Merge pull request #371 from kjsanger/feature/npg-python-lib

Refactor to depend on npg-python-lib
wtsi-npg · Sep 24, 2024 · 9ceb94c · 9ceb94c
2 parents 60da9e8 + 47113d7
commit 9ceb94c
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Showing 18 changed files with 96 additions and 393 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,7 @@
 cryptography==43.0.1
 npg_id_generation@https://github.com/wtsi-npg/npg_id_generation/releases/download/5.0.1/npg_id_generation-5.0.1.tar.gz
-partisan@https://github.com/wtsi-npg/partisan/releases/download/2.11.1/partisan-2.11.1.tar.gz
+npg-python-lib@https://github.com/wtsi-npg/npg-python-lib/releases/download/0.2.0/npg_python_lib-0.2.0.tar.gz
+partisan@https://github.com/wtsi-npg/partisan/releases/download/2.12.0/partisan-2.12.0.tar.gz
 pymysql==1.1.1
 python-dateutil==2.9.0.post0
 rich==13.7.1

diff --git a/src/npg_irods/cli/apply_ont_metadata.py b/src/npg_irods/cli/apply_ont_metadata.py
@@ -22,14 +22,14 @@
 
 import sqlalchemy
 import structlog
-from sqlalchemy.orm import Session
-
-from npg_irods.cli.util import (
+from npg.cli import (
     add_date_range_arguments,
     add_db_config_arguments,
     add_logging_arguments,
-    configure_logging,
 )
+from npg.log import configure_structlog
+from sqlalchemy.orm import Session
+
 from npg_irods.db import DBConfig
 from npg_irods.ont import apply_metadata
 from npg_irods.version import version
@@ -68,7 +68,7 @@
 )
 
 args = parser.parse_args()
-configure_logging(
+configure_structlog(
     config_file=args.log_config,
     debug=args.debug,
     verbose=args.verbose,

diff --git a/src/npg_irods/cli/check_checksums.py b/src/npg_irods/cli/check_checksums.py
@@ -21,13 +21,10 @@
 import sys
 
 import structlog
+from npg.cli import add_io_arguments, add_logging_arguments
+from npg.log import configure_structlog
 
 from npg_irods.utilities import check_checksums
-from npg_irods.cli.util import (
-    add_io_arguments,
-    add_logging_arguments,
-    configure_logging,
-)
 from npg_irods.version import version
 
 description = """
@@ -84,7 +81,7 @@
 )
 
 args = parser.parse_args()
-configure_logging(
+configure_structlog(
     config_file=args.log_config,
     debug=args.debug,
     verbose=args.verbose,

diff --git a/src/npg_irods/cli/check_common_metadata.py b/src/npg_irods/cli/check_common_metadata.py
@@ -21,13 +21,10 @@
 import sys
 
 import structlog
+from npg.cli import add_io_arguments, add_logging_arguments
+from npg.log import configure_structlog
 
 from npg_irods.utilities import check_common_metadata
-from npg_irods.cli.util import (
-    add_io_arguments,
-    add_logging_arguments,
-    configure_logging,
-)
 from npg_irods.version import version
 
 description = """
@@ -83,7 +80,7 @@
 )
 
 args = parser.parse_args()
-configure_logging(
+configure_structlog(
     config_file=args.log_config,
     debug=args.debug,
     verbose=args.verbose,

diff --git a/src/npg_irods/cli/check_consent_withdrawn.py b/src/npg_irods/cli/check_consent_withdrawn.py
@@ -21,15 +21,12 @@
 import sys
 
 import structlog
+from npg.cli import add_io_arguments, add_logging_arguments
+from npg.log import configure_structlog
 
 from npg_irods.utilities import (
     check_consent_withdrawn,
 )
-from npg_irods.cli.util import (
-    add_io_arguments,
-    add_logging_arguments,
-    configure_logging,
-)
 from npg_irods.version import version
 
 description = """
@@ -79,7 +76,7 @@
 
 
 args = parser.parse_args()
-configure_logging(
+configure_structlog(
     config_file=args.log_config,
     debug=args.debug,
     verbose=args.verbose,

diff --git a/src/npg_irods/cli/check_replicas.py b/src/npg_irods/cli/check_replicas.py
@@ -21,13 +21,10 @@
 import sys
 
 import structlog
+from npg.cli import add_io_arguments, add_logging_arguments
+from npg.log import configure_structlog
 
 from npg_irods.utilities import check_replicas
-from npg_irods.cli.util import (
-    add_io_arguments,
-    add_logging_arguments,
-    configure_logging,
-)
 from npg_irods.version import version
 
 description = """
@@ -92,7 +89,7 @@
 )
 
 args = parser.parse_args()
-configure_logging(
+configure_structlog(
     config_file=args.log_config,
     debug=args.debug,
     verbose=args.verbose,

diff --git a/src/npg_irods/cli/copy_confirm.py b/src/npg_irods/cli/copy_confirm.py
@@ -21,11 +21,13 @@
 import sys
 
 import structlog
+from npg.cli import add_logging_arguments
+from npg.log import configure_structlog
 from partisan.exception import RodsError
 
+from npg_irods.common import rods_path
 from npg_irods.exception import ChecksumError
 from npg_irods.utilities import copy
-from npg_irods.cli.util import add_logging_arguments, configure_logging, rods_path
 from npg_irods.version import version
 
 description = """
@@ -86,7 +88,7 @@
 )
 
 args = parser.parse_args()
-configure_logging(
+configure_structlog(
     config_file=args.log_config,
     debug=args.debug,
     verbose=args.verbose,

diff --git a/src/npg_irods/cli/locate_data_objects.py b/src/npg_irods/cli/locate_data_objects.py
@@ -25,18 +25,18 @@
 
 import sqlalchemy
 import structlog
-from partisan.irods import AVU, DataObject, query_metadata
-from sqlalchemy.orm import Session
-
-from npg_irods import illumina, ont, pacbio, sequenom
-from npg_irods.cli.util import (
+from npg.cli import (
     add_date_range_arguments,
     add_db_config_arguments,
     add_logging_arguments,
-    configure_logging,
     integer_in_range,
-    with_previous,
 )
+from npg.iter import with_previous
+from npg.log import configure_structlog
+from partisan.irods import AVU, DataObject, query_metadata
+from sqlalchemy.orm import Session
+
+from npg_irods import illumina, ont, pacbio, sequenom
 from npg_irods.db import DBConfig
 from npg_irods.db.mlwh import (
     find_consent_withdrawn_samples,
@@ -648,7 +648,7 @@ def main():
     squp_parser.set_defaults(func=sequenom_updates_cli)
 
     args = parser.parse_args()
-    configure_logging(
+    configure_structlog(
         config_file=args.log_config,
         debug=args.debug,
         verbose=args.verbose,

diff --git a/src/npg_irods/cli/repair_checksums.py b/src/npg_irods/cli/repair_checksums.py
@@ -21,13 +21,10 @@
 import sys
 
 import structlog
+from npg.cli import add_io_arguments, add_logging_arguments
+from npg.log import configure_structlog
 
 from npg_irods.utilities import repair_checksums
-from npg_irods.cli.util import (
-    add_io_arguments,
-    add_logging_arguments,
-    configure_logging,
-)
 from npg_irods.version import version
 
 description = """
@@ -89,7 +86,7 @@
 )
 
 args = parser.parse_args()
-configure_logging(
+configure_structlog(
     config_file=args.log_config,
     debug=args.debug,
     verbose=args.verbose,

diff --git a/src/npg_irods/cli/repair_common_metadata.py b/src/npg_irods/cli/repair_common_metadata.py
@@ -21,13 +21,10 @@
 import sys
 
 import structlog
+from npg.cli import add_io_arguments, add_logging_arguments
+from npg.log import configure_structlog
 
 from npg_irods.utilities import repair_common_metadata
-from npg_irods.cli.util import (
-    add_io_arguments,
-    add_logging_arguments,
-    configure_logging,
-)
 from npg_irods.version import version
 
 description = """
@@ -86,7 +83,7 @@
 )
 
 args = parser.parse_args()
-configure_logging(
+configure_structlog(
     config_file=args.log_config,
     debug=args.debug,
     verbose=args.verbose,

diff --git a/src/npg_irods/cli/repair_replicas.py b/src/npg_irods/cli/repair_replicas.py
@@ -21,13 +21,10 @@
 import sys
 
 import structlog
+from npg.cli import add_io_arguments, add_logging_arguments
+from npg.log import configure_structlog
 
 from npg_irods.utilities import repair_replicas
-from npg_irods.cli.util import (
-    add_io_arguments,
-    add_logging_arguments,
-    configure_logging,
-)
 from npg_irods.version import version
 
 description = """
@@ -88,7 +85,7 @@
 )
 
 args = parser.parse_args()
-configure_logging(
+configure_structlog(
     config_file=args.log_config,
     debug=args.debug,
     verbose=args.verbose,

diff --git a/src/npg_irods/cli/safe_remove_script.py b/src/npg_irods/cli/safe_remove_script.py
@@ -21,9 +21,10 @@
 import sys
 
 import structlog
+from npg.cli import add_logging_arguments
+from npg.log import configure_structlog
 
 from npg_irods.utilities import write_safe_remove_script
-from npg_irods.cli.util import add_logging_arguments, configure_logging
 from npg_irods.version import version
 
 description = """
@@ -76,7 +77,7 @@
 )
 
 args = parser.parse_args()
-configure_logging(
+configure_structlog(
     config_file=args.log_config,
     debug=args.debug,
     verbose=args.verbose,

diff --git a/src/npg_irods/cli/update_secondary_metadata.py b/src/npg_irods/cli/update_secondary_metadata.py
@@ -22,13 +22,9 @@
 
 import sqlalchemy
 import structlog
+from npg.cli import add_db_config_arguments, add_io_arguments, add_logging_arguments
+from npg.log import configure_structlog
 
-from npg_irods.cli.util import (
-    add_db_config_arguments,
-    add_io_arguments,
-    add_logging_arguments,
-    configure_logging,
-)
 from npg_irods.db import DBConfig
 from npg_irods.utilities import update_secondary_metadata
 from npg_irods.version import version
@@ -103,7 +99,7 @@ def main():
     )
 
     args = parser.parse_args()
-    configure_logging(
+    configure_structlog(
         config_file=args.log_config,
         debug=args.debug,
         verbose=args.verbose,