renamed base logger back to 'logger'

Australian-Imaging-Service · Jun 19, 2024 · 4029d56 · 4029d56
1 parent 6f8e7bb
commit 4029d56
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Showing 4 changed files with 53 additions and 12 deletions.
diff --git a/xnat_ingest/cli/stage.py b/xnat_ingest/cli/stage.py
@@ -127,6 +127,18 @@
         "mail and log level are delimited by ',' and separate destinations by ';'"
     ),
 )
+@click.option(
+    "--add-logger",
+    type=str,
+    multiple=True,
+    default=(),
+    envvar="XNAT_INGEST_UPLOAD_LOGGERS",
+    help=(
+        "The loggers to use for logging. By default just the 'xnat-ingest' logger is used. "
+        "But additional loggers can be included (e.g. 'xnat') can be "
+        "specified here"
+    ),
+)
 @click.option(
     "--mail-server",
     type=MailServer.cli_type,
@@ -173,6 +185,7 @@ def stage(
     log_level: str,
     log_files: ty.List[LogFile],
     log_emails: ty.List[LogEmail],
+    add_logger: ty.List[str],
     mail_server: MailServer,
     raise_errors: bool,
     deidentify: bool,
@@ -183,6 +196,7 @@ def stage(
         log_emails=log_emails,
         log_files=log_files,
         mail_server=mail_server,
+        add_logger=add_logger,
     )
 
     if xnat_login:

diff --git a/xnat_ingest/cli/upload.py b/xnat_ingest/cli/upload.py
@@ -83,6 +83,18 @@
         "mail and log level are delimited by ',' and separate destinations by ';'"
     ),
 )
+@click.option(
+    "--add-logger",
+    type=str,
+    multiple=True,
+    default=(),
+    envvar="XNAT_INGEST_UPLOAD_LOGGERS",
+    help=(
+        "The loggers to use for logging. By default just the 'xnat-ingest' logger is used. "
+        "But additional loggers can be included (e.g. 'xnat') can be "
+        "specified here"
+    ),
+)
 @click.option(
     "--mail-server",
     type=MailServer.cli_type,
@@ -166,6 +178,7 @@ def upload(
     log_emails: ty.List[LogEmail],
     mail_server: MailServer,
     always_include: ty.Sequence[str],
+    add_logger: ty.List[str],
     raise_errors: bool,
     store_credentials: ty.Tuple[str, str],
     temp_dir: ty.Optional[Path],
@@ -179,6 +192,7 @@ def upload(
         log_emails=log_emails,
         log_files=log_files,
         mail_server=mail_server,
+        add_logger=add_logger,
     )
     if temp_dir:
         tempfile.tempdir = str(temp_dir)

diff --git a/xnat_ingest/tests/test_cli.py b/xnat_ingest/tests/test_cli.py
@@ -196,9 +196,10 @@ def test_stage_and_upload(
             str(associated_files_dir)
             + "/{PatientName.given_name}_{PatientName.family_name}*.ptd",
             r".*/[^\.]+.[^\.]+.[^\.]+.(?P<id>\d+)\.[A-Z]+_(?P<resource>[^\.]+).*",
-            # "--log-file",
-            # str(log_file),
-            # "info",
+            "--log-file",
+            str(log_file),
+            "info",
+            "--add-logger",
             "--raise-errors",
             "--delete",
             "--xnat-login",
@@ -214,9 +215,10 @@ def test_stage_and_upload(
         upload,
         [
             str(staging_dir),
-            # "--log-file",
-            # str(log_file),
-            # "info",
+            "--log-file",
+            str(log_file),
+            "info",
+            "--add-logger",
             "--always-include",
             "medimage/dicom-series",
             "--raise-errors",

diff --git a/xnat_ingest/utils.py b/xnat_ingest/utils.py
@@ -134,14 +134,22 @@ def set_logger_handling(
     log_emails: ty.List[LogEmail] | None,
     log_files: ty.List[LogFile] | None,
     mail_server: MailServer,
+    add_logger: ty.Sequence[str] = (),
 ):
+    loggers = [logger]
+    for log in add_logger:
+        loggers.append(logging.getLogger(log))
 
     levels = [log_level]
-    levels.extend(le.loglevel for le in log_emails)
-    levels.extend(lf.loglevel for lf in log_files)
+    if log_emails:
+        levels.extend(le.loglevel for le in log_emails)
+    if log_files:
+        levels.extend(lf.loglevel for lf in log_files)
 
     min_log_level = min(getattr(logging, ll.upper()) for ll in levels)
-    logger.setLevel(min_log_level)
+
+    for logr in loggers:
+        logr.setLevel(min_log_level)
 
     # Configure the email logger
     if log_emails:
@@ -161,7 +169,8 @@ def set_logger_handling(
                 secure=None,
             )
             smtp_hdle.setLevel(getattr(logging, log_email.loglevel.upper()))
-            logger.addHandler(smtp_hdle)
+            for logr in loggers:
+                logr.addHandler(smtp_hdle)
 
     # Configure the file logger
     for log_file in log_files:
@@ -172,14 +181,16 @@ def set_logger_handling(
         log_file_hdle.setFormatter(
             logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
         )
-        logger.addHandler(log_file_hdle)
+        for logr in loggers:
+            logr.addHandler(log_file_hdle)
 
     console_hdle = logging.StreamHandler(sys.stdout)
     console_hdle.setLevel(getattr(logging, log_level.upper()))
     console_hdle.setFormatter(
         logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
     )
-    logger.addHandler(console_hdle)
+    for logr in loggers:
+        logr.addHandler(console_hdle)
 
 
 def get_checksums(xresource) -> ty.Dict[str, str]: