Examples with StudyGroupClassBean org.akaza.openclinica.bean.managestudy.StudyGroupClassBean used on opensource projects

Example 16 with StudyGroupClassBean

use of org.akaza.openclinica.bean.managestudy.StudyGroupClassBean in project OpenClinica by OpenClinica.

the class ListStudySubjectServlet method processRequest.

// >>
// < ResourceBundleresword;
@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    locale = LocaleResolver.getLocale(request);
    // < resword =
    // ResourceBundle.getBundle("org.akaza.openclinica.i18n.words",locale);
    // BWP 3098 << close the info side panel and show icons
    request.setAttribute("closeInfoShowIcons", true);
    // >>
    // BWP 3195, 3330 : designed to address pagination issues
    String pageNumber = fp.getString(SUBJECT_PAGE_NUMBER);
    StringBuilder paginatingQuery = new StringBuilder("");
    String filterKeyword = fp.getString(FILTER_KEYWORD);
    String tmpSearch = fp.getString(SEARCH_SUBMITTED);
    boolean searchSubmitted = !(tmpSearch == null || "".equalsIgnoreCase(tmpSearch)) && !"".equalsIgnoreCase(filterKeyword) && !"+".equalsIgnoreCase(filterKeyword);
    if (pageNumber != null && !"".equalsIgnoreCase(pageNumber)) {
        int tempNum = 0;
        try {
            tempNum = Integer.parseInt(pageNumber);
        } catch (NumberFormatException nfe) {
        // tempNum is already initialized to 0
        }
        if (tempNum > 0) {
            paginatingQuery = new StringBuilder(SUBJECT_PAGE_NUMBER).append("=").append(pageNumber);
            paginatingQuery.append("&ebl_paginated=1");
        }
    }
    // 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) {
        paginatingQuery.append("&ebl_sortColumnInd=0&submitted=1&ebl_sortAscending=1&ebl_filtered=1");
        paginatingQuery.append("&").append(FILTER_KEYWORD).append("=").append(filterKeywordURLEncode);
    }
    request.setAttribute(PAGINATING_QUERY, paginatingQuery.toString());
    StudyDAO stdao = new StudyDAO(sm.getDataSource());
    StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource());
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
    StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
    StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
    StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
    // YW << update study parameters of current study.
    // "collectDob" and "genderRequired" are set as the same as the parent
    // study
    // tbh, also add the params "subjectPersonIdRequired",
    // "subjectIdGeneration", "subjectIdPrefixSuffix"
    int parentStudyId = currentStudy.getParentStudyId();
    ArrayList studyGroupClasses = new ArrayList();
    ArrayList allDefs = new ArrayList();
    // tbh
    if (parentStudyId > 0) {
        StudyBean parentStudy = (StudyBean) stdao.findByPK(parentStudyId);
        studyGroupClasses = sgcdao.findAllActiveByStudy(parentStudy);
        allDefs = seddao.findAllActiveByStudy(parentStudy);
    } else {
        parentStudyId = currentStudy.getId();
        studyGroupClasses = sgcdao.findAllActiveByStudy(currentStudy);
        allDefs = seddao.findAllActiveByStudy(currentStudy);
    }
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
    StudyParameterValueBean parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "collectDob");
    currentStudy.getStudyParameterConfig().setCollectDob(parentSPV.getValue());
    parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "genderRequired");
    currentStudy.getStudyParameterConfig().setGenderRequired(parentSPV.getValue());
    parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectPersonIdRequired");
    currentStudy.getStudyParameterConfig().setSubjectPersonIdRequired(parentSPV.getValue());
    parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectIdGeneration");
    currentStudy.getStudyParameterConfig().setSubjectIdGeneration(parentSPV.getValue());
    parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectIdPrefixSuffix");
    currentStudy.getStudyParameterConfig().setSubjectIdPrefixSuffix(parentSPV.getValue());
    // for all the study groups for each group class
    for (int i = 0; i < studyGroupClasses.size(); i++) {
        StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
        ArrayList groups = sgdao.findAllByGroupClass(sgc);
        sgc.setStudyGroups(groups);
    }
    request.setAttribute("studyGroupClasses", studyGroupClasses);
    // information for the event tabs
    session.setAttribute("allDefsArray", allDefs);
    session.setAttribute("allDefsNumber", new Integer(allDefs.size()));
    session.setAttribute("groupSize", new Integer(studyGroupClasses.size()));
    // find all the subjects in current study
    ArrayList subjects = sdao.findAllByStudyId(currentStudy.getId());
    ArrayList<DisplayStudySubjectBean> displayStudySubs = new ArrayList<DisplayStudySubjectBean>();
    // BEGIN LOOPING THROUGH SUBJECTS
    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());
            }
        }
        ArrayList subEvents = new ArrayList();
        // find all events order by definition ordinal
        ArrayList events = sedao.findAllByStudySubject(studySub);
        for (int j = 0; j < allDefs.size(); j++) {
            StudyEventDefinitionBean sed = (StudyEventDefinitionBean) allDefs.get(j);
            boolean hasDef = false;
            // logger.info("...set blank to "+blankid);
            for (int k = 0; k < events.size(); k++) {
                StudyEventBean se = (StudyEventBean) events.get(k);
                if (se.getStudyEventDefinitionId() == sed.getId()) {
                    se.setStudyEventDefinition(sed);
                    // logger.info(">>>found assigned id "+sed.getId()+" sed
                    // name: "+sed.getName()+" "+se.getId());
                    subEvents.add(se);
                    hasDef = true;
                }
            }
            if (!hasDef) {
                StudyEventBean blank = new StudyEventBean();
                blank.setSubjectEventStatus(SubjectEventStatus.NOT_SCHEDULED);
                blank.setStudyEventDefinitionId(sed.getId());
                // how can we set the following:
                // logger.info("...resetting blank id: "+blank.getId()+" to
                // "+blankid);
                // blank.setId(blankid);
                blank.setStudyEventDefinition(sed);
                // logger.info(">>>blank id: "+blank.getId());
                // logger.info(">>>found unassigned id "+sed.getId()+" sed
                // name: "+sed.getName()+" ");
                subEvents.add(blank);
            }
        }
        // logger.info("subevents size after all adds: "+subEvents.size());
        // reorganize the events and find the repeating ones
        // subEvents:[aa bbb cc d ee]
        // finalEvents:[a(2) b(3) c(2) d e(2)]
        int prevDefId = 0;
        int currDefId = 0;
        ArrayList finalEvents = new ArrayList();
        int repeatingNum = 1;
        int count = 0;
        StudyEventBean event = new StudyEventBean();
        // begin looping through subject events
        for (int j = 0; j < subEvents.size(); j++) {
            StudyEventBean se = (StudyEventBean) subEvents.get(j);
            currDefId = se.getStudyEventDefinitionId();
            if (currDefId != prevDefId) {
                // find a new event
                if (repeatingNum > 1) {
                    event.setRepeatingNum(repeatingNum);
                    repeatingNum = 1;
                }
                // add current event to final
                finalEvents.add(se);
                event = se;
                count++;
            // logger.info("event id? "+event.getId());
            } else {
                // repeating event
                repeatingNum++;
                event.getRepeatEvents().add(se);
                // event.getRepeatEvents().size());
                if (j == subEvents.size() - 1) {
                    event.setRepeatingNum(repeatingNum);
                    repeatingNum = 1;
                }
            }
            prevDefId = currDefId;
        }
        // end looping through subject events
        DisplayStudySubjectBean dssb = new DisplayStudySubjectBean();
        // logger.info("final events size: "+finalEvents.size());
        dssb.setStudyEvents(finalEvents);
        dssb.setStudySubject(studySub);
        dssb.setStudyGroups(subGClasses);
        displayStudySubs.add(dssb);
    }
    // END LOOPING THROUGH SUBJECTS
    // Set a subject property to determine whether to show a signed-type
    // icon (electronic signature)
    // in the JSP view or not
    // Get all event crfs by studyevent id; then use
    // EventDefinitionCRFDAO.isRequired to
    // determine whether any uncompleted CRFs are required.
    boolean isRequiredUncomplete = false;
    for (DisplayStudySubjectBean subject : displayStudySubs) {
        for (Iterator it = subject.getStudyEvents().iterator(); it.hasNext(); ) {
            StudyEventBean event = (StudyEventBean) it.next();
            if (event.getSubjectEventStatus() != null && event.getSubjectEventStatus().getId() == 3) {
                // disallow the subject from signing any studies
                subject.setStudySignable(false);
                break;
            } else {
                // determine whether the subject has any required,
                // uncompleted event CRFs
                isRequiredUncomplete = eventHasRequiredUncompleteCRFs(event);
                if (isRequiredUncomplete) {
                    subject.setStudySignable(false);
                    break;
                }
            }
        }
    }
    fp = new FormProcessor(request);
    EntityBeanTable table = fp.getEntityBeanTable();
    ArrayList allStudyRows = DisplayStudySubjectRow.generateRowsFromBeans(displayStudySubs);
    ArrayList columnArray = new ArrayList();
    columnArray.add(resword.getString("study_subject_ID"));
    columnArray.add(resword.getString("subject_status"));
    columnArray.add(resword.getString("OID"));
    columnArray.add(resword.getString("gender"));
    // new
    columnArray.add(resword.getString("secondary_ID"));
    for (int i = 0; i < studyGroupClasses.size(); i++) {
        StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
        columnArray.add(sgc.getName());
    }
    for (int i = 0; i < allDefs.size(); i++) {
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) allDefs.get(i);
        columnArray.add(sed.getName());
    }
    columnArray.add(resword.getString("actions"));
    String[] columns = new String[columnArray.size()];
    columnArray.toArray(columns);
    // String[] columns = {"ID", "Subject Status", "Gender", "Enrollment
    // Date",
    // "Study Events", "Actions" };
    table.setColumns(new ArrayList(Arrays.asList(columns)));
    table.setQuery(getBaseURL(), new HashMap());
    table.hideColumnLink(columnArray.size() - 1);
    // table.addLink("Enroll a new subject",
    // "javascript:leftnavExpand('addSubjectRowExpress');");
    table.setRows(allStudyRows);
    if (filterKeyword != null && !"".equalsIgnoreCase(filterKeyword)) {
        table.setKeywordFilter(filterKeyword);
    }
    table.computeDisplay();
    request.setAttribute("table", table);
    // request.setAttribute("subjects", subjects);
    String idSetting = currentStudy.getStudyParameterConfig().getSubjectIdGeneration();
    // set up auto study subject id
    if (idSetting.equals("auto editable") || idSetting.equals("auto non-editable")) {
        //Shaoyu Su
        //int nextLabel = ssdao.findTheGreatestLabel() + 1;
        //request.setAttribute("label", new Integer(nextLabel).toString());
        request.setAttribute("label", resword.getString("id_generated_Save_Add"));
    }
    FormDiscrepancyNotes discNotes = new FormDiscrepancyNotes();
    session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
    forwardPage(getJSP());
}

Example 17 with StudyGroupClassBean

use of org.akaza.openclinica.bean.managestudy.StudyGroupClassBean in project OpenClinica by OpenClinica.

the class CreateSubjectGroupClassServlet method confirmGroup.

/**
     * Validates the first section of study inputs and save it into study bean
     *
     * @param request
     * @param response
     * @throws Exception
     */
private void confirmGroup() throws Exception {
    Validator v = new Validator(request);
    FormProcessor fp = new FormProcessor(request);
    v.addValidation("name", Validator.NO_BLANKS);
    v.addValidation("subjectAssignment", Validator.NO_BLANKS);
    v.addValidation("name", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 30);
    v.addValidation("subjectAssignment", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 30);
    ArrayList studyGroups = new ArrayList();
    for (int i = 0; i < 10; i++) {
        String name = fp.getString("studyGroup" + i);
        String description = fp.getString("studyGroupDescription" + i);
        if (!StringUtil.isBlank(name)) {
            StudyGroupBean group = new StudyGroupBean();
            group.setName(name);
            group.setDescription(description);
            studyGroups.add(group);
            if (name.length() > 255) {
                request.setAttribute("studyGroupError", respage.getString("group_name_cannot_be_more_255"));
                break;
            }
            if (description.length() > 1000) {
                request.setAttribute("studyGroupError", respage.getString("group_description_cannot_be_more_100"));
                break;
            }
        }
    }
    errors = v.validate();
    if (fp.getInt("groupClassTypeId") == 0) {
        Validator.addError(errors, "groupClassTypeId", resexception.getString("group_class_type_is_required"));
    }
    StudyGroupClassBean group = new StudyGroupClassBean();
    group.setName(fp.getString("name"));
    group.setGroupClassTypeId(fp.getInt("groupClassTypeId"));
    group.setSubjectAssignment(fp.getString("subjectAssignment"));
    session.setAttribute("group", group);
    session.setAttribute("studyGroups", studyGroups);
    if (errors.isEmpty()) {
        logger.info("no errors in the first section");
        group.setGroupClassTypeName(GroupClassType.get(group.getGroupClassTypeId()).getName());
        forwardPage(Page.CREATE_SUBJECT_GROUP_CLASS_CONFIRM);
    } else {
        logger.info("has validation errors in the first section");
        request.setAttribute("formMessages", errors);
        request.setAttribute("groupTypes", GroupClassType.toArrayList());
        forwardPage(Page.CREATE_SUBJECT_GROUP_CLASS);
    }
}

Example 18 with StudyGroupClassBean

use of org.akaza.openclinica.bean.managestudy.StudyGroupClassBean in project OpenClinica by OpenClinica.

the class CreateSubjectGroupClassServlet method processRequest.

@Override
public void processRequest() throws Exception {
    String action = request.getParameter("action");
    if (StringUtil.isBlank(action)) {
        ArrayList studyGroups = new ArrayList();
        for (int i = 0; i < 10; i++) {
            studyGroups.add(new StudyGroupBean());
        }
        StudyGroupClassBean group = new StudyGroupClassBean();
        request.setAttribute("groupTypes", GroupClassType.toArrayList());
        session.setAttribute("group", group);
        session.setAttribute("studyGroups", studyGroups);
        forwardPage(Page.CREATE_SUBJECT_GROUP_CLASS);
    } else {
        if ("confirm".equalsIgnoreCase(action)) {
            confirmGroup();
        } else if ("submit".equalsIgnoreCase(action)) {
            submitGroup();
        }
    }
}

Example 19 with StudyGroupClassBean

use of org.akaza.openclinica.bean.managestudy.StudyGroupClassBean in project OpenClinica by OpenClinica.

the class ListEventsForSubjectTableFactory method configureColumns.

@Override
protected void configureColumns(TableFacade tableFacade, Locale locale) {
    resword = ResourceBundleProvider.getWordsBundle(locale);
    resformat = ResourceBundleProvider.getFormatBundle(locale);
    tableFacade.setColumnProperties(columnNames);
    Row row = tableFacade.getTable().getRow();
    int index = 0;
    configureColumn(row.getColumn(columnNames[index]), resword.getString("study_subject_ID"), null, null);
    ++index;
    configureColumn(row.getColumn(columnNames[index]), resword.getString("subject_status"), new StatusCellEditor(), new StatusDroplistFilterEditor());
    ++index;
    configureColumn(row.getColumn(columnNames[index]), resword.getString("site_id"), null, null);
    ++index;
    configureColumn(row.getColumn(columnNames[index]), resword.getString("gender"), null, null, true, false);
    ++index;
    // group class columns
    for (int i = index; i < index + studyGroupClasses.size(); i++) {
        StudyGroupClassBean studyGroupClass = studyGroupClasses.get(i - index);
        configureColumn(row.getColumn(columnNames[i]), studyGroupClass.getName(), new StudyGroupClassCellEditor(studyGroupClass), new SubjectGroupClassDroplistFilterEditor(studyGroupClass), true, false);
    }
    configureColumn(row.getColumn(columnNames[index + studyGroupClasses.size()]), resword.getString("event_status"), new EventStatusCellEditor(), new SubjectEventStatusDroplistFilterEditor(), true, false);
    ++index;
    configureColumn(row.getColumn(columnNames[index + studyGroupClasses.size()]), resword.getString("event_date"), new EventStartDateCellEditor(), null);
    ++index;
    // crf columns
    for (int i = index + studyGroupClasses.size(); i < columnNames.length - 1; i++) {
        CRFBean crfBean = crfBeans.get(i - (index + studyGroupClasses.size()));
        configureColumn(row.getColumn(columnNames[i]), crfBean.getName(), new EventCrfCellEditor(), new SubjectEventCRFStatusDroplistFilterEditor(), true, false);
    }
    String actionsHeader = resword.getString("rule_actions") + "&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;";
    configureColumn(row.getColumn(columnNames[columnNames.length - 1]), actionsHeader, new ActionsCellEditor(), new DefaultActionsEditor(locale), true, false);
}

Example 20 with StudyGroupClassBean

use of org.akaza.openclinica.bean.managestudy.StudyGroupClassBean in project OpenClinica by OpenClinica.

the class ListSubjectGroupClassServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
    // YW <<
    StudyDAO stdao = new StudyDAO(sm.getDataSource());
    int parentStudyId = currentStudy.getParentStudyId();
    ArrayList groups = new ArrayList();
    if (parentStudyId > 0) {
        StudyBean parentStudy = (StudyBean) stdao.findByPK(parentStudyId);
        groups = sgcdao.findAllByStudy(parentStudy);
    } else {
        groups = sgcdao.findAllByStudy(currentStudy);
    }
    // YW >>
    String isReadOnly = request.getParameter("read");
    StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
    for (int i = 0; i < groups.size(); i++) {
        StudyGroupClassBean group = (StudyGroupClassBean) groups.get(i);
        ArrayList studyGroups = sgdao.findAllByGroupClass(group);
        group.setStudyGroups(studyGroups);
    }
    EntityBeanTable table = fp.getEntityBeanTable();
    ArrayList allGroupRows = StudyGroupClassRow.generateRowsFromBeans(groups);
    boolean isParentStudy = currentStudy.getParentStudyId() > 0 ? false : true;
    request.setAttribute("isParentStudy", isParentStudy);
    String[] columns = { resword.getString("subject_group_class"), resword.getString("type"), resword.getString("subject_assignment"), resword.getString("study_name"), resword.getString("subject_groups"), resword.getString("status"), resword.getString("actions") };
    table.setColumns(new ArrayList(Arrays.asList(columns)));
    table.hideColumnLink(4);
    table.hideColumnLink(6);
    table.setQuery("ListSubjectGroupClass", new HashMap());
    // if (isParentStudy && (!currentStudy.getStatus().isLocked())) {
    // table.addLink(resword.getString("create_a_subject_group_class"),
    // "CreateSubjectGroupClass");
    // }
    table.setRows(allGroupRows);
    table.computeDisplay();
    request.setAttribute("table", table);
    if (request.getParameter("read") != null && request.getParameter("read").equals("true")) {
        request.setAttribute("readOnly", true);
    }
    forwardPage(Page.SUBJECT_GROUP_CLASS_LIST);
}