#5188

Committed 10 Jul 2024 02:12PM UTC coverage: 77.026% (+0.08%) from 76.943%

Build # #5188

Build Type

push

Committed by

Commit Message

[DCJ-481] Add "Broad DAA" flag to appropriate DAA (#2351)

Run Details

46 of 46 new or added lines in 4 files covered. (100.0%)

2 existing lines in 2 files now uncovered.

9988 of 12967 relevant lines covered (77.03%)

0.77 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

96.67

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

package org.broadinstitute.consent.http.service;

import com.google.cloud.storage.BlobId;
import com.google.gson.Gson;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.inject.Inject;
import jakarta.ws.rs.BadRequestException;
import jakarta.ws.rs.NotFoundException;
import jakarta.ws.rs.ServerErrorException;
import jakarta.ws.rs.core.MediaType;
import java.io.IOException;
import java.io.InputStream;
import java.util.Comparator;
import java.util.List;
import java.util.Optional;
import java.util.UUID;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import org.broadinstitute.consent.http.cloudstore.GCSService;
import org.broadinstitute.consent.http.db.DaaDAO;
import org.broadinstitute.consent.http.db.DacDAO;
import org.broadinstitute.consent.http.db.InstitutionDAO;
import org.broadinstitute.consent.http.enumeration.FileCategory;
import org.broadinstitute.consent.http.models.Dac;
import org.broadinstitute.consent.http.models.DataAccessAgreement;
import org.broadinstitute.consent.http.models.FileStorageObject;
import org.broadinstitute.consent.http.models.Institution;
import org.broadinstitute.consent.http.models.User;
import org.broadinstitute.consent.http.service.UserService.SimplifiedUser;
import org.broadinstitute.consent.http.service.dao.DaaServiceDAO;
import org.broadinstitute.consent.http.util.ConsentLogger;
import org.glassfish.jersey.media.multipart.FormDataContentDisposition;

public class DaaService implements ConsentLogger {

  private final DaaServiceDAO daaServiceDAO;
  private final DaaDAO daaDAO;
  private final GCSService gcsService;
  private final EmailService emailService;
  private final UserService userService;
  private final InstitutionDAO institutionDAO;
  private final DacDAO dacDAO;

  @Inject
  public DaaService(DaaServiceDAO daaServiceDAO, DaaDAO daaDAO, GCSService gcsService, EmailService emailService, UserService userService, InstitutionDAO institutionDAO, DacDAO dacDAO) {
    this.daaServiceDAO = daaServiceDAO;
    this.daaDAO = daaDAO;
    this.gcsService = gcsService;
    this.emailService = emailService;
    this.userService = userService;
    this.institutionDAO = institutionDAO;
    this.dacDAO = dacDAO;
  }

  /**
   * Create a new DataAccessAgreement with file content.
   *
   * @param userId The create User ID
   * @param dacId The initial DAC ID
   * @param inputStream The file content
   * @param fileDetail The file details
   * @return The created DataAccessAgreement
   * @throws ServerErrorException The Exception
   */
  public DataAccessAgreement createDaaWithFso(Integer userId, Integer dacId,
      InputStream inputStream,
      FormDataContentDisposition fileDetail)
      throws ServerErrorException {
    UUID id = UUID.randomUUID();
    BlobId blobId;
    try {
      blobId = gcsService.storeDocument(inputStream, fileDetail.getType(), id);
    } catch (IOException e) {
      logException(String.format("Error storing DAA file in GCS. User ID: %s; Dac ID: %s. ", userId, dacId), e);
      throw new ServerErrorException("Error storing DAA file in GCS.", 500);
    }
    Integer daaId;
    try {
      String mediaType = switch (StringUtils.substringAfterLast(fileDetail.getFileName(), ".")) {
        case "png", "gif", "jpg", "jpeg" -> "image";
        default -> MediaType.APPLICATION_OCTET_STREAM;
      };
      FileStorageObject fso = new FileStorageObject();
      fso.setBlobId(blobId);
      fso.setFileName(fileDetail.getFileName());
      fso.setCategory(FileCategory.DATA_ACCESS_AGREEMENT);
      fso.setMediaType(mediaType);
      daaId = daaServiceDAO.createDaaWithFso(userId, dacId, fso);
    } catch (Exception e) {
      try {
        gcsService.deleteDocument(blobId.getName());
      } catch (Exception ex) {
        logException(String.format("Error deleting DAA file from GCS. User ID: %s; Dac ID: %s. ", userId, dacId), ex);
      }
      logException(String.format("Error saving DAA. User ID: %s; Dac ID: %s. ", userId, dacId), e);
      throw new ServerErrorException("Error saving DAA.", 500);
    }
    return daaDAO.findById(daaId);
  }

  public void addDacToDaa(Integer dacId, Integer daaId) {
    daaDAO.createDacDaaRelation(dacId, daaId);
  }

  public void removeDacFromDaa(Integer dacId, Integer daaId) {
    daaDAO.deleteDacDaaRelation(dacId, daaId);
  }

  // Note: This method/implementation is not the permanent solution to identifying the Broad DAA.
  // Work is ticketed to refactor this logic.
  public boolean isBroadDAA(int daaId, List<DataAccessAgreement> allDaas, List<Dac> allDacs) {
    // Artificially tag the Broad/DUOS DAA as a reference DAA.
    Optional<Dac> broadDac = allDacs.stream()
        .filter(dac -> dac.getName().toLowerCase().contains("broad")).findFirst();
    if (broadDac.isPresent()) {
      Optional<DataAccessAgreement> broadDAA = allDaas.stream()
          .filter(daa -> daa.getInitialDacId().equals(broadDac.get().getDacId())).findFirst();
      broadDAA.ifPresent(daa -> daa.setBroadDaa(true));
    } else {
      // In this case, we want the first created DAA to be the Broad default DAA.
      allDaas.stream().min(Comparator.comparing(DataAccessAgreement::getDaaId))
          .ifPresent(daa -> daa.setBroadDaa(true));
    }
    Optional<DataAccessAgreement> broadDaa = allDaas.stream().filter(daa -> daa.getDaaId().equals(daaId)).findFirst();
    if (broadDaa.isPresent()) {
      return broadDaa.get().getBroadDaa();
    } else {
      return false;
    }
  }

  public List<DataAccessAgreement> findAll() {
      List<DataAccessAgreement> daas = daaDAO.findAll();
      List<Dac> allDacs = dacDAO.findAll();
      if (daas != null) {
        daas.forEach(daa -> {
          daa.setBroadDaa(
              isBroadDAA(daa.getDaaId(), daas, allDacs)
          );
        });
        return daas;
      }
    return List.of();
  }

  public DataAccessAgreement findById(Integer daaId) {
    DataAccessAgreement daa = daaDAO.findById(daaId);
    if (daa != null) {
      return daa;
    }
    throw new NotFoundException("Could not find DAA with the provided ID: " + daaId);
  }

  public void sendDaaRequestEmails(User user, Integer daaId) throws Exception {
    try {
      Institution institution = institutionDAO.findInstitutionWithSOById(user.getInstitutionId());
      if (institution == null) {
        throw new BadRequestException("This user has not set their institution: " + user.getDisplayName());
      }
      List<SimplifiedUser> signingOfficials = institution.getSigningOfficials();
      if (signingOfficials.isEmpty()) {
        throw new NotFoundException("No signing officials found for user: " + user.getDisplayName());
      }
      int userId = user.getUserId();
      String userName = user.getDisplayName();
      for (SimplifiedUser signingOfficial : signingOfficials) {
        DataAccessAgreement daa = findById(daaId);
        String daaName = daa.getFile().getFileName();
        emailService.sendDaaRequestMessage( signingOfficial.displayName, signingOfficial.email,
            userName, daaName, daaId, userId);
      }
    } catch (Exception e) {
      logException(e);
      throw(e);
    }
  }

  public void sendNewDaaEmails(User user, Integer daaId, String dacName, String newDaaName) throws Exception {
    try {
      DataAccessAgreement daa = findById(daaId);
      if (daa != null) {
        String previousDaaName = daa.getFile().getFileName();
        List<SimplifiedUser> researchers = userService.getUsersByDaaId(daaId);
        List<SimplifiedUser> signingOfficials = researchers.stream()
            .flatMap(researcher -> userService.findSOsByInstitutionId(researcher.institutionId).stream())
            .distinct()
            .collect(Collectors.toList());

        for (SimplifiedUser researcher : researchers) {
          emailService.sendNewDAAUploadResearcherMessage(researcher.displayName, researcher.email,
              dacName, previousDaaName, newDaaName, user.getUserId());
        }
        for (SimplifiedUser signingOfficial : signingOfficials) {
          emailService.sendNewDAAUploadSOMessage(signingOfficial.displayName, signingOfficial.email,
              dacName, previousDaaName, newDaaName, user.getUserId());
        }
      }
    } catch (Exception e) {
      logException(e);
      throw(e);
    }
  }

  public InputStream findFileById(Integer daaId) {
    DataAccessAgreement daa = daaDAO.findById(daaId);
    if (daa != null) {
      FileStorageObject file = daa.getFile();
      if (file != null) {
        return gcsService.getDocument(file.getBlobId().getName());
      }
    }
    throw new NotFoundException("Could not find DAA File with the provided ID: " + daaId);
  }

  public List<DataAccessAgreement> findDAAsInJsonArray(String json, String arrayKey) {
    List<JsonElement> jsonElementList;
    try {
      JsonObject jsonObject = new Gson().fromJson(json, JsonObject.class);
      jsonElementList = jsonObject.getAsJsonArray(arrayKey).asList();
    } catch (Exception e) {
      throw new BadRequestException("Invalid JSON or missing array with key: " + arrayKey);
    }
    return jsonElementList.stream().distinct().map(e -> findById(e.getAsInt())).toList();
  }

  public void deleteDaa(Integer daaId) {
    DataAccessAgreement daa = daaDAO.findById(daaId);
    if (daa != null) {
      daaDAO.deleteDaa(daaId);
    } else {
      throw new NotFoundException("Could not find DAA with the provided ID: " + daaId);
    }
  }
}

1	package org.broadinstitute.consent.http.service;
2
3	import com.google.cloud.storage.BlobId;
4	import com.google.gson.Gson;
5	import com.google.gson.JsonElement;
6	import com.google.gson.JsonObject;
7	import com.google.inject.Inject;
8	import jakarta.ws.rs.BadRequestException;
9	import jakarta.ws.rs.NotFoundException;
10	import jakarta.ws.rs.ServerErrorException;
11	import jakarta.ws.rs.core.MediaType;
12	import java.io.IOException;
13	import java.io.InputStream;
14	import java.util.Comparator;
15	import java.util.List;
16	import java.util.Optional;
17	import java.util.UUID;
18	import java.util.stream.Collectors;
19	import org.apache.commons.lang3.StringUtils;
20	import org.broadinstitute.consent.http.cloudstore.GCSService;
21	import org.broadinstitute.consent.http.db.DaaDAO;
22	import org.broadinstitute.consent.http.db.DacDAO;
23	import org.broadinstitute.consent.http.db.InstitutionDAO;
24	import org.broadinstitute.consent.http.enumeration.FileCategory;
25	import org.broadinstitute.consent.http.models.Dac;
26	import org.broadinstitute.consent.http.models.DataAccessAgreement;
27	import org.broadinstitute.consent.http.models.FileStorageObject;
28	import org.broadinstitute.consent.http.models.Institution;
29	import org.broadinstitute.consent.http.models.User;
30	import org.broadinstitute.consent.http.service.UserService.SimplifiedUser;
31	import org.broadinstitute.consent.http.service.dao.DaaServiceDAO;
32	import org.broadinstitute.consent.http.util.ConsentLogger;
33	import org.glassfish.jersey.media.multipart.FormDataContentDisposition;
34
35	public class DaaService implements ConsentLogger {
36
37	private final DaaServiceDAO daaServiceDAO;
38	private final DaaDAO daaDAO;
39	private final GCSService gcsService;
40	private final EmailService emailService;
41	private final UserService userService;
42	private final InstitutionDAO institutionDAO;
43	private final DacDAO dacDAO;
44
45	@Inject
46	public DaaService(DaaServiceDAO daaServiceDAO, DaaDAO daaDAO, GCSService gcsService, EmailService emailService, UserService userService, InstitutionDAO institutionDAO, DacDAO dacDAO) {	1✔
47	this.daaServiceDAO = daaServiceDAO;	1✔
48	this.daaDAO = daaDAO;	1✔
49	this.gcsService = gcsService;	1✔
50	this.emailService = emailService;	1✔
51	this.userService = userService;	1✔
52	this.institutionDAO = institutionDAO;	1✔
53	this.dacDAO = dacDAO;	1✔
54	}	1✔
55
56	/**
57	* Create a new DataAccessAgreement with file content.
58	*
59	* @param userId The create User ID
60	* @param dacId The initial DAC ID
61	* @param inputStream The file content
62	* @param fileDetail The file details
63	* @return The created DataAccessAgreement
64	* @throws ServerErrorException The Exception
65	*/
66	public DataAccessAgreement createDaaWithFso(Integer userId, Integer dacId,
67	InputStream inputStream,
68	FormDataContentDisposition fileDetail)
69	throws ServerErrorException {
70	UUID id = UUID.randomUUID();	1✔
71	BlobId blobId;
72	try {
73	blobId = gcsService.storeDocument(inputStream, fileDetail.getType(), id);	1✔
74	} catch (IOException e) {	1✔
75	logException(String.format("Error storing DAA file in GCS. User ID: %s; Dac ID: %s. ", userId, dacId), e);	1✔
76	throw new ServerErrorException("Error storing DAA file in GCS.", 500);	1✔
77	}	1✔
78	Integer daaId;
79	try {
80	String mediaType = switch (StringUtils.substringAfterLast(fileDetail.getFileName(), ".")) {	1✔
81	case "png", "gif", "jpg", "jpeg" -> "image";	×
82	default -> MediaType.APPLICATION_OCTET_STREAM;	1✔
83	};
84	FileStorageObject fso = new FileStorageObject();	1✔
85	fso.setBlobId(blobId);	1✔
86	fso.setFileName(fileDetail.getFileName());	1✔
87	fso.setCategory(FileCategory.DATA_ACCESS_AGREEMENT);	1✔
88	fso.setMediaType(mediaType);	1✔
89	daaId = daaServiceDAO.createDaaWithFso(userId, dacId, fso);	1✔
90	} catch (Exception e) {	1✔
91	try {
92	gcsService.deleteDocument(blobId.getName());	×
93	} catch (Exception ex) {	1✔
94	logException(String.format("Error deleting DAA file from GCS. User ID: %s; Dac ID: %s. ", userId, dacId), ex);	1✔
95	}	×
96	logException(String.format("Error saving DAA. User ID: %s; Dac ID: %s. ", userId, dacId), e);	1✔
97	throw new ServerErrorException("Error saving DAA.", 500);	1✔
98	}	1✔
99	return daaDAO.findById(daaId);	1✔
100	}
101
102	public void addDacToDaa(Integer dacId, Integer daaId) {
103	daaDAO.createDacDaaRelation(dacId, daaId);	1✔
104	}	1✔
105
106	public void removeDacFromDaa(Integer dacId, Integer daaId) {
107	daaDAO.deleteDacDaaRelation(dacId, daaId);	1✔
108	}	1✔
109
110	// Note: This method/implementation is not the permanent solution to identifying the Broad DAA.
111	// Work is ticketed to refactor this logic.
112	public boolean isBroadDAA(int daaId, List<DataAccessAgreement> allDaas, List<Dac> allDacs) {
113	// Artificially tag the Broad/DUOS DAA as a reference DAA.
114	Optional<Dac> broadDac = allDacs.stream()	1✔
115	.filter(dac -> dac.getName().toLowerCase().contains("broad")).findFirst();	1✔
116	if (broadDac.isPresent()) {	1✔
117	Optional<DataAccessAgreement> broadDAA = allDaas.stream()	1✔
118	.filter(daa -> daa.getInitialDacId().equals(broadDac.get().getDacId())).findFirst();	1✔
119	broadDAA.ifPresent(daa -> daa.setBroadDaa(true));	1✔
120	} else {	1✔
121	// In this case, we want the first created DAA to be the Broad default DAA.
122	allDaas.stream().min(Comparator.comparing(DataAccessAgreement::getDaaId))	1✔
123	.ifPresent(daa -> daa.setBroadDaa(true));	1✔
124	}
125	Optional<DataAccessAgreement> broadDaa = allDaas.stream().filter(daa -> daa.getDaaId().equals(daaId)).findFirst();	1✔
126	if (broadDaa.isPresent()) {	1✔
127	return broadDaa.get().getBroadDaa();	1✔
128	} else {
129	return false;	1✔
130	}
131	}
132
133	public List<DataAccessAgreement> findAll() {
134	List<DataAccessAgreement> daas = daaDAO.findAll();	1✔
135	List<Dac> allDacs = dacDAO.findAll();	1✔
136	if (daas != null) {	1✔
137	daas.forEach(daa -> {	1✔
138	daa.setBroadDaa(	1✔
139	isBroadDAA(daa.getDaaId(), daas, allDacs)	1✔
140	);
141	});	1✔
142	return daas;	1✔
143	}
UNCOV 144	return List.of();	×
145	}
146
147	public DataAccessAgreement findById(Integer daaId) {
148	DataAccessAgreement daa = daaDAO.findById(daaId);	1✔
149	if (daa != null) {	1✔
150	return daa;	1✔
151	}
152	throw new NotFoundException("Could not find DAA with the provided ID: " + daaId);	1✔
153	}
154
155	public void sendDaaRequestEmails(User user, Integer daaId) throws Exception {
156	try {
157	Institution institution = institutionDAO.findInstitutionWithSOById(user.getInstitutionId());	1✔
158	if (institution == null) {	1✔
159	throw new BadRequestException("This user has not set their institution: " + user.getDisplayName());	1✔
160	}
161	List<SimplifiedUser> signingOfficials = institution.getSigningOfficials();	1✔
162	if (signingOfficials.isEmpty()) {	1✔
163	throw new NotFoundException("No signing officials found for user: " + user.getDisplayName());	1✔
164	}
165	int userId = user.getUserId();	1✔
166	String userName = user.getDisplayName();	1✔
167	for (SimplifiedUser signingOfficial : signingOfficials) {	1✔
168	DataAccessAgreement daa = findById(daaId);	1✔
169	String daaName = daa.getFile().getFileName();	1✔
170	emailService.sendDaaRequestMessage( signingOfficial.displayName, signingOfficial.email,	1✔
171	userName, daaName, daaId, userId);	1✔
172	}	1✔
173	} catch (Exception e) {	1✔
174	logException(e);	1✔
175	throw(e);	1✔
176	}	1✔
177	}	1✔
178
179	public void sendNewDaaEmails(User user, Integer daaId, String dacName, String newDaaName) throws Exception {
180	try {
181	DataAccessAgreement daa = findById(daaId);	1✔
182	if (daa != null) {	1✔
183	String previousDaaName = daa.getFile().getFileName();	1✔
184	List<SimplifiedUser> researchers = userService.getUsersByDaaId(daaId);	1✔
185	List<SimplifiedUser> signingOfficials = researchers.stream()	1✔
186	.flatMap(researcher -> userService.findSOsByInstitutionId(researcher.institutionId).stream())	1✔
187	.distinct()	1✔
188	.collect(Collectors.toList());	1✔
189
190	for (SimplifiedUser researcher : researchers) {	1✔
191	emailService.sendNewDAAUploadResearcherMessage(researcher.displayName, researcher.email,	1✔
192	dacName, previousDaaName, newDaaName, user.getUserId());	1✔
193	}	1✔
194	for (SimplifiedUser signingOfficial : signingOfficials) {	1✔
195	emailService.sendNewDAAUploadSOMessage(signingOfficial.displayName, signingOfficial.email,	1✔
196	dacName, previousDaaName, newDaaName, user.getUserId());	1✔
197	}	1✔
198	}
199	} catch (Exception e) {	1✔
200	logException(e);	1✔
201	throw(e);	1✔
202	}	1✔
203	}	1✔
204
205	public InputStream findFileById(Integer daaId) {
206	DataAccessAgreement daa = daaDAO.findById(daaId);	1✔
207	if (daa != null) {	1✔
208	FileStorageObject file = daa.getFile();	1✔
209	if (file != null) {	1✔
210	return gcsService.getDocument(file.getBlobId().getName());	1✔
211	}
212	}
213	throw new NotFoundException("Could not find DAA File with the provided ID: " + daaId);	1✔
214	}
215
216	public List<DataAccessAgreement> findDAAsInJsonArray(String json, String arrayKey) {
217	List<JsonElement> jsonElementList;
218	try {
219	JsonObject jsonObject = new Gson().fromJson(json, JsonObject.class);	1✔
220	jsonElementList = jsonObject.getAsJsonArray(arrayKey).asList();	1✔
221	} catch (Exception e) {	1✔
222	throw new BadRequestException("Invalid JSON or missing array with key: " + arrayKey);	1✔
223	}	1✔
224	return jsonElementList.stream().distinct().map(e -> findById(e.getAsInt())).toList();	1✔
225	}
226
227	public void deleteDaa(Integer daaId) {
228	DataAccessAgreement daa = daaDAO.findById(daaId);	1✔
229	if (daa != null) {	1✔
230	daaDAO.deleteDaa(daaId);	1✔
231	} else {
232	throw new NotFoundException("Could not find DAA with the provided ID: " + daaId);	1✔
233	}
234	}	1✔
235	}

DataBiosphere / consent / #5188

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous