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

Example 11 with ItemFormMetadataDAO

use of org.akaza.openclinica.dao.submit.ItemFormMetadataDAO 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 12 with ItemFormMetadataDAO

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

the class ViewCRFVersionServlet method processRequest.

@Override
public void processRequest() throws Exception {
    // CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    FormLayoutDAO fldao = new FormLayoutDAO(sm.getDataSource());
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    // checks which module the requests are from
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);
    // int crfVersionId = fp.getInt("id");
    int formLayoutId = fp.getInt("id");
    if (formLayoutId == 0) {
        addPageMessage(respage.getString("please_choose_a_crf_to_view_details"));
        forwardPage(Page.CRF_LIST_SERVLET);
    } else {
        // CRFVersionBean version = (CRFVersionBean) cvdao.findByPK(crfVersionId);
        FormLayoutBean formLayout = (FormLayoutBean) fldao.findByPK(formLayoutId);
        // tbh
        CRFDAO crfdao = new CRFDAO(sm.getDataSource());
        CRFBean crf = (CRFBean) crfdao.findByPK(formLayout.getCrfId());
        CRFVersionMetadataUtil metadataUtil = new CRFVersionMetadataUtil(sm.getDataSource());
        ArrayList<SectionBean> sections = metadataUtil.retrieveFormMetadata(formLayout);
        request.setAttribute("sections", sections);
        request.setAttribute("version", formLayout);
        // tbh
        request.setAttribute("crfname", crf.getName());
        // tbh
        forwardPage(Page.VIEW_CRF_VERSION);
    }
}

Example 13 with ItemFormMetadataDAO

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

the class CRFVersionMetadataUtil method retrieveFormMetadata.

/**
     * Builds and returns an ArrayList of SectionBeans that comprise the metadata of a CRFVersion.
     */
public ArrayList<SectionBean> retrieveFormMetadata(FormLayoutBean formLayout) throws Exception {
    ItemDAO idao = new ItemDAO(dataSource);
    ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(dataSource);
    // tbh, 102007
    SectionDAO sdao = new SectionDAO(dataSource);
    ItemGroupDAO igdao = new ItemGroupDAO(dataSource);
    ItemGroupMetadataDAO igmdao = new ItemGroupMetadataDAO(dataSource);
    ArrayList sections = (ArrayList) sdao.findByLayoutId(formLayout.getId());
    HashMap versionMap = new HashMap();
    for (int i = 0; i < sections.size(); i++) {
        SectionBean section = (SectionBean) sections.get(i);
        versionMap.put(new Integer(section.getId()), section.getItems());
        // YW 08-21-2007, add group metadata
        ArrayList<ItemGroupBean> igs = (ArrayList<ItemGroupBean>) igdao.findGroupByLayoutId(formLayout.getId());
        for (int j = 0; j < igs.size(); ++j) {
            ArrayList<ItemGroupMetadataBean> igms = (ArrayList<ItemGroupMetadataBean>) igmdao.findMetaByGroupAndSection(igs.get(j).getId(), section.getCRFVersionId(), section.getId());
            if (!igms.isEmpty()) {
                // Note, the following logic has been adapted here -
                // "for a given crf version,
                // all the items in the same group have the same group
                // metadata
                // so we can get one of them and set metadata for the
                // group"
                igs.get(j).setMeta(igms.get(0));
                igs.get(j).setItemGroupMetaBeans(igms);
            }
        }
        ((SectionBean) sections.get(i)).setGroups(igs);
    // YW >>
    }
    ArrayList items = idao.findAllItemsByLayoutId(formLayout.getId());
    // then different query will be used
    if (igmdao.versionIncluded(formLayout.getId())) {
        for (int i = 0; i < items.size(); i++) {
            ItemBean item = (ItemBean) items.get(i);
            ItemFormMetadataBean ifm = ifmdao.findByItemIdAndFormLayoutId(item.getId(), formLayout.getId());
            item.setItemMeta(ifm);
            // logger.info("option******" +
            // ifm.getResponseSet().getOptions().size());
            ArrayList its = (ArrayList) versionMap.get(new Integer(ifm.getSectionId()));
            its.add(item);
        }
    } else {
        for (int i = 0; i < items.size(); i++) {
            ItemBean item = (ItemBean) items.get(i);
            ItemFormMetadataBean ifm = ifmdao.findByItemIdAndFormLayoutIdNotInIGM(item.getId(), formLayout.getId());
            item.setItemMeta(ifm);
            // logger.info("option******" +
            // ifm.getResponseSet().getOptions().size());
            ArrayList its = (ArrayList) versionMap.get(new Integer(ifm.getSectionId()));
            its.add(item);
        }
    }
    for (int i = 0; i < sections.size(); i++) {
        SectionBean section = (SectionBean) sections.get(i);
        section.setItems((ArrayList) versionMap.get(new Integer(section.getId())));
    }
    return sections;
}

Example 14 with ItemFormMetadataDAO

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

the class ImportCRFDataService method lookupValidationErrors.

public List<DisplayItemBeanWrapper> lookupValidationErrors(HttpServletRequest request, ODMContainer odmContainer, UserAccountBean ub, HashMap<String, String> totalValidationErrors, HashMap<String, String> hardValidationErrors, ArrayList<Integer> permittedEventCRFIds) throws OpenClinicaException {
    DisplayItemBeanWrapper displayItemBeanWrapper = null;
    HashMap validationErrors = new HashMap();
    List<DisplayItemBeanWrapper> wrappers = new ArrayList<DisplayItemBeanWrapper>();
    ImportHelper importHelper = new ImportHelper();
    FormDiscrepancyNotes discNotes = new FormDiscrepancyNotes();
    DiscrepancyValidator discValidator = new DiscrepancyValidator(request, discNotes);
    // create a second Validator, this one for hard edit checks
    HashMap<String, String> hardValidator = new HashMap<String, String>();
    StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
    StudyDAO studyDAO = new StudyDAO(ds);
    StudyBean studyBean = studyDAO.findByOid(odmContainer.getCrfDataPostImportContainer().getStudyOID());
    StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
    StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(ds);
    HashMap<String, ItemDataBean> blankCheck = new HashMap<String, ItemDataBean>();
    String hardValidatorErrorMsgs = "";
    ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
    int totalEventCRFCount = 0;
    int totalItemDataBeanCount = 0;
    for (SubjectDataBean subjectDataBean : subjectDataBeans) {
        ArrayList<DisplayItemBean> displayItemBeans = new ArrayList<DisplayItemBean>();
        logger.debug("iterating through subject data beans: found " + subjectDataBean.getSubjectOID());
        ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
        totalEventCRFCount += studyEventDataBeans.size();
        StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
        for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
            int parentStudyId = studyBean.getParentStudyId();
            StudyEventDefinitionBean sedBean = sedDao.findByOidAndStudy(studyEventDataBean.getStudyEventOID(), studyBean.getId(), parentStudyId);
            ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
            logger.debug("iterating through study event data beans: found " + studyEventDataBean.getStudyEventOID());
            int ordinal = 1;
            try {
                ordinal = new Integer(studyEventDataBean.getStudyEventRepeatKey()).intValue();
            } catch (Exception e) {
            // trying to catch NPEs, because tags can be without the
            // repeat key
            }
            StudyEventBean studyEvent = (StudyEventBean) studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubjectBean.getId(), sedBean.getId(), ordinal);
            displayItemBeans = new ArrayList<DisplayItemBean>();
            for (FormDataBean formDataBean : formDataBeans) {
                Map<String, Integer> groupMaxOrdinals = new HashMap<String, Integer>();
                displayItemBeanWrapper = null;
                CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
                EventCRFDAO eventCRFDAO = new EventCRFDAO(ds);
                ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formDataBean.getFormOID());
                ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
                if ((crfVersionBeans == null) || (crfVersionBeans.size() == 0)) {
                    MessageFormat mf = new MessageFormat("");
                    mf.applyPattern(respage.getString("your_crf_version_oid_did_not_generate"));
                    Object[] arguments = { formDataBean.getFormOID() };
                    throw new OpenClinicaException(mf.format(arguments), "");
                }
                CRFVersionBean crfVersion = crfVersionBeans.get(0);
                // if you have a mispelled form oid you get an error here
                // need to error out gracefully and post an error
                logger.debug("iterating through form beans: found " + crfVersion.getOid());
                // may be the point where we cut off item groups etc and
                // instead work on sections
                EventCRFBean eventCRFBean = eventCRFDAO.findByEventCrfVersion(studyEvent, crfVersion);
                EventDefinitionCRFDAO eventDefinitionCRFDAO = new EventDefinitionCRFDAO(ds);
                EventDefinitionCRFBean eventDefinitionCRF = eventDefinitionCRFDAO.findByStudyEventIdAndCRFVersionId(studyBean, studyEvent.getId(), crfVersion.getId());
                if (eventCRFBean != null) {
                    if (permittedEventCRFIds.contains(new Integer(eventCRFBean.getId()))) {
                        for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
                            groupMaxOrdinals.put(itemGroupDataBean.getItemGroupOID(), 1);
                        }
                        // correctness, tbh
                        for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
                            ArrayList<ItemBean> blankCheckItems = new ArrayList<ItemBean>();
                            ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
                            logger.debug("iterating through group beans: " + itemGroupDataBean.getItemGroupOID());
                            // put a checker in here
                            ItemGroupDAO itemGroupDAO = new ItemGroupDAO(ds);
                            ItemGroupBean testBean = itemGroupDAO.findByOid(itemGroupDataBean.getItemGroupOID());
                            if (testBean == null) {
                                // TODO i18n of message
                                MessageFormat mf = new MessageFormat("");
                                mf.applyPattern(respage.getString("your_item_group_oid_for_form_oid"));
                                Object[] arguments = { itemGroupDataBean.getItemGroupOID(), formDataBean.getFormOID() };
                                throw new OpenClinicaException(mf.format(arguments), "");
                            }
                            totalItemDataBeanCount += itemDataBeans.size();
                            for (ImportItemDataBean importItemDataBean : itemDataBeans) {
                                logger.debug("   iterating through item data beans: " + importItemDataBean.getItemOID());
                                ItemDAO itemDAO = new ItemDAO(ds);
                                ItemFormMetadataDAO itemFormMetadataDAO = new ItemFormMetadataDAO(ds);
                                List<ItemBean> itemBeans = itemDAO.findByOid(importItemDataBean.getItemOID());
                                if (!itemBeans.isEmpty()) {
                                    ItemBean itemBean = itemBeans.get(0);
                                    logger.debug("   found " + itemBean.getName());
                                    // throw a null pointer? hopefully not if its been checked...
                                    DisplayItemBean displayItemBean = new DisplayItemBean();
                                    displayItemBean.setItem(itemBean);
                                    ArrayList<ItemFormMetadataBean> metadataBeans = itemFormMetadataDAO.findAllByItemId(itemBean.getId());
                                    logger.debug("      found metadata item beans: " + metadataBeans.size());
                                    int groupOrdinal = 1;
                                    if (itemGroupDataBean.getItemGroupRepeatKey() != null) {
                                        try {
                                            groupOrdinal = new Integer(itemGroupDataBean.getItemGroupRepeatKey()).intValue();
                                            if (groupOrdinal > groupMaxOrdinals.get(itemGroupDataBean.getItemGroupOID())) {
                                                groupMaxOrdinals.put(itemGroupDataBean.getItemGroupOID(), groupOrdinal);
                                            }
                                        } catch (Exception e) {
                                            // do nothing here currently, we are
                                            // looking for a number format
                                            // exception
                                            // from the above.
                                            logger.debug("found npe for group ordinals, line 344!");
                                        }
                                    }
                                    ItemDataBean itemDataBean = createItemDataBean(itemBean, eventCRFBean, importItemDataBean.getValue(), ub, groupOrdinal);
                                    blankCheckItems.add(itemBean);
                                    String newKey = groupOrdinal + "_" + itemGroupDataBean.getItemGroupOID() + "_" + itemBean.getOid() + "_" + subjectDataBean.getSubjectOID();
                                    blankCheck.put(newKey, itemDataBean);
                                    logger.info("adding " + newKey + " to blank checks");
                                    if (!metadataBeans.isEmpty()) {
                                        ItemFormMetadataBean metadataBean = metadataBeans.get(0);
                                        // also possible nullpointer
                                        displayItemBean.setData(itemDataBean);
                                        displayItemBean.setMetadata(metadataBean);
                                        displayItemBean.setEventDefinitionCRF(eventDefinitionCRF);
                                        String eventCRFRepeatKey = studyEventDataBean.getStudyEventRepeatKey();
                                        // if you do indeed leave off this in the XML it will pass but return 'null'
                                        // tbh
                                        attachValidator(displayItemBean, importHelper, discValidator, hardValidator, request, eventCRFRepeatKey, studySubjectBean.getOid());
                                        displayItemBeans.add(displayItemBean);
                                    } else {
                                        MessageFormat mf = new MessageFormat("");
                                        mf.applyPattern(respage.getString("no_metadata_could_be_found"));
                                        Object[] arguments = { importItemDataBean.getItemOID() };
                                        throw new OpenClinicaException(mf.format(arguments), "");
                                    }
                                } else {
                                    // report the error there
                                    MessageFormat mf = new MessageFormat("");
                                    mf.applyPattern(respage.getString("no_item_could_be_found"));
                                    Object[] arguments = { importItemDataBean.getItemOID() };
                                    throw new OpenClinicaException(mf.format(arguments), "");
                                }
                            }
                            // end item data beans
                            logger.debug(".. found blank check: " + blankCheck.toString());
                            for (int i = 1; i <= groupMaxOrdinals.get(itemGroupDataBean.getItemGroupOID()); i++) {
                                for (ItemBean itemBean : blankCheckItems) {
                                    String newKey = i + "_" + itemGroupDataBean.getItemGroupOID() + "_" + itemBean.getOid() + "_" + subjectDataBean.getSubjectOID();
                                    if (blankCheck.get(newKey) == null) {
                                        // if it already exists, Do Not Add It.
                                        ItemDataBean itemDataCheck = getItemDataDao().findByItemIdAndEventCRFIdAndOrdinal(itemBean.getId(), eventCRFBean.getId(), i);
                                        logger.debug("found item data bean id: " + itemDataCheck.getId() + " for ordinal " + i);
                                        if (itemDataCheck.getId() == 0) {
                                            ItemDataBean blank = createItemDataBean(itemBean, eventCRFBean, "", ub, i);
                                            DisplayItemBean displayItemBean = new DisplayItemBean();
                                            displayItemBean.setItem(itemBean);
                                            displayItemBean.setData(blank);
                                            // displayItemBean.setMetadata(metadataBean);
                                            // set event def crf?
                                            displayItemBean.setEventDefinitionCRF(eventDefinitionCRF);
                                            String eventCRFRepeatKey = studyEventDataBean.getStudyEventRepeatKey();
                                            // if you do indeed leave off this in the XML it will pass but return
                                            // 'null'
                                            // tbh
                                            displayItemBeans.add(displayItemBean);
                                            logger.debug("... adding display item bean");
                                        }
                                    }
                                    logger.debug("found a blank at " + i + ", adding " + blankCheckItems.size() + " blank items");
                                }
                            }
                            // << tbh #5548
                            blankCheckItems = new ArrayList<ItemBean>();
                        }
                    // end item group data beans
                    }
                    // matches if on permittedCRFIDs
                    CRFDAO crfDAO = new CRFDAO(ds);
                    CRFBean crfBean = crfDAO.findByVersionId(crfVersion.getCrfId());
                    // seems like an extravagance, but is not contained in crf
                    // version or event crf bean
                    validationErrors = discValidator.validate();
                    // totalValidationErrors.addAll(validationErrors);
                    for (Object errorKey : validationErrors.keySet()) {
                        // JN: to avoid duplicate errors
                        if (!totalValidationErrors.containsKey(errorKey.toString()))
                            totalValidationErrors.put(errorKey.toString(), validationErrors.get(errorKey).toString());
                        // assuming that this will be put back in to the core
                        // method's hashmap, updating statically, tbh 06/2008
                        logger.debug("+++ adding " + errorKey.toString());
                    }
                    logger.debug("-- hard validation checks: --");
                    for (Object errorKey : hardValidator.keySet()) {
                        logger.debug(errorKey.toString() + " -- " + hardValidator.get(errorKey));
                        hardValidationErrors.put(errorKey.toString(), hardValidator.get(errorKey));
                        // updating here 'statically' tbh 06/2008
                        hardValidatorErrorMsgs += hardValidator.get(errorKey) + "<br/><br/>";
                    }
                    String studyEventId = studyEvent.getId() + "";
                    String crfVersionId = crfVersion.getId() + "";
                    logger.debug("creation of wrapper: original count of display item beans " + displayItemBeans.size() + ", count of item data beans " + totalItemDataBeanCount + " count of validation errors " + validationErrors.size() + " count of study subjects " + subjectDataBeans.size() + " count of event crfs " + totalEventCRFCount + " count of hard error checks " + hardValidator.size());
                    // check if we need to overwrite
                    DataEntryStage dataEntryStage = eventCRFBean.getStage();
                    Status eventCRFStatus = eventCRFBean.getStatus();
                    boolean overwrite = false;
                    // //JN: Commenting out the following 2 lines, coz the prompt should come in the cases on
                    if (// eventCRFStatus.equals(Status.UNAVAILABLE) ||
                    dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
                        overwrite = true;
                    }
                    // << tbh, adding extra statuses to prevent appending, 06/2009
                    // SummaryStatsBean ssBean = new SummaryStatsBean();
                    // ssBean.setDiscNoteCount(totalValidationErrors);
                    // ssBean.setEventCrfCount(totalEventCRFCount);
                    // ssBean.setStudySubjectCount(subjectDataBeans.size());
                    // // add other stats here, tbh
                    // not working here, need to do it in a different method,
                    // tbh
                    // summary stats added tbh 05/2008
                    // JN: Changed from validationErrors to totalValidationErrors to create discrepancy notes for
                    // all
                    // the
                    displayItemBeanWrapper = new DisplayItemBeanWrapper(displayItemBeans, true, overwrite, validationErrors, studyEventId, crfVersionId, studyEventDataBean.getStudyEventOID(), studySubjectBean.getLabel(), eventCRFBean.getCreatedDate(), crfBean.getName(), crfVersion.getName(), studySubjectBean.getOid(), studyEventDataBean.getStudyEventRepeatKey());
                    // JN: Commenting out the following code, since we shouldn't re-initialize at this point, as
                    // validationErrors would get overwritten and the
                    // older errors will be overriden. Moving it after the form.
                    // Removing the comments for now, since it seems to be creating duplicate Discrepancy Notes.
                    validationErrors = new HashMap();
                    discValidator = new DiscrepancyValidator(request, discNotes);
                // reset to allow for new errors...
                }
            }
            // discValidator = new DiscrepancyValidator(request, discNotes);
            if (displayItemBeanWrapper != null && displayItemBeans.size() > 0)
                wrappers.add(displayItemBeanWrapper);
        }
    // after study events
    // remove repeats here? remove them below by only forwarding the
    // first
    // each wrapper represents an Event CRF and a Form, but we don't
    // have all events for all forms
    // need to not add a wrapper for every event + form combination,
    // but instead for every event + form combination which is present
    // look at the hack below and see what happens
    }
    // thrown, tbh 06/2008
    if (!hardValidator.isEmpty()) {
    // throw new OpenClinicaException(hardValidatorErrorMsgs, "");
    }
    return wrappers;
}

Example 15 with ItemFormMetadataDAO

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

the class SelectItemsServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int crfId = fp.getInt("crfId");
    int defId = fp.getInt("defId");
    int eventAttr = fp.getInt("eventAttr");
    int subAttr = fp.getInt("subAttr");
    int CRFAttr = fp.getInt("CRFAttr");
    int groupAttr = fp.getInt("groupAttr");
    int discAttr = fp.getInt("discAttr");
    CRFDAO crfdao = new CRFDAO(sm.getDataSource());
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    ItemFormMetadataDAO imfdao = new ItemFormMetadataDAO(sm.getDataSource());
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    HashMap events = (HashMap) session.getAttribute(CreateDatasetServlet.EVENTS_FOR_CREATE_DATASET);
    if (events == null) {
        events = new HashMap();
    }
    request.setAttribute("eventlist", events);
    logger.info("found dob setting: " + currentStudy.getStudyParameterConfig().getCollectDob());
    if (crfId == 0) {
        // no crf selected
        if (eventAttr == 0 && subAttr == 0 && CRFAttr == 0 && groupAttr == 0 && discAttr == 0) {
            forwardPage(Page.CREATE_DATASET_2);
        } else if (eventAttr > 0) {
            request.setAttribute("subjectAgeAtEvent", "1");
            if (currentStudy.getStudyParameterConfig().getCollectDob().equals("3")) {
                request.setAttribute("subjectAgeAtEvent", "0");
                logger.info("dob not collected, setting age at event to 0");
            }
            forwardPage(Page.CREATE_DATASET_EVENT_ATTR);
        } else if (subAttr > 0) {
            if (currentStudy.getStudyParameterConfig().getCollectDob().equals("3")) {
                logger.info("dob not collected, setting age at event to 0");
            }
            forwardPage(Page.CREATE_DATASET_SUB_ATTR);
        } else if (CRFAttr > 0) {
            forwardPage(Page.CREATE_DATASET_CRF_ATTR);
        } else if (groupAttr > 0) {
            // TODO set up subject group classes here?
            setUpStudyGroupPage();
            forwardPage(Page.CREATE_DATASET_GROUP_ATTR);
        } else // else if (discAttr > 0) {
        // forwardPage(Page.CREATE_DATASET_DISC_ATTR);
        // }
        {
            forwardPage(Page.CREATE_DATASET_2);
        }
        return;
    }
    CRFBean crf = (CRFBean) crfdao.findByPK(crfId);
    StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(defId);
    session.setAttribute("crf", crf);
    session.setAttribute("definition", sed);
    DatasetBean db = (DatasetBean) session.getAttribute("newDataset");
    if (db == null) {
        db = new DatasetBean();
    }
    session.setAttribute("newDataset", db);
    // save current def id in the seesion to avoid duplicated def id in
    // dataset
    // bean
    // session.setAttribute(CURRENT_DEF_ID, new Integer(defId));
    ArrayList items = idao.findAllActiveByCRF(crf);
    for (int i = 0; i < items.size(); i++) {
        ItemBean item = (ItemBean) items.get(i);
        /*
             * logger.info("testing on item id "+ item.getId()+ " crf version id "+
             * item.getItemMeta().getCrfVersionId());
             */
        ItemFormMetadataBean meta = imfdao.findByItemIdAndCRFVersionId(item.getId(), item.getItemMeta().getCrfVersionId());
        // TODO change the above data access function, tbh
        // ArrayList metas = imfdao.findAllByItemId(item.getId());
        meta.setCrfVersionName(item.getItemMeta().getCrfVersionName());
        // logger.info("crf versionname" + meta.getCrfVersionName());
        item.getItemMetas().add(meta);
    // item.setItemMetas(metas);
    }
    HashMap itemMap = new HashMap();
    for (int i = 0; i < items.size(); i++) {
        ItemBean item = (ItemBean) items.get(i);
        if (!itemMap.containsKey(defId + "_" + item.getId())) {
            if (db.getItemMap().containsKey(defId + "_" + item.getId())) {
                item.setSelected(true);
                item.setDatasetItemMapKey(defId + "_" + item.getId());
            // logger.info("Item got selected already11");
            }
            // itemMap.put(new Integer(item.getId()), item);
            itemMap.put(defId + "_" + item.getId(), item);
        } else {
            // same item,combine the metadata
            ItemBean uniqueItem = (ItemBean) itemMap.get(defId + "_" + item.getId());
            uniqueItem.getItemMetas().add(item.getItemMetas().get(0));
            if (db.getItemMap().containsKey(defId + "_" + uniqueItem.getId())) {
                uniqueItem.setSelected(true);
            // logger.info("Item got selected already22");
            }
        }
    }
    ArrayList itemArray = new ArrayList(itemMap.values());
    // now sort them by ordinal/name
    Collections.sort(itemArray);
    session.setAttribute("allItems", itemArray);
    forwardPage(Page.CREATE_DATASET_2);
}