Merge pull request #47 from alliance-genome/API-deployment-KANBAN-558

Refactored API image repo CDK stack KANBAN-558

.github/workflows/PR-validation.yml

@@ -404,9 +404,6 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: "3.12"
-    - name: CDK resource assertions (unit tests)
-      run: |
-        make run-unit-tests
     - name: Python typing test
       run: |
         make run-python-type-check
@@ -428,4 +425,4 @@ jobs:
         role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-cdk-test
         aws-region: us-east-1
     - name: Validate production CDK stack code
-      run: cdk diff PaviApiCdkStack
+      run: make validate

.github/workflows/main-build-and-deploy.yml

@@ -48,8 +48,8 @@ jobs:
       run: make validate
     - name: cdk deploy
       run: cdk deploy PaviPipelineCdkStack --require-approval never
-  api-deploy-aws-infra:
-    name: Deploy/update AWS infrastructure for API
+  api-deploy-image-repo:
+    name: Deploy/update container image repository stack for API
     needs: [on-merge-and-deploy]
     permissions:
       id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
@@ -81,7 +81,7 @@ jobs:
     - name: CDK validations (resource assertions and cdk diff)
       run: make validate
     - name: cdk deploy
-      run: cdk deploy PaviApiCdkStack --require-approval never
+      run: cdk deploy PaviApiImageRepoCdkStack --require-approval never
   pipeline-seq-retrieval-build-and-push-docker-image:
     needs: [on-merge-and-deploy, pipeline-deploy-aws-infra]
     permissions:
@@ -155,7 +155,7 @@ jobs:
           ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_alignment:${{ github.event.pull_request.base.ref }}
         platforms: linux/amd64
   api-build-and-push-docker-image:
-    needs: [on-merge-and-deploy, api-deploy-aws-infra]
+    needs: [on-merge-and-deploy, api-deploy-image-repo]
     permissions:
       id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
     runs-on: ubuntu-22.04

api/aws_infra/Makefile

@@ -41,7 +41,7 @@ run-python-style-check: python-dependencies python-test-dependencies
 
 validate: check-node run-unit-tests
 # Validate production stack code
-	cdk diff PaviApiCdkStack
+	cdk diff PaviApiImageRepoCdkStack
 
 validate-dev: check-venv-active validate
 	@:

api/aws_infra/cdk_app.py

@@ -4,7 +4,7 @@
 from pathlib import Path
 from sys import path as sys_path
 
-from cdk_classes.cdk_infra_stack import CdkInfraStack
+from cdk_classes.cdk_image_repo_stack import CdkImageRepoStack
 
 repo_root_path = Path(__file__).parent.parent.parent.parent
 sys_path.append(str(repo_root_path))
@@ -13,11 +13,11 @@
 
 
 app = App()
-CdkInfraStack(app, "PaviApiCdkStack",
-              env=agr_aws_environment)
+CdkImageRepoStack(app, "PaviApiImageRepoCdkStack",
+                  env=agr_aws_environment)
 
-CdkInfraStack(app, "PaviApiCdkStack-dev", env_suffix="dev",
-              shared_api_image_repo='agr_pavi/api',
-              env=agr_aws_environment)
+CdkImageRepoStack(app, "PaviApiImageRepoCdkStack-dev", env_suffix="dev",
+                  shared_api_image_repo='agr_pavi/api',
+                  env=agr_aws_environment)
 
 app.synth()

api/aws_infra/cdk_classes/cdk_infra_stack.py → api/aws_infra/cdk_classes/cdk_image_repo_stack.py

@@ -16,7 +16,7 @@
 from shared_aws_infra.shared_cdk_classes.pavi_ecr_repo import PaviEcrRepository  # noqa: E402
 
 
-class CdkInfraStack(Stack):
+class CdkImageRepoStack(Stack):
 
     api_ecr_repo: ecr.Repository | ecr.IRepository
 

api/aws_infra/tests/unit/test_cdk_infra_stack.py → api/aws_infra/tests/unit/test_cdk_image_repo_stack.py

@@ -8,7 +8,7 @@
 from aws_cdk.aws_config import ResourceType
 import aws_cdk.assertions as assertions
 
-from cdk_classes.cdk_infra_stack import CdkInfraStack
+from cdk_classes.cdk_image_repo_stack import CdkImageRepoStack
 
 from pathlib import Path
 from sys import path as sys_path
@@ -19,7 +19,7 @@
 from shared_aws_infra.agr_aws_env import agr_aws_environment  # noqa: E402
 
 app = App()
-stack = CdkInfraStack(app, "pytest-stack", env=agr_aws_environment)
+stack = CdkImageRepoStack(app, "pytest-stack", env=agr_aws_environment)
 template = assertions.Template.from_stack(stack)
 
 

api/pytest.ini

@@ -0,0 +1,5 @@
+[pytest]
+addopts =
+    --import-mode=importlib
+    --ignore=aws_infra
+pythonpath = src

pipeline/seq_retrieval/pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+addopts =
+    --import-mode=importlib
+pythonpath = src

shared_aws_infra/.flake8

@@ -0,0 +1,6 @@
+[flake8]
+ignore = E266, E501, W503
+max-complexity = 18
+select = B,C,E,F,W,T4
+exclude = venv,node_modules
+per-file-ignores = __init__.py:F401