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Managed s3 bucket permissions #29

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merged 4 commits into from
May 9, 2024
Merged

Managed s3 bucket permissions #29

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be9d3be
Moved Nextflow bucket permissions into managed policy.
mluypaert May 9, 2024
dc9fe5b
Refactored NF output bucket variable
mluypaert May 9, 2024
877a300
Ignore more Resource vs IResource CDK typing mismatches
mluypaert May 9, 2024
46d03d9
Python style fixes
mluypaert May 9, 2024
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45 changes: 25 additions & 20 deletions pipeline/aws_infra/cdk_classes/aws_batch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,8 @@ class PaviExecutionEnvironment:

compute_environment: aws_batch.ManagedEc2EcsComputeEnvironment
job_queue: aws_batch.JobQueue
nf_workdir_bucket: s3.Bucket | s3.IBucket
nf_output_bucket: s3.Bucket | s3.IBucket
nf_bucket_access_policy: iam.ManagedPolicy

def __init__(self, scope: Stack, env_suffix: str, shared_work_dir_bucket: Optional[str]) -> None:
"""
Expand All @@ -36,7 +37,7 @@ def __init__(self, scope: Stack, env_suffix: str, shared_work_dir_bucket: Option
bucket_name = 'agr-pavi-pipeline-nextflow'
if env_suffix:
bucket_name += f'-{env_suffix}'
self.nf_workdir_bucket = s3.Bucket(
self.nf_output_bucket = s3.Bucket(
scope=scope, id='pavi-pipeline-nf-workdir-bucket',
bucket_name=bucket_name,
access_control=s3.BucketAccessControl.PRIVATE,
Expand All @@ -46,10 +47,10 @@ def __init__(self, scope: Stack, env_suffix: str, shared_work_dir_bucket: Option
removal_policy=RemovalPolicy.RETAIN,
versioned=False
)
cdk_tags.of(self.nf_workdir_bucket).add("Product", "PAVI")
cdk_tags.of(self.nf_workdir_bucket).add("Managed_by", "PAVI")
cdk_tags.of(self.nf_output_bucket).add("Product", "PAVI") # type: ignore
cdk_tags.of(self.nf_output_bucket).add("Managed_by", "PAVI") # type: ignore
else:
self.nf_workdir_bucket = s3.Bucket.from_bucket_name(
self.nf_output_bucket = s3.Bucket.from_bucket_name(
scope=scope, id='pavi-pipeline-nf-workdir-bucket',
bucket_name=shared_work_dir_bucket)

Expand All @@ -60,31 +61,35 @@ def __init__(self, scope: Stack, env_suffix: str, shared_work_dir_bucket: Option
sid="S3BucketWriteAll",
effect=iam.Effect.ALLOW,
actions=['s3:Put*'],
resources=[self.nf_workdir_bucket.bucket_arn + '/*']
resources=[self.nf_output_bucket.bucket_arn + '/*']
),
iam.PolicyStatement(
sid="S3BucketReadAll",
effect=iam.Effect.ALLOW,
actions=['s3:ListBucket*', 's3:Get*'],
resources=[self.nf_workdir_bucket.bucket_arn, self.nf_workdir_bucket.bucket_arn + '/*']
resources=[self.nf_output_bucket.bucket_arn, self.nf_output_bucket.bucket_arn + '/*']
)
]
)
cdk_tags.of(s3_workdir_bucket_policy_doc).add("Product", "PAVI")
cdk_tags.of(s3_workdir_bucket_policy_doc).add("Managed_by", "PAVI")
s3_workdir_bucket_policy = iam.ManagedPolicy(scope, 'pavi-s3-nextflow-bucket-policy',
managed_policy_name='agr-pavi-pipeline-nf-bucket-access',
description='Grant required access to PAVI pipeline nextflow bucket to run nextflow pipelines using it.',
document=s3_workdir_bucket_policy_doc)
cdk_tags.of(s3_workdir_bucket_policy).add("Product", "PAVI") # type: ignore
cdk_tags.of(s3_workdir_bucket_policy).add("Managed_by", "PAVI") # type: ignore

self.nf_bucket_access_policy = s3_workdir_bucket_policy

instance_role = iam.Role(scope, 'pavi-pipeline-compute-environment-instance-role',
description='Role granting permissions for Nextflow ECS execution',
assumed_by=iam.ServicePrincipal('ec2.amazonaws.com'), # type: ignore
managed_policies=[
iam.ManagedPolicy.from_aws_managed_policy_name("service-role/AmazonEC2ContainerServiceforEC2Role"),
iam.ManagedPolicy.from_managed_policy_name(scope, "iam-ecr-read-policy", "ReadOnlyAccessECR")
],
inline_policies={
's3-workdir-policy': s3_workdir_bucket_policy_doc
})
cdk_tags.of(instance_role).add("Product", "PAVI")
cdk_tags.of(instance_role).add("Managed_by", "PAVI")
iam.ManagedPolicy.from_managed_policy_name(scope, "iam-ecr-read-policy", "ReadOnlyAccessECR"),
self.nf_bucket_access_policy
])
cdk_tags.of(instance_role).add("Product", "PAVI") # type: ignore
cdk_tags.of(instance_role).add("Managed_by", "PAVI") # type: ignore

ce_name = 'pavi_pipeline_ecs'
if env_suffix:
Expand All @@ -100,8 +105,8 @@ def __init__(self, scope: Stack, env_suffix: str, shared_work_dir_bucket: Option

self.compute_environment.apply_removal_policy(RemovalPolicy.DESTROY)

cdk_tags.of(self.compute_environment).add("Product", "PAVI")
cdk_tags.of(self.compute_environment).add("Managed_by", "PAVI")
cdk_tags.of(self.compute_environment).add("Product", "PAVI") # type: ignore
cdk_tags.of(self.compute_environment).add("Managed_by", "PAVI") # type: ignore

self.compute_environment.tags.set_tag('Name', 'PAVI pipeline execution worker', priority=None, apply_to_launched_instances=True)

Expand All @@ -116,5 +121,5 @@ def __init__(self, scope: Stack, env_suffix: str, shared_work_dir_bucket: Option

self.job_queue.add_compute_environment(self.compute_environment, order=1) # type: ignore

cdk_tags.of(self.job_queue).add("Product", "PAVI")
cdk_tags.of(self.job_queue).add("Managed_by", "PAVI")
cdk_tags.of(self.job_queue).add("Product", "PAVI") # type: ignore
cdk_tags.of(self.job_queue).add("Managed_by", "PAVI") # type: ignore
10 changes: 10 additions & 0 deletions pipeline/aws_infra/tests/unit/test_cdk_infra_stack.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,16 @@ def test_pipeline_nf_s3_bucket() -> None:
})


# The S3 bucket policy is assigned to the GH-actions role for PAVI, in addition to PAVI-managed resources.
# Changing the name of this policy might require the gh-actions role to be updated to include the new role.
def test_pipeline_nf_s3_bucket_policy() -> None:
template.has_resource(type=ResourceType.of('AWS::IAM::ManagedPolicy').compliance_resource_type, props={
"Properties": {
"ManagedPolicyName": "agr-pavi-pipeline-nf-bucket-access"
}
})


# Below tests check for resource that must be available in the stack,
# but which can be replaced/renamed without manual interventions other than
# updating all references to those resources to use the new name (check all code).
Expand Down