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CORE-188: batch upsert tracing #3147

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merged 4 commits into from
Dec 6, 2024
Merged

CORE-188: batch upsert tracing #3147

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4e46c0d
connect batchUpsert tracing contexts
davidangb Dec 5, 2024
e4bb6b7
fix ordering of traces in updateAction
davidangb Dec 5, 2024
28b516d
add more detail
davidangb Dec 5, 2024
08258f0
Merge branch 'develop' into da_CORE-188_batchUpsertTracing
davidangb Dec 5, 2024
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140 changes: 71 additions & 69 deletions core/src/main/scala/org/broadinstitute/dsde/rawls/dataaccess/slick/AttributeComponent.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -695,81 +695,81 @@ trait AttributeComponent {
*/
def rewriteAttrsAction(attributesToSave: Traversable[RECORD],
existingAttributes: Traversable[RECORD],
insertFunction: Seq[RECORD] => () => WriteAction[Int]
insertFunction: Seq[RECORD] => () => WriteAction[Int],
parentContext: RawlsTracingContext = RawlsTracingContext()
): ReadWriteAction[Set[OWNER_ID]] =
traceDBIOWithParent("AttributeComponent.rewriteAttrsAction", RawlsTracingContext(Option.empty)) {
tracingContext =>
val toSaveAttrMap = toPrimaryKeyMap(attributesToSave)
val existingAttrMap = toPrimaryKeyMap(existingAttributes)

// note that currently-existing attributes will have a populated id e.g. "1234", but to-save will have an id of "0"
// therefore, we use this ComparableRecord class which omits the id when checking equality between existing and to-save.
object ComparableRecord {
def fromRecord(rec: RECORD): ComparableRecord =
new ComparableRecord(
rec.ownerId,
rec.namespace,
rec.name,
rec.valueString,
rec.valueNumber,
rec.valueBoolean,
rec.valueJson,
rec.valueEntityRef,
rec.listIndex,
rec.listLength,
rec.deleted,
rec.deletedDate
)
}
traceDBIOWithParent("AttributeComponent.rewriteAttrsAction", parentContext) { tracingContext =>
val toSaveAttrMap = toPrimaryKeyMap(attributesToSave)
val existingAttrMap = toPrimaryKeyMap(existingAttributes)

// note that currently-existing attributes will have a populated id e.g. "1234", but to-save will have an id of "0"
// therefore, we use this ComparableRecord class which omits the id when checking equality between existing and to-save.
object ComparableRecord {
def fromRecord(rec: RECORD): ComparableRecord =
new ComparableRecord(
rec.ownerId,
rec.namespace,
rec.name,
rec.valueString,
rec.valueNumber,
rec.valueBoolean,
rec.valueJson,
rec.valueEntityRef,
rec.listIndex,
rec.listLength,
rec.deleted,
rec.deletedDate
)
}

case class ComparableRecord(
ownerId: OWNER_ID,
namespace: String,
name: String,
valueString: Option[String],
valueNumber: Option[Double],
valueBoolean: Option[Boolean],
valueJson: Option[String],
valueEntityRef: Option[Long],
listIndex: Option[Int],
listLength: Option[Int],
deleted: Boolean,
deletedDate: Option[Timestamp]
)
case class ComparableRecord(
ownerId: OWNER_ID,
namespace: String,
name: String,
valueString: Option[String],
valueNumber: Option[Double],
valueBoolean: Option[Boolean],
valueJson: Option[String],
valueEntityRef: Option[Long],
listIndex: Option[Int],
listLength: Option[Int],
deleted: Boolean,
deletedDate: Option[Timestamp]
)

// create a set of ComparableRecords representing the existing attributes
val existingAttributesSet: Set[ComparableRecord] =
existingAttributes.toSet.map(r => ComparableRecord.fromRecord(r))
// create a set of ComparableRecords representing the existing attributes
val existingAttributesSet: Set[ComparableRecord] =
existingAttributes.toSet.map(r => ComparableRecord.fromRecord(r))

val existingKeys = existingAttrMap.keySet
val existingKeys = existingAttrMap.keySet

// insert attributes which are in save but not exists
val attributesToInsert = toSaveAttrMap.filterKeys(!existingKeys.contains(_))
// insert attributes which are in save but not exists
val attributesToInsert = toSaveAttrMap.filterKeys(!existingKeys.contains(_))

// delete attributes which are in exists but not save
val attributesToDelete = existingAttrMap.filterKeys(!toSaveAttrMap.keySet.contains(_))
// delete attributes which are in exists but not save
val attributesToDelete = existingAttrMap.filterKeys(!toSaveAttrMap.keySet.contains(_))

val attributesToUpdate = toSaveAttrMap.filter { case (k, v) =>
existingKeys.contains(k) && // if the attribute doesn't already exist, don't attempt to update it
!existingAttributesSet.contains(
ComparableRecord.fromRecord(v)
) // if the attribute exists and is unchanged, don't update it
}
val attributesToUpdate = toSaveAttrMap.filter { case (k, v) =>
existingKeys.contains(k) && // if the attribute doesn't already exist, don't attempt to update it
!existingAttributesSet.contains(
ComparableRecord.fromRecord(v)
) // if the attribute exists and is unchanged, don't update it
}

// collect the parent objects (e.g. entity, workspace) that have writes, so we know which object rows to re-calculate
val ownersWithWrites: Set[OWNER_ID] = (attributesToInsert.values.map(_.ownerId) ++
attributesToUpdate.values.map(_.ownerId) ++
attributesToDelete.values.map(_.ownerId)).toSet

// perform the inserts/updates/deletes
patchAttributesAction(
attributesToInsert.values,
attributesToUpdate.values,
attributesToDelete.values.map(_.id),
insertFunction,
tracingContext
)
.map(_ => ownersWithWrites)
// collect the parent objects (e.g. entity, workspace) that have writes, so we know which object rows to re-calculate
val ownersWithWrites: Set[OWNER_ID] = (attributesToInsert.values.map(_.ownerId) ++
attributesToUpdate.values.map(_.ownerId) ++
attributesToDelete.values.map(_.ownerId)).toSet

// perform the inserts/updates/deletes
patchAttributesAction(
attributesToInsert.values,
attributesToUpdate.values,
attributesToDelete.values.map(_.id),
insertFunction,
tracingContext
)
.map(_ => ownersWithWrites)
}

// noinspection SqlDialectInspection
Expand Down Expand Up @@ -804,8 +804,10 @@ trait AttributeComponent {

def updateAction(insertIntoScratchFunction: () => WriteAction[Int], tracingContext: RawlsTracingContext) =
traceDBIOWithParent("updateAction", tracingContext) { span =>
traceDBIOWithParent("insertIntoScratchFunction", span)(_ => insertIntoScratchFunction()) andThen
traceDBIOWithParent("updateInMasterAction", span)(_ => updateInMasterAction())
for {
_ <- traceDBIOWithParent("insertIntoScratchFunction", span)(_ => insertIntoScratchFunction())
numUpdates <- traceDBIOWithParent("updateInMasterAction", span)(_ => updateInMasterAction())
} yield numUpdates
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the change from andThen to for ... yield ensures the second "updateInMasterAction" trace does not start eagerly

}
}

Expand Down
42 changes: 28 additions & 14 deletions core/src/main/scala/org/broadinstitute/dsde/rawls/dataaccess/slick/EntityComponent.scala
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Expand Up @@ -1026,25 +1026,35 @@ trait EntityComponent {
def save(workspaceContext: Workspace, entity: Entity): ReadWriteAction[Entity] =
save(workspaceContext, Seq(entity)).map(_.head)

def save(workspaceContext: Workspace, entities: Traversable[Entity]): ReadWriteAction[Traversable[Entity]] = {
def save(workspaceContext: Workspace,
entities: Traversable[Entity],
parentContext: RawlsTracingContext = RawlsTracingContext()
): ReadWriteAction[Traversable[Entity]] = {
entities.foreach(validateEntity)

for {
_ <- workspaceQuery.updateLastModified(workspaceContext.workspaceIdAsUUID)
preExistingEntityRecs <- getEntityRecords(workspaceContext.workspaceIdAsUUID, entities.map(_.toReference).toSet)
savingEntityRecs <- entityQueryWithInlineAttributes
.insertNewEntities(workspaceContext, entities, preExistingEntityRecs.map(_.toReference))
.map(_ ++ preExistingEntityRecs)
referencedAndSavingEntityRecs <- lookupNotYetLoadedReferences(workspaceContext,
entities,
savingEntityRecs.map(_.toReference)
).map(_ ++ savingEntityRecs)
_ <- traceDBIOWithParent("updateLastModified", parentContext)(_ =>
workspaceQuery.updateLastModified(workspaceContext.workspaceIdAsUUID)
)
preExistingEntityRecs <- traceDBIOWithParent("getEntityRecords", parentContext)(_ =>
getEntityRecords(workspaceContext.workspaceIdAsUUID, entities.map(_.toReference).toSet)
)
savingEntityRecs <- traceDBIOWithParent("insertNewEntities", parentContext)(_ =>
entityQueryWithInlineAttributes
.insertNewEntities(workspaceContext, entities, preExistingEntityRecs.map(_.toReference))
.map(_ ++ preExistingEntityRecs)
)
referencedAndSavingEntityRecs <- traceDBIOWithParent("lookupNotYetLoadedReferences", parentContext)(_ =>
lookupNotYetLoadedReferences(workspaceContext, entities, savingEntityRecs.map(_.toReference))
.map(_ ++ savingEntityRecs)
)

actuallyUpdatedEntityIds <- rewriteAttributes(
workspaceContext.workspaceIdAsUUID,
entities,
savingEntityRecs.map(_.id),
referencedAndSavingEntityRecs.map(e => e.toReference -> e.id).toMap
referencedAndSavingEntityRecs.map(e => e.toReference -> e.id).toMap,
parentContext
)
// find the pre-existing records that we updated
actuallyUpdatedPreExistingEntityRecs = preExistingEntityRecs.filter(e =>
Expand All @@ -1064,7 +1074,9 @@ trait EntityComponent {
// 2) were repeated in the input payload, causing one insert and subsequent update(s)
recsToUpdate = (actuallyUpdatedPreExistingEntityRecs ++ insertedRepeats).distinct

_ <- entityQueryWithInlineAttributes.optimisticLockUpdate(recsToUpdate, entities)
_ <- traceDBIOWithParent("optimisticLockUpdate", parentContext)(_ =>
entityQueryWithInlineAttributes.optimisticLockUpdate(recsToUpdate, entities)
)
} yield entities
}

Expand Down Expand Up @@ -1112,7 +1124,8 @@ trait EntityComponent {
private def rewriteAttributes(workspaceId: UUID,
entitiesToSave: Traversable[Entity],
entityIds: Seq[Long],
entityIdsByRef: Map[AttributeEntityReference, Long]
entityIdsByRef: Map[AttributeEntityReference, Long],
parentContext: RawlsTracingContext = RawlsTracingContext()
) = {
val attributesToSave = for {
entity <- entitiesToSave
Expand All @@ -1127,7 +1140,8 @@ trait EntityComponent {
entityAttributeShardQuery(workspaceId).findByOwnerQuery(entityIds).result flatMap { existingAttributes =>
entityAttributeShardQuery(workspaceId).rewriteAttrsAction(attributesToSave,
existingAttributes,
entityAttributeTempQuery.insertScratchAttributes
entityAttributeTempQuery.insertScratchAttributes,
parentContext
)
}
}
Expand Down
10 changes: 6 additions & 4 deletions core/src/main/scala/org/broadinstitute/dsde/rawls/entities/local/LocalEntityProvider.scala
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Expand Up @@ -497,13 +497,15 @@ class LocalEntityProvider(requestArguments: EntityRequestArguments,
} else {
val t = updateTrials.collect { case (entityUpdate, Success(entity)) => entity }

dataAccess.entityQuery
.save(workspaceContext, t)
.withStatementParameters(statementInit = _.setQueryTimeout(queryTimeoutSeconds))
traceDBIOWithParent("saveAction", localContext) { subContext =>
dataAccess.entityQuery
.save(workspaceContext, t, subContext.toTracingContext)
.withStatementParameters(statementInit = _.setQueryTimeout(queryTimeoutSeconds))
}
}
}

traceDBIOWithParent("saveAction", localContext)(_ => saveAction)
saveAction
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moving the trace wrapper up ensures it does not start eagerly

} recover {
case icve: java.sql.SQLIntegrityConstraintViolationException =>
val userMessage =
Expand Down
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