From 4878a204878c20a153f2cdf20ed05e083ffe1936 Mon Sep 17 00:00:00 2001
From: Keith James <kdj@sanger.ac.uk>
Date: Mon, 4 Nov 2024 13:48:54 +0000
Subject: [PATCH] Add log entries for the application and CLI names

Bump npg-python-lib from 0.3.1 to 0.3.3
---
 requirements.txt                              |  2 +-
 src/npg_irods/__init__.py                     | 20 +++++++++++++++++++
 src/npg_irods/cli/__init__.py                 | 19 ++++++++++++++++++
 src/npg_irods/cli/apply_ont_metadata.py       |  3 ++-
 src/npg_irods/cli/check_checksums.py          |  3 ++-
 src/npg_irods/cli/check_common_metadata.py    |  3 ++-
 src/npg_irods/cli/check_consent_withdrawn.py  |  3 ++-
 src/npg_irods/cli/check_replicas.py           |  3 ++-
 src/npg_irods/cli/copy_confirm.py             |  3 ++-
 src/npg_irods/cli/locate_data_objects.py      | 11 +++++++++-
 src/npg_irods/cli/repair_checksums.py         |  3 ++-
 src/npg_irods/cli/repair_common_metadata.py   |  3 ++-
 src/npg_irods/cli/repair_replicas.py          |  3 ++-
 src/npg_irods/cli/safe_remove_script.py       |  3 ++-
 .../cli/update_secondary_metadata.py          |  3 ++-
 src/npg_irods/cli/withdraw_consent.py         |  3 ++-
 src/npg_irods/cli/write_html_report.py        |  3 ++-
 17 files changed, 76 insertions(+), 15 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 1c1fefb..c0db006 100644
--- a/requirements.txt
+++ b/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
diff --git a/src/npg_irods/__init__.py b/src/npg_irods/__init__.py
index 813f5e9..e7c8cd0 100644
--- a/src/npg_irods/__init__.py
+++ b/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__
diff --git a/src/npg_irods/cli/__init__.py b/src/npg_irods/cli/__init__.py
index e630e89..bd09e95 100644
--- a/src/npg_irods/cli/__init__.py
+++ b/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."""
diff --git a/src/npg_irods/cli/apply_ont_metadata.py b/src/npg_irods/cli/apply_ont_metadata.py
index e39519f..dadeb0d 100755
--- a/src/npg_irods/cli/apply_ont_metadata.py
+++ b/src/npg_irods/cli/apply_ont_metadata.py
@@ -32,7 +32,7 @@
 from npg.log import configure_structlog
 from sqlalchemy.orm import Session
 
-from npg_irods import db, version
+from npg_irods import add_appinfo_structlog_processor, db, version
 from npg_irods.ont import apply_metadata
 
 description = """
@@ -76,6 +76,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")
 
 
diff --git a/src/npg_irods/cli/check_checksums.py b/src/npg_irods/cli/check_checksums.py
index 66f451e..4a9d8af 100755
--- a/src/npg_irods/cli/check_checksums.py
+++ b/src/npg_irods/cli/check_checksums.py
@@ -24,7 +24,7 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
-from npg_irods import version
+from npg_irods import add_appinfo_structlog_processor, version
 from npg_irods.utilities import check_checksums
 
 description = """
@@ -88,6 +88,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")
 
 
diff --git a/src/npg_irods/cli/check_common_metadata.py b/src/npg_irods/cli/check_common_metadata.py
index efc1f43..3388dab 100755
--- a/src/npg_irods/cli/check_common_metadata.py
+++ b/src/npg_irods/cli/check_common_metadata.py
@@ -24,7 +24,7 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
-from npg_irods import version
+from npg_irods import add_appinfo_structlog_processor, version
 from npg_irods.utilities import check_common_metadata
 
 description = """
@@ -87,6 +87,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")
 
 
diff --git a/src/npg_irods/cli/check_consent_withdrawn.py b/src/npg_irods/cli/check_consent_withdrawn.py
index 654f5a1..5dc323c 100755
--- a/src/npg_irods/cli/check_consent_withdrawn.py
+++ b/src/npg_irods/cli/check_consent_withdrawn.py
@@ -24,7 +24,7 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
-from npg_irods import version
+from npg_irods import add_appinfo_structlog_processor, version
 from npg_irods.utilities import (
     check_consent_withdrawn,
 )
@@ -84,6 +84,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")
 
 
diff --git a/src/npg_irods/cli/check_replicas.py b/src/npg_irods/cli/check_replicas.py
index a282a9a..c500e07 100755
--- a/src/npg_irods/cli/check_replicas.py
+++ b/src/npg_irods/cli/check_replicas.py
@@ -24,7 +24,7 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
-from npg_irods import version
+from npg_irods import add_appinfo_structlog_processor, version
 from npg_irods.utilities import check_replicas
 
 description = """
@@ -96,6 +96,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")
 
 
diff --git a/src/npg_irods/cli/copy_confirm.py b/src/npg_irods/cli/copy_confirm.py
index 72f2e65..f869710 100755
--- a/src/npg_irods/cli/copy_confirm.py
+++ b/src/npg_irods/cli/copy_confirm.py
@@ -25,7 +25,7 @@
 from npg.log import configure_structlog
 from partisan.exception import RodsError
 
-from npg_irods import version
+from npg_irods import add_appinfo_structlog_processor, version
 from npg_irods.common import rods_path
 from npg_irods.exception import ChecksumError
 from npg_irods.utilities import copy
@@ -95,6 +95,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")
 
 
diff --git a/src/npg_irods/cli/locate_data_objects.py b/src/npg_irods/cli/locate_data_objects.py
index 0bc9858..b338921 100644
--- a/src/npg_irods/cli/locate_data_objects.py
+++ b/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)
 
diff --git a/src/npg_irods/cli/repair_checksums.py b/src/npg_irods/cli/repair_checksums.py
index ce66e0c..475dc8c 100755
--- a/src/npg_irods/cli/repair_checksums.py
+++ b/src/npg_irods/cli/repair_checksums.py
@@ -24,7 +24,7 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
-from npg_irods import version
+from npg_irods import add_appinfo_structlog_processor, version
 from npg_irods.utilities import repair_checksums
 
 description = """
@@ -93,6 +93,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")
 
 
diff --git a/src/npg_irods/cli/repair_common_metadata.py b/src/npg_irods/cli/repair_common_metadata.py
index 26560ab..10396bc 100755
--- a/src/npg_irods/cli/repair_common_metadata.py
+++ b/src/npg_irods/cli/repair_common_metadata.py
@@ -24,7 +24,7 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
-from npg_irods import version
+from npg_irods import add_appinfo_structlog_processor, version
 from npg_irods.utilities import repair_common_metadata
 
 description = """
@@ -90,6 +90,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")
 
 
diff --git a/src/npg_irods/cli/repair_replicas.py b/src/npg_irods/cli/repair_replicas.py
index 4cb8146..39c286a 100755
--- a/src/npg_irods/cli/repair_replicas.py
+++ b/src/npg_irods/cli/repair_replicas.py
@@ -24,7 +24,7 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
-from npg_irods import version
+from npg_irods import add_appinfo_structlog_processor, version
 from npg_irods.utilities import repair_replicas
 
 description = """
@@ -92,6 +92,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")
 
 
diff --git a/src/npg_irods/cli/safe_remove_script.py b/src/npg_irods/cli/safe_remove_script.py
index eab7a12..7336982 100755
--- a/src/npg_irods/cli/safe_remove_script.py
+++ b/src/npg_irods/cli/safe_remove_script.py
@@ -24,7 +24,7 @@
 from npg.cli import add_logging_arguments
 from npg.log import configure_structlog
 
-from npg_irods import version
+from npg_irods import add_appinfo_structlog_processor, version
 from npg_irods.utilities import write_safe_remove_script
 
 description = """
@@ -84,6 +84,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")
 
 
diff --git a/src/npg_irods/cli/update_secondary_metadata.py b/src/npg_irods/cli/update_secondary_metadata.py
index 961abfc..9633abb 100755
--- a/src/npg_irods/cli/update_secondary_metadata.py
+++ b/src/npg_irods/cli/update_secondary_metadata.py
@@ -26,7 +26,7 @@
 from npg.conf import IniData
 from npg.log import configure_structlog
 
-from npg_irods import db, version
+from npg_irods import add_appinfo_structlog_processor, db, version
 from npg_irods.utilities import update_secondary_metadata
 
 description = """
@@ -109,6 +109,7 @@ def main():
         colour=args.colour,
         json=args.json,
     )
+    add_appinfo_structlog_processor()
 
     dbconfig = IniData(db.Config).from_file(args.db_config.name, "mlwh_ro")
     engine = sqlalchemy.create_engine(
diff --git a/src/npg_irods/cli/withdraw_consent.py b/src/npg_irods/cli/withdraw_consent.py
index 6235aed..4f07f33 100755
--- a/src/npg_irods/cli/withdraw_consent.py
+++ b/src/npg_irods/cli/withdraw_consent.py
@@ -24,7 +24,7 @@
 from npg.cli import add_logging_arguments
 from npg.log import configure_structlog
 
-from npg_irods import version
+from npg_irods import add_appinfo_structlog_processor, version
 from npg_irods.utilities import (
     withdraw_consent,
 )
@@ -89,6 +89,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")
 
 
diff --git a/src/npg_irods/cli/write_html_report.py b/src/npg_irods/cli/write_html_report.py
index b661436..4f4e2b9 100644
--- a/src/npg_irods/cli/write_html_report.py
+++ b/src/npg_irods/cli/write_html_report.py
@@ -26,7 +26,7 @@
 from partisan.exception import RodsError
 from yattag import indent
 
-from npg_irods import version
+from npg_irods import add_appinfo_structlog_processor, version
 from npg_irods.html_reports import ont_runs_html_report_this_year
 
 description = """Writes an HTML report summarising data in iRODS.
@@ -80,6 +80,7 @@
     colour=args.colour,
     json=args.json,
 )
+add_appinfo_structlog_processor()
 log = structlog.get_logger("main")