Example usage for org.hibernate SessionFactory close

List of usage examples for org.hibernate SessionFactory close

  1. HOME
  2. Java
  3. org.hibernate
  4. org.hibernate.*
  5. SessionFactory
  6. close

Introduction

In this page you can find the example usage for org.hibernate SessionFactory close.

Prototype

void close() throws HibernateException;

Source Link

Document

Destroy this SessionFactory and release all resources (caches, connection pools, etc).

Usage

From source file:ctd.services.addReference.java

License:Apache License

/**
 *
 * @return message/*w  w w  . j  a  v  a2 s.  c o  m*/
 */
public String addReference() {
    String message = "";
    //open hibernate connection
    SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
    Session session = sessionFactory.openSession();

    Query q = session.createQuery("from Ticket where password='" + getPassword() + "'");
    Ticket ticket = (Ticket) q.uniqueResult();

    Iterator it1 = ticket.getStudySampleAssaies().iterator();
    while (it1.hasNext()) {
        StudySampleAssay ssa = (StudySampleAssay) it1.next();
        String name = ssa.getNameRawfile();
        name = name.replace(".CEL", "");
        if (name.equals(getName_RAWFILE())) {
            ssa.setXREF(getReference());
        }
    }

    Transaction tr = session.beginTransaction();
    session.saveOrUpdate(ticket);
    session.persist(ticket);
    tr.commit();
    session.close();
    sessionFactory.close();

    message = getReference() + " is added.";

    return message;
}

From source file:ctd.services.deleteData.java

License:Apache License

public String deleteData() throws NoImplementationException, SerializerException {

    //init parameters
    ResourceBundle res = ResourceBundle.getBundle("settings");
    String webservice_password = res.getString("ws.password");

    DeleteDataResult ddr = new DeleteDataResult();

    if (webservice_password.equals(getWsPassword())) {
        //open hibernate connection
        SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
        Session session = sessionFactory.openSession();

        Query q = session.createQuery("from Ticket where password='" + getPassword() + "'");
        Ticket ticket = (Ticket) q.uniqueResult();

        //if password is incorrect, stop and give error message.
        if (ticket == null) {
            ddr.setErrorMessage("password from this ticket is not found in the database.");
        }//www. j a v a2  s .  c o  m
        //Delete, if ticket is retrieved.
        if (ticket != null) {
            //gather study_sampel_assay_ids to be deleted in the expression table
            Iterator it1 = ticket.getStudySampleAssaies().iterator();
            while (it1.hasNext()) {
                StudySampleAssay ssa = (StudySampleAssay) it1.next();
                Integer id = ssa.getId();
                session.delete(ssa);

            }
            //Delete ticket and its connected samples
            Transaction tx = (Transaction) session.beginTransaction();
            session.delete(ticket);
            tx.commit();
            ddr.setMessage("Data from this ticket is deleted.");
        }
        session.close();
        sessionFactory.close();
    }

    if (webservice_password.equals(getWsPassword()) == false) {
        ddr.setErrorMessage("wrong password for using webservice, change the settings.properties file.");
    }

    ////////////////////
    //SKARINGA
    ObjectTransformer trans = null;
    try {
        trans = ObjectTransformerFactory.getInstance().getImplementation();
    } catch (NoImplementationException ex) {
        Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE, null, ex);
    }
    String text = trans.serializeToString(ddr);
    return text;
}

From source file:ctd.services.getExperimentInfo.java

License:Apache License

public String getExperimentInfo() throws NoImplementationException, SerializerException {
    String message = "";
    ArrayList<AssayInfo> array = new ArrayList<AssayInfo>();

    //open hibernate connection
    SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
    Session session = sessionFactory.openSession();

    Ticket ticket = null;/*from w  w w. ja  v  a 2s .  c o m*/

    Query q1 = session.createQuery("from Ticket where password='" + getPassword() + "'");
    ticket = (Ticket) q1.uniqueResult();

    Iterator it1 = ticket.getStudySampleAssaies().iterator();
    while (it1.hasNext()) {
        AssayInfo ai = new AssayInfo();
        StudySampleAssay ssa = (StudySampleAssay) it1.next();
        String x_ref_name = ssa.getXREF();
        String raw_name = ssa.getNameRawfile();
        Double avg = ssa.getAverage();
        Double std = ssa.getStd();

        ai.setAverage(avg);
        ai.setNameRawfile(raw_name);
        ai.setXREF(x_ref_name);
        ai.setStd(std);

        array.add(ai);
    }
    session.close();
    sessionFactory.close();
    ////////////////////
    //SKARINGA
    ObjectTransformer trans = null;
    try {
        trans = ObjectTransformerFactory.getInstance().getImplementation();
    } catch (NoImplementationException ex) {
        Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE, null, ex);
    }
    message = trans.serializeToString(array);

    return message;
}

From source file:ctd.services.getExpressionByProbeSetId.java

License:Apache License

public String getExpressionByProbeSetId() throws NoImplementationException, SerializerException {

    //init parameters
    ResourceBundle res = ResourceBundle.getBundle("settings");
    String webservice_password = res.getString("ws.password");

    String message = "";
    ArrayList<ProbeSetExpressionInfo> pseia = new ArrayList<ProbeSetExpressionInfo>();

    if (webservice_password.contains(getWsPassword())) {

        //open hibernate connection
        SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
        Session session = sessionFactory.openSession();

        String psi = getProbeSetId();
        SQLQuery q = session.createSQLQuery(
                "Select chip.name,expression.expression,study_sample_assay.X_REF,study_sample_assay.average,study_sample_assay.std,ticket.password FROM chip,chip_annotation,expression,study_sample_assay,ticket WHERE chip.id=chip_annotation.chip_id AND probeset='"
                        + psi//  w  w w  .jav  a  2  s .c om
                        + "' AND chip_annotation.id=expression.chip_annotation_id AND expression.study_sample_assay_id=study_sample_assay.id AND study_sample_assay.ticket_id=ticket.id");

        Iterator it1 = q.list().iterator();
        while (it1.hasNext()) {
            ProbeSetExpressionInfo psei = new ProbeSetExpressionInfo();
            Object[] data = (Object[]) it1.next();
            String chip_name = (String) data[0];
            Double log2value = (Double) data[1];
            String local_accession = (String) data[2];
            Double average = (Double) data[3];
            Double std = (Double) data[4];
            String password = (String) data[5];

            psei.setChipName(chip_name);
            psei.setLog2Value(log2value);
            psei.setLocalAccession(local_accession);
            psei.setSTD(std);
            psei.setAverage(average);
            psei.setTicketPassword(password);

            pseia.add(psei);
        }

        session.close();
        sessionFactory.close();
    }
    ////////////////////
    //SKARINGA
    ObjectTransformer trans = null;
    try {
        trans = ObjectTransformerFactory.getInstance().getImplementation();
    } catch (NoImplementationException ex) {
        Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE, null, ex);
    }
    message = trans.serializeToString(pseia);
    return message;
}

From source file:ctd.services.getExpressionByProbeSetId.java

License:Apache License

public ArrayList<ProbeSetExpressionInfo> getExpressionByProbeSetIdInternal()
        throws NoImplementationException, SerializerException {

    //init parameters
    ResourceBundle res = ResourceBundle.getBundle("settings");
    String webservice_password = res.getString("ws.password");

    String message = "";
    ArrayList<ProbeSetExpressionInfo> pseia = new ArrayList<ProbeSetExpressionInfo>();

    if (webservice_password.contains(getWsPassword())) {

        //open hibernate connection
        SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
        Session session = sessionFactory.openSession();

        String psi = getProbeSetId();
        SQLQuery q = session.createSQLQuery(
                "Select chip.name,expression.expression,study_sample_assay.X_REF,study_sample_assay.average,study_sample_assay.std,ticket.password,ticket.title,ticket.id,study_sample_assay.group_name FROM chip,chip_annotation,expression,study_sample_assay,ticket WHERE chip.id=chip_annotation.chip_id AND probeset='"
                        + psi// ww w  . j  a va  2 s . co  m
                        + "' AND chip_annotation.id=expression.chip_annotation_id AND expression.study_sample_assay_id=study_sample_assay.id AND study_sample_assay.ticket_id=ticket.id ORDER BY study_sample_assay.ticket_id,study_sample_assay.group_name ASC");

        Iterator it1 = q.list().iterator();
        while (it1.hasNext()) {
            ProbeSetExpressionInfo psei = new ProbeSetExpressionInfo();
            Object[] data = (Object[]) it1.next();
            String chip_name = (String) data[0];
            Double log2value = (Double) data[1];
            String local_accession = (String) data[2];
            Double average = (Double) data[3];
            Double std = (Double) data[4];
            String password = (String) data[5];
            String title = (String) data[6];
            Integer ticket_id = (Integer) data[7];
            String group_name = (String) data[8];

            psei.setChipName(chip_name);
            psei.setLog2Value(log2value);
            psei.setLocalAccession(local_accession);
            psei.setSTD(std);
            psei.setAverage(average);
            psei.setTicketPassword(password);
            psei.setTitle(title);
            psei.setGroupName(group_name);
            psei.setTicketId(ticket_id);

            pseia.add(psei);
        }

        session.close();
        sessionFactory.close();
    }

    return pseia;
}

From source file:ctd.services.getJsonExperimentInfo.java

License:Apache License

public String getJsonExperimentInfo() throws NoImplementationException, SerializerException {
    String message = "";
    ArrayList<AssayInfo> array = new ArrayList<AssayInfo>();

    //open hibernate connection
    SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
    Session session = sessionFactory.openSession();

    Ticket ticket = null;/*from  w w w . ja  v a2s .c  om*/

    Query q1 = session.createQuery("from Ticket where password='" + getTicketPassword() + "'");
    ticket = (Ticket) q1.uniqueResult();

    Iterator it1 = ticket.getStudySampleAssaies().iterator();
    while (it1.hasNext()) {
        AssayInfo ai = new AssayInfo();
        StudySampleAssay ssa = (StudySampleAssay) it1.next();
        String x_ref_name = ssa.getXREF();
        String raw_name = ssa.getNameRawfile();
        Double avg = ssa.getAverage();
        Double std = ssa.getStd();

        ai.setAverage(avg);
        ai.setNameRawfile(raw_name);
        ai.setXREF(x_ref_name);
        ai.setStd(std);

        array.add(ai);
    }
    session.close();
    sessionFactory.close();
    ////////////////////
    //SKARINGA
    ObjectTransformer trans = null;
    try {
        trans = ObjectTransformerFactory.getInstance().getImplementation();
    } catch (NoImplementationException ex) {
        Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE, null, ex);
    }
    message = trans.serializeToJsonString(array);

    return message;
}

From source file:ctd.services.getJsonExpressionByProbeSetId.java

License:Apache License

public String getExpressionByProbeSetId() throws NoImplementationException, SerializerException {

    //init parameters
    ResourceBundle res = ResourceBundle.getBundle("settings");
    String webservice_password = res.getString("ws.password");

    String message = "";
    ArrayList<ProbeSetExpressionInfo> pseia = new ArrayList<ProbeSetExpressionInfo>();

    if (webservice_password.contains(getWsPassword())) {

        //open hibernate connection
        SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
        Session session = sessionFactory.openSession();

        String psi = getProbeSetId();
        SQLQuery q = session.createSQLQuery(
                "Select chip.name,expression.expression,study_sample_assay.X_REF,study_sample_assay.average,study_sample_assay.std,ticket.password FROM chip,chip_annotation,expression,study_sample_assay,ticket WHERE chip.id=chip_annotation.chip_id AND probeset='"
                        + psi/*from  w ww.java 2s. co  m*/
                        + "' AND chip_annotation.id=expression.chip_annotation_id AND expression.study_sample_assay_id=study_sample_assay.id AND study_sample_assay.ticket_id=ticket.id");

        Iterator it1 = q.list().iterator();
        while (it1.hasNext()) {
            ProbeSetExpressionInfo psei = new ProbeSetExpressionInfo();
            Object[] data = (Object[]) it1.next();
            String chip_name = (String) data[0];
            Double log2value = (Double) data[1];
            String local_accession = (String) data[2];
            Double average = (Double) data[3];
            Double std = (Double) data[4];
            String password = (String) data[5];

            psei.setChipName(chip_name);
            psei.setLog2Value(log2value);
            psei.setLocalAccession(local_accession);
            psei.setSTD(std);
            psei.setAverage(average);
            psei.setTicketPassword(password);

            pseia.add(psei);
        }

        session.close();
        sessionFactory.close();
    }
    ////////////////////
    //SKARINGA
    ObjectTransformer trans = null;
    try {
        trans = ObjectTransformerFactory.getInstance().getImplementation();
    } catch (NoImplementationException ex) {
        Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE, null, ex);
    }
    message = trans.serializeToJsonString(pseia);
    return message;
}

From source file:ctd.services.getJsonExpressionByProbeSetId.java

License:Apache License

public ArrayList<ProbeSetExpressionInfo> getExpressionByProbeSetIdInternal()
        throws NoImplementationException, SerializerException {

    //init parameters
    ResourceBundle res = ResourceBundle.getBundle("settings");
    String webservice_password = res.getString("ws.password");

    String message = "";
    ArrayList<ProbeSetExpressionInfo> pseia = new ArrayList<ProbeSetExpressionInfo>();

    if (webservice_password.contains(getWsPassword())) {

        //open hibernate connection
        SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
        Session session = sessionFactory.openSession();

        String psi = getProbeSetId();
        SQLQuery q = session.createSQLQuery(
                "Select chip.name,expression.expression,study_sample_assay.X_REF,study_sample_assay.average,study_sample_assay.std,ticket.password FROM chip,chip_annotation,expression,study_sample_assay,ticket WHERE chip.id=chip_annotation.chip_id AND probeset='"
                        + psi/*from   w  w w. jav  a2 s  .co  m*/
                        + "' AND chip_annotation.id=expression.chip_annotation_id AND expression.study_sample_assay_id=study_sample_assay.id AND study_sample_assay.ticket_id=ticket.id ORDER BY study_sample_assay.X_REF ASC");

        Iterator it1 = q.list().iterator();
        while (it1.hasNext()) {
            ProbeSetExpressionInfo psei = new ProbeSetExpressionInfo();
            Object[] data = (Object[]) it1.next();
            String chip_name = (String) data[0];
            Double log2value = (Double) data[1];
            String local_accession = (String) data[2];
            Double average = (Double) data[3];
            Double std = (Double) data[4];
            String password = (String) data[5];

            psei.setChipName(chip_name);
            psei.setLog2Value(log2value);
            psei.setLocalAccession(local_accession);
            psei.setSTD(std);
            psei.setAverage(average);
            psei.setTicketPassword(password);

            pseia.add(psei);
        }

        session.close();
        sessionFactory.close();
    }

    return pseia;
}

From source file:ctd.services.getJsonTicket.java

License:Apache License

public String getTicket() throws SerializerException {

    //init parameters
    ResourceBundle res = ResourceBundle.getBundle("settings");

    String webservice_password = res.getString("ws.password");

    String ftp_folder = res.getString("ws.ftp_folder");
    String prefix_ctd_reference = res.getString("ws.prefix_ticket_reference");
    String prefix_ftp_subfolder = res.getString("ws.prefix_ftp_subfolders");
    String ftp_username = res.getString("ws.ftp_username");
    String group = res.getString("ws.group");
    String hostname = res.getString("ws.hostname");

    TicketClient ticket_client = new TicketClient();
    String new_folder = "";
    String message = "";

    String password_client = getWsPassword();

    if (webservice_password.equals(password_client)) {
        //open hibernate connection
        SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
        Session session = sessionFactory.openSession();
        Transaction tr = session.beginTransaction();

        Integer id = 1;/*from   w ww . jav  a  2  s .  c  o m*/
        SQLQuery q1 = session.createSQLQuery("Select MAX(id) FROM ticket");
        Iterator it1 = q1.list().iterator();
        while (it1.hasNext()) {
            id = (Integer) it1.next();
            if (id != null) {
                id++;
            }
            if (id == null) {
                id = 1;
            }
        }

        ///Get unique password for processing the submitted celfiles
        UUID uuid = null;

        ///check if this uuid is not allready used in this database
        Boolean check = true;
        while (check) {
            uuid = UUID.randomUUID();
            Query q2 = session.createQuery("from Ticket where password='" + uuid.toString() + "'");
            if (q2.list().isEmpty()) {
                check = false;
            }
        }

        //String db_password = password_client+"_"+webservice_password;//uuid.toString();
        String db_password = uuid.toString();
        //ctd reference id
        String ctd_ref = prefix_ctd_reference + String.valueOf(id);
        //ctd ftp subfolder
        String ctd_ftp_folder = prefix_ftp_subfolder + String.valueOf(id);

        //create subdir
        new_folder = ftp_folder + ctd_ftp_folder;
        boolean success = (new File(new_folder)).mkdir();
        //change owner from root to cleandata for this new directory

        //Adjust permissions
        String command1 = "chown " + ftp_username + " " + new_folder;
        String command4 = "chgrp " + group + " " + new_folder;
        String command2 = "chmod 700 " + new_folder;
        String command3 = "chmod +t " + new_folder;

        Process child;
        try {
            child = Runtime.getRuntime().exec(command1);
            child = Runtime.getRuntime().exec(command4);
            child = Runtime.getRuntime().exec(command2);
            child = Runtime.getRuntime().exec(command3);
        } catch (IOException ex) {
            Logger.getLogger(getJsonTicket.class.getName()).log(Level.SEVERE, null, ex);
        }

        //location ftp folder
        String link = "sftp://" + ftp_username + "@" + hostname + ":" + new_folder + "/";
        ticket_client.setLocationFTPFolder(link);

        Ticket ticket = new Ticket();
        ticket.setFolder(ctd_ftp_folder);
        ticket.setPassword(db_password);
        ticket.setCtdRef(ctd_ref);
        ticket.setClosed("no");

        ticket_client.setCtdRef(ctd_ref);
        ticket_client.setFolder(ctd_ftp_folder);
        ticket_client.setPassword(db_password);

        session.save(ticket);
        session.persist(ticket);
        tr.commit();

        session.close();
        sessionFactory.close();
        session = null;
        sessionFactory = null;
    }

    ////////////////////
    //SKARINGA
    ObjectTransformer trans = null;
    try {
        trans = ObjectTransformerFactory.getInstance().getImplementation();
    } catch (NoImplementationException ex) {
        Logger.getLogger(getJsonTicket.class.getName()).log(Level.SEVERE, null, ex);
    }
    message = trans.serializeToJsonString(ticket_client);

    return message;
}

From source file:ctd.services.getMeasurementDataProbeset.java

License:Apache License

public String getMeasurementDataProbeset() throws NoImplementationException, SerializerException {
    //init parameters
    ResourceBundle res = ResourceBundle.getBundle("settings");
    String webservice_password = res.getString("ws.password");

    String message = "";
    ArrayList<ProbeSetExpressionInfo> pseia = new ArrayList<ProbeSetExpressionInfo>();

    if (webservice_password.contains(getWsPassword())) {

        //open hibernate connection
        SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
        Session session = sessionFactory.openSession();

        String psi = getMeasurementToken();
        SQLQuery q = session.createSQLQuery(
                "Select chip.name,expression.expression,study_sample_assay.X_REF,study_sample_assay.average,study_sample_assay.std,ticket.password FROM chip,chip_annotation,expression,study_sample_assay,ticket WHERE chip.id=chip_annotation.chip_id AND probeset='"
                        + psi// www.j av  a2  s  . c  o m
                        + "' AND chip_annotation.id=expression.chip_annotation_id AND expression.study_sample_assay_id=study_sample_assay.id AND study_sample_assay.ticket_id=ticket.id");

        Iterator it1 = q.list().iterator();
        while (it1.hasNext()) {
            ProbeSetExpressionInfo psei = new ProbeSetExpressionInfo();
            Object[] data = (Object[]) it1.next();
            String chip_name = (String) data[0];
            Double log2value = (Double) data[1];
            String local_accession = (String) data[2];
            Double average = (Double) data[3];
            Double std = (Double) data[4];
            String password = (String) data[5];

            psei.setChipName(chip_name);
            psei.setLog2Value(log2value);
            psei.setLocalAccession(local_accession);
            psei.setSTD(std);
            psei.setAverage(average);
            psei.setTicketPassword(password);

            pseia.add(psei);
        }

        session.close();
        sessionFactory.close();
    }
    ////////////////////
    //SKARINGA
    ObjectTransformer trans = null;
    try {
        trans = ObjectTransformerFactory.getInstance().getImplementation();
    } catch (NoImplementationException ex) {
        Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE, null, ex);
    }
    message = trans.serializeToJsonString(pseia);
    return message;
}