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

Example 11 with CRFVersionBean

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

the class CRFVersionDAO method findAllByCRF.

public Collection findAllByCRF(int crfId) {
    this.setTypesExpected();
    HashMap variables = new HashMap();
    variables.put(new Integer(1), new Integer(crfId));
    String sql = digester.getQuery("findAllByCRF");
    ArrayList alist = this.select(sql, variables);
    ArrayList al = new ArrayList();
    Iterator it = alist.iterator();
    while (it.hasNext()) {
        CRFVersionBean eb = (CRFVersionBean) this.getEntityFromHashMap((HashMap) it.next());
        al.add(eb);
    }
    return al;
}

Example 12 with CRFVersionBean

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

the class ImportDataHelper method createEventCRF.

public EventCRFBean createEventCRF(HashMap<String, String> importedObject) {
    EventCRFBean eventCrfBean = null;
    int studyEventId = importedObject.get("study_event_id") == null ? -1 : Integer.parseInt(importedObject.get("study_event_id"));
    String crfVersionName = importedObject.get("crf_version_name") == null ? "" : importedObject.get("crf_version_name").toString();
    String crfName = importedObject.get("crf_name") == null ? "" : importedObject.get("crf_name").toString();
    String eventDefinitionCRFName = importedObject.get("event_definition_crf_name") == null ? "" : importedObject.get("event_definition_crf_name").toString();
    String subjectName = importedObject.get("subject_name") == null ? "" : importedObject.get("subject_name").toString();
    String studyName = importedObject.get("study_name") == null ? "" : importedObject.get("study_name").toString();
    logger.info("found the following: study event id " + studyEventId + ", crf version name " + crfVersionName + ", crf name " + crfName + ", event def crf name " + eventDefinitionCRFName + ", subject name " + subjectName + ", study name " + studyName);
    // << tbh
    int eventCRFId = 0;
    EventCRFDAO eventCrfDao = new EventCRFDAO(sm.getDataSource());
    StudyDAO studyDao = new StudyDAO(sm.getDataSource());
    StudySubjectDAO studySubjectDao = new StudySubjectDAO(sm.getDataSource());
    StudyEventDefinitionDAO studyEventDefinistionDao = new StudyEventDefinitionDAO(sm.getDataSource());
    CRFVersionDAO crfVersionDao = new CRFVersionDAO(sm.getDataSource());
    StudyEventDAO studyEventDao = new StudyEventDAO(sm.getDataSource());
    CRFDAO crfdao = new CRFDAO(sm.getDataSource());
    SubjectDAO subjectDao = new SubjectDAO(sm.getDataSource());
    StudyBean studyBean = (StudyBean) studyDao.findByName(studyName);
    // .findByPK(studyId);
    // generate the subject bean first, so that we can have the subject id
    // below...
    SubjectBean subjectBean = // .findByUniqueIdentifierAndStudy(subjectName,
    subjectDao.findByUniqueIdentifier(subjectName);
    StudySubjectBean studySubjectBean = studySubjectDao.findBySubjectIdAndStudy(subjectBean.getId(), studyBean);
    // .findByLabelAndStudy(subjectName, studyBean);
    logger.info("::: found study subject id here: " + studySubjectBean.getId() + " with the following: subject ID " + subjectBean.getId() + " study bean name " + studyBean.getName());
    StudyEventBean studyEventBean = (StudyEventBean) studyEventDao.findByPK(studyEventId);
    // TODO need to replace, can't really replace
    logger.info("found study event status: " + studyEventBean.getStatus().getName());
    // [study] event should be scheduled, event crf should be not started
    CRFVersionBean crfVersion = (CRFVersionBean) crfVersionDao.findByFullName(crfVersionName, crfName);
    // .findByPK(crfVersionId);
    // replaced by findByName(name, version)
    logger.info("found crf version name here: " + crfVersion.getName());
    EntityBean crf = crfdao.findByPK(crfVersion.getCrfId());
    logger.info("found crf name here: " + crf.getName());
    // trying it again up here since down there doesn't seem to work, tbh
    StudyEventDefinitionBean studyEventDefinitionBean = (StudyEventDefinitionBean) studyEventDefinistionDao.findByName(eventDefinitionCRFName);
    if (studySubjectBean.getId() <= 0 && studyEventBean.getId() <= 0 && crfVersion.getId() <= 0 && studyBean.getId() <= 0 && studyEventDefinitionBean.getId() <= 0) {
        logger.info("Throw an Exception, One of the provided ids is not valid");
    }
    // >> tbh repeating items:
    ArrayList eventCrfBeans = eventCrfDao.findByEventSubjectVersion(studyEventBean, studySubjectBean, crfVersion);
    // TODO repeating items here? not yet
    if (eventCrfBeans.size() > 1) {
        logger.info("found more than one");
    }
    if (!eventCrfBeans.isEmpty() && eventCrfBeans.size() == 1) {
        eventCrfBean = (EventCRFBean) eventCrfBeans.get(0);
        logger.info("This EventCrfBean was found");
    }
    if (!eventCrfBeans.isEmpty() && eventCrfBeans.size() > 1) {
        logger.info("Throw a System exception , result should either be 0 or 1");
    }
    if (eventCrfBean == null) {
        StudyBean studyWithSED = studyBean;
        if (studyBean.getParentStudyId() > 0) {
            studyWithSED = new StudyBean();
            studyWithSED.setId(studyBean.getParentStudyId());
        }
        AuditableEntityBean studyEvent = studyEventDao.findByPKAndStudy(studyEventId, studyWithSED);
        if (studyEvent.getId() <= 0) {
            logger.info("Hello Exception");
        }
        eventCrfBean = new EventCRFBean();
        // eventCrfBean.setCrfVersion(crfVersion);
        if (eventCRFId == 0) {
            // ???
            if (studyBean.getStudyParameterConfig().getInterviewerNameDefault().equals("blank")) {
                eventCrfBean.setInterviewerName("");
            } else {
                // default will be event's owner name
                eventCrfBean.setInterviewerName(studyEventBean.getOwner().getName());
            }
            if (!studyBean.getStudyParameterConfig().getInterviewDateDefault().equals("blank")) {
                if (studyEventBean.getDateStarted() != null) {
                    // default
                    eventCrfBean.setDateInterviewed(studyEventBean.getDateStarted());
                // date
                } else {
                    // logger.info("evnet start date is null, so date
                    // interviewed is null");
                    eventCrfBean.setDateInterviewed(null);
                }
            } else {
                eventCrfBean.setDateInterviewed(null);
            }
            eventCrfBean.setAnnotations("");
            eventCrfBean.setCreatedDate(new Date());
            eventCrfBean.setCRFVersionId(crfVersion.getId());
            // eventCrfBean.setCrfVersion((CRFVersionBean)crfVersion);
            eventCrfBean.setOwner(ub);
            // eventCrfBean.setCrf((CRFBean)crf);
            eventCrfBean.setStatus(Status.AVAILABLE);
            eventCrfBean.setCompletionStatusId(1);
            // problem with the line below
            eventCrfBean.setStudySubjectId(studySubjectBean.getId());
            eventCrfBean.setStudyEventId(studyEventId);
            eventCrfBean.setValidateString("");
            eventCrfBean.setValidatorAnnotations("");
            try {
                eventCrfBean = (EventCRFBean) eventCrfDao.create(eventCrfBean);
            // TODO review
            // eventCrfBean.setCrfVersion((CRFVersionBean)crfVersion);
            // eventCrfBean.setCrf((CRFBean)crf);
            } catch (Exception ee) {
                logger.info(ee.getMessage());
                logger.info("throws with crf version id " + crfVersion.getId() + " and study event id " + studyEventId + " study subject id " + studySubjectBean.getId());
            }
        // note that you need to catch an exception if the numbers are
        // bogus, ie you can throw an error here
        // however, putting the try catch allows you to pass which is
        // also bad
        // logger.info("CREATED EVENT CRF");
        } else {
            // there is an event CRF already, only need to update
            // is the status not started???
            logger.info("*** already-started event CRF with msg: " + eventCrfBean.getStatus().getName());
            if (eventCrfBean.getStatus().equals(Status.PENDING)) {
                logger.info("Not Started???");
            }
            eventCrfBean = (EventCRFBean) eventCrfDao.findByPK(eventCRFId);
            eventCrfBean.setCRFVersionId(crfVersion.getId());
            eventCrfBean.setUpdatedDate(new Date());
            eventCrfBean.setUpdater(ub);
            eventCrfBean = (EventCRFBean) eventCrfDao.update(eventCrfBean);
        // eventCrfBean.setCrfVersion((CRFVersionBean)crfVersion);
        // eventCrfBean.setCrf((CRFBean)crf);
        }
        if (eventCrfBean.getId() <= 0) {
            logger.info("error");
        } else {
            // TODO change status here, tbh
            // 2/08 this part seems to work, tbh
            studyEventBean.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED);
            studyEventBean.setUpdater(ub);
            studyEventBean.setUpdatedDate(new Date());
            studyEventDao.update(studyEventBean);
        }
    }
    eventCrfBean.setCrfVersion(crfVersion);
    eventCrfBean.setCrf((CRFBean) crf);
    // repeating?
    return eventCrfBean;
}

Example 13 with CRFVersionBean

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

the class Key method populateForCrfBasedRulesView.

/**
     * Organize objects in a certain way so that we can show to Users on UI.
     * step1 : Get StudyEvent , eventCrf , crfVersion from studyEventId.
     * 
     * @param crfViewSpecificOrderedObjects
     * @param ruleSet
     * @param rule
     * @return
     */
private HashMap<RuleBulkExecuteContainer, HashMap<RuleBulkExecuteContainerTwo, Set<String>>> populateForCrfBasedRulesView(HashMap<RuleBulkExecuteContainer, HashMap<RuleBulkExecuteContainerTwo, Set<String>>> crfViewSpecificOrderedObjects, RuleSetBean ruleSet, RuleBean rule, String result, StudyBean currentStudy, List<RuleActionBean> actions) {
    // step1
    StudyEventBean studyEvent = (StudyEventBean) getStudyEventDao().findByPK(Integer.valueOf(getExpressionService().getStudyEventDefenitionOrdninalCurated(ruleSet.getTarget().getValue())));
    EventCRFBean eventCrf = (EventCRFBean) getEventCrfDao().findAllByStudyEventAndCrfOrCrfVersionOid(studyEvent, getExpressionService().getCrfOid(ruleSet.getTarget().getValue())).get(0);
    CRFVersionBean crfVersion = (CRFVersionBean) getCrfVersionDao().findByPK(eventCrf.getCRFVersionId());
    RuleBulkExecuteContainer key = new RuleBulkExecuteContainer(crfVersion.getName(), rule, result, actions);
    String key2String = getExpressionService().getCustomExpressionUsedToCreateView(ruleSet.getTarget().getValue(), studyEvent.getSampleOrdinal());
    String studyEventDefinitionName = getExpressionService().getStudyEventDefinitionFromExpression(ruleSet.getTarget().getValue(), currentStudy).getName();
    studyEventDefinitionName += " [" + studyEvent.getSampleOrdinal() + "]";
    // String itemGroupName = getExpressionService().getItemGroupNameAndOrdinal(ruleSet.getTarget().getValue());
    // String itemName = getExpressionService().getItemGroupExpression(ruleSet.getTarget().getValue()).getName();
    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();
    RuleBulkExecuteContainerTwo key2 = new RuleBulkExecuteContainerTwo(key2String, studyEvent, studyEventDefinitionName, itemGroupName, itemName);
    StudySubjectBean studySubject = (StudySubjectBean) getStudySubjectDao().findByPK(studyEvent.getStudySubjectId());
    if (crfViewSpecificOrderedObjects.containsKey(key)) {
        HashMap<RuleBulkExecuteContainerTwo, Set<String>> k = crfViewSpecificOrderedObjects.get(key);
        if (k.containsKey(key2)) {
            k.get(key2).add(String.valueOf(studySubject.getLabel()));
        } else {
            HashSet<String> values = new HashSet<String>();
            values.add(String.valueOf(studySubject.getLabel()));
            k.put(key2, values);
        }
    } else {
        HashMap<RuleBulkExecuteContainerTwo, Set<String>> k = new HashMap<RuleBulkExecuteContainerTwo, Set<String>>();
        HashSet<String> values = new HashSet<String>();
        values.add(String.valueOf(studySubject.getLabel()));
        k.put(key2, values);
        crfViewSpecificOrderedObjects.put(key, k);
    }
    return crfViewSpecificOrderedObjects;
}

Example 14 with CRFVersionBean

use of org.akaza.openclinica.bean.submit.CRFVersionBean 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 15 with CRFVersionBean

use of org.akaza.openclinica.bean.submit.CRFVersionBean 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;
}