def mock_create_labbooks(fixture_working_dir):
# Create a labbook in the temporary directory
config_file = fixture_working_dir[0]
lb = LabBook(fixture_working_dir[0])
lb.new(owner={"username": UT_USERNAME},
name=UT_LBNAME,
description="Cats labbook 1")
# Create a file in the dir
with open(os.path.join(fixture_working_dir[1], 'unittest-examplefile'),
'w') as sf:
sf.write("test data")
sf.seek(0)
FileOperations.insert_file(lb, 'code', sf.name)
assert os.path.isfile(
os.path.join(lb.root_dir, 'code', 'unittest-examplefile'))
# Create test client
schema = graphene.Schema(query=LabbookQuery, mutation=LabbookMutations)
with patch.object(Configuration, 'find_default_config',
lambda self: config_file):
app = Flask("lmsrvlabbook")
app.config["LABMGR_CONFIG"] = Configuration()
app.config["LABMGR_ID_MGR"] = get_identity_manager(Configuration())
with app.app_context():
flask.g.user_obj = app.config["LABMGR_ID_MGR"].get_user_profile()
client = Client(
schema,
middleware=[LabBookLoaderMiddleware(), error_middleware],
context_value=ContextMock())
yield lb, client, schema
shutil.rmtree(fixture_working_dir, ignore_errors=True)
def fixture_working_dir_with_cached_user():
"""A pytest fixture that creates a temporary working directory, config file, schema, and local user identity
"""
# Create temp dir
config_file, temp_dir = _create_temp_work_dir()
# Create user identity
user_dir = os.path.join(temp_dir, '.labmanager', 'identity')
os.makedirs(user_dir)
with open(os.path.join(user_dir, 'user.json'), 'wt') as user_file:
json.dump(
{
"username": "******",
"email": "*****@*****.**",
"given_name": "Jane",
"family_name": "Doe"
}, user_file)
with patch.object(Configuration, 'find_default_config',
lambda self: config_file):
app = Flask("lmsrvlabbook")
# Load configuration class into the flask application
app.config["LABMGR_CONFIG"] = Configuration()
app.config["LABMGR_ID_MGR"] = get_identity_manager(Configuration())
with app.app_context():
# within this block, current_app points to app.
yield config_file, temp_dir # name of the config file, temporary working directory
# Remove the temp_dir
shutil.rmtree(temp_dir)
def fixture_working_dir_env_repo_scoped():
"""A pytest fixture that creates a temporary working directory, a config file to match, creates the schema,
and populates the environment component repository.
Class scope modifier attached
"""
# Create temp dir
config_file, temp_dir = _create_temp_work_dir()
# Create user identity
user_dir = os.path.join(temp_dir, '.labmanager', 'identity')
os.makedirs(user_dir)
with open(os.path.join(user_dir, 'user.json'), 'wt') as user_file:
json.dump(
{
"username": "******",
"email": "*****@*****.**",
"given_name": "Jane",
"family_name": "Doe"
}, user_file)
# Create test client
schema = graphene.Schema(query=LabbookQuery, mutation=LabbookMutations)
# get environment data and index
erm = RepositoryManager(config_file)
erm.update_repositories()
erm.index_repositories()
with patch.object(Configuration, 'find_default_config',
lambda self: config_file):
# Load User identity into app context
app = Flask("lmsrvlabbook")
app.config["LABMGR_CONFIG"] = Configuration()
app.config["LABMGR_ID_MGR"] = get_identity_manager(Configuration())
with app.app_context():
# within this block, current_app points to app. Set current user explicitly (this is done in the middleware)
flask.g.user_obj = app.config["LABMGR_ID_MGR"].get_user_profile()
# Create a test client
client = Client(
schema,
middleware=[LabBookLoaderMiddleware(), error_middleware],
context_value=ContextMock())
yield config_file, temp_dir, client, schema # name of the config file, temporary working directory, the schema
# Remove the temp_dir
shutil.rmtree(temp_dir)
def fixture_working_dir_lfs_disabled():
"""A pytest fixture that creates a temporary working directory, config file, schema, and local user identity
"""
# Create temp dir
config_file, temp_dir = _create_temp_work_dir(lfs_enabled=False)
# Create user identity
user_dir = os.path.join(temp_dir, '.labmanager', 'identity')
os.makedirs(user_dir)
with open(os.path.join(user_dir, 'user.json'), 'wt') as user_file:
json.dump(
{
"username": "******",
"email": "*****@*****.**",
"given_name": "Jane",
"family_name": "Doe"
}, user_file)
# Create test client
schema = graphene.Schema(query=LabbookQuery, mutation=LabbookMutations)
with patch.object(Configuration, 'find_default_config',
lambda self: config_file):
# Load User identity into app context
app = Flask("lmsrvlabbook")
app.config["LABMGR_CONFIG"] = Configuration()
app.config["LABMGR_ID_MGR"] = get_identity_manager(Configuration())
with app.app_context():
# within this block, current_app points to app. Set current usert explicitly(this is done in the middleware)
flask.g.user_obj = app.config["LABMGR_ID_MGR"].get_user_profile()
# Create a test client
client = Client(schema,
middleware=[LabBookLoaderMiddleware()],
context_value=ContextMock())
yield config_file, temp_dir, client, schema # name of the config file, temporary working directory, the schema
# Remove the temp_dir
shutil.rmtree(temp_dir)
from lmcommon.environment import RepositoryManager
from lmcommon.auth.identity import AuthenticationError, get_identity_manager
from lmcommon.labbook.lock import reset_all_locks
from lmcommon.labbook import LabBook
from lmsrvcore.auth.user import get_logged_in_author
logger = LMLogger.get_logger()
# Create Flask app
app = Flask("lmsrvlabbook")
# Load configuration class into the flask application
random_bytes = os.urandom(32)
app.config["SECRET_KEY"] = base64.b64encode(random_bytes).decode('utf-8')
app.config["LABMGR_CONFIG"] = config = Configuration()
app.config["LABMGR_ID_MGR"] = get_identity_manager(Configuration())
if config.config["flask"]["allow_cors"]:
# Allow CORS
CORS(app, max_age=7200)
# Set Debug mode
app.config['DEBUG'] = config.config["flask"]["DEBUG"]
# Register LabBook service
app.register_blueprint(blueprint.complete_labbook_service)
# Configure CHP
try:
api_prefix = app.config["LABMGR_CONFIG"].config['proxy'][
"labmanager_api_prefix"]
def build_image_for_jupyterlab():
# Create temp dir
config_file, temp_dir = _create_temp_work_dir()
# Create user identity
user_dir = os.path.join(temp_dir, '.labmanager', 'identity')
os.makedirs(user_dir)
with open(os.path.join(user_dir, 'user.json'), 'wt') as user_file:
json.dump(
{
"username": "******",
"email": "*****@*****.**",
"given_name": "unittester",
"family_name": "tester"
}, user_file)
# Create test client
schema = graphene.Schema(query=LabbookQuery, mutation=LabbookMutations)
# get environment data and index
erm = RepositoryManager(config_file)
erm.update_repositories()
erm.index_repositories()
with patch.object(Configuration, 'find_default_config',
lambda self: config_file):
# Load User identity into app context
app = Flask("lmsrvlabbook")
app.config["LABMGR_CONFIG"] = Configuration()
app.config["LABMGR_ID_MGR"] = get_identity_manager(Configuration())
with app.app_context():
# within this block, current_app points to app. Set current user explicitly (this is done in the middleware)
flask.g.user_obj = app.config["LABMGR_ID_MGR"].get_user_profile()
# Create a test client
client = Client(
schema,
middleware=[LabBookLoaderMiddleware(), error_middleware],
context_value=ContextMock())
# Create a labook
lb = LabBook(config_file)
lb.new(name="containerunittestbook",
description="Testing docker building.",
owner={"username": "******"})
# Create Component Manager
cm = ComponentManager(lb)
# Add a component
cm.add_component("base", ENV_UNIT_TEST_REPO, ENV_UNIT_TEST_BASE,
ENV_UNIT_TEST_REV)
cm.add_packages("pip3", [{
"manager": "pip3",
"package": "requests",
"version": "2.18.4"
}])
ib = ImageBuilder(lb)
ib.assemble_dockerfile(write=True)
docker_client = get_docker_client()
try:
lb, docker_image_id = ContainerOperations.build_image(
labbook=lb, username="******")
yield lb, ib, docker_client, docker_image_id, client, "unittester"
finally:
shutil.rmtree(lb.root_dir)
try:
docker_client.containers.get(docker_image_id).stop()
docker_client.containers.get(docker_image_id).remove()
except:
pass
try:
docker_client.images.remove(docker_image_id,
force=True,
noprune=False)
except:
pass
def fixture_working_dir_populated_scoped():
"""A pytest fixture that creates a temporary working directory, a config file to match, creates the schema,
and populates the environment component repository.
Class scope modifier attached
"""
# Create temp dir
config_file, temp_dir = _create_temp_work_dir()
# Create user identity
user_dir = os.path.join(temp_dir, '.labmanager', 'identity')
os.makedirs(user_dir)
with open(os.path.join(user_dir, 'user.json'), 'wt') as user_file:
json.dump(
{
"username": "******",
"email": "*****@*****.**",
"given_name": "Jane",
"family_name": "Doe"
}, user_file)
# Create test client
schema = graphene.Schema(query=LabbookQuery, mutation=LabbookMutations)
# Create a bunch of lab books
lb = LabBook(config_file)
lb.new(owner={"username": "******"},
name="labbook1",
description="Cats labbook 1")
time.sleep(1.1)
lb.new(owner={"username": "******"},
name="labbook2",
description="Dogs labbook 2")
time.sleep(1.1)
lb.new(owner={"username": "******"},
name="labbook3",
description="Mice labbook 3")
time.sleep(1.1)
lb.new(owner={"username": "******"},
name="labbook4",
description="Horses labbook 4")
time.sleep(1.1)
lb.new(owner={"username": "******"},
name="labbook5",
description="Cheese labbook 5")
time.sleep(1.1)
lb.new(owner={"username": "******"},
name="labbook6",
description="Goat labbook 6")
time.sleep(1.1)
lb.new(owner={"username": "******"},
name="labbook7",
description="Turtle labbook 7")
time.sleep(1.1)
lb.new(owner={"username": "******"},
name="labbook8",
description="Lamb labbook 8")
time.sleep(1.1)
lb.new(owner={"username": "******"},
name="labbook9",
description="Taco labbook 9")
time.sleep(1.1)
lb.new(owner={"username": "******"},
name="labbook-0",
description="This should not show up.")
with patch.object(Configuration, 'find_default_config',
lambda self: config_file):
# Load User identity into app context
app = Flask("lmsrvlabbook")
app.config["LABMGR_CONFIG"] = Configuration()
app.config["LABMGR_ID_MGR"] = get_identity_manager(Configuration())
with app.app_context():
# within this block, current_app points to app. Set current user explicitly (this is done in the middleware)
flask.g.user_obj = app.config["LABMGR_ID_MGR"].get_user_profile()
# Create a test client
client = Client(schema,
middleware=[LabBookLoaderMiddleware()],
context_value=ContextMock())
yield config_file, temp_dir, client, schema
# Remove the temp_dir
shutil.rmtree(temp_dir)
