set up logging levels correctly

scripts/logging_testing.py

@@ -0,0 +1,21 @@
+from click.testing import CliRunner
+from xnat_ingest.cli.stage import stage
+from xnat_ingest.utils import show_cli_trace
+
+runner = CliRunner()
+result = runner.invoke(
+    stage,
+    [
+        "/Users/tclose/.medimages4tests/cache/dicom/mri/t1w/siemens/skyra/syngo_d13c",
+        "/Users/tclose/test-stage",
+        "--project-id",
+        "TESTSTAGE",
+        "--log-level",
+        "INFO"
+    ],
+    catch_exceptions=False
+)
+
+assert result.exit_code == 0, show_cli_trace(result)
+
+print(result.stdout)

xnat_ingest/cli/stage.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+import typing as ty
 import traceback
 import click
 from tqdm import tqdm
@@ -144,8 +145,8 @@ def stage(
     project_id: str | None,
     delete: bool,
     log_level: str,
-    log_file: Path,
-    log_emails: LogEmail,
+    log_file: LogFile | None,
+    log_emails: ty.List[LogEmail],
     mail_server: MailServer,
     raise_errors: bool,
 ):

xnat_ingest/utils.py

@@ -90,8 +90,18 @@ class AssociatedFiles(CliType):
 
 
 def set_logger_handling(
-    log_level: str, log_emails: LogEmail, log_file: LogFile, mail_server: MailServer
+    log_level: str, log_emails: ty.List[LogEmail] | None, log_file: LogFile | None, mail_server: MailServer
 ):
+
+    levels = [log_level]
+    if log_emails:
+        levels.extend(le.loglevel for le in log_emails)
+    if log_file:
+        levels.append(log_file.loglevel)
+
+    min_log_level = min(getattr(logging, ll.upper()) for ll in levels)
+    logger.setLevel(min_log_level)
+
     # Configure the email logger
     if log_emails:
         if not mail_server: