#5724

Committed 23 Apr 2025 07:05PM UTC coverage: 79.021% (+0.04%) from 78.981%

Build # #5724

Build Type

push

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Commit Message

[DT-1520] DAR Expiration. (#2491)

Run Details

25 of 27 new or added lines in 4 files covered. (92.59%)

1 existing line in 1 file now uncovered.

10234 of 12951 relevant lines covered (79.02%)

0.79 hits per line

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92.81

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

package org.broadinstitute.consent.http.models;

import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonInclude.Include;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.google.common.base.CaseFormat;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive;
import com.google.gson.JsonSerializer;
import com.google.gson.reflect.TypeToken;
import java.lang.reflect.Type;
import java.sql.Timestamp;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.concurrent.TimeUnit;
import java.util.stream.Collectors;
import java.util.stream.Stream;

@JsonInclude(Include.NON_NULL)
public class DataAccessRequest {

  public static final long EXPIRATION_DURATION_MILLIS = TimeUnit.DAYS.toMillis(365);

  @JsonProperty
  public Integer id;

  @JsonProperty
  public String referenceId;

  @JsonProperty
  public Integer collectionId;

  @JsonProperty
  public String parentId;

  @JsonProperty
  public DataAccessRequestData data;

  @JsonProperty
  public Boolean draft = true;

  @JsonProperty
  public Boolean expired = false;

  @JsonProperty
  public Timestamp expiresAt;

  @JsonProperty
  public Integer userId;

  @JsonProperty
  public Timestamp createDate;

  /*
   * Legacy property on DARs. Used to display the sort order for a DAR. In practice, this also
   * functions as the Update Date. See also https://broadinstitute.atlassian.net/browse/DUOS-728
   */
  @JsonProperty
  public Timestamp sortDate;

  @JsonProperty
  public Timestamp submissionDate;

  @JsonProperty
  public Timestamp updateDate;
  @JsonProperty
  public List<Integer> datasetIds;
  @JsonProperty
  private Map<Integer, Election> elections;

  public DataAccessRequest() {
    this.elections = new HashMap<>();
  }

  public static boolean isCanceled(DataAccessRequest dar) {
    return
        Objects.nonNull(dar) &&
            Objects.nonNull(dar.getData()) &&
            Objects.nonNull(dar.getData().getStatus()) &&
            dar.getData().getStatus().equalsIgnoreCase("canceled");
  }

  public Integer getId() {
    return id;
  }

  public void setId(Integer id) {
    this.id = id;
  }

  public String getReferenceId() {
    return referenceId;
  }

  public void setReferenceId(String referenceId) {
    this.referenceId = referenceId;
  }

  public Integer getCollectionId() {
    return collectionId;
  }

  public void setCollectionId(Integer collectionId) {
    this.collectionId = collectionId;
  }

  public String getParentId() {
    return parentId;
  }

  public void setParentId(String parentId) {
    this.parentId = parentId;
  }

  public DataAccessRequestData getData() {
    return data;
  }

  public void setData(DataAccessRequestData data) {
    this.data = data;
  }

  public Boolean getDraft() {
    return draft;
  }

  public boolean getExpired() {
    return expired;
  }

  public Timestamp getExpiresAt() {
    return expiresAt;
  }

  public Integer getUserId() {
    return userId;
  }

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

  public Date getCreateDate() {
    return createDate;
  }

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

  public Date getSortDate() {
    return sortDate;
  }

  public void setSortDate(Timestamp sortDate) {
    this.sortDate = sortDate;
  }

  public Timestamp getSubmissionDate() {
    return submissionDate;
  }

  public void setSubmissionDate(Timestamp submissionDate) {
    this.submissionDate = submissionDate;
    draft = submissionDate == null;
    expired = submissionDate != null
        && submissionDate.before(
        new Timestamp(System.currentTimeMillis() - EXPIRATION_DURATION_MILLIS));
    expiresAt = (submissionDate != null) ? new Timestamp(
        submissionDate.getTime() + EXPIRATION_DURATION_MILLIS) : null;
  }

  public Timestamp getUpdateDate() {
    return updateDate;
  }

  public void setUpdateDate(Timestamp updateDate) {
    this.updateDate = updateDate;
  }

  public Map<Integer, Election> getElections() {
    return elections;
  }

  public void setElections(Map<Integer, Election> elections) {
    this.elections = elections;
  }

  public void addElection(Election election) {
    if (Objects.isNull(elections)) {
      this.setElections(new HashMap<>());
    }
    if (Objects.nonNull(election)) {
      Integer electionId = election.getElectionId();
      Election savedRecord = elections.get(electionId);
      if (Objects.isNull(savedRecord)) {
        elections.put(electionId, election);
      }
    }
  }

  public List<Integer> getDatasetIds() {
    if (Objects.isNull(datasetIds)) {
      return List.of();
    }
    return datasetIds;
  }

  public void setDatasetIds(List<Integer> datasetIds) {
    this.datasetIds = datasetIds;
  }

  public void addDatasetId(Integer id) {
    if (Objects.isNull(datasetIds)) {
      datasetIds = new ArrayList<>();
    }
    if (!datasetIds.contains(id)) {
      datasetIds.add(id);
    }
  }

  public void addDatasetIds(List<Integer> ids) {
    if (Objects.isNull(datasetIds)) {
      datasetIds = new ArrayList<>();
    }
    if (Objects.nonNull(ids) && !ids.isEmpty()) {
      datasetIds = Stream.of(datasetIds, ids)
          .flatMap(List::stream)
          .distinct()
          .collect(Collectors.toList());
    }
  }

  /**
   * Merges the DAR and the DAR Data into a single Map Ignores a series of deprecated keys Null
   * values are ignored by default
   *
   * @return Map<String, Object> Dar in simple map format
   */
  public Map<String, Object> convertToSimplifiedDar() {
    // Serialize dates/timestamps as longs, but do not deserialize longs into dates so we can
    // output long values in the final result.
    Gson gson = new GsonBuilder()
        .registerTypeAdapter(Date.class,
            (JsonSerializer<Date>) (date, type, jsonSerializationContext) -> new JsonPrimitive(
                date.getTime()))
        .registerTypeAdapter(Timestamp.class,
            (JsonSerializer<Timestamp>) (timestamp, type, jsonSerializationContext) -> new JsonPrimitive(
                timestamp.getTime()))
        .create();
    DataAccessRequestData dataCopy = this.getData();
    this.setData(null);

    String serializedDar = gson.toJson(shallowCopy(this));
    JsonObject dar = gson.fromJson(serializedDar, JsonObject.class);

    String serializedDarData = gson.toJson(dataCopy);
    JsonObject darData = gson.fromJson(serializedDarData, JsonObject.class);

    DataAccessRequestData.DEPRECATED_PROPS.forEach(darData::remove);
    for (String dataKey : darData.keySet()) {
      String camelCasedDataKey =
          dataKey.contains("_")
              ? CaseFormat.LOWER_UNDERSCORE.to(CaseFormat.LOWER_CAMEL, dataKey)
              : dataKey;
      if (!dar.has(camelCasedDataKey)) {
        dar.add(camelCasedDataKey, darData.get(dataKey));
      }
    }
    Type darMapType = new TypeToken<Map<String, Object>>() {
    }.getType();
    return gson.fromJson(dar.toString(), darMapType);
  }

  public boolean requiresManualReview() {
    return
        Objects.nonNull(this.getData()) && (
            (Objects.nonNull(this.getData().getPoa()) && this.getData().getPoa()) ||
                (Objects.nonNull(this.getData().getPopulation()) && this.getData().getPopulation())
                ||
                (Objects.nonNull(this.getData().getOther()) && this.getData().getOther()) ||
                (Objects.nonNull(this.getData().getOtherText()) && !this.getData().getOtherText()
                    .isBlank()) ||
                (Objects.nonNull(this.getData().getIllegalBehavior()) && this.getData()
                    .getIllegalBehavior()) ||
                (Objects.nonNull(this.getData().getAddiction()) && this.getData().getAddiction()) ||
                (Objects.nonNull(this.getData().getSexualDiseases()) && this.getData()
                    .getSexualDiseases()) ||
                (Objects.nonNull(this.getData().getStigmatizedDiseases()) && this.getData()
                    .getStigmatizedDiseases()) ||
                (Objects.nonNull(this.getData().getVulnerablePopulation()) && this.getData()
                    .getVulnerablePopulation()) ||
                (Objects.nonNull(this.getData().getPopulationMigration()) && this.getData()
                    .getPopulationMigration()) ||
                (Objects.nonNull(this.getData().getPsychiatricTraits()) && this.getData()
                    .getPsychiatricTraits()) ||
                (Objects.nonNull(this.getData().getNotHealth()) && this.getData().getNotHealth())
        );
  }

  /**
   * Make a shallow copy of the dar. This is mostly a workaround for problems serializing dates when
   * calling Gson.toJson on `this`
   *
   * @param dar DataAccessRequest
   * @return Shallow copy of DataAccessRequest
   */
  private Map<String, Object> shallowCopy(DataAccessRequest dar) {
    Map<String, Object> copy = new HashMap<>();
    if (Objects.nonNull(dar.getCreateDate())) {
      copy.put("createDate", dar.getCreateDate().getTime());
    }
    if (Objects.nonNull(dar.getDraft())) {
      copy.put("draft", dar.getDraft());
    }
    copy.put("expired", dar.getExpired());
    copy.put("expiredAt", dar.getExpiresAt());
    if (Objects.nonNull(dar.getId())) {
      copy.put("id", dar.getId());
    }
    if (Objects.nonNull(dar.getReferenceId())) {
      copy.put("referenceId", dar.getReferenceId());
    }
    if (Objects.nonNull(dar.getSortDate())) {
      copy.put("sortDate", dar.getSortDate().getTime());
    }
    if (Objects.nonNull(dar.getSubmissionDate())) {
      copy.put("submissionDate", dar.getSubmissionDate().getTime());
    }
    if (Objects.nonNull(dar.getUpdateDate())) {
      copy.put("updateDate", dar.getUpdateDate().getTime());
    }
    if (Objects.nonNull(dar.getUserId())) {
      copy.put("userId", dar.getUserId());
    }
    if (Objects.nonNull(dar.getCollectionId())) {
      copy.put("collectionId", dar.getCollectionId());
    }
    if (Objects.nonNull(dar.getDatasetIds())) {
      copy.put("datasetIds", dar.getDatasetIds());
    }
    if (Objects.nonNull(dar.getParentId())) {
      copy.put("parentId", dar.getParentId());
    }
    return copy;
  }
}

1	package org.broadinstitute.consent.http.models;
2
3	import com.fasterxml.jackson.annotation.JsonInclude;
4	import com.fasterxml.jackson.annotation.JsonInclude.Include;
5	import com.fasterxml.jackson.annotation.JsonProperty;
6	import com.google.common.base.CaseFormat;
7	import com.google.gson.Gson;
8	import com.google.gson.GsonBuilder;
9	import com.google.gson.JsonObject;
10	import com.google.gson.JsonPrimitive;
11	import com.google.gson.JsonSerializer;
12	import com.google.gson.reflect.TypeToken;
13	import java.lang.reflect.Type;
14	import java.sql.Timestamp;
15	import java.util.ArrayList;
16	import java.util.Date;
17	import java.util.HashMap;
18	import java.util.List;
19	import java.util.Map;
20	import java.util.Objects;
21	import java.util.concurrent.TimeUnit;
22	import java.util.stream.Collectors;
23	import java.util.stream.Stream;
24
25	@JsonInclude(Include.NON_NULL)
26	public class DataAccessRequest {
27
28	public static final long EXPIRATION_DURATION_MILLIS = TimeUnit.DAYS.toMillis(365);	1✔
29
30	@JsonProperty
31	public Integer id;
32
33	@JsonProperty
34	public String referenceId;
35
36	@JsonProperty
37	public Integer collectionId;
38
39	@JsonProperty
40	public String parentId;
41
42	@JsonProperty
43	public DataAccessRequestData data;
44
45	@JsonProperty	1✔
46	public Boolean draft = true;	1✔
47
48	@JsonProperty	1✔
49	public Boolean expired = false;	1✔
50
51	@JsonProperty
52	public Timestamp expiresAt;
53
54	@JsonProperty
55	public Integer userId;
56
57	@JsonProperty
58	public Timestamp createDate;
59
60	/*
61	* Legacy property on DARs. Used to display the sort order for a DAR. In practice, this also
62	* functions as the Update Date. See also https://broadinstitute.atlassian.net/browse/DUOS-728
63	*/
64	@JsonProperty
65	public Timestamp sortDate;
66
67	@JsonProperty
68	public Timestamp submissionDate;
69
70	@JsonProperty
71	public Timestamp updateDate;
72	@JsonProperty
73	public List<Integer> datasetIds;
74	@JsonProperty
75	private Map<Integer, Election> elections;
76
77	public DataAccessRequest() {	1✔
78	this.elections = new HashMap<>();	1✔
79	}	1✔
80
81	public static boolean isCanceled(DataAccessRequest dar) {
82	return	1✔
83	Objects.nonNull(dar) &&	1✔
84	Objects.nonNull(dar.getData()) &&	1✔
85	Objects.nonNull(dar.getData().getStatus()) &&	1✔
86	dar.getData().getStatus().equalsIgnoreCase("canceled");	1✔
87	}
88
89	public Integer getId() {
90	return id;	1✔
91	}
92
93	public void setId(Integer id) {
94	this.id = id;	1✔
95	}	1✔
96
97	public String getReferenceId() {
98	return referenceId;	1✔
99	}
100
101	public void setReferenceId(String referenceId) {
102	this.referenceId = referenceId;	1✔
103	}	1✔
104
105	public Integer getCollectionId() {
106	return collectionId;	1✔
107	}
108
109	public void setCollectionId(Integer collectionId) {
110	this.collectionId = collectionId;	1✔
111	}	1✔
112
113	public String getParentId() {
114	return parentId;	1✔
115	}
116
117	public void setParentId(String parentId) {
118	this.parentId = parentId;	1✔
119	}	1✔
120
121	public DataAccessRequestData getData() {
122	return data;	1✔
123	}
124
125	public void setData(DataAccessRequestData data) {
126	this.data = data;	1✔
127	}	1✔
128
129	public Boolean getDraft() {
130	return draft;	1✔
131	}
132
133	public boolean getExpired() {
134	return expired;	1✔
135	}
136
137	public Timestamp getExpiresAt() {
138	return expiresAt;	1✔
139	}
140
141	public Integer getUserId() {
142	return userId;	1✔
143	}
144
145	public void setUserId(Integer userId) {
146	this.userId = userId;	1✔
147	}	1✔
148
149	public Date getCreateDate() {
150	return createDate;	1✔
151	}
152
153	public void setCreateDate(Timestamp createDate) {
154	this.createDate = createDate;	1✔
155	}	1✔
156
157	public Date getSortDate() {
158	return sortDate;	1✔
159	}
160
161	public void setSortDate(Timestamp sortDate) {
162	this.sortDate = sortDate;	1✔
163	}	1✔
164
165	public Timestamp getSubmissionDate() {
166	return submissionDate;	1✔
167	}
168
169	public void setSubmissionDate(Timestamp submissionDate) {
170	this.submissionDate = submissionDate;	1✔
171	draft = submissionDate == null;	1✔
172	expired = submissionDate != null	1✔
173	&& submissionDate.before(	1✔
174	new Timestamp(System.currentTimeMillis() - EXPIRATION_DURATION_MILLIS));	1✔
175	expiresAt = (submissionDate != null) ? new Timestamp(	1✔
176	submissionDate.getTime() + EXPIRATION_DURATION_MILLIS) : null;	1✔
177	}	1✔
178
179	public Timestamp getUpdateDate() {
180	return updateDate;	1✔
181	}
182
183	public void setUpdateDate(Timestamp updateDate) {
184	this.updateDate = updateDate;	1✔
185	}	1✔
186
187	public Map<Integer, Election> getElections() {
188	return elections;	1✔
189	}
190
191	public void setElections(Map<Integer, Election> elections) {
NEW 192	this.elections = elections;	×
NEW 193	}	×
194
195	public void addElection(Election election) {
196	if (Objects.isNull(elections)) {	1✔
197	this.setElections(new HashMap<>());	×
198	}
199	if (Objects.nonNull(election)) {	1✔
200	Integer electionId = election.getElectionId();	1✔
201	Election savedRecord = elections.get(electionId);	1✔
202	if (Objects.isNull(savedRecord)) {	1✔
203	elections.put(electionId, election);	1✔
204	}
205	}
206	}	1✔
207
208	public List<Integer> getDatasetIds() {
209	if (Objects.isNull(datasetIds)) {	1✔
210	return List.of();	1✔
211	}
212	return datasetIds;	1✔
213	}
214
215	public void setDatasetIds(List<Integer> datasetIds) {
216	this.datasetIds = datasetIds;	1✔
217	}	1✔
218
219	public void addDatasetId(Integer id) {
220	if (Objects.isNull(datasetIds)) {	1✔
221	datasetIds = new ArrayList<>();	1✔
222	}
223	if (!datasetIds.contains(id)) {	1✔
224	datasetIds.add(id);	1✔
225	}
226	}	1✔
227
228	public void addDatasetIds(List<Integer> ids) {
229	if (Objects.isNull(datasetIds)) {	1✔
230	datasetIds = new ArrayList<>();	1✔
231	}
232	if (Objects.nonNull(ids) && !ids.isEmpty()) {	1✔
233	datasetIds = Stream.of(datasetIds, ids)	1✔
234	.flatMap(List::stream)	1✔
235	.distinct()	1✔
236	.collect(Collectors.toList());	1✔
237	}
238	}	1✔
239
240	/**
241	* Merges the DAR and the DAR Data into a single Map Ignores a series of deprecated keys Null
242	* values are ignored by default
243	*
244	* @return Map<String, Object> Dar in simple map format
245	*/
246	public Map<String, Object> convertToSimplifiedDar() {
247	// Serialize dates/timestamps as longs, but do not deserialize longs into dates so we can
248	// output long values in the final result.
249	Gson gson = new GsonBuilder()	1✔
250	.registerTypeAdapter(Date.class,	1✔
251	(JsonSerializer<Date>) (date, type, jsonSerializationContext) -> new JsonPrimitive(	×
252	date.getTime()))	×
253	.registerTypeAdapter(Timestamp.class,	1✔
254	(JsonSerializer<Timestamp>) (timestamp, type, jsonSerializationContext) -> new JsonPrimitive(	×
255	timestamp.getTime()))	×
256	.create();	1✔
257	DataAccessRequestData dataCopy = this.getData();	1✔
258	this.setData(null);	1✔
259
260	String serializedDar = gson.toJson(shallowCopy(this));	1✔
261	JsonObject dar = gson.fromJson(serializedDar, JsonObject.class);	1✔
262
263	String serializedDarData = gson.toJson(dataCopy);	1✔
264	JsonObject darData = gson.fromJson(serializedDarData, JsonObject.class);	1✔
265
266	DataAccessRequestData.DEPRECATED_PROPS.forEach(darData::remove);	1✔
267	for (String dataKey : darData.keySet()) {	1✔
268	String camelCasedDataKey =
269	dataKey.contains("_")	1✔
270	? CaseFormat.LOWER_UNDERSCORE.to(CaseFormat.LOWER_CAMEL, dataKey)	×
271	: dataKey;	1✔
272	if (!dar.has(camelCasedDataKey)) {	1✔
273	dar.add(camelCasedDataKey, darData.get(dataKey));	1✔
274	}
275	}	1✔
276	Type darMapType = new TypeToken<Map<String, Object>>() {	1✔
277	}.getType();	1✔
278	return gson.fromJson(dar.toString(), darMapType);	1✔
279	}
280
281	public boolean requiresManualReview() {
282	return	1✔
283	Objects.nonNull(this.getData()) && (	1✔
284	(Objects.nonNull(this.getData().getPoa()) && this.getData().getPoa()) \|\|	1✔
285	(Objects.nonNull(this.getData().getPopulation()) && this.getData().getPopulation())	1✔
286	\|\|
287	(Objects.nonNull(this.getData().getOther()) && this.getData().getOther()) \|\|	1✔
288	(Objects.nonNull(this.getData().getOtherText()) && !this.getData().getOtherText()	1✔
289	.isBlank()) \|\|	1✔
290	(Objects.nonNull(this.getData().getIllegalBehavior()) && this.getData()	1✔
291	.getIllegalBehavior()) \|\|	1✔
292	(Objects.nonNull(this.getData().getAddiction()) && this.getData().getAddiction()) \|\|	1✔
293	(Objects.nonNull(this.getData().getSexualDiseases()) && this.getData()	1✔
294	.getSexualDiseases()) \|\|	1✔
295	(Objects.nonNull(this.getData().getStigmatizedDiseases()) && this.getData()	1✔
296	.getStigmatizedDiseases()) \|\|	1✔
297	(Objects.nonNull(this.getData().getVulnerablePopulation()) && this.getData()	1✔
298	.getVulnerablePopulation()) \|\|	1✔
299	(Objects.nonNull(this.getData().getPopulationMigration()) && this.getData()	1✔
300	.getPopulationMigration()) \|\|	1✔
301	(Objects.nonNull(this.getData().getPsychiatricTraits()) && this.getData()	1✔
302	.getPsychiatricTraits()) \|\|	1✔
303	(Objects.nonNull(this.getData().getNotHealth()) && this.getData().getNotHealth())	1✔
304	);
305	}
306
307	/**
308	* Make a shallow copy of the dar. This is mostly a workaround for problems serializing dates when
309	* calling Gson.toJson on `this`
310	*
311	* @param dar DataAccessRequest
312	* @return Shallow copy of DataAccessRequest
313	*/
314	private Map<String, Object> shallowCopy(DataAccessRequest dar) {
315	Map<String, Object> copy = new HashMap<>();	1✔
316	if (Objects.nonNull(dar.getCreateDate())) {	1✔
317	copy.put("createDate", dar.getCreateDate().getTime());	1✔
318	}
319	if (Objects.nonNull(dar.getDraft())) {	1✔
320	copy.put("draft", dar.getDraft());	1✔
321	}
322	copy.put("expired", dar.getExpired());	1✔
323	copy.put("expiredAt", dar.getExpiresAt());	1✔
324	if (Objects.nonNull(dar.getId())) {	1✔
325	copy.put("id", dar.getId());	×
326	}
327	if (Objects.nonNull(dar.getReferenceId())) {	1✔
328	copy.put("referenceId", dar.getReferenceId());	1✔
329	}
330	if (Objects.nonNull(dar.getSortDate())) {	1✔
331	copy.put("sortDate", dar.getSortDate().getTime());	1✔
332	}
333	if (Objects.nonNull(dar.getSubmissionDate())) {	1✔
334	copy.put("submissionDate", dar.getSubmissionDate().getTime());	×
335	}
336	if (Objects.nonNull(dar.getUpdateDate())) {	1✔
337	copy.put("updateDate", dar.getUpdateDate().getTime());	1✔
338	}
339	if (Objects.nonNull(dar.getUserId())) {	1✔
340	copy.put("userId", dar.getUserId());	1✔
341	}
342	if (Objects.nonNull(dar.getCollectionId())) {	1✔
343	copy.put("collectionId", dar.getCollectionId());	1✔
344	}
345	if (Objects.nonNull(dar.getDatasetIds())) {	1✔
346	copy.put("datasetIds", dar.getDatasetIds());	1✔
347	}
348	if (Objects.nonNull(dar.getParentId())) {	1✔
349	copy.put("parentId", dar.getParentId());	×
350	}
351	return copy;	1✔
352	}
353	}

DataBiosphere / consent / #5724

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