misc. scoping fixes

bento_beacon/app.py

@@ -3,6 +3,7 @@
 from flask import Flask, current_app, request
 from urllib.parse import urlunsplit
 from .endpoints.info import info
+from .endpoints.info_permissions_required import info_permissions_required
 from .endpoints.individuals import individuals
 from .endpoints.variants import variants
 from .endpoints.biosamples import biosamples
@@ -40,8 +41,8 @@
 
 # blueprints
 # always load info endpoints, load everything else based on config
-
 app.register_blueprint(info)
+app.register_blueprint(info_permissions_required)
 
 endpoint_blueprints = {
     "biosamples": biosamples,
@@ -66,12 +67,13 @@
 
 @app.before_request
 async def before_request():
-    if request.blueprint != "info":
-        validate_request()
-        await verify_permissions()
-        await save_request_data()
-        await set_censorship()
-        init_response_data()
+    if request.blueprint == "info":
+        return 
+    validate_request()
+    await verify_permissions()
+    await save_request_data()
+    await set_censorship()
+    init_response_data()
 
 
 @app.errorhandler(Exception)

bento_beacon/config_files/config.py

@@ -146,7 +146,7 @@ class Config:
     KATSU_BASE_URL = os.environ.get("KATSU_BASE_URL")
     KATSU_BIOSAMPLES_ENDPOINT = "/api/biosamples"
     KATSU_INDIVIDUALS_ENDPOINT = "/api/individuals"
-    KATSU_BATCH_INDIVIDUALS_ENDPOINT = "/api/batch/individuals"
+    KATSU_PROJECTS_ENDPOINT = "/api/projects"
     KATSU_DATASETS_ENDPOINT = "/api/datasets"
     KATSU_SEARCH_ENDPOINT = "/private/search"
     KATSU_RESOURCES_ENDPOINT = "/api/resources"

bento_beacon/endpoints/info.py

@@ -1,13 +1,10 @@
 from flask import Blueprint, current_app
 from ..authz.middleware import authz_middleware
-from ..utils.beacon_response import beacon_info_response, add_info_to_response, summary_stats
+from ..utils.beacon_response import beacon_info_response
 from ..utils.katsu_utils import (
-    get_filtering_terms,
-    katsu_total_individuals_count,
     katsu_get,
     katsu_datasets,
 )
-from ..utils.gohan_utils import gohan_counts_for_overview
 from ..utils.scope import scoped_route_decorator_for_blueprint
 
 
@@ -42,7 +39,7 @@ async def service_info(project_id=None):
 async def beacon_info(project_id=None):
     """
     service info in beacon format
-    dataset info is scoped, rest of response unscoped
+    description field is scoped, rest of response unscoped
     """
     return beacon_info_response(await beacon_format_service_details(project_id))
 

bento_beacon/endpoints/info_permissions_required.py

@@ -1,6 +1,6 @@
 from flask import Blueprint, current_app
 from ..authz.middleware import authz_middleware
-from .info import beacon_format_service_details 
+from .info import beacon_format_service_details
 from ..utils.beacon_response import beacon_info_response, add_info_to_response, summary_stats
 from ..utils.katsu_utils import (
     get_filtering_terms,
@@ -15,29 +15,26 @@
 
 
 @route_with_optional_project_id("/info")
-@authz_middleware.deco_public_endpoint
 async def beacon_info_with_overview(project_id=None):
     """
-    as above but with beacon overview details
-    unscoped, overview details currently node-level only
+    returns same beacon-format service info served from root endpoint, but with an overview added
+    overview is unscoped, no overview info is returned for scoped requests
+    description field is scoped (this is pulled from datasets data)
     """
-
     service_info = await beacon_format_service_details(project_id)
     return beacon_info_response({**service_info, "overview": await overview()})
 
 
 @route_with_optional_project_id("/overview")
-@authz_middleware.deco_public_endpoint
 async def beacon_overview(project_id=None):
     """
     Custom endpoint not in beacon spec
-    currently node-level overview only 
+    currently node-level overview only
     """
     service_info = await beacon_format_service_details(project_id)
     return beacon_info_response({**service_info, "overview": await overview(project_id)})
 
 
-# xxxxxxxxxxxxxxxx move this to its own blueprint, since this now looks at permissions xxxxxxxxxxxxxxxxx
 # could be scoped by dataset only by adding query params for dataset (endpoint is GET only)
 # this endpoint normally doesn't take queries at all, the only params it recognizes are for pagination
 # could also annotating filtering terms with a dataset id in cases where it's limited to a particular dataset
@@ -54,7 +51,7 @@ async def filtering_terms(project_id=None):
 
 
 # -------------------------------------------------------
-#  
+#
 # -------------------------------------------------------
 
 
@@ -72,11 +69,10 @@ async def overview(project_id=None, dataset_id=None):
     else:
         variants = {}
 
-    # can be removed once bento_public is updated (it reads from counts.variants for assemblyIDs)
+    # can be removed once bento_public and beacon network nodes are updated (it reads from counts.variants for assemblyIDs)
     legacy_format_overview = {"counts": {"individuals": await katsu_total_individuals_count(), "variants": variants}}
 
     katsu_stats = await summary_stats(None)
     beacon_overview = {"variants": variants, **katsu_stats}
 
     return {**legacy_format_overview, **beacon_overview}
-

bento_beacon/utils/beacon_response.py

@@ -1,4 +1,4 @@
-from flask import current_app, g, request
+from flask import current_app, g, request, url_for
 from .katsu_utils import search_summary_statistics, overview_statistics
 from .censorship import (
     get_censorship_threshold,
@@ -28,23 +28,30 @@ def add_message(message_obj):
 
 def add_no_results_censorship_message_to_response():
     add_info_to_response(MESSAGE_FOR_CENSORED_QUERY_WITH_NO_RESULTS)
-    add_info_to_response(f"censorship threshold: {current_app.config['COUNT_THRESHOLD']}")
+    add_info_to_response(f"censorship threshold: {g.count_threshold}")
 
 
 async def add_stats_to_response(ids):
+    stats = await summary_stats(ids)
+    if stats: 
+        g.response_info["bento"] = await summary_stats(ids)
+
+
+async def add_overview_stats_to_response():
+    await add_stats_to_response(None)
+
+
+async def summary_stats(ids):
     if ids is not None and len(ids) <= (await get_censorship_threshold()):
-        return
+        return None
 
     if ids is None:
         stats = await overview_statistics()
     else:
         stats = await search_summary_statistics(ids)
     packaged_stats = await package_biosample_and_experiment_stats(stats)
-    g.response_info["bento"] = packaged_stats
-
+    return packaged_stats
 
-async def add_overview_stats_to_response():
-    await add_stats_to_response(None)
 
 
 async def package_biosample_and_experiment_stats(stats):
@@ -137,7 +144,7 @@ async def build_query_response(ids=None, numTotalResults=None, full_record_handl
         if full_record_handler is None:
             # user asked for full response where it doesn't exist yet, e.g. in variants
             raise InvalidQuery("record response not available for this entry type")
-        result_sets, numTotalResults = full_record_handler(ids)
+        result_sets, numTotalResults = await full_record_handler(ids)
         return beacon_result_set_response(result_sets, numTotalResults)
 
 
@@ -260,7 +267,8 @@ def response_info():
 
 
 def info_endpoint_schema():
-    return [current_app.config["INFO_ENDPOINTS_SCHEMAS"][request.path]]
+    path_without_optional_project_id = url_for(request.endpoint)
+    return [current_app.config["INFO_ENDPOINTS_SCHEMAS"][path_without_optional_project_id]]
 
 
 def schemas_this_query():

bento_beacon/utils/censorship.py

@@ -70,7 +70,7 @@ async def reject_if_too_many_filters() -> None:
     if g.permission_query_data:
         return
     max_filters = await get_max_filters()
-    request_filters = g.get("request_data", {}).get("filters")
+    request_filters = g.get("request_data", {}).get("filters", [])
     if len(request_filters) > max_filters:
         raise InvalidQuery(f"too many filters in request, maximum of {max_filters} permitted")
 

bento_beacon/utils/scope.py

@@ -1,12 +1,12 @@
-def scoped_route_decorator_generator(blueprint):
+def scoped_route_decorator_for_blueprint(blueprint):
     """
-    # Generates a decorator equivalent to two flask "@route" decorators, one with a project_id prefix, and one without
+    Generates a decorator equivalent to two flask "@route" decorators, one with a project_id prefix, and one without.
 
-    # input: a flask blueprint (all beacon routes belong to a particular blueprint)
+    input: a flask blueprint (all beacon routes belong to a particular blueprint)
 
-    # output: a decorator that's equivalent to invoking these two flask decorators together:
-        # @my_blueprint.route("my_route", **options)
-        # @my_blueprint.route("/<project_id>/my_route", **options)
+    output: a decorator that's equivalent to invoking these two flask decorators together:
+        @my_blueprint.route("my_route", **options)
+        @my_blueprint.route("/<project_id>/my_route", **options)
     """
 
     def scoped_route(rule, **options):