Example usage for org.hibernate.criterion DetachedCriteria forClass

List of usage examples for org.hibernate.criterion DetachedCriteria forClass

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Introduction

In this page you can find the example usage for org.hibernate.criterion DetachedCriteria forClass.

Prototype

public static DetachedCriteria forClass(Class clazz)

Source Link

Document

Static builder to create a DetachedCriteria for the given entity, by its Class.

Usage

From source file:GCTestClient.java

License:BSD License

/**
 * Use case : Basic Genomic ID Search /*from w  ww . j  a  v a  2 s  . c  o m*/
 * Search on one more attribute within a Gene,MessengerRNA or Protein and 
 * return result from that search as a list of objects of the same class
 *  
 *  Query in this Method:
 *  Search on Gene where ensemblGeneId='ENS2' and get associated MessengerRNA 
 *  and print GenbankAccession.
 *   
 */
static void querySimple() throws Exception {

    /**
     * Create a DetachedCriteria for Gene with ensemblGeneId=ENS2
     */
    DetachedCriteria geneCriteria = DetachedCriteria.forClass(Gene.class);
    geneCriteria.add(Restrictions.eq("ensemblGeneId", "ENS2"));

    List resultList = appService.query(geneCriteria, Gene.class.getName());

    for (Iterator iter1 = resultList.iterator(); iter1.hasNext();) {
        /** get Gene Object form resultList*/
        Gene gene = (Gene) iter1.next();
        System.out.println("EnsemblGeneId : " + gene.getEnsemblGeneId());
        /** get associated mRNAColelction from Gene*/
        Collection coll = gene.getMessengerRNACollection();
        for (Iterator iter = coll.iterator(); iter.hasNext();) {
            MessengerRNA mrna = (MessengerRNA) iter.next();

            /** Print value of GenbankAccession attribute of MessengerRNA object */
            System.out.println("GenbankAccession : " + mrna.getGenbankAccession());
        }
    }

}

From source file:GCTestClient.java

License:BSD License

/**
 * Use case : Query Based on Confidence 
 * Search on one more attribute within a Gene,MessengerRNA or Protein class
 * with a given or higher confidence score (from GenomicIdentifierSet).
 * Traverse the model to get data from the other classes.
 *  /*from w w w  .java  2  s .c  o m*/
 *  Query in this method:
 *  Search on Protein where ensemblGeneId='ENS2' AND unigene,ensemblPeptide as output 
 *  AND confidenceScore > 0.2
 *  Print Set ID,Confidenscore and associated Gene,mRNA values with this Set 
 *  
 */

static void queryConfScore() throws Exception {
    /**
     * Create Detached for GenomicIdentifierSet Object and add restriction on confidence score
     * confidenceScore>0.2
     */
    DetachedCriteria genomicIdSetCriteria = DetachedCriteria.forClass(GenomicIdentifierSet.class);
    genomicIdSetCriteria.add(Restrictions.gt("confidenceScore", new Float("0.1")));

    /**
     * Create Criteria for search on ensemblGeneId = ENS2 AND unigeneAsOutput = true
     * AND ensemblPeptideAsOutput=true
     */

    DetachedCriteria geneCriteria = genomicIdSetCriteria.createCriteria("gene");
    geneCriteria.add(Restrictions.eq("ensemblGeneId", "ENS2"));

    geneCriteria.add(Restrictions.eq("unigeneAsOutput", new Boolean(true)));

    DetachedCriteria proteinCriteria = genomicIdSetCriteria.createCriteria("protein");
    proteinCriteria.add(Restrictions.eq("ensemblPeptideAsOutput", new Boolean(true)));
    /**
     * Execute the Query
     */
    List resultList = appService.query(genomicIdSetCriteria,
            "edu.wustl.geneconnect.domain.GenomicIdentifierSet");
    System.out.println("Result Size: " + resultList.size());
    for (Iterator iter = resultList.iterator(); iter.hasNext();) {

        GenomicIdentifierSet gset = (GenomicIdentifierSet) iter.next();
        /**Print Set Id and Confidence Score*/
        System.out.println(
                "\nSet Id: " + gset.getId() + "  Confidence Score: " + gset.getConfidenceScore() + "\n");
        Gene gene = gset.getGene();
        MessengerRNA mrna = gset.getMessengerRNA();
        Protein protein = gset.getProtein();

        System.out.println("Ensembl Gene ID | UniGene cluster ID | Ensembl Peptide ID");
        System.out.println(gene.getEnsemblGeneId() + "           | " + gene.getUnigeneClusterId()
                + "            | " + protein.getEnsemblPeptideId());

        System.out
                .println("-----------------------------------------------------------------------------------");
    }
}

From source file:GCTestClient.java

License:BSD License

/**
 * @throws Exception/*from ww  w. j a  va  2  s  .c  o  m*/
 */
static void querybyNodeTraversal() throws Exception {
    /*Detached Criteria for GenomicIdentifier Set object*/
    DetachedCriteria genomicIdSetCriteria = DetachedCriteria.forClass(GenomicIdentifierSet.class);

    /**
     * Create criteria for ONT where Set should contain a ONT as 
     * EnsemblGene ---Direct---> Entrez Gene ---Direct---> UniGene
     * and optionally can also specify link type between each data source pair.
     */

    /**
     * Create criteria for ONT as:
     * EnsemblGene ---Direct
     */
    DetachedCriteria ontCrit = genomicIdSetCriteria.createCriteria("orderOfNodeTraversalCollection");
    DetachedCriteria ontCritF = ontCrit.createCriteria("sourceDataSource")
            .add(Restrictions.eq("name", "Ensembl Gene"));
    ontCrit.createCriteria("linkType").add(Restrictions.eq("type", "DIRECT"));

    /**
     * Create criteria for ONT as:
     * EnsemblGene ---Direct---> Entrez Gene ---Direct
     */
    DetachedCriteria ontCritF1 = ontCrit.createCriteria("childOrderOfNodeTraversal");

    ontCritF1.createCriteria("sourceDataSource").add(Restrictions.eq("name", "Entrez Gene"));
    ontCritF1.createCriteria("linkType").add(Restrictions.eq("type", "DIRECT"));

    /**
     * Create criteria for ONT as:
     * EnsemblGene ---Direct---> Entrez Gene ---Direct---> UniGene
     */
    DetachedCriteria ontCritF2 = ontCritF1.createCriteria("childOrderOfNodeTraversal");
    DetachedCriteria ontCritF3 = ontCritF2.createCriteria("sourceDataSource");
    ontCritF3.add(Restrictions.eq("name", "UniGene"));
    ontCritF2.add(Restrictions.isNull("childOrderOfNodeTraversal"));

    /**
     * Create Critria for ensemblTranscriptId = ENST1 AND
     * ensemblGeneAsOutput = true AND ensemblPeptideAsOutput = true
     */
    DetachedCriteria mrnaCriteria = genomicIdSetCriteria.createCriteria("messengerRNA");
    mrnaCriteria.add(Restrictions.eq("ensemblTranscriptId", "ENST1"));

    DetachedCriteria geneCriteria = genomicIdSetCriteria.createCriteria("gene");
    geneCriteria.add(Restrictions.eq("ensemblGeneAsOutput", new Boolean(true)));

    DetachedCriteria proteinCriteria = genomicIdSetCriteria.createCriteria("protein");
    proteinCriteria.add(Restrictions.eq("ensemblPeptideAsOutput", new Boolean(true)));

    // load all GenomicIdentifierSet objects with Gene.entrezgeneID = A1 and ONT A->C->D->B

    List resultList = appService.query(genomicIdSetCriteria,
            "edu.wustl.geneconnect.domain.GenomicIdentifierSet");

    System.out.println("Result Size: " + resultList.size());
    for (Iterator iter = resultList.iterator(); iter.hasNext();) {
        GenomicIdentifierSet gset = (GenomicIdentifierSet) iter.next();
        System.out.println("**************************************************************");
        System.out.println("Set id: " + gset.getId() + "  Confidence Score: " + gset.getConfidenceScore());
        //         System.out.println("Gid: " + gset.getGene().getEntrezgeneID());
        Collection coll = gset.getOrderOfNodeTraversalCollection();

        /*Get and Print the Order of Node Traveersal associated with this GenomicIdentifierSet*/
        System.out.println("________________________________________________________");
        for (Iterator iter1 = coll.iterator(); iter1.hasNext();) {
            System.out.println("ONT Id----DataSource-------LinkType");
            OrderOfNodeTraversal ont = (OrderOfNodeTraversal) iter1.next();

            OrderOfNodeTraversal tempont = ont;
            while (tempont != null) {
                LinkType ltype = tempont.getLinkType();
                String linkType = null;
                if (ltype != null)
                    linkType = ltype.getType();
                System.out.println(tempont.getId() + "----" + tempont.getSourceDataSource().getName() + "------"
                        + linkType);
                OrderOfNodeTraversal nextont = tempont.getChildOrderOfNodeTraversal();
                tempont = nextont;
            }
            System.out.println("________________________________________________________");
        }
        System.out.println("**************************************************************");
    }
}

From source file:GCTestClient.java

License:BSD License

/**
 * Use case : Query By Limiting ID Frequency 
 * Search on one ensemblPeptideId attribute within a Protein 
 * with a given higher frequency (from GenomicIdentifierData) for Entrez Gene 
 * data source.//from   w w  w .  j  a v  a  2s.  c o  m
 *  
 * Display the result contining Genomic IDs and associated Frequency
 *   
 * @throws Exception
 */
public static void queryByLimitingIDFrequency() throws Exception {

    /**
     * Create DetachedCriteria for GenomicIdentifierSet with restriction for confidenceScore >=0.2 
     */
    DetachedCriteria genomicIdSetCriteria = DetachedCriteria.forClass(GenomicIdentifierSet.class);

    /**
     * Create Criteria to search on guven frequency of given data source 
     */

    DetachedCriteria freqCriteria = genomicIdSetCriteria.createCriteria("consensusIdentifierDataCollection");

    freqCriteria.add(Restrictions.gt("frequency", new Float("0.1")));
    freqCriteria.add(Restrictions.gt("frequency", new Float("0.1")));

    /** 
     * The dataSource value should be one of the Data Source Name
     * 
     */
    DetachedCriteria genomicIdCriteria = freqCriteria.createCriteria("genomicIdentifier");

    genomicIdCriteria.add(Restrictions.eq("dataSource", "Ensembl Gene"));
    genomicIdCriteria.add(Restrictions.eq("dataSource", "Entrez Gene"));

    /**
     * Create Criteria for ensemblGene selected as ouput 
     */
    DetachedCriteria geneCriteria = genomicIdSetCriteria.createCriteria("gene");
    geneCriteria.add(Restrictions.eq("ensemblGeneAsOutput", new Boolean(true)));

    /**
     * Create Criteria for search on ensemblPeptideId attribute
     */
    DetachedCriteria proteinCriteria = genomicIdSetCriteria.createCriteria("protein");
    proteinCriteria.add(Restrictions.eq("ensemblPeptideId", "ENSP1"));

    /**
     * Create Criteria for refseqmRNA selected as ouput 
     */
    DetachedCriteria mranCriteria = genomicIdSetCriteria.createCriteria("messengerRNA");
    mranCriteria.add(Restrictions.eq("refseqmRNAAsOutput", new Boolean(true)));

    List resultList = appService.query(genomicIdSetCriteria, GenomicIdentifierSet.class.getName());
    System.out.println("ResultSet Size: " + resultList.size());

    for (Iterator iter = resultList.iterator(); iter.hasNext();) {
        GenomicIdentifierSet gset = (GenomicIdentifierSet) iter.next();
        /*Print Set Id and Confidence Score*/
        System.out.println(
                "\nSet Id: " + gset.getId() + "  Confidence Score: " + gset.getConfidenceScore() + "\n");
        Gene gene = gset.getGene();
        MessengerRNA mrna = gset.getMessengerRNA();
        Protein p = gset.getProtein();

        System.out.println("Ensembl Gene ID | Ensembl Peptide ID | RefSeq mRNA ID");
        System.out.println(gene.getEnsemblGeneId() + "           | " + p.getEnsemblPeptideId()
                + "            | " + mrna.getRefseqId());

        System.out
                .println("-----------------------------------------------------------------------------------");
    }
    /*
     * Print the Genomic identiifer and its frequency throughout the GenomicIdentifierSolution
     */
    System.out.println(
            "Following is  a list of all genomic identifers (occured in this result)and its frequency");
    if (resultList.size() > 0) {
        GenomicIdentifierSet set = (GenomicIdentifierSet) resultList.get(0);

        GenomicIdentifierSolution solution = set.getGenomicIdentifierSolution();
        Collection coll = solution.getConsensusIdentifierDataCollection();
        System.out.println("Genomic Identifer\tFrequency");
        for (Iterator iter1 = coll.iterator(); iter1.hasNext();) {
            //OrderOfNodeTraversal ont = (OrderOfNodeTraversal)iter1.next();
            ConsensusIdentifierData ont = (ConsensusIdentifierData) iter1.next();
            GenomicIdentifier g = ont.getGenomicIdentifier();
            if (g != null)
                System.out.println("\t" + g.getGenomicIdentifier() + "\t\t\t" + ont.getFrequency());
        }
    }
}

From source file:TechGuideExamples.java

License:BSD License

public static void main(String[] args) throws Exception {

    System.out.println("*** Tech Guide Examples");

    ApplicationService appService = ApplicationServiceProvider.getApplicationService();

    /** Examples used in Developer Guide */

    try {//  ww  w .  ja va  2s. c  o  m
        System.out.println("\nExample One: Simple Search (Single Criteria Object)");
        Gene gene = new Gene();
        // searching for all genes whose symbol starts with brca
        gene.setSymbol("brca*");

        List resultList = appService.search(Gene.class, gene);

        for (Iterator resultsIterator = resultList.iterator(); resultsIterator.hasNext();) {
            Gene returnedGene = (Gene) resultsIterator.next();
            System.out.println("Symbol: " + returnedGene.getSymbol() + "\tTaxon:"
                    + returnedGene.getTaxon().getScientificName() + "\tName " + returnedGene.getFullName());
        }
    } catch (RuntimeException e) {
        e.printStackTrace();
    }

    try {
        System.out.println("\nExample Two: Simple Search (Criteria Object Collection)");
        Taxon taxon1 = new Taxon();
        taxon1.setAbbreviation("hs"); // Homo sapiens
        Taxon taxon2 = new Taxon();
        taxon2.setAbbreviation("m"); // Mus musculus
        List<Taxon> taxonList = new ArrayList<Taxon>();
        taxonList.add(taxon1);
        taxonList.add(taxon2);
        List resultList = appService.search(Gene.class, taxonList);
        System.out.println("Total # of records = " + resultList.size());

    } catch (Exception e) {
        e.printStackTrace();
    }

    try {
        System.out.println("\nExample Three: Simple Search (Compound Criteria Object)");
        Taxon taxon = new Taxon();
        taxon.setAbbreviation("hs"); // Homo sapiens
        Gene gene = new Gene();
        gene.setTaxon(taxon);
        gene.setSymbol("IL5"); // Interleukin 5
        List<Gene> geneList = new ArrayList<Gene>();
        geneList.add(gene);
        Pathway pathway = new Pathway();
        pathway.setGeneCollection(geneList);
        List resultList = appService.search("gov.nih.nci.cabio.domain.Pathway", pathway);
        for (Iterator resultsIterator = resultList.iterator(); resultsIterator.hasNext();) {
            Pathway returnedPathway = (Pathway) resultsIterator.next();
            System.out.println("Name: " + returnedPathway.getName() + "\tDisplayValue: "
                    + returnedPathway.getDisplayValue());
        }
    } catch (Exception e) {
        e.printStackTrace();
    }

    try {
        System.out.println("\nExample Four: Nested Search");
        Gene gene = new Gene();
        gene.setSymbol("TP53"); // Tumor protein p53 (Li-Fraumeni syndrome)   
        List resultList = appService
                .search("gov.nih.nci.cabio.domain.ProteinSequence,gov.nih.nci.cabio.domain.Protein", gene);
        for (Iterator resultsIterator = resultList.iterator(); resultsIterator.hasNext();) {
            ProteinSequence returnedProtSeq = (ProteinSequence) resultsIterator.next();
            System.out.println("Id: " + returnedProtSeq.getId() + "\tLength: " + returnedProtSeq.getLength());
        }
    } catch (Exception e) {
        e.printStackTrace();
    }

    try {
        System.out.println("\nExample Five: Detached Criteria Search");
        DetachedCriteria criteria = DetachedCriteria.forClass(PhysicalLocation.class);
        criteria = criteria.add(Restrictions.gt("chromosomalStartPosition", new Long(86851632)));
        criteria = criteria.add(Restrictions.lt("chromosomalEndPosition", new Long(86861632)));
        criteria = criteria.add(Restrictions.ilike("assembly", "reference"));
        criteria = criteria.createCriteria("chromosome").add(Restrictions.eq("number", "1"));
        List resultList = appService.query(criteria);
        System.out.println("Total # of  records = " + resultList.size());
    } catch (Exception e) {
        e.printStackTrace();
    }

    try {
        System.out.println("\nExample Six: HQL Search");
        String hqlString = "FROM gov.nih.nci.cabio.domain.Gene g WHERE g.symbol LIKE ?";
        List<String> params = new ArrayList<String>();
        params.add("BRCA%");
        HQLCriteria hqlC = new HQLCriteria(hqlString, params);
        List resultList = appService.query(hqlC);
        System.out.println("Total # of records = " + resultList.size());
    } catch (Exception e) {
        e.printStackTrace();
    }

}

From source file:TestClientWithTimestamps.java

License:BSD License

/**
 * This example demonstrates the use of Hibernate detached criteria objects
 * to formulate and perform more sophisticated searches. for more
 * information, please consult the Hibernate documentation at
 * http://www.hibernate.org/hib_docs/v3/api/org/hibernate/criterion/DetachedCriteria.html
 *//*from w  w  w. j av a2  s. c om*/
@SuppressWarnings("unused")
private static void searchSNPAnnoation() {
    DetachedCriteria criteria = DetachedCriteria.forClass(SNPAnnotation.class);
    criteria.add(Restrictions.ge("chromosomeLocation", new Integer(4000000)));
    criteria.add(Restrictions.le("chromosomeLocation", new Integer(4200000)));
    criteria.add(Restrictions.eq("chromosomeName", "1"));
    try {
        System.out.println("______________________________________________________________________");
        System.out.println("Retrieving all SNPAnnotations for Chr 1,4000000 - 4200000");
        ApplicationService appService = ApplicationServiceProvider.getApplicationService();

        List resultList = appService.query(criteria, SNPAnnotation.class.getName());
        if (resultList != null) {
            System.out.println("Number of results returned: " + resultList.size());
            System.out.println("DbsnpId" + "\t" + "ChromosomeName" + "\t" + "ChromosomeLocation" + "\t"
                    + "GenomeBuild" + "\t" + "ReferenceSequence" + "\t" + "ReferenceStrand" + "\t"
                    + "GeneBiomarker(s)" + "\n");
            for (Iterator resultsIterator = resultList.iterator(); resultsIterator.hasNext();) {
                SNPAnnotation returnedObj = (SNPAnnotation) resultsIterator.next();
                System.out.println(returnedObj.getDbsnpId() + "\t" + returnedObj.getChromosomeName() + "\t"
                        + returnedObj.getChromosomeLocation() + "\t" + returnedObj.getGenomeBuild() + "\t"
                        + returnedObj.getReferenceSequence() + "\t" + returnedObj.getReferenceStrand() + "\t"
                        + pipeGeneBiomarkers(returnedObj.getGeneBiomarkerCollection()) + "\n");
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:TestClientWithTimestamps.java

License:BSD License

@SuppressWarnings({ "unused", "unchecked" })
private static void searchGeneBiomarker() {
    /*/* ww w  .  j  a  v  a  2  s. c om*/
     * This example demonstrates the use of Hibernate detached criteria
     * objects to formulate and perform more sophisticated searches. A
     * detailed description of detached criteria is beyond the scope of this
     * example; for more information, please consult the Hibernate
     * documentation at
     * http://www.hibernate.org/hib_docs/v3/api/org/hibernate/criterion/DetachedCriteria.html
     */

    DetachedCriteria criteria = DetachedCriteria.forClass(GeneBiomarker.class);
    criteria.add(Restrictions.gt("startPhyscialLocation", new Long(6000000)));
    criteria.add(Restrictions.lt("endPhysicalLocation", new Long(6300000)));
    criteria.add(Restrictions.eq("chromosome", "19"));

    try {
        System.out.println("______________________________________________________________________");
        System.out.println("Retrieving all GeneBiomarker objects for Chr 19,6000000 - 6300000");
        ApplicationService appService = ApplicationServiceProvider.getApplicationService();

        List resultList = appService.query(criteria, GeneBiomarker.class.getName());
        if (resultList != null) {
            System.out.println("Number of results returned: " + resultList.size());
            System.out.println("ChromosomeName" + "\t" + "StartPhyscialLocation" + "\t" + "EndPhysicalLocation"
                    + "\t" + "HugoGeneSymbol" + "\n");
            for (Iterator resultsIterator = resultList.iterator(); resultsIterator.hasNext();) {
                GeneBiomarker returnedObj = (GeneBiomarker) resultsIterator.next();
                System.out.println(returnedObj.getChromosome() + "\t" + returnedObj.getStartPhyscialLocation()
                        + "\t" + returnedObj.getEndPhysicalLocation() + "\t" + returnedObj.getHugoGeneSymbol()
                        + "\n");
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:Example5.java

License:BSD License

private void testSearchSpecimen(ApplicationService appService) {

    DetachedCriteria criteria = DetachedCriteria.forClass(Specimen.class);
    criteria.add(Restrictions.gt("quantity", new Quantity("50")));

    try {//from  w  w w . jav  a  2s  .  com
        List resultList = appService.query(criteria, Specimen.class.getName());

        System.out.println("No of specimens found: " + resultList.size());
        for (Iterator resultsIterator = resultList.iterator(); resultsIterator.hasNext();) {
            Specimen returnedspecimen = (Specimen) resultsIterator.next();
            System.out.println(
                    "Label: " + returnedspecimen.getLabel() + "Type: " + returnedspecimen.getType() + " ");
            System.out.println("\tQuantity: " + returnedspecimen.getQuantity().getValue() + " ");
        }
    } catch (Exception e) {
        System.out.println(e.getMessage());
        e.printStackTrace();
    }
}

From source file:$.UserServiceImpl.java

License:Apache License

public List<User> listUser(User user) {
        DetachedCriteria detachedCriteria = DetachedCriteria.forClass(User.class);
        detachedCriteria.add(Restrictions.eq("user", user));
        detachedCriteria.addOrder(Order.asc("id"));
        return userDao.findByCriteria(detachedCriteria);
    }/* w  w  w .ja v  a 2 s. co m*/

From source file:aplicacion.datos.hibernate.dao.imp.GuiaPrecioDAOImpl.java

public ArrayList<GuiaPrecio> getGuias() {
    DetachedCriteria criteria = DetachedCriteria.forClass(GuiaPrecio.class);
    return (ArrayList) getHibernateTemplate().findByCriteria(criteria);
    //        GuiaPrecio g1 = new GuiaPrecio();
    //        g1.setCodigo(1);
    //        g1.setTipoVehiculo("Moto");
    //        g1.setPrecio(11.4);
    //        resultado.add(g1);
    //        GuiaPrecio g2 = new GuiaPrecio();
    //        g2.setCodigo(2);
    //        g2.setTipoVehiculo("Auto");
    //        g2.setPrecio(25);
    //        resultado.add(g2);
    //return resultado;
}