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

Example 11 with ItemBean

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

the class ImportDataRuleRunnerContainer method initRuleSetsAndTargets.

/**
     * Populate importDataTrueRuleSets and variableAndValue.
     * Precondition: import data file passed validation which means all OIDs are not empty.
     * @param ds
     * @param studyBean
     * @param subjectDataBean
     * @param ruleSetService
     */
@Transactional
public void initRuleSetsAndTargets(DataSource ds, StudyBean studyBean, SubjectDataBean subjectDataBean, RuleSetServiceInterface ruleSetService) {
    this.shouldRunRules = this.shouldRunRules == null ? Boolean.FALSE : this.shouldRunRules;
    this.importDataTrueRuleSets = this.importDataTrueRuleSets == null ? new ArrayList<RuleSetBean>() : this.importDataTrueRuleSets;
    this.variableAndValue = this.variableAndValue == null ? new HashMap<String, String>() : this.variableAndValue;
    studyOid = studyBean.getOid();
    studySubjectOid = subjectDataBean.getSubjectOID();
    StudySubjectBean studySubject = new StudySubjectDAO<String, ArrayList>(ds).findByOid(studySubjectOid);
    HashMap<String, StudyEventDefinitionBean> seds = new HashMap<String, StudyEventDefinitionBean>();
    HashMap<String, CRFVersionBean> cvs = new HashMap<String, CRFVersionBean>();
    ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
    for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
        String sedOid = studyEventDataBean.getStudyEventOID();
        StudyEventDefinitionBean sed;
        if (seds.containsKey(sedOid))
            sed = seds.get(sedOid);
        else {
            sed = new StudyEventDefinitionDAO<String, ArrayList>(ds).findByOid(sedOid);
            seds.put(sedOid, sed);
        }
        ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
        for (FormDataBean formDataBean : formDataBeans) {
            String cvOid = formDataBean.getFormOID();
            CRFVersionBean crfVersion;
            if (cvs.containsKey(cvOid))
                crfVersion = cvs.get(cvOid);
            else {
                crfVersion = new CRFVersionDAO<String, ArrayList>(ds).findByOid(cvOid);
                cvs.put(cvOid, crfVersion);
            }
            String sedOrd = studyEventDataBean.getStudyEventRepeatKey();
            Integer sedOrdinal = sedOrd != null && !sedOrd.isEmpty() ? Integer.valueOf(sedOrd) : 1;
            StudyEventBean studyEvent = (StudyEventBean) new StudyEventDAO(ds).findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubject.getId(), sed.getId(), sedOrdinal);
            List<RuleSetBean> ruleSets = ruleSetService.getRuleSetsByCrfStudyAndStudyEventDefinition(studyBean, sed, crfVersion);
            //Set<String> targetItemOids = new HashSet<String>();
            if (ruleSets != null && !ruleSets.isEmpty()) {
                ruleSets = filterByImportDataEntryTrue(ruleSets);
                if (ruleSets != null && !ruleSets.isEmpty()) {
                    ruleSets = ruleSetService.filterByStatusEqualsAvailable(ruleSets);
                    ruleSets = ruleSetService.filterRuleSetsByStudyEventOrdinal(ruleSets, studyEvent, crfVersion, sed);
                    //ruleSets = ruleSetService.filterRuleSetsByHiddenItems(ruleSets, eventCrfBean, crfVersion, new ArrayList<ItemBean>());
                    shouldRunRules = ruleSetService.shouldRunRulesForRuleSets(ruleSets, Phase.IMPORT);
                    if (shouldRunRules != null && shouldRunRules == Boolean.TRUE) {
                        //targetItemOids = collectTargetItemOids(ruleSets);
                        HashMap<String, Integer> grouped = new HashMap<String, Integer>();
                        ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
                        for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
                            ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
                            for (ImportItemDataBean importItemDataBean : itemDataBeans) {
                                //if(targetItemOids.contains(importItemDataBean.getItemOID())) {
                                ItemBean item = new ItemDAO<String, ArrayList>(ds).findByOid(importItemDataBean.getItemOID()).get(0);
                                String igOid = itemGroupDataBean.getItemGroupOID();
                                String igOrd = itemGroupDataBean.getItemGroupRepeatKey();
                                Integer igOrdinal = igOrd != null && !igOrd.isEmpty() ? Integer.valueOf(igOrd) : 1;
                                //logic from DataEntryServlet method: populateRuleSpecificHashMaps()
                                if (isRepeatIGForSure(ds, crfVersion.getId(), igOid, igOrdinal, item.getId())) {
                                    String key1 = igOid + "[" + igOrdinal + "]." + importItemDataBean.getItemOID();
                                    String key = igOid + "." + importItemDataBean.getItemOID();
                                    variableAndValue.put(key1, importItemDataBean.getValue());
                                    if (grouped.containsKey(key)) {
                                        grouped.put(key, grouped.get(key) + 1);
                                    } else {
                                        grouped.put(key, 1);
                                    }
                                } else {
                                    variableAndValue.put(importItemDataBean.getItemOID(), importItemDataBean.getValue());
                                    grouped.put(importItemDataBean.getItemOID(), 1);
                                }
                            //
                            //}
                            }
                        }
                        ruleSets = ruleSetService.solidifyGroupOrdinalsUsingFormProperties(ruleSets, grouped);
                        importDataTrueRuleSets.addAll(ruleSets);
                    }
                }
            }
        }
    }
}

Example 12 with ItemBean

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

the class RuleRunner method prepareEmailContents.

HashMap<String, String> prepareEmailContents(RuleSetBean ruleSet, RuleSetRuleBean ruleSetRule, StudyBean currentStudy, RuleActionBean ruleAction) {
    // get the Study Event
    StudyEventBean studyEvent = (StudyEventBean) getStudyEventDao().findByPK(Integer.valueOf(getExpressionService().getStudyEventDefenitionOrdninalCurated(ruleSet.getTarget().getValue())));
    // get the Study Subject
    StudySubjectBean studySubject = (StudySubjectBean) getStudySubjectDao().findByPK(studyEvent.getStudySubjectId());
    // get Study/Site Associated with Subject
    StudyBean theStudy = (StudyBean) getStudyDao().findByPK(studySubject.getStudyId());
    String theStudyName, theSiteName = "";
    if (theStudy.getParentStudyId() > 0) {
        StudyBean theParentStudy = (StudyBean) getStudyDao().findByPK(theStudy.getParentStudyId());
        theStudyName = theParentStudy.getName() + " / " + theParentStudy.getIdentifier();
        theSiteName = theStudy.getName() + " / " + theStudy.getIdentifier();
    } else {
        theStudyName = theStudy.getName() + " / " + theStudy.getIdentifier();
    }
    // get the eventCrf & subsequently the CRF Version
    //EventCRFBean eventCrf = (EventCRFBean) getEventCrfDao().findAllByStudyEvent(studyEvent).get(0);
    EventCRFBean eventCrf = (EventCRFBean) getEventCrfDao().findAllByStudyEventAndCrfOrCrfVersionOid(studyEvent, getExpressionService().getCrfOid(ruleSet.getTarget().getValue())).get(0);
    CRFVersionBean crfVersion = (CRFVersionBean) getCrfVersionDao().findByPK(eventCrf.getCRFVersionId());
    CRFBean crf = (CRFBean) getCrfDao().findByPK(crfVersion.getCrfId());
    String studyEventDefinitionName = getExpressionService().getStudyEventDefinitionFromExpression(ruleSet.getTarget().getValue(), currentStudy).getName();
    studyEventDefinitionName += " [" + studyEvent.getSampleOrdinal() + "]";
    String itemGroupName = getExpressionService().getItemGroupNameAndOrdinal(ruleSet.getTarget().getValue());
    ItemGroupBean itemGroupBean = getExpressionService().getItemGroupExpression(ruleSet.getTarget().getValue());
    ItemBean itemBean = getExpressionService().getItemExpression(ruleSet.getTarget().getValue(), itemGroupBean);
    String itemName = itemBean.getName();
    SectionBean section = (SectionBean) getSectionDAO().findByPK(getItemFormMetadataDAO().findByItemIdAndCRFVersionId(itemBean.getId(), crfVersion.getId()).getSectionId());
    StringBuffer sb = new StringBuffer();
    ResourceBundle respage = ResourceBundleProvider.getPageMessagesBundle();
    sb.append(respage.getString("email_header_1"));
    sb.append(" " + contextPath + " ");
    sb.append(respage.getString("email_header_2"));
    sb.append(" '" + currentStudy.getName() + "' ");
    sb.append(respage.getString("email_header_3"));
    sb.append(" \n\n ");
    sb.append(respage.getString("email_body_1") + " " + theStudyName + " \n ");
    sb.append(respage.getString("email_body_1_a") + " " + theSiteName + " \n ");
    sb.append(respage.getString("email_body_2") + " " + studySubject.getName() + " \n ");
    sb.append(respage.getString("email_body_3") + " " + studyEventDefinitionName + " \n ");
    sb.append(respage.getString("email_body_4") + " " + crf.getName() + " " + crfVersion.getName() + " \n ");
    sb.append(respage.getString("email_body_5") + " " + section.getTitle() + " \n ");
    sb.append(respage.getString("email_body_6") + " " + itemGroupName + " \n ");
    sb.append(respage.getString("email_body_7") + " " + itemName + " \n ");
    sb.append(respage.getString("email_body_8") + " " + ruleAction.getCuratedMessage() + " \n ");
    sb.append(" \n\n ");
    sb.append(respage.getString("email_body_9"));
    sb.append(" " + contextPath + " ");
    sb.append(respage.getString("email_body_10"));
    sb.append(" \n");
    requestURLMinusServletPath = requestURLMinusServletPath == null ? "" : requestURLMinusServletPath;
    sb.append(requestURLMinusServletPath + "/ViewSectionDataEntry?ecId=" + eventCrf.getId() + "&sectionId=" + section.getId() + "&tabId=" + section.getOrdinal());
    // &eventId="+ studyEvent.getId());
    sb.append("\n\n");
    sb.append(respage.getString("email_footer"));
    String subject = contextPath + " - [" + currentStudy.getName() + "] ";
    String ruleSummary = ruleAction.getSummary() != null ? ruleAction.getSummary() : "";
    String message = ruleSummary.length() < 20 ? ruleSummary : ruleSummary.substring(0, 20) + " ... ";
    subject += message;
    HashMap<String, String> emailContents = new HashMap<String, String>();
    emailContents.put("body", sb.toString());
    emailContents.put("subject", subject);
    return emailContents;
}

Example 13 with ItemBean

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

the class ScoreCalculator method redoCalculations.

/**
     * Re-do calculations if funcs include changed item(s) and funcs are not
     * included in the current section. If calculation can not sucessfully redo,
     * old value will be erased and "<erased>" will be saved in database. <br>
     * The parameter 'itemdata' might be overwritten.
     * 
     * @param itemGroupSizes
     * @param items
     * @param itemdata
     * @param oldItemdata
     * @param updatedData
     * @param sectionId
     * @return ArrayList<String> which records left_item_text of items who
     *         failed to be updated into database.
     */
public ArrayList<String> redoCalculations(HashMap<String, ItemBean> items, HashMap<String, String> itemdata, TreeSet<String> changedItems, HashMap<Integer, TreeSet<Integer>> itemOrdinals, int sectionId) {
    ArrayList<String> updateFailedItems = new ArrayList<String>();
    if (itemdata == null) {
        logger.error("In ScoreCalculator redoCalculations(), itemdata is empty!");
        errors.add("In ScoreCalculator redoCalculations(), 'itemdata' map is empty!");
        return updateFailedItems;
    }
    if (changedItems == null) {
        logger.error("In ScoreCalculator redoCalculations(), 'changeItems' set is empty!");
        errors.add("In ScoreCalculator redoCalculations(), 'changeItems' set is empty!");
        return updateFailedItems;
    }
    ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
    NumberFormat nf = NumberFormat.getInstance();
    Parser parser = new Parser(items, itemdata);
    try {
        // for calculation type
        List<ItemFormMetadataBean> derivedItemList = ifmdao.findAllByCRFVersionIdAndResponseTypeId(ecb.getCRFVersionId(), ResponseType.CALCULATION.getId());
        if (derivedItemList.size() > 0) {
            Collections.sort(derivedItemList);
            for (ItemFormMetadataBean ifmb : derivedItemList) {
                if (ifmb.getSectionId() != sectionId) {
                    ItemBean ib = (ItemBean) idao.findByPK(ifmb.getItemId());
                    ResponseOptionBean rob = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
                    int groupsize = 1;
                    if (itemOrdinals.containsKey(ib.getId())) {
                        groupsize = itemOrdinals.get(ib.getId()).size();
                    }
                    String value = "";
                    ArrayList<ScoreToken> parsedExp = new ArrayList<ScoreToken>();
                    for (int i = 0; i < groupsize; ++i) {
                        ItemDataBean idb = iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb.getItemId(), ecb.getId(), i + 1);
                        // is there any changed item
                        Parser p = new Parser(items, itemdata);
                        parsedExp = parser.parseScoreTokens(rob.getValue());
                        if (p.isChanged(changedItems, parsedExp)) {
                            StringBuffer err = new StringBuffer();
                            parsedExp = parser.assignVariables(parsedExp, i + 1);
                            // before, set "<erased>"
                            if (parser.getErrors().length() > 0) {
                                err.append(parser.getErrors());
                                if (idb.isActive()) {
                                    idb.setValue("<erased>");
                                    idb.setStatus(Status.UNAVAILABLE);
                                    idb = (ItemDataBean) iddao.update(idb);
                                    if (!idb.isActive()) {
                                        String key = i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
                                        updateFailedItems.add(key);
                                    }
                                }
                                parser.setErrors(new StringBuffer());
                            } else // otherwise do calculation
                            {
                                try {
                                    value = ScoreUtil.eval(parsedExp);
                                } catch (ScoreException se) {
                                    logger.error(se.getMessage());
                                }
                                String exp = rob.getValue();
                                exp = exp.replace("##", ",");
                                if (writeToDB(ib, ifmb, idb, exp, value, err)) {
                                    changedItems.add(ib.getName());
                                    itemdata.put(ib.getId() + "_" + (i + 1), idb.getValue());
                                } else {
                                    String key = i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
                                    updateFailedItems.add(key);
                                }
                            }
                            if (err.length() > 0) {
                                String key = i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
                                errors.add("Item " + key + " contains calculation errors: " + err.toString());
                            }
                        }
                    }
                }
            }
        }
        List<ItemFormMetadataBean> itemList = ifmdao.findAllByCRFVersionIdAndResponseTypeId(ecb.getCRFVersionId(), ResponseType.GROUP_CALCULATION.getId());
        if (itemList.size() > 0) {
            Collections.sort(itemList);
            for (ItemFormMetadataBean ifmb : itemList) {
                if (ifmb.getSectionId() != sectionId) {
                    ItemBean ib = (ItemBean) idao.findByPK(ifmb.getItemId());
                    ResponseOptionBean rob = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
                    String value = "";
                    Parser p = new Parser(items, itemdata);
                    ArrayList<ScoreToken> parsedExp = parser.parseScoreTokens(rob.getValue());
                    if (p.isChanged(changedItems, parsedExp)) {
                        StringBuffer err = new StringBuffer();
                        parser.setErrors(err);
                        parsedExp = parser.assignVariables(parsedExp, itemOrdinals);
                        ItemDataBean idb = iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb.getItemId(), ecb.getId(), 1);
                        if (parser.getErrors().length() > 0) {
                            err.append(parser.getErrors());
                            if (idb.isActive()) {
                                idb.setValue("<erased>");
                                idb.setStatus(Status.UNAVAILABLE);
                                idb = (ItemDataBean) iddao.update(idb);
                                if (!idb.isActive()) {
                                    updateFailedItems.add(ifmb.getLeftItemText());
                                }
                            }
                        } else {
                            try {
                                value = ScoreUtil.eval(parsedExp);
                            } catch (ScoreException se) {
                                logger.error(se.getMessage());
                            }
                            String exp = rob.getValue();
                            exp = exp.replace("##", ",");
                            if (writeToDB(ib, ifmb, idb, exp, value, err)) {
                                changedItems.add(ib.getName());
                                itemdata.put(ib.getId() + "_" + idb.getOrdinal(), idb.getValue());
                            } else {
                                updateFailedItems.add(ifmb.getLeftItemText());
                            }
                        }
                        if (err.length() > 0) {
                            errors.add("Item " + ifmb.getLeftItemText() + " contains calculation errors: " + err.toString());
                        }
                    }
                }
            }
        }
    } catch (OpenClinicaException e) {
        logger.error(e.getMessage());
    }
    return updateFailedItems;
}

Example 14 with ItemBean

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

the class RandomizeService method getExpressionValue.

private String getExpressionValue(String expr, EventCRFBean eventCrfBean, RuleSetBean ruleSet) {
    String expression = getExpressionService().constructFullExpressionIfPartialProvided(expr, ruleSet.getTarget().getValue());
    ItemDataBean itemData = null;
    if (expression != null && !expression.isEmpty()) {
        ItemBean itemBean = getExpressionService().getItemBeanFromExpression(expression);
        String itemGroupBOrdinal = getExpressionService().getGroupOrdninalCurated(expression);
        itemData = getItemDataDAO().findByItemIdAndEventCRFIdAndOrdinal(itemBean.getId(), eventCrfBean.getId(), itemGroupBOrdinal == "" ? 1 : Integer.valueOf(itemGroupBOrdinal));
    }
    return itemData.getValue();
}

Example 15 with ItemBean

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

the class DynamicsMetadataService method getValue.

private String getValue(PropertyBean property, RuleSetBean ruleSet, EventCRFBean eventCrfBean, List<StratificationFactorBean> stratificationFactorBeans) {
    String value = null;
    if (property.getValue() != null && property.getValue().length() > 0) {
        logger.info("Value from property value is : {}", value);
        value = property.getValue();
    }
    if (property.getValueExpression() == null) {
        logger.info("There is no ValueExpression for property =" + property.getOid());
        if (stratificationFactorBeans != null)
            try {
                value = getRandomizeService().getRandomizationCode(eventCrfBean, stratificationFactorBeans, ruleSet);
            } catch (JSONException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
    } else {
        String expression = getExpressionService().constructFullExpressionIfPartialProvided(property.getValueExpression().getValue(), ruleSet.getTarget().getValue());
        if (expression != null && !expression.isEmpty()) {
            ItemBean itemBean = getExpressionService().getItemBeanFromExpression(expression);
            String itemGroupBOrdinal = getExpressionService().getGroupOrdninalCurated(expression);
            ItemDataBean itemData = getItemDataDAO().findByItemIdAndEventCRFIdAndOrdinal(itemBean.getId(), eventCrfBean.getId(), itemGroupBOrdinal == "" ? 1 : Integer.valueOf(itemGroupBOrdinal));
            if (itemData.getId() == 0) {
                logger.info("Cannot get Value for ExpressionValue {}", expression);
            } else {
                value = itemData.getValue();
                logger.info("Value from ExpressionValue '{}'  is : {}", expression, value);
            }
        }
    }
    return value;
}