Merge pull request #21983 from jmchilton/concise_logging

More concise test logging

lib/galaxy/config/__init__.py

@@ -5,6 +5,7 @@ Universe configuration builder.
 # absolute_import needed for tool_shed package.
 
 import configparser
+import copy
 import json
 import locale
 import logging
@@ -117,9 +118,9 @@ LOGGING_CONFIG_DEFAULT: dict[str, Any] = {
             "level": "ERROR",
             "qualname": "py.warnings",
         },
-        "celery.utils.functional": {
+        "celery": {
             "level": "INFO",
-            "qualname": "celery.utils.functional",
+            "qualname": "celery",
         },
         "sentry_sdk.errors": {
             "level": "INFO",
@@ -162,6 +163,13 @@ DEFAULT_EMAIL_FROM_LOCAL_PART = "galaxy-no-reply"
 DISABLED_FLAG = "disabled"  # Used to mark a config option as disabled
 
 
+def default_log_config(log_level: str = "DEBUG") -> dict[str, Any]:
+    logging_conf = copy.deepcopy(LOGGING_CONFIG_DEFAULT)
+    if log_level != "DEBUG":
+        logging_conf["handlers"]["console"]["level"] = log_level
+    return logging_conf
+
+
 def configure_logging(config, facts=None):
     """Allow some basic logging configuration to be read from ini file.
 
@@ -186,9 +194,7 @@ def configure_logging(config, facts=None):
         logging_conf = config.get("logging", None)
         if logging_conf is None:
             # if using the default logging config, honor the log_level setting
-            logging_conf = LOGGING_CONFIG_DEFAULT
-            if config.get("log_level", "DEBUG") != "DEBUG":
-                logging_conf["handlers"]["console"]["level"] = config.get("log_level", "DEBUG")
+            logging_conf = default_log_config(config.get("log_level", "DEBUG"))
         # configure logging with logging dict in config, template *FileHandler handler filenames with the `filename_template` option
         for name, conf in logging_conf.get("handlers", {}).items():
             if (

lib/galaxy/dependencies/pinned-requirements.txt

@@ -206,7 +206,7 @@ pydantic-core==2.41.5
 pydantic-evals==1.63.0
 pydantic-graph==1.63.0
 pydantic-settings==2.13.1
-pydantic-tes==0.2.0
+pydantic-tes==0.3.0
 pydicom==3.0.1
 pydot==4.0.1
 pyeventsystem==0.1.0

lib/galaxy/schema/generics.py

@@ -26,8 +26,8 @@ class GenericModel(BaseModel):
         return f"{class_name}{suffix}"
 
     @classmethod
-    def __get_pydantic_core_schema__(cls, *args, **kwargs):
-        result = super().__get_pydantic_core_schema__(*args, **kwargs)
+    def __get_pydantic_core_schema__(cls, source, handler):
+        result = handler(source)
         ref_to_name[result["ref"]] = cls.__name__
         return result
 

lib/galaxy/schema/schema.py

@@ -1987,27 +1987,25 @@ class ExportObjectResultMetadata(Model):
     error: Optional[str] = None
 
     @model_validator(mode="after")
-    @classmethod
-    def validate_success(cls, model):
+    def validate_success(self):
         """
         Ensure successful exports do not have error text.
         """
-        if model.success and model.error is not None:
+        if self.success and self.error is not None:
             raise ValueError("successful exports cannot have error text")
 
-        return model
+        return self
 
     @model_validator(mode="after")
-    @classmethod
-    def validate_uri(cls, model):
+    def validate_uri(self):
         """
         Ensure unsuccessful exports do not have a URI.
         """
 
-        if not model.success and model.uri:
+        if not self.success and self.uri:
             raise ValueError("unsuccessful exports cannot have a URI")
 
-        return model
+        return self
 
 
 class ExportObjectMetadata(Model):

lib/galaxy_test/driver/driver_util.py

@@ -21,7 +21,7 @@ from typing import (
 from urllib.parse import urlparse
 
 from galaxy.app import UniverseApplication as GalaxyUniverseApplication
-from galaxy.config import LOGGING_CONFIG_DEFAULT
+from galaxy.config import default_log_config
 from galaxy.model import mapping
 from galaxy.model.database_utils import (
     create_database,
@@ -192,7 +192,8 @@ def setup_galaxy_config(
     data_manager_config_file = _resolve_relative_config_paths(data_manager_config_file)
     tool_config_file = _resolve_relative_config_paths(tool_conf)
     tool_data_table_config_path = _resolve_relative_config_paths(tool_data_table_config_path)
-
+    log_level = os.environ.get("GALAXY_TEST_LOG_LEVEL", "DEBUG").upper()
+    logging = default_log_config(log_level)
     config = dict(
         admin_users="test@bx.psu.edu",
         allow_library_path_paste=True,
@@ -232,7 +233,7 @@ def setup_galaxy_config(
         use_heartbeat=False,
         user_library_import_dir=user_library_import_dir,
         webhooks_dir=TEST_WEBHOOKS_DIR,
-        logging=LOGGING_CONFIG_DEFAULT,
+        logging=logging,
         monitor_thread_join_timeout=5,
         object_store_store_by="uuid",
         fetch_url_allowlist=["127.0.0.0/24"],

pytest.ini

@@ -2,6 +2,10 @@
 addopts = --doctest-continue-on-failure --verbosity=1 --showlocals
 asyncio_mode = auto
 log_level = DEBUG
+filterwarnings =
+    ignore::DeprecationWarning:pkg_resources
+    ignore::DeprecationWarning:refgenconf
+    ignore::UserWarning:refgenconf
 # Install pytest-memray and set memray to true here to enable memory profiling of tests
 # memray = true
 pythonpath = lib

run_tests.sh

@@ -293,7 +293,9 @@ TOOL_SHED_TEST_TMP_DIR          Defaults to random /tmp directory - place for
                                 tool shed test server files to be placed.
 TOOL_SHED_TEST_OMIT_GALAXY      Do not launch a Galaxy server for tool shed
                                 testing.
-GALAXY_TEST_DISABLE_ACCESS_LOG  Do not log access messages
+GALAXY_TEST_DISABLE_ACCESS_LOG  Do not log access messages.
+GALAXY_TEST_LOG_LEVEL           Set Galaxy server log level for tests
+                                (default: DEBUG). E.g. WARNING to reduce output.
 GALAXY_TEST_AXE_SCRIPT_URL      URL of aXe script to use for accessibility testing.
 GALAXY_TEST_SKIP_AXE            Set this to '1' to skip aXe accessibilty testing when
                                 running selenium tests.