Examples with CRFBean org.akaza.openclinica.bean.admin.CRFBean used on opensource projects

Example 81 with CRFBean

use of org.akaza.openclinica.bean.admin.CRFBean in project OpenClinica by OpenClinica.

the class RandomizeActionValidator method validateOidInPropertyBean.

public void validateOidInPropertyBean(PropertyBean propertyBean, Errors e, String p) {
    if (getExpressionService().isExpressionPartial(getRuleSetBean().getTarget().getValue())) {
        if (getExpressionService().getExpressionSize(propertyBean.getOid()).intValue() > 3) {
            e.rejectValue(p + "oid", "oid.invalid", "OID: " + propertyBean.getOid() + " is Invalid.");
        }
        try {
            getExpressionService().isExpressionValid(propertyBean.getOid());
        } catch (OpenClinicaSystemException ose) {
            e.rejectValue(p + "oid", "oid.invalid", "OID: " + propertyBean.getOid() + " is Invalid.");
        }
        // Use OID in destinationProperty to get CRF
        CRFBean destinationPropertyOidCrf = getExpressionService().getCRFFromExpression(propertyBean.getOid());
        if (destinationPropertyOidCrf == null) {
            ItemBean item = getExpressionService().getItemBeanFromExpression(propertyBean.getOid());
            destinationPropertyOidCrf = getCrfDAO().findByItemOid(item.getOid());
        }
        // Use Target get CRF
        CRFBean targetCrf = getExpressionService().getCRFFromExpression(getRuleSetBean().getTarget().getValue());
        if (targetCrf == null) {
            ItemBean item = getExpressionService().getItemBeanFromExpression(getRuleSetBean().getTarget().getValue());
            targetCrf = getCrfDAO().findByItemOid(item.getOid());
        }
        // Get All event definitions the selected CRF belongs to
        List<StudyEventDefinitionBean> destinationPropertyStudyEventDefinitions = getStudyEventDefinitionDAO().findAllByCrf(destinationPropertyOidCrf);
        List<StudyEventDefinitionBean> targetStudyEventDefinitions = getStudyEventDefinitionDAO().findAllByCrf(targetCrf);
        Collection intersection = CollectionUtils.intersection(destinationPropertyStudyEventDefinitions, targetStudyEventDefinitions);
        if (intersection.size() == 0) {
            e.rejectValue(p + "oid", "oid.invalid", "OID: " + propertyBean.getOid() + " is Invalid.");
        }
    } else {
        String expression = getExpressionService().constructFullExpressionIfPartialProvided(propertyBean.getOid(), getRuleSetBean().getTarget().getValue());
        ItemBean item = getExpressionService().getItemBeanFromExpression(expression);
        if (!getExpressionService().isRandomizeActionExpressionValid(propertyBean.getOid(), getRuleSetBean(), 3) || item == null) {
            e.rejectValue(p + "oid", "oid.invalid", "OID: " + propertyBean.getOid() + " is Invalid.");
        }
    }
}

Example 82 with CRFBean

use of org.akaza.openclinica.bean.admin.CRFBean in project OpenClinica by OpenClinica.

the class ExpressionService method getEventDefinitionCRF.

public EventDefinitionCRFBean getEventDefinitionCRF(String expression) {
    if (expression.split(ESCAPED_SEPERATOR).length < 4) {
        return null;
    }
    StudyEventDefinitionBean studyEventDefinition = getStudyEventDefinitionFromExpression(expression);
    CRFBean crf = getCRFFromExpression(expression);
    if (studyEventDefinition == null || crf == null)
        throw new OpenClinicaSystemException("OCRERR_0020");
    return getEventDefinitionCRFDao().findByStudyEventDefinitionIdAndCRFId(this.expressionWrapper.getStudyBean(), studyEventDefinition.getId(), crf.getId());
}

Example 83 with CRFBean

use of org.akaza.openclinica.bean.admin.CRFBean in project OpenClinica by OpenClinica.

the class EditSelectedServlet method selectAll.

/**
 * Finds all the items in a study giving all events in the study
 *
 * @param events
 * @return
 */
public static ArrayList selectAll(HashMap events, CRFDAO crfdao, ItemDAO idao) {
    ArrayList allItems = new ArrayList();
    Iterator it = events.keySet().iterator();
    while (it.hasNext()) {
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) it.next();
        ArrayList crfs = (ArrayList) crfdao.findAllActiveByDefinition(sed);
        for (int i = 0; i < crfs.size(); i++) {
            CRFBean crf = (CRFBean) crfs.get(i);
            ArrayList items = idao.findAllActiveByCRF(crf);
            for (int j = 0; j < items.size(); j++) {
                ItemBean item = (ItemBean) items.get(j);
                item.setCrfName(crf.getName());
                item.setDefName(sed.getName());
                item.setDefId(sed.getId());
                item.setSelected(true);
            }
            allItems.addAll(items);
        }
    }
    return allItems;
}

Example 84 with CRFBean

use of org.akaza.openclinica.bean.admin.CRFBean 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);
}

Example 85 with CRFBean

use of org.akaza.openclinica.bean.admin.CRFBean in project OpenClinica by OpenClinica.

the class DiscrepancyNoteOutputServlet method populateRowsWithAttachedData.

private ArrayList<DiscrepancyNoteBean> populateRowsWithAttachedData(ArrayList<DiscrepancyNoteBean> noteRows) {
    Locale l = LocaleResolver.getLocale(request);
    resword = ResourceBundleProvider.getWordsBundle(l);
    resformat = ResourceBundleProvider.getFormatBundle(l);
    SimpleDateFormat sdf = new SimpleDateFormat(resformat.getString("date_format_string"), ResourceBundleProvider.getLocale());
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
    StudySubjectDAO studySubjectDAO = new StudySubjectDAO(sm.getDataSource());
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    CRFDAO cdao = new CRFDAO(sm.getDataSource());
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    StudyDAO studyDao = new StudyDAO(sm.getDataSource());
    ItemGroupMetadataDAO<String, ArrayList> igmdao = new ItemGroupMetadataDAO<String, ArrayList>(sm.getDataSource());
    ItemGroupDAO<String, ArrayList> igdao = new ItemGroupDAO<String, ArrayList>(sm.getDataSource());
    ArrayList<DiscrepancyNoteBean> allNotes = new ArrayList<DiscrepancyNoteBean>();
    for (int i = 0; i < noteRows.size(); i++) {
        DiscrepancyNoteBean dnb = noteRows.get(i);
        dnb.setCreatedDateString(dnb.getCreatedDate() == null ? "" : sdf.format(dnb.getCreatedDate()));
        if (dnb.getParentDnId() == 0) {
            ArrayList children = dndao.findAllByStudyAndParent(currentStudy, dnb.getId());
            children = children == null ? new ArrayList() : children;
            dnb.setNumChildren(children.size());
            dnb.setChildren(children);
            int lastDnId = dnb.getId();
            int lastChild = 0;
            for (int j = 0; j < children.size(); j++) {
                DiscrepancyNoteBean child = (DiscrepancyNoteBean) children.get(j);
                child.setCreatedDateString(child.getCreatedDate() == null ? "" : sdf.format(child.getCreatedDate()));
                child.setUpdatedDateString(child.getCreatedDate() != null ? sdf.format(child.getCreatedDate()) : "");
                if (child.getId() > lastDnId) {
                    lastDnId = child.getId();
                    lastChild = j;
                }
            }
            if (children.size() > 0) {
                DiscrepancyNoteBean lastdn = (DiscrepancyNoteBean) children.get(lastChild);
                // dnb.setResStatus(ResolutionStatus.get(lastdn.getResolutionStatusId()));
                /*
                     * The update date is the date created of the latest child
                     * note
                     */
                dnb.setUpdatedDate(lastdn.getCreatedDate());
                dnb.setUpdatedDateString(dnb.getUpdatedDate() != null ? sdf.format(dnb.getUpdatedDate()) : "");
            }
        }
        String entityType = dnb.getEntityType();
        if (dnb.getEntityId() > 0 && !entityType.equals("")) {
            AuditableEntityBean aeb = dndao.findEntity(dnb);
            dnb.setEntityName(aeb.getName());
            if (entityType.equalsIgnoreCase("subject")) {
                // allNotes.add(dnb);
                SubjectBean sb = (SubjectBean) aeb;
                StudySubjectBean ssb = studySubjectDAO.findBySubjectIdAndStudy(sb.getId(), currentStudy);
                dnb.setStudySub(ssb);
                dnb.setSubjectName(ssb.getLabel());
                String column = dnb.getColumn().trim();
                if (!StringUtil.isBlank(column)) {
                    if ("gender".equalsIgnoreCase(column)) {
                        dnb.setEntityValue(sb.getGender() + "");
                        dnb.setEntityName(resword.getString("gender"));
                    } else if ("date_of_birth".equals(column)) {
                        if (sb.getDateOfBirth() != null) {
                            dnb.setEntityValue(sb.getDateOfBirth().toString());
                        }
                        dnb.setEntityName(resword.getString("date_of_birth"));
                    } else if ("unique_identifier".equalsIgnoreCase(column)) {
                        dnb.setEntityName(resword.getString("unique_identifier"));
                        dnb.setEntityValue(sb.getUniqueIdentifier());
                    }
                }
            } else if (entityType.equalsIgnoreCase("studySub")) {
                // allNotes.add(dnb);
                StudySubjectBean ssb = (StudySubjectBean) aeb;
                dnb.setStudySub(ssb);
                dnb.setSubjectName(ssb.getLabel());
                String column = dnb.getColumn().trim();
                if (!StringUtil.isBlank(column)) {
                    if ("enrollment_date".equals(column)) {
                        if (ssb.getEnrollmentDate() != null) {
                            dnb.setEntityValue(ssb.getEnrollmentDate().toString());
                        }
                        dnb.setEntityName(resword.getString("enrollment_date"));
                    }
                }
            } else if (entityType.equalsIgnoreCase("eventCRF")) {
                StudyEventBean se = (StudyEventBean) sedao.findByPK(dnb.getEntityId());
                StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
                EventCRFBean ecb = (EventCRFBean) aeb;
                CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(ecb.getCRFVersionId());
                CRFBean cb = (CRFBean) cdao.findByPK(cvb.getCrfId());
                dnb.setStageId(ecb.getStage().getId());
                dnb.setEntityName(cb.getName() + " (" + cvb.getName() + ")");
                StudySubjectBean ssub = (StudySubjectBean) studySubjectDAO.findByPK(ecb.getStudySubjectId());
                dnb.setStudySub(ssub);
                dnb.setSubjectName(ssub.getLabel());
                if (se != null) {
                    dnb.setEventStart(se.getDateStarted());
                    dnb.setEventName(se.getName());
                }
                dnb.setCrfName(cb.getName());
                String crfStatus = resword.getString(ecb.getStage().getNameRaw());
                if (crfStatus.equals("Invalid")) {
                    crfStatus = "";
                } else if (crfStatus.equals("Data Entry Complete")) {
                    crfStatus = "Complete";
                }
                dnb.setCrfStatus(crfStatus);
                String column = dnb.getColumn().trim();
                if (!StringUtil.isBlank(column)) {
                    if ("date_interviewed".equals(column)) {
                        if (ecb.getDateInterviewed() != null) {
                            dnb.setEntityValue(ecb.getDateInterviewed().toString());
                        }
                        dnb.setEntityName(resword.getString("date_interviewed"));
                    } else if ("interviewer_name".equals(column)) {
                        dnb.setEntityValue(ecb.getInterviewerName());
                        dnb.setEntityName(resword.getString("interviewer_name"));
                    }
                }
                dnb.setEvent(se);
                dnb.setStudyEventDefinitionBean(sedb);
            // }
            } else if (entityType.equalsIgnoreCase("studyEvent")) {
                // allNotes.add(dnb);
                StudyEventBean se = (StudyEventBean) sedao.findByPK(dnb.getEntityId());
                StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
                se.setName(sedb.getName());
                dnb.setEntityName(sedb.getName());
                StudySubjectBean ssub = (StudySubjectBean) studySubjectDAO.findByPK(se.getStudySubjectId());
                dnb.setStudySub(ssub);
                dnb.setEventStart(se.getDateStarted());
                dnb.setEventName(se.getName());
                dnb.setSubjectName(ssub.getLabel());
                String column = dnb.getColumn().trim();
                if (!StringUtil.isBlank(column)) {
                    if ("date_start".equals(column)) {
                        if (se.getDateStarted() != null) {
                            dnb.setEntityValue(se.getDateStarted().toString());
                        }
                        dnb.setEntityName(resword.getString("start_date"));
                    } else if ("date_end".equals(column)) {
                        if (se.getDateEnded() != null) {
                            dnb.setEntityValue(se.getDateEnded().toString());
                        }
                        dnb.setEntityName(resword.getString("end_date"));
                    } else if ("location".equals(column)) {
                        dnb.setEntityValue(se.getLocation());
                        dnb.setEntityName(resword.getString("location"));
                    }
                }
                dnb.setEvent(se);
                dnb.setStudyEventDefinitionBean(sedb);
            } else if (entityType.equalsIgnoreCase("itemData")) {
                ItemDataBean idb = (ItemDataBean) iddao.findByPK(dnb.getEntityId());
                ItemBean ib = (ItemBean) idao.findByPK(idb.getItemId());
                EventCRFBean ec = (EventCRFBean) ecdao.findByPK(idb.getEventCRFId());
                CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(ec.getCRFVersionId());
                CRFBean cb = (CRFBean) cdao.findByPK(cvb.getCrfId());
                ItemGroupMetadataBean itemGroupMetadataBean = (ItemGroupMetadataBean) igmdao.findByItemAndCrfVersion(ib.getId(), cvb.getId());
                Boolean isRepeatForSure = itemGroupMetadataBean.isRepeatingGroup();
                if (isRepeatForSure) {
                    ItemGroupBean ig = (ItemGroupBean) igdao.findByPK(itemGroupMetadataBean.getItemGroupId());
                    dnb.setItemDataOrdinal(idb.getOrdinal());
                    dnb.setItemGroupName(ig.getName());
                }
                // allNotes.add(dnb);
                dnb.setStageId(ec.getStage().getId());
                dnb.setEntityName(ib.getName());
                dnb.setEntityValue(idb.getValue());
                StudyEventBean se = (StudyEventBean) sedao.findByPK(ec.getStudyEventId());
                StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
                se.setName(sedb.getName());
                StudySubjectBean ssub = (StudySubjectBean) studySubjectDAO.findByPK(ec.getStudySubjectId());
                dnb.setStudySub(ssub);
                dnb.setSubjectName(ssub.getLabel());
                dnb.setEventStart(se.getDateStarted());
                dnb.setEventName(se.getName());
                dnb.setCrfName(cb.getName());
                String crfStatus = resword.getString(ec.getStage().getNameRaw());
                if (crfStatus.equals("Invalid")) {
                    crfStatus = "";
                } else if (crfStatus.equals("Data Entry Complete")) {
                    crfStatus = "Complete";
                }
                dnb.setCrfStatus(crfStatus);
                dnb.setEvent(se);
                dnb.setStudyEventDefinitionBean(sedb);
            }
        }
        dnb.setStudy((StudyBean) studyDao.findByPK(dnb.getStudyId()));
        if (dnb.getParentDnId() == 0 && dnb.getChildren().size() > 0) {
            ArrayList<DiscrepancyNoteBean> children = dnb.getChildren();
            int childrenSize = children.size();
            for (int j = 0; j < childrenSize; j++) {
                DiscrepancyNoteBean child = children.get(j);
                child.setSubjectName(dnb.getSubjectName());
                child.setEventName(dnb.getEventName());
                child.setCrfName(dnb.getCrfName());
                child.setCrfStatus(dnb.getCrfStatus());
                child.setEntityName(dnb.getEntityName());
                child.setEntityValue(dnb.getEntityValue());
                child.setStudySub(dnb.getStudySub());
                child.setStudy(dnb.getStudy());
            }
        }
        allNotes.add(dnb);
    }
    return allNotes;
}