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

Example 31 with DiscrepancyNoteDAO

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

the class DataImportService method createDiscrepancyNote.

public DiscrepancyNoteBean createDiscrepancyNote(ItemBean itemBean, String message, EventCRFBean eventCrfBean, DisplayItemBean displayItemBean, Integer parentId, UserAccountBean uab, DataSource ds, StudyBean study) {
    DiscrepancyNoteBean note = new DiscrepancyNoteBean();
    StudySubjectDAO ssdao = new StudySubjectDAO(ds);
    note.setDescription(message);
    note.setDetailedNotes("Failed Validation Check");
    note.setOwner(uab);
    note.setCreatedDate(new Date());
    note.setResolutionStatusId(ResolutionStatus.OPEN.getId());
    note.setDiscrepancyNoteTypeId(DiscrepancyNoteType.FAILEDVAL.getId());
    if (parentId != null) {
        note.setParentDnId(parentId);
    }
    note.setField(itemBean.getName());
    note.setStudyId(study.getId());
    note.setEntityName(itemBean.getName());
    note.setEntityType("ItemData");
    note.setEntityValue(displayItemBean.getData().getValue());
    note.setEventName(eventCrfBean.getName());
    note.setEventStart(eventCrfBean.getCreatedDate());
    note.setCrfName(displayItemBean.getEventDefinitionCRF().getCrfName());
    StudySubjectBean ss = (StudySubjectBean) ssdao.findByPK(eventCrfBean.getStudySubjectId());
    note.setSubjectName(ss.getName());
    note.setEntityId(displayItemBean.getData().getId());
    note.setColumn("value");
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(ds);
    note = (DiscrepancyNoteBean) dndao.create(note);
    // so that the below method works, need to set the entity above
    logger.debug("trying to create mapping with " + note.getId() + " " + note.getEntityId() + " " + note.getColumn() + " " + note.getEntityType());
    dndao.createMapping(note);
    logger.debug("just created mapping");
    return note;
}

Example 32 with DiscrepancyNoteDAO

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

the class ResolveDiscrepancyServlet method processRequest.

/*
     * (non-Javadoc)
     *
     * @see org.akaza.openclinica.control.core.SecureController#processRequest()
     */
@Override
protected void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int noteId = fp.getInt(INPUT_NOTE_ID);
    String module = (String) session.getAttribute("module");
    StudySubjectDAO studySubjectDAO = new StudySubjectDAO(sm.getDataSource());
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
    dndao.setFetchMapping(true);
    // check that the note exists
    DiscrepancyNoteBean discrepancyNoteBean = (DiscrepancyNoteBean) dndao.findByPK(noteId);
    if (!discrepancyNoteBean.isActive()) {
        throw new InconsistentStateException(Page.MANAGE_STUDY_SERVLET, resexception.getString("you_are_trying_resolve_discrepancy_not_exist"));
    }
    // check that the note has not already been closed
    ArrayList children = dndao.findAllByParent(discrepancyNoteBean);
    discrepancyNoteBean.setChildren(children);
    // This logic has been reverted, issue-7459
    // if (parentNoteIsClosed(discrepancyNoteBean)) {
    // throw new InconsistentStateException(Page.VIEW_DISCREPANCY_NOTES_IN_STUDY_SERVLET, respage
    // .getString("the_discrepancy_choose_has_been_closed_resolved_create_new"));
    // }
    // all clear, send the user to the resolved screen
    String entityType = discrepancyNoteBean.getEntityType().toLowerCase();
    discrepancyNoteBean.setResStatus(ResolutionStatus.get(discrepancyNoteBean.getResolutionStatusId()));
    discrepancyNoteBean.setDisType(DiscrepancyNoteType.get(discrepancyNoteBean.getDiscrepancyNoteTypeId()));
    // View Study Events <<
    if (currentRole.getRole().equals(Role.MONITOR) && !"itemdata".equalsIgnoreCase(entityType) && !"eventcrf".equalsIgnoreCase(entityType)) {
        redirectMonitor(module, discrepancyNoteBean);
        return;
    }
    // If Study is Frozen or Locked
    if (currentStudy.getStatus().isFrozen() && !"itemdata".equalsIgnoreCase(entityType) && !"eventcrf".equalsIgnoreCase(entityType)) {
        redirectMonitor(module, discrepancyNoteBean);
        return;
    }
    boolean toView = false;
    boolean isCompleted = false;
    if ("itemdata".equalsIgnoreCase(entityType)) {
        ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
        ItemDataBean idb = (ItemDataBean) iddao.findByPK(discrepancyNoteBean.getEntityId());
        EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
        EventCRFBean ecb = (EventCRFBean) ecdao.findByPK(idb.getEventCRFId());
        StudySubjectBean studySubjectBean = (StudySubjectBean) studySubjectDAO.findByPK(ecb.getStudySubjectId());
        discrepancyNoteBean.setSubjectId(studySubjectBean.getId());
        discrepancyNoteBean.setItemId(idb.getItemId());
        if (ecb.getStatus().equals(Status.UNAVAILABLE)) {
            isCompleted = true;
        }
        // we want to go to view note page if the note is
        toView = true;
    // for item data
    }
    // logger.info("set up pop up url: " + createNoteURL);
    // System.out.println("set up pop up url: " + createNoteURL);
    boolean goNext = prepareRequestForResolution(request, sm.getDataSource(), currentStudy, discrepancyNoteBean, isCompleted);
    Page p = getPageForForwarding(discrepancyNoteBean, isCompleted);
    // logger.info("found page for forwarding: " + p.getFileName());
    if (p == null) {
        throw new InconsistentStateException(Page.VIEW_DISCREPANCY_NOTES_IN_STUDY_SERVLET, resexception.getString("the_discrepancy_note_triying_resolve_has_invalid_type"));
    } else {
        if (p.getFileName().contains("?")) {
            if (!p.getFileName().contains("fromViewNotes=1")) {
                p.setFileName(p.getFileName() + "&fromViewNotes=1");
            }
        } else {
            p.setFileName(p.getFileName() + "?fromViewNotes=1");
        }
        String createNoteURL = CreateDiscrepancyNoteServlet.getAddChildURL(discrepancyNoteBean, ResolutionStatus.CLOSED, true);
        setPopUpURL(createNoteURL);
    }
    if (!goNext) {
        setPopUpURL("");
        addPageMessage(respage.getString("you_may_not_perform_admin_edit_on_CRF_not_completed_by_user"));
        p = Page.VIEW_DISCREPANCY_NOTES_IN_STUDY_SERVLET;
    }
    forwardPage(p);
}

Example 33 with DiscrepancyNoteDAO

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

the class DataEntryServlet method setTotals.

/**
     * To set the totals of each resolution status on the DisplayItemBean for each item.
     * @param dib
         * @param notes
         * @param ecbId TODO
     */
private DisplayItemBean setTotals(DisplayItemBean dib, int itemDataId, ArrayList<DiscrepancyNoteBean> notes, int ecbId) {
    long t = System.currentTimeMillis();
    logMe("Method::::::setTotals" + t);
    int resolutionStatus;
    int totNew = 0, totRes = 0, totClosed = 0, totUpdated = 0, totNA = 0;
    boolean hasOtherThread = false;
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource());
    ArrayList<DiscrepancyNoteBean> existingNotes = dndao.findExistingNotesForToolTip(itemDataId);
    dib.setDiscrepancyNotes(existingNotes);
    for (DiscrepancyNoteBean obj : dib.getDiscrepancyNotes()) {
        DiscrepancyNoteBean note = obj;
        if (note.getParentDnId() == 0) {
            resolutionStatus = note.getResolutionStatusId();
            //using totNew to show the total parent threads
            totNew++;
        /* if(resolutionStatus==ResolutionStatus.UPDATED.getId())totUpdated++;
                 else if(resolutionStatus==ResolutionStatus.RESOLVED.getId())totRes++;//Resolution proposed count
                 else if(resolutionStatus==ResolutionStatus.CLOSED.getId())totClosed++;
                 else if(resolutionStatus==ResolutionStatus.NOT_APPLICABLE.getId())totNA++;*/
        // not needed any more
        }
    }
    ArrayList parentNotes = dndao.findExistingNotesForItemData(itemDataId);
    //Adding this to show the value of only parent threads on discrepancy notes tool tip
    for (Object obj : parentNotes) {
        DiscrepancyNoteBean note = (DiscrepancyNoteBean) obj;
        if (note.getParentDnId() == 0) {
            if (hasOtherThread) {
                totNew++;
            }
            hasOtherThread = true;
        }
    }
    logMe("time taken thus far, before audit log check" + (System.currentTimeMillis() - t));
    long t1 = System.currentTimeMillis();
    AuditDAO adao = new AuditDAO(getDataSource());
    ArrayList itemAuditEvents = adao.checkItemAuditEventsExist(dib.getItem().getId(), "item_data", ecbId);
    if (itemAuditEvents.size() > 0) {
        AuditBean itemFirstAudit = (AuditBean) itemAuditEvents.get(0);
        String firstRFC = itemFirstAudit.getReasonForChange();
        String oldValue = itemFirstAudit.getOldValue();
        if (firstRFC != null && "initial value".equalsIgnoreCase(firstRFC) && (oldValue == null || oldValue.isEmpty())) {
            dib.getData().setAuditLog(false);
        } else {
            dib.getData().setAuditLog(true);
        }
    }
    logMe("time taken thus far, after audit log check" + (System.currentTimeMillis() - t));
    logMe("Only for audit check::" + (System.currentTimeMillis() - t1));
    //totNew is used for parent thread count
    dib.setTotNew(totNew);
    dib.setTotRes(totRes);
    dib.setTotUpdated(totUpdated);
    dib.setTotClosed(totClosed);
    dib.setTotNA(totNA);
    logMe("returning back..time taken" + (System.currentTimeMillis() - t));
    return dib;
}

Example 34 with DiscrepancyNoteDAO

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

the class DataEntryServlet method isEachRequiredFieldFillout.

protected boolean isEachRequiredFieldFillout(HttpServletRequest request) {
    HttpSession session = request.getSession();
    EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource());
    // need to update this method to accomodate dynamics, tbh
    ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale);
    ItemDAO idao = new ItemDAO(getDataSource());
    ItemFormMetadataDAO itemFormMetadataDao = new ItemFormMetadataDAO(getDataSource());
    // Below code will iterate all shown and hidden required fields/items in a crf version and verify if the data field is filled up with value or if not , then it is a hidden field with no show rule triggered for the item.        
    ArrayList<ItemFormMetadataBean> shownRequiredAllItemsInCrfVersion = itemFormMetadataDao.findAllItemsRequiredAndShownByCrfVersionId(ecb.getCRFVersionId());
    ArrayList<ItemFormMetadataBean> hiddenRequiredAllItemsInCrfVersion = itemFormMetadataDao.findAllItemsRequiredAndHiddenByCrfVersionId(ecb.getCRFVersionId());
    ItemGroupMetadataDAO<String, ArrayList> igdao = new ItemGroupMetadataDAO<String, ArrayList>(dataSource);
    ArrayList<ItemDataBean> itemdatas = null;
    for (ItemFormMetadataBean shownItemMeta : shownRequiredAllItemsInCrfVersion) {
        ItemGroupMetadataBean igBean = (ItemGroupMetadataBean) igdao.findByItemAndCrfVersion(shownItemMeta.getItemId(), ecb.getCRFVersionId());
        // verifies if the group that the item belongs to is not hidden.
        if (igBean != null && igBean.isShowGroup()) {
            itemdatas = iddao.findAllByEventCRFIdAndItemId(ecb.getId(), shownItemMeta.getItemId());
            if (itemdatas == null || itemdatas.size() == 0)
                return false;
            for (ItemDataBean itemdata : itemdatas) {
                System.out.println(itemdata.getItemId() + "  :  " + itemdata.getValue());
                if ((itemdata.getValue() == null || itemdata.getValue().equals("") || itemdata.getValue().trim().length() == 0) && dndao.findNumExistingNotesForItem(itemdata.getId()) < 1) {
                    return false;
                }
            }
        }
        ArrayList<DynamicsItemFormMetadataBean> dynamicsItemFormMetadataBeans = null;
        for (ItemFormMetadataBean hiddenItemMeta : hiddenRequiredAllItemsInCrfVersion) {
            itemdatas = iddao.findAllByEventCRFIdAndItemId(ecb.getId(), hiddenItemMeta.getItemId());
            dynamicsItemFormMetadataBeans = getItemMetadataService().getDynamicsItemFormMetadataDao().findByItemAndEventCrfShown(ecb, hiddenItemMeta.getItemId());
            if (itemdatas.size() == 0 && dynamicsItemFormMetadataBeans.size() > 0) {
                return false;
            }
            for (ItemDataBean itemdata : itemdatas) {
                if ((itemdata.getValue() == null || itemdata.getValue().equals("") || itemdata.getValue().trim().length() == 0) && dndao.findNumExistingNotesForItem(itemdata.getId()) < 1 && dynamicsItemFormMetadataBeans.size() > 0) {
                    return false;
                }
            }
        }
    }
    // had to change the query below to allow for hidden items here, tbh 04/2010
    ArrayList allFilled = iddao.findAllBlankRequiredByEventCRFId(ecb.getId(), ecb.getCRFVersionId());
    int numNotes = 0;
    if (!allFilled.isEmpty()) {
        LOGGER.trace("allFilled is not empty");
        FormDiscrepancyNotes fdn = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
        HashMap idNotes = fdn.getIdNotes();
        for (int i = 0; i < allFilled.size(); i++) {
            ItemDataBean idb = (ItemDataBean) allFilled.get(i);
            int exsitingNotes = dndao.findNumExistingNotesForItem(idb.getId());
            if (exsitingNotes > 0) {
                LOGGER.trace("has existing note");
                numNotes++;
            } else if (idNotes.containsKey(idb.getId())) {
                LOGGER.trace("has note in session");
                numNotes++;
            }
        }
        LOGGER.trace("numNotes allFilled.size:" + numNotes + " " + allFilled.size());
        if (numNotes >= allFilled.size()) {
            LOGGER.trace("all required are filled out");
            return true;
        } else {
            LOGGER.debug("numNotes < allFilled.size() " + numNotes + ": " + allFilled.size());
            return false;
        }
    }
    return true;
}

Example 35 with DiscrepancyNoteDAO

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

the class ImportSpringJob method createDiscrepancyNote.

public static DiscrepancyNoteBean createDiscrepancyNote(ItemBean itemBean, String message, EventCRFBean eventCrfBean, DisplayItemBean displayItemBean, Integer parentId, UserAccountBean uab, DataSource ds, StudyBean study) {
    // DisplayItemBean displayItemBean) {
    DiscrepancyNoteBean note = new DiscrepancyNoteBean();
    StudySubjectDAO ssdao = new StudySubjectDAO(ds);
    note.setDescription(message);
    note.setDetailedNotes("Failed Validation Check");
    note.setOwner(uab);
    note.setCreatedDate(new Date());
    note.setResolutionStatusId(ResolutionStatus.OPEN.getId());
    note.setDiscrepancyNoteTypeId(DiscrepancyNoteType.FAILEDVAL.getId());
    if (parentId != null) {
        note.setParentDnId(parentId);
    }
    note.setField(itemBean.getName());
    note.setStudyId(study.getId());
    note.setEntityName(itemBean.getName());
    note.setEntityType(DiscrepancyNoteBean.ITEM_DATA);
    note.setEntityValue(displayItemBean.getData().getValue());
    note.setEventName(eventCrfBean.getName());
    note.setEventStart(eventCrfBean.getCreatedDate());
    note.setCrfName(displayItemBean.getEventDefinitionCRF().getCrfName());
    StudySubjectBean ss = (StudySubjectBean) ssdao.findByPK(eventCrfBean.getStudySubjectId());
    note.setSubjectName(ss.getName());
    note.setEntityId(displayItemBean.getData().getId());
    note.setColumn("value");
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(ds);
    note = (DiscrepancyNoteBean) dndao.create(note);
    // so that the below method works, need to set the entity above
    // System.out.println("trying to create mapping with " + note.getId() +
    // " " + note.getEntityId() + " " + note.getColumn() + " " +
    // note.getEntityType());
    dndao.createMapping(note);
    return note;
}