Examples with ODM org.cdisc.ns.odm.v130.ODM used on opensource projects

Example 1 with ODM

use of org.cdisc.ns.odm.v130.ODM in project OpenClinica by OpenClinica.

the class OdmController method getODM.

private ODM getODM(String studyOID, String subjectKey) {
    ODM odm = new ODM();
    String ssoid = subjectKey;
    if (ssoid == null) {
        return null;
    }
    FormLayoutDAO formLayoutDAO = new FormLayoutDAO(dataSource);
    StudyDAO studyDAO = new StudyDAO(dataSource);
    StudySubjectDAO studySubjectDAO = new StudySubjectDAO(dataSource);
    EventCRFDAO eventCRFDAO = new EventCRFDAO(dataSource);
    ItemDataDAO itemDataDAO = new ItemDataDAO(dataSource);
    CRFDAO crfDAO = new CRFDAO(dataSource);
    List<ODMcomplexTypeDefinitionFormData> formDatas = new ArrayList<>();
    try {
        // Retrieve crfs for next event
        StudySubjectBean studySubjectBean = studySubjectDAO.findByOid(ssoid);
        ParticipantEventService participantEventService = new ParticipantEventService(dataSource);
        StudyEventBean nextEvent = participantEventService.getNextParticipantEvent(studySubjectBean);
        if (nextEvent != null) {
            logger.debug("Found event: " + nextEvent.getName() + " - ID: " + nextEvent.getId());
            List<EventCRFBean> eventCrfs = eventCRFDAO.findAllByStudyEvent(nextEvent);
            StudyBean study = studyDAO.findByOid(studyOID);
            if (!mayProceed(studyOID, studySubjectBean))
                return odm;
            List<EventDefinitionCRFBean> eventDefCrfs = participantEventService.getEventDefCrfsForStudyEvent(studySubjectBean, nextEvent);
            for (EventDefinitionCRFBean eventDefCrf : eventDefCrfs) {
                if (eventDefCrf.isParticipantForm()) {
                    EventCRFBean eventCRF = participantEventService.getExistingEventCRF(studySubjectBean, nextEvent, eventDefCrf);
                    boolean itemDataExists = false;
                    boolean validStatus = true;
                    FormLayoutBean formLayout = null;
                    if (eventCRF != null) {
                        if (eventCRF.getStatus().getId() != 1 && eventCRF.getStatus().getId() != 2)
                            validStatus = false;
                        if (itemDataDAO.findAllByEventCRFId(eventCRF.getId()).size() > 0)
                            itemDataExists = true;
                        formLayout = (FormLayoutBean) formLayoutDAO.findByPK(eventCRF.getFormLayoutId());
                    } else
                        formLayout = (FormLayoutBean) formLayoutDAO.findByPK(eventDefCrf.getDefaultVersionId());
                    if (validStatus) {
                        String formUrl = null;
                        if (!itemDataExists)
                            formUrl = createEnketoUrl(studyOID, formLayout, nextEvent, ssoid);
                        else
                            formUrl = createEditUrl(studyOID, formLayout, nextEvent, ssoid);
                        formDatas.add(getFormDataPerCrf(formLayout, nextEvent, eventCrfs, crfDAO, formUrl, itemDataExists));
                    }
                }
            }
            return createOdm(study, studySubjectBean, nextEvent, formDatas);
        } else {
            logger.debug("Unable to find next event for subject.");
        }
    } catch (Exception e) {
        logger.error(e.getMessage());
        logger.error(ExceptionUtils.getStackTrace(e));
    }
    return odm;
}

Example 2 with ODM

use of org.cdisc.ns.odm.v130.ODM in project OpenClinica by OpenClinica.

the class MetadataCollectorResource method collectODMMetadata.

public String collectODMMetadata(String studyOID) {
    StudyBean studyBean = getStudyDao().findByOid(studyOID);
    MetaDataCollector mdc = new MetaDataCollector(this.dataSource, studyBean, getRuleSetRuleDao());
    AdminDataCollector adc = new AdminDataCollector(this.dataSource, studyBean);
    MetaDataCollector.setTextLength(200);
    ODM odm = new ODM();
    ODMBean odmb = mdc.getODMBean();
    odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0-OC3-0.xsd");
    ArrayList<String> xmlnsList = new ArrayList<String>();
    xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.3\"");
    // xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/openclinica_odm/v1.3\"");
    xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/odm_ext_v130/v3.1\"");
    xmlnsList.add("xmlns:OpenClinicaRules=\"http://www.openclinica.org/ns/rules/v3.1\"");
    odmb.setXmlnsList(xmlnsList);
    odmb.setODMVersion("oc1.3");
    mdc.setODMBean(odmb);
    adc.setOdmbean(odmb);
    mdc.collectFileData();
    adc.collectFileData();
    FullReportBean report = new FullReportBean();
    report.setAdminDataMap(adc.getOdmAdminDataMap());
    report.setOdmStudyMap(mdc.getOdmStudyMap());
    report.setCoreResources(getCoreResources());
    report.setOdmBean(mdc.getODMBean());
    report.setODMVersion("oc1.3");
    report.createStudyMetaOdmXml(Boolean.FALSE);
    return report.getXmlOutput().toString().trim();
}

Example 3 with ODM

use of org.cdisc.ns.odm.v130.ODM in project OpenClinica by OpenClinica.

the class OdmImportServiceImpl method importOdmToOC.

@Transactional
public void importOdmToOC(ODM odm) {
    UserAccount userAccount = getCurrentUser();
    // TODO add validation to all entities
    ODMcomplexTypeDefinitionStudy odmStudy = odm.getStudy().get(0);
    Study study = saveOrUpdateStudy(odm, userAccount, odmStudy);
    ParticipantPortalRegistrar portal = new ParticipantPortalRegistrar();
    portal.registerStudy(study.getOc_oid(), study.getOc_oid(), study.getName());
    StudyParameterValue spv = getStudyParameterValueDao().findByStudyIdParameter(study.getStudyId(), "participantPortal");
    // Update OC Study configuration
    if (spv == null) {
        spv = new StudyParameterValue();
        spv.setStudy(study);
    }
    spv.setValue("enabled");
    spv = getStudyParameterValueDao().saveOrUpdate(spv);
    StudyUserRole studyUserRole = null;
    StudyUserRoleId studyUserRoleId = null;
    Form[] fmCrfs = getAllCrfsByProtIdFromFormManager(study);
    ArrayList<StudyUserRole> surRoles = getStudyUserRoleDao().findAllUserRolesByUserAccount(userAccount, study.getStudyId(), study.getStudyId());
    if (surRoles.size() == 0) {
        studyUserRoleId = new StudyUserRoleId();
        studyUserRole = new StudyUserRole();
        studyUserRole = getStudyUserRoleDao().saveOrUpdate(populateUserRole(study, userAccount, studyUserRole, studyUserRoleId));
    }
    StudyEventDefinition studyEventDefinition = null;
    List<ODMcomplexTypeDefinitionMetaDataVersion> odmMetadataVersions = odmStudy.getMetaDataVersion();
    List<ODMcomplexTypeDefinitionStudyEventDef> odmStudyEventDefs = saveOrUpdateEvent(userAccount, study, odmMetadataVersions);
    CrfBean crf = null;
    FormLayout formLayout = null;
    saveOrUpdateCrf(userAccount, study, odmMetadataVersions, fmCrfs);
    List<ODMcomplexTypeDefinitionStudyEventRef> odmStudyEventRefs = odmMetadataVersions.get(0).getProtocol().getStudyEventRef();
    for (ODMcomplexTypeDefinitionStudyEventRef odmStudyEventRef : odmStudyEventRefs) {
        for (ODMcomplexTypeDefinitionStudyEventDef odmStudyEventDef : odmStudyEventDefs) {
            if (odmStudyEventDef.getOID().equals(odmStudyEventRef.getStudyEventOID())) {
                studyEventDefinition = getStudyEventDefDao().findByOcOID(odmStudyEventDef.getOID());
                studyEventDefinition.setOrdinal(odmStudyEventRef.getOrderNumber().intValue());
                studyEventDefinition = getStudyEventDefDao().saveOrUpdate(studyEventDefinition);
                List<EventDefinitionCrf> jsonEventDefCrfList = new ArrayList<>();
                EventDefinitionCrf eventDefinitionCrf = null;
                for (ODMcomplexTypeDefinitionFormRef odmFormRef : odmStudyEventDef.getFormRef()) {
                    crf = getCrfDao().findByOcOID(odmFormRef.getFormOID());
                    eventDefinitionCrf = getEventDefinitionCrfDao().findByStudyEventDefinitionIdAndCRFIdAndStudyId(studyEventDefinition.getStudyEventDefinitionId(), crf.getCrfId(), study.getStudyId());
                    String defaultVersionName = null;
                    OCodmComplexTypeDefinitionConfigurationParameters conf = odmFormRef.getConfigurationParameters();
                    List<OCodmComplexTypeDefinitionFormLayoutRef> formLayoutRefs = odmFormRef.getFormLayoutRef();
                    if (formLayoutRefs.size() == 1 && formLayoutRefs.get(0).getIsDefaultVersion() == null) {
                        defaultVersionName = formLayoutRefs.get(0).getOID();
                    } else {
                        for (OCodmComplexTypeDefinitionFormLayoutRef formLayoutRef : formLayoutRefs) {
                            if (formLayoutRef.getIsDefaultVersion().equalsIgnoreCase("Yes")) {
                                defaultVersionName = formLayoutRef.getOID();
                            }
                        }
                    }
                    if (defaultVersionName == null) {
                        defaultVersionName = formLayoutRefs.get(0).getOID();
                    }
                    formLayout = getFormLayoutDao().findByNameCrfId(defaultVersionName, crf.getCrfId());
                    EventDefinitionCrfDTO edcObj = new EventDefinitionCrfDTO();
                    edcObj.setUserAccount(userAccount);
                    edcObj.setConf(conf);
                    edcObj.setCrf(crf);
                    edcObj.setEventDefinitionCrf(eventDefinitionCrf);
                    edcObj.setOdmFormRef(odmFormRef);
                    edcObj.setStudy(study);
                    edcObj.setFormLayout(formLayout);
                    edcObj.setStudyEventDefinition(studyEventDefinition);
                    EDCTagDTO populateEDCTagParameter = new EDCTagDTO();
                    populateEDCTagParameter.setConf(conf);
                    populateEDCTagParameter.setConf(conf);
                    populateEDCTagParameter.setEventDefinitionCrf(eventDefinitionCrf);
                    populateEDCTagParameter.setUserAccount(userAccount);
                    eventDefinitionCrf = saveOrUpdateEventDefnCrf(new EventDefinitionCrfDTO(edcObj));
                    saveOrUpdateEDCTag(new EDCTagDTO(populateEDCTagParameter), studyEventDefinition, crf);
                    jsonEventDefCrfList.add(eventDefinitionCrf);
                }
                List<EventDefinitionCrf> ocEventDefCrfList = getEventDefinitionCrfDao().findAvailableByStudyEventDefStudy(studyEventDefinition.getStudyEventDefinitionId(), study.getStudyId());
                for (EventDefinitionCrf ocEventDefCrf : ocEventDefCrfList) {
                    if (!jsonEventDefCrfList.contains(ocEventDefCrf)) {
                        ocEventDefCrf.setStatusId(Status.DELETED.getCode());
                        getEventDefinitionCrfDao().saveOrUpdate(ocEventDefCrf);
                    }
                }
            }
        }
    }
}

Example 4 with ODM

use of org.cdisc.ns.odm.v130.ODM in project OpenClinica by OpenClinica.

the class OdmImportServiceImpl method saveOrUpdateStudy.

private Study saveOrUpdateStudy(ODM odm, UserAccount userAccount, ODMcomplexTypeDefinitionStudy odmStudy) {
    ODMcomplexTypeDefinitionGlobalVariables odmGlobalVariables = odmStudy.getGlobalVariables();
    String studyOid = odm.getStudy().get(0).getOID();
    Study study = getStudyDao().findByOcOID(studyOid);
    if (study == null || study.getStudyId() == 0) {
        study = new Study();
        study.setOc_oid(studyOid);
        study = getStudyDao().saveOrUpdate(populateStudy(odmGlobalVariables, userAccount, study));
    } else {
        study = getStudyDao().saveOrUpdate(updateStudy(odmGlobalVariables, userAccount, study));
    }
    return study;
}

Example 5 with ODM

use of org.cdisc.ns.odm.v130.ODM in project OpenClinica by OpenClinica.

the class OdmController method createOdm.

private ODM createOdm(StudyBean study, StudySubjectBean studySubjectBean, StudyEventBean nextEvent, List<ODMcomplexTypeDefinitionFormData> formDatas) {
    ODM odm = new ODM();
    ODMcomplexTypeDefinitionClinicalData clinicalData = generateClinicalData(study);
    ODMcomplexTypeDefinitionSubjectData subjectData = generateSubjectData(studySubjectBean);
    ODMcomplexTypeDefinitionStudyEventData studyEventData = generateStudyEventData(nextEvent);
    // Create the object graph
    studyEventData.getFormData().addAll(formDatas);
    subjectData.getStudyEventData().add(studyEventData);
    clinicalData.getSubjectData().add(subjectData);
    odm.getClinicalData().add(clinicalData);
    return odm;
}