Merge pull request #259 from kjsanger/bug/safe-remove-script-options

Bug: add default for --output CLI option of safe-remove-script

src/npg_irods/cli/apply_ont_metadata.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2023, 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
@@ -81,7 +81,7 @@
     "--db-config",
     "--db_config",
     help="Configuration file for database connection.",
-    type=argparse.FileType("r"),
+    type=argparse.FileType("r", encoding="UTF-8"),
     required=True,
 )
 

src/npg_irods/cli/check_checksums.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2022, 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2022, 2023, 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
@@ -61,7 +61,7 @@
     "-o",
     "--output",
     help="Output filename.",
-    type=argparse.FileType("w"),
+    type=argparse.FileType("w", encoding="UTF-8"),
     default=sys.stdout,
 )
 parser.add_argument(

src/npg_irods/cli/check_common_metadata.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2022, 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2022, 2023, 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
@@ -60,7 +60,7 @@
     "-o",
     "--output",
     help="Output filename.",
-    type=argparse.FileType("w"),
+    type=argparse.FileType("w", encoding="UTF-8"),
     default=sys.stdout,
 )
 parser.add_argument(

src/npg_irods/cli/check_consent_withdrawn.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2023, 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
@@ -69,7 +69,7 @@
     "-o",
     "--output",
     help="Output filename.",
-    type=argparse.FileType("w"),
+    type=argparse.FileType("w", encoding="UTF-8"),
     default=sys.stdout,
 )
 parser.add_argument(

src/npg_irods/cli/check_replicas.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2023, 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
@@ -62,7 +62,7 @@
     "-o",
     "--output",
     help="Output filename.",
-    type=argparse.FileType("w"),
+    type=argparse.FileType("w", encoding="UTF-8"),
     default=sys.stdout,
 )
 parser.add_argument(

src/npg_irods/cli/repair_checksums.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2022, 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2022, 2023, 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
@@ -59,14 +59,14 @@
     "-i",
     "--input",
     help="Input filename.",
-    type=argparse.FileType("r"),
+    type=argparse.FileType("r", encoding="UTF-8"),
     default=sys.stdin,
 )
 parser.add_argument(
     "-o",
     "--output",
     help="Output filename.",
-    type=argparse.FileType("w"),
+    type=argparse.FileType("w", encoding="UTF-8"),
     default=sys.stdout,
 )
 parser.add_argument(

src/npg_irods/cli/repair_common_metadata.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2022, 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2022, 2023, 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
@@ -57,7 +57,7 @@
     "-o",
     "--output",
     help="Output filename.",
-    type=argparse.FileType("w"),
+    type=argparse.FileType("w", encoding="UTF-8"),
     default=sys.stdout,
 )
 parser.add_argument(

src/npg_irods/cli/repair_replicas.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2023, 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
@@ -51,14 +51,14 @@
     "-i",
     "--input",
     help="Input filename.",
-    type=argparse.FileType("r"),
+    type=argparse.FileType("r", encoding="UTF-8"),
     default=sys.stdin,
 )
 parser.add_argument(
     "-o",
     "--output",
     help="Output filename.",
-    type=argparse.FileType("w"),
+    type=argparse.FileType("w", encoding="UTF-8"),
     default=sys.stdout,
 )
 parser.add_argument(

src/npg_irods/cli/safe_remove_script.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2022, 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2022, 2023, 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
@@ -18,6 +18,7 @@
 # @author Keith James <[email protected]>
 
 import argparse
+import sys
 
 import structlog
 
@@ -57,6 +58,8 @@
     "-o",
     "--output",
     help="Output filename.",
+    type=argparse.FileType("w", encoding="UTF-8"),
+    default=sys.stdout,
 )
 parser.add_argument(
     "--echo-commands",

src/npg_irods/cli/update_secondary_metadata.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2023, 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
@@ -70,14 +70,14 @@ def main():
         "-i",
         "--input",
         help="Input filename.",
-        type=argparse.FileType("r"),
+        type=argparse.FileType("r", encoding="UTF-8"),
         default=sys.stdin,
     )
     parser.add_argument(
         "-o",
         "--output",
         help="Output filename.",
-        type=argparse.FileType("w"),
+        type=argparse.FileType("w", encoding="UTF-8"),
         default=sys.stdout,
     )
     parser.add_argument(

src/npg_irods/cli/withdraw_consent.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# Copyright © 2023 Genome Research Ltd. All rights reserved.
+# Copyright © 2023, 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
@@ -54,14 +54,14 @@
     "-i",
     "--input",
     help="Input filename.",
-    type=argparse.FileType("r"),
+    type=argparse.FileType("r", encoding="UTF-8"),
     default=sys.stdin,
 )
 parser.add_argument(
     "-o",
     "--output",
     help="Output filename.",
-    type=argparse.FileType("w"),
+    type=argparse.FileType("w", encoding="UTF-8"),
     default=sys.stdout,
 )
 parser.add_argument(

src/npg_irods/utilities.py

@@ -20,6 +20,7 @@
 import io
 import os
 import shlex
+import sys
 import threading
 from multiprocessing.pool import ThreadPool
 from pathlib import PurePath
@@ -1020,7 +1021,7 @@ def _log_print(cmd, path):
         _log_print("irmdir", target)
 
 
-def write_safe_remove_script(path, root, stop_on_error=True, verbose=False):
+def write_safe_remove_script(writer, root, stop_on_error=True, verbose=False):
     """Write a shell script that will safely and remove a collection and contents (or a
     data object) from iRODS. It will generate irm commands for data objects and irmdir
     commands for collections. None of the commands generated are themselves recursive.
@@ -1029,20 +1030,24 @@ def write_safe_remove_script(path, root, stop_on_error=True, verbose=False):
     system. The script uses the interpreter "/bin/bash".
 
     Args:
-        path: The path of the script to be generated. Any existing file at this path will
+        writer: Writer to which the script is written. Any existing file there will
             be overwritten without warning.
         root: A DataObject, Collection, PurePath or str path to remove.
         stop_on_error: Add "set -e" to the script to stop on the first error.
         verbose: Add "set -x" to the script to echo commands to STDERR as they are run.
     """
-    with open(path, "w", encoding="utf-8") as f:
-        print(f"#!/bin/bash", file=f)
-        print(f"# Generated by npg-irods {version()}", file=f)
 
-        if stop_on_error:
-            print("set -e", file=f)
-        if verbose:
-            print("set -x", file=f)
+    print(f"#!/bin/bash", file=writer)
+    print(f"# Generated by npg-irods {version()}", file=writer)
 
-        write_safe_remove_commands(root, f)
-        os.chmod(path, 0o755)
+    if stop_on_error:
+        print("set -e", file=writer)
+    if verbose:
+        print("set -x", file=writer)
+
+    write_safe_remove_commands(root, writer)
+
+    if writer is not sys.stdout:
+        writer.close()
+        os.chmod(writer.name, 0o755)
+        log.info(f"Script written to {writer.name}")

tests/test_utilities.py

@@ -586,7 +586,8 @@ def test_write_safe_remove_commands(self, annotated_collection_tree):
     @m.it("Removes the expected collections and data objects")
     def test_write_safe_remove_script(self, tmp_path, annotated_collection_tree):
         script = Path(tmp_path, "safe_rm.sh")
-        write_safe_remove_script(script, annotated_collection_tree)
+        with open(script, "w", encoding="UTF-8") as writer:
+            write_safe_remove_script(writer, annotated_collection_tree)
         subprocess.run([script.as_posix()], check=True)
 
         assert not Collection(annotated_collection_tree).exists()
@@ -626,7 +627,8 @@ def test_write_safe_remove_commands_special(self, challenging_paths_irods):
     @m.it("Removes the expected collections and data objects")
     def test_write_safe_remove_script_special(self, tmp_path, challenging_paths_irods):
         script = Path(tmp_path, "safe_rm.sh")
-        write_safe_remove_script(script, challenging_paths_irods)
+        with open(script, "w", encoding="UTF-8") as writer:
+            write_safe_remove_script(writer, challenging_paths_irods)
         subprocess.run([script.as_posix()], check=True)
 
         assert not Collection(challenging_paths_irods).exists()