Merge pull request #719 from broadinstitute/mw/fix_v3_autoclass_warn

Show the GCS migration warning only once

Author: mike-w-wilson

gnomad_qc/v3/resources/annotations.py

@@ -19,6 +19,7 @@
     RELEASES,
     VERSIONS,
 )
+from gnomad_qc.v3.resources.resource_utils import show_v3_migration_warning
 
 SUBSETS = SUBSETS["v3"]
 
@@ -36,12 +37,7 @@ def _annotations_root(version: str = CURRENT_VERSION) -> str:
     :param version: Version of annotation path to return
     :return: root path of the variant annotation files
     """
-    logging.warning(
-        "Most objects in 'gs://gnomad/annotations' were moved to either "
-        "'gs://gnomad-archive' or 'gs://gnomad-autoclass'. This function now returns "
-        "'gs://gnomad-autoclass/annotations' paths, if no resource is found there, "
-        "please check 'gs://gnomad-archive/annotations'."
-    )
+    show_v3_migration_warning("annotations")
     return f"gs://gnomad-autoclass/annotations/hail-0.2/ht/genomes_v{version}"
 
 

gnomad_qc/v3/resources/resource_utils.py

@@ -0,0 +1,20 @@
+"""Centralized migration warnings for v3 resources moved to new GCS locations."""
+
+import functools
+import logging
+from typing import Literal
+
+
+@functools.lru_cache(maxsize=2)
+def show_v3_migration_warning(target: Literal["annotations", "sample_qc"]) -> None:
+    """
+    Show GCS migration warning for v3 resources (only once per target per session).
+
+    :param target: Type of resource that was migrated ("annotations" or "sample_qc")
+    """
+    logging.warning(
+        f"Most objects in 'gs://gnomad/{target}' were moved to either "
+        f"'gs://gnomad-archive' or 'gs://gnomad-autoclass'. This function now returns "
+        f"'gs://gnomad-autoclass/{target}' paths, if no resource is found there, "
+        f"please check 'gs://gnomad-archive/{target}'."
+    )

gnomad_qc/v3/resources/sample_qc.py

@@ -11,6 +11,7 @@
 from gnomad.sample_qc.relatedness import get_relationship_expr
 
 from gnomad_qc.v3.resources.constants import CURRENT_VERSION, VERSIONS
+from gnomad_qc.v3.resources.resource_utils import show_v3_migration_warning
 
 ########################################################################################
 # Note: Some of the resources in this file have been moved to gs://gnomad-archive,
@@ -27,12 +28,7 @@ def get_sample_qc_root(version: str = CURRENT_VERSION, mt: bool = False) -> str:
     :param mt: Whether path is for a MatrixTable, default is False
     :return: Root to sample QC path
     """
-    logging.warning(
-        "Most objects in 'gs://gnomad/sample_qc' were moved to either "
-        "'gs://gnomad-archive' or 'gs://gnomad-autoclass'. This function now returns "
-        "'gs://gnomad-autoclass/sample_qc' paths, if no resource is found there, "
-        "please check 'gs://gnomad-archive/sample_qc'."
-    )
+    show_v3_migration_warning("sample_qc")
     return f"gs://gnomad-autoclass/sample_qc/{'mt' if mt else 'ht'}/genomes_v{version}"
 
 

gnomad_qc/v5/data_ingestion/field_md_to_html.py

@@ -27,7 +27,7 @@
 final_sections = []
 
 
-elements = soup.find_all(["p", "table", "h1", "h2"])
+elements = list(soup.find_all(["p", "table", "h1", "h2"]))
 
 paragraphs_before_first_table = []
 paragraphs_before_second_table = []