Examples with StudyBean org.akaza.openclinica.bean.managestudy.StudyBean used on opensource projects

Example 61 with StudyBean

use of org.akaza.openclinica.bean.managestudy.StudyBean in project OpenClinica by OpenClinica.

the class ListDiscNotesSubjectTableFactory method setDataAndLimitVariables.

@Override
public void setDataAndLimitVariables(TableFacade tableFacade) {
    StudyBean study = this.getStudyBean();
    Limit limit = tableFacade.getLimit();
    ListDiscNotesSubjectFilter subjectFilter = getSubjectFilter(limit);
    subjectFilter.addFilter("dn.discrepancy_note_type_id", this.discNoteType);
    StringBuffer constraints = new StringBuffer();
    if (this.discNoteType > 0 && this.discNoteType < 10) {
        constraints.append(" and dn.discrepancy_note_type_id=" + this.discNoteType);
    }
    if (this.resolutionStatusIds != null && this.resolutionStatusIds.size() > 0) {
        String s = " and (";
        for (Integer resolutionStatusId : this.resolutionStatusIds) {
            s += "dn.resolution_status_id = " + resolutionStatusId + " or ";
        }
        s = s.substring(0, s.length() - 3) + " )";
        subjectFilter.addFilter("dn.resolution_status_id", s);
        constraints.append(s);
    }
    if (!limit.isComplete()) {
        int totalRows = getStudySubjectDAO().getCountWithFilter(subjectFilter, study);
        tableFacade.setTotalRows(totalRows);
    }
    ListDiscNotesSubjectSort subjectSort = getSubjectSort(limit);
    int rowStart = limit.getRowSelect().getRowStart();
    int rowEnd = limit.getRowSelect().getRowEnd();
    Collection<StudySubjectBean> items = getStudySubjectDAO().getWithFilterAndSort(study, subjectFilter, subjectSort, rowStart, rowEnd);
    Collection<HashMap<Object, Object>> theItems = new ArrayList<HashMap<Object, Object>>();
    boolean hasDN = false;
    for (StudySubjectBean studySubjectBean : items) {
        HashMap<Object, Object> theItem = new HashMap<Object, Object>();
        theItem.put("studySubject", studySubjectBean);
        theItem.put("studySubject.label", studySubjectBean.getLabel());
        theItem.put("studySubject.status", studySubjectBean.getStatus());
        theItem.put("enrolledAt", ((StudyBean) getStudyDAO().findByPK(studySubjectBean.getStudyId())).getIdentifier());
        // Get All study events for this study subject and then put list in
        // HashMap with study event definition id as
        // key and a list of study events as the value.
        List<StudyEventBean> allStudyEventsForStudySubject = getStudyEventDAO().findAllByStudySubject(studySubjectBean);
        HashMap<Integer, List<StudyEventBean>> allStudyEventsForStudySubjectBySedId = new HashMap<Integer, List<StudyEventBean>>();
        theItem.put("isSignable", isSignable(allStudyEventsForStudySubject));
        for (StudyEventBean studyEventBean : allStudyEventsForStudySubject) {
            if (allStudyEventsForStudySubjectBySedId.get(studyEventBean.getStudyEventDefinitionId()) == null) {
                ArrayList<StudyEventBean> a = new ArrayList<StudyEventBean>();
                a.add(studyEventBean);
                allStudyEventsForStudySubjectBySedId.put(studyEventBean.getStudyEventDefinitionId(), a);
            } else {
                allStudyEventsForStudySubjectBySedId.get(studyEventBean.getStudyEventDefinitionId()).add(studyEventBean);
            }
        }
        for (StudyEventDefinitionBean studyEventDefinition : getStudyEventDefinitions()) {
            List<StudyEventBean> studyEvents = allStudyEventsForStudySubjectBySedId.get(studyEventDefinition.getId());
            SubjectEventStatus subjectEventStatus = null;
            HashMap<ResolutionStatus, Integer> discCounts = new HashMap<ResolutionStatus, Integer>();
            studyEvents = studyEvents == null ? new ArrayList<StudyEventBean>() : studyEvents;
            if (studyEvents.size() < 1) {
                subjectEventStatus = SubjectEventStatus.NOT_SCHEDULED;
            } else {
                for (StudyEventBean studyEventBean : studyEvents) {
                    discCounts = countAll(discCounts, studyEventBean, constraints, study.isSite(study.getParentStudyId()));
                    hasDN = hasDN == false ? discCounts.size() > 0 : hasDN;
                    if (studyEventBean.getSampleOrdinal() == 1) {
                        subjectEventStatus = studyEventBean.getSubjectEventStatus();
                    // break;
                    }
                }
            }
            theItem.put("sed_" + studyEventDefinition.getId() + "_discCounts", discCounts);
            theItem.put("sed_" + studyEventDefinition.getId(), subjectEventStatus.getId());
            theItem.put("sed_" + studyEventDefinition.getId() + "_studyEvents", studyEvents);
            theItem.put("sed_" + studyEventDefinition.getId() + "_object", studyEventDefinition);
        }
        theItems.add(theItem);
    }
    // Do not forget to set the items back on the tableFacade.
    tableFacade.setItems(theItems);
    setStudyHasDiscNotes(hasDN);
}

Example 62 with StudyBean

use of org.akaza.openclinica.bean.managestudy.StudyBean in project OpenClinica by OpenClinica.

the class ListDiscNotesSubjectTableFactory method getStudyEventDefinitions.

@SuppressWarnings("unchecked")
private ArrayList<StudyEventDefinitionBean> getStudyEventDefinitions() {
    if (this.studyEventDefinitions == null) {
        if (studyBean.getParentStudyId() > 0) {
            StudyBean parentStudy = (StudyBean) getStudyDAO().findByPK(studyBean.getParentStudyId());
            studyEventDefinitions = getStudyEventDefinitionDao().findAllByStudy(parentStudy);
        } else {
            studyEventDefinitions = getStudyEventDefinitionDao().findAllByStudy(studyBean);
        }
    }
    return this.studyEventDefinitions;
}

Example 63 with StudyBean

use of org.akaza.openclinica.bean.managestudy.StudyBean in project OpenClinica by OpenClinica.

the class ListDiscNotesForCRFTableFactory method getStudyGroupClasses.

@SuppressWarnings("unchecked")
private ArrayList<StudyGroupClassBean> getStudyGroupClasses() {
    if (this.studyGroupClasses == null) {
        if (studyBean.getParentStudyId() > 0) {
            StudyBean parentStudy = (StudyBean) getStudyDAO().findByPK(studyBean.getParentStudyId());
            studyGroupClasses = getStudyGroupClassDAO().findAllActiveByStudy(parentStudy);
        } else {
            studyGroupClasses = getStudyGroupClassDAO().findAllActiveByStudy(studyBean);
        }
    }
    return studyGroupClasses;
}

Example 64 with StudyBean

use of org.akaza.openclinica.bean.managestudy.StudyBean in project OpenClinica by OpenClinica.

the class TableOfContentsServlet method createEventCRF.

/**
 * Creates a new Event CRF or update the exsiting one, that is, an event CRF
 * can be created but not item data yet, in this case, still consider it is
 * not started(called uncompleted before)
 *
 * @return
 * @throws Exception
 */
private EventCRFBean createEventCRF() throws Exception {
    EventCRFBean ecb;
    ecdao = new EventCRFDAO(sm.getDataSource());
    int crfVersionId = fp.getInt(INPUT_CRF_VERSION_ID);
    int studyEventId = fp.getInt(INPUT_STUDY_EVENT_ID);
    int eventDefinitionCRFId = fp.getInt(INPUT_EVENT_DEFINITION_CRF_ID);
    int subjectId = fp.getInt(INPUT_SUBJECT_ID);
    int eventCRFId = fp.getInt(INPUT_EVENT_CRF_ID);
    logger.info("Creating event CRF within Table of Contents.  Study id: " + currentStudy.getId() + "; CRF Version id: " + crfVersionId + "; Study Event id: " + studyEventId + "; Event Definition CRF id: " + eventDefinitionCRFId + "; Subject: " + subjectId);
    StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
    StudySubjectBean ssb = ssdao.findBySubjectIdAndStudy(subjectId, currentStudy);
    if (!ssb.isActive()) {
        throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("trying_to_begin_DE1"));
    }
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    StudyEventDefinitionBean sedb = seddao.findByEventDefinitionCRFId(eventDefinitionCRFId);
    if (!ssb.isActive() || !sedb.isActive()) {
        throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("trying_to_begin_DE2"));
    }
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    EntityBean eb = cvdao.findByPK(crfVersionId);
    if (!eb.isActive()) {
        throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("trying_to_begin_DE3"));
    }
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudyEventBean sEvent = (StudyEventBean) sedao.findByPK(studyEventId);
    StudyBean studyWithSED = currentStudy;
    if (currentStudy.getParentStudyId() > 0) {
        studyWithSED = new StudyBean();
        studyWithSED.setId(currentStudy.getParentStudyId());
    }
    AuditableEntityBean aeb = sedao.findByPKAndStudy(studyEventId, studyWithSED);
    if (!aeb.isActive()) {
        throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("trying_to_begin_DE4"));
    }
    ecb = new EventCRFBean();
    if (eventCRFId == 0) {
        // no event CRF created yet
        ecb.setAnnotations("");
        ecb.setCreatedDate(new Date());
        ecb.setCRFVersionId(crfVersionId);
        ecb.setInterviewerName("");
        if (sEvent.getDateStarted() != null) {
            // default date
            ecb.setDateInterviewed(sEvent.getDateStarted());
        } else {
            ecb.setDateInterviewed(null);
        }
        ecb.setOwnerId(ub.getId());
        ecb.setStatus(Status.AVAILABLE);
        ecb.setCompletionStatusId(1);
        ecb.setStudySubjectId(ssb.getId());
        ecb.setStudyEventId(studyEventId);
        ecb.setValidateString("");
        ecb.setValidatorAnnotations("");
        ecb = (EventCRFBean) ecdao.create(ecb);
        logger.info("CREATED EVENT CRF");
    } else {
        // there is an event CRF already, only need to update
        ecb = (EventCRFBean) ecdao.findByPK(eventCRFId);
        ecb.setCRFVersionId(crfVersionId);
        ecb.setUpdatedDate(new Date());
        ecb.setUpdater(ub);
        ecb = (EventCRFBean) ecdao.update(ecb);
    }
    if (!ecb.isActive()) {
        throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("new_event_CRF_not_created_database_error"));
    } else {
        sEvent.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED);
        sEvent.setUpdater(ub);
        sEvent.setUpdatedDate(new Date());
        sedao.update(sEvent);
    }
    return ecb;
}

Example 65 with StudyBean

use of org.akaza.openclinica.bean.managestudy.StudyBean in project OpenClinica by OpenClinica.

the class EditFormController method mayProceed.

private boolean mayProceed(String studyOid) throws Exception {
    boolean accessPermission = false;
    StudyBean siteStudy = getStudy(studyOid);
    StudyBean study = getParentStudy(studyOid);
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(dataSource);
    StudyParameterValueBean pStatus = spvdao.findByHandleAndStudy(study.getId(), "participantPortal");
    participantPortalRegistrar = new ParticipantPortalRegistrar();
    // ACTIVE ,
    String pManageStatus = participantPortalRegistrar.getRegistrationStatus(study.getOid()).toString();
    // PENDING ,
    // INACTIVE
    // enabled , disabled
    String participateStatus = pStatus.getValue().toString();
    // available , pending , frozen , locked
    String studyStatus = study.getStatus().getName().toString();
    // available , pending , frozen , locked
    String siteStatus = siteStudy.getStatus().getName().toString();
    System.out.println("pManageStatus: " + pManageStatus + "  participantStatus: " + participateStatus + "   studyStatus: " + studyStatus + "   siteStatus: " + siteStatus);
    logger.info("pManageStatus: " + pManageStatus + "  participantStatus: " + participateStatus + "   studyStatus: " + studyStatus + "   siteStatus: " + siteStatus);
    if (participateStatus.equalsIgnoreCase("enabled") && studyStatus.equalsIgnoreCase("available") && siteStatus.equalsIgnoreCase("available") && pManageStatus.equalsIgnoreCase("ACTIVE")) {
        accessPermission = true;
    }
    return accessPermission;
}