Examples with ItemDAO org.akaza.openclinica.dao.submit.ItemDAO used on opensource projects

Example 26 with ItemDAO

use of org.akaza.openclinica.dao.submit.ItemDAO in project OpenClinica by OpenClinica.

the class DataImportService method submitData.

public ArrayList<String> submitData(ODMContainer odmContainer, DataSource dataSource, StudyBean studyBean, UserAccountBean userBean, List<DisplayItemBeanWrapper> displayItemBeanWrappers, Map<Integer, String> importedCRFStatuses) throws Exception {
    boolean discNotesGenerated = false;
    ItemDataDAO itemDataDao = new ItemDataDAO(dataSource);
    itemDataDao.setFormatDates(false);
    EventCRFDAO eventCrfDao = new EventCRFDAO(dataSource);
    StringBuffer auditMsg = new StringBuffer();
    int eventCrfBeanId = -1;
    EventCRFBean eventCrfBean = null;
    ArrayList<Integer> eventCrfInts;
    ItemDataBean itemDataBean;
    CrfBusinessLogicHelper crfBusinessLogicHelper = new CrfBusinessLogicHelper(dataSource);
    for (DisplayItemBeanWrapper wrapper : displayItemBeanWrappers) {
        boolean resetSDV = false;
        logger.debug("right before we check to make sure it is savable: " + wrapper.isSavable());
        if (wrapper.isSavable()) {
            eventCrfInts = new ArrayList<Integer>();
            logger.debug("wrapper problems found : " + wrapper.getValidationErrors().toString());
            if (wrapper.getDisplayItemBeans() != null && wrapper.getDisplayItemBeans().size() == 0) {
                return getReturnList("fail", "", "No items to submit. Please check your XML.");
            }
            for (DisplayItemBean displayItemBean : wrapper.getDisplayItemBeans()) {
                eventCrfBeanId = displayItemBean.getData().getEventCRFId();
                eventCrfBean = (EventCRFBean) eventCrfDao.findByPK(eventCrfBeanId);
                logger.debug("found value here: " + displayItemBean.getData().getValue());
                logger.debug("found status here: " + eventCrfBean.getStatus().getName());
                itemDataBean = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
                if (wrapper.isOverwrite() && itemDataBean.getStatus() != null) {
                    if (!itemDataBean.getValue().equals(displayItemBean.getData().getValue()))
                        resetSDV = true;
                    logger.debug("just tried to find item data bean on item name " + displayItemBean.getItem().getName());
                    itemDataBean.setUpdatedDate(new Date());
                    itemDataBean.setUpdater(userBean);
                    itemDataBean.setValue(displayItemBean.getData().getValue());
                    // set status?
                    itemDataDao.update(itemDataBean);
                    logger.debug("updated: " + itemDataBean.getItemId());
                    // need to set pk here in order to create dn
                    displayItemBean.getData().setId(itemDataBean.getId());
                } else {
                    resetSDV = true;
                    itemDataDao.create(displayItemBean.getData());
                    logger.debug("created: " + displayItemBean.getData().getItemId());
                    itemDataBean = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
                    // logger.debug("found: id " + itemDataBean2.getId() + " name " + itemDataBean2.getName());
                    displayItemBean.getData().setId(itemDataBean.getId());
                }
                ItemDAO idao = new ItemDAO(dataSource);
                ItemBean ibean = (ItemBean) idao.findByPK(displayItemBean.getData().getItemId());
                // logger.debug("*** checking for validation errors: " + ibean.getName());
                String itemOid = displayItemBean.getItem().getOid() + "_" + wrapper.getStudyEventRepeatKey() + "_" + displayItemBean.getData().getOrdinal() + "_" + wrapper.getStudySubjectOid();
                // wrapper.getValidationErrors().toString());
                if (wrapper.getValidationErrors().containsKey(itemOid)) {
                    ArrayList<String> messageList = (ArrayList<String>) wrapper.getValidationErrors().get(itemOid);
                    for (String message : messageList) {
                        DiscrepancyNoteBean parentDn = createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, null, userBean, dataSource, studyBean);
                        createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, parentDn.getId(), userBean, dataSource, studyBean);
                        discNotesGenerated = true;
                        logger.debug("*** created disc note with message: " + message);
                        auditMsg.append(wrapper.getStudySubjectOid() + ": " + ibean.getOid() + ": " + message + "---");
                    // split by this ? later, tbh
                    // displayItemBean);
                    }
                }
                if (!eventCrfInts.contains(new Integer(eventCrfBean.getId()))) {
                    String eventCRFStatus = importedCRFStatuses.get(new Integer(eventCrfBean.getId()));
                    if (eventCRFStatus != null && eventCRFStatus.equals(DataEntryStage.INITIAL_DATA_ENTRY.getName()) && eventCrfBean.getStatus().isAvailable()) {
                        crfBusinessLogicHelper.markCRFStarted(eventCrfBean, userBean, true);
                    } else {
                        crfBusinessLogicHelper.markCRFComplete(eventCrfBean, userBean, true);
                    }
                    eventCrfInts.add(new Integer(eventCrfBean.getId()));
                }
            }
            // Reset the SDV status if item data has been changed or added
            if (eventCrfBean != null && resetSDV)
                eventCrfDao.setSDVStatus(false, userBean.getId(), eventCrfBean.getId());
        }
    }
    if (!discNotesGenerated) {
        return getReturnList("success", "", auditMsg.toString());
    } else {
        return getReturnList("warn", "", auditMsg.toString());
    }
}

Example 27 with ItemDAO

use of org.akaza.openclinica.dao.submit.ItemDAO in project OpenClinica by OpenClinica.

the class GenerateExtractFileService method createSPSSFile.

/**
     * createSPSSFile, added by tbh, 01/2009
     *
     * @param db
     * @param eb
     * @param currentstudyid
     * @param parentstudy
     * @return
     */
public HashMap<String, Integer> createSPSSFile(DatasetBean db, ExtractBean eb2, StudyBean currentStudy, StudyBean parentStudy, long sysTimeBegin, String generalFileDir, SPSSReportBean answer, String generalFileDirCopy, UserAccountBean userBean) {
    setUpResourceBundles();
    String SPSSFileName = db.getName() + "_data_spss.dat";
    String DDLFileName = db.getName() + "_ddl_spss.sps";
    String ZIPFileName = db.getName() + "_spss";
    SPSSVariableNameValidator svnv = new SPSSVariableNameValidator();
    answer.setDatFileName(SPSSFileName);
    // DatasetDAO dsdao = new DatasetDAO(ds);
    // create the extract bean here, tbh
    // ExtractBean eb = this.generateExtractBean(db, currentStudy,
    // parentStudy);
    // eb = dsdao.getDatasetData(eb, currentStudy.getId(),
    // parentStudy.getId());
    // eb.getMetadata();
    // eb.computeReport(answer);
    // set up items here to get
    answer.setItems(eb2.getItemNames());
    // itemMetadata
    // set up response sets for each item here
    ItemDAO itemdao = new ItemDAO(ds);
    ItemFormMetadataDAO imfdao = new ItemFormMetadataDAO(ds);
    ArrayList items = answer.getItems();
    for (int i = 0; i < items.size(); i++) {
        DisplayItemHeaderBean dih = (DisplayItemHeaderBean) items.get(i);
        ItemBean item = dih.getItem();
        ArrayList metas = imfdao.findAllByItemId(item.getId());
        // for (int h = 0; h < metas.size(); h++) {
        // ItemFormMetadataBean ifmb = (ItemFormMetadataBean)
        // metas.get(h);
        // logger.info("group name found:
        // "+ifmb.getGroupLabel());
        // }
        // logger.info("crf versionname" +
        // meta.getCrfVersionName());
        item.setItemMetas(metas);
    }
    HashMap eventDescs = new HashMap<String, String>();
    eventDescs = eb2.getEventDescriptions();
    eventDescs.put("SubjID", resword.getString("study_subject_ID"));
    eventDescs.put("ProtocolID", resword.getString("protocol_ID_site_ID"));
    eventDescs.put("DOB", resword.getString("date_of_birth"));
    eventDescs.put("YOB", resword.getString("year_of_birth"));
    eventDescs.put("Gender", resword.getString("gender"));
    answer.setDescriptions(eventDescs);
    ArrayList generatedReports = new ArrayList<String>();
    try {
        // YW <<
        generatedReports.add(answer.getMetadataFile(svnv, eb2).toString());
        generatedReports.add(answer.getDataFile().toString());
    // YW >>
    } catch (IndexOutOfBoundsException i) {
        generatedReports.add(answer.getMetadataFile(svnv, eb2).toString());
        logger.debug("throw the error here");
    }
    long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
    ArrayList titles = new ArrayList();
    // YW <<
    titles.add(DDLFileName);
    titles.add(SPSSFileName);
    // YW >>
    // create new createFile method that accepts array lists to
    // put into zip files
    int fId = this.createFile(ZIPFileName, titles, generalFileDir, generatedReports, db, sysTimeEnd, ExportFormatBean.TXTFILE, true, userBean);
    if (!"".equals(generalFileDirCopy)) {
        int fId2 = this.createFile(ZIPFileName, titles, generalFileDirCopy, generatedReports, db, sysTimeEnd, ExportFormatBean.TXTFILE, false, userBean);
    }
    // return DDLFileName;
    HashMap answerMap = new HashMap<String, Integer>();
    answerMap.put(DDLFileName, new Integer(fId));
    return answerMap;
}

Example 28 with ItemDAO

use of org.akaza.openclinica.dao.submit.ItemDAO in project OpenClinica by OpenClinica.

the class DatasetDAO method initialDatasetData.

/**
     * Initialize itemMap, itemIds, itemDefCrf and groupIds for a DatasetBean
     *
     * @param db
     * @return
     * @author ywang (Feb., 2008)
     */
public DatasetBean initialDatasetData(int datasetId) {
    ItemDAO idao = new ItemDAO(ds);
    DatasetBean db = (DatasetBean) findByPK(datasetId);
    String sql = db.getSQLStatement();
    sql = sql.split("study_event_definition_id in")[1];
    String[] ss = sql.split("and item_id in");
    String sedIds = ss[0];
    String[] sss = ss[1].split("and");
    String itemIds = sss[0];
    this.setDefinitionCrfItemTypesExpected();
    logger.debug("begin to execute GetDefinitionCrfItemSql");
    ArrayList alist = select(getDefinitionCrfItemSql(sedIds, itemIds));
    Iterator it = alist.iterator();
    while (it.hasNext()) {
        HashMap row = (HashMap) it.next();
        ItemBean ib = (ItemBean) idao.getEntityFromHashMap(row);
        Integer defId = (Integer) row.get("sed_id");
        String defName = (String) row.get("sed_name");
        String crfName = (String) row.get("crf_name");
        Integer itemId = ib.getId();
        String key = defId + "_" + itemId;
        if (!db.getItemMap().containsKey(key)) {
            ib.setSelected(true);
            ib.setDefName(defName);
            ib.setCrfName(crfName);
            ib.setDatasetItemMapKey(key);
            // contains study_event_definition_ids
            if (!db.getEventIds().contains(defId)) {
                db.getEventIds().add(defId);
            }
            db.getItemIds().add(itemId);
            db.getItemDefCrf().add(ib);
            db.getItemMap().put(key, ib);
        }
    }
    db.setSubjectGroupIds(getGroupIds(db.getId()));
    return db;
}

Example 29 with ItemDAO

use of org.akaza.openclinica.dao.submit.ItemDAO in project OpenClinica by OpenClinica.

the class CreateCRFVersionServlet method isItemSame.

/**
     * Checks whether the item with same name has the same other fields: units, phi_status if no, they are two different
     * items, cannot have the same same
     * 
     * @param items
     *            items from excel
     * @return the items found
     */
private ArrayList isItemSame(HashMap items, CRFVersionBean version) {
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    ArrayList diffItems = new ArrayList();
    Set names = items.keySet();
    Iterator it = names.iterator();
    while (it.hasNext()) {
        String name = (String) it.next();
        ItemBean newItem = (ItemBean) idao.findByNameAndCRFId(name, version.getCrfId());
        ItemBean item = (ItemBean) items.get(name);
        if (newItem.getId() > 0) {
            if (!item.getUnits().equalsIgnoreCase(newItem.getUnits()) || item.isPhiStatus() != newItem.isPhiStatus() || item.getDataType().getId() != newItem.getDataType().getId() || !item.getDescription().equalsIgnoreCase(newItem.getDescription())) {
                logger.debug("found two items with same name but different units/phi/datatype/description");
                diffItems.add(newItem);
            }
        }
    }
    return diffItems;
}

Example 30 with ItemDAO

use of org.akaza.openclinica.dao.submit.ItemDAO in project OpenClinica by OpenClinica.

the class ViewNoteServlet method processRequest.

@Override
protected void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    Locale locale = LocaleResolver.getLocale(request);
    DateFormat dateFormatter = DateFormat.getDateInstance(DateFormat.DEFAULT, locale);
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
    dndao.setFetchMapping(true);
    int noteId = fp.getInt(NOTE_ID, true);
    DiscrepancyNoteBean note = (DiscrepancyNoteBean) dndao.findByPK(noteId);
    String entityType = note.getEntityType();
    if (note.getEntityId() > 0 && !entityType.equals("")) {
        if (!StringUtil.isBlank(entityType)) {
            if ("itemData".equalsIgnoreCase(entityType)) {
                ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
                ItemDataBean itemData = (ItemDataBean) iddao.findByPK(note.getEntityId());
                ItemDAO idao = new ItemDAO(sm.getDataSource());
                ItemBean item = (ItemBean) idao.findByPK(itemData.getItemId());
                note.setEntityValue(itemData.getValue());
                note.setEntityName(item.getName());
                //Mantis Issue 5165. It should be itemData.getId() instead of item.getId()
                note.setEntityId(itemData.getId());
                EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
                EventCRFBean ec = (EventCRFBean) ecdao.findByPK(itemData.getEventCRFId());
                StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
                StudyEventBean se = (StudyEventBean) sed.findByPK(ec.getStudyEventId());
                StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
                StudySubjectBean ssub = (StudySubjectBean) ssdao.findByPK(se.getStudySubjectId());
                note.setStudySub(ssub);
                StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
                StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
                se.setName(sedb.getName());
                note.setEvent(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());
                note.setCrfName(crf.getName());
            } else if ("studySub".equalsIgnoreCase(entityType)) {
                StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
                StudySubjectBean ssub = (StudySubjectBean) ssdao.findByPK(note.getEntityId());
                note.setStudySub(ssub);
                // System.out.println("column" + note.getColumn());
                SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
                SubjectBean sub = (SubjectBean) sdao.findByPK(ssub.getSubjectId());
                if (!StringUtil.isBlank(note.getColumn())) {
                    if ("enrollment_date".equalsIgnoreCase(note.getColumn())) {
                        if (ssub.getEnrollmentDate() != null) {
                            note.setEntityValue(dateFormatter.format(ssub.getEnrollmentDate()));
                        }
                        note.setEntityName(resword.getString("enrollment_date"));
                    } else if ("gender".equalsIgnoreCase(note.getColumn())) {
                        note.setEntityValue(sub.getGender() + "");
                        note.setEntityName(resword.getString("gender"));
                    } else if ("date_of_birth".equalsIgnoreCase(note.getColumn())) {
                        if (sub.getDateOfBirth() != null) {
                            note.setEntityValue(dateFormatter.format(sub.getDateOfBirth()));
                        }
                        note.setEntityName(resword.getString("date_of_birth"));
                    }
                }
            } else if ("subject".equalsIgnoreCase(entityType)) {
                SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
                SubjectBean sub = (SubjectBean) sdao.findByPK(note.getEntityId());
                StudySubjectBean ssub = new StudySubjectBean();
                ssub.setLabel(sub.getUniqueIdentifier());
                note.setStudySub(ssub);
                if (!StringUtil.isBlank(note.getColumn())) {
                    if ("gender".equalsIgnoreCase(note.getColumn())) {
                        note.setEntityValue(sub.getGender() + "");
                        note.setEntityName(resword.getString("gender"));
                    } else if ("date_of_birth".equalsIgnoreCase(note.getColumn())) {
                        if (sub.getDateOfBirth() != null) {
                            note.setEntityValue(dateFormatter.format(sub.getDateOfBirth()));
                        }
                        note.setEntityName(resword.getString("date_of_birth"));
                    } else if ("unique_identifier".equalsIgnoreCase(note.getColumn())) {
                        note.setEntityName(resword.getString("unique_identifier"));
                        note.setEntityValue(sub.getUniqueIdentifier());
                    }
                }
            } else if ("studyEvent".equalsIgnoreCase(entityType)) {
                StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
                StudyEventBean se = (StudyEventBean) sed.findByPK(note.getEntityId());
                StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
                StudySubjectBean ssub = (StudySubjectBean) ssdao.findByPK(se.getStudySubjectId());
                note.setStudySub(ssub);
                StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
                StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
                se.setName(sedb.getName());
                note.setEvent(se);
                if (!StringUtil.isBlank(note.getColumn())) {
                    if ("location".equalsIgnoreCase(note.getColumn())) {
                        request.setAttribute("entityValue", se.getLocation());
                        request.setAttribute("entityName", resword.getString("location"));
                        note.setEntityName(resword.getString("location"));
                        note.setEntityValue(se.getLocation());
                    } else if ("date_start".equalsIgnoreCase(note.getColumn())) {
                        if (se.getDateStarted() != null) {
                            note.setEntityValue(dateFormatter.format(se.getDateStarted()));
                        }
                        note.setEntityName(resword.getString("start_date"));
                    } else if ("date_end".equalsIgnoreCase(note.getColumn())) {
                        if (se.getDateEnded() != null) {
                            note.setEntityValue(dateFormatter.format(se.getDateEnded()));
                        }
                        note.setEntityName(resword.getString("end_date"));
                    }
                }
            } else if ("eventCrf".equalsIgnoreCase(entityType)) {
                EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
                EventCRFBean ec = (EventCRFBean) ecdao.findByPK(note.getEntityId());
                StudySubjectBean ssub = (StudySubjectBean) new StudySubjectDAO(sm.getDataSource()).findByPK(ec.getStudySubjectId());
                note.setStudySub(ssub);
                StudyEventBean event = (StudyEventBean) new StudyEventDAO(sm.getDataSource()).findByPK(ec.getStudyEventId());
                note.setEvent(event);
                if (!StringUtil.isBlank(note.getColumn())) {
                    if ("date_interviewed".equals(note.getColumn())) {
                        if (ec.getDateInterviewed() != null) {
                            note.setEntityValue(dateFormatter.format(ec.getDateInterviewed()));
                        }
                        note.setEntityName(resword.getString("date_interviewed"));
                    } else if ("interviewer_name".equals(note.getColumn())) {
                        note.setEntityValue(ec.getInterviewerName());
                        note.setEntityName(resword.getString("interviewer_name"));
                    }
                }
            }
        }
    }
    // Mantis Issue 8495.
    if (note.getStudyId() != currentStudy.getId()) {
        if (currentStudy.getParentStudyId() > 0) {
            if (currentStudy.getId() != note.getStudySub().getStudyId()) {
                addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                forwardPage(Page.MENU_SERVLET);
                return;
            }
        } else {
            // The SubjectStudy is not belong to currentstudy and current study is not a site.
            StudyDAO studydao = new StudyDAO(sm.getDataSource());
            Collection sites;
            sites = studydao.findOlnySiteIdsByStudy(currentStudy);
            if (!sites.contains(note.getStudySub().getStudyId())) {
                addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                forwardPage(Page.MENU_SERVLET);
                return;
            }
        }
    }
    // Check end
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    ArrayList<DiscrepancyNoteBean> notes = dndao.findAllEntityByPK(note.getEntityType(), noteId);
    Date lastUpdatedDate = note.getCreatedDate();
    UserAccountBean lastUpdator = (UserAccountBean) udao.findByPK(note.getOwnerId());
    /*
         * for (int i = 0; i < notes.size(); i++) { DiscrepancyNoteBean n =
         * (DiscrepancyNoteBean) notes.get(i); int pId = n.getParentDnId(); if
         * (pId == 0) { note = n; note.setLastUpdator((UserAccountBean)
         * udao.findByPK(n.getOwnerId()));
         * note.setLastDateUpdated(n.getCreatedDate()); lastUpdatedDate =
         * note.getLastDateUpdated(); lastUpdator = note.getLastUpdator(); } }
         */
    // BWP 3029 >> This algorithm needs to be changed to properly set
    // the parent note's status and updated date
    // First sort the notes on their ID; this will put the parent note
    // first; and
    // the note with the latest status and updated date last
    java.util.Collections.sort(notes);
    DiscrepancyNoteBean lastChild = notes.get(notes.size() - 1);
    lastUpdatedDate = lastChild.getCreatedDate();
    lastUpdator = (UserAccountBean) udao.findByPK(lastChild.getOwnerId());
    note.setLastUpdator(lastUpdator);
    note.setLastDateUpdated(lastUpdatedDate);
    note.setUpdatedDate(lastUpdatedDate);
    for (DiscrepancyNoteBean dnBean : notes) {
        if (dnBean.getParentDnId() > 0) {
            note.getChildren().add(dnBean);
        }
    }
    /*
         * for (int i = 0; i < notes.size(); i++) { DiscrepancyNoteBean n =
         * (DiscrepancyNoteBean) notes.get(i); int pId = n.getParentDnId(); if
         * (pId > 0) { note.getChildren().add(n);
         *
         * if (!n.getCreatedDate().before(lastUpdatedDate)) { lastUpdatedDate =
         * n.getCreatedDate(); lastUpdator = (UserAccountBean)
         * udao.findByPK(n.getOwnerId()); note.setLastUpdator(lastUpdator);
         * note.setLastDateUpdated(lastUpdatedDate);
         * note.setResolutionStatusId(n.getResolutionStatusId());
         * note.setResStatus(ResolutionStatus.get(n.getResolutionStatusId())); } } }
         */
    note.setNumChildren(note.getChildren().size());
    note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
    request.setAttribute(DIS_NOTE, note);
    forwardPage(Page.VIEW_SINGLE_NOTE);
}