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

Example 26 with DatasetBean

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

the class DatasetDAO method findAllOrderByStudyIdAndName.

public Collection findAllOrderByStudyIdAndName() {
    this.setTypesExpected();
    ArrayList alist = this.select(digester.getQuery("findAllOrderByStudyIdAndName"));
    ArrayList al = new ArrayList();
    Iterator it = alist.iterator();
    while (it.hasNext()) {
        DatasetBean eb = (DatasetBean) this.getEntityFromHashMap((HashMap) it.next());
        al.add(eb);
    }
    return al;
}

Example 27 with DatasetBean

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

the class DatasetDAO method findByOwnerId.

/**
     * find by owner id, reports a list of datasets by user account id.
     *
     * @param ownerId
     *            studyId
     */
public Collection findByOwnerId(int ownerId, int studyId) {
    // TODO add an findbyadminownerid?
    this.setTypesExpected();
    HashMap variables = new HashMap();
    variables.put(Integer.valueOf(1), Integer.valueOf(studyId));
    variables.put(Integer.valueOf(2), Integer.valueOf(studyId));
    variables.put(Integer.valueOf(3), Integer.valueOf(ownerId));
    ArrayList alist = this.select(digester.getQuery("findByOwnerId"), variables);
    ArrayList al = new ArrayList();
    Iterator it = alist.iterator();
    while (it.hasNext()) {
        DatasetBean eb = (DatasetBean) this.getEntityFromHashMap((HashMap) it.next());
        al.add(eb);
    }
    return al;
}

Example 28 with DatasetBean

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

the class DatasetDAO method findTopFive.

public Collection findTopFive(StudyBean currentStudy) {
    int studyId = currentStudy.getId();
    this.setTypesExpected();
    HashMap variables = new HashMap();
    variables.put(Integer.valueOf(1), Integer.valueOf(studyId));
    variables.put(Integer.valueOf(2), Integer.valueOf(studyId));
    ArrayList alist = this.select(digester.getQuery("findTopFive"), variables);
    ArrayList al = new ArrayList();
    Iterator it = alist.iterator();
    while (it.hasNext()) {
        DatasetBean eb = (DatasetBean) this.getEntityFromHashMap((HashMap) it.next());
        al.add(eb);
    }
    return al;
}

Example 29 with DatasetBean

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

the class StudyInfoPanel method setData.

/**
     * setData, the external function which creates data for the panel to
     * reflect.
     *
     * @param page
     * @param session
     * @param request
     */
public void setData(Page page, HttpSession session, HttpServletRequest request) {
    Locale locale = request.getLocale();
    resword = ResourceBundleProvider.getWordsBundle();
    local_sdf = new SimpleDateFormat(ResourceBundleProvider.getFormatBundle(locale).getString("date_format_string"));
    try {
        // defaults, can be reset by mistake by running through one page,
        // tbh
        this.setStudyInfoShown(true);
        this.setOrderedData(false);
        // try to avoid errors, tbh
        if (page.equals(Page.CREATE_DATASET_1)) {
            this.reset();
        // this.setData("Number of Steps", "5");
        } else if (page.equals(Page.CREATE_DATASET_2) || page.equals(Page.CREATE_DATASET_EVENT_ATTR) || page.equals(Page.CREATE_DATASET_SUB_ATTR) || page.equals(Page.CREATE_DATASET_CRF_ATTR) || page.equals(Page.CREATE_DATASET_GROUP_ATTR) || page.equals(Page.CREATE_DATASET_VIEW_SELECTED)) {
            HashMap eventlist = (HashMap) request.getAttribute("eventlist");
            ArrayList displayData = generateEventTree(eventlist);
            this.reset();
            this.setUserOrderedData(displayData);
            this.setStudyInfoShown(false);
            this.setOrderedData(true);
            this.setCreateDataset(true);
            this.setSubmitDataModule(false);
            this.setExtractData(false);
        } else if (page.equals(Page.CREATE_DATASET_3)) {
            this.reset();
            this.setStudyInfoShown(false);
            this.setOrderedData(false);
            this.setCreateDataset(true);
            this.setSubmitDataModule(false);
            this.setExtractData(false);
            DatasetBean dsb = (DatasetBean) session.getAttribute("newDataset");
            int ev_count = dsb.getItemIds().size();
            this.setData(resword.getString("items_selected"), new Integer(ev_count).toString());
        } else if (page.equals(Page.CREATE_DATASET_4)) {
            this.reset();
            this.setStudyInfoShown(false);
            this.setOrderedData(false);
            this.setCreateDataset(true);
            this.setSubmitDataModule(false);
            this.setExtractData(false);
            this.removeData(resword.getString("beginning_date"));
            this.removeData(resword.getString("ending_date"));
            DatasetBean dsb = (DatasetBean) session.getAttribute("newDataset");
            int ev_count = dsb.getItemIds().size();
            this.setData(resword.getString("items_selected"), new Integer(ev_count).toString());
            if ("01/01/1900".equals(english_sdf.format(dsb.getDateStart()))) {
                this.setData(resword.getString("beginning_date"), resword.getString("not_specified"));
            } else {
                this.setData(resword.getString("beginning_date"), local_sdf.format(dsb.getDateStart()));
            }
            if ("12/31/2100".equals(english_sdf.format(dsb.getDateEnd()))) {
                this.setData(resword.getString("ending_date"), resword.getString("not_specified"));
            } else {
                this.setData(resword.getString("ending_date"), local_sdf.format(dsb.getDateEnd()));
            }
            FilterBean fb = (FilterBean) session.getAttribute("newFilter");
            if (fb != null) {
                this.setData("Added Filter", fb.getName());
            }
        } else if (page.equals(Page.APPLY_FILTER)) {
            DatasetBean dsb = (DatasetBean) session.getAttribute("newDataset");
            this.setData(resword.getString("beginning_date"), local_sdf.format(dsb.getDateStart()));
            this.setData(resword.getString("ending_date"), local_sdf.format(dsb.getDateEnd()));
        } else if (page.equals(Page.CONFIRM_DATASET)) {
            this.reset();
            this.setStudyInfoShown(false);
            this.setOrderedData(false);
            this.setCreateDataset(true);
            this.setSubmitDataModule(false);
            this.setExtractData(false);
            DatasetBean dsb = (DatasetBean) session.getAttribute("newDataset");
            this.setData(resword.getString("dataset_name"), dsb.getName());
            this.setData(resword.getString("dataset_description"), dsb.getDescription());
            int ev_count = dsb.getItemIds().size();
            this.setData(resword.getString("items_selected"), new Integer(ev_count).toString());
            if ("01/01/1900".equals(english_sdf.format(dsb.getDateStart()))) {
                this.setData(resword.getString("beginning_date"), resword.getString("not_specified"));
            } else {
                this.setData(resword.getString("beginning_date"), local_sdf.format(dsb.getDateStart()));
            }
            if ("12/31/2100".equals(english_sdf.format(dsb.getDateEnd()))) {
                this.setData(resword.getString("ending_date"), resword.getString("not_specified"));
            } else {
                this.setData(resword.getString("ending_date"), local_sdf.format(dsb.getDateEnd()));
            }
            FilterBean fb = (FilterBean) session.getAttribute("newFilter");
            if (fb != null) {
                this.setData(resword.getString("added_filter"), fb.getName());
            }
        } else if (page.equals(Page.CREATE_FILTER_SCREEN_3_1)) {
            CRFVersionBean cvBean = (CRFVersionBean) session.getAttribute("cvBean");
            this.setData(resword.getString("CRF_version_selected"), cvBean.getName());
        } else if (page.equals(Page.CREATE_FILTER_SCREEN_3_2)) {
            SectionBean secBean = (SectionBean) session.getAttribute("secBean");
            this.setData(resword.getString("section_selected"), secBean.getName());
            Collection metadatas = (Collection) request.getAttribute("metadatas");
            this.setData(resword.getString("number_of_questions"), new Integer(metadatas.size()).toString());
        } else if (page.equals(Page.CREATE_FILTER_SCREEN_4)) {
        } else if (page.equals(Page.CREATE_FILTER_SCREEN_5)) {
        // blank here to prevent data reset, tbh
        } else if (page.equals(Page.ADMIN_SYSTEM)) {
        // blank here , info set in servlet itself
        } else if (page.equals(Page.VIEW_STUDY_SUBJECT) || page.equals(Page.LIST_EVENTS_FOR_SUBJECT)) {
            // special case, unlocks study name, subject name, and
            // visits
            // TODO set all this up, tbh
            /*
                 * set up the side info panel to create the following upon entry
                 * from the ViewStudyServlet Study X Subject Y StudyEventDef Z1
                 * StudyEventDef Z2 <status-tag> CRF A1 <status-tag> CRF A2 Z1
                 * should be collapsible/expandible, etc.
                 *
                 * We can pull things from the session and the request:
                 */
            /*
                 * StudyBean study = (StudyBean) request.getAttribute("study");
                 * StudySubjectBean studySubject = (StudySubjectBean)
                 * request.getAttribute("studySub"); EntityBeanTable table =
                 * (EntityBeanTable) request.getAttribute("table"); EventCRFBean
                 * ecb = (EventCRFBean)request.getAttribute("eventCRF");
                 * this.reset(); ArrayList rows = table.getRows(); ArrayList
                 * beans = DisplayStudyEventBean.generateBeansFromRows(rows);
                 *
                 *
                 * addStudyEventTree(study, studySubject, beans, ecb);
                 */
            // this.setIconInfoShown(false);
            // this.setManageSubject(true);
            this.reset();
            this.setStudyInfoShown(true);
            this.setOrderedData(true);
            this.setExtractData(false);
            this.setSubmitDataModule(false);
            this.setCreateDataset(false);
            this.setIconInfoShown(false);
            this.setManageSubject(true);
            request.setAttribute("showDDEIcon", Boolean.TRUE);
        } else if (page.equals(Page.ENTER_DATA_FOR_STUDY_EVENT) || page.equals(Page.ENTER_DATA_FOR_STUDY_EVENT_SERVLET)) {
            StudyBean study = (StudyBean) session.getAttribute("study");
            StudySubjectBean studySubject = (StudySubjectBean) request.getAttribute("studySubject");
            ArrayList beans = (ArrayList) request.getAttribute("beans");
            EventCRFBean ecb = (EventCRFBean) request.getAttribute("eventCRF");
            this.reset();
            addStudyEventTree(study, studySubject, beans, ecb, true);
            this.setStudyInfoShown(false);
            this.setOrderedData(true);
            this.setSubmitDataModule(true);
            this.setExtractData(false);
            this.setCreateDataset(false);
            this.setIconInfoShown(false);
        } else if (page.equals(Page.INTERVIEWER) || page.equals(Page.TABLE_OF_CONTENTS) || page.equals(Page.TABLE_OF_CONTENTS_SERVLET) || page.equals(Page.INITIAL_DATA_ENTRY) || page.equals(Page.INITIAL_DATA_ENTRY_SERVLET) || page.equals(Page.DOUBLE_DATA_ENTRY) || page.equals(Page.DOUBLE_DATA_ENTRY_SERVLET) || page.equals(Page.ADMIN_EDIT) || page.equals(Page.ADMIN_EDIT_SERVLET)) {
            /*
                 * pages designed to also follow the above format; check to see
                 * if they are in the session already, and does not refresh.
                 * TODO refine and test
                 */
            StudyBean study = (StudyBean) session.getAttribute("study");
            StudySubjectBean studySubject = (StudySubjectBean) request.getAttribute("studySubject");
            ArrayList beans = (ArrayList) request.getAttribute("beans");
            EventCRFBean ecb = (EventCRFBean) request.getAttribute("eventCRF");
            this.reset();
            addStudyEventTree(study, studySubject, beans, ecb, false);
            this.setStudyInfoShown(false);
            this.setOrderedData(true);
            this.setSubmitDataModule(true);
            this.setExtractData(false);
            this.setCreateDataset(false);
            this.setIconInfoShown(true);
        } else if (page.equals(Page.EDIT_DATASET)) {
            this.reset();
            // HashMap eventlist = (HashMap)
            // request.getAttribute("eventlist");
            HashMap eventlist = (LinkedHashMap) session.getAttribute("eventsForCreateDataset");
            ArrayList displayData = generateEventTree(eventlist);
            this.setCreateDataset(true);
            this.setOrderedData(true);
            this.setUserOrderedData(displayData);
            this.setStudyInfoShown(true);
            this.setSubmitDataModule(false);
            this.setExtractData(false);
            DatasetBean dsb = (DatasetBean) request.getAttribute("dataset");
            this.setData(resword.getString("dataset_name"), dsb.getName());
            this.setData(resword.getString("date_created"), local_sdf.format(dsb.getCreatedDate()));
            this.setData(resword.getString("dataset_owner"), dsb.getOwner().getName());
            this.setData(resword.getString("date_last_run"), local_sdf.format(dsb.getDateLastRun()));
        } else if (page.equals(Page.EXPORT_DATASETS)) {
            this.setCreateDataset(false);
        } else if (page.equals(Page.GENERATE_DATASET_HTML)) {
            DatasetBean db = (DatasetBean) request.getAttribute("dataset");
            ExtractBean exbean = (ExtractBean) request.getAttribute("extractBean");
            this.reset();
            ArrayList displayData = new ArrayList();
            displayData = generateDatasetTree(exbean, db);
            this.setUserOrderedData(displayData);
            this.setStudyInfoShown(false);
            this.setOrderedData(true);
            this.setExtractData(true);
            this.setSubmitDataModule(false);
            this.setCreateDataset(false);
        } else if (page.equals(Page.LIST_STUDY_SUBJECT) || page.equals(Page.LIST_STUDY_SUBJECTS) || page.equals(Page.SUBMIT_DATA) || page.equals(Page.SUBMIT_DATA_SERVLET)) {
            this.reset();
            this.setStudyInfoShown(true);
            this.setOrderedData(true);
            this.setExtractData(false);
            this.setSubmitDataModule(false);
            this.setCreateDataset(false);
            this.setIconInfoShown(false);
            this.setManageSubject(true);
            // don't want to show DDE icon key for subject matrix page
            request.setAttribute("showDDEIcon", Boolean.FALSE);
        } else if (page.equals(Page.VIEW_SECTION_DATA_ENTRY) || page.equals(Page.VIEW_SECTION_DATA_ENTRY_SERVLET)) {
            this.reset();
            this.setStudyInfoShown(true);
            this.setOrderedData(true);
            this.setExtractData(false);
            this.setSubmitDataModule(false);
            this.setCreateDataset(false);
            this.setIconInfoShown(true);
            this.setManageSubject(false);
        } else if (page.equals(Page.CREATE_SUBJECT_GROUP_CLASS) || page.equals(Page.CREATE_SUBJECT_GROUP_CLASS_CONFIRM) || page.equals(Page.UPDATE_SUBJECT_GROUP_CLASS) || page.equals(Page.UPDATE_SUBJECT_GROUP_CLASS_CONFIRM)) {
            this.reset();
            this.setStudyInfoShown(true);
            this.setOrderedData(true);
            this.setExtractData(false);
            this.setSubmitDataModule(false);
            this.setCreateDataset(false);
            this.setIconInfoShown(true);
            this.setManageSubject(false);
        } else {
            // automatically reset if we don't know what's happening
            this.reset();
            this.setStudyInfoShown(true);
            this.setOrderedData(true);
            this.setExtractData(false);
            this.setSubmitDataModule(false);
            this.setCreateDataset(false);
            this.setIconInfoShown(true);
            this.setManageSubject(false);
        }
    } catch (Exception e) {
        this.reset();
    }
}

Example 30 with DatasetBean

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

the class SelectItemsServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int crfId = fp.getInt("crfId");
    int defId = fp.getInt("defId");
    int eventAttr = fp.getInt("eventAttr");
    int subAttr = fp.getInt("subAttr");
    int CRFAttr = fp.getInt("CRFAttr");
    int groupAttr = fp.getInt("groupAttr");
    int discAttr = fp.getInt("discAttr");
    CRFDAO crfdao = new CRFDAO(sm.getDataSource());
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    ItemFormMetadataDAO imfdao = new ItemFormMetadataDAO(sm.getDataSource());
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    HashMap events = (HashMap) session.getAttribute(CreateDatasetServlet.EVENTS_FOR_CREATE_DATASET);
    if (events == null) {
        events = new HashMap();
    }
    request.setAttribute("eventlist", events);
    logger.info("found dob setting: " + currentStudy.getStudyParameterConfig().getCollectDob());
    if (crfId == 0) {
        // no crf selected
        if (eventAttr == 0 && subAttr == 0 && CRFAttr == 0 && groupAttr == 0 && discAttr == 0) {
            forwardPage(Page.CREATE_DATASET_2);
        } else if (eventAttr > 0) {
            request.setAttribute("subjectAgeAtEvent", "1");
            if (currentStudy.getStudyParameterConfig().getCollectDob().equals("3")) {
                request.setAttribute("subjectAgeAtEvent", "0");
                logger.info("dob not collected, setting age at event to 0");
            }
            forwardPage(Page.CREATE_DATASET_EVENT_ATTR);
        } else if (subAttr > 0) {
            if (currentStudy.getStudyParameterConfig().getCollectDob().equals("3")) {
                logger.info("dob not collected, setting age at event to 0");
            }
            forwardPage(Page.CREATE_DATASET_SUB_ATTR);
        } else if (CRFAttr > 0) {
            forwardPage(Page.CREATE_DATASET_CRF_ATTR);
        } else if (groupAttr > 0) {
            // TODO set up subject group classes here?
            setUpStudyGroupPage();
            forwardPage(Page.CREATE_DATASET_GROUP_ATTR);
        } else // else if (discAttr > 0) {
        // forwardPage(Page.CREATE_DATASET_DISC_ATTR);
        // }
        {
            forwardPage(Page.CREATE_DATASET_2);
        }
        return;
    }
    CRFBean crf = (CRFBean) crfdao.findByPK(crfId);
    StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(defId);
    session.setAttribute("crf", crf);
    session.setAttribute("definition", sed);
    DatasetBean db = (DatasetBean) session.getAttribute("newDataset");
    if (db == null) {
        db = new DatasetBean();
    }
    session.setAttribute("newDataset", db);
    // save current def id in the seesion to avoid duplicated def id in
    // dataset
    // bean
    // session.setAttribute(CURRENT_DEF_ID, new Integer(defId));
    ArrayList items = idao.findAllActiveByCRF(crf);
    for (int i = 0; i < items.size(); i++) {
        ItemBean item = (ItemBean) items.get(i);
        /*
             * logger.info("testing on item id "+ item.getId()+ " crf version id "+
             * item.getItemMeta().getCrfVersionId());
             */
        ItemFormMetadataBean meta = imfdao.findByItemIdAndCRFVersionId(item.getId(), item.getItemMeta().getCrfVersionId());
        // TODO change the above data access function, tbh
        // ArrayList metas = imfdao.findAllByItemId(item.getId());
        meta.setCrfVersionName(item.getItemMeta().getCrfVersionName());
        // logger.info("crf versionname" + meta.getCrfVersionName());
        item.getItemMetas().add(meta);
    // item.setItemMetas(metas);
    }
    HashMap itemMap = new HashMap();
    for (int i = 0; i < items.size(); i++) {
        ItemBean item = (ItemBean) items.get(i);
        if (!itemMap.containsKey(defId + "_" + item.getId())) {
            if (db.getItemMap().containsKey(defId + "_" + item.getId())) {
                item.setSelected(true);
                item.setDatasetItemMapKey(defId + "_" + item.getId());
            // logger.info("Item got selected already11");
            }
            // itemMap.put(new Integer(item.getId()), item);
            itemMap.put(defId + "_" + item.getId(), item);
        } else {
            // same item,combine the metadata
            ItemBean uniqueItem = (ItemBean) itemMap.get(defId + "_" + item.getId());
            uniqueItem.getItemMetas().add(item.getItemMetas().get(0));
            if (db.getItemMap().containsKey(defId + "_" + uniqueItem.getId())) {
                uniqueItem.setSelected(true);
            // logger.info("Item got selected already22");
            }
        }
    }
    ArrayList itemArray = new ArrayList(itemMap.values());
    // now sort them by ordinal/name
    Collections.sort(itemArray);
    session.setAttribute("allItems", itemArray);
    forwardPage(Page.CREATE_DATASET_2);
}