#5834

Committed 02 May 2025 06:55PM UTC coverage: 78.772% (+0.04%) from 78.733%

Build # #5834

Build Type

push

Committed by

Commit Message

[DT-1601] Add a check that all datasets in a progress report must be approved (#2510)

Run Details

5 of 5 new or added lines in 1 file covered. (100.0%)

54 existing lines in 6 files now uncovered.

10075 of 12790 relevant lines covered (78.77%)

0.79 hits per line

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87.2

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

package org.broadinstitute.consent.http.service;

import static org.broadinstitute.consent.http.service.DataAccessRequestService.EXPIRE_NOTICE_INTERVAL;
import static org.broadinstitute.consent.http.service.DataAccessRequestService.EXPIRE_WARN_INTERVAL;

import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Streams;
import com.google.inject.Inject;
import com.sendgrid.Response;
import com.sendgrid.helpers.mail.Mail;
import com.sendgrid.helpers.mail.objects.Content;
import com.sendgrid.helpers.mail.objects.Email;
import freemarker.template.Template;
import freemarker.template.TemplateException;
import jakarta.ws.rs.NotFoundException;
import java.io.IOException;
import java.io.StringWriter;
import java.io.Writer;
import java.sql.Timestamp;
import java.time.Instant;
import java.time.LocalDate;
import java.time.LocalTime;
import java.time.ZoneOffset;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;
import javax.annotation.Nullable;
import org.broadinstitute.consent.http.configurations.ConsentConfiguration;
import org.broadinstitute.consent.http.db.DacDAO;
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.MailMessageDAO;
import org.broadinstitute.consent.http.db.UserDAO;
import org.broadinstitute.consent.http.db.VoteDAO;
import org.broadinstitute.consent.http.enumeration.EmailType;
import org.broadinstitute.consent.http.enumeration.UserRoles;
import org.broadinstitute.consent.http.mail.SendGridAPI;
import org.broadinstitute.consent.http.mail.freemarker.FreeMarkerTemplateHelper;
import org.broadinstitute.consent.http.mail.message.DaaRequestMessage;
import org.broadinstitute.consent.http.mail.message.DarExpirationReminderMessage;
import org.broadinstitute.consent.http.mail.message.DarExpiredMessage;
import org.broadinstitute.consent.http.mail.message.DataCustodianApprovalMessage;
import org.broadinstitute.consent.http.mail.message.DatasetApprovedMessage;
import org.broadinstitute.consent.http.mail.message.DatasetDeniedMessage;
import org.broadinstitute.consent.http.mail.message.DatasetSubmittedMessage;
import org.broadinstitute.consent.http.mail.message.MailMessage;
import org.broadinstitute.consent.http.mail.message.NewCaseMessage;
import org.broadinstitute.consent.http.mail.message.NewDAAUploadResearcherMessage;
import org.broadinstitute.consent.http.mail.message.NewDAAUploadSOMessage;
import org.broadinstitute.consent.http.mail.message.NewDARRequestMessage;
import org.broadinstitute.consent.http.mail.message.NewResearcherLibraryRequestMessage;
import org.broadinstitute.consent.http.mail.message.ReminderMessage;
import org.broadinstitute.consent.http.mail.message.ResearcherApprovedMessage;
import org.broadinstitute.consent.http.models.Dac;
import org.broadinstitute.consent.http.models.DarCollection;
import org.broadinstitute.consent.http.models.DataAccessRequest;
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.models.UserRole;
import org.broadinstitute.consent.http.models.Vote;
import org.broadinstitute.consent.http.models.dto.DatasetMailDTO;
import org.broadinstitute.consent.http.util.ConsentLogger;

public class EmailService implements ConsentLogger {

  public static final Timestamp MINIMUM_SUBMITTED_DATE_FOR_DAR_EXPIRATIONS = Timestamp.from(
      Instant.ofEpochSecond(
          LocalDate.of(2024, 9, 30).toEpochSecond(LocalTime.of(0, 0, 0, 0), ZoneOffset.UTC)));
  private final DarCollectionDAO collectionDAO;
  private final DataAccessRequestDAO dataAccessRequestDAO;
  private final UserDAO userDAO;
  private final ElectionDAO electionDAO;
  private final MailMessageDAO emailDAO;
  private final VoteDAO voteDAO;
  private final DatasetDAO datasetDAO;
  private final DacDAO dacDAO;
  private final FreeMarkerTemplateHelper templateHelper;
  private final SendGridAPI sendGridAPI;
  private final String fromAccount;
  private final String serverUrl;

  @Inject
  public EmailService(
      DarCollectionDAO collectionDAO,
      VoteDAO voteDAO,
      ElectionDAO electionDAO,
      UserDAO userDAO,
      MailMessageDAO emailDAO,
      DatasetDAO datasetDAO,
      DacDAO dacDAO,
      DataAccessRequestDAO dataAccessRequestDAO,
      SendGridAPI sendGridAPI,
      FreeMarkerTemplateHelper helper,
      ConsentConfiguration config) {
    this.collectionDAO = collectionDAO;
    this.userDAO = userDAO;
    this.electionDAO = electionDAO;
    this.voteDAO = voteDAO;
    this.templateHelper = helper;
    this.emailDAO = emailDAO;
    this.datasetDAO = datasetDAO;
    this.dacDAO = dacDAO;
    this.dataAccessRequestDAO = dataAccessRequestDAO;
    this.sendGridAPI = sendGridAPI;
    this.serverUrl = config.getServicesConfiguration().getLocalURL();
    this.fromAccount = config.getMailConfiguration().getGoogleAccount();
  }

  /**
   * This method saves an email (either sent or unsent) with all available metadata from the
   * SendGrid response.
   */
  private void saveEmailAndResponse(
      @Nullable Response response,
      @Nullable String entityReferenceId,
      @Nullable Integer voteId,
      Integer userId,
      EmailType emailType,
      String content) {
    Instant now = Instant.now();
    Instant dateSent = (Objects.nonNull(response) && response.getStatusCode() < 400) ? now : null;
    emailDAO.insert(
        entityReferenceId,
        voteId,
        userId,
        emailType.getTypeInt(),
        dateSent,
        content,
        Objects.nonNull(response) ? response.getBody() : null,
        Objects.nonNull(response) ? response.getStatusCode() : null,
        now);
  }

  @VisibleForTesting
  protected void sendMessage(MailMessage mailMessage, Integer userId)
      throws IOException, TemplateException {
    Writer out = new StringWriter();
    Template template = templateHelper.getTemplate(mailMessage.getTemplateName());
    template.process(mailMessage.createModel(serverUrl), out);
    String content = out.toString();
    Mail message = new Mail(new Email(fromAccount), mailMessage.createSubject(),
        new Email(mailMessage.toUser.getEmail()), new Content("text/html", content));
    Response response = sendGridAPI.sendMessage(message, mailMessage.toUser.getEmail());
    saveEmailAndResponse(
        response,
        mailMessage.getEntityReferenceId(),
        mailMessage.getVoteId(),
        userId,
        mailMessage.emailType,
        content);
  }

  public List<org.broadinstitute.consent.http.models.mail.MailMessage> fetchEmailMessagesByType(
      EmailType emailType, Integer limit,
      Integer offset) {
    return emailDAO.fetchMessagesByType(emailType.getTypeInt(), limit, offset);
  }

  public List<org.broadinstitute.consent.http.models.mail.MailMessage> fetchEmailMessagesByCreateDate(
      Date start, Date end, Integer limit,
      Integer offset) {
    return emailDAO.fetchMessagesByCreateDate(start, end, limit, offset);
  }

  public void sendNewDARCollectionMessage(Integer collectionId)
      throws IOException, TemplateException {
    DarCollection collection = collectionDAO.findDARCollectionByCollectionId(collectionId);
    if (collection == null) {
      logWarn(
          "Sending new DAR Collection message: Could not find collection for specified collection id: "
              + collectionId);
      return;
    }
    List<User> distinctUsers = getDistinctAdminAndChairUsersForCollection(collection);
    User researcher = userDAO.findUserById(collection.getCreateUserId());
    if (researcher == null) {
      logWarn(
          "Sending new DAR Collection message: Could not find researcher for specified user id: "
              + collection.getCreateUserId());
    }
    String researcherName = researcher == null ? "Unknown" : researcher.getDisplayName();
    Collection<Dac> dacsInDAR = dacDAO.findDacsForCollectionId(collectionId);
    List<Integer> datasetIds = collection.getDatasets().stream().map(Dataset::getDatasetId)
        .toList();
    List<Dataset> datasetsInDAR =
        datasetIds.isEmpty() ? List.of() : datasetDAO.findDatasetsByIdList(datasetIds);

    Map<String, List<String>> sendList = new HashMap<>();
    for (User user : distinctUsers) {
      List<Dac> matchingDacsForUser = getMatchingDacs(user, dacsInDAR);
      for (Dac dac : matchingDacsForUser) {
        List<String> matchingDatasetsForDac = getMatchingDatasets(dac, datasetsInDAR);
        if (matchingDatasetsForDac != null) {
          sendList.put(dac.getName(), matchingDatasetsForDac);
        }
      }
      sendNewDARRequestEmail(user, sendList, researcherName, collection.getDarCode());
    }
  }

  private List<User> getDistinctAdminAndChairUsersForCollection(DarCollection collection) {
    List<User> admins = userDAO.describeUsersByRoleAndEmailPreference(UserRoles.ADMIN.getRoleName(),
        true);
    List<Integer> datasetIds = collection.getDars().values().stream()
        .map(DataAccessRequest::getDatasetIds)
        .flatMap(List::stream)
        .collect(Collectors.toList());
    Set<User> chairPersons = userDAO.findUsersForDatasetsByRole(datasetIds,
        Collections.singletonList(UserRoles.CHAIRPERSON.getRoleName()));
    // Ensure that admins/chairs are not double emailed
    // and filter users that don't want to receive email
    return Streams.concat(admins.stream(), chairPersons.stream())
        .filter(u -> Boolean.TRUE.equals(u.getEmailPreference()))
        .distinct()
        .toList();
  }

  private List<Dac> getMatchingDacs(User user, Collection<Dac> dacsInDAR) {
    List<Integer> dacIDs = user.getRoles().stream()
        .filter(ur -> ur.getDacId() != null)
        .map(UserRole::getDacId)
        .toList();
    return dacsInDAR.stream()
        .filter(dac -> dacIDs.contains(dac.getDacId()))
        .toList();
  }

  private List<String> getMatchingDatasets(Dac dac, List<Dataset> datasetsInDAR) {
    return datasetsInDAR.stream()
        .filter(dataset -> dataset.getDacId() == dac.getDacId())
        .map(dataset -> dataset.getDatasetIdentifier())
        .toList();
  }

  private void sendNewDARRequestEmail(
      User user, Map<String, List<String>> sendList, String researcherName, String darCode)
      throws TemplateException, IOException {
    sendMessage(new NewDARRequestMessage(user, darCode, sendList, researcherName),
        user.getUserId());
  }

  public void sendExpirationNotices() {
    sendDARExpirationReminderNotices();
    sendDARExpirationNotices();
  }

  private void sendDARExpirationNotices() {
    EmailType emailType = EmailType.DAR_EXPIRED;
    sendDARMessageToList(emailType, EXPIRE_NOTICE_INTERVAL);
  }

  private void sendDARExpirationReminderNotices() {
    EmailType emailType = EmailType.DAR_EXPIRATION_REMINDER;
    sendDARMessageToList(emailType, EXPIRE_WARN_INTERVAL);
  }

  private void sendDARMessageToList(EmailType type, String interval) {
    List<DataAccessRequest> expiredDars = dataAccessRequestDAO.findAgedDARsByEmailTypeOlderThanInterval(
        type.getTypeInt(), interval, MINIMUM_SUBMITTED_DATE_FOR_DAR_EXPIRATIONS);
    expiredDars.forEach(expiredDar -> {
      try {
        String referenceId = expiredDar.getReferenceId();
        User user = userDAO.findUserById(expiredDar.getUserId());
        String darCode = expiredDar.getDarCode();
        String userName = user.getDisplayName();
        if (user.getEmail() == null) {
          // Do not throw here.  Log information about the DAR since this will continue
          // to appear broken until manual intervention is taken to resolve the missing user
          // email address
          logException(new Exception(String.format(
              "Email address for user %d (%s) not found for expiring warning.  DAR reference id: %s",
              expiredDar.getUserId(), userName, referenceId)));
        } else {
          switch (type) {
            case DAR_EXPIRATION_REMINDER:
              sendDarExpirationReminderMessage(user, darCode, user.getUserId(), referenceId);
              break;
            case DAR_EXPIRED:
              sendDarExpiredMessage(user, darCode, user.getUserId(), referenceId);
          }
        }
      } catch (Exception e) {
        logException(e);
      }
    });
  }

  public void sendReminderMessage(Integer voteId) throws IOException, TemplateException {
    Vote vote = voteDAO.findVoteById(voteId);
    Election election = electionDAO.findElectionWithFinalVoteById(vote.getElectionId());
    DarCollection collection = collectionDAO.findDARCollectionByReferenceId(
        election.getReferenceId());
    User user = findUserById(vote.getUserId());
    String voteUrl = serverUrl + "dar_collection/%d".formatted(collection.getDarCollectionId());
    sendMessage(new ReminderMessage(user, vote, collection.getDarCode(), election.getElectionType(),
        voteUrl), user.getUserId());
    voteDAO.updateVoteReminderFlag(voteId, true);
  }

  public void sendDarNewCollectionElectionMessage(List<User> users, DarCollection darCollection)
      throws IOException, TemplateException {
    String electionType = "Data Access Request";
    String darCode = darCollection.getDarCode();
    for (User user : users) {
      sendMessage(new NewCaseMessage(user, darCode, electionType), user.getUserId());
    }
  }

  public void sendResearcherDarApproved(
      String darCode,
      Integer researcherId,
      List<DatasetMailDTO> datasets,
      String dataUseRestriction)
      throws TemplateException, IOException {
    User user = userDAO.findUserById(researcherId);
    sendMessage(
        new ResearcherApprovedMessage(user, darCode, datasets, dataUseRestriction), researcherId);
  }

  public void sendDataCustodianApprovalMessage(
      User custodian,
      String darCode,
      List<DatasetMailDTO> datasets,
      String dataDepositorName,
      String researcherEmail)
      throws TemplateException, IOException {
    sendMessage(
        new DataCustodianApprovalMessage(
            custodian, darCode, datasets, dataDepositorName, researcherEmail),
        custodian.getUserId());
  }

  public void sendDatasetSubmittedMessage(
      User dacChair, User dataSubmitter, String dacName, String datasetName)
      throws TemplateException, IOException {
    sendMessage(
        new DatasetSubmittedMessage(dacChair, dataSubmitter.getDisplayName(), datasetName, dacName),
        dacChair.getUserId());
  }

  public void sendDatasetApprovedMessage(User user, String dacName, String datasetName)
      throws TemplateException, IOException {
    sendMessage(new DatasetApprovedMessage(user, dacName, datasetName), user.getUserId());
  }

  public void sendDatasetDeniedMessage(
      User user, String dacName, String datasetName, String dacEmail)
      throws TemplateException, IOException {
    sendMessage(new DatasetDeniedMessage(user, dacName, datasetName, dacEmail), user.getUserId());
  }

  public void sendNewResearcherMessage(User researcher, User signingOfficial)
      throws TemplateException, IOException {
    sendMessage(
        new NewResearcherLibraryRequestMessage(signingOfficial, researcher),
        researcher.getUserId());
  }

  public void sendDaaRequestMessage(
      User signingOfficial, User requestUser, String daaName, Integer daaId)
      throws TemplateException, IOException {
    sendMessage(
        new DaaRequestMessage(signingOfficial, requestUser, daaName, daaId),
        requestUser.getUserId());
  }

  public void sendNewDAAUploadSOMessage(
      User signingOfficial,
      String dacName,
      String previousDaaName,
      String newDaaName,
      Integer userId)
      throws TemplateException, IOException {
    sendMessage(
        new NewDAAUploadSOMessage(signingOfficial, dacName, previousDaaName, newDaaName), userId);
  }

  public void sendNewDAAUploadResearcherMessage(
      User researcher, String dacName, String previousDaaName, String newDaaName, Integer userId)
      throws TemplateException, IOException {
    sendMessage(
        new NewDAAUploadResearcherMessage(
            researcher, dacName, previousDaaName, newDaaName),
        userId);
  }

  private User findUserById(Integer id) throws IllegalArgumentException {
    User user = userDAO.findUserById(id);
    if (user == null) {
      throw new NotFoundException("Could not find dacUser for specified id : " + id);
    }
    return user;
  }

  /**
   * Send a message to a researcher that their data access request has expired.
   *
   * @param researcher  the researcher to send the message to
   * @param darCode     the data access request code that's expired
   * @param userId      the user id of the person sending the message
   * @param referenceId the data access request reference id that's expired
   */
  public void sendDarExpiredMessage(User researcher, String darCode, Integer userId,
      String referenceId)
      throws TemplateException, IOException {
    sendMessage(new DarExpiredMessage(researcher, darCode, referenceId), userId);
  }

  /**
   * Remind the user that their data access request is about to expire.
   *
   * @param user        the user to send the message to
   * @param darCode     the data access request code that's about to expire
   * @param userId      the user id of the person sending the message
   * @param referenceId the data access request reference id that is expiring
   */
  public void sendDarExpirationReminderMessage(User user, String darCode, Integer userId,
      String referenceId)
      throws TemplateException, IOException {
    sendMessage(new DarExpirationReminderMessage(user, darCode, referenceId), userId);
  }
}

1	package org.broadinstitute.consent.http.service;
2
3	import static org.broadinstitute.consent.http.service.DataAccessRequestService.EXPIRE_NOTICE_INTERVAL;
4	import static org.broadinstitute.consent.http.service.DataAccessRequestService.EXPIRE_WARN_INTERVAL;
5
6	import com.google.common.annotations.VisibleForTesting;
7	import com.google.common.collect.Streams;
8	import com.google.inject.Inject;
9	import com.sendgrid.Response;
10	import com.sendgrid.helpers.mail.Mail;
11	import com.sendgrid.helpers.mail.objects.Content;
12	import com.sendgrid.helpers.mail.objects.Email;
13	import freemarker.template.Template;
14	import freemarker.template.TemplateException;
15	import jakarta.ws.rs.NotFoundException;
16	import java.io.IOException;
17	import java.io.StringWriter;
18	import java.io.Writer;
19	import java.sql.Timestamp;
20	import java.time.Instant;
21	import java.time.LocalDate;
22	import java.time.LocalTime;
23	import java.time.ZoneOffset;
24	import java.util.Collection;
25	import java.util.Collections;
26	import java.util.Date;
27	import java.util.HashMap;
28	import java.util.List;
29	import java.util.Map;
30	import java.util.Objects;
31	import java.util.Set;
32	import java.util.stream.Collectors;
33	import javax.annotation.Nullable;
34	import org.broadinstitute.consent.http.configurations.ConsentConfiguration;
35	import org.broadinstitute.consent.http.db.DacDAO;
36	import org.broadinstitute.consent.http.db.DarCollectionDAO;
37	import org.broadinstitute.consent.http.db.DataAccessRequestDAO;
38	import org.broadinstitute.consent.http.db.DatasetDAO;
39	import org.broadinstitute.consent.http.db.ElectionDAO;
40	import org.broadinstitute.consent.http.db.MailMessageDAO;
41	import org.broadinstitute.consent.http.db.UserDAO;
42	import org.broadinstitute.consent.http.db.VoteDAO;
43	import org.broadinstitute.consent.http.enumeration.EmailType;
44	import org.broadinstitute.consent.http.enumeration.UserRoles;
45	import org.broadinstitute.consent.http.mail.SendGridAPI;
46	import org.broadinstitute.consent.http.mail.freemarker.FreeMarkerTemplateHelper;
47	import org.broadinstitute.consent.http.mail.message.DaaRequestMessage;
48	import org.broadinstitute.consent.http.mail.message.DarExpirationReminderMessage;
49	import org.broadinstitute.consent.http.mail.message.DarExpiredMessage;
50	import org.broadinstitute.consent.http.mail.message.DataCustodianApprovalMessage;
51	import org.broadinstitute.consent.http.mail.message.DatasetApprovedMessage;
52	import org.broadinstitute.consent.http.mail.message.DatasetDeniedMessage;
53	import org.broadinstitute.consent.http.mail.message.DatasetSubmittedMessage;
54	import org.broadinstitute.consent.http.mail.message.MailMessage;
55	import org.broadinstitute.consent.http.mail.message.NewCaseMessage;
56	import org.broadinstitute.consent.http.mail.message.NewDAAUploadResearcherMessage;
57	import org.broadinstitute.consent.http.mail.message.NewDAAUploadSOMessage;
58	import org.broadinstitute.consent.http.mail.message.NewDARRequestMessage;
59	import org.broadinstitute.consent.http.mail.message.NewResearcherLibraryRequestMessage;
60	import org.broadinstitute.consent.http.mail.message.ReminderMessage;
61	import org.broadinstitute.consent.http.mail.message.ResearcherApprovedMessage;
62	import org.broadinstitute.consent.http.models.Dac;
63	import org.broadinstitute.consent.http.models.DarCollection;
64	import org.broadinstitute.consent.http.models.DataAccessRequest;
65	import org.broadinstitute.consent.http.models.Dataset;
66	import org.broadinstitute.consent.http.models.Election;
67	import org.broadinstitute.consent.http.models.User;
68	import org.broadinstitute.consent.http.models.UserRole;
69	import org.broadinstitute.consent.http.models.Vote;
70	import org.broadinstitute.consent.http.models.dto.DatasetMailDTO;
71	import org.broadinstitute.consent.http.util.ConsentLogger;
72
73	public class EmailService implements ConsentLogger {
74
75	public static final Timestamp MINIMUM_SUBMITTED_DATE_FOR_DAR_EXPIRATIONS = Timestamp.from(	1✔
76	Instant.ofEpochSecond(	1✔
77	LocalDate.of(2024, 9, 30).toEpochSecond(LocalTime.of(0, 0, 0, 0), ZoneOffset.UTC)));	1✔
78	private final DarCollectionDAO collectionDAO;
79	private final DataAccessRequestDAO dataAccessRequestDAO;
80	private final UserDAO userDAO;
81	private final ElectionDAO electionDAO;
82	private final MailMessageDAO emailDAO;
83	private final VoteDAO voteDAO;
84	private final DatasetDAO datasetDAO;
85	private final DacDAO dacDAO;
86	private final FreeMarkerTemplateHelper templateHelper;
87	private final SendGridAPI sendGridAPI;
88	private final String fromAccount;
89	private final String serverUrl;
90
91	@Inject
92	public EmailService(
93	DarCollectionDAO collectionDAO,
94	VoteDAO voteDAO,
95	ElectionDAO electionDAO,
96	UserDAO userDAO,
97	MailMessageDAO emailDAO,
98	DatasetDAO datasetDAO,
99	DacDAO dacDAO,
100	DataAccessRequestDAO dataAccessRequestDAO,
101	SendGridAPI sendGridAPI,
102	FreeMarkerTemplateHelper helper,
103	ConsentConfiguration config) {	1✔
104	this.collectionDAO = collectionDAO;	1✔
105	this.userDAO = userDAO;	1✔
106	this.electionDAO = electionDAO;	1✔
107	this.voteDAO = voteDAO;	1✔
108	this.templateHelper = helper;	1✔
109	this.emailDAO = emailDAO;	1✔
110	this.datasetDAO = datasetDAO;	1✔
111	this.dacDAO = dacDAO;	1✔
112	this.dataAccessRequestDAO = dataAccessRequestDAO;	1✔
113	this.sendGridAPI = sendGridAPI;	1✔
114	this.serverUrl = config.getServicesConfiguration().getLocalURL();	1✔
115	this.fromAccount = config.getMailConfiguration().getGoogleAccount();	1✔
116	}	1✔
117
118	/**
119	* This method saves an email (either sent or unsent) with all available metadata from the
120	* SendGrid response.
121	*/
122	private void saveEmailAndResponse(
123	@Nullable Response response,
124	@Nullable String entityReferenceId,
125	@Nullable Integer voteId,
126	Integer userId,
127	EmailType emailType,
128	String content) {
129	Instant now = Instant.now();	1✔
130	Instant dateSent = (Objects.nonNull(response) && response.getStatusCode() < 400) ? now : null;	1✔
131	emailDAO.insert(	1✔
132	entityReferenceId,
133	voteId,
134	userId,
135	emailType.getTypeInt(),	1✔
136	dateSent,
137	content,
138	Objects.nonNull(response) ? response.getBody() : null,	1✔
139	Objects.nonNull(response) ? response.getStatusCode() : null,	1✔
140	now);
141	}	1✔
142
143	@VisibleForTesting
144	protected void sendMessage(MailMessage mailMessage, Integer userId)
145	throws IOException, TemplateException {
146	Writer out = new StringWriter();	1✔
147	Template template = templateHelper.getTemplate(mailMessage.getTemplateName());	1✔
148	template.process(mailMessage.createModel(serverUrl), out);	1✔
149	String content = out.toString();	1✔
150	Mail message = new Mail(new Email(fromAccount), mailMessage.createSubject(),	1✔
151	new Email(mailMessage.toUser.getEmail()), new Content("text/html", content));	1✔
152	Response response = sendGridAPI.sendMessage(message, mailMessage.toUser.getEmail());	1✔
153	saveEmailAndResponse(	1✔
154	response,
155	mailMessage.getEntityReferenceId(),	1✔
156	mailMessage.getVoteId(),	1✔
157	userId,
158	mailMessage.emailType,
159	content);
160	}	1✔
161
162	public List<org.broadinstitute.consent.http.models.mail.MailMessage> fetchEmailMessagesByType(
163	EmailType emailType, Integer limit,
164	Integer offset) {
165	return emailDAO.fetchMessagesByType(emailType.getTypeInt(), limit, offset);	1✔
166	}
167
168	public List<org.broadinstitute.consent.http.models.mail.MailMessage> fetchEmailMessagesByCreateDate(
169	Date start, Date end, Integer limit,
170	Integer offset) {
171	return emailDAO.fetchMessagesByCreateDate(start, end, limit, offset);	1✔
172	}
173
174	public void sendNewDARCollectionMessage(Integer collectionId)
175	throws IOException, TemplateException {
176	DarCollection collection = collectionDAO.findDARCollectionByCollectionId(collectionId);	1✔
177	if (collection == null) {	1✔
UNCOV 178	logWarn(	×
179	"Sending new DAR Collection message: Could not find collection for specified collection id: "
180	+ collectionId);
UNCOV 181	return;	×
182	}
183	List<User> distinctUsers = getDistinctAdminAndChairUsersForCollection(collection);	1✔
184	User researcher = userDAO.findUserById(collection.getCreateUserId());	1✔
185	if (researcher == null) {	1✔
UNCOV 186	logWarn(	×
187	"Sending new DAR Collection message: Could not find researcher for specified user id: "
UNCOV 188	+ collection.getCreateUserId());	×
189	}
190	String researcherName = researcher == null ? "Unknown" : researcher.getDisplayName();	1✔
191	Collection<Dac> dacsInDAR = dacDAO.findDacsForCollectionId(collectionId);	1✔
192	List<Integer> datasetIds = collection.getDatasets().stream().map(Dataset::getDatasetId)	1✔
193	.toList();	1✔
194	List<Dataset> datasetsInDAR =
195	datasetIds.isEmpty() ? List.of() : datasetDAO.findDatasetsByIdList(datasetIds);	1✔
196
197	Map<String, List<String>> sendList = new HashMap<>();	1✔
198	for (User user : distinctUsers) {	1✔
199	List<Dac> matchingDacsForUser = getMatchingDacs(user, dacsInDAR);	1✔
200	for (Dac dac : matchingDacsForUser) {	1✔
201	List<String> matchingDatasetsForDac = getMatchingDatasets(dac, datasetsInDAR);	1✔
202	if (matchingDatasetsForDac != null) {	1✔
203	sendList.put(dac.getName(), matchingDatasetsForDac);	1✔
204	}
205	}	1✔
206	sendNewDARRequestEmail(user, sendList, researcherName, collection.getDarCode());	1✔
207	}	1✔
208	}	1✔
209
210	private List<User> getDistinctAdminAndChairUsersForCollection(DarCollection collection) {
211	List<User> admins = userDAO.describeUsersByRoleAndEmailPreference(UserRoles.ADMIN.getRoleName(),	1✔
212	true);	1✔
213	List<Integer> datasetIds = collection.getDars().values().stream()	1✔
214	.map(DataAccessRequest::getDatasetIds)	1✔
215	.flatMap(List::stream)	1✔
216	.collect(Collectors.toList());	1✔
217	Set<User> chairPersons = userDAO.findUsersForDatasetsByRole(datasetIds,	1✔
218	Collections.singletonList(UserRoles.CHAIRPERSON.getRoleName()));	1✔
219	// Ensure that admins/chairs are not double emailed
220	// and filter users that don't want to receive email
221	return Streams.concat(admins.stream(), chairPersons.stream())	1✔
222	.filter(u -> Boolean.TRUE.equals(u.getEmailPreference()))	1✔
223	.distinct()	1✔
224	.toList();	1✔
225	}
226
227	private List<Dac> getMatchingDacs(User user, Collection<Dac> dacsInDAR) {
228	List<Integer> dacIDs = user.getRoles().stream()	1✔
229	.filter(ur -> ur.getDacId() != null)	1✔
230	.map(UserRole::getDacId)	1✔
231	.toList();	1✔
232	return dacsInDAR.stream()	1✔
233	.filter(dac -> dacIDs.contains(dac.getDacId()))	1✔
234	.toList();	1✔
235	}
236
237	private List<String> getMatchingDatasets(Dac dac, List<Dataset> datasetsInDAR) {
238	return datasetsInDAR.stream()	1✔
239	.filter(dataset -> dataset.getDacId() == dac.getDacId())	1✔
240	.map(dataset -> dataset.getDatasetIdentifier())	1✔
241	.toList();	1✔
242	}
243
244	private void sendNewDARRequestEmail(
245	User user, Map<String, List<String>> sendList, String researcherName, String darCode)
246	throws TemplateException, IOException {
247	sendMessage(new NewDARRequestMessage(user, darCode, sendList, researcherName),	1✔
248	user.getUserId());	1✔
249	}	1✔
250
251	public void sendExpirationNotices() {
252	sendDARExpirationReminderNotices();	1✔
253	sendDARExpirationNotices();	1✔
254	}	1✔
255
256	private void sendDARExpirationNotices() {
257	EmailType emailType = EmailType.DAR_EXPIRED;	1✔
258	sendDARMessageToList(emailType, EXPIRE_NOTICE_INTERVAL);	1✔
259	}	1✔
260
261	private void sendDARExpirationReminderNotices() {
262	EmailType emailType = EmailType.DAR_EXPIRATION_REMINDER;	1✔
263	sendDARMessageToList(emailType, EXPIRE_WARN_INTERVAL);	1✔
264	}	1✔
265
266	private void sendDARMessageToList(EmailType type, String interval) {
267	List<DataAccessRequest> expiredDars = dataAccessRequestDAO.findAgedDARsByEmailTypeOlderThanInterval(	1✔
268	type.getTypeInt(), interval, MINIMUM_SUBMITTED_DATE_FOR_DAR_EXPIRATIONS);	1✔
269	expiredDars.forEach(expiredDar -> {	1✔
270	try {
271	String referenceId = expiredDar.getReferenceId();	1✔
272	User user = userDAO.findUserById(expiredDar.getUserId());	1✔
273	String darCode = expiredDar.getDarCode();	1✔
274	String userName = user.getDisplayName();	1✔
275	if (user.getEmail() == null) {	1✔
276	// Do not throw here. Log information about the DAR since this will continue
277	// to appear broken until manual intervention is taken to resolve the missing user
278	// email address
279	logException(new Exception(String.format(	1✔
280	"Email address for user %d (%s) not found for expiring warning. DAR reference id: %s",
281	expiredDar.getUserId(), userName, referenceId)));	1✔
282	} else {
283	switch (type) {	1✔
284	case DAR_EXPIRATION_REMINDER:
285	sendDarExpirationReminderMessage(user, darCode, user.getUserId(), referenceId);	1✔
286	break;	1✔
287	case DAR_EXPIRED:
288	sendDarExpiredMessage(user, darCode, user.getUserId(), referenceId);	1✔
289	}
290	}
291	} catch (Exception e) {	1✔
292	logException(e);	1✔
293	}	1✔
294	});	1✔
295	}	1✔
296
297	public void sendReminderMessage(Integer voteId) throws IOException, TemplateException {
298	Vote vote = voteDAO.findVoteById(voteId);	1✔
299	Election election = electionDAO.findElectionWithFinalVoteById(vote.getElectionId());	1✔
300	DarCollection collection = collectionDAO.findDARCollectionByReferenceId(	1✔
301	election.getReferenceId());	1✔
302	User user = findUserById(vote.getUserId());	1✔
303	String voteUrl = serverUrl + "dar_collection/%d".formatted(collection.getDarCollectionId());	1✔
304	sendMessage(new ReminderMessage(user, vote, collection.getDarCode(), election.getElectionType(),	1✔
305	voteUrl), user.getUserId());	1✔
306	voteDAO.updateVoteReminderFlag(voteId, true);	1✔
307	}	1✔
308
309	public void sendDarNewCollectionElectionMessage(List<User> users, DarCollection darCollection)
310	throws IOException, TemplateException {
UNCOV 311	String electionType = "Data Access Request";	×
UNCOV 312	String darCode = darCollection.getDarCode();	×
UNCOV 313	for (User user : users) {	×
UNCOV 314	sendMessage(new NewCaseMessage(user, darCode, electionType), user.getUserId());	×
UNCOV 315	}	×
UNCOV 316	}	×
317
318	public void sendResearcherDarApproved(
319	String darCode,
320	Integer researcherId,
321	List<DatasetMailDTO> datasets,
322	String dataUseRestriction)
323	throws TemplateException, IOException {
UNCOV 324	User user = userDAO.findUserById(researcherId);	×
UNCOV 325	sendMessage(	×
326	new ResearcherApprovedMessage(user, darCode, datasets, dataUseRestriction), researcherId);
UNCOV 327	}	×
328
329	public void sendDataCustodianApprovalMessage(
330	User custodian,
331	String darCode,
332	List<DatasetMailDTO> datasets,
333	String dataDepositorName,
334	String researcherEmail)
335	throws TemplateException, IOException {
UNCOV 336	sendMessage(	×
337	new DataCustodianApprovalMessage(
338	custodian, darCode, datasets, dataDepositorName, researcherEmail),
UNCOV 339	custodian.getUserId());	×
UNCOV 340	}	×
341
342	public void sendDatasetSubmittedMessage(
343	User dacChair, User dataSubmitter, String dacName, String datasetName)
344	throws TemplateException, IOException {
345	sendMessage(	1✔
346	new DatasetSubmittedMessage(dacChair, dataSubmitter.getDisplayName(), datasetName, dacName),	1✔
347	dacChair.getUserId());	1✔
348	}	1✔
349
350	public void sendDatasetApprovedMessage(User user, String dacName, String datasetName)
351	throws TemplateException, IOException {
UNCOV 352	sendMessage(new DatasetApprovedMessage(user, dacName, datasetName), user.getUserId());	×
UNCOV 353	}	×
354
355	public void sendDatasetDeniedMessage(
356	User user, String dacName, String datasetName, String dacEmail)
357	throws TemplateException, IOException {
UNCOV 358	sendMessage(new DatasetDeniedMessage(user, dacName, datasetName, dacEmail), user.getUserId());	×
UNCOV 359	}	×
360
361	public void sendNewResearcherMessage(User researcher, User signingOfficial)
362	throws TemplateException, IOException {
363	sendMessage(	1✔
364	new NewResearcherLibraryRequestMessage(signingOfficial, researcher),
365	researcher.getUserId());	1✔
366	}	1✔
367
368	public void sendDaaRequestMessage(
369	User signingOfficial, User requestUser, String daaName, Integer daaId)
370	throws TemplateException, IOException {
371	sendMessage(	1✔
372	new DaaRequestMessage(signingOfficial, requestUser, daaName, daaId),
373	requestUser.getUserId());	1✔
374	}	1✔
375
376	public void sendNewDAAUploadSOMessage(
377	User signingOfficial,
378	String dacName,
379	String previousDaaName,
380	String newDaaName,
381	Integer userId)
382	throws TemplateException, IOException {
383	sendMessage(	1✔
384	new NewDAAUploadSOMessage(signingOfficial, dacName, previousDaaName, newDaaName), userId);
385	}	1✔
386
387	public void sendNewDAAUploadResearcherMessage(
388	User researcher, String dacName, String previousDaaName, String newDaaName, Integer userId)
389	throws TemplateException, IOException {
390	sendMessage(	1✔
391	new NewDAAUploadResearcherMessage(
392	researcher, dacName, previousDaaName, newDaaName),
393	userId);
394	}	1✔
395
396	private User findUserById(Integer id) throws IllegalArgumentException {
397	User user = userDAO.findUserById(id);	1✔
398	if (user == null) {	1✔
UNCOV 399	throw new NotFoundException("Could not find dacUser for specified id : " + id);	×
400	}
401	return user;	1✔
402	}
403
404	/**
405	* Send a message to a researcher that their data access request has expired.
406	*
407	* @param researcher the researcher to send the message to
408	* @param darCode the data access request code that's expired
409	* @param userId the user id of the person sending the message
410	* @param referenceId the data access request reference id that's expired
411	*/
412	public void sendDarExpiredMessage(User researcher, String darCode, Integer userId,
413	String referenceId)
414	throws TemplateException, IOException {
415	sendMessage(new DarExpiredMessage(researcher, darCode, referenceId), userId);	1✔
416	}	1✔
417
418	/**
419	* Remind the user that their data access request is about to expire.
420	*
421	* @param user the user to send the message to
422	* @param darCode the data access request code that's about to expire
423	* @param userId the user id of the person sending the message
424	* @param referenceId the data access request reference id that is expiring
425	*/
426	public void sendDarExpirationReminderMessage(User user, String darCode, Integer userId,
427	String referenceId)
428	throws TemplateException, IOException {
429	sendMessage(new DarExpirationReminderMessage(user, darCode, referenceId), userId);	1✔
430	}	1✔
431	}

DataBiosphere / consent / #5834

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