1370

Committed 26 Jun 2024 06:59AM UTC coverage: 25.503% (-0.004%) from 25.507%

Build # 1370

Build Type

push

jenkins

Committed by

web-flow

Commit Message

Closes #2496: Make the banner link optional (#2503)

Run Details

17782 of 69725 relevant lines covered (25.5%)

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44.62

/dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/dataset/DatasetService.java

package edu.harvard.iq.dataverse.dataset;

import edu.harvard.iq.dataverse.DatasetDao;
import edu.harvard.iq.dataverse.DatasetPage;
import edu.harvard.iq.dataverse.DataverseRequestServiceBean;
import edu.harvard.iq.dataverse.DataverseSession;
import edu.harvard.iq.dataverse.EjbDataverseEngine;
import edu.harvard.iq.dataverse.PermissionServiceBean;
import edu.harvard.iq.dataverse.annotations.PermissionNeeded;
import edu.harvard.iq.dataverse.api.AbstractApiBean;
import edu.harvard.iq.dataverse.engine.command.exception.NotAuthenticatedException;
import edu.harvard.iq.dataverse.engine.command.impl.CreateNewDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetGuestbookCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetThumbnailCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand;
import edu.harvard.iq.dataverse.ingest.IngestServiceBean;
import edu.harvard.iq.dataverse.interceptors.LoggedCall;
import edu.harvard.iq.dataverse.interceptors.Restricted;
import edu.harvard.iq.dataverse.interceptors.SuperuserRequired;
import edu.harvard.iq.dataverse.notification.NotificationObjectType;
import edu.harvard.iq.dataverse.notification.UserNotificationService;
import edu.harvard.iq.dataverse.persistence.datafile.DataFile;
import edu.harvard.iq.dataverse.persistence.dataset.Dataset;
import edu.harvard.iq.dataverse.persistence.dataset.DatasetLock;
import edu.harvard.iq.dataverse.persistence.dataset.Template;
import edu.harvard.iq.dataverse.persistence.user.AuthenticatedUser;
import edu.harvard.iq.dataverse.persistence.user.NotificationType;
import edu.harvard.iq.dataverse.persistence.user.Permission;
import edu.harvard.iq.dataverse.provenance.ProvPopupFragmentBean;
import edu.harvard.iq.dataverse.search.index.SolrIndexServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;

import javax.ejb.Stateless;
import javax.ejb.TransactionAttribute;
import javax.ejb.TransactionAttributeType;
import javax.inject.Inject;
import java.io.InputStream;
import java.time.Clock;
import java.time.Instant;
import java.util.Date;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;

@Stateless
public class DatasetService {

    private static final Logger logger = Logger.getLogger(DatasetPage.class.getCanonicalName());
    private static final String DATASET_LOCKED_FOR_UPDATE_MESSAGE = "Update embargo date failed. Dataset is locked. ";
    private static final String DATASET_IN_WRONG_STATE_MESSAGE = "Setting embargo date failed. Dataset is in a non-editable state.";

    private EjbDataverseEngine commandEngine;
    private UserNotificationService userNotificationService;
    private DatasetDao datasetDao;
    private DataverseSession session;
    private DataverseRequestServiceBean dvRequestService;
    private IngestServiceBean ingestService;
    private SettingsServiceBean settingsService;
    private ProvPopupFragmentBean provPopupFragmentBean;
    private SolrIndexServiceBean solrIndexService;


    // -------------------- CONSTRUCTORS --------------------

    @Deprecated
    public DatasetService() {
    }

    @Inject
    public DatasetService(EjbDataverseEngine commandEngine, UserNotificationService userNotificationService,
                          DatasetDao datasetDao, DataverseSession session, DataverseRequestServiceBean dvRequestService,
                          IngestServiceBean ingestService, SettingsServiceBean settingsService,
                          ProvPopupFragmentBean provPopupFragmentBean, PermissionServiceBean permissionService,
                          SolrIndexServiceBean solrIndexService) {
        this.commandEngine = commandEngine;
        this.userNotificationService = userNotificationService;
        this.datasetDao = datasetDao;
        this.session = session;
        this.dvRequestService = dvRequestService;
        this.ingestService = ingestService;
        this.settingsService = settingsService;
        this.provPopupFragmentBean = provPopupFragmentBean;
        this.solrIndexService = solrIndexService;
    }


    // -------------------- LOGIC --------------------

    public Dataset createDataset(Dataset dataset, Template usedTemplate) {

        AuthenticatedUser user = retrieveAuthenticatedUser();

        CreateNewDatasetCommand createCommand = new CreateNewDatasetCommand(dataset, dvRequestService.getDataverseRequest(), false, usedTemplate);
        dataset = commandEngine.submit(createCommand);


        userNotificationService.sendNotificationWithEmail(user, dataset.getCreateDate(), NotificationType.CREATEDS,
                                                          dataset.getLatestVersion().getId(), NotificationObjectType.DATASET_VERSION);

        return dataset;
    }

    @TransactionAttribute(TransactionAttributeType.NOT_SUPPORTED)
    public AddFilesResult addFilesToDataset(long datasetId, List<DataFile> newFiles) {

        Dataset dataset = datasetDao.find(datasetId);
        AuthenticatedUser user = retrieveAuthenticatedUser();

        if (settingsService.isTrueForKey(SettingsServiceBean.Key.ProvCollectionEnabled)) {
            provPopupFragmentBean.saveStageProvFreeformToLatestVersion();
        }

        List<DataFile> savedFiles = ingestService.saveAndAddFilesToDataset(dataset.getEditVersion(), newFiles);

        int notSavedFilesCount = newFiles.size() - savedFiles.size();

        if (savedFiles.size() == 0) {
            return new AddFilesResult(dataset, notSavedFilesCount, false);
        }

        dataset = commandEngine.submit(new UpdateDatasetVersionCommand(dataset, dvRequestService.getDataverseRequest()));


        // Call Ingest Service one more time, to
        // queue the data ingest jobs for asynchronous execution:
        ingestService.startIngestJobsForDataset(dataset, user);

        //After dataset saved, then persist prov json data
        boolean hasProvenanceErrors = false;

        if (settingsService.isTrueForKey(SettingsServiceBean.Key.ProvCollectionEnabled)) {
            try {
                provPopupFragmentBean.saveStagedProvJson(false, dataset.getLatestVersion().getFileMetadatas());
            } catch (AbstractApiBean.WrappedResponse ex) {
                logger.log(Level.SEVERE, null, ex);
                hasProvenanceErrors = true;
            }
        }

        return new AddFilesResult(dataset, notSavedFilesCount, hasProvenanceErrors);
    }

    /**
     * Replaces thumbnail (default if none is set) with the one provided.
     *
     * @param datasetForNewThumbnail dataset that will have new thumbnail
     * @param thumbnailFile          thumbnail that will be set for dataset
     */
    public DatasetThumbnail changeDatasetThumbnail(Dataset datasetForNewThumbnail, DataFile thumbnailFile) {
        return commandEngine.submit(new UpdateDatasetThumbnailCommand(dvRequestService.getDataverseRequest(),
                                                                      datasetForNewThumbnail,
                                                                      UpdateDatasetThumbnailCommand.UserIntent.setDatasetFileAsThumbnail,
                                                                      thumbnailFile.getId(),
                                                                      null));

    }

    /**
     * Replaces thumbnail (default if none is set) with the one provided.
     *
     * @param datasetForNewThumbnail dataset that will have new thumbnail
     * @param fileStream             thumbnail that will be set for dataset
     */
    public DatasetThumbnail changeDatasetThumbnail(Dataset datasetForNewThumbnail, InputStream fileStream) {
        return commandEngine.submit(new UpdateDatasetThumbnailCommand(dvRequestService.getDataverseRequest(),
                                                                      datasetForNewThumbnail,
                                                                      UpdateDatasetThumbnailCommand.UserIntent.setNonDatasetFileAsThumbnail,
                                                                      null,
                                                                      fileStream));

    }

    public DatasetThumbnail removeDatasetThumbnail(Dataset datasetWithThumbnail) {
        return commandEngine.submit(new UpdateDatasetThumbnailCommand(dvRequestService.getDataverseRequest(),
                                                                      datasetWithThumbnail,
                                                                      UpdateDatasetThumbnailCommand.UserIntent.removeThumbnail,
                                                                      null,
                                                                      null));

    }

    public Dataset updateDatasetGuestbook(Dataset editedDataset) {
        return commandEngine.submit(new UpdateDatasetGuestbookCommand(dvRequestService.getDataverseRequest(), editedDataset));
    }

    @LoggedCall
    @Restricted(@PermissionNeeded(needs = {Permission.EditDataset}))
    public Dataset setDatasetEmbargoDate(@PermissionNeeded Dataset dataset, Date embargoDate) throws IllegalStateException {
        if(dataset.hasEverBeenPublished() && !session.getUser().isSuperuser()) {
            throw new IllegalStateException(getDatasetInWrongStateMessage());
        }
        return updateDatasetEmbargoDate(dataset, embargoDate);
    }

    @LoggedCall
    @Restricted(@PermissionNeeded(needs = {Permission.EditDataset}))
    public Dataset liftDatasetEmbargoDate(@PermissionNeeded Dataset dataset) {
        return updateDatasetEmbargoDate(dataset, null);
    }

    String getDatasetLockedMessage(Dataset dataset) {
        return DATASET_LOCKED_FOR_UPDATE_MESSAGE + dataset.getLocks().toString();
    }

    String getDatasetInWrongStateMessage() {
        return DATASET_IN_WRONG_STATE_MESSAGE;
    }

    @SuperuserRequired
    public void updateAllLastChangeForExporterTime() {
        datasetDao.updateAllLastChangeForExporterTime();
    }

    @SuperuserRequired
    public void updateLastChangeForExporterTime(Dataset dataset) {
        dataset.setLastChangeForExporterTime(new Date());
        datasetDao.merge(dataset);
    }

    // -------------------- PRIVATE --------------------

    private AuthenticatedUser retrieveAuthenticatedUser() {
        if (!session.getUser().isAuthenticated()) {
            throw new NotAuthenticatedException();
        }
        return (AuthenticatedUser) session.getUser();
    }

    private Dataset updateDatasetEmbargoDate(Dataset dataset, Date embargoDate) throws IllegalStateException {
        if(dataset.isLocked() && dataset.getLocks().stream().anyMatch(l -> l.getReason() != DatasetLock.Reason.InReview)) {
            logger.log(Level.WARNING, "Dataset is locked. Cannot perform update embargo date");
            throw new IllegalStateException(getDatasetLockedMessage(dataset));
        }

        dataset.setEmbargoDate(embargoDate);
        dataset.setLastChangeForExporterTime(Date.from(Instant.now(Clock.systemDefaultZone())));
        dataset = datasetDao.mergeAndFlush(dataset);

        solrIndexService.indexPermissionsForDatasetWithDataFiles(dataset);

        return dataset;
    }

}

1	package edu.harvard.iq.dataverse.dataset;
2
3	import edu.harvard.iq.dataverse.DatasetDao;
4	import edu.harvard.iq.dataverse.DatasetPage;
5	import edu.harvard.iq.dataverse.DataverseRequestServiceBean;
6	import edu.harvard.iq.dataverse.DataverseSession;
7	import edu.harvard.iq.dataverse.EjbDataverseEngine;
8	import edu.harvard.iq.dataverse.PermissionServiceBean;
9	import edu.harvard.iq.dataverse.annotations.PermissionNeeded;
10	import edu.harvard.iq.dataverse.api.AbstractApiBean;
11	import edu.harvard.iq.dataverse.engine.command.exception.NotAuthenticatedException;
12	import edu.harvard.iq.dataverse.engine.command.impl.CreateNewDatasetCommand;
13	import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetGuestbookCommand;
14	import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetThumbnailCommand;
15	import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand;
16	import edu.harvard.iq.dataverse.ingest.IngestServiceBean;
17	import edu.harvard.iq.dataverse.interceptors.LoggedCall;
18	import edu.harvard.iq.dataverse.interceptors.Restricted;
19	import edu.harvard.iq.dataverse.interceptors.SuperuserRequired;
20	import edu.harvard.iq.dataverse.notification.NotificationObjectType;
21	import edu.harvard.iq.dataverse.notification.UserNotificationService;
22	import edu.harvard.iq.dataverse.persistence.datafile.DataFile;
23	import edu.harvard.iq.dataverse.persistence.dataset.Dataset;
24	import edu.harvard.iq.dataverse.persistence.dataset.DatasetLock;
25	import edu.harvard.iq.dataverse.persistence.dataset.Template;
26	import edu.harvard.iq.dataverse.persistence.user.AuthenticatedUser;
27	import edu.harvard.iq.dataverse.persistence.user.NotificationType;
28	import edu.harvard.iq.dataverse.persistence.user.Permission;
29	import edu.harvard.iq.dataverse.provenance.ProvPopupFragmentBean;
30	import edu.harvard.iq.dataverse.search.index.SolrIndexServiceBean;
31	import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
32
33	import javax.ejb.Stateless;
34	import javax.ejb.TransactionAttribute;
35	import javax.ejb.TransactionAttributeType;
36	import javax.inject.Inject;
37	import java.io.InputStream;
38	import java.time.Clock;
39	import java.time.Instant;
40	import java.util.Date;
41	import java.util.List;
42	import java.util.logging.Level;
43	import java.util.logging.Logger;
44
45	@Stateless
46	public class DatasetService {
47
48	private static final Logger logger = Logger.getLogger(DatasetPage.class.getCanonicalName());	1✔
49	private static final String DATASET_LOCKED_FOR_UPDATE_MESSAGE = "Update embargo date failed. Dataset is locked. ";
50	private static final String DATASET_IN_WRONG_STATE_MESSAGE = "Setting embargo date failed. Dataset is in a non-editable state.";
51
52	private EjbDataverseEngine commandEngine;
53	private UserNotificationService userNotificationService;
54	private DatasetDao datasetDao;
55	private DataverseSession session;
56	private DataverseRequestServiceBean dvRequestService;
57	private IngestServiceBean ingestService;
58	private SettingsServiceBean settingsService;
59	private ProvPopupFragmentBean provPopupFragmentBean;
60	private SolrIndexServiceBean solrIndexService;
61
62
63	// -------------------- CONSTRUCTORS --------------------
64
65	@Deprecated
66	public DatasetService() {	×
67	}	×
68
69	@Inject
70	public DatasetService(EjbDataverseEngine commandEngine, UserNotificationService userNotificationService,
71	DatasetDao datasetDao, DataverseSession session, DataverseRequestServiceBean dvRequestService,
72	IngestServiceBean ingestService, SettingsServiceBean settingsService,
73	ProvPopupFragmentBean provPopupFragmentBean, PermissionServiceBean permissionService,
74	SolrIndexServiceBean solrIndexService) {	1✔
75	this.commandEngine = commandEngine;	1✔
76	this.userNotificationService = userNotificationService;	1✔
77	this.datasetDao = datasetDao;	1✔
78	this.session = session;	1✔
79	this.dvRequestService = dvRequestService;	1✔
80	this.ingestService = ingestService;	1✔
81	this.settingsService = settingsService;	1✔
82	this.provPopupFragmentBean = provPopupFragmentBean;	1✔
83	this.solrIndexService = solrIndexService;	1✔
84	}	1✔
85
86
87	// -------------------- LOGIC --------------------
88
89	public Dataset createDataset(Dataset dataset, Template usedTemplate) {
90
91	AuthenticatedUser user = retrieveAuthenticatedUser();	×
92
93	CreateNewDatasetCommand createCommand = new CreateNewDatasetCommand(dataset, dvRequestService.getDataverseRequest(), false, usedTemplate);	×
94	dataset = commandEngine.submit(createCommand);	×
95
96
97	userNotificationService.sendNotificationWithEmail(user, dataset.getCreateDate(), NotificationType.CREATEDS,	×
98	dataset.getLatestVersion().getId(), NotificationObjectType.DATASET_VERSION);	×
99
100	return dataset;	×
101	}
102
103	@TransactionAttribute(TransactionAttributeType.NOT_SUPPORTED)
104	public AddFilesResult addFilesToDataset(long datasetId, List<DataFile> newFiles) {
105
106	Dataset dataset = datasetDao.find(datasetId);	×
107	AuthenticatedUser user = retrieveAuthenticatedUser();	×
108
109	if (settingsService.isTrueForKey(SettingsServiceBean.Key.ProvCollectionEnabled)) {	×
110	provPopupFragmentBean.saveStageProvFreeformToLatestVersion();	×
111	}
112
113	List<DataFile> savedFiles = ingestService.saveAndAddFilesToDataset(dataset.getEditVersion(), newFiles);	×
114
115	int notSavedFilesCount = newFiles.size() - savedFiles.size();	×
116
117	if (savedFiles.size() == 0) {	×
118	return new AddFilesResult(dataset, notSavedFilesCount, false);	×
119	}
120
121	dataset = commandEngine.submit(new UpdateDatasetVersionCommand(dataset, dvRequestService.getDataverseRequest()));	×
122
123
124	// Call Ingest Service one more time, to
125	// queue the data ingest jobs for asynchronous execution:
126	ingestService.startIngestJobsForDataset(dataset, user);	×
127
128	//After dataset saved, then persist prov json data
129	boolean hasProvenanceErrors = false;	×
130
131	if (settingsService.isTrueForKey(SettingsServiceBean.Key.ProvCollectionEnabled)) {	×
132	try {
133	provPopupFragmentBean.saveStagedProvJson(false, dataset.getLatestVersion().getFileMetadatas());	×
134	} catch (AbstractApiBean.WrappedResponse ex) {	×
135	logger.log(Level.SEVERE, null, ex);	×
136	hasProvenanceErrors = true;	×
137	}	×
138	}
139
140	return new AddFilesResult(dataset, notSavedFilesCount, hasProvenanceErrors);	×
141	}
142
143	/**
144	* Replaces thumbnail (default if none is set) with the one provided.
145	*
146	* @param datasetForNewThumbnail dataset that will have new thumbnail
147	* @param thumbnailFile thumbnail that will be set for dataset
148	*/
149	public DatasetThumbnail changeDatasetThumbnail(Dataset datasetForNewThumbnail, DataFile thumbnailFile) {
150	return commandEngine.submit(new UpdateDatasetThumbnailCommand(dvRequestService.getDataverseRequest(),	1✔
151	datasetForNewThumbnail,
152	UpdateDatasetThumbnailCommand.UserIntent.setDatasetFileAsThumbnail,
153	thumbnailFile.getId(),	1✔
154	null));
155
156	}
157
158	/**
159	* Replaces thumbnail (default if none is set) with the one provided.
160	*
161	* @param datasetForNewThumbnail dataset that will have new thumbnail
162	* @param fileStream thumbnail that will be set for dataset
163	*/
164	public DatasetThumbnail changeDatasetThumbnail(Dataset datasetForNewThumbnail, InputStream fileStream) {
165	return commandEngine.submit(new UpdateDatasetThumbnailCommand(dvRequestService.getDataverseRequest(),	1✔
166	datasetForNewThumbnail,
167	UpdateDatasetThumbnailCommand.UserIntent.setNonDatasetFileAsThumbnail,
168	null,
169	fileStream));
170
171	}
172
173	public DatasetThumbnail removeDatasetThumbnail(Dataset datasetWithThumbnail) {
174	return commandEngine.submit(new UpdateDatasetThumbnailCommand(dvRequestService.getDataverseRequest(),	1✔
175	datasetWithThumbnail,
176	UpdateDatasetThumbnailCommand.UserIntent.removeThumbnail,
177	null,
178	null));
179
180	}
181
182	public Dataset updateDatasetGuestbook(Dataset editedDataset) {
183	return commandEngine.submit(new UpdateDatasetGuestbookCommand(dvRequestService.getDataverseRequest(), editedDataset));	×
184	}
185
186	@LoggedCall
187	@Restricted(@PermissionNeeded(needs = {Permission.EditDataset}))
188	public Dataset setDatasetEmbargoDate(@PermissionNeeded Dataset dataset, Date embargoDate) throws IllegalStateException {
189	if(dataset.hasEverBeenPublished() && !session.getUser().isSuperuser()) {	1✔
190	throw new IllegalStateException(getDatasetInWrongStateMessage());	1✔
191	}
192	return updateDatasetEmbargoDate(dataset, embargoDate);	1✔
193	}
194
195	@LoggedCall
196	@Restricted(@PermissionNeeded(needs = {Permission.EditDataset}))
197	public Dataset liftDatasetEmbargoDate(@PermissionNeeded Dataset dataset) {
198	return updateDatasetEmbargoDate(dataset, null);	×
199	}
200
201	String getDatasetLockedMessage(Dataset dataset) {
202	return DATASET_LOCKED_FOR_UPDATE_MESSAGE + dataset.getLocks().toString();	1✔
203	}
204
205	String getDatasetInWrongStateMessage() {
206	return DATASET_IN_WRONG_STATE_MESSAGE;	1✔
207	}
208
209	@SuperuserRequired
210	public void updateAllLastChangeForExporterTime() {
211	datasetDao.updateAllLastChangeForExporterTime();	×
212	}	×
213
214	@SuperuserRequired
215	public void updateLastChangeForExporterTime(Dataset dataset) {
216	dataset.setLastChangeForExporterTime(new Date());	×
217	datasetDao.merge(dataset);	×
218	}	×
219
220	// -------------------- PRIVATE --------------------
221
222	private AuthenticatedUser retrieveAuthenticatedUser() {
223	if (!session.getUser().isAuthenticated()) {	×
224	throw new NotAuthenticatedException();	×
225	}
226	return (AuthenticatedUser) session.getUser();	×
227	}
228
229	private Dataset updateDatasetEmbargoDate(Dataset dataset, Date embargoDate) throws IllegalStateException {
230	if(dataset.isLocked() && dataset.getLocks().stream().anyMatch(l -> l.getReason() != DatasetLock.Reason.InReview)) {	1✔
231	logger.log(Level.WARNING, "Dataset is locked. Cannot perform update embargo date");	1✔
232	throw new IllegalStateException(getDatasetLockedMessage(dataset));	1✔
233	}
234
235	dataset.setEmbargoDate(embargoDate);	1✔
236	dataset.setLastChangeForExporterTime(Date.from(Instant.now(Clock.systemDefaultZone())));	1✔
237	dataset = datasetDao.mergeAndFlush(dataset);	1✔
238
239	solrIndexService.indexPermissionsForDatasetWithDataFiles(dataset);	1✔
240
241	return dataset;	1✔
242	}
243
244	}

CeON / dataverse / 1370

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