1371

Committed 28 Jun 2024 05:54AM UTC coverage: 25.453% (-0.05%) from 25.503%

Build # 1371

Build Type

push

jenkins

Committed by

web-flow

Commit Message

Closes #2474: Store the entity id in saml session once user logs in with the identity provider (#2486)

Run Details

49 of 54 new or added lines in 4 files covered. (90.74%)

860 existing lines in 14 files now uncovered.

17805 of 69953 relevant lines covered (25.45%)

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9.35

/dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/EjbDataverseEngine.java

package edu.harvard.iq.dataverse;

import edu.harvard.iq.dataverse.actionlogging.ActionLogServiceBean;
import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
import edu.harvard.iq.dataverse.authorization.groups.GroupServiceBean;
import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroupServiceBean;
import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUserServiceBean;
import edu.harvard.iq.dataverse.bannersandmessages.messages.DataverseTextMessageServiceBean;
import edu.harvard.iq.dataverse.citation.CitationFactory;
import edu.harvard.iq.dataverse.dataaccess.DataAccess;
import edu.harvard.iq.dataverse.datacapturemodule.DataCaptureModuleServiceBean;
import edu.harvard.iq.dataverse.datafile.FileDownloadServiceBean;
import edu.harvard.iq.dataverse.dataset.DatasetThumbnailService;
import edu.harvard.iq.dataverse.dataset.DownloadDatasetLogDao;
import edu.harvard.iq.dataverse.dataset.datasetversion.DatasetVersionServiceBean;
import edu.harvard.iq.dataverse.dataverse.template.TemplateDao;
import edu.harvard.iq.dataverse.engine.DataverseEngine;
import edu.harvard.iq.dataverse.engine.command.Command;
import edu.harvard.iq.dataverse.engine.command.CommandContext;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
import edu.harvard.iq.dataverse.engine.command.exception.PermissionException;
import edu.harvard.iq.dataverse.featured.FeaturedDataverseServiceBean;
import edu.harvard.iq.dataverse.globalid.DOIDataCiteServiceBean;
import edu.harvard.iq.dataverse.globalid.DOIEZIdServiceBean;
import edu.harvard.iq.dataverse.globalid.FakePidProviderServiceBean;
import edu.harvard.iq.dataverse.globalid.HandlenetServiceBean;
import edu.harvard.iq.dataverse.guestbook.GuestbookResponseServiceBean;
import edu.harvard.iq.dataverse.guestbook.GuestbookServiceBean;
import edu.harvard.iq.dataverse.ingest.IngestServiceBean;
import edu.harvard.iq.dataverse.notification.UserNotificationService;
import edu.harvard.iq.dataverse.persistence.ActionLogRecord;
import edu.harvard.iq.dataverse.persistence.DvObject;
import edu.harvard.iq.dataverse.persistence.user.Permission;
import edu.harvard.iq.dataverse.privateurl.PrivateUrlServiceBean;
import edu.harvard.iq.dataverse.search.SearchServiceBean;
import edu.harvard.iq.dataverse.search.index.IndexBatchServiceBean;
import edu.harvard.iq.dataverse.search.index.IndexServiceBean;
import edu.harvard.iq.dataverse.search.index.SolrIndexServiceBean;
import edu.harvard.iq.dataverse.search.savedsearch.SavedSearchServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.SystemConfig;
import edu.harvard.iq.dataverse.validation.DatasetFieldValidationService;
import edu.harvard.iq.dataverse.workflow.WorkflowServiceBean;
import edu.harvard.iq.dataverse.workflow.execution.WorkflowExecutionFacade;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.collections4.SetUtils;

import javax.annotation.Resource;
import javax.ejb.EJB;
import javax.ejb.EJBContext;
import javax.ejb.EJBException;
import javax.ejb.Stateless;
import javax.ejb.TransactionAttribute;
import javax.inject.Inject;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.validation.ConstraintViolation;
import javax.validation.ConstraintViolationException;
import java.util.EnumSet;
import java.util.Map;
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;

import static javax.ejb.TransactionAttributeType.REQUIRES_NEW;

/**
 * An EJB capable of executing {@link Command}s in a JEE environment.
 *
 * @author michael
 */
@Stateless
public class EjbDataverseEngine {

    private static final Logger logger = Logger.getLogger(EjbDataverseEngine.class.getCanonicalName());

    @EJB
    DatasetDao datasetDao;

    @EJB
    DataverseDao dataverseDao;

    @EJB
    DataverseRoleServiceBean rolesService;

    @EJB
    BuiltinUserServiceBean usersService;

    @EJB
    IndexServiceBean indexService;

    @EJB
    IndexBatchServiceBean indexBatchService;

    @EJB
    SolrIndexServiceBean solrIndexService;

    @EJB
    SearchServiceBean searchService;

    @EJB
    IngestServiceBean ingestService;

    @EJB
    PermissionServiceBean permissionService;

    @EJB
    DvObjectServiceBean dvObjectService;

    @EJB
    DataverseFacetServiceBean dataverseFacetService;

    @EJB
    FeaturedDataverseServiceBean featuredDataverseService;

    @EJB
    DataFileServiceBean dataFileService;

    @EJB
    TemplateDao templateDao;

    @EJB
    SavedSearchServiceBean savedSearchService;

    @EJB
    DataverseFieldTypeInputLevelServiceBean fieldTypeInputLevels;

    @EJB
    DOIEZIdServiceBean doiEZId;

    @EJB
    DOIDataCiteServiceBean doiDataCite;

    @EJB
    FakePidProviderServiceBean fakePidProvider;

    @EJB
    HandlenetServiceBean handleNet;

    @Inject
    SettingsServiceBean settings;

    @EJB
    GuestbookServiceBean guestbookService;

    @EJB
    GuestbookResponseServiceBean responses;

    @EJB
    DatasetLinkingServiceBean dsLinking;

    @EJB
    ExplicitGroupServiceBean explicitGroups;

    @EJB
    GroupServiceBean groups;

    @EJB
    RoleAssigneeServiceBean roleAssignees;

    @EJB
    UserNotificationService userNotificationService;

    @EJB
    AuthenticationServiceBean authentication;

    @EJB
    SystemConfig systemConfig;

    @EJB
    PrivateUrlServiceBean privateUrlService;

    @EJB
    DatasetVersionServiceBean datasetVersionService;

    @EJB
    MapLayerMetadataServiceBean mapLayerMetadata;

    @EJB
    DataCaptureModuleServiceBean dataCaptureModule;

    @PersistenceContext(unitName = "VDCNet-ejbPU")
    private EntityManager em;

    @EJB
    ActionLogServiceBean logSvc;

    @Inject
    WorkflowServiceBean workflowService;

    @Inject
    WorkflowExecutionFacade workflowExecutionFacade;

    @EJB
    FileDownloadServiceBean fileDownloadService;

    @EJB
    DataverseTextMessageServiceBean dataverseTextMessageServiceBean;

    @Inject
    DatasetThumbnailService datasetThumbnailService;

    @Inject
    CitationFactory citationFactory;

    @Inject
    DownloadDatasetLogDao downloadDatasetLogDao;

    @Inject
    DatasetFieldValidationService fieldValidationService;


    @Resource
    EJBContext ejbCtxt;

    private DataAccess dataAccess = DataAccess.dataAccess();

    private CommandContext ctxt;

    @TransactionAttribute(REQUIRES_NEW)
    public <R> R submitInNewTransaction(Command<R> aCommand)  {
        return submit(aCommand);
    }

    public <R> R submit(Command<R> aCommand)  {

        final ActionLogRecord logRec = new ActionLogRecord(ActionLogRecord.ActionType.Command, aCommand.getClass().getCanonicalName());

        try {
            logRec.setUserIdentifier(aCommand.getRequest().getUser().getIdentifier());

            // Check permissions - or throw an exception
            Map<String, ? extends Set<Permission>> requiredMap = aCommand.getRequiredPermissions();
            if (requiredMap == null) {
                throw new RuntimeException("Command " + aCommand + " does not define required permissions.");
            }

            DataverseRequest dvReq = aCommand.getRequest();

            Map<String, DvObject> affectedDvObjects = aCommand.getAffectedDvObjects();
            logRec.setInfo(aCommand.describe());
            for (Map.Entry<String, ? extends Set<Permission>> pair : requiredMap.entrySet()) {
                String dvName = pair.getKey();
                if (!affectedDvObjects.containsKey(dvName)) {
                    throw new RuntimeException("Command instance " + aCommand + " does not have a DvObject named '" + dvName + "'");
                }
                DvObject dvo = affectedDvObjects.get(dvName);

                Set<Permission> granted = (dvo != null) ? permissionService.permissionsFor(dvReq, dvo)
                        : EnumSet.allOf(Permission.class);
                Set<Permission> required = requiredMap.get(dvName);

                if ((!aCommand.isAllPermissionsRequired() && !CollectionUtils.containsAny(granted, required) ||
                        (aCommand.isAllPermissionsRequired() && !granted.containsAll(required)))) {
                    Set<Permission> missingPermissions = SetUtils.difference(required, granted);
                    logRec.setActionResult(ActionLogRecord.Result.PermissionError);
                    /**
                     * @todo Is there any harm in showing the "granted" set
                     * since we already show "required"? It would help people
                     * reason about the mismatch.
                     */
                    throw new PermissionException("Can't execute command " + aCommand
                                                          + ", because request " + aCommand.getRequest()
                                                          + " is missing permissions " + missingPermissions
                                                          + " on Object " + dvo.accept(DvObject.NamePrinter),
                                                  aCommand,
                                                  missingPermissions, dvo);
                }
            }
            try {
                return aCommand.execute(getContext());

            } catch (EJBException ejbe) {
                throw new CommandException("Command " + aCommand.toString() + " failed: " + ejbe.getMessage(), ejbe.getCausedByException(), aCommand);
            }
        } catch (CommandException cmdEx) {
            if (!(cmdEx instanceof PermissionException)) {
                logRec.setActionResult(ActionLogRecord.Result.InternalError);
            }
            logRec.setInfo(logRec.getInfo() + " (" + cmdEx.getMessage() + ")");
            throw cmdEx;
        } catch (RuntimeException re) {
            logRec.setActionResult(ActionLogRecord.Result.InternalError);
            logRec.setInfo(logRec.getInfo() + " (" + re.getMessage() + ")");

            Throwable cause = re;
            while (cause != null) {
                if (cause instanceof ConstraintViolationException) {
                    StringBuilder sb = new StringBuilder();
                    sb.append("Unexpected bean validation constraint exception:");
                    ConstraintViolationException constraintViolationException = (ConstraintViolationException) cause;
                    for (ConstraintViolation<?> violation : constraintViolationException.getConstraintViolations()) {
                        sb.append(" Invalid value: <<<").append(violation.getInvalidValue()).append(">>> for ").append(violation.getPropertyPath()).append(" at ").append(violation.getLeafBean()).append(" - ").append(violation.getMessage());
                    }
                    logger.log(Level.SEVERE, sb.toString());
                    // set this more detailed info in action log
                    logRec.setInfo(logRec.getInfo() + " (" + sb.toString() + ")");
                }
                cause = cause.getCause();
            }

            throw re;

        } finally {
            if (logRec.getActionResult() == null) {
                logRec.setActionResult(ActionLogRecord.Result.OK);
            } else {
                ejbCtxt.setRollbackOnly();
            }
            logRec.setEndTime(new java.util.Date());
            logSvc.log(logRec);
        }

    }

    public CommandContext getContext() {
        if (ctxt == null) {
            ctxt = new CommandContext() {

                @Override
                public DatasetDao datasets() {
                    return datasetDao;
                }

                @Override
                public DataverseDao dataverses() {
                    return dataverseDao;
                }

                @Override
                public DataverseRoleServiceBean roles() {
                    return rolesService;
                }

                @Override
                public BuiltinUserServiceBean builtinUsers() {
                    return usersService;
                }

                @Override
                public IndexServiceBean index() {
                    return indexService;
                }

                @Override
                public IndexBatchServiceBean indexBatch() {
                    return indexBatchService;
                }

                @Override
                public SolrIndexServiceBean solrIndex() {
                    return solrIndexService;
                }

                @Override
                public SearchServiceBean search() {
                    return searchService;
                }

                @Override
                public IngestServiceBean ingest() {
                    return ingestService;
                }

                @Override
                public PermissionServiceBean permissions() {
                    return permissionService;
                }

                @Override
                public DvObjectServiceBean dvObjects() {
                    return dvObjectService;
                }

                @Override
                public DataFileServiceBean files() {
                    return dataFileService;
                }

                @Override
                public EntityManager em() {
                    return em;
                }

                @Override
                public DataAccess dataAccess() {
                    return dataAccess;
                }

                @Override
                public DataverseFacetServiceBean facets() {
                    return dataverseFacetService;
                }

                @Override
                public FeaturedDataverseServiceBean featuredDataverses() {
                    return featuredDataverseService;
                }

                @Override
                public TemplateDao templates() {
                    return templateDao;
                }

                @Override
                public SavedSearchServiceBean savedSearches() {
                    return savedSearchService;
                }

                @Override
                public DataverseFieldTypeInputLevelServiceBean fieldTypeInputLevels() {
                    return fieldTypeInputLevels;
                }

                @Override
                public DOIEZIdServiceBean doiEZId() {
                    return doiEZId;
                }

                @Override
                public DOIDataCiteServiceBean doiDataCite() {
                    return doiDataCite;
                }

                @Override
                public FakePidProviderServiceBean fakePidProvider() {
                    return fakePidProvider;
                }

                @Override
                public HandlenetServiceBean handleNet() {
                    return handleNet;
                }

                @Override
                public SettingsServiceBean settings() {
                    return settings;
                }

                @Override
                public GuestbookServiceBean guestbooks() {
                    return guestbookService;
                }

                @Override
                public GuestbookResponseServiceBean responses() {
                    return responses;
                }

                @Override
                public DatasetLinkingServiceBean dsLinking() {
                    return dsLinking;
                }

                @Override
                public DataverseEngine engine() {
                    return new DataverseEngine() {
                        @Override
                        public <R> R submit(Command<R> aCommand)  {
                            return EjbDataverseEngine.this.submit(aCommand);
                        }
                    };
                }

                @Override
                public ExplicitGroupServiceBean explicitGroups() {
                    return explicitGroups;
                }

                @Override
                public GroupServiceBean groups() {
                    return groups;
                }

                @Override
                public RoleAssigneeServiceBean roleAssignees() {
                    return roleAssignees;
                }

                @Override
                public UserNotificationService notifications() {
                    return userNotificationService;
                }

                @Override
                public AuthenticationServiceBean authentication() {
                    return authentication;
                }

                @Override
                public SystemConfig systemConfig() {
                    return systemConfig;
                }

                @Override
                public PrivateUrlServiceBean privateUrl() {
                    return privateUrlService;
                }

                @Override
                public DatasetVersionServiceBean datasetVersion() {
                    return datasetVersionService;
                }

                @Override
                public WorkflowServiceBean workflows() {
                    return workflowService;
                }

                @Override
                public WorkflowExecutionFacade workflowExecutions() {
                    return workflowExecutionFacade;
                }

                @Override
                public MapLayerMetadataServiceBean mapLayerMetadata() {
                    return mapLayerMetadata;
                }

                @Override
                public DataCaptureModuleServiceBean dataCaptureModule() {
                    return dataCaptureModule;
                }

                @Override
                public FileDownloadServiceBean fileDownload() {
                    return fileDownloadService;
                }

                @Override
                public DataverseTextMessageServiceBean dataverseTextMessages() {
                    return dataverseTextMessageServiceBean;
                }

                @Override
                public DatasetThumbnailService datasetThumailService() {
                    return datasetThumbnailService;
                }

                @Override
                public CitationFactory citationFactory() {
                    return citationFactory;
                }

                @Override
                public DownloadDatasetLogDao downloadDatasetDao() {
                    return downloadDatasetLogDao;
                }

                @Override
                public DatasetFieldValidationService fieldValidationService() {
                    return fieldValidationService;
                }
            };
        }

        return ctxt;
    }

}

1	package edu.harvard.iq.dataverse;
2
3	import edu.harvard.iq.dataverse.actionlogging.ActionLogServiceBean;
4	import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
5	import edu.harvard.iq.dataverse.authorization.groups.GroupServiceBean;
6	import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroupServiceBean;
7	import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUserServiceBean;
8	import edu.harvard.iq.dataverse.bannersandmessages.messages.DataverseTextMessageServiceBean;
9	import edu.harvard.iq.dataverse.citation.CitationFactory;
10	import edu.harvard.iq.dataverse.dataaccess.DataAccess;
11	import edu.harvard.iq.dataverse.datacapturemodule.DataCaptureModuleServiceBean;
12	import edu.harvard.iq.dataverse.datafile.FileDownloadServiceBean;
13	import edu.harvard.iq.dataverse.dataset.DatasetThumbnailService;
14	import edu.harvard.iq.dataverse.dataset.DownloadDatasetLogDao;
15	import edu.harvard.iq.dataverse.dataset.datasetversion.DatasetVersionServiceBean;
16	import edu.harvard.iq.dataverse.dataverse.template.TemplateDao;
17	import edu.harvard.iq.dataverse.engine.DataverseEngine;
18	import edu.harvard.iq.dataverse.engine.command.Command;
19	import edu.harvard.iq.dataverse.engine.command.CommandContext;
20	import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
21	import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
22	import edu.harvard.iq.dataverse.engine.command.exception.PermissionException;
23	import edu.harvard.iq.dataverse.featured.FeaturedDataverseServiceBean;
24	import edu.harvard.iq.dataverse.globalid.DOIDataCiteServiceBean;
25	import edu.harvard.iq.dataverse.globalid.DOIEZIdServiceBean;
26	import edu.harvard.iq.dataverse.globalid.FakePidProviderServiceBean;
27	import edu.harvard.iq.dataverse.globalid.HandlenetServiceBean;
28	import edu.harvard.iq.dataverse.guestbook.GuestbookResponseServiceBean;
29	import edu.harvard.iq.dataverse.guestbook.GuestbookServiceBean;
30	import edu.harvard.iq.dataverse.ingest.IngestServiceBean;
31	import edu.harvard.iq.dataverse.notification.UserNotificationService;
32	import edu.harvard.iq.dataverse.persistence.ActionLogRecord;
33	import edu.harvard.iq.dataverse.persistence.DvObject;
34	import edu.harvard.iq.dataverse.persistence.user.Permission;
35	import edu.harvard.iq.dataverse.privateurl.PrivateUrlServiceBean;
36	import edu.harvard.iq.dataverse.search.SearchServiceBean;
37	import edu.harvard.iq.dataverse.search.index.IndexBatchServiceBean;
38	import edu.harvard.iq.dataverse.search.index.IndexServiceBean;
39	import edu.harvard.iq.dataverse.search.index.SolrIndexServiceBean;
40	import edu.harvard.iq.dataverse.search.savedsearch.SavedSearchServiceBean;
41	import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
42	import edu.harvard.iq.dataverse.util.SystemConfig;
43	import edu.harvard.iq.dataverse.validation.DatasetFieldValidationService;
44	import edu.harvard.iq.dataverse.workflow.WorkflowServiceBean;
45	import edu.harvard.iq.dataverse.workflow.execution.WorkflowExecutionFacade;
46	import org.apache.commons.collections4.CollectionUtils;
47	import org.apache.commons.collections4.SetUtils;
48
49	import javax.annotation.Resource;
50	import javax.ejb.EJB;
51	import javax.ejb.EJBContext;
52	import javax.ejb.EJBException;
53	import javax.ejb.Stateless;
54	import javax.ejb.TransactionAttribute;
55	import javax.inject.Inject;
56	import javax.persistence.EntityManager;
57	import javax.persistence.PersistenceContext;
58	import javax.validation.ConstraintViolation;
59	import javax.validation.ConstraintViolationException;
60	import java.util.EnumSet;
61	import java.util.Map;
62	import java.util.Set;
63	import java.util.logging.Level;
64	import java.util.logging.Logger;
65
66	import static javax.ejb.TransactionAttributeType.REQUIRES_NEW;
67
68	/**
69	* An EJB capable of executing {@link Command}s in a JEE environment.
70	*
71	* @author michael
72	*/
73	@Stateless
UNCOV 74	public class EjbDataverseEngine {	×
75
76	private static final Logger logger = Logger.getLogger(EjbDataverseEngine.class.getCanonicalName());	1✔
77
78	@EJB
79	DatasetDao datasetDao;
80
81	@EJB
82	DataverseDao dataverseDao;
83
84	@EJB
85	DataverseRoleServiceBean rolesService;
86
87	@EJB
88	BuiltinUserServiceBean usersService;
89
90	@EJB
91	IndexServiceBean indexService;
92
93	@EJB
94	IndexBatchServiceBean indexBatchService;
95
96	@EJB
97	SolrIndexServiceBean solrIndexService;
98
99	@EJB
100	SearchServiceBean searchService;
101
102	@EJB
103	IngestServiceBean ingestService;
104
105	@EJB
106	PermissionServiceBean permissionService;
107
108	@EJB
109	DvObjectServiceBean dvObjectService;
110
111	@EJB
112	DataverseFacetServiceBean dataverseFacetService;
113
114	@EJB
115	FeaturedDataverseServiceBean featuredDataverseService;
116
117	@EJB
118	DataFileServiceBean dataFileService;
119
120	@EJB
121	TemplateDao templateDao;
122
123	@EJB
124	SavedSearchServiceBean savedSearchService;
125
126	@EJB
127	DataverseFieldTypeInputLevelServiceBean fieldTypeInputLevels;
128
129	@EJB
130	DOIEZIdServiceBean doiEZId;
131
132	@EJB
133	DOIDataCiteServiceBean doiDataCite;
134
135	@EJB
136	FakePidProviderServiceBean fakePidProvider;
137
138	@EJB
139	HandlenetServiceBean handleNet;
140
141	@Inject
142	SettingsServiceBean settings;
143
144	@EJB
145	GuestbookServiceBean guestbookService;
146
147	@EJB
148	GuestbookResponseServiceBean responses;
149
150	@EJB
151	DatasetLinkingServiceBean dsLinking;
152
153	@EJB
154	ExplicitGroupServiceBean explicitGroups;
155
156	@EJB
157	GroupServiceBean groups;
158
159	@EJB
160	RoleAssigneeServiceBean roleAssignees;
161
162	@EJB
163	UserNotificationService userNotificationService;
164
165	@EJB
166	AuthenticationServiceBean authentication;
167
168	@EJB
169	SystemConfig systemConfig;
170
171	@EJB
172	PrivateUrlServiceBean privateUrlService;
173
174	@EJB
175	DatasetVersionServiceBean datasetVersionService;
176
177	@EJB
178	MapLayerMetadataServiceBean mapLayerMetadata;
179
180	@EJB
181	DataCaptureModuleServiceBean dataCaptureModule;
182
183	@PersistenceContext(unitName = "VDCNet-ejbPU")
184	private EntityManager em;
185
186	@EJB
187	ActionLogServiceBean logSvc;
188
189	@Inject
190	WorkflowServiceBean workflowService;
191
192	@Inject
193	WorkflowExecutionFacade workflowExecutionFacade;
194
195	@EJB
196	FileDownloadServiceBean fileDownloadService;
197
198	@EJB
199	DataverseTextMessageServiceBean dataverseTextMessageServiceBean;
200
201	@Inject
202	DatasetThumbnailService datasetThumbnailService;
203
204	@Inject
205	CitationFactory citationFactory;
206
207	@Inject
208	DownloadDatasetLogDao downloadDatasetLogDao;
209
210	@Inject
211	DatasetFieldValidationService fieldValidationService;
212
213
214	@Resource
215	EJBContext ejbCtxt;
216
UNCOV 217	private DataAccess dataAccess = DataAccess.dataAccess();	×
218
219	private CommandContext ctxt;
220
221	@TransactionAttribute(REQUIRES_NEW)
222	public <R> R submitInNewTransaction(Command<R> aCommand) {
UNCOV 223	return submit(aCommand);	×
224	}
225
226	public <R> R submit(Command<R> aCommand) {
227
228	final ActionLogRecord logRec = new ActionLogRecord(ActionLogRecord.ActionType.Command, aCommand.getClass().getCanonicalName());	1✔
229
230	try {
UNCOV 231	logRec.setUserIdentifier(aCommand.getRequest().getUser().getIdentifier());	×
232
233	// Check permissions - or throw an exception
234	Map<String, ? extends Set<Permission>> requiredMap = aCommand.getRequiredPermissions();	×
235	if (requiredMap == null) {	×
UNCOV 236	throw new RuntimeException("Command " + aCommand + " does not define required permissions.");	×
237	}
238
UNCOV 239	DataverseRequest dvReq = aCommand.getRequest();	×
240
241	Map<String, DvObject> affectedDvObjects = aCommand.getAffectedDvObjects();	×
242	logRec.setInfo(aCommand.describe());	×
243	for (Map.Entry<String, ? extends Set<Permission>> pair : requiredMap.entrySet()) {	×
244	String dvName = pair.getKey();	×
245	if (!affectedDvObjects.containsKey(dvName)) {	×
UNCOV 246	throw new RuntimeException("Command instance " + aCommand + " does not have a DvObject named '" + dvName + "'");	×
247	}
UNCOV 248	DvObject dvo = affectedDvObjects.get(dvName);	×
249
250	Set<Permission> granted = (dvo != null) ? permissionService.permissionsFor(dvReq, dvo)	×
251	: EnumSet.allOf(Permission.class);	×
UNCOV 252	Set<Permission> required = requiredMap.get(dvName);	×
253
254	if ((!aCommand.isAllPermissionsRequired() && !CollectionUtils.containsAny(granted, required) \|\|	×
255	(aCommand.isAllPermissionsRequired() && !granted.containsAll(required)))) {	×
256	Set<Permission> missingPermissions = SetUtils.difference(required, granted);	×
UNCOV 257	logRec.setActionResult(ActionLogRecord.Result.PermissionError);	×
258	/**
259	* @todo Is there any harm in showing the "granted" set
260	* since we already show "required"? It would help people
261	* reason about the mismatch.
262	*/
263	throw new PermissionException("Can't execute command " + aCommand	×
UNCOV 264	+ ", because request " + aCommand.getRequest()	×
265	+ " is missing permissions " + missingPermissions
UNCOV 266	+ " on Object " + dvo.accept(DvObject.NamePrinter),	×
267	aCommand,
268	missingPermissions, dvo);
269	}
UNCOV 270	}	×
271	try {
UNCOV 272	return aCommand.execute(getContext());	×
273
274	} catch (EJBException ejbe) {	×
UNCOV 275	throw new CommandException("Command " + aCommand.toString() + " failed: " + ejbe.getMessage(), ejbe.getCausedByException(), aCommand);	×
276	}
277	} catch (CommandException cmdEx) {	×
278	if (!(cmdEx instanceof PermissionException)) {	×
UNCOV 279	logRec.setActionResult(ActionLogRecord.Result.InternalError);	×
280	}
281	logRec.setInfo(logRec.getInfo() + " (" + cmdEx.getMessage() + ")");	×
UNCOV 282	throw cmdEx;	×
283	} catch (RuntimeException re) {	1✔
284	logRec.setActionResult(ActionLogRecord.Result.InternalError);	1✔
285	logRec.setInfo(logRec.getInfo() + " (" + re.getMessage() + ")");	1✔
286
287	Throwable cause = re;	1✔
288	while (cause != null) {	1✔
289	if (cause instanceof ConstraintViolationException) {	1✔
290	StringBuilder sb = new StringBuilder();	×
291	sb.append("Unexpected bean validation constraint exception:");	×
292	ConstraintViolationException constraintViolationException = (ConstraintViolationException) cause;	×
293	for (ConstraintViolation<?> violation : constraintViolationException.getConstraintViolations()) {	×
294	sb.append(" Invalid value: <<<").append(violation.getInvalidValue()).append(">>> for ").append(violation.getPropertyPath()).append(" at ").append(violation.getLeafBean()).append(" - ").append(violation.getMessage());	×
295	}	×
UNCOV 296	logger.log(Level.SEVERE, sb.toString());	×
297	// set this more detailed info in action log
UNCOV 298	logRec.setInfo(logRec.getInfo() + " (" + sb.toString() + ")");	×
299	}
300	cause = cause.getCause();	1✔
301	}
302
303	throw re;	1✔
304
305	} finally {
306	if (logRec.getActionResult() == null) {	×
UNCOV 307	logRec.setActionResult(ActionLogRecord.Result.OK);	×
308	} else {
UNCOV 309	ejbCtxt.setRollbackOnly();	×
310	}
311	logRec.setEndTime(new java.util.Date());	×
UNCOV 312	logSvc.log(logRec);	×
313	}
314
315	}
316
317	public CommandContext getContext() {
318	if (ctxt == null) {	×
UNCOV 319	ctxt = new CommandContext() {	×
320
321	@Override
322	public DatasetDao datasets() {
UNCOV 323	return datasetDao;	×
324	}
325
326	@Override
327	public DataverseDao dataverses() {
UNCOV 328	return dataverseDao;	×
329	}
330
331	@Override
332	public DataverseRoleServiceBean roles() {
UNCOV 333	return rolesService;	×
334	}
335
336	@Override
337	public BuiltinUserServiceBean builtinUsers() {
UNCOV 338	return usersService;	×
339	}
340
341	@Override
342	public IndexServiceBean index() {
UNCOV 343	return indexService;	×
344	}
345
346	@Override
347	public IndexBatchServiceBean indexBatch() {
UNCOV 348	return indexBatchService;	×
349	}
350
351	@Override
352	public SolrIndexServiceBean solrIndex() {
UNCOV 353	return solrIndexService;	×
354	}
355
356	@Override
357	public SearchServiceBean search() {
UNCOV 358	return searchService;	×
359	}
360
361	@Override
362	public IngestServiceBean ingest() {
UNCOV 363	return ingestService;	×
364	}
365
366	@Override
367	public PermissionServiceBean permissions() {
UNCOV 368	return permissionService;	×
369	}
370
371	@Override
372	public DvObjectServiceBean dvObjects() {
UNCOV 373	return dvObjectService;	×
374	}
375
376	@Override
377	public DataFileServiceBean files() {
UNCOV 378	return dataFileService;	×
379	}
380
381	@Override
382	public EntityManager em() {
UNCOV 383	return em;	×
384	}
385
386	@Override
387	public DataAccess dataAccess() {
UNCOV 388	return dataAccess;	×
389	}
390
391	@Override
392	public DataverseFacetServiceBean facets() {
UNCOV 393	return dataverseFacetService;	×
394	}
395
396	@Override
397	public FeaturedDataverseServiceBean featuredDataverses() {
UNCOV 398	return featuredDataverseService;	×
399	}
400
401	@Override
402	public TemplateDao templates() {
UNCOV 403	return templateDao;	×
404	}
405
406	@Override
407	public SavedSearchServiceBean savedSearches() {
UNCOV 408	return savedSearchService;	×
409	}
410
411	@Override
412	public DataverseFieldTypeInputLevelServiceBean fieldTypeInputLevels() {
UNCOV 413	return fieldTypeInputLevels;	×
414	}
415
416	@Override
417	public DOIEZIdServiceBean doiEZId() {
UNCOV 418	return doiEZId;	×
419	}
420
421	@Override
422	public DOIDataCiteServiceBean doiDataCite() {
UNCOV 423	return doiDataCite;	×
424	}
425
426	@Override
427	public FakePidProviderServiceBean fakePidProvider() {
UNCOV 428	return fakePidProvider;	×
429	}
430
431	@Override
432	public HandlenetServiceBean handleNet() {
UNCOV 433	return handleNet;	×
434	}
435
436	@Override
437	public SettingsServiceBean settings() {
UNCOV 438	return settings;	×
439	}
440
441	@Override
442	public GuestbookServiceBean guestbooks() {
UNCOV 443	return guestbookService;	×
444	}
445
446	@Override
447	public GuestbookResponseServiceBean responses() {
UNCOV 448	return responses;	×
449	}
450
451	@Override
452	public DatasetLinkingServiceBean dsLinking() {
UNCOV 453	return dsLinking;	×
454	}
455
456	@Override
457	public DataverseEngine engine() {
UNCOV 458	return new DataverseEngine() {	×
459	@Override
460	public <R> R submit(Command<R> aCommand) {
UNCOV 461	return EjbDataverseEngine.this.submit(aCommand);	×
462	}
463	};
464	}
465
466	@Override
467	public ExplicitGroupServiceBean explicitGroups() {
UNCOV 468	return explicitGroups;	×
469	}
470
471	@Override
472	public GroupServiceBean groups() {
UNCOV 473	return groups;	×
474	}
475
476	@Override
477	public RoleAssigneeServiceBean roleAssignees() {
UNCOV 478	return roleAssignees;	×
479	}
480
481	@Override
482	public UserNotificationService notifications() {
UNCOV 483	return userNotificationService;	×
484	}
485
486	@Override
487	public AuthenticationServiceBean authentication() {
UNCOV 488	return authentication;	×
489	}
490
491	@Override
492	public SystemConfig systemConfig() {
UNCOV 493	return systemConfig;	×
494	}
495
496	@Override
497	public PrivateUrlServiceBean privateUrl() {
UNCOV 498	return privateUrlService;	×
499	}
500
501	@Override
502	public DatasetVersionServiceBean datasetVersion() {
UNCOV 503	return datasetVersionService;	×
504	}
505
506	@Override
507	public WorkflowServiceBean workflows() {
UNCOV 508	return workflowService;	×
509	}
510
511	@Override
512	public WorkflowExecutionFacade workflowExecutions() {
UNCOV 513	return workflowExecutionFacade;	×
514	}
515
516	@Override
517	public MapLayerMetadataServiceBean mapLayerMetadata() {
UNCOV 518	return mapLayerMetadata;	×
519	}
520
521	@Override
522	public DataCaptureModuleServiceBean dataCaptureModule() {
UNCOV 523	return dataCaptureModule;	×
524	}
525
526	@Override
527	public FileDownloadServiceBean fileDownload() {
UNCOV 528	return fileDownloadService;	×
529	}
530
531	@Override
532	public DataverseTextMessageServiceBean dataverseTextMessages() {
UNCOV 533	return dataverseTextMessageServiceBean;	×
534	}
535
536	@Override
537	public DatasetThumbnailService datasetThumailService() {
UNCOV 538	return datasetThumbnailService;	×
539	}
540
541	@Override
542	public CitationFactory citationFactory() {
UNCOV 543	return citationFactory;	×
544	}
545
546	@Override
547	public DownloadDatasetLogDao downloadDatasetDao() {
UNCOV 548	return downloadDatasetLogDao;	×
549	}
550
551	@Override
552	public DatasetFieldValidationService fieldValidationService() {
UNCOV 553	return fieldValidationService;	×
554	}
555	};
556	}
557
UNCOV 558	return ctxt;	×
559	}
560
561	}

CeON / dataverse / 1371

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