Merge branch 'master' into features/filtering-terms-from-config

bento_beacon/config_files/config.py

@@ -143,12 +143,13 @@ class Config:
     KATSU_DISEASES_TERMS_ENDPOINT = "/api/disease_term_autocomplete"
     KATSU_SAMPLED_TISSUES_TERMS_ENDPOINT = "/api/biosample_sampled_tissue_autocomplete"
     KATSU_PUBLIC_CONFIG_ENDPOINT = "/api/public_search_fields"
-    KATSU_INDIVIDUAL_SCHEMA_ENDPOINT = "/api/chord_phenopacket_schema"
-    KATSU_EXPERIMENT_SCHEMA_ENDPOINT = "/api/experiment_schema"
+    KATSU_INDIVIDUAL_SCHEMA_ENDPOINT = "/api/schemas/phenopacket"
+    KATSU_EXPERIMENT_SCHEMA_ENDPOINT = "/api/schemas/experiment"
     KATSU_BEACON_SEARCH = "/api/beacon_search"
     KATSU_SEARCH_OVERVIEW = "/api/search_overview"
     KATSU_PRIVATE_OVERVIEW = "/api/overview"
     KATSU_PUBLIC_OVERVIEW = "/api/public_overview"
+    KATSU_PUBLIC_RULES = "/api/public_rules"
     KATSU_TIMEOUT = int(os.environ.get("BEACON_KATSU_TIMEOUT", 180))
 
     MAP_EXTRA_PROPERTIES_TO_INFO = os.environ.get("MAP_EXTRA_PROPERTIES_TO_INFO", True)

bento_beacon/endpoints/info.py

@@ -143,7 +143,7 @@ def build_ga4gh_service_info():
         "name": info["name"],
         "type": {"artifact": "Beacon v2", "group": "org.ga4gh", "version": info["apiVersion"]},
         "environment": info["environment"],
-        "organization": {"name": info["organization"]["name"], "url": info["organization"]["welcomeUrl"]},
+        "organization": {"name": info["organization"]["name"], "url": info["organization"].get("welcomeUrl", "")},
         "contactUrl": info["organization"]["contactUrl"],
         "version": info["version"],
         "bento": {"serviceKind": "beacon"},

bento_beacon/utils/katsu_utils.py

@@ -289,9 +289,10 @@ def overview_statistics():
 
 
 def katsu_censorship_settings() -> tuple[int | None, int | None]:
-    overview = katsu_get(current_app.config["KATSU_PUBLIC_OVERVIEW"])
-    max_filters = overview.get("max_query_parameters")
-    count_threshold = overview.get("count_threshold")
+    # TODO: should be project-dataset scoped
+    rules = katsu_get(current_app.config["KATSU_PUBLIC_RULES"])
+    max_filters = rules.get("max_query_parameters")
+    count_threshold = rules.get("count_threshold")
     # return even if None
     return max_filters, count_threshold
 

bento_beacon/utils/search.py

@@ -1,6 +1,8 @@
+from flask import current_app
 from functools import reduce
 from .gohan_utils import query_gohan
 from .katsu_utils import katsu_filters_query, search_from_config, biosample_ids_for_individuals
+from .beacon_response import add_info_to_response
 
 
 # TODO: search by linked field set elements instead of hardcoding
@@ -11,6 +13,10 @@ def biosample_id_search(variants_query=None, phenopacket_filters=None, experimen
         return []
 
     if variants_query:
+        if not current_app.config["BEACON_CONFIG"].get("useGohan"):
+            # variants query even though there are no variants in this beacon, this can happen in a network context
+            add_info_to_response("No variants available at this beacon, query by metadata values only")
+            return []
         variant_sample_ids = query_gohan(variants_query, "count", ids_only=True)
         if not variant_sample_ids:
             return []

requirements.txt

@@ -1,12 +1,12 @@
-aiohttp==3.9.5
+aiohttp==3.10.2
 aiosignal==1.3.1
 annotated-types==0.6.0
 arrow==1.2.3
 async-timeout==4.0.3
 attrs==22.2.0
 autopep8==1.6.0
 bento-lib==10.1.1
-certifi==2024.6.2
+certifi==2024.7.4
 cffi==1.15.1
 charset-normalizer==2.1.1
 click==8.1.7
@@ -49,4 +49,4 @@ urllib3==1.26.19
 webcolors==1.12
 Werkzeug==2.2.3
 yarl==1.9.3
-zipp==3.17.0
+zipp==3.19.1