Added permissions fixing after running scratch-copy and implemented a new module

CHANGELOG.md

@@ -68,6 +68,7 @@ Code contributions to the new version:
 - Added full execution support for the MAG template [#321](https://github.com/BU-ISCIII/buisciii-tools/pull/321).
 - Added labels to services.json and updated bioinfo_doc.py and jinja_template_delivery.j2 so that software versions data is displayed in the delivery pdf [#330](https://github.com/BU-ISCIII/buisciii-tools/pull/330).
 - Updated several templates (singularity images, outdated paths, improvements, etc) [#331](https://github.com/BU-ISCIII/buisciii-tools/pull/331)
+- Added permissions fixing after running scratch_copy, as well as a new fix-permissions module in the tools [#332](https://github.com/BU-ISCIII/buisciii-tools/pull/332).
 
 ### Modules
 

bu_isciii/__main__.py

@@ -649,5 +649,31 @@ def autoclean_sftp(ctx, sftp_folder, days):
     sftp_clean.handle_autoclean_sftp()
 
 
+# FIX PERMISSIONS
+@bu_isciii_cli.command(help_priority=9)
+@click.option(
+    "-d",
+    "--input_directory",
+    type=click.Path(),
+    default=None,
+    required=True,
+    help="Input directory to fix permissions (absolute path)",
+)
+@click.pass_context
+def fix_permissions(ctx, input_directory):
+    """
+    Fix permissions
+    """
+    if not os.path.isdir(input_directory):
+        exit("Invalid input directory")
+    conf = bu_isciii.config_json.ConfigJson()
+    permissions = conf.get_configuration("global").get("permissions")
+    bu_isciii.utils.remake_permissions(input_directory, permissions)
+    stderr = rich.console.Console(
+        stderr=True, force_terminal=bu_isciii.utils.rich_force_colors()
+    )
+    stderr.print(f"[green]Correct permissions were applied to {input_directory}")
+
+
 if __name__ == "__main__":
     run_bu_isciii()

bu_isciii/conf/configuration.json

@@ -2,7 +2,11 @@
     "global": {
         "data_path": "/data/bi",
         "archived_path": "/archived/bi",
-        "yaml_conf_path": "~/buisciii_config.yml"
+        "yaml_conf_path": "~/buisciii_config.yml",
+        "permissions": {
+        "directory_chmod": "2775",
+        "file_chmod": "664"
+        }
     },
     "sftp_copy": {
         "protocol": "rsync",

bu_isciii/scratch.py

@@ -187,6 +187,16 @@ def revert_copy_scratch(self):
                             sync_source_contents=False,
                         )
                         self.srun_command(self.srun_settings, rsync_command)
+
+                        # After successful rsync, apply correct permissions
+                        conf = bu_isciii.config_json.ConfigJson()
+                        permissions_config = conf.get_configuration("global").get(
+                            "permissions"
+                        )
+                        bu_isciii.utils.remake_permissions(
+                            self.full_path, permissions_config
+                        )
+
                         stderr.print(
                             "[green]Successfully copied the directory to %s"
                             % dest_folder,

bu_isciii/utils.py

@@ -7,6 +7,7 @@
 import os
 import tarfile
 import sys
+import subprocess
 
 import questionary
 import rich
@@ -495,3 +496,32 @@ def process_yaml_file(yaml_file):
 
 def validate_date(date_previous, date_posterior):
     return
+
+
+def remake_permissions(copied_folder_path, permissions_config):
+    """
+    Change permissions of all files and directories in a given absolute path.
+
+    Args:
+        copied_folder_path: The path to the folder that was copied
+        permissions_config: Dictionary containing permissions configuration (e.g., {'directory_chmod': '755', 'file_chmod': '664'})
+    """
+    subprocess.run(
+        f"chown -R $(whoami):bi {copied_folder_path}", shell=True, check=True
+    )
+
+    # Change permissions for directories
+    if "directory_chmod" in permissions_config:
+        subprocess.run(
+            f"find {copied_folder_path} -type d -exec chmod {permissions_config['directory_chmod']} {{}} \;",
+            shell=True,
+            check=True,
+        )
+
+    # Change permissions for files
+    if "file_chmod" in permissions_config:
+        subprocess.run(
+            f"find {copied_folder_path} -type f -exec chmod {permissions_config['file_chmod']} {{}} \;",
+            shell=True,
+            check=True,
+        )