Java tutorial
/* Copyright 2010 Wageningen University, Division of Human Nutrition. * Drs. R. Kerkhoven, robert.kerkhoven@wur.nl * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package ctd.services; import com.skaringa.javaxml.NoImplementationException; import com.skaringa.javaxml.ObjectTransformer; import com.skaringa.javaxml.ObjectTransformerFactory; import com.skaringa.javaxml.SerializerException; import ctd.ws.model.ProbeSetExpressionInfo; import java.util.ArrayList; import java.util.Iterator; import java.util.ResourceBundle; import java.util.logging.Level; import java.util.logging.Logger; import org.hibernate.SQLQuery; import org.hibernate.Session; import org.hibernate.SessionFactory; import org.hibernate.cfg.Configuration; /** * * @author kerkh010 */ public class getExpressionByProbeSetId { private String probeSetId; private String wsPassword; 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 + "' 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; } 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 + "' 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; } /** * @return the probeSetId */ public String getProbeSetId() { return probeSetId; } /** * @param probeSetId the probeSetId to set */ public void setProbeSetId(String probeSetId) { this.probeSetId = probeSetId; } /** * @return the password */ public String getWsPassword() { return wsPassword; } /** * @param password the password to set */ public void setWsPassword(String password) { this.wsPassword = password; } }