Set Library Permissions

.github/workflows/ci.yaml

@@ -7,7 +7,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.6']
+        python-version: ['3.7']
         tox-action:
           - lint
           - pytest
@@ -37,7 +37,7 @@ jobs:
           submodules: true
       - uses: actions/setup-python@v1
         with:
-          python-version: '3.6'
+          python-version: '3.7'
       - name: Install dependencies
         run: |
           python3 -m pip install --upgrade pip setuptools

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.
@@ -76,6 +77,7 @@ def get_var(var_name):
     install_requires=requirements,
     license="AFL",
     zip_safe=False,
+    python_requires=">=3.7",
     keywords='galaxy',
     classifiers=[
         'Development Status :: 5 - Production/Stable',
@@ -88,9 +90,10 @@ def get_var(var_name):
         'Topic :: Software Development :: Testing',
         'Natural Language :: English',
         "Programming Language :: Python :: 3",
-        'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
     ],
     test_suite=TEST_DIR,
     tests_require=test_requirements

src/ephemeris/set_library_permissions.py

@@ -0,0 +1,132 @@
+#!/usr/bin/env python
+"""Tool to set permissions for all datasets of a given Galaxy Data Library"""
+
+import argparse
+import logging as log
+import sys
+
+from bioblend import galaxy
+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, auto):
+    log.info("Your library_id is %s", library_id)
+    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 %0.02f min\n",
+        total,
+        est,
+    )
+    if auto:
+        for current in range(total):
+            log.debug(
+                "Processing dataset %d of %d, ID=%s", current, total, datasets[current]
+            )
+            gi.libraries.set_dataset_permissions(
+                dataset_id=datasets[current],
+                access_in=role_ids,
+                modify_in=role_ids,
+                manage_in=role_ids,
+            )
+    else:
+        if input("Do you want to continue? (y/n) ") == "y":
+            with Progress() as progress:
+                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],
+                    )
+                    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)
+        else:
+            log.info("Operation cancelled by user. No changes were applied.\n")
+
+
+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", nargs="+", help="Specify a list of comma separated role IDs")
+    parser.add_argument(
+        "-y",
+        "--yes",
+        default=False,
+        action="store_true",
+        help="Set the -y flag for auto-accept and skip manual approvement",
+    )
+    parser.add_argument(
+        "-s",
+        "--silent",
+        default=False,
+        action="store_true",
+        help="sets loglevel to ERROR",
+    )
+    return parser
+
+
+def main():
+    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)
+    elif args.silent:
+        log.basicConfig(level=log.ERROR)
+    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, auto=args.yes)
+    log.info(
+        "\nThis script uses bioblend to update ALL permissions of ALL datasets in a"
+        "specified library to the given roles. Be careful and cancel if unsure\n"
+    )
+
+
+if __name__ == "__main__":
+    main()

tox.ini

@@ -1,21 +1,21 @@
 # TODO: implement doc linting
 [tox]
-envlist = py{36}-lint, py{36}-pytest, py{36}, py{36}-integration
+envlist = py{37}-lint, py{37}-pytest, py{37}, py{37}-integration
 source_dir = src/ephemeris
 test_dir = tests
 
 [testenv]
 commands = {envpython} setup.py nosetests []
 whitelist_externals = bash
 
-[testenv:py36-lint]
+[testenv:py37-lint]
 commands = flake8 {[tox]source_dir} {[tox]test_dir}
 skip_install = True
 deps =
     flake8
     flake8-import-order
 
-[testenv:py36-pytest]
+[testenv:py37-pytest]
 deps =
     -r requirements.txt
     pytest
@@ -32,12 +32,12 @@ commands =
     # Unfortunately this has to run in the tox env to have access to envsitepackagesdir
     sed -i 's#{envsitepackagesdir}#src#' coverage.xml
 
-[testenv:py36]
+[testenv:py37]
 deps =
     -r requirements.txt
 commands = bash {[tox]test_dir}/test.sh
 
-[testenv:py36-integration]
+[testenv:py37-integration]
 deps =
     -r requirements.txt
 commands = bash {[tox]test_dir}/test.sh