#5580

Committed 07 Mar 2025 08:35PM UTC coverage: 79.278% (+0.004%) from 79.274%

Build # #5580

Build Type

push

Committed by

Commit Message

DT-1284: Improve dataset query performance (#2464)

Run Details

9 of 10 new or added lines in 4 files covered. (90.0%)

2 existing lines in 2 files now uncovered.

10253 of 12933 relevant lines covered (79.28%)

0.79 hits per line

Source File
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82.29

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

package org.broadinstitute.consent.http.models;

import com.google.gson.JsonArray;
import com.google.gson.JsonPrimitive;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.broadinstitute.consent.http.models.dataset_registration_v1.ConsentGroup.AccessManagement;
import org.broadinstitute.consent.http.models.dataset_registration_v1.builder.DatasetRegistrationSchemaV1Builder;
import org.broadinstitute.consent.http.util.ConsentLogger;
import org.checkerframework.checker.nullness.qual.NonNull;

public class Dataset implements ConsentLogger {

  private Integer datasetId;

  private String objectId;

  private String name;

  // For backwards compatibility with DatasetDTO, this is an alias to the name property.
  private String datasetName;

  private Date createDate;

  private Integer createUserId;

  private Date updateDate;

  private Integer updateUserId;

  private Integer alias;

  private String datasetIdentifier;

  public DataUse dataUse;

  private String translatedDataUse;
  private Integer dacId;

  private Boolean deletable;

  private FileStorageObject nihInstitutionalCertificationFile;

  private Set<DatasetProperty> properties;

  List<String> propertyName;
  private Boolean dacApproval;

  private User createUser;

  private Integer studyId;

  private Study study;

  public Dataset() {
  }

  public Dataset(Integer datasetId, String objectId, String name, Date createDate,
      Integer createUserId, Date updateDate, Integer updateUserId, Integer alias) {
    this.datasetId = datasetId;
    this.objectId = objectId;
    this.name = name;
    this.datasetName = name;
    this.createDate = createDate;
    this.createUserId = createUserId;
    this.updateDate = updateDate;
    this.updateUserId = updateUserId;
    this.alias = alias;
  }

  public Dataset(Integer datasetId, String objectId, String name, Date createDate, Integer alias) {
    this.datasetId = datasetId;
    this.objectId = objectId;
    this.name = name;
    this.datasetName = name;
    this.createDate = createDate;
    this.alias = alias;
  }

  public Dataset(Integer datasetId, String objectId, String name, Date createDate) {
    this.datasetId = datasetId;
    this.objectId = objectId;
    this.name = name;
    this.datasetName = name;
    this.createDate = createDate;
  }

  private static final String PREFIX = "DUOS-";

  public Dataset(String objectId) {
    this.objectId = objectId;
  }

  public Integer getDatasetId() {
    return datasetId;
  }

  public void setDatasetId(Integer datasetId) {
    this.datasetId = datasetId;
  }

  public String getObjectId() {
    return objectId;
  }

  public void setObjectId(String objectId) {
    this.objectId = objectId;
  }

  public String getName() {
    return name;
  }

  public void setName(String name) {
    this.name = name;
  }

  public String getDatasetName() {
    return datasetName;
  }

  public void setDatasetName(String datasetName) {
    this.datasetName = datasetName;
  }

  public Date getCreateDate() {
    return createDate;
  }

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

  public Integer getCreateUserId() {
    return createUserId;
  }

  public void setCreateUserId(Integer createUserId) {
    this.createUserId = createUserId;
  }

  public Date getUpdateDate() {
    return updateDate;
  }

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

  public Integer getUpdateUserId() {
    return updateUserId;
  }

  public void setUpdateUserId(Integer updateUserId) {
    this.updateUserId = updateUserId;
  }

  public Set<DatasetProperty> getProperties() {
    return properties;
  }

  public List<String> getPropertyName() {
    return propertyName;
  }


  public void setProperties(Set<DatasetProperty> properties) {
    this.properties = properties;
  }

  public void addProperty(DatasetProperty property) {
    if (Objects.isNull(this.properties)) {
      this.properties = new HashSet<>();
    }
    this.properties.add(property);
  }

  public Boolean getDacApproval() {
    return dacApproval;
  }

  public void setDacApproval(Boolean dacApproval) {
    this.dacApproval = dacApproval;
  }

  public Integer getAlias() {
    return alias;
  }

  public void setAlias(Integer alias) {
    this.alias = alias;
  }

  public DataUse getDataUse() {
    return dataUse;
  }

  public void setDataUse(DataUse dataUse) {
    this.dataUse = dataUse;
  }

  public void setDatasetIdentifier() {
    this.datasetIdentifier = parseAliasToIdentifier(this.getAlias());
  }

  public String getDatasetIdentifier() {
    if (Objects.isNull(this.getAlias())) {
      return null;
    }

    return parseAliasToIdentifier(this.getAlias());
  }

  public static String parseAliasToIdentifier(Integer alias) {
    return PREFIX + StringUtils.leftPad(alias.toString(), 6, "0");
  }

  public static Integer parseIdentifierToAlias(String identifier) throws IllegalArgumentException {
    try {
      String givenPrefix = identifier.substring(0, PREFIX.length());
      if (!givenPrefix.equals(PREFIX)) {
        throw new IllegalArgumentException("Invalid prefix.");
      }

      String aliasAsString = identifier.substring(PREFIX.length()); // cut off DUOS-
      return Integer.parseInt(aliasAsString); // parse remaining as integer
    } catch (Exception e) {
      throw new IllegalArgumentException(
          "Could not parse identifier (" + identifier + "). Proper format: " + PREFIX + "XXXXXX");
    }
  }

  public Integer getDacId() {
    return dacId;
  }

  public void setDacId(Integer dacId) {
    this.dacId = dacId;
  }

  public String getTranslatedDataUse() {
    return translatedDataUse;
  }

  public void setTranslatedDataUse(String translatedDataUse) {
    this.translatedDataUse = translatedDataUse;
  }

  public Boolean getDeletable() {
    return deletable;
  }

  public void setDeletable(Boolean deletable) {
    this.deletable = deletable;
  }

  /**
   * Checks if the Dataset matches a raw search query. Searches on all dataset properties and some
   * data use properties. Has optional parameter accessManagement which will search datasets on both
   * the raw search query and the access management type.
   *
   * @param query            Raw string query
   * @param accessManagement One of controlled, open, or external
   * @return if the Dataset matched query
   */

  // TODO: investigate whether we can try to coerce getPropertyValue to a boolean instead of comparing strings
  public boolean isDatasetMatch(@NonNull String query, AccessManagement accessManagement) {
    String lowerCaseQuery = query.toLowerCase();
    List<String> queryTerms = List.of(lowerCaseQuery.split("\\s+"));

    List<String> matchTerms = new ArrayList<>();
    matchTerms.add(this.getName());
    matchTerms.add(this.getDatasetIdentifier());

    if (Objects.nonNull(getProperties()) && !getProperties().isEmpty()) {
      Optional<DatasetProperty> accessManagementProp = getProperties()
          .stream()
          .filter((dp) -> Objects.nonNull(dp.getPropertyValue()))
          .filter((dp) -> Objects.equals(dp.getPropertyName(), "Access Management"))
          .findFirst();

      if (accessManagementProp.isEmpty()) {
        if (accessManagement.equals(AccessManagement.OPEN)) {
          return false;
        }
      } else if (!accessManagement.toString()
          .equals(accessManagementProp.get().getPropertyValueAsString())) {
        return false;
      }

      List<String> propVals = getProperties()
          .stream()
          .filter((dp) -> Objects.nonNull(dp.getPropertyValue()))
          .map(DatasetProperty::getPropertyValueAsString)
          .map(String::toLowerCase)
          .toList();
      matchTerms.addAll(propVals);
    }

    if (Objects.nonNull(dataUse)) {
      if (Objects.nonNull(dataUse.getEthicsApprovalRequired())
          && dataUse.getEthicsApprovalRequired()) {
        matchTerms.add("irb");
      }

      if (Objects.nonNull(dataUse.getCollaboratorRequired())
          && dataUse.getCollaboratorRequired()) {
        matchTerms.add("collaborator");
      }

      if (Objects.nonNull(dataUse.getDiseaseRestrictions())) {
        matchTerms.addAll(dataUse.getDiseaseRestrictions());
      }
    }

    return queryTerms
        .stream()
        .filter(Objects::nonNull)
        // all terms must match at least one thing
        .allMatch((q) ->
            matchTerms
                .stream()
                .filter(Objects::nonNull)
                .map(String::toLowerCase)
                .anyMatch(
                    (t) -> t.contains(q))
        );
  }

  public Study getStudy() {
    return study;
  }

  public void setStudy(Study study) {
    this.study = study;
  }

  public Integer getStudyId() {
    return studyId;
  }

  public void setStudyId(Integer studyId) {
    this.studyId = studyId;
  }

  /**
   * Determine if the user is a dataset/study creator
   *
   * @param user User
   * @return User is a creator of the dataset/study
   */
  public boolean isCustodian(User user) {
    if (getStudy() != null && getStudy().getProperties() != null) {
      Optional<StudyProperty> dataCustodians = getStudy()
          .getProperties()
          .stream()
          .filter(p -> p.getKey().equals(DatasetRegistrationSchemaV1Builder.dataCustodianEmail))
          .findFirst();
      if (dataCustodians.isPresent()) {
        JsonArray jsonArray = (JsonArray) dataCustodians.get().getValue();
        return jsonArray.contains(new JsonPrimitive(user.getEmail()));
      } else {
        logWarn(
            "No data custodians found for dataset: %s".formatted(getDatasetIdentifier()));
      }
    } else {
      logWarn(
          "No study properties found for dataset: %s".formatted(getDatasetIdentifier()));
    }
    return false;
  }

  public boolean isCreator(User user) {
    if (Objects.equals(user.getUserId(), getCreateUserId())) {
      return true;
    }
    return getStudy() != null && Objects.equals(user.getUserId(),
        getStudy().getCreateUserId());
  }

  @Override
  public boolean equals(Object o) {
    if (this == o) {
      return true;
    }
    if (o == null || getClass() != o.getClass()) {
      return false;
    }
    Dataset dataset = (Dataset) o;
    return com.google.common.base.Objects.equal(datasetId, dataset.datasetId);
  }

  @Override
  public int hashCode() {
    return com.google.common.base.Objects.hashCode(datasetId);
  }

  public FileStorageObject getNihInstitutionalCertificationFile() {
    return nihInstitutionalCertificationFile;
  }

  public void setNihInstitutionalCertificationFile(
      FileStorageObject nihInstitutionalCertificationFile) {
    this.nihInstitutionalCertificationFile = nihInstitutionalCertificationFile;
  }

  public User getCreateUser() {
    return createUser;
  }

  public void setCreateUser(User createUser) {
    this.createUser = createUser;
  }

}

1	package org.broadinstitute.consent.http.models;
2
3	import com.google.gson.JsonArray;
4	import com.google.gson.JsonPrimitive;
5	import java.util.ArrayList;
6	import java.util.Date;
7	import java.util.HashSet;
8	import java.util.List;
9	import java.util.Objects;
10	import java.util.Optional;
11	import java.util.Set;
12	import org.apache.commons.lang3.StringUtils;
13	import org.broadinstitute.consent.http.models.dataset_registration_v1.ConsentGroup.AccessManagement;
14	import org.broadinstitute.consent.http.models.dataset_registration_v1.builder.DatasetRegistrationSchemaV1Builder;
15	import org.broadinstitute.consent.http.util.ConsentLogger;
16	import org.checkerframework.checker.nullness.qual.NonNull;
17
18	public class Dataset implements ConsentLogger {
19
20	private Integer datasetId;
21
22	private String objectId;
23
24	private String name;
25
26	// For backwards compatibility with DatasetDTO, this is an alias to the name property.
27	private String datasetName;
28
29	private Date createDate;
30
31	private Integer createUserId;
32
33	private Date updateDate;
34
35	private Integer updateUserId;
36
37	private Integer alias;
38
39	private String datasetIdentifier;
40
41	public DataUse dataUse;
42
43	private String translatedDataUse;
44	private Integer dacId;
45
46	private Boolean deletable;
47
48	private FileStorageObject nihInstitutionalCertificationFile;
49
50	private Set<DatasetProperty> properties;
51
52	List<String> propertyName;
53	private Boolean dacApproval;
54
55	private User createUser;
56
57	private Integer studyId;
58
59	private Study study;
60
61	public Dataset() {	1✔
62	}	1✔
63
64	public Dataset(Integer datasetId, String objectId, String name, Date createDate,
65	Integer createUserId, Date updateDate, Integer updateUserId, Integer alias) {	×
66	this.datasetId = datasetId;	×
67	this.objectId = objectId;	×
68	this.name = name;	×
69	this.datasetName = name;	×
70	this.createDate = createDate;	×
71	this.createUserId = createUserId;	×
72	this.updateDate = updateDate;	×
73	this.updateUserId = updateUserId;	×
74	this.alias = alias;	×
75	}	×
76
77	public Dataset(Integer datasetId, String objectId, String name, Date createDate, Integer alias) {	×
78	this.datasetId = datasetId;	×
79	this.objectId = objectId;	×
80	this.name = name;	×
81	this.datasetName = name;	×
82	this.createDate = createDate;	×
83	this.alias = alias;	×
84	}	×
85
86	public Dataset(Integer datasetId, String objectId, String name, Date createDate) {	1✔
87	this.datasetId = datasetId;	1✔
88	this.objectId = objectId;	1✔
89	this.name = name;	1✔
90	this.datasetName = name;	1✔
91	this.createDate = createDate;	1✔
92	}	1✔
93
94	private static final String PREFIX = "DUOS-";
95
96	public Dataset(String objectId) {	×
97	this.objectId = objectId;	×
98	}	×
99
100	public Integer getDatasetId() {
101	return datasetId;	1✔
102	}
103
104	public void setDatasetId(Integer datasetId) {
105	this.datasetId = datasetId;	1✔
106	}	1✔
107
108	public String getObjectId() {
109	return objectId;	×
110	}
111
112	public void setObjectId(String objectId) {
113	this.objectId = objectId;	1✔
114	}	1✔
115
116	public String getName() {
117	return name;	1✔
118	}
119
120	public void setName(String name) {
121	this.name = name;	1✔
122	}	1✔
123
124	public String getDatasetName() {
125	return datasetName;	1✔
126	}
127
128	public void setDatasetName(String datasetName) {
129	this.datasetName = datasetName;	1✔
130	}	1✔
131
132	public Date getCreateDate() {
133	return createDate;	×
134	}
135
136	public void setCreateDate(Date createDate) {
137	this.createDate = createDate;	1✔
138	}	1✔
139
140	public Integer getCreateUserId() {
141	return createUserId;	1✔
142	}
143
144	public void setCreateUserId(Integer createUserId) {
145	this.createUserId = createUserId;	1✔
146	}	1✔
147
148	public Date getUpdateDate() {
149	return updateDate;	1✔
150	}
151
152	public void setUpdateDate(Date updateDate) {
153	this.updateDate = updateDate;	1✔
154	}	1✔
155
156	public Integer getUpdateUserId() {
157	return updateUserId;	1✔
158	}
159
160	public void setUpdateUserId(Integer updateUserId) {
161	this.updateUserId = updateUserId;	1✔
162	}	1✔
163
164	public Set<DatasetProperty> getProperties() {
165	return properties;	1✔
166	}
167
168	public List<String> getPropertyName() {
169	return propertyName;	×
170	}
171
172
173	public void setProperties(Set<DatasetProperty> properties) {
174	this.properties = properties;	1✔
175	}	1✔
176
177	public void addProperty(DatasetProperty property) {
178	if (Objects.isNull(this.properties)) {	1✔
179	this.properties = new HashSet<>();	1✔
180	}
181	this.properties.add(property);	1✔
182	}	1✔
183
184	public Boolean getDacApproval() {
185	return dacApproval;	1✔
186	}
187
188	public void setDacApproval(Boolean dacApproval) {
189	this.dacApproval = dacApproval;	1✔
190	}	1✔
191
192	public Integer getAlias() {
193	return alias;	1✔
194	}
195
196	public void setAlias(Integer alias) {
197	this.alias = alias;	1✔
198	}	1✔
199
200	public DataUse getDataUse() {
201	return dataUse;	1✔
202	}
203
204	public void setDataUse(DataUse dataUse) {
205	this.dataUse = dataUse;	1✔
206	}	1✔
207
208	public void setDatasetIdentifier() {
209	this.datasetIdentifier = parseAliasToIdentifier(this.getAlias());	1✔
210	}	1✔
211
212	public String getDatasetIdentifier() {
213	if (Objects.isNull(this.getAlias())) {	1✔
214	return null;	1✔
215	}
216
217	return parseAliasToIdentifier(this.getAlias());	1✔
218	}
219
220	public static String parseAliasToIdentifier(Integer alias) {
221	return PREFIX + StringUtils.leftPad(alias.toString(), 6, "0");	1✔
222	}
223
224	public static Integer parseIdentifierToAlias(String identifier) throws IllegalArgumentException {
225	try {
226	String givenPrefix = identifier.substring(0, PREFIX.length());	1✔
227	if (!givenPrefix.equals(PREFIX)) {	1✔
228	throw new IllegalArgumentException("Invalid prefix.");	1✔
229	}
230
231	String aliasAsString = identifier.substring(PREFIX.length()); // cut off DUOS-	1✔
232	return Integer.parseInt(aliasAsString); // parse remaining as integer	1✔
233	} catch (Exception e) {	1✔
234	throw new IllegalArgumentException(	1✔
235	"Could not parse identifier (" + identifier + "). Proper format: " + PREFIX + "XXXXXX");
236	}
237	}
238
239	public Integer getDacId() {
240	return dacId;	1✔
241	}
242
243	public void setDacId(Integer dacId) {
244	this.dacId = dacId;	1✔
245	}	1✔
246
247	public String getTranslatedDataUse() {
248	return translatedDataUse;	1✔
249	}
250
251	public void setTranslatedDataUse(String translatedDataUse) {
252	this.translatedDataUse = translatedDataUse;	1✔
253	}	1✔
254
255	public Boolean getDeletable() {
256	return deletable;	1✔
257	}
258
259	public void setDeletable(Boolean deletable) {
260	this.deletable = deletable;	1✔
261	}	1✔
262
263	/**
264	* Checks if the Dataset matches a raw search query. Searches on all dataset properties and some
265	* data use properties. Has optional parameter accessManagement which will search datasets on both
266	* the raw search query and the access management type.
267	*
268	* @param query Raw string query
269	* @param accessManagement One of controlled, open, or external
270	* @return if the Dataset matched query
271	*/
272
273	// TODO: investigate whether we can try to coerce getPropertyValue to a boolean instead of comparing strings
274	public boolean isDatasetMatch(@NonNull String query, AccessManagement accessManagement) {
275	String lowerCaseQuery = query.toLowerCase();	1✔
276	List<String> queryTerms = List.of(lowerCaseQuery.split("\\s+"));	1✔
277
278	List<String> matchTerms = new ArrayList<>();	1✔
279	matchTerms.add(this.getName());	1✔
280	matchTerms.add(this.getDatasetIdentifier());	1✔
281
282	if (Objects.nonNull(getProperties()) && !getProperties().isEmpty()) {	1✔
283	Optional<DatasetProperty> accessManagementProp = getProperties()	1✔
284	.stream()	1✔
285	.filter((dp) -> Objects.nonNull(dp.getPropertyValue()))	1✔
286	.filter((dp) -> Objects.equals(dp.getPropertyName(), "Access Management"))	1✔
287	.findFirst();	1✔
288
289	if (accessManagementProp.isEmpty()) {	1✔
290	if (accessManagement.equals(AccessManagement.OPEN)) {	1✔
291	return false;	×
292	}
293	} else if (!accessManagement.toString()	1✔
294	.equals(accessManagementProp.get().getPropertyValueAsString())) {	1✔
295	return false;	1✔
296	}
297
298	List<String> propVals = getProperties()	1✔
299	.stream()	1✔
300	.filter((dp) -> Objects.nonNull(dp.getPropertyValue()))	1✔
301	.map(DatasetProperty::getPropertyValueAsString)	1✔
302	.map(String::toLowerCase)	1✔
303	.toList();	1✔
304	matchTerms.addAll(propVals);	1✔
305	}
306
307	if (Objects.nonNull(dataUse)) {	1✔
308	if (Objects.nonNull(dataUse.getEthicsApprovalRequired())	1✔
309	&& dataUse.getEthicsApprovalRequired()) {	1✔
310	matchTerms.add("irb");	1✔
311	}
312
313	if (Objects.nonNull(dataUse.getCollaboratorRequired())	1✔
314	&& dataUse.getCollaboratorRequired()) {	1✔
315	matchTerms.add("collaborator");	1✔
316	}
317
318	if (Objects.nonNull(dataUse.getDiseaseRestrictions())) {	1✔
319	matchTerms.addAll(dataUse.getDiseaseRestrictions());	1✔
320	}
321	}
322
323	return queryTerms	1✔
324	.stream()	1✔
325	.filter(Objects::nonNull)	1✔
326	// all terms must match at least one thing
327	.allMatch((q) ->	1✔
328	matchTerms	1✔
329	.stream()	1✔
330	.filter(Objects::nonNull)	1✔
331	.map(String::toLowerCase)	1✔
332	.anyMatch(	1✔
333	(t) -> t.contains(q))	1✔
334	);
335	}
336
337	public Study getStudy() {
338	return study;	1✔
339	}
340
341	public void setStudy(Study study) {
342	this.study = study;	1✔
343	}	1✔
344
345	public Integer getStudyId() {
NEW 346	return studyId;	×
347	}
348
349	public void setStudyId(Integer studyId) {
350	this.studyId = studyId;	1✔
351	}	1✔
352
353	/**
354	* Determine if the user is a dataset/study creator
355	*
356	* @param user User
357	* @return User is a creator of the dataset/study
358	*/
359	public boolean isCustodian(User user) {
360	if (getStudy() != null && getStudy().getProperties() != null) {	1✔
361	Optional<StudyProperty> dataCustodians = getStudy()	1✔
362	.getProperties()	1✔
363	.stream()	1✔
364	.filter(p -> p.getKey().equals(DatasetRegistrationSchemaV1Builder.dataCustodianEmail))	1✔
365	.findFirst();	1✔
366	if (dataCustodians.isPresent()) {	1✔
367	JsonArray jsonArray = (JsonArray) dataCustodians.get().getValue();	1✔
368	return jsonArray.contains(new JsonPrimitive(user.getEmail()));	1✔
369	} else {
370	logWarn(	×
371	"No data custodians found for dataset: %s".formatted(getDatasetIdentifier()));	×
372	}
373	} else {	×
374	logWarn(	1✔
375	"No study properties found for dataset: %s".formatted(getDatasetIdentifier()));	1✔
376	}
377	return false;	1✔
378	}
379
380	public boolean isCreator(User user) {
381	if (Objects.equals(user.getUserId(), getCreateUserId())) {	1✔
382	return true;	1✔
383	}
384	return getStudy() != null && Objects.equals(user.getUserId(),	1✔
385	getStudy().getCreateUserId());	1✔
386	}
387
388	@Override
389	public boolean equals(Object o) {
390	if (this == o) {	1✔
391	return true;	1✔
392	}
393	if (o == null \|\| getClass() != o.getClass()) {	1✔
394	return false;	×
395	}
396	Dataset dataset = (Dataset) o;	1✔
397	return com.google.common.base.Objects.equal(datasetId, dataset.datasetId);	1✔
398	}
399
400	@Override
401	public int hashCode() {
402	return com.google.common.base.Objects.hashCode(datasetId);	1✔
403	}
404
405	public FileStorageObject getNihInstitutionalCertificationFile() {
406	return nihInstitutionalCertificationFile;	1✔
407	}
408
409	public void setNihInstitutionalCertificationFile(
410	FileStorageObject nihInstitutionalCertificationFile) {
411	this.nihInstitutionalCertificationFile = nihInstitutionalCertificationFile;	1✔
412	}	1✔
413
414	public User getCreateUser() {
415	return createUser;	1✔
416	}
417
418	public void setCreateUser(User createUser) {
419	this.createUser = createUser;	1✔
420	}	1✔
421
422	}

DataBiosphere / consent / #5580

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