringUtils.isBlank(sdvOption)) {
int id = Integer.valueOf(sdvOption);
edcBean.setSourceDataVerification(SourceDataVerification.getByCode(id));
}
if (!StringUtils.isBlank(requiredCRF) && "yes".equalsIgnoreCase(requiredCRF.trim())) {
edcBean.setRequiredCRF(true);
} else {
edcBean.setRequiredCRF(false);
}
if (!StringUtils.isBlank(participantForm) && "yes".equalsIgnoreCase(participantForm.trim())) {
edcBean.setParticipantForm(true);
} else {
edcBean.setParticipantForm(false);
}
// when participant form is not selected, force allow anonymous to be not selected
if (edcBean.isParticipantForm() && !StringUtils.isBlank(allowAnonymousSubmission) && "yes".equalsIgnoreCase(allowAnonymousSubmission.trim())) {
edcBean.setAllowAnonymousSubmission(true);
} else {
edcBean.setAllowAnonymousSubmission(false);
}
if (!StringUtils.isBlank(offline) && "yes".equalsIgnoreCase(offline.trim())) {
edcBean.setOffline(true);
} else {
edcBean.setOffline(false);
}
if (!StringUtils.isBlank(doubleEntry) && "yes".equalsIgnoreCase(doubleEntry.trim())) {
edcBean.setDoubleEntry(true);
} else {
edcBean.setDoubleEntry(false);
}
if (!StringUtils.isBlank(decisionCondition) && "yes".equalsIgnoreCase(decisionCondition.trim())) {
edcBean.setDecisionCondition(true);
} else {
edcBean.setDecisionCondition(false);
}
if (!StringUtils.isBlank(electronicSignature) && "yes".equalsIgnoreCase(electronicSignature.trim())) {
edcBean.setElectronicSignature(true);
} else {
edcBean.setElectronicSignature(false);
}
// also useful to protect from naughty submission not coming from our html form
if (edcBean.isParticipantForm() && edcBean.isAllowAnonymousSubmission()) {
edcBean.setSubmissionUrl(submissionUrl.trim());
}
ArrayList<CRFVersionBean> versions = fldao.findAllByCRFId(crfId);
edcBean.setVersions(versions);
String nullString = "";
// process null values
ArrayList nulls = NullValue.toArrayList();
for (int a = 0; a < nulls.size(); a++) {
NullValue n = (NullValue) nulls.get(a);
String myNull = fp.getString(n.getName().toLowerCase() + i);
if (!StringUtils.isBlank(myNull) && "yes".equalsIgnoreCase(myNull.trim())) {
nullString = nullString + n.getName().toUpperCase() + ",";
}
}
edcBean.setNullValues(nullString);
edcBean.setStudyId(ub.getActiveStudyId());
eventDefinitionCRFs.add(edcBean);
}
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
request.setAttribute("participateFormStatus", participateFormStatus);
if (participateFormStatus.equals("enabled"))
baseUrl();
request.setAttribute("participateFormStatus", participateFormStatus);
request.setAttribute("eventDefinitionCRFs", eventDefinitionCRFs);
// not used on page
session.setAttribute("edCRFs", eventDefinitionCRFs);
ArrayList<EventDefinitionCRFBean> edcsInSession = (ArrayList<EventDefinitionCRFBean>) session.getAttribute("edCRFs");
int parentStudyId = sed.getStudyId();
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
ArrayList<EventDefinitionCRFBean> eventDefCrfList = (ArrayList<EventDefinitionCRFBean>) edcdao.findAllActiveSitesAndStudiesPerParentStudy(parentStudyId);
if (eventDefCrfList.size() != 0)
validateSubmissionUrl(edcsInSession, eventDefCrfList, v);
errors = v.validate();
if (!errors.isEmpty()) {
ArrayList<String> sdvOptions = new ArrayList<String>();
sdvOptions.add(SourceDataVerification.AllREQUIRED.toString());
sdvOptions.add(SourceDataVerification.PARTIALREQUIRED.toString());
sdvOptions.add(SourceDataVerification.NOTREQUIRED.toString());
sdvOptions.add(SourceDataVerification.NOTAPPLICABLE.toString());
request.setAttribute("sdvOptions", sdvOptions);
logger.info("has errors");
session.setAttribute("eventDefinitionCRFs", eventDefinitionCRFs);
request.setAttribute("formMessages", errors);
forwardPage(Page.DEFINE_STUDY_EVENT4);
}
forwardPage(Page.DEFINE_STUDY_EVENT_CONFIRM);
}
use of org.akaza.openclinica.dao.service.StudyParameterValueDAO in project OpenClinica by OpenClinica.
the class DefineStudyEventServlet method confirmDefinition2.
private void confirmDefinition2() throws Exception {
FormProcessor fp = new FormProcessor(request);
FormLayoutDAO fldao = new FormLayoutDAO(sm.getDataSource());
ArrayList crfArray = new ArrayList();
Map tmpCRFIdMap = (HashMap) session.getAttribute("tmpCRFIdMap");
// trying to avoid NPE not sure why we would get it there ((tmpCRFIdMap.containsKey(id))), tbh
if (tmpCRFIdMap == null) {
tmpCRFIdMap = new HashMap();
}
ArrayList crfsWithVersion = (ArrayList) session.getAttribute("crfsWithVersion");
for (int i = 0; i < crfsWithVersion.size(); i++) {
int id = fp.getInt("id" + i);
String name = fp.getString("name" + i);
// String label = fp.getString("label" + i);
String selected = fp.getString("selected" + i);
// logger.info("selected:" + selected);
if (!StringUtils.isBlank(selected) && "yes".equalsIgnoreCase(selected.trim())) {
logger.debug("one crf selected");
CRFBean cb = new CRFBean();
cb.setId(id);
cb.setName(name);
// only find active verions
ArrayList versions = (ArrayList) fldao.findAllActiveByCRF(cb.getId());
cb.setVersions(versions);
crfArray.add(cb);
} else {
if (tmpCRFIdMap.containsKey(id)) {
tmpCRFIdMap.remove(id);
}
}
}
for (Iterator tmpCRFIterator = tmpCRFIdMap.keySet().iterator(); tmpCRFIterator.hasNext(); ) {
int id = (Integer) tmpCRFIterator.next();
String name = (String) tmpCRFIdMap.get(id);
boolean isExists = false;
for (Iterator it = crfArray.iterator(); it.hasNext(); ) {
CRFBean cb = (CRFBean) it.next();
if (id == cb.getId()) {
isExists = true;
}
}
if (!isExists) {
CRFBean cb = new CRFBean();
cb.setId(id);
cb.setName(name);
// only find active verions
ArrayList versions = (ArrayList) fldao.findAllActiveByCRF(cb.getId());
cb.setVersions(versions);
crfArray.add(cb);
}
}
session.removeAttribute("tmpCRFIdMap");
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
if (crfArray.size() == 0) {
// no crf seleted
// addPageMessage("At least one CRF must be selected.");
addPageMessage(respage.getString("no_CRF_selected_for_definition_add_later"));
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) session.getAttribute("definition");
sed.setCrfs(new ArrayList());
String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
request.setAttribute("participateFormStatus", participateFormStatus);
session.setAttribute("definition", sed);
request.setAttribute("eventDefinitionCRFs", new ArrayList());
// not used on page
session.setAttribute("edCRFs", new ArrayList());
forwardPage(Page.DEFINE_STUDY_EVENT_CONFIRM);
// forwardPage(Page.DEFINE_STUDY_EVENT2);
} else {
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) session.getAttribute("definition");
// crfs selected by user
sed.setCrfs(crfArray);
session.setAttribute("eventDefinitionCRFs", new ArrayList());
session.setAttribute("definition", sed);
String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
if (participateFormStatus.equals("enabled"))
baseUrl();
request.setAttribute("participateFormStatus", participateFormStatus);
ArrayList<String> sdvOptions = new ArrayList<String>();
sdvOptions.add(SourceDataVerification.AllREQUIRED.toString());
sdvOptions.add(SourceDataVerification.PARTIALREQUIRED.toString());
sdvOptions.add(SourceDataVerification.NOTREQUIRED.toString());
sdvOptions.add(SourceDataVerification.NOTAPPLICABLE.toString());
request.setAttribute("sdvOptions", sdvOptions);
forwardPage(Page.DEFINE_STUDY_EVENT3);
}
}
use of org.akaza.openclinica.dao.service.StudyParameterValueDAO in project OpenClinica by OpenClinica.
the class CreateSubStudyServlet method initDefinitions.
private ArrayList<StudyEventDefinitionBean> initDefinitions(StudyBean site) throws MalformedURLException {
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>();
StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource());
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
FormLayoutDAO fldao = new FormLayoutDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
StudyBean parentStudy = (StudyBean) new StudyDAO(sm.getDataSource()).findByPK(site.getParentStudyId());
seds = sedDao.findAllByStudy(parentStudy);
int start = 0;
for (StudyEventDefinitionBean sed : seds) {
String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
if (participateFormStatus.equals("enabled"))
baseUrl();
request.setAttribute("participateFormStatus", participateFormStatus);
int defId = sed.getId();
ArrayList<EventDefinitionCRFBean> edcs = (ArrayList<EventDefinitionCRFBean>) edcdao.findAllByDefinitionAndSiteIdAndParentStudyId(defId, site.getId(), parentStudy.getId());
ArrayList<EventDefinitionCRFBean> defCrfs = new ArrayList<EventDefinitionCRFBean>();
// sed.setCrfNum(edcs.size());
for (EventDefinitionCRFBean edcBean : edcs) {
CRFBean cBean = (CRFBean) cdao.findByPK(edcBean.getCrfId());
String crfPath = sed.getOid() + "." + cBean.getOid();
edcBean.setOffline(getEventDefinitionCrfTagService().getEventDefnCrfOfflineStatus(2, crfPath, true));
int edcStatusId = edcBean.getStatus().getId();
CRFBean crf = (CRFBean) cdao.findByPK(edcBean.getCrfId());
int crfStatusId = crf.getStatusId();
if (edcStatusId == 5 || edcStatusId == 7 || crfStatusId == 5 || crfStatusId == 7) {
} else {
ArrayList<FormLayoutBean> versions = (ArrayList<FormLayoutBean>) fldao.findAllActiveByCRF(edcBean.getCrfId());
edcBean.setVersions(versions);
edcBean.setCrfName(crf.getName());
FormLayoutBean defaultVersion = (FormLayoutBean) fldao.findByPK(edcBean.getDefaultVersionId());
edcBean.setDefaultVersionName(defaultVersion.getName());
edcBean.setSubmissionUrl("");
/*
* EventDefinitionCRFBean eBean = (EventDefinitionCRFBean) edcdao.findByPK(edcBean.getId());
* if (eBean.isActive()){
* edcBean.setSubmissionUrl(eBean.getSubmissionUrl());
* }else{
* edcBean.setSubmissionUrl("");
* }
*/
String sversionIds = edcBean.getSelectedVersionIds();
ArrayList<Integer> idList = new ArrayList<Integer>();
if (sversionIds.length() > 0) {
String[] ids = sversionIds.split("\\,");
for (String id : ids) {
idList.add(Integer.valueOf(id));
}
}
edcBean.setSelectedVersionIdList(idList);
defCrfs.add(edcBean);
++start;
}
}
logger.debug("definitionCrfs size=" + defCrfs.size() + " total size=" + edcs.size());
sed.setCrfs(defCrfs);
sed.setCrfNum(defCrfs.size());
}
return seds;
}
use of org.akaza.openclinica.dao.service.StudyParameterValueDAO in project OpenClinica by OpenClinica.
the class InitUpdateSubStudyServlet method createEventDefinitions.
private void createEventDefinitions(StudyBean parentStudy) throws MalformedURLException {
FormProcessor fp = new FormProcessor(request);
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
int siteId = Integer.valueOf(request.getParameter("id").trim());
ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>();
StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource());
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
// CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
FormLayoutDAO fldao = new FormLayoutDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
seds = sedDao.findAllByStudy(parentStudy);
int start = 0;
for (StudyEventDefinitionBean sed : seds) {
String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
if (participateFormStatus.equals("enabled"))
baseUrl();
request.setAttribute("participateFormStatus", participateFormStatus);
int defId = sed.getId();
ArrayList<EventDefinitionCRFBean> edcs = (ArrayList<EventDefinitionCRFBean>) edcdao.findAllByDefinitionAndSiteIdAndParentStudyId(defId, siteId, parentStudy.getId());
ArrayList<EventDefinitionCRFBean> defCrfs = new ArrayList<EventDefinitionCRFBean>();
// sed.setCrfNum(edcs.size());
for (EventDefinitionCRFBean edcBean : edcs) {
CRFBean cBean = (CRFBean) cdao.findByPK(edcBean.getCrfId());
String crfPath = sed.getOid() + "." + cBean.getOid();
edcBean.setOffline(getEventDefinitionCrfTagService().getEventDefnCrfOfflineStatus(2, crfPath, true));
int edcStatusId = edcBean.getStatus().getId();
CRFBean crf = (CRFBean) cdao.findByPK(edcBean.getCrfId());
int crfStatusId = crf.getStatusId();
if (edcStatusId == 5 || edcStatusId == 7 || crfStatusId == 5 || crfStatusId == 7) {
} else {
// ArrayList<CRFVersionBean> versions = (ArrayList<CRFVersionBean>)
// cvdao.findAllActiveByCRF(edcBean.getCrfId());
ArrayList<FormLayoutBean> versions = (ArrayList<FormLayoutBean>) fldao.findAllActiveByCRF(edcBean.getCrfId());
edcBean.setVersions(versions);
edcBean.setCrfName(crf.getName());
if (edcBean.getParentId() == 0)
edcBean.setSubmissionUrl("");
// CRFVersionBean defaultVersion = (CRFVersionBean) cvdao.findByPK(edcBean.getDefaultVersionId());
FormLayoutBean defaultVersion = (FormLayoutBean) fldao.findByPK(edcBean.getDefaultVersionId());
edcBean.setDefaultVersionName(defaultVersion.getName());
String sversionIds = edcBean.getSelectedVersionIds();
ArrayList<Integer> idList = new ArrayList<Integer>();
if (sversionIds.length() > 0) {
String[] ids = sversionIds.split("\\,");
for (String id : ids) {
idList.add(Integer.valueOf(id));
}
}
edcBean.setSelectedVersionIdList(idList);
defCrfs.add(edcBean);
++start;
}
}
logger.debug("definitionCrfs size=" + defCrfs.size() + " total size=" + edcs.size());
sed.setCrfs(defCrfs);
sed.setCrfNum(defCrfs.size());
}
// not sure if request is better, since not sure if there is another
// process using this.
session.setAttribute("definitions", seds);
session.setAttribute("sdvOptions", this.setSDVOptions());
}
use of org.akaza.openclinica.dao.service.StudyParameterValueDAO in project OpenClinica by OpenClinica.
the class RemoveCRFFromDefinitionServlet method processRequest.
@Override
public void processRequest() throws Exception {
ArrayList edcs = (ArrayList) session.getAttribute("eventDefinitionCRFs");
ArrayList updatedEdcs = new ArrayList();
String crfName = "";
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) session.getAttribute("definition");
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
request.setAttribute("participateFormStatus", participateFormStatus);
if (edcs != null && edcs.size() > 1) {
String idString = request.getParameter("id");
logger.info("crf id:" + idString);
if (StringUtil.isBlank(idString)) {
addPageMessage(respage.getString("please_choose_a_crf_to_remove"));
forwardPage(Page.UPDATE_EVENT_DEFINITION1);
} else {
// crf id
int id = Integer.valueOf(idString.trim()).intValue();
for (int i = 0; i < edcs.size(); i++) {
EventDefinitionCRFBean edc = (EventDefinitionCRFBean) edcs.get(i);
if (edc.getCrfId() == id) {
edc.setStatus(Status.DELETED);
crfName = edc.getCrfName();
}
if (edc.getId() > 0 || !edc.getStatus().equals(Status.DELETED)) {
updatedEdcs.add(edc);
logger.info("\nversion:" + edc.getDefaultVersionId());
}
}
session.setAttribute("eventDefinitionCRFs", updatedEdcs);
addPageMessage(respage.getString("has_been_removed_need_confirmation"));
forwardPage(Page.UPDATE_EVENT_DEFINITION1);
}
} else {
addPageMessage(respage.getString("an_ED_needs_to_have_least_one_CRF"));
forwardPage(Page.UPDATE_EVENT_DEFINITION1);
}
}
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