Features/new auth

bento_beacon/app.py

@@ -11,7 +11,7 @@
 from .endpoints.datasets import datasets
 from .utils.exceptions import APIException
 from werkzeug.exceptions import HTTPException
-from .authz import authz_middleware
+from .authz.middleware import authz_middleware
 from .config_files.config import Config
 from .utils.beacon_response import beacon_error_response
 from .utils.beacon_request import save_request_data, validate_request

bento_beacon/authz/headers.py

@@ -0,0 +1,10 @@
+from flask import request, Request
+
+
+def auth_header_getter(r: Request) -> dict[str, str]:
+    token = r.headers.get("authorization")
+    return {"Authorization": token} if token else {}
+
+
+def auth_header_from_request() -> dict[str, str]:
+    return auth_header_getter(request)

bento_beacon/authz.py → bento_beacon/authz/middleware.py

@@ -1,6 +1,7 @@
+from flask import request
 from bento_lib.auth.middleware.flask import FlaskAuthMiddleware
-from .config_files.config import Config
-from .utils.beacon_response import build_response_meta
+from ..config_files.config import Config
+from ..utils.beacon_response import build_response_meta
 
 __all__ = [
     "authz_middleware",
@@ -10,13 +11,16 @@
     "PERMISSION_QUERY_DATASET_LEVEL_COUNTS",
     "PERMISSION_QUERY_DATA",
     "PERMISSION_DOWNLOAD_DATA",
+    "check_permissions",
+    "check_permission"
 ]
 
 
 authz_middleware = FlaskAuthMiddleware(
     Config.AUTHZ_URL,
     enabled=Config.AUTHZ_ENABLED,
     beacon_meta_callback=build_response_meta,
+    debug_mode=Config.BENTO_DEBUG
 )
 
 # for now, these will go unused - Beacon currently does not have a strong concept of Bento projects/datasets
@@ -27,3 +31,17 @@
 # these permissions can open up various aspects of handoff / full-search
 PERMISSION_QUERY_DATA = "query:data"
 PERMISSION_DOWNLOAD_DATA = "download:data"
+
+
+def check_permissions(permissions: list[str]) -> bool:
+    auth_res = authz_middleware.authz_post(request, "/policy/evaluate", body={
+        "requested_resource": {"everything": True},
+        "required_permissions": permissions,
+        },
+    )["result"]
+    authz_middleware.mark_authz_done(request)
+    return auth_res
+
+
+def check_permission(permission: str) -> bool:
+    return check_permissions([permission])

bento_beacon/config_files/config.py

@@ -20,6 +20,9 @@ class Config:
 
     DEFAULT_PAGINATION_PAGE_SIZE = 10
 
+    BENTO_DEBUG = os.environ.get("BENTO_DEBUG", os.environ.get(
+        "FLASK_DEBUG", "false")).strip().lower() in ('true', '1', 't')
+
     BENTO_DOMAIN = os.environ.get("BENTOV2_DOMAIN")
     BEACON_BASE_URL = os.environ.get("BEACON_BASE_URL")
     BENTO_PUBLIC_URL = os.environ.get("BENTOV2_PUBLIC_URL")
@@ -140,8 +143,7 @@ class Config:
 # -------------------
 # drs
 
-    DRS_INTERNAL_URL = os.environ.get("DRS_INTERNAL_URL")
-    DRS_EXTERNAL_URL = os.environ.get("DRS_EXTERNAL_URL")
+    DRS_URL = os.environ.get("DRS_URL")
 
 # -------------------
 # authorization

bento_beacon/endpoints/cohorts.py

@@ -1,5 +1,5 @@
 from flask import Blueprint, current_app
-from ..authz import authz_middleware
+from ..authz.middleware import authz_middleware
 from ..utils.exceptions import NotImplemented
 from ..utils.beacon_response import beacon_response
 

bento_beacon/endpoints/datasets.py

@@ -1,5 +1,5 @@
 from flask import Blueprint, current_app
-from ..authz import authz_middleware
+from ..authz.middleware import authz_middleware
 from ..utils.exceptions import NotImplemented
 from ..utils.beacon_response import beacon_response
 from ..utils.katsu_utils import katsu_datasets

bento_beacon/endpoints/individuals.py

@@ -1,37 +1,43 @@
 from flask import Blueprint
 from functools import reduce
-from ..authz import authz_middleware
+from ..authz.middleware import authz_middleware, PERMISSION_DOWNLOAD_DATA, PERMISSION_QUERY_DATA, check_permission
 from ..utils.beacon_request import (
     query_parameters_from_request,
     summary_stats_requested,
-    )
+)
 from ..utils.beacon_response import (
     beacon_response,
     add_info_to_response,
     add_stats_to_response,
     add_overview_stats_to_response,
-    zero_count_response
+    zero_count_response,
+    beacon_full_response
 )
 from ..utils.katsu_utils import (
     katsu_filters_and_sample_ids_query,
     katsu_total_individuals_count,
-    search_from_config
+    search_from_config,
+    phenopackets_for_ids
 )
 from ..utils.search import biosample_id_search
+from ..utils.handover_utils import handover_for_ids
 
 individuals = Blueprint("individuals", __name__)
 
 
 @individuals.route("/individuals", methods=['GET', 'POST'])
-@authz_middleware.deco_public_endpoint  # TODO: authz - for now. eventually, return more depending on permissions
 def get_individuals():
+
+    full_response = check_permission(PERMISSION_QUERY_DATA)
+
     variants_query, phenopacket_filters, experiment_filters, config_filters = query_parameters_from_request()
 
     no_query = not (variants_query or phenopacket_filters or experiment_filters or config_filters)
     search_sample_ids = variants_query or experiment_filters
     config_search_only = config_filters and not (variants_query or phenopacket_filters or experiment_filters)
 
     # return total count of individuals if no query
+    # TODO: return default granularity rather than count (default could be bool rather than count)
     if no_query:
         add_info_to_response("no query found, returning total count")
         total_count = katsu_total_individuals_count()
@@ -73,41 +79,61 @@ def get_individuals():
     # baroque syntax but covers all cases
     individual_ids = list(reduce(set.intersection, (set(ids) for ids in individual_results.values())))
 
-    # conditionally add summary statistics to response
     if summary_stats_requested():
         add_stats_to_response(individual_ids)
 
+    if full_response:
+        return individuals_full_response(individual_ids)
+
     return beacon_response({"count": len(individual_ids), "results": individual_ids})
 
 
-# -------------------------------------------------------
-#       unimplemented endpoints
-# -------------------------------------------------------
-# these would be appropriate for full-access beacons only
+# TODO: pagination (ideally after katsu search gets paginated)
+def individuals_full_response(ids):
+
+    # temp
+    # if len(ids) > 100:
+    #     return {"message": "too many ids for full response"}
 
-# replace this one once auth is in place
-# @individuals.route("/individuals/<id>", methods=['GET', 'POST'])
-# @authn_token_required_flask_wrapper
-# def individual_by_id(id):
-#     # get one individual by id, with handover if available
-#     return individuals_full_response([id])
+    handover_permission = check_permission(PERMISSION_DOWNLOAD_DATA)
+    handover = handover_for_ids(ids) if handover_permission else {}
+    phenopackets_by_result_set = phenopackets_for_ids(ids).get("results", {})
+    result_ids = list(phenopackets_by_result_set.keys())
+    result_sets = {}
 
+    for r_id in result_ids:
+        results_this_id = phenopackets_by_result_set.get(r_id, {}).get("matches", [])
+        results_count = len(results_this_id)
+        result = {
+            "id": r_id,
+            "setType": "individual",
+            "exists": results_count > 0,
+            "resultsCount": results_count,
+            "results": results_this_id,
+        }
+        handover_this_id = handover.get(r_id, [])
+        if handover_this_id:
+            result["resultsHandovers"] = handover_this_id
+        result_sets[r_id] = result
 
-# @individuals.route("/individuals/<id>/g_variants", methods=['GET', 'POST'])
-# def individual_variants(id):
-#     # all variants for a particular individual
-#     # may never be implemented, bad match for our use case (download vcf instead)
-#     raise NotImplemented()
+    return beacon_full_response(result_sets)
 
 
-# @individuals.route("/individuals/<id>/biosamples", methods=['GET', 'POST'])
-# def individual_biosamples(id):
-#     # all biosamples for a particular individual
-#     pass
+@individuals.route("/individuals/<id>", methods=['GET', 'POST'])
+@authz_middleware.deco_require_permissions_on_resource({PERMISSION_QUERY_DATA})
+def individual_by_id(id):
+    # forbidden / unauthorized if no permissions
+    return individuals_full_response([id])
 
 
-# @individuals.route("/individuals/<id>/filtering_terms", methods=['GET', 'POST'])
-# def individual_filtering_terms(id):
-#     # filtering terms for a particular individual
-#     # note that this involves private data   
-#     pass
+# -------------------------------------------------------
+#       endpoints in beacon model not yet implemented:
+#
+#       /individuals/<id>/g_variants
+#           - may be simpler to download vcf instead
+#       /individuals/<id>/biosamples
+#           - requires full response code for biosamples (could just serve phenopackets again here)
+#       /individuals/<id>/filtering_terms
+#           - unclear use case, isn't reading the full response better?
+#           - requires better ontology support / better filtering terms implementation
+# -------------------------------------------------------

bento_beacon/endpoints/info.py

@@ -1,7 +1,7 @@
 import json
 from copy import deepcopy
 from flask import Blueprint, current_app
-from ..authz import authz_middleware
+from ..authz.middleware import authz_middleware
 from ..utils.beacon_response import beacon_info_response
 from ..utils.katsu_utils import (
     get_filtering_terms,

bento_beacon/endpoints/variants.py

@@ -1,5 +1,5 @@
 from flask import Blueprint
-from ..authz import authz_middleware
+from ..authz.middleware import authz_middleware
 from ..utils.beacon_request import query_parameters_from_request
 from ..utils.beacon_response import beacon_response, add_info_to_response
 from ..utils.gohan_utils import query_gohan, gohan_total_variants_count, gohan_totals_by_sample_id

bento_beacon/utils/beacon_response.py

@@ -20,6 +20,7 @@ def init_response_data():
     g.response_info = {}
 
 
+# TODO: handle multiple messages
 def add_info_to_response(info):
     g.response_info["message"] = info
 
@@ -83,7 +84,7 @@ def beacon_response(results, collection_response=False):
     return r
 
 
-def beacon_response_with_handover(result_sets):
+def beacon_full_response(result_sets):
     g.request_data["requestedGranularity"] = "record"
     r = {
         "meta": build_response_meta(),
@@ -121,7 +122,7 @@ def build_response_meta():
     received_request_summary = received_request()
     return {
         "beaconId": current_app.config["BEACON_ID"],
-        "apiVersion": current_app.config["BEACON_SPEC_VERSION"],   
+        "apiVersion": current_app.config["BEACON_SPEC_VERSION"],
         "returnedSchemas": returned_schemas,
         "returnedGranularity": returned_granularity,
         "receivedRequestSummary": received_request_summary

bento_beacon/utils/gohan_utils.py

@@ -1,6 +1,6 @@
 from flask import current_app
 from .exceptions import APIException, InvalidQuery, NotImplemented
-from .nested_query_utils import auth_header_from_request
+from ..authz.headers import auth_header_from_request
 import requests
 
 # -------------------------------------------------------