Examples with CRFVersionDAO org.akaza.openclinica.dao.submit.CRFVersionDAO used on opensource projects

Example 71 with CRFVersionDAO

use of org.akaza.openclinica.dao.submit.CRFVersionDAO in project OpenClinica by OpenClinica.

the class CreateFiltersTwoServlet method processRequest.

// < ResourceBundle restext,resword,respage,resexception;
@Override
public void processRequest() throws Exception {
    // we can't get to here without an action:
    // begin--takes us to specify parameters,
    // where the user will select CRF, then section,
    // then parameters of the section: a little tricky
    // to do entirely with javascript, but can be done.
    // possible to set up the CRF-section relationship,
    // and then have a screen 3.5 with the parameters?
    // criteria--takes us to specify criteria, that is,
    // to specify and, or, not and, etc. here we'll take the
    // list we just generated online and generate a chain
    // of filterobjectbeans, which will in turn,
    // generate the SQL add on for the dataset.
    String action = request.getParameter("action");
    StudyBean studyWithEventDefs = currentStudy;
    if (currentStudy.getParentStudyId() > 0) {
        studyWithEventDefs = new StudyBean();
        studyWithEventDefs.setId(currentStudy.getParentStudyId());
    }
    if (StringUtil.isBlank(action)) {
    // throw an error
    } else if ("begin".equalsIgnoreCase(action)) {
        StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
        HashMap events = sedao.findCRFsByStudy(studyWithEventDefs);
        // if events are empty -- resend to first filter page with message
        if (events.isEmpty()) {
            addPageMessage(respage.getString("no_CRF_assigned_pick_another"));
            FormProcessor fp = new FormProcessor(request);
            FilterDAO fdao = new FilterDAO(sm.getDataSource());
            EntityBeanTable table = fp.getEntityBeanTable();
            ArrayList 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);
            forwardPage(Page.CREATE_FILTER_SCREEN_1);
        } else {
            // else, send to the following page:
            request.setAttribute("events", events);
            forwardPage(Page.CREATE_FILTER_SCREEN_3);
        }
    } else if ("crfselected".equalsIgnoreCase(action)) {
        // get the crf id, return to a new page with sections
        // and parameters attached, tbh
        FormProcessor fp = new FormProcessor(request);
        HashMap errors = new HashMap();
        int crfId = fp.getInt("crfId");
        if (crfId > 0) {
            CRFVersionDAO cvDAO = new CRFVersionDAO(sm.getDataSource());
            CRFDAO cDAO = new CRFDAO(sm.getDataSource());
            SectionDAO secDAO = new SectionDAO(sm.getDataSource());
            Collection sections = secDAO.findByVersionId(crfId);
            CRFVersionBean cvBean = (CRFVersionBean) cvDAO.findByPK(crfId);
            CRFBean cBean = (CRFBean) cDAO.findByPK(cvBean.getCrfId());
            request.setAttribute("sections", sections);
            session.setAttribute("cBean", cBean);
            // for further pages,
            session.setAttribute("cvBean", cvBean);
            // tbh
            forwardPage(Page.CREATE_FILTER_SCREEN_3_1);
        } else {
            addPageMessage(respage.getString("select_a_CRF_before_picking"));
            StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
            HashMap events = sedao.findCRFsByStudy(studyWithEventDefs);
            request.setAttribute("events", events);
            forwardPage(Page.CREATE_FILTER_SCREEN_3);
        }
    } else if ("sectionselected".equalsIgnoreCase(action)) {
        // TODO set the crf and the section into session,
        // allow for the user to go back and forth,
        // set up the questions to be picked,
        // allow the user to move on to create_filter_screen_4
        FormProcessor fp = new FormProcessor(request);
        int sectionId = fp.getInt("sectionId");
        if (sectionId > 0) {
            SectionDAO secDAO = new SectionDAO(sm.getDataSource());
            SectionBean secBean = (SectionBean) secDAO.findByPK(sectionId);
            session.setAttribute("secBean", secBean);
            ItemFormMetadataDAO ifmDAO = new ItemFormMetadataDAO(sm.getDataSource());
            Collection metadatas = ifmDAO.findAllBySectionId(sectionId);
            if (metadatas.size() > 0) {
                request.setAttribute("metadatas", metadatas);
                forwardPage(Page.CREATE_FILTER_SCREEN_3_2);
            } else {
                CRFVersionBean cvBean = (CRFVersionBean) session.getAttribute("cvBean");
                addPageMessage(respage.getString("section_not_have_questions_select_another"));
                // SectionDAO secDAO = new SectionDAO(sm.getDataSource());
                Collection sections = secDAO.findByVersionId(cvBean.getId());
                request.setAttribute("sections", sections);
                forwardPage(Page.CREATE_FILTER_SCREEN_3_1);
            }
        } else {
            CRFVersionBean cvBean = (CRFVersionBean) session.getAttribute("cvBean");
            addPageMessage(respage.getString("select_section_before_select_question"));
            SectionDAO secDAO = new SectionDAO(sm.getDataSource());
            Collection sections = secDAO.findByVersionId(cvBean.getId());
            request.setAttribute("sections", sections);
            forwardPage(Page.CREATE_FILTER_SCREEN_3_1);
        }
    } else if ("questionsselected".equalsIgnoreCase(action)) {
        ArrayList alist = this.extractIdsFromForm();
        // and send the user to create_filter_screen_4
        if (alist.size() > 0) {
            ItemFormMetadataDAO ifmDAO = new ItemFormMetadataDAO(sm.getDataSource());
            Collection questions = ifmDAO.findByMultiplePKs(alist);
            session.setAttribute("questions", questions);
            forwardPage(Page.CREATE_FILTER_SCREEN_4);
        } else {
            SectionBean secBean = (SectionBean) session.getAttribute("secBean");
            addPageMessage(respage.getString("select_questions_before_set_parameters"));
            ItemFormMetadataDAO ifmDAO = new ItemFormMetadataDAO(sm.getDataSource());
            Collection metadatas = ifmDAO.findAllBySectionId(secBean.getId());
            request.setAttribute("metadatas", metadatas);
            forwardPage(Page.CREATE_FILTER_SCREEN_3_2);
        }
    } else if ("validatecriteria".equalsIgnoreCase(action)) {
        // TODO look at the criteria and create a list of filterobjectdata
        // beans, so that we can create the SQL later on in
        // the process.
        // also, throw the user back to the process or throw
        // them forward into the createServletThree process
        FormProcessor fp = new FormProcessor(request);
        String logical = fp.getString("logical");
        ArrayList questions = (ArrayList) session.getAttribute("questions");
        ArrayList filterobjects = new ArrayList();
        // (ArrayList)session.getAttribute("filterobjects");
        Iterator q_it = questions.iterator();
        int arrCnt = 0;
        while (q_it.hasNext()) {
            ItemFormMetadataBean ifmBean = (ItemFormMetadataBean) q_it.next();
            String opString = "operator:" + ifmBean.getId();
            String valString = "value:" + ifmBean.getId();
            String remString = "remove:" + ifmBean.getId();
            if ("remove".equals(fp.getString(remString))) {
                logger.info("found the string: " + remString);
                // TODO remove the question from from the list,
                // redirect to that page again????? <--maybe not?
                // questions.remove(arrCnt);
                // shouldn't have to remove the above, just do nothing
                arrCnt++;
            } else {
                String operator = fp.getString(opString);
                String value = fp.getString(valString);
                FilterObjectBean fob = new FilterObjectBean();
                fob.setItemId(ifmBean.getId());
                fob.setItemName(ifmBean.getHeader() + " " + ifmBean.getLeftItemText() + " " + ifmBean.getRightItemText());
                // case operator:
                if ("equal to".equalsIgnoreCase(operator)) {
                    fob.setOperand("=");
                } else if ("greater than".equalsIgnoreCase(operator)) {
                    fob.setOperand(">");
                } else if ("less than".equalsIgnoreCase(operator)) {
                    fob.setOperand("<");
                } else if ("greater than or equal".equalsIgnoreCase(operator)) {
                    fob.setOperand(">=");
                } else if ("less than or equal".equalsIgnoreCase(operator)) {
                    fob.setOperand("<=");
                } else if ("like".equalsIgnoreCase(operator)) {
                    fob.setOperand(" like ");
                } else if ("not like".equalsIgnoreCase(operator)) {
                    fob.setOperand(" not like ");
                } else {
                    fob.setOperand("!=");
                }
                fob.setValue(value);
                filterobjects.add(fob);
            }
        // end else
        // 
        }
        // end while
        session.setAttribute("questions", questions);
        // TODO where does the connector come into play?
        // session.setAttribute("filterobjects",filterobjects);
        FilterDAO fDAO = new FilterDAO(sm.getDataSource());
        String newSQL = (String) session.getAttribute("newSQL");
        ArrayList newExp = (ArrayList) session.getAttribute("newExp");
        // human readable explanation
        String newNewSQL = fDAO.genSQLStatement(newSQL, logical, filterobjects);
        ArrayList newNewExp = fDAO.genExplanation(newExp, logical, filterobjects);
        if (arrCnt == questions.size()) {
            newNewSQL = newSQL;
            newNewExp = newExp;
        // don't change anything, if we've removed everything from this
        // list
        }
        logger.info("new SQL Generated: " + newNewSQL);
        String sub = fp.getString("submit");
        if ("Specify Filter Metadata".equals(sub)) {
            // add new params, create the filter object,
            // and go to create metadata
            FilterBean fb = new FilterBean();
            fb.setSQLStatement(newNewSQL + ")");
            // adding parens here to finish off other
            // statement--might add first part of statement here
            // for legibility's sake
            // tbh 06-02-2005
            session.removeAttribute("newSQL");
            // end of the road
            session.setAttribute("newFilter", fb);
            request.setAttribute("statuses", getStatuses());
            forwardPage(Page.CREATE_FILTER_SCREEN_5);
        } else {
            // replace the 'old' sql with the new sql gathered from the
            // session
            session.setAttribute("newSQL", newNewSQL);
            session.setAttribute("newExp", newNewExp);
            // add new params, and go back
            StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
            HashMap events = sedao.findCRFsByStudy(currentStudy);
            // 
            request.setAttribute("events", events);
            forwardPage(Page.CREATE_FILTER_SCREEN_3);
        }
    }
}

Example 72 with CRFVersionDAO

use of org.akaza.openclinica.dao.submit.CRFVersionDAO in project OpenClinica by OpenClinica.

the class ViewStudySubjectServlet method populateUncompletedCRFsWithCRFAndVersions.

public static void populateUncompletedCRFsWithCRFAndVersions(DataSource ds, ArrayList uncompletedEventDefinitionCRFs) {
    CRFDAO cdao = new CRFDAO(ds);
    CRFVersionDAO cvdao = new CRFVersionDAO(ds);
    int size = uncompletedEventDefinitionCRFs.size();
    for (int i = 0; i < size; i++) {
        DisplayEventDefinitionCRFBean dedcrf = (DisplayEventDefinitionCRFBean) uncompletedEventDefinitionCRFs.get(i);
        CRFBean cb = (CRFBean) cdao.findByPK(dedcrf.getEdc().getCrfId());
        dedcrf.getEdc().setCrf(cb);
        ArrayList theVersions = (ArrayList) cvdao.findAllActiveByCRF(dedcrf.getEdc().getCrfId());
        ArrayList versions = new ArrayList();
        HashMap<String, CRFVersionBean> crfVersionIds = new HashMap<String, CRFVersionBean>();
        for (int j = 0; j < theVersions.size(); j++) {
            CRFVersionBean crfVersion = (CRFVersionBean) theVersions.get(j);
            crfVersionIds.put(String.valueOf(crfVersion.getId()), crfVersion);
        }
        if (!dedcrf.getEdc().getSelectedVersionIds().equals("")) {
            String[] kk = dedcrf.getEdc().getSelectedVersionIds().split(",");
            for (String string : kk) {
                if (crfVersionIds.get(string) != null) {
                    versions.add(crfVersionIds.get(string));
                }
            }
        } else {
            versions = theVersions;
        }
        dedcrf.getEdc().setVersions(versions);
        uncompletedEventDefinitionCRFs.set(i, dedcrf);
    }
}

Example 73 with CRFVersionDAO

use of org.akaza.openclinica.dao.submit.CRFVersionDAO in project OpenClinica by OpenClinica.

the class ViewStudySubjectServlet method getDisplayEventCRFs.

/**
 * Each of the event CRFs with its corresponding CRFBean. Then generates a
 * list of DisplayEventCRFBeans, one for each event CRF.
 *
 * @param eventCRFs
 *            The list of event CRFs for this study event.
 * @param eventDefinitionCRFs
 *            The list of event definition CRFs for this study event.
 * @return The list of DisplayEventCRFBeans for this study event.
 */
public static ArrayList getDisplayEventCRFs(DataSource ds, ArrayList eventCRFs, ArrayList eventDefinitionCRFs, UserAccountBean ub, StudyUserRoleBean currentRole, SubjectEventStatus status, StudyBean study) {
    ArrayList answer = new ArrayList();
    // HashMap definitionsById = new HashMap();
    int i;
    /*
         * for (i = 0; i < eventDefinitionCRFs.size(); i++) {
         * EventDefinitionCRFBean edc = (EventDefinitionCRFBean)
         * eventDefinitionCRFs.get(i); definitionsById.put(new
         * Integer(edc.getStudyEventDefinitionId()), edc); }
         */
    StudyEventDAO sedao = new StudyEventDAO(ds);
    CRFDAO cdao = new CRFDAO(ds);
    CRFVersionDAO cvdao = new CRFVersionDAO(ds);
    ItemDataDAO iddao = new ItemDataDAO(ds);
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(ds);
    for (i = 0; i < eventCRFs.size(); i++) {
        EventCRFBean ecb = (EventCRFBean) eventCRFs.get(i);
        // populate the event CRF with its crf bean
        int crfVersionId = ecb.getCRFVersionId();
        CRFBean cb = cdao.findByVersionId(crfVersionId);
        ecb.setCrf(cb);
        CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(crfVersionId);
        ecb.setCrfVersion(cvb);
        // then get the definition so we can call
        // DisplayEventCRFBean.setFlags
        int studyEventId = ecb.getStudyEventId();
        int studyEventDefinitionId = sedao.getDefinitionIdFromStudyEventId(studyEventId);
        // EventDefinitionCRFBean edc = (EventDefinitionCRFBean)
        // definitionsById.get(new Integer(
        // studyEventDefinitionId));
        // fix problem of the above code(commented out), find the correct
        // edc, note that on definitionId can be related to multiple
        // eventdefinitioncrfBeans
        EventDefinitionCRFBean edc = edcdao.findByStudyEventDefinitionIdAndCRFId(study, studyEventDefinitionId, cb.getId());
        // rules updated 112007 tbh
        if (status.equals(SubjectEventStatus.LOCKED) || status.equals(SubjectEventStatus.SKIPPED) || status.equals(SubjectEventStatus.STOPPED)) {
            ecb.setStage(DataEntryStage.LOCKED);
        // we need to set a SED-wide flag here, because other edcs
        // in this event can be filled in and change the status, tbh
        } else if (status.equals(SubjectEventStatus.INVALID)) {
            ecb.setStage(DataEntryStage.LOCKED);
        } else if (!cb.getStatus().equals(Status.AVAILABLE)) {
            ecb.setStage(DataEntryStage.LOCKED);
        } else if (!cvb.getStatus().equals(Status.AVAILABLE)) {
            ecb.setStage(DataEntryStage.LOCKED);
        }
        // TODO need to refactor since this is similar to other code, tbh
        if (edc != null) {
            // System.out.println("edc is not null, need to set flags");
            DisplayEventCRFBean dec = new DisplayEventCRFBean();
            dec.setEventDefinitionCRF(edc);
            // System.out.println("edc.isDoubleEntry()" +
            // edc.isDoubleEntry() + ecb.getId());
            dec.setFlags(ecb, ub, currentRole, edc.isDoubleEntry());
            if (dec.isLocked()) {
            // System.out.println("*** found a locked DEC:
            // "+edc.getCrfName());
            }
            ArrayList idata = iddao.findAllByEventCRFId(ecb.getId());
            if (!idata.isEmpty()) {
                // consider an event crf started only if item data get
                // created
                answer.add(dec);
            }
        }
    }
    return answer;
}

Example 74 with CRFVersionDAO

use of org.akaza.openclinica.dao.submit.CRFVersionDAO in project OpenClinica by OpenClinica.

the class DataEntryServlet method getAllDisplayBeans.

/**
 * Retrieve the DisplaySectionBean which will be used to display the Event CRF Section on the JSP, and also is used to controll processRequest.
 * @param request TODO
 */
protected ArrayList getAllDisplayBeans(HttpServletRequest request) throws Exception {
    EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
    ArrayList sections = new ArrayList();
    HttpSession session = request.getSession();
    StudyBean study = (StudyBean) session.getAttribute("study");
    SectionDAO sdao = new SectionDAO(getDataSource());
    ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale);
    // ALL_SECTION_BEANS
    ArrayList<SectionBean> allSectionBeans = (ArrayList<SectionBean>) request.getAttribute(ALL_SECTION_BEANS);
    for (int j = 0; j < allSectionBeans.size(); j++) {
        SectionBean sb = allSectionBeans.get(j);
        DisplaySectionBean section = new DisplaySectionBean();
        section.setEventCRF(ecb);
        if (sb.getParentId() > 0) {
            SectionBean parent = (SectionBean) sdao.findByPK(sb.getParentId());
            sb.setParent(parent);
        }
        section.setSection(sb);
        CRFVersionDAO cvdao = new CRFVersionDAO(getDataSource());
        CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(ecb.getCRFVersionId());
        section.setCrfVersion(cvb);
        CRFDAO cdao = new CRFDAO(getDataSource());
        CRFBean cb = (CRFBean) cdao.findByPK(cvb.getCrfId());
        section.setCrf(cb);
        EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource());
        EventDefinitionCRFBean edcb = edcdao.findByStudyEventIdAndCRFVersionId(study, ecb.getStudyEventId(), cvb.getId());
        section.setEventDefinitionCRF(edcb);
        // setup DAO's here to avoid creating too many objects
        ItemDAO idao = new ItemDAO(getDataSource());
        ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(getDataSource());
        iddao = new ItemDataDAO(getDataSource(), locale);
        // get all the display item beans
        ArrayList displayItems = getParentDisplayItems(false, sb, edcb, idao, ifmdao, iddao, false, request);
        LOGGER.debug("222 just ran get parent display, has group " + " FALSE has ungrouped FALSE");
        // now sort them by ordinal
        Collections.sort(displayItems);
        // now get the child DisplayItemBeans
        for (int i = 0; i < displayItems.size(); i++) {
            DisplayItemBean dib = (DisplayItemBean) displayItems.get(i);
            dib.setChildren(getChildrenDisplayItems(dib, edcb, request));
            if (shouldLoadDBValues(dib)) {
                LOGGER.trace("should load db values is true, set value");
                dib.loadDBValue();
            }
            displayItems.set(i, dib);
        }
        section.setItems(displayItems);
        sections.add(section);
    }
    return sections;
}

Example 75 with CRFVersionDAO

use of org.akaza.openclinica.dao.submit.CRFVersionDAO in project OpenClinica by OpenClinica.

the class EnterDataForStudyEventServlet method getDisplayEventCRFs.

/**
 * Each of the event CRFs with its corresponding CRFBean. Then generates a
 * list of DisplayEventCRFBeans, one for each event CRF.
 *
 * @param eventCRFs
 *            The list of event CRFs for this study event.
 * @param eventDefinitionCRFs
 *            The list of event definition CRFs for this study event.
 * @return The list of DisplayEventCRFBeans for this study event.
 */
private ArrayList getDisplayEventCRFs(ArrayList eventCRFs, ArrayList eventDefinitionCRFs, SubjectEventStatus status) {
    ArrayList answer = new ArrayList();
    HashMap definitionsByCRFId = new HashMap();
    int i;
    for (i = 0; i < eventDefinitionCRFs.size(); i++) {
        EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i);
        definitionsByCRFId.put(new Integer(edc.getCrfId()), edc);
    }
    CRFDAO cdao = new CRFDAO(sm.getDataSource());
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
    for (i = 0; i < eventCRFs.size(); i++) {
        EventCRFBean ecb = (EventCRFBean) eventCRFs.get(i);
        logger.debug("0. found event crf bean: " + ecb.getName());
        // populate the event CRF with its crf bean
        int crfVersionId = ecb.getCRFVersionId();
        CRFBean cb = cdao.findByVersionId(crfVersionId);
        logger.debug("1. found crf bean: " + cb.getName());
        ecb.setCrf(cb);
        CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(crfVersionId);
        logger.debug("2. found crf version bean: " + cvb.getName());
        ecb.setCrfVersion(cvb);
        logger.debug("found subj event status: " + status.getName() + " cb status: " + cb.getStatus().getName() + " cvb status: " + cvb.getStatus().getName());
        // below added tbh 092007
        boolean invalidate = false;
        if (status.isLocked()) {
            ecb.setStage(DataEntryStage.LOCKED);
        } else if (status.isInvalid()) {
            ecb.setStage(DataEntryStage.LOCKED);
        // invalidate = true;
        } else if (!cb.getStatus().equals(Status.AVAILABLE)) {
            logger.debug("got to the CB version of the logic");
            ecb.setStage(DataEntryStage.LOCKED);
        // invalidate= true;
        } else if (!cvb.getStatus().equals(Status.AVAILABLE)) {
            logger.debug("got to the CVB version of the logic");
            ecb.setStage(DataEntryStage.LOCKED);
        // invalidate = true;
        }
        logger.debug("found ecb stage of " + ecb.getStage().getName());
        // above added tbh, 092007-102007
        try {
            // event crf collection will pull up events that have
            // been started, but contain no data
            // this creates problems if we remove CRFs from
            // event definitions
            EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) definitionsByCRFId.get(new Integer(cb.getId()));
            logger.debug("3. found event def crf bean: " + edcb.getName());
            DisplayEventCRFBean dec = new DisplayEventCRFBean();
            dec.setFlags(ecb, ub, currentRole, edcb.isDoubleEntry());
            ArrayList idata = iddao.findAllByEventCRFId(ecb.getId());
            if (!idata.isEmpty()) {
                // consider an event crf started only if item data get
                // created
                answer.add(dec);
            }
        } catch (NullPointerException npe) {
            logger.debug("5. got to NPE on this time around!");
        }
    }
    return answer;
}