diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 5c3cc55e78..ae634dd85d 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,14 @@ cgap-portal Change Log ---------- +14.1.1 +====== +`PR 743: Purge permissions fix `_ + +* Update set_user_info_property to true to allow admins to purge items +* Bring in updated snovault to fix impersonation bug + + 14.1.0 ====== `PR 739: Bm babel updates `_ diff --git a/poetry.lock b/poetry.lock index d861176454..224f84378a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. 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"pytest-cov", "pytest-xdist"] [[package]] name = "websocket-client" -version = "1.5.1" +version = "1.6.1" description = "WebSocket client for Python with low level API options" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "websocket-client-1.5.1.tar.gz", hash = "sha256:3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40"}, - {file = "websocket_client-1.5.1-py3-none-any.whl", hash = "sha256:cdf5877568b7e83aa7cf2244ab56a3213de587bbe0ce9d8b9600fc77b455d89e"}, + {file = "websocket-client-1.6.1.tar.gz", hash = "sha256:c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd"}, + {file = "websocket_client-1.6.1-py3-none-any.whl", hash = "sha256:f1f9f2ad5291f0225a49efad77abf9e700b6fef553900623060dad6e26503b9d"}, ] [package.extras] @@ -3613,18 +3653,18 @@ watchdog = ["watchdog"] [[package]] name = "wheel" -version = "0.40.0" +version = "0.41.0" description = "A built-package format for Python" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "wheel-0.40.0-py3-none-any.whl", hash = "sha256:d236b20e7cb522daf2390fa84c55eea81c5c30190f90f29ae2ca1ad8355bf247"}, - {file = "wheel-0.40.0.tar.gz", hash = "sha256:cd1196f3faee2b31968d626e1731c94f99cbdb67cf5a46e4f5656cbee7738873"}, + {file = "wheel-0.41.0-py3-none-any.whl", hash = "sha256:7e9be3bbd0078f6147d82ed9ed957e323e7708f57e134743d2edef3a7b7972a9"}, + {file = "wheel-0.41.0.tar.gz", hash = "sha256:55a0f0a5a84869bce5ba775abfd9c462e3a6b1b7b7ec69d72c0b83d673a5114d"}, ] [package.extras] -test = ["pytest (>=6.0.0)"] +test = ["pytest (>=6.0.0)", "setuptools (>=65)"] [[package]] name = "wsgiproxy2" @@ -3667,19 +3707,19 @@ files = [ [[package]] name = "zipp" -version = "3.15.0" +version = "3.16.2" description = "Backport of pathlib-compatible object wrapper for zip files" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"}, - {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"}, + {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"}, + {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [[package]] name = "zope-deprecation" @@ -3778,4 +3818,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.10" -content-hash = "16441100f9c0207eadd0220e5aa96d27c4abef40c314adcda746ce5605e47b47" +content-hash = "19a019157def3938b8f7796e250daa003013fb25e77840ef9a2744b31404ec0f" diff --git a/pyproject.toml b/pyproject.toml index ec0ff35c21..2ad1f43388 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "cgap-portal". name = "encoded" -version = "14.1.0" +version = "14.1.1" description = "Computational Genome Analysis Platform" authors = ["4DN-DCIC Team "] license = "MIT" @@ -49,7 +49,7 @@ codeguru-profiler-agent = "^1.2.4" cryptography = "39.0.2" colorama = "0.3.3" dcicpyvcf = "1.0.0.1b0" # "^1.0.0" -dcicsnovault = "9.0.0" +dcicsnovault = "9.1.1" #dcicutils = "^7.4.0" #dcicutils = "7.4.4.5b21" dcicutils = "^7.5.0" diff --git a/src/encoded/commands/owltools.py b/src/encoded/commands/owltools.py index 98845e5a27..4e55208efe 100644 --- a/src/encoded/commands/owltools.py +++ b/src/encoded/commands/owltools.py @@ -76,7 +76,7 @@ def get_last_bit(uri_string): def isBlankNode(aClass): ''' Checks for an RDF blank node ''' - if type(aClass) == BNode: + if type(aClass) is BNode: return True else: return False diff --git a/src/encoded/project/authentication.py b/src/encoded/project/authentication.py index 1205c8d7a8..5180bfc0c3 100644 --- a/src/encoded/project/authentication.py +++ b/src/encoded/project/authentication.py @@ -8,7 +8,7 @@ def login(self, context, request, *, samesite): return super().login(context, request, samesite=samesite) def namespaced_authentication_policy_authenticated_userid(self, namespaced_authentication_policy, request, set_user_info_property): - set_user_info_property = False + set_user_info_property = True return super().namespaced_authentication_policy_authenticated_userid(namespaced_authentication_policy, request, set_user_info_property) def note_auth0_authentication_policy_unauthenticated_userid(self, auth0_authentication_policy, request, email, id_token): diff --git a/src/encoded/search/search.py b/src/encoded/search/search.py index eae3b8b4a3..26b09f38cb 100644 --- a/src/encoded/search/search.py +++ b/src/encoded/search/search.py @@ -1017,7 +1017,7 @@ def build_table_columns(self): type_infos = [self.request.registry[TYPES][t] for t in self.doc_types if t != 'Item'] for ti in type_infos: # We use `type` instead of `isinstance` since we don't want to catch subclasses. - if type(ti) == AbstractTypeInfo: + if type(ti) is AbstractTypeInfo: any_abstract_types = True break diff --git a/src/encoded/tests/test_permissions.py b/src/encoded/tests/test_permissions.py index 62ec251f8f..6145b7d5a2 100644 --- a/src/encoded/tests/test_permissions.py +++ b/src/encoded/tests/test_permissions.py @@ -1,10 +1,10 @@ +from typing import Any, Dict + import pytest -# import webtest +from webtest.app import TestApp -# from datetime import date -# from urllib.parse import urlencode -# from ..types.institution import Institution from .datafixtures import remote_user_testapp +from .utils import get_identifier_path pytestmark = [pytest.mark.setone, pytest.mark.working, pytest.mark.schema] @@ -461,3 +461,9 @@ def test_public_item_wo_project_can_be_posted_by_project_member(bgm_user_testapp # need to have a uniquename to_post['name'] = 'another section name' bgm_user_testapp.post_json('/static_section', to_post, status=201) + + +def test_admin_can_purge(testapp: TestApp, file: Dict[str, Any]) -> None: + file_path = get_identifier_path(file.get("uuid")) + testapp.patch_json(file_path, {"status": "deleted"}, status=200) + testapp.delete_json(f"{file_path}/?purge=True", {}, status=200)