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Update fastq unarchiver step function to chunk fastq ids to prevent lambda timeouts #973

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merged 1 commit into from
May 7, 2025
Merged

Update fastq unarchiver step function to chunk fastq ids to prevent lambda timeouts #973

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70 changes: 47 additions & 23 deletions ...stq-unarchiving/app/step_functions_templates/run_s3_steps_copy_sfns_sfn_template.asl.json
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Original file line number Diff line number Diff line change
Expand Up @@ -45,32 +45,56 @@
"JitterStrategy": "FULL"
}
],
"Next": "Split fastq ids by instrument run id"
"Next": "For each fastq id (Batched)"
},
"Split fastq ids by instrument run id": {
"Type": "Task",
"Resource": "arn:aws:states:::lambda:invoke",
"Output": "{% $states.result.Payload %}",
"Arguments": {
"FunctionName": "${__split_fastq_ids_by_instrument_run_id_lambda_function_arn__}",
"Payload": {
"fastqIdList": "{% $fastqIdList %}"
}
"For each fastq id (Batched)": {
"Type": "Map",
"Label": "ForeachfastqidBatched",
"Items": "{% $fastqIdList %}",
"ItemBatcher": {
"MaxItemsPerBatch": 10
},
"Retry": [
{
"ErrorEquals": [
"Lambda.ServiceException",
"Lambda.AWSLambdaException",
"Lambda.SdkClientException",
"Lambda.TooManyRequestsException"
],
"IntervalSeconds": 1,
"MaxAttempts": 3,
"BackoffRate": 2,
"JitterStrategy": "FULL"
"MaxConcurrency": 1,
"ItemProcessor": {
"ProcessorConfig": {
"Mode": "DISTRIBUTED",
"ExecutionType": "STANDARD"
},
"StartAt": "Split fastq ids by instrument run id",
"States": {
"Split fastq ids by instrument run id": {
"Type": "Task",
"Resource": "arn:aws:states:::lambda:invoke",
"Arguments": {
"FunctionName": "${__split_fastq_ids_by_instrument_run_id_lambda_function_arn__}",
"Payload": {
"fastqIdList": "{% $states.input.Items %}"
}
},
"Retry": [
{
"ErrorEquals": [
"Lambda.ServiceException",
"Lambda.AWSLambdaException",
"Lambda.SdkClientException",
"Lambda.TooManyRequestsException"
],
"IntervalSeconds": 1,
"MaxAttempts": 3,
"BackoffRate": 2,
"JitterStrategy": "FULL"
}
],
"End": true,
"Output": {
"fastqIdsByInstrumentRunId": "{% $states.result.Payload.fastqIdsByInstrumentRunId %}"
}
}
}
],
},
"Output": {
"fastqIdsByInstrumentRunId": "{% /* https://try.jsonata.org/TdN5_ctqk */\n(\n /* Functions */\n $appendDistinct := function($i, $j){$distinct($append($i, $j))};\n $flattenedResultList := [\n $reduce(\n [\n $map($states.result, function($v){\n [\n $v.fastqIdsByInstrumentRunId\n ]\n })\n ],\n $append\n )\n ];\n\n /* Collect all instrument run ids */\n $allInstrumentRunIds := [\n $reduce(\n [\n $map(\n [\n $flattenedResultList\n ], \n function($v){\n $v.instrumentRunId\n }\n )\n ],\n $appendDistinct\n )\n ];\n\n /* Iterate over each instrumentRunId and combine with any fastq id lists */\n [\n $map(\n $allInstrumentRunIds, \n function($v){\n {\n \"instrumentRunId\": $v,\n \"fastqIdList\": [\n /* Append all into one list */\n $reduce(\n [\n $map(\n /* Any results with this instrument run id */\n [\n $filter(\n $flattenedResultList,\n function($y){\n $y.instrumentRunId = $v\n }\n )\n ],\n /* Get the fastq id lists */\n function($z){\n $z.fastqIdList\n }\n )\n ],\n $append\n )\n ]\n }\n }\n )\n ]\n) %}"
},
"Next": "For each instrument run id"
},
"For each instrument run id": {
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10 changes: 8 additions & 2 deletions lib/workload/stateless/stacks/fastq-unarchiving/deploy/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -374,7 +374,13 @@ export class FastqUnarchivingManagerStack extends Stack {
statements: [
new iam.PolicyStatement({
resources: [runUnarchivingStateMachine.stateMachineArn],
actions: ['states:StartExecution', 'states:DescribeExecution', 'states:StopExecution'],
actions: ['states:StartExecution'],
}),
new iam.PolicyStatement({
resources: [
`arn:aws:states:${cdk.Aws.REGION}:${cdk.Aws.ACCOUNT_ID}:execution:${runUnarchivingStateMachine.stateMachineName}/*:*`,
],
actions: ['states:RedriveExecution'],
}),
],
}),
Expand All @@ -400,7 +406,7 @@ export class FastqUnarchivingManagerStack extends Stack {
);

NagSuppressions.addResourceSuppressions(
runUnarchivingStateMachine,
[runUnarchivingStateMachine, distributedMapPolicy],
[
{
id: 'AwsSolutions-IAM5',
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