Examples with HideCRFManager org.akaza.openclinica.service.crfdata.HideCRFManager used on opensource projects

Example 1 with HideCRFManager

use of org.akaza.openclinica.service.crfdata.HideCRFManager 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 2 with HideCRFManager

use of org.akaza.openclinica.service.crfdata.HideCRFManager in project OpenClinica by OpenClinica.

the class EnterDataForStudyEventServlet method processRequest.

/*
     * (non-Javadoc)
     *
     * @see org.akaza.openclinica.control.core.SecureController#processRequest()
     */
@Override
protected void processRequest() throws Exception {
    // removeLockedCRF(ub.getId());
    getCrfLocker().unlockAllForUser(ub.getId());
    FormProcessor fp = new FormProcessor(request);
    int eventId = fp.getInt(INPUT_EVENT_ID, true);
    request.setAttribute("eventId", eventId + "");
    request.setAttribute("originatingPage", URLEncoder.encode("EnterDataForStudyEvent?eventId=" + eventId, "UTF-8"));
    // so we can display the event for which we're entering data
    StudyEventBean seb = getStudyEvent(eventId);
    // so we can display the subject's label
    StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
    StudySubjectBean studySubjectBean = (StudySubjectBean) ssdao.findByPK(seb.getStudySubjectId());
    int studyId = studySubjectBean.getStudyId();
    StudyDAO studydao = new StudyDAO(sm.getDataSource());
    StudyBean study = (StudyBean) studydao.findByPK(studyId);
    // If the study subject derives from a site, and is being viewed from a
    // parent study,
    // then the study IDs will be different. However, since each note is
    // saved with the specific
    // study ID, then its study ID may be different than the study subject's
    // ID.
    boolean subjectStudyIsCurrentStudy = studyId == currentStudy.getId();
    boolean isParentStudy = study.getParentStudyId() < 1;
    // Get any disc notes for this study event
    DiscrepancyNoteDAO discrepancyNoteDAO = new DiscrepancyNoteDAO(sm.getDataSource());
    ArrayList<DiscrepancyNoteBean> allNotesforSubjectAndEvent = new ArrayList<DiscrepancyNoteBean>();
    // These methods return only parent disc notes
    if (subjectStudyIsCurrentStudy && isParentStudy) {
        allNotesforSubjectAndEvent = discrepancyNoteDAO.findAllStudyEventByStudyAndId(currentStudy, studySubjectBean.getId());
    } else {
        // findAllStudyEventByStudiesAndSubjectId
        if (!isParentStudy) {
            StudyBean stParent = (StudyBean) studydao.findByPK(study.getParentStudyId());
            allNotesforSubjectAndEvent = discrepancyNoteDAO.findAllStudyEventByStudiesAndSubjectId(stParent, study, studySubjectBean.getId());
        } else {
            allNotesforSubjectAndEvent = discrepancyNoteDAO.findAllStudyEventByStudiesAndSubjectId(currentStudy, study, studySubjectBean.getId());
        }
    }
    if (!allNotesforSubjectAndEvent.isEmpty()) {
        setRequestAttributesForNotes(allNotesforSubjectAndEvent);
    }
    // prepare to figure out what the display should look like
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    ArrayList<EventCRFBean> eventCRFs = ecdao.findAllByStudyEvent(seb);
    ArrayList<Boolean> doRuleSetsExist = new ArrayList<Boolean>();
    RuleSetDAO ruleSetDao = new RuleSetDAO(sm.getDataSource());
    for (EventCRFBean eventCrfBean : eventCRFs) {
    // Boolean result = ruleSetDao.findByEventCrf(eventCrfBean) != null
    // ? Boolean.TRUE : Boolean.FALSE;
    // doRuleSetsExist.add(result);
    }
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
    ArrayList eventDefinitionCRFs = (ArrayList) edcdao.findAllActiveByEventDefinitionId(study, seb.getStudyEventDefinitionId());
    // get the event definition CRFs for which no event CRF exists
    // the event definition CRFs must be populated with versions so we can
    // let the user choose which version he will enter data for
    // However, this method seems to be returning DisplayEventDefinitionCRFs
    // that contain valid eventCRFs??
    ArrayList uncompletedEventDefinitionCRFs = getUncompletedCRFs(eventDefinitionCRFs, eventCRFs);
    populateUncompletedCRFsWithCRFAndVersions(uncompletedEventDefinitionCRFs);
    // BWP 2816 << Attempt to provide the DisplayEventDefinitionCRF with a
    // valid owner
    // only if its container eventCRf has a valid id
    populateUncompletedCRFsWithAnOwner(uncompletedEventDefinitionCRFs);
    // >>BWP
    // for the event definition CRFs for which event CRFs exist, get
    // DisplayEventCRFBeans, which the JSP will use to determine what
    // the user will see for each event CRF
    // removing the below row in exchange for the ViewStudySubjectServlet
    // version, for two
    // reasons:
    // 1. concentrate all business logic in one place
    // 2. VSSS seems to handle the javascript creation correctly
    // ArrayList displayEventCRFs = getDisplayEventCRFs(eventCRFs,
    // eventDefinitionCRFs, seb.getSubjectEventStatus());
    ArrayList displayEventCRFs = ViewStudySubjectServlet.getDisplayEventCRFs(sm.getDataSource(), eventCRFs, eventDefinitionCRFs, ub, currentRole, seb.getSubjectEventStatus(), study);
    // Issue 3212 BWP << hide certain CRFs at the site level
    if (currentStudy.getParentStudyId() > 0) {
        HideCRFManager hideCRFManager = HideCRFManager.createHideCRFManager();
        uncompletedEventDefinitionCRFs = hideCRFManager.removeHiddenEventDefinitionCRFBeans(uncompletedEventDefinitionCRFs);
        displayEventCRFs = hideCRFManager.removeHiddenEventCRFBeans(displayEventCRFs);
    }
    // >>
    request.setAttribute(BEAN_STUDY_EVENT, seb);
    request.setAttribute("doRuleSetsExist", doRuleSetsExist);
    request.setAttribute(BEAN_STUDY_SUBJECT, studySubjectBean);
    request.setAttribute(BEAN_UNCOMPLETED_EVENTDEFINITIONCRFS, uncompletedEventDefinitionCRFs);
    request.setAttribute(BEAN_DISPLAY_EVENT_CRFS, displayEventCRFs);
    // @pgawade 31-Aug-2012 fix for issue #15315: Reverting to set the request variable "beans" back
    // this is for generating side info panel
    ArrayList beans = ViewStudySubjectServlet.getDisplayStudyEventsForStudySubject(studySubjectBean, sm.getDataSource(), ub, currentRole);
    request.setAttribute("beans", beans);
    EventCRFBean ecb = new EventCRFBean();
    ecb.setStudyEventId(eventId);
    request.setAttribute("eventCRF", ecb);
    // Make available the study
    request.setAttribute("study", currentStudy);
    forwardPage(Page.ENTER_DATA_FOR_STUDY_EVENT);
}

Example 3 with HideCRFManager

use of org.akaza.openclinica.service.crfdata.HideCRFManager in project OpenClinica by OpenClinica.

the class ViewStudySubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    // studySubjectId
    int studySubId = fp.getInt("id", true);
    String from = fp.getString("from");
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);
    // if coming from change crf version -> display message
    String crfVersionChangeMsg = fp.getString("isFromCRFVersionChange");
    if (crfVersionChangeMsg != null && !crfVersionChangeMsg.equals("")) {
        addPageMessage(crfVersionChangeMsg);
    }
    if (studySubId == 0) {
        addPageMessage(respage.getString("please_choose_a_subject_to_view"));
        forwardPage(Page.LIST_STUDY_SUBJECTS);
    } else {
        if (!StringUtil.isBlank(from)) {
            // form ListSubject or
            request.setAttribute("from", from);
        // ListStudySubject
        } else {
            request.setAttribute("from", "");
        }
        StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
        request.setAttribute("studySub", studySub);
        request.setAttribute("originatingPage", URLEncoder.encode("ViewStudySubject?id=" + studySub.getId(), "UTF-8"));
        int studyId = studySub.getStudyId();
        int subjectId = studySub.getSubjectId();
        StudyDAO studydao = new StudyDAO(sm.getDataSource());
        StudyBean study = (StudyBean) studydao.findByPK(studyId);
        // Check if this StudySubject would be accessed from the Current Study
        if (studySub.getStudyId() != currentStudy.getId()) {
            if (currentStudy.getParentStudyId() > 0) {
                addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                forwardPage(Page.MENU_SERVLET);
                return;
            } else {
                // The SubjectStudy is not belong to currentstudy and current study is not a site.
                Collection sites = studydao.findOlnySiteIdsByStudy(currentStudy);
                if (!sites.contains(study.getId())) {
                    addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                    forwardPage(Page.MENU_SERVLET);
                    return;
                }
            }
        }
        // If the study subject derives from a site, and is being viewed
        // from a parent study,
        // then the study IDs will be different. However, since each note is
        // saved with the specific
        // study ID, then its study ID may be different than the study
        // subject's ID.
        boolean subjectStudyIsCurrentStudy = studyId == currentStudy.getId();
        boolean isParentStudy = study.getParentStudyId() < 1;
        // Get any disc notes for this subject : studySubId
        DiscrepancyNoteDAO discrepancyNoteDAO = new DiscrepancyNoteDAO(sm.getDataSource());
        List<DiscrepancyNoteBean> allNotesforSubject = new ArrayList<DiscrepancyNoteBean>();
        // These methods return only parent disc notes
        if (subjectStudyIsCurrentStudy && isParentStudy) {
            allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudyAndId(study, subjectId);
            allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudyAndId(study, studySubId));
        } else {
            if (!isParentStudy) {
                StudyBean stParent = (StudyBean) studydao.findByPK(study.getParentStudyId());
                allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudiesAndSubjectId(stParent, study, subjectId);
                allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudiesAndStudySubjectId(stParent, study, studySubId));
            } else {
                allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudiesAndSubjectId(currentStudy, study, subjectId);
                allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudiesAndStudySubjectId(currentStudy, study, studySubId));
            }
        }
        if (!allNotesforSubject.isEmpty()) {
            setRequestAttributesForNotes(allNotesforSubject);
        }
        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);
             */
        // YW 11-26-2007 <<
        StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
        study.getStudyParameterConfig().setCollectDob(spvdao.findByHandleAndStudy(studyId, "collectDob").getValue());
        // YW >>
        request.setAttribute("subjectStudy", study);
        if (study.getParentStudyId() > 0) {
            // this is a site,find parent
            StudyBean parentStudy2 = (StudyBean) studydao.findByPK(study.getParentStudyId());
            request.setAttribute("parentStudy", parentStudy2);
        } 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());
        StudySubjectService studySubjectService = (StudySubjectService) WebApplicationContextUtils.getWebApplicationContext(getServletContext()).getBean("studySubjectService");
        List<DisplayStudyEventBean> displayEvents = studySubjectService.getDisplayStudyEventsForStudySubject(studySub, ub, currentRole);
        for (int i = 0; i < displayEvents.size(); i++) {
            DisplayStudyEventBean decb = displayEvents.get(i);
            if (!(currentRole.isDirector() || currentRole.isCoordinator()) && decb.getStudyEvent().getSubjectEventStatus().isLocked()) {
                decb.getStudyEvent().setEditable(false);
            }
        }
        if (currentStudy.getParentStudyId() > 0) {
            HideCRFManager hideCRFManager = HideCRFManager.createHideCRFManager();
            for (DisplayStudyEventBean displayStudyEventBean : displayEvents) {
                hideCRFManager.removeHiddenEventCRF(displayStudyEventBean);
            }
        }
        EntityBeanTable table = fp.getEntityBeanTable();
        // sort by start
        table.setSortingIfNotExplicitlySet(1, false);
        // date, 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())) {
            if (currentStudy.getStatus().isAvailable() && !currentRole.getRole().equals(Role.MONITOR)) {
                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);
        // find audit log for events
        AuditEventDAO aedao = new AuditEventDAO(sm.getDataSource());
        ArrayList logs = aedao.findEventStatusLogByStudySubject(studySubId);
        // logger.warning("^^^ retrieved logs");
        UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
        ArrayList eventLogs = new ArrayList();
        // logger.warning("^^^ starting to iterate");
        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) {
                e.printStackTrace();
            }
            UserAccountBean updater = (UserAccountBean) udao.findByPK(avb.getUserId());
            sea.setUpdater(updater);
            eventLogs.add(sea);
        }
        request.setAttribute("eventLogs", eventLogs);
        forwardPage(Page.VIEW_STUDY_SUBJECT);
    }
}

Example 4 with HideCRFManager

use of org.akaza.openclinica.service.crfdata.HideCRFManager in project OpenClinica by OpenClinica.

the class ListEventsForSubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    // checks which module the requests are from
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);
    String pageNumber = fp.getString(ListStudySubjectServlet.SUBJECT_PAGE_NUMBER);
    String filterKeyword = fp.getString(ListStudySubjectServlet.FILTER_KEYWORD);
    String tmpSearch = fp.getString(ListStudySubjectServlet.SEARCH_SUBMITTED);
    boolean searchSubmitted = !(tmpSearch == null || "".equalsIgnoreCase(tmpSearch)) && !"".equalsIgnoreCase(filterKeyword);
    SubjectMatrixUtil matrixUtil = new SubjectMatrixUtil();
    String query = matrixUtil.createPaginatingQuery(pageNumber);
    StringBuilder extendedQuery = new StringBuilder(query);
    // URL encode the search keyword, since it will be a parameter in the
    // URL
    String filterKeywordURLEncode = java.net.URLEncoder.encode(filterKeyword, "UTF-8");
    if (searchSubmitted) {
        extendedQuery.append("&ebl_sortColumnInd=0&submitted=1&ebl_sortAscending=1&ebl_filtered=1");
        extendedQuery.append("&").append(ListStudySubjectServlet.FILTER_KEYWORD).append("=").append(filterKeywordURLEncode);
    }
    request.setAttribute(ListStudySubjectServlet.PAGINATING_QUERY, extendedQuery.toString());
    int definitionId = fp.getInt("defId");
    int tabId = fp.getInt("tab");
    if (definitionId <= 0) {
        addPageMessage(respage.getString("please_choose_an_ED_ta_to_vies_details"));
        forwardPage(Page.LIST_STUDY_SUBJECTS);
        return;
    }
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(definitionId);
    StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource());
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
    StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
    CRFDAO crfdao = new CRFDAO(sm.getDataSource());
    // find all the groups in the current study
    ArrayList studyGroupClasses = sgcdao.findAllActiveByStudy(currentStudy);
    // information for the event tabs
    ArrayList allDefs = seddao.findAllActiveByStudy(currentStudy);
    boolean isASite = false;
    if (currentStudy.getParentStudyId() > 0) {
        StudyDAO stdao = new StudyDAO(sm.getDataSource());
        StudyBean parent = (StudyBean) stdao.findByPK(currentStudy.getParentStudyId());
        allDefs = seddao.findAllActiveByStudy(parent);
    }
    ArrayList eventDefinitionCRFs = (ArrayList) edcdao.findAllActiveByEventDefinitionId(this.currentStudy, definitionId);
    for (int i = 0; i < eventDefinitionCRFs.size(); i++) {
        EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i);
        CRFBean crf = (CRFBean) crfdao.findByPK(edc.getCrfId());
        edc.setCrf(crf);
    }
    request.setAttribute("studyGroupClasses", studyGroupClasses);
    request.setAttribute("allDefsArray", allDefs);
    request.setAttribute("allDefsNumber", new Integer(allDefs.size()));
    request.setAttribute("groupSize", new Integer(studyGroupClasses.size()));
    request.setAttribute("eventDefCRFSize", new Integer(eventDefinitionCRFs.size()));
    request.setAttribute("tabId", new Integer(tabId));
    request.setAttribute("studyEventDef", sed);
    request.setAttribute("eventDefCRFs", eventDefinitionCRFs);
    // find all the subjects in current study
    ArrayList subjects = sdao.findAllByStudyId(currentStudy.getId());
    ArrayList displayStudySubs = new ArrayList();
    for (int i = 0; i < subjects.size(); i++) {
        StudySubjectBean studySub = (StudySubjectBean) subjects.get(i);
        ArrayList groups = (ArrayList) sgmdao.findAllByStudySubject(studySub.getId());
        ArrayList subGClasses = new ArrayList();
        for (int j = 0; j < studyGroupClasses.size(); j++) {
            StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(j);
            boolean hasClass = false;
            for (int k = 0; k < groups.size(); k++) {
                SubjectGroupMapBean sgmb = (SubjectGroupMapBean) groups.get(k);
                if (sgmb.getGroupClassName().equalsIgnoreCase(sgc.getName())) {
                    subGClasses.add(sgmb);
                    hasClass = true;
                    break;
                }
            }
            if (!hasClass) {
                subGClasses.add(new SubjectGroupMapBean());
            }
        }
        // find all eventcrfs for each event, for each event tab
        ArrayList displaySubjectEvents = new ArrayList();
        ArrayList<DisplayStudyEventBean> displayEvents = new ArrayList<DisplayStudyEventBean>();
        ArrayList events = sedao.findAllByStudySubjectAndDefinition(studySub, sed);
        for (int k = 0; k < events.size(); k++) {
            StudyEventBean seb = (StudyEventBean) events.get(k);
            DisplayStudyEventBean dseb = ListStudySubjectServlet.getDisplayStudyEventsForStudySubject(studySub, seb, sm.getDataSource(), ub, currentRole, this.currentStudy);
            // ArrayList eventCRFs = ecdao.findAllByStudyEvent(seb);
            // ArrayList al =
            // ViewStudySubjectServlet.getUncompletedCRFs(sm.getDataSource(),
            // eventDefinitionCRFs, eventCRFs);
            // dseb.getUncompletedCRFs().add(al);
            displayEvents.add(dseb);
        }
        ArrayList al = new ArrayList();
        for (int k = 0; k < displayEvents.size(); k++) {
            DisplayStudyEventBean dseb = displayEvents.get(k);
            ArrayList eventCRFs = dseb.getDisplayEventCRFs();
            for (int a = 0; a < eventDefinitionCRFs.size(); a++) {
                EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(a);
                int crfId = edc.getCrfId();
                boolean hasCRF = false;
                for (int b = 0; b < eventCRFs.size(); b++) {
                    DisplayEventCRFBean decb = (DisplayEventCRFBean) eventCRFs.get(b);
                    // decb.getStage().getName() );
                    if (decb.getEventCRF().getCrf().getId() == crfId) {
                        dseb.getAllEventCRFs().add(decb);
                        // logger.info("hasCRf" + crfId +
                        // decb.getEventCRF().getCrf().getName());
                        hasCRF = true;
                        break;
                    }
                }
                if (hasCRF == false) {
                    DisplayEventCRFBean db = new DisplayEventCRFBean();
                    db.setEventDefinitionCRF(edc);
                    db.getEventDefinitionCRF().setCrf(edc.getCrf());
                    dseb.getAllEventCRFs().add(db);
                // logger.info("noCRf" + crfId);
                }
            }
            // Issue 3212 BWP <<
            if (currentStudy.getParentStudyId() > 0) {
                // check each eventDefCRFBean and set its isHidden property
                // to true, if its
                // persistent/database-derived hideCrf is true (domain rule:
                // hide the CRF from users logged into a site)
                HideCRFManager hideCRFManager = HideCRFManager.createHideCRFManager();
                hideCRFManager.optionallyCheckHideCRFProperty(dseb);
                // remove a DisplayEventCRFBean from a DisplayStudyEventBean
                // in the list
                // if it contains a hidden CRF in its event definition
                hideCRFManager.removeHiddenEventCRF(dseb);
                // generate a boolean request attribute indicating whether
                // any of the CRFs
                // should be hidden
                boolean hideCRFs = hideCRFManager.studyEventHasAHideCRFProperty(dseb);
                request.setAttribute("hideCRFs", hideCRFs);
            }
        // >>
        }
        DisplayStudySubjectBean dssb = new DisplayStudySubjectBean();
        dssb.setStudySubject(studySub);
        dssb.setStudyGroups(subGClasses);
        dssb.setStudyEvents(displayEvents);
        if (definitionId > 0) {
            dssb.setSedId(definitionId);
        } else {
            dssb.setSedId(-1);
        }
        displayStudySubs.add(dssb);
    }
    EntityBeanTable table = fp.getEntityBeanTable();
    ArrayList allStudyRows = DisplayStudySubjectEventsRow.generateRowsFromBeans(displayStudySubs);
    ArrayList columnArray = new ArrayList();
    columnArray.add(resword.getString("ID"));
    columnArray.add(resword.getString("subject_status"));
    columnArray.add(resword.getString("gender"));
    for (int i = 0; i < studyGroupClasses.size(); i++) {
        StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
        columnArray.add(sgc.getName());
    }
    // columnArray.add("Event Sequence");
    columnArray.add(resword.getString("event_status"));
    columnArray.add(resword.getString("event_date"));
    // Issue 3212 BWP <<
    HideCRFManager hideCRFMgr = HideCRFManager.createHideCRFManager();
    hideCRFMgr.hideSpecifiedEventCRFDefBeans(eventDefinitionCRFs);
    for (int i = 0; i < eventDefinitionCRFs.size(); i++) {
        EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i);
        // Issue 3212 BWP <<
        if (!(currentStudy.getParentStudyId() > 0)) {
            columnArray.add(edc.getCrf().getName());
        } else {
            if (!edc.isHideCrf()) {
                columnArray.add(edc.getCrf().getName());
            }
        }
    // >>
    }
    columnArray.add(resword.getString("actions"));
    String[] columns = new String[columnArray.size()];
    columnArray.toArray(columns);
    table.setColumns(new ArrayList(Arrays.asList(columns)));
    table.setQuery("ListEventsForSubject?module=" + module + "&defId=" + definitionId + "&tab=" + tabId, new HashMap());
    table.hideColumnLink(columnArray.size() - 1);
    // if(currentStudy.getStatus().isAvailable()){
    // table.addLink(resword.getString("add_new_subject"), "AddNewSubject");
    // }
    table.setRows(allStudyRows);
    if (filterKeyword != null && !"".equalsIgnoreCase(filterKeyword)) {
        table.setKeywordFilter(filterKeyword);
    }
    table.computeDisplay();
    request.setAttribute("table", table);
    forwardPage(Page.LIST_EVENTS_FOR_SUBJECT);
}

Example 5 with HideCRFManager

use of org.akaza.openclinica.service.crfdata.HideCRFManager in project OpenClinica by OpenClinica.

the class ViewRuleAssignmentNewServlet method createStudyEventForInfoPanel.

private void createStudyEventForInfoPanel() {
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    ItemDAO itemdao = new ItemDAO(sm.getDataSource());
    StudyBean studyWithEventDefinitions = currentStudy;
    if (currentStudy.getParentStudyId() > 0) {
        studyWithEventDefinitions = new StudyBean();
        studyWithEventDefinitions.setId(currentStudy.getParentStudyId());
    }
    CRFDAO crfdao = new CRFDAO(sm.getDataSource());
    ArrayList seds = seddao.findAllActiveByStudy(studyWithEventDefinitions);
    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);
        }
    }
    request.setAttribute("eventlist", events);
    request.setAttribute("crfCount", crfdao.getCountofActiveCRFs());
    request.setAttribute("itemCount", itemdao.getCountofActiveItems());
    request.setAttribute("ruleSetCount", getRuleSetService().getRuleSetDao().count(currentStudy));
}