def test_it_outputs_csv_to_file_without_entity_parent_id_for_projects(
capsys, syn_test_helper, syn_project, syn_folder, syn_file,
mk_tempdir):
folder_team = syn_test_helper.create_team()
file_team = syn_test_helper.create_team()
SynapseProxy.client().setPermissions(
syn_folder,
folder_team.id,
accessType=SynapseProxy.Permissions.CAN_EDIT_AND_DELETE,
warn_if_inherits=False)
SynapseProxy.client().setPermissions(
syn_file,
file_team.id,
accessType=SynapseProxy.Permissions.CAN_EDIT_AND_DELETE,
warn_if_inherits=False)
out_file = os.path.join(mk_tempdir(), 'outfile.csv')
report = BenefactorPermissionsReport(syn_project.id, out_path=out_file)
report.execute()
assert report._csv_full_path == out_file
assert_success_from_print(capsys, syn_project)
assert_success_from_csv(report._csv_full_path, syn_project, syn_folder,
syn_file)
with open(out_file, newline='') as csvfile:
reader = csv.DictReader(csvfile)
for row in reader:
if row['entity_type'] == 'Project':
assert row['entity_parent_id'] == ''
else:
assert row['entity_parent_id'] == syn_project.id
def test__extract_concrete_type():
assert SynapseProxy._extract_concrete_type(
syn.Project()) == 'org.sagebionetworks.repo.model.Project'
assert SynapseProxy._extract_concrete_type({
'concreteType':
'org.sagebionetworks.repo.model.Project'
}) == 'org.sagebionetworks.repo.model.Project'
assert SynapseProxy._extract_concrete_type({
'type':
'org.sagebionetworks.repo.model.Project'
}) == 'org.sagebionetworks.repo.model.Project'
with pytest.raises(ValueError) as err:
SynapseProxy._extract_concrete_type({})
assert 'Cannot extract type from' in str(err)
def test_it_reports_on_uniq_permissions(capsys, syn_project, syn_folder,
syn_file, syn_test_helper):
folder_team = syn_test_helper.create_team()
file_team = syn_test_helper.create_team()
SynapseProxy.client().setPermissions(
syn_folder,
folder_team.id,
accessType=SynapseProxy.Permissions.CAN_EDIT_AND_DELETE,
warn_if_inherits=False)
SynapseProxy.client().setPermissions(
syn_file,
file_team.id,
accessType=SynapseProxy.Permissions.CAN_EDIT_AND_DELETE,
warn_if_inherits=False)
BenefactorPermissionsReport(syn_project.name).execute()
assert_success_from_print(capsys, syn_project, syn_folder, syn_file)
def assert_success_from_print(capsys, *entities):
captured = capsys.readouterr()
assert captured.err == ''
for entity in entities:
log_msg = '{0}: {1} ({2}) found.'.format(SynapseProxy.entity_type_display_name(entity),
entity.name,
entity.id)
assert log_msg in captured.out
def test_with_cache_get_user(syn_test_helper):
user_id = SynapseProxy.client().getUserProfile().get('ownerId')
user = SynapseProxy.WithCache.get_user(user_id)
assert user['ownerId'] == user_id
# Returns None if the user does not exist
assert SynapseProxy.WithCache.get_user('-9999999') is None
assert SynapseProxy.WithCache.get_user('000') is None
assert SynapseProxy.WithCache.get_user(
syn_test_helper.uniq_name(prefix='notarealname')) is None
def create_project(self, **kwargs):
"""Creates a new Project and adds it to the trash queue."""
if 'name' not in kwargs:
kwargs['name'] = self.uniq_name(prefix=kwargs.get('prefix', ''))
kwargs.pop('prefix', None)
project = SynapseProxy.client().store(Project(**kwargs))
self.dispose_of(project)
return project
def create_file(self, **kwargs):
"""Creates a new File and adds it to the trash queue."""
if 'name' not in kwargs:
kwargs['name'] = self.uniq_name(prefix=kwargs.get('prefix', ''))
kwargs.pop('prefix', None)
file = SynapseProxy.client().store(File(**kwargs))
self.dispose_of(file)
return file
def create_wiki(self, **kwargs):
"""Creates a new Wiki and adds it to the trash queue."""
if 'title' not in kwargs:
kwargs['title'] = self.uniq_name(prefix=kwargs.get('prefix', ''))
kwargs.pop('prefix', None)
if 'markdown' not in kwargs:
kwargs['markdown'] = 'My Wiki {0}'.format(kwargs['title'])
wiki = SynapseProxy.client().store(Wiki(**kwargs))
self.dispose_of(wiki)
return wiki
def test_is_synapse_id():
assert SynapseProxy.is_synapse_id('SyN1230') is True
assert SynapseProxy.is_synapse_id(' sYn1230 ') is True
assert SynapseProxy.is_synapse_id('syn') is False
assert SynapseProxy.is_synapse_id('syn 1230') is False
assert SynapseProxy.is_synapse_id('1230') is False
assert SynapseProxy.is_synapse_id('1230syn') is False
def create_team(self, **kwargs):
"""Creates a new Team and adds it to the trash queue."""
if 'name' not in kwargs:
kwargs['name'] = self.uniq_name(prefix=kwargs.get('prefix', ''))
kwargs.pop('prefix', None)
team = SynapseProxy.client().store(Team(**kwargs))
# Wait for the team to be available in Synapse.
tries = 0
while True:
tries += 1
try:
SynapseProxy.client().getTeam(team.name)
break
except ValueError:
if tries >= 10:
raise Exception('Timed out waiting for Team to be available in Synapse.')
else:
time.sleep(3)
self.dispose_of(team)
return team
def test_with_cache_get_user_or_team(syn_test_helper):
user_id = SynapseProxy.client().getUserProfile().get('ownerId')
team_id = syn_test_helper.create_team().get('id')
user = SynapseProxy.WithCache.get_user_or_team(user_id)
assert isinstance(user, syn.UserProfile)
assert user['ownerId'] == user_id
team = SynapseProxy.WithCache.get_user_or_team(team_id)
assert isinstance(team, syn.Team)
assert team['id'] == team_id
# Returns None if the user and team do not exist
assert SynapseProxy.WithCache.get_user_or_team('-9999999') is None
assert SynapseProxy.WithCache.get_user_or_team('000') is None
assert SynapseProxy.WithCache.get_user_or_team(
syn_test_helper.uniq_name(prefix='notarealname')) is None
assert SynapseProxy.WithCache.get_user_or_team(
syn_test_helper.uniq_name(prefix='notarealname')) is None
def test_is_file():
assert SynapseProxy.is_file(
'org.sagebionetworks.repo.model.FileEntity') is True
assert SynapseProxy.is_file(syn.File(parentId='syn0')) is True
assert SynapseProxy.is_file(
{'concreteType': 'org.sagebionetworks.repo.model.FileEntity'}) is True
def test_is_folder():
assert SynapseProxy.is_folder(
'org.sagebionetworks.repo.model.Folder') is True
assert SynapseProxy.is_folder(syn.Folder(parentId='syn0')) is True
assert SynapseProxy.is_folder(
{'concreteType': 'org.sagebionetworks.repo.model.Folder'}) is True
def test_is_project():
assert SynapseProxy.is_project(
'org.sagebionetworks.repo.model.Project') is True
assert SynapseProxy.is_project(syn.Project()) is True
assert SynapseProxy.is_project(
{'concreteType': 'org.sagebionetworks.repo.model.Project'}) is True
def test_entity_type_display_name():
assert SynapseProxy.entity_type_display_name(
'org.sagebionetworks.repo.model.Project'
) == SynapseProxy.PROJECT_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name(
syn.Project()) == SynapseProxy.PROJECT_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name({
'concreteType':
'org.sagebionetworks.repo.model.Project'
}) == SynapseProxy.PROJECT_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name(
'org.sagebionetworks.repo.model.Folder'
) == SynapseProxy.FOLDER_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name(
syn.Folder(parentId='syn0')) == SynapseProxy.FOLDER_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name({
'concreteType':
'org.sagebionetworks.repo.model.Folder'
}) == SynapseProxy.FOLDER_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name(
'org.sagebionetworks.repo.model.FileEntity'
) == SynapseProxy.FILE_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name(
syn.File(parentId='syn0')) == SynapseProxy.FILE_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name({
'concreteType':
'org.sagebionetworks.repo.model.FileEntity'
}) == SynapseProxy.FILE_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name(
'org.sagebionetworks.repo.model.Link'
) == SynapseProxy.LINK_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name(
syn.Link(parentId='syn0',
targetId='syn0')) == SynapseProxy.LINK_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name({
'concreteType':
'org.sagebionetworks.repo.model.Link'
}) == SynapseProxy.LINK_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name(
'org.sagebionetworks.repo.model.table.TableEntity'
) == SynapseProxy.TABLE_TYPE_DISPLAY_NAME
assert SynapseProxy.entity_type_display_name({
'concreteType':
'org.sagebionetworks.repo.model.table.TableEntity'
}) == SynapseProxy.TABLE_TYPE_DISPLAY_NAME
def dispose(self):
"""Cleans up any Synapse objects that were created during testing.
This method needs to be manually called after each or all tests are done.
"""
projects = []
folders = []
files = []
teams = []
wikis = []
others = []
for obj in self._trash:
if isinstance(obj, Project):
projects.append(obj)
elif isinstance(obj, Folder):
folders.append(obj)
elif isinstance(obj, File):
files.append(obj)
elif isinstance(obj, Team):
teams.append(obj)
elif isinstance(obj, Wiki):
wikis.append(obj)
else:
others.append(obj)
for syn_obj in wikis:
try:
SynapseProxy.client().delete(syn_obj)
except:
pass
self._trash.remove(syn_obj)
for syn_obj in files:
try:
SynapseProxy.client().delete(syn_obj)
except:
pass
self._trash.remove(syn_obj)
for syn_obj in folders:
try:
SynapseProxy.client().delete(syn_obj)
except:
pass
self._trash.remove(syn_obj)
for syn_obj in projects:
try:
SynapseProxy.client().delete(syn_obj)
except:
pass
self._trash.remove(syn_obj)
for syn_obj in teams:
try:
SynapseProxy.client().delete(syn_obj)
except:
pass
self._trash.remove(syn_obj)
for obj in others:
print('WARNING: Non-Supported object found: {0}'.format(obj))
self._trash.remove(obj)
def syn_client():
return SynapseProxy.client()