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

Example 1 with DisplayItemBeanWrapper

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

the class ImportCRFDataServlet method processRequest.

@Override
public void processRequest() throws Exception {
    resetPanel();
    panel.setStudyInfoShown(false);
    panel.setOrderedData(true);
    FormProcessor fp = new FormProcessor(request);
    // checks which module the requests are from
    String module = fp.getString(MODULE);
    // keep the module in the session
    session.setAttribute(MODULE, module);
    String action = request.getParameter("action");
    CRFVersionBean version = (CRFVersionBean) session.getAttribute("version");
    File xsdFile = new File(SpringServletAccess.getPropertiesDir(context) + "ODM1-3-0.xsd");
    File xsdFile2 = new File(SpringServletAccess.getPropertiesDir(context) + "ODM1-2-1.xsd");
    if (StringUtil.isBlank(action)) {
        logger.info("action is blank");
        request.setAttribute("version", version);
        forwardPage(Page.IMPORT_CRF_DATA);
    }
    if ("confirm".equalsIgnoreCase(action)) {
        String dir = SQLInitServlet.getField("filePath");
        if (!new File(dir).exists()) {
            logger.info("The filePath in datainfo.properties is invalid " + dir);
            addPageMessage(respage.getString("filepath_you_defined_not_seem_valid"));
            forwardPage(Page.IMPORT_CRF_DATA);
        }
        // All the uploaded files will be saved in filePath/crf/original/
        String theDir = dir + "crf" + File.separator + "original" + File.separator;
        if (!new File(theDir).isDirectory()) {
            new File(theDir).mkdirs();
            logger.info("Made the directory " + theDir);
        }
        // MultipartRequest multi = new MultipartRequest(request, theDir, 50 * 1024 * 1024);
        File f = null;
        try {
            f = uploadFile(theDir, version);
        } catch (Exception e) {
            logger.warn("*** Found exception during file upload***");
            e.printStackTrace();
        }
        if (f == null) {
            forwardPage(Page.IMPORT_CRF_DATA);
        }
        // TODO
        // validation steps
        // 1. valid xml - validated by file uploader below
        // LocalConfiguration config = LocalConfiguration.getInstance();
        // config.getProperties().setProperty(
        // "org.exolab.castor.parser.namespaces",
        // "true");
        // config
        // .getProperties()
        // .setProperty("org.exolab.castor.sax.features",
        // "http://xml.org/sax/features/validation,
        // http://apache.org/xml/features/validation/schema,
        // http://apache.org/xml/features/validation/schema-full-checking");
        // // above sets to validate against namespace
        Mapping myMap = new Mapping();
        // @pgawade 18-April-2011 Fix for issue 8394
        String ODM_MAPPING_DIRPath = CoreResources.ODM_MAPPING_DIR;
        myMap.loadMapping(ODM_MAPPING_DIRPath + File.separator + "cd_odm_mapping.xml");
        Unmarshaller um1 = new Unmarshaller(myMap);
        // um1.addNamespaceToPackageMapping("http://www.openclinica.org/ns/odm_ext_v130/v3.1", "OpenClinica");
        // um1.addNamespaceToPackageMapping("http://www.cdisc.org/ns/odm/v1.3"
        // ,
        // "ODMContainer");
        boolean fail = false;
        ODMContainer odmContainer = new ODMContainer();
        session.removeAttribute("odmContainer");
        try {
            // schemaValidator.validateAgainstSchema(f, xsdFile);
            // utf-8 compliance, tbh 06/2009
            InputStreamReader isr = new InputStreamReader(new FileInputStream(f), "UTF-8");
            odmContainer = (ODMContainer) um1.unmarshal(isr);
            logger.debug("Found crf data container for study oid: " + odmContainer.getCrfDataPostImportContainer().getStudyOID());
            logger.debug("found length of subject list: " + odmContainer.getCrfDataPostImportContainer().getSubjectData().size());
            // 2. validates against ODM 1.3
            // check it all below, throw an exception and route to a
            // different
            // page if not working
            // TODO this block of code needs the xerces serializer in order
            // to
            // work
            // StringWriter myWriter = new StringWriter();
            // Marshaller m1 = new Marshaller(myWriter);
            // 
            // m1.setProperty("org.exolab.castor.parser.namespaces",
            // "true");
            // m1
            // .setProperty("org.exolab.castor.sax.features",
            // "http://xml.org/sax/features/validation,
            // http://apache.org/xml/features/validation/schema,
            // http://apache.org/xml/features/validation/schema-full-checking
            // ");
            // 
            // m1.setMapping(myMap);
            // m1.setNamespaceMapping("",
            // "http://www.cdisc.org/ns/odm/v1.3");
            // m1.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3
            // ODM1-3.xsd");
            // m1.marshal(odmContainer);
            // if you havent thrown it, you wont throw it here
            addPageMessage(respage.getString("passed_xml_validation"));
        } catch (Exception me1) {
            me1.printStackTrace();
            // expanding it to all exceptions, but hoping to catch Marshal
            // Exception or SAX Exceptions
            logger.info("found exception with xml transform");
            // 
            logger.info("trying 1.2.1");
            try {
                schemaValidator.validateAgainstSchema(f, xsdFile2);
                // for backwards compatibility, we also try to validate vs
                // 1.2.1 ODM 06/2008
                InputStreamReader isr = new InputStreamReader(new FileInputStream(f), "UTF-8");
                odmContainer = (ODMContainer) um1.unmarshal(isr);
            } catch (Exception me2) {
                // not sure if we want to report me2
                MessageFormat mf = new MessageFormat("");
                mf.applyPattern(respage.getString("your_xml_is_not_well_formed"));
                Object[] arguments = { me1.getMessage() };
                addPageMessage(mf.format(arguments));
                // 
                // addPageMessage("Your XML is not well-formed, and does not
                // comply with the ODM 1.3 Schema. Please check it, and try
                // again. It returned the message: "
                // + me1.getMessage());
                // me1.printStackTrace();
                forwardPage(Page.IMPORT_CRF_DATA);
            // you can't really wait to forward because then you throw
            // NPEs
            // in the next few parts of the code
            }
        }
        // TODO need to output further here
        // 2.a. is the study the same one that the user is in right now?
        // 3. validates against study metadata
        // 3.a. is that study subject in that study?
        // 3.b. is that study event def in that study?
        // 3.c. is that site in that study?
        // 3.d. is that crf version in that study event def?
        // 3.e. are those item groups in that crf version?
        // 3.f. are those items in that item group?
        List<String> errors = getImportCRFDataService().validateStudyMetadata(odmContainer, ub.getActiveStudyId());
        if (errors != null) {
            // add to session
            // forward to another page
            logger.info(errors.toString());
            for (String error : errors) {
                addPageMessage(error);
            }
            if (errors.size() > 0) {
                // fail = true;
                forwardPage(Page.IMPORT_CRF_DATA);
            } else {
                addPageMessage(respage.getString("passed_study_check"));
                addPageMessage(respage.getString("passed_oid_metadata_check"));
            }
        }
        logger.debug("passed error check");
        // TODO ADD many validation steps before we get to the
        // session-setting below
        // 4. is the event in the correct status to accept data import?
        // -- scheduled, data entry started, completed
        // (and the event should already be created)
        // (and the event should be independent, ie not affected by other
        // events)
        Boolean eventCRFStatusesValid = getImportCRFDataService().eventCRFStatusesValid(odmContainer, ub);
        ImportCRFInfoContainer importCrfInfo = new ImportCRFInfoContainer(odmContainer, sm.getDataSource());
        // The eventCRFBeans list omits EventCRFs that don't match UpsertOn rules. If EventCRF did not exist and
        // doesn't match upsert, it won't be created.
        List<EventCRFBean> eventCRFBeans = getImportCRFDataService().fetchEventCRFBeans(odmContainer, ub);
        List<DisplayItemBeanWrapper> displayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
        HashMap<String, String> totalValidationErrors = new HashMap<String, String>();
        HashMap<String, String> hardValidationErrors = new HashMap<String, String>();
        // The following map is used for setting the EventCRF status post import.
        HashMap<Integer, String> importedCRFStatuses = getImportCRFDataService().fetchEventCRFStatuses(odmContainer);
        // method in the ImportCRFDataService is modified for this fix.
        if (eventCRFBeans == null) {
            fail = true;
            addPageMessage(respage.getString("no_event_status_matching"));
        } else {
            ArrayList<Integer> permittedEventCRFIds = new ArrayList<Integer>();
            logger.info("found a list of eventCRFBeans: " + eventCRFBeans.toString());
            // List<DisplayItemBeanWrapper> displayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
            // HashMap<String, String> totalValidationErrors = new
            // HashMap<String, String>();
            // HashMap<String, String> hardValidationErrors = new
            // HashMap<String, String>();
            logger.debug("found event crfs " + eventCRFBeans.size());
            // -- does the event already exist? if not, fail
            if (!eventCRFBeans.isEmpty()) {
                for (EventCRFBean eventCRFBean : eventCRFBeans) {
                    DataEntryStage dataEntryStage = eventCRFBean.getStage();
                    Status eventCRFStatus = eventCRFBean.getStatus();
                    logger.info("Event CRF Bean: id " + eventCRFBean.getId() + ", data entry stage " + dataEntryStage.getName() + ", status " + eventCRFStatus.getName());
                    if (eventCRFStatus.equals(Status.AVAILABLE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
                        // actually want the negative
                        // was status == available and the stage questions, but
                        // when you are at 'data entry complete' your status is
                        // set to 'unavailable'.
                        // >> tbh 09/2008
                        // HOWEVER, when one event crf is removed and the rest
                        // are good, what happens???
                        // need to create a list and inform that one is blocked
                        // and the rest are not...
                        // 
                        permittedEventCRFIds.add(new Integer(eventCRFBean.getId()));
                    } else {
                    // fail = true;
                    // addPageMessage(respage.getString(
                    // "the_event_crf_not_correct_status"));
                    // forwardPage(Page.IMPORT_CRF_DATA);
                    }
                }
                // did we exclude all the event CRFs? if not, pass, else fail
                if (eventCRFBeans.size() >= permittedEventCRFIds.size()) {
                    addPageMessage(respage.getString("passed_event_crf_status_check"));
                } else {
                    fail = true;
                    addPageMessage(respage.getString("the_event_crf_not_correct_status"));
                }
                try {
                    List<DisplayItemBeanWrapper> tempDisplayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
                    tempDisplayItemBeanWrappers = getImportCRFDataService().lookupValidationErrors(request, odmContainer, ub, totalValidationErrors, hardValidationErrors, permittedEventCRFIds);
                    logger.debug("generated display item bean wrappers " + tempDisplayItemBeanWrappers.size());
                    logger.debug("size of total validation errors: " + totalValidationErrors.size());
                    displayItemBeanWrappers.addAll(tempDisplayItemBeanWrappers);
                } catch (NullPointerException npe1) {
                    // what if you have 2 event crfs but the third is a fake?
                    fail = true;
                    logger.debug("threw a NPE after calling lookup validation errors");
                    System.out.println(ExceptionUtils.getStackTrace(npe1));
                    addPageMessage(respage.getString("an_error_was_thrown_while_validation_errors"));
                // npe1.printStackTrace();
                } catch (OpenClinicaException oce1) {
                    fail = true;
                    logger.debug("threw an OCE after calling lookup validation errors " + oce1.getOpenClinicaMessage());
                    addPageMessage(oce1.getOpenClinicaMessage());
                }
            } else if (!eventCRFStatusesValid) {
                fail = true;
                addPageMessage(respage.getString("the_event_crf_not_correct_status"));
            } else {
                fail = true;
                addPageMessage(respage.getString("no_event_crfs_matching_the_xml_metadata"));
            }
        // for (HashMap<String, String> crfData : importedData) {
        // DisplayItemBeanWrapper displayItemBeanWrapper =
        // testing(request,
        // crfData);
        // displayItemBeanWrappers.add(displayItemBeanWrapper);
        // errors = displayItemBeanWrapper.getValidationErrors();
        // 
        // }
        }
        if (fail) {
            logger.debug("failed here - forwarding...");
            forwardPage(Page.IMPORT_CRF_DATA);
        } else {
            addPageMessage(respage.getString("passing_crf_edit_checks"));
            session.setAttribute("odmContainer", odmContainer);
            session.setAttribute("importedData", displayItemBeanWrappers);
            session.setAttribute("validationErrors", totalValidationErrors);
            session.setAttribute("hardValidationErrors", hardValidationErrors);
            session.setAttribute("importedCRFStatuses", importedCRFStatuses);
            session.setAttribute("importCrfInfo", importCrfInfo);
            // above are updated 'statically' by the method that originally
            // generated the wrappers; soon the only thing we will use
            // wrappers for is the 'overwrite' flag
            logger.debug("+++ content of total validation errors: " + totalValidationErrors.toString());
            SummaryStatsBean ssBean = getImportCRFDataService().generateSummaryStatsBean(odmContainer, displayItemBeanWrappers, importCrfInfo);
            session.setAttribute("summaryStats", ssBean);
            // will have to set hard edit checks here as well
            session.setAttribute("subjectData", odmContainer.getCrfDataPostImportContainer().getSubjectData());
            forwardPage(Page.VERIFY_IMPORT_SERVLET);
        }
    // }
    }
}

Example 2 with DisplayItemBeanWrapper

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

the class VerifyImportedCRFDataServlet method processRequest.

@Override
@SuppressWarnings(value = "unchecked")
public void processRequest() throws Exception {
    ItemDataDAO itemDataDao = new ItemDataDAO(sm.getDataSource());
    itemDataDao.setFormatDates(false);
    EventCRFDAO eventCrfDao = new EventCRFDAO(sm.getDataSource());
    CrfBusinessLogicHelper crfBusinessLogicHelper = new CrfBusinessLogicHelper(sm.getDataSource());
    String action = request.getParameter("action");
    FormProcessor fp = new FormProcessor(request);
    // checks which module the requests are from
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);
    resetPanel();
    panel.setStudyInfoShown(false);
    panel.setOrderedData(true);
    setToPanel(resword.getString("create_CRF"), respage.getString("br_create_new_CRF_entering"));
    setToPanel(resword.getString("create_CRF_version"), respage.getString("br_create_new_CRF_uploading"));
    setToPanel(resword.getString("revise_CRF_version"), respage.getString("br_if_you_owner_CRF_version"));
    setToPanel(resword.getString("CRF_spreadsheet_template"), respage.getString("br_download_blank_CRF_spreadsheet_from"));
    setToPanel(resword.getString("example_CRF_br_spreadsheets"), respage.getString("br_download_example_CRF_instructions_from"));
    if ("confirm".equalsIgnoreCase(action)) {
        List<DisplayItemBeanWrapper> displayItemBeanWrappers = (List<DisplayItemBeanWrapper>) session.getAttribute("importedData");
        logger.info("Size of displayItemBeanWrappers : " + displayItemBeanWrappers.size());
        forwardPage(Page.VERIFY_IMPORT_CRF_DATA);
    }
    if ("save".equalsIgnoreCase(action)) {
        // setup ruleSets to run if applicable
        RuleSetServiceInterface ruleSetService = (RuleSetServiceInterface) SpringServletAccess.getApplicationContext(context).getBean("ruleSetService");
        List<ImportDataRuleRunnerContainer> containers = this.ruleRunSetup(sm.getDataSource(), currentStudy, ub, ruleSetService);
        List<DisplayItemBeanWrapper> displayItemBeanWrappers = (List<DisplayItemBeanWrapper>) session.getAttribute("importedData");
        // System.out.println("Size of displayItemBeanWrappers : " +
        // displayItemBeanWrappers.size());
        HashMap<Integer, String> importedCRFStatuses = (HashMap<Integer, String>) session.getAttribute("importedCRFStatuses");
        for (DisplayItemBeanWrapper wrapper : displayItemBeanWrappers) {
            boolean resetSDV = false;
            int eventCrfBeanId = -1;
            EventCRFBean eventCrfBean = new EventCRFBean();
            // TODO : tom , the wrapper object has all the necessary data -
            // as you see we check the
            // is to see if this data is Savable if it is then we go ahead
            // and save it. if not we discard.
            // So the change needs to happen here , instead of discarding we
            // need to file discrepancy notes
            // and save the data. If you look in the
            // Page.VERIFY_IMPORT_CRF_DATA jsp file you can see how I am
            // pulling the errors. and use that in the same way.
            logger.info("right before we check to make sure it is savable: " + wrapper.isSavable());
            if (wrapper.isSavable()) {
                ArrayList<Integer> eventCrfInts = new ArrayList<Integer>();
                // wrapper.getValidationErrors().toString());
                for (DisplayItemBean displayItemBean : wrapper.getDisplayItemBeans()) {
                    eventCrfBeanId = displayItemBean.getData().getEventCRFId();
                    eventCrfBean = (EventCRFBean) eventCrfDao.findByPK(eventCrfBeanId);
                    logger.info("found value here: " + displayItemBean.getData().getValue());
                    logger.info("found status here: " + eventCrfBean.getStatus().getName());
                    // System.out.println("found event crf bean name here: "
                    // +
                    // eventCrfBean.getEventName()+" id "+eventCrfBean.getId
                    // ());
                    // SO, items can be created in a wrapper which is set to
                    // overwrite
                    // we get around this by checking the bean first, to
                    // make sure it's not null
                    ItemDataBean itemDataBean = new ItemDataBean();
                    itemDataBean = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
                    if (wrapper.isOverwrite() && itemDataBean.getStatus() != null) {
                        if (!itemDataBean.getValue().equals(displayItemBean.getData().getValue()))
                            resetSDV = true;
                        logger.info("just tried to find item data bean on item name " + displayItemBean.getItem().getName());
                        itemDataBean.setUpdatedDate(new Date());
                        itemDataBean.setUpdater(ub);
                        itemDataBean.setValue(displayItemBean.getData().getValue());
                        // set status?
                        itemDataDao.update(itemDataBean);
                        logger.info("updated: " + itemDataBean.getItemId());
                        // need to set pk here in order to create dn
                        displayItemBean.getData().setId(itemDataBean.getId());
                    } else {
                        resetSDV = true;
                        itemDataDao.create(displayItemBean.getData());
                        logger.info("created: " + displayItemBean.getData().getItemId() + "event CRF ID = " + eventCrfBean.getId() + "CRF VERSION ID =" + eventCrfBean.getCRFVersionId());
                        // does this dao function work for repeating
                        // events/groups?
                        // ItemDataBean itemDataBean =
                        // itemDataDao.findByEventCRFIdAndItemName(
                        // eventCrfBean,
                        // displayItemBean.getItem().getName());
                        ItemDataBean itemDataBean2 = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
                        logger.info("found: id " + itemDataBean2.getId() + " name " + itemDataBean2.getName());
                        displayItemBean.getData().setId(itemDataBean2.getId());
                    }
                    // logger.info("created item data bean:
                    // "+displayItemBean.getData().getId());
                    // logger.info("created:
                    // "+displayItemBean.getData().getName());
                    // logger.info("continued:
                    // "+displayItemBean.getData().getItemId());
                    ItemDAO idao = new ItemDAO(sm.getDataSource());
                    ItemBean ibean = (ItemBean) idao.findByPK(displayItemBean.getData().getItemId());
                    // logger.info("continued2: getName " +
                    // ibean.getName());
                    // System.out.println("*** checking for validation errors: "
                    // + ibean.getName());
                    String itemOid = displayItemBean.getItem().getOid() + "_" + wrapper.getStudyEventRepeatKey() + "_" + displayItemBean.getData().getOrdinal() + "_" + wrapper.getStudySubjectOid();
                    if (wrapper.getValidationErrors().containsKey(itemOid)) {
                        ArrayList messageList = (ArrayList) wrapper.getValidationErrors().get(itemOid);
                        // could it be more than one? tbh 08/2008
                        for (int iter = 0; iter < messageList.size(); iter++) {
                            String message = (String) messageList.get(iter);
                            DiscrepancyNoteBean parentDn = ImportSpringJob.createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, null, ub, sm.getDataSource(), currentStudy);
                            ImportSpringJob.createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, parentDn.getId(), ub, sm.getDataSource(), currentStudy);
                        // System.out.println("*** created disc note with message: "
                        // + message);
                        // displayItemBean);
                        }
                    }
                    // "+displayItemBean.getDbData().getName());
                    if (!eventCrfInts.contains(new Integer(eventCrfBean.getId()))) {
                        String eventCRFStatus = importedCRFStatuses.get(new Integer(eventCrfBean.getId()));
                        if (eventCRFStatus != null && eventCRFStatus.equals(DataEntryStage.INITIAL_DATA_ENTRY.getName()) && eventCrfBean.getStatus().isAvailable()) {
                            crfBusinessLogicHelper.markCRFStarted(eventCrfBean, ub);
                        } else {
                            crfBusinessLogicHelper.markCRFComplete(eventCrfBean, ub);
                        }
                        eventCrfInts.add(new Integer(eventCrfBean.getId()));
                    }
                }
                // Reset the SDV status if item data has been changed or added
                if (eventCrfBean != null && resetSDV)
                    eventCrfDao.setSDVStatus(false, ub.getId(), eventCrfBean.getId());
            // end of item datas, tbh
            // crfBusinessLogicHelper.markCRFComplete(eventCrfBean, ub);
            // System .out.println("*** just updated event crf bean: "+
            // eventCrfBean.getId());
            // need to update the study event status as well, tbh
            // crfBusinessLogicHelper.updateStudyEvent(eventCrfBean,
            // ub);
            // above should do it for us, tbh 08/2008
            }
        }
        addPageMessage(respage.getString("data_has_been_successfully_import"));
        addPageMessage(this.ruleActionWarnings(this.runRules(currentStudy, ub, containers, ruleSetService, ExecutionMode.SAVE)));
        // forwardPage(Page.SUBMIT_DATA_SERVLET);
        forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
    // replaced tbh, 06/2009
    }
}

Example 3 with DisplayItemBeanWrapper

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

the class DataImportService method submitData.

public ArrayList<String> submitData(ODMContainer odmContainer, DataSource dataSource, StudyBean studyBean, UserAccountBean userBean, List<DisplayItemBeanWrapper> displayItemBeanWrappers, Map<Integer, String> importedCRFStatuses) throws Exception {
    boolean discNotesGenerated = false;
    ItemDataDAO itemDataDao = new ItemDataDAO(dataSource);
    itemDataDao.setFormatDates(false);
    EventCRFDAO eventCrfDao = new EventCRFDAO(dataSource);
    StringBuffer auditMsg = new StringBuffer();
    int eventCrfBeanId = -1;
    EventCRFBean eventCrfBean = null;
    ArrayList<Integer> eventCrfInts;
    ItemDataBean itemDataBean;
    CrfBusinessLogicHelper crfBusinessLogicHelper = new CrfBusinessLogicHelper(dataSource);
    for (DisplayItemBeanWrapper wrapper : displayItemBeanWrappers) {
        boolean resetSDV = false;
        logger.debug("right before we check to make sure it is savable: " + wrapper.isSavable());
        if (wrapper.isSavable()) {
            eventCrfInts = new ArrayList<Integer>();
            logger.debug("wrapper problems found : " + wrapper.getValidationErrors().toString());
            if (wrapper.getDisplayItemBeans() != null && wrapper.getDisplayItemBeans().size() == 0) {
                return getReturnList("fail", "", "No items to submit. Please check your XML.");
            }
            for (DisplayItemBean displayItemBean : wrapper.getDisplayItemBeans()) {
                eventCrfBeanId = displayItemBean.getData().getEventCRFId();
                eventCrfBean = (EventCRFBean) eventCrfDao.findByPK(eventCrfBeanId);
                logger.debug("found value here: " + displayItemBean.getData().getValue());
                logger.debug("found status here: " + eventCrfBean.getStatus().getName());
                itemDataBean = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
                if (wrapper.isOverwrite() && itemDataBean.getStatus() != null) {
                    if (!itemDataBean.getValue().equals(displayItemBean.getData().getValue()))
                        resetSDV = true;
                    logger.debug("just tried to find item data bean on item name " + displayItemBean.getItem().getName());
                    itemDataBean.setUpdatedDate(new Date());
                    itemDataBean.setUpdater(userBean);
                    itemDataBean.setValue(displayItemBean.getData().getValue());
                    // set status?
                    itemDataDao.update(itemDataBean);
                    logger.debug("updated: " + itemDataBean.getItemId());
                    // need to set pk here in order to create dn
                    displayItemBean.getData().setId(itemDataBean.getId());
                } else {
                    resetSDV = true;
                    itemDataDao.create(displayItemBean.getData());
                    logger.debug("created: " + displayItemBean.getData().getItemId());
                    itemDataBean = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
                    // logger.debug("found: id " + itemDataBean2.getId() + " name " + itemDataBean2.getName());
                    displayItemBean.getData().setId(itemDataBean.getId());
                }
                ItemDAO idao = new ItemDAO(dataSource);
                ItemBean ibean = (ItemBean) idao.findByPK(displayItemBean.getData().getItemId());
                // logger.debug("*** checking for validation errors: " + ibean.getName());
                String itemOid = displayItemBean.getItem().getOid() + "_" + wrapper.getStudyEventRepeatKey() + "_" + displayItemBean.getData().getOrdinal() + "_" + wrapper.getStudySubjectOid();
                // wrapper.getValidationErrors().toString());
                if (wrapper.getValidationErrors().containsKey(itemOid)) {
                    ArrayList<String> messageList = (ArrayList<String>) wrapper.getValidationErrors().get(itemOid);
                    for (String message : messageList) {
                        DiscrepancyNoteBean parentDn = createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, null, userBean, dataSource, studyBean);
                        createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, parentDn.getId(), userBean, dataSource, studyBean);
                        discNotesGenerated = true;
                        logger.debug("*** created disc note with message: " + message);
                        auditMsg.append(wrapper.getStudySubjectOid() + ": " + ibean.getOid() + ": " + message + "---");
                    // split by this ? later, tbh
                    // displayItemBean);
                    }
                }
                if (!eventCrfInts.contains(new Integer(eventCrfBean.getId()))) {
                    String eventCRFStatus = importedCRFStatuses.get(new Integer(eventCrfBean.getId()));
                    if (eventCRFStatus != null && eventCRFStatus.equals(DataEntryStage.INITIAL_DATA_ENTRY.getName()) && eventCrfBean.getStatus().isAvailable()) {
                        crfBusinessLogicHelper.markCRFStarted(eventCrfBean, userBean, true);
                    } else {
                        crfBusinessLogicHelper.markCRFComplete(eventCrfBean, userBean, true);
                    }
                    eventCrfInts.add(new Integer(eventCrfBean.getId()));
                }
            }
            // Reset the SDV status if item data has been changed or added
            if (eventCrfBean != null && resetSDV)
                eventCrfDao.setSDVStatus(false, userBean.getId(), eventCrfBean.getId());
        }
    }
    if (!discNotesGenerated) {
        return getReturnList("success", "", auditMsg.toString());
    } else {
        return getReturnList("warn", "", auditMsg.toString());
    }
}

Example 4 with DisplayItemBeanWrapper

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

the class ImportCRFDataService method lookupValidationErrors.

public List<DisplayItemBeanWrapper> lookupValidationErrors(HttpServletRequest request, ODMContainer odmContainer, UserAccountBean ub, HashMap<String, String> totalValidationErrors, HashMap<String, String> hardValidationErrors, ArrayList<Integer> permittedEventCRFIds) throws OpenClinicaException {
    DisplayItemBeanWrapper displayItemBeanWrapper = null;
    HashMap validationErrors = new HashMap();
    List<DisplayItemBeanWrapper> wrappers = new ArrayList<DisplayItemBeanWrapper>();
    ImportHelper importHelper = new ImportHelper();
    FormDiscrepancyNotes discNotes = new FormDiscrepancyNotes();
    DiscrepancyValidator discValidator = new DiscrepancyValidator(request, discNotes);
    // create a second Validator, this one for hard edit checks
    HashMap<String, String> hardValidator = new HashMap<String, String>();
    StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
    StudyDAO studyDAO = new StudyDAO(ds);
    StudyBean studyBean = studyDAO.findByOid(odmContainer.getCrfDataPostImportContainer().getStudyOID());
    StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
    StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(ds);
    HashMap<String, ItemDataBean> blankCheck = new HashMap<String, ItemDataBean>();
    String hardValidatorErrorMsgs = "";
    ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
    int totalEventCRFCount = 0;
    int totalItemDataBeanCount = 0;
    for (SubjectDataBean subjectDataBean : subjectDataBeans) {
        ArrayList<DisplayItemBean> displayItemBeans = new ArrayList<DisplayItemBean>();
        logger.debug("iterating through subject data beans: found " + subjectDataBean.getSubjectOID());
        ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
        totalEventCRFCount += studyEventDataBeans.size();
        StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
        for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
            int parentStudyId = studyBean.getParentStudyId();
            StudyEventDefinitionBean sedBean = sedDao.findByOidAndStudy(studyEventDataBean.getStudyEventOID(), studyBean.getId(), parentStudyId);
            ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
            logger.debug("iterating through study event data beans: found " + studyEventDataBean.getStudyEventOID());
            int ordinal = 1;
            try {
                ordinal = new Integer(studyEventDataBean.getStudyEventRepeatKey()).intValue();
            } catch (Exception e) {
            // trying to catch NPEs, because tags can be without the
            // repeat key
            }
            StudyEventBean studyEvent = (StudyEventBean) studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubjectBean.getId(), sedBean.getId(), ordinal);
            displayItemBeans = new ArrayList<DisplayItemBean>();
            for (FormDataBean formDataBean : formDataBeans) {
                Map<String, Integer> groupMaxOrdinals = new HashMap<String, Integer>();
                displayItemBeanWrapper = null;
                CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
                EventCRFDAO eventCRFDAO = new EventCRFDAO(ds);
                ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formDataBean.getFormOID());
                ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
                if ((crfVersionBeans == null) || (crfVersionBeans.size() == 0)) {
                    MessageFormat mf = new MessageFormat("");
                    mf.applyPattern(respage.getString("your_crf_version_oid_did_not_generate"));
                    Object[] arguments = { formDataBean.getFormOID() };
                    throw new OpenClinicaException(mf.format(arguments), "");
                }
                CRFVersionBean crfVersion = crfVersionBeans.get(0);
                // if you have a mispelled form oid you get an error here
                // need to error out gracefully and post an error
                logger.debug("iterating through form beans: found " + crfVersion.getOid());
                // may be the point where we cut off item groups etc and
                // instead work on sections
                EventCRFBean eventCRFBean = eventCRFDAO.findByEventCrfVersion(studyEvent, crfVersion);
                EventDefinitionCRFDAO eventDefinitionCRFDAO = new EventDefinitionCRFDAO(ds);
                EventDefinitionCRFBean eventDefinitionCRF = eventDefinitionCRFDAO.findByStudyEventIdAndCRFVersionId(studyBean, studyEvent.getId(), crfVersion.getId());
                if (eventCRFBean != null) {
                    if (permittedEventCRFIds.contains(new Integer(eventCRFBean.getId()))) {
                        for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
                            groupMaxOrdinals.put(itemGroupDataBean.getItemGroupOID(), 1);
                        }
                        // correctness, tbh
                        for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
                            ArrayList<ItemBean> blankCheckItems = new ArrayList<ItemBean>();
                            ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
                            logger.debug("iterating through group beans: " + itemGroupDataBean.getItemGroupOID());
                            // put a checker in here
                            ItemGroupDAO itemGroupDAO = new ItemGroupDAO(ds);
                            ItemGroupBean testBean = itemGroupDAO.findByOid(itemGroupDataBean.getItemGroupOID());
                            if (testBean == null) {
                                // TODO i18n of message
                                MessageFormat mf = new MessageFormat("");
                                mf.applyPattern(respage.getString("your_item_group_oid_for_form_oid"));
                                Object[] arguments = { itemGroupDataBean.getItemGroupOID(), formDataBean.getFormOID() };
                                throw new OpenClinicaException(mf.format(arguments), "");
                            }
                            totalItemDataBeanCount += itemDataBeans.size();
                            for (ImportItemDataBean importItemDataBean : itemDataBeans) {
                                logger.debug("   iterating through item data beans: " + importItemDataBean.getItemOID());
                                ItemDAO itemDAO = new ItemDAO(ds);
                                ItemFormMetadataDAO itemFormMetadataDAO = new ItemFormMetadataDAO(ds);
                                List<ItemBean> itemBeans = itemDAO.findByOid(importItemDataBean.getItemOID());
                                if (!itemBeans.isEmpty()) {
                                    ItemBean itemBean = itemBeans.get(0);
                                    logger.debug("   found " + itemBean.getName());
                                    // throw a null pointer? hopefully not if its been checked...
                                    DisplayItemBean displayItemBean = new DisplayItemBean();
                                    displayItemBean.setItem(itemBean);
                                    ArrayList<ItemFormMetadataBean> metadataBeans = itemFormMetadataDAO.findAllByItemId(itemBean.getId());
                                    logger.debug("      found metadata item beans: " + metadataBeans.size());
                                    int groupOrdinal = 1;
                                    if (itemGroupDataBean.getItemGroupRepeatKey() != null) {
                                        try {
                                            groupOrdinal = new Integer(itemGroupDataBean.getItemGroupRepeatKey()).intValue();
                                            if (groupOrdinal > groupMaxOrdinals.get(itemGroupDataBean.getItemGroupOID())) {
                                                groupMaxOrdinals.put(itemGroupDataBean.getItemGroupOID(), groupOrdinal);
                                            }
                                        } catch (Exception e) {
                                            // do nothing here currently, we are
                                            // looking for a number format
                                            // exception
                                            // from the above.
                                            logger.debug("found npe for group ordinals, line 344!");
                                        }
                                    }
                                    ItemDataBean itemDataBean = createItemDataBean(itemBean, eventCRFBean, importItemDataBean.getValue(), ub, groupOrdinal);
                                    blankCheckItems.add(itemBean);
                                    String newKey = groupOrdinal + "_" + itemGroupDataBean.getItemGroupOID() + "_" + itemBean.getOid() + "_" + subjectDataBean.getSubjectOID();
                                    blankCheck.put(newKey, itemDataBean);
                                    logger.info("adding " + newKey + " to blank checks");
                                    if (!metadataBeans.isEmpty()) {
                                        ItemFormMetadataBean metadataBean = metadataBeans.get(0);
                                        // also possible nullpointer
                                        displayItemBean.setData(itemDataBean);
                                        displayItemBean.setMetadata(metadataBean);
                                        displayItemBean.setEventDefinitionCRF(eventDefinitionCRF);
                                        String eventCRFRepeatKey = studyEventDataBean.getStudyEventRepeatKey();
                                        // if you do indeed leave off this in the XML it will pass but return 'null'
                                        // tbh
                                        attachValidator(displayItemBean, importHelper, discValidator, hardValidator, request, eventCRFRepeatKey, studySubjectBean.getOid());
                                        displayItemBeans.add(displayItemBean);
                                    } else {
                                        MessageFormat mf = new MessageFormat("");
                                        mf.applyPattern(respage.getString("no_metadata_could_be_found"));
                                        Object[] arguments = { importItemDataBean.getItemOID() };
                                        throw new OpenClinicaException(mf.format(arguments), "");
                                    }
                                } else {
                                    // report the error there
                                    MessageFormat mf = new MessageFormat("");
                                    mf.applyPattern(respage.getString("no_item_could_be_found"));
                                    Object[] arguments = { importItemDataBean.getItemOID() };
                                    throw new OpenClinicaException(mf.format(arguments), "");
                                }
                            }
                            // end item data beans
                            logger.debug(".. found blank check: " + blankCheck.toString());
                            for (int i = 1; i <= groupMaxOrdinals.get(itemGroupDataBean.getItemGroupOID()); i++) {
                                for (ItemBean itemBean : blankCheckItems) {
                                    String newKey = i + "_" + itemGroupDataBean.getItemGroupOID() + "_" + itemBean.getOid() + "_" + subjectDataBean.getSubjectOID();
                                    if (blankCheck.get(newKey) == null) {
                                        // if it already exists, Do Not Add It.
                                        ItemDataBean itemDataCheck = getItemDataDao().findByItemIdAndEventCRFIdAndOrdinal(itemBean.getId(), eventCRFBean.getId(), i);
                                        logger.debug("found item data bean id: " + itemDataCheck.getId() + " for ordinal " + i);
                                        if (itemDataCheck.getId() == 0) {
                                            ItemDataBean blank = createItemDataBean(itemBean, eventCRFBean, "", ub, i);
                                            DisplayItemBean displayItemBean = new DisplayItemBean();
                                            displayItemBean.setItem(itemBean);
                                            displayItemBean.setData(blank);
                                            // displayItemBean.setMetadata(metadataBean);
                                            // set event def crf?
                                            displayItemBean.setEventDefinitionCRF(eventDefinitionCRF);
                                            String eventCRFRepeatKey = studyEventDataBean.getStudyEventRepeatKey();
                                            // if you do indeed leave off this in the XML it will pass but return
                                            // 'null'
                                            // tbh
                                            displayItemBeans.add(displayItemBean);
                                            logger.debug("... adding display item bean");
                                        }
                                    }
                                    logger.debug("found a blank at " + i + ", adding " + blankCheckItems.size() + " blank items");
                                }
                            }
                            // << tbh #5548
                            blankCheckItems = new ArrayList<ItemBean>();
                        }
                    // end item group data beans
                    }
                    // matches if on permittedCRFIDs
                    CRFDAO crfDAO = new CRFDAO(ds);
                    CRFBean crfBean = crfDAO.findByVersionId(crfVersion.getCrfId());
                    // seems like an extravagance, but is not contained in crf
                    // version or event crf bean
                    validationErrors = discValidator.validate();
                    // totalValidationErrors.addAll(validationErrors);
                    for (Object errorKey : validationErrors.keySet()) {
                        // JN: to avoid duplicate errors
                        if (!totalValidationErrors.containsKey(errorKey.toString()))
                            totalValidationErrors.put(errorKey.toString(), validationErrors.get(errorKey).toString());
                        // assuming that this will be put back in to the core
                        // method's hashmap, updating statically, tbh 06/2008
                        logger.debug("+++ adding " + errorKey.toString());
                    }
                    logger.debug("-- hard validation checks: --");
                    for (Object errorKey : hardValidator.keySet()) {
                        logger.debug(errorKey.toString() + " -- " + hardValidator.get(errorKey));
                        hardValidationErrors.put(errorKey.toString(), hardValidator.get(errorKey));
                        // updating here 'statically' tbh 06/2008
                        hardValidatorErrorMsgs += hardValidator.get(errorKey) + "<br/><br/>";
                    }
                    String studyEventId = studyEvent.getId() + "";
                    String crfVersionId = crfVersion.getId() + "";
                    logger.debug("creation of wrapper: original count of display item beans " + displayItemBeans.size() + ", count of item data beans " + totalItemDataBeanCount + " count of validation errors " + validationErrors.size() + " count of study subjects " + subjectDataBeans.size() + " count of event crfs " + totalEventCRFCount + " count of hard error checks " + hardValidator.size());
                    // check if we need to overwrite
                    DataEntryStage dataEntryStage = eventCRFBean.getStage();
                    Status eventCRFStatus = eventCRFBean.getStatus();
                    boolean overwrite = false;
                    // //JN: Commenting out the following 2 lines, coz the prompt should come in the cases on
                    if (// eventCRFStatus.equals(Status.UNAVAILABLE) ||
                    dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
                        overwrite = true;
                    }
                    // << tbh, adding extra statuses to prevent appending, 06/2009
                    // SummaryStatsBean ssBean = new SummaryStatsBean();
                    // ssBean.setDiscNoteCount(totalValidationErrors);
                    // ssBean.setEventCrfCount(totalEventCRFCount);
                    // ssBean.setStudySubjectCount(subjectDataBeans.size());
                    // // add other stats here, tbh
                    // not working here, need to do it in a different method,
                    // tbh
                    // summary stats added tbh 05/2008
                    // JN: Changed from validationErrors to totalValidationErrors to create discrepancy notes for
                    // all
                    // the
                    displayItemBeanWrapper = new DisplayItemBeanWrapper(displayItemBeans, true, overwrite, validationErrors, studyEventId, crfVersionId, studyEventDataBean.getStudyEventOID(), studySubjectBean.getLabel(), eventCRFBean.getCreatedDate(), crfBean.getName(), crfVersion.getName(), studySubjectBean.getOid(), studyEventDataBean.getStudyEventRepeatKey());
                    // JN: Commenting out the following code, since we shouldn't re-initialize at this point, as
                    // validationErrors would get overwritten and the
                    // older errors will be overriden. Moving it after the form.
                    // Removing the comments for now, since it seems to be creating duplicate Discrepancy Notes.
                    validationErrors = new HashMap();
                    discValidator = new DiscrepancyValidator(request, discNotes);
                // reset to allow for new errors...
                }
            }
            // discValidator = new DiscrepancyValidator(request, discNotes);
            if (displayItemBeanWrapper != null && displayItemBeans.size() > 0)
                wrappers.add(displayItemBeanWrapper);
        }
    // after study events
    // remove repeats here? remove them below by only forwarding the
    // first
    // each wrapper represents an Event CRF and a Form, but we don't
    // have all events for all forms
    // need to not add a wrapper for every event + form combination,
    // but instead for every event + form combination which is present
    // look at the hack below and see what happens
    }
    // thrown, tbh 06/2008
    if (!hardValidator.isEmpty()) {
    // throw new OpenClinicaException(hardValidatorErrorMsgs, "");
    }
    return wrappers;
}

Example 5 with DisplayItemBeanWrapper

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

the class ImportCRFDataService method generateSummaryStatsBean.

public SummaryStatsBean generateSummaryStatsBean(ODMContainer odmContainer, List<DisplayItemBeanWrapper> wrappers, ImportCRFInfoContainer importCrfInfo) {
    int countSubjects = 0;
    int countEventCRFs = 0;
    int discNotesGenerated = 0;
    for (DisplayItemBeanWrapper wr : wrappers) {
        HashMap validations = wr.getValidationErrors();
        discNotesGenerated += validations.size();
    }
    ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
    countSubjects += subjectDataBeans.size();
    for (SubjectDataBean subjectDataBean : subjectDataBeans) {
        ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
        for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
            ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
            // this would be the place to add more stats
            for (FormDataBean formDataBean : formDataBeans) {
                countEventCRFs += 1;
            }
        }
    }
    SummaryStatsBean ssBean = new SummaryStatsBean();
    ssBean.setDiscNoteCount(discNotesGenerated);
    ssBean.setEventCrfCount(countEventCRFs);
    ssBean.setStudySubjectCount(countSubjects);
    ssBean.setSkippedCrfCount(importCrfInfo.getCountSkippedEventCrfs());
    return ssBean;
}