Examples with DatasetBean org.akaza.openclinica.bean.extract.DatasetBean used on opensource projects

Example 21 with DatasetBean

use of org.akaza.openclinica.bean.extract.DatasetBean in project OpenClinica by OpenClinica.

the class ViewJobServlet method processRequest.

@Override
protected void processRequest() throws Exception {
    // TODO single stage servlet where we get the list of jobs
    // and push them out to the JSP page
    // related classes will be required to generate the table rows
    // and eventually links to view and edit the jobs as well
    FormProcessor fp = new FormProcessor(request);
    // First we must get a reference to a scheduler
    scheduler = getScheduler();
    XsltTriggerService xsltTriggerSrvc = new XsltTriggerService();
    // Scheduler sched = sfb.getScheduler();
    Set<TriggerKey> triggerKeys = scheduler.getTriggerKeys(GroupMatcher.triggerGroupEquals(xsltTriggerSrvc.getTriggerGroupNameForExportJobs()));
    String[] triggerNames = triggerKeys.stream().toArray(String[]::new);
    //      String[]    triggerNames          =           scheduler.getJobNames(XsltTriggerService.TRIGGER_GROUP_NAME);
    // logger.info("trigger list: "+triggerNames.length);
    // logger.info("trigger names: "+triggerNames.toString());
    ArrayList triggerBeans = new ArrayList();
    for (String triggerName : triggerNames) {
        Trigger trigger = scheduler.getTrigger(TriggerKey.triggerKey(triggerName, xsltTriggerSrvc.getTriggerGroupNameForExportJobs()));
        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
        }
        // logger.info(trigger.getDescription());
        // logger.info("");//getJobDataMap()
        TriggerBean triggerBean = new TriggerBean();
        triggerBean.setFullName(trigger.getKey().getName());
        triggerBean.setPreviousDate(trigger.getPreviousFireTime());
        triggerBean.setNextDate(trigger.getNextFireTime());
        if (trigger.getDescription() != null) {
            triggerBean.setDescription(trigger.getDescription());
        }
        // setting: frequency, dataset name
        JobDataMap dataMap = new JobDataMap();
        DatasetDAO datasetDAO = new DatasetDAO(sm.getDataSource());
        StudyDAO studyDao = new StudyDAO(sm.getDataSource());
        if (trigger.getJobDataMap().size() > 0) {
            dataMap = trigger.getJobDataMap();
            int dsId = dataMap.getInt(ExampleSpringJob.DATASET_ID);
            String periodToRun = dataMap.getString(ExampleSpringJob.PERIOD);
            triggerBean.setPeriodToRun(periodToRun);
            DatasetBean dataset = (DatasetBean) datasetDAO.findByPK(dsId);
            triggerBean.setDataset(dataset);
            triggerBean.setDatasetName(dataset.getName());
            StudyBean study = (StudyBean) studyDao.findByPK(dataset.getStudyId());
            triggerBean.setStudyName(study.getName());
        // triggerBean.setStudyName(dataMap.getString(ExampleSpringJob.STUDY_NAME));
        }
        logger.debug("Trigger Priority: " + trigger.getKey().getName() + " " + trigger.getPriority());
        if (scheduler.getTriggerState(TriggerKey.triggerKey(triggerName, XsltTriggerService.TRIGGER_GROUP_NAME)) == Trigger.TriggerState.PAUSED) {
            triggerBean.setActive(false);
            logger.debug("setting active to false for trigger: " + trigger.getKey().getName());
        } else {
            triggerBean.setActive(true);
            logger.debug("setting active to TRUE for trigger: " + trigger.getKey().getName());
        }
        triggerBeans.add(triggerBean);
    // our wrapper to show triggers
    }
    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("period_to_run"), resword.getString("dataset"), resword.getString("study"), resword.getString("actions") };
    table.setColumns(new ArrayList(Arrays.asList(columns)));
    table.hideColumnLink(3);
    table.hideColumnLink(7);
    table.setQuery("ViewJob", new HashMap());
    // table.addLink("", "CreateUserAccount");
    table.setSortingColumnInd(0);
    table.setRows(allRows);
    table.computeDisplay();
    request.setAttribute("table", table);
    // throw new NullPointerException("faking an error here");
    forwardPage(Page.VIEW_JOB);
}

Example 22 with DatasetBean

use of org.akaza.openclinica.bean.extract.DatasetBean in project OpenClinica by OpenClinica.

the class ViewSingleJobServlet method processRequest.

@Override
protected void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    // changes to this servlet, we now look at group name too, tbh 05/2009
    String triggerName = fp.getString("tname");
    String gName = fp.getString("gname");
    String groupName = "";
    if (gName.equals("") || gName.equals("0")) {
        groupName = XsltTriggerService.TRIGGER_GROUP_NAME;
    } else {
        // if (gName.equals("1")) {
        groupName = TRIGGER_IMPORT_GROUP;
    }
    // << tbh 09/03/2009 #4143
    scheduler = getScheduler();
    Trigger trigger = scheduler.getTrigger(new TriggerKey(triggerName, groupName));
    if (trigger == null) {
        groupName = XsltTriggerService.TRIGGER_GROUP_NAME;
        trigger = scheduler.getTrigger(new TriggerKey(triggerName.trim(), groupName));
    }
    // << tbh 09/03/2009 #4143
    // above is a hack, if we add more trigger groups this will have
    // to be redone
    logger.debug("found trigger name: " + triggerName);
    logger.debug("found group name: " + groupName);
    TriggerBean triggerBean = new TriggerBean();
    JobDataMap dataMap = new JobDataMap();
    AuditEventDAO auditEventDAO = new AuditEventDAO(sm.getDataSource());
    try {
        triggerBean.setFullName(trigger.getKey().getName());
        triggerBean.setPreviousDate(trigger.getPreviousFireTime());
        triggerBean.setNextDate(trigger.getNextFireTime());
        // >> set active here, tbh 10/08/2009
        if (scheduler.getTriggerState(new TriggerKey(triggerName, groupName)) == Trigger.TriggerState.PAUSED) {
            triggerBean.setActive(false);
            logger.debug("setting active to false for trigger: " + trigger.getKey().getName());
        } else {
            triggerBean.setActive(true);
            logger.debug("setting active to TRUE for trigger: " + trigger.getKey().getName());
        }
        // <<
        if (trigger.getDescription() != null) {
            triggerBean.setDescription(trigger.getDescription());
        }
        if (trigger.getJobDataMap().size() > 0) {
            dataMap = trigger.getJobDataMap();
            String contactEmail = dataMap.getString(XsltTriggerService.EMAIL);
            logger.debug("found email: " + contactEmail);
            // int dsId = new Integer(datasetId).intValue();
            if (gName.equals("") || gName.equals("0")) {
                String exportFormat = dataMap.getString(XsltTriggerService.EXPORT_FORMAT);
                String periodToRun = dataMap.getString(ExampleSpringJob.PERIOD);
                // int userId = new Integer(userAcctId).intValue();
                int dsId = dataMap.getInt(ExampleSpringJob.DATASET_ID);
                triggerBean.setExportFormat(exportFormat);
                triggerBean.setPeriodToRun(periodToRun);
                DatasetDAO datasetDAO = new DatasetDAO(sm.getDataSource());
                DatasetBean dataset = (DatasetBean) datasetDAO.findByPK(dsId);
                triggerBean.setDataset(dataset);
            }
            int userId = dataMap.getInt(ExampleSpringJob.USER_ID);
            // need to set information, extract bean, user account bean
            UserAccountDAO userAccountDAO = new UserAccountDAO(sm.getDataSource());
            triggerBean.setContactEmail(contactEmail);
            UserAccountBean userAccount = (UserAccountBean) userAccountDAO.findByPK(userId);
            triggerBean.setUserAccount(userAccount);
            ArrayList<AuditEventBean> triggerLogs = auditEventDAO.findAllByAuditTable(trigger.getKey().getName());
            // set the table for the audit event beans here
            ArrayList allRows = AuditEventRow.generateRowsFromBeans(triggerLogs);
            EntityBeanTable table = fp.getEntityBeanTable();
            String[] columns = { resword.getString("date_and_time"), resword.getString("action_message"), resword.getString("entity_operation"), // resword.getString("study_subject_ID"),
            resword.getString("changes_and_additions"), resword.getString("actions") };
            table.setColumns(new ArrayList(Arrays.asList(columns)));
            table.setAscendingSort(false);
            table.hideColumnLink(1);
            table.hideColumnLink(3);
            table.hideColumnLink(4);
            table.setQuery("ViewSingleJob?tname=" + triggerName + "&gname=" + gName, new HashMap());
            table.setRows(allRows);
            table.computeDisplay();
            request.setAttribute("table", table);
        }
    } catch (NullPointerException e) {
        // TODO Auto-generated catch block
        logger.debug(" found NPE " + e.getMessage());
        e.printStackTrace();
    }
    // need to show the extract for which this runs, which files, etc
    // in other words the job data map
    request.setAttribute("triggerBean", triggerBean);
    request.setAttribute("groupName", groupName);
    forwardPage(Page.VIEW_SINGLE_JOB);
}

Example 23 with DatasetBean

use of org.akaza.openclinica.bean.extract.DatasetBean in project OpenClinica by OpenClinica.

the class DatasetDAO method initialDatasetData.

/**
     * Initialize itemMap, itemIds, itemDefCrf and groupIds for a DatasetBean
     *
     * @param db
     * @return
     * @author ywang (Feb., 2008)
     */
public DatasetBean initialDatasetData(int datasetId) {
    ItemDAO idao = new ItemDAO(ds);
    DatasetBean db = (DatasetBean) findByPK(datasetId);
    String sql = db.getSQLStatement();
    sql = sql.split("study_event_definition_id in")[1];
    String[] ss = sql.split("and item_id in");
    String sedIds = ss[0];
    String[] sss = ss[1].split("and");
    String itemIds = sss[0];
    this.setDefinitionCrfItemTypesExpected();
    logger.debug("begin to execute GetDefinitionCrfItemSql");
    ArrayList alist = select(getDefinitionCrfItemSql(sedIds, itemIds));
    Iterator it = alist.iterator();
    while (it.hasNext()) {
        HashMap row = (HashMap) it.next();
        ItemBean ib = (ItemBean) idao.getEntityFromHashMap(row);
        Integer defId = (Integer) row.get("sed_id");
        String defName = (String) row.get("sed_name");
        String crfName = (String) row.get("crf_name");
        Integer itemId = ib.getId();
        String key = defId + "_" + itemId;
        if (!db.getItemMap().containsKey(key)) {
            ib.setSelected(true);
            ib.setDefName(defName);
            ib.setCrfName(crfName);
            ib.setDatasetItemMapKey(key);
            // contains study_event_definition_ids
            if (!db.getEventIds().contains(defId)) {
                db.getEventIds().add(defId);
            }
            db.getItemIds().add(itemId);
            db.getItemDefCrf().add(ib);
            db.getItemMap().put(key, ib);
        }
    }
    db.setSubjectGroupIds(getGroupIds(db.getId()));
    return db;
}

Example 24 with DatasetBean

use of org.akaza.openclinica.bean.extract.DatasetBean in project OpenClinica by OpenClinica.

the class DatasetDAO method findByPK.

public EntityBean findByPK(int ID) {
    DatasetBean eb = new DatasetBean();
    this.setTypesExpected();
    HashMap variables = new HashMap();
    variables.put(Integer.valueOf(1), Integer.valueOf(ID));
    String sql = digester.getQuery("findByPK");
    ArrayList alist = this.select(sql, variables);
    Iterator it = alist.iterator();
    if (it.hasNext()) {
        eb = (DatasetBean) this.getEntityFromHashMap((HashMap) it.next());
    } else {
        logger.warn("found no object: " + sql + " " + ID);
    }
    return eb;
}

Example 25 with DatasetBean

use of org.akaza.openclinica.bean.extract.DatasetBean in project OpenClinica by OpenClinica.

the class DatasetDAO method getEntityFromHashMap.

public Object getEntityFromHashMap(HashMap hm) {
    DatasetBean eb = new DatasetBean();
    this.setEntityAuditInformation(eb, hm);
    eb.setDescription((String) hm.get("description"));
    eb.setStudyId(((Integer) hm.get("study_id")).intValue());
    eb.setName((String) hm.get("name"));
    eb.setId(((Integer) hm.get("dataset_id")).intValue());
    eb.setSQLStatement((String) hm.get("sql_statement"));
    eb.setNumRuns(((Integer) hm.get("num_runs")).intValue());
    eb.setDateStart((Date) hm.get("date_start"));
    eb.setDateEnd((Date) hm.get("date_end"));
    eb.setApproverId(((Integer) hm.get("approver_id")).intValue());
    eb.setDateLastRun((Date) hm.get("date_last_run"));
    eb.setShowEventEnd(((Boolean) hm.get("show_event_end")).booleanValue());
    eb.setShowEventStart(((Boolean) hm.get("show_event_start")).booleanValue());
    eb.setShowEventLocation(((Boolean) hm.get("show_event_location")).booleanValue());
    eb.setShowSubjectDob(((Boolean) hm.get("show_subject_dob")).booleanValue());
    eb.setShowSubjectGender(((Boolean) hm.get("show_subject_gender")).booleanValue());
    eb.setShowEventStatus(((Boolean) hm.get("show_event_status")).booleanValue());
    eb.setShowSubjectStatus(((Boolean) hm.get("show_subject_status")).booleanValue());
    eb.setShowSubjectUniqueIdentifier(((Boolean) hm.get("show_subject_unique_id")).booleanValue());
    eb.setShowSubjectAgeAtEvent(((Boolean) hm.get("show_subject_age_at_event")).booleanValue());
    eb.setShowCRFstatus(((Boolean) hm.get("show_crf_status")).booleanValue());
    eb.setShowCRFversion(((Boolean) hm.get("show_crf_version")).booleanValue());
    eb.setShowCRFinterviewerName(((Boolean) hm.get("show_crf_int_name")).booleanValue());
    eb.setShowCRFinterviewerDate(((Boolean) hm.get("show_crf_int_date")).booleanValue());
    eb.setShowSubjectGroupInformation(((Boolean) hm.get("show_group_info")).booleanValue());
    // eb.setShowDiscrepancyInformation(((Boolean)
    // hm.get("show_disc_info")).booleanValue());
    // do we want to find group info here? looks like the best place for
    // non-repeats...
    // if (eb.isShowSubjectGroupInformation()) {
    eb.setSubjectGroupIds(getGroupIds(eb.getId()));
    // }
    eb.setODMMetaDataVersionName((String) hm.get("odm_metadataversion_name"));
    eb.setODMMetaDataVersionOid((String) hm.get("odm_metadataversion_oid"));
    eb.setODMPriorStudyOid((String) hm.get("odm_prior_study_oid"));
    eb.setODMPriorMetaDataVersionOid((String) hm.get("odm_prior_metadataversion_oid"));
    eb.setShowSubjectSecondaryId((Boolean) hm.get("show_secondary_id"));
    int isId = ((Integer) hm.get("dataset_item_status_id")).intValue();
    isId = isId > 0 ? isId : 1;
    DatasetItemStatus dis = DatasetItemStatus.get(isId);
    eb.setDatasetItemStatus(dis);
    return eb;
}