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

Example 1 with ODMcomplexTypeDefinitionMetaDataVersion

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

the class OdmImportServiceImpl method saveOrUpdateCrf.

private void saveOrUpdateCrf(UserAccount userAccount, Study study, List<ODMcomplexTypeDefinitionMetaDataVersion> odmMetadataVersions, Form[] fmCrfs) {
    for (ODMcomplexTypeDefinitionFormDef odmFormDef : odmMetadataVersions.get(0).getFormDef()) {
        String crfOid = odmFormDef.getOID();
        List<OCodmComplexTypeDefinitionFormLayoutDef> formLayoutDefs = odmFormDef.getFormLayoutDef();
        // String crfDescription = odmFormDef.getFormDetails().getDescription();
        String crfName = odmFormDef.getName();
        saveOrUpdateCrfAndFormLayouts(crfOid, formLayoutDefs, fmCrfs, userAccount, study, crfName);
    }
}

Example 2 with ODMcomplexTypeDefinitionMetaDataVersion

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

the class OdmImportServiceImpl method saveOrUpdateEvent.

private List<ODMcomplexTypeDefinitionStudyEventDef> saveOrUpdateEvent(UserAccount userAccount, Study study, List<ODMcomplexTypeDefinitionMetaDataVersion> odmMetadataVersions) {
    StudyEventDefinition studyEventDefinition;
    List<ODMcomplexTypeDefinitionStudyEventDef> odmStudyEventDefs = odmMetadataVersions.get(0).getStudyEventDef();
    List<StudyEventDefinition> jsonEventList = new ArrayList<>();
    for (ODMcomplexTypeDefinitionStudyEventDef odmStudyEventDef : odmStudyEventDefs) {
        studyEventDefinition = getStudyEventDefDao().findByOcOID(odmStudyEventDef.getOID());
        if (studyEventDefinition == null || studyEventDefinition.getStudyEventDefinitionId() == 0) {
            studyEventDefinition = new StudyEventDefinition();
            studyEventDefinition.setOc_oid(odmStudyEventDef.getOID());
            studyEventDefinition = getStudyEventDefDao().saveOrUpdate(populateEvent(odmStudyEventDef, userAccount, studyEventDefinition, study));
        } else {
            studyEventDefinition = getStudyEventDefDao().saveOrUpdate(updateEvent(odmStudyEventDef, userAccount, studyEventDefinition, study));
        }
        jsonEventList.add(studyEventDefinition);
    }
    // findAllNonRemovedEvents
    List<StudyEventDefinition> ocEventList = getStudyEventDefDao().findAll();
    for (StudyEventDefinition ocEvent : ocEventList) {
        if (!jsonEventList.contains(ocEvent)) {
            ocEvent.setStatus(Status.DELETED);
            getStudyEventDefDao().saveOrUpdate(ocEvent);
        }
    }
    return odmStudyEventDefs;
}

Example 3 with ODMcomplexTypeDefinitionMetaDataVersion

use of org.cdisc.ns.odm.v130.ODMcomplexTypeDefinitionMetaDataVersion 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);
                    }
                }
            }
        }
    }
}