Merge branch 'master' into features/beacon-network

.github/workflows/lint.yml

@@ -18,4 +18,4 @@ jobs:
       - name: Install black
         run: python -m pip install black
       - name: Run linter
-        run: black --check --line-length=120 ./bento_beacon
+        run: black --check --line-length=120 ./bento_beacon

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.04.01
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.06.01
 
 SHELL ["/bin/bash", "-c"]
 

bento_beacon/config_files/config.py

@@ -143,8 +143,8 @@ 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"

bento_beacon/endpoints/info.py

@@ -146,7 +146,7 @@ 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/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 []

dev.Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.04.01
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.06.01
 
 LABEL org.opencontainers.image.description="Local development image for the Bento Beacon service."
 LABEL devcontainer.metadata='[{ \

requirements.txt

@@ -6,11 +6,11 @@ async-timeout==4.0.3
 attrs==22.2.0
 autopep8==1.6.0
 bento-lib==10.1.1
-certifi==2024.2.2
+certifi==2024.7.4
 cffi==1.15.1
 charset-normalizer==2.1.1
 click==8.1.7
-cryptography==42.0.5
+cryptography==42.0.8
 flake8==6.1.0
 Flask==2.2.5
 Flask-Cors==4.0.1
@@ -45,8 +45,8 @@ six==1.16.0
 toml==0.10.2
 typing_extensions==4.8.0
 uri-template==1.2.0
-urllib3==1.26.18
+urllib3==1.26.19
 webcolors==1.12
 Werkzeug==2.2.3
 yarl==1.9.3
-zipp==3.17.0
+zipp==3.19.1