/*
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.UserGroup;
import edu.harvard.iq.dvn.core.admin.VDCUser;
import edu.harvard.iq.dvn.core.mail.MailServiceLocal;
import edu.harvard.iq.dvn.core.util.PropertyUtil;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import javax.ejb.EJB;
import javax.ejb.Remove;
import javax.ejb.Stateful;
import javax.ejb.TransactionAttribute;
import javax.ejb.TransactionAttributeType;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
/**
*
* @author Ellen Kraffmiller
*/
@Stateful
@TransactionAttribute(TransactionAttributeType.NOT_SUPPORTED)
public class EditStudyPermissionsServiceBean implements EditStudyPermissionsService, java.io.Serializable {
@PersistenceContext(type = PersistenceContextType.EXTENDED,unitName="VDCNet-ejbPU")
EntityManager em;
@EJB StudyServiceLocal studyService;
@EJB StudyFileServiceLocal studyFileService;
@EJB MailServiceLocal mailService;
private boolean currentVersionFiles;
public boolean isCurrentVersionFiles() {
return currentVersionFiles;
}
public void setCurrentVersionFiles(boolean currentVersionFiles) {
this.currentVersionFiles = currentVersionFiles;
}
Study study;
public void setStudy(Long id) {
study = em.find(Study.class,id);
if (study==null) {
throw new IllegalArgumentException("Unknown study id: "+id);
}
}
/**
* Initialize the bean with a Study for editing
*/
public void setStudy(Long id, Long versionNumber ) {
study = em.find(Study.class,id);
if (study==null) {
throw new IllegalArgumentException("Unknown study id: "+id);
}
studyPermissions = new ArrayList<PermissionBean>();
fileDetails = new ArrayList<FileDetailBean>();
studyRequests = new ArrayList<StudyRequestBean>();
currentVersionFiles = true;
Map<Long,String> studyFileNames = new HashMap();
// general study restriction
if (study.isRestricted()) {
setStudyRestriction("Restricted");
} else {
setStudyRestriction("Public");
}
// and users/groups with access to study
for (Iterator it = study.getAllowedUsers().iterator(); it.hasNext();) {
VDCUser user = (VDCUser) it.next();
studyPermissions.add(new PermissionBean(user));
}
for (Iterator it2 = study.getAllowedGroups().iterator(); it2.hasNext();) {
UserGroup group = (UserGroup) it2.next();
studyPermissions.add(new PermissionBean(group));
}
// to populate the file details, we make one db call to get all filemetadata obejcts
// for each studyfile; we then loop through list, creating a new FileDetailBean when
// we encounter a new studyfile.id
//
// we also use this query call to create a Map of files and names that we can
//then use for the study requests
Long loopStudyFileId = null;
FileDetailBean fd = null;
// elements of array are studyfile.id, filemetadata.id, studyversion.versionNumber
for ( Object[] sfArray : studyFileService.getOrderedFilesByStudy(study.getId()) ) {
if (sfArray[0].equals(loopStudyFileId)) { // another filemetadata for current studyfile
// all we modify is the String of file versions this file pertains to
fd.setFileVersions( sfArray[2].toString() + "," + fd.getFileVersions());
} else { // first time with this id
loopStudyFileId = (Long) sfArray[0]; // set the id of the loop var
StudyFile elem = em.find(StudyFile.class,loopStudyFileId);
FileMetadata fmd = em.find(FileMetadata.class, sfArray[1]);
fd = new FileDetailBean(); // create a new File Detail Bean
fd.setStudyFile(elem);
fd.setFileMetadata(fmd);
fd.setCurrentVersion( versionNumber != null && versionNumber.equals((sfArray[2])) );
fd.setFilePermissions(new ArrayList<PermissionBean>());
for (Iterator it4 = elem.getAllowedUsers().iterator(); it4.hasNext();) {
VDCUser elem2 = (VDCUser) it4.next();
fd.getFilePermissions().add(new PermissionBean(elem2));
}
for (Iterator it5 = elem.getAllowedGroups().iterator(); it5.hasNext();) {
UserGroup elem2 = (UserGroup) it5.next();
fd.getFilePermissions().add(new PermissionBean(elem2));
}
fd.setFileVersions( sfArray[2].toString() );
fileDetails.add(fd);
// add file name to the studyFileNames map for use by study requests
studyFileNames.put(loopStudyFileId, fmd.getLabel());
}
}
// file level restrictions
for (Iterator detailIter = fileDetails.iterator(); detailIter.hasNext();) {
FileDetailBean elem = (FileDetailBean) detailIter.next();
if (elem.getStudyFile().isRestricted()) {
elem.setFileRestriction("Restricted");
} else {
elem.setFileRestriction("Public");
}
}
fileDetailsCopy = new ArrayList<FileDetailBean>(fileDetails);
// study requests
for (StudyAccessRequest elem : study.getStudyRequests()) {
StudyRequestBean srb = new StudyRequestBean(elem);
srb.setFileName(studyFileNames.get(elem.getStudyFile().getId()));
studyRequests.add(srb);
}
}
public void removeCollectionElement(Collection coll, Object elem) {
coll.remove(elem);
em.remove(elem);
}
public void removeCollectionElement(Iterator iter, Object elem) {
iter.remove();
em.remove(elem);
}
public Study getStudy() {
return study;
}
Map<VDCUser,List<StudyRequestBean>> requestsToMail = new HashMap();
public void updateRequests() {
List removeBeans = new ArrayList();
for (StudyRequestBean elem : studyRequests) {
VDCUser requestUser = elem.getStudyRequest().getVdcUser();
if (Boolean.TRUE.equals(elem.getAccept()) ){
this.addFileUser(requestUser.getId(), elem.getStudyRequest().getStudyFile().getId(), true);
em.remove(elem.getStudyRequest());
study.getStudyRequests().remove(elem.getStudyRequest());
removeBeans.add(elem);
// add to queue to mail on save
List userRequests = requestsToMail.get(requestUser);
if (userRequests == null) {
userRequests = new ArrayList();
}
userRequests.add(elem);
requestsToMail.put(requestUser, userRequests);
} else if (Boolean.FALSE.equals(elem.getAccept()) ){
em.remove(elem.getStudyRequest());
study.getStudyRequests().remove(elem.getStudyRequest());
removeBeans.add(elem);
// add to queue to mail on save
List userRequests = requestsToMail.get(requestUser);
if (userRequests == null) {
userRequests = new ArrayList();
}
userRequests.add(elem);
requestsToMail.put(requestUser, userRequests);
}
}
for (Iterator it2 = removeBeans.iterator(); it2.hasNext();) {
StudyRequestBean elem = (StudyRequestBean) it2.next();
studyRequests.remove(elem);
}
}
@Remove
@TransactionAttribute(TransactionAttributeType.REQUIRES_NEW)
public void save() {
if (this.studyRestriction.equals("Restricted")) {
study.setRestricted(true);
} else {
study.setRestricted(false);
}
for (Iterator it = fileDetails.iterator(); it.hasNext();) {
FileDetailBean elem = (FileDetailBean) it.next();
if (elem.getFileRestriction().equals("Restricted")) {
elem.getStudyFile().setRestricted(true);
int users = elem.getStudyFile().getAllowedUsers().size();
} else {
elem.getStudyFile().setRestricted(false);
}
}
// Don't really need to do call flush(), because a method that
// requires a transaction will automatically trigger a flush to the database,
// but include this just to show what's happening here
em.flush();
String studyUrl = study.getPersistentURL();
// if save succeeds, send out all accept/reject mail messages
for (Entry<VDCUser,List<StudyRequestBean>> requestEntry : requestsToMail.entrySet()) {
List<String> acceptedFiles = new ArrayList();
List<String> rejectedFiles = new ArrayList();
for (StudyRequestBean elem : requestEntry.getValue()) {
if (Boolean.TRUE.equals(elem.getAccept()) ){
acceptedFiles.add(elem.getFileName());
} else if (Boolean.FALSE.equals(elem.getAccept()) ){
rejectedFiles.add("File Name: " + elem.getFileName() + ", Message: "+ elem.getInputDenyMessage());
}
}
mailService.sendFileAccessResolvedNotification(requestEntry.getKey().getEmail(), study.getReleasedVersion().getMetadata().getTitle(), study.getGlobalId(), acceptedFiles,rejectedFiles, studyUrl, study.getOwner().getContactEmail());
}
}
/**
* Remove this Stateful Session bean from the EJB Container without
* saving updates to the database.
*/
@Remove
public void cancel() {
}
/**
* Creates a new instance of EditStudyServiceBean
*/
public EditStudyPermissionsServiceBean() {
}
/**
* Holds value of property studyPermissions.
*/
private Collection<PermissionBean> studyPermissions;
/**
* Getter for property studyPermissions.
* @return Value of property studyPermissions.
*/
public Collection<PermissionBean> getStudyPermissions() {
return this.studyPermissions;
}
/**
* Setter for property studyPermissions.
* @param studyPermissions New value of property studyPermissions.
*/
public void setStudyPermissions(Collection<PermissionBean> studyPermissions) {
this.studyPermissions = studyPermissions;
}
/**
* Holds value of property fileDetails.
*/
private Collection<FileDetailBean> fileDetails;
private Collection<FileDetailBean> fileDetailsReturn;
/**
* Getter for property filePermissions.
* @return Value of property filePermissions.
*/
public Collection<FileDetailBean> getFileDetails() {
fileDetailsReturn = new ArrayList<FileDetailBean>();
if (!currentVersionFiles){
return this.fileDetails;
} else {
for (Object obj : fileDetails){
FileDetailBean fdb = (FileDetailBean) obj;
if(fdb.isCurrentVerstion()){
fileDetailsReturn.add(fdb);
}
}
return this.fileDetailsReturn;
}
}
/**
* Setter for property filePermissions.
* @param filePermissions New value of property filePermissions.
*/
public void setFileDetails(Collection<FileDetailBean> fileDetails) {
this.fileDetails = fileDetails;
}
private Collection<FileDetailBean> fileDetailsCopy;
public String updateAllFilesList(String filterTerm){
List fileIds = studyFileService.findAllFileIdsSearch(study.getId(), filterTerm);
if (!fileIds.isEmpty()) {
fileDetails = new ArrayList();
ArrayList<FileDetailBean> myFileDetails = new ArrayList<FileDetailBean>(fileDetailsCopy);
for (Iterator it = fileIds.iterator(); it.hasNext();) {
Long elem = (Long) it.next();
for (Iterator it2 = myFileDetails.iterator(); it2.hasNext();) {
FileDetailBean fdb = (FileDetailBean) it2.next();
if (((Long) fdb.getStudyFile().getId()).equals(elem)) {
fileDetails.add(fdb);
break;
}
}
}
}
return "";
}
/**
* Holds value of property studyRestriction.
*/
private String studyRestriction;
/**
* Getter for property studyRestriction.
* @return Value of property studyRestriction.
*/
public String getStudyRestriction() {
return this.studyRestriction;
}
/**
* Setter for property studyRestriction.
* @param studyRestriction New value of property studyRestriction.
*/
public void setStudyRestriction(String studyRestriction) {
this.studyRestriction = studyRestriction;
}
/**
* Holds value of property studyRequests.
*/
private Collection<StudyRequestBean> studyRequests;
/**
* Getter for property studyRequests.
* @return Value of property studyRequests.
*/
public Collection<StudyRequestBean> getStudyRequests() {
return this.studyRequests;
}
/**
* Setter for property studyRequests.
* @param studyRequests New value of property studyRequests.
*/
public void setStudyRequests(Collection<StudyRequestBean> studyRequests) {
this.studyRequests = studyRequests;
}
public void addStudyUser(Long userId ) {
VDCUser user = (VDCUser)em.find(VDCUser.class, userId);
study.getAllowedUsers().add(user);
studyPermissions.add(new PermissionBean(user));
}
public void addStudyGroup(Long groupId ) {
UserGroup group = (UserGroup)em.find(UserGroup.class, groupId);
study.getAllowedGroups().add(group);
studyPermissions.add(new PermissionBean(group));
}
public void addFileUser(Long id) {
boolean restrictedOnly=false;
addFileUser(id, restrictedOnly);
}
public void addFileUser(Long userId, Long fileId) {
boolean restrictedOnly=false;
addFileUser(userId, fileId, restrictedOnly);
}
public void addFileUser(Long id, boolean restrictedOnly) {
VDCUser user = (VDCUser)em.find(VDCUser.class, id);
for (Iterator it = fileDetails.iterator(); it.hasNext();) {
FileDetailBean elem = (FileDetailBean) it.next();
if ((!restrictedOnly && elem.isChecked()) || (restrictedOnly && elem.getStudyFile().isRestricted())) {
StudyFile studyFile = elem.getStudyFile();
if (!studyFile.isUserInAllowedUsers(user.getId())) {
studyFile.getAllowedUsers().add(user);
elem.getFilePermissions().add(new PermissionBean(user));
}
}
}
}
public void addFileUser(Long userId, Long fileId, boolean restrictedOnly) {
VDCUser user = (VDCUser)em.find(VDCUser.class, userId);
StudyFile studyFile = (StudyFile)em.find(StudyFile.class, fileId);
for (Iterator it = fileDetails.iterator(); it.hasNext();) {
FileDetailBean elem = (FileDetailBean) it.next();
if ((!restrictedOnly && elem.isChecked()) || (restrictedOnly && elem.getStudyFile().isRestricted())) {
if (!studyFile.isUserInAllowedUsers(user.getId())) {
studyFile.getAllowedUsers().add(user);
elem.getFilePermissions().add(new PermissionBean(user));
}
}
}
}
public void addFileGroup(Long id) {
UserGroup group = (UserGroup)em.find(UserGroup.class, id);
for (Iterator it = fileDetails.iterator(); it.hasNext();) {
FileDetailBean elem = (FileDetailBean) it.next();
if (elem.isChecked()) {
StudyFile studyFile = elem.getStudyFile();
if (!studyFile.isGroupInAllowedGroups(id)) {
studyFile.getAllowedGroups().add(group);
elem.getFilePermissions().add(new PermissionBean(group));
}
}
}
}
public void setFileRestriction( boolean restricted) {
for (Iterator it = fileDetails.iterator(); it.hasNext();) {
FileDetailBean elem = (FileDetailBean) it.next();
if (elem.isChecked()) {
StudyFile studyFile = elem.getStudyFile();
studyFile.setRestricted(restricted);
if (restricted) {
elem.setFileRestriction("Restricted");
} else {
elem.setFileRestriction("Public");
}
}
}
}
private Collection<PermissionBean> filePermissionsReturn;
public Collection<PermissionBean> getFilePermissions(Long fileId) {
for (Iterator it = this.fileDetails.iterator(); it.hasNext();) {
FileDetailBean fdb = (FileDetailBean) it.next();
if (fdb.getStudyFile().getId().equals(fileId)) {
filePermissionsReturn = new ArrayList<PermissionBean>(fdb.getFilePermissions());
fileDetail = fdb;
break;
}
}
return filePermissionsReturn;
}
private FileDetailBean fileDetail;
public void removeFilePermissions(boolean removeChecked) {
List checkedBeans = new ArrayList();
for (Iterator it2 = fileDetail.getFilePermissions().iterator(); it2.hasNext();) {
PermissionBean elem = (PermissionBean) it2.next();
if (elem.isChecked()) {
if (elem.getUser()!=null) {
VDCUser foundUser = null;
// Note: need to do this extra step of finding the user by checking the ID,
// because this does not work:
// fileDetail.getStudyFile().getAllowedGroups().remove(elem.getUser());
// (Some wierdness in EJB where it doesn't think elem.getUser() is equivalent to the user in the list.)
for (Iterator userIt = fileDetail.getStudyFile().getAllowedUsers().iterator(); userIt.hasNext();) {
VDCUser user = (VDCUser) userIt.next();
if (user.getId().equals(elem.getUser().getId())) {
foundUser= user;
}
}
if (foundUser!=null) {
if (!removeChecked) {
fileDetail.getStudyFile().getAllowedUsers().remove(foundUser);
foundUser.getStudyFiles().remove(fileDetail.getStudyFile());
} else {
for (StudyFile sf : fileDetail.getStudyFile().getStudy().getStudyFiles()) {
sf.getAllowedUsers().remove(foundUser);
foundUser.getStudyFiles().remove(sf);
}
}
}
} else if (elem.getGroup()!=null) {
// See above note for removing elem.getUser()
UserGroup foundGroup = null;
for (Iterator groupIt = fileDetail.getStudyFile().getAllowedGroups().iterator(); groupIt.hasNext();) {
UserGroup group = (UserGroup) groupIt.next();
if (group.getId().equals(elem.getGroup().getId())) {
foundGroup = group;
}
}
if (foundGroup!=null) {
if (!removeChecked) {
fileDetail.getStudyFile().getAllowedGroups().remove(foundGroup);
foundGroup.getStudyFiles().remove(fileDetail.getStudyFile());
} else {
for (StudyFile sf : fileDetail.getStudyFile().getStudy().getStudyFiles()) {
sf.getAllowedGroups().remove(foundGroup);
foundGroup.getStudyFiles().remove(sf);
}
}
}
}
checkedBeans.add(elem);
}
}
for (Iterator it3 = checkedBeans.iterator(); it3.hasNext();) {
PermissionBean elem = (PermissionBean)it3.next();
if (elem.isChecked()) {
fileDetail.getFilePermissions().remove(elem);
}
}
}
public void removeStudyPermissions() {
List checkedBeans = new ArrayList();
for (Iterator<PermissionBean> it = studyPermissions.iterator(); it.hasNext();) {
PermissionBean elem = it.next();
if (elem.isChecked()) {
if (elem.getUser()!=null) {
study.getAllowedUsers().remove(elem.getUser());
elem.getUser().getStudies().remove(study);
} else if (elem.getGroup()!=null) {
study.getAllowedGroups().remove(elem.getGroup());
elem.getGroup().getStudies().remove(study);
}
checkedBeans.add(elem);
}
}
for (Iterator it = checkedBeans.iterator(); it.hasNext();) {
PermissionBean elem = (PermissionBean) it.next();
if (elem.isChecked()) {
studyPermissions.remove(elem);
}
}
}
}