#22002

Committed 01 Apr 2024 07:56PM CUT coverage: 20.716% (+0.5%) from 20.173%

Build # #22002

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web-flow

Commit Message

Merge pull request #10453 from IQSS/develop

Merge 6.2 into master

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81 existing lines in 49 files now uncovered.

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/src/main/java/edu/harvard/iq/dataverse/DvObjectServiceBean.java

package edu.harvard.iq.dataverse;

import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.pidproviders.PidProvider;
import edu.harvard.iq.dataverse.pidproviders.PidProviderFactoryBean;
import edu.harvard.iq.dataverse.pidproviders.PidUtil;
import java.sql.Timestamp;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;

import jakarta.ejb.EJB;
import jakarta.ejb.Stateless;
import jakarta.ejb.TransactionAttribute;
import static jakarta.ejb.TransactionAttributeType.REQUIRES_NEW;
import jakarta.inject.Named;
import jakarta.persistence.EntityManager;
import jakarta.persistence.NoResultException;
import jakarta.persistence.NonUniqueResultException;
import jakarta.persistence.PersistenceContext;
import jakarta.persistence.Query;
import jakarta.persistence.StoredProcedureQuery;

import org.apache.commons.lang3.StringUtils;

/**
 * Your goto bean for everything {@link DvObject}, that's not tied to any
 * concrete subclass.
 *
 * @author michael
 */
@Stateless
@Named
public class DvObjectServiceBean implements java.io.Serializable {

    @PersistenceContext(unitName = "VDCNet-ejbPU")
    private EntityManager em;
    
    @EJB
    PidProviderFactoryBean pidProviderFactoryBean;
    
    private static final Logger logger = Logger.getLogger(DvObjectServiceBean.class.getCanonicalName());
    /**
     * @param dvoc The object we check
     * @return {@code true} iff the passed object is the owner of any
     * {@link DvObject}.
     */
    public boolean hasData(DvObjectContainer dvoc) {
        return em.createNamedQuery("DvObject.ownedObjectsById", Long.class)
                .setParameter("id", dvoc.getId())
                .getSingleResult() > 0;
    }

    public DvObject findDvObject(Long id) {
        try {
            return em.createNamedQuery("DvObject.findById", DvObject.class)
                    .setParameter("id", id)
                    .getSingleResult();
        } catch (NoResultException | NonUniqueResultException ex) {
            return null;
        }
    }

    public List<DvObject> findAll() {
        return em.createNamedQuery("DvObject.findAll", DvObject.class).getResultList();
    }
    
    
    public List<DvObject> findByOwnerId(Long ownerId) {
        return em.createNamedQuery("DvObject.findByOwnerId").setParameter("ownerId", ownerId).getResultList();
    }
    
    public List<DvObject> findByAuthenticatedUserId(AuthenticatedUser user) {
        Query query = em.createNamedQuery("DvObject.findByAuthenticatedUserId"); 
        query.setParameter("ownerId", user.getId());
        query.setParameter("releaseUserId", user.getId());
        return query.getResultList();
    }
    
    public boolean checkExists(Long id) {
        Query query = em.createNamedQuery("DvObject.checkExists");
        query.setParameter("id", id);
        Long result =(Long)query.getSingleResult();
        return result > 0;
    }   

    public DvObject findByGlobalId(String globalIdString, DvObject.DType dtype) {
        try {
            GlobalId gid = PidUtil.parseAsGlobalID(globalIdString);
            return findByGlobalId(gid, dtype);
        } catch (IllegalArgumentException iae) {
            logger.fine("Invalid identifier: " + globalIdString);
            return null;
        }

    }
    
    public DvObject findByAltGlobalId(String globalIdString, DvObject.DType dtype) {
        try {
            GlobalId gid = PidUtil.parseAsGlobalID(globalIdString);
            return findByAltGlobalId(gid, dtype);
        } catch (IllegalArgumentException iae) {
            logger.fine("Invalid alternate identifier: " + globalIdString);
            return null;
        }

    }

    public DvObject findByGlobalId(GlobalId globalId, DvObject.DType dtype) {
        Query query = em.createNamedQuery("DvObject.findByGlobalId");
        return runFindByGlobalId(query, globalId, dtype);
    }

    public DvObject findByAltGlobalId(GlobalId globalId, DvObject.DType dtype) {
        Query query = em.createNamedQuery("DvObject.findByAlternativeGlobalId");
        return runFindByGlobalId(query, globalId, dtype);
    }

    public Long findIdByGlobalId(GlobalId globalId, DvObject.DType dtype) {
        Query query = em.createNamedQuery("DvObject.findIdByGlobalId");
        return runFindIdByGlobalId(query, globalId, dtype);
    }

    public Long findIdByAltGlobalId(GlobalId globalId, DvObject.DType dtype) {
        Query query = em.createNamedQuery("DvObject.findIdByAlternativeGlobalId");
        return runFindIdByGlobalId(query, globalId, dtype);
    }

    private DvObject runFindByGlobalId(Query query, GlobalId gid, DvObject.DType dtype) {
        DvObject foundDvObject = null;
        try {
            query.setParameter("identifier", gid.getIdentifier());
            query.setParameter("protocol", gid.getProtocol());
            query.setParameter("authority", gid.getAuthority());
            query.setParameter("dtype", dtype.getDType());
            foundDvObject = (DvObject) query.getSingleResult();
        } catch (NoResultException e) {
            // (set to .info, this can fill the log file with thousands of
            // these messages during a large harvest run)
            logger.fine("no dvObject found: " + gid.asString());
            // DO nothing, just return null.
            return null;
        } catch (Exception ex) {
            logger.info("Exception caught in findByGlobalId: " + ex.getLocalizedMessage());
            return null;
        }
        return foundDvObject;
    }

    private Long runFindIdByGlobalId(Query query, GlobalId gid, DvObject.DType dtype) {
        Long foundDvObject = null;
        try {
            query.setParameter("identifier", gid.getIdentifier());
            query.setParameter("protocol", gid.getProtocol());
            query.setParameter("authority", gid.getAuthority());
            query.setParameter("dtype", dtype.getDType());
            foundDvObject = (Long) query.getSingleResult();
        } catch (NoResultException e) {
            // (set to .info, this can fill the log file with thousands of
            // these messages during a large harvest run)
            logger.fine("no dvObject found: " + gid.asString());
            // DO nothing, just return null.
            return null;
        } catch (Exception ex) {
            logger.info("Exception caught in findByGlobalId: " + ex.getLocalizedMessage());
            return null;
        }
        return foundDvObject;
    }
    
    public DvObject findByGlobalId(GlobalId globalId) {
        try {
            return (DvObject) em.createNamedQuery("DvObject.findByProtocolIdentifierAuthority")
                    .setParameter("identifier", globalId.getIdentifier())
                    .setParameter("authority", globalId.getAuthority()).setParameter("protocol", globalId.getProtocol())
                    .getSingleResult();
        } catch (NoResultException nre) {
            return null;
        }
    }
    
    public boolean isGlobalIdLocallyUnique(GlobalId globalId) {
        return em.createNamedQuery("DvObject.findByProtocolIdentifierAuthority")
            .setParameter("identifier", globalId.getIdentifier())
            .setParameter("authority", globalId.getAuthority())
            .setParameter("protocol", globalId.getProtocol())
            .getResultList().isEmpty();
    }

    public DvObject updateContentIndexTime(DvObject dvObject) {
        /**
         * @todo to avoid a possible OptimisticLockException, should we merge
         * dvObject before we try to setIndexTime? See
         * https://github.com/IQSS/dataverse/commit/6ad0ebb272c8cb46368cb76784b55dbf33eea947
         */
        DvObject dvObjectToModify = findDvObject(dvObject.getId());
        dvObjectToModify.setIndexTime(new Timestamp(new Date().getTime()));
        DvObject savedDvObject = em.merge(dvObjectToModify);
        return savedDvObject;
    }

    /**
     * @param dvObject
     * @return 
     * @todo DRY! Perhaps we should merge this with the older
     * updateContentIndexTime method.
     */
    public DvObject updatePermissionIndexTime(DvObject dvObject) {
        /**
         * @todo to avoid a possible OptimisticLockException, should we merge
         * dvObject before we try to set this timestamp? See
         * https://github.com/IQSS/dataverse/commit/6ad0ebb272c8cb46368cb76784b55dbf33eea947
         */
        Long dvObjectId = dvObject.getId();
        DvObject dvObjectToModify = findDvObject(dvObjectId);
        if (dvObjectToModify == null) {
            logger.log(Level.FINE, "Unable to update permission index time on DvObject with id of {0}", dvObjectId);
            return dvObject;
        }
        dvObjectToModify.setPermissionIndexTime(new Timestamp(new Date().getTime()));
        DvObject savedDvObject = em.merge(dvObjectToModify);
        logger.log(Level.FINE, "Updated permission index time for DvObject id {0}", dvObjectId);
        return savedDvObject;
    }

    @TransactionAttribute(REQUIRES_NEW)
    public int clearAllIndexTimes() {
        Query clearIndexTimes = em.createQuery("UPDATE DvObject o SET o.indexTime = NULL, o.permissionIndexTime = NULL");
        int numRowsUpdated = clearIndexTimes.executeUpdate();
        return numRowsUpdated;
    }

    public int clearIndexTimes(long dvObjectId) {
        Query clearIndexTimes = em.createQuery("UPDATE DvObject o SET o.indexTime = NULL, o.permissionIndexTime = NULL WHERE o.id =:dvObjectId");
        clearIndexTimes.setParameter("dvObjectId", dvObjectId);
        int numRowsUpdated = clearIndexTimes.executeUpdate();
        return numRowsUpdated;
    }
    
    private String getDvObjectIdListClause(List<Long> dvObjectIdList){
        if (dvObjectIdList == null){
            return null;
        }
        List<String> outputList = new ArrayList<>();
        
        for(Long id : dvObjectIdList){
            if (id != null){
                outputList.add(id.toString());
            }
        }
        if (outputList.isEmpty()){
            return null;
        }        
        return " (" + StringUtils.join(outputList, ",") + ")";        
    }
    
    public List<Object[]> getDvObjectInfoForMyData(List<Long> dvObjectIdList){
        //msgt("getAssigneeAndRoleIdListFor");

        String dvObjectClause = getDvObjectIdListClause(dvObjectIdList);
        if (dvObjectClause==null){
            return null;
        }
        
        String qstr = "SELECT dv.id, dv.dtype, dv.owner_id"; // dv.modificationtime,
        qstr += " FROM dvobject dv";
        qstr += " WHERE  dv.id IN " + dvObjectClause;
        qstr += ";";

        return em.createNativeQuery(qstr).getResultList();
        
    }
    
    /**
     * Used for retrieving DvObject based on a list of parent Ids
     *  MyData use case: The Dataverse has file permissions and we want to know 
     *  the Datasets under that Dataverse (and subsequently query files by
     *  their parent id--but in solr)
     * 
     * @param dvObjectParentIdList
     * @return 
     */
    public List<Object[]> getDvObjectInfoByParentIdForMyData(List<Long> dvObjectParentIdList){
        //msgt("getAssigneeAndRoleIdListFor");

        String dvObjectClause = getDvObjectIdListClause(dvObjectParentIdList);
        if (dvObjectClause==null){
            return null;
        }
        
        String qstr = "SELECT dv.id, dv.dtype, dv.owner_id"; // dv.modificationtime,
        qstr += " FROM dvobject dv";
        qstr += " WHERE  dv.owner_id IN " + dvObjectClause;
        qstr += ";";

        return em.createNativeQuery(qstr).getResultList();
        
    }
    
    /**
     * Used to exclude Harvested Data from the Mydata page
     * 
     * @return 
     */
    public List<Long> getAllHarvestedDataverseIds(){
        
        String qstr = "SELECT h.dataverse_id FROM harvestingclient h;";

        return em.createNativeQuery(qstr).getResultList();
        
    }
    
    /**
     * Used to calculate the dvObject tree paths for the search results on the
     * dataverse page. (In order to determine if "linked" or not).
     * *done in recursive 1 query!*
     * 
     * @param objectIds
     * @return 
     */
    public Map<Long, String> getObjectPathsByIds(Set<Long> objectIds){
        if (objectIds == null || objectIds.size() < 1) {
            return null;
        }
        
        String datasetIdStr = StringUtils.join(objectIds, ", ");
        
        String qstr = "WITH RECURSIVE path_elements AS ((" +
            " SELECT id, owner_id FROM dvobject WHERE id in (" + datasetIdStr + "))" +
            " UNION\n" +
            " SELECT o.id, o.owner_id FROM path_elements p, dvobject o WHERE o.id = p.owner_id) " +
            "SELECT id, owner_id FROM path_elements WHERE owner_id IS NOT NULL;"; // ORDER by id ASC;";
        
        List<Object[]> searchResults;
        
        try {
            searchResults = em.createNativeQuery(qstr).getResultList();
        } catch (Exception ex) {
            searchResults = null;
        }
        
        if (searchResults == null || searchResults.size() < 1) {
            return null;
        }
        
        Map<Long, Long> treeMap = new HashMap<>();
        
        for (Object[] result : searchResults) {
            Long objectId;
            Long ownerId;
            if (result[0] != null) {
                try {
                    objectId = ((Integer) result[0]).longValue();
                } catch (Exception ex) {
                    logger.warning("OBJECT PATH: could not cast result[0] (dvobject id) to Integer!");
                    objectId = null;
                }
                if (objectId == null) {
                    continue;
                }
                
                ownerId = (Long)result[1];
                logger.fine("OBJECT PATH: id: "+objectId+", owner: "+ownerId);
                if (ownerId != null && (ownerId != 1L)) {
                    treeMap.put(objectId, ownerId);
                }
            }
        }
        
        Map<Long, String> ret = new HashMap<>();
        
        for (Long objectId : objectIds) {
            String treePath = "/" + objectId;
            Long treePosition = treeMap.get(objectId);
            
            while (treePosition != null) {
                treePath = "/" + treePosition + treePath;
                treePosition = treeMap.get(treePosition);
            }
            
            logger.fine("OBJECT PATH: returning "+treePath+" for "+objectId);
            ret.put(objectId, treePath);
        }
        return ret;        
    }
    
    public String generateNewIdentifierByStoredProcedure() {
        StoredProcedureQuery query = this.em.createNamedStoredProcedureQuery("Dataset.generateIdentifierFromStoredProcedure");
        query.execute();
        return (String) query.getOutputParameterValue(1);
    }
    
    /** @deprecated Backward-compatibility method to get the effective pid generator for a DvObjectContainer.
     * If the dvObjectContainer method fails, this method will check for the old global default settings.
     * If/when those are no longer supported, this method can be removed and replaced with calls directly 
     * to dvObjectContainer.getEffectivePidGenerator();
     * 
     */
    @Deprecated(forRemoval = true, since = "2024-02-09")
    public PidProvider getEffectivePidGenerator(DvObjectContainer dvObjectContainer) {
        PidProvider pidGenerator = dvObjectContainer.getEffectivePidGenerator();
        if (pidGenerator == null) {
            pidGenerator = pidProviderFactoryBean.getDefaultPidGenerator();
        }
        return pidGenerator;
    }
    
}

1	package edu.harvard.iq.dataverse;
2
3	import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
4	import edu.harvard.iq.dataverse.pidproviders.PidProvider;
5	import edu.harvard.iq.dataverse.pidproviders.PidProviderFactoryBean;
6	import edu.harvard.iq.dataverse.pidproviders.PidUtil;
7	import java.sql.Timestamp;
8	import java.util.ArrayList;
9	import java.util.Date;
10	import java.util.HashMap;
11	import java.util.List;
12	import java.util.Map;
13	import java.util.Set;
14	import java.util.logging.Level;
15	import java.util.logging.Logger;
16
17	import jakarta.ejb.EJB;
18	import jakarta.ejb.Stateless;
19	import jakarta.ejb.TransactionAttribute;
20	import static jakarta.ejb.TransactionAttributeType.REQUIRES_NEW;
21	import jakarta.inject.Named;
22	import jakarta.persistence.EntityManager;
23	import jakarta.persistence.NoResultException;
24	import jakarta.persistence.NonUniqueResultException;
25	import jakarta.persistence.PersistenceContext;
26	import jakarta.persistence.Query;
27	import jakarta.persistence.StoredProcedureQuery;
28
29	import org.apache.commons.lang3.StringUtils;
30
31	/**
32	* Your goto bean for everything {@link DvObject}, that's not tied to any
33	* concrete subclass.
34	*
35	* @author michael
36	*/
37	@Stateless
38	@Named
39	public class DvObjectServiceBean implements java.io.Serializable {	×
40
41	@PersistenceContext(unitName = "VDCNet-ejbPU")
42	private EntityManager em;
43
44	@EJB
45	PidProviderFactoryBean pidProviderFactoryBean;
46
UNCOV 47	private static final Logger logger = Logger.getLogger(DvObjectServiceBean.class.getCanonicalName());	×
48	/**
49	* @param dvoc The object we check
50	* @return {@code true} iff the passed object is the owner of any
51	* {@link DvObject}.
52	*/
53	public boolean hasData(DvObjectContainer dvoc) {
54	return em.createNamedQuery("DvObject.ownedObjectsById", Long.class)	×
55	.setParameter("id", dvoc.getId())	×
56	.getSingleResult() > 0;	×
57	}
58
59	public DvObject findDvObject(Long id) {
60	try {
61	return em.createNamedQuery("DvObject.findById", DvObject.class)	×
62	.setParameter("id", id)	×
63	.getSingleResult();	×
64	} catch (NoResultException \| NonUniqueResultException ex) {	×
65	return null;	×
66	}
67	}
68
69	public List<DvObject> findAll() {
70	return em.createNamedQuery("DvObject.findAll", DvObject.class).getResultList();	×
71	}
72
73
74	public List<DvObject> findByOwnerId(Long ownerId) {
75	return em.createNamedQuery("DvObject.findByOwnerId").setParameter("ownerId", ownerId).getResultList();	×
76	}
77
78	public List<DvObject> findByAuthenticatedUserId(AuthenticatedUser user) {
79	Query query = em.createNamedQuery("DvObject.findByAuthenticatedUserId");	×
80	query.setParameter("ownerId", user.getId());	×
81	query.setParameter("releaseUserId", user.getId());	×
82	return query.getResultList();	×
83	}
84
85	public boolean checkExists(Long id) {
86	Query query = em.createNamedQuery("DvObject.checkExists");	×
87	query.setParameter("id", id);	×
88	Long result =(Long)query.getSingleResult();	×
89	return result > 0;	×
90	}
91
92	public DvObject findByGlobalId(String globalIdString, DvObject.DType dtype) {
93	try {
94	GlobalId gid = PidUtil.parseAsGlobalID(globalIdString);	×
95	return findByGlobalId(gid, dtype);	×
96	} catch (IllegalArgumentException iae) {	×
97	logger.fine("Invalid identifier: " + globalIdString);	×
98	return null;	×
99	}
100
101	}
102
103	public DvObject findByAltGlobalId(String globalIdString, DvObject.DType dtype) {
104	try {
105	GlobalId gid = PidUtil.parseAsGlobalID(globalIdString);	×
106	return findByAltGlobalId(gid, dtype);	×
107	} catch (IllegalArgumentException iae) {	×
108	logger.fine("Invalid alternate identifier: " + globalIdString);	×
109	return null;	×
110	}
111
112	}
113
114	public DvObject findByGlobalId(GlobalId globalId, DvObject.DType dtype) {
115	Query query = em.createNamedQuery("DvObject.findByGlobalId");	×
116	return runFindByGlobalId(query, globalId, dtype);	×
117	}
118
119	public DvObject findByAltGlobalId(GlobalId globalId, DvObject.DType dtype) {
120	Query query = em.createNamedQuery("DvObject.findByAlternativeGlobalId");	×
121	return runFindByGlobalId(query, globalId, dtype);	×
122	}
123
124	public Long findIdByGlobalId(GlobalId globalId, DvObject.DType dtype) {
125	Query query = em.createNamedQuery("DvObject.findIdByGlobalId");	×
126	return runFindIdByGlobalId(query, globalId, dtype);	×
127	}
128
129	public Long findIdByAltGlobalId(GlobalId globalId, DvObject.DType dtype) {
130	Query query = em.createNamedQuery("DvObject.findIdByAlternativeGlobalId");	×
131	return runFindIdByGlobalId(query, globalId, dtype);	×
132	}
133
134	private DvObject runFindByGlobalId(Query query, GlobalId gid, DvObject.DType dtype) {
135	DvObject foundDvObject = null;	×
136	try {
137	query.setParameter("identifier", gid.getIdentifier());	×
138	query.setParameter("protocol", gid.getProtocol());	×
139	query.setParameter("authority", gid.getAuthority());	×
140	query.setParameter("dtype", dtype.getDType());	×
141	foundDvObject = (DvObject) query.getSingleResult();	×
142	} catch (NoResultException e) {	×
143	// (set to .info, this can fill the log file with thousands of
144	// these messages during a large harvest run)
145	logger.fine("no dvObject found: " + gid.asString());	×
146	// DO nothing, just return null.
147	return null;	×
148	} catch (Exception ex) {	×
149	logger.info("Exception caught in findByGlobalId: " + ex.getLocalizedMessage());	×
150	return null;	×
151	}	×
152	return foundDvObject;	×
153	}
154
155	private Long runFindIdByGlobalId(Query query, GlobalId gid, DvObject.DType dtype) {
156	Long foundDvObject = null;	×
157	try {
158	query.setParameter("identifier", gid.getIdentifier());	×
159	query.setParameter("protocol", gid.getProtocol());	×
160	query.setParameter("authority", gid.getAuthority());	×
161	query.setParameter("dtype", dtype.getDType());	×
162	foundDvObject = (Long) query.getSingleResult();	×
163	} catch (NoResultException e) {	×
164	// (set to .info, this can fill the log file with thousands of
165	// these messages during a large harvest run)
166	logger.fine("no dvObject found: " + gid.asString());	×
167	// DO nothing, just return null.
168	return null;	×
169	} catch (Exception ex) {	×
170	logger.info("Exception caught in findByGlobalId: " + ex.getLocalizedMessage());	×
171	return null;	×
172	}	×
173	return foundDvObject;	×
174	}
175
176	public DvObject findByGlobalId(GlobalId globalId) {
177	try {
178	return (DvObject) em.createNamedQuery("DvObject.findByProtocolIdentifierAuthority")	×
179	.setParameter("identifier", globalId.getIdentifier())	×
180	.setParameter("authority", globalId.getAuthority()).setParameter("protocol", globalId.getProtocol())	×
181	.getSingleResult();	×
182	} catch (NoResultException nre) {	×
183	return null;	×
184	}
185	}
186
187	public boolean isGlobalIdLocallyUnique(GlobalId globalId) {
188	return em.createNamedQuery("DvObject.findByProtocolIdentifierAuthority")	×
189	.setParameter("identifier", globalId.getIdentifier())	×
190	.setParameter("authority", globalId.getAuthority())	×
191	.setParameter("protocol", globalId.getProtocol())	×
192	.getResultList().isEmpty();	×
193	}
194
195	public DvObject updateContentIndexTime(DvObject dvObject) {
196	/**
197	* @todo to avoid a possible OptimisticLockException, should we merge
198	* dvObject before we try to setIndexTime? See
199	* https://github.com/IQSS/dataverse/commit/6ad0ebb272c8cb46368cb76784b55dbf33eea947
200	*/
201	DvObject dvObjectToModify = findDvObject(dvObject.getId());	×
202	dvObjectToModify.setIndexTime(new Timestamp(new Date().getTime()));	×
203	DvObject savedDvObject = em.merge(dvObjectToModify);	×
204	return savedDvObject;	×
205	}
206
207	/**
208	* @param dvObject
209	* @return
210	* @todo DRY! Perhaps we should merge this with the older
211	* updateContentIndexTime method.
212	*/
213	public DvObject updatePermissionIndexTime(DvObject dvObject) {
214	/**
215	* @todo to avoid a possible OptimisticLockException, should we merge
216	* dvObject before we try to set this timestamp? See
217	* https://github.com/IQSS/dataverse/commit/6ad0ebb272c8cb46368cb76784b55dbf33eea947
218	*/
219	Long dvObjectId = dvObject.getId();	×
220	DvObject dvObjectToModify = findDvObject(dvObjectId);	×
221	if (dvObjectToModify == null) {	×
222	logger.log(Level.FINE, "Unable to update permission index time on DvObject with id of {0}", dvObjectId);	×
223	return dvObject;	×
224	}
225	dvObjectToModify.setPermissionIndexTime(new Timestamp(new Date().getTime()));	×
226	DvObject savedDvObject = em.merge(dvObjectToModify);	×
227	logger.log(Level.FINE, "Updated permission index time for DvObject id {0}", dvObjectId);	×
228	return savedDvObject;	×
229	}
230
231	@TransactionAttribute(REQUIRES_NEW)
232	public int clearAllIndexTimes() {
233	Query clearIndexTimes = em.createQuery("UPDATE DvObject o SET o.indexTime = NULL, o.permissionIndexTime = NULL");	×
234	int numRowsUpdated = clearIndexTimes.executeUpdate();	×
235	return numRowsUpdated;	×
236	}
237
238	public int clearIndexTimes(long dvObjectId) {
239	Query clearIndexTimes = em.createQuery("UPDATE DvObject o SET o.indexTime = NULL, o.permissionIndexTime = NULL WHERE o.id =:dvObjectId");	×
240	clearIndexTimes.setParameter("dvObjectId", dvObjectId);	×
241	int numRowsUpdated = clearIndexTimes.executeUpdate();	×
242	return numRowsUpdated;	×
243	}
244
245	private String getDvObjectIdListClause(List<Long> dvObjectIdList){
246	if (dvObjectIdList == null){	×
247	return null;	×
248	}
249	List<String> outputList = new ArrayList<>();	×
250
251	for(Long id : dvObjectIdList){	×
252	if (id != null){	×
253	outputList.add(id.toString());	×
254	}
255	}	×
256	if (outputList.isEmpty()){	×
257	return null;	×
258	}
259	return " (" + StringUtils.join(outputList, ",") + ")";	×
260	}
261
262	public List<Object[]> getDvObjectInfoForMyData(List<Long> dvObjectIdList){
263	//msgt("getAssigneeAndRoleIdListFor");
264
265	String dvObjectClause = getDvObjectIdListClause(dvObjectIdList);	×
266	if (dvObjectClause==null){	×
267	return null;	×
268	}
269
270	String qstr = "SELECT dv.id, dv.dtype, dv.owner_id"; // dv.modificationtime,	×
271	qstr += " FROM dvobject dv";	×
272	qstr += " WHERE dv.id IN " + dvObjectClause;	×
273	qstr += ";";	×
274
275	return em.createNativeQuery(qstr).getResultList();	×
276
277	}
278
279	/**
280	* Used for retrieving DvObject based on a list of parent Ids
281	* MyData use case: The Dataverse has file permissions and we want to know
282	* the Datasets under that Dataverse (and subsequently query files by
283	* their parent id--but in solr)
284	*
285	* @param dvObjectParentIdList
286	* @return
287	*/
288	public List<Object[]> getDvObjectInfoByParentIdForMyData(List<Long> dvObjectParentIdList){
289	//msgt("getAssigneeAndRoleIdListFor");
290
291	String dvObjectClause = getDvObjectIdListClause(dvObjectParentIdList);	×
292	if (dvObjectClause==null){	×
293	return null;	×
294	}
295
296	String qstr = "SELECT dv.id, dv.dtype, dv.owner_id"; // dv.modificationtime,	×
297	qstr += " FROM dvobject dv";	×
298	qstr += " WHERE dv.owner_id IN " + dvObjectClause;	×
299	qstr += ";";	×
300
301	return em.createNativeQuery(qstr).getResultList();	×
302
303	}
304
305	/**
306	* Used to exclude Harvested Data from the Mydata page
307	*
308	* @return
309	*/
310	public List<Long> getAllHarvestedDataverseIds(){
311
312	String qstr = "SELECT h.dataverse_id FROM harvestingclient h;";	×
313
314	return em.createNativeQuery(qstr).getResultList();	×
315
316	}
317
318	/**
319	* Used to calculate the dvObject tree paths for the search results on the
320	* dataverse page. (In order to determine if "linked" or not).
321	* done in recursive 1 query!
322	*
323	* @param objectIds
324	* @return
325	*/
326	public Map<Long, String> getObjectPathsByIds(Set<Long> objectIds){
327	if (objectIds == null \|\| objectIds.size() < 1) {	×
328	return null;	×
329	}
330
331	String datasetIdStr = StringUtils.join(objectIds, ", ");	×
332
333	String qstr = "WITH RECURSIVE path_elements AS ((" +	×
334	" SELECT id, owner_id FROM dvobject WHERE id in (" + datasetIdStr + "))" +
335	" UNION\n" +
336	" SELECT o.id, o.owner_id FROM path_elements p, dvobject o WHERE o.id = p.owner_id) " +
337	"SELECT id, owner_id FROM path_elements WHERE owner_id IS NOT NULL;"; // ORDER by id ASC;";
338
339	List<Object[]> searchResults;
340
341	try {
342	searchResults = em.createNativeQuery(qstr).getResultList();	×
343	} catch (Exception ex) {	×
344	searchResults = null;	×
345	}	×
346
347	if (searchResults == null \|\| searchResults.size() < 1) {	×
348	return null;	×
349	}
350
351	Map<Long, Long> treeMap = new HashMap<>();	×
352
353	for (Object[] result : searchResults) {	×
354	Long objectId;
355	Long ownerId;
356	if (result[0] != null) {	×
357	try {
358	objectId = ((Integer) result[0]).longValue();	×
359	} catch (Exception ex) {	×
360	logger.warning("OBJECT PATH: could not cast result[0] (dvobject id) to Integer!");	×
361	objectId = null;	×
362	}	×
363	if (objectId == null) {	×
364	continue;	×
365	}
366
367	ownerId = (Long)result[1];	×
368	logger.fine("OBJECT PATH: id: "+objectId+", owner: "+ownerId);	×
369	if (ownerId != null && (ownerId != 1L)) {	×
370	treeMap.put(objectId, ownerId);	×
371	}
372	}
373	}	×
374
375	Map<Long, String> ret = new HashMap<>();	×
376
377	for (Long objectId : objectIds) {	×
378	String treePath = "/" + objectId;	×
379	Long treePosition = treeMap.get(objectId);	×
380
381	while (treePosition != null) {	×
382	treePath = "/" + treePosition + treePath;	×
383	treePosition = treeMap.get(treePosition);	×
384	}
385
386	logger.fine("OBJECT PATH: returning "+treePath+" for "+objectId);	×
387	ret.put(objectId, treePath);	×
388	}	×
389	return ret;	×
390	}
391
392	public String generateNewIdentifierByStoredProcedure() {
393	StoredProcedureQuery query = this.em.createNamedStoredProcedureQuery("Dataset.generateIdentifierFromStoredProcedure");	×
394	query.execute();	×
395	return (String) query.getOutputParameterValue(1);	×
396	}
397
398	/** @deprecated Backward-compatibility method to get the effective pid generator for a DvObjectContainer.
399	* If the dvObjectContainer method fails, this method will check for the old global default settings.
400	* If/when those are no longer supported, this method can be removed and replaced with calls directly
401	* to dvObjectContainer.getEffectivePidGenerator();
402	*
403	*/
404	@Deprecated(forRemoval = true, since = "2024-02-09")
405	public PidProvider getEffectivePidGenerator(DvObjectContainer dvObjectContainer) {
NEW 406	PidProvider pidGenerator = dvObjectContainer.getEffectivePidGenerator();	×
NEW 407	if (pidGenerator == null) {	×
NEW 408	pidGenerator = pidProviderFactoryBean.getDefaultPidGenerator();	×
409	}
NEW 410	return pidGenerator;	×
411	}
412
413	}

IQSS / dataverse / #22002

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