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DatasetVersionServiceBean.java
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package edu.harvard.iq.dataverse;
import edu.harvard.iq.dataverse.DatasetVersion.VersionState;
import edu.harvard.iq.dataverse.ingest.IngestUtil;
import edu.harvard.iq.dataverse.pidproviders.PidUtil;
import edu.harvard.iq.dataverse.search.IndexServiceBean;
import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import static edu.harvard.iq.dataverse.batch.jobs.importer.filesystem.FileRecordJobListener.SEP;
import edu.harvard.iq.dataverse.batch.util.LoggingUtil;
import edu.harvard.iq.dataverse.search.SolrSearchResult;
import edu.harvard.iq.dataverse.settings.FeatureFlags;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.MarkupChecker;
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
import jakarta.ejb.EJB;
import jakarta.ejb.EJBException;
import jakarta.ejb.Stateless;
import jakarta.inject.Named;
import jakarta.json.Json;
import jakarta.json.JsonObjectBuilder;
import jakarta.persistence.EntityManager;
import jakarta.persistence.NoResultException;
import jakarta.persistence.PersistenceContext;
import jakarta.persistence.Query;
import jakarta.persistence.TypedQuery;
import org.apache.commons.lang3.StringUtils;
/**
*
* @author skraffmiller
*/
@Stateless
@Named
public class DatasetVersionServiceBean implements java.io.Serializable {
private static final Logger logger = Logger.getLogger(DatasetVersionServiceBean.class.getCanonicalName());
private static final SimpleDateFormat logFormatter = new SimpleDateFormat("yyyy-MM-dd'T'HH-mm-ss");
@EJB
DatasetServiceBean datasetService;
@EJB
DataFileServiceBean datafileService;
@EJB
SettingsServiceBean settingsService;
@EJB
AuthenticationServiceBean authService;
@EJB
SystemConfig systemConfig;
@EJB
IndexServiceBean indexService;
@PersistenceContext(unitName = "VDCNet-ejbPU")
private EntityManager em;
/**
* Response to a successful request from the DatasetPage
*
* Used to help display messages in the cases when:
* (1) A specific dataset version (including a DRAFT) is requested
* (2) A different dataset is returned b/c the first one doesn't exist
*
* Simple example: "DRAFT" requested but no longer exists b/c it
* was published and is now version "1.0"
*/
public class RetrieveDatasetVersionResponse{
private DatasetVersion datasetVersionForResponse;
private boolean wasSpecificVersionRequested = false;
private boolean didSpecificVersionMatch = false;
private String actualVersion = null;
private String requestedVersion = null;
public RetrieveDatasetVersionResponse(DatasetVersion datasetVersion, String requestedVersion){
if (datasetVersion == null){
throw new IllegalArgumentException("datasetVersion cannot be null");
}
//logger.fine("RetrieveDatasetVersionResponse: datasetVersion: " + datasetVersion.getSemanticVersion() + " requestedVersion: " + requestedVersion);
//logger.fine("chosenVersion id: " + datasetVersion.getId() + " getFriendlyVersionNumber: " + datasetVersion.getFriendlyVersionNumber());
this.datasetVersionForResponse = datasetVersion;
this.actualVersion = datasetVersion.getSemanticVersion();
this.requestedVersion = requestedVersion;
this.checkVersion();
}
public String getDifferentVersionMessage(){
if (this.wasSpecificVersionRequested && !this.didSpecificVersionMatch){
String userMsg;
if (DatasetVersionServiceBean.this.isVersionAskingForDraft(this.requestedVersion)){
userMsg = BundleUtil.getStringFromBundle("file.viewDiffDialog.msg.draftNotFound");
}else{
userMsg = BundleUtil.getStringFromBundle("file.viewDiffDialog.msg.versionNotFound", Arrays.asList(MarkupChecker.escapeHtml(this.requestedVersion)));
}
if (DatasetVersionServiceBean.this.isVersionAskingForDraft(this.actualVersion)){
userMsg += BundleUtil.getStringFromBundle("file.viewDiffDialog.msg.draftFound");
}else{
userMsg += BundleUtil.getStringFromBundle("file.viewDiffDialog.msg.versionFound", Arrays.asList(this.actualVersion));
}
return userMsg;
}
return null;
}
private void checkVersion(){
if (actualVersion==null){ // this shouldn't happen
return;
}
//logger.fine("check version. requested: " + this.requestedVersion + " returned: " + actualVersion);
// This may often be the case if version is not specified
//
if (requestedVersion == null || requestedVersion.isEmpty()){
this.wasSpecificVersionRequested = false;
return;
}
this.wasSpecificVersionRequested = true;
this.didSpecificVersionMatch = this.requestedVersion.equalsIgnoreCase(actualVersion);
}
public boolean wasRequestedVersionRetrieved(){
return !(this.wasSpecificVersionRequested && !this.didSpecificVersionMatch);
}
public DatasetVersion getDatasetVersion(){
return this.datasetVersionForResponse;
}
} // end RetrieveDatasetVersionResponse
public DatasetVersion find(Object pk) {
return em.find(DatasetVersion.class, pk);
}
public DatasetVersion findDeep(Object pk) {
return (DatasetVersion) em.createNamedQuery("DatasetVersion.findById")
.setParameter("id", pk)
// Optimization hints: retrieve all data in one query; this prevents point queries when iterating over the files
.setHint("eclipselink.left-join-fetch", "o.fileMetadatas.dataFile.ingestRequest")
.setHint("eclipselink.left-join-fetch", "o.fileMetadatas.dataFile.thumbnailForDataset")
.setHint("eclipselink.left-join-fetch", "o.fileMetadatas.dataFile.dataTables")
.setHint("eclipselink.left-join-fetch", "o.fileMetadatas.fileCategories")
.setHint("eclipselink.left-join-fetch", "o.fileMetadatas.dataFile.embargo")
.setHint("eclipselink.left-join-fetch", "o.fileMetadatas.dataFile.retention")
.setHint("eclipselink.left-join-fetch", "o.fileMetadatas.datasetVersion")
.setHint("eclipselink.left-join-fetch", "o.fileMetadatas.dataFile.releaseUser")
.setHint("eclipselink.left-join-fetch", "o.fileMetadatas.dataFile.creator")
.setHint("eclipselink.left-join-fetch", "o.fileMetadatas.dataFile.dataFileTags")
.getSingleResult();
}
/**
* Performs the same database lookup as the one behind Dataset.getVersions().
* Additionally, provides the arguments for selecting a partial list of
* (length-offset) versions for pagination, plus the ability to pre-select
* only the publicly-viewable versions.
* It is recommended that individual software components utilize the
* ListVersionsCommand, instead of calling this service method directly.
* @param datasetId
* @param offset for pagination through long lists of versions
* @param length for pagination through long lists of versions
* @param includeUnpublished retrieves all the versions, including drafts and deaccessioned.
* @return (partial) list of versions
*/
public List<DatasetVersion> findVersions(Long datasetId, Integer offset, Integer length, boolean includeUnpublished) {
TypedQuery<DatasetVersion> query;
if (includeUnpublished) {
query = em.createNamedQuery("DatasetVersion.findByDataset", DatasetVersion.class);
} else {
query = em.createNamedQuery("DatasetVersion.findReleasedByDataset", DatasetVersion.class)
.setParameter("datasetId", datasetId);
}
query.setParameter("datasetId", datasetId);
if (offset != null) {
query.setFirstResult(offset);
}
if (length != null) {
query.setMaxResults(length);
}
return query.getResultList();
}
public DatasetVersion findByFriendlyVersionNumber(Long datasetId, String friendlyVersionNumber) {
Long majorVersionNumber = null;
Long minorVersionNumber = null;
String[] versions = friendlyVersionNumber.split("\\.");
try {
if (versions.length == 1) {
majorVersionNumber = Long.parseLong(versions[0]);
} else if (versions.length == 2) {
majorVersionNumber = Long.parseLong(versions[0]);
minorVersionNumber = Long.parseLong(versions[1]);
} else {
return null;
}
} catch (NumberFormatException n) {
return null;
}
if (minorVersionNumber != null) {
String queryStr = "SELECT v from DatasetVersion v where v.dataset.id = :datasetId and v.versionNumber= :majorVersionNumber and v.minorVersionNumber= :minorVersionNumber";
DatasetVersion foundDatasetVersion = null;
try {
Query query = em.createQuery(queryStr);
query.setParameter("datasetId", datasetId);
query.setParameter("majorVersionNumber", majorVersionNumber);
query.setParameter("minorVersionNumber", minorVersionNumber);
foundDatasetVersion = (DatasetVersion) query.getSingleResult();
} catch (NoResultException e) {
logger.warning("no ds version found: " + datasetId + " " + friendlyVersionNumber);
// DO nothing, just return null.
}
return foundDatasetVersion;
}
if (majorVersionNumber == null && minorVersionNumber == null) {
return null;
}
if (majorVersionNumber != null && minorVersionNumber == null) {
try {
TypedQuery<DatasetVersion> typedQuery = em.createQuery("SELECT v from DatasetVersion v where v.dataset.id = :datasetId and v.versionNumber= :majorVersionNumber", DatasetVersion.class);
typedQuery.setParameter("datasetId", datasetId);
typedQuery.setParameter("majorVersionNumber", majorVersionNumber);
DatasetVersion retVal = null;
List<DatasetVersion> versionsList = typedQuery.getResultList();
for (DatasetVersion dsvTest : versionsList) {
if (retVal == null) {
retVal = dsvTest;
} else {
if (retVal.getMinorVersionNumber().intValue() < dsvTest.getMinorVersionNumber().intValue()) {
retVal = dsvTest;
}
}
}
return retVal;
} catch (NoResultException e) {
logger.warning("no ds version found: " + datasetId + " " + friendlyVersionNumber);
// DO nothing, just return null.
}
}
return null;
}
/**
* Parse a Persistent Id and return as 3 strings.
*
* Example: 1.0, 1.1. 3.4, etc.
*
* @param version
* @return Long[] with [ major_version, minor_version ]
* - either or both may be null
*/
public Long[] parseVersionNumber(String version){
if (version == null){
return null;
}
Long majorVersion;
Long minorVersion = null;
String[] vparts = version.split("\\.");
if (vparts.length == 1){
try{
majorVersion = Long.parseLong(vparts[0]);
}catch (NumberFormatException n) {
return null;
}
}else if (vparts.length == 2){
try{
majorVersion = Long.parseLong(vparts[0]);
minorVersion = Long.parseLong(vparts[1]);
}catch (NumberFormatException n) {
return null;
}
}else{
return null;
}
Long versionNumbers[] = { majorVersion, minorVersion };
return versionNumbers;
}
private void msg(String s){
//logger.fine(s);
}
public boolean isVersionDefaultCustomTerms(DatasetVersion datasetVersion) {
//SEK - belt and suspenders here, but this is where the bug 10719 first manifested
if (datasetVersion != null && datasetVersion.getId() != null) {
try {
TermsOfUseAndAccess toua = (TermsOfUseAndAccess) em.createNamedQuery("TermsOfUseAndAccess.findByDatasetVersionIdAndDefaultTerms")
.setParameter("id", datasetVersion.getId()).setParameter("defaultTerms", TermsOfUseAndAccess.DEFAULT_NOTERMS).getSingleResult();
if (toua != null && datasetVersion.getTermsOfUseAndAccess().getLicense() == null) {
return true;
}
} catch (NoResultException e) {
return false;
}
}
return false;
}
/**
* Does the version identifier in the URL ask for a "DRAFT"?
*
* @param version
* @return boolean
*/
public boolean isVersionAskingForDraft(String version){
if (version == null){
return false;
}
return version.toUpperCase().equals(VersionState.DRAFT.toString());
}
private String getDatasetVersionBasicQuery(String identifierClause, String extraClause){
if (identifierClause == null){
return null;
}
if (extraClause == null){
extraClause = "";
}
String queryStr = "SELECT dv.* FROM DatasetVersion dv";
queryStr += " INNER JOIN Dataset ds";
queryStr += " ON dv.dataset_id=ds.id";
queryStr += identifierClause; // either persistentId or id
queryStr += extraClause; // may be an empty string
queryStr += " ORDER BY versionNumber DESC, minorVersionNumber DESC";
queryStr += " LIMIT 1;";
return queryStr;
}
public String getContributorsNames(DatasetVersion version) {
String contNames = "";
for (String id : version.getVersionContributorIdentifiers()) {
id = id.startsWith("@") ? id.substring(1) : id;
AuthenticatedUser au = authService.getAuthenticatedUser(id);
if (au != null) {
if (contNames.isEmpty()) {
contNames = au.getName();
} else {
contNames = contNames + ", " + au.getName();
}
}
}
return contNames;
}
public List<DatasetVersionUser> getDatasetVersionUsersByAuthenticatedUser(AuthenticatedUser user){
TypedQuery<DatasetVersionUser> typedQuery = em.createQuery("SELECT u from DatasetVersionUser u where u.authenticatedUser.id = :authenticatedUserId", DatasetVersionUser.class);
typedQuery.setParameter("authenticatedUserId", user.getId());
return typedQuery.getResultList();
}
/**
* Query to return the last Released DatasetVersion by Persistent ID
*
* @param identifierClause - query clause to retrieve via DatasetVersion.Id or DatasetVersion.persistentId
* @return String fullQuery
*/
private String getLatestReleasedDatasetVersionQuery(String identifierClause){
if (identifierClause == null){
return null;
}
String releasedClause = " AND dv.versionstate = '" + VersionState.RELEASED.toString() + "'";
return getDatasetVersionBasicQuery(identifierClause, releasedClause);
}
/**
* Query to return a DatasetVersion by Specific Version
*
* @param identifierClause - query clause to retrieve via DatasetVersion.Id or DatasetVersion.persistentId
* @return String fullQuery
*/
private String getNumericDatasetVersionQueryByIdentifier(String identifierClause, Long majorVersion, Long minorVersion){
if (identifierClause == null){
return null;
}
String extraQueryClause = "";
// For an exact version: retrieve either RELEASED or DEACCESSIONED
//
if (majorVersion != null && minorVersion != null){
extraQueryClause += " AND dv.versionNumber= " + majorVersion;
extraQueryClause += " AND dv.minorVersionNumber= " + minorVersion;
extraQueryClause += " AND (dv.versionstate = '" + VersionState.RELEASED.toString() + "' or dv.versionstate = '" + VersionState.DEACCESSIONED.toString() + "')";
} else {
// Last released major version
//
extraQueryClause += " AND dv.versionNumber= " + majorVersion;
extraQueryClause += " AND dv.versionstate = '" + VersionState.RELEASED.toString() + "'";
}
return getDatasetVersionBasicQuery(identifierClause, extraQueryClause);
}
/**
* Query to return a Draft DatasetVersion by Persistent ID
*
* @param identifierClause - query clause to retrieve via DatasetVersion.Id or DatasetVersion.persistentId
* @return String fullQuery
*/
private String getDraftDatasetVersionQuery(String identifierClause){
if (identifierClause == null){
return null;
}
String draftClause = " AND dv.versionstate = '" + VersionState.DRAFT.toString() + "'";
return getDatasetVersionBasicQuery(identifierClause, draftClause);
}
/**
* Query to return a DEACCESSIONED DatasetVersion by Persistent ID
*
* @param identifierClause - query clause to retrieve via DatasetVersion.Id or DatasetVersion.persistentId
* @return String fullQuery
*/
private String getDeaccessionedDatasetVersionQuery(String identifierClause){
if (identifierClause == null){
return null;
}
String draftClause = " AND dv.versionstate = '" + VersionState.DEACCESSIONED.toString() + "'";
return getDatasetVersionBasicQuery(identifierClause, draftClause);
}
/**
* Execute a query to return DatasetVersion
*
* @param queryString
* @return
*/
private DatasetVersion getDatasetVersionByQuery(String queryString){
msg("getDatasetVersionByQuery queryString: " + queryString);
if (queryString == null){
return null;
}
// Inexact check to see if one of the selected tables is DATASETVERSION
//
if (!queryString.toUpperCase().contains("FROM DATASETVERSION")){
throw new IllegalArgumentException("This query does not select from the table DATASETVERSION");
}
try{
Query query = em.createNativeQuery(queryString, DatasetVersion.class);
DatasetVersion ds = (DatasetVersion) query.getSingleResult();
msg("Found: " + ds);
return ds;
} catch (NoResultException e) {
msg("DatasetVersion not found: " + queryString);
logger.log(Level.FINE, "DatasetVersion not found: {0}", queryString);
return null;
} catch (EJBException e) {
logger.log(Level.WARNING, "EJBException exception: {0}", e.getMessage());
return null;
}
} // end getDatasetVersionByQuery
/**
* @deprecated because of a typo; use {@link #retrieveDatasetVersionByIdentifierClause(String, String) retrieveDatasetVersionByIdentifierClause} instead
* @see #retrieveDatasetVersionByIdentifierClause(String, String)
* @param identifierClause
* @param version
* @return a DatasetVersion if found, or {@code null} otherwise
*/
@Deprecated
public DatasetVersion retrieveDatasetVersionByIdentiferClause(String identifierClause, String version) {
return retrieveDatasetVersionByIdentifierClause(identifierClause, version);
}
/**
* @param identifierClause
* @param version
* @return a DatasetVersion if found, or {@code null} otherwise
*/
public DatasetVersion retrieveDatasetVersionByIdentifierClause(String identifierClause, String version) {
if (identifierClause == null){
return null;
}
DatasetVersion chosenVersion;
/* --------------------------------------------
(1) Scenario: User asking for a DRAFT?
- (1a) Look for draft
- (1b) Not found: Get Latest Release
- Permissions: check on DatasetPage
-------------------------------------------- */
if (DatasetVersionServiceBean.this.isVersionAskingForDraft(version)){
// (1a) Try to retrieve a draft
msg("(1a) Try to retrieve a draft");
String draftQuery = this.getDraftDatasetVersionQuery(identifierClause);
chosenVersion = this.getDatasetVersionByQuery(draftQuery);
// Draft Exists! Return it!
msg("Draft Exists! Return it!");
if (chosenVersion != null){
return chosenVersion; // let DatasetPage check permissions
}
// (1b) No draft found - check for last released
msg("(1b) No draft found - check for last released");
String lastReleasedQuery = this.getLatestReleasedDatasetVersionQuery(identifierClause);
chosenVersion = this.getDatasetVersionByQuery(lastReleasedQuery);
return chosenVersion; // This may be null -- let DatasetPage check
}
// END: User asking for a Draft
/* --------------------------------------------
(2) Scenario: Version specified
- (2a) Look for major and minor version - RELEASE OR DEACCESSIONED
- OR Look for major version - RELEASE
- (2c) Not found: look for latest released version
- (2c) Not found: look for DEACCESSIONED
- (2d) Not found: look for draft
- Permissions: check on DatasetPage
(3) Scenario: No version specified
- Same as (2c)(2d) above
- Permissions: check on DatasetPage
-------------------------------------------- */
Long[] versionNumbers = parseVersionNumber(version);
if (versionNumbers != null && versionNumbers.length == 2){ // At least a major version found
// (2a) Look for major and minor version - RELEASE OR DEACCESSIONED
msg("(2a) Look for major and minor version -" + Arrays.toString(versionNumbers));
String specificVersionQuery = this.getNumericDatasetVersionQueryByIdentifier(identifierClause, versionNumbers[0], versionNumbers[1]);
chosenVersion = this.getDatasetVersionByQuery(specificVersionQuery);
if (chosenVersion != null){
return chosenVersion;
}
}
// (2b) Look for latest released version
msg("(2b) Look for latest released version");
String latestVersionQuery = this.getLatestReleasedDatasetVersionQuery(identifierClause);
//msg("latestVersionQuery: " + latestVersionQuery);
chosenVersion = this.getDatasetVersionByQuery(latestVersionQuery);
if (chosenVersion != null){
return chosenVersion;
}
// (2c) Look for DEACCESSIONED
msg("(2c) Look for draft");
String dQuery = this.getDeaccessionedDatasetVersionQuery(identifierClause);
//msg("draftQuery: " + draftQuery);
chosenVersion = this.getDatasetVersionByQuery(dQuery);
if (chosenVersion != null){
return chosenVersion;
}
// (2d) Look for draft
msg("(2d) Look for draft");
String draftQuery = this.getDraftDatasetVersionQuery(identifierClause);
//msg("draftQuery: " + draftQuery);
chosenVersion = this.getDatasetVersionByQuery(draftQuery);
return chosenVersion; // This may be null -- let DatasetPage check
} // end: retrieveDatasetVersionByPersistentId
/**
* Find a DatasetVersion using the persisentID and version string
*
* @param persistentId doi:10.5072/FK2/BYM3IW
* @param version "DRAFT", 1.0, 2, 3.4, null, etc
* @return
*/
public RetrieveDatasetVersionResponse retrieveDatasetVersionByPersistentId(String persistentId, String version){
msg("retrieveDatasetVersionByPersistentId: " + persistentId + " " + version);
if (persistentId==null){
return null;
}
/*
Parse the persistent id
*/
GlobalId parsedId;
try{
parsedId = PidUtil.parseAsGlobalID(persistentId); // [ protocol, authority, identifier]
} catch (IllegalArgumentException e){
logger.log(Level.WARNING, "Failed to parse persistentID: {0}", persistentId);
return null;
}
String identifierClause = " AND ds.protocol= '" + parsedId.getProtocol() + "'";
identifierClause += " AND ds.authority = '" + parsedId.getAuthority() + "'";
identifierClause += " AND ds.identifier = '" + parsedId.getIdentifier() + "'";
DatasetVersion ds = retrieveDatasetVersionByIdentifierClause(identifierClause, version);
if (ds != null){
msg("retrieved dataset: " + ds.getId() + " semantic: " + ds.getSemanticVersion());
return new RetrieveDatasetVersionResponse(ds, version);
}
return null;
}
public RetrieveDatasetVersionResponse selectRequestedVersion(List<DatasetVersion> versions, String versionTag) {
Long[] versionNumbers = parseVersionNumber(versionTag);
Long majorVersion = null;
Long minorVersion = null;
if (versionNumbers != null && versionNumbers.length == 2) {
majorVersion = versionNumbers[0];
minorVersion = versionNumbers[1];
}
for (DatasetVersion version : versions) {
if (this.isVersionAskingForDraft(versionTag)) {
if (version.isDraft()) {
return new RetrieveDatasetVersionResponse(version, versionTag);
}
} else if (majorVersion != null && minorVersion != null) {
if (majorVersion.equals(version.getVersionNumber()) && minorVersion.equals(version.getMinorVersionNumber()) && (version.isReleased() || version.isDeaccessioned())) {
return new RetrieveDatasetVersionResponse(version, versionTag);
}
} else if (majorVersion != null) {
if (majorVersion.equals(version.getVersionNumber()) && version.isReleased()) {
return new RetrieveDatasetVersionResponse(version, versionTag);
}
//
}
}
// second pass - grab the first released version:
for (DatasetVersion version : versions) {
if (version.isReleased()) {
return new RetrieveDatasetVersionResponse(version, versionTag);
}
}
// third pass - grab the first (latest!) deaccessioned version
for (DatasetVersion version : versions) {
if (version.isDeaccessioned()) {
return new RetrieveDatasetVersionResponse(version, versionTag);
}
}
// fourth pass - draft is the last choice:
for (DatasetVersion version : versions) {
if (version.isDraft()) {
return new RetrieveDatasetVersionResponse(version, versionTag);
}
}
return null;
}
/**
* Find a DatasetVersion using the persisentID and version string
*
* @param datasetId
* @param version "DRAFT", 1.0, 2, 3.4, null, etc
* @return
*/
public RetrieveDatasetVersionResponse retrieveDatasetVersionById(Long datasetId, String version){
msg("retrieveDatasetVersionById: " + datasetId + " " + version);
DatasetVersion ds = getDatasetVersionById(datasetId, version);
if (ds != null){
return new RetrieveDatasetVersionResponse(ds, version);
}
return null;
} // end: retrieveDatasetVersionById
public DatasetVersion getDatasetVersionById(Long datasetId, String version){
msg("retrieveDatasetVersionById: " + datasetId + " " + version);
if (datasetId==null){
return null;
}
String identifierClause = this.getIdClause(datasetId);
DatasetVersion ds = retrieveDatasetVersionByIdentifierClause(identifierClause, version);
return ds;
} // end: getDatasetVersionById
public DatasetVersion getLatestReleasedVersionFast(Long datasetId) {
String identifierClause = this.getIdClause(datasetId);
String latestVersionQuery = this.getLatestReleasedDatasetVersionQuery(identifierClause);
return this.getDatasetVersionByQuery(latestVersionQuery);
}
private String getIdClause(Long datasetId) {
return " AND ds.id = " + datasetId;
}
/**
* Find a DatasetVersion using the dataset versionId
*
* @param versionId DatasetVersion id
* @return
*/
public RetrieveDatasetVersionResponse retrieveDatasetVersionByVersionId(Long versionId){
//msg("retrieveDatasetVersionById: " + datasetId + " " + versionId);
if (versionId==null ){
return null;
}
// Try versionId - release state doesn't matte
//
String retrieveSpecifiedDSVQuery = "SELECT dv.* FROM DatasetVersion dv WHERE dv.id = " + versionId;
DatasetVersion chosenVersion = this.getDatasetVersionByQuery(retrieveSpecifiedDSVQuery);
if (chosenVersion != null) {
return new RetrieveDatasetVersionResponse(chosenVersion, "");
}
return null;
} // end: retrieveDatasetVersionByVersionId
// This is an optimized, native query-based method for picking an image
// that can be used as the thumbnail for a given dataset/version.
// It is primarily designed to be used when thumbnails are requested
// from the Dataverse page, which is Solr search object based; meaning we
// may not have the Dataset, DatasetVersion, etc. entities initialized.
// And since we may need to look up/generate these thumbnails for a large
// number of search results, actually instantiating full entities for each
// one may be prohibitively expensive. It is also used by the DatasetPage,
// when in read-only, optimized mode, when we similarly try to serve the
// page while minimizing full lookup of entities via EJB.
// (in both cases above the method is called via ThumbnailServiceWrapper)
public Long getThumbnailByVersionId(Long versionId) {
if (versionId == null) {
return null;
}
if (!FeatureFlags.DISABLE_DATASET_THUMBNAIL_AUTOSELECT.enabled()) {
Long thumbnailFileId;
// First, let's see if there are thumbnails that have already been
// generated:
try {
thumbnailFileId = (Long) em.createNativeQuery("SELECT df.id "
+ "FROM datafile df, filemetadata fm, datasetversion dv, dvobject o "
+ "WHERE dv.id = " + versionId + " "
+ "AND df.id = o.id "
+ "AND fm.datasetversion_id = dv.id "
+ "AND fm.datafile_id = df.id "
+ "AND df.restricted = false "
+ "AND df.embargo_id is null "
+ "AND df.retention_id is null "
+ "AND o.previewImageAvailable = true "
+ "ORDER BY df.id LIMIT 1;").getSingleResult();
} catch (Exception ex) {
thumbnailFileId = null;
}
if (thumbnailFileId != null) {
logger.fine("DatasetVersionService,getThumbnailByVersionid(): found already generated thumbnail for version " + versionId + ": " + thumbnailFileId);
assignDatasetThumbnailByNativeQuery(versionId, thumbnailFileId);
return thumbnailFileId;
}
if (!systemConfig.isThumbnailGenerationDisabledForImages()) {
// OK, let's try and generate an image thumbnail!
long imageThumbnailSizeLimit = systemConfig.getThumbnailSizeLimitImage();
try {
thumbnailFileId = (Long) em.createNativeQuery("SELECT df.id "
+ "FROM datafile df, filemetadata fm, datasetversion dv, dvobject o "
+ "WHERE dv.id = " + versionId + " "
+ "AND df.id = o.id "
+ "AND fm.datasetversion_id = dv.id "
+ "AND fm.datafile_id = df.id "
+ "AND o.previewimagefail = false "
+ "AND df.restricted = false "
+ "AND df.embargo_id is null "
+ "AND df.retention_id is null "
+ "AND df.contenttype LIKE 'image/%' "
+ "AND NOT df.contenttype = 'image/fits' "
+ "AND df.filesize < " + imageThumbnailSizeLimit + " "
+ "ORDER BY df.filesize ASC LIMIT 1;").getSingleResult();
} catch (Exception ex) {
thumbnailFileId = null;
}
if (thumbnailFileId != null) {
logger.fine("obtained file id: " + thumbnailFileId);
DataFile thumbnailFile = datafileService.find(thumbnailFileId);
if (thumbnailFile != null) {
if (datafileService.isThumbnailAvailable(thumbnailFile)) {
assignDatasetThumbnailByNativeQuery(versionId, thumbnailFileId);
return thumbnailFileId;
}
}
}
}
// And if that didn't work, try the same thing for PDFs:
if (!systemConfig.isThumbnailGenerationDisabledForPDF()) {
// OK, let's try and generate an image thumbnail!
long imageThumbnailSizeLimit = systemConfig.getThumbnailSizeLimitPDF();
try {
thumbnailFileId = (Long) em.createNativeQuery("SELECT df.id "
+ "FROM datafile df, filemetadata fm, datasetversion dv, dvobject o "
+ "WHERE dv.id = " + versionId + " "
+ "AND df.id = o.id "
+ "AND fm.datasetversion_id = dv.id "
+ "AND fm.datafile_id = df.id "
+ "AND o.previewimagefail = false "
+ "AND df.restricted = false "
+ "AND df.embargo_id is null "
+ "AND df.retention_id is null "
+ "AND df.contenttype = 'application/pdf' "
+ "AND df.filesize < " + imageThumbnailSizeLimit + " "
+ "ORDER BY df.filesize ASC LIMIT 1;").getSingleResult();
} catch (Exception ex) {
thumbnailFileId = null;
}
if (thumbnailFileId != null) {
DataFile thumbnailFile = datafileService.find(thumbnailFileId);
if (thumbnailFile != null) {
if (datafileService.isThumbnailAvailable(thumbnailFile)) {
assignDatasetThumbnailByNativeQuery(versionId, thumbnailFileId);
return thumbnailFileId;
}
}
}
}
}
return null;
}
private void assignDatasetThumbnailByNativeQuery(Long versionId, Long dataFileId) {
try {
em.createNativeQuery("UPDATE dataset SET thumbnailfile_id=" + dataFileId + " WHERE id in (SELECT dataset_id FROM datasetversion WHERE id=" + versionId + ")").executeUpdate();
} catch (Exception ex) {
// it's ok to just ignore...
}
}
public void writeEditVersionLog(DatasetVersionDifference dvd, AuthenticatedUser au) {
String logDir = System.getProperty("com.sun.aas.instanceRoot") + SEP + "logs" + SEP + "edit-drafts" + SEP;
String identifier = dvd.getOriginalVersion().getDataset().getIdentifier();
identifier = identifier.substring(identifier.indexOf("/") + 1);
String datasetId = dvd.getOriginalVersion().getDataset().getId().toString();
String summary = au.getFirstName() + " " + au.getLastName() + " (" + au.getIdentifier() + ") updated " + dvd.getEditSummaryForLog();
String logTimestamp = logFormatter.format(new Date());
String fileName = "/edit-draft-" + datasetId + "-" + identifier + "-" + logTimestamp + ".txt";
LoggingUtil.saveLogFile(summary, logDir, fileName);
}
public void populateDatasetSearchCard(SolrSearchResult solrSearchResult) {
Long dataverseId = Long.parseLong(solrSearchResult.getParent().get("id"));
Long datasetVersionId = solrSearchResult.getDatasetVersionId();
Long datasetId = solrSearchResult.getEntityId();
if (dataverseId == 0) {
return;
}
Object[] searchResult;
try {
if (datasetId != null) {
searchResult = (Object[]) em.createNativeQuery("SELECT t0.VERSIONSTATE, t1.ALIAS, t2.THUMBNAILFILE_ID, t2.USEGENERICTHUMBNAIL, t3.STORAGEIDENTIFIER FROM DATASETVERSION t0, DATAVERSE t1, DATASET t2, DVOBJECT t3 WHERE t0.ID = "
+ datasetVersionId
+ " AND t1.ID = "
+ dataverseId
+ " AND t2.ID = "
+ datasetId
+ " AND t2.ID = t3.ID").getSingleResult()
;
} else {
// Why is this method ever called with dataset_id = null? -- L.A.
searchResult = (Object[]) em.createNativeQuery("SELECT t0.VERSIONSTATE, t1.ALIAS FROM DATASETVERSION t0, DATAVERSE t1 WHERE t0.ID = " + datasetVersionId + " AND t1.ID = " + dataverseId).getSingleResult();
}
} catch (Exception ex) {
return;
}
if (searchResult == null) {
return;
}
if (searchResult[0] != null) {
String versionState = (String)searchResult[0];
if ("DEACCESSIONED".equals(versionState)) {
solrSearchResult.setDeaccessionedState(true);
}
}
/**
* @todo (from pdurbin) can a dataverse alias ever be null?
*/
if (searchResult[1] != null) {
solrSearchResult.setDataverseAlias((String) searchResult[1]);
}
if (searchResult.length == 5) {
Dataset datasetEntity = new Dataset();
String globalIdentifier = solrSearchResult.getIdentifier();
GlobalId globalId = PidUtil.parseAsGlobalID(globalIdentifier);
datasetEntity.setProtocol(globalId.getProtocol());
datasetEntity.setAuthority(globalId.getAuthority());
datasetEntity.setIdentifier(globalId.getIdentifier());
if (searchResult[4] != null) {
datasetEntity.setStorageIdentifier(searchResult[4].toString());
}
solrSearchResult.setEntity(datasetEntity);
if (searchResult[2] != null) {
// This is the image file specifically assigned as the "icon" for
// the dataset:
Long thumbnailFile_id = (Long) searchResult[2];
if (thumbnailFile_id != null) {
DataFile thumbnailFile;
try {
thumbnailFile = datafileService.findCheapAndEasy(thumbnailFile_id);
} catch (Exception ex) {
thumbnailFile = null;