use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.
the class ImportCRFDataService method validateStudyMetadata.
/*
* meant to answer the following questions 3.a. is that study subject in that study? 3.b. is that study event def in
* that study? 3.c. is that site in that study? 3.d. is that crf version in that study event def? 3.e. are those
* item groups in that crf version? 3.f. are those items in that item group?
*/
public List<String> validateStudyMetadata(ODMContainer odmContainer, int currentStudyId) {
List<String> errors = new ArrayList<String>();
MessageFormat mf = new MessageFormat("");
// throw new OpenClinicaException(mf.format(arguments), "");
try {
StudyDAO studyDAO = new StudyDAO(ds);
String studyOid = odmContainer.getCrfDataPostImportContainer().getStudyOID();
StudyBean studyBean = studyDAO.findByOid(studyOid);
if (studyBean == null) {
mf.applyPattern(respage.getString("your_study_oid_does_not_reference_an_existing"));
Object[] arguments = { studyOid };
errors.add(mf.format(arguments));
// errors.add("Your Study OID " + studyOid + " does not
// reference an existing Study or Site in the database. Please
// check it and try again.");
// throw an error here because getting the ID would be difficult
// otherwise
logger.debug("unknown study OID");
throw new OpenClinicaException("Unknown Study OID", "");
} else if (studyBean.getId() != currentStudyId) {
mf.applyPattern(respage.getString("your_current_study_is_not_the_same_as"));
Object[] arguments = { studyBean.getName() };
//
// errors.add("Your current study is not the same as the Study "
// + studyBean.getName()
// + ", for which you are trying to enter data. Please log out
// of your current study and into the study for which the data
// is keyed.");
errors.add(mf.format(arguments));
}
ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
ItemGroupDAO itemGroupDAO = new ItemGroupDAO(ds);
ItemDAO itemDAO = new ItemDAO(ds);
if (subjectDataBeans != null) {
// report all available errors, tbh
for (SubjectDataBean subjectDataBean : subjectDataBeans) {
String oid = subjectDataBean.getSubjectOID();
StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(oid, studyBean.getId());
if (studySubjectBean == null) {
mf.applyPattern(respage.getString("your_subject_oid_does_not_reference"));
Object[] arguments = { oid };
errors.add(mf.format(arguments));
// errors.add("Your Subject OID " + oid + " does not
// reference an existing Subject in the Study.");
logger.debug("logged an error with subject oid " + oid);
}
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
if (studyEventDataBeans != null) {
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
String sedOid = studyEventDataBean.getStudyEventOID();
StudyEventDefinitionBean studyEventDefintionBean = studyEventDefinitionDAO.findByOidAndStudy(sedOid, studyBean.getId(), studyBean.getParentStudyId());
if (studyEventDefintionBean == null) {
mf.applyPattern(respage.getString("your_study_event_oid_for_subject_oid"));
Object[] arguments = { sedOid, oid };
errors.add(mf.format(arguments));
// errors.add("Your Study Event OID " + sedOid +
// " for Subject OID " + oid
// + " does not reference an existing Study
// Event in the Study.");
logger.debug("logged an error with se oid " + sedOid + " and subject oid " + oid);
}
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
if (formDataBeans != null) {
for (FormDataBean formDataBean : formDataBeans) {
String formOid = formDataBean.getFormOID();
ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formOid);
// right now just check nulls
if (crfVersionBeans != null) {
for (CRFVersionBean crfVersionBean : crfVersionBeans) {
if (crfVersionBean == null) {
mf.applyPattern(respage.getString("your_crf_version_oid_for_study_event_oid"));
Object[] arguments = { formOid, sedOid };
errors.add(mf.format(arguments));
// errors.add("Your CRF Version
// OID " + formOid + " for Study
// Event OID " + sedOid
// + " does not reference a
// proper CRF Version in that
// Study Event.");
logger.debug("logged an error with form " + formOid + " and se oid " + sedOid);
}
}
} else {
mf.applyPattern(respage.getString("your_crf_version_oid_did_not_generate"));
Object[] arguments = { formOid };
errors.add(mf.format(arguments));
// errors.add("Your CRF Version OID " +
// formOid
// + " did not generate any results in
// the database. Please check it and try
// again.");
}
ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
if (itemGroupDataBeans != null) {
for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
String itemGroupOID = itemGroupDataBean.getItemGroupOID();
List<ItemGroupBean> itemGroupBeans = itemGroupDAO.findAllByOid(itemGroupOID);
if (itemGroupBeans != null) {
logger.debug("number of item group beans: " + itemGroupBeans.size());
logger.debug("item group oid: " + itemGroupOID);
for (ItemGroupBean itemGroupBean : itemGroupBeans) {
if (itemGroupBean == null) {
mf.applyPattern(respage.getString("your_item_group_oid_for_form_oid"));
Object[] arguments = { itemGroupOID, formOid };
errors.add(mf.format(arguments));
// errors.add("Your Item
// Group OID " +
// itemGroupOID + " for
// Form OID " + formOid
// + " does not
// reference a proper
// Item Group in that
// CRF Version.");
}
}
} else {
mf.applyPattern(respage.getString("the_item_group_oid_did_not"));
Object[] arguments = { itemGroupOID };
errors.add(mf.format(arguments));
// errors.add("The Item Group
// OID " + itemGroupOID
// + " did not generate any
// results in the database,
// please check it and try
// again.");
}
ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
if (itemDataBeans != null) {
for (ImportItemDataBean itemDataBean : itemDataBeans) {
String itemOID = itemDataBean.getItemOID();
List<ItemBean> itemBeans = itemDAO.findByOid(itemOID);
if (itemBeans != null) {
logger.debug("found itembeans: ");
for (ItemBean itemBean : itemBeans) {
if (itemBean == null) {
mf.applyPattern(respage.getString("your_item_oid_for_item_group_oid"));
Object[] arguments = { itemOID, itemGroupOID };
errors.add(mf.format(arguments));
// errors.add(
// "Your
// Item OID " +
// itemOID + "
// for Item
// Group OID " +
// itemGroupOID
// + " does not
// reference a
// proper Item
// in the Item
// Group.");
} else {
logger.debug("found " + itemBean.getOid() + ", passing");
}
}
}
}
} else {
mf.applyPattern(respage.getString("the_item_group_oid_did_not_contain_item_data"));
Object[] arguments = { itemGroupOID };
errors.add(mf.format(arguments));
// errors.add("The Item Group
// OID " + itemGroupOID
// + " did not contain any Item
// Data in the XML file, please
// check it and try again.");
}
}
} else {
mf.applyPattern(respage.getString("your_study_event_contains_no_form_data"));
Object[] arguments = { sedOid };
errors.add(mf.format(arguments));
// errors.add("Your Study Event " +
// sedOid
// + " contains no Form Data, or the
// Form OIDs are incorrect. Please check
// it and try again.");
}
}
}
}
}
}
}
} catch (OpenClinicaException oce) {
} catch (NullPointerException npe) {
logger.debug("found a nullpointer here");
}
// if errors == null you pass, if not you fail
return errors;
}
use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.
the class ImportCRFDataService method eventCRFStatusesValid.
/*
* purpose: returns false if any of the forms/EventCRFs fail the UpsertOnBean rules.
*/
public boolean eventCRFStatusesValid(ODMContainer odmContainer, UserAccountBean ub) {
ArrayList<EventCRFBean> eventCRFBeans = new ArrayList<EventCRFBean>();
ArrayList<Integer> eventCRFBeanIds = new ArrayList<Integer>();
EventCRFDAO eventCrfDAO = new EventCRFDAO(ds);
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
StudyDAO studyDAO = new StudyDAO(ds);
StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
UpsertOnBean upsert = odmContainer.getCrfDataPostImportContainer().getUpsertOn();
// If Upsert bean is not present, create one with default settings
if (upsert == null)
upsert = new UpsertOnBean();
String studyOID = odmContainer.getCrfDataPostImportContainer().getStudyOID();
StudyBean studyBean = studyDAO.findByOid(studyOID);
ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
for (SubjectDataBean subjectDataBean : subjectDataBeans) {
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
String sampleOrdinal = studyEventDataBean.getStudyEventRepeatKey() == null ? "1" : studyEventDataBean.getStudyEventRepeatKey();
StudyEventDefinitionBean studyEventDefinitionBean = studyEventDefinitionDAO.findByOidAndStudy(studyEventDataBean.getStudyEventOID(), studyBean.getId(), studyBean.getParentStudyId());
logger.info("find all by def and subject " + studyEventDefinitionBean.getName() + " study subject " + studySubjectBean.getName());
StudyEventBean studyEventBean = (StudyEventBean) studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubjectBean.getId(), studyEventDefinitionBean.getId(), Integer.parseInt(sampleOrdinal));
// locked
if (studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.LOCKED) || studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SIGNED) || studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.STOPPED)) {
return true;
}
for (FormDataBean formDataBean : formDataBeans) {
CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formDataBean.getFormOID());
for (CRFVersionBean crfVersionBean : crfVersionBeans) {
ArrayList<EventCRFBean> eventCrfBeans = eventCrfDAO.findByEventSubjectVersion(studyEventBean, studySubjectBean, crfVersionBean);
// event crf, yet.
if (eventCrfBeans.isEmpty()) {
logger.debug(" found no event crfs from Study Event id " + studyEventBean.getId() + ", location " + studyEventBean.getLocation());
if ((studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SCHEDULED) || studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.DATA_ENTRY_STARTED) || studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.COMPLETED))) {
if (!upsert.isNotStarted())
return false;
}
}
for (EventCRFBean ecb : eventCrfBeans) {
Integer ecbId = new Integer(ecb.getId());
if (!(ecb.getStage().equals(DataEntryStage.INITIAL_DATA_ENTRY) && upsert.isDataEntryStarted()) && !(ecb.getStage().equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) && upsert.isDataEntryComplete()))
return false;
}
}
}
}
}
return true;
}
use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.
the class StudySubjectEndpoint method doesSubjectExist.
/**
* @param subjectTransferBean
* @return
*/
private boolean doesSubjectExist(SubjectTransferBean subjectTransferBean) {
// TODO: Implement this
StudySubjectDAO ssdao = new StudySubjectDAO(dataSource);
StudyDAO studyDao = new StudyDAO(dataSource);
StudyBean studyBean = studyDao.findByUniqueIdentifier(subjectTransferBean.getStudy().getIdentifier());
StudySubjectBean ssbean = ssdao.findByLabelAndStudy(subjectTransferBean.getStudySubjectId(), studyBean);
return ssbean.getId() > 0 ? true : false;
}
use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.
the class SystemController method getStudyList.
public ArrayList<StudyBean> getStudyList() {
StudyDAO sdao = new StudyDAO(dataSource);
ArrayList<StudyBean> sBeans = (ArrayList<StudyBean>) sdao.findAllParents();
return sBeans;
}
use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.
the class StudyModuleController method deactivateParticipate.
@RequestMapping(value = "/{study}/deactivate", method = RequestMethod.GET)
public String deactivateParticipate(@PathVariable("study") String studyOid, HttpServletRequest request) throws Exception {
studyDao = new StudyDAO(dataSource);
StudyBean study = studyDao.findByOid(studyOid);
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(dataSource);
StudyParameterValueBean spv = spvdao.findByHandleAndStudy(study.getId(), "participantPortal");
spv.setStudyId(study.getId());
spv.setParameter("participantPortal");
spv.setValue("disabled");
if (spv.getId() > 0)
spvdao.update(spv);
else
spvdao.create(spv);
StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
currentStudy.getStudyParameterConfig().setParticipantPortal("disabled");
return "redirect:/pages/studymodule";
}
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