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fix and update tests (#1607)
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@mikkonie
mikkonie committed Jul 26, 2023
1 parent 4af6d61 commit bd2451d
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Showing 5 changed files with 228 additions and 89 deletions.
109 changes: 108 additions & 1 deletion samplesheets/tests/test_permissions_api.py
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Original file line number Diff line number Diff line change
@@ -1,16 +1,25 @@
"""Tests for REST API View permissions in the samplesheets app"""

import os
import uuid

from django.test import override_settings
from django.urls import reverse

# Projectroles dependency
from projectroles.models import SODAR_CONSTANTS
from projectroles.plugins import get_backend_api
from projectroles.tests.test_models import RemoteSiteMixin, RemoteProjectMixin
from projectroles.tests.test_permissions import TestProjectPermissionBase
from projectroles.tests.test_permissions_api import TestProjectAPIPermissionBase

from samplesheets.models import Investigation
from samplesheets.models import (
Investigation,
IRODS_REQUEST_ACTION_DELETE,
IRODS_REQUEST_STATUS_ACTIVE,
)
from samplesheets.tests.test_io import SampleSheetIOMixin
from samplesheets.tests.test_models import IrodsDataRequestMixin
from samplesheets.tests.test_permissions import (
SHEET_PATH,
REMOTE_SITE_NAME,
Expand All @@ -20,6 +29,10 @@
)


# Local constants
IRODS_FILE_NAME = 'test1.txt'


class TestInvestigationRetrieveAPIView(
SampleSheetIOMixin,
RemoteSiteMixin,
Expand Down Expand Up @@ -354,6 +367,100 @@ def test_get_archive(self):
self.assert_response_api(url, self.anonymous, 401)


class TestIrodsDataRequestDestroyAPIView(
SampleSheetIOMixin, IrodsDataRequestMixin, TestProjectAPIPermissionBase
):
"""Test permissions for IrodsDataRequestDestroyAPIView"""

def _make_request(self):
# TODO: Create as contributor instead
self.request = self.make_irods_request(
project=self.project,
action=IRODS_REQUEST_ACTION_DELETE,
path=self.obj_path,
status=IRODS_REQUEST_STATUS_ACTIVE,
user=self.superuser,
)
self.request.sodar_uuid = self.request_uuid
self.request.save()
self.url = reverse(
'samplesheets:api_irods_request_delete',
kwargs={'irodsdatarequest': self.request.sodar_uuid},
)

def setUp(self):
super().setUp()
# Import investigation
self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
self.study = self.investigation.studies.first()
self.assay = self.study.assays.first()
# Set up iRODS data
self.irods_backend = get_backend_api('omics_irods')
self.assay_path = self.irods_backend.get_path(self.assay)
self.obj_path = os.path.join(self.assay_path, IRODS_FILE_NAME)
self.request_uuid = uuid.uuid4()
self._make_request()

def test_delete(self):
"""Test delete() in IrodsDataRequestDestroyAPIView"""
good_users = [
self.superuser,
self.user_owner_cat,
self.user_delegate_cat,
self.user_owner,
self.user_delegate,
]
bad_users = [
self.user_contributor_cat,
self.user_guest_cat,
self.user_finder_cat,
self.user_contributor,
self.user_guest,
self.user_no_roles,
]
self.assert_response_api(
self.url,
good_users,
204,
method='DELETE',
cleanup_method=self._make_request,
)
self.assert_response_api(self.url, bad_users, 403, method='DELETE')
self.assert_response_api(self.url, self.anonymous, 401, method='DELETE')

@override_settings(PROJECTROLES_ALLOW_ANONYMOUS=True)
def test_delete_anon(self):
"""Test delete() in IrodsDataRequestDestroyAPIView with anonymous access"""
self.project.set_public()
self.assert_response_api(self.url, self.anonymous, 401, method='DELETE')

def test_delete_archived(self):
"""Test delete() in IrodsDataRequestDestroyAPIView with archived project"""
self.project.set_archive()
good_users = [self.superuser]
bad_users = [
self.user_owner_cat,
self.user_delegate_cat,
self.user_contributor_cat,
self.user_guest_cat,
self.user_finder_cat,
self.user_owner,
self.user_delegate,
self.user_contributor,
self.user_guest,
self.user_no_roles,
]
self.assert_response_api(
self.url,
good_users,
204,
method='DELETE',
cleanup_method=self._make_request,
)
self.assert_response_api(self.url, bad_users, 403, method='DELETE')
self.assert_response_api(self.url, self.anonymous, 401, method='DELETE')


class TestRemoteSheetGetAPIView(
SampleSheetIOMixin,
RemoteSiteMixin,
Expand Down
177 changes: 99 additions & 78 deletions samplesheets/tests/test_permissions_api_taskflow.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,47 @@
)


# Base Classes and Mixins ------------------------------------------------------


class TestIrodsDataRequestAPIViewBase(
SampleSheetIOMixin, SampleSheetTaskflowMixin, TaskflowAPIPermissionTestBase
):
"""Base class for iRODS data request API view permission tests"""

def create_request(self):
"""Helper function to create a request"""
url = reverse(
'samplesheets:api_irods_request_create',
kwargs={'project': self.project.sodar_uuid},
)
# TODO: Create as contributor instead
# TODO: Remove these "bla" things once #1735 has been fixed
post_data = {'path': self.obj_path + '/', 'description': 'bla'}
with self.login(self.superuser):
self.client.post(url, post_data)
obj = IrodsDataRequest.objects.first()
return obj

def setUp(self):
super().setUp()
# Import investigation
self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
self.study = self.investigation.studies.first()
self.assay = self.study.assays.first()
# Set up iRODS data
self.make_irods_colls(self.investigation)
self.assay_path = self.irods_backend.get_path(self.assay)
self.obj_path = os.path.join(self.assay_path, IRODS_FILE_NAME)
self.md5_path = os.path.join(self.assay_path, IRODS_FILE_NAME + '.md5')
# Create objects
self.file_obj = self.irods.data_objects.create(self.obj_path)
self.md5_obj = self.irods.data_objects.create(self.md5_path)


# Test Classes -----------------------------------------------------------------


class TestSampleDataFileExistsAPIView(
SampleSheetIOMixin, SampleSheetTaskflowMixin, TaskflowAPIPermissionTestBase
):
Expand Down Expand Up @@ -62,6 +103,8 @@ def test_get(self):
self.assert_response_api(url, good_users, 200, data=self.post_data)
self.assert_response_api(url, self.anonymous, 401, data=self.post_data)

# TODO: Test get anonymous

def test_get_archive(self):
"""Test get() with archived project"""
self.project.set_archive()
Expand All @@ -83,53 +126,79 @@ def test_get_archive(self):
self.assert_response_api(url, self.anonymous, 401, data=self.post_data)


class TestIrodsDataRequestAPIViewBase(
class TestIrodsDataRequestListAPIView(
SampleSheetIOMixin, SampleSheetTaskflowMixin, TaskflowAPIPermissionTestBase
):
"""Base class for iRODS data request API view permission tests"""

def create_request(self):
"""Helper function to create a request"""
url = reverse(
'samplesheets:api_irods_request_create',
kwargs={'project': self.project.sodar_uuid},
)
# Set up post data
post_data = {'path': self.path + '/', 'description': 'bla'}
with self.login(self.superuser):
self.client.post(url, post_data)
obj = IrodsDataRequest.objects.first()
return obj
"""Tests for IrodsDataRequestListAPIView permissions"""

def setUp(self):
super().setUp()
# Import investigation
self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
self.study = self.investigation.studies.first()
self.assay = self.study.assays.first()

# Set up iRODS data
self.make_irods_colls(self.investigation)
self.assay_path = self.irods_backend.get_path(self.assay)
self.path = os.path.join(self.assay_path, IRODS_FILE_NAME)
self.path_md5 = os.path.join(self.assay_path, f'{IRODS_FILE_NAME}.md5')
# Create objects
self.file_obj = self.irods.data_objects.create(self.path)
self.md5_obj = self.irods.data_objects.create(self.path_md5)
self.url = reverse(
'samplesheets:api_irods_request_list',
kwargs={'project': self.project.sodar_uuid},
)

def test_get(self):
"""Test get() in IrodsDataRequestListAPIView"""
good_users = [
self.superuser,
self.user_owner_cat,
self.user_delegate_cat,
self.user_contributor_cat,
self.user_owner,
self.user_delegate,
self.user_contributor,
]
bad_users = [
self.user_guest_cat,
self.user_finder_cat,
self.user_guest,
self.user_no_roles,
]
self.assert_response_api(self.url, good_users, 200)
self.assert_response_api(self.url, bad_users, 403)
self.assert_response_api(self.url, self.anonymous, 401)

@override_settings(PROJECTROLES_ALLOW_ANONYMOUS=True)
def test_get_anon(self):
"""Test get() in IrodsDataRequestListAPIView with anonymous access"""
self.assert_response_api(self.url, self.anonymous, 401)

def test_get_archived(self):
"""Test get() in IrodsDataRequestListAPIView with archived project"""
self.project.set_archive()
good_users = [self.superuser]
bad_users = [
self.user_owner_cat,
self.user_delegate_cat,
self.user_contributor_cat,
self.user_owner,
self.user_delegate,
self.user_contributor,
self.user_guest_cat,
self.user_finder_cat,
self.user_guest,
self.user_no_roles,
]
self.assert_response_api(self.url, good_users, 200)
self.assert_response_api(self.url, bad_users, 403)
self.assert_response_api(self.url, self.anonymous, 401)


class TestIrodsDataRequestCreateAPIView(TestIrodsDataRequestAPIViewBase):
"""Test permissions for IrodsDataRequestCreateAPIView"""

def setUp(self):
super().setUp()
# Set up URLs
self.url = reverse(
'samplesheets:api_irods_request_create',
kwargs={'project': self.project.sodar_uuid},
)
# Set up post data
self.post_data = {'path': self.path + '/', 'description': 'bla'}
self.post_data = {'path': self.obj_path + '/', 'description': 'bla'}

def test_create(self):
"""Test post() in IrodsDataRequestCreateAPIView"""
Expand Down Expand Up @@ -209,7 +278,7 @@ def setUp(self):
'samplesheets:api_irods_request_update',
kwargs={'irodsdatarequest': self.irods_request.sodar_uuid},
)
self.update_data = {'path': self.path, 'description': 'Updated'}
self.update_data = {'path': self.obj_path, 'description': 'Updated'}

def test_update(self):
"""Test post() in IrodsDataRequestUpdateAPIView"""
Expand Down Expand Up @@ -273,56 +342,7 @@ def test_update_archived(self):
)


class TestIrodsDataRequestDeleteAPIView(TestIrodsDataRequestAPIViewBase):
"""Test permissions for IrodsDataRequestDeleteAPIView"""

def test_delete(self):
"""Test delete() in IrodsDataRequestDeleteAPIView"""
good_users = [
self.superuser,
self.user_owner_cat,
self.user_delegate_cat,
self.user_owner,
self.user_delegate,
]
bad_users = [
self.user_contributor_cat,
self.user_guest_cat,
self.user_finder_cat,
self.user_contributor,
self.user_guest,
self.user_no_roles,
]

for user in good_users:
obj = self.create_request()
self.url_delete = reverse(
'samplesheets:api_irods_request_delete',
kwargs={'irodsdatarequest': obj.sodar_uuid},
)
self.assert_response_api(
self.url_delete, user, 200, method='DELETE'
)

obj = self.create_request()
self.url_delete = reverse(
'samplesheets:api_irods_request_delete',
kwargs={'irodsdatarequest': obj.sodar_uuid},
)
self.assert_response_api(
self.url_delete, bad_users, 403, method='DELETE'
)

# Test with anonymous access
with self.login(self.superuser):
obj = self.create_request()
self.url_delete = reverse(
'samplesheets:api_irods_request_delete',
kwargs={'irodsdatarequest': obj.sodar_uuid},
)
self.assert_response_api(
self.url_delete, self.anonymous, 401, method='DELETE'
)
# NOTE: For IrodsDataRequestDestroyAPIView, see test_permissions_api


class TestIrodsDataRequestAcceptAPIView(TestIrodsDataRequestAPIViewBase):
Expand Down Expand Up @@ -451,6 +471,7 @@ def test_accept_archived(self):
)


# TODO: Move to test_permissions_api
class TestIrodsDataRequestRejectAPIView(TestIrodsDataRequestAPIViewBase):
"""Test permissions for TestIrodsDataRequestRejectAPIView"""

Expand Down
5 changes: 4 additions & 1 deletion samplesheets/tests/test_views_ajax_taskflow.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
from samplesheets.tests.test_views_taskflow import (
TestIrodsDataRequestViewsBase,
SampleSheetTaskflowMixin,
IRODS_FILE_NAME,
IRODS_FILE_NAME2,
)
from samplesheets.views import IRODS_REQ_CREATE_ALERT as CREATE_ALERT
Expand Down Expand Up @@ -641,7 +642,9 @@ def test_get_coll_obj_delete_request(self):
)

self.assertEqual(response.status_code, 200)
self.assertEqual(response.json()['irods_data'][0]['name'], 'test1')
self.assertEqual(
response.json()['irods_data'][0]['name'], IRODS_FILE_NAME
)
self.assertEqual(
response.json()['irods_data'][0]['path'], self.obj_path
)
Expand Down
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