61 get our openapi spec working for the data analysis pipeline api

Pulumi.cape-cod-dev.yaml

@@ -108,9 +108,58 @@ config:
                     # each item should have:
                     #   - desc: A description for the api. Will be used in
                     #           description tags.
-                    # TODO: ISSUE #61 - openapi spec file would go here
+                    #   - spec_file: An OpenApi 3.0.1 yaml specification. This
+                    #                should include *no* AWS id's, names,
+                    #                account info, etc
+                    #   - env_vars: a list of swimlane-exposed env vars that the
+                    #               API requires access to. the env vars will be
+                    #               passed into the environment of the lambda
+                    #               and basic permissions will be given to the
+                    #               lambda to access the resources referenced by
+                    #               the env var.
+                    #   - handlers: a list of objects containing
+                    #       - id:
+                    #           the id in the spec file that will be replaced
+                    #           with the arn of the created lambda function
+                    #       - name:
+                    #           a short name that will be used in resource
+                    #           creation (naming of the resources)
+                    #       - code:
+                    #           the path in the repo for the lambda that
+                    #           implements the endpoint
+                    #       - funct_args:
+                    #           arguments to pass *as is* to the lambda
+                    #           function constructor. the keys used need to map
+                    #           to actual argument names of the pulumi lambda
+                    #           function constructor. additionally, most args
+                    #           will be ignored (e.g. environment, role) as
+                    #           they are dynamically injected in code or not
+                    #           used currently. If not provided, the handler
+                    #           will default to  "index.index_handler" and the
+                    #           runtime will default to "python3.10". The
+                    #           following arguments are supported:
+                    #           - architectures (list, defaults to ["x86_64"])
+                    #           - description
+                    #           - handler (defaults to "index.index_handler")
+                    #           - memory_size (MB,  defaults to 128)
+                    #           - runtime (defaults to "python3.10")
+                    #           - timeout (seconds, defaults to 3)
                     dap:
                         desc: "Data Analysis Pipeline API"
+                        spec_file: "assets/api/data-analysis-pipeline/dap-openapi-301.yaml.j2"
+                        env_vars:
+                            - "DAP_QUEUE_NAME"
+                            - "DAP_REG_DDB_TABLE"
+                        handlers:
+                            - id: "list_daps_handler"
+                              name: "lsdaps"
+                              code: "assets/api/data-analysis-pipeline/handlers/list_daps.py"
+                            - id: "list_dap_executors_handler"
+                              name: "lsexec"
+                              code: "assets/api/data-analysis-pipeline/handlers/list_dap_executors.py"
+                            - id: "submit_dap_run_handler"
+                              name: "sbmtdap"
+                              code: "assets/api/data-analysis-pipeline/handlers/submit_dap_run.py"
             # static apps are deployed to s3 as html/js/css bundles and are
             # exposed through an application load balancer. these may hit API
             # endpoints (assuming the required permissions/roles are available),

assets/api/data-analysis-pipeline/dap-openapi-301.yaml.j2

@@ -0,0 +1,212 @@
+openapi: "3.0.1"
+info:
+    title: "CAPE Data Analysis Pipeline API"
+    description:
+        "CAPE Data Analysis Pipeline API (***TODO: add more comment***)"
+    version: "2024-11-04T20:50:49Z"
+servers:
+    # we do not provide x-amazon-apigateway-endpoint-configuration here (setting up the vpc endpoint)
+    # as we expect that to be set in the pulumi code setting up the RestApi. Don't want AWS ids in the
+    # repo
+    - url: "https://api.cape-dev.org/{basePath}"
+      variables:
+          basePath:
+              # This value needs to map to the stage name exposed via the ALB
+              default: "dap-dev"
+paths:
+    /analysispipelines:
+        get:
+            responses:
+                "200":
+                    # TODO: need the response headers (i.e. cors)
+                    description: "Success"
+                    content:
+                        application/json:
+                            schema:
+                                type: array
+                                description:
+                                    "An array of available pipelines to run."
+                                items:
+                                    type: object
+                                    properties:
+                                        pipeline_name:
+                                            type: string
+                                            description: The pipeline name
+                                        pipeline_type:
+                                            type: string
+                                            description:
+                                                The type of pipeline execution
+                                                environment (e.g. 'nextflow')
+                                        version:
+                                            type: string
+                                            description: The pipeline version
+                "500":
+                    description:
+                        "Server Error - Unable to read the pipeline registry."
+            x-amazon-apigateway-integration:
+                # this is the integration http method, not the endpoint http method. all lambda backed
+                # integrations are post
+                httpMethod: "POST"
+                uri: "arn:aws:apigateway:${AWS::Region}:lambda:path/2015-03-31/functions/{{ list_daps_handler }}/invocations"
+                passthroughBehavior: "when_no_match"
+                timeoutInMillis: 29000
+                type: "aws_proxy"
+        options:
+            responses:
+                "200":
+                    $ref: "#/components/responses/200OptionsCors"
+            x-amazon-apigateway-integration:
+              responses:
+                default:
+                    statusCode: "200"
+                    responseParameters:
+                        method.response.header.Access-Control-Allow-Methods: "'OPTIONS,POST'"
+                        method.response.header.Access-Control-Allow-Headers: "'Content-Type,X-Amz-Date,Authorization,X-Api-Key,X-Amz-Security-Token'"
+                        method.response.header.Access-Control-Allow-Origin: "'*'"
+              requestTemplates:
+                  application/json: "{'statusCode':200}"
+              passthroughBehavior: "when_no_match"
+              timeoutInMillis: 29000
+              type: "mock"
+    /pipelineexecutors:
+        get:
+            responses:
+                "200":
+                    # TODO: need the response headers (i.e. cors)
+                    description: "Success"
+                    content:
+                        application/json:
+                            schema:
+                                type: array
+                                description:
+                                    "An array of available pipeline executors."
+                                items:
+                                    type: object
+                                    properties:
+                                        instance_id:
+                                            type: string
+                                            description:
+                                                The ID of the executor EC2
+                                                instance
+                                        instance_name:
+                                            type: string
+                                            description:
+                                                The name of the executor EC2
+                                                instance
+                                        pipeline_type:
+                                            type: string
+                                            description:
+                                                The type of pipeline supported
+                                                by the executor EC2 instance.
+                "500":
+                    description:
+                        "Server error while getting list of available executors."
+            x-amazon-apigateway-integration:
+                httpMethod: "POST"
+                uri: "arn:aws:apigateway:${AWS::Region}:lambda:path/2015-03-31/functions/{{ list_dap_executors_handler }}/invocations"
+                passthroughBehavior: "when_no_match"
+                timeoutInMillis: 29000
+                type: "aws_proxy"
+        options:
+            responses:
+                "200":
+                    $ref: "#/components/responses/200OptionsCors"
+            x-amazon-apigateway-integration:
+              responses:
+                default:
+                    statusCode: "200"
+                    responseParameters:
+                        method.response.header.Access-Control-Allow-Methods: "'OPTIONS,POST'"
+                        method.response.header.Access-Control-Allow-Headers: "'Content-Type,X-Amz-Date,Authorization,X-Api-Key,X-Amz-Security-Token'"
+                        method.response.header.Access-Control-Allow-Origin: "'*'"
+              requestTemplates:
+                  application/json: "{'statusCode':200}"
+              passthroughBehavior: "when_no_match"
+              timeoutInMillis: 29000
+              type: "mock"
+    /analysispipeline:
+        post:
+            requestBody:
+                description: Submit a data analysis pipeline for execution.
+                required: true
+                content:
+                    application/json:
+                        schema:
+                            type: object
+                            properties:
+                                pipelineName:
+                                    type: string
+                                    description: The name of the pipeline to run
+                                pipelineVersion:
+                                    type: string
+                                    description:
+                                        The version of the pipeline to run
+                                outputPath:
+                                    type: string
+                                    description: >
+                                        The S3 location to put pipeline output.
+                                        Assumes permissions are set correctly.
+                                # TODO: ISSUE #TBD all below fields are specific to bactopia right now. also, the
+                                #       descriptions are bunk if we keep using these params
+                                r1Path:
+                                    type: string
+                                    description: The R1 path.
+                                r2Path:
+                                    type: string
+                                    description: The R2 path.
+                                ec2Id:
+                                    type: string
+                                    description:
+                                        The id of the EC2 instance serving as
+                                        executor.
+                                sample:
+                                    type: string
+                                    description: >
+                                        The name of the sample being processed.
+                                        Affects output directory and file names
+            responses:
+                "200":
+                    # TODO: need the response headers (i.e. cors)
+                    description: "Success submitting pipeline for execution."
+            x-amazon-apigateway-integration:
+                httpMethod: "POST"
+                uri: "arn:aws:apigateway:${AWS::Region}:lambda:path/2015-03-31/functions/{{ submit_dap_run_handler }}/invocations"
+                passthroughBehavior: "when_no_match"
+                timeoutInMillis: 29000
+                type: "aws_proxy"
+        options:
+            responses:
+                "200":
+                    $ref: "#/components/responses/200OptionsCors"
+            x-amazon-apigateway-integration:
+              responses:
+                default:
+                    statusCode: "200"
+                    responseParameters:
+                        method.response.header.Access-Control-Allow-Methods: "'OPTIONS,POST'"
+                        method.response.header.Access-Control-Allow-Headers: "'Content-Type,X-Amz-Date,Authorization,X-Api-Key,X-Amz-Security-Token'"
+                        method.response.header.Access-Control-Allow-Origin: "'*'"
+              requestTemplates:
+                  application/json: "{'statusCode':200}"
+              passthroughBehavior: "when_no_match"
+              timeoutInMillis: 29000
+              type: "mock"
+# resusable components that follow OpenApi 3.0.1 spec
+components:
+    responses:
+        200OptionsCors:
+            description: "200 response"
+            headers:
+                Access-Control-Allow-Origin:
+                    schema:
+                        type: "string"
+                Access-Control-Allow-Methods:
+                    schema:
+                        type: "string"
+                Access-Control-Allow-Headers:
+                    schema:
+                        type: "string"
+            content: {}
+# we do not provide x-amazon-apigateway-policy here (setting up the policy for using the API)
+# as we expect that to be set in the pulumi code setting up the RestApi. Don't want AWS ids and
+# perms in the repo