#5929

Committed 19 May 2025 12:36PM UTC coverage: 78.551% (-0.2%) from 78.727%

Build # #5929

Build Type

push

Committed by

Commit Message

DT-1564, Progress Report DAC flow (#2523)

Run Details

175 of 228 new or added lines in 17 files covered. (76.75%)

5 existing lines in 3 files now uncovered.

10027 of 12765 relevant lines covered (78.55%)

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60.53

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

package org.broadinstitute.consent.http.service;

import com.google.common.annotations.VisibleForTesting;
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 java.io.IOException;
import java.io.StringWriter;
import java.io.Writer;
import java.time.Instant;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import javax.annotation.Nullable;
import org.broadinstitute.consent.http.configurations.ConsentConfiguration;
import org.broadinstitute.consent.http.db.MailMessageDAO;
import org.broadinstitute.consent.http.db.UserDAO;
import org.broadinstitute.consent.http.enumeration.EmailType;
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.NewProgressReportCaseMessage;
import org.broadinstitute.consent.http.mail.message.NewProgressReportRequestMessage;
import org.broadinstitute.consent.http.mail.message.NewResearcherLibraryRequestMessage;
import org.broadinstitute.consent.http.mail.message.ReminderMessage;
import org.broadinstitute.consent.http.mail.message.ResearcherDarApprovedMessage;
import org.broadinstitute.consent.http.mail.message.ResearcherApprovedProgressReportMessage;
import org.broadinstitute.consent.http.models.User;
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 {

  private final UserDAO userDAO;
  private final MailMessageDAO emailDAO;
  private final FreeMarkerTemplateHelper templateHelper;
  private final SendGridAPI sendGridAPI;
  private final String fromAccount;
  private final String serverUrl;

  @Inject
  public EmailService(
      UserDAO userDAO,
      MailMessageDAO emailDAO,
      SendGridAPI sendGridAPI,
      FreeMarkerTemplateHelper helper,
      ConsentConfiguration config) {
    this.userDAO = userDAO;
    this.templateHelper = helper;
    this.emailDAO = emailDAO;
    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 sendResearcherDarApproved(
      String darCode,
      Integer researcherId,
      List<DatasetMailDTO> datasets,
      String dataUseRestriction)
      throws TemplateException, IOException {
    User user = userDAO.findUserById(researcherId);
    sendMessage(
        new ResearcherDarApprovedMessage(user, darCode, datasets, dataUseRestriction), researcherId);
  }

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

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

  public void sendProgressReportNewCollectionElectionMessage(List<User> users, String darCode)
      throws IOException, TemplateException {
    for (User user : users) {
      sendMessage(new NewProgressReportCaseMessage(user, darCode), user.getUserId());
    }
  }

  public 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 sendNewProgressReportRequestEmail(
      User user, Map<String, List<String>> sendList, String researcherName, String darCode, String referenceId)
      throws TemplateException, IOException {
      sendMessage(new NewProgressReportRequestMessage(user, darCode, referenceId, sendList, researcherName),
        user.getUserId());
  }

  /**
   * 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);
  }

  public void sendReminderMessage(User user, Vote vote, String darCode, String electionType, String url)
      throws TemplateException, IOException {
    sendMessage(new ReminderMessage(user, vote, darCode, electionType, url), user.getUserId());
  }

}

1	package org.broadinstitute.consent.http.service;
2
3	import com.google.common.annotations.VisibleForTesting;
4	import com.google.inject.Inject;
5	import com.sendgrid.Response;
6	import com.sendgrid.helpers.mail.Mail;
7	import com.sendgrid.helpers.mail.objects.Content;
8	import com.sendgrid.helpers.mail.objects.Email;
9	import freemarker.template.Template;
10	import freemarker.template.TemplateException;
11	import java.io.IOException;
12	import java.io.StringWriter;
13	import java.io.Writer;
14	import java.time.Instant;
15	import java.util.Date;
16	import java.util.List;
17	import java.util.Map;
18	import java.util.Objects;
19	import javax.annotation.Nullable;
20	import org.broadinstitute.consent.http.configurations.ConsentConfiguration;
21	import org.broadinstitute.consent.http.db.MailMessageDAO;
22	import org.broadinstitute.consent.http.db.UserDAO;
23	import org.broadinstitute.consent.http.enumeration.EmailType;
24	import org.broadinstitute.consent.http.mail.SendGridAPI;
25	import org.broadinstitute.consent.http.mail.freemarker.FreeMarkerTemplateHelper;
26	import org.broadinstitute.consent.http.mail.message.DaaRequestMessage;
27	import org.broadinstitute.consent.http.mail.message.DarExpirationReminderMessage;
28	import org.broadinstitute.consent.http.mail.message.DarExpiredMessage;
29	import org.broadinstitute.consent.http.mail.message.DataCustodianApprovalMessage;
30	import org.broadinstitute.consent.http.mail.message.DatasetApprovedMessage;
31	import org.broadinstitute.consent.http.mail.message.DatasetDeniedMessage;
32	import org.broadinstitute.consent.http.mail.message.DatasetSubmittedMessage;
33	import org.broadinstitute.consent.http.mail.message.MailMessage;
34	import org.broadinstitute.consent.http.mail.message.NewCaseMessage;
35	import org.broadinstitute.consent.http.mail.message.NewDAAUploadResearcherMessage;
36	import org.broadinstitute.consent.http.mail.message.NewDAAUploadSOMessage;
37	import org.broadinstitute.consent.http.mail.message.NewDARRequestMessage;
38	import org.broadinstitute.consent.http.mail.message.NewProgressReportCaseMessage;
39	import org.broadinstitute.consent.http.mail.message.NewProgressReportRequestMessage;
40	import org.broadinstitute.consent.http.mail.message.NewResearcherLibraryRequestMessage;
41	import org.broadinstitute.consent.http.mail.message.ReminderMessage;
42	import org.broadinstitute.consent.http.mail.message.ResearcherDarApprovedMessage;
43	import org.broadinstitute.consent.http.mail.message.ResearcherApprovedProgressReportMessage;
44	import org.broadinstitute.consent.http.models.User;
45	import org.broadinstitute.consent.http.models.Vote;
46	import org.broadinstitute.consent.http.models.dto.DatasetMailDTO;
47	import org.broadinstitute.consent.http.util.ConsentLogger;
48
49	public class EmailService implements ConsentLogger {
50
51	private final UserDAO userDAO;
52	private final MailMessageDAO emailDAO;
53	private final FreeMarkerTemplateHelper templateHelper;
54	private final SendGridAPI sendGridAPI;
55	private final String fromAccount;
56	private final String serverUrl;
57
58	@Inject
59	public EmailService(
60	UserDAO userDAO,
61	MailMessageDAO emailDAO,
62	SendGridAPI sendGridAPI,
63	FreeMarkerTemplateHelper helper,
64	ConsentConfiguration config) {	1✔
65	this.userDAO = userDAO;	1✔
66	this.templateHelper = helper;	1✔
67	this.emailDAO = emailDAO;	1✔
68	this.sendGridAPI = sendGridAPI;	1✔
69	this.serverUrl = config.getServicesConfiguration().getLocalURL();	1✔
70	this.fromAccount = config.getMailConfiguration().getGoogleAccount();	1✔
71	}	1✔
72
73	/**
74	* This method saves an email (either sent or unsent) with all available metadata from the
75	* SendGrid response.
76	*/
77	private void saveEmailAndResponse(
78	@Nullable Response response,
79	@Nullable String entityReferenceId,
80	@Nullable Integer voteId,
81	Integer userId,
82	EmailType emailType,
83	String content) {
84	Instant now = Instant.now();	1✔
85	Instant dateSent = (Objects.nonNull(response) && response.getStatusCode() < 400) ? now : null;	1✔
86	emailDAO.insert(	1✔
87	entityReferenceId,
88	voteId,
89	userId,
90	emailType.getTypeInt(),	1✔
91	dateSent,
92	content,
93	Objects.nonNull(response) ? response.getBody() : null,	1✔
94	Objects.nonNull(response) ? response.getStatusCode() : null,	1✔
95	now);
96	}	1✔
97
98	@VisibleForTesting
99	protected void sendMessage(MailMessage mailMessage, Integer userId)
100	throws IOException, TemplateException {
101	Writer out = new StringWriter();	1✔
102	Template template = templateHelper.getTemplate(mailMessage.getTemplateName());	1✔
103	template.process(mailMessage.createModel(serverUrl), out);	1✔
104	String content = out.toString();	1✔
105	Mail message = new Mail(new Email(fromAccount), mailMessage.createSubject(),	1✔
106	new Email(mailMessage.toUser.getEmail()), new Content("text/html", content));	1✔
107	Response response = sendGridAPI.sendMessage(message, mailMessage.toUser.getEmail());	1✔
108	saveEmailAndResponse(	1✔
109	response,
110	mailMessage.getEntityReferenceId(),	1✔
111	mailMessage.getVoteId(),	1✔
112	userId,
113	mailMessage.emailType,
114	content);
115	}	1✔
116
117	public List<org.broadinstitute.consent.http.models.mail.MailMessage> fetchEmailMessagesByType(
118	EmailType emailType, Integer limit,
119	Integer offset) {
120	return emailDAO.fetchMessagesByType(emailType.getTypeInt(), limit, offset);	1✔
121	}
122
123	public List<org.broadinstitute.consent.http.models.mail.MailMessage> fetchEmailMessagesByCreateDate(
124	Date start, Date end, Integer limit,
125	Integer offset) {
126	return emailDAO.fetchMessagesByCreateDate(start, end, limit, offset);	1✔
127	}
128
129
130	public void sendResearcherDarApproved(
131	String darCode,
132	Integer researcherId,
133	List<DatasetMailDTO> datasets,
134	String dataUseRestriction)
135	throws TemplateException, IOException {
NEW 136	User user = userDAO.findUserById(researcherId);	×
NEW 137	sendMessage(	×
138	new ResearcherDarApprovedMessage(user, darCode, datasets, dataUseRestriction), researcherId);
UNCOV 139	}	×
140
141	public void sendResearcherProgressReportApproved(
142	String darCode,
143	Integer researcherId,
144	List<DatasetMailDTO> datasets,
145	String dataUseRestriction)
146	throws TemplateException, IOException {
147	User user = userDAO.findUserById(researcherId);	×
148	sendMessage(	×
149	new ResearcherApprovedProgressReportMessage(user, darCode, datasets, dataUseRestriction), researcherId);
150	}	×
151
152	public void sendDataCustodianApprovalMessage(
153	User custodian,
154	String darCode,
155	List<DatasetMailDTO> datasets,
156	String dataDepositorName,
157	String researcherEmail)
158	throws TemplateException, IOException {
159	sendMessage(	×
160	new DataCustodianApprovalMessage(
161	custodian, darCode, datasets, dataDepositorName, researcherEmail),
162	custodian.getUserId());	×
163	}	×
164
165	public void sendDatasetSubmittedMessage(
166	User dacChair, User dataSubmitter, String dacName, String datasetName)
167	throws TemplateException, IOException {
168	sendMessage(	1✔
169	new DatasetSubmittedMessage(dacChair, dataSubmitter.getDisplayName(), datasetName, dacName),	1✔
170	dacChair.getUserId());	1✔
171	}	1✔
172
173	public void sendDatasetApprovedMessage(User user, String dacName, String datasetName)
174	throws TemplateException, IOException {
175	sendMessage(new DatasetApprovedMessage(user, dacName, datasetName), user.getUserId());	×
176	}	×
177
178	public void sendDatasetDeniedMessage(
179	User user, String dacName, String datasetName, String dacEmail)
180	throws TemplateException, IOException {
181	sendMessage(new DatasetDeniedMessage(user, dacName, datasetName, dacEmail), user.getUserId());	×
182	}	×
183
184	public void sendNewResearcherMessage(User researcher, User signingOfficial)
185	throws TemplateException, IOException {
186	sendMessage(	1✔
187	new NewResearcherLibraryRequestMessage(signingOfficial, researcher),
188	researcher.getUserId());	1✔
189	}	1✔
190
191	public void sendDaaRequestMessage(
192	User signingOfficial, User requestUser, String daaName, Integer daaId)
193	throws TemplateException, IOException {
194	sendMessage(	1✔
195	new DaaRequestMessage(signingOfficial, requestUser, daaName, daaId),
196	requestUser.getUserId());	1✔
197	}	1✔
198
199	public void sendNewDAAUploadSOMessage(
200	User signingOfficial,
201	String dacName,
202	String previousDaaName,
203	String newDaaName,
204	Integer userId)
205	throws TemplateException, IOException {
206	sendMessage(	1✔
207	new NewDAAUploadSOMessage(signingOfficial, dacName, previousDaaName, newDaaName), userId);
208	}	1✔
209
210	public void sendNewDAAUploadResearcherMessage(
211	User researcher, String dacName, String previousDaaName, String newDaaName, Integer userId)
212	throws TemplateException, IOException {
213	sendMessage(	1✔
214	new NewDAAUploadResearcherMessage(
215	researcher, dacName, previousDaaName, newDaaName),
216	userId);
217	}	1✔
218
219	public void sendDarNewCollectionElectionMessage(List<User> users, String darCode)
220	throws IOException, TemplateException {
NEW 221	String electionType = "Data Access Request";	×
NEW 222	for (User user : users) {	×
NEW 223	sendMessage(new NewCaseMessage(user, darCode, electionType), user.getUserId());	×
UNCOV 224	}	×
NEW 225	}	×
226
227	public void sendProgressReportNewCollectionElectionMessage(List<User> users, String darCode)
228	throws IOException, TemplateException {
NEW 229	for (User user : users) {	×
NEW 230	sendMessage(new NewProgressReportCaseMessage(user, darCode), user.getUserId());	×
NEW 231	}	×
NEW 232	}	×
233
234	public void sendNewDARRequestEmail(
235	User user, Map<String, List<String>> sendList, String researcherName, String darCode)
236	throws TemplateException, IOException {
NEW 237	sendMessage(new NewDARRequestMessage(user, darCode, sendList, researcherName),	×
NEW 238	user.getUserId());	×
NEW 239	}	×
240
241	public void sendNewProgressReportRequestEmail(
242	User user, Map<String, List<String>> sendList, String researcherName, String darCode, String referenceId)
243	throws TemplateException, IOException {
NEW 244	sendMessage(new NewProgressReportRequestMessage(user, darCode, referenceId, sendList, researcherName),	×
NEW 245	user.getUserId());	×
UNCOV 246	}	×
247
248	/**
249	* Send a message to a researcher that their data access request has expired.
250	*
251	* @param researcher the researcher to send the message to
252	* @param darCode the data access request code that's expired
253	* @param userId the user id of the person sending the message
254	* @param referenceId the data access request reference id that's expired
255	*/
256	public void sendDarExpiredMessage(User researcher, String darCode, Integer userId,
257	String referenceId)
258	throws TemplateException, IOException {
259	sendMessage(new DarExpiredMessage(researcher, darCode, referenceId), userId);	1✔
260	}	1✔
261
262	/**
263	* Remind the user that their data access request is about to expire.
264	*
265	* @param user the user to send the message to
266	* @param darCode the data access request code that's about to expire
267	* @param userId the user id of the person sending the message
268	* @param referenceId the data access request reference id that is expiring
269	*/
270	public void sendDarExpirationReminderMessage(User user, String darCode, Integer userId,
271	String referenceId)
272	throws TemplateException, IOException {
273	sendMessage(new DarExpirationReminderMessage(user, darCode, referenceId), userId);	1✔
274	}	1✔
275
276	public void sendReminderMessage(User user, Vote vote, String darCode, String electionType, String url)
277	throws TemplateException, IOException {
NEW 278	sendMessage(new ReminderMessage(user, vote, darCode, electionType, url), user.getUserId());	×
NEW 279	}	×
280
281	}

DataBiosphere / consent / #5929

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