/*
Copyright (C) 2005-2012, by the President and Fellows of Harvard College.
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.
Dataverse Network - A web application to share, preserve and analyze research data.
Developed at the Institute for Quantitative Social Science, Harvard University.
Version 3.0.
*/
/*
* EditStudyServiceBean.java
*
* Created on September 29, 2006, 1:27 PM
*
* To change this template, choose Tools | Template Manager
* and open the template in the editor.
*/
package edu.harvard.iq.dvn.core.study;
import edu.harvard.iq.dvn.core.admin.VDCUser;
import edu.harvard.iq.dvn.core.doi.DOIEZIdServiceLocal;
import edu.harvard.iq.dvn.ingest.dsb.DSBWrapper;
import edu.harvard.iq.dvn.core.gnrs.GNRSServiceLocal;
import edu.harvard.iq.dvn.core.index.IndexServiceLocal;
import edu.harvard.iq.dvn.core.mail.MailServiceLocal;
import edu.harvard.iq.dvn.core.vdc.VDC;
import edu.harvard.iq.dvn.core.vdc.VDCNetwork;
import edu.harvard.iq.dvn.core.vdc.VDCNetworkServiceLocal;
import java.io.File;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.*;
import javax.annotation.Resource;
import javax.ejb.EJB;
import javax.ejb.EJBException;
import javax.ejb.Remove;
import javax.ejb.Stateful;
import javax.ejb.TransactionAttribute;
import javax.ejb.TransactionAttributeType;
import javax.jms.Queue;
import javax.jms.QueueConnectionFactory;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
/**
*
* @author Ellen Kraffmiller
*/
@Stateful
@TransactionAttribute(TransactionAttributeType.NOT_SUPPORTED)
public class EditStudyServiceBean implements edu.harvard.iq.dvn.core.study.EditStudyService, java.io.Serializable {
@EJB IndexServiceLocal indexService;
@EJB MailServiceLocal mailService;
@EJB VDCNetworkServiceLocal vdcNetworkService;
@EJB StudyServiceLocal studyService;
@EJB StudyFileServiceLocal studyFileService;
@EJB GNRSServiceLocal gnrsService;
@EJB DOIEZIdServiceLocal doiEZIdServiceLocal;
@PersistenceContext(type = PersistenceContextType.EXTENDED,unitName="VDCNet-ejbPU")
EntityManager em;
@Resource(mappedName="jms/DSBIngest") Queue queue;
@Resource(mappedName="jms/DSBQueueConnectionFactory") QueueConnectionFactory factory;
StudyVersion studyVersion;
private boolean newStudy=false;
private List currentFiles = new ArrayList();
private List newFiles = new ArrayList();
private String ingestEmail;
/**
* Initialize the bean with a studyVersion for editing
*/
public void setStudyVersion(Long studyId ) {
Study study = em.find(Study.class,studyId);
if (study==null) {
throw new IllegalArgumentException("Unknown study id: "+studyId);
}
studyVersion = study.getEditVersion();
for (FileMetadata fm: studyVersion.getFileMetadatas()) {
StudyFileEditBean fileBean = new StudyFileEditBean(fm);
getCurrentFiles().add(fileBean);
}
}
public void setStudyVersionByGlobalId(String globalId ) {
Study study = getStudyByGlobalId(globalId);
if (study==null) {
throw new IllegalArgumentException("Unknown Global id: "+globalId);
}
studyVersion = study.getEditVersion();
for (FileMetadata fm: studyVersion.getFileMetadatas()) {
StudyFileEditBean fileBean = new StudyFileEditBean(fm);
getCurrentFiles().add(fileBean);
}
}
public void newStudy(Long vdcId, Long userId, Long templateId) {
newStudy=true;
VDC vdc = em.find(VDC.class, vdcId);
VDCUser creator = em.find(VDCUser.class,userId);
Study study = new Study(vdc, creator, StudyVersion.VersionState.DRAFT, em.find(Template.class,templateId));
em.persist(study);
// set default protocol and authority
VDCNetwork vdcNetwork = vdcNetworkService.find();
study.setProtocol(vdcNetwork.getProtocol());
study.setAuthority(vdcNetwork.getAuthority());
studyVersion = study.getLatestVersion();
}
public void removeCollectionElement(Collection coll, Object elem) {
coll.remove(elem);
em.remove(elem);
}
public void removeCollectionElement(List list,int index) {
System.out.println("index is "+index+", list size is "+list.size());
em.remove(list.get(index));
list.remove(index);
}
public void removeCollectionElement(Iterator iter, Object elem) {
iter.remove();
em.remove(elem);
}
public Study getStudy() {
return studyVersion.getStudy();
}
public StudyVersion getStudyVersion() {
return studyVersion;
}
private HashMap studyMap;
public HashMap getStudyMap() {
return studyMap;
}
public void setStudyMap(HashMap studyMap) {
this.studyMap=studyMap;
}
@Remove
@TransactionAttribute(TransactionAttributeType.REQUIRED)
public void save(Long vdcId, Long userId) {
VDCUser user = em.find(VDCUser.class, userId);
try {
Metadata m = studyVersion.getMetadata();
if (m.getStudyFieldValues() != null) {
for (StudyFieldValue sfv : m.getStudyFieldValues()) {
if (sfv.getId() == null) {
em.persist(sfv);
}
}
}
editFiles();
studyService.saveStudyVersion(studyVersion, userId);
// if new, register the handle or doi identifier
if (isNewStudy() && vdcNetworkService.find().isHandleRegistration()) {
if (vdcNetworkService.findRootNetwork().getProtocol().equals("hdl")) {
String handle = studyVersion.getStudy().getAuthority() + "/" + studyVersion.getStudy().getStudyId();
gnrsService.createHandle(handle);
}
if (vdcNetworkService.findRootNetwork().getProtocol().equals("doi")) {
doiEZIdServiceLocal.createIdentifier(studyVersion.getStudy());
}
}
em.flush(); // Always call flush(), so that we can detect an OptimisticLockException
} catch (EJBException e) {
System.out.println("EJBException " + e.getMessage() + " saving studyVersion " + studyVersion.getId() + " edited by " + user.getUserName() + " at " + new Date().toString());
e.printStackTrace();
throw e;
}
}
/**
* Remove this Stateful Session bean from the EJB Container without
* saving updates to the database.
*/
@Remove
public void cancel() {
}
/*
private void addFiles(VDCUser user) {
// step 0: start with some initialization
File newDir = new File(FileUtil.getStudyFileDir(), study.getAuthority() + File.separator + study.getStudyId());
if (!newDir.exists()) {
newDir.mkdirs();
}
// step 1: divide the files, based on subsettable or not
List subsettableFiles = new ArrayList();
List otherFiles = new ArrayList();
Iterator iter = newFiles.iterator();
while (iter.hasNext()) {
StudyFileEditBean fileBean = (StudyFileEditBean) iter.next();
if ( fileBean.getStudyFile().isSubsettable() ) {
subsettableFiles.add(fileBean);
} else {
otherFiles.add(fileBean);
// also add to category, so that it will be flushed for the ids
addFileToCategory(fileBean.getStudyFile(), fileBean.getFileCategoryName(), study);
}
}
// step 2: iterate through nonsubsettable files, moving from temp to new location
iter = otherFiles.iterator();
while (iter.hasNext()) {
StudyFileEditBean fileBean = (StudyFileEditBean) iter.next();
StudyFile f = fileBean.getStudyFile();
File tempFile = new File(fileBean.getTempSystemFileLocation());
File newLocationFile = new File(newDir, f.getFileSystemName());
try {
FileUtil.copyFile( tempFile, newLocationFile );
tempFile.delete();
f.setFileSystemLocation(newLocationFile.getAbsolutePath());
} catch (IOException ex) {
throw new EJBException(ex);
}
}
// step 3: iterate through subsettable files, sending a message via JMS
if (subsettableFiles.size() > 0) {
QueueConnection conn = null;
QueueSession session = null;
QueueSender sender = null;
try {
conn = factory.createQueueConnection();
session = conn.createQueueSession(false,0);
sender = session.createSender(queue);
DSBIngestMessage ingestMessage = new DSBIngestMessage();
ingestMessage.setFileBeans(subsettableFiles);
ingestMessage.setIngestEmail(ingestEmail);
ingestMessage.setIngestUserId(user.getId());
ingestMessage.setStudyId(study.getId());
Message message = session.createObjectMessage(ingestMessage);
String detail = "Ingest processing for " + subsettableFiles.size() + " file(s).";
studyService.addStudyLock(study.getId(), user.getId(), detail);
try {
sender.send(message);
} catch(Exception ex) {
// If anything goes wrong, remove the study lock.
studyService.removeStudyLock(study.getId());
ex.printStackTrace();
}
// send an e-mail
mailService.sendIngestRequestedNotification(ingestEmail, subsettableFiles);
} catch (JMSException ex) {
ex.printStackTrace();
} finally {
try {
if (sender != null) {sender.close();}
if (session != null) {session.close();}
if (conn != null) {conn.close();}
} catch (JMSException ex) {
ex.printStackTrace();
}
}
}
}
*/
private void editFiles() {
boolean recalculateStudyUNF = false;
List filesToBeDeleted = new ArrayList();
Iterator iter = currentFiles.iterator();
while (iter.hasNext()) {
StudyFileEditBean fileBean = (StudyFileEditBean) iter.next();
StudyFile f = em.find(StudyFile.class,fileBean.getStudyFile().getId());
if (fileBean.isDeleteFlag()) {
recalculateStudyUNF = f.isUNFable() ? true : recalculateStudyUNF;
// If there is only one study version that points to the file,
// delete the file metadata and the file.
// Else, just delete the file metadata.
if (f.getFileMetadatas().size()==1) {
f.getAllowedGroups().clear();
f.getAllowedUsers().clear();
filesToBeDeleted.add(f);
}
studyVersion.getFileMetadatas().remove(fileBean.getFileMetadata());
em.remove(fileBean.getFileMetadata());
}
}
em.flush();
// and recalculate study UNF, if needed
if (recalculateStudyUNF) {
try {
studyVersion.getMetadata().setUNF( new DSBWrapper().calculateUNF(studyVersion) );
} catch (IOException e) {
throw new EJBException("Could not calculate new study UNF");
}
}
// finally delete the physical files
Iterator tbdIter = filesToBeDeleted.iterator();
while (tbdIter.hasNext()) {
StudyFile f = (StudyFile) tbdIter.next();
File physicalFile = new File(f.getFileSystemLocation());
if ( f.isSubsettable() ) {
// preserved original datafile, if available:
//File originalPhysicalFile = new File(physicalFile.getParent(), "_" + f.getId().toString());
File originalPhysicalFile = new File(physicalFile.getParent(), "_" + f.getFileSystemName());
if ( originalPhysicalFile.exists() ) {
originalPhysicalFile.delete();
}
// TODO: Delete DataVariables and related data thru nativeSQL:
// and any cached copies of this file in formats other
// than tab-delimited:
for (DataFileFormatType type : studyService.getDataFileFormatTypes()) {
File cachedDataFile = new File(f.getFileSystemLocation() + "." + type.getValue());
if ( cachedDataFile.exists() ) {
cachedDataFile.delete();
}
}
}
if ( physicalFile.exists() ) {
physicalFile.delete();
}
}
}
/**
* Creates a new instance of EditStudyServiceBean
*/
public EditStudyServiceBean() {
}
public List getCurrentFiles() {
return currentFiles;
}
public void setCurrentFiles(List currentFiles) {
this.currentFiles = currentFiles;
}
public List getNewFiles() {
return newFiles;
}
public void setNewFiles(List newFiles) {
this.newFiles = newFiles;
}
public String getIngestEmail() {
return ingestEmail;
}
public void setIngestEmail(String ingestEmail) {
this.ingestEmail = ingestEmail;
}
public boolean isNewStudy() {
return newStudy;
}
public void changeTemplate(Long templateId) {
Template newTemplate = em.find(Template.class, templateId);
// we have to clear out the studyFieldValues from the transient StudyField list
// (otherwise they hang on to the metadata object)
for (StudyField sf : studyVersion.getMetadata().getStudyFields()) {
sf.getStudyFieldValues().clear();
}
// then remove the existing metadata from study version
em.remove(studyVersion.getMetadata());
// Copy Template Metadata into Study Metadata
studyVersion.setMetadata(new Metadata(newTemplate.getMetadata(), false, false));
studyVersion.getStudy().setTemplate(newTemplate);
// prefill date of deposit
studyVersion.getMetadata().setDateOfDeposit( new SimpleDateFormat("yyyy-MM-dd").format( new Date() ) );
// Add empty row for entering data in currently empty collections
studyVersion.getMetadata().initCollections();
}
private void clearCollection(Collection collection) {
if (collection!=null) {
for (Iterator it = collection.iterator(); it.hasNext();) {
Object elem = it.next();
it.remove();
em.remove(elem);
}
}
}
public Study getStudyByGlobalId(String globalId) {
return studyService.getStudyByGlobalId(globalId);
}
}