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Added AWS resource tagging #24

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merged 2 commits into from
Apr 30, 2024
Merged

Added AWS resource tagging #24

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e386afd
Added Managed_by and Product AWS tags on PAVI-managed AWS resources.
mluypaert Apr 30, 2024
8f34eae
Name launched EC2 execution workers
mluypaert Apr 30, 2024
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17 changes: 16 additions & 1 deletion pipeline/aws_infra/cdk_classes/aws_batch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,8 @@
aws_iam as iam,
RemovalPolicy,
Stack,
aws_s3 as s3
aws_s3 as s3,
Tags as cdk_tags
)

from typing import Optional
Expand Down Expand Up @@ -45,6 +46,8 @@ 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")
else:
self.nf_workdir_bucket = s3.Bucket.from_bucket_name(
scope=scope, id='pavi-pipeline-nf-workdir-bucket',
Expand All @@ -67,6 +70,8 @@ def __init__(self, scope: Stack, env_suffix: str, shared_work_dir_bucket: Option
)
]
)
cdk_tags.of(s3_workdir_bucket_policy_doc).add("Product", "PAVI")
cdk_tags.of(s3_workdir_bucket_policy_doc).add("Managed_by", "PAVI")

instance_role = iam.Role(scope, 'pavi-pipeline-compute-environment-instance-role',
description='Role granting permissions for Nextflow ECS execution',
Expand All @@ -78,6 +83,8 @@ def __init__(self, scope: Stack, env_suffix: str, shared_work_dir_bucket: Option
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")

ce_name = 'pavi_pipeline_ecs'
if env_suffix:
Expand All @@ -93,6 +100,11 @@ 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")

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

# Create the job queue
jq_name = 'pavi_pipeline'
if env_suffix:
Expand All @@ -103,3 +115,6 @@ 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")
7 changes: 6 additions & 1 deletion pipeline/aws_infra/cdk_classes/cdk_infra_stack.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
from aws_cdk import (
Stack,
aws_ecr as ecr
aws_ecr as ecr,
Tags as cdk_tags
)

from constructs import Construct
Expand Down Expand Up @@ -39,12 +40,16 @@ def __init__(self, scope: Construct, construct_id: str, env_suffix: str = "",
env_suffix=env_suffix)
else:
self.seq_retrieval_ecr_repo = ecr.Repository.from_repository_name(self, id='PAVI-pipeline-seq-retrieval-repo', repository_name=shared_seq_retrieval_image_repo)
cdk_tags.of(self.seq_retrieval_ecr_repo).add("Product", "PAVI")
cdk_tags.of(self.seq_retrieval_ecr_repo).add("Managed_by", "PAVI")

# Import or create shared_alignment_image_repo
if not shared_alignment_image_repo:
self.alignment_ecr_repo = PaviEcrRepository(self, id='PAVI-pipeline-alignment-repo', component_name='pipeline_alignment',
env_suffix=env_suffix)
else:
self.alignment_ecr_repo = ecr.Repository.from_repository_name(self, id='PAVI-pipeline-alignment-repo', repository_name=shared_alignment_image_repo)
cdk_tags.of(self.alignment_ecr_repo).add("Product", "PAVI")
cdk_tags.of(self.alignment_ecr_repo).add("Managed_by", "PAVI")

self.execution_environment = PaviExecutionEnvironment(self, env_suffix=env_suffix, shared_work_dir_bucket=shared_work_dir_bucket)