Set Library Permissions

requirements.txt

@@ -5,3 +5,4 @@ Jinja2
 galaxy-tool-util>=20.9.1
 galaxy-util>=20.9.0
 pysam
+rich

setup.py

@@ -37,6 +37,7 @@ def get_var(var_name):
         setup-data-libraries=ephemeris.setup_data_libraries:main
         galaxy-wait=ephemeris.sleep:main
         install_tool_deps=ephemeris.install_tool_deps:main
+        set_library_permissions=ephemeris.set_library_permissions:main
 '''
 PACKAGE_DATA = {
     # Be sure to update MANIFEST.in for source dist.

src/ephemeris/set_library_permissions.py

@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+'''Tool to set permissions for all datasets of a given Galaxy Data Library'''
+
+import argparse
+import logging as log
+from bioblend import galaxy
+import sys, time, os
+from rich.progress import Progress
+from .common_parser import get_common_args
+# Print iterations progress
+
+
+def get_datasets(gi, library_id) -> [str]:
+    objects = gi.libraries.show_dataset(library_id=library_id, dataset_id='')
+    datasets = []
+    for index in range(len(objects)):
+       if objects[index]['type'] == 'file':
+           datasets.append(objects[index]['id'])
+    if datasets == []:
+        sys.exit("No datasets in library!")
+    else:
+        return datasets
+
+def set_permissions(gi, library_id, role_ids):
+    log.info("Your library_id is " + library_id + "\n")
+    log.info("Your roles are: %s", " ".join(role_ids))
+    datasets = get_datasets(gi, library_id)
+    total = len(datasets)
+    est = total*3/60
+    # Give User time to abort
+    log.info('\nSuccess! %d datasets found. Processing can take up to %f min', total, est)
+    t = 5
+    with Progress() as progress:
+        task_countdown = progress.add_task("[red]Starting in 5 seconds...", total=total)
+        t = 5
+        while t:
+            time.sleep(1)
+            t -= 1
+            progress.update(task_countdown, advance=1)
+    # Process datasets
+        task = progress.add_task("[green]Processing datasets...", total=total)
+        for current in range(total):
+            log.debug('Processing dataset %d of %d, ID=%s', current, total, datasets[current])
+            rows, columns = os.popen('stty size', 'r').read().split()
+            gi.libraries.set_dataset_permissions(dataset_id=datasets[current], access_in=role_ids, modify_in=role_ids, manage_in=role_ids)  
+            progress.update(task, advance=1)
+
+def _parser():
+    '''Constructs the parser object'''
+    parent = get_common_args()
+    parser = argparse.ArgumentParser(
+        parents=[parent],
+        description='Populate the Galaxy data library with data.'
+    )
+    parser.add_argument('--library', help="Specify the data library ID")
+    parser.add_argument('--roles', help="Specify a list of comma separated role IDs")
+    return parser
+
+def main():
+    print("\nThis command script uses bioblend galaxyAPI to set ALL permissions of ALL datasets")
+    print("in given library to given roles. Be careful and cancel with Crtl+C if unsure.\n")
+    args = _parser().parse_args()
+    if args.user and args.password:
+        gi = galaxy.GalaxyInstance(url=args.galaxy, email=args.user, password=args.password)
+    elif args.api_key:
+        gi = galaxy.GalaxyInstance(url=args.galaxy, key=args.api_key)
+    else:
+        sys.exit('Please specify either a valid Galaxy username/password or an API key.')
+
+    if args.verbose:
+        log.basicConfig(level=log.DEBUG)
+    else:
+        log.basicConfig(level=log.INFO)
+
+    if args.roles and args.library:
+        args.roles = [r.strip() for r in args.roles.split(",")]
+    else:
+        sys.exit("Specify library ID (--library myLibraryID) and (list of) role(s) (--roles roleId1,roleId2)")
+    set_permissions(gi, library_id=args.library, role_ids=args.roles)
+
+
+if __name__ == '__main__':
+    main()