def get_user_details(self, response):
authenticated_panoptes = Panoptes(
endpoint=PanoptesUtils.base_url(),
client_id=PanoptesUtils.client_id(),
client_secret=PanoptesUtils.client_secret())
authenticated_panoptes.bearer_token = response['access_token']
authenticated_panoptes.logged_in = True
authenticated_panoptes.refresh_token = response['refresh_token']
bearer_expiry = datetime.now() + timedelta(
seconds=response['expires_in'])
authenticated_panoptes.bearer_expires = (bearer_expiry)
with authenticated_panoptes:
user = authenticated_panoptes.get('/me')[0]['users'][0]
ids = ['admin user']
if not user['admin']:
ids = [
project.href for project in Project.where(
current_user_roles='collaborator')
]
return {
'username': user['login'],
'email': user['email'],
'is_superuser': user['admin'],
'projects': ids
}
def get_authenticated_panoptes(bearer_token, bearer_expiry):
guest_authenticated_panoptes = Panoptes(endpoint=PanoptesUtils.base_url())
guest_authenticated_panoptes.bearer_token = bearer_token
guest_authenticated_panoptes.logged_in = True
bearer_expiry = datetime.strptime(bearer_expiry, "%Y-%m-%d %H:%M:%S.%f")
guest_authenticated_panoptes.bearer_expires = (bearer_expiry)
return guest_authenticated_panoptes
def get_user_details(self, response):
with Panoptes() as p:
p.bearer_token = response['access_token']
p.logged_in = True
p.refresh_token = response['refresh_token']
p.bearer_expires = (datetime.now() +
timedelta(seconds=response['expires_in']))
user = p.get('/me')[0]['users'][0]
ids = ['admin user']
if not user['admin']:
ids = [project.id for project in Project.where()]
return {
'username': user['login'],
'email': user['email'],
'is_superuser': user['admin'],
'projects': ids,
}
def apply(self, filenames):
if self.pipeline.multiple_subject_sets:
scope = self.bundle
else:
scope = self.pipeline
theia_authenticated_client = Panoptes(
endpoint=PanoptesUtils.base_url(),
client_id=PanoptesUtils.client_id(),
client_secret=PanoptesUtils.client_secret()
)
with theia_authenticated_client:
target_set = self._get_subject_set(scope, self.project.id, scope.name_subject_set())
using_manifest = False
metadata_dictionary = {}
path_example = filenames[0]
manifest_file_location = path.join((path.dirname(path_example) + "_interstitial_products"), "manifest.csv")
if self.include_metadata and path.exists(manifest_file_location):
using_manifest = True
with open(manifest_file_location, newline='') as csvfile:
reader = csv.DictReader(csvfile)
for row in reader:
metadata_dictionary[row['#filename']] = row
for filename in filenames:
img = Image.open(filename)
img.save(filename, 'png')
#This line might have to be done with os.path to translate across OSes
name_only = filename.split("/")[len(filename.split("/")) - 1]
metadata = {}
if using_manifest:
metadata = metadata_dictionary[name_only]
new_subject = self._create_subject(self.project.id, filename, metadata=metadata)
target_set.add(new_subject)
class TestUploadSubject:
@patch('theia.operations.panoptes_operations.UploadSubject.config',
return_value=False)
@patch('theia.api.models.Pipeline.name_subject_set',
return_value='pipeline name')
@patch(
'theia.operations.panoptes_operations.UploadSubject._get_subject_set',
return_value=SubjectSet())
@patch(
'theia.operations.panoptes_operations.UploadSubject._create_subject',
return_value=Subject())
@patch('panoptes_client.SubjectSet.add')
@patch('PIL.Image.open', return_value=Mock())
def test_apply_single(self, mockOpen, mockAdd, mockCreate, mockGet,
mockGetName, mockIncludeMetadata, *args):
project = Project(id=8)
pipeline = Pipeline(project=project)
bundle = JobBundle(pipeline=pipeline)
operation = UploadSubject(bundle)
operation.apply(['some_file'])
mockOpen.assert_called_once()
mockGetName.assert_called_once()
mockGet.assert_called_once_with(pipeline, 8, 'pipeline name')
mockCreate.assert_called_once_with(8, 'some_file', metadata={})
mockAdd.assert_called_once_with(mockCreate.return_value)
@patch('theia.operations.panoptes_operations.UploadSubject.config',
return_value=False)
@patch('theia.api.models.JobBundle.name_subject_set',
return_value='bundle name')
@patch(
'theia.operations.panoptes_operations.UploadSubject._get_subject_set',
return_value=SubjectSet())
@patch(
'theia.operations.panoptes_operations.UploadSubject._create_subject',
return_value=Subject())
@patch('panoptes_client.SubjectSet.add')
@patch('PIL.Image.open', return_value=Mock())
def test_apply_multiple(self, mockOpen, mockAdd, mockCreate, mockGet,
mockGetName, mockIncludeMetadata, *args):
project = Project(id=8)
pipeline = Pipeline(project=project, multiple_subject_sets=True)
bundle = JobBundle(pipeline=pipeline)
operation = UploadSubject(bundle)
operation.apply(['some_file'])
mockOpen.assert_called_once()
mockGetName.assert_called_once()
mockGet.assert_called_once_with(bundle, 8, 'bundle name')
mockCreate.assert_called_once_with(8, 'some_file', metadata={})
mockAdd.assert_called_once_with(mockCreate.return_value)
@patch('theia.api.models.JobBundle.save')
@patch('theia.api.models.Pipeline.save')
@patch(
'theia.operations.panoptes_operations.UploadSubject._create_subject_set'
)
@patch('panoptes_client.SubjectSet.find', autospec=True)
@patch('panoptes_client.Panoptes', return_value=Panoptes())
def test__get_subject_set(self, mock_client, mockFind, mockCreateSet,
*args):
mockFind.reset_mock()
mockCreateSet.reset_mock()
emptyJobBundle = JobBundle()
linkedJobBundle = JobBundle(subject_set_id=3)
emptyPipeline = Pipeline()
linkedPipeline = Pipeline(subject_set_id=3)
operation = UploadSubject(emptyJobBundle)
result = operation._get_subject_set(emptyJobBundle, 8, 'some name')
mockFind.assert_not_called()
mockCreateSet.assert_called_once_with(8, 'some name')
mockFind.reset_mock()
mockCreateSet.reset_mock()
operation = UploadSubject(linkedJobBundle)
result = operation._get_subject_set(linkedJobBundle, 8, 'some name')
mockFind.assert_called_once_with(3)
mockCreateSet.assert_not_called()
mockFind.reset_mock()
mockCreateSet.reset_mock()
operation = UploadSubject(emptyPipeline)
result = operation._get_subject_set(emptyPipeline, 8, 'some name')
mockFind.assert_not_called()
mockCreateSet.assert_called_once_with(8, 'some name')
mockFind.reset_mock()
mockCreateSet.reset_mock()
operation = UploadSubject(linkedPipeline)
result = operation._get_subject_set(linkedPipeline, 8, 'some name')
mockFind.assert_called_once_with(3)
mockCreateSet.assert_not_called()
@patch('panoptes_client.Project.find', return_value=Mock())
@patch('panoptes_client.Subject.save', autospec=True)
@patch('panoptes_client.Subject.add_location', autospec=True)
def test__create_subject_no_metadata(self, mockAdd, mockSave, mockFind):
operation = UploadSubject(None)
created_subject = operation._create_subject(1, 'some_file')
mockFind.assert_called_once_with(1)
mockAdd.assert_called_once_with(created_subject, 'some_file') # weird
mockSave.assert_called_once()
assert (mockFind.return_value == created_subject.links.project.id
) # weird
@patch('panoptes_client.Project.find', return_value=Mock())
@patch('panoptes_client.Subject.save', autospec=True)
@patch('panoptes_client.Subject.add_location', autospec=True)
def test__create_subject_with_metadata(self, mockAdd, mockSave, mockFind):
operation = UploadSubject(None)
created_subject = operation._create_subject(1, 'some_file',
{'foo': 'bar'})
mockFind.assert_called_once_with(1)
mockAdd.assert_called_once_with(created_subject, 'some_file') # weird
mockSave.assert_called_once()
assert (mockFind.return_value == created_subject.links.project.id
) # weird
assert (created_subject.metadata == {'foo': 'bar'})
@patch('panoptes_client.Project.find', return_value=Mock())
@patch('panoptes_client.SubjectSet.save', autospec=True)
def test__create_subject_set(self, mockSave, mockFind):
operation = UploadSubject(None)
created_set = operation._create_subject_set(1, 'some name')
mockFind.assert_called_once_with(1)
mockSave.assert_called_once()
assert (created_set.display_name == 'some name')
assert (mockFind.return_value == created_set.links.project.id) # weird