/*
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.
*/
/*
* Study.java
*
* Created on July 28, 2006, 2:44 PM
*
*/
package edu.harvard.iq.dvn.core.study;
import edu.harvard.iq.dvn.core.admin.*;
import edu.harvard.iq.dvn.core.vdc.VDC;
import edu.harvard.iq.dvn.core.vdc.VDCCollection;
import edu.harvard.iq.dvn.core.vdc.VDCNetwork;
import java.net.URL;
import java.net.URLConnection;
//import edu.ucsb.nceas.ezid.EZIDService;
import java.util.*;
import javax.ejb.EJBException;
import javax.persistence.*;
import org.apache.commons.codec.binary.Base64;
/**
*
* @author Ellen Kraffmiller
*/
@Entity
@Table(uniqueConstraints=@UniqueConstraint(columnNames={"authority,protocol,studyId"}))
public class Study implements java.io.Serializable {
@OneToOne(mappedBy = "study", cascade={CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
private StudyDownload studyDownload;
@OneToOne(mappedBy = "study", cascade={CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
private StudyLock studyLock;
@Temporal(value = TemporalType.TIMESTAMP)
private Date createTime;
@Temporal(value = TemporalType.TIMESTAMP)
private Date lastUpdateTime;
@Temporal(value = TemporalType.TIMESTAMP)
private Date lastExportTime;
@ManyToMany(cascade={CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST })
private Collection<UserGroup> allowedGroups;
@ManyToOne
@JoinColumn(nullable=false)
private VDCUser creator;
@ManyToOne
private VDCUser lastUpdater;
private boolean isHarvested;
@ManyToMany( cascade={CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST })
private Collection<StudyField> summaryFields;
@OneToMany(mappedBy="study", cascade={CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
private Collection<StudyAccessRequest> studyRequests;
@Temporal(value = TemporalType.TIMESTAMP)
private Date lastIndexTime;
@OneToMany(mappedBy="study", cascade={CascadeType.REMOVE, CascadeType.PERSIST})
@OrderBy("versionNumber DESC")
private List<StudyVersion> studyVersions;
public Study () {
StudyVersion sv = new StudyVersion();
sv.setStudy(this);
studyVersions = new ArrayList<StudyVersion>();
studyVersions.add( sv );
}
public Study(VDC vdc, VDCUser creator, StudyVersion.VersionState versionState) {
this(vdc,creator,versionState,null);
}
public Study(VDC vdc, VDCUser creator, StudyVersion.VersionState versionState, Template initTemplate) {
if (vdc==null) {
throw new EJBException("Cannot create study with null VDC");
}
this.setOwner(vdc);
if (initTemplate == null ){
setTemplate(vdc.getDefaultTemplate());
} else {
this.setTemplate(initTemplate);
}
StudyVersion sv = new StudyVersion();
sv.setVersionNumber(new Long(1));
sv.setVersionState(versionState);
sv.setStudy(this);
sv.setMetadata(new Metadata(template.getMetadata(),false,false));
sv.getMetadata().setStudyVersion(sv);
studyVersions = new ArrayList<StudyVersion>();
studyVersions.add( sv );
//if (vdc != null) {
// vdc.getOwnedStudies().add(this);
//}
// commented the lines above: with the EJB caching off,
// getOwnedStudies results in actually looking up the studies
// in the database, then looking up the metadata, the studylock, and
// a couple of other things *for every study in the DV*; resulting
// in 5*N SQL queries where N = number of studies already in the DV!
// -L.A.
this.setCreator(creator);
this.setLastUpdater(creator);
}
public String getGlobalId() {
return protocol+":"+authority+"/"+getStudyId();
}
public String getPersistentURL() {
if (this.getProtocol().equals("hdl")){
return getHandleURL();
} else if (this.getProtocol().equals("doi")){
return getEZIdURL();
} else {
return "";
}
}
private String getHandleURL() {
return "http://hdl.handle.net/"+authority+"/"+getStudyId();
}
private String getEZIdURL() {
return "http://dx.doi.org/"+authority+"/"+getStudyId();
}
private String studyId;
public String getStudyId() {
return studyId;
}
public void setStudyId(String studyId) {
this.studyId = (studyId != null ? studyId.toUpperCase() : null);
}
public Date getCreateTime() {
return createTime;
}
public void setCreateTime(Date createTime) {
this.createTime = createTime;
}
public Date getLastUpdateTime() {
return lastUpdateTime;
}
public void setLastUpdateTime(Date lastUpdateTime) {
this.lastUpdateTime = lastUpdateTime;
if (createTime==null) {
setCreateTime(lastUpdateTime);
}
}
public StudyVersion getLatestVersion() {
int size = studyVersions.size();
if (size==0){
return null;
} else {
// The versions are retrieved from the database
// in descending versionNumber order, so the first element in the list
// is the latest version
return studyVersions.get(0);
}
}
public StudyVersion getStudyVersionByNumber (Long versionNumber) {
for (StudyVersion studyVersion : getStudyVersions()) {
if (studyVersion.getVersionNumber().equals(versionNumber)) {
return studyVersion;
}
}
return null;
}
public boolean isInReview() {
return this.getLatestVersion().isInReview();
}
public boolean isDraft() {
return this.getLatestVersion().isDraft();
}
public boolean isDeaccessioned() {
return this.getDeaccessionedVersion() != null;
}
public boolean isReleased() {
return this.getReleasedVersion() != null;
}
public Collection<UserGroup> getAllowedGroups() {
return allowedGroups;
}
public void setAllowedGroups(Collection<UserGroup> allowedGroups) {
this.allowedGroups = allowedGroups;
}
public VDCUser getCreator() {
return creator;
}
public void setCreator(VDCUser creator) {
this.creator = creator;
}
public VDCUser getLastUpdater() {
return lastUpdater;
}
public void setLastUpdater(VDCUser lastUpdater) {
this.lastUpdater = lastUpdater;
}
public boolean isIsHarvested() {
return isHarvested;
}
public void setIsHarvested(boolean isHarvested) {
this.isHarvested = isHarvested;
}
public Collection<StudyField> getSummaryFields() {
return summaryFields;
}
public void setSummaryFields(Collection<StudyField> summaryFields) {
this.summaryFields = summaryFields;
}
private long numberOfDownloads;
/**
* Getter for property numberOfDownloads.
* @return Value of property numberOfDownloads.
*/
public long getNumberOfDownloads() {
return this.numberOfDownloads;
}
/**
* Setter for property numberOfDownloads.
* @param numberOfDownloads New value of property numberOfDownloads.
*/
public void setNumberOfDownloads(long numberOfDownloads) {
this.numberOfDownloads = numberOfDownloads;
}
/**
* Holds value of property id.
*/
@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
private Long id;
/**
* Getter for property id.
* @return Value of property id.
*/
public Long getId() {
return this.id;
}
/**
* Setter for property id.
* @param id New value of property id.
*/
public void setId(Long id) {
this.id = id;
}
@OneToMany(mappedBy="study", cascade={CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
private java.util.List<edu.harvard.iq.dvn.core.study.StudyFile> studyFiles;
public List<StudyFile> getStudyFiles() {
return studyFiles;
}
public void setStudyFiles(List<StudyFile> studyFiles) {
this.studyFiles = studyFiles;
}
/**
* Holds value of property version.
*/
@Version
private Long version;
/**
* Getter for property version.
* @return Value of property version.
*/
public Long getVersion() {
return this.version;
}
/**
* Setter for property version.
* @param version New value of property version.
*/
public void setVersion(Long version) {
this.version = version;
}
@ManyToMany(mappedBy="studies")
private Collection<VDCCollection> studyColls;
public Collection<VDCCollection> getStudyColls() {
return studyColls;
}
public void setStudyColls(Collection<VDCCollection> studyColls) {
this.studyColls = studyColls;
}
/*
* Similar mechanism for keeping a list of (sub)Networks, to which the
* study may be attached via a "linked" collection; i.e., in additon to
* the network to which it belongs directly, through the DV owner id and
* parent network of the DV.
* [experimental]
*/
@ManyToMany
@JoinTable(name = "LINKED_NETWORK_STUDIES",
joinColumns = @JoinColumn(name = "study_id"),
inverseJoinColumns = @JoinColumn(name = "vdcnetwork_id"))
private List<VDCNetwork> linkedToNetworks;
public List<VDCNetwork> getLinkedToNetworks() {
return this.linkedToNetworks;
}
public void setLinkedToNetworks(List<VDCNetwork> linkedNetworks) {
this.linkedToNetworks = linkedNetworks;
}
public List<Long> getLinkedToNetworkIds() {
if (this.linkedToNetworks == null || this.linkedToNetworks.size() == 0) {
return null;
}
ArrayList<Long> retlist = new ArrayList<Long>();
Iterator iter = this.linkedToNetworks.iterator();
VDCNetwork linkedToNetwork = null;
while (iter.hasNext()) {
linkedToNetwork = (VDCNetwork) iter.next();
if (linkedToNetwork != null) {
retlist.add(linkedToNetwork.getId());
}
}
if (retlist.size() == 0) {
retlist = null;
}
return retlist;
}
/*
public void setLinkedToNetwork (VDCNetwork network) {
if (this.linkedToNetworks == null) {
this.linkedToNetworks = new ArrayList<VDCNetwork>();
}
if (!linkedToNetworks.contains(network)) {
linkedToNetworks.add(network);
}
}
public void unsetLinkedToNetwork (VDCNetwork network) {
if (linkedToNetworks.contains(network)) {
linkedToNetworks.remove(network);
}
}*/
/**
* Holds value of property template.
*/
@ManyToOne
@JoinColumn(nullable=false)
private Template template;
/**
* Getter for property template.
* @return Value of property template.
*/
public Template getTemplate() {
return this.template;
}
/**
* Setter for property template.
* @param template New value of property template.
*/
public void setTemplate(Template template) {
this.template = template;
}
/**
* Holds value of property restricted.
*/
private boolean restricted;
/**
* Getter for property restricted.
* @return Value of property restricted.
*/
public boolean isRestricted() {
return this.restricted;
}
/**
* Setter for property restricted.
* @param restricted New value of property restricted.
*/
public void setRestricted(boolean restricted) {
this.restricted = restricted;
}
/**
* Holds value of property allowedUsers.
*/
@ManyToMany(cascade={CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST })
private Collection<VDCUser> allowedUsers;
/**
* Getter for property allowedUsers.
* @return Value of property allowedUsers.
*/
public Collection<VDCUser> getAllowedUsers() {
return this.allowedUsers;
}
/**
* Setter for property allowedUsers.
* @param allowedUsers New value of property allowedUsers.
*/
public void setAllowedUsers(Collection<VDCUser> allowedUsers) {
this.allowedUsers = allowedUsers;
}
/**
* Holds value of property requestAccess.
* If this value is true, then the user can send an email
* to the vdc administrator requesting access to the study
*/
private boolean requestAccess;
/**
* Getter for property requestAccess.
* @return Value of property requestAccess.
*/
public boolean isRequestAccess() {
return this.requestAccess;
}
/**
* Setter for property requestAccess.
* @param requestAccess New value of property requestAccess.
*/
public void setRequestAccess(boolean requestAccess) {
this.requestAccess = requestAccess;
}
/**
* Holds value of property owner.
*/
@ManyToOne
@JoinColumn(nullable=false)
private VDC owner;
/**
* Getter for property owner.
* @return Value of property owner.
*/
public VDC getOwner() {
return this.owner;
}
/**
* Setter for property owner.
* @param owner New value of property owner.
*/
public void setOwner(VDC owner) {
this.owner = owner;
}
/**
* Holds value of property reviewer.
*/
@ManyToOne
private VDCUser reviewer;
/**
* Getter for property reviewer.
* @return Value of property reviewer.
*/
public VDCUser getReviewer() {
return this.reviewer;
}
/**
* Setter for property reviewer.
* @param reviewer New value of property reviewer.
*/
public void setReviewer(VDCUser reviewer) {
this.reviewer = reviewer;
}
public Collection<StudyAccessRequest> getStudyRequests() {
return studyRequests;
}
public void setStudyRequests(Collection<StudyAccessRequest> studyRequests) {
this.studyRequests = studyRequests;
}
public boolean isStudyRestrictedForUser( VDCUser user) {
return isStudyRestrictedForUser(user, null);
}
public boolean isStudyRestrictedForGroup(UserGroup usergroup) {
return isStudyRestrictedForUser(null, usergroup);
}
public boolean isStudyRestrictedForUser(VDCUser user, UserGroup ipUserGroup) {
// the restrictions should be checked on the owner of the study, not the currentVDC (needs cleanup)
VDC vdc = this.getOwner();
// first check restrictions at the dataverse level
if (this.getOwner().isVDCRestrictedForUser(user, null) ) {
return true;
}
// otherwise check for restriction on study itself
if ( isRestricted() ) {
if (user == null) {
if (ipUserGroup==null) {
return true;
} else {
Iterator iter = this.getAllowedGroups().iterator();
while (iter.hasNext()) {
UserGroup allowedGroup = (UserGroup) iter.next();
if (allowedGroup.equals(ipUserGroup)) {
return false;
}
}
return true;
}
}
// 1. check network role
if (user.getNetworkRole()!=null && user.getNetworkRole().getName().equals(NetworkRoleServiceLocal.ADMIN) ) {
// If you are network admin, you can do anything!
return false;
}
// 2. check vdc role
VDCRole userRole = user.getVDCRole(vdc);
if (userRole != null) {
String userRoleName = userRole.getRole().getName();
if ( userRoleName.equals(RoleServiceLocal.ADMIN) || userRoleName.equals(RoleServiceLocal.CURATOR) ) {
return false;
}
}
// 2a. check if creator
if (user.getId().equals(this.getCreator().getId())) {
return false;
}
// 3. check user
Iterator iter = this.getAllowedUsers().iterator();
while (iter.hasNext()) {
VDCUser allowedUser = (VDCUser) iter.next();
if ( allowedUser.getId().equals(user.getId()) ) {
return false;
}
}
// 4. check groups
iter = this.getAllowedGroups().iterator();
while (iter.hasNext()) {
UserGroup allowedGroup = (UserGroup) iter.next();
if (user.getUserGroups().contains(allowedGroup)) {
return false;
}
}
return true;
}
else {
return false;
}
}
/**
* Holds value of property protocol.
*/
@Column(columnDefinition="TEXT")
private String protocol;
/**
* Getter for property protocol.
* @return Value of property protocol.
*/
public String getProtocol() {
return this.protocol;
}
/**
* Setter for property protocol.
* @param protocol New value of property protocol.
*/
public void setProtocol(String protocol) {
this.protocol = protocol;
}
/**
* Holds value of property authority.
*/
@Column(columnDefinition="TEXT")
private String authority;
/**
* Getter for property authority.
* @return Value of property authority.
*/
public String getAuthority() {
return this.authority;
}
/**
* Setter for property authority.
* @param authority New value of property authority.
*/
public void setAuthority(String authority) {
this.authority = authority;
}
private String harvestIdentifier;
public String getHarvestIdentifier() {
return harvestIdentifier;
}
public void setHarvestIdentifier(String harvestIdentifier) {
this.harvestIdentifier = harvestIdentifier;
}
public boolean isUserAuthorizedToEdit(VDCUser user) {
// No users are allowed to edit a Harvested Study
if (owner.isHarvestingDv()) {
return false;
}
if (user.getNetworkRole()!=null && user.getNetworkRole().getName().equals(NetworkRoleServiceLocal.ADMIN)) {
return true;
}
if (user.isCurator(owner) || user.isAdmin(owner)) {
return true;
}
if (isUserStudyContributor(user)) {
return true;
}
return false;
}
public boolean isUserStudyContributor(VDCUser user) {
if ((owner.isAllowRegisteredUsersToContribute() || user.isContributor(owner))
&&(creator.getId().equals(user.getId()) || owner.isAllowContributorsEditAll()) ) {
return true;
}
return false;
}
public boolean isUserAuthorizedToRelease(VDCUser user) {
// No users are allowed to edit a Harvested Study
if (owner.isHarvestingDv()) {
return false;
}
if (user.getNetworkRole()!=null && user.getNetworkRole().getName().equals(NetworkRoleServiceLocal.ADMIN)) {
return true;
}
if (user.isCurator(owner) || user.isAdmin(owner)) {
return true;
}
return false;
}
public StudyLock getStudyLock() {
return studyLock;
}
public void setStudyLock(StudyLock studyLock) {
this.studyLock = studyLock;
}
public int hashCode() {
int hash = 0;
hash += (this.id != null ? this.id.hashCode() : 0);
return hash;
}
public boolean equals(Object object) {
// TODO: Warning - this method won't work in the case the id fields are not set
if (!(object instanceof Study)) {
return false;
}
Study other = (Study)object;
if (this.id != other.id && (this.id == null || !this.id.equals(other.id))) return false;
return true;
}
public StudyDownload getStudyDownload() {
return studyDownload;
}
public void setStudyDownload(StudyDownload studyDownload) {
this.studyDownload = studyDownload;
}
public Date getLastExportTime() {
return lastExportTime;
}
public void setLastExportTime(Date lastExportTime) {
this.lastExportTime = lastExportTime;
}
public Date getLastIndexTime() {
return lastIndexTime;
}
public void setLastIndexTime(Date lastIndexTime) {
this.lastIndexTime = lastIndexTime;
}
@OneToMany(mappedBy = "study", cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
private List<StudyFileActivity> studyFileActivity;
public List<StudyFileActivity> getStudyFileActivity() {
return studyFileActivity;
}
public void setStudyFileActivity(List<StudyFileActivity> studyFileActivity) {
this.studyFileActivity = studyFileActivity;
}
public List<StudyVersion> getStudyVersions() {
return studyVersions;
}
public void setStudyVersions(List<StudyVersion> studyVersions) {
this.studyVersions = studyVersions;
}
public StudyVersion getReleasedVersion() {
for (StudyVersion studyVersion : getStudyVersions()) {
if (studyVersion.getVersionState().equals(StudyVersion.VersionState.RELEASED) ) {
return studyVersion;
}
}
return null;
}
/**
* Create a new Study version based on the metadata of the latest version
*/
private StudyVersion createNewStudyVersion() {
StudyVersion sv = new StudyVersion();
sv.setVersionState(StudyVersion.VersionState.DRAFT);
StudyVersion latestVersion = getLatestVersion();
sv.setMetadata(new Metadata(latestVersion.getMetadata()));
sv.getMetadata().setStudyVersion(sv);
sv.setFileMetadatas(new ArrayList<FileMetadata>());
for(FileMetadata fm : latestVersion.getFileMetadatas()) {
FileMetadata newFm = new FileMetadata();
newFm.setCategory(fm.getCategory());
newFm.setDescription(fm.getDescription());
newFm.setLabel(fm.getLabel());
newFm.setStudyFile(fm.getStudyFile());
newFm.setStudyVersion(sv);
sv.getFileMetadatas().add(newFm);
}
sv.setVersionNumber(latestVersion.getVersionNumber()+1);
// I'm adding the version to the list so it will be persisted when
// the study object is persisted.
getStudyVersions().add(0, sv);
sv.setStudy(this);
return sv;
}
public StudyVersion getEditVersion() {
StudyVersion latestVersion = this.getLatestVersion();
if (!latestVersion.isWorkingCopy()) {
// if the latest version is released or archived, create a new version for editing
return createNewStudyVersion();
} else {
// else, edit existing working copy
return latestVersion;
}
}
/**
*
* @return The latest archived version of a deaccessioned study. If the study
* has not been deaccessioned, this method will return null.
*/
public StudyVersion getDeaccessionedVersion() {
for (StudyVersion studyVersion : getStudyVersions()) {
if (studyVersion.getVersionState().equals(StudyVersion.VersionState.DEACCESSIONED) ) {
return studyVersion;
}
}
return null;
}
// @Override
// public String toString() {
// return ToStringBuilder.reflectionToString(this,
// ToStringStyle.MULTI_LINE_STYLE);
// }
}