Merge pull request #383 from kjsanger/feature/ont-creation-time

Add command line option to find recently created ONT run collections

src/npg_irods/__init__.py

@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright © 2022, 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/>.
+#
+# @author Keith James <[email protected]>
+
+
+import importlib.metadata
+
+__version__ = importlib.metadata.version("npg-irods-python")
+
+
+def version() -> str:
+    """Return the current version."""
+    return __version__

src/npg_irods/cli/apply_ont_metadata.py

@@ -32,9 +32,8 @@
 from npg.log import configure_structlog
 from sqlalchemy.orm import Session
 
-from npg_irods import db
+from npg_irods import db, version
 from npg_irods.ont import apply_metadata
-from npg_irods.version import version
 
 description = """
 Applies metadata and data access permissions on ONT run collections in iRODS, to reflect
@@ -66,7 +65,7 @@
     type=str,
 )
 parser.add_argument(
-    "--version", help="Print the version and exit.", action="store_true"
+    "--version", help="Print the version and exit.", action="version", version=version()
 )
 
 args = parser.parse_args()
@@ -81,10 +80,6 @@
 
 
 def main():
-    if args.version:
-        print(version())
-        sys.exit(0)
-
     dbconfig = IniData(db.Config).from_file(args.db_config.name, "mlwh_ro")
     engine = sqlalchemy.create_engine(
         dbconfig.url, pool_pre_ping=True, pool_recycle=3600

src/npg_irods/cli/check_checksums.py

@@ -24,8 +24,8 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
+from npg_irods import version
 from npg_irods.utilities import check_checksums
-from npg_irods.version import version
 
 description = """
 Reads iRODS data object paths from a file or STDIN, one per line and performs
@@ -77,7 +77,7 @@
     default=4,
 )
 parser.add_argument(
-    "--version", help="Print the version and exit.", action="store_true"
+    "--version", help="Print the version and exit.", action="version", version=version()
 )
 
 args = parser.parse_args()
@@ -92,10 +92,6 @@
 
 
 def main():
-    if args.version:
-        print(version())
-        sys.exit(0)
-
     num_processed, num_passed, num_errors = check_checksums(
         args.input,
         args.output,

src/npg_irods/cli/check_common_metadata.py

@@ -24,8 +24,8 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
+from npg_irods import version
 from npg_irods.utilities import check_common_metadata
-from npg_irods.version import version
 
 description = """
 Reads iRODS data object paths from a file or STDIN, one per line and performs
@@ -76,7 +76,7 @@
     default=4,
 )
 parser.add_argument(
-    "--version", help="Print the version and exit.", action="store_true"
+    "--version", help="Print the version and exit.", action="version", version=version()
 )
 
 args = parser.parse_args()
@@ -91,10 +91,6 @@
 
 
 def main():
-    if args.version:
-        print(version())
-        sys.exit(0)
-
     num_processed, num_passed, num_errors = check_common_metadata(
         args.input,
         args.output,

src/npg_irods/cli/check_consent_withdrawn.py

@@ -24,10 +24,11 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
+from npg_irods import version
 from npg_irods.utilities import (
     check_consent_withdrawn,
 )
-from npg_irods.version import version
+
 
 description = """
 Reads iRODS data object paths from a file or STDIN, one per line and checks that each
@@ -71,7 +72,7 @@
     action="store_true",
 )
 parser.add_argument(
-    "--version", help="Print the version and exit.", action="store_true"
+    "--version", help="Print the version and exit.", action="version", version=version()
 )
 
 
@@ -87,10 +88,6 @@
 
 
 def main():
-    if args.version:
-        print(version())
-        sys.exit(0)
-
     num_processed, num_passed, num_errors = check_consent_withdrawn(
         args.input,
         args.output,

src/npg_irods/cli/check_replicas.py

@@ -24,8 +24,8 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
+from npg_irods import version
 from npg_irods.utilities import check_replicas
-from npg_irods.version import version
 
 description = """
 Reads iRODS data object paths from a file or STDIN, one per line and performs
@@ -85,7 +85,7 @@
     default=4,
 )
 parser.add_argument(
-    "--version", help="Print the version and exit.", action="store_true"
+    "--version", help="Print the version and exit.", action="version", version=version()
 )
 
 args = parser.parse_args()
@@ -100,10 +100,6 @@
 
 
 def main():
-    if args.version:
-        print(version())
-        sys.exit(0)
-
     num_processed, num_passed, num_errors = check_replicas(
         args.input,
         args.output,

src/npg_irods/cli/copy_confirm.py

@@ -25,10 +25,10 @@
 from npg.log import configure_structlog
 from partisan.exception import RodsError
 
+from npg_irods import version
 from npg_irods.common import rods_path
 from npg_irods.exception import ChecksumError
 from npg_irods.utilities import copy
-from npg_irods.version import version
 
 description = """
 Copies iRODS collections and data objects from one path to another, optionally
@@ -84,7 +84,7 @@
     action="store_true",
 )
 parser.add_argument(
-    "--version", help="Print the version and exit.", action="store_true"
+    "--version", help="Print the version and exit.", action="version", version=version()
 )
 
 args = parser.parse_args()
@@ -99,10 +99,6 @@
 
 
 def main():
-    if args.version:
-        print(version())
-        sys.exit(0)
-
     try:
         num_processed, num_copied = copy(
             args.source,

src/npg_irods/cli/locate_data_objects.py

@@ -37,7 +37,7 @@
 from partisan.irods import AVU, DataObject, RodsItem, query_metadata
 from sqlalchemy.orm import Session
 
-from npg_irods import db, illumina, ont, pacbio, sequenom
+from npg_irods import db, illumina, ont, pacbio, sequenom, version
 
 from npg_irods.db.mlwh import (
     find_consent_withdrawn_samples,
@@ -51,7 +51,6 @@
 from npg_irods.metadata.illumina import Instrument
 from npg_irods.metadata.lims import TrackedSample, TrackedStudy
 from npg_irods.ont import barcode_collections
-from npg_irods.version import version
 
 description = """
 A utility for locating sets of data objects in iRODS.
@@ -630,7 +629,10 @@ def main():
         type=str,
     )
     parser.add_argument(
-        "--version", help="Print the version and exit.", action="store_true"
+        "--version",
+        help="Print the version and exit.",
+        action="version",
+        version=version(),
     )
 
     subparsers = parser.add_subparsers(title="Sub-commands", required=True)
@@ -673,6 +675,20 @@ def main():
     )
     ilup_parser.set_defaults(func=illumina_updates_cli)
 
+    ontcre_parser = subparsers.add_parser(
+        "ont-run-creation",
+        help="Find ONT runfolder collections created in iRODS within a specified time "
+        "range.",
+    )
+    add_date_range_arguments(ontcre_parser)
+    ontcre_parser.add_argument(
+        "--report-json",
+        "--report_json",
+        help="Print output in JSON format.",
+        action="store_true",
+    )
+    ontcre_parser.set_defaults(func=ont_run_collections_created_cli)
+
     ontup_parser = subparsers.add_parser(
         "ont-updates",
         help="Find collections, containing data objects for ONT runs, whose tracking"
@@ -755,9 +771,6 @@ def main():
         json=args.json,
     )
 
-    if args.version:
-        print(version())
-        sys.exit(0)
     args.func(args)
 
 

src/npg_irods/cli/repair_checksums.py

@@ -24,8 +24,8 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
+from npg_irods import version
 from npg_irods.utilities import repair_checksums
-from npg_irods.version import version
 
 description = """
 Reads iRODS data object paths from a file or STDIN, one per line and repairs
@@ -82,7 +82,7 @@
     default=4,
 )
 parser.add_argument(
-    "--version", help="Print the version and exit.", action="store_true"
+    "--version", help="Print the version and exit.", action="version", version=version()
 )
 
 args = parser.parse_args()
@@ -97,10 +97,6 @@
 
 
 def main():
-    if args.version:
-        print(version())
-        sys.exit(0)
-
     num_processed, num_repaired, num_errors = repair_checksums(
         args.input,
         args.output,

src/npg_irods/cli/repair_common_metadata.py

@@ -24,8 +24,8 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
+from npg_irods import version
 from npg_irods.utilities import repair_common_metadata
-from npg_irods.version import version
 
 description = """
 Reads iRODS data object paths from a file or STDIN, one per line and repairs
@@ -79,7 +79,7 @@
     default=4,
 )
 parser.add_argument(
-    "--version", help="Print the version and exit.", action="store_true"
+    "--version", help="Print the version and exit.", action="version", version=version()
 )
 
 args = parser.parse_args()
@@ -94,10 +94,6 @@
 
 
 def main():
-    if args.version:
-        print(version())
-        sys.exit(0)
-
     num_processed, num_repaired, num_errors = repair_common_metadata(
         args.input,
         args.output,

src/npg_irods/cli/repair_replicas.py

@@ -24,8 +24,8 @@
 from npg.cli import add_io_arguments, add_logging_arguments
 from npg.log import configure_structlog
 
+from npg_irods import version
 from npg_irods.utilities import repair_replicas
-from npg_irods.version import version
 
 description = """
 Reads iRODS data object paths from a file or STDIN, one per line and repairs their
@@ -81,7 +81,7 @@
     default=4,
 )
 parser.add_argument(
-    "--version", help="Print the version and exit.", action="store_true"
+    "--version", help="Print the version and exit.", action="version", version=version()
 )
 
 args = parser.parse_args()
@@ -96,10 +96,6 @@
 
 
 def main():
-    if args.version:
-        print(version())
-        sys.exit(0)
-
     num_processed, num_repaired, num_errors = repair_replicas(
         args.input,
         args.output,

src/npg_irods/cli/safe_remove_script.py

@@ -24,8 +24,8 @@
 from npg.cli import add_logging_arguments
 from npg.log import configure_structlog
 
+from npg_irods import version
 from npg_irods.utilities import write_safe_remove_script
-from npg_irods.version import version
 
 description = """
 Writes a shell script to allow safe recursive deletion of collections and data objects
@@ -73,7 +73,7 @@
     action="store_true",
 )
 parser.add_argument(
-    "--version", help="Print the version and exit.", action="store_true"
+    "--version", help="Print the version and exit.", action="version", version=version()
 )
 
 args = parser.parse_args()
@@ -88,10 +88,6 @@
 
 
 def main():
-    if args.version:
-        print(version())
-        sys.exit(0)
-
     try:
         write_safe_remove_script(
             args.output,