Merge pull request #482 from nuwang/add_support_for_access_tokens

Add support for API auth with access token

Author: nsoranzo

bioblend/galaxy/__init__.py

@@ -40,6 +40,7 @@ def __init__(
         email: Optional[str] = None,
         password: Optional[str] = None,
         *,
+        token: Optional[str] = None,
         verify: bool = True,
         user_agent: Optional[str] = None,
     ) -> None:
@@ -81,10 +82,18 @@ def __init__(
         :param password: Password of Galaxy account corresponding to the above
                          e-mail address. Ignored if key is supplied directly.
 
+        :type token: str
+        :param token: An OIDC access token obtained from an OIDC provider
+                      configured in `oidc_backends_config.xml`. Can be used
+                      as a substitue for an API key. You must make sure the access
+                      token has not expired when making an API call.
+
         :param verify: Whether to verify the server's TLS certificate
         :type verify: bool
         """
-        super().__init__(url, key=key, email=email, password=password, verify=verify, user_agent=user_agent)
+        super().__init__(
+            url, key=key, email=email, password=password, token=token, verify=verify, user_agent=user_agent
+        )
         self.libraries = libraries.LibraryClient(self)
         self.histories = histories.HistoryClient(self)
         self.workflows = workflows.WorkflowClient(self)

bioblend/galaxy/objects/galaxy_instance.py

@@ -54,11 +54,12 @@ def __init__(
         email: Optional[str] = None,
         password: Optional[str] = None,
         *,
+        token: Optional[str] = None,
         verify: bool = True,
         user_agent: Optional[str] = None,
     ) -> None:
         self.gi = bioblend.galaxy.GalaxyInstance(
-            url, key=api_key, email=email, password=password, verify=verify, user_agent=user_agent
+            url, key=api_key, email=email, password=password, token=token, verify=verify, user_agent=user_agent
         )
         self.log = bioblend.log
         self.datasets = client.ObjDatasetClient(self)

bioblend/galaxyclient.py

@@ -39,6 +39,7 @@ def __init__(
         email: Optional[str] = None,
         password: Optional[str] = None,
         *,
+        token: Optional[str] = None,
         verify: bool = True,
         timeout: Optional[float] = None,
         user_agent: Optional[str] = None,
@@ -76,6 +77,8 @@ def __init__(
         # password and grab user's key before first request.
         if key:
             self._key: Optional[str] = key
+        elif token:
+            self.token: Optional[str] = token
         else:
             self._key = None
             self.email = email
@@ -84,7 +87,10 @@ def __init__(
         if user_agent:
             self.json_headers["User-Agent"] = user_agent
         # json_headers needs to be set before key can be defined, otherwise authentication with email/password causes an error
-        self.json_headers["x-api-key"] = self.key
+        if token:
+            self.json_headers["Authorization"] = f"Bearer {token}"
+        else:
+            self.json_headers["x-api-key"] = self.key
         # Number of attempts before giving up on a GET request.
         self._max_get_attempts = 1
         # Delay in seconds between subsequent retries.