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

Example 51 with StudyBean

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

the class ViewStudySubjectServlet method getDisplayStudyEventsForStudySubject.

public static ArrayList<DisplayStudyEventBean> getDisplayStudyEventsForStudySubject(StudySubjectBean studySub, DataSource ds, UserAccountBean ub, StudyUserRoleBean currentRole) {
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(ds);
    StudyEventDAO sedao = new StudyEventDAO(ds);
    EventCRFDAO ecdao = new EventCRFDAO(ds);
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(ds);
    StudySubjectDAO ssdao = new StudySubjectDAO(ds);
    StudyDAO sdao = new StudyDAO(ds);
    ArrayList events = sedao.findAllByStudySubject(studySub);
    ArrayList displayEvents = new ArrayList();
    for (int i = 0; i < events.size(); i++) {
        StudyEventBean event = (StudyEventBean) events.get(i);
        StudySubjectBean studySubject = (StudySubjectBean) ssdao.findByPK(event.getStudySubjectId());
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(event.getStudyEventDefinitionId());
        event.setStudyEventDefinition(sed);
        // find all active crfs in the definition
        StudyBean study = (StudyBean) sdao.findByPK(studySubject.getStudyId());
        ArrayList eventDefinitionCRFs = (ArrayList) edcdao.findAllActiveByEventDefinitionId(study, sed.getId());
        ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
        // construct info needed on view study event page
        DisplayStudyEventBean de = new DisplayStudyEventBean();
        de.setStudyEvent(event);
        de.setDisplayEventCRFs(getDisplayEventCRFs(ds, eventCRFs, eventDefinitionCRFs, ub, currentRole, event.getSubjectEventStatus(), study));
        ArrayList al = getUncompletedCRFs(ds, eventDefinitionCRFs, eventCRFs, event.getSubjectEventStatus());
        populateUncompletedCRFsWithCRFAndVersions(ds, al);
        de.setUncompletedCRFs(al);
        de.setMaximumSampleOrdinal(sedao.getMaxSampleOrdinal(sed, studySubject));
        displayEvents.add(de);
    // event.setEventCRFs(createAllEventCRFs(eventCRFs,
    // eventDefinitionCRFs));
    }
    return displayEvents;
}

Example 52 with StudyBean

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

the class ViewSubjectGroupClassServlet method processRequest.

@Override
public void processRequest() throws Exception {
    String action = request.getParameter("action");
    FormProcessor fp = new FormProcessor(request);
    int classId = fp.getInt("id");
    if (classId == 0) {
        addPageMessage(respage.getString("please_choose_a_subject_group_class_to_view"));
        forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
    } else {
        StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
        StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
        SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
        StudyDAO studyDao = new StudyDAO(sm.getDataSource());
        StudyGroupClassBean sgcb = (StudyGroupClassBean) sgcdao.findByPK(classId);
        StudyBean study = (StudyBean) studyDao.findByPK(sgcb.getStudyId());
        checkRoleByUserAndStudy(ub, sgcb.getStudyId(), study.getParentStudyId());
        // YW 09-19-2007 <<
        sgcb.setGroupClassTypeName(GroupClassType.get(sgcb.getGroupClassTypeId()).getName());
        // YW >>
        ArrayList groups = sgdao.findAllByGroupClass(sgcb);
        ArrayList studyGroups = new ArrayList();
        for (int i = 0; i < groups.size(); i++) {
            StudyGroupBean sg = (StudyGroupBean) groups.get(i);
            ArrayList subjectMaps = sgmdao.findAllByStudyGroupClassAndGroup(sgcb.getId(), sg.getId());
            sg.setSubjectMaps(subjectMaps);
            // YW<<
            studyGroups.add(sg);
        // YW>>
        }
        request.setAttribute("group", sgcb);
        // request.setAttribute("studyGroups", groups);
        request.setAttribute("studyGroups", studyGroups);
        forwardPage(Page.VIEW_SUBJECT_GROUP_CLASS);
    }
}

Example 53 with StudyBean

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

the class EnterDataForStudyEventServlet method processRequest.

/*
     * (non-Javadoc)
     *
     * @see org.akaza.openclinica.control.core.SecureController#processRequest()
     */
@Override
protected void processRequest() throws Exception {
    // removeLockedCRF(ub.getId());
    getCrfLocker().unlockAllForUser(ub.getId());
    FormProcessor fp = new FormProcessor(request);
    int eventId = fp.getInt(INPUT_EVENT_ID, true);
    request.setAttribute("eventId", eventId + "");
    // so we can display the event for which we're entering data
    StudyEventBean seb = getStudyEvent(eventId);
    // so we can display the subject's label
    StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
    StudySubjectBean studySubjectBean = (StudySubjectBean) ssdao.findByPK(seb.getStudySubjectId());
    int studyId = studySubjectBean.getStudyId();
    StudyDAO studydao = new StudyDAO(sm.getDataSource());
    StudyBean study = (StudyBean) studydao.findByPK(studyId);
    // If the study subject derives from a site, and is being viewed from a
    // parent study,
    // then the study IDs will be different. However, since each note is
    // saved with the specific
    // study ID, then its study ID may be different than the study subject's
    // ID.
    boolean subjectStudyIsCurrentStudy = studyId == currentStudy.getId();
    boolean isParentStudy = study.getParentStudyId() < 1;
    // Get any disc notes for this study event
    DiscrepancyNoteDAO discrepancyNoteDAO = new DiscrepancyNoteDAO(sm.getDataSource());
    ArrayList<DiscrepancyNoteBean> allNotesforSubjectAndEvent = new ArrayList<DiscrepancyNoteBean>();
    // These methods return only parent disc notes
    if (subjectStudyIsCurrentStudy && isParentStudy) {
        allNotesforSubjectAndEvent = discrepancyNoteDAO.findAllStudyEventByStudyAndId(currentStudy, studySubjectBean.getId());
    } else {
        // findAllStudyEventByStudiesAndSubjectId
        if (!isParentStudy) {
            StudyBean stParent = (StudyBean) studydao.findByPK(study.getParentStudyId());
            allNotesforSubjectAndEvent = discrepancyNoteDAO.findAllStudyEventByStudiesAndSubjectId(stParent, study, studySubjectBean.getId());
        } else {
            allNotesforSubjectAndEvent = discrepancyNoteDAO.findAllStudyEventByStudiesAndSubjectId(currentStudy, study, studySubjectBean.getId());
        }
    }
    if (!allNotesforSubjectAndEvent.isEmpty()) {
        setRequestAttributesForNotes(allNotesforSubjectAndEvent);
    }
    // prepare to figure out what the display should look like
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    ArrayList<EventCRFBean> eventCRFs = ecdao.findAllByStudyEvent(seb);
    ArrayList<Boolean> doRuleSetsExist = new ArrayList<Boolean>();
    RuleSetDAO ruleSetDao = new RuleSetDAO(sm.getDataSource());
    for (EventCRFBean eventCrfBean : eventCRFs) {
    // Boolean result = ruleSetDao.findByEventCrf(eventCrfBean) != null
    // ? Boolean.TRUE : Boolean.FALSE;
    // doRuleSetsExist.add(result);
    }
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
    ArrayList eventDefinitionCRFs = (ArrayList) edcdao.findAllActiveByEventDefinitionId(study, seb.getStudyEventDefinitionId());
    // get the event definition CRFs for which no event CRF exists
    // the event definition CRFs must be populated with versions so we can
    // let the user choose which version he will enter data for
    // However, this method seems to be returning DisplayEventDefinitionCRFs
    // that contain valid eventCRFs??
    ArrayList uncompletedEventDefinitionCRFs = getUncompletedCRFs(eventDefinitionCRFs, eventCRFs);
    populateUncompletedCRFsWithCRFAndVersions(uncompletedEventDefinitionCRFs);
    // BWP 2816 << Attempt to provide the DisplayEventDefinitionCRF with a
    // valid owner
    // only if its container eventCRf has a valid id
    populateUncompletedCRFsWithAnOwner(uncompletedEventDefinitionCRFs);
    // >>BWP
    // for the event definition CRFs for which event CRFs exist, get
    // DisplayEventCRFBeans, which the JSP will use to determine what
    // the user will see for each event CRF
    // removing the below row in exchange for the ViewStudySubjectServlet
    // version, for two
    // reasons:
    // 1. concentrate all business logic in one place
    // 2. VSSS seems to handle the javascript creation correctly
    // ArrayList displayEventCRFs = getDisplayEventCRFs(eventCRFs,
    // eventDefinitionCRFs, seb.getSubjectEventStatus());
    ArrayList displayEventCRFs = ViewStudySubjectServlet.getDisplayEventCRFs(sm.getDataSource(), eventCRFs, eventDefinitionCRFs, ub, currentRole, seb.getSubjectEventStatus(), study);
    // Issue 3212 BWP << hide certain CRFs at the site level
    if (currentStudy.getParentStudyId() > 0) {
        HideCRFManager hideCRFManager = HideCRFManager.createHideCRFManager();
        uncompletedEventDefinitionCRFs = hideCRFManager.removeHiddenEventDefinitionCRFBeans(uncompletedEventDefinitionCRFs);
        displayEventCRFs = hideCRFManager.removeHiddenEventCRFBeans(displayEventCRFs);
    }
    // >>
    request.setAttribute(BEAN_STUDY_EVENT, seb);
    request.setAttribute("doRuleSetsExist", doRuleSetsExist);
    request.setAttribute(BEAN_STUDY_SUBJECT, studySubjectBean);
    request.setAttribute(BEAN_UNCOMPLETED_EVENTDEFINITIONCRFS, uncompletedEventDefinitionCRFs);
    request.setAttribute(BEAN_DISPLAY_EVENT_CRFS, displayEventCRFs);
    // @pgawade 31-Aug-2012 fix for issue #15315: Reverting to set the request variable "beans" back
    // this is for generating side info panel
    ArrayList beans = ViewStudySubjectServlet.getDisplayStudyEventsForStudySubject(studySubjectBean, sm.getDataSource(), ub, currentRole);
    request.setAttribute("beans", beans);
    EventCRFBean ecb = new EventCRFBean();
    ecb.setStudyEventId(eventId);
    request.setAttribute("eventCRF", ecb);
    // Make available the study
    request.setAttribute("study", currentStudy);
    forwardPage(Page.ENTER_DATA_FOR_STUDY_EVENT);
}

Example 54 with StudyBean

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

the class DiscNotesSubjectStatisticsFactory 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(6);
    }
    int rowStart = limit.getRowSelect().getRowStart();
    int rowEnd = 6;
    ListDiscNotesSubjectSort subjectSort = getSubjectSort(limit);
    HashMap<Object, Map> items = (HashMap<Object, Map>) getDiscrepancyMap();
    Collection<HashMap<Object, Object>> theItems = new ArrayList<HashMap<Object, Object>>();
    Collection<HashMap<Object, Object>> theItemsKeys = new ArrayList<HashMap<Object, Object>>();
    Collection<HashMap<Object, Object>> theItemsVals = new ArrayList<HashMap<Object, Object>>();
    Iterator keyIt = null;
    if (items.values().iterator().hasNext())
        keyIt = items.values().iterator().next().keySet().iterator();
    HashMap<Object, Object> theItem = new HashMap();
    Set theKeys = items.keySet();
    List<Object> existingKey = new ArrayList();
    Iterator theKeysItr = theKeys.iterator();
    while (keyIt.hasNext()) {
        String key = "", val = "";
        key = keyIt.next().toString();
        for (Map<String, String[]> firstVals : items.values()) {
            theItem = new HashMap();
            Iterator it = firstVals.values().iterator();
            // keyIt = firstVals.keySet().iterator();
            String label = (String) theKeysItr.next();
            while (it.hasNext()) {
                theItem.put("_", key);
                theItem.put(label, it.next());
            }
            theItems.add(theItem);
        }
        theItemsVals.addAll(theItems);
        tableFacade.setItems(theItemsVals);
    }
}

Example 55 with StudyBean

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

the class CreateDiscrepancyNoteServlet method generateUserAccounts.

private ArrayList generateUserAccounts(int studyId, int subjectId) {
    UserAccountDAO userAccountDAO = new UserAccountDAO(sm.getDataSource());
    StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
    StudyBean subjectStudy = studyDAO.findByStudySubjectId(subjectId);
    // study id, tbh 03/2009
    ArrayList userAccounts = new ArrayList();
    if (currentStudy.getParentStudyId() > 0) {
        userAccounts = userAccountDAO.findAllUsersByStudyOrSite(studyId, currentStudy.getParentStudyId(), subjectId);
    } else if (subjectStudy.getParentStudyId() > 0) {
        userAccounts = userAccountDAO.findAllUsersByStudyOrSite(subjectStudy.getId(), subjectStudy.getParentStudyId(), subjectId);
    } else {
        userAccounts = userAccountDAO.findAllUsersByStudyOrSite(studyId, 0, subjectId);
    }
    return userAccounts;
}