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

Example 56 with CRFVersionDAO

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

the class ExtractBean method getMetadata.

/**
 * Implements the Column algorithm in "Dataset Export Algorithms" Must be
 * called after DatasetDAO.getDatasetData();
 */
public void getMetadata() {
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(ds);
    CRFDAO cdao = new CRFDAO(ds);
    CRFVersionDAO cvdao = new CRFVersionDAO(ds);
    ItemDAO idao = new ItemDAO(ds);
    ItemFormMetadataDAO ifmDAO = new ItemFormMetadataDAO(this.ds);
    StudyGroupDAO studygroupDAO = new StudyGroupDAO(ds);
    StudyGroupClassDAO studygroupclassDAO = new StudyGroupClassDAO(ds);
    // SubjectGroupMapDAO subjectGroupMapDAO = new SubjectGroupMapDAO(ds);
    studyGroupClasses = new ArrayList();
    studyGroupMap = new HashMap();
    studyGroupMaps = new HashMap<Integer, ArrayList>();
    sedCrfColumns = new HashMap();
    displayed = new HashMap();
    sedCrfItemFormMetadataBeans = new HashMap();
    studyEvents = seddao.findAllByStudy(study);
    ArrayList finalStudyEvents = new ArrayList();
    if (dataset.isShowSubjectGroupInformation()) {
        // logger.info("found study id for maps: "+study.getId());
        studyGroupMaps = studygroupDAO.findSubjectGroupMaps(study.getId());
        // below is for a given subject; we need a data structure for
        // all subjects
        // studyGroupMap = studygroupDAO.findByStudySubject(currentSubject);
        // problem: can't use currentSubject here, since it's not 'set up'
        // properly
        // how to get the current subject?
        logger.info("found subject group ids: " + dataset.getSubjectGroupIds().toString());
        // studyGroupClasses = dataset.getSubjectGroupIds();
        for (int h = 0; h < dataset.getSubjectGroupIds().size(); h++) {
            Integer groupId = (Integer) dataset.getSubjectGroupIds().get(h);
            StudyGroupClassBean sgclass = (StudyGroupClassBean) studygroupclassDAO.findByPK(groupId.intValue());
            // logger.info();
            // hmm how to link groups to subjects though? only through
            // subject group map
            logger.info("found a studygroupclass bean: " + sgclass.getName());
            studyGroupClasses.add(sgclass);
        }
    }
    for (int i = 0; i < studyEvents.size(); i++) {
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) studyEvents.get(i);
        if (!selectedSED(sed)) {
            continue;
        }
        ArrayList CRFs = (ArrayList) cdao.findAllActiveByDefinition(sed);
        ArrayList CRFsDisplayedInThisSED = new ArrayList();
        for (int j = 0; j < CRFs.size(); j++) {
            CRFBean cb = (CRFBean) CRFs.get(j);
            if (!selectedSEDCRF(sed, cb)) {
                continue;
            } else {
                CRFsDisplayedInThisSED.add(cb);
                ArrayList CRFVersions = cvdao.findAllByCRFId(cb.getId());
                for (int k = 0; k < CRFVersions.size(); k++) {
                    CRFVersionBean cvb = (CRFVersionBean) CRFVersions.get(k);
                    ArrayList Items = idao.findAllItemsByVersionId(cvb.getId());
                    // sort by ordinal/name
                    Collections.sort(Items);
                    for (int l = 0; l < Items.size(); l++) {
                        ItemBean ib = (ItemBean) Items.get(l);
                        if (selected(ib) && !getDisplayed(sed, cb, ib)) {
                            // logger.info("found at
                            // itemformmetadatadao: "+ib.getId()+",
                            // "+cvb.getId());
                            ItemFormMetadataBean ifmb = ifmDAO.findByItemIdAndCRFVersionId(ib.getId(), cvb.getId());
                            addColumn(sed, cb, ib);
                            addItemFormMetadataBeans(sed, cb, ifmb);
                            markDisplayed(sed, cb, ib);
                        }
                    }
                }
            }
        // else
        }
        // for
        sed.setCrfs(CRFsDisplayedInThisSED);
        // make the setCrfs call "stick"
        finalStudyEvents.add(sed);
    }
    this.studyEvents = finalStudyEvents;
}

Example 57 with CRFVersionDAO

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

the class DeleteCRFVersionServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int versionId = fp.getInt(VERSION_ID, true);
    String action = request.getParameter("action");
    if (versionId == 0) {
        addPageMessage(respage.getString("please_choose_a_CRF_version_to_delete"));
        forwardPage(Page.CRF_LIST_SERVLET);
    } else {
        CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
        CRFDAO cdao = new CRFDAO(sm.getDataSource());
        EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
        StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource());
        StudyEventDAO seDao = new StudyEventDAO(sm.getDataSource());
        ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
        EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
        StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
        CRFVersionBean version = (CRFVersionBean) cvdao.findByPK(versionId);
        // find definitions using this version
        ArrayList definitions = edcdao.findByDefaultVersion(version.getId());
        for (Object edcBean : definitions) {
            StudyEventDefinitionBean sedBean = (StudyEventDefinitionBean) sedDao.findByPK(((EventDefinitionCRFBean) edcBean).getStudyEventDefinitionId());
            ((EventDefinitionCRFBean) edcBean).setEventName(sedBean.getName());
        }
        // find event crfs using this version
        ArrayList<ItemDataBean> idBeans = iddao.findByCRFVersion(version);
        ArrayList<EventCRFBean> eCRFs = ecdao.findAllByCRF(version.getCrfId());
        for (EventCRFBean eCRF : eCRFs) {
            StudySubjectBean ssBean = (StudySubjectBean) ssdao.findByPK(eCRF.getStudySubjectId());
            eCRF.setStudySubject(ssBean);
            StudyEventBean seBean = (StudyEventBean) seDao.findByPK(eCRF.getStudyEventId());
            StudyEventDefinitionBean sedBean = (StudyEventDefinitionBean) sedDao.findByPK(seBean.getStudyEventDefinitionId());
            seBean.setStudyEventDefinition(sedBean);
            eCRF.setStudyEvent(seBean);
        }
        ArrayList eventCRFs = ecdao.findAllByCRFVersion(versionId);
        boolean canDelete = true;
        if (!definitions.isEmpty()) {
            // used in definition
            canDelete = false;
            request.setAttribute("definitions", definitions);
            addPageMessage(respage.getString("this_CRF_version") + " " + version.getName() + respage.getString("has_associated_study_events_definitions_cannot_delete"));
        } else if (!idBeans.isEmpty()) {
            canDelete = false;
            request.setAttribute("eventCRFs", eCRFs);
            request.setAttribute("itemDataForVersion", idBeans);
            addPageMessage(respage.getString("this_CRF_version") + " " + version.getName() + respage.getString("has_associated_item_data_cannot_delete"));
        } else if (!eventCRFs.isEmpty()) {
            canDelete = false;
            request.setAttribute("eventsForVersion", eventCRFs);
            addPageMessage(respage.getString("this_CRF_version") + " " + version.getName() + respage.getString("has_associated_study_events_cannot_delete"));
        }
        if ("confirm".equalsIgnoreCase(action)) {
            request.setAttribute(VERSION_TO_DELETE, version);
            forwardPage(Page.DELETE_CRF_VERSION);
        } else {
            // submit
            if (canDelete) {
                ArrayList items = cvdao.findNotSharedItemsByVersion(versionId);
                NewCRFBean nib = new NewCRFBean(sm.getDataSource(), version.getCrfId());
                nib.setDeleteQueries(cvdao.generateDeleteQueries(versionId, items));
                nib.deleteFromDB();
                addPageMessage(respage.getString("the_CRF_version_has_been_deleted_succesfully"));
            } else {
                addPageMessage(respage.getString("the_CRF_version_cannot_be_deleted"));
            }
            forwardPage(Page.CRF_LIST_SERVLET);
        }
    }
}

Example 58 with CRFVersionDAO

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

the class CreateCRFVersionServlet method canDeleteVersion.

/**
 * Checks whether the version can be deleted
 *
 * @param previousVersionId
 * @return
 */
private boolean canDeleteVersion(int previousVersionId) {
    CRFVersionDAO cdao = new CRFVersionDAO(sm.getDataSource());
    ArrayList items = null;
    ArrayList itemsHaveData = new ArrayList();
    // boolean isItemUsedByOtherVersion =
    // cdao.isItemUsedByOtherVersion(previousVersionId);
    // if (isItemUsedByOtherVersion) {
    // ArrayList itemsUsedByOtherVersion = (ArrayList)
    // cdao.findItemUsedByOtherVersion(previousVersionId);
    // session.setAttribute("itemsUsedByOtherVersion",itemsUsedByOtherVersion);
    // return false;
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    ArrayList events = ecdao.findAllByCRFVersion(previousVersionId);
    if (!events.isEmpty()) {
        session.setAttribute("eventsForVersion", events);
        return false;
    }
    items = cdao.findNotSharedItemsByVersion(previousVersionId);
    for (int i = 0; i < items.size(); i++) {
        ItemBean item = (ItemBean) items.get(i);
        if (ub.getId() != item.getOwner().getId()) {
            logger.debug("not owner" + item.getOwner().getId() + "<>" + ub.getId());
            return false;
        }
        if (cdao.hasItemData(item.getId())) {
            itemsHaveData.add(item);
            logger.debug("item has data");
            session.setAttribute("itemsHaveData", itemsHaveData);
            return false;
        }
    }
    // user is the owner and item not have data,
    // delete previous version with non-shared items
    NewCRFBean nib = (NewCRFBean) session.getAttribute("nib");
    nib.setDeleteQueries(cdao.generateDeleteQueries(previousVersionId, items));
    session.setAttribute("nib", nib);
    return true;
}

Example 59 with CRFVersionDAO

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

the class StudySubjectServiceImpl method getDisplayStudyEventsForStudySubject.

@Override
@SuppressWarnings({ "unchecked", "rawtypes" })
public List<DisplayStudyEventBean> getDisplayStudyEventsForStudySubject(StudySubjectBean studySubject, UserAccountBean userAccount, StudyUserRoleBean currentRole) {
    StudyEventDAO studyEventDao = new StudyEventDAO(dataSource);
    StudyEventDefinitionDAO studyEventDefinitionDao = new StudyEventDefinitionDAO(dataSource);
    StudyDAO studyDao = new StudyDAO(dataSource);
    EventDefinitionCRFDAO eventDefinitionCrfDao = new EventDefinitionCRFDAO(dataSource);
    EventCRFDAO eventCrfDao = new EventCRFDAO(dataSource);
    CRFDAO crfDao = new CRFDAO(dataSource);
    CRFVersionDAO crfVersionDao = new CRFVersionDAO(dataSource);
    ArrayList events = studyEventDao.findAllByStudySubject(studySubject);
    Map<Integer, StudyEventDefinitionBean> eventDefinitionByEvent = studyEventDefinitionDao.findByStudySubject(studySubject.getId());
    StudyBean study = (StudyBean) studyDao.findByPK(studySubject.getStudyId());
    Map<Integer, SortedSet<EventDefinitionCRFBean>> eventDefinitionCrfByStudyEventDefinition;
    if (study.getParentStudyId() < 1) {
        // Is a study
        eventDefinitionCrfByStudyEventDefinition = eventDefinitionCrfDao.buildEventDefinitionCRFListByStudyEventDefinitionForStudy(studySubject.getId());
    } else {
        // Is a site
        eventDefinitionCrfByStudyEventDefinition = eventDefinitionCrfDao.buildEventDefinitionCRFListByStudyEventDefinition(studySubject.getId(), study.getId(), study.getParentStudyId());
    }
    Map<Integer, SortedSet<EventCRFBean>> eventCrfListByStudyEvent = eventCrfDao.buildEventCrfListByStudyEvent(studySubject.getId());
    Map<Integer, Integer> maxOrdinalByStudyEvent = studyEventDefinitionDao.buildMaxOrdinalByStudyEvent(studySubject.getId());
    Set<Integer> nonEmptyEventCrf = eventCrfDao.buildNonEmptyEventCrfIds(studySubject.getId());
    Map<Integer, CRFVersionBean> crfVersionById = crfVersionDao.buildCrfVersionById(studySubject.getId());
    Map<Integer, CRFBean> crfById = crfDao.buildCrfById(studySubject.getId());
    ArrayList<DisplayStudyEventBean> displayEvents = new ArrayList<DisplayStudyEventBean>();
    for (int i = 0; i < events.size(); i++) {
        StudyEventBean event = (StudyEventBean) events.get(i);
        StudyEventDefinitionBean sed = eventDefinitionByEvent.get(event.getStudyEventDefinitionId());
        event.setStudyEventDefinition(sed);
        List eventDefinitionCRFs = new ArrayList((eventDefinitionCrfByStudyEventDefinition.containsKey(sed.getId()) ? eventDefinitionCrfByStudyEventDefinition.get(sed.getId()) : Collections.EMPTY_LIST));
        List eventCRFs = new ArrayList((eventCrfListByStudyEvent.containsKey(event.getId())) ? eventCrfListByStudyEvent.get(event.getId()) : Collections.EMPTY_LIST);
        // construct info needed on view study event page
        DisplayStudyEventBean de = new DisplayStudyEventBean();
        de.setStudyEvent(event);
        de.setDisplayEventCRFs((ArrayList<DisplayEventCRFBean>) getDisplayEventCRFs(eventCRFs, userAccount, currentRole, event.getSubjectEventStatus(), study, nonEmptyEventCrf, crfVersionById, crfById, event.getStudyEventDefinitionId(), eventDefinitionCRFs));
        ArrayList<DisplayEventDefinitionCRFBean> al = getUncompletedCRFs(eventDefinitionCRFs, eventCRFs, event.getSubjectEventStatus(), nonEmptyEventCrf, crfVersionById, crfById);
        populateUncompletedCRFsWithCRFAndVersions(al, crfVersionById, crfById);
        de.setUncompletedCRFs(al);
        // de.setMaximumSampleOrdinal(studyEventDao.getMaxSampleOrdinal(sed,
        // studySubject));
        de.setMaximumSampleOrdinal(maxOrdinalByStudyEvent.get(event.getStudyEventDefinitionId()));
        displayEvents.add(de);
    // event.setEventCRFs(createAllEventCRFs(eventCRFs,
    // eventDefinitionCRFs));
    }
    return displayEvents;
}

Example 60 with CRFVersionDAO

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

the class ViewItemDetailServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int itemId = fp.getInt(ITEM_ID);
    String itemOid = fp.getString(ITEM_OID);
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
    ItemGroupMetadataDAO igmdao = new ItemGroupMetadataDAO(sm.getDataSource());
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    CRFDAO cdao = new CRFDAO(sm.getDataSource());
    SectionDAO sectionDao = new SectionDAO(sm.getDataSource());
    if (itemId == 0 && itemOid == null) {
        addPageMessage(respage.getString("please_choose_an_item_first"));
        forwardPage(Page.ITEM_DETAIL);
        return;
    }
    ItemBean item = itemId > 0 ? (ItemBean) idao.findByPK(itemId) : (ItemBean) idao.findByOid(itemOid).get(0);
    ArrayList versions = idao.findAllVersionsByItemId(item.getId());
    ArrayList versionItems = new ArrayList();
    CRFBean crf = null;
    ItemFormMetadataBean imfBean = null;
    // finds each item metadata for each version
    for (int i = 0; i < versions.size(); i++) {
        Integer versionId = (Integer) versions.get(i);
        CRFVersionBean version = (CRFVersionBean) cvdao.findByPK(versionId.intValue());
        if (versionId != null && versionId.intValue() > 0) {
            // YW 08-22-2007
            if (igmdao.versionIncluded(versionId)) {
                imfBean = ifmdao.findByItemIdAndCRFVersionId(item.getId(), versionId.intValue());
                imfBean.setCrfVersionName(version.getName());
                crf = (CRFBean) cdao.findByPK(version.getCrfId());
                imfBean.setCrfName(crf.getName());
                versionItems.add(imfBean);
            } else {
                imfBean = ifmdao.findByItemIdAndCRFVersionIdNotInIGM(item.getId(), versionId.intValue());
                imfBean.setCrfVersionName(version.getName());
                crf = (CRFBean) cdao.findByPK(version.getCrfId());
                imfBean.setCrfName(crf.getName());
                versionItems.add(imfBean);
            }
        }
    }
    SectionBean section = (SectionBean) sectionDao.findByPK(imfBean.getSectionId());
    request.setAttribute(VERSION_ITEMS, versionItems);
    request.setAttribute(ITEM_BEAN, item);
    request.setAttribute("crf", crf);
    request.setAttribute("section", section);
    request.setAttribute("ifmdBean", imfBean);
    forwardPage(Page.ITEM_DETAIL);
}