forked from google/android-fhir
-
Notifications
You must be signed in to change notification settings - Fork 0
/
LocalChangeDao.kt
545 lines (502 loc) · 18.1 KB
/
LocalChangeDao.kt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
/*
* Copyright 2023-2024 Google LLC
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http:https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package com.google.android.fhir.db.impl.dao
import androidx.room.Dao
import androidx.room.Insert
import androidx.room.OnConflictStrategy
import androidx.room.Query
import androidx.room.Transaction
import ca.uhn.fhir.parser.IParser
import ca.uhn.fhir.util.FhirTerser
import ca.uhn.fhir.util.ResourceReferenceInfo
import com.fasterxml.jackson.databind.JsonNode
import com.fasterxml.jackson.databind.ObjectMapper
import com.github.fge.jsonpatch.diff.JsonDiff
import com.google.android.fhir.LocalChangeToken
import com.google.android.fhir.db.impl.addUpdatedReferenceToResource
import com.google.android.fhir.db.impl.entities.LocalChangeEntity
import com.google.android.fhir.db.impl.entities.LocalChangeEntity.Type
import com.google.android.fhir.db.impl.entities.LocalChangeResourceReferenceEntity
import com.google.android.fhir.db.impl.entities.ResourceEntity
import com.google.android.fhir.db.impl.replaceJsonValue
import com.google.android.fhir.logicalId
import com.google.android.fhir.versionId
import java.time.Instant
import java.util.Date
import java.util.UUID
import org.hl7.fhir.r4.model.Resource
import org.hl7.fhir.r4.model.ResourceType
import org.json.JSONArray
import timber.log.Timber
/**
* Dao for local changes made to a resource. One row in LocalChangeEntity corresponds to one change
* e.g. an INSERT or UPDATE. The UPDATES (diffs) are stored as RFC 6902 JSON patches.
*/
@Dao
internal abstract class LocalChangeDao {
lateinit var iParser: IParser
lateinit var fhirTerser: FhirTerser
@Insert(onConflict = OnConflictStrategy.REPLACE)
abstract suspend fun addLocalChange(localChangeEntity: LocalChangeEntity): Long
@Query(
"""
UPDATE LocalChangeEntity
SET resourceId = :updatedResourceId
WHERE id = :localChangeId
""",
)
abstract suspend fun updateResourceId(localChangeId: Long, updatedResourceId: String): Int
@Transaction
open suspend fun addInsert(resource: Resource, resourceUuid: UUID, timeOfLocalChange: Instant) {
val resourceId = resource.logicalId
val resourceType = resource.resourceType
val resourceString = iParser.encodeResourceToString(resource)
val localChangeEntity =
LocalChangeEntity(
id = DEFAULT_ID_VALUE,
resourceType = resourceType.name,
resourceId = resourceId,
resourceUuid = resourceUuid,
timestamp = timeOfLocalChange,
type = Type.INSERT,
payload = resourceString,
versionId = resource.versionId,
)
val localChangeReferences =
extractResourceReferences(resource).mapNotNull { resourceReferenceInfo ->
if (resourceReferenceInfo.resourceReference.referenceElement.value != null) {
LocalChangeResourceReferenceEntity(
id = DEFAULT_ID_VALUE,
localChangeId = DEFAULT_ID_VALUE,
resourceReferencePath = resourceReferenceInfo.name,
resourceReferenceValue = resourceReferenceInfo.resourceReference.referenceElement.value,
)
} else {
null
}
}
createLocalChange(localChangeEntity, localChangeReferences)
}
private suspend fun createLocalChange(
localChange: LocalChangeEntity,
localChangeReferences: List<LocalChangeResourceReferenceEntity>,
) {
val localChangeId = addLocalChange(localChange)
if (localChangeReferences.isNotEmpty()) {
insertLocalChangeResourceReferences(
localChangeReferences.map { it.copy(localChangeId = localChangeId) },
)
}
}
suspend fun addUpdate(
oldEntity: ResourceEntity,
updatedResource: Resource,
timeOfLocalChange: Instant,
) {
val resourceId = updatedResource.logicalId
val resourceType = updatedResource.resourceType
if (
!localChangeIsEmpty(resourceId, resourceType) &&
lastChangeType(resourceId, resourceType)!! == Type.DELETE
) {
throw InvalidLocalChangeException(
"Unexpected DELETE when updating $resourceType/$resourceId. UPDATE failed.",
)
}
val oldResource = iParser.parseResource(oldEntity.serializedResource) as Resource
val jsonDiff = diff(iParser, oldResource, updatedResource)
if (jsonDiff.length() == 0) {
Timber.i(
"New resource ${updatedResource.resourceType}/${updatedResource.id} is same as old resource. " +
"Not inserting UPDATE LocalChange.",
)
return
}
val localChangeEntity =
LocalChangeEntity(
id = DEFAULT_ID_VALUE,
resourceType = resourceType.name,
resourceId = resourceId,
resourceUuid = oldEntity.resourceUuid,
timestamp = timeOfLocalChange,
type = Type.UPDATE,
payload = jsonDiff.toString(),
versionId = oldEntity.versionId,
)
val localChangeReferences =
extractReferencesDiff(oldResource, updatedResource).map { resourceReferenceInfo ->
LocalChangeResourceReferenceEntity(
id = DEFAULT_ID_VALUE,
localChangeId = DEFAULT_ID_VALUE,
resourceReferencePath = resourceReferenceInfo.name,
resourceReferenceValue = resourceReferenceInfo.resourceReference.referenceElement.value,
)
}
createLocalChange(localChangeEntity, localChangeReferences)
}
suspend fun addDelete(
resourceId: String,
resourceUuid: UUID,
resourceType: ResourceType,
remoteVersionId: String?,
) {
createLocalChange(
LocalChangeEntity(
id = DEFAULT_ID_VALUE,
resourceType = resourceType.name,
resourceId = resourceId,
resourceUuid = resourceUuid,
timestamp = Date().toInstant(),
type = Type.DELETE,
payload = "",
versionId = remoteVersionId,
),
emptyList(),
)
}
private fun extractResourceReferences(resource: Resource) =
fhirTerser.getAllResourceReferences(resource).toSet()
/**
* Extract the difference in the [ResourceReferenceInfo]s in the two versions of the resource.
*
* Two versions of a resource can vary in two ways in terms of the resources they refer:
* 1) A reference present in oldVersionResource is removed, hence, not present in
* newVersionResource.
* 2) A new reference is added to the oldVersionResource, hence, the reference is present in
* newVersionResource and not in oldVersionResource.
*
* We compute the differences of both the above kinds to return the entire set of differences.
*
* This method is useful to extract differences for UPDATE kind of [LocalChange]
*
* @param oldVersionResource: The older version of the resource
* @param newVersionResource: The new version of the resource
* @return A set of [ResourceReferenceInfo] containing the differences in references between the
* two resource versions.
*/
private fun extractReferencesDiff(
oldVersionResource: Resource,
newVersionResource: Resource,
): Set<ResourceReferenceInfo> {
require(oldVersionResource.resourceType.equals(newVersionResource.resourceType))
val oldVersionResourceReferences = extractResourceReferences(oldVersionResource).toSet()
val newVersionResourceReferences = extractResourceReferences(newVersionResource).toSet()
return oldVersionResourceReferences.minus(newVersionResourceReferences) +
newVersionResourceReferences.minus(oldVersionResourceReferences)
}
private fun Set<ResourceReferenceInfo>.minus(set: Set<ResourceReferenceInfo>) =
filter { ref ->
set.none {
it.name == ref.name &&
it.resourceReference.referenceElement.value ==
ref.resourceReference.referenceElement.value
}
}
.toSet()
@Query(
"""
SELECT type
FROM LocalChangeEntity
WHERE resourceId = :resourceId
AND resourceType = :resourceType
ORDER BY id ASC
LIMIT 1
""",
)
abstract suspend fun lastChangeType(resourceId: String, resourceType: ResourceType): Type?
@Query(
"""
SELECT COUNT(type)
FROM LocalChangeEntity
WHERE resourceId = :resourceId
AND resourceType = :resourceType
LIMIT 1
""",
)
abstract suspend fun countLastChange(resourceId: String, resourceType: ResourceType): Int
private suspend fun localChangeIsEmpty(resourceId: String, resourceType: ResourceType): Boolean =
countLastChange(resourceId, resourceType) == 0
@Query(
"""
SELECT *
FROM LocalChangeEntity
ORDER BY timestamp ASC""",
)
abstract suspend fun getAllLocalChanges(): List<LocalChangeEntity>
@Query(
"""
SELECT *
FROM LocalChangeEntity
WHERE LocalChangeEntity.id IN (:ids)
ORDER BY timestamp ASC""",
)
abstract suspend fun getLocalChanges(ids: List<Long>): List<LocalChangeEntity>
@Query(
"""
SELECT COUNT(*)
FROM LocalChangeEntity
""",
)
abstract suspend fun getLocalChangesCount(): Int
@Query(
"""
DELETE FROM LocalChangeEntity
WHERE LocalChangeEntity.id = (:id)
""",
)
abstract suspend fun discardLocalChanges(id: Long)
@Transaction
open suspend fun discardLocalChanges(token: LocalChangeToken) {
token.ids.forEach { discardLocalChanges(it) }
}
@Query(
"""
DELETE FROM LocalChangeEntity
WHERE resourceId = (:resourceId)
AND resourceType = :resourceType
""",
)
abstract suspend fun discardLocalChanges(resourceId: String, resourceType: ResourceType)
suspend fun discardLocalChanges(resources: List<Resource>) {
resources.forEach { discardLocalChanges(it.logicalId, it.resourceType) }
}
@Query(
"""
SELECT *
FROM LocalChangeEntity
WHERE resourceId = :resourceId AND resourceType = :resourceType
ORDER BY timestamp ASC
""",
)
abstract suspend fun getLocalChanges(
resourceType: ResourceType,
resourceId: String,
): List<LocalChangeEntity>
@Query(
"""
SELECT *
FROM LocalChangeEntity
WHERE resourceUuid = :resourceUuid
ORDER BY timestamp ASC
""",
)
abstract suspend fun getLocalChanges(
resourceUuid: UUID,
): List<LocalChangeEntity>
@Query(
"""
SELECT *
FROM LocalChangeResourceReferenceEntity
WHERE resourceReferenceValue = :resourceReferenceValue
""",
)
abstract suspend fun getLocalChangeReferencesWithValue(
resourceReferenceValue: String,
): List<LocalChangeResourceReferenceEntity>
@Query(
"""
SELECT *
FROM LocalChangeResourceReferenceEntity
WHERE localChangeId = :localChangeId
""",
)
abstract suspend fun getReferencesForLocalChange(
localChangeId: Long,
): List<LocalChangeResourceReferenceEntity>
@Query(
"""
SELECT *
FROM LocalChangeResourceReferenceEntity
WHERE localChangeId = (:localChangeId)
""",
)
abstract suspend fun getReferencesForLocalChanges(
localChangeId: List<Long>,
): List<LocalChangeResourceReferenceEntity>
@Insert(onConflict = OnConflictStrategy.REPLACE)
abstract suspend fun insertLocalChangeResourceReferences(
resourceReferences: List<LocalChangeResourceReferenceEntity>,
)
/**
* Updates the resource IDs of the [LocalChange] of the updated resource. Updates [LocalChange]
* with references to the updated resource.
*/
suspend fun updateResourceIdAndReferences(
resourceUuid: UUID,
oldResource: Resource,
updatedResource: Resource,
): List<UUID> {
updateResourceIdInResourceLocalChanges(
resourceUuid = resourceUuid,
updatedResourceId = updatedResource.logicalId,
)
return updateReferencesInLocalChange(
oldResource = oldResource,
updatedResource = updatedResource,
)
}
/**
* Updates the [LocalChangeEntity]s for the updated resource by updating the
* [LocalChangeEntity.resourceId].
*/
private suspend fun updateResourceIdInResourceLocalChanges(
resourceUuid: UUID,
updatedResourceId: String,
) =
getLocalChanges(resourceUuid).forEach { localChangeEntity ->
updateResourceId(localChangeEntity.id, updatedResourceId)
}
/**
* Looks for [LocalChangeEntity] which refer to the updated resource through
* [LocalChangeResourceReferenceEntity]. For each [LocalChangeEntity] which contains reference to
* the updated resource in its payload, we update the payload with the reference and also update
* the corresponding [LocalChangeResourceReferenceEntity]. We delete the original
* [LocalChangeEntity] and create a new one with new [LocalChangeResourceReferenceEntity]s in its
* place. This method returns a list of the [ResourceEntity.resourceUuid] for all the resources
* whose [LocalChange] contained references to the oldResource
*/
private suspend fun updateReferencesInLocalChange(
oldResource: Resource,
updatedResource: Resource,
): List<UUID> {
val oldReferenceValue = "${oldResource.resourceType.name}/${oldResource.logicalId}"
val updatedReferenceValue = "${updatedResource.resourceType.name}/${updatedResource.logicalId}"
val referringLocalChangeIds =
getLocalChangeReferencesWithValue(oldReferenceValue).map { it.localChangeId }.distinct()
val referringLocalChanges = getLocalChanges(referringLocalChangeIds)
referringLocalChanges.forEach { existingLocalChangeEntity ->
val updatedLocalChangeEntity =
replaceReferencesInLocalChangePayload(
localChange = existingLocalChangeEntity,
oldReference = oldReferenceValue,
updatedReference = updatedReferenceValue,
)
.copy(id = DEFAULT_ID_VALUE)
val updatedLocalChangeReferences =
getReferencesForLocalChange(existingLocalChangeEntity.id).map {
localChangeResourceReferenceEntity ->
if (localChangeResourceReferenceEntity.resourceReferenceValue == oldReferenceValue) {
LocalChangeResourceReferenceEntity(
id = DEFAULT_ID_VALUE,
localChangeId = DEFAULT_ID_VALUE,
resourceReferencePath = localChangeResourceReferenceEntity.resourceReferencePath,
resourceReferenceValue = updatedReferenceValue,
)
} else {
localChangeResourceReferenceEntity.copy(
id = DEFAULT_ID_VALUE,
localChangeId = DEFAULT_ID_VALUE,
)
}
}
discardLocalChanges(existingLocalChangeEntity.id)
createLocalChange(updatedLocalChangeEntity, updatedLocalChangeReferences)
}
return referringLocalChanges.map { it.resourceUuid }.distinct()
}
private fun replaceReferencesInLocalChangePayload(
localChange: LocalChangeEntity,
oldReference: String,
updatedReference: String,
): LocalChangeEntity {
return when (localChange.type) {
LocalChangeEntity.Type.INSERT -> {
val insertResourcePayload = iParser.parseResource(localChange.payload) as Resource
val updatedResourcePayload =
addUpdatedReferenceToResource(
iParser,
insertResourcePayload,
oldReference,
updatedReference,
)
return localChange.copy(
payload = iParser.encodeResourceToString(updatedResourcePayload),
)
}
LocalChangeEntity.Type.UPDATE -> {
val patchArray = JSONArray(localChange.payload)
val updatedPatchArray = JSONArray()
for (i in 0 until patchArray.length()) {
val updatedPatch =
replaceJsonValue(patchArray.getJSONObject(i), oldReference, updatedReference)
updatedPatchArray.put(updatedPatch)
}
return localChange.copy(
payload = updatedPatchArray.toString(),
)
}
LocalChangeEntity.Type.DELETE -> localChange
}
}
@Query(
"""
SELECT *
FROM LocalChangeEntity
WHERE resourceUuid = (
SELECT resourceUuid
FROM LocalChangeEntity
ORDER BY timestamp ASC
LIMIT 1)
ORDER BY timestamp ASC
""",
)
abstract suspend fun getAllChangesForEarliestChangedResource(): List<LocalChangeEntity>
class InvalidLocalChangeException(message: String?) : Exception(message)
companion object {
const val DEFAULT_ID_VALUE = 0L
}
}
/** Calculates the JSON patch between two [Resource] s. */
internal fun diff(parser: IParser, source: Resource, target: Resource): JSONArray {
val objectMapper = ObjectMapper()
return getFilteredJSONArray(
JsonDiff.asJson(
objectMapper.readValue(parser.encodeResourceToString(source), JsonNode::class.java),
objectMapper.readValue(parser.encodeResourceToString(target), JsonNode::class.java),
),
)
}
/**
* This function returns the json diff as a json array of operation objects. We remove the "/meta"
* and "/text" paths as they cause path not found issue when we update the resource. They are
* usually present in the downloaded resource object but are missing in the edited object as these
* aren't supposed to be edited. Thus, the Json diff creates a DELETE- OP for "/meta" and "/text"
* and causes the issue with server update.
*
* An unfiltered JSON Array for family name update looks like
*
* ```
* [{"op":"remove","path":"/meta"}, {"op":"remove","path":"/text"},
* {"op":"replace","path":"/name/0/family","value":"Nucleus"}]
* ```
*
* A filtered JSON Array for family name update looks like
*
* ```
* [{"op":"replace","path":"/name/0/family","value":"Nucleus"}]
* ```
*/
private fun getFilteredJSONArray(jsonDiff: JsonNode) =
with(JSONArray(jsonDiff.toString())) {
val ignorePaths = setOf("/meta", "/text")
return@with JSONArray(
(0 until length())
.map { optJSONObject(it) }
.filterNot { jsonObject ->
ignorePaths.any { jsonObject.optString("path").startsWith(it) }
},
)
}