#5119

Committed 24 May 2024 05:31PM UTC coverage: 76.36% (+0.08%) from 76.282%

Build # #5119

Build Type

push

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Commit Message

[DCJ-49][DCJ-50][risk=no] New APIs for DAA Enforced DAR Create/Update (#2330)

Co-authored-by: fboulnois <fboulnois@users.noreply.github.com>

Run Details

88 of 93 new or added lines in 6 files covered. (94.62%)

1 existing line in 1 file now uncovered.

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95.33

/src/main/java/org/broadinstitute/consent/http/models/User.java

package org.broadinstitute.consent.http.models;

import com.fasterxml.jackson.annotation.JsonProperty;
import com.google.gson.Gson;
import com.google.gson.JsonObject;
import java.beans.Transient;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.EnumSet;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import net.gcardone.junidecode.Junidecode;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.broadinstitute.consent.http.enumeration.UserRoles;
import org.broadinstitute.consent.http.util.gson.GsonUtil;

public class User {

  public static final String QUERY_FIELDS_WITH_U_PREFIX =
      " u.user_id as u_user_id, " +
          " u.email as u_email, " +
          " u.display_name as u_display_name, " +
          " u.create_date as u_create_date, " +
          " u.email_preference as u_email_preference, " +
          " u.institution_id as u_institution_id," +
          " u.era_commons_id as u_era_commons_id ";

  @JsonProperty
  private Integer userId;

  @JsonProperty
  private String email;

  @JsonProperty
  private String displayName;

  @JsonProperty
  private Date createDate;

  @JsonProperty
  private List<UserRole> roles;

  @JsonProperty
  private List<UserProperty> properties;

  @JsonProperty
  private Boolean emailPreference;

  @JsonProperty
  private Integer institutionId;

  @JsonProperty
  private String eraCommonsId;

  private Institution institution;

  private List<LibraryCard> libraryCards;

  public User() {
  }

  public Integer getUserId() {
    return userId;
  }

  public void setUserId(Integer userId) {
    this.userId = userId;
  }

  public User(Integer userId, String email, String displayName, Date createDate) {
    this.userId = userId;
    this.email = email;
    this.displayName = displayName;
    this.createDate = createDate;
  }

  public User(Integer userId, String email, String displayName, Date createDate,
      List<UserRole> roles) {
    this.userId = userId;
    this.email = email;
    this.displayName = displayName;
    this.createDate = createDate;
    this.roles = roles;
  }

  /**
   * Convenience method for backwards compatibility support for older clients. This method is
   * intended to reconstruct a User object from a supplied JSON string for primary fields and roles.
   * Other associated objects are not intended to be parsed using this method since it comes from
   * user-supplied data and may conflict with what the system knows about those associations.
   *
   * @param json A json string that may or may not be correctly structured as a DACUser
   */
  public User(String json) {
    Gson gson = GsonUtil.getInstance();
    JsonObject userJsonObject = gson.fromJson(json, JsonObject.class);
    // There are no cases where we want to pull the create date/update date from user-provided data.
    // Nor do we need to retrieve the full institution object from user-provided data.
    JsonObject filteredUserJsonObject = filterFields(
        userJsonObject,
        Arrays.asList("createDate", "institution", "libraryCards"));
    User u = gson.fromJson(filteredUserJsonObject.toString(), User.class);
    setUserId(u);
    setEmail(u);
    setDisplayName(u);
    setEmailPreference(u);
    setRoles(u);
    setInstitutionId(u);
  }

  /**
   * Private method to filter out fields that we do not want to parse from json objects.
   *
   * @param obj    The json object
   * @param fields The fields to remove
   * @return Filtered Clone of the object.
   */
  private JsonObject filterFields(JsonObject obj, List<String> fields) {
    JsonObject copy = obj.deepCopy();
    fields.forEach(f -> {
      if (copy.has(f)) {
        copy.remove(f);
      }
    });
    return copy;
  }

  private void setUserId(User u) {
    if (Objects.nonNull(u.getUserId())) {
      this.setUserId(u.getUserId());
    }
  }

  private void setEmail(User u) {
    if (!StringUtils.isEmpty(u.getEmail()) && u.getEmail() != null) {
      this.setEmail(Junidecode.unidecode(u.getEmail()));
    }
  }

  private void setDisplayName(User u) {
    if (!StringUtils.isEmpty(u.getDisplayName())) {
      this.setDisplayName(u.getDisplayName());
    }
  }

  private void setEmailPreference(User u) {
    if (Objects.nonNull(u.getEmailPreference())) {
      this.setEmailPreference(u.getEmailPreference());
    }
  }

  private void setRoles(User u) {
    if (CollectionUtils.isNotEmpty(u.getRoles())) {
      this.setRoles(u.getRoles());
    }
  }

  private void setInstitutionId(User u) {
    if (Objects.nonNull(u.getInstitutionId())) {
      this.setInstitutionId(u.getInstitutionId());
    }
  }

  public String getEmail() {
    return email;
  }

  public void setEmail(String email) {
    this.email = email;
  }

  public String getDisplayName() {
    return displayName;
  }

  public void setDisplayName(String displayName) {
    this.displayName = displayName;
  }

  public List<UserRole> getRoles() {
    return roles;
  }

  public void setRoles(List<UserRole> roles) {
    this.roles = roles;
  }

  public void setAdminRole() {
    this.roles = List.of(UserRoles.Admin());
  }

  public void setChairpersonRole() {
    this.roles = List.of(UserRoles.Chairperson());
  }

  public void setChairpersonRoleWithDAC(int dacId) {
    UserRole chairpersonRole = UserRoles.Chairperson();
    chairpersonRole.setDacId(dacId);
    this.roles = List.of(chairpersonRole);
  }

  public void setITDirectorRole() {
    this.roles = List.of(UserRoles.ITDirector());
  }

  public void setMemberRole() {
    this.roles = List.of(UserRoles.Member());
  }

  public void setResearcherRole() {
    this.roles = List.of(UserRoles.Researcher());
  }

  public void setSigningOfficialRole() {
    this.roles = List.of(UserRoles.SigningOfficial());
  }

  public List<UserProperty> getProperties() {
    return properties;
  }

  public void setProperties(List<UserProperty> properties) {
    this.properties = properties;
  }

  public Date getCreateDate() {
    return createDate;
  }

  public void setCreateDate(Date createDate) {
    this.createDate = createDate;
  }

  public Boolean getEmailPreference() {
    return emailPreference;
  }

  public void setEmailPreference(Boolean emailPreference) {
    this.emailPreference = emailPreference;
  }

  public Integer getInstitutionId() {
    return institutionId;
  }

  public void setInstitutionId(Integer institutionId) {
    this.institutionId = institutionId;
  }

  public String getEraCommonsId() {
    return eraCommonsId;
  }

  public void setEraCommonsId(String eraCommonsId) {
    this.eraCommonsId = eraCommonsId;
  }

  public void setInstitution(Institution institution) {
    this.institution = institution;
  }

  public void setInstitution(User user) {
    if (Objects.nonNull(user.getInstitution())) {
      this.institution = user.institution;
    }
  }

  public Institution getInstitution() {
    return institution;
  }

  public void setLibraryCards(List<LibraryCard> cards) {
    this.libraryCards = cards;
  }

  public List<LibraryCard> getLibraryCards() {
    return this.libraryCards;
  }

  public void addRole(UserRole userRole) {
    if (Objects.isNull(this.getRoles())) {
      this.setRoles(new ArrayList<>());
    }

    if (!this.getRoles().contains(userRole)) {
      this.getRoles().add(userRole);
    }
  }

  public void addProperty(UserProperty userProp) {
    if (Objects.isNull(this.getProperties())) {
      this.setProperties(new ArrayList<>());
    }
    if (!this.getProperties().contains(userProp)) {
      this.getProperties().add(userProp);
    }
  }

  public void addLibraryCard(LibraryCard card) {
    if (Objects.isNull(this.getLibraryCards())) {
      this.setLibraryCards(new ArrayList<>());
    }
    if (!this.getLibraryCards().contains(card)) {
      this.getLibraryCards().add(card);
    }
  }

  @Override
  public int hashCode() {
    return this.getUserId();
  }

  @Override
  public boolean equals(Object obj) {
    if (this == obj) {
      return true;
    }
    if (obj == null) {
      return false;
    }
    if (getClass() != obj.getClass()) {
      return false;
    }

    User other = (User) obj;
    return new EqualsBuilder().append(getUserId(), other.getUserId()).isEquals();
  }

  @Override
  public String toString() {
    return GsonUtil.gsonBuilderWithAdapters().create().toJson(this);
  }

  public boolean hasUserRole(UserRoles role) {
    if (Objects.isNull(this.getRoles())) {
      return false;
    } else {
      return this.getRoles().stream().anyMatch((r) -> r.getRoleId().equals(role.getRoleId()));
    }
  }

  @Transient
  public List<Integer> getUserRoleIdsFromUser() {
    if (Objects.isNull(this.getRoles())) {
      return List.of();
    }
    return this.getRoles()
        .stream()
        .map(UserRole::getRoleId)
        .collect(Collectors.toList());
  }

  @Transient
  public boolean doesUserHaveAnyRoleInSet(EnumSet<UserRoles> userRoles) {
    List<Integer> queriedRoleIds = userRoles.stream().map(UserRoles::getRoleId)
        .collect(Collectors.toList());
    return getUserRoleIdsFromUser().stream().anyMatch(queriedRoleIds::contains);
  }

  @Transient
  public Boolean checkIfUserHasRole(String roleName, Integer dacId) {
    UserRoles role = UserRoles.getUserRoleFromName(roleName);
    List<UserRole> roles = getRoles();
    List<UserRole> targetRoles = roles.stream()
        .filter((r) -> {
          return r.getName().equals(role.getRoleName())
              && r.getRoleId().equals(role.getRoleId())
              && Objects.equals(r.getDacId(), dacId);
        })
        .collect(Collectors.toList());
    return !targetRoles.isEmpty();

  }

}

1	package org.broadinstitute.consent.http.models;
2
3	import com.fasterxml.jackson.annotation.JsonProperty;
4	import com.google.gson.Gson;
5	import com.google.gson.JsonObject;
6	import java.beans.Transient;
7	import java.util.ArrayList;
8	import java.util.Arrays;
9	import java.util.Date;
10	import java.util.EnumSet;
11	import java.util.List;
12	import java.util.Objects;
13	import java.util.stream.Collectors;
14	import net.gcardone.junidecode.Junidecode;
15	import org.apache.commons.collections4.CollectionUtils;
16	import org.apache.commons.lang3.StringUtils;
17	import org.apache.commons.lang3.builder.EqualsBuilder;
18	import org.broadinstitute.consent.http.enumeration.UserRoles;
19	import org.broadinstitute.consent.http.util.gson.GsonUtil;
20
21	public class User {
22
23	public static final String QUERY_FIELDS_WITH_U_PREFIX =
24	" u.user_id as u_user_id, " +
25	" u.email as u_email, " +
26	" u.display_name as u_display_name, " +
27	" u.create_date as u_create_date, " +
28	" u.email_preference as u_email_preference, " +
29	" u.institution_id as u_institution_id," +
30	" u.era_commons_id as u_era_commons_id ";
31
32	@JsonProperty
33	private Integer userId;
34
35	@JsonProperty
36	private String email;
37
38	@JsonProperty
39	private String displayName;
40
41	@JsonProperty
42	private Date createDate;
43
44	@JsonProperty
45	private List<UserRole> roles;
46
47	@JsonProperty
48	private List<UserProperty> properties;
49
50	@JsonProperty
51	private Boolean emailPreference;
52
53	@JsonProperty
54	private Integer institutionId;
55
56	@JsonProperty
57	private String eraCommonsId;
58
59	private Institution institution;
60
61	private List<LibraryCard> libraryCards;
62
63	public User() {	1✔
64	}	1✔
65
66	public Integer getUserId() {
67	return userId;	1✔
68	}
69
70	public void setUserId(Integer userId) {
71	this.userId = userId;	1✔
72	}	1✔
73
74	public User(Integer userId, String email, String displayName, Date createDate) {	1✔
75	this.userId = userId;	1✔
76	this.email = email;	1✔
77	this.displayName = displayName;	1✔
78	this.createDate = createDate;	1✔
79	}	1✔
80
81	public User(Integer userId, String email, String displayName, Date createDate,
82	List<UserRole> roles) {	1✔
83	this.userId = userId;	1✔
84	this.email = email;	1✔
85	this.displayName = displayName;	1✔
86	this.createDate = createDate;	1✔
87	this.roles = roles;	1✔
88	}	1✔
89
90	/**
91	* Convenience method for backwards compatibility support for older clients. This method is
92	* intended to reconstruct a User object from a supplied JSON string for primary fields and roles.
93	* Other associated objects are not intended to be parsed using this method since it comes from
94	* user-supplied data and may conflict with what the system knows about those associations.
95	*
96	* @param json A json string that may or may not be correctly structured as a DACUser
97	*/
98	public User(String json) {	1✔
99	Gson gson = GsonUtil.getInstance();	1✔
100	JsonObject userJsonObject = gson.fromJson(json, JsonObject.class);	1✔
101	// There are no cases where we want to pull the create date/update date from user-provided data.
102	// Nor do we need to retrieve the full institution object from user-provided data.
103	JsonObject filteredUserJsonObject = filterFields(	1✔
104	userJsonObject,
105	Arrays.asList("createDate", "institution", "libraryCards"));	1✔
106	User u = gson.fromJson(filteredUserJsonObject.toString(), User.class);	1✔
107	setUserId(u);	1✔
108	setEmail(u);	1✔
109	setDisplayName(u);	1✔
110	setEmailPreference(u);	1✔
111	setRoles(u);	1✔
112	setInstitutionId(u);	1✔
113	}	1✔
114
115	/**
116	* Private method to filter out fields that we do not want to parse from json objects.
117	*
118	* @param obj The json object
119	* @param fields The fields to remove
120	* @return Filtered Clone of the object.
121	*/
122	private JsonObject filterFields(JsonObject obj, List<String> fields) {
123	JsonObject copy = obj.deepCopy();	1✔
124	fields.forEach(f -> {	1✔
125	if (copy.has(f)) {	1✔
126	copy.remove(f);	1✔
127	}
128	});	1✔
129	return copy;	1✔
130	}
131
132	private void setUserId(User u) {
133	if (Objects.nonNull(u.getUserId())) {	1✔
134	this.setUserId(u.getUserId());	1✔
135	}
136	}	1✔
137
138	private void setEmail(User u) {
139	if (!StringUtils.isEmpty(u.getEmail()) && u.getEmail() != null) {	1✔
140	this.setEmail(Junidecode.unidecode(u.getEmail()));	1✔
141	}
142	}	1✔
143
144	private void setDisplayName(User u) {
145	if (!StringUtils.isEmpty(u.getDisplayName())) {	1✔
146	this.setDisplayName(u.getDisplayName());	1✔
147	}
148	}	1✔
149
150	private void setEmailPreference(User u) {
151	if (Objects.nonNull(u.getEmailPreference())) {	1✔
152	this.setEmailPreference(u.getEmailPreference());	1✔
153	}
154	}	1✔
155
156	private void setRoles(User u) {
157	if (CollectionUtils.isNotEmpty(u.getRoles())) {	1✔
158	this.setRoles(u.getRoles());	1✔
159	}
160	}	1✔
161
162	private void setInstitutionId(User u) {
163	if (Objects.nonNull(u.getInstitutionId())) {	1✔
164	this.setInstitutionId(u.getInstitutionId());	×
165	}
166	}	1✔
167
168	public String getEmail() {
169	return email;	1✔
170	}
171
172	public void setEmail(String email) {
173	this.email = email;	1✔
174	}	1✔
175
176	public String getDisplayName() {
177	return displayName;	1✔
178	}
179
180	public void setDisplayName(String displayName) {
181	this.displayName = displayName;	1✔
182	}	1✔
183
184	public List<UserRole> getRoles() {
185	return roles;	1✔
186	}
187
188	public void setRoles(List<UserRole> roles) {
189	this.roles = roles;	1✔
190	}	1✔
191
192	public void setAdminRole() {
193	this.roles = List.of(UserRoles.Admin());	1✔
194	}	1✔
195
196	public void setChairpersonRole() {
197	this.roles = List.of(UserRoles.Chairperson());	1✔
198	}	1✔
199
200	public void setChairpersonRoleWithDAC(int dacId) {
201	UserRole chairpersonRole = UserRoles.Chairperson();	1✔
202	chairpersonRole.setDacId(dacId);	1✔
203	this.roles = List.of(chairpersonRole);	1✔
204	}	1✔
205
206	public void setITDirectorRole() {
207	this.roles = List.of(UserRoles.ITDirector());	1✔
208	}	1✔
209
210	public void setMemberRole() {
211	this.roles = List.of(UserRoles.Member());	1✔
212	}	1✔
213
214	public void setResearcherRole() {
215	this.roles = List.of(UserRoles.Researcher());	1✔
216	}	1✔
217
218	public void setSigningOfficialRole() {
219	this.roles = List.of(UserRoles.SigningOfficial());	1✔
220	}	1✔
221
222	public List<UserProperty> getProperties() {
223	return properties;	1✔
224	}
225
226	public void setProperties(List<UserProperty> properties) {
227	this.properties = properties;	1✔
228	}	1✔
229
230	public Date getCreateDate() {
231	return createDate;	1✔
232	}
233
234	public void setCreateDate(Date createDate) {
235	this.createDate = createDate;	1✔
236	}	1✔
237
238	public Boolean getEmailPreference() {
239	return emailPreference;	1✔
240	}
241
242	public void setEmailPreference(Boolean emailPreference) {
243	this.emailPreference = emailPreference;	1✔
244	}	1✔
245
246	public Integer getInstitutionId() {
247	return institutionId;	1✔
248	}
249
250	public void setInstitutionId(Integer institutionId) {
251	this.institutionId = institutionId;	1✔
252	}	1✔
253
254	public String getEraCommonsId() {
255	return eraCommonsId;	1✔
256	}
257
258	public void setEraCommonsId(String eraCommonsId) {
259	this.eraCommonsId = eraCommonsId;	1✔
260	}	1✔
261
262	public void setInstitution(Institution institution) {
263	this.institution = institution;	1✔
264	}	1✔
265
266	public void setInstitution(User user) {
267	if (Objects.nonNull(user.getInstitution())) {	×
268	this.institution = user.institution;	×
269	}
270	}	×
271
272	public Institution getInstitution() {
273	return institution;	1✔
274	}
275
276	public void setLibraryCards(List<LibraryCard> cards) {
277	this.libraryCards = cards;	1✔
278	}	1✔
279
280	public List<LibraryCard> getLibraryCards() {
281	return this.libraryCards;	1✔
282	}
283
284	public void addRole(UserRole userRole) {
285	if (Objects.isNull(this.getRoles())) {	1✔
286	this.setRoles(new ArrayList<>());	1✔
287	}
288
289	if (!this.getRoles().contains(userRole)) {	1✔
290	this.getRoles().add(userRole);	1✔
291	}
292	}	1✔
293
294	public void addProperty(UserProperty userProp) {
295	if (Objects.isNull(this.getProperties())) {	1✔
296	this.setProperties(new ArrayList<>());	1✔
297	}
298	if (!this.getProperties().contains(userProp)) {	1✔
299	this.getProperties().add(userProp);	1✔
300	}
301	}	1✔
302
303	public void addLibraryCard(LibraryCard card) {
304	if (Objects.isNull(this.getLibraryCards())) {	1✔
305	this.setLibraryCards(new ArrayList<>());	1✔
306	}
307	if (!this.getLibraryCards().contains(card)) {	1✔
308	this.getLibraryCards().add(card);	1✔
309	}
310	}	1✔
311
312	@Override
313	public int hashCode() {
314	return this.getUserId();	1✔
315	}
316
317	@Override
318	public boolean equals(Object obj) {
319	if (this == obj) {	1✔
320	return true;	1✔
321	}
322	if (obj == null) {	1✔
323	return false;	×
324	}
325	if (getClass() != obj.getClass()) {	1✔
326	return false;	×
327	}
328
329	User other = (User) obj;	1✔
330	return new EqualsBuilder().append(getUserId(), other.getUserId()).isEquals();	1✔
331	}
332
333	@Override
334	public String toString() {
NEW 335	return GsonUtil.gsonBuilderWithAdapters().create().toJson(this);	×
336	}
337
338	public boolean hasUserRole(UserRoles role) {
339	if (Objects.isNull(this.getRoles())) {	1✔
340	return false;	1✔
341	} else {
342	return this.getRoles().stream().anyMatch((r) -> r.getRoleId().equals(role.getRoleId()));	1✔
343	}
344	}
345
346	@Transient
347	public List<Integer> getUserRoleIdsFromUser() {
348	if (Objects.isNull(this.getRoles())) {	1✔
349	return List.of();	1✔
350	}
351	return this.getRoles()	1✔
352	.stream()	1✔
353	.map(UserRole::getRoleId)	1✔
354	.collect(Collectors.toList());	1✔
355	}
356
357	@Transient
358	public boolean doesUserHaveAnyRoleInSet(EnumSet<UserRoles> userRoles) {
359	List<Integer> queriedRoleIds = userRoles.stream().map(UserRoles::getRoleId)	1✔
360	.collect(Collectors.toList());	1✔
361	return getUserRoleIdsFromUser().stream().anyMatch(queriedRoleIds::contains);	1✔
362	}
363
364	@Transient
365	public Boolean checkIfUserHasRole(String roleName, Integer dacId) {
366	UserRoles role = UserRoles.getUserRoleFromName(roleName);	1✔
367	List<UserRole> roles = getRoles();	1✔
368	List<UserRole> targetRoles = roles.stream()	1✔
369	.filter((r) -> {	1✔
370	return r.getName().equals(role.getRoleName())	1✔
371	&& r.getRoleId().equals(role.getRoleId())	1✔
372	&& Objects.equals(r.getDacId(), dacId);	1✔
373	})
374	.collect(Collectors.toList());	1✔
375	return !targetRoles.isEmpty();	1✔
376
377	}
378
379	}

DataBiosphere / consent / #5119

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