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

Example 21 with ItemDAO

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

the class FormBeanUtil method createDisplaySectionWithItemGroups.

/**
     * Create a DisplaySectionBean with a list of ItemGroupBeans. NOTE:
     * unGrouped Items are not included
     * 
     * @param study
     *            The StudyBean
     * @param sectionId
     *            The Section ID associated with the Items, which end up
     *            providing the content of the tables.
     * @param crfVersionId
     *            The CRF version ID associated with the Items.
     * @param studyEventId
     *            The Study Event ID associated with the CRF Version ID.
     * @param sm
     *            A SessionManager, from which DataSources are acquired for the
     *            DAO objects.
     * @return A DisplaySectionBean.
     */
public DisplaySectionBean createDisplaySectionWithItemGroups(StudyBean study, int sectionId, EventCRFBean eventCrfBean, int studyEventId, SessionManager sm, int eventDefinitionCRFId, ServletContext context) {
    DisplaySectionBean dBean = new DisplaySectionBean();
    ItemGroupDAO formGroupDAO = new ItemGroupDAO(sm.getDataSource());
    ItemGroupMetadataDAO igMetaDAO = new ItemGroupMetadataDAO(sm.getDataSource());
    ItemDAO itemDao = new ItemDAO(sm.getDataSource());
    ItemFormMetadataDAO metaDao = new ItemFormMetadataDAO(sm.getDataSource());
    List<ItemGroupBean> arrList = formGroupDAO.findLegitGroupBySectionId(sectionId);
    // all items associated with the section, including those not in a group
    List<ItemFormMetadataBean> allMetas = new ArrayList<ItemFormMetadataBean>();
    try {
        allMetas = metaDao.findAllBySectionId(sectionId);
    } catch (OpenClinicaException oce) {
        logger.info("oce.getOpenClinicaMessage() = " + oce.getOpenClinicaMessage());
    }
    // Collections.sort(allMetas);
    if (arrList.isEmpty())
        return dBean;
    // Find out whether there are any checkboxes/radios/select elements
    // and if so, get any null values
    // associated with them
    List<String> nullValuesList = new ArrayList<String>();
    boolean itemsHaveChecksRadios = itemsIncludeChecksRadiosSelects(allMetas);
    // "+eventDefinitionCRFId);
    if (eventDefinitionCRFId <= 0) {
        EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
        EventDefinitionCRFBean edcBean = edcdao.findByStudyEventIdAndCRFVersionId(study, studyEventId, eventCrfBean.getCRFVersionId());
        eventDefinitionCRFId = edcBean.getId();
    }
    // "+eventDefinitionCRFId);
    if (itemsHaveChecksRadios && eventDefinitionCRFId > 0) {
        // method returns null values as a List<String>
        nullValuesList = this.getNullValuesByEventCRFDefId(eventDefinitionCRFId, sm.getDataSource());
    }
    // Get the items associated with each group
    List<ItemBean> itBeans;
    List<DisplayItemBean> displayItems;
    List<DisplayItemGroupBean> displayFormBeans = new ArrayList<DisplayItemGroupBean>();
    DisplayItemGroupBean displayItemGBean;
    for (ItemGroupBean itemGroup : arrList) {
        itBeans = itemDao.findAllItemsByGroupId(itemGroup.getId(), eventCrfBean.getCRFVersionId());
        List<ItemGroupMetadataBean> metadata = igMetaDAO.findMetaByGroupAndSection(itemGroup.getId(), eventCrfBean.getCRFVersionId(), sectionId);
        if (!metadata.isEmpty()) {
            // 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
            ItemGroupMetadataBean meta = metadata.get(0);
            itemGroup.setMeta(meta);
        }
        // include arrayList parameter until I determine difference in
        // classes
        displayItems = getDisplayBeansFromItems(itBeans, sm.getDataSource(), eventCrfBean, sectionId, nullValuesList, context);
        displayItemGBean = this.createDisplayFormGroup(displayItems, itemGroup);
        displayFormBeans.add(displayItemGBean);
    }
    // We still have to sort these display item group beans on their
    // ItemGroupMetadataBean?
    // then number their ordinals accordingly
    Collections.sort(displayFormBeans, new Comparator<DisplayItemGroupBean>() {

        public int compare(DisplayItemGroupBean displayItemGroupBean, DisplayItemGroupBean displayItemGroupBean1) {
            return displayItemGroupBean.getGroupMetaBean().compareTo(displayItemGroupBean1.getGroupMetaBean());
        }
    });
    // Now provide the display item group beans with an ordinal
    int digOrdinal = 0;
    for (DisplayItemGroupBean digBean : displayFormBeans) {
        digBean.setOrdinal(++digOrdinal);
    }
    dBean.setDisplayFormGroups(displayFormBeans);
    return dBean;
}

Example 22 with ItemDAO

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

the class FormBeanUtil method createDisplaySectionBWithFormGroups.

/**
     * Create a DisplaySectionBean with a list of ItemGroupBeans. This List will
     * include any ItemGroupBeans that are associated with ungrouped items; in
     * other words, the DisplaySectionBean will represent a section that has
     * both ungrouped and grouped tables.
     * 
     * @param sectionId
     *            The Section ID associated with the Items, which end up
     *            providing the content of the tables.
     * @param crfVersionId
     *            The CRF version ID associated with the Items.
     * @param dataSource
     * @param eventCRFDefId
     *            The id for the Event CRF Definition.
     * @return A DisplaySectionBean with sorted ItemGroupBeans, meaning the
     *         ItemGroupBeans should be listed in the order that they appear on
     *         the CRF section.
     * @return A DisplaySectionBean representing a CRF section.
     */
public DisplaySectionBean createDisplaySectionBWithFormGroups(int sectionId, int crfVersionId, DataSource dataSource, int eventCRFDefId, EventCRFBean eventCrfBean, ServletContext context) {
    DisplaySectionBean displaySectionBean = new DisplaySectionBean();
    ItemGroupDAO formGroupDAO = new ItemGroupDAO(dataSource);
    ItemGroupMetadataDAO igMetaDAO = new ItemGroupMetadataDAO(dataSource);
    ItemDAO itemDao = new ItemDAO(dataSource);
    ItemFormMetadataDAO metaDao = new ItemFormMetadataDAO(dataSource);
    SectionDAO sectionDao = new SectionDAO(dataSource);
    // Give the DisplaySectionBean a legitimate SectionBean
    SectionBean secBean = (SectionBean) sectionDao.findByPK(sectionId);
    displaySectionBean.setSection(secBean);
    // changed from: findGroupBySectionId
    List<ItemGroupBean> itemGroupBeans = formGroupDAO.findLegitGroupAllBySectionId(sectionId);
    // all items associated with the section, including those not in a group
    List<ItemFormMetadataBean> allMetas = new ArrayList<ItemFormMetadataBean>();
    try {
        allMetas = metaDao.findAllBySectionId(sectionId);
    } catch (OpenClinicaException oce) {
        logger.info("oce.getOpenClinicaMessage() = " + oce.getOpenClinicaMessage());
    }
    // Sort these items according to their position on the CRF; their
    // ordinal
    Collections.sort(allMetas);
    // The DisplayItemGroupBean(s) for "nongrouped" items
    List<DisplayItemGroupBean> nonGroupBeans = null;
    // if(itemGroupBeans.isEmpty()) return displaySectionBean;
    // Find out whether there are any checkboxes/radios/select elements
    // and if so, get any null values
    // associated with them
    List<String> nullValuesList = new ArrayList<String>();
    boolean itemsHaveChecksRadios = itemsIncludeChecksRadiosSelects(allMetas);
    if (itemsHaveChecksRadios && eventCRFDefId > 0) {
        // method returns null values as a List<String>
        nullValuesList = this.getNullValuesByEventCRFDefId(eventCRFDefId, dataSource);
    }
    // Get the items associated with each group
    List<ItemBean> itBeans;
    List<DisplayItemBean> displayItems;
    List<DisplayItemGroupBean> displayFormBeans = new ArrayList<DisplayItemGroupBean>();
    DisplayItemGroupBean displayItemGBean;
    for (ItemGroupBean itemGroup : itemGroupBeans) {
        itBeans = itemDao.findAllItemsByGroupId(itemGroup.getId(), crfVersionId);
        logger.debug("just ran find all by group id " + itemGroup.getId() + " found " + itBeans.size() + " item beans");
        List<ItemGroupMetadataBean> metadata = igMetaDAO.findMetaByGroupAndSection(itemGroup.getId(), crfVersionId, sectionId);
        if (!metadata.isEmpty()) {
            // for a given crf version, all the items in the same group
            // have the same group metadata info
            // so we can get one of the metadata and set the metadata for
            // the group
            ItemGroupMetadataBean meta = metadata.get(0);
            itemGroup.setMeta(meta);
        }
        displayItems = getDisplayBeansFromItems(itBeans, dataSource, eventCrfBean, sectionId, nullValuesList, context);
        displayItemGBean = this.createDisplayFormGroup(displayItems, itemGroup);
        displayFormBeans.add(displayItemGBean);
    }
    // We still have to sort these display item group beans on their
    // ItemGroupMetadataBean?
    // then number their ordinals accordingly
    Collections.sort(displayFormBeans, new Comparator<DisplayItemGroupBean>() {

        public int compare(DisplayItemGroupBean displayItemGroupBean, DisplayItemGroupBean displayItemGroupBean1) {
            return displayItemGroupBean.getGroupMetaBean().compareTo(displayItemGroupBean1.getGroupMetaBean());
        }
    });
    // Now provide the display item group beans with an ordinal
    int digOrdinal = 0;
    for (DisplayItemGroupBean digBean : displayFormBeans) {
        digBean.setOrdinal(++digOrdinal);
    }
    // find out whether there are any ungrouped items by comparing the
    // number of
    // grouped items to allMetas.size()
    // List<DisplayItemGroupBean> nonGroupBeans=null;
    int tempCount = 0;
    for (DisplayItemGroupBean groupBean : displayFormBeans) {
        tempCount += groupBean.getItems().size();
    }
    if (tempCount < allMetas.size()) {
        nonGroupBeans = createGroupBeansForNongroupedItems(allMetas, displayFormBeans, sectionId, dataSource, nullValuesList, eventCrfBean, context);
    }
    if (nonGroupBeans != null) {
        displayFormBeans.addAll(nonGroupBeans);
    }
    // sort the list according to the ordinal of the contained
    // DisplayItemGroupBeans
    Collections.sort(displayFormBeans, new Comparator<DisplayItemGroupBean>() {

        public int compare(DisplayItemGroupBean disFormGroupBean, DisplayItemGroupBean disFormGroupBean1) {
            Integer compInt = disFormGroupBean1.getOrdinal();
            Integer compInt2 = disFormGroupBean.getOrdinal();
            return compInt2.compareTo(compInt);
        }
    });
    displaySectionBean.setDisplayFormGroups(displayFormBeans);
    return displaySectionBean;
}

Example 23 with ItemDAO

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

the class FormBeanUtil method createDisplaySectionBeanWithItemGroups.

/**
     * Create a DisplaySectionBean with a list of FormGroupBeans.
     * 
     * @param crfVersionId
     *            The CRF version ID associated with the Items.
     * @param sectionBean
     *            The SectionBean with an ID associated with the Items, which
     *            end up providing the content of the tables.
     * @param sm
     *            A SessionManager, from which DataSources are acquired for the
     *            DAO objects.
     * @return A DisplaySectionBean.
     */
public DisplaySectionBean createDisplaySectionBeanWithItemGroups(int sectionId, EventCRFBean eventCrfBean, SectionBean sectionBean, SessionManager sm, ServletContext context) {
    DisplaySectionBean dBean = new DisplaySectionBean();
    ItemGroupDAO formGroupDAO = new ItemGroupDAO(sm.getDataSource());
    ItemGroupMetadataDAO igMetaDAO = new ItemGroupMetadataDAO(sm.getDataSource());
    ItemDAO itemDao = new ItemDAO(sm.getDataSource());
    // Get all items associated with this crfVersion ID; divide them up into
    // items with a group, and those without a group.
    // get all items associated with a section id, then split them up into
    // grouped
    // and non-grouped items
    List<ItemBean> allItems = itemDao.findAllParentsBySectionId(sectionId);
    // Get a List of FormGroupBeans for each group associated with
    // this crfVersionId.
    // List<ItemGroupBean> arrList =
    // formGroupDAO.findGroupByCRFVersionIDMap(crfVersionId);
    List<ItemGroupBean> arrList = formGroupDAO.findLegitGroupBySectionId(sectionId);
    if (arrList.isEmpty())
        return dBean;
    // Get the items associated with each group
    List<ItemBean> itBeans;
    List<DisplayItemBean> displayItems;
    List<DisplayItemGroupBean> displayFormBeans = new ArrayList<DisplayItemGroupBean>();
    DisplayItemGroupBean displayFormGBean;
    for (ItemGroupBean itemGroup : arrList) {
        itBeans = itemDao.findAllItemsByGroupId(itemGroup.getId(), eventCrfBean.getCRFVersionId());
        List<ItemGroupMetadataBean> metadata = igMetaDAO.findMetaByGroupAndSection(itemGroup.getId(), eventCrfBean.getCRFVersionId(), sectionId);
        // this requirement
        if (!metadata.isEmpty()) {
            // 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
            ItemGroupMetadataBean meta = metadata.get(0);
            itemGroup.setMeta(meta);
        }
        // TODO: the last arg is a list of null value strings
        displayItems = getDisplayBeansFromItems(itBeans, sm.getDataSource(), eventCrfBean, sectionBean.getId(), null, context);
        displayFormGBean = this.createDisplayFormGroup(displayItems, itemGroup);
        displayFormBeans.add(displayFormGBean);
    }
    // sort the list according to the ordinal of the contained
    // FormGroupBeans
    Collections.sort(displayFormBeans, new Comparator<DisplayItemGroupBean>() {

        public int compare(DisplayItemGroupBean disFormGroupBean, DisplayItemGroupBean disFormGroupBean1) {
            return disFormGroupBean.getGroupMetaBean().getOrdinal().compareTo(disFormGroupBean1.getGroupMetaBean().getOrdinal());
        }
    });
    dBean.setDisplayFormGroups(displayFormBeans);
    return dBean;
}

Example 24 with ItemDAO

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

the class OpenRosaXmlGenerator method getItemBean.

@SuppressWarnings({ "rawtypes", "unchecked" })
private ItemBean getItemBean(String itemOid) {
    ArrayList<ItemBean> itemBean = null;
    idao = new ItemDAO(dataSource);
    itemBean = (ArrayList<ItemBean>) idao.findByOid(itemOid);
    return itemBean.get(0);
}

Example 25 with ItemDAO

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

the class ImportCRFDataService method validateStudyMetadata.

/*
     * meant to answer the following questions 3.a. is that study subject in that study? 3.b. is that study event def in
     * that study? 3.c. is that site in that study? 3.d. is that crf version in that study event def? 3.e. are those
     * item groups in that crf version? 3.f. are those items in that item group?
     */
public List<String> validateStudyMetadata(ODMContainer odmContainer, int currentStudyId) {
    List<String> errors = new ArrayList<String>();
    MessageFormat mf = new MessageFormat("");
    // throw new OpenClinicaException(mf.format(arguments), "");
    try {
        StudyDAO studyDAO = new StudyDAO(ds);
        String studyOid = odmContainer.getCrfDataPostImportContainer().getStudyOID();
        StudyBean studyBean = studyDAO.findByOid(studyOid);
        if (studyBean == null) {
            mf.applyPattern(respage.getString("your_study_oid_does_not_reference_an_existing"));
            Object[] arguments = { studyOid };
            errors.add(mf.format(arguments));
            // errors.add("Your Study OID " + studyOid + " does not
            // reference an existing Study or Site in the database. Please
            // check it and try again.");
            // throw an error here because getting the ID would be difficult
            // otherwise
            logger.debug("unknown study OID");
            throw new OpenClinicaException("Unknown Study OID", "");
        } else if (studyBean.getId() != currentStudyId) {
            mf.applyPattern(respage.getString("your_current_study_is_not_the_same_as"));
            Object[] arguments = { studyBean.getName() };
            //
            // errors.add("Your current study is not the same as the Study "
            // + studyBean.getName()
            // + ", for which you are trying to enter data. Please log out
            // of your current study and into the study for which the data
            // is keyed.");
            errors.add(mf.format(arguments));
        }
        ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
        StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
        StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
        CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
        ItemGroupDAO itemGroupDAO = new ItemGroupDAO(ds);
        ItemDAO itemDAO = new ItemDAO(ds);
        if (subjectDataBeans != null) {
            // report all available errors, tbh
            for (SubjectDataBean subjectDataBean : subjectDataBeans) {
                String oid = subjectDataBean.getSubjectOID();
                StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(oid, studyBean.getId());
                if (studySubjectBean == null) {
                    mf.applyPattern(respage.getString("your_subject_oid_does_not_reference"));
                    Object[] arguments = { oid };
                    errors.add(mf.format(arguments));
                    // errors.add("Your Subject OID " + oid + " does not
                    // reference an existing Subject in the Study.");
                    logger.debug("logged an error with subject oid " + oid);
                }
                ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
                if (studyEventDataBeans != null) {
                    for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
                        String sedOid = studyEventDataBean.getStudyEventOID();
                        StudyEventDefinitionBean studyEventDefintionBean = studyEventDefinitionDAO.findByOidAndStudy(sedOid, studyBean.getId(), studyBean.getParentStudyId());
                        if (studyEventDefintionBean == null) {
                            mf.applyPattern(respage.getString("your_study_event_oid_for_subject_oid"));
                            Object[] arguments = { sedOid, oid };
                            errors.add(mf.format(arguments));
                            // errors.add("Your Study Event OID " + sedOid +
                            // " for Subject OID " + oid
                            // + " does not reference an existing Study
                            // Event in the Study.");
                            logger.debug("logged an error with se oid " + sedOid + " and subject oid " + oid);
                        }
                        ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
                        if (formDataBeans != null) {
                            for (FormDataBean formDataBean : formDataBeans) {
                                String formOid = formDataBean.getFormOID();
                                ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formOid);
                                // right now just check nulls
                                if (crfVersionBeans != null) {
                                    for (CRFVersionBean crfVersionBean : crfVersionBeans) {
                                        if (crfVersionBean == null) {
                                            mf.applyPattern(respage.getString("your_crf_version_oid_for_study_event_oid"));
                                            Object[] arguments = { formOid, sedOid };
                                            errors.add(mf.format(arguments));
                                            // errors.add("Your CRF Version
                                            // OID " + formOid + " for Study
                                            // Event OID " + sedOid
                                            // + " does not reference a
                                            // proper CRF Version in that
                                            // Study Event.");
                                            logger.debug("logged an error with form " + formOid + " and se oid " + sedOid);
                                        }
                                    }
                                } else {
                                    mf.applyPattern(respage.getString("your_crf_version_oid_did_not_generate"));
                                    Object[] arguments = { formOid };
                                    errors.add(mf.format(arguments));
                                // errors.add("Your CRF Version OID " +
                                // formOid
                                // + " did not generate any results in
                                // the database. Please check it and try
                                // again.");
                                }
                                ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
                                if (itemGroupDataBeans != null) {
                                    for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
                                        String itemGroupOID = itemGroupDataBean.getItemGroupOID();
                                        List<ItemGroupBean> itemGroupBeans = itemGroupDAO.findAllByOid(itemGroupOID);
                                        if (itemGroupBeans != null) {
                                            logger.debug("number of item group beans: " + itemGroupBeans.size());
                                            logger.debug("item group oid: " + itemGroupOID);
                                            for (ItemGroupBean itemGroupBean : itemGroupBeans) {
                                                if (itemGroupBean == null) {
                                                    mf.applyPattern(respage.getString("your_item_group_oid_for_form_oid"));
                                                    Object[] arguments = { itemGroupOID, formOid };
                                                    errors.add(mf.format(arguments));
                                                // errors.add("Your Item
                                                // Group OID " +
                                                // itemGroupOID + " for
                                                // Form OID " + formOid
                                                // + " does not
                                                // reference a proper
                                                // Item Group in that
                                                // CRF Version.");
                                                }
                                            }
                                        } else {
                                            mf.applyPattern(respage.getString("the_item_group_oid_did_not"));
                                            Object[] arguments = { itemGroupOID };
                                            errors.add(mf.format(arguments));
                                        // errors.add("The Item Group
                                        // OID " + itemGroupOID
                                        // + " did not generate any
                                        // results in the database,
                                        // please check it and try
                                        // again.");
                                        }
                                        ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
                                        if (itemDataBeans != null) {
                                            for (ImportItemDataBean itemDataBean : itemDataBeans) {
                                                String itemOID = itemDataBean.getItemOID();
                                                List<ItemBean> itemBeans = itemDAO.findByOid(itemOID);
                                                if (itemBeans != null) {
                                                    logger.debug("found itembeans: ");
                                                    for (ItemBean itemBean : itemBeans) {
                                                        if (itemBean == null) {
                                                            mf.applyPattern(respage.getString("your_item_oid_for_item_group_oid"));
                                                            Object[] arguments = { itemOID, itemGroupOID };
                                                            errors.add(mf.format(arguments));
                                                        // errors.add(
                                                        // "Your
                                                        // Item OID " +
                                                        // itemOID + "
                                                        // for Item
                                                        // Group OID " +
                                                        // itemGroupOID
                                                        // + " does not
                                                        // reference a
                                                        // proper Item
                                                        // in the Item
                                                        // Group.");
                                                        } else {
                                                            logger.debug("found " + itemBean.getOid() + ", passing");
                                                        }
                                                    }
                                                }
                                            }
                                        } else {
                                            mf.applyPattern(respage.getString("the_item_group_oid_did_not_contain_item_data"));
                                            Object[] arguments = { itemGroupOID };
                                            errors.add(mf.format(arguments));
                                        // errors.add("The Item Group
                                        // OID " + itemGroupOID
                                        // + " did not contain any Item
                                        // Data in the XML file, please
                                        // check it and try again.");
                                        }
                                    }
                                } else {
                                    mf.applyPattern(respage.getString("your_study_event_contains_no_form_data"));
                                    Object[] arguments = { sedOid };
                                    errors.add(mf.format(arguments));
                                // errors.add("Your Study Event " +
                                // sedOid
                                // + " contains no Form Data, or the
                                // Form OIDs are incorrect. Please check
                                // it and try again.");
                                }
                            }
                        }
                    }
                }
            }
        }
    } catch (OpenClinicaException oce) {
    } catch (NullPointerException npe) {
        logger.debug("found a nullpointer here");
    }
    // if errors == null you pass, if not you fail
    return errors;
}