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

Example 1 with ExportFormDataBean

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

the class OdmExtractDAO method setOCFormDataAuditLogs.

protected void setOCFormDataAuditLogs(StudyBean study, OdmClinicalDataBean data, String studySubjectOids, String ecIds, HashMap<Integer, String> formOidPoses) {
    this.setOCFormDataAuditsTypesExpected();
    String dbName = CoreResources.getDBName();
    logger.debug("Begin to execute GetOCFormDataAuditsSql");
    logger.debug("getOCFormDataAuditsSql= " + this.getOCFormDataAuditsSql(studySubjectOids, ecIds));
    ArrayList rows = select(this.getOCFormDataAuditsSql(studySubjectOids, ecIds));
    Iterator iter = rows.iterator();
    while (iter.hasNext()) {
        HashMap row = (HashMap) iter.next();
        Integer ecId = (Integer) row.get("event_crf_id");
        Integer auditId = (Integer) row.get("audit_id");
        String type = (String) row.get("name");
        Integer userId = (Integer) row.get("user_id");
        Date auditDate = (Date) row.get("audit_date");
        String auditReason = (String) row.get("reason_for_change");
        String oldValue = (String) row.get("old_value");
        String newValue = (String) row.get("new_value");
        Integer typeId = (Integer) row.get("audit_log_event_type_id");
        if (formOidPoses.containsKey(ecId)) {
            String[] poses = formOidPoses.get(ecId).split("---");
            ExportFormDataBean form = data.getExportSubjectData().get(Integer.parseInt(poses[0])).getExportStudyEventData().get(Integer.parseInt(poses[1])).getExportFormData().get(Integer.parseInt(poses[2]));
            AuditLogBean auditLog = new AuditLogBean();
            auditLog.setOid("AL_" + auditId);
            auditLog.setUserId("USR_" + userId);
            auditLog.setDatetimeStamp(auditDate);
            auditLog.setType(type);
            auditLog.setReasonForChange(auditReason);
            if (typeId == 8 || typeId == 10 || typeId == 11 || typeId == 14 || typeId == 15 || typeId == 16) {
                if ("0".equals(newValue)) {
                    auditLog.setNewValue(Status.INVALID.getName());
                } else {
                    auditLog.setNewValue(Status.getFromMap(Integer.parseInt(newValue)).getName());
                }
                if ("0".equals(oldValue)) {
                    auditLog.setOldValue(Status.INVALID.getName());
                } else {
                    auditLog.setOldValue(Status.getFromMap(Integer.parseInt(oldValue)).getName());
                }
            } else if ((typeId == 32) && ("oracle".equalsIgnoreCase(dbName))) {
                if ("1".equals(newValue)) {
                    auditLog.setNewValue("TRUE");
                } else {
                    auditLog.setNewValue("FALSE");
                }
                if ("1".equals(oldValue)) {
                    auditLog.setOldValue("TRUE");
                } else {
                    auditLog.setOldValue("FALSE");
                }
            } else {
                auditLog.setNewValue(newValue);
                auditLog.setOldValue(oldValue);
            }
            AuditLogsBean logs = form.getAuditLogs();
            if (logs.getEntityID() == null || logs.getEntityID().length() <= 0) {
                logs.setEntityID(form.getFormOID());
            }
            logs.getAuditLogs().add(auditLog);
            form.setAuditLogs(logs);
        }
    }
}

Example 2 with ExportFormDataBean

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

the class OdmExtractDAO method getClinicalData.

public void getClinicalData(StudyBean study, DatasetBean dataset, OdmClinicalDataBean data, String odmVersion, String studySubjectIds, String odmType) {
    String dbName = CoreResources.getDBName();
    String subprev = "";
    HashMap<String, Integer> sepos = new HashMap<String, Integer>();
    String seprev = "";
    String formprev = "";
    HashMap<String, Integer> igpos = new HashMap<String, Integer>();
    String igprev = "";
    String oidPos = "";
    HashMap<Integer, String> oidPoses = new HashMap<Integer, String>();
    HashMap<Integer, String> idataOidPoses = new HashMap<Integer, String>();
    // String studyIds = "";
    // if (study.getParentStudyId() > 0) {
    // studyIds += study.getId();
    // } else {
    // ArrayList<Integer> ids = (ArrayList<Integer>) (new
    // StudyDAO(this.ds)).findAllSiteIdsByStudy(study);
    // for (int i = 0; i < ids.size() - 1; ++i) {
    // studyIds += ids.get(i) + ",";
    // }
    // studyIds += ids.get(ids.size() - 1);
    // }
    String studyIds = study.getId() + "";
    int datasetItemStatusId = dataset.getDatasetItemStatus().getId();
    String sql = dataset.getSQLStatement().split("order by")[0].trim();
    sql = sql.split("study_event_definition_id in")[1];
    String[] ss = sql.split("and item_id in");
    String sedIds = ss[0];
    String[] sss = ss[1].split("and");
    String itemIds = sss[0];
    String dateConstraint = "";
    if ("postgres".equalsIgnoreCase(dbName)) {
        dateConstraint = "and " + sss[1] + " and " + sss[2];
        dateConstraint = dateConstraint.replace("date_created", "ss.enrollment_date");
    } else if ("oracle".equalsIgnoreCase(dbName)) {
        String[] os = (sss[1] + sss[2]).split("'");
        dateConstraint = "and trunc(ss.enrollment_date) >= to_date('" + os[1] + "') and trunc(ss.enrollment_date) <= to_date('" + os[3] + "')";
    }
    logger.debug("Begin to GetSubjectEventFormSql");
    if (odmVersion.startsWith("oc")) {
        logger.debug("getOCSubjectEventFormSql=" + getOCSubjectEventFormSqlSS(studyIds, sedIds, itemIds, dateConstraint, datasetItemStatusId, studySubjectIds));
        this.setSubjectEventFormDataTypesExpected(odmVersion);
        ArrayList viewRows = select(getOCSubjectEventFormSqlSS(studyIds, sedIds, itemIds, dateConstraint, datasetItemStatusId, studySubjectIds));
        Iterator iter = viewRows.iterator();
        this.setDataWithOCAttributes(study, dataset, data, odmVersion, iter, oidPoses, odmType);
    } else {
        logger.debug("getSubjectEventFormSql=" + getSubjectEventFormSqlSS(studyIds, sedIds, itemIds, dateConstraint, datasetItemStatusId, studySubjectIds));
        this.setSubjectEventFormDataTypesExpected();
        ArrayList viewRows = select(getSubjectEventFormSqlSS(studyIds, sedIds, itemIds, dateConstraint, datasetItemStatusId, studySubjectIds));
        Iterator iter = viewRows.iterator();
        // updated as well because this method came from here.
        while (iter.hasNext()) {
            JobTerminationMonitor.check();
            HashMap row = (HashMap) iter.next();
            String studySubjectLabel = (String) row.get("study_subject_oid");
            String sedOID = (String) row.get("definition_oid");
            Boolean studyEventRepeating = (Boolean) row.get("definition_repeating");
            Integer sampleOrdinal = (Integer) row.get("sample_ordinal");
            String cvOID = (String) row.get("crf_version_oid");
            // ecId
            Integer ecId = (Integer) row.get("event_crf_id");
            CRFVersionBean cvBean = cvdao.findByOid(cvOID);
            CRFBean cBean = (CRFBean) crfdao.findByPK(cvBean.getCrfId());
            // should
            // be unique;
            String key = studySubjectLabel;
            ExportSubjectDataBean sub = new ExportSubjectDataBean();
            if (subprev.equals(studySubjectLabel)) {
                int p = data.getExportSubjectData().size() - 1;
                sub = data.getExportSubjectData().get(p);
            } else {
                subprev = studySubjectLabel;
                sub.setSubjectOID(studySubjectLabel);
                data.getExportSubjectData().add(sub);
                seprev = "";
                formprev = "";
                igprev = "";
            }
            oidPos = data.getExportSubjectData().size() - 1 + "";
            ExportStudyEventDataBean se = new ExportStudyEventDataBean();
            // key += sedOID + sampleOrdinal;
            key += sedOID;
            if (!seprev.equals(key) || !sepos.containsKey(key + sampleOrdinal)) {
                sepos.put(key + sampleOrdinal, sub.getExportStudyEventData().size());
                seprev = key;
                se.setStudyEventOID(sedOID);
                se.setStudyEventRepeatKey(studyEventRepeating ? sampleOrdinal + "" : "-1");
                sub.getExportStudyEventData().add(se);
                formprev = "";
                igprev = "";
            } else {
                se = sub.getExportStudyEventData().get(sepos.get(key + sampleOrdinal));
            }
            oidPos += "---" + (sub.getExportStudyEventData().size() - 1);
            ExportFormDataBean form = new ExportFormDataBean();
            key += cvOID;
            if (formprev.equals(key)) {
                form = se.getExportFormData().get(se.getExportFormData().size() - 1);
            } else {
                formprev = key;
                form.setFormOID(cBean.getOid());
                se.getExportFormData().add(form);
                igprev = "";
            }
            oidPos += "---" + (se.getExportFormData().size() - 1);
            // ecId should be distinct
            oidPoses.put(ecId, oidPos);
            oidPos = "";
        }
    }
    this.setEventGroupItemDataWithUnitTypesExpected();
    logger.debug("Begin to GetEventGroupItemWithUnitSql");
    ArrayList viewRows = select(getEventGroupItemWithUnitSql(studyIds, sedIds, itemIds, dateConstraint, datasetItemStatusId, studySubjectIds));
    logger.debug("getEventGroupItemWithUnitSql : " + getEventGroupItemWithUnitSql(studyIds, sedIds, itemIds, dateConstraint, datasetItemStatusId, studySubjectIds));
    String idataIds = "";
    if (viewRows.size() > 0) {
        Iterator iter = viewRows.iterator();
        ExportSubjectDataBean sub = new ExportSubjectDataBean();
        ExportStudyEventDataBean se = new ExportStudyEventDataBean();
        ExportFormDataBean form = new ExportFormDataBean();
        int ecprev = -1;
        igprev = "";
        boolean goon = true;
        String itprev = "";
        // HashMap<String, String> nullValueMap =
        // ClinicalDataUnit.getNullValueMap();
        HashMap<String, String> nullValueCVs = this.getNullValueCVs(study);
        HashSet<Integer> itemDataIds = new HashSet<Integer>();
        String yearMonthFormat = StringUtil.parseDateFormat(ResourceBundleProvider.getFormatBundle(locale).getString("date_format_year_month"));
        String yearFormat = StringUtil.parseDateFormat(ResourceBundleProvider.getFormatBundle(locale).getString("date_format_year"));
        while (iter.hasNext()) {
            JobTerminationMonitor.check();
            HashMap row = (HashMap) iter.next();
            Integer ecId = (Integer) row.get("event_crf_id");
            Integer igId = (Integer) row.get("item_group_id");
            String igOID = (String) row.get("item_group_oid");
            String igName = (String) row.get("item_group_name");
            Integer itId = (Integer) row.get("item_id");
            String itOID = (String) row.get("item_oid");
            Integer itDataOrdinal = (Integer) row.get("item_data_ordinal");
            String itValue = (String) row.get("value");
            Integer datatypeid = (Integer) row.get("item_data_type_id");
            Integer idataId = (Integer) row.get("item_data_id");
            String muOid = (String) row.get("mu_oid");
            String key = "";
            if (ecId != ecprev) {
                logger.debug("Found ecId=" + ecId + " in subjectEventFormSql is:" + oidPoses.containsKey(ecId));
                if (oidPoses.containsKey(ecId)) {
                    goon = true;
                    String[] poses = oidPoses.get(ecId).split("---");
                    sub = data.getExportSubjectData().get(Integer.valueOf(poses[0]));
                    se = sub.getExportStudyEventData().get(Integer.valueOf(poses[1]));
                    form = se.getExportFormData().get(Integer.valueOf(poses[2]));
                } else {
                    goon = false;
                }
                ecprev = ecId;
            }
            if (goon) {
                ImportItemGroupDataBean ig = new ImportItemGroupDataBean();
                // key = ecId + igOID;
                key = ecId + "-" + igId;
                if (!igprev.equals(key) || !igpos.containsKey(key + itDataOrdinal)) {
                    igpos.put(key + itDataOrdinal, form.getItemGroupData().size());
                    igprev = key;
                    ig.setItemGroupOID(igOID + "");
                    ig.setItemGroupRepeatKey("ungrouped".equalsIgnoreCase(igName) ? "-1" : itDataOrdinal + "");
                    form.getItemGroupData().add(ig);
                } else {
                    ig = form.getItemGroupData().get(igpos.get(key + itDataOrdinal));
                }
                String newpos = oidPoses.get(ecId) + "---" + igpos.get(key + itDataOrdinal);
                // item should be distinct; but duplicated item data have
                // been reported because "save" have been clicked twice.
                // those duplicated item data have been arranged together by
                // "distinct" because of their same
                // ecId+igOID+itOID+itDataOrdinal (08-2008)
                key = itId + "_" + itDataOrdinal + key;
                if (!itprev.equals(key)) {
                    itprev = key;
                    ImportItemDataBean it = new ImportItemDataBean();
                    it.setItemOID(itOID);
                    it.setTransactionType("Insert");
                    String nullKey = study.getId() + "-" + se.getStudyEventOID() + "-" + form.getFormOID();
                    if (ClinicalDataUtil.isNull(itValue, nullKey, nullValueCVs)) {
                        // if
                        // (nullValueMap.containsKey(itValue.trim().toUpperCase()))
                        // {
                        // itValue =
                        // nullValueMap.get(itValue.trim().toUpperCase());
                        it.setIsNull("Yes");
                        String nullvalues = ClinicalDataUtil.presetNullValueStr(nullValueCVs.get(nullKey));
                        boolean hasValueWithNull = ClinicalDataUtil.isValueWithNull(itValue, nullvalues);
                        it.setHasValueWithNull(hasValueWithNull);
                        if (hasValueWithNull) {
                            it.setValue(itValue);
                            it.setReasonForNull(ClinicalDataUtil.getNullsInValue(itValue, nullvalues));
                        } else {
                            it.setReasonForNull(itValue.trim());
                        }
                    } else {
                        if (datatypeid == 9) {
                            try {
                                itValue = new SimpleDateFormat("yyyy-MM-dd").format(new SimpleDateFormat(oc_df_string).parse(itValue));
                            } catch (Exception fe) {
                                logger.debug("Item -" + itOID + " value " + itValue + " might not be ODM date format yyyy-MM-dd.");
                            }
                        }
                        /*
                             * not be supported in openclinica-3.0.40.1
                             * else if (datatypeid == 10 && odmVersion.contains("1.3")) {
                             * if (StringUtil.isFormatDate(itValue, oc_df_string)) {
                             * try {
                             * itValue = new SimpleDateFormat("yyyy-MM-dd").format(new
                             * SimpleDateFormat(oc_df_string).parse(itValue));
                             * } catch (Exception e) {
                             * logger.info("Item -" + itOID + " value " + itValue +
                             * " might not be ODM partialDate format yyyy[-MM[-dd]].");
                             * }
                             * } else {
                             * if (StringUtil.isPartialYearMonth(itValue, yearMonthFormat)) {
                             * try {
                             * itValue = new SimpleDateFormat("yyyy-MM").format(new
                             * SimpleDateFormat(yearMonthFormat).parse(itValue));
                             * } catch (Exception e) {
                             * logger.info("Item -" + itOID + " value " + itValue +
                             * " might not be ODM partialDate format yyyy[-MM[-dd]].");
                             * }
                             * } else {
                             * try {
                             * itValue = new SimpleDateFormat("yyyy").format(new
                             * SimpleDateFormat(yearFormat).parse(itValue));
                             * } catch (Exception e) {
                             * logger.info("Item -" + itOID + " value " + itValue +
                             * " might not be ODM partialDate format yyyy[-MM[-dd]].");
                             * }
                             * }
                             * }
                             * }
                             */
                        it.setValue(itValue);
                    }
                    if (muOid != null && muOid.length() > 0) {
                        ElementRefBean measurementUnitRef = new ElementRefBean();
                        measurementUnitRef.setElementDefOID(muOid);
                        it.setMeasurementUnitRef(measurementUnitRef);
                    }
                    ig.getItemData().add(it);
                    newpos += "---" + (ig.getItemData().size() - 1);
                    idataOidPoses.put(idataId, newpos);
                }
                idataIds += "'" + idataId + "', ";
            }
        }
    }
    idataIds = idataIds.length() > 0 ? idataIds.substring(0, idataIds.length() - 2) : idataIds;
    if (idataIds.length() > 0 && itemIds.length() > 0) {
        this.setErasedScoreItemDataValues(data, itemIds, idataIds, idataOidPoses, odmVersion);
    } else {
        logger.info("OdmExtractDAO.setScoreItemDataNullValues was not called because of empty item_data_ids or/and item_ids");
    }
    if (odmType != null && odmType.equalsIgnoreCase("clinical_data")) {
        logger.debug("Do not create discrepancy notes");
    } else if (odmVersion.startsWith("oc")) {
        if (idataIds.length() > 0) {
            setOCItemDataAuditLogs(study, data, idataIds, idataOidPoses);
            setOCItemDataDNs(data, idataIds, idataOidPoses);
        } else {
            logger.info("OdmExtractDAO.setOCItemDataAuditLogs & setOCItemDataDNs weren't called because of empty idataIds");
        }
    }
}

Example 3 with ExportFormDataBean

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

the class GenerateClinicalDataServiceImpl method getFormDataForClinicalStudy.

private ArrayList<ExportFormDataBean> getFormDataForClinicalStudy(StudySubject ss, StudyEvent se, String formVersionOID) {
    List<ExportFormDataBean> formDataBean = new ArrayList<ExportFormDataBean>();
    boolean formCheck = true;
    if (formVersionOID != null)
        formCheck = false;
    boolean hiddenCrfCheckPassed = true;
    List<CrfBean> hiddenCrfs = new ArrayList<CrfBean>();
    for (EventCrf ecrf : se.getEventCrfs()) {
        List<EventDefinitionCrf> edcs = se.getStudyEventDefinition().getEventDefinitionCrfs();
        hiddenCrfCheckPassed = true;
        int siteId = 0;
        int parentStudyId = 0;
        Study study = ss.getStudy();
        if (study.getStudy() != null && isActiveRoleAtSite) {
            // it is site subject
            siteId = study.getStudyId();
            parentStudyId = study.getStudy().getStudyId();
            hiddenCrfs = listOfHiddenCrfs(siteId, parentStudyId, edcs, ecrf);
            if (hiddenCrfs.contains(ecrf.getCrfVersion().getCrf())) {
                hiddenCrfCheckPassed = false;
            }
        }
        // This logic is to use the same method for both S_OID/SS_OID/*/* and full path
        if (hiddenCrfCheckPassed) {
            if (!formCheck) {
                if (ecrf.getCrfVersion().getOcOid().equals(formVersionOID))
                    formCheck = true;
                else
                    formCheck = false;
            }
            if (formCheck) {
                ExportFormDataBean dataBean = new ExportFormDataBean();
                dataBean.setItemGroupData(fetchItemData(ecrf.getCrfVersion().getItemGroupMetadatas(), ecrf.getEventCrfId(), ecrf.getCrfVersion().getVersioningMaps(), ecrf));
                dataBean.setFormOID(ecrf.getCrfVersion().getCrf().getOcOid());
                if (ecrf.getDateInterviewed() != null)
                    dataBean.setInterviewDate(ecrf.getDateInterviewed() + "");
                if (ecrf.getInterviewerName() != null)
                    dataBean.setInterviewerName(ecrf.getInterviewerName());
                // dataBean.setStatus(EventCRFStatus.getByCode(Integer.valueOf(ecrf.getStatus().getCode())).getI18nDescription(getLocale()));
                dataBean.setStatus(fetchEventCRFStatus(ecrf));
                if (ecrf.getFormLayout().getName() != null)
                    dataBean.setFormLayout(ecrf.getFormLayout().getName());
                if (collectAudits)
                    dataBean.setAuditLogs(fetchAuditLogs(ecrf.getEventCrfId(), "event_crf", ecrf.getCrfVersion().getCrf().getOcOid(), null));
                if (collectDns)
                    dataBean.setDiscrepancyNotes(fetchDiscrepancyNotes(ecrf));
                formDataBean.add(dataBean);
                if (formVersionOID != null)
                    formCheck = false;
            }
        }
    }
    return (ArrayList<ExportFormDataBean>) formDataBean;
}

Example 4 with ExportFormDataBean

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

the class ClinicalDataReportBean method addNodeClinicalData.

public void addNodeClinicalData(boolean header, boolean footer) {
    String ODMVersion = this.getODMVersion();
    // when collecting data, only item with value has been collected.
    StringBuffer xml = this.getXmlOutput();
    String indent = this.getIndent();
    String nls = System.getProperty("line.separator");
    if (header) {
        xml.append(indent + "<ClinicalData StudyOID=\"" + StringEscapeUtils.escapeXml(clinicalData.getStudyOID()) + "\" MetaDataVersionOID=\"" + StringEscapeUtils.escapeXml(this.clinicalData.getMetaDataVersionOID()) + "\">");
        xml.append(nls);
    }
    ArrayList<ExportSubjectDataBean> subs = (ArrayList<ExportSubjectDataBean>) this.clinicalData.getExportSubjectData();
    for (ExportSubjectDataBean sub : subs) {
        xml.append(indent + indent + "<SubjectData SubjectKey=\"" + StringEscapeUtils.escapeXml(sub.getSubjectOID()));
        if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) {
            xml.append("\" OpenClinica:StudySubjectID=\"" + StringEscapeUtils.escapeXml(sub.getStudySubjectId()));
            String uniqueIdentifier = sub.getUniqueIdentifier();
            if (uniqueIdentifier != null && uniqueIdentifier.length() > 0) {
                xml.append("\" OpenClinica:UniqueIdentifier=\"" + StringEscapeUtils.escapeXml(uniqueIdentifier));
            }
            String status = sub.getStatus();
            if (status != null && status.length() > 0) {
                xml.append("\" OpenClinica:Status=\"" + StringEscapeUtils.escapeXml(status));
            }
            String secondaryId = sub.getSecondaryId();
            if (secondaryId != null && secondaryId.length() > 0) {
                xml.append("\"  OpenClinica:SecondaryID=\"" + StringEscapeUtils.escapeXml(secondaryId));
            }
            Integer year = sub.getYearOfBirth();
            if (year != null) {
                xml.append("\" OpenClinica:YearOfBirth=\"" + sub.getYearOfBirth());
            } else {
                if (sub.getDateOfBirth() != null) {
                    xml.append("\" OpenClinica:DateOfBirth=\"" + sub.getDateOfBirth());
                }
            }
            String gender = sub.getSubjectGender();
            if (gender != null && gender.length() > 0) {
                xml.append("\" OpenClinica:Sex=\"" + StringEscapeUtils.escapeXml(gender));
            }
            String enrollmentDate = sub.getEnrollmentDate();
            if (enrollmentDate != null && enrollmentDate.length() > 0) {
                xml.append("\" OpenClinica:EnrollmentDate=\"" + enrollmentDate);
            }
        }
        xml.append("\">");
        xml.append(nls);
        //
        ArrayList<ExportStudyEventDataBean> ses = (ArrayList<ExportStudyEventDataBean>) sub.getExportStudyEventData();
        for (ExportStudyEventDataBean se : ses) {
            xml.append(indent + indent + indent + "<StudyEventData StudyEventOID=\"" + StringEscapeUtils.escapeXml(se.getStudyEventOID()));
            if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) {
                String location = se.getLocation();
                if (location != null && location.length() > 0) {
                    xml.append("\" OpenClinica:StudyEventLocation=\"" + StringEscapeUtils.escapeXml(location));
                }
                String startDate = se.getStartDate();
                if (startDate != null && startDate.length() > 0) {
                    xml.append("\" OpenClinica:StartDate=\"" + startDate);
                }
                String endDate = se.getEndDate();
                if (endDate != null && endDate.length() > 0) {
                    xml.append("\" OpenClinica:EndDate=\"" + endDate);
                }
                String status = se.getStatus();
                if (status != null && status.length() > 0) {
                    xml.append("\" OpenClinica:Status=\"" + StringEscapeUtils.escapeXml(status));
                }
                if (se.getAgeAtEvent() != null) {
                    xml.append("\" OpenClinica:SubjectAgeAtEvent=\"" + se.getAgeAtEvent());
                }
            }
            xml.append("\"");
            if (!"-1".equals(se.getStudyEventRepeatKey())) {
                xml.append(" StudyEventRepeatKey=\"" + se.getStudyEventRepeatKey() + "\"");
            }
            xml.append(">");
            xml.append(nls);
            //
            ArrayList<ExportFormDataBean> forms = se.getExportFormData();
            for (ExportFormDataBean form : forms) {
                xml.append(indent + indent + indent + indent + "<FormData FormOID=\"" + StringEscapeUtils.escapeXml(form.getFormOID()));
                if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) {
                    String formLayout = form.getFormLayout();
                    if (!StringUtils.isEmpty(formLayout)) {
                        xml.append("\" OpenClinica:FormLayoutOID=\"" + StringEscapeUtils.escapeXml(formLayout));
                    }
                    String interviewerName = form.getInterviewerName();
                    if (interviewerName != null && interviewerName.length() > 0) {
                        xml.append("\" OpenClinica:InterviewerName=\"" + StringEscapeUtils.escapeXml(interviewerName));
                    }
                    if (form.getInterviewDate() != null && form.getInterviewDate().length() > 0) {
                        xml.append("\" OpenClinica:InterviewDate=\"" + form.getInterviewDate());
                    }
                    String status = form.getStatus();
                    if (status != null && status.length() > 0) {
                        xml.append("\" OpenClinica:Status=\"" + StringEscapeUtils.escapeXml(status));
                    }
                }
                xml.append("\">");
                xml.append(nls);
                //
                ArrayList<ImportItemGroupDataBean> igs = form.getItemGroupData();
                sortImportItemGroupDataBeanList(igs);
                for (ImportItemGroupDataBean ig : igs) {
                    xml.append(indent + indent + indent + indent + indent + "<ItemGroupData ItemGroupOID=\"" + StringEscapeUtils.escapeXml(ig.getItemGroupOID()) + "\" ");
                    if (!"-1".equals(ig.getItemGroupRepeatKey())) {
                        xml.append("ItemGroupRepeatKey=\"" + ig.getItemGroupRepeatKey() + "\" ");
                    }
                    if (ig.getItemData().get(0).isDeleted()) {
                        xml.append("OpenClinica:Removed=\"" + (ig.getItemData().get(0).isDeleted() ? "Yes" : "No") + "\" ");
                    }
                    xml.append("TransactionType=\"Insert\">");
                    xml.append(nls);
                    ArrayList<ImportItemDataBean> items = ig.getItemData();
                    sortImportItemDataBeanList(items);
                    for (ImportItemDataBean item : items) {
                        boolean printValue = true;
                        xml.append(indent + indent + indent + indent + indent + indent + "<ItemData ItemOID=\"" + StringEscapeUtils.escapeXml(item.getItemOID()) + "\" ");
                        if ("Yes".equals(item.getIsNull())) {
                            xml.append("IsNull=\"Yes\"");
                            if (!item.isHasValueWithNull()) {
                                printValue = false;
                            }
                            if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) {
                                xml.append(" OpenClinica:ReasonForNull=\"" + StringEscapeUtils.escapeXml(item.getReasonForNull()) + "\" ");
                                if (!printValue) {
                                    xml.append("/>");
                                    xml.append(nls);
                                }
                            }
                        }
                        if (printValue) {
                            Boolean hasElm = false;
                            xml.append("Value=\"" + StringEscapeUtils.escapeXml(item.getValue()) + "\"");
                            String muRefOid = item.getMeasurementUnitRef().getElementDefOID();
                            if (muRefOid != null && muRefOid.length() > 0) {
                                if (hasElm) {
                                } else {
                                    xml.append(">");
                                    xml.append(nls);
                                    hasElm = true;
                                }
                                xml.append(indent + indent + indent + indent + indent + indent + indent + "<MeasurementUnitRef MeasurementUnitOID=\"" + StringEscapeUtils.escapeXml(muRefOid) + "\"/>");
                                xml.append(nls);
                            }
                            if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) {
                                if (item.getAuditLogs() != null && item.getAuditLogs().getAuditLogs().size() > 0) {
                                    if (hasElm) {
                                    } else {
                                        xml.append(">");
                                        xml.append(nls);
                                        hasElm = true;
                                    }
                                    this.addAuditLogs(item.getAuditLogs(), indent + indent + indent + indent + indent + indent + indent, "item");
                                }
                                //
                                if (item.getDiscrepancyNotes() != null && item.getDiscrepancyNotes().getDiscrepancyNotes().size() > 0) {
                                    if (hasElm) {
                                    } else {
                                        xml.append(">");
                                        xml.append(nls);
                                        hasElm = true;
                                    }
                                    this.addDiscrepancyNotes(item.getDiscrepancyNotes(), indent + indent + indent + indent + indent + indent + indent);
                                }
                            }
                            if (hasElm) {
                                xml.append(indent + indent + indent + indent + indent + indent + "</ItemData>");
                                xml.append(nls);
                                hasElm = false;
                            } else {
                                xml.append("/>");
                                xml.append(nls);
                            }
                        }
                    }
                    xml.append(indent + indent + indent + indent + indent + "</ItemGroupData>");
                    xml.append(nls);
                }
                //
                if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) {
                    if (form.getAuditLogs() != null && form.getAuditLogs().getAuditLogs().size() > 0) {
                        this.addAuditLogs(form.getAuditLogs(), indent + indent + indent + indent + indent, "form");
                    }
                    //
                    if (form.getDiscrepancyNotes() != null && form.getDiscrepancyNotes().getDiscrepancyNotes().size() > 0) {
                        this.addDiscrepancyNotes(form.getDiscrepancyNotes(), indent + indent + indent + indent + indent);
                    }
                }
                xml.append(indent + indent + indent + indent + "</FormData>");
                xml.append(nls);
            }
            //
            if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) {
                if (se.getAuditLogs() != null && se.getAuditLogs().getAuditLogs().size() > 0) {
                    this.addAuditLogs(se.getAuditLogs(), indent + indent + indent + indent, "se");
                }
                //
                if (se.getDiscrepancyNotes() != null && se.getDiscrepancyNotes().getDiscrepancyNotes().size() > 0) {
                    this.addDiscrepancyNotes(se.getDiscrepancyNotes(), indent + indent + indent + indent);
                }
            }
            xml.append(indent + indent + indent + "</StudyEventData>");
            xml.append(nls);
        }
        if ("oc1.2".equalsIgnoreCase(ODMVersion) || "oc1.3".equalsIgnoreCase(ODMVersion)) {
            ArrayList<SubjectGroupDataBean> sgddata = (ArrayList<SubjectGroupDataBean>) sub.getSubjectGroupData();
            if (sgddata.size() > 0) {
                for (SubjectGroupDataBean sgd : sgddata) {
                    String cid = sgd.getStudyGroupClassId() != null ? "OpenClinica:StudyGroupClassID=\"" + StringEscapeUtils.escapeXml(sgd.getStudyGroupClassId()) + "\" " : "";
                    if (cid.length() > 0) {
                        String cn = sgd.getStudyGroupClassName() != null ? "OpenClinica:StudyGroupClassName=\"" + StringEscapeUtils.escapeXml(sgd.getStudyGroupClassName()) + "\" " : "";
                        String gn = sgd.getStudyGroupName() != null ? "OpenClinica:StudyGroupName=\"" + StringEscapeUtils.escapeXml(sgd.getStudyGroupName()) + "\" " : "";
                        xml.append(indent + indent + indent + "<OpenClinica:SubjectGroupData " + cid + cn + gn);
                    }
                    xml.append(" />");
                    xml.append(nls);
                }
            }
            //
            if (sub.getAuditLogs() != null && sub.getAuditLogs().getAuditLogs().size() > 0) {
                this.addAuditLogs(sub.getAuditLogs(), indent + indent + indent, "sub");
            }
            //
            if (sub.getDiscrepancyNotes() != null && sub.getDiscrepancyNotes().getDiscrepancyNotes().size() > 0) {
                this.addDiscrepancyNotes(sub.getDiscrepancyNotes(), indent + indent + indent);
            }
        }
        xml.append(indent + indent + "</SubjectData>");
        xml.append(nls);
    }
    if (footer) {
        xml.append(indent + "</ClinicalData>");
        xml.append(nls);
    }
}

Example 5 with ExportFormDataBean

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

the class OdmExtractDAO method setDataWithOCAttributes.

protected void setDataWithOCAttributes(StudyBean study, DatasetBean dataset, OdmClinicalDataBean data, String odmVersion, Iterator iter, HashMap<Integer, String> oidPoses, String odmType) {
    String subprev = "";
    HashMap<String, Integer> sepos = new HashMap<String, Integer>();
    String seprev = "";
    String formprev = "";
    HashMap<String, Integer> igpos = new HashMap<String, Integer>();
    String igprev = "";
    String oidPos = "";
    StudyBean parentStudy = study.getParentStudyId() > 0 ? (StudyBean) new StudyDAO(this.ds).findByPK(study.getParentStudyId()) : study;
    setStudyParemeterConfig(parentStudy);
    HashSet<Integer> sgcIdSet = new HashSet<Integer>();
    HashMap<String, String> subOidPoses = new HashMap<String, String>();
    HashMap<String, String> evnOidPoses = new HashMap<String, String>();
    String studySubjectOids = "";
    String sedOids = "";
    String ecIds = "";
    while (iter.hasNext()) {
        HashMap row = (HashMap) iter.next();
        String studySubjectLabel = (String) row.get("study_subject_oid");
        // String label = (String) row.get("label");
        Integer sgcId = (Integer) row.get("sgc_id");
        String sgcName = (String) row.get("sgc_name");
        String sgName = (String) row.get("sg_name");
        String sedOID = (String) row.get("definition_oid");
        Boolean studyEventRepeating = (Boolean) row.get("definition_repeating");
        Integer sampleOrdinal = (Integer) row.get("sample_ordinal");
        Date startDate = (Date) row.get("date_start");
        String cvOID = (String) row.get("crf_version_oid");
        // ecId should
        Integer ecId = (Integer) row.get("event_crf_id");
        // be unique;
        Date dob = (Date) row.get("date_of_birth");
        CRFVersionBean cvBean = cvdao.findByOid(cvOID);
        CRFBean cBean = (CRFBean) crfdao.findByPK(cvBean.getCrfId());
        String key = studySubjectLabel;
        ExportSubjectDataBean sub = new ExportSubjectDataBean();
        if (subprev.equals(studySubjectLabel)) {
            int p = data.getExportSubjectData().size() - 1;
            sub = data.getExportSubjectData().get(p);
            // ------ add openclinica subject_group
            if (sgcId > 0) {
                int presize = sgcIdSet.size();
                sgcIdSet.add(sgcId);
                if (sgcIdSet.size() > presize) {
                    sgcIdSet.add(sgcId);
                    SubjectGroupDataBean sgd = new SubjectGroupDataBean();
                    sgd.setStudyGroupClassId("SGC_" + sgcId);
                    sgd.setStudyGroupClassName(sgcName);
                    sgd.setStudyGroupName(sgName);
                    sub.getSubjectGroupData().add(sgd);
                }
            }
        // ------ finish adding openclinica subject_group
        } else {
            subprev = studySubjectLabel;
            studySubjectOids += "'" + studySubjectLabel + "', ";
            sub.setSubjectOID(studySubjectLabel);
            // ----- add openclinica subject attributes
            sub.setStudySubjectId((String) row.get("label"));
            if (dataset.isShowSubjectUniqueIdentifier()) {
                sub.setUniqueIdentifier((String) row.get("unique_identifier"));
            }
            if (dataset.isShowSubjectSecondaryId()) {
                sub.setSecondaryId((String) row.get("secondary_label"));
            }
            if (dob != null) {
                if (dataset.isShowSubjectDob()) {
                    if (parentStudy.getStudyParameterConfig().getCollectDob().equals("2")) {
                        Calendar cal = Calendar.getInstance();
                        cal.setTime(dob);
                        int year = cal.get(Calendar.YEAR);
                        if (year > 0) {
                            sub.setYearOfBirth(year);
                        }
                    } else {
                        sub.setDateOfBirth(new SimpleDateFormat("yyyy-MM-dd").format(dob));
                    }
                }
            }
            if (dataset.isShowSubjectGender()) {
                sub.setSubjectGender((String) row.get("gender"));
            }
            if (dataset.isShowSubjectStatus()) {
                sub.setStatus(Status.get((Integer) row.get("status_id")).getName());
            }
            // ------ add openclinica subject_group
            if (sgcId > 0) {
                sgcIdSet.clear();
                sgcIdSet.add(sgcId);
                SubjectGroupDataBean sgd = new SubjectGroupDataBean();
                sgd.setStudyGroupClassId("SGC_" + sgcId);
                sgd.setStudyGroupClassName(sgcName);
                sgd.setStudyGroupName(sgName);
                sub.getSubjectGroupData().add(sgd);
            }
            // ------ finish adding openclinica subject_group
            data.getExportSubjectData().add(sub);
            seprev = "";
            formprev = "";
            igprev = "";
        }
        oidPos = data.getExportSubjectData().size() - 1 + "";
        subOidPoses.put(studySubjectLabel, oidPos);
        ExportStudyEventDataBean se = new ExportStudyEventDataBean();
        // key += sedOID + sampleOrdinal;
        key += sedOID;
        if (!seprev.equals(key) || !sepos.containsKey(key + sampleOrdinal)) {
            sepos.put(key + sampleOrdinal, sub.getExportStudyEventData().size());
            seprev = key;
            sedOids += "'" + sedOID + "', ";
            se.setStudyEventOID(sedOID);
            // ----- add openclinica study event attributes
            if (startDate != null && dataset.isShowSubjectAgeAtEvent() && dob != null) {
                se.setAgeAtEvent(Utils.getAge(dob, startDate));
            }
            if (dataset.isShowEventLocation()) {
                se.setLocation((String) row.get("se_location"));
            }
            if (dataset.isShowEventStart() && startDate != null) {
                if ((Boolean) row.get("start_time_flag") == Boolean.TRUE) {
                    se.setStartDate(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss").format(startDate));
                } else {
                    se.setStartDate(new SimpleDateFormat("yyyy-MM-dd").format(startDate));
                }
            }
            Date endDate = (Date) row.get("date_end");
            if (dataset.isShowEventEnd() && endDate != null) {
                if ((Boolean) row.get("end_time_flag") == Boolean.TRUE) {
                    se.setEndDate(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss").format(endDate));
                } else {
                    se.setEndDate(new SimpleDateFormat("yyyy-MM-dd").format(endDate));
                }
            }
            if (dataset.isShowEventStatus()) {
                se.setStatus(SubjectEventStatus.get((Integer) row.get("event_status_id")).getName());
            }
            // ----- finish adding study event attributes
            se.setStudyEventRepeatKey(studyEventRepeating ? sampleOrdinal + "" : "-1");
            sub.getExportStudyEventData().add(se);
            formprev = "";
            igprev = "";
        } else {
            se = sub.getExportStudyEventData().get(sepos.get(key + sampleOrdinal));
        }
        oidPos += "---" + (sub.getExportStudyEventData().size() - 1);
        evnOidPoses.put(key, oidPos);
        ExportFormDataBean form = new ExportFormDataBean();
        key += cvOID;
        if (formprev.equals(key)) {
            form = se.getExportFormData().get(se.getExportFormData().size() - 1);
        } else {
            formprev = key;
            ecIds += "'" + ecId + "', ";
            form.setFormOID(cBean.getOid());
            // ----- add openclinica crf attributes
            if (dataset.isShowCRFversion()) {
                form.setCrfVersion((String) row.get("crf_version"));
            }
            if (dataset.isShowCRFstatus()) {
                form.setStatus(this.getCrfVersionStatus(se.getStatus(), (Integer) row.get("cv_status_id"), (Integer) row.get("ec_status_id"), (Integer) row.get("validator_id")));
            }
            if (dataset.isShowCRFinterviewerName()) {
                form.setInterviewerName((String) row.get("interviewer_name"));
            }
            if (dataset.isShowCRFinterviewerDate()) {
                try {
                    form.setInterviewDate(new SimpleDateFormat("yyyy-MM-dd").format((Date) row.get("date_interviewed")));
                } catch (NullPointerException npe) {
                    logger.debug("caught NPE for interviewDate");
                // Comment it out for: 11592. For this exaction function, interviewDate should be kept as the
                // same as in database.
                // form.setInterviewDate(new SimpleDateFormat("yyyy-MM-dd").format(new Date()));
                }
            }
            // ----- finish adding crf attributes
            se.getExportFormData().add(form);
            igprev = "";
        }
        oidPos += "---" + (se.getExportFormData().size() - 1);
        // ecId should be distinct
        oidPoses.put(ecId, oidPos);
        oidPos = "";
    }
    studySubjectOids = studySubjectOids.length() > 0 ? studySubjectOids.substring(0, studySubjectOids.length() - 2).trim() : studySubjectOids;
    sedOids = sedOids.length() > 0 ? sedOids.substring(0, sedOids.length() - 2).trim() : sedOids;
    ecIds = ecIds.length() > 0 ? ecIds.substring(0, ecIds.length() - 2).trim() : ecIds;
    if (odmType != null && odmType.equalsIgnoreCase("clinical_data")) {
        logger.debug("No Audit logs or discrepancy Notes");
    } else {
        if (studySubjectOids.length() > 0) {
            this.setOCSubjectDataAuditLogs(parentStudy, data, studySubjectOids, subOidPoses);
            this.setOCEventDataAuditLogs(parentStudy, data, studySubjectOids, evnOidPoses);
            if (ecIds.length() > 0) {
                this.setOCFormDataAuditLogs(parentStudy, data, studySubjectOids, ecIds, oidPoses);
            } else {
                logger.debug("OdmExtractDAO.setOCFormDataAuditLogs wasn't called because of empty ecIds");
            }
            this.setOCSubjectDataDNs(data, studySubjectOids, subOidPoses);
            if (sedOids.length() > 0) {
                this.setOCEventDataDNs(data, sedOids, studySubjectOids, evnOidPoses);
            } else {
                logger.info("OdmExtractDAO.setOCEventDataDNs wasn't called because of empty sedOids");
            }
        } else {
            logger.debug("OdmExtractDAO methods(setOCSubjectDataAuditLogs,setOCEventDataAuditLogs,setOCFormDataAuditLogs," + "setOCSubjectDataDNs,setOCEventDataDNs) weren't called because of empty studySubjectOids");
        }
        if (ecIds.length() > 0) {
            this.setOCFormDataDNs(data, ecIds, oidPoses);
        } else {
            logger.debug("OdmExtractDAO.setOCFormDataDNs wasn't called because of empty ecIds");
        }
    }
}