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Refactor the authentication code; add an "interactive=False" option f…
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…or using the client in headless scripts where we can't prompt for passwords
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@apdavison
apdavison committed Oct 25, 2024
1 parent 23e56bd commit d84f4a0
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Showing 4 changed files with 88 additions and 67 deletions.
8 changes: 4 additions & 4 deletions codemeta.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,12 @@
"@type": "SoftwareSourceCode",
"license": "https://spdx.org/licenses/BSD-3-Clause.html",
"codeRepository": "https://github.com/HumanBrainProject/ebrains-validation-client",
"dateModified": "2024-10-09",
"downloadUrl": "https://files.pythonhosted.org/packages/be/17/e483a75b4b94dcc69e8b1be21ef11667ec74c8d8d1e7858bbeee71d62d1e/ebrains_validation_framework-0.9.1.tar.gz",
"dateModified": "2024-10-25",
"downloadUrl": null,
"issueTracker": "https://github.com/HumanBrainProject/ebrains-validation-client/issues",
"name": "ebrains-validation-framework",
"version": "0.9.1",
"identifier": "https://pypi.org/project/ebrains-validation-framework/0.9.1/",
"version": "0.9.2",
"identifier": "https://pypi.org/project/ebrains-validation-framework/0.9.2/",
"description": "Python client for the EBRAINS Validation Framework web services.",
"applicationCategory": "neuroscience",
"funding": "https://cordis.europa.eu/project/id/945539",
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2 changes: 1 addition & 1 deletion docs/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@
# The short X.Y version.
version = "0.9"
# The full version, including alpha/beta/rc tags.
release = "0.9.1"
release = "0.9.2"

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
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143 changes: 82 additions & 61 deletions ebrains_validation_framework/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
have_collab_token_handler = False


__version__ = "0.9.1"
__version__ = "0.9.2"


TOKENFILE = os.path.expanduser("~/.ebrainstoken")
Expand Down Expand Up @@ -90,7 +90,7 @@ class BaseClient(object):

__test__ = False

def __init__(self, username=None, password=None, environment="production", token=None):
def __init__(self, username=None, password=None, environment="production", token=None, interactive=True):
self.username = username
self.verify = True
self.environment = environment
Expand Down Expand Up @@ -118,79 +118,85 @@ def __init__(self, username=None, password=None, environment="production", token
raise KeyError(f"{err_msg_base} does not contain environment = {environment}")
else:
raise IOError(f"{err_msg_base} not found in the current directory.")
if self.token:
pass
elif password is None:
self.token = None
self._authenticate(password, interactive)

def _authenticate(self, password, interactive):
# If a token is provided, we try using it.
# If not, we try to get a token from the environment
# or from a local cache
if not self.token:
if have_collab_token_handler:
# if are we running in a Jupyter notebook within the Collaboratory
# the token is already available
self.token = oauth.get_token()
elif os.path.exists(TOKENFILE):
if username:
# check for a stored token
if self.username:
with open(TOKENFILE) as fp:
data = json.load(fp).get(username, None)
data = json.load(fp).get(self.username, None)
if data and "access_token" in data:
self.token = data["access_token"]
if not self._check_token_valid():
print(
"EBRAINS authentication token is invalid or has expired. "
"Will need to re-authenticate."
)
self.token = None
else:
print(f"EBRAINS authentication token file not having required JSON data. data = {data}")
print(f"No token for {self.username} found in {TOKENFILE}")
else:
print("Authentication token file found, but you have not provided your username.")
else:
print("EBRAINS authentication token file not found locally.")

if self.token is None:
if not username:
print("\n==============================================")
print("Please enter your EBRAINS username.")
username = input("EBRAINS Username: ")

password = os.environ.get("EBRAINS_PASS")
if password is not None:
try:
self._ebrains_auth(username, password)
except Exception:
print(
"Authentication Failure. "
"Possibly incorrect EBRAINS password saved in environment variable 'EBRAINS_PASS'."
)
if not hasattr(self, "config"):
# If we don't have a token, we try to authenticate with username and password
if not self._check_token_valid():
print(
"EBRAINS authentication token is invalid or has expired. "
"Will need to re-authenticate."
)
if (not self.username) and interactive:
print("\n==============================================")
print("Please enter your EBRAINS username.")
self.username = input("EBRAINS Username: ")

if self.username:
password = password or os.environ.get("EBRAINS_PASS")
if (not password) and interactive:
# prompt for password
print("Please enter your EBRAINS password: ")
password = getpass.getpass()

if password:
try:
# prompt for password
print("Please enter your EBRAINS password: ")
password = getpass.getpass()
self._ebrains_auth(username, password)
self._ebrains_auth(self.username, password)
except Exception:
print("Authentication Failure! Password entered is possibly incorrect.")
raise
with open(TOKENFILE, "w") as fp:
json.dump({username: {"access_token": self.config["access_token"]}}, fp)
os.chmod(TOKENFILE, 0o600)
else:
try:
self._ebrains_auth(username, password)
except Exception:
print("Authentication Failure! Password entered is possibly incorrect.")
raise

if self.token:
self.auth = EBRAINSAuth(self.token)

# store token in local cache
if os.path.exists(TOKENFILE):
with open(TOKENFILE, "r") as fp:
token_data = json.load(fp)
else:
token_data = {}
token_data[self.username] = {"access_token": self.token}

with open(TOKENFILE, "w") as fp:
json.dump({username: {"access_token": self.config["access_token"]}}, fp)
json.dump(token_data, fp)
fp.write("\n")
os.chmod(TOKENFILE, 0o600)
self.auth = EBRAINSAuth(self.token)
else:
self.auth = None

def _check_token_valid(self):
url = "https://iam.ebrains.eu/auth/realms/hbp/protocol/openid-connect/userinfo"
data = requests.get(url, auth=EBRAINSAuth(self.token), verify=self.verify)
if data.status_code == 200:
return True
else:
return False
if self.token:
url = "https://iam.ebrains.eu/auth/realms/hbp/protocol/openid-connect/userinfo"
data = requests.get(url, auth=EBRAINSAuth(self.token), verify=self.verify)
if data.status_code == 200:
remote_username = data.json()["preferred_username"]
if self.username and self.username != remote_username:
raise Exception("Username does not match token")
else:
self.username = remote_username
return True
return False

def _format_people_name(self, names):
# converts a string of people names separated by semi-colons
Expand Down Expand Up @@ -447,7 +453,7 @@ class TestLibrary(BaseClient):
}
token : string, optional
You may directly input a valid authenticated token from Collaboratory v1 or v2.
You may directly input a valid authenticated EBRAINS access token.
Note: you should use the `access_token` and NOT `refresh_token`.
Examples
Expand All @@ -460,8 +466,8 @@ class TestLibrary(BaseClient):

__test__ = False

def __init__(self, username=None, password=None, environment="production", token=None):
super(TestLibrary, self).__init__(username, password, environment, token)
def __init__(self, username=None, password=None, environment="production", token=None, interactive=True):
super(TestLibrary, self).__init__(username, password, environment, token, interactive)
self._set_app_info()

def _set_app_info(self):
Expand Down Expand Up @@ -1580,8 +1586,13 @@ def register_result(self, test_result, data_store=None, collab_id=None):
files_to_upload.extend(test_result.related_data["figures"])
if files_to_upload:
list_dict_files_uploaded = [
{"download_url": f["filepath"], "size": f["filesize"]}
for f in data_store.upload_data(files_to_upload)
{
"download_url": ftu["filepath"],
"size": ftu["filesize"],
"hash": ftu["hash"],
"local_path": ftu["local_path"]
}
for ftu in data_store.upload_data(files_to_upload)
]
results_storage.extend(list_dict_files_uploaded)

Expand Down Expand Up @@ -1729,8 +1740,8 @@ class ModelCatalog(BaseClient):

__test__ = False

def __init__(self, username=None, password=None, environment="production", token=None):
super(ModelCatalog, self).__init__(username, password, environment, token)
def __init__(self, username=None, password=None, environment="production", token=None, interactive=True):
super(ModelCatalog, self).__init__(username, password, environment, token, interactive)
self._set_app_info()

def _set_app_info(self):
Expand Down Expand Up @@ -2541,6 +2552,7 @@ def add_model_instance(
hash="",
morphology="",
license="",
collab_id=None
):
"""Register a new model instance.
Expand Down Expand Up @@ -2569,6 +2581,10 @@ def add_model_instance(
URL(s) to the morphology file(s) employed in this model.
license : string
Indicates the license applicable for this model instance.
collab_id : string
Specifies the ID of the host collab in the EBRAINS Collaboratory
(the model instance would belong to this collab).
If not provided, defaults to the collab of the parent model project.
Returns
-------
Expand All @@ -2590,6 +2606,7 @@ def add_model_instance(

instance_data = locals()
instance_data.pop("self")
instance_data["project_id"] = instance_data.pop("collab_id")

for key, val in instance_data.items():
if val == "":
Expand All @@ -2614,7 +2631,7 @@ def add_model_instance(
else:
handle_response_error("Error in adding model instance", response)

def find_model_instance_else_add(self, model_obj):
def find_model_instance_else_add(self, model_obj, collab_id=None):
"""Find existing model instance; else create a new instance
This checks if the input model object has an associated model instance.
Expand All @@ -2624,6 +2641,9 @@ def find_model_instance_else_add(self, model_obj):
----------
model_obj : object
Python object representing a model.
collab_id : str
In case of adding a new model instance, add it to this collab.
If None, add to the same collab as the parent model.
Returns
-------
Expand Down Expand Up @@ -2664,6 +2684,7 @@ def find_model_instance_else_add(self, model_obj):
source=getattr(model_obj, "remote_url", ""),
version=model_obj.model_version,
parameters=getattr(model_obj, "parameters", ""),
collab_id=collab_id or getattr(model_obj, "collab_id", None)
)
else:
model_instance = self.get_model_instance(instance_id=model_obj.model_instance_uuid)
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[project]
name = "ebrains_validation_framework"
version = "0.9.1"
version = "0.9.2"
description = "Python client for the EBRAINS Validation Framework web services."
readme = "README.md"
authors = [
Expand Down

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