DataBiosphere / consent / #5697

coverage: 78.956% (-0.02%) from 78.975%
#5697

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[DT-1487]Req. 10 - Enable Int. Collab. Approvals via DAR when LCA = Yes (#2484)

Co-authored-by: rjohanek <rjohanek@broadinstitute.org>

49 of 50 new or added lines in 5 files covered. (98.0%)

14 existing lines in 4 files now uncovered.

10209 of 12930 relevant lines covered (78.96%)

0.79 hits per line

Source File
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86.05
/src/main/java/org/broadinstitute/consent/http/service/TDRService.java
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package org.broadinstitute.consent.http.service;
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import com.google.inject.Inject;










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import jakarta.ws.rs.NotAuthorizedException;










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import jakarta.ws.rs.NotFoundException;










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import java.sql.Timestamp;










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import java.util.Arrays;










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import java.util.Collection;










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import java.util.Comparator;










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import java.util.Date;










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import java.util.List;










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import java.util.Objects;










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import java.util.UUID;










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import java.util.stream.Stream;










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import org.broadinstitute.consent.http.db.DatasetDAO;










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import org.broadinstitute.consent.http.db.SamDAO;










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import org.broadinstitute.consent.http.db.UserDAO;










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import org.broadinstitute.consent.http.models.AuthUser;










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import org.broadinstitute.consent.http.models.Collaborator;










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import org.broadinstitute.consent.http.models.DataAccessRequest;










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import org.broadinstitute.consent.http.models.DataAccessRequestData;










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import org.broadinstitute.consent.http.models.Dataset;










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import org.broadinstitute.consent.http.models.User;










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import org.broadinstitute.consent.http.models.tdr.ApprovedUser;










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import org.broadinstitute.consent.http.models.tdr.ApprovedUsers;










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import org.broadinstitute.consent.http.util.ConsentLogger;










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public class TDRService implements ConsentLogger {










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  private final DataAccessRequestService dataAccessRequestService;










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  private final DatasetDAO datasetDAO;










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  private final SamDAO samDAO;










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  private final UserDAO userDAO;










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  @Inject










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  public TDRService(DataAccessRequestService dataAccessRequestService, DatasetDAO datasetDAO,










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      SamDAO samDAO, UserDAO userDAO) {




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    this.dataAccessRequestService = dataAccessRequestService;




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    this.datasetDAO = datasetDAO;




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    this.samDAO = samDAO;




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    this.userDAO = userDAO;




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  }




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  public ApprovedUsers getApprovedUsersForDataset(AuthUser authUser, Dataset dataset) {










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    Collection<DataAccessRequest> dars = dataAccessRequestService.getApprovedDARsForDataset(




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        dataset);










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    List<String> labCollaborators = dars.stream()




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        .map(DataAccessRequest::getData)




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        .filter(Objects::nonNull)




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        .map(DataAccessRequestData::getLabAndInternalCollaborators)




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        .flatMap(List::stream)




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        .filter(Objects::nonNull)




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        .map(Collaborator::getEmail)




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        .filter(email -> !email.isBlank())




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        // Sam has an endpoint for validating a single email at a time










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        .map(email -> {




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          try {










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            samDAO.getV1UserByEmail(authUser, email);




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            return email;




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          } catch (NotAuthorizedException e) {




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            logWarn("User " + authUser.getEmail() + " is not authorized to look for users in Sam");




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            return null;




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          } catch (Exception e) {




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            logWarn("Collaborator: " + email + " does not exist in Sam");




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            return null;




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          }










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        })










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        .filter(Objects::nonNull)




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        .toList();




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    List<Integer> userIds = dars.stream().map(DataAccessRequest::getUserId).toList();




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    Collection<User> users = userIds.isEmpty() ? List.of() : userDAO.findUsers(userIds);




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    List<String> userEmails = users.stream()




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        .map(User::getEmail)




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        .filter(email -> !email.isBlank())




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        .toList();




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    List<ApprovedUser> approvedUsers = Stream.of(labCollaborators, userEmails)




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        .flatMap(List::stream)




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        .distinct()




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        .map(ApprovedUser::new)




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        .sorted(Comparator.comparing(ApprovedUser::email))




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        .toList();




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    return new ApprovedUsers(approvedUsers);




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  }










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  public List<Dataset> getDatasetsByIdentifier(List<Integer> aliases) {










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    return datasetDAO.findDatasetsByAlias(aliases)




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        .stream()




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        // technically, it is possible to have two dataset identifiers which










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        // have the same alias but are not the same: e.g., DUOS-5 and DUOS-00005










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        .filter(d -> aliases.contains(d.getAlias()))




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        .toList();




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  }










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}
























    

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