Examples with CrfBean org.akaza.openclinica.domain.datamap.CrfBean used on opensource projects

Example 1 with CrfBean

use of org.akaza.openclinica.domain.datamap.CrfBean in project OpenClinica by OpenClinica.

the class XformMetaDataService method createCRFMetaData.

@Transactional
public FormLayout createCRFMetaData(CrfMetaDataObject cmdObject) throws Exception {
    CrfVersion crfVersion = null;
    FormLayout formLayout = null;
    CrfBean crfBean = null;
    Section section = null;
    crfBean = (CrfBean) crfDao.findByOcOID(cmdObject.crf.getOcoid());
    if (crfBean != null) {
        crfBean.setUpdateId(cmdObject.ub.getId());
        crfBean.setDateUpdated(new Date());
        crfBean = crfDao.saveOrUpdate(crfBean);
        formLayout = formLayoutDao.findByOcOID(cmdObject.version.getOcoid());
        if (formLayout == null) {
            formLayout = new FormLayout();
            formLayout = populateFormLayout(formLayout, crfBean, cmdObject);
            formLayout = formLayoutDao.saveOrUpdate(formLayout);
        }
        crfVersion = crfVersionDao.findAllByCrfId(crfBean.getCrfId()).get(0);
        section = sectionDao.findByCrfVersionOrdinal(crfVersion.getCrfVersionId(), 1);
    } else {
        crfBean = new CrfBean();
        crfBean = populateCrf(crfBean, cmdObject);
        Integer crfId = (Integer) crfDao.save(crfBean);
        crfBean.setCrfId(crfId);
        // Create new Form Layout
        formLayout = new FormLayout();
        formLayout = populateFormLayout(formLayout, crfBean, cmdObject);
        formLayout = formLayoutDao.saveOrUpdate(formLayout);
        // Create new CRF Version
        crfVersion = new CrfVersion();
        crfVersion = populateCrfVersion(crfBean, crfVersion, cmdObject);
        crfVersion = crfVersionDao.saveOrUpdate(crfVersion);
        // Create Section
        section = sectionDao.findByCrfVersionOrdinal(crfVersion.getCrfVersionId(), 1);
        if (section == null) {
            section = new Section();
            section = populateCrfVersion(section, crfVersion, cmdObject);
            sectionDao.saveOrUpdate(section);
            section = sectionDao.findByCrfVersionOrdinal(crfVersion.getCrfVersionId(), 1);
        }
    }
    createGroups(cmdObject.container, crfBean, crfVersion, formLayout, section, cmdObject.ub, cmdObject.errors);
    if (cmdObject.errors.hasErrors()) {
        logger.error("Encounter validation errors while saving CRF.  Rolling back transaction.");
        throw new RuntimeException("Encountered validation errors while saving CRF.");
    }
    return formLayout;
}

Example 2 with CrfBean

use of org.akaza.openclinica.domain.datamap.CrfBean in project OpenClinica by OpenClinica.

the class EnketoUrlService method populateInstance.

private String populateInstance(CrfVersion crfVersion, FormLayout formLayout, EventCrf eventCrf, String studyOid, String flavor) throws Exception {
    Map<String, Object> data = new HashMap<String, Object>();
    List<ItemGroup> igs = itemGroupDao.findByCrfVersionId(crfVersion.getCrfVersionId());
    for (ItemGroup ig : igs) {
        List<HashMap<String, Object>> hashMapList = new ArrayList<HashMap<String, Object>>();
        List<ItemGroupMetadata> igms = itemGroupMetadataDao.findByItemGroupCrfVersion(ig.getItemGroupId(), crfVersion.getCrfVersionId());
        int maxRowCount = itemDataDao.getMaxCountByEventCrfGroup(eventCrf.getEventCrfId(), ig.getItemGroupId());
        HashMap<String, Object> hashMap = null;
        if (igms.get(0).isRepeatingGroup() && maxRowCount == 0) {
            hashMap = new HashMap<>();
            hashMap.put("index", 1);
            hashMap.put("lastUsedOrdinal", 1);
            for (ItemGroupMetadata igm : igms) {
                hashMap.put(igm.getItem().getName(), "");
                if (flavor.equals(QUERY_FLAVOR))
                    hashMap.put(igm.getItem().getName() + QUERY_SUFFIX, "");
            }
            hashMapList.add(hashMap);
            data.put(ig.getName(), hashMapList);
        }
        boolean rowDeleted = false;
        if (igms.get(0).isRepeatingGroup()) {
            for (int i = 0; i < maxRowCount; i++) {
                rowDeleted = false;
                for (ItemGroupMetadata igm : igms) {
                    ItemData itemData = itemDataDao.findByItemEventCrfOrdinalDeleted(igm.getItem().getItemId(), eventCrf.getEventCrfId(), i + 1);
                    if (itemData != null) {
                        rowDeleted = true;
                        break;
                    }
                }
                if (!rowDeleted) {
                    hashMap = new HashMap<>();
                    hashMap.put("index", i + 1);
                    if (i == 0) {
                        hashMap.put("lastUsedOrdinal", maxRowCount);
                    }
                    for (ItemGroupMetadata igm : igms) {
                        ItemData itemData = itemDataDao.findByItemEventCrfOrdinal(igm.getItem().getItemId(), eventCrf.getEventCrfId(), i + 1);
                        String itemValue = getItemValue(itemData, crfVersion);
                        hashMap.put(igm.getItem().getName(), itemData != null ? itemValue : "");
                        if (flavor.equals(QUERY_FLAVOR)) {
                            if (itemData != null) {
                                ObjectMapper mapper = new ObjectMapper();
                                QueriesBean queriesBean = buildQueryElement(itemData);
                                hashMap.put(igm.getItem().getName() + QUERY_SUFFIX, queriesBean != null ? mapper.writeValueAsString(queriesBean) : "");
                            } else {
                                hashMap.put(igm.getItem().getName() + QUERY_SUFFIX, "");
                            }
                        }
                    }
                    hashMapList.add(hashMap);
                }
            }
        }
        if (igms.get(0).isRepeatingGroup() && maxRowCount != 0) {
            data.put(ig.getName(), hashMapList);
        }
        if (!igms.get(0).isRepeatingGroup()) {
            for (ItemGroupMetadata igm : igms) {
                ItemData itemData = itemDataDao.findByItemEventCrfOrdinal(igm.getItem().getItemId(), eventCrf.getEventCrfId(), 1);
                String itemValue = getItemValue(itemData, crfVersion);
                data.put(igm.getItem().getName(), itemData != null ? itemValue : "");
                if (flavor.equals(QUERY_FLAVOR)) {
                    if (itemData != null) {
                        ObjectMapper mapper = new ObjectMapper();
                        QueriesBean queriesBean = buildQueryElement(itemData);
                        data.put(igm.getItem().getName() + QUERY_SUFFIX, queriesBean != null ? mapper.writeValueAsString(queriesBean) : "");
                    } else {
                        data.put(igm.getItem().getName() + QUERY_SUFFIX, "");
                    }
                }
            }
        }
    }
    String templateStr = null;
    CrfBean crfBean = crfDao.findById(formLayout.getCrf().getCrfId());
    String directoryPath = Utils.getCrfMediaFilePath(crfBean.getOcOid(), formLayout.getOcOid());
    File dir = new File(directoryPath);
    File[] directoryListing = dir.listFiles();
    if (directoryListing != null) {
        for (File child : directoryListing) {
            if (flavor.equals(QUERY_FLAVOR) && child.getName().endsWith(INSTANCE_QUERIES_SUFFIX) || flavor.equals(NO_FLAVOR) && child.getName().endsWith(INSTANCE_SUFFIX)) {
                templateStr = new String(Files.readAllBytes(Paths.get(child.getPath())));
                break;
            }
        }
    }
    Template template = new Template("template name", new StringReader(templateStr), new Configuration());
    StringWriter wtr = new StringWriter();
    template.process(data, wtr);
    String instance = wtr.toString();
    System.out.println(instance);
    return instance;
}

Example 3 with CrfBean

use of org.akaza.openclinica.domain.datamap.CrfBean in project OpenClinica by OpenClinica.

the class OpenRosaServices method getForm.

@GET
@Path("/{studyOID}/form")
@Produces(MediaType.TEXT_XML)
public XFormList getForm(@Context HttpServletRequest request, @Context HttpServletResponse response, @PathParam("studyOID") String studyOID, @QueryParam("formID") String uniqueId, @RequestHeader("Authorization") String authorization, @Context ServletContext context) throws Exception {
    LoggerContext lc = (LoggerContext) LoggerFactory.getILoggerFactory();
    // print logback's internal status
    StatusPrinter.print(lc);
    if (!mayProceedPreview(studyOID))
        return null;
    String flavor = getQuerySet(uniqueId);
    String formLayoutOid = getFormLayoutOid(uniqueId);
    FormLayout formLayout = formLayoutDao.findByOcOID(formLayoutOid);
    CrfBean crf = crfDao.findById(formLayout.getCrf().getCrfId());
    String xformOutput = "";
    String directoryPath = Utils.getCrfMediaFilePath(crf.getOcOid(), formLayout.getOcOid());
    File dir = new File(directoryPath);
    File[] directoryListing = dir.listFiles();
    if (directoryListing != null) {
        for (File child : directoryListing) {
            if (flavor.equals(QUERY_FLAVOR) && child.getName().endsWith(QUERY_SUFFIX) || flavor.equals(NO_FLAVOR) && child.getName().endsWith(NO_SUFFIX)) {
                xformOutput = new String(Files.readAllBytes(Paths.get(child.getPath())));
                break;
            }
        }
    }
    XFormList formList = null;
    try {
        formList = new XFormList();
        XForm form = new XForm(crf, formLayout);
        // TODO Uncomment this before checking in
        if (StringUtils.isNotEmpty(xformOutput)) {
            form.setHash(DigestUtils.md5Hex(xformOutput));
        }
        String urlBase = getCoreResources().getDataInfo().getProperty("sysURL").split("/MainMenu")[0];
        List<FormLayoutMedia> mediaList = formLayoutMediaDao.findByFormLayoutIdForNoteTypeMedia(formLayout.getFormLayoutId());
        if (flavor.equals(QUERY_FLAVOR)) {
            form.setDownloadURL(urlBase + "/rest2/openrosa/" + studyOID + "/formXml?formId=" + formLayout.getOcOid() + QUERY);
            form.setManifestURL(urlBase + "/rest2/openrosa/" + studyOID + "/manifest?formId=" + formLayout.getOcOid() + QUERY);
            form.setFormID(formLayout.getOcOid() + QUERY);
        } else {
            form.setDownloadURL(urlBase + "/rest2/openrosa/" + studyOID + "/formXml?formId=" + formLayout.getOcOid());
            form.setManifestURL(urlBase + "/rest2/openrosa/" + studyOID + "/manifest?formId=" + formLayout.getOcOid());
        }
        formList.add(form);
    } catch (Exception e) {
        LOGGER.error(e.getMessage());
        LOGGER.error(ExceptionUtils.getStackTrace(e));
    // return "<Error>" + e.getMessage() + "</Error>";
    }
    return formList;
}

Example 4 with CrfBean

use of org.akaza.openclinica.domain.datamap.CrfBean 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().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.getCrfVersion().getName() != null)
                    dataBean.setCrfVersion(ecrf.getCrfVersion().getName());
                if (collectAudits)
                    dataBean.setAuditLogs(fetchAuditLogs(ecrf.getEventCrfId(), "event_crf", ecrf.getCrfVersion().getOcOid(), null));
                if (collectDns)
                    dataBean.setDiscrepancyNotes(fetchDiscrepancyNotes(ecrf));
                formDataBean.add(dataBean);
                if (formVersionOID != null)
                    formCheck = false;
            }
        }
    }
    return (ArrayList<ExportFormDataBean>) formDataBean;
}

Example 5 with CrfBean

use of org.akaza.openclinica.domain.datamap.CrfBean in project OpenClinica by OpenClinica.

the class XformMetaDataService method createCRFMetaData.

@Transactional
public CrfVersion createCRFMetaData(CRFVersionBean version, XformContainer container, StudyBean currentStudy, UserAccountBean ub, Html html, String submittedCrfName, String submittedCrfVersionName, String submittedCrfVersionDescription, String submittedRevisionNotes, String submittedXformText, List<FileItem> formItems, Errors errors) throws Exception {
    // Retrieve CrfBean. Create one if it doesn't exist yet.
    CrfBean crf = null;
    if (version.getCrfId() > 0) {
        crf = (CrfBean) crfDao.findById(version.getCrfId());
        crf.setUpdateId(ub.getId());
        crf.setDateUpdated(new Date());
        crfDao.saveOrUpdate(crf);
    } else {
        crf = new CrfBean();
        crf.setName(submittedCrfName);
        crf.setDescription(submittedCrfVersionDescription);
        crf.setUserAccount(userDao.findById(ub.getId()));
        crf.setStatus(org.akaza.openclinica.domain.Status.AVAILABLE);
        crf.setStudy(studyDao.findById(currentStudy.getId()));
        crf.setOcOid(crfDao.getValidOid(new CrfBean(), submittedCrfName));
        crf.setUpdateId(ub.getId());
        crf.setDateUpdated(new Date());
        Integer crfId = (Integer) crfDao.save(crf);
        crf.setCrfId(crfId);
    }
    // Create new CRF Version
    CrfVersion crfVersion = new CrfVersion();
    crfVersion.setName(submittedCrfVersionName);
    crfVersion.setDescription(submittedCrfVersionDescription);
    crfVersion.setCrf(crf);
    crfVersion.setUserAccount(userDao.findById(ub.getId()));
    crfVersion.setStatus(org.akaza.openclinica.domain.Status.AVAILABLE);
    crfVersion.setRevisionNotes(submittedRevisionNotes);
    crfVersion.setOcOid(crfVersionDao.getValidOid(new CrfVersion(), crf.getOcOid(), crfVersion.getName()));
    crfVersion.setXform(submittedXformText);
    crfVersion.setXformName(container.getInstanceName());
    Integer crfVersionId = (Integer) crfVersionDao.save(crfVersion);
    crfVersion.setCrfVersionId(crfVersionId);
    // Create Section
    Section section = new Section();
    section.setCrfVersion(crfVersion);
    section.setStatus(org.akaza.openclinica.domain.Status.AVAILABLE);
    section.setLabel("");
    section.setTitle("");
    section.setSubtitle("");
    section.setPageNumberLabel("");
    section.setOrdinal(1);
    // not null
    section.setUserAccount(userDao.findById(ub.getId()));
    section.setBorders(0);
    sectionDao.saveOrUpdate(section);
    section = sectionDao.findByCrfVersionOrdinal(crfVersion.getCrfVersionId(), 1);
    createGroups(container, html, submittedXformText, crf, crfVersion, section, ub, errors);
    saveMedia(formItems, crf, crfVersion);
    if (errors.hasErrors()) {
        logger.error("Encounter validation errors while saving CRF.  Rolling back transaction.");
        throw new RuntimeException("Encountered validation errors while saving CRF.");
    }
    return crfVersion;
}