Merge pull request #75 from bento-platform/persist-censorship-functional

Re-attempt censorship settings on query

bento_beacon/app.py

@@ -17,6 +17,7 @@
 from .utils.beacon_request import save_request_data, validate_request, verify_permissions
 from .utils.beacon_response import init_response_data
 from .utils.katsu_utils import katsu_censorship_settings
+from .utils.censorship import set_censorship_settings
 
 REQUEST_SPEC_RELATIVE_PATH = "beacon-v2/framework/json/requests/"
 BEACON_MODELS = ["analyses", "biosamples", "cohorts", "datasets", "individuals", "runs", "variants"]
@@ -92,8 +93,7 @@
             f"retrieved censorship params: max_filter {max_filters}, count_threshold: {count_threshold}")
 
     # save even if None
-    current_app.config["MAX_FILTERS"] = max_filters
-    current_app.config["COUNT_THRESHOLD"] = count_threshold
+    set_censorship_settings(max_filters, count_threshold)
 
 
 @app.before_request

bento_beacon/config_files/config.py

@@ -160,7 +160,7 @@ class Config:
         "schema": "phenopackets v1"
     }
 
-    MAX_RETRIES_FOR_CENSORSHIP_PARAMS = 5
+    MAX_RETRIES_FOR_CENSORSHIP_PARAMS = 2
 # -------------------
 # gohan
 

bento_beacon/utils/censorship.py

@@ -1,17 +1,44 @@
 from flask import current_app, g
 from .exceptions import APIException, InvalidQuery
+from .katsu_utils import katsu_censorship_settings
 
 
 MESSAGE_FOR_CENSORED_QUERY_WITH_NO_RESULTS = "No results. Either none were found, or the query produced results numbering at or below the threshold for censorship."
 
 
+def set_censorship_settings(max_filters, count_threshold):
+    current_app.config["MAX_FILTERS"] = max_filters
+    current_app.config["COUNT_THRESHOLD"] = count_threshold
+
+
+# saves settings to config as a side effect
+def censorship_retry() -> tuple[int | None, int | None]:
+    max_filters, count_threshold = katsu_censorship_settings()
+    if max_filters is None or count_threshold is None:
+        raise APIException(message="error reading censorship settings from katsu: "
+                           + f"max_filters: {max_filters}, count_threshold: {count_threshold}")
+
+    current_app.logger.info(
+        f"setting censorship parameters max_filters: {max_filters}, count_threshold: {count_threshold}")
+    set_censorship_settings(max_filters, count_threshold)
+    return max_filters, count_threshold
+
+
+def threshold_retry() -> int | None:
+    _, count_threshold = censorship_retry()
+    return count_threshold
+
+
+def max_filters_retry() -> int | None:
+    max_filters, _ = censorship_retry()
+    return max_filters
+
+
 def get_censorship_threshold():
     if g.permission_query_data:
         return 0
     threshold = current_app.config["COUNT_THRESHOLD"]
-    if threshold is None:
-        raise APIException(message="unable to retrieve 'count_threshold' censorship parameter from katsu")
-    return threshold
+    return threshold if threshold is not None else threshold_retry()
 
 
 def censored_count(count):
@@ -24,9 +51,7 @@ def censored_count(count):
 # we don't have the same option of returning zero here
 def get_max_filters():
     max_filters = current_app.config["MAX_FILTERS"]
-    if max_filters is None:
-        raise APIException(message="unable to retrieve 'max_query_parameters' censorship setting from katsu")
-    return max_filters
+    return max_filters if max_filters is not None else max_filters_retry()
 
 
 # ugly side-effect code, but keeps censorship code together