Revert "fix(migrate): improve acl->authz migration, remove deprecated…

bin/migrate_acl_authz.py

@@ -34,9 +34,8 @@
 
 from indexd.index.drivers.alchemy import IndexRecord, IndexRecordAuthz
 
-from yaml import safe_load
 
-logger = get_logger("migrate_acl_authz", log_level="debug")
+logger = get_logger("migrate_acl_authz")
 
 
 def main():
@@ -50,10 +49,7 @@ def main():
     driver = settings["config"]["INDEX"]["driver"]
     try:
         acl_converter = ACLConverter(
-            args.arborist,
-            getattr(args, "sheepdog"),
-            getattr(args, "use_tags"),
-            getattr(args, "user_yaml_path"),
+            args.arborist, getattr(args, "sheepdog"), getattr(args, "use_tags")
         )
     except EnvironmentError:
         logger.error("can't continue without database connection")
@@ -123,18 +119,11 @@ def parse_args():
         dest="start_did",
         help="did to start at (records processed in lexographical order)",
     )
-    parser.add_argument(
-        "--user-yaml-path",
-        dest="user_yaml_path",
-        help="path to user yaml for pulling authz mapping",
-    )
     return parser.parse_args()
 
 
 class ACLConverter(object):
-    def __init__(
-        self, arborist_url, sheepdog_db=None, use_tags=False, user_yaml_path=None
-    ):
+    def __init__(self, arborist_url, sheepdog_db=None, use_tags=False):
         self.arborist_url = arborist_url.rstrip("/")
         self.programs = set()
         self.projects = dict()
@@ -145,21 +134,6 @@ def __init__(
         else:
             logger.info("not using any auth namespace")
         self.use_sheepdog_db = bool(sheepdog_db)
-        self.mapping = {}
-
-        if user_yaml_path:
-            with open(user_yaml_path, "r") as f:
-                user_yaml = safe_load(f)
-                user_yaml_authz = user_yaml.get("authz", dict())
-                if not user_yaml_authz:
-                    user_yaml_authz = user_yaml.get("rbac", dict())
-
-                project_to_resource = user_yaml_authz.get(
-                    "user_project_to_resource", dict()
-                )
-                self.mapping = project_to_resource
-
-        logger.info(f"got mapping: {self.mapping}")
 
         # if "use_tags" is True, map resource paths to tags in arborist so
         # we can save http calls
@@ -220,10 +194,6 @@ def acl_to_authz(self, record):
             if not acl_item:
                 # ignore empty string
                 continue
-            # prefer user.yaml authz mapping if provided
-            elif acl_item in self.mapping:
-                path = self.mapping[acl_item]
-                projects_found += 1
             elif acl_item == "*":
                 # if there's a * it should just be open. return early
                 path = "/open"

indexd/app.py

@@ -7,6 +7,7 @@
 from .guid.blueprint import blueprint as indexd_drs_blueprint
 from .blueprint import blueprint as cross_blueprint
 
+from indexd.fence_client import FenceClient
 from indexd.urls.blueprint import blueprint as index_urls_blueprint
 
 import os
@@ -21,6 +22,10 @@ def app_init(app, settings=None):
         from .default_settings import settings
     app.config.update(settings["config"])
     app.auth = settings["auth"]
+    app.fence_client = FenceClient(
+        url=os.environ.get("PRESIGNED_FENCE_URL")
+        or "http://presigned-url-fence-service"
+    )
     app.hostname = os.environ.get("HOSTNAME") or "http://example.io"
     app.register_blueprint(indexd_bulk_blueprint)
     app.register_blueprint(indexd_index_blueprint)

indexd/drs/blueprint.py

@@ -64,6 +64,26 @@ def list_drs_records():
     return flask.jsonify(ret), 200
 
 
+@blueprint.route(
+    "/ga4gh/drs/v1/objects/<path:object_id>/access",
+    defaults={"access_id": None},
+    methods=["GET"],
+)
+@blueprint.route(
+    "/ga4gh/drs/v1/objects/<path:object_id>/access/<path:access_id>", methods=["GET"]
+)
+def get_signed_url(object_id, access_id):
+    if not access_id:
+        raise (UserError("Access ID/Protocol is required."))
+    res = flask.current_app.fence_client.get_signed_url_for_object(
+        object_id=object_id, access_id=access_id
+    )
+    if not res:
+        raise IndexNoRecordFound("No signed url found")
+
+    return res, 200
+
+
 def create_drs_uri(did):
     """
     Return ga4gh-compilant drs format uri

indexd/fence_client.py

@@ -0,0 +1,55 @@
+from cdislogging import get_logger
+
+import flask
+import requests
+
+
+from indexd.index.errors import NoRecordFound as IndexNoRecordFound
+from indexd.errors import IndexdUnexpectedError
+from indexd.auth.errors import AuthError, AuthzError
+
+
+logger = get_logger(__name__)
+
+
+class FenceClient(object):
+    def __init__(self, url):
+        self.url = url
+
+    def get_signed_url_for_object(self, object_id, access_id):
+        fence_server = self.url
+        api_url = fence_server.rstrip("/") + "/data/download/"
+        url = api_url + object_id
+        headers = flask.request.headers
+        if "AUTHORIZATION" not in headers:
+            logger.error("Bearer Token not available.")
+            raise AuthError("Not Authorized. Access Token Required.")
+        if access_id:
+            url += "?protocol=" + access_id
+            if flask.request.query_string:
+                url = f"{url}&{flask.request.query_string.decode()}"
+        try:
+            req = requests.get(url, headers=headers)
+        except Exception as e:
+            logger.error("failed to reach fence at {0}: {1}".format(url + object_id, e))
+            raise IndexdUnexpectedError("Failed to retrieve access url")
+        if req.status_code == 404:
+            logger.error(
+                "Not found. Fence could not find {}: {} with access id: {}".format(
+                    url + object_id, req.text, access_id
+                )
+            )
+            raise IndexNoRecordFound(
+                "No document with id:{} with access_id:{}".format(object_id, access_id)
+            )
+        if req.status_code == 401:
+            raise AuthzError("Unauthorized: Access denied due to invalid credentials.")
+        elif req.status_code != 200:
+            err_msg = "Unable to get presigned URL from Fence"
+            logger.error(
+                "{} - code: {} - details:\n{}".format(
+                    err_msg, req.status_code, req.text
+                )
+            )
+            raise IndexdUnexpectedError(code=req.status_code, message=err_msg)
+        return req.json()

openapis/swagger.yaml

@@ -1101,6 +1101,70 @@ paths:
         - authToken: []
       tags:
         - DRS
+  '/ga4gh/drs/v1/objects/{object_id}/access/{access_id}':
+    get:
+      summary: Get a URL for fetching bytes.
+      description: >-
+        Returns a URL that can be used to fetch the bytes of a DrsObject.
+        This method only needs to be called when using an AccessMethod that contains an access_id
+        (e.g., for servers that use signed URLs for fetching object bytes).
+      operationId: GetAccessURL
+      responses:
+        '200':
+          description: The access URL was found successfully.
+          schema:
+            $ref: '#/definitions/AccessURL'
+        # '202':
+        #   description: >
+        #     The operation is delayed and will continue asynchronously.
+        #     The client should retry this same request after the delay specified by Retry-After header.
+        #   headers:
+        #     Retry-After:
+        #       description: >
+        #         Delay in seconds. The client should retry this same request after waiting for this duration.
+        #         To simplify client response processing, this must be an integral relative time in seconds.
+        #         This value SHOULD represent the minimum duration the client should wait before attempting
+        #         the operation again with a reasonable expectation of success. When it is not feasible
+        #         for the server to determine the actual expected delay, the server may return a
+        #         brief, fixed value instead.
+        #       type: integer
+        #       format: int64
+        '400':
+          description: The request is malformed.
+          schema:
+            $ref: '#/definitions/Error'
+        '401':
+          description: The request is unauthorized.
+          schema:
+            $ref: '#/definitions/Error'
+        '404':
+          description: The requested access URL wasn't found
+          schema:
+            $ref: '#/definitions/Error'
+        '403':
+          description: The requester is not authorized to perform this action.
+          schema:
+            $ref: '#/definitions/Error'
+        '500':
+          description: An unexpected error occurred.
+          schema:
+            $ref: '#/definitions/Error'
+      parameters:
+        - name: object_id
+          in: path
+          required: true
+          type: string
+          description: An id of a DrsObject
+        - name: access_id
+          in: path
+          required: true
+          type: string
+          description: An access_id from the access_methods list of a DrsObject
+      security:
+        - authToken: []
+      tags:
+        - DRS
+      x-swagger-router-controller: ga4gh.drs.server
   '/bundle':
     post:
       tags: