Examples with ImportItemGroupDataBean org.akaza.openclinica.bean.submit.crfdata.ImportItemGroupDataBean used on opensource projects

Example 6 with ImportItemGroupDataBean

use of org.akaza.openclinica.bean.submit.crfdata.ImportItemGroupDataBean 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 7 with ImportItemGroupDataBean

use of org.akaza.openclinica.bean.submit.crfdata.ImportItemGroupDataBean in project OpenClinica by OpenClinica.

the class TriggerService method generateHardValidationErrorMessage.

public String generateHardValidationErrorMessage(ArrayList<SubjectDataBean> subjectData, HashMap<String, String> hardValidationErrors, boolean isValid) {
    StringBuffer sb = new StringBuffer();
    String studyEventRepeatKey = "1";
    String groupRepeatKey = "1";
    sb.append("<table border=\'0\' cellpadding=\'0\' cellspacing=\'0\' width=\'100%\'>");
    for (SubjectDataBean subjectDataBean : subjectData) {
        sb.append("<tr valign=\'top\'> <td class=\'table_header_row\' colspan=\'4\'>Study Subject: " + subjectDataBean.getSubjectOID() + "</td> </tr>");
        // next step here
        ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
        for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
            sb.append("<tr valign=\'top\'> <td class=\'table_header_row\'>Event CRF OID</td> <td class=\'table_header_row\' colspan=\'3\'></td>");
            sb.append("</tr> <tr valign=\'top\'> <td class=\'table_cell_left\'>");
            sb.append(studyEventDataBean.getStudyEventOID());
            if (studyEventDataBean.getStudyEventRepeatKey() != null) {
                studyEventRepeatKey = studyEventDataBean.getStudyEventRepeatKey();
                sb.append(" (Repeat key " + studyEventDataBean.getStudyEventRepeatKey() + ")");
            } else {
                // reset
                studyEventRepeatKey = "1";
            }
            sb.append("</td> <td class=\'table_cell\' colspan=\'3\'></td> </tr>");
            ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
            for (FormDataBean formDataBean : formDataBeans) {
                sb.append("<tr valign=\'top\'> <td class=\'table_header_row\'></td> ");
                sb.append("<td class=\'table_header_row\'>CRF Version OID</td> <td class=\'table_header_row\' colspan=\'2\'></td></tr>");
                sb.append("<tr valign=\'top\'> <td class=\'table_cell_left\'></td> <td class=\'table_cell\'>");
                sb.append(formDataBean.getFormOID());
                sb.append("</td> <td class=\'table_cell\' colspan=\'2\'></td> </tr>");
                ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
                for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
                    sb.append("<tr valign=\'top\'> <td class=\'table_header_row\'></td>");
                    sb.append("<td class=\'table_header_row\'></td> <td class=\'table_header_row\' colspan=\'2\'>");
                    sb.append(itemGroupDataBean.getItemGroupOID());
                    if (itemGroupDataBean.getItemGroupRepeatKey() != null) {
                        groupRepeatKey = itemGroupDataBean.getItemGroupRepeatKey();
                        sb.append(" (Repeat key " + itemGroupDataBean.getItemGroupRepeatKey() + ")");
                    } else {
                        groupRepeatKey = "1";
                    }
                    sb.append("</td></tr>");
                    ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
                    for (ImportItemDataBean itemDataBean : itemDataBeans) {
                        String oidKey = itemDataBean.getItemOID() + "_" + studyEventRepeatKey + "_" + groupRepeatKey + "_" + subjectDataBean.getSubjectOID();
                        if (!isValid) {
                            if (hardValidationErrors.containsKey(oidKey)) {
                                sb.append("<tr valign=\'top\'> <td class=\'table_cell_left\'></td>");
                                sb.append("<td class=\'table_cell\'></td> <td class=\'table_cell\'><font color=\'red\'>");
                                sb.append(itemDataBean.getItemOID());
                                sb.append("</font></td> <td class=" + "\'table_cell\'>");
                                sb.append(itemDataBean.getValue() + "<br/>");
                                sb.append(hardValidationErrors.get(oidKey));
                                sb.append("</td></tr>");
                            /*
                                     * <tr valign="top"> <td class="table_cell_left"></td> <td class="table_cell"></td>
                                     * <td class="table_cell"><font color="red"><c:out
                                     * value="${itemData.itemOID}"/></font></td> <td class="table_cell"> <c:out
                                     * value="${itemData.value}"/><br/> <c:out value="${hardValidationErrors[oidKey]}"/>
                                     * </td> </tr>
                                     */
                            }
                        } else {
                            if (!hardValidationErrors.containsKey(oidKey)) {
                                sb.append("<tr valign=\'top\'> <td class=\'table_cell_left\'></td>");
                                sb.append("<td class=\'table_cell\'></td> <td class=\'table_cell\'>");
                                sb.append(itemDataBean.getItemOID());
                                sb.append("</td> <td class=" + "\'table_cell\'>");
                                sb.append(itemDataBean.getValue());
                                sb.append("</td></tr>");
                            }
                        }
                    }
                }
            }
        }
    }
    sb.append("</table>");
    return sb.toString();
}

Example 8 with ImportItemGroupDataBean

use of org.akaza.openclinica.bean.submit.crfdata.ImportItemGroupDataBean in project OpenClinica by OpenClinica.

the class TriggerService method generateHardValidationErrorMessage.

public String generateHardValidationErrorMessage(ArrayList<SubjectDataBean> subjectData, HashMap<String, String> hardValidationErrors, String groupRepeatKey) {
    StringBuffer sb = new StringBuffer();
    String studyEventRepeatKey = null;
    sb.append("");
    for (SubjectDataBean subjectDataBean : subjectData) {
        ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
        for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
            studyEventRepeatKey = studyEventDataBean.getStudyEventRepeatKey();
            ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
            for (FormDataBean formDataBean : formDataBeans) {
                ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
                for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
                    ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
                    for (ImportItemDataBean itemDataBean : itemDataBeans) {
                        String oidKey = itemDataBean.getItemOID() + "_" + studyEventRepeatKey + "_" + groupRepeatKey + "_" + subjectDataBean.getSubjectOID();
                        if (hardValidationErrors.containsKey(oidKey)) {
                            // What about event repeat ordinal and item group and item group repeat ordinal?
                            sb.append(subjectDataBean.getSubjectOID() + "." + studyEventDataBean.getStudyEventOID());
                            if (studyEventDataBean.getStudyEventRepeatKey() != null)
                                sb.append("(" + studyEventDataBean.getStudyEventRepeatKey() + ")");
                            sb.append("." + formDataBean.getFormOID() + "." + itemGroupDataBean.getItemGroupOID());
                            if (itemGroupDataBean.getItemGroupRepeatKey() != null)
                                sb.append("(" + itemGroupDataBean.getItemGroupRepeatKey() + ")");
                            sb.append("." + itemDataBean.getItemOID());
                            sb.append(": ");
                            sb.append(itemDataBean.getValue() + " -- ");
                            sb.append(hardValidationErrors.get(oidKey));
                            sb.append("");
                        }
                    }
                }
            }
        }
    }
    sb.append("");
    return sb.toString();
}