Examples with StudyDAO org.akaza.openclinica.dao.managestudy.StudyDAO used on opensource projects

Example 91 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class OdmController method getODM.

private ODM getODM(String studyOID, String subjectKey) {
    ODM odm = new ODM();
    String ssoid = subjectKey;
    if (ssoid == null) {
        return null;
    }
    CRFVersionDAO versionDAO = new CRFVersionDAO(dataSource);
    StudyDAO studyDAO = new StudyDAO(dataSource);
    StudySubjectDAO studySubjectDAO = new StudySubjectDAO(dataSource);
    EventCRFDAO eventCRFDAO = new EventCRFDAO(dataSource);
    ItemDataDAO itemDataDAO = new ItemDataDAO(dataSource);
    CRFDAO crfDAO = new CRFDAO(dataSource);
    List<ODMcomplexTypeDefinitionFormData> formDatas = new ArrayList<>();
    try {
        // Retrieve crfs for next event
        StudySubjectBean studySubjectBean = studySubjectDAO.findByOid(ssoid);
        ParticipantEventService participantEventService = new ParticipantEventService(dataSource);
        StudyEventBean nextEvent = participantEventService.getNextParticipantEvent(studySubjectBean);
        if (nextEvent != null) {
            logger.debug("Found event: " + nextEvent.getName() + " - ID: " + nextEvent.getId());
            List<EventCRFBean> eventCrfs = eventCRFDAO.findAllByStudyEvent(nextEvent);
            StudyBean study = studyDAO.findByOid(studyOID);
            if (!mayProceed(studyOID, studySubjectBean))
                return odm;
            List<EventDefinitionCRFBean> eventDefCrfs = participantEventService.getEventDefCrfsForStudyEvent(studySubjectBean, nextEvent);
            for (EventDefinitionCRFBean eventDefCrf : eventDefCrfs) {
                if (eventDefCrf.isParticipantForm()) {
                    EventCRFBean eventCRF = participantEventService.getExistingEventCRF(studySubjectBean, nextEvent, eventDefCrf);
                    boolean itemDataExists = false;
                    boolean validStatus = true;
                    CRFVersionBean crfVersion = null;
                    if (eventCRF != null) {
                        if (eventCRF.getStatus().getId() != 1 && eventCRF.getStatus().getId() != 2)
                            validStatus = false;
                        if (itemDataDAO.findAllByEventCRFId(eventCRF.getId()).size() > 0)
                            itemDataExists = true;
                        crfVersion = (CRFVersionBean) versionDAO.findByPK(eventCRF.getCRFVersionId());
                    } else
                        crfVersion = (CRFVersionBean) versionDAO.findByPK(eventDefCrf.getDefaultVersionId());
                    if (validStatus) {
                        String formUrl = null;
                        if (!itemDataExists)
                            formUrl = createEnketoUrl(studyOID, crfVersion, nextEvent, ssoid);
                        else
                            formUrl = createEditUrl(studyOID, crfVersion, nextEvent, ssoid);
                        formDatas.add(getFormDataPerCrf(crfVersion, nextEvent, eventCrfs, crfDAO, formUrl, itemDataExists));
                    }
                }
            }
            return createOdm(study, studySubjectBean, nextEvent, formDatas);
        } else {
            logger.debug("Unable to find next event for subject.");
        }
    } catch (Exception e) {
        logger.error(e.getMessage());
        logger.error(ExceptionUtils.getStackTrace(e));
    }
    return odm;
}

Example 92 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class ViewDiscrepancyNoteServlet method processRequest.

@Override
@SuppressWarnings("unchecked")
protected void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int eventCRFId = fp.getInt(CreateDiscrepancyNoteServlet.EVENT_CRF_ID);
    request.setAttribute(CreateDiscrepancyNoteServlet.EVENT_CRF_ID, new Integer(eventCRFId));
    request.setAttribute(DIS_TYPES, DiscrepancyNoteType.list);
    if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2) || currentRole.getRole().equals(Role.INVESTIGATOR)) {
        ArrayList<ResolutionStatus> resStatuses = new ArrayList();
        resStatuses.add(ResolutionStatus.UPDATED);
        resStatuses.add(ResolutionStatus.RESOLVED);
        request.setAttribute(RES_STATUSES, resStatuses);
        // it's for parentDNId is null or 0
        request.setAttribute(WHICH_RES_STATUSES, "22");
        ArrayList<ResolutionStatus> resStatuses2 = new ArrayList<ResolutionStatus>();
        resStatuses2.add(ResolutionStatus.OPEN);
        resStatuses2.add(ResolutionStatus.RESOLVED);
        request.setAttribute(RES_STATUSES2, resStatuses2);
        List<DiscrepancyNoteType> types2 = new ArrayList<DiscrepancyNoteType>(DiscrepancyNoteType.list);
        types2.remove(DiscrepancyNoteType.QUERY);
        request.setAttribute(DIS_TYPES2, types2);
    } else if (currentRole.getRole().equals(Role.MONITOR)) {
        ArrayList<ResolutionStatus> resStatuses = new ArrayList();
        resStatuses.add(ResolutionStatus.OPEN);
        resStatuses.add(ResolutionStatus.UPDATED);
        resStatuses.add(ResolutionStatus.CLOSED);
        request.setAttribute(RES_STATUSES, resStatuses);
        request.setAttribute(WHICH_RES_STATUSES, "1");
        ArrayList<DiscrepancyNoteType> types2 = new ArrayList<DiscrepancyNoteType>();
        types2.add(DiscrepancyNoteType.QUERY);
        request.setAttribute(DIS_TYPES2, types2);
    } else {
        // Role.STUDYDIRECTOR Role.COORDINATOR
        List<ResolutionStatus> resStatuses = new ArrayList<ResolutionStatus>(ResolutionStatus.list);
        resStatuses.remove(ResolutionStatus.NOT_APPLICABLE);
        request.setAttribute(RES_STATUSES, resStatuses);
        ;
        // it's for parentDNId is null or 0 and FVC
        request.setAttribute(WHICH_RES_STATUSES, "2");
        ArrayList<ResolutionStatus> resStatuses2 = new ArrayList<ResolutionStatus>();
        resStatuses2.add(ResolutionStatus.OPEN);
        resStatuses2.add(ResolutionStatus.RESOLVED);
        request.setAttribute(RES_STATUSES2, resStatuses2);
    }
    // logic from CreateDiscrepancyNoteServlet
    request.setAttribute("unlock", "0");
    fp.getBoolean(IS_REASON_FOR_CHANGE);
    fp.getBoolean(ERROR_FLAG);
    String monitor = fp.getString("monitor");
    // } else if ("1".equalsIgnoreCase(monitor)) {// change to allow user to
    if ("1".equalsIgnoreCase(monitor)) {
        // change to allow user to
        // enter note for all items,
        // not just blank items
        request.setAttribute(CAN_MONITOR, "1");
        request.setAttribute("monitor", monitor);
    } else {
        request.setAttribute(CAN_MONITOR, "0");
    }
    Boolean fromBox = fp.getBoolean(FROM_BOX);
    if (fromBox == null || !fromBox) {
        session.removeAttribute(BOX_TO_SHOW);
        session.removeAttribute(BOX_DN_MAP);
        session.removeAttribute(AUTOVIEWS);
    }
    Boolean refresh = fp.getBoolean("refresh");
    request.setAttribute("refresh", refresh + "");
    String ypos = fp.getString("y");
    if (ypos == null || ypos.length() == 0) {
        ypos = "0";
    }
    request.setAttribute("y", ypos);
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
    int entityId = fp.getInt(ENTITY_ID, true);
    String name = fp.getString(ENTITY_TYPE, true);
    String column = fp.getString(ENTITY_COLUMN, true);
    String field = fp.getString(ENTITY_FIELD, true);
    String isLocked = fp.getString(LOCKED_FLAG);
    if (!StringUtil.isBlank(isLocked) && "yes".equalsIgnoreCase(isLocked)) {
        request.setAttribute(LOCKED_FLAG, "yes");
    } else {
        request.setAttribute(LOCKED_FLAG, "no");
    }
    DateFormat dateFormatter = DateFormat.getDateInstance(DateFormat.DEFAULT, locale);
    int subjectId = fp.getInt(CreateDiscrepancyNoteServlet.SUBJECT_ID, true);
    int itemId = fp.getInt(CreateDiscrepancyNoteServlet.ITEM_ID, true);
    StudySubjectBean ssub = new StudySubjectBean();
    if (subjectId > 0) {
        StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
        ssub = (StudySubjectBean) ssdao.findByPK(subjectId);
        request.setAttribute("noteSubject", ssub);
    }
    ItemBean item = new ItemBean();
    if (itemId > 0) {
        ItemDAO idao = new ItemDAO(sm.getDataSource());
        item = (ItemBean) idao.findByPK(itemId);
        request.setAttribute("item", item);
        request.setAttribute("entityName", item.getName());
    }
    ItemDataBean itemData = new ItemDataBean();
    SimpleDateFormat sdf = new SimpleDateFormat("dd-MMM-yyyy");
    int preUserId = 0;
    if (!StringUtil.isBlank(name)) {
        if ("itemData".equalsIgnoreCase(name)) {
            ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
            itemData = (ItemDataBean) iddao.findByPK(entityId);
            request.setAttribute("entityValue", itemData.getValue());
            request.setAttribute("entityName", item.getName());
            EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
            EventCRFBean ec = (EventCRFBean) ecdao.findByPK(itemData.getEventCRFId());
            preUserId = ec.getOwnerId() > 0 ? ec.getOwnerId() : 0;
            request.setAttribute("entityCreatedDate", sdf.format(ec.getCreatedDate()));
            StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
            StudyEventBean se = (StudyEventBean) sed.findByPK(ec.getStudyEventId());
            StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
            StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
            se.setName(sedb.getName());
            request.setAttribute("studyEvent", se);
            CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
            CRFVersionBean cv = (CRFVersionBean) cvdao.findByPK(ec.getCRFVersionId());
            CRFDAO cdao = new CRFDAO(sm.getDataSource());
            CRFBean crf = (CRFBean) cdao.findByPK(cv.getCrfId());
            request.setAttribute("crf", crf);
        } else if ("studySub".equalsIgnoreCase(name)) {
            StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
            ssub = (StudySubjectBean) ssdao.findByPK(entityId);
            SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
            SubjectBean sub = (SubjectBean) sdao.findByPK(ssub.getSubjectId());
            request.setAttribute("noteSubject", ssub);
            if (!StringUtil.isBlank(column)) {
                if ("enrollment_date".equalsIgnoreCase(column)) {
                    if (ssub.getEnrollmentDate() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(ssub.getEnrollmentDate()));
                    }
                    request.setAttribute("entityName", resword.getString("enrollment_date"));
                } else if ("gender".equalsIgnoreCase(column)) {
                    request.setAttribute("entityValue", sub.getGender() + "");
                    request.setAttribute("entityName", resword.getString("gender"));
                } else if ("date_of_birth".equalsIgnoreCase(column)) {
                    if (sub.getDateOfBirth() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(sub.getDateOfBirth()));
                    }
                    request.setAttribute("entityName", resword.getString("date_of_birth"));
                } else if ("unique_identifier".equalsIgnoreCase(column)) {
                    if (sub.getUniqueIdentifier() != null) {
                        request.setAttribute("entityValue", sub.getUniqueIdentifier());
                    }
                    request.setAttribute("entityName", resword.getString("unique_identifier"));
                }
            }
            preUserId = ssub.getOwnerId() > 0 ? ssub.getOwnerId() : 0;
            request.setAttribute("entityCreatedDate", sdf.format(ssub.getCreatedDate()));
        } else if ("subject".equalsIgnoreCase(name)) {
            SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
            SubjectBean sub = (SubjectBean) sdao.findByPK(entityId);
            // be caution: here for subject, noteSubject is SubjectBean and
            // label is unique_identifier
            sub.setLabel(sub.getUniqueIdentifier());
            request.setAttribute("noteSubject", sub);
            if (!StringUtil.isBlank(column)) {
                if ("gender".equalsIgnoreCase(column)) {
                    request.setAttribute("entityValue", ssub.getGender() + "");
                    request.setAttribute("entityName", resword.getString("gender"));
                } else if ("date_of_birth".equalsIgnoreCase(column)) {
                    if (sub.getDateOfBirth() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(sub.getDateOfBirth()));
                    }
                    request.setAttribute("entityName", resword.getString("date_of_birth"));
                } else if ("unique_identifier".equalsIgnoreCase(column)) {
                    request.setAttribute("entityValue", sub.getUniqueIdentifier());
                    request.setAttribute("entityName", resword.getString("unique_identifier"));
                }
            }
            preUserId = sub.getOwnerId() > 0 ? sub.getOwnerId() : 0;
            request.setAttribute("entityCreatedDate", sdf.format(sub.getCreatedDate()));
        } else if ("studyEvent".equalsIgnoreCase(name)) {
            StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
            StudyEventBean se = (StudyEventBean) sed.findByPK(entityId);
            StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
            StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
            se.setName(sedb.getName());
            request.setAttribute("studyEvent", se);
            request.setAttribute("noteSubject", new StudySubjectDAO(sm.getDataSource()).findByPK(se.getStudySubjectId()));
            if (!StringUtil.isBlank(column)) {
                if ("location".equalsIgnoreCase(column)) {
                    request.setAttribute("entityValue", se.getLocation());
                    request.setAttribute("entityName", resword.getString("location"));
                } else if ("start_date".equalsIgnoreCase(column)) {
                    if (se.getDateStarted() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(se.getDateStarted()));
                    }
                    request.setAttribute("entityName", resword.getString("start_date"));
                } else if ("end_date".equalsIgnoreCase(column)) {
                    if (se.getDateEnded() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(se.getDateEnded()));
                    }
                    request.setAttribute("entityName", resword.getString("end_date"));
                }
            }
            preUserId = se.getOwnerId() > 0 ? se.getOwnerId() : 0;
            request.setAttribute("entityCreatedDate", sdf.format(se.getCreatedDate()));
        } else if ("eventCrf".equalsIgnoreCase(name)) {
            EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
            EventCRFBean ec = (EventCRFBean) ecdao.findByPK(entityId);
            if (!StringUtil.isBlank(column)) {
                if ("date_interviewed".equals(column)) {
                    if (ec.getDateInterviewed() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(ec.getDateInterviewed()));
                    }
                    request.setAttribute("entityName", resword.getString("date_interviewed"));
                } else if ("interviewer_name".equals(column)) {
                    request.setAttribute("entityValue", ec.getInterviewerName());
                    request.setAttribute("entityName", resword.getString("interviewer_name"));
                }
            }
            setupStudyEventCRFAttributes(ec);
            preUserId = ec.getOwnerId() > 0 ? ec.getOwnerId() : 0;
            request.setAttribute("entityCreatedDate", sdf.format(ec.getCreatedDate()));
        }
    }
    boolean writeToDB = fp.getBoolean(CreateDiscrepancyNoteServlet.WRITE_TO_DB, true);
    HashMap<Integer, Integer> autoviews = (HashMap<Integer, Integer>) session.getAttribute(AUTOVIEWS);
    autoviews = autoviews == null ? new HashMap<Integer, Integer>() : autoviews;
    HashMap<Integer, DiscrepancyNoteBean> boxDNMap = (HashMap<Integer, DiscrepancyNoteBean>) session.getAttribute(BOX_DN_MAP);
    if (boxDNMap == null || !boxDNMap.containsKey(0)) {
        boxDNMap = new HashMap<Integer, DiscrepancyNoteBean>();
        // initialize dn for a new thread
        DiscrepancyNoteBean dnb = new DiscrepancyNoteBean();
        if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2) || currentRole.getRole().equals(Role.INVESTIGATOR)) {
            dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.ANNOTATION.getId());
            dnb.setResolutionStatusId(ResolutionStatus.NOT_APPLICABLE.getId());
            autoviews.put(0, 0);
        // request.setAttribute("autoView", "0");
        } else {
            dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.QUERY.getId());
            dnb.setAssignedUserId(preUserId);
            autoviews.put(0, 1);
        // request.setAttribute("autoView", "1");
        }
        boxDNMap.put(0, dnb);
    } else if (boxDNMap.containsKey(0)) {
        int dnTypeId = boxDNMap.get(0).getDiscrepancyNoteTypeId();
        autoviews.put(0, dnTypeId == 3 ? 1 : 0);
    }
    if (boxDNMap.containsKey(0)) {
        int dnTypeId0 = boxDNMap.get(0).getDiscrepancyNoteTypeId();
        if (dnTypeId0 == 2 || dnTypeId0 == 4) {
            request.setAttribute("typeID0", dnTypeId0 + "");
        }
    }
    // request.setAttribute("enterData", enterData);
    request.setAttribute("monitor", monitor);
    request.setAttribute(ENTITY_ID, entityId + "");
    request.setAttribute(ENTITY_TYPE, name);
    request.setAttribute(ENTITY_FIELD, field);
    request.setAttribute(ENTITY_COLUMN, column);
    request.setAttribute(CreateDiscrepancyNoteServlet.WRITE_TO_DB, writeToDB ? "1" : "0");
    ArrayList notes = (ArrayList) dndao.findAllByEntityAndColumn(name, entityId, column);
    if (notes.size() > 0) {
        notes.get(0);
        // @pgawade 21-May-2011 Corrected the condition to throw no access
        // error
        StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
        int parentStudyForNoteSub = 0;
        // @pgawade #9801: 07-June-2011 corrected the way to get study
        // subject id associated with discrepancy note
        // int noteSubId = note.getOwnerId();
        StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
        // StudySubjectBean notessub = (StudySubjectBean)
        // ssdao.findByPK(noteSubId);
        StudySubjectBean notessub = (StudySubjectBean) ssdao.findByPK(subjectId);
        StudyBean studyBeanSub = (StudyBean) studyDAO.findByPK(notessub.getStudyId());
        if (null != studyBeanSub) {
            parentStudyForNoteSub = studyBeanSub.getParentStudyId();
        }
        if (notessub.getStudyId() != currentStudy.getId() && currentStudy.getId() != parentStudyForNoteSub) {
            addPageMessage(noAccessMessage);
            throw new InsufficientPermissionException(Page.MENU_SERVLET, exceptionName, "1");
        }
    }
    FormDiscrepancyNotes newNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
    Map<Integer, DiscrepancyNoteBean> noteTree = new LinkedHashMap<Integer, DiscrepancyNoteBean>();
    String session_key = eventCRFId + "_" + field;
    ArrayList newFieldNotes = null;
    if (newNotes != null && (!newNotes.getNotes(field).isEmpty() || !newNotes.getNotes(session_key).isEmpty())) {
        newFieldNotes = newNotes.getNotes(field);
        if (newFieldNotes == null || newFieldNotes.size() == 0) {
            newFieldNotes = newNotes.getNotes(session_key);
        }
        // System.out.println("how many notes:" + newFieldNotes.size());
        for (int i = 0; i < newFieldNotes.size(); i++) {
            DiscrepancyNoteBean note = (DiscrepancyNoteBean) newFieldNotes.get(i);
            note.setLastUpdator(ub);
            note.setLastDateUpdated(new Date());
            note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
            note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
            note.setSaved(false);
            if (itemId > 0) {
                note.setEntityName(item.getName());
                note.setEntityValue(itemData.getValue());
            }
            note.setSubjectName(ssub.getName());
            note.setEntityType(name);
            int pId = note.getParentDnId();
            if (pId == 0) {
                // we can only keep one unsaved note because
                // note.id == 0
                noteTree.put(note.getId(), note);
            }
        }
        for (int i = 0; i < newFieldNotes.size(); i++) {
            DiscrepancyNoteBean note = (DiscrepancyNoteBean) newFieldNotes.get(i);
            int pId = note.getParentDnId();
            if (pId > 0) {
                note.setSaved(false);
                note.setLastUpdator(ub);
                note.setLastDateUpdated(new Date());
                note.setEntityName(item.getName());
                note.setSubjectName(ssub.getName());
                note.setEntityType(name);
                note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
                note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
                DiscrepancyNoteBean parent = noteTree.get(new Integer(pId));
                if (parent != null) {
                    parent.getChildren().add(note);
                }
            }
        }
    }
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    HashMap<Integer, String> fvcInitAssigns = new HashMap<Integer, String>();
    for (int i = 0; i < notes.size(); i++) {
        DiscrepancyNoteBean note = (DiscrepancyNoteBean) notes.get(i);
        note.setColumn(column);
        note.setEntityId(entityId);
        note.setEntityType(name);
        note.setField(field);
        Date lastUpdatedDate = note.getCreatedDate();
        UserAccountBean lastUpdator = (UserAccountBean) udao.findByPK(note.getOwnerId());
        note.setLastUpdator(lastUpdator);
        note.setLastDateUpdated(lastUpdatedDate);
        int pId = note.getParentDnId();
        note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
        note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
        if (pId == 0) {
            noteTree.put(new Integer(note.getId()), note);
        }
    }
    for (int i = 0; i < notes.size(); i++) {
        DiscrepancyNoteBean note = (DiscrepancyNoteBean) notes.get(i);
        int pId = note.getParentDnId();
        if (itemId > 0) {
            note.setEntityName(item.getName());
            note.setEntityValue(itemData.getValue());
        }
        note.setSubjectName(ssub.getName());
        note.setEntityType(name);
        Date lastUpdatedDate = note.getCreatedDate();
        UserAccountBean lastUpdator = (UserAccountBean) udao.findByPK(note.getOwnerId());
        note.setLastUpdator(lastUpdator);
        note.setLastDateUpdated(lastUpdatedDate);
        note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
        note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
        if (pId > 0) {
            DiscrepancyNoteBean parent = noteTree.get(new Integer(pId));
            if (parent != null) {
                parent.getChildren().add(note);
                if (!note.getCreatedDate().before(parent.getLastDateUpdated())) {
                    parent.setLastDateUpdated(note.getCreatedDate());
                }
                if (note.getDiscrepancyNoteTypeId() == 1 && note.getAssignedUserId() > 0) {
                    int ownerId = note.getOwnerId();
                    if (fvcInitAssigns.containsKey(pId)) {
                        String f = fvcInitAssigns.get(pId);
                        String fn = note.getId() + "." + ownerId;
                        if (fn.compareTo(f) < 0) {
                            fvcInitAssigns.put(pId, fn);
                        }
                    } else {
                        fvcInitAssigns.put(pId, note.getId() + "." + ownerId);
                    }
                }
            }
        }
    }
    Set parents = noteTree.keySet();
    Iterator it = parents.iterator();
    while (it.hasNext()) {
        Integer key = (Integer) it.next();
        DiscrepancyNoteBean note = noteTree.get(key);
        note.setNumChildren(note.getChildren().size());
        note.setEntityType(name);
        if (!boxDNMap.containsKey(key)) {
            DiscrepancyNoteBean dn = new DiscrepancyNoteBean();
            dn.setId(key);
            int dnTypeId = note.getDiscrepancyNoteTypeId();
            dn.setDiscrepancyNoteTypeId(dnTypeId);
            if (dnTypeId == 3) {
                // Query
                dn.setAssignedUserId(note.getOwnerId());
            } else if (dnTypeId == 1) {
                // FVC
                if (fvcInitAssigns.containsKey(key)) {
                    String[] s = fvcInitAssigns.get(key).split("\\.");
                    int i = Integer.parseInt(s.length == 2 ? s[1].trim() : "0");
                    dn.setAssignedUserId(i);
                }
            }
            Role r = currentRole.getRole();
            // currentStudy.getId() != currentStudy.getParentStudyId()) {
            if (r.equals(Role.RESEARCHASSISTANT) || r.equals(Role.RESEARCHASSISTANT2) || r.equals(Role.INVESTIGATOR)) {
                if (dn.getDiscrepancyNoteTypeId() == DiscrepancyNoteType.QUERY.getId() && note.getResStatus().getId() == ResolutionStatus.UPDATED.getId()) {
                    dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
                } else {
                    dn.setResolutionStatusId(ResolutionStatus.RESOLVED.getId());
                }
                if (dn.getAssignedUserId() > 0) {
                    autoviews.put(key, 1);
                } else {
                    autoviews.put(key, 0);
                }
            // copied from CreateDiscrepancyNoteServlet
            // request.setAttribute("autoView", "0");
            // hide the panel, tbh
            } else {
                if (note.getResStatus().getId() == ResolutionStatus.RESOLVED.getId()) {
                    dn.setResolutionStatusId(ResolutionStatus.CLOSED.getId());
                } else if (note.getResStatus().getId() == ResolutionStatus.CLOSED.getId()) {
                    dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
                } else if (r.equals(Role.MONITOR)) {
                    dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
                } else if (dn.getDiscrepancyNoteTypeId() == 1) {
                    dn.setResolutionStatusId(ResolutionStatus.RESOLVED.getId());
                } else {
                    dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
                }
                autoviews.put(key, 1);
                if (dn.getAssignedUserId() > 0) {
                } else {
                    dn.setAssignedUserId(preUserId);
                }
            }
            boxDNMap.put(key, dn);
        }
    }
    session.setAttribute(BOX_DN_MAP, boxDNMap);
    session.setAttribute(AUTOVIEWS, autoviews);
    // noteTree is a Hashmap mapping note id to a parent note, with all the
    // child notes
    // stored in the children List.
    // BWP 3029>>make sure the parent note has an updated resolution status
    // and
    // updated date
    fixStatusUpdatedDate(noteTree);
    request.setAttribute(DIS_NOTES, noteTree);
    // copied from CreatediscrepancyNoteServlet generateUserAccounts
    StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
    StudyBean subjectStudy = studyDAO.findByStudySubjectId(subjectId);
    int studyId = currentStudy.getId();
    ArrayList<UserAccountBean> userAccounts = new ArrayList();
    if (currentStudy.getParentStudyId() > 0) {
        userAccounts = udao.findAllUsersByStudyOrSite(studyId, currentStudy.getParentStudyId(), subjectId);
    } else if (subjectStudy.getParentStudyId() > 0) {
        userAccounts = udao.findAllUsersByStudyOrSite(subjectStudy.getId(), subjectStudy.getParentStudyId(), subjectId);
    } else {
        userAccounts = udao.findAllUsersByStudyOrSite(studyId, 0, subjectId);
    }
    request.setAttribute(USER_ACCOUNTS, userAccounts);
    request.setAttribute(VIEW_DN_LINK, this.getPageServletFileName());
    // audit log items (from ViewItemAuditLogServlet.java)
    AuditDAO adao = new AuditDAO(sm.getDataSource());
    if (name.equalsIgnoreCase("studysub")) {
        name = "study_subject";
    } else if (name.equalsIgnoreCase("eventcrf")) {
        name = "event_crf";
    } else if (name.equalsIgnoreCase("studyevent")) {
        name = "study_event";
    } else if (name.equalsIgnoreCase("itemdata")) {
        name = "item_data";
    }
    ArrayList itemAuditEvents = adao.findItemAuditEvents(entityId, name);
    request.setAttribute("itemAudits", itemAuditEvents);
    forwardPage(Page.VIEW_DISCREPANCY_NOTE);
}

Example 93 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class UrlRewriteServlet method getOpenClinicaResourceFromURL.

/**
 * Method to parse the request URL parameters and get the respective
 * database identifiers
 *
 * @param URLPath
 *            - example "S_CPCS/320999/SE_CPCS%5B1%5D/F_CPCS_1"
 * @param queryString
 *            - example
 *            "format=html&mode=view&tabId=1&exitTo=ViewStudySubject"
 * @return
 */
public OpenClinicaResource getOpenClinicaResourceFromURL(String URLPath) /*
                                                                            * ,
                                                                            * String
                                                                            * queryString
                                                                            */
{
    OpenClinicaResource openClinicaResource = new OpenClinicaResource();
    if ((null != URLPath) && (!URLPath.equals(""))) {
        if (URLPath.contains("/")) {
            String[] tokens = URLPath.split("/");
            if (tokens.length != 0) {
                String URLParamValue = "";
                StudyDAO stdao = new StudyDAO(getDataSource());
                StudySubjectDAO ssubdao = new StudySubjectDAO(getDataSource());
                StudyEventDefinitionDAO sedefdao = new StudyEventDefinitionDAO(getDataSource());
                CRFDAO crfdao = new CRFDAO(getDataSource());
                CRFVersionDAO crfvdao = new CRFVersionDAO(getDataSource());
                ItemDAO idao = new ItemDAO(getDataSource());
                ItemGroupDAO igdao = new ItemGroupDAO(getDataSource());
                StudyEventDAO sedao = new StudyEventDAO(getDataSource());
                StudyBean study = null;
                StudySubjectBean subject = null;
                StudyEventDefinitionBean sed = null;
                CRFBean c = null;
                CRFVersionBean cv = null;
                ItemBean item = null;
                ItemGroupBean ig = null;
                StudyEventBean studyEvent = null;
                Integer studySubjectId = 0;
                Integer eventDefId = 0;
                Integer eventRepeatKey = 0;
                for (int i = 0; i < tokens.length; i++) {
                    // when interpreting these request URL parameters, the
                    // assumption is that the position of
                    // each type of parameters will be fixed. Meaning, study
                    // OID is always going to be at the start
                    // followed by StudySubjectKey followed by study event
                    // definition OID followed by
                    // study event repeat key followed by form OID followed
                    // by item group OID followed by
                    // item group repeat key followed by item OID
                    // It can also be done based on the start of OID value
                    // (example study OID presently
                    // starts with 'S_' but we will have to change it if we
                    // change the method of generating
                    // oID values in future.
                    URLParamValue = tokens[i].trim();
                    // System.out.println("URLParamValue::"+URLParamValue);
                    logger.info("URLPAramValue::" + URLParamValue);
                    if ((null != URLParamValue) && (!URLParamValue.equals(""))) {
                        switch(i) {
                            case 0:
                                {
                                    // study OID
                                    study = stdao.findByOid(URLParamValue);
                                    // validate study OID
                                    if (study == null) {
                                        openClinicaResource.setInValid(true);
                                        openClinicaResource.getMessages().add(resexception.getString("invalid_study_oid"));
                                        return openClinicaResource;
                                    } else {
                                        openClinicaResource.setStudyOID(URLParamValue);
                                        if (null != study) {
                                            openClinicaResource.setStudyID(study.getId());
                                        }
                                    }
                                    break;
                                }
                            case 1:
                                {
                                    // StudySubjectKey
                                    subject = ssubdao.findByOidAndStudy(URLParamValue, study.getId());
                                    // validate subject OID
                                    if (subject == null) {
                                        openClinicaResource.setInValid(true);
                                        openClinicaResource.getMessages().add(resexception.getString("invalid_subject_oid"));
                                        return openClinicaResource;
                                    } else {
                                        openClinicaResource.setStudySubjectOID(URLParamValue);
                                        if (null != subject) {
                                            studySubjectId = subject.getId();
                                            openClinicaResource.setStudySubjectID(studySubjectId);
                                        }
                                    }
                                    break;
                                }
                            case 2:
                                {
                                    // study event definition OID
                                    // separate study event OID and study event
                                    // repeat key
                                    String seoid = "";
                                    String eventOrdinal = "";
                                    if (URLParamValue.contains("%5B") && URLParamValue.contains("%5D")) {
                                        seoid = URLParamValue.substring(0, URLParamValue.indexOf("%5B"));
                                        openClinicaResource.setStudyEventDefOID(seoid);
                                        eventOrdinal = URLParamValue.substring(URLParamValue.indexOf("%5B") + 3, URLParamValue.indexOf("%5D"));
                                    } else if (URLParamValue.contains("[") && URLParamValue.contains("]")) {
                                        seoid = URLParamValue.substring(0, URLParamValue.indexOf("["));
                                        logger.info("seoid" + seoid);
                                        openClinicaResource.setStudyEventDefOID(seoid);
                                        eventOrdinal = URLParamValue.substring(URLParamValue.indexOf("[") + 1, URLParamValue.indexOf("]"));
                                        logger.info("eventOrdinal::" + eventOrdinal);
                                    } else {
                                        // event ordinal not specified
                                        openClinicaResource.setInValid(true);
                                        openClinicaResource.getMessages().add(resexception.getString("event_ordinal_not_specified"));
                                        return openClinicaResource;
                                    }
                                    if ((null != seoid) && (null != study)) {
                                        sed = sedefdao.findByOidAndStudy(seoid, study.getId(), study.getParentStudyId());
                                        // validate study event oid
                                        if (null == sed) {
                                            openClinicaResource.setInValid(true);
                                            openClinicaResource.getMessages().add(resexception.getString("invalid_event_oid"));
                                            return openClinicaResource;
                                        } else {
                                            eventDefId = sed.getId();
                                            openClinicaResource.setStudyEventDefID(eventDefId);
                                        }
                                    }
                                    if (null != eventRepeatKey) {
                                        eventRepeatKey = Integer.parseInt(eventOrdinal.trim());
                                        // validate the event ordinal specified exists in database
                                        studyEvent = (StudyEventBean) sedao.findByStudySubjectIdAndDefinitionIdAndOrdinal(subject.getId(), sed.getId(), eventRepeatKey);
                                        // this method return new StudyEvent (not null) even if no studyEvent can be found
                                        if (null == studyEvent || studyEvent.getId() == 0) {
                                            openClinicaResource.setInValid(true);
                                            openClinicaResource.getMessages().add(resexception.getString("invalid_event_ordinal"));
                                            return openClinicaResource;
                                        } else {
                                            openClinicaResource.setStudyEventRepeatKey(eventRepeatKey);
                                        }
                                    }
                                    break;
                                }
                            case 3:
                                {
                                    // form OID
                                    openClinicaResource.setFormVersionOID(URLParamValue);
                                    // validate the crf version oid
                                    cv = crfvdao.findByOid(URLParamValue);
                                    if (cv == null) {
                                        openClinicaResource.setInValid(true);
                                        openClinicaResource.getMessages().add(resexception.getString("invalid_crf_oid"));
                                        return openClinicaResource;
                                    } else {
                                        openClinicaResource.setFormVersionID(cv.getId());
                                        // validate if crf is removed
                                        if (cv.getStatus().equals(Status.DELETED)) {
                                            openClinicaResource.setInValid(true);
                                            openClinicaResource.getMessages().add(resexception.getString("removed_crf"));
                                            return openClinicaResource;
                                        } else {
                                            if (null != study) {
                                                // cv =
                                                // crfvdao.findByCrfVersionOidAndStudy(URLParamValue,
                                                // study.getId());
                                                // if (null != cv) {
                                                // openClinicaResource.setFormVersionID(cv.getId());
                                                // openClinicaResource.setFormID(cv.getCrfId());
                                                // }
                                                HashMap studySubjectCRFDataDetails = sedao.getStudySubjectCRFData(study, studySubjectId, eventDefId, URLParamValue, eventRepeatKey);
                                                if ((null != studySubjectCRFDataDetails) && (studySubjectCRFDataDetails.size() != 0)) {
                                                    if (studySubjectCRFDataDetails.containsKey("event_crf_id")) {
                                                        openClinicaResource.setEventCrfId((Integer) studySubjectCRFDataDetails.get("event_crf_id"));
                                                    }
                                                    if (studySubjectCRFDataDetails.containsKey("event_definition_crf_id")) {
                                                        openClinicaResource.setEventDefinitionCrfId((Integer) studySubjectCRFDataDetails.get("event_definition_crf_id"));
                                                    }
                                                    if (studySubjectCRFDataDetails.containsKey("study_event_id")) {
                                                        openClinicaResource.setStudyEventId((Integer) studySubjectCRFDataDetails.get("study_event_id"));
                                                    }
                                                } else {
                                                    // no data was found in the database for the combination of parameters in the RESTful URL. There are 2 possible reasons:
                                                    // a. The data entry is not started yet for this event CRF. As of OpenClinica 3.1.3 we have not implemented the
                                                    // RESTful URL functionality in this case.
                                                    // b. The form version OID entered in the URL could be different than the one used in the data entry
                                                    openClinicaResource.setInValid(true);
                                                    openClinicaResource.getMessages().add(resexception.getString("either_no_data_for_crf_or_data_entry_not_started"));
                                                    return openClinicaResource;
                                                }
                                            }
                                        }
                                    }
                                    break;
                                }
                            case 4:
                                {
                                    // item group OID
                                    // separate item group OID and item group
                                    // repeat key
                                    String igoid = "";
                                    String igRepeatKey = "";
                                    if (URLParamValue.contains("[")) {
                                        igoid = URLParamValue.substring(1, URLParamValue.indexOf("["));
                                        igRepeatKey = URLParamValue.substring(URLParamValue.indexOf("["), URLParamValue.indexOf("}]"));
                                    }
                                    if ((null != igoid) && (null != cv)) {
                                        ig = igdao.findByOidAndCrf(URLParamValue, cv.getCrfId());
                                        if (null != ig) {
                                            openClinicaResource.setItemGroupID(ig.getId());
                                        }
                                    }
                                    if (null != igRepeatKey) {
                                        openClinicaResource.setItemGroupRepeatKey(Integer.parseInt(igRepeatKey));
                                    }
                                    break;
                                }
                            case 5:
                                {
                                    // item = idao.find
                                    break;
                                }
                        }
                    // switch end
                    }
                }
            }
        }
    }
    return openClinicaResource;
}

Example 94 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class RuleController method create.

@RequestMapping(value = "/studies/{study}/connect", method = RequestMethod.POST)
@ResponseBody
public org.openclinica.ns.response.v31.Response create(@RequestBody org.openclinica.ns.response.v31.Response responeType, Model model, HttpSession session, @PathVariable("study") String studyOid) throws Exception {
    ResourceBundleProvider.updateLocale(new Locale("en_US"));
    StudyDAO studyDao = new StudyDAO(dataSource);
    StudyBean currentStudy = studyDao.findByOid(studyOid);
    UserAccountBean userAccount = getUserAccount();
    mayProceed(userAccount, currentStudy);
    Response response = new Response();
    response.setValid(Boolean.TRUE);
    org.openclinica.ns.response.v31.MessagesType theMessageType = new MessagesType();
    theMessageType.setMessage("Hello");
    response.getMessages().add(theMessageType);
    logger.debug("RPIC READY");
    return response;
// model.addAttribute("response", response);
}

Example 95 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class RuleController method studyMetadata.

@RequestMapping(value = "/studies/{study}/metadata", method = RequestMethod.GET)
public ModelAndView studyMetadata(Model model, HttpSession session, @PathVariable("study") String studyOid, HttpServletResponse response) throws Exception {
    ResourceBundleProvider.updateLocale(new Locale("en_US"));
    StudyBean currentStudy = (StudyBean) session.getAttribute("study");
    UserAccountBean userAccount = (UserAccountBean) session.getAttribute("userBean");
    UserAccountDAO userAccountDao = new UserAccountDAO(dataSource);
    userAccount = (UserAccountBean) userAccountDao.findByUserName("root");
    StudyDAO studyDao = new StudyDAO(dataSource);
    currentStudy = studyDao.findByOid(studyOid);
    MetaDataCollector mdc = new MetaDataCollector(dataSource, currentStudy, getRuleSetRuleDao());
    AdminDataCollector adc = new AdminDataCollector(dataSource, currentStudy);
    // RulesDataCollector rdc = new RulesDataCollector(sm.getDataSource(), currentStudy,getRuleSetRuleDao());
    MetaDataCollector.setTextLength(200);
    ODMBean odmb = mdc.getODMBean();
    odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0-OC2-0.xsd");
    ArrayList<String> xmlnsList = new ArrayList<String>();
    xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.3\"");
    // xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/openclinica_odm/v1.3\"");
    xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/odm_ext_v130/v3.1\"");
    xmlnsList.add("xmlns:OpenClinicaRules=\"http://www.openclinica.org/ns/rules/v3.1\"");
    odmb.setXmlnsList(xmlnsList);
    odmb.setODMVersion("oc1.3");
    mdc.setODMBean(odmb);
    adc.setOdmbean(odmb);
    // rdc.setOdmbean(odmb);
    mdc.collectFileData();
    MetaDataReportBean metaReport = new MetaDataReportBean(mdc.getOdmStudyMap(), coreResources);
    metaReport.setODMVersion("oc1.3");
    metaReport.setOdmBean(mdc.getODMBean());
    metaReport.createChunkedOdmXml(Boolean.FALSE);
    adc.collectFileData();
    AdminDataReportBean adminReport = new AdminDataReportBean(adc.getOdmAdminDataMap());
    adminReport.setODMVersion("oc1.3");
    adminReport.setOdmBean(mdc.getODMBean());
    adminReport.createChunkedOdmXml(Boolean.FALSE);
    // rdc.collectFileData();
    // RulesDataReportBean rulesReport = new RulesDataReportBean(rdc.getOdmRulesDataMap(),getCoreResources());
    // rulesReport.setODMVersion("oc1.3");
    // rulesReport.setOdmBean(mdc.getODMBean());
    // rulesReport.createChunkedOdmXml(Boolean.FALSE);
    FullReportBean report = new FullReportBean();
    report.setAdminDataMap(adc.getOdmAdminDataMap());
    report.setOdmStudyMap(mdc.getOdmStudyMap());
    report.setCoreResources(coreResources);
    // report.setRulesDataMap(rdc.getOdmRulesDataMap());
    report.setOdmBean(mdc.getODMBean());
    report.setODMVersion("oc1.3");
    report.createStudyMetaOdmXml(Boolean.FALSE);
    response.setContentType("application/xml");
    PrintWriter out = response.getWriter();
    out.print(report.getXmlOutput().toString().trim());
    return null;
}