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

Example 26 with ItemBean

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

the class ExpressionService method getItemExpression.

/*
     * public ItemGroupBean getItemGroupFromExpression(String expression) {
     * logger.debug("Expression : " + expression); logger.debug("Expression : "
     * + getItemGroupOidFromExpression(expression)); return
     * getItemGroupDao().findByOid(getItemGroupOidFromExpression(expression)); }
     */
public ItemBean getItemExpression(String expression, ItemGroupBean itemGroup) {
    String itemKey = getItemOidFromExpression(expression);
    logger.debug("Expression : {} , Item OID : {}", expression, itemKey);
    if (items.containsKey(itemKey)) {
        return items.get(itemKey);
    } else {
        ItemBean item = getItemDao().findItemByGroupIdandItemOid(itemGroup.getId(), itemKey);
        if (item != null) {
            items.put(itemKey, item);
            return item;
        } else {
            return null;
        }
    }
}

Example 27 with ItemBean

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

the class ExpressionService method getValueFromDb.

public String getValueFromDb(String expression, List<ItemDataBean> itemData) throws OpenClinicaSystemException {
    if (isExpressionPartial(expression)) {
        throw new OpenClinicaSystemException("getValueFromDb:We cannot get the Value of a PARTIAL expression : " + expression);
    }
    try {
        Integer index = getItemGroupOidOrdinalFromExpression(expression).equals("") ? 0 : Integer.valueOf(getItemGroupOidOrdinalFromExpression(expression)) - 1;
        ItemDataBean itemDataBean = itemData.get(index);
        ItemBean itemBean = (ItemBean) getItemDao().findByPK(itemDataBean.getItemId());
        String value = itemData.get(index).getValue();
        value = ifValueIsDate(itemBean, value);
        return value;
    } catch (NullPointerException npe) {
        logger.error("NullPointerException was thrown ");
        return null;
    } catch (IndexOutOfBoundsException ioobe) {
        logger.error("IndexOutOfBoundsException was thrown ");
        return null;
    }
}

Example 28 with ItemBean

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

the class InsertActionValidator method validateOidInPropertyBean.

public void validateOidInPropertyBean(PropertyBean propertyBean, Errors e, String p) {
    if (getExpressionService().isExpressionPartial(getRuleSetBean().getTarget().getValue())) {
        if (getExpressionService().getExpressionSize(propertyBean.getOid()).intValue() > 3) {
            e.rejectValue(p + "oid", "oid.invalid", "OID: " + propertyBean.getOid() + " is Invalid.");
        }
        try {
            getExpressionService().isExpressionValid(propertyBean.getOid());
        } catch (OpenClinicaSystemException ose) {
            e.rejectValue(p + "oid", "oid.invalid", "OID: " + propertyBean.getOid() + " is Invalid.");
        }
        // Use OID in destinationProperty to get CRF
        CRFBean destinationPropertyOidCrf = getExpressionService().getCRFFromExpression(propertyBean.getOid());
        if (destinationPropertyOidCrf == null) {
            ItemBean item = getExpressionService().getItemBeanFromExpression(propertyBean.getOid());
            destinationPropertyOidCrf = getCrfDAO().findByItemOid(item.getOid());
        }
        // Use Target get CRF
        CRFBean targetCrf = getExpressionService().getCRFFromExpression(getRuleSetBean().getTarget().getValue());
        if (targetCrf == null) {
            ItemBean item = getExpressionService().getItemBeanFromExpression(getRuleSetBean().getTarget().getValue());
            targetCrf = getCrfDAO().findByItemOid(item.getOid());
        }
        // Get All event definitions the selected CRF belongs to
        List<StudyEventDefinitionBean> destinationPropertyStudyEventDefinitions = getStudyEventDefinitionDAO().findAllByCrf(destinationPropertyOidCrf);
        List<StudyEventDefinitionBean> targetStudyEventDefinitions = getStudyEventDefinitionDAO().findAllByCrf(targetCrf);
        Collection intersection = CollectionUtils.intersection(destinationPropertyStudyEventDefinitions, targetStudyEventDefinitions);
        if (intersection.size() == 0) {
            e.rejectValue(p + "oid", "oid.invalid", "OID: " + propertyBean.getOid() + " is Invalid.");
        }
    } else {
        String expression = getExpressionService().constructFullExpressionIfPartialProvided(propertyBean.getOid(), getRuleSetBean().getTarget().getValue());
        ItemBean item = getExpressionService().getItemBeanFromExpression(expression);
        if (!getExpressionService().isInsertActionExpressionValid(propertyBean.getOid(), getRuleSetBean(), 3) || item == null) {
            e.rejectValue(p + "oid", "oid.invalid", "OID: " + propertyBean.getOid() + " is Invalid.");
        }
    }
}

Example 29 with ItemBean

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

the class CreateCRFVersionServlet method processRequest.

@SuppressWarnings("unchecked")
@Override
public void processRequest() throws Exception {
    resetPanel();
    panel.setStudyInfoShown(true);
    CRFDAO cdao = new CRFDAO(sm.getDataSource());
    CRFVersionDAO vdao = new CRFVersionDAO(sm.getDataSource());
    EventDefinitionCRFDAO edao = new EventDefinitionCRFDAO(sm.getDataSource());
    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);
    request.setAttribute("xformEnabled", CoreResources.getField("xform.enabled"));
    String action = request.getParameter("action");
    CRFVersionBean version = (CRFVersionBean) session.getAttribute("version");
    if (StringUtil.isBlank(action)) {
        logger.debug("action is blank");
        request.setAttribute("version", version);
        forwardPage(Page.CREATE_CRF_VERSION);
    } else if ("confirm".equalsIgnoreCase(action)) {
        String dir = SQLInitServlet.getField("filePath");
        if (!new File(dir).exists()) {
            logger.debug("The filePath in datainfo.properties is invalid " + dir);
            addPageMessage(resword.getString("the_filepath_you_defined"));
            forwardPage(Page.CREATE_CRF_VERSION);
            // BWP 01/13/2009 >>
            return;
        // >>
        }
        // 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.debug("Made the directory " + theDir);
        }
        // MultipartRequest multi = new MultipartRequest(request, theDir, 50 * 1024 * 1024);
        String tempFile = "";
        try {
            tempFile = uploadFile(theDir, version);
        } catch (CRFReadingException crfException) {
            Validator.addError(errors, "excel_file", crfException.getMessage());
            String msg = crfException.getMessage();
            request.setAttribute("formMessages", errors);
            forwardPage(Page.CREATE_CRF_VERSION);
            return;
        } catch (Exception e) {
            //
            logger.warn("*** Found exception during file upload***");
            e.printStackTrace();
        }
        session.setAttribute("tempFileName", tempFile);
        // provided and/or not xls format
        if (errors.isEmpty()) {
            String s = ((NewCRFBean) session.getAttribute("nib")).getVersionName();
            if (s.length() > 255) {
                Validator.addError(errors, "excel_file", resword.getString("the_version_CRF_version_more_than_255"));
            } else if (s.length() <= 0) {
                Validator.addError(errors, "excel_file", resword.getString("the_VERSION_column_was_blank"));
            }
            version.setName(s);
            if (version.getCrfId() == 0) {
                version.setCrfId(fp.getInt("crfId"));
            }
            session.setAttribute("version", version);
        }
        if (!errors.isEmpty()) {
            logger.debug("has validation errors ");
            request.setAttribute("formMessages", errors);
            forwardPage(Page.CREATE_CRF_VERSION);
        } else {
            CRFBean crf = (CRFBean) cdao.findByPK(version.getCrfId());
            ArrayList versions = (ArrayList) vdao.findAllByCRF(crf.getId());
            for (int i = 0; i < versions.size(); i++) {
                CRFVersionBean version1 = (CRFVersionBean) versions.get(i);
                if (version.getName().equals(version1.getName())) {
                    // version already exists
                    logger.debug("Version already exists; owner or not:" + ub.getId() + "," + version1.getOwnerId());
                    if (ub.getId() != version1.getOwnerId()) {
                        // not owner
                        addPageMessage(respage.getString("CRF_version_try_upload_exists_database") + version1.getOwner().getName() + respage.getString("please_contact_owner_to_delete"));
                        forwardPage(Page.CREATE_CRF_VERSION);
                        return;
                    } else {
                        // owner,
                        ArrayList definitions = edao.findByDefaultVersion(version1.getId());
                        if (!definitions.isEmpty()) {
                            // used in
                            // definition
                            request.setAttribute("definitions", definitions);
                            forwardPage(Page.REMOVE_CRF_VERSION_DEF);
                            return;
                        } else {
                            // not used in definition
                            int previousVersionId = version1.getId();
                            version.setId(previousVersionId);
                            session.setAttribute("version", version);
                            session.setAttribute("previousVersionId", new Integer(previousVersionId));
                            forwardPage(Page.REMOVE_CRF_VERSION_CONFIRM);
                            return;
                        }
                    }
                }
            }
            // didn't find same version in the DB,let user upload the excel
            // file
            logger.debug("didn't find same version in the DB,let user upload the excel file.");
            // List excelErr =
            // ((ArrayList)request.getAttribute("excelErrors"));
            List excelErr = (ArrayList) session.getAttribute("excelErrors");
            logger.debug("excelErr.isEmpty()=" + excelErr.isEmpty());
            if (excelErr != null && excelErr.isEmpty()) {
                addPageMessage(resword.getString("congratulations_your_spreadsheet_no_errors"));
                forwardPage(Page.VIEW_SECTION_DATA_ENTRY_PREVIEW);
            } else {
                logger.debug("OpenClinicaException thrown, forwarding to CREATE_CRF_VERSION_CONFIRM.");
                forwardPage(Page.CREATE_CRF_VERSION_CONFIRM);
            }
            return;
        }
    } else if ("confirmsql".equalsIgnoreCase(action)) {
        NewCRFBean nib = (NewCRFBean) session.getAttribute("nib");
        if (nib != null && nib.getItemQueries() != null) {
            request.setAttribute("openQueries", nib.getItemQueries());
        } else {
            request.setAttribute("openQueries", new HashMap());
        }
        boolean canDelete = false;
        // check whether need to delete previous version
        Boolean deletePreviousVersion = (Boolean) session.getAttribute("deletePreviousVersion");
        Integer previousVersionId = (Integer) session.getAttribute("previousVersionId");
        if (deletePreviousVersion != null && deletePreviousVersion.equals(Boolean.TRUE) && previousVersionId != null && previousVersionId.intValue() > 0) {
            logger.debug("Need to delete previous version");
            // whether we can delete
            canDelete = canDeleteVersion(previousVersionId.intValue());
            if (!canDelete) {
                logger.debug("but cannot delete previous version");
                if (session.getAttribute("itemsHaveData") == null && session.getAttribute("eventsForVersion") == null) {
                    addPageMessage(respage.getString("you_are_not_owner_some_items_cannot_delete"));
                }
                if (session.getAttribute("itemsHaveData") == null) {
                    session.setAttribute("itemsHaveData", new ArrayList());
                }
                if (session.getAttribute("eventsForVersion") == null) {
                    session.setAttribute("eventsForVersion", new ArrayList());
                }
                forwardPage(Page.CREATE_CRF_VERSION_NODELETE);
                return;
            }
            ArrayList<ItemBean> nonSharedItems = (ArrayList<ItemBean>) vdao.findNotSharedItemsByVersion(previousVersionId.intValue());
            // htaycher: here is the trick we need to put in nib1.setItemQueries()
            // update statements for shared items and insert for nonShared that were just deleted 5927
            HashMap item_table_statements = new HashMap();
            ArrayList<String> temp = new ArrayList<String>(nonSharedItems.size());
            for (ItemBean item : nonSharedItems) {
                temp.add(item.getName());
                item_table_statements.put(item.getName(), nib.getBackupItemQueries().get(item.getName()));
            }
            for (String item_name : (Set<String>) nib.getItemQueries().keySet()) {
                // check if item shared
                if (!temp.contains(item_name)) {
                    item_table_statements.put(item_name, nib.getItemQueries().get(item_name));
                }
            }
            // statements to run
            if (!nonSharedItems.isEmpty()) {
                request.setAttribute("openQueries", item_table_statements);
            }
            // htaycher: put all statements in
            nib.setItemQueries(item_table_statements);
            session.setAttribute("nib", nib);
        }
        // submit
        logger.debug("commit sql");
        NewCRFBean nib1 = (NewCRFBean) session.getAttribute("nib");
        if (nib1 != null) {
            try {
                if (canDelete) {
                    nib1.deleteInsertToDB();
                } else {
                    nib1.insertToDB();
                }
                request.setAttribute("queries", nib1.getQueries());
                // YW << for add a link to "View CRF Version Data Entry".
                // For this purpose, CRFVersion id is needed.
                // So the latest CRFVersion Id of A CRF Id is it.
                CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
                ArrayList crfvbeans = new ArrayList();
                logger.debug("CRF-ID [" + version.getCrfId() + "]");
                int crfVersionId = 0;
                String versionOID = null;
                if (version.getCrfId() != 0) {
                    crfvbeans = cvdao.findAllByCRFId(version.getCrfId());
                    CRFVersionBean cvbean = (CRFVersionBean) crfvbeans.get(crfvbeans.size() - 1);
                    crfVersionId = cvbean.getId();
                    versionOID = cvbean.getOid();
                    for (Iterator iter = crfvbeans.iterator(); iter.hasNext(); ) {
                        cvbean = (CRFVersionBean) iter.next();
                        if (crfVersionId < cvbean.getId()) {
                            crfVersionId = cvbean.getId();
                        }
                    }
                }
                // Not needed; crfVersionId will be autoboxed in Java 5
                // this was added for the old CVS java compiler
                Integer cfvID = new Integer(crfVersionId);
                if (cfvID == 0) {
                    cfvID = cvdao.findCRFVersionId(nib1.getCrfId(), nib1.getVersionName());
                }
                CRFVersionBean finalVersion = (CRFVersionBean) cvdao.findByPK(cfvID);
                version.setCrfId(nib1.getCrfId());
                version.setOid(finalVersion.getOid());
                CRFBean crfBean = (CRFBean) cdao.findByPK(version.getCrfId());
                crfBean.setUpdatedDate(version.getCreatedDate());
                crfBean.setUpdater(ub);
                cdao.update(crfBean);
                // workaround to get a correct file name below, tbh 06/2008
                request.setAttribute("crfVersionId", cfvID);
                // YW >>
                // return those properties to initial values
                session.removeAttribute("version");
                session.removeAttribute("eventsForVersion");
                session.removeAttribute("itemsHaveData");
                session.removeAttribute("nib");
                session.removeAttribute("deletePreviousVersion");
                session.removeAttribute("previousVersionId");
                // save new version spreadsheet
                String tempFile = (String) session.getAttribute("tempFileName");
                if (tempFile != null) {
                    logger.debug("*** ^^^ *** saving new version spreadsheet" + tempFile);
                    try {
                        String dir = SQLInitServlet.getField("filePath");
                        File f = new File(dir + "crf" + File.separator + "original" + File.separator + tempFile);
                        // check to see whether crf/new/ folder exists
                        // inside, if not,
                        // creates
                        // the crf/new/ folder
                        String finalDir = dir + "crf" + File.separator + "new" + File.separator;
                        if (!new File(finalDir).isDirectory()) {
                            logger.debug("need to create folder for excel files" + finalDir);
                            new File(finalDir).mkdirs();
                        }
                        // String newFile = version.getCrfId() +
                        // version.getName() + ".xls";
                        String newFile = version.getCrfId() + version.getOid() + ".xls";
                        logger.debug("*** ^^^ *** new file: " + newFile);
                        File nf = new File(finalDir + newFile);
                        logger.debug("copying old file " + f.getName() + " to new file " + nf.getName());
                        copy(f, nf);
                    // ?
                    } catch (IOException ie) {
                        logger.debug("==============");
                        addPageMessage(respage.getString("CRF_version_spreadsheet_could_not_saved_contact"));
                    }
                }
                session.removeAttribute("tempFileName");
                session.removeAttribute(MODULE);
                session.removeAttribute("excelErrors");
                session.removeAttribute("htmlTab");
                forwardPage(Page.CREATE_CRF_VERSION_DONE);
            } catch (OpenClinicaException pe) {
                logger.debug("--------------");
                session.setAttribute("excelErrors", nib1.getErrors());
                // request.setAttribute("excelErrors", nib1.getErrors());
                forwardPage(Page.CREATE_CRF_VERSION_ERROR);
            }
        } else {
            forwardPage(Page.CREATE_CRF_VERSION);
        }
    } else if ("delete".equalsIgnoreCase(action)) {
        logger.debug("user wants to delete previous version");
        List excelErr = (ArrayList) session.getAttribute("excelErrors");
        logger.debug("for overwrite CRF version, excelErr.isEmpty()=" + excelErr.isEmpty());
        if (excelErr != null && excelErr.isEmpty()) {
            addPageMessage(resword.getString("congratulations_your_spreadsheet_no_errors"));
            // should be moved to excelErr != null block
            session.setAttribute("deletePreviousVersion", Boolean.TRUE);
            forwardPage(Page.VIEW_SECTION_DATA_ENTRY_PREVIEW);
        } else {
            // should be moved to excelErr != null
            session.setAttribute("deletePreviousVersion", Boolean.FALSE);
            // block
            logger.debug("OpenClinicaException thrown, forwarding to CREATE_CRF_VERSION_CONFIRM.");
            forwardPage(Page.CREATE_CRF_VERSION_CONFIRM);
        }
    }
}

Example 30 with ItemBean

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

the class CreateCRFVersionServlet method isResponseValid.

private ItemBean isResponseValid(HashMap items, CRFVersionBean version) {
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    ItemFormMetadataDAO metadao = new ItemFormMetadataDAO(sm.getDataSource());
    Set names = items.keySet();
    Iterator it = names.iterator();
    while (it.hasNext()) {
        String name = (String) it.next();
        ItemBean oldItem = (ItemBean) idao.findByNameAndCRFId(name, version.getCrfId());
        ItemBean item = (ItemBean) items.get(name);
        if (oldItem.getId() > 0) {
            // found same item in DB
            ArrayList metas = metadao.findAllByItemId(oldItem.getId());
            for (int i = 0; i < metas.size(); i++) {
                ItemFormMetadataBean ifmb = (ItemFormMetadataBean) metas.get(i);
                ResponseSetBean rsb = ifmb.getResponseSet();
                if (hasDifferentOption(rsb, item.getItemMeta().getResponseSet()) != null) {
                    return item;
                }
            }
        }
    }
    return null;
}