Example usage for org.hibernate Session persist

List of usage examples for org.hibernate Session persist

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Introduction

In this page you can find the example usage for org.hibernate Session persist.

Prototype

void persist(Object object);

Source Link

Document

Make a transient instance persistent.

Usage

From source file:cs544.blog.dao.UserDAOHibernate.java

@Override
public void saveUser(User user) {
    Session session = sessionFactory.getCurrentSession();
    session.persist(user);

}

From source file:cs544.blog.dao.UserDAOHibernate.java

@Override
public void updateUser(User user) {
    Session session = sessionFactory.getCurrentSession();
    // session.update(user);
    User userExisted = loadUser(user.getId());
    //        Session session = sessionFactory.getCurrentSession();
    if (userExisted != null) {
        session.delete(userExisted);/*w w w  .  j  ava  2 s  .  c om*/
        session.persist(user);
    }
    //saveUser(user);
}

From source file:cs544.exercise02_1.AppBook.java

public static void main(String[] args) {
    // Hibernate placeholders
    Session session = null;
    Transaction tx = null;/*ww w .ja va 2s  . c  om*/

    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();

        // Create new instance of Book and set values in it
        Book book1 = new Book("Spring in Action", "8574524578451", "Rob Jhonshon", 54.21, new Date());
        // save the book1
        session.persist(book1);

        // Create new instance of Book2 and set values in it
        Book book2 = new Book("Expert in Spring", "3434524578451", "Habibur Rahman", 74.21, new Date());
        // save the book1
        session.persist(book2);

        // Create new instance of Book3 and set values in it
        Book book3 = new Book("Spring in Spring", "533524578451", "Amit Jhonshon", 44.21, new Date());
        // save the book1
        session.persist(book3);
        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

    //retrieve book list from db
    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();

        // retieve all books
        @SuppressWarnings("unchecked")
        List<Book> bookList = session.createQuery("from Book").list();
        for (Book book : bookList) {
            System.out.println(
                    "name= " + book.getTitle() + ", ISBN= " + book.getISBN() + ", author= " + book.getAuthor());
        }
        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

    //retrieve one book list from db
    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();

        // retieve all books
        @SuppressWarnings("unchecked")

        Book book = (Book) session.get(Book.class, 1);

        System.out.println(
                "name= " + book.getTitle() + ", ISBN= " + book.getISBN() + ", author= " + book.getAuthor());

        //set new author name for book id 1
        book.setAuthor("Masudur Rahman");

        //update new book attribute
        session.update(book);

        //retrive one book again and will delete
        Book bookInstance = (Book) session.load(Book.class, 3);

        //remove data from database
        session.delete(bookInstance);

        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

    //retrieve book list from db
    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();

        // retieve all books
        @SuppressWarnings("unchecked")
        List<Book> bookList = session.createQuery("from Book").list();
        for (Book book : bookList) {
            System.out.println(
                    "name= " + book.getTitle() + ", ISBN= " + book.getISBN() + ", author= " + book.getAuthor());
        }
        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

    // Close the SessionFactory (not mandatory)
    sessionFactory.close();
    System.exit(0);
}

From source file:cs544.exercise03_1.AppOwner.java

public static void main(String[] args) {
    // Hibernate placeholders
    Session session = null;
    Transaction tx = null;/*from  ww  w . ja v a  2 s . c om*/

    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();

        // Create new instance of Object and set values in it
        Owner owner = new Owner("Masudur Rahman", "Fairfield, IA");
        session.persist(owner);

        Owner owner2 = new Owner("Fahim Muntasir", "Dhaka, BD");

        session.persist(owner2);
        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

    //retrieve book list from db
    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();

        // retieve all books
        @SuppressWarnings("unchecked")
        List<Owner> ownerList = session.createQuery("from Owner").list();
        for (Owner owner : ownerList) {
            System.out.println("name= " + owner.getName() + ", address= " + owner.getAddress());
        }
        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

}

From source file:cs544.exercise04_1.AppEmployee.java

public static void main(String[] args) {
    // Hibernate placeholders
    Session session = null;
    Transaction tx = null;// w ww  . ja  va2s  .  com

    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();

        // Create new instance of Object and set values in it
        Laptop laptop1 = new Laptop("Sonny", "VAIO");
        Laptop laptop2 = new Laptop("Dell", "INSPIRON");

        Set<Laptop> laptops = new HashSet<Laptop>();

        laptops.add(laptop1);
        laptops.add(laptop2);

        Employee employee = new Employee("Fahim", "Muntasir");
        laptop1.setEmployee(employee);
        laptop2.setEmployee(employee);
        employee.setLaptop(laptops);
        session.persist(employee);
        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

    //retrieve book list from db
    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();

        // retieve all books
        @SuppressWarnings("unchecked")
        List<Employee> employeeList = session.createQuery("from Employee").list();
        for (Employee empployee : employeeList) {
            System.out.println(
                    "FirstName= " + empployee.getFirstname() + ", lastName= " + empployee.getLastname());
        }

        List<Laptop> laptopList = session.createQuery("from Laptop").list();
        for (Laptop laptop : laptopList) {
            System.out.println("Brand= " + laptop.getBrand() + ", Type= " + laptop.getType());
        }

        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

}

From source file:cs544.exercise04_1.AppPassenger.java

public static void main(String[] args) {
    // Hibernate placeholders
    Session session = null;
    Transaction tx = null;/*w w w  . j  a  v  a2 s  .  c  o m*/

    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();

        // Create new instance of Object and set values in it
        Flight flight1 = new Flight("FL001", new Date(), new Date(), new Date());
        Flight flight2 = new Flight("FL002", new Date(), new Date(), new Date());

        List<Flight> flights = new ArrayList<Flight>();

        flights.add(flight1);
        flights.add(flight2);

        Passenger passenger = new Passenger("Masudur Rahman");
        passenger.setFlights(flights);

        session.persist(passenger);
        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

    //retrieve book list from db
    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();

        // retieve all books
        @SuppressWarnings("unchecked")
        List<Passenger> passList = session.createQuery("from Passenger").list();
        for (Passenger pass : passList) {
            System.out.println("Name= " + pass.getName());
        }

        List<Flight> flList = session.createQuery("from Flight").list();
        for (Flight fl : flList) {
            System.out.println("No= " + fl.getFlightnumber() + ", from= " + fl.getFrom() + " To= " + fl.getTo()
                    + ", date= " + fl.getDate());
        }

        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

}

From source file:cs544.exercise04_1.AppSchool.java

public static void main(String[] args) {
    // Hibernate placeholders
    Session session = null;
    Transaction tx = null;/*from w  w  w . j  a  v  a 2  s  .  c o  m*/

    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();
        School school = new School("Maharishi University");
        // Create new instance of Object and set values in it

        Student st1 = new Student("Masudur", "Rahman");
        Student st2 = new Student("Habibur", "Rahman");

        Map<Integer, Student> studentMap = new HashMap<Integer, Student>();

        studentMap.put(st1.getStudentid(), st1);
        studentMap.put(st2.getStudentid(), st2);

        school.setStudents(studentMap);

        session.persist(school);
        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

    //retrieve book list from db
    try {
        session = sessionFactory.openSession();
        tx = session.beginTransaction();

        // retieve all books
        @SuppressWarnings("unchecked")
        List<School> schoolList = session.createQuery("from School").list();
        for (School school : schoolList) {
            System.out.println("Name= " + school.getName());
        }

        List<Student> stList = session.createQuery("from Student").list();
        for (Student st : stList) {
            System.out.println("Student First Name= " + st.getFirstname() + ", Last Name= " + st.getLastname());
        }

        tx.commit();

    } catch (HibernateException e) {
        if (tx != null) {
            System.err.println("Rolling back: " + e.getMessage());
            tx.rollback();
        }
    } finally {
        if (session != null) {
            session.close();
        }
    }

}

From source file:ctd.services.addReference.java

License:Apache License

/**
 *
 * @return message/*from  www. j  a  va2 s . c om*/
 */
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.getCleanData.java

License:Apache License

public String cleanData() throws IOException, NoImplementationException, SerializerException {

    CleanDataResult result = new CleanDataResult();

    String message = "";
    String error_message = "";
    //get parameters.
    ResourceBundle res = ResourceBundle.getBundle("settings");
    ResourceBundle cdf_list = ResourceBundle.getBundle("cdf");

    //Base directory ftp folder: Here the subfolders are found for each set of CEL-files.
    String ftp_folder = res.getString("ws.ftp_folder");
    String rscript_cleandata = res.getString("ws.rscript_cleandata");
    String rscript = res.getString("ws.rscript");
    //db//from  w ww .  j  a v  a  2 s  .c  om
    String db_username = res.getString("db.username");
    String db_password = res.getString("db.password");
    String db_database = res.getString("db.database");

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

    Query q = session.createQuery(
            "from Ticket where password='" + getPassword() + "' AND ctd_REF='" + getCTD_REF() + "'");

    Ticket ticket = null;
    String closed = "";
    if (q.list().size() != 0) {
        ticket = (Ticket) q.list().get(0);
        closed = ticket.getClosed();
    }
    if (ticket == null) {
        error_message = "Ticket password and CTD_REF don't match.";
    }
    if (closed.equals("yes")) {
        error_message = "Ticket is allready used for normalization of these CEL-files.";
        ticket = null;
    }
    if (ticket != null) {
        //get the folder
        String folder = ticket.getFolder();
        //create subfolder containing the derived zip file
        String zip_folder = ftp_folder + folder;
        //get content
        File dir = new File(zip_folder);
        String[] files = dir.list();
        //find the zip file.
        String cel_zip_file = "";
        String zip_file = "";
        String gct_file = "";

        for (int i = 0; i < files.length; i++) {
            String file = files[i];
            if (file.contains("zip")) {
                cel_zip_file = file;
                zip_file = zip_folder + "/" + cel_zip_file;
                gct_file = zip_folder + "/gctfile_" + folder;
            }
        }
        Process p3 = Runtime.getRuntime().exec("chmod 777 " + zip_file);

        //////////////////////////////////////////////////////////////////
        //Do a system call to normalize. R. (zip_folder zip_file gct_file rscript)
        String args = rscript + " --vanilla " + rscript_cleandata + " -i" + zip_file + " -o" + gct_file + " -w"
                + zip_folder;
        Process p = Runtime.getRuntime().exec(args);

        //Check if CEL files are unzipped allready
        boolean do_loop = true;
        while (do_loop) {
            File dir2 = new File(zip_folder);
            String[] files2 = dir2.list();
            //Check if CEL files are allready there
            for (int i = 0; i < files2.length; i++) {
                String file = files2[i];
                if (file.endsWith("chip")) {
                    do_loop = false;
                    try {
                        Thread.sleep(5000);
                    } catch (InterruptedException ex) {
                        Logger.getLogger(getCleanData.class.getName()).log(Level.SEVERE, null, ex);
                    }
                }
            }
        }

        File dir2 = new File(zip_folder);
        String[] files2 = dir2.list();
        String chip_file = "";
        String chip_file_db = "";
        ArrayList<String> unziped_files = new ArrayList<String>();
        for (int i = 0; i < files2.length; i++) {
            String file = files2[i];
            if (file.endsWith("CEL")) {
                unziped_files.add(file);
            }
            if (file.endsWith("chip")) {
                chip_file = file;

                chip_file_db = chip_file.split("_CDF_")[1];
            }
        }

        //Check if all CEL files are derived from the same chip.
        //This is essential for normalization.
        //initiate check hashmap. This map contains all the unique chip definition file names. There should be only one per analysis.

        ArrayList<StudySampleAssay> map = new ArrayList<StudySampleAssay>();

        for (int i = 0; i < unziped_files.size(); i++) {
            String cel_file = unziped_files.get(i);

            StudySampleAssay ssa = new StudySampleAssay();
            // Open the file that is the first
            // command line parameter
            String cel_file_path = zip_folder + "/" + cel_file;
            String name = cel_file.replaceAll(".CEL", "");
            ssa.setNameRawfile(name);
            ssa.setXREF(name);
            map.add(ssa);
        }

        ticket.getStudySampleAssaies().addAll(map);
        session.saveOrUpdate(ticket);
        session.persist(ticket);
        tr.commit();
        session.close();

        //Storage chip definition file (CDF), creation gct file and database storage.
        SessionFactory sessionFactory1 = new Configuration().configure().buildSessionFactory();
        Session session1 = sessionFactory1.openSession();

        List<ChipAnnotation> chip_annotation = null;

        //check if cdf (chip definition file) is allready stored, if not, store it.

        Query q2 = session1.createQuery("from Chip Where Name='" + chip_file_db + "'");
        if (q2.uniqueResult() != null) {
            Chip chip = (Chip) q2.list().get(0);
            chip_annotation = chip.getChipAnnotation();
        }

        if (q2.uniqueResult() == null) {
            //Add this chip and its annotation
            Chip chip_new = new Chip();
            chip_new.setName(chip_file_db);

            //read chip file
            String chip_file_path = zip_folder + "/" + chip_file;
            chip_annotation = readChip(chip_file_path);

            //Store the whole
            chip_new.getChipAnnotation().addAll(chip_annotation);

            Transaction tr1 = session1.beginTransaction();
            session1.save(chip_new);
            session1.persist(chip_new);
            tr1.commit();
            session1.close();
        }

        //create the temp file for storage of the data_insert file.
        String data_file = zip_folder + "/expression.txt";
        FileOutputStream out = null;
        PrintStream pr = null;
        out = new FileOutputStream(data_file);
        pr = new PrintStream(out);

        //create array data input file for the database table, find correct foreign keys.
        //get the study_sample_assay id and the probeset ids.
        SessionFactory sessionFactory2 = new Configuration().configure().buildSessionFactory();
        Session session2 = sessionFactory2.openSession();

        //Get the cip_annotation_id
        Query q3 = session2.createQuery("from Chip Where Name='" + chip_file_db + "'");
        Chip chip = (Chip) q3.list().get(0);
        chip_annotation = chip.getChipAnnotation();
        Iterator it2 = chip_annotation.iterator();
        //for speed, put the chip annotation id in a hashmap
        HashMap<String, String> chip_annotation_ids = new HashMap<String, String>();
        while (it2.hasNext()) {
            ChipAnnotation ca = (ChipAnnotation) it2.next();
            String id = ca.getId().toString();
            String ps = ca.getProbeset();
            chip_annotation_ids.put(ps, id);
        }

        try {

            Query qt = session2.createQuery(
                    "from Ticket where password='" + getPassword() + "' AND ctd_REF='" + getCTD_REF() + "'");

            ticket = null;

            if (qt.list().size() != 0) {
                ticket = (Ticket) qt.list().get(0);
            }

            Iterator it3 = ticket.getStudySampleAssaies().iterator();
            while (it3.hasNext()) {
                StudySampleAssay ssa = (StudySampleAssay) it3.next();
                String name_raw_file = ssa.getNameRawfile();
                String ssa_id = ssa.getId().toString();
                error_message = error_message + name_raw_file;

                String gct_file_generated = gct_file + ".gct";
                ArrayList<Double> values = writeFile(pr, chip_annotation_ids, ssa_id, gct_file_generated,
                        name_raw_file);

                Statistics stat = new Statistics();
                stat.setData(values);
                Double average = stat.getAverage();
                Double std = stat.getSTD();

                ssa.setXREF(name_raw_file);
                ssa.setAverage(average);
                ssa.setStd(std);
            }

        } catch (IOException e) {
        }
        pr.close();
        out.close();

        Transaction tr2 = session2.beginTransaction();
        session2.update(ticket);
        session2.persist(ticket);
        tr2.commit();

        session2.close();

        String u = "--user=" + db_username;
        String passw = "--password=" + db_password;
        String[] commands = new String[] { "mysqlimport", u, passw, "--local", db_database, data_file };

        Process p4 = Runtime.getRuntime().exec(commands);

        message = message + " RMA and GRSN on the CEL-files is done, data is stored.";

        //close the ticket when finished, normalization can only be performed once by the client.
        CloseTicket();

        //remove data_file
        Process p5 = Runtime.getRuntime().exec("rm -f " + data_file);
        Process p6 = Runtime.getRuntime().exec("rm -f " + zip_folder + "/*.CEL");

    }

    ////////////////////
    //SKARINGA
    result.setErrorMessage(error_message);

    result.setMessage(message);
    ObjectTransformer trans = null;
    try {
        trans = ObjectTransformerFactory.getInstance().getImplementation();
    } catch (NoImplementationException ex) {
        Logger.getLogger(getTicket.class.getName()).log(Level.SEVERE, null, ex);
    }
    message = trans.serializeToString(result);
    return message;
}

From source file:ctd.services.getCleanData.java

License:Apache License

private void CloseTicket() {

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

    Query q = session.createQuery(
            "from Ticket where password='" + getPassword() + "' AND ctd_REF='" + getCTD_REF() + "'");

    Ticket ticket = null;/*from w w  w.j  a va  2 s .  c om*/

    if (q.list().size() != 0) {
        ticket = (Ticket) q.list().get(0);
        ticket.setClosed("yes");
    }

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

}