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

Example 6 with FormLayout

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

the class BatchCRFMigrationController method executeMigrationAction.

public void executeMigrationAction(HelperObject helperObject, EventCRFBean eventCRFBean) {
    Session session = helperObject.getSession();
    EventCrf eventCrf = helperObject.getEventCrfDao().findById(eventCRFBean.getId());
    StudyEvent studyEvent = helperObject.getStudyEventDao().findById(eventCRFBean.getStudyEventId());
    FormLayout formLayout = helperObject.getFormLayoutDao().findById(helperObject.getTargetCrfVersionBean().getId());
    StudySubject studySubject = helperObject.getStudySubjectDao().findById(eventCRFBean.getStudySubjectId());
    eventCrf.setSdvStatus(false);
    eventCrf.setDateUpdated(new Date());
    eventCrf.setSdvUpdateId(helperObject.getUserAccountBean().getId());
    eventCrf.setUpdateId(helperObject.getUserAccountBean().getId());
    eventCrf.setFormLayout(formLayout);
    session.saveOrUpdate(eventCrf);
    String status_before_update = null;
    SubjectEventStatus eventStatus = null;
    if (studySubject.getStatus() == Status.SIGNED) {
        status_before_update = auditDao().findLastStatus("study_subject", studySubject.getStudySubjectId(), "8");
        if (status_before_update != null && status_before_update.length() == 1) {
            int subject_status = Integer.parseInt(status_before_update);
            Status status = Status.getByCode(subject_status);
            studySubject.setStatus(status);
        }
        studySubject.setUpdateId(helperObject.getUserAccountBean().getId());
        session.saveOrUpdate(studySubject);
    }
    studyEvent.setUpdateId(helperObject.getUserAccountBean().getId());
    studyEvent.setDateUpdated(new Date());
    status_before_update = auditDao().findLastStatus("study_event", studyEvent.getStudyEventId(), "8");
    if (status_before_update != null && status_before_update.length() == 1) {
        int status = Integer.parseInt(status_before_update);
        eventStatus = SubjectEventStatus.get(status);
        studyEvent.setSubjectEventStatusId(eventStatus.getId());
    }
    session.saveOrUpdate(studyEvent);
}

Example 7 with FormLayout

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

the class FSItemProcessor method processFieldSubmissionGroupItems.

private void processFieldSubmissionGroupItems(ArrayList<HashMap> listOfUploadFilePaths, Node repeatNode, Node itemNode, SubmissionContainer container, ItemGroup itemGroup) throws Exception {
    String itemName;
    Integer itemOrdinal = 1;
    String itemValue;
    // Node repeatGroupNode = itemNode.getParentNode();
    if (repeatNode != null) {
        final NamedNodeMap attributes = repeatNode.getAttributes();
        // check to see if groupNode has any enketo attributes
        for (int attrIndex = 0; attrIndex < attributes.getLength(); attrIndex++) {
            if (attributes.item(attrIndex).getNodeName().equals(ENKETO_ORDINAL)) {
                logger.debug("found enketo attribute");
                logger.debug(attributes.item(attrIndex).getNodeName());
                logger.debug(attributes.item(attrIndex).getNodeValue());
                itemOrdinal = new Integer(attributes.item(attrIndex).getNodeValue());
            }
        }
    } else {
        itemOrdinal = 1;
    }
    FormLayout formLayout = container.getFormLayout();
    CrfVersion crfVersion = crfVersionDao.findAllByCrfId(formLayout.getCrf().getCrfId()).get(0);
    container.setCrfVersion(crfVersion);
    Item item = null;
    ItemGroupMetadata igm = null;
    if (container.getRequestType() == FieldRequestTypeEnum.DELETE_FIELD) {
        List<ItemGroupMetadata> igms = itemGroupMetadataDao.findByItemGroupCrfVersion(itemGroup.getItemGroupId(), crfVersion.getCrfVersionId());
        for (ItemGroupMetadata ig : igms) {
            ItemData existingItemData = itemDataDao.findByItemEventCrfOrdinal(ig.getItem().getItemId(), container.getEventCrf().getEventCrfId(), itemOrdinal);
            // ItemData existingItemData = lookupFieldItemData(itemGroup, itemOrdinal, container);
            if (existingItemData != null) {
                existingItemData.setDeleted(true);
                existingItemData.setValue("");
                existingItemData.setOldStatus(existingItemData.getStatus());
                existingItemData.setUserAccount(container.getUser());
                existingItemData.setStatus(Status.AVAILABLE);
                existingItemData.setUpdateId(container.getUser().getUserId());
                existingItemData.setInstanceId(container.getInstanceId());
                existingItemData = itemDataDao.saveOrUpdate(existingItemData);
                resetSdvStatus(container);
                // Close discrepancy notes
                closeItemDiscrepancyNotes(container, existingItemData);
            }
        }
        return;
    }
    // igm = itemGroupMetadataDao.findByItemCrfVersion(item.getItemId(), crfVersion.getCrfVersionId());
    // Item loop
    QueryServiceHelperBean helperBean = new QueryServiceHelperBean();
    if (queryService.getQueryAttribute(helperBean, itemNode) != null) {
        queryService.process(helperBean, container, itemNode, itemOrdinal);
    } else if (shouldProcessItemNode(itemNode)) {
        itemName = itemNode.getNodeName().trim();
        itemValue = itemNode.getTextContent();
        item = itemDao.findByNameCrfId(itemNode.getNodeName(), crfVersion.getCrf().getCrfId());
        if (item == null) {
            logger.error("Failed to lookup item: '" + itemName + "'.  Continuing with submission.");
        }
        ItemFormMetadata itemFormMetadata = itemFormMetadataDao.findByItemCrfVersion(item.getItemId(), crfVersion.getCrfVersionId());
        // Convert space separated Enketo multiselect values to comma separated OC multiselect values
        Integer responseTypeId = itemFormMetadata.getResponseSet().getResponseType().getResponseTypeId();
        if (responseTypeId == 3 || responseTypeId == 7) {
            itemValue = itemValue.replaceAll(" ", ",");
        }
        if (responseTypeId == 4) {
            /*
                 * for (HashMap uploadFilePath : listOfUploadFilePaths) {
                 * if ((boolean) uploadFilePath.containsKey(itemValue) && itemValue != "") {
                 * itemValue = (String) uploadFilePath.get(itemValue);
                 * break;
                 * }
                 * }
                 */
            FormLayoutMedia media = formLayoutMediaDao.findByEventCrfIdAndFileName(container.getEventCrf().getEventCrfId(), itemValue);
            if (media == null) {
                media = new FormLayoutMedia();
            }
            media.setName(itemValue);
            media.setFormLayout(formLayout);
            media.setEventCrfId(container.getEventCrf().getEventCrfId());
            media.setPath("/" + container.getStudy().getOc_oid() + "/");
            formLayoutMediaDao.saveOrUpdate(media);
        }
        ItemData newItemData = createItemData(item, itemValue, itemOrdinal, container);
        Errors itemErrors = validateItemData(newItemData, item, responseTypeId);
        if (itemErrors.hasErrors()) {
            container.getErrors().addAllErrors(itemErrors);
            throw new Exception("Item validation error.  Rolling back submission changes.");
        }
        ItemData existingItemData = itemDataDao.findByItemEventCrfOrdinal(item.getItemId(), container.getEventCrf().getEventCrfId(), itemOrdinal);
        if (existingItemData == null) {
            newItemData.setStatus(Status.UNAVAILABLE);
            itemDataDao.saveOrUpdate(newItemData);
            resetSdvStatus(container);
        } else if (existingItemData.getValue().equals(newItemData.getValue())) {
        } else {
            // Existing item. Value changed. Update existing value.
            existingItemData.setInstanceId(container.getInstanceId());
            existingItemData.setValue(newItemData.getValue());
            existingItemData.setUpdateId(container.getUser().getUserId());
            existingItemData.setDateUpdated(new Date());
            itemDataDao.saveOrUpdate(existingItemData);
            resetSdvStatus(container);
        }
    }
}

Example 8 with FormLayout

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

the class EventProcessor method processAnonymous.

private void processAnonymous(SubmissionContainer container, Errors errors, StudySubject studySubject, StudyEventDefinition studyEventDefinition) throws Exception {
    // Integer.valueOf(container.getSubjectContext().get("studyEventOrdinal"));
    Integer ordinal = 1;
    Integer maxExistingOrdinal = studyEventDao.findMaxOrdinalByStudySubjectStudyEventDefinition(studySubject.getStudySubjectId(), studyEventDefinition.getStudyEventDefinitionId());
    FormLayout formLayout = formLayoutDao.findByOcOID(container.getSubjectContext().get("formLayoutOID"));
    while (ordinal <= maxExistingOrdinal + 1) {
        StudyEvent existingStudyEvent = studyEventDao.fetchByStudyEventDefOIDAndOrdinal(studyEventDefinition.getOc_oid(), ordinal, studySubject.getStudySubjectId());
        if (existingStudyEvent == null) {
            container.setStudyEvent(createStudyEvent(studySubject, studyEventDefinition, ordinal, container.getUser()));
            container.setEventCrf(createEventCrf(formLayout, container.getStudyEvent(), container.getSubject(), container.getUser()));
            break;
        } else if (!existingStudyEvent.getStatusId().equals(Status.AVAILABLE.getCode()) || (!existingStudyEvent.getSubjectEventStatusId().equals(SubjectEventStatus.SCHEDULED.getCode()) && !existingStudyEvent.getSubjectEventStatusId().equals(SubjectEventStatus.NOT_SCHEDULED.getCode()) && !existingStudyEvent.getSubjectEventStatusId().equals(SubjectEventStatus.DATA_ENTRY_STARTED.getCode()))) {
            if (studyEventDefinition.getRepeating()) {
                ordinal++;
                continue;
            } else {
                errors.reject("Existing StudyEvent is not Available and EventDef is not repeating");
                logger.info("***  Existing StudyEvent is not Available and EventDef is not repeating  ***");
                throw new Exception("***  Existing StudyEvent is not Available and EventDef is not repeating  ***");
            }
        } else {
            EventCrf existingEventCrf = eventCrfDao.findByStudyEventIdStudySubjectIdCrfId(existingStudyEvent.getStudyEventId(), container.getSubject().getStudySubjectId(), formLayout.getCrf().getCrfId());
            if (existingEventCrf == null) {
                container.setStudyEvent(existingStudyEvent);
                container.setEventCrf(createEventCrf(formLayout, container.getStudyEvent(), container.getSubject(), container.getUser()));
                break;
            } else {
                List<ItemData> itemDataList = itemDataDao.findByEventCrfId(existingEventCrf.getEventCrfId());
                if (existingEventCrf.getStatusId().equals(Status.AVAILABLE.getCode()) && itemDataList.size() == 0) {
                    container.setStudyEvent(existingStudyEvent);
                    container.setEventCrf(existingEventCrf);
                    break;
                } else if (studyEventDefinition.getRepeating()) {
                    ordinal++;
                    continue;
                } else {
                    errors.reject("Existing EventCRF is not usable and EventDef is not repeating");
                    logger.info("***  Existing EventCRF is not usable and EventDef is not repeating  ***");
                    throw new Exception("***  Existing EventCRF is not usable and EventDef is not repeating  ***");
                }
            }
        }
    }
    if (container.getStudyEvent() == null || container.getEventCrf() == null) {
        errors.reject("Unable to identify StudyEvent or EventCrf.");
        logger.info("***  Unable to identify StudyEvent or EventCrf.  ***");
        throw new Exception("***  Unable to identify StudyEvent or EventCrf.  ***");
    }
}

Example 9 with FormLayout

use of org.akaza.openclinica.domain.datamap.FormLayout 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 10 with FormLayout

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

the class OpenRosaServices method getFormList.

/**
     * @api {get} /rest2/openrosa/:studyOID/formList Get Form List
     * @apiName getFormList
     * @apiPermission admin
     * @apiVersion 3.8.0
     * @apiParam {String} studyOID Study Oid.
     * @apiGroup Form
     * @apiDescription Retrieves a listing of the available OpenClinica forms.
     * @apiParamExample {json} Request-Example:
     *                  {
     *                  "studyOid": "S_SAMPLTE",
     *                  }
     * @apiSuccessExample {xml} Success-Response:
     *                    HTTP/1.1 200 OK
     *                    {
     *                    <xforms xmlns="http://openrosa.org/xforms/xformsList">
     *                    <xform>
     *                    <formID>F_FIRSTFORM_1</formID>
     *                    <name>First Form</name>
     *                    <majorMinorVersion>1</majorMinorVersion>
     *                    <version>1</version>
     *                    <hash>8678370cd92814d4e3216d58d821403f</hash>
     *                    <downloadUrl>http://oc1.openclinica.com/OpenClinica-web/rest2/openrosa/S_SAMPLTE/formXml?
     *                    formId=F_FIRSTFORM_1</downloadUrl>
     *                    </xform>
     *                    <xform>
     *                    <formID>F_SECONDFORM_1</formID>
     *                    <name>Second Form</name>
     *                    <majorMinorVersion>1</majorMinorVersion>
     *                    <version>1</version>
     *                    <hash>7ee60d1c6516b730bbe9bdbd7cad942f</hash>
     *                    <downloadUrl>http://oc1.openclinica.com/OpenClinica-web/rest2/openrosa/S_SAMPLTE/formXml?
     *                    formId=F_SECONDFORM_1</downloadUrl>
     *                    </xform>
     *                    </xforms>
     */
@GET
@Path("/{studyOID}/formList")
@Produces(MediaType.TEXT_XML)
public String getFormList(@Context HttpServletRequest request, @Context HttpServletResponse response, @PathParam("studyOID") String studyOID, @QueryParam("formID") String uniqueId, @RequestHeader("Authorization") String authorization, @Context ServletContext context) throws Exception {
    if (!mayProceedPreview(studyOID))
        return null;
    XFormList formList = null;
    try {
        if (StringUtils.isEmpty(uniqueId)) {
            List<CrfBean> crfs = crfDao.findAll();
            List<FormLayout> formLayouts = formLayoutDao.findAll();
            formList = new XFormList();
            for (CrfBean crf : crfs) {
                for (FormLayout formLayout : formLayouts) {
                    if (formLayout.getCrf().getCrfId() == crf.getCrfId()) {
                        XForm form = new XForm(crf, formLayout);
                        // TODO: Need to generate hash based on contents of
                        // XForm. Will be done in a later story.
                        // TODO: For now all XForms get a date based hash to
                        // trick Enketo into always downloading
                        // TODO: them.
                        String urlBase = getCoreResources().getDataInfo().getProperty("sysURL").split("/MainMenu")[0];
                        form.setDownloadURL(urlBase + "/rest2/openrosa/" + studyOID + "/formXml?formId=" + formLayout.getOcOid());
                        List<FormLayoutMedia> mediaList = formLayoutMediaDao.findByFormLayoutIdForNoteTypeMedia(formLayout.getFormLayoutId());
                        if (mediaList != null && mediaList.size() > 0) {
                            form.setManifestURL(urlBase + "/rest2/openrosa/" + studyOID + "/manifest?formId=" + formLayout.getOcOid());
                        }
                        formList.add(form);
                    }
                }
            }
        } else {
            formList = getForm(request, response, studyOID, uniqueId, authorization, context);
        }
        // Create the XML formList using a Castor mapping file.
        XMLContext xmlContext = new XMLContext();
        Mapping mapping = xmlContext.createMapping();
        mapping.loadMapping(getCoreResources().getURL("openRosaFormListMapping.xml"));
        xmlContext.addMapping(mapping);
        Marshaller marshaller = xmlContext.createMarshaller();
        StringWriter writer = new StringWriter();
        marshaller.setWriter(writer);
        marshaller.marshal(formList);
        // Set response headers
        Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("GMT"));
        Date currentDate = new Date();
        cal.setTime(currentDate);
        SimpleDateFormat format = new SimpleDateFormat("E, dd MMM yyyy HH:mm:ss zz");
        format.setCalendar(cal);
        response.setHeader("Content-Type", "text/xml; charset=UTF-8");
        response.setHeader("Date", format.format(currentDate));
        response.setHeader("X-OpenRosa-Version", "1.0");
        return writer.toString();
    } catch (Exception e) {
        LOGGER.error(e.getMessage());
        LOGGER.error(ExceptionUtils.getStackTrace(e));
        return "<Error>" + e.getMessage() + "</Error>";
    }
}