Examples with EntityBeanTable org.akaza.openclinica.web.bean.EntityBeanTable used on opensource projects

Example 1 with EntityBeanTable

use of org.akaza.openclinica.web.bean.EntityBeanTable in project OpenClinica by OpenClinica.

the class SignStudySubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    String action = fp.getString("action");
    // studySubjectId
    int studySubId = fp.getInt("id", true);
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);
    if (studySubId == 0) {
        addPageMessage(respage.getString("please_choose_a_subject_to_view"));
        forwardPage(Page.LIST_STUDY_SUBJECTS);
        return;
    }
    StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
    if (!permitSign(studySub, sm.getDataSource())) {
        addPageMessage(respage.getString("subject_event_cannot_signed"));
        // forwardPage(Page.SUBMIT_DATA_SERVLET);
        forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
        // >> changed tbh, 06/2009
        return;
    }
    if (action.equalsIgnoreCase("confirm")) {
        String username = request.getParameter("j_user");
        String password = request.getParameter("j_pass");
        SecurityManager securityManager = ((SecurityManager) SpringServletAccess.getApplicationContext(context).getBean("securityManager"));
        // String encodedUserPass =
        // org.akaza.openclinica.core.SecurityManager
        // .getInstance().encrytPassword(password);
        UserAccountBean ub = (UserAccountBean) session.getAttribute("userBean");
        if (securityManager.verifyPassword(password, getUserDetails()) && ub.getName().equals(username)) {
            if (signSubjectEvents(studySub, sm.getDataSource(), ub)) {
                // Making the StudySubject signed as all the events have
                // become signed.
                studySub.setStatus(Status.SIGNED);
                studySub.setUpdater(ub);
                subdao.update(studySub);
                addPageMessage(respage.getString("subject_event_signed"));
                // forwardPage(Page.SUBMIT_DATA_SERVLET);
                forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
                // >> changed tbh, 06/2009
                return;
            } else {
                addPageMessage(respage.getString("errors_in_submission_see_below"));
                forwardPage(Page.LIST_STUDY_SUBJECTS);
                return;
            }
        } else {
            request.setAttribute("id", new Integer(studySubId).toString());
            addPageMessage(restext.getString("password_match"));
            forwardPage(Page.LIST_STUDY_SUBJECTS);
            return;
        }
    }
    request.setAttribute("studySub", studySub);
    int studyId = studySub.getStudyId();
    int subjectId = studySub.getSubjectId();
    SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
    if (currentStudy.getStudyParameterConfig().getCollectDob().equals("2")) {
        Date dob = subject.getDateOfBirth();
        if (dob != null) {
            Calendar cal = Calendar.getInstance();
            cal.setTime(dob);
            int year = cal.get(Calendar.YEAR);
            request.setAttribute("yearOfBirth", new Integer(year));
        } else {
            request.setAttribute("yearOfBirth", "");
        }
    }
    request.setAttribute("subject", subject);
    StudyDAO studydao = new StudyDAO(sm.getDataSource());
    StudyBean study = (StudyBean) studydao.findByPK(studyId);
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
    study.getStudyParameterConfig().setCollectDob(spvdao.findByHandleAndStudy(studyId, "collectDob").getValue());
    if (study.getParentStudyId() > 0) {
        // this is a site,find parent
        StudyBean parentStudy = (StudyBean) studydao.findByPK(study.getParentStudyId());
        request.setAttribute("parentStudy", parentStudy);
    } else {
        request.setAttribute("parentStudy", new StudyBean());
    }
    ArrayList children = (ArrayList) sdao.findAllChildrenByPK(subjectId);
    request.setAttribute("children", children);
    // find study events
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
    // find all eventcrfs for each event
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    ArrayList<DisplayStudyEventBean> displayEvents = getDisplayStudyEventsForStudySubject(study, studySub, sm.getDataSource(), ub, currentRole);
    DiscrepancyNoteUtil discNoteUtil = new DiscrepancyNoteUtil();
    // Don't filter for now; disc note beans are returned with eventCRFId
    // set
    discNoteUtil.injectParentDiscNotesIntoDisplayStudyEvents(displayEvents, new HashSet(), sm.getDataSource(), 0);
    // All the displaystudyevents for one subject
    request.setAttribute("displayStudyEvents", displayEvents);
    // Set up a Map for the JSP view, mapping the eventCRFId to another Map:
    // the
    // inner Map maps the resolution status name to the number of notes for
    // that
    // eventCRF id, as in New --> 2
    Map discNoteByEventCRFid = discNoteUtil.createDiscNoteMapByEventCRF(displayEvents);
    request.setAttribute("discNoteByEventCRFid", discNoteByEventCRFid);
    EntityBeanTable table = fp.getEntityBeanTable();
    // sort by start date,
    table.setSortingIfNotExplicitlySet(1, false);
    // desc
    ArrayList allEventRows = DisplayStudyEventRow.generateRowsFromBeans(displayEvents);
    String[] columns = { resword.getString("event") + " (" + resword.getString("occurrence_number") + ")", resword.getString("start_date1"), resword.getString("location"), resword.getString("status"), resword.getString("actions"), resword.getString("CRFs_atrib") };
    table.setColumns(new ArrayList(Arrays.asList(columns)));
    table.hideColumnLink(4);
    table.hideColumnLink(5);
    if (!"removed".equalsIgnoreCase(studySub.getStatus().getName()) && !"auto-removed".equalsIgnoreCase(studySub.getStatus().getName())) {
        table.addLink(resword.getString("add_new_event"), "CreateNewStudyEvent?" + CreateNewStudyEventServlet.INPUT_STUDY_SUBJECT_ID_FROM_VIEWSUBJECT + "=" + studySub.getId());
    }
    HashMap args = new HashMap();
    args.put("id", new Integer(studySubId).toString());
    table.setQuery("ViewStudySubject", args);
    table.setRows(allEventRows);
    table.computeDisplay();
    request.setAttribute("table", table);
    SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
    ArrayList groupMaps = (ArrayList) sgmdao.findAllByStudySubject(studySubId);
    request.setAttribute("groups", groupMaps);
    AuditEventDAO aedao = new AuditEventDAO(sm.getDataSource());
    ArrayList logs = aedao.findEventStatusLogByStudySubject(studySubId);
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    ArrayList eventLogs = new ArrayList();
    for (int i = 0; i < logs.size(); i++) {
        AuditEventBean avb = (AuditEventBean) logs.get(i);
        StudyEventAuditBean sea = new StudyEventAuditBean();
        sea.setAuditEvent(avb);
        StudyEventBean se = (StudyEventBean) sedao.findByPK(avb.getEntityId());
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
        sea.setDefinition(sed);
        String old = avb.getOldValue().trim();
        try {
            if (!StringUtil.isBlank(old)) {
                SubjectEventStatus oldStatus = SubjectEventStatus.get(new Integer(old).intValue());
                sea.setOldSubjectEventStatus(oldStatus);
            }
            String newValue = avb.getNewValue().trim();
            if (!StringUtil.isBlank(newValue)) {
                SubjectEventStatus newStatus = SubjectEventStatus.get(new Integer(newValue).intValue());
                sea.setNewSubjectEventStatus(newStatus);
            }
        } catch (NumberFormatException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        // logger.warning("^^^ caught NFE");
        }
        UserAccountBean updater = (UserAccountBean) udao.findByPK(avb.getUserId());
        sea.setUpdater(updater);
        eventLogs.add(sea);
    }
    // logger.warning("^^^ finished iteration");
    request.setAttribute("eventLogs", eventLogs);
    forwardPage(Page.SIGN_STUDY_SUBJECT);
}

Example 2 with EntityBeanTable

use of org.akaza.openclinica.web.bean.EntityBeanTable in project OpenClinica by OpenClinica.

the class ViewImportJobServlet method processRequest.

@Override
protected void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    // First we must get a reference to a scheduler
    scheduler = getScheduler();
    // then we pull all the triggers that are specifically named
    // IMPORT_TRIGGER.
    Set<TriggerKey> triggerKeys = scheduler.getTriggerKeys(GroupMatcher.groupEquals(IMPORT_TRIGGER));
    // the next bit goes out and processes all the triggers
    ArrayList triggerBeans = new ArrayList<TriggerBean>();
    for (TriggerKey triggerKey : triggerKeys) {
        String triggerName = triggerKey.getName();
        Trigger trigger = scheduler.getTrigger(triggerKey);
        logger.debug("found trigger, full name: " + triggerName);
        try {
            logger.debug("prev fire time " + trigger.getPreviousFireTime().toString());
            logger.debug("next fire time " + trigger.getNextFireTime().toString());
            logger.debug("final fire time: " + trigger.getFinalFireTime().toString());
        } catch (NullPointerException npe) {
        // could be nulls in the dates, etc
        }
        TriggerBean triggerBean = new TriggerBean();
        triggerBean.setFullName(triggerName);
        triggerBean.setPreviousDate(trigger.getPreviousFireTime());
        triggerBean.setNextDate(trigger.getNextFireTime());
        if (trigger.getDescription() != null) {
            triggerBean.setDescription(trigger.getDescription());
        }
        // this next bit of code looks at the job data map and pulls out
        // specific items
        JobDataMap dataMap = new JobDataMap();
        if (trigger.getJobDataMap().size() > 0) {
            dataMap = trigger.getJobDataMap();
            triggerBean.setStudyName(dataMap.getString(ExampleSpringJob.STUDY_NAME));
            String oid = dataMap.getString("study_oid");
        }
        // this next bit of code looks to see if the trigger is paused
        logger.debug("Trigger Priority: " + triggerName + " " + trigger.getPriority());
        if (scheduler.getTriggerState(new TriggerKey(triggerName, IMPORT_TRIGGER)) == Trigger.TriggerState.PAUSED) {
            triggerBean.setActive(false);
            logger.debug("setting active to false for trigger: " + triggerName);
        } else {
            triggerBean.setActive(true);
            logger.debug("setting active to TRUE for trigger: " + triggerName);
        }
        triggerBeans.add(triggerBean);
    // our wrapper to show triggers
    }
    // set up the table here and get ready to send to the web page
    ArrayList allRows = TriggerRow.generateRowsFromBeans(triggerBeans);
    EntityBeanTable table = fp.getEntityBeanTable();
    String[] columns = { resword.getString("name"), resword.getString("previous_fire_time"), resword.getString("next_fire_time"), resword.getString("description"), resword.getString("study"), resword.getString("actions") };
    table.setColumns(new ArrayList(Arrays.asList(columns)));
    table.hideColumnLink(3);
    table.hideColumnLink(5);
    table.setQuery("ViewImportJob", new HashMap());
    // table.addLink("", "CreateUserAccount");
    table.setSortingColumnInd(0);
    table.setRows(allRows);
    table.computeDisplay();
    request.setAttribute("table", table);
    forwardPage(Page.VIEW_IMPORT_JOB);
}

Example 3 with EntityBeanTable

use of org.akaza.openclinica.web.bean.EntityBeanTable in project OpenClinica by OpenClinica.

the class ExportDatasetServlet method processRequest.

@Override
public void processRequest() throws Exception {
    DatasetDAO dsdao = new DatasetDAO(sm.getDataSource());
    ArchivedDatasetFileDAO asdfdao = new ArchivedDatasetFileDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    GenerateExtractFileService generateFileService = new GenerateExtractFileService(sm.getDataSource(), (CoreResources) SpringServletAccess.getApplicationContext(context).getBean("coreResources"), (RuleSetRuleDao) SpringServletAccess.getApplicationContext(context).getBean("ruleSetRuleDao"));
    String action = fp.getString("action");
    int datasetId = fp.getInt("datasetId");
    int adfId = fp.getInt("adfId");
    if (datasetId == 0) {
        try {
            DatasetBean dsb = (DatasetBean) session.getAttribute("newDataset");
            datasetId = dsb.getId();
            logger.info("dataset id was zero, trying session: " + datasetId);
        } catch (NullPointerException e) {
            e.printStackTrace();
            logger.info("tripped over null pointer exception");
        }
    }
    DatasetBean db = (DatasetBean) dsdao.findByPK(datasetId);
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    StudyBean study = (StudyBean) sdao.findByPK(db.getStudyId());
    checkRoleByUserAndStudy(ub, study.getParentStudyId(), study.getId());
    //Checks if the study is current study or child of current study
    if (study.getId() != currentStudy.getId() && study.getParentStudyId() != currentStudy.getId()) {
        addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
        forwardPage(Page.MENU_SERVLET);
        return;
    }
    /**
         * @vbc 08/06/2008 NEW EXTRACT DATA IMPLEMENTATION get study_id and
         *      parentstudy_id int currentstudyid = currentStudy.getId(); int
         *      parentstudy = currentStudy.getParentStudyId(); if (parentstudy >
         *      0) { // is OK } else { // same parentstudy = currentstudyid; } //
         */
    int currentstudyid = currentStudy.getId();
    // YW 11-09-2008 << modified logic here.
    int parentstudy = currentstudyid;
    // YW 11-09-2008 >>
    StudyBean parentStudy = new StudyBean();
    if (currentStudy.getParentStudyId() > 0) {
        //StudyDAO sdao = new StudyDAO(sm.getDataSource());
        parentStudy = (StudyBean) sdao.findByPK(currentStudy.getParentStudyId());
    }
    ExtractBean eb = generateFileService.generateExtractBean(db, currentStudy, parentStudy);
    if (StringUtil.isBlank(action)) {
        loadList(db, asdfdao, datasetId, fp, eb);
        forwardPage(Page.EXPORT_DATASETS);
    } else if ("delete".equalsIgnoreCase(action) && adfId > 0) {
        boolean success = false;
        ArchivedDatasetFileBean adfBean = (ArchivedDatasetFileBean) asdfdao.findByPK(adfId);
        File file = new File(adfBean.getFileReference());
        if (!file.canWrite()) {
            addPageMessage(respage.getString("write_protected"));
        } else {
            success = file.delete();
            if (success) {
                asdfdao.deleteArchiveDataset(adfBean);
                addPageMessage(respage.getString("file_removed"));
            } else {
                addPageMessage(respage.getString("error_removing_file"));
            }
        }
        loadList(db, asdfdao, datasetId, fp, eb);
        forwardPage(Page.EXPORT_DATASETS);
    } else {
        logger.info("**** found action ****: " + action);
        String generateReport = "";
        // generate file, and show screen export
        // String generalFileDir = DATASET_DIR + db.getId() +
        // File.separator;
        // change this up, so that we don't overwrite anything
        String pattern = "yyyy" + File.separator + "MM" + File.separator + "dd" + File.separator + "HHmmssSSS" + File.separator;
        SimpleDateFormat sdfDir = new SimpleDateFormat(pattern);
        String generalFileDir = DATASET_DIR + db.getId() + File.separator + sdfDir.format(new java.util.Date());
        String fileName = "";
        db.setName(db.getName().replaceAll(" ", "_"));
        Page finalTarget = Page.GENERATE_DATASET;
        finalTarget = Page.EXPORT_DATA_CUSTOM;
        // now display report according to format specified
        // TODO revise final target to set to fileReference????
        long sysTimeBegin = System.currentTimeMillis();
        int fId = 0;
        if ("sas".equalsIgnoreCase(action)) {
            // generateReport =
            // dsdao.generateDataset(db,
            // ExtractBean.SAS_FORMAT,
            // currentStudy,
            // parentStudy);
            long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
            String SASFileName = db.getName() + "_sas.sas";
            // logger.info("found data set: "+generateReport);
            generateFileService.createFile(SASFileName, generalFileDir, generateReport, db, sysTimeEnd, ExportFormatBean.TXTFILE, true, ub);
            logger.info("created sas file");
            request.setAttribute("generate", generalFileDir + SASFileName);
            finalTarget.setFileName(generalFileDir + SASFileName);
            fileName = SASFileName;
        // won't work since page creator is private
        } else if ("odm".equalsIgnoreCase(action)) {
            String odmVersion = fp.getString("odmVersion");
            String ODMXMLFileName = "";
            // DRY
            // HashMap answerMap = generateFileService.createODMFile(odmVersion, sysTimeBegin, generalFileDir, db, this.currentStudy, "");
            HashMap answerMap = generateFileService.createODMFile(odmVersion, sysTimeBegin, generalFileDir, db, this.currentStudy, "", eb, currentStudy.getId(), currentStudy.getParentStudyId(), "99", true, true, true, null, ub);
            for (Iterator it = answerMap.entrySet().iterator(); it.hasNext(); ) {
                java.util.Map.Entry entry = (java.util.Map.Entry) it.next();
                Object key = entry.getKey();
                Object value = entry.getValue();
                ODMXMLFileName = (String) key;
                Integer fileID = (Integer) value;
                fId = fileID.intValue();
            }
            fileName = ODMXMLFileName;
            request.setAttribute("generate", generalFileDir + ODMXMLFileName);
            logger.debug("+++ set the following: " + generalFileDir + ODMXMLFileName);
            // send a link with the SQL file? put the generated SQL file with the dataset?
            if (fp.getString("xalan") != null) {
                XalanTriggerService xts = new XalanTriggerService();
                String propertiesPath = SQLInitServlet.getField("filePath");
                // the trick there, we need to open up the zipped file and get at the XML
                openZipFile(generalFileDir + ODMXMLFileName + ".zip");
                // need to find out how to copy this xml file from /bin to the generalFileDir
                SimpleTrigger simpleTrigger = xts.generateXalanTrigger(propertiesPath + File.separator + "ODMReportStylesheet.xsl", ODMXMLFileName, generalFileDir + "output.sql", db.getId());
                scheduler = getScheduler();
                JobDetailFactoryBean JobDetailFactoryBean = new JobDetailFactoryBean();
                JobDetailFactoryBean.setGroup(xts.TRIGGER_GROUP_NAME);
                JobDetailFactoryBean.setName(simpleTrigger.getKey().getName());
                JobDetailFactoryBean.setJobClass(org.akaza.openclinica.web.job.XalanStatefulJob.class);
                JobDetailFactoryBean.setJobDataMap(simpleTrigger.getJobDataMap());
                // need durability?
                JobDetailFactoryBean.setDurability(true);
                try {
                    Date dateStart = scheduler.scheduleJob(JobDetailFactoryBean.getObject(), simpleTrigger);
                    logger.info("== found job date: " + dateStart.toString());
                } catch (SchedulerException se) {
                    se.printStackTrace();
                }
            }
        } else if ("txt".equalsIgnoreCase(action)) {
            // generateReport =
            // dsdao.generateDataset(db,
            // ExtractBean.TXT_FORMAT,
            // currentStudy,
            // parentStudy);
            // eb = dsdao.getDatasetData(eb, currentstudyid, parentstudy);
            String TXTFileName = "";
            HashMap answerMap = generateFileService.createTabFile(eb, sysTimeBegin, generalFileDir, db, currentstudyid, parentstudy, "", ub);
            // and of course DRY
            for (Iterator it = answerMap.entrySet().iterator(); it.hasNext(); ) {
                java.util.Map.Entry entry = (java.util.Map.Entry) it.next();
                Object key = entry.getKey();
                Object value = entry.getValue();
                TXTFileName = (String) key;
                Integer fileID = (Integer) value;
                fId = fileID.intValue();
            }
            fileName = TXTFileName;
            request.setAttribute("generate", generalFileDir + TXTFileName);
            // finalTarget.setFileName(generalFileDir+TXTFileName);
            logger.debug("+++ set the following: " + generalFileDir + TXTFileName);
        } else if ("html".equalsIgnoreCase(action)) {
            // html based dataset browser
            TabReportBean answer = new TabReportBean();
            eb = dsdao.getDatasetData(eb, currentstudyid, parentstudy);
            eb.getMetadata();
            eb.computeReport(answer);
            request.setAttribute("dataset", db);
            request.setAttribute("extractBean", eb);
            finalTarget = Page.GENERATE_DATASET_HTML;
        } else if ("spss".equalsIgnoreCase(action)) {
            SPSSReportBean answer = new SPSSReportBean();
            // removed three lines here and put them in generate file
            // service, createSPSSFile method. tbh 01/2009
            eb = dsdao.getDatasetData(eb, currentstudyid, parentstudy);
            eb.getMetadata();
            eb.computeReport(answer);
            // System.out.println("*** isShowCRFversion:
            // "+db.isShowCRFversion());
            // TODO in the spirit of DRY, if this works we need to remove
            // lines 443-776 in this servlet, tbh 01/2009
            String DDLFileName = "";
            HashMap answerMap = generateFileService.createSPSSFile(db, eb, currentStudy, parentStudy, sysTimeBegin, generalFileDir, answer, "", ub);
            // hmm, DRY?
            for (Iterator it = answerMap.entrySet().iterator(); it.hasNext(); ) {
                java.util.Map.Entry entry = (java.util.Map.Entry) it.next();
                Object key = entry.getKey();
                Object value = entry.getValue();
                DDLFileName = (String) key;
                Integer fileID = (Integer) value;
                fId = fileID.intValue();
            }
            request.setAttribute("generate", generalFileDir + DDLFileName);
            logger.debug("+++ set the following: " + generalFileDir + DDLFileName);
        } else if ("csv".equalsIgnoreCase(action)) {
            CommaReportBean answer = new CommaReportBean();
            eb = dsdao.getDatasetData(eb, currentstudyid, parentstudy);
            eb.getMetadata();
            eb.computeReport(answer);
            long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
            // logger.info("found data set: "+generateReport);
            String CSVFileName = db.getName() + "_comma.txt";
            fId = generateFileService.createFile(CSVFileName, generalFileDir, answer.toString(), db, sysTimeEnd, ExportFormatBean.CSVFILE, true, ub);
            fileName = CSVFileName;
            logger.info("just created csv file");
            request.setAttribute("generate", generalFileDir + CSVFileName);
        // finalTarget.setFileName(generalFileDir+CSVFileName);
        } else if ("excel".equalsIgnoreCase(action)) {
            // HSSFWorkbook excelReport = dsdao.generateExcelDataset(db,
            // ExtractBean.XLS_FORMAT,
            // currentStudy,
            // parentStudy);
            long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
            // TODO this will change and point to a created excel
            // spreadsheet, tbh
            String excelFileName = db.getName() + "_excel.xls";
            // fId = this.createFile(excelFileName,
            // generalFileDir,
            // excelReport,
            // db, sysTimeEnd,
            // ExportFormatBean.EXCELFILE);
            // logger.info("just created csv file, for excel output");
            // response.setHeader("Content-disposition","attachment;
            // filename="+CSVFileName);
            // logger.info("csv file name: "+CSVFileName);
            finalTarget = Page.GENERATE_EXCEL_DATASET;
            // response.setContentType("application/vnd.ms-excel");
            response.setHeader("Content-Disposition", "attachment; filename=" + db.getName() + "_excel.xls");
            request.setAttribute("generate", generalFileDir + excelFileName);
            logger.info("set 'generate' to :" + generalFileDir + excelFileName);
            fileName = excelFileName;
        // excelReport.write(stream);
        // stream.flush();
        // stream.close();
        // finalTarget.setFileName(WEB_DIR+db.getId()+"/"+excelFileName);
        }
        // <%@page contentType="application/vnd.ms-excel"%>
        if (!finalTarget.equals(Page.GENERATE_EXCEL_DATASET) && !finalTarget.equals(Page.GENERATE_DATASET_HTML)) {
            // to catch all the others and try to set a new path for file
            // capture
            // tbh, 4-18-05
            // request.setAttribute("generate",finalTarget.getFileName());
            // TODO changing path to show refresh page, then window with
            // link to download file, tbh 06-08-05
            // finalTarget.setFileName(
            // "/WEB-INF/jsp/extract/generatedFileDataset.jsp");
            finalTarget.setFileName("" + "/WEB-INF/jsp/extract/generateMetadataCore.jsp");
            // also set up table here???
            asdfdao = new ArchivedDatasetFileDAO(sm.getDataSource());
            ArchivedDatasetFileBean asdfBean = (ArchivedDatasetFileBean) asdfdao.findByPK(fId);
            // *** do we need this below? tbh
            ArrayList newFileList = new ArrayList();
            newFileList.add(asdfBean);
            // request.setAttribute("filelist",newFileList);
            ArrayList filterRows = ArchivedDatasetFileRow.generateRowsFromBeans(newFileList);
            EntityBeanTable table = fp.getEntityBeanTable();
            // sort by date
            table.setSortingIfNotExplicitlySet(3, false);
            String[] columns = { resword.getString("file_name"), resword.getString("run_time"), resword.getString("file_size"), resword.getString("created_date"), resword.getString("created_by") };
            table.setColumns(new ArrayList(Arrays.asList(columns)));
            table.hideColumnLink(0);
            table.hideColumnLink(1);
            table.hideColumnLink(2);
            table.hideColumnLink(3);
            table.hideColumnLink(4);
            // table.setQuery("ExportDataset?datasetId=" +db.getId(), new
            // HashMap());
            // trying to continue...
            // session.setAttribute("newDataset",db);
            request.setAttribute("dataset", db);
            request.setAttribute("file", asdfBean);
            table.setRows(filterRows);
            table.computeDisplay();
            request.setAttribute("table", table);
        // *** do we need this above? tbh
        }
        logger.info("set first part of 'generate' to :" + generalFileDir);
        logger.info("found file name: " + finalTarget.getFileName());
        //            String del = CoreResources.getField("dataset_file_delete");
        //            if (del.equalsIgnoreCase("true") || del.equals("")) {
        //                File deleteFile = new File(generalFileDir + fileName);
        //                deleteFile.delete();
        //            }
        forwardPage(finalTarget);
    }
}

Example 4 with EntityBeanTable

use of org.akaza.openclinica.web.bean.EntityBeanTable in project OpenClinica by OpenClinica.

the class CreateDatasetServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    String action = fp.getString("action");
    if (StringUtil.isBlank(action)) {
        // step 1 -- instructions, and continue button
        session.setAttribute("newDataset", new DatasetBean());
        session.setAttribute("allItems", new ArrayList());
        session.setAttribute("crf", new CRFBean());
        session.setAttribute("allSelectedItems", new ArrayList());
        forwardPage(Page.CREATE_DATASET_1);
    } else {
        StudyBean studyWithEventDefs = currentStudy;
        if (currentStudy.getParentStudyId() > 0) {
            studyWithEventDefs = new StudyBean();
            studyWithEventDefs.setId(currentStudy.getParentStudyId());
        }
        if ("begin".equalsIgnoreCase(action)) {
            // step 2 -- select study events/crfs
            StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
            StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
            EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
            StudyBean studyWithEventDefinitions = currentStudy;
            if (currentStudy.getParentStudyId() > 0) {
                studyWithEventDefinitions = new StudyBean();
                studyWithEventDefinitions.setId(currentStudy.getParentStudyId());
            }
            ArrayList seds = seddao.findAllActiveByStudy(studyWithEventDefinitions);
            CRFDAO crfdao = new CRFDAO(sm.getDataSource());
            HashMap events = new LinkedHashMap();
            for (int i = 0; i < seds.size(); i++) {
                StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seds.get(i);
                ArrayList<CRFBean> crfs = (ArrayList<CRFBean>) crfdao.findAllActiveByDefinition(sed);
                if (currentStudy.getParentStudyId() > 0) {
                    // sift through these CRFs and see which ones are hidden
                    HideCRFManager hideCRFs = HideCRFManager.createHideCRFManager();
                    crfs = hideCRFs.removeHiddenCRFBeans(studyWithEventDefinitions, sed, crfs, sm.getDataSource());
                }
                if (!crfs.isEmpty()) {
                    events.put(sed, crfs);
                }
            }
            // datasets
            if (events.isEmpty()) {
                addPageMessage(respage.getString("not_have_study_definitions_assigned"));
                forwardPage(Page.CREATE_DATASET_1);
            } else {
                crfdao = new CRFDAO(sm.getDataSource());
                ItemDAO idao = new ItemDAO(sm.getDataSource());
                ArrayList sedItemIds = CreateDatasetServlet.allSedItemIdsInStudy(events, crfdao, idao);
                session.setAttribute("numberOfStudyItems", Integer.toString(sedItemIds.size()));
                request.setAttribute("eventlist", events);
                session.setAttribute(EVENTS_FOR_CREATE_DATASET, events);
                session.setAttribute("newDataset", new DatasetBean());
                session.setAttribute("allItems", new ArrayList());
                session.setAttribute("crf", new CRFBean());
                forwardPage(Page.CREATE_DATASET_2);
            }
        } else if ("beginsubmit".equalsIgnoreCase(action)) {
            String saveItems = fp.getString(SAVE_BUTTON);
            String saveContinue = fp.getString(SAVE_CONTINUE_BUTTON);
            DatasetBean db = (DatasetBean) session.getAttribute("newDataset");
            if (db == null) {
                db = new DatasetBean();
            }
            extractIdsFromForm(db);
            extractEventIds(db);
            session.setAttribute("newDataset", db);
            // +"");
            if (!StringUtil.isBlank(saveItems)) {
                request.setAttribute("eventlist", session.getAttribute(EVENTS_FOR_CREATE_DATASET));
                // BWP 3095>>
                String summary = respage.getString("you_have_selected") + " " + db.getItemIds().size() + " " + respage.getString("items_so_far");
                summary += genAttMsg(db);
                addPageMessage(summary);
                int crfId = fp.getInt("crfId");
                if (crfId > 0) {
                    // user choose a crf and select items
                    forwardPage(Page.CREATE_DATASET_2);
                } else {
                    ArrayList sgclasses = (ArrayList) session.getAttribute("allSelectedGroups");
                    if (sgclasses == null || sgclasses.size() == 0) {
                        sgclasses = setUpStudyGroups();
                    }
                    session.setAttribute("allSelectedGroups", sgclasses);
                    request.setAttribute("allSelectedGroups", sgclasses);
                    // TODO push out list of subject groups here???
                    // form submitted from "view selected item ' or
                    // attribute page, so
                    // forward back to "view selected item " page
                    forwardPage(Page.CREATE_DATASET_VIEW_SELECTED);
                }
            } else {
                if (db.getItemIds().size() == 0) {
                    request.setAttribute("eventlist", session.getAttribute(EVENTS_FOR_CREATE_DATASET));
                    addPageMessage(respage.getString("should_select_one_item_to_create_dataset"));
                    forwardPage(Page.CREATE_DATASET_2);
                } else {
                    String summary = respage.getString("you_have_selected") + " " + db.getItemIds().size() + " " + respage.getString("items_totally_for_this_dataset");
                    summary += genAttMsg(db);
                    addPageMessage(summary);
                    // 0 means using
                    fp.addPresetValue("firstmonth", 0);
                    // default month
                    fp.addPresetValue("firstyear", 1900);
                    fp.addPresetValue("lastmonth", 0);
                    fp.addPresetValue("lastyear", 2100);
                    setPresetValues(fp.getPresetValues());
                    logger.warn("found preset values while setting date: " + fp.getPresetValues().toString());
                    request.setAttribute(BEAN_MONTHS, getMonths());
                    request.setAttribute(BEAN_YEARS, getYears());
                    forwardPage(Page.CREATE_DATASET_3);
                }
            }
        } else if ("scopesubmit".equalsIgnoreCase(action)) {
            ArrayList months = getMonths();
            ArrayList years = getYears();
            int firstMonth = fp.getInt("firstmonth");
            int firstYear = fp.getInt("firstyear");
            int lastMonth = fp.getInt("lastmonth");
            int lastYear = fp.getInt("lastyear");
            if (fp.getInt("firstmonth") == 0) {
                // default value
                firstMonth = 1;
            }
            if (fp.getInt("lastmonth") == 0) {
                // default value
                lastMonth = 12;
            }
            errors = new HashMap();
            if (fp.getInt("firstmonth") > 0 && firstYear == 1900) {
                Validator.addError(errors, "firstmonth", restext.getString("if_specify_month_also_specify_year"));
            }
            if (fp.getInt("lastmonth") > 0 && lastYear == 2100) {
                Validator.addError(errors, "lastmonth", restext.getString("if_specify_month_also_specify_year"));
            }
            Date dateStart = getFirstDayOfMonth(firstYear, firstMonth);
            Date dateEnd = getLastDayOfMonth(lastYear, lastMonth);
            if (dateEnd.compareTo(dateStart) < 0) {
                Validator.addError(errors, "firstmonth", restext.getString("the_from_should_be_come_before_to"));
            }
            if (!errors.isEmpty()) {
                String[] fieldNames = { "firstmonth", "firstyear", "lastmonth", "lastyear" };
                fp.setCurrentIntValuesAsPreset(fieldNames);
                setInputMessages(errors);
                addPageMessage(respage.getString("errors_in_submission_see_below"));
                setPresetValues(fp.getPresetValues());
                request.setAttribute(BEAN_MONTHS, getMonths());
                request.setAttribute(BEAN_YEARS, getYears());
                forwardPage(Page.CREATE_DATASET_3);
            } else {
                DatasetBean dsb = (DatasetBean) session.getAttribute("newDataset");
                dsb.setDateStart(dateStart);
                dsb.setDateEnd(dateEnd);
                session.setAttribute("newDataset", dsb);
                if (fp.getString("submit").equals(resword.getString("continue_to_apply_filter"))) {
                    // FilterDAO fdao = new FilterDAO(sm.getDataSource());
                    // Collection filters = fdao.findAll();
                    // TODO make findAllByProject
                    // request.setAttribute("filters",filters);
                    EntityBeanTable table = getFilterTable();
                    session.setAttribute("partOfCreateDataset", new Integer(1));
                    // to be used in createFiltersThree servlet, tbh
                    request.setAttribute("table", table);
                    forwardPage(Page.APPLY_FILTER);
                } else {
                    request.setAttribute("statuses", Status.toActiveArrayList());
                    // YW, 2-20-2008 <<these attributes will show on the
                    // CREATE_DATASET_4
                    String temp = dsb.getODMMetaDataVersionOid();
                    request.setAttribute("mdvOID", temp != null && temp.length() > 0 ? temp : "v1.0.0");
                    temp = dsb.getODMMetaDataVersionName();
                    request.setAttribute("mdvName", temp != null && temp.length() > 0 ? temp : "MetaDataVersion_v1.0.0");
                    request.setAttribute("mdvPrevStudy", dsb.getODMPriorStudyOid());
                    request.setAttribute("mdvPrevOID", dsb.getODMPriorMetaDataVersionOid());
                    // YW >>
                    forwardPage(Page.CREATE_DATASET_4);
                }
            }
        } else if ("specifysubmit".equalsIgnoreCase(action)) {
            Validator v = new Validator(request);
            v.addValidation("dsName", Validator.NO_BLANKS);
            v.addValidation("dsName", Validator.NO_SEMI_COLONS_OR_COLONS);
            v.addValidation("dsDesc", Validator.NO_BLANKS);
            v.addValidation("dsStatus", Validator.IS_VALID_TERM, TermType.STATUS);
            v.addValidation("dsName", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255);
            v.addValidation("dsDesc", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 2000);
            String mdvOID = fp.getString("mdvOID");
            String mdvName = fp.getString("mdvName");
            String mdvPrevStudy = fp.getString("mdvPrevStudy");
            if (mdvPrevStudy != null && mdvPrevStudy.length() > 0) {
                v.addValidation("mdvPrevOID", Validator.NO_BLANKS);
            }
            String mdvPrevOID = fp.getString("mdvPrevOID");
            errors = v.validate();
            String dsName = fp.getString("dsName");
            if (!StringUtil.isBlank(dsName)) {
                // YW, << 3-19-2008
                if (dsName.contains("/") || dsName.contains("\\")) {
                    v.addError(errors, "dsName", restext.getString("slash_not_allowed"));
                }
                // 2-20-2008, no check for editing dataset
                if (((DatasetBean) session.getAttribute("newDataset")).getId() <= 0) {
                    // YW >>
                    // logger.info("dsName" + fp.getString("dsName"));
                    DatasetDAO dsdao = new DatasetDAO(sm.getDataSource());
                    DatasetBean dsBean = (DatasetBean) dsdao.findByNameAndStudy(fp.getString("dsName").trim(), currentStudy);
                    if (dsBean.getId() > 0) {
                        Validator.addError(errors, "dsName", restext.getString("dataset_name_used_by_another_choose_unique"));
                    }
                }
            }
            if (!errors.isEmpty()) {
                String[] fieldNames = { "dsName", "dsDesc" };
                fp.setCurrentStringValuesAsPreset(fieldNames);
                fp.addPresetValue("dsStatusId", fp.getInt("dsStatus"));
                fp.addPresetValue("mdvOID", mdvOID);
                fp.addPresetValue("mdvName", mdvName);
                fp.addPresetValue("mdvPrevStudy", mdvPrevStudy);
                fp.addPresetValue("mdvPrevOID", mdvPrevOID);
                addPageMessage(respage.getString("errors_in_submission_see_below"));
                setInputMessages(errors);
                setPresetValues(fp.getPresetValues());
                request.setAttribute("statuses", Status.toActiveArrayList());
                forwardPage(Page.CREATE_DATASET_4);
            } else {
                session.setAttribute("mdvOID", mdvOID);
                session.setAttribute("mdvName", mdvName);
                session.setAttribute("mdvPrevStudy", mdvPrevStudy);
                session.setAttribute("mdvPrevOID", mdvPrevOID);
                if (mdvPrevOID != null && mdvPrevOID.length() > 0 && (mdvPrevStudy == null || mdvPrevStudy.length() <= 0)) {
                    mdvPrevStudy = currentStudy.getId() + "";
                }
                DatasetBean dsb = (DatasetBean) session.getAttribute("newDataset");
                dsb.setSQLStatement(dsb.generateQuery());
                String dbName = SQLInitServlet.getField("dataBase");
                if ("oracle".equals(dbName)) {
                    dsb.setSQLStatement(dsb.generateOracleQuery());
                }
                // TODO set up oracle syntax for the query, grab the
                // database
                // from the session manager and feed it to the dataset bean
                // possibly done, tbh 1/4/2005
                // TODO look for the filter here, re-create the sql
                // statement
                // and put it in here
                // possibly done need to test, tbh 1/7/2005
                FilterBean fb = (FilterBean) session.getAttribute("newFilter");
                if (fb != null) {
                    // FilterDAO fDAO = new FilterDAO(sm.getDataSource());
                    dsb.setSQLStatement(dsb.getSQLStatement() + " " + fb.getSQLStatement());
                }
                // dataset if dataset name has been changed.
                if (dsb.getId() > 0 && !dsb.getName().equals(fp.getString("dsName"))) {
                    dsb.setId(0);
                }
                // YW >>
                dsb.setODMMetaDataVersionName(mdvName);
                dsb.setODMMetaDataVersionOid(mdvOID);
                dsb.setODMPriorMetaDataVersionOid(mdvPrevOID);
                dsb.setODMPriorStudyOid(mdvPrevStudy);
                dsb.setName(fp.getString("dsName"));
                dsb.setDescription(fp.getString("dsDesc"));
                dsb.setStatus(Status.get(fp.getInt("dsStatus")));
                dsb.setDatasetItemStatus(DatasetItemStatus.get(fp.getInt("itemStatus")));
                session.removeAttribute("partOfCreateDataset");
                Date ddate = new SimpleDateFormat("MM/dd/yyyy").parse("01/01/1900");
                // done to remove the set up of going to get the filter, tbh
                // set up dataset here, grab primary key???!!!???
                // added by jxu
                request.setAttribute("defaultStart", local_df.parse(local_df.format(ddate)));
                request.setAttribute("defaultEnd", getLastDayOfMonth(2100, 12));
                session.setAttribute("newDataset", dsb);
                forwardPage(Page.CONFIRM_DATASET);
            }
        } else if ("confirmall".equalsIgnoreCase(action)) {
            String submit = fp.getString("btnSubmit");
            logger.info("reached confirm all");
            if (!resword.getString("confirm_and_save").equalsIgnoreCase(submit)) {
                // we're going back, so we should not destroy the
                // data we've created, tbh
                // session.removeAttribute("newDataset");
                // session.removeAttribute("newFilter");
                forwardPage(Page.CREATE_DATASET_4);
            } else {
                DatasetDAO ddao = new DatasetDAO(sm.getDataSource());
                DatasetBean dsb = (DatasetBean) session.getAttribute("newDataset");
                dsb.setStudyId(this.currentStudy.getId());
                dsb.setOwner(ub);
                // dsb.setOwnerId(ub.getId());
                //
                // at this point, dataset itemId will still be kept
                // uniquely.
                dsb = finalUpateDatasetBean(dsb);
                if (dsb.getId() == 0) {
                    // if the bean hasn't been created already that is...
                    logger.info("*** about to create the dataset bean");
                    dsb = (DatasetBean) ddao.create(dsb);
                    logger.info("created dataset bean: " + dsb.getId() + ", name: " + dsb.getName());
                    if (!dsb.isActive()) {
                        addPageMessage(restext.getString("problem_creating_dataset_try_again"));
                        forwardPage(Page.EXTRACT_DATASETS_MAIN);
                    }
                } else // YW, 2-20-2008 << for editing existing dataset
                if (dsb.getId() > 0) {
                    dsb = (DatasetBean) ddao.updateAll(dsb);
                    if (!dsb.isActive()) {
                        addPageMessage(restext.getString("problem_creating_dataset_try_again"));
                        forwardPage(Page.EXTRACT_DATASETS_MAIN);
                    }
                    dsb = (DatasetBean) ddao.updateGroupMap(dsb);
                    if (!dsb.isActive()) {
                        addPageMessage(restext.getString("problem_updating_subject_group_class_when_updating_dataset"));
                        forwardPage(Page.EXTRACT_DATASETS_MAIN);
                    }
                }
                // YW >>
                logger.info("setting data set id here");
                // may be easier to just set the dataset bean
                // back into the session?
                request.setAttribute("dataset", dsb);
                forwardPage(Page.EXPORT_DATASETS);
            }
        } else {
            // refine this bit to catch errors, hopefully
            addPageMessage(restext.getString("creating_new_dataset_cancelled"));
            forwardPage(Page.CREATE_DATASET_1);
        }
    }
}

Example 5 with EntityBeanTable

use of org.akaza.openclinica.web.bean.EntityBeanTable in project OpenClinica by OpenClinica.

the class CreateFiltersOneServlet method processRequest.

// < ResourceBundlerestext,resword,respage,resexception;
@Override
public void processRequest() throws Exception {
    // clean up the previous setup, if necessary
    session.removeAttribute("newExp");
    // removes the new explanation for setting up the create dataset
    // covers the plan if you cancel out of a process then want to get in
    // again, tbh
    String action = request.getParameter("action");
    if (StringUtil.isBlank(action)) {
        // our start page:
        // note that this is now set up to accept the
        // tabling classes created in View.
        FormProcessor fp = new FormProcessor(request);
        FilterDAO fdao = new FilterDAO(sm.getDataSource());
        EntityBeanTable table = fp.getEntityBeanTable();
        ArrayList filters = new ArrayList();
        if (ub.isSysAdmin()) {
            filters = (ArrayList) fdao.findAllAdmin();
        } else {
            filters = (ArrayList) fdao.findAll();
        }
        ArrayList filterRows = FilterRow.generateRowsFromBeans(filters);
        String[] columns = { resword.getString("filter_name"), resword.getString("description"), resword.getString("created_by"), resword.getString("created_date"), resword.getString("status"), resword.getString("actions") };
        table.setColumns(new ArrayList(Arrays.asList(columns)));
        table.hideColumnLink(5);
        table.addLink(resword.getString("create_new_filter"), "CreateFiltersOne?action=begin");
        table.setQuery("CreateFiltersOne", new HashMap());
        table.setRows(filterRows);
        table.computeDisplay();
        request.setAttribute("table", table);
        // the code above replaces the following line:
        // request.setAttribute("filters",filters);
        forwardPage(Page.CREATE_FILTER_SCREEN_1);
    } else if ("begin".equalsIgnoreCase(action)) {
        forwardPage(Page.CREATE_FILTER_SCREEN_2);
    }
}