Add credential handling to UserClient and ToolClient#534
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dannon wants to merge 4 commits intogalaxyproject:mainfrom
Open
Add credential handling to UserClient and ToolClient#534dannon wants to merge 4 commits intogalaxyproject:mainfrom
dannon wants to merge 4 commits intogalaxyproject:mainfrom
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Add get_credentials, create_credentials, and get_credentials_for_tool methods to UserClient for managing stored credentials (API keys, etc.) via Galaxy's credentials API. Also add credentials_context parameter to ToolClient.run_tool() so credentials can be passed through when executing tools that require them.
The get_credentials_for_tool helper was using wrong field names from the Galaxy API response -- service_name/service_version instead of name/version, and current_group (an object) instead of current_group_id (an ID) with a groups list lookup. Verified against Galaxy's schema in credentials.py. Also widened run_tool payload type annotation and added integration tests for the credential methods.
Galaxy doesn't auto-set current_group_id when credentials are created,
so the get_credentials_for_tool helper was broken out of the box. Add
select_credential_group wrapping PUT /api/users/{id}/credentials so
callers can activate a group after creation.
Also fix truthiness checks to use 'is not None' instead of truthy
evaluation, clarify create_credentials return docstring, and update
tests to call select_credential_group before get_credentials_for_tool.
…ssing credential tools Ruff format with default line-length was reformatting existing code that black with line-length=120 left alone, causing lint failures. Reverted all formatting-only changes to existing code. Bumped test version gate from release_25.0 to release_25.1 since the credentials API doesn't exist in 25.0. The create/get_for_tool tests now use a real tool ID and gracefully skip when the tool doesn't have credential definitions (which is the case for standard test tools).
nsoranzo
reviewed
Apr 10, 2026
| ) | ||
| except ConnectionError as e: | ||
| if "does not require any credentials" in str(e) or "not defined" in str(e): | ||
| self.skipTest("Test tool does not have credential definitions") |
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This and the following tests are always skipped because random_lines1 doesn't require credentials, can we use secret_tool instead (which is used in Galaxy's test/integration/test_credentials.py)?
nsoranzo
reviewed
Apr 10, 2026
| ) -> None: | ||
| """ | ||
| Select the active credential group for a set of user credentials. | ||
| This must be called after ``create_credentials()`` before the |
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Suggested change
| This must be called after ``create_credentials()`` before the | |
| This must be called after credentials have been created but before the |
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Summary
get_credentials,create_credentials,select_credential_group, andget_credentials_for_toolmethods toUserClientwrapping Galaxy's/api/users/{id}/credentialsendpointscredentials_contextparameter toToolClient.run_tool()for passing stored credentials when executing tools that require themget_credentials_for_toolis a convenience method that builds thecredentials_contextlist from stored credentials, ready to pass directly torun_tool()Test plan
release_25.1)create_credentials+select_credential_group+get_credentials_for_tool+run_tool(credentials_context=...)workflow against a Galaxy instance with credential supportruff checkandruff formatpass