Add log entries for the application and CLI names

Bump npg-python-lib from 0.3.1 to 0.3.3

requirements.txt

@@ -1,6 +1,6 @@
 cryptography==43.0.3
 npg_id_generation@https://github.com/wtsi-npg/npg_id_generation/releases/download/5.0.1/npg_id_generation-5.0.1.tar.gz
-npg-python-lib@https://github.com/wtsi-npg/npg-python-lib/releases/download/0.3.1/npg_python_lib-0.3.1.tar.gz
+npg-python-lib@https://github.com/wtsi-npg/npg-python-lib/releases/download/0.3.3/npg_python_lib-0.3.3.tar.gz
 partisan@https://github.com/wtsi-npg/partisan/releases/download/2.13.0/partisan-2.13.0.tar.gz
 pymysql==1.1.1
 python-dateutil==2.9.0.post0

src/npg_irods/__init__.py

@@ -19,10 +19,30 @@
 
 
 import importlib.metadata
+import sys
+
+import structlog
 
 __version__ = importlib.metadata.version("npg-irods-python")
 
 
+# If this proves generally useful, it could be moved to npg-python-lib
+def add_appinfo_structlog_processor():
+    """Add a custom structlog processor reporting executable information to the
+    configuration."""
+
+    def _add_executable_info(_logger, _method_name, event: dict):
+        """Add executable name and version to all log entries."""
+        event["application"] = "npg-irods-python"
+        event["executable"] = sys.argv[0]
+        event["version"] = version()
+        return event
+
+    c = structlog.get_config()
+    c["processors"] = [_add_executable_info] + c["processors"]
+    structlog.configure(**c)
+
+
 def version() -> str:
     """Return the current version."""
     return __version__

src/npg_irods/cli/__init__.py

@@ -1 +1,20 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright © 2024 Genome Research Ltd. All rights reserved.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+
 """Command line interface for npg-irods-python."""

src/npg_irods/cli/locate_data_objects.py

@@ -37,7 +37,15 @@
 from partisan.irods import AVU, DataObject, RodsItem, query_metadata
 from sqlalchemy.orm import Session
 
-from npg_irods import db, illumina, ont, pacbio, sequenom, version
+from npg_irods import (
+    add_appinfo_structlog_processor,
+    db,
+    illumina,
+    ont,
+    pacbio,
+    sequenom,
+    version,
+)
 
 from npg_irods.db.mlwh import (
     find_consent_withdrawn_samples,
@@ -770,6 +778,7 @@ def main():
         colour=args.colour,
         json=args.json,
     )
+    add_appinfo_structlog_processor()
 
     args.func(args)