#5676

Committed 17 Apr 2025 12:57PM UTC coverage: 79.034% (-0.04%) from 79.075%

Build # #5676

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Commit Message

[DT-1502] Enforce Library card rule on all DAR creation; return specific Error text when this rule is being enforced. (#2481)

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82 of 92 new or added lines in 8 files covered. (89.13%)

1 existing line in 1 file now uncovered.

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/src/main/java/org/broadinstitute/consent/http/service/DataAccessRequestService.java

package org.broadinstitute.consent.http.service;

import com.google.gson.Gson;
import com.google.inject.Inject;
import jakarta.ws.rs.NotAcceptableException;
import jakarta.ws.rs.NotFoundException;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.Objects;
import java.util.UUID;
import org.broadinstitute.consent.http.db.DAOContainer;
import org.broadinstitute.consent.http.db.DarCollectionDAO;
import org.broadinstitute.consent.http.db.DataAccessRequestDAO;
import org.broadinstitute.consent.http.db.DatasetDAO;
import org.broadinstitute.consent.http.db.ElectionDAO;
import org.broadinstitute.consent.http.db.InstitutionDAO;
import org.broadinstitute.consent.http.db.MatchDAO;
import org.broadinstitute.consent.http.db.UserDAO;
import org.broadinstitute.consent.http.db.VoteDAO;
import org.broadinstitute.consent.http.enumeration.DarStatus;
import org.broadinstitute.consent.http.enumeration.UserRoles;
import org.broadinstitute.consent.http.exceptions.LibraryCardRequiredException;
import org.broadinstitute.consent.http.exceptions.NIHComplianceRuleException;
import org.broadinstitute.consent.http.models.DarCollection;
import org.broadinstitute.consent.http.models.DarDataset;
import org.broadinstitute.consent.http.models.DataAccessRequest;
import org.broadinstitute.consent.http.models.DataAccessRequestData;
import org.broadinstitute.consent.http.models.Dataset;
import org.broadinstitute.consent.http.models.Election;
import org.broadinstitute.consent.http.models.User;
import org.broadinstitute.consent.http.service.dao.DataAccessRequestServiceDAO;
import org.broadinstitute.consent.http.util.ConsentLogger;
import org.jdbi.v3.core.statement.UnableToExecuteStatementException;

public class DataAccessRequestService implements ConsentLogger {

  private final CounterService counterService;
  private final DatasetDAO datasetDAO;
  private final DataAccessRequestDAO dataAccessRequestDAO;
  private final DarCollectionDAO darCollectionDAO;
  private final ElectionDAO electionDAO;
  private final MatchDAO matchDAO;
  private final UserDAO userDAO;
  private final VoteDAO voteDAO;
  private final InstitutionDAO institutionDAO;
  private final DataAccessRequestServiceDAO dataAccessRequestServiceDAO;

  private final DacService dacService;
  private final DataAccessReportsParser dataAccessReportsParser;

  @Inject
  public DataAccessRequestService(CounterService counterService, DAOContainer container,
      DacService dacService, DataAccessRequestServiceDAO dataAccessRequestServiceDAO,
      UseRestrictionConverter useRestrictionConverter) {
    this.counterService = counterService;
    this.dataAccessRequestDAO = container.getDataAccessRequestDAO();
    this.darCollectionDAO = container.getDarCollectionDAO();
    this.datasetDAO = container.getDatasetDAO();
    this.electionDAO = container.getElectionDAO();
    this.matchDAO = container.getMatchDAO();
    this.userDAO = container.getUserDAO();
    this.voteDAO = container.getVoteDAO();
    this.institutionDAO = container.getInstitutionDAO();
    this.dacService = dacService;
    this.dataAccessReportsParser = new DataAccessReportsParser(datasetDAO, useRestrictionConverter);
    this.dataAccessRequestServiceDAO = dataAccessRequestServiceDAO;
  }

  public List<DataAccessRequest> findAllDraftDataAccessRequests() {
    return dataAccessRequestDAO.findAllDraftDataAccessRequests();
  }

  public List<DataAccessRequest> findAllDraftDataAccessRequestsByUser(Integer userId) {
    return dataAccessRequestDAO.findAllDraftsByUserId(userId);
  }

  public void deleteByReferenceId(User user, String referenceId) throws NotAcceptableException {
    List<Election> elections = electionDAO.findElectionsByReferenceId(referenceId);
    if (!elections.isEmpty()) {
      // If the user is an admin, delete all votes and elections
      if (user.hasUserRole(UserRoles.ADMIN)) {
        voteDAO.deleteVotesByReferenceId(referenceId);
        List<Integer> electionIds = elections.stream().map(Election::getElectionId).toList();
        electionDAO.deleteElectionsByIds(electionIds);
      } else {
        String message = String.format(
            "Unable to delete DAR: '%s', there are existing elections that reference it.",
            referenceId);
        logWarn(message);
        throw new NotAcceptableException(message);
      }
    }
    matchDAO.deleteRationalesByPurposeIds(List.of(referenceId));
    matchDAO.deleteMatchesByPurposeId(referenceId);
    dataAccessRequestDAO.deleteDARDatasetRelationByReferenceId(referenceId);
    dataAccessRequestDAO.deleteByReferenceId(referenceId);
  }

  public DataAccessRequest findByReferenceId(String referencedId) {
    DataAccessRequest dar = dataAccessRequestDAO.findByReferenceId(referencedId);
    if (Objects.isNull(dar)) {
      throw new NotFoundException("There does not exist a DAR with the given reference Id");
    }
    return dar;
  }

  //NOTE: rewrite method into new servicedao method on another ticket
  public DataAccessRequest insertDraftDataAccessRequest(User user, DataAccessRequest dar) {
    if (Objects.isNull(user) || Objects.isNull(dar) || Objects.isNull(
        dar.getReferenceId()) || Objects.isNull(dar.getData())) {
      throw new IllegalArgumentException("User and DataAccessRequest are required");
    }

    if (user.getLibraryCards().isEmpty()) {
      throw new LibraryCardRequiredException();
    }

    Date now = new Date();
    dataAccessRequestDAO.insertDraftDataAccessRequest(
        dar.getReferenceId(),
        user.getUserId(),
        now,
        now,
        null,
        now,
        dar.getData()
    );
    syncDataAccessRequestDatasets(dar.getDatasetIds(), dar.getReferenceId());

    return findByReferenceId(dar.getReferenceId());
  }

  /**
   * First delete any rows with the current reference id. This will allow us to keep (referenceId,
   * dataset_id) unique Takes in a list of datasetIds and a referenceId and adds them to the
   * dar_dataset collection
   *
   * @param datasetIds  List of Integers that represent the datasetIds
   * @param referenceId ReferenceId of the corresponding DAR
   */
  private void syncDataAccessRequestDatasets(List<Integer> datasetIds, String referenceId) {
    List<DarDataset> darDatasets = datasetIds.stream()
        .map(datasetId -> new DarDataset(referenceId, datasetId))
        .toList();
    dataAccessRequestDAO.deleteDARDatasetRelationByReferenceId(referenceId);

    if (!darDatasets.isEmpty()) {
      dataAccessRequestDAO.insertAllDarDatasets(darDatasets);
    }
  }

  /**
   * Create a new Draft DAR from the canceled DARs present in source DarCollection.
   *
   * @param user             The User
   * @param sourceCollection The source DarCollection
   * @return New DataAccessRequest in draft status
   */
  public DataAccessRequest createDraftDarFromCanceledCollection(User user,
      DarCollection sourceCollection) {
    if (Objects.isNull(sourceCollection.getDars()) || sourceCollection.getDars().isEmpty()) {
      throw new IllegalArgumentException("Source Collection must contain at least a single DAR");
    }
    if (user.getLibraryCards().isEmpty()) {
      throw new LibraryCardRequiredException();
    }
    DataAccessRequest sourceDar = new ArrayList<>(sourceCollection.getDars().values()).get(0);
    DataAccessRequestData sourceData = sourceDar.getData();
    if (Objects.isNull(sourceData)) {
      throw new IllegalArgumentException(
          "Source Collection must contain at least a single DAR with a populated data");
    }

    // Find all dataset ids for canceled DARs in the collection
    List<Integer> datasetIds = sourceCollection
        .getDars().values().stream()
        .filter(d -> DarStatus.CANCELED.getValue().equalsIgnoreCase(d.getData().getStatus()))
        .map(DataAccessRequest::getDatasetIds)
        .flatMap(Collection::stream)
        .toList();
    if (datasetIds.isEmpty()) {
      throw new IllegalArgumentException(
          "Source Collection must contain references to at least a single canceled DAR's dataset");
    }

    List<String> canceledReferenceIds = sourceCollection
        .getDars().values().stream()
        .filter(d -> DarStatus.CANCELED.getValue().equalsIgnoreCase(d.getData().getStatus()))
        .map(DataAccessRequest::getReferenceId)
        .toList();
    List<Integer> electionIds = electionDAO.getElectionIdsByReferenceIds(canceledReferenceIds);
    if (!electionIds.isEmpty()) {
      String errorMessage = "Found 'Open' elections for canceled DARs in collection id: "
          + sourceCollection.getDarCollectionId();
      logWarn(errorMessage);
      throw new IllegalArgumentException(errorMessage);
    }

    List<String> sourceReferenceIds = sourceCollection
        .getDars().values().stream()
        .map(DataAccessRequest::getReferenceId)
        .toList();
    dataAccessRequestDAO.archiveByReferenceIds(sourceReferenceIds);

    String referenceId = UUID.randomUUID().toString();
    Date now = new Date();
    // Clone the dar's data object and reset values that need to be updated for the clone
    DataAccessRequestData newData = new Gson().fromJson(sourceData.toString(),
        DataAccessRequestData.class);
    newData.setDarCode(null);
    newData.setStatus(null);
    newData.setReferenceId(referenceId);
    newData.setCreateDate(now.getTime());
    newData.setSortDate(now.getTime());
    dataAccessRequestDAO.insertDraftDataAccessRequest(
        referenceId,
        user.getUserId(),
        now,
        now,
        null,
        now,
        newData
    );
    syncDataAccessRequestDatasets(datasetIds, referenceId);

    return findByReferenceId(referenceId);
  }

  /**
   * @param user User
   * @return List<DataAccessRequest>
   */
  public List<DataAccessRequest> getDataAccessRequestsByUserRole(User user) {
    List<DataAccessRequest> dars = dataAccessRequestDAO.findAllDataAccessRequests();
    return dacService.filterDataAccessRequestsByDac(dars, user);
  }

  /**
   * Generate a DataAccessRequest from the provided DAR. The provided DAR may or may not exist in
   * draft form, so it covers both cases of converting an existing draft to submitted and creating a
   * brand new DAR from scratch.
   *
   * @param user              The create User
   * @param dataAccessRequest DataAccessRequest with populated DAR data
   * @return The created DAR.
   */
  public DataAccessRequest createDataAccessRequest(User user, DataAccessRequest dataAccessRequest) {
    if (Objects.isNull(user) || Objects.isNull(dataAccessRequest) || Objects.isNull(
        dataAccessRequest.getReferenceId()) || Objects.isNull(dataAccessRequest.getData())) {
      throw new IllegalArgumentException("User and DataAccessRequest are required");
    }

    if (user.getLibraryCards().isEmpty()) {
      throw new NIHComplianceRuleException();
    }

    Date now = new Date();
    long nowTime = now.getTime();
    DataAccessRequestData darData = dataAccessRequest.getData();
    if (Objects.isNull(darData.getCreateDate())) {
      darData.setCreateDate(nowTime);
    }
    darData.setSortDate(nowTime);
    DataAccessRequest existingDar = dataAccessRequestDAO.findByReferenceId(
        dataAccessRequest.getReferenceId());
    Integer collectionId;
    // Only create a new DarCollection if we haven't done so already
    if (Objects.nonNull(existingDar) && Objects.nonNull(existingDar.getCollectionId())) {
      collectionId = existingDar.getCollectionId();
    } else {
      String darCodeSequence = "DAR-" + counterService.getNextDarSequence();
      collectionId = darCollectionDAO.insertDarCollection(darCodeSequence, user.getUserId(), now);
      darData.setDarCode(darCodeSequence);
    }
    String referenceId;
    List<Integer> datasetIds = dataAccessRequest.getDatasetIds();
    if (Objects.nonNull(existingDar)) {
      referenceId = dataAccessRequest.getReferenceId();
      dataAccessRequestDAO.updateDraftForCollection(collectionId,
          referenceId);
      dataAccessRequestDAO.updateDataByReferenceId(
          referenceId,
          user.getUserId(),
          new Date(darData.getSortDate()),
          now,
          now,
          darData);
    } else {
      referenceId = UUID.randomUUID().toString();
      dataAccessRequestDAO.insertDataAccessRequest(
          collectionId,
          referenceId,
          user.getUserId(),
          new Date(darData.getCreateDate()),
          new Date(darData.getSortDate()),
          now,
          now,
          darData);
    }
    syncDataAccessRequestDatasets(datasetIds, referenceId);
    return findByReferenceId(referenceId);
  }

  /**
   * Update an existing DataAccessRequest. Replaces DataAccessRequestData.
   *
   * @param user The User
   * @param dar  The DataAccessRequest
   * @return The updated DataAccessRequest
   */
  public DataAccessRequest updateByReferenceId(User user, DataAccessRequest dar) {
    try {
      return dataAccessRequestServiceDAO.updateByReferenceId(user, dar);
    } catch (SQLException e) {
      // If I simply rethrow the error then I'll have to redefine any method that
      // calls this function to "throw SQLException"
      //Instead I'm going to throw an UnableToExecuteStatementException
      //Response class will catch it, log it, and throw a 500 through the "unableToExecuteExceptionHandler"
      //on the Resource class, just like it would with a SQLException
      throw new UnableToExecuteStatementException(e.getMessage());
    }
  }

  public Collection<DataAccessRequest> getApprovedDARsForDataset(Dataset dataset) {
    return dataAccessRequestDAO.findApprovedDARsByDatasetId(dataset.getDatasetId());
  }

}

1	package org.broadinstitute.consent.http.service;
2
3	import com.google.gson.Gson;
4	import com.google.inject.Inject;
5	import jakarta.ws.rs.NotAcceptableException;
6	import jakarta.ws.rs.NotFoundException;
7	import java.sql.SQLException;
8	import java.util.ArrayList;
9	import java.util.Collection;
10	import java.util.Date;
11	import java.util.List;
12	import java.util.Objects;
13	import java.util.UUID;
14	import org.broadinstitute.consent.http.db.DAOContainer;
15	import org.broadinstitute.consent.http.db.DarCollectionDAO;
16	import org.broadinstitute.consent.http.db.DataAccessRequestDAO;
17	import org.broadinstitute.consent.http.db.DatasetDAO;
18	import org.broadinstitute.consent.http.db.ElectionDAO;
19	import org.broadinstitute.consent.http.db.InstitutionDAO;
20	import org.broadinstitute.consent.http.db.MatchDAO;
21	import org.broadinstitute.consent.http.db.UserDAO;
22	import org.broadinstitute.consent.http.db.VoteDAO;
23	import org.broadinstitute.consent.http.enumeration.DarStatus;
24	import org.broadinstitute.consent.http.enumeration.UserRoles;
25	import org.broadinstitute.consent.http.exceptions.LibraryCardRequiredException;
26	import org.broadinstitute.consent.http.exceptions.NIHComplianceRuleException;
27	import org.broadinstitute.consent.http.models.DarCollection;
28	import org.broadinstitute.consent.http.models.DarDataset;
29	import org.broadinstitute.consent.http.models.DataAccessRequest;
30	import org.broadinstitute.consent.http.models.DataAccessRequestData;
31	import org.broadinstitute.consent.http.models.Dataset;
32	import org.broadinstitute.consent.http.models.Election;
33	import org.broadinstitute.consent.http.models.User;
34	import org.broadinstitute.consent.http.service.dao.DataAccessRequestServiceDAO;
35	import org.broadinstitute.consent.http.util.ConsentLogger;
36	import org.jdbi.v3.core.statement.UnableToExecuteStatementException;
37
38	public class DataAccessRequestService implements ConsentLogger {
39
40	private final CounterService counterService;
41	private final DatasetDAO datasetDAO;
42	private final DataAccessRequestDAO dataAccessRequestDAO;
43	private final DarCollectionDAO darCollectionDAO;
44	private final ElectionDAO electionDAO;
45	private final MatchDAO matchDAO;
46	private final UserDAO userDAO;
47	private final VoteDAO voteDAO;
48	private final InstitutionDAO institutionDAO;
49	private final DataAccessRequestServiceDAO dataAccessRequestServiceDAO;
50
51	private final DacService dacService;
52	private final DataAccessReportsParser dataAccessReportsParser;
53
54	@Inject
55	public DataAccessRequestService(CounterService counterService, DAOContainer container,
56	DacService dacService, DataAccessRequestServiceDAO dataAccessRequestServiceDAO,
57	UseRestrictionConverter useRestrictionConverter) {	1✔
58	this.counterService = counterService;	1✔
59	this.dataAccessRequestDAO = container.getDataAccessRequestDAO();	1✔
60	this.darCollectionDAO = container.getDarCollectionDAO();	1✔
61	this.datasetDAO = container.getDatasetDAO();	1✔
62	this.electionDAO = container.getElectionDAO();	1✔
63	this.matchDAO = container.getMatchDAO();	1✔
64	this.userDAO = container.getUserDAO();	1✔
65	this.voteDAO = container.getVoteDAO();	1✔
66	this.institutionDAO = container.getInstitutionDAO();	1✔
67	this.dacService = dacService;	1✔
68	this.dataAccessReportsParser = new DataAccessReportsParser(datasetDAO, useRestrictionConverter);	1✔
69	this.dataAccessRequestServiceDAO = dataAccessRequestServiceDAO;	1✔
70	}	1✔
71
72	public List<DataAccessRequest> findAllDraftDataAccessRequests() {
73	return dataAccessRequestDAO.findAllDraftDataAccessRequests();	1✔
74	}
75
76	public List<DataAccessRequest> findAllDraftDataAccessRequestsByUser(Integer userId) {
77	return dataAccessRequestDAO.findAllDraftsByUserId(userId);	1✔
78	}
79
80	public void deleteByReferenceId(User user, String referenceId) throws NotAcceptableException {
81	List<Election> elections = electionDAO.findElectionsByReferenceId(referenceId);	1✔
82	if (!elections.isEmpty()) {	1✔
83	// If the user is an admin, delete all votes and elections
84	if (user.hasUserRole(UserRoles.ADMIN)) {	1✔
85	voteDAO.deleteVotesByReferenceId(referenceId);	1✔
86	List<Integer> electionIds = elections.stream().map(Election::getElectionId).toList();	1✔
87	electionDAO.deleteElectionsByIds(electionIds);	1✔
88	} else {	1✔
89	String message = String.format(	1✔
90	"Unable to delete DAR: '%s', there are existing elections that reference it.",
91	referenceId);
92	logWarn(message);	1✔
93	throw new NotAcceptableException(message);	1✔
94	}
95	}
96	matchDAO.deleteRationalesByPurposeIds(List.of(referenceId));	1✔
97	matchDAO.deleteMatchesByPurposeId(referenceId);	1✔
98	dataAccessRequestDAO.deleteDARDatasetRelationByReferenceId(referenceId);	1✔
99	dataAccessRequestDAO.deleteByReferenceId(referenceId);	1✔
100	}	1✔
101
102	public DataAccessRequest findByReferenceId(String referencedId) {
103	DataAccessRequest dar = dataAccessRequestDAO.findByReferenceId(referencedId);	1✔
104	if (Objects.isNull(dar)) {	1✔
105	throw new NotFoundException("There does not exist a DAR with the given reference Id");	×
106	}
107	return dar;	1✔
108	}
109
110	//NOTE: rewrite method into new servicedao method on another ticket
111	public DataAccessRequest insertDraftDataAccessRequest(User user, DataAccessRequest dar) {
112	if (Objects.isNull(user) \|\| Objects.isNull(dar) \|\| Objects.isNull(	1✔
113	dar.getReferenceId()) \|\| Objects.isNull(dar.getData())) {	1✔
114	throw new IllegalArgumentException("User and DataAccessRequest are required");	1✔
115	}
116
117	if (user.getLibraryCards().isEmpty()) {	1✔
NEW 118	throw new LibraryCardRequiredException();	×
119	}
120
121	Date now = new Date();	1✔
122	dataAccessRequestDAO.insertDraftDataAccessRequest(	1✔
123	dar.getReferenceId(),	1✔
124	user.getUserId(),	1✔
125	now,
126	now,
127	null,
128	now,
129	dar.getData()	1✔
130	);
131	syncDataAccessRequestDatasets(dar.getDatasetIds(), dar.getReferenceId());	1✔
132
133	return findByReferenceId(dar.getReferenceId());	1✔
134	}
135
136	/**
137	* First delete any rows with the current reference id. This will allow us to keep (referenceId,
138	* dataset_id) unique Takes in a list of datasetIds and a referenceId and adds them to the
139	* dar_dataset collection
140	*
141	* @param datasetIds List of Integers that represent the datasetIds
142	* @param referenceId ReferenceId of the corresponding DAR
143	*/
144	private void syncDataAccessRequestDatasets(List<Integer> datasetIds, String referenceId) {
145	List<DarDataset> darDatasets = datasetIds.stream()	1✔
146	.map(datasetId -> new DarDataset(referenceId, datasetId))	1✔
147	.toList();	1✔
148	dataAccessRequestDAO.deleteDARDatasetRelationByReferenceId(referenceId);	1✔
149
150	if (!darDatasets.isEmpty()) {	1✔
151	dataAccessRequestDAO.insertAllDarDatasets(darDatasets);	1✔
152	}
153	}	1✔
154
155	/**
156	* Create a new Draft DAR from the canceled DARs present in source DarCollection.
157	*
158	* @param user The User
159	* @param sourceCollection The source DarCollection
160	* @return New DataAccessRequest in draft status
161	*/
162	public DataAccessRequest createDraftDarFromCanceledCollection(User user,
163	DarCollection sourceCollection) {
164	if (Objects.isNull(sourceCollection.getDars()) \|\| sourceCollection.getDars().isEmpty()) {	1✔
165	throw new IllegalArgumentException("Source Collection must contain at least a single DAR");	1✔
166	}
167	if (user.getLibraryCards().isEmpty()) {	1✔
168	throw new LibraryCardRequiredException();	1✔
169	}
170	DataAccessRequest sourceDar = new ArrayList<>(sourceCollection.getDars().values()).get(0);	1✔
171	DataAccessRequestData sourceData = sourceDar.getData();	1✔
172	if (Objects.isNull(sourceData)) {	1✔
173	throw new IllegalArgumentException(	1✔
174	"Source Collection must contain at least a single DAR with a populated data");
175	}
176
177	// Find all dataset ids for canceled DARs in the collection
178	List<Integer> datasetIds = sourceCollection	1✔
179	.getDars().values().stream()	1✔
180	.filter(d -> DarStatus.CANCELED.getValue().equalsIgnoreCase(d.getData().getStatus()))	1✔
181	.map(DataAccessRequest::getDatasetIds)	1✔
182	.flatMap(Collection::stream)	1✔
183	.toList();	1✔
184	if (datasetIds.isEmpty()) {	1✔
185	throw new IllegalArgumentException(	1✔
186	"Source Collection must contain references to at least a single canceled DAR's dataset");
187	}
188
189	List<String> canceledReferenceIds = sourceCollection	1✔
190	.getDars().values().stream()	1✔
191	.filter(d -> DarStatus.CANCELED.getValue().equalsIgnoreCase(d.getData().getStatus()))	1✔
192	.map(DataAccessRequest::getReferenceId)	1✔
193	.toList();	1✔
194	List<Integer> electionIds = electionDAO.getElectionIdsByReferenceIds(canceledReferenceIds);	1✔
195	if (!electionIds.isEmpty()) {	1✔
196	String errorMessage = "Found 'Open' elections for canceled DARs in collection id: "	1✔
197	+ sourceCollection.getDarCollectionId();	1✔
198	logWarn(errorMessage);	1✔
199	throw new IllegalArgumentException(errorMessage);	1✔
200	}
201
202	List<String> sourceReferenceIds = sourceCollection	1✔
203	.getDars().values().stream()	1✔
204	.map(DataAccessRequest::getReferenceId)	1✔
205	.toList();	1✔
206	dataAccessRequestDAO.archiveByReferenceIds(sourceReferenceIds);	1✔
207
208	String referenceId = UUID.randomUUID().toString();	1✔
209	Date now = new Date();	1✔
210	// Clone the dar's data object and reset values that need to be updated for the clone
211	DataAccessRequestData newData = new Gson().fromJson(sourceData.toString(),	1✔
212	DataAccessRequestData.class);
213	newData.setDarCode(null);	1✔
214	newData.setStatus(null);	1✔
215	newData.setReferenceId(referenceId);	1✔
216	newData.setCreateDate(now.getTime());	1✔
217	newData.setSortDate(now.getTime());	1✔
218	dataAccessRequestDAO.insertDraftDataAccessRequest(	1✔
219	referenceId,
220	user.getUserId(),	1✔
221	now,
222	now,
223	null,
224	now,
225	newData
226	);
227	syncDataAccessRequestDatasets(datasetIds, referenceId);	1✔
228
229	return findByReferenceId(referenceId);	1✔
230	}
231
232	/**
233	* @param user User
234	* @return List<DataAccessRequest>
235	*/
236	public List<DataAccessRequest> getDataAccessRequestsByUserRole(User user) {
237	List<DataAccessRequest> dars = dataAccessRequestDAO.findAllDataAccessRequests();	1✔
238	return dacService.filterDataAccessRequestsByDac(dars, user);	1✔
239	}
240
241	/**
242	* Generate a DataAccessRequest from the provided DAR. The provided DAR may or may not exist in
243	* draft form, so it covers both cases of converting an existing draft to submitted and creating a
244	* brand new DAR from scratch.
245	*
246	* @param user The create User
247	* @param dataAccessRequest DataAccessRequest with populated DAR data
248	* @return The created DAR.
249	*/
250	public DataAccessRequest createDataAccessRequest(User user, DataAccessRequest dataAccessRequest) {
251	if (Objects.isNull(user) \|\| Objects.isNull(dataAccessRequest) \|\| Objects.isNull(	1✔
252	dataAccessRequest.getReferenceId()) \|\| Objects.isNull(dataAccessRequest.getData())) {	1✔
253	throw new IllegalArgumentException("User and DataAccessRequest are required");	×
254	}
255
256	if (user.getLibraryCards().isEmpty()) {	1✔
257	throw new NIHComplianceRuleException();	1✔
258	}
259
260	Date now = new Date();	1✔
261	long nowTime = now.getTime();	1✔
262	DataAccessRequestData darData = dataAccessRequest.getData();	1✔
263	if (Objects.isNull(darData.getCreateDate())) {	1✔
264	darData.setCreateDate(nowTime);	1✔
265	}
266	darData.setSortDate(nowTime);	1✔
267	DataAccessRequest existingDar = dataAccessRequestDAO.findByReferenceId(	1✔
268	dataAccessRequest.getReferenceId());	1✔
269	Integer collectionId;
270	// Only create a new DarCollection if we haven't done so already
271	if (Objects.nonNull(existingDar) && Objects.nonNull(existingDar.getCollectionId())) {	1✔
272	collectionId = existingDar.getCollectionId();	×
273	} else {
274	String darCodeSequence = "DAR-" + counterService.getNextDarSequence();	1✔
275	collectionId = darCollectionDAO.insertDarCollection(darCodeSequence, user.getUserId(), now);	1✔
276	darData.setDarCode(darCodeSequence);	1✔
277	}
278	String referenceId;
279	List<Integer> datasetIds = dataAccessRequest.getDatasetIds();	1✔
280	if (Objects.nonNull(existingDar)) {	1✔
281	referenceId = dataAccessRequest.getReferenceId();	1✔
282	dataAccessRequestDAO.updateDraftForCollection(collectionId,	1✔
283	referenceId);
284	dataAccessRequestDAO.updateDataByReferenceId(	1✔
285	referenceId,
286	user.getUserId(),	1✔
287	new Date(darData.getSortDate()),	1✔
288	now,
289	now,
290	darData);
291	} else {
292	referenceId = UUID.randomUUID().toString();	1✔
293	dataAccessRequestDAO.insertDataAccessRequest(	1✔
294	collectionId,
295	referenceId,
296	user.getUserId(),	1✔
297	new Date(darData.getCreateDate()),	1✔
298	new Date(darData.getSortDate()),	1✔
299	now,
300	now,
301	darData);
302	}
303	syncDataAccessRequestDatasets(datasetIds, referenceId);	1✔
304	return findByReferenceId(referenceId);	1✔
305	}
306
307	/**
308	* Update an existing DataAccessRequest. Replaces DataAccessRequestData.
309	*
310	* @param user The User
311	* @param dar The DataAccessRequest
312	* @return The updated DataAccessRequest
313	*/
314	public DataAccessRequest updateByReferenceId(User user, DataAccessRequest dar) {
315	try {
316	return dataAccessRequestServiceDAO.updateByReferenceId(user, dar);	1✔
317	} catch (SQLException e) {	×
318	// If I simply rethrow the error then I'll have to redefine any method that
319	// calls this function to "throw SQLException"
320	//Instead I'm going to throw an UnableToExecuteStatementException
321	//Response class will catch it, log it, and throw a 500 through the "unableToExecuteExceptionHandler"
322	//on the Resource class, just like it would with a SQLException
323	throw new UnableToExecuteStatementException(e.getMessage());	×
324	}
325	}
326
327	public Collection<DataAccessRequest> getApprovedDARsForDataset(Dataset dataset) {
328	return dataAccessRequestDAO.findApprovedDARsByDatasetId(dataset.getDatasetId());	1✔
329	}
330
331	}

DataBiosphere / consent / #5676

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