From 26875e52c67690015f7942f93236bb2cb37cebfd Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 30 Jul 2024 14:02:32 -0400
Subject: [PATCH] Fixup the type signatures of authnz backends.

---
 lib/galaxy/authnz/__init__.py      | 4 ++--
 lib/galaxy/authnz/custos_authnz.py | 2 +-
 lib/galaxy/authnz/managers.py      | 2 +-
 lib/galaxy/authnz/psa_authnz.py    | 4 ++--
 lib/galaxy/model/deferred.py       | 3 +++
 5 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/authnz/__init__.py b/lib/galaxy/authnz/__init__.py
index c2c5685e3180..071b09784bfe 100644
--- a/lib/galaxy/authnz/__init__.py
+++ b/lib/galaxy/authnz/__init__.py
@@ -43,7 +43,7 @@ def __init__(self, provider, config, backend_config):
     def refresh(self, trans, token):
         raise NotImplementedError()
 
-    def authenticate(self, provider, trans):
+    def authenticate(self, trans, idphint=None):
         """Runs for authentication process. Checks the database if a
         valid identity exists in the database; if yes, then the  user
         is authenticated, if not, it generates a provider-specific
@@ -72,7 +72,7 @@ def callback(self, state_token: str, authz_code: str, trans, login_redirect_url)
         """
         raise NotImplementedError()
 
-    def disconnect(self, provider, trans, disconnect_redirect_url=None):
+    def disconnect(self, provider, trans, disconnect_redirect_url=None, email=None, association_id=None):
         raise NotImplementedError()
 
     def logout(self, trans, post_user_logout_href=None):
diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py
index 806f6e1cafba..d6fdf22c8b31 100644
--- a/lib/galaxy/authnz/custos_authnz.py
+++ b/lib/galaxy/authnz/custos_authnz.py
@@ -343,7 +343,7 @@ def create_user(self, token, trans, login_redirect_url):
             trans.sa_session.commit()
         return login_redirect_url, user
 
-    def disconnect(self, provider, trans, email=None, disconnect_redirect_url=None):
+    def disconnect(self, provider, trans, disconnect_redirect_url=None, email=None, association_id=None):
         try:
             user = trans.user
             index = 0
diff --git a/lib/galaxy/authnz/managers.py b/lib/galaxy/authnz/managers.py
index 93fc3c010ac3..7ec758fd3cac 100644
--- a/lib/galaxy/authnz/managers.py
+++ b/lib/galaxy/authnz/managers.py
@@ -432,7 +432,7 @@ def disconnect(self, provider, trans, email=None, disconnect_redirect_url=None,
             if success is False:
                 return False, message, None
             elif provider in KEYCLOAK_BACKENDS:
-                return backend.disconnect(provider, trans, email, disconnect_redirect_url)
+                return backend.disconnect(provider, trans, disconnect_redirect_url, email=email)
             return backend.disconnect(provider, trans, disconnect_redirect_url)
         except Exception:
             msg = f"An error occurred when disconnecting authentication with `{provider}` identity provider for user `{trans.user.username}`"
diff --git a/lib/galaxy/authnz/psa_authnz.py b/lib/galaxy/authnz/psa_authnz.py
index b8a34b68e710..c222e76ebe09 100644
--- a/lib/galaxy/authnz/psa_authnz.py
+++ b/lib/galaxy/authnz/psa_authnz.py
@@ -193,7 +193,7 @@ def refresh(self, trans, user_authnz_token):
             return True
         return False
 
-    def authenticate(self, trans):
+    def authenticate(self, trans, idphint=None):
         on_the_fly_config(trans.sa_session)
         strategy = Strategy(trans.request, trans.session, Storage, self.config)
         backend = self._load_backend(strategy, self.config["redirect_uri"])
@@ -224,7 +224,7 @@ def callback(self, state_token, authz_code, trans, login_redirect_url):
 
         return redirect_url, self.config.get("user", None)
 
-    def disconnect(self, provider, trans, disconnect_redirect_url=None, association_id=None):
+    def disconnect(self, provider, trans, disconnect_redirect_url=None, email=None, association_id=None):
         on_the_fly_config(trans.sa_session)
         self.config[setting_name("DISCONNECT_REDIRECT_URL")] = (
             disconnect_redirect_url if disconnect_redirect_url is not None else ()
diff --git a/lib/galaxy/model/deferred.py b/lib/galaxy/model/deferred.py
index d73517fb756a..6cfaa75a0dcb 100644
--- a/lib/galaxy/model/deferred.py
+++ b/lib/galaxy/model/deferred.py
@@ -177,6 +177,9 @@ def ensure_materialized(
         return materialized_dataset_instance
 
     def _stream_source(self, target_source: DatasetSource, datatype) -> str:
+        source_uri = target_source.source_uri
+        if source_uri is None:
+            raise Exception("Cannot stream from dataset source without specified source_uri")
         path = stream_url_to_file(target_source.source_uri, file_sources=self._file_sources)
         transform = target_source.transform or []
         to_posix_lines = False