Allow specifying the User-Agent when creating a GalaxyClient

bioblend/galaxy/__init__.py

@@ -41,6 +41,7 @@ def __init__(
         password: Optional[str] = None,
         *,
         verify: bool = True,
+        user_agent: Optional[str] = None,
     ) -> None:
         """
         A base representation of a connection to a Galaxy instance, identified
@@ -83,7 +84,7 @@ def __init__(
         :param verify: Whether to verify the server's TLS certificate
         :type verify: bool
         """
-        super().__init__(url, key=key, email=email, password=password, verify=verify)
+        super().__init__(url, key=key, email=email, password=password, 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

@@ -58,8 +58,11 @@ def __init__(
         password: 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)
+        self.gi = bioblend.galaxy.GalaxyInstance(
+            url, key=api_key, email=email, password=password, verify=verify, user_agent=user_agent
+        )
         self.log = bioblend.log
         self.datasets = client.ObjDatasetClient(self)
         self.dataset_collections = client.ObjDatasetCollectionClient(self)

bioblend/galaxyclient.py

@@ -12,7 +12,9 @@
 import logging
 from typing import (
     Any,
+    Dict,
     Optional,
+    Union,
 )
 
 import requests
@@ -40,6 +42,7 @@ def __init__(
         *,
         verify: bool = True,
         timeout: Optional[float] = None,
+        user_agent: Optional[str] = None,
     ) -> None:
         """
         :param verify: Whether to verify the server's TLS certificate
@@ -78,7 +81,9 @@ def __init__(
             self._key = None
             self.email = email
             self.password = password
-        self.json_headers: dict = {"Content-Type": "application/json"}
+        self.json_headers: Dict[str, Union[str, bytes, None]] = {"Content-Type": "application/json"}
+        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
         # Number of attempts before giving up on a GET request.
@@ -330,15 +335,14 @@ def get_tus_uploader(
         """
         headers = {"x-api-key": self.key}
         client = tusclient.client.TusClient(self.url + url, headers=headers)
-        if storage:
-            storage = tusclient.storage.filestorage.FileStorage(storage)
+        url_storage = tusclient.storage.filestorage.FileStorage(storage) if storage else None
         try:
             return client.uploader(
                 file_path=path,
                 chunk_size=chunk_size,
                 metadata=metadata,
-                store_url=storage is not None,
-                url_storage=storage,
+                store_url=url_storage is not None,
+                url_storage=url_storage,
             )
         except tusclient.exceptions.TusCommunicationError as exc:
             raise ConnectionError(
@@ -374,6 +378,7 @@ def key(self) -> Optional[str]:
 
 
 def _tus_uploader_session_id(self: tusclient.uploader.Uploader) -> str:
+    assert self.url
     return self.url.rsplit("/", 1)[1]
 
 

bioblend/toolshed/__init__.py

@@ -21,6 +21,7 @@ def __init__(
         password: Optional[str] = None,
         *,
         verify: bool = True,
+        user_agent: Optional[str] = None,
     ) -> None:
         """
         A base representation of a connection to a ToolShed instance, identified
@@ -61,7 +62,7 @@ def __init__(
         :param verify: Whether to verify the server's TLS certificate
         :type verify: bool
         """
-        super().__init__(url, key=key, email=email, password=password, verify=verify)
+        super().__init__(url, key=key, email=email, password=password, verify=verify, user_agent=user_agent)
         self.categories = categories.ToolShedCategoryClient(self)
         self.repositories = repositories.ToolShedRepositoryClient(self)
         self.tools = tools.ToolShedToolClient(self)