private boolean mayProceedPreview(String studyOid) throws Exception {
boolean accessPermission = false;
StudyBean study = getParentStudy(studyOid);
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(dataSource);
StudyParameterValueBean pStatus =
spvdao.findByHandleAndStudy(study.getId(), "participantPortal");
participantPortalRegistrar = new ParticipantPortalRegistrar();
String pManageStatus =
participantPortalRegistrar.getRegistrationStatus(studyOid).toString(); // ACTIVE ,
// PENDING ,
// INACTIVE
String participateStatus = pStatus.getValue().toString(); // enabled , disabled
String studyStatus =
study.getStatus().getName().toString(); // available , pending , frozen , locked
logger.info(
"pManageStatus: "
+ pManageStatus
+ " participantStatus: "
+ participateStatus
+ " studyStatus: "
+ studyStatus);
if (participateStatus.equalsIgnoreCase("enabled")
&& (studyStatus.equalsIgnoreCase("available")
|| studyStatus.equalsIgnoreCase("pending")
|| studyStatus.equalsIgnoreCase("frozen")
|| studyStatus.equalsIgnoreCase("locked"))
&& (pManageStatus.equalsIgnoreCase("ACTIVE")
|| pManageStatus.equalsIgnoreCase("PENDING")
|| pManageStatus.equalsIgnoreCase("INACTIVE"))) {
accessPermission = true;
}
return accessPermission;
}
private void updateParameter(StudyParameterValueDAO spvdao, StudyParameterValueBean spv) {
StudyParameterValueBean spv1 =
spvdao.findByHandleAndStudy(spv.getStudyId(), spv.getParameter());
if (spv1.getId() > 0) {
spvdao.update(spv);
} else {
spvdao.create(spv);
}
}
private void updateParameter(StudyParameterValueDAO spvdao, StudyParameterValueBean spv) {
StudyParameterValueBean spv1 =
spvdao.findByHandleAndStudy(spv.getStudyId(), spv.getParameter());
System.out.println("found parameter: " + spv.getParameter());
if (spv1.getId() > 0) {
spvdao.update(spv);
System.out.println("updating");
} else {
spvdao.create(spv);
System.out.println("creating");
}
}
/** Inserts the new study into database */
private void submitStudy() {
FormProcessor fp = new FormProcessor(request);
StudyDAO sdao = new StudyDAO(sm.getDataSource());
StudyBean study = (StudyBean) session.getAttribute("newStudy");
ArrayList parameters = study.getStudyParameters();
logger.info("study bean to be created:\n");
logger.info(
study.getName()
+ "\n"
+ study.getIdentifier()
+ "\n"
+ study.getParentStudyId()
+ "\n"
+ study.getSummary()
+ "\n"
+ study.getPrincipalInvestigator()
+ "\n"
+ study.getDatePlannedStart()
+ "\n"
+ study.getDatePlannedEnd()
+ "\n"
+ study.getFacilityName()
+ "\n"
+ study.getFacilityCity()
+ "\n"
+ study.getFacilityState()
+ "\n"
+ study.getFacilityZip()
+ "\n"
+ study.getFacilityCountry()
+ "\n"
+ study.getFacilityRecruitmentStatus()
+ "\n"
+ study.getFacilityContactName()
+ "\n"
+ study.getFacilityContactEmail()
+ "\n"
+ study.getFacilityContactPhone()
+ "\n"
+ study.getFacilityContactDegree());
study.setOwner(ub);
study.setCreatedDate(new Date());
StudyBean parent = (StudyBean) sdao.findByPK(study.getParentStudyId());
study.setType(parent.getType());
// YW 10-10-2007, enable setting site status
study.setStatus(study.getStatus());
// YW >>
study.setGenetic(parent.isGenetic());
study = (StudyBean) sdao.create(study);
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
for (int i = 0; i < parameters.size(); i++) {
StudyParamsConfig config = (StudyParamsConfig) parameters.get(i);
StudyParameterValueBean spv = config.getValue();
spv.setStudyId(study.getId());
spv = (StudyParameterValueBean) spvdao.create(config.getValue());
}
// YW << here only "collectDob" and "genderRequired" have been corrected
// for sites.
StudyParameterValueBean spv = new StudyParameterValueBean();
StudyParameterValueBean parentSPV = spvdao.findByHandleAndStudy(parent.getId(), "collectDob");
spv.setStudyId(study.getId());
spv.setParameter("collectDob");
spv.setValue(parentSPV.getValue());
spvdao.create(spv);
parentSPV = spvdao.findByHandleAndStudy(parent.getId(), "genderRequired");
spv.setParameter("genderRequired");
spv.setValue(parentSPV.getValue());
spvdao.create(spv);
// YW >>
// switch user to the newly created site
session.setAttribute("study", session.getAttribute("newStudy"));
currentStudy = (StudyBean) session.getAttribute("study");
session.removeAttribute("newStudy");
addPageMessage(respage.getString("the_new_site_created_succesfully_current"));
forwardPage(Page.SITE_LIST_SERVLET);
}
private void collectMetaDataVersion() {
ArrayList<StudyEventDefinitionBean> sedBeansInStudy =
(ArrayList<StudyEventDefinitionBean>) studyBase.getSedBeansInStudy();
if (sedBeansInStudy == null || sedBeansInStudy.size() < 1) {
logger.info("null, because there is no study event definition in this study.");
return;
}
StudyBean study = studyBase.getStudy();
MetaDataVersionBean metadata = this.odmStudy.getMetaDataVersion();
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(this.ds);
int parentId = study.getParentStudyId() > 0 ? study.getParentStudyId() : study.getId();
StudyParameterValueBean spv = spvdao.findByHandleAndStudy(parentId, "discrepancyManagement");
metadata.setSoftHard(spv.getValue().equalsIgnoreCase("true") ? "Hard" : "Soft");
OdmExtractDAO oedao = new OdmExtractDAO(this.ds);
int studyId = study.getId();
int parentStudyId = study.getParentStudyId() > 0 ? study.getParentStudyId() : studyId;
if (this.getCategory() == 1 && study.isSite(study.getParentStudyId())) {
// populate MetaDataVersion attributes
if (dataset != null) {
metadata.setOid(dataset.getODMMetaDataVersionOid() + "-" + study.getOid());
metadata.setName(dataset.getODMMetaDataVersionName() + "-" + study.getOid());
this.setParentMetaDataVersionOid(dataset.getODMMetaDataVersionOid());
}
if (metadata.getOid() == null || metadata.getOid().length() <= 0) {
metadata.setOid("v1.0.0" + "-" + study.getOid());
this.setParentMetaDataVersionOid("v1.0.0");
}
if (metadata.getName() == null || metadata.getName().length() <= 0) {
metadata.setName("MetaDataVersion_v1.0.0" + "-" + study.getOid());
}
// populate Include
this.collectIncludeFromParentInSameFile();
// populate protocol
oedao.getUpdatedSiteMetadata(parentStudyId, studyId, metadata, this.odmBean.getODMVersion());
} else {
if (dataset != null) {
metadata.setOid(dataset.getODMMetaDataVersionOid());
metadata.setName(dataset.getODMMetaDataVersionName());
}
if (metadata.getOid() == null || metadata.getOid().length() <= 0) {
metadata.setOid("v1.0.0");
}
if (metadata.getName() == null || metadata.getName().length() <= 0) {
metadata.setName("MetaDataVersion_v1.0.0");
}
// populate Include
String psOid = new String();
String pmOid = new String();
if (dataset != null) {
psOid = dataset.getODMPriorStudyOid();
pmOid = dataset.getODMPriorMetaDataVersionOid();
}
if (pmOid != null && pmOid.length() > 0) {
MetaDataVersionIncludeBean ib = metadata.getInclude();
ib.setMetaDataVersionOID(pmOid);
if (psOid != null && psOid.length() > 0) {
ib.setStudyOID(psOid);
} else {
ib.setStudyOID(study.getOid());
}
}
// populate protocol
// Set<Integer> nullCodeSet = oedao.getMetadata(parentStudyId,
// studyId,
// metadata, this.getODMBean().getODMVersion());
// studyBase.setNullClSet(nullCodeSet);
oedao.getMetadata(parentStudyId, studyId, metadata, this.odmBean.getODMVersion());
}
}
public boolean validate(SubjectTransferBean subjectTransferBean)
throws OpenClinicaSystemException {
StudyDAO stdao = new StudyDAO(this.getDataSource());
StudyBean study = stdao.findByUniqueIdentifier(subjectTransferBean.getStudyOid());
if (study == null) {
throw new OpenClinicaSystemException("Study you specified does not exist");
}
UserAccountBean ua = subjectTransferBean.getOwner();
StudyUserRoleBean role = ua.getRoleByStudy(study);
if (role.getId() == 0 || role.getRole().equals(Role.MONITOR)) {
throw new OpenClinicaSystemException(
"You do not have sufficient priviliges to run this service");
}
if (subjectTransferBean.getSiteIdentifier() != null) {
study =
stdao.findSiteByUniqueIdentifier(
subjectTransferBean.getStudyOid(), subjectTransferBean.getSiteIdentifier());
}
subjectTransferBean.setStudy(study);
if (study == null) {
throw new OpenClinicaSystemException("Site you specified does not exist");
}
int handleStudyId = study.getParentStudyId() > 0 ? study.getParentStudyId() : study.getId();
org.akaza.openclinica.dao.service.StudyParameterValueDAO spvdao =
new StudyParameterValueDAO(this.getDataSource());
StudyParameterValueBean studyParameter =
spvdao.findByHandleAndStudy(handleStudyId, "subjectPersonIdRequired");
String personId = subjectTransferBean.getPersonId();
if ("required".equals(studyParameter.getValue())
&& (personId == null || personId.length() < 1)) {
throw new OpenClinicaSystemException(
"personId is required for the study: " + study.getName());
// return false;
}
if (personId != null && personId.length() > 255) {
throw new OpenClinicaSystemException("personId should not be longer than 255.");
// return false;
}
String idSetting = "";
StudyParameterValueBean subjectIdGenerationParameter =
spvdao.findByHandleAndStudy(handleStudyId, "subjectIdGeneration");
idSetting = subjectIdGenerationParameter.getValue();
if (idSetting.equals("auto editable") || idSetting.equals("auto non-editable")) {
int nextLabel = getStudySubjectDao().findTheGreatestLabel() + 1;
subjectTransferBean.setStudySubjectId(new Integer(nextLabel).toString());
}
String studySubjectId = subjectTransferBean.getStudySubjectId();
if (studySubjectId == null || studySubjectId.length() < 1) {
logger.info("studySubjectId is required.");
throw new OpenClinicaSystemException("studySubjectId is required.");
// return false;
} else if (studySubjectId.length() > 30) {
throw new OpenClinicaSystemException("studySubjectId should not be longer than 30.");
// return false;
}
String secondaryId = subjectTransferBean.getSecondaryId();
if (secondaryId != null && secondaryId.length() > 30) {
throw new OpenClinicaSystemException("secondaryId should not be longer than 30.");
// return false;
}
String gender = subjectTransferBean.getGender() + "";
studyParameter = spvdao.findByHandleAndStudy(handleStudyId, "genderRequired");
if ("true".equals(studyParameter.getValue()) && (gender == null || gender.length() < 1)) {
throw new OpenClinicaSystemException("gender is required for the study:" + study.getName());
// return false;
}
Date dateOfBirth = subjectTransferBean.getDateOfBirth();
String yearOfBirth = subjectTransferBean.getYearOfBirth();
studyParameter = spvdao.findByHandleAndStudy(handleStudyId, "collectDob");
if ("1".equals(studyParameter.getValue()) && (dateOfBirth == null)) {
throw new OpenClinicaSystemException("date Of Birth is required:" + study.getName());
// return false;
} else if ("2".equals(studyParameter.getValue()) && (yearOfBirth == null)) {
throw new OpenClinicaSystemException("Year Of Birth is required:" + study.getName());
} else if ("2".equals(studyParameter.getValue()) && (yearOfBirth != null)) {
try {
SimpleDateFormat sdf = new SimpleDateFormat("yyyy");
subjectTransferBean.setDateOfBirth(sdf.parse(subjectTransferBean.getYearOfBirth()));
} catch (ParseException e) {
throw new OpenClinicaSystemException("Year Of Birth not Valid:" + study.getName());
}
}
Date enrollmentDate = subjectTransferBean.getEnrollmentDate();
if (enrollmentDate == null) {
throw new OpenClinicaSystemException("enrollmentDate is required.");
// return false;
} else {
if ((new Date()).compareTo(enrollmentDate) < 0) {
throw new OpenClinicaSystemException("enrollmentDate should be in the past.");
// return false;
}
}
return true;
}
