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Address review comments
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3 files changed

+11
-3
lines changed

3 files changed

+11
-3
lines changed

bioblend/galaxy/__init__.py

Lines changed: 8 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -40,6 +40,7 @@ def __init__(
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email: Optional[str] = None,
4141
password: Optional[str] = None,
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*,
43+
token: Optional[str] = None,
4344
verify: bool = True,
4445
user_agent: Optional[str] = None,
4546
) -> None:
@@ -81,10 +82,16 @@ def __init__(
8182
:param password: Password of Galaxy account corresponding to the above
8283
e-mail address. Ignored if key is supplied directly.
8384
85+
:type token: str
86+
:param token: An OIDC access token obtained from an OIDC provider
87+
configured in `oidc_backends_config.xml`. Can be used
88+
as a substitue for an API key. You must make sure the access
89+
token has not expired when making an API call.
90+
8491
:param verify: Whether to verify the server's TLS certificate
8592
:type verify: bool
8693
"""
87-
super().__init__(url, key=key, email=email, password=password, verify=verify, user_agent=user_agent)
94+
super().__init__(url, key=key, email=email, password=password, token=token, verify=verify, user_agent=user_agent)
8895
self.libraries = libraries.LibraryClient(self)
8996
self.histories = histories.HistoryClient(self)
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self.workflows = workflows.WorkflowClient(self)

bioblend/galaxy/objects/galaxy_instance.py

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -54,11 +54,12 @@ def __init__(
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email: Optional[str] = None,
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password: Optional[str] = None,
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*,
57+
token: Optional[str] = None,
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verify: bool = True,
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user_agent: Optional[str] = None,
5960
) -> None:
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self.gi = bioblend.galaxy.GalaxyInstance(
61-
url, key=api_key, email=email, password=password, verify=verify, user_agent=user_agent
62+
url, key=api_key, email=email, password=password, token=token, verify=verify, user_agent=user_agent
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)
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self.log = bioblend.log
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self.datasets = client.ObjDatasetClient(self)

bioblend/galaxyclient.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -36,10 +36,10 @@ def __init__(
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self,
3737
url: str,
3838
key: Optional[str] = None,
39-
token: Optional[str] = None,
4039
email: Optional[str] = None,
4140
password: Optional[str] = None,
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*,
42+
token: Optional[str] = None,
4343
verify: bool = True,
4444
timeout: Optional[float] = None,
4545
user_agent: Optional[str] = None,

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