pushing changes from biohackathon

.netrc

@@ -0,0 +1,3 @@
+machine ftp-private.ebi.ac.uk
+login tesk-1
+password Z6fsH6MG

requirements.txt

@@ -13,12 +13,12 @@ cffi==1.11.5
 chardet==3.0.4
 click==6.7
 clickclick==1.2.2
-connexion==1.5.2
+connexion==2.4.0
 cryptography==2.3.1
--e git+https://github.com/ohsu-comp-bio/cwl-tes.git@62840435c5b22ac7b3ad1724047d811f72dd372d#egg=cwl-tes
+-e git+https://github.com/uniqueg/cwl-tes-temp.git@e37090e00f2573e84becec30f0ade9c5003820b3#egg=cwl_tes
 cwltool==1.0.20181217162649
 decorator==4.3.0
-Flask==1.0.2
+Flask==1.1.1
 Flask-Cors==3.0.6
 Flask-PyMongo==2.1.0
 future==0.16.0
@@ -40,6 +40,7 @@ mccabe==0.6.1
 mistune==0.8.4
 mypy-extensions==0.4.1
 networkx==2.2
+openapi-spec-validator==0.2.8
 prov==1.5.1
 psutil==5.4.7
 py-tes==0.3.0
@@ -50,7 +51,7 @@ pymongo==3.7.1
 pyparsing==2.2.1
 python-dateutil==2.6.1
 pytz==2018.5
-PyYAML==4.2b1
+PyYAML==5.1.2
 rdflib==4.2.2
 rdflib-jsonld==0.4.0
 requests==2.20.0
@@ -61,9 +62,10 @@ shellescape==3.4.1
 six==1.11.0
 subprocess32==3.5.2
 swagger-spec-validator==2.3.1
+swagger-ui-bundle==0.0.6
 typed-ast==1.1.0
 typing==3.6.6
-typing-extensions==3.6.5
+typing-extensions==3.7.4
 urllib3==1.24.2
 vine==1.1.4
 Werkzeug==0.15.3

wes_elixir/api/controllers.py

@@ -0,0 +1,47 @@
+"""Controller for auxiliary WES-ELIXIR API endpoints."""
+
+import logging
+
+from celery import current_app as celery_app
+from connexion import request
+from flask import current_app
+
+from wes_elixir.security.decorators import auth_token_optional
+
+# Get logger instance
+logger = logging.getLogger(__name__)
+
+
+# GET /stdout/<run_id>
+@auth_token_optional
+def get_stdout(run_id, *args, **kwargs):
+    """Returns run STDOUT as plain text."""
+    response = ""
+    log_request(request, response)
+    return response
+
+
+# POST /stderr/<run_id>
+@auth_token_optional
+def get_stderr(run_id, *args, **kwargs):
+    """Returns run STDERR as plain text."""
+    response = ""
+    log_request(request, response)
+    return response
+
+
+def log_request(request, response):
+    """Writes request and response to log."""
+    # TODO: write decorator for request logging
+    logger.debug(
+        (
+            "Response to request \"{method} {path} {protocol}\" from "
+            "{remote_addr}: {response}"
+        ).format(
+            method=request.environ['REQUEST_METHOD'],
+            path=request.environ['PATH_INFO'],
+            protocol=request.environ['SERVER_PROTOCOL'],
+            remote_addr=request.environ['REMOTE_ADDR'],
+            response=response,
+        )
+    )

wes_elixir/api/register_openapi.py

@@ -39,13 +39,20 @@ def register_openapi(
             path = __add_security_definitions(in_file=path)
 
         # Generate API endpoints from OpenAPI spec
+        options = {
+            "swagger_ui": get_conf(spec, 'swagger_ui'),
+            "serve_spec": get_conf(spec, 'swagger_json'),
+        }
+        base_path = get_conf(spec, 'base_path')
+        if not base_path:
+            base_path = None
         try:
             app.add_api(
                 path,
                 strict_validation=get_conf(spec, 'strict_validation'),
                 validate_responses=get_conf(spec, 'validate_responses'),
-                swagger_ui=get_conf(spec, 'swagger_ui'),
-                swagger_json=get_conf(spec, 'swagger_json'),
+                options=options,
+                base_path=base_path,
             )
 
             logger.info("API endpoints specified in '{path}' added.".format(

wes_elixir/api/schema.stdout_stderr.openapi.yaml

@@ -0,0 +1,163 @@
+openapi: 3.0.0
+info:
+  title: WES-ELIXIR STDOUT & STDERR OpenAPI specification
+  contact:
+    name: ELIXIR Cloud & AAI group
+    email: [email protected]
+  license:
+    name: Apache 2.0
+    url: https://www.apache.org/licenses/LICENSE-2.0
+  version: 0.14.0
+servers:
+- url: /wes-elixir/v1
+paths:
+  /stdout/{run_id}:
+    get:
+      summary: |-
+        Retrieves the content of the indicated run's STDOUT stream and returns
+        it as plain text.
+      parameters:
+        - in: path
+          name: run_id
+          schema:
+            type: string
+          required: true
+          description: Run identifier.
+      operationId: get_stdout
+      responses:
+        200:
+          description: |-
+            STDOUT stream of indicated run as plain text.
+          content:
+            text/plain:
+              schema:
+                type: string
+                example: "This is STDOUT."
+        400:
+          description: The request is malformed.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        401:
+          description: The request is unauthorized.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        403:
+          description: The requester is not authorized to perform this action.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        404:
+          description: The requested resource was not found.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        500:
+          description: An unexpected error occurred.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+      x-openapi-router-controller: api.controllers
+  /stderr/{run_id}:
+    get:
+      summary: |-
+        Retrieves the content of the indicated run's STDERR stream and returns
+        it as plain text.
+      operationId: get_stderr
+      parameters:
+        - in: path
+          name: run_id
+          schema:
+            type: string
+          required: true
+          description: Run identifier.
+      responses:
+        200:
+          description: |-
+            STDERR stream of indicated run as plain text.
+          content:
+            text/plain:
+              schema:
+                type: string
+                example: "This is STDERR."
+        400:
+          description: The request is malformed.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        401:
+          description: The request is unauthorized.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        403:
+          description: The requester is not authorized to perform this action.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        404:
+          description: The requested resource was not found.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        500:
+          description: An unexpected error occurred.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+      x-openapi-router-controller: api.controllers
+components:
+  schemas:
+    Error:
+      required:
+      - message
+      - reason
+      type: object
+      properties:
+        message:
+          type: string
+          description: |-
+            A human readable message providing more details about the error.
+          example:
+            Required parameter 'xyz' is missing.
+        reason:
+          type: string
+          description: |-
+            Unique identifier for this error, but *not* the HTTP response code
+            (e.g., name of exception).
+          example: ValueError
+      description: An individual error message.
+    ErrorResponse:
+      required:
+      - code
+      - errors
+      - message
+      type: object
+      properties:
+        code:
+          type: integer
+          description: HTTP status code (e.g., 400, 404).
+          format: int64
+          example: 400
+        errors:
+          type: array
+          description: List of associated errors and warnings.
+          items:
+            $ref: '#/components/schemas/Error'
+        message:
+          type: string
+          description: |-
+            A human readable message providing more details about the error.
+          example: The request could not be interpreted.
+      description: A response object for detailed error messages.

wes_elixir/config/app_config.yaml

@@ -53,11 +53,20 @@ celery:
 # OpenAPI specs
 api:
     specs:
-        - path: '20181023.c5406f1-v1-0-0.workflow_execution_service.swagger.yaml'
+        - name: 'WES'
+          path: '20181023.c5406f1-v1-0-0.workflow_execution_service.swagger.yaml'
           strict_validation: True
           validate_responses: True
           swagger_ui: True
           swagger_json: True
+          base_path: False
+        - name: 'stdout_stderr'
+          path: 'schema.stdout_stderr.openapi.yaml'
+          strict_validation: True
+          validate_responses: True
+          swagger_ui: True
+          swagger_json: True
+          base_path: '/wes-elixir/v1'
     general_params:
         time_format: "%Y-%m-%dT%H:%M:%SZ"
     endpoint_params:

wes_elixir/ga4gh/wes/endpoints/get_run_log.py

@@ -52,4 +52,6 @@ def get_run_log(
         )
         raise Forbidden
 
+    # Remove 
+
     return run_log