Example usage for org.hibernate Criteria list

List of usage examples for org.hibernate Criteria list

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In this page you can find the example usage for org.hibernate Criteria list.

Prototype

public List list() throws HibernateException;

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Usage

From source file:au.org.theark.core.dao.StudyDao.java

License:Open Source License

public Collection<BiospecimenField> getAllBiospecimenFields() {
    Criteria criteria = getSession().createCriteria(BiospecimenField.class);
    return criteria.list();
}

From source file:au.org.theark.core.dao.StudyDao.java

License:Open Source License

public Collection<BiocollectionField> getAllBiocollectionFields() {
    Criteria criteria = getSession().createCriteria(BiocollectionField.class);
    return criteria.list();
}

From source file:au.org.theark.core.dao.StudyDao.java

License:Open Source License

public void runSearch(Long searchId, String currentUser) {
    DataExtractionVO allTheData = new DataExtractionVO();
    Search search = (Search) getSession().get(Search.class, searchId);
    if (search == null) {
        // TODO errors and reports
    } else {/*  ww w .  j  a  va2s. co m*/
        //getMaxAddressesForTheseSubjects(null, null); chris doesn't need this right now
        List<DemographicField> addressDFs = getSelectedDemographicFieldsForSearch(search, Entity.Address);
        List<DemographicField> lssDFs = getSelectedDemographicFieldsForSearch(search, Entity.LinkSubjectStudy);
        List<DemographicField> personDFs = getSelectedDemographicFieldsForSearch(search, Entity.Person);
        List<DemographicField> phoneDFs = getSelectedDemographicFieldsForSearch(search, Entity.Phone);
        List<DemographicField> otherIDDFs = getSelectedDemographicFieldsForSearch(search, Entity.OtherID);
        //added on 2015-11-03 include the twin subject uid and the twin type.
        List<DemographicField> twinDetailDFs = getSelectedDemographicFieldsForSearch(search,
                Entity.LinkSubjectTwin);

        List<DemographicField> allSubjectFields = new ArrayList<DemographicField>();
        allSubjectFields.addAll(addressDFs);
        allSubjectFields.addAll(lssDFs);
        allSubjectFields.addAll(personDFs);
        allSubjectFields.addAll(phoneDFs);
        allSubjectFields.addAll(twinDetailDFs);

        List<BiospecimenField> bsfs = getSelectedBiospecimenFieldsForSearch(search);
        List<BiocollectionField> bcfs = getSelectedBiocollectionFieldsForSearch(search);
        List<CustomFieldDisplay> bccfds = getSelectedBiocollectionCustomFieldDisplaysForSearch(search);
        List<CustomFieldDisplay> bscfds = getSelectedBiospecimenCustomFieldDisplaysForSearch(search);
        List<CustomFieldDisplay> scfds = getSelectedSubjectCustomFieldDisplaysForSearch(search);
        List<PhenoDataSetFieldDisplay> pfds = getSelectedPhenoDataSetFieldDisplaysForSearch(search);

        List<ConsentStatusField> consentStatus = (List<ConsentStatusField>) getSelectedConsentStatusFieldsForSearch(
                search);

        /* Making this stuff into an xml document THEN converting it generically to xls/csv/pdf/etc might be an option
         * other options;
         *  1 get each of these and apply a filter every time 
         *  2 a megaquery to get EVERYTHING FOR EVERYONE into our "report/value object/model" 
         *  3 use the filters to create a set of subjectUIDs and maybe apply that, though may also needs a set of pheno_data_id, subj_custom_ids, etc
         */

        //DEMOGRAPHIC FILTERING - but not data
        List<Long> idsAfterFiltering = applyDemographicFilters(search); //from here we need to add 
        log.info("uids afterFilteringdemo=" + idsAfterFiltering.size());

        //CONSENT STATUS FILTERING - still being worked on not complete...but doesn't break anything
        //         List<Long> consentAfterFiltering = 
        if (!idsAfterFiltering.isEmpty()) {
            idsAfterFiltering = applyConsentStatusFilters(allTheData, search, idsAfterFiltering);
        }
        log.info("consent idsAfterFiltering=" + idsAfterFiltering.size());

        //BIOCOLLECTION
        List<Long> bioCollectionIdsAfterFiltering = new ArrayList<Long>();
        if (!idsAfterFiltering.isEmpty()) {
            bioCollectionIdsAfterFiltering = addDataFromMegaBiocollectionQuery(allTheData, bcfs, bccfds, search,
                    idsAfterFiltering, bioCollectionIdsAfterFiltering);
        }
        log.info("uidsafterFiltering doing the construction of megaobject=" + idsAfterFiltering.size());
        log.info("uidsafterFiltering biocol=" + idsAfterFiltering.size());

        //BIOCOL CUSTOM
        if (!idsAfterFiltering.isEmpty()) {
            idsAfterFiltering = applyBioCollectionCustomFilters(allTheData, search, idsAfterFiltering,
                    bioCollectionIdsAfterFiltering); //change will be applied to referenced object
        }
        log.info("uidsafterFiltering biocol cust=" + idsAfterFiltering.size());

        //BIOSPECIMEN
        List<Long> biospecimenIdsAfterFiltering = new ArrayList<Long>();

        if (!idsAfterFiltering.isEmpty()) {
            biospecimenIdsAfterFiltering = addDataFromMegaBiospecimenQuery(allTheData, bsfs, search,
                    idsAfterFiltering, biospecimenIdsAfterFiltering, bioCollectionIdsAfterFiltering);
        }
        log.info("biospecimenIdsAfterFiltering size: " + biospecimenIdsAfterFiltering.size());
        log.info("uidsafterFilteringbiospec=" + idsAfterFiltering.size());

        //BIOSPEC CUSTOM
        if (!idsAfterFiltering.isEmpty()) {
            idsAfterFiltering = applyBiospecimenCustomFilters(allTheData, search, idsAfterFiltering,
                    biospecimenIdsAfterFiltering); //change will be applied to referenced object
        }
        log.info("uidsafterFiltering=Biospec cust" + idsAfterFiltering.size()
                + "biospecimenIdsAfterFiltering custom size: " + biospecimenIdsAfterFiltering.size());

        //PHENO CUSTOM

        if (!idsAfterFiltering.isEmpty()) {
            idsAfterFiltering = applyPhenoDataSetFilters(allTheData, search, idsAfterFiltering); //change will be applied to referenced object
        }
        log.info("uidsafterFiltering pheno cust=" + idsAfterFiltering.size());

        //DEMOGRAPHIC DATA
        idsAfterFiltering = applySubjectCustomFilters(allTheData, search, idsAfterFiltering); //change will be applied to referenced object

        wipeBiospecimenDataNotMatchingThisList(search.getStudy(), allTheData, biospecimenIdsAfterFiltering,
                bioCollectionIdsAfterFiltering, idsAfterFiltering);
        wipeBiocollectionDataNotMatchThisList(search.getStudy(), allTheData, bioCollectionIdsAfterFiltering,
                idsAfterFiltering, biospecimenIdsAfterFiltering, getBiospecimenQueryFilters(search));

        //2015-11-03 include the Twin subject uid with the twin type after the otherIDFs
        addDataFromMegaDemographicQuery(allTheData, personDFs, lssDFs, addressDFs, phoneDFs, otherIDDFs,
                twinDetailDFs, scfds, search, idsAfterFiltering);//This must go last, as the number of joining tables is going to affect performance

        log.info("uidsafterFiltering SUBJECT cust=" + idsAfterFiltering.size());

        Map<Long, Long> maxInputList = new HashMap<Long, Long>();//pass the index and do a max comparison to minimize a simple grid which will be too bulky
        Map<Long, Long> maxOutputList = new HashMap<Long, Long>();
        Long maxProcessesPerPipeline = new Long(0L);
        if (search.getIncludeGeno()) {
            maxProcessesPerPipeline = addGenoData(allTheData, search, idsAfterFiltering, maxInputList,
                    maxOutputList, maxProcessesPerPipeline);//TODO: test
        }
        prettyLoggingOfWhatIsInOurMegaObject(allTheData.getDemographicData(), FieldCategory.DEMOGRAPHIC_FIELD);
        prettyLoggingOfWhatIsInOurMegaObject(allTheData.getSubjectCustomData(), FieldCategory.SUBJECT_CFD);
        prettyLoggingOfWhatIsInOurMegaObject(allTheData.getBiospecimenData(), FieldCategory.BIOSPECIMEN_FIELD);
        prettyLoggingOfWhatIsInOurMegaObject(allTheData.getBiospecimenData(),
                FieldCategory.BIOCOLLECTION_FIELD);
        // prettyLoggingOfWhatIsInOurMegaObject(allTheData.getConsentStatusData(), FieldCategory.CONSENT_STATUS_FIELD);

        // CREATE CSVs - later will offer options xml, pdf, etc
        SearchResult searchResult = new SearchResult();
        searchResult.setSearch(search);
        Criteria criteria = getSession().createCriteria(SearchResult.class);
        criteria.add(Restrictions.eq("search", search));
        List<SearchResult> searchResults = criteria.list();
        for (SearchResult sr : searchResults) {
            deleteSearchResult(sr);
        }

        createSearchResult(search, iDataExtractionDao.createSubjectDemographicCSV(search, allTheData,
                allSubjectFields, scfds, FieldCategory.DEMOGRAPHIC_FIELD), currentUser);
        createSearchResult(search, iDataExtractionDao.createBiocollectionCSV(search, allTheData, bccfds,
                FieldCategory.BIOCOLLECTION_FIELD), currentUser);
        createSearchResult(search, iDataExtractionDao.createBiospecimenCSV(search, allTheData, bsfs, bscfds,
                FieldCategory.BIOSPECIMEN_FIELD), currentUser);
        createSearchResult(search,
                iDataExtractionDao.createPhenotypicCSV(search, allTheData, pfds, FieldCategory.PHENO_FD),
                currentUser);
        if (search.getIncludeGeno()) {
            createSearchResult(search, iDataExtractionDao.createGenoCSV(search, allTheData, FieldCategory.GENO,
                    maxProcessesPerPipeline, maxInputList, maxOutputList), currentUser);
        }
        createSearchResult(search, iDataExtractionDao.createConsentStatusCSV(search, allTheData, consentStatus,
                FieldCategory.CONSENT_STATUS_FIELD), currentUser);
        createSearchResult(search, iDataExtractionDao.createMegaCSV(search, allTheData, allSubjectFields,
                bccfds, bscfds, pfds, consentStatus), currentUser);
        try {
            search.setFinishTime(new java.util.Date(System.currentTimeMillis()));
            search.setStatus("FINISHED");
            update(search);
        } catch (EntityExistsException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
            //TODO don't catch exceptions without doing something - and for that matter we should really start having statuses on our extractions so people can know what happened
            log.error("Error while updating search with finish time.");
        }
    }
}

From source file:au.org.theark.core.dao.StudyDao.java

License:Open Source License

private List<Long> applyConsentStatusFilters(DataExtractionVO allTheData, Search search,
        List<Long> idsToInclude) {

    //for(Long l : idsToInclude) {
    //   log.info("including: " + l);
    //}// w  w  w  .jav a 2 s .  c o m
    boolean hasConsentFilters = false;
    if (search.getQueryFilters().isEmpty()) {
        return idsToInclude;
    } else {
        for (QueryFilter filter : search.getQueryFilters()) {
            if (filter.getConsentStatusField() != null) {
                hasConsentFilters = true;
            }
        }
    }
    Criteria filter = getSession().createCriteria(Consent.class, "c");
    filter.add(Restrictions.eq("c.study.id", search.getStudy().getId()));
    filter.createAlias("c.linkSubjectStudy", "lss");
    if (!idsToInclude.isEmpty()) {
        filter.add(Restrictions.in("lss.id", idsToInclude));
    }
    filter.createAlias("c.studyComponentStatus", "cscs");
    filter.createAlias("c.studyComp", "csc");

    if (!hasConsentFilters) {

        for (QueryFilter qf : search.getQueryFilters()) {
            if (qf.getConsentStatusField() != null) {
                switch (qf.getOperator()) {
                case EQUAL:
                    filter.add(Restrictions.eq(getConsentFilterFieldName(qf), qf.getValue()));
                    break;
                case BETWEEN:
                    filter.add(Restrictions.between(getConsentFilterFieldName(qf), qf.getValue(),
                            qf.getSecondValue()));
                    break;
                case GREATER_THAN:
                    filter.add(Restrictions.gt(getConsentFilterFieldName(qf), qf.getValue()));
                    break;
                case GREATER_THAN_OR_EQUAL:
                    filter.add(Restrictions.ge(getConsentFilterFieldName(qf), qf.getValue()));
                    break;
                case IS_EMPTY:
                    filter.add(Restrictions.isEmpty(getConsentFilterFieldName(qf)));
                    break;
                case IS_NOT_EMPTY:
                    filter.add(Restrictions.isNotEmpty(getConsentFilterFieldName(qf)));
                    break;
                case LESS_THAN:
                    filter.add(Restrictions.lt(getConsentFilterFieldName(qf), qf.getValue()));
                    break;
                case LESS_THAN_OR_EQUAL:
                    filter.add(Restrictions.le(getConsentFilterFieldName(qf), qf.getValue()));
                    break;
                case LIKE:
                    filter.add(Restrictions.like(getConsentFilterFieldName(qf), qf.getValue(),
                            MatchMode.ANYWHERE));
                    break;
                case NOT_EQUAL:
                    filter.add(Restrictions.ne(getConsentFilterFieldName(qf), qf.getValue()));
                    break;
                default:
                    break;
                }
            }
        }
    }
    filter.setProjection(
            Projections.distinct(Projections.projectionList().add(Projections.property("lss.id"))));

    List<Long> consentStatusIDs = filter.list();

    Collection<Consent> csData = Collections.EMPTY_LIST;

    if (!consentStatusIDs.isEmpty()) {
        Criteria consentData = getSession().createCriteria(Consent.class, "c");
        consentData.add(Restrictions.eq("c.study.id", search.getStudy().getId()));
        consentData.createAlias("c.linkSubjectStudy", "lss");
        consentData.add(Restrictions.in("lss.id", consentStatusIDs));
        csData = consentData.list();
    }

    HashMap<String, ExtractionVO> hashOfConsentStatusData = allTheData.getConsentStatusData();

    ExtractionVO valuesForThisLss = new ExtractionVO();
    HashMap<String, String> map = null;
    LinkSubjectStudy previousLss = null;
    int count = 0;
    //will try to order our results and can therefore just compare to last LSS and either add to or create new Extraction VO
    for (Consent data : csData) {
        if (previousLss == null) {
            map = new HashMap<String, String>();
            previousLss = data.getLinkSubjectStudy();
            count = 0;
        } else if (data.getLinkSubjectStudy().getId().equals(previousLss.getId())) {
            //then just put the data in
            count++;
        } else { //if its a new LSS finalize previous map, etc
            valuesForThisLss.setKeyValues(map);
            valuesForThisLss.setSubjectUid(previousLss.getSubjectUID());
            hashOfConsentStatusData.put(previousLss.getSubjectUID(), valuesForThisLss);
            previousLss = data.getLinkSubjectStudy();
            map = new HashMap<String, String>();//reset
            valuesForThisLss = new ExtractionVO();
            count = 0;
        }
        if (data.getStudyComp().getName() != null) {
            map.put(count + "_Study Component Name", data.getStudyComp().getName());
        }
        if (data.getStudyComponentStatus() != null) {
            map.put(count + "_Study Component Status", data.getStudyComponentStatus().getName());
        }
        if (data.getConsentDate() != null) {
            map.put(count + "_Consent Date", data.getConsentDate().toString());
        }
        if (data.getConsentedBy() != null) {
            map.put(count + "_Consented By", data.getConsentedBy());
        }
    }

    //finalize the last entered key value sets/extraction VOs
    if (map != null && previousLss != null) {
        valuesForThisLss.setKeyValues(map);
        valuesForThisLss.setSubjectUid(previousLss.getSubjectUID());
        hashOfConsentStatusData.put(previousLss.getSubjectUID(), valuesForThisLss);
    }

    //can probably now go ahead and add these to the dataVO...even though inevitable further filters may further axe this list or parts of it.
    allTheData.setConsentStatusData(hashOfConsentStatusData);
    if (hasConsentFilters) {
        return consentStatusIDs;
    } else {
        return idsToInclude;
    }
}

From source file:au.org.theark.core.dao.StudyDao.java

License:Open Source License

public List<QueryFilterVO> getQueryFilterVOs(Search search) {
    List<QueryFilterVO> filterVOs = new ArrayList<QueryFilterVO>();
    Criteria criteria = getSession().createCriteria(QueryFilter.class);

    if (search != null && search.getId() != null) {
        criteria.add(Restrictions.eq("search", search));
        List<QueryFilter> filters = criteria.list();

        for (QueryFilter filter : filters) {
            QueryFilterVO filterVO = new QueryFilterVO();
            filterVO.setQueryFilter(filter);
            if (filter.getDemographicField() != null) {
                filterVO.setFieldCategory(FieldCategory.DEMOGRAPHIC_FIELD);
            } else if (filter.getBiocollectionField() != null) {
                filterVO.setFieldCategory(FieldCategory.BIOCOLLECTION_FIELD);
            } else if (filter.getBiospecimenField() != null) {
                filterVO.setFieldCategory(FieldCategory.BIOSPECIMEN_FIELD);
            } else if (filter.getCustomFieldDisplay() != null) {
                filterVO.setFieldCategory(
                        getFieldCategoryFor(filter.getCustomFieldDisplay().getCustomField().getArkFunction()));
            } else if (filter.getConsentStatusField() != null) {
                filterVO.setFieldCategory(FieldCategory.CONSENT_STATUS_FIELD);
            }//from   w  ww  . ja  va2  s.  c  om
            filterVOs.add(filterVO);
        }
    }
    return filterVOs;
}

From source file:au.org.theark.core.dao.StudyDao.java

License:Open Source License

public List<Study> getParentAndChildStudies(Long id) {
    Criteria studyCriteria = getSession().createCriteria(Study.class);
    Study study = getStudy(id);/* w  w  w  .ja v  a  2 s .  c  o  m*/

    if (study.getStudyStatus() != null) {
        studyCriteria.add(Restrictions.eq(Constants.STUDY_STATUS, study.getStudyStatus()));
        try {
            StudyStatus status = getStudyStatus("Archive");
            studyCriteria.add(Restrictions.ne(Constants.STUDY_STATUS, status));
        } catch (StatusNotAvailableException notAvailable) {
            log.error("Cannot look up and filter on archive status. Reference data could be missing");
        }
    } else {
        try {
            StudyStatus status = getStudyStatus("Archive");
            studyCriteria.add(Restrictions.ne(Constants.STUDY_STATUS, status));
        } catch (StatusNotAvailableException notAvailable) {
            log.error("Cannot look up and filter on archive status. Reference data could be missing");
        }

    }

    if (study.getParentStudy() != null && !study.getParentStudy().equals(study)) {
        studyCriteria.add(
                Restrictions.or(Restrictions.idEq(id), Restrictions.eq("parentStudy", study.getParentStudy())));
    } else {
        studyCriteria.add(Restrictions.or(Restrictions.idEq(id), Restrictions.eq("parentStudy", study)));
    }

    studyCriteria.addOrder(Order.asc("id"));
    studyCriteria.addOrder(Order.asc(Constants.STUDY_NAME));
    return studyCriteria.list();
}

From source file:au.org.theark.core.dao.StudyDao.java

License:Open Source License

public List<SearchResult> getSearchResultList(Long searchResultId) {
    Criteria criteria = getSession().createCriteria(SearchResult.class);
    criteria.add(Restrictions.eq("search.id", searchResultId));
    return criteria.list();
}

From source file:au.org.theark.core.dao.StudyDao.java

License:Open Source License

public List<Relationship> getFamilyRelationships() {
    Criteria criteria = getSession().createCriteria(Relationship.class);
    return criteria.list();
}

From source file:au.org.theark.core.dao.StudyDao.java

License:Open Source License

public List<SearchSubject> getSearchSubjects() {
    Criteria criteria = getSession().createCriteria(SearchSubject.class);
    return criteria.list();
}

From source file:au.org.theark.core.dao.StudyDao.java

License:Open Source License

public List<Long> getSubjectIdsforSearch(Search search) {
    Criteria criteria = getSession().createCriteria(SearchSubject.class);
    criteria.add(Restrictions.eq("search", search));
    criteria.setProjection(Projections.property("linkSubjectStudy.id"));
    return criteria.list();
}