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

Example 46 with ItemFormMetadataBean

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

the class ExtractBean method getMetadata.

/**
 * Implements the Column algorithm in "Dataset Export Algorithms" Must be
 * called after DatasetDAO.getDatasetData();
 */
public void getMetadata() {
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(ds);
    CRFDAO cdao = new CRFDAO(ds);
    CRFVersionDAO cvdao = new CRFVersionDAO(ds);
    ItemDAO idao = new ItemDAO(ds);
    ItemFormMetadataDAO ifmDAO = new ItemFormMetadataDAO(this.ds);
    StudyGroupDAO studygroupDAO = new StudyGroupDAO(ds);
    StudyGroupClassDAO studygroupclassDAO = new StudyGroupClassDAO(ds);
    // SubjectGroupMapDAO subjectGroupMapDAO = new SubjectGroupMapDAO(ds);
    studyGroupClasses = new ArrayList();
    studyGroupMap = new HashMap();
    studyGroupMaps = new HashMap<Integer, ArrayList>();
    sedCrfColumns = new HashMap();
    displayed = new HashMap();
    sedCrfItemFormMetadataBeans = new HashMap();
    studyEvents = seddao.findAllByStudy(study);
    ArrayList finalStudyEvents = new ArrayList();
    if (dataset.isShowSubjectGroupInformation()) {
        // logger.info("found study id for maps: "+study.getId());
        studyGroupMaps = studygroupDAO.findSubjectGroupMaps(study.getId());
        // below is for a given subject; we need a data structure for
        // all subjects
        // studyGroupMap = studygroupDAO.findByStudySubject(currentSubject);
        // problem: can't use currentSubject here, since it's not 'set up'
        // properly
        // how to get the current subject?
        logger.info("found subject group ids: " + dataset.getSubjectGroupIds().toString());
        // studyGroupClasses = dataset.getSubjectGroupIds();
        for (int h = 0; h < dataset.getSubjectGroupIds().size(); h++) {
            Integer groupId = (Integer) dataset.getSubjectGroupIds().get(h);
            StudyGroupClassBean sgclass = (StudyGroupClassBean) studygroupclassDAO.findByPK(groupId.intValue());
            // logger.info();
            // hmm how to link groups to subjects though? only through
            // subject group map
            logger.info("found a studygroupclass bean: " + sgclass.getName());
            studyGroupClasses.add(sgclass);
        }
    }
    for (int i = 0; i < studyEvents.size(); i++) {
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) studyEvents.get(i);
        if (!selectedSED(sed)) {
            continue;
        }
        ArrayList CRFs = (ArrayList) cdao.findAllActiveByDefinition(sed);
        ArrayList CRFsDisplayedInThisSED = new ArrayList();
        for (int j = 0; j < CRFs.size(); j++) {
            CRFBean cb = (CRFBean) CRFs.get(j);
            if (!selectedSEDCRF(sed, cb)) {
                continue;
            } else {
                CRFsDisplayedInThisSED.add(cb);
                ArrayList CRFVersions = cvdao.findAllByCRFId(cb.getId());
                for (int k = 0; k < CRFVersions.size(); k++) {
                    CRFVersionBean cvb = (CRFVersionBean) CRFVersions.get(k);
                    ArrayList Items = idao.findAllItemsByVersionId(cvb.getId());
                    // sort by ordinal/name
                    Collections.sort(Items);
                    for (int l = 0; l < Items.size(); l++) {
                        ItemBean ib = (ItemBean) Items.get(l);
                        if (selected(ib) && !getDisplayed(sed, cb, ib)) {
                            // logger.info("found at
                            // itemformmetadatadao: "+ib.getId()+",
                            // "+cvb.getId());
                            ItemFormMetadataBean ifmb = ifmDAO.findByItemIdAndCRFVersionId(ib.getId(), cvb.getId());
                            addColumn(sed, cb, ib);
                            addItemFormMetadataBeans(sed, cb, ifmb);
                            markDisplayed(sed, cb, ib);
                        }
                    }
                }
            }
        // else
        }
        // for
        sed.setCrfs(CRFsDisplayedInThisSED);
        // make the setCrfs call "stick"
        finalStudyEvents.add(sed);
    }
    this.studyEvents = finalStudyEvents;
}

Example 47 with ItemFormMetadataBean

use of org.akaza.openclinica.bean.submit.ItemFormMetadataBean 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 48 with ItemFormMetadataBean

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

the class OpenRosaXmlGenerator method buildInstance.

// method
/**
     * @param model
     * @param crfVersion
     * @param crfSections
     * @return
     * @throws Exception
     */
private String buildInstance(Model model, FormLayoutBean formLayout, CRFVersionBean crfVersion, ArrayList<SectionBean> crfSections) throws Exception {
    DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
    DocumentBuilder build = docFactory.newDocumentBuilder();
    Document doc = build.newDocument();
    Element crfElement = doc.createElement(formLayout.getOid());
    crfElement.setAttribute("id", formLayout.getOid());
    doc.appendChild(crfElement);
    crfElement.setAttributeNS("http://www.w3.org/2000/xmlns/", "xmlns:jr", "http://openrosa.org/javarosa");
    for (SectionBean section : crfSections) {
        Element sectionSubTitle = doc.createElement("SECTION_" + section.getId() + ".SUBTITLE");
        Element sectionInstructions = doc.createElement("SECTION_" + section.getId() + ".INSTRUCTIONS");
        Element sectionElm = doc.createElement("SECTION_" + section.getLabel().replaceAll("\\W", "_"));
        crfElement.appendChild(sectionSubTitle);
        crfElement.appendChild(sectionInstructions);
        crfElement.appendChild(sectionElm);
    }
    ArrayList<ItemGroupBean> itemGroupBeans = getItemGroupBeansByFormLayout(formLayout);
    for (ItemGroupBean itemGroupBean : itemGroupBeans) {
        ItemGroupMetadataBean itemGroupMetadataBean = getItemGroupMetadataByGroup(itemGroupBean, crfVersion);
        String repeatGroupMin = itemGroupMetadataBean.getRepeatNum().toString();
        Boolean isrepeating = itemGroupMetadataBean.isRepeatingGroup();
        Element groupElement = doc.createElement(itemGroupBean.getOid());
        if (isrepeating) {
            groupElement.setTextContent(repeatGroupMin);
            groupElement.setAttribute("jr:template", "");
            Element hiddenOrdinalItem = doc.createElement("OC.REPEAT_ORDINAL");
            groupElement.appendChild(hiddenOrdinalItem);
        }
        crfElement.appendChild(groupElement);
        idao = new ItemDAO(dataSource);
        ArrayList<ItemBean> items = (ArrayList<ItemBean>) idao.findAllItemsByGroupIdOrdered(itemGroupBean.getId(), crfVersion.getId());
        for (ItemBean item : items) {
            ItemFormMetadataBean itemMetaData = getItemFormMetadata(item, crfVersion);
            if (itemMetaData.getHeader() != null && !itemMetaData.getHeader().equals("")) {
                Element header = doc.createElement(item.getOid() + ".HEADER");
                groupElement.appendChild(header);
            }
            if (itemMetaData.getHeader() != null && !itemMetaData.getSubHeader().equals("")) {
                Element subHeader = doc.createElement(item.getOid() + ".SUBHEADER");
                groupElement.appendChild(subHeader);
            }
            Element question = doc.createElement(item.getOid());
            groupElement.appendChild(question);
        }
    // end of item
    }
    // end of group
    // add meta
    Element meta = doc.createElement("meta");
    // add instanceId
    Element instanceId = doc.createElement("instanceID");
    meta.appendChild(instanceId);
    crfElement.appendChild(meta);
    TransformerFactory transformFactory = TransformerFactory.newInstance();
    Transformer transformer = transformFactory.newTransformer();
    transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
    transformer.setOutputProperty(OutputKeys.INDENT, "yes");
    StringWriter writer = new StringWriter();
    StreamResult result = new StreamResult(writer);
    DOMSource source = new DOMSource(doc);
    transformer.transform(source, result);
    return writer.toString();
}

Example 49 with ItemFormMetadataBean

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

the class DynamicsMetadataService method showNew.

public void showNew(Integer itemDataId, List<PropertyBean> properties, UserAccountBean ub, RuleSetBean ruleSet) {
    ItemDataBean itemDataBeanA = (ItemDataBean) getItemDataDAO().findByPK(itemDataId);
    EventCRFBean eventCrfBeanA = (EventCRFBean) getEventCRFDAO().findByPK(itemDataBeanA.getEventCRFId());
    ItemGroupMetadataBean itemGroupMetadataBeanA = (ItemGroupMetadataBean) getItemGroupMetadataDAO().findByItemAndCrfVersion(itemDataBeanA.getItemId(), eventCrfBeanA.getCRFVersionId());
    Boolean isGroupARepeating = isGroupRepeating(itemGroupMetadataBeanA);
    String itemGroupAOrdinal = getExpressionService().getGroupOrdninalCurated(ruleSet.getTarget().getValue());
    for (PropertyBean propertyBean : properties) {
        String oid = propertyBean.getOid();
        ItemOrItemGroupHolder itemOrItemGroup = getItemOrItemGroup(oid);
        // OID is an item
        if (itemOrItemGroup.getItemBean() != null) {
            String expression = getExpressionService().constructFullExpressionIfPartialProvided(propertyBean.getOid(), ruleSet.getTarget().getValue());
            ItemBean itemBeanB = getExpressionService().getItemBeanFromExpression(expression);
            ItemGroupBean itemGroupBeanB = getExpressionService().getItemGroupExpression(expression);
            EventCRFBean eventCrfBeanB = eventCrfBeanA;
            ItemGroupMetadataBean itemGroupMetadataBeanB = (ItemGroupMetadataBean) getItemGroupMetadataDAO().findByItemAndCrfVersion(itemBeanB.getId(), eventCrfBeanB.getCRFVersionId());
            Boolean isGroupBRepeating = isGroupRepeating(itemGroupMetadataBeanB);
            String itemGroupBOrdinal = getExpressionService().getGroupOrdninalCurated(expression);
            List<ItemDataBean> itemDataBeans = new ArrayList<ItemDataBean>();
            // If A and B are both non repeating groups
            if (!isGroupARepeating && !isGroupBRepeating) {
                ItemDataBean oidBasedItemData = oneToOne(itemDataBeanA, eventCrfBeanA, itemGroupMetadataBeanA, itemBeanB, itemGroupMetadataBeanB, eventCrfBeanB, ub, 1);
                itemDataBeans.add(oidBasedItemData);
            }
            // If A is not repeating group & B is a repeating group with no index selected
            if (!isGroupARepeating && isGroupBRepeating && itemGroupBOrdinal.equals("")) {
                List<ItemDataBean> oidBasedItemDatas = oneToMany(itemDataBeanA, eventCrfBeanA, itemGroupMetadataBeanA, itemBeanB, itemGroupBeanB, itemGroupMetadataBeanB, eventCrfBeanB, ub);
                itemDataBeans.addAll(oidBasedItemDatas);
            }
            // If A is not repeating group & B is a repeating group with index selected
            if (!isGroupARepeating && isGroupBRepeating && !itemGroupBOrdinal.equals("")) {
                ItemDataBean oidBasedItemData = oneToIndexedMany(itemDataBeanA, eventCrfBeanA, itemGroupMetadataBeanA, itemBeanB, itemGroupBeanB, itemGroupMetadataBeanB, eventCrfBeanB, ub, Integer.valueOf(itemGroupBOrdinal));
                itemDataBeans.add(oidBasedItemData);
            }
            // If A is repeating group with index & B is a repeating group with index selected
            if (isGroupARepeating && isGroupBRepeating && !itemGroupBOrdinal.equals("")) {
                ItemDataBean oidBasedItemData = oneToIndexedMany(itemDataBeanA, eventCrfBeanA, itemGroupMetadataBeanA, itemBeanB, itemGroupBeanB, itemGroupMetadataBeanB, eventCrfBeanB, ub, Integer.valueOf(itemGroupBOrdinal));
                itemDataBeans.add(oidBasedItemData);
            }
            // If A is repeating group with index & B is a repeating group with no index selected
            if (isGroupARepeating && isGroupBRepeating && itemGroupBOrdinal.equals("")) {
                ItemDataBean oidBasedItemData = oneToIndexedMany(itemDataBeanA, eventCrfBeanA, itemGroupMetadataBeanA, itemBeanB, itemGroupBeanB, itemGroupMetadataBeanB, eventCrfBeanB, ub, Integer.valueOf(itemGroupAOrdinal));
                itemDataBeans.add(oidBasedItemData);
            }
            logger.debug("** found item data beans: " + itemDataBeans.toString());
            for (ItemDataBean oidBasedItemData : itemDataBeans) {
                ItemFormMetadataBean itemFormMetadataBean = getItemFormMetadataDAO().findByItemIdAndCRFVersionId(itemBeanB.getId(), eventCrfBeanB.getCRFVersionId());
                DynamicsItemFormMetadataBean dynamicsMetadataBean = getDynamicsItemFormMetadataBean(itemFormMetadataBean, eventCrfBeanA, oidBasedItemData);
                if (dynamicsMetadataBean == null) {
                    showItem(itemFormMetadataBean, eventCrfBeanA, oidBasedItemData);
                // itemsAlreadyShown.add(new Integer(oidBasedItemData.getId()));
                } else if (dynamicsMetadataBean != null && !dynamicsMetadataBean.isShowItem()) {
                    dynamicsMetadataBean.setShowItem(true);
                    getDynamicsItemFormMetadataDao().saveOrUpdate(dynamicsMetadataBean);
                // itemsAlreadyShown.add(new Integer(oidBasedItemData.getId()));
                } else if (eventCrfBeanA.getStage().equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
                    logger.debug("hit DDE here: idb " + oidBasedItemData.getId());
                    // need a guard clause to guarantee DDE
                    // if we get there, it means that we've hit DDE and the bean exists
                    // setVersion(1);// version 1 = passed DDE
                    dynamicsMetadataBean.setPassedDde(1);
                    getDynamicsItemFormMetadataDao().saveOrUpdate(dynamicsMetadataBean);
                }
            }
        } else // OID is a group
        {
            logger.debug("found item group id 1 " + oid);
            ItemGroupBean itemGroupBean = itemOrItemGroup.getItemGroupBean();
            ArrayList sectionBeans = getSectionDAO().findAllByCRFVersionId(eventCrfBeanA.getCRFVersionId());
            for (int i = 0; i < sectionBeans.size(); i++) {
                SectionBean sectionBean = (SectionBean) sectionBeans.get(i);
                // System.out.println("found section " + sectionBean.getId());
                List<ItemGroupMetadataBean> itemGroupMetadataBeans = getItemGroupMetadataDAO().findMetaByGroupAndSection(itemGroupBean.getId(), eventCrfBeanA.getCRFVersionId(), sectionBean.getId());
                for (ItemGroupMetadataBean itemGroupMetadataBean : itemGroupMetadataBeans) {
                    if (itemGroupMetadataBean.getItemGroupId() == itemGroupBean.getId()) {
                        // System.out.println("found item group id 2 " + oid);
                        DynamicsItemGroupMetadataBean dynamicsGroupBean = getDynamicsItemGroupMetadataBean(itemGroupMetadataBean, eventCrfBeanA);
                        if (dynamicsGroupBean == null) {
                            showGroup(itemGroupMetadataBean, eventCrfBeanA);
                        } else if (dynamicsGroupBean != null && !dynamicsGroupBean.isShowGroup()) {
                            dynamicsGroupBean.setShowGroup(true);
                            getDynamicsItemGroupMetadataDao().saveOrUpdate(dynamicsGroupBean);
                        } else if (eventCrfBeanA.getStage().equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
                            // setVersion(1); // version 1 = passed DDE
                            dynamicsGroupBean.setPassedDde(1);
                            getDynamicsItemGroupMetadataDao().saveOrUpdate(dynamicsGroupBean);
                        }
                    }
                }
            }
        }
    }
}

Example 50 with ItemFormMetadataBean

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

the class DynamicsMetadataService method updateGroupDynItemsInASection.

private void updateGroupDynItemsInASection(DisplayItemWithGroupBean itemWithGroup, List<Integer> showItemIds, int groupId, int sectionId, int crfVersionId, int eventCrfId) {
    List<DisplayItemGroupBean> digbs = itemWithGroup.getItemGroups();
    List<Integer> showDataIds = this.dynamicsItemFormMetadataDao.findShowItemDataIdsForAGroupInSection(groupId, sectionId, crfVersionId, eventCrfId);
    List<Integer> hideDataIds = this.dynamicsItemFormMetadataDao.findHideItemDataIdsForAGroupInSection(groupId, sectionId, crfVersionId, eventCrfId);
    for (int n = 0; n < digbs.size(); ++n) {
        DisplayItemGroupBean dg = digbs.get(n);
        ArrayList<DisplayItemBean> items = (ArrayList<DisplayItemBean>) dg.getItems();
        for (int m = 0; m < items.size(); ++m) {
            DisplayItemBean dib = items.get(m);
            ItemFormMetadataBean meta = dib.getMetadata();
            dib.setBlankDwelt(false);
            if (hideDataIds != null && hideDataIds.contains(dib.getData().getId())) {
                meta.setShowItem(false);
            }
            if (showDataIds != null && showDataIds.contains(dib.getData().getId())) {
                meta.setShowItem(true);
            }
            if (!meta.isShowItem() && showItemIds != null && showItemIds.contains(dib.getItem().getId())) {
                dib.setBlankDwelt(true);
            }
        }
    }
}