From 342321485e6cd3eec36744eb644649de3a12c6ec Mon Sep 17 00:00:00 2001
From: Leonardo Schwarz <leonardo.schwarz@fgcz.ethz.ch>
Date: Mon, 5 Aug 2024 10:10:42 +0200
Subject: [PATCH] use the harmonized logging setup

---
 bfabric/cli_formatting.py                            | 12 ++++++++++++
 ...fabric_list_not_available_proteomics_workunits.py |  9 +++++++++
 2 files changed, 21 insertions(+)

diff --git a/bfabric/cli_formatting.py b/bfabric/cli_formatting.py
index b8acc7f..f986f07 100644
--- a/bfabric/cli_formatting.py
+++ b/bfabric/cli_formatting.py
@@ -1,3 +1,6 @@
+import sys
+
+from loguru import logger
 from rich.highlighter import RegexHighlighter
 from rich.theme import Theme
 
@@ -10,3 +13,12 @@ class HostnameHighlighter(RegexHighlighter):
 
 
 DEFAULT_THEME = Theme({"bfabric.hostname": "bold red"})
+
+
+def setup_script_logging(debug: bool = False) -> None:
+    """Sets up the logging for the command line scripts."""
+    logger.remove()
+    if not debug:
+        logger.add(sys.stderr, filter="bfabric", level="INFO", format="{level} {message}")
+    else:
+        logger.add(sys.stderr, filter="bfabric", level="DEBUG")
diff --git a/bfabric/scripts/bfabric_list_not_available_proteomics_workunits.py b/bfabric/scripts/bfabric_list_not_available_proteomics_workunits.py
index cdbaaad..a833f5a 100755
--- a/bfabric/scripts/bfabric_list_not_available_proteomics_workunits.py
+++ b/bfabric/scripts/bfabric_list_not_available_proteomics_workunits.py
@@ -16,10 +16,12 @@
 from datetime import datetime, timedelta
 from typing import Any
 
+from loguru import logger
 from rich.console import Console
 from rich.table import Column, Table
 
 from bfabric import Bfabric, BfabricClientConfig
+from bfabric.cli_formatting import setup_script_logging
 
 
 def render_output(workunits_by_status: dict[str, list[dict[str, Any]]], config: BfabricClientConfig) -> None:
@@ -60,6 +62,12 @@ def render_output(workunits_by_status: dict[str, list[dict[str, Any]]], config:
 def list_not_available_proteomics_workunits(date_cutoff: datetime) -> None:
     """Lists proteomics work units that are not available on bfabric."""
     client = Bfabric.from_config()
+    console = Console()
+    with console.capture() as capture:
+        console.print(
+            f"listing not available proteomics work units created after {date_cutoff}", style="bright_yellow", end=""
+        )
+    logger.info(capture.get())
 
     workunits_by_status = {}
     for status in ["Pending", "Processing", "Failed"]:
@@ -73,6 +81,7 @@ def list_not_available_proteomics_workunits(date_cutoff: datetime) -> None:
 
 def main() -> None:
     """Parses the command line arguments and calls `list_not_available_proteomics_workunits`."""
+    setup_script_logging()
     parser = ArgumentParser(description="Lists proteomics work units that are not available on bfabric.")
     parser.add_argument("--max-age", type=int, help="Max age of work units in days", default=14)
     args = parser.parse_args()