gov.nih.nci.caintegrator.studyQueryService.germline.FindingsHandler.java Source code

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Here is the source code for gov.nih.nci.caintegrator.studyQueryService.germline.FindingsHandler.java

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/*L
 *  Copyright SAIC
 *
 *  Distributed under the OSI-approved BSD 3-Clause License.
 *  See http://ncip.github.com/stats-analysis/LICENSE.txt for details.
 */

package gov.nih.nci.caintegrator.studyQueryService.germline;

import gov.nih.nci.caintegrator.domain.annotation.snp.bean.SNPAnnotation;
import gov.nih.nci.caintegrator.domain.finding.bean.Finding;
import gov.nih.nci.caintegrator.studyQueryService.dto.FindingCriteriaDTO;
import gov.nih.nci.caintegrator.studyQueryService.dto.annotation.AnnotationCriteria;
import gov.nih.nci.caintegrator.util.HibernateUtil;

import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.hibernate.Session;
import org.hibernate.SessionFactory;

/**
 * Author: Ram Bhattaru
 * Date:   Jul 5, 2006
 * Time:   2:34:18 PM
 */
abstract public class FindingsHandler extends BatchFindingsHandler {

    private SessionFactory sessionFactory;
    protected static final String TARGET_FINDING_ALIAS = " finding";

    protected abstract Class getTargeFindingType();

    protected abstract StringBuffer getTargetFindingHQL();

    protected abstract void initializeProxies(Collection<? extends Finding> findings, Session session);

    protected abstract Collection<? extends Finding> executeFindingSetQuery(FindingCriteriaDTO critDTO,
            StringBuffer targetHQL, Session session, int start, int end) throws Exception;

    public Collection<? extends Finding> getFindings(FindingCriteriaDTO critDTO, int fromIndex, int toIndex)
            throws Exception {
        Collection<? extends Finding> findings;
        Session session = getSessionFactory().getCurrentSession();
        StringBuffer targetHQL = getTargetFindingHQL();
        findings = executeFindingSetQuery(critDTO, targetHQL, session, fromIndex, toIndex);
        initializeProxies(findings, session);
        session.clear();
        return findings;
    }

    protected Collection<? extends Finding> getMyFindings(FindingCriteriaDTO critDTO, Session session,
            int startIndex, int endIndex) throws Exception {
        StringBuffer targetHQL = getTargetFindingHQL();
        Collection<? extends Finding> findings = executeFindingSetQuery(critDTO, targetHQL, session, startIndex,
                endIndex);
        return findings;
    }

    protected void appendAnnotationCritHQL(FindingCriteriaDTO critDTO, HashMap params, StringBuffer snpAnnotCond)
            throws Exception {
        if (critDTO.getAnnotationCriteria() != null) {
            StringBuffer annotJoin = SNPAnnotationCriteriaHandler
                    .getAnnotHQLWithParams(critDTO.getAnnotationCriteria(), params);
            snpAnnotCond
                    .append(TARGET_FINDING_ALIAS + ".snpAnnotation.id IN ( " + annotJoin.toString() + " ) AND ");
        }
    }

    public void getFindingForFTP(FindingCriteriaDTO critDTO, List toBePopulated) throws Exception {
        Session session = getSessionFactory().getCurrentSession();
        Collection findings;
        int start = 0;
        int end = BATCH_OBJECT_INCREMENT;
        Set toBeSent;
        do {
            findings = getMyFindings(critDTO, session, start, end);
            initializeProxies(findings, session);
            toBeSent = new HashSet();
            toBeSent.addAll(findings);
            process(toBePopulated, toBeSent, session);
            start += BATCH_OBJECT_INCREMENT;
            end += BATCH_OBJECT_INCREMENT;
            ;
        } while (findings.size() >= BATCH_OBJECT_INCREMENT);

        /* send empty data object to let the client know that no more results are present */
        process(toBePopulated, getConcreteTypedFindingSet(), session);
        return;
    }

    public List<SNPAnnotation> getSNPAnnotations(AnnotationCriteria annotCrit) throws Exception {
        List<SNPAnnotation> snpAnnotationObjs;
        Session session = getSessionFactory().getCurrentSession();
        /*  TODO: refer to the below method implementation  */
        snpAnnotationObjs = SNPAnnotationCriteriaHandler.getSNPAnnotations(annotCrit, session);
        return snpAnnotationObjs;
    }

    protected boolean isOnlyPanelCriteria(AnnotationCriteria annotCrit) {
        if ((annotCrit.getGeneSymbols() == null) && (annotCrit.getPhysicalPositionCriteria() == null)
                && (annotCrit.getSnpIdentifiers() == null) && (annotCrit.getPanelCriteria() != null))
            return true;
        else
            return false;
    }

    public SessionFactory getSessionFactory() {
        return sessionFactory;
    }

    public void setSessionFactory(SessionFactory sessionFactory) {
        this.sessionFactory = sessionFactory;
    }

}