From 25488e4aa1cb969b1cd3467c47c8bc4c84fb02dc Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Fri, 20 Dec 2024 14:02:53 +0100
Subject: [PATCH] remove vault in evaluation and MinimalToolApp

---
 lib/galaxy/structured_app.py   | 1 -
 lib/galaxy/tools/evaluation.py | 6 ++----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/structured_app.py b/lib/galaxy/structured_app.py
index 473c11e00d4e..1d1986dee1a8 100644
--- a/lib/galaxy/structured_app.py
+++ b/lib/galaxy/structured_app.py
@@ -90,7 +90,6 @@ class MinimalToolApp(Protocol):
     tool_data_tables: "ToolDataTableManager"
     file_sources: ConfiguredFileSources
     security: IdEncodingHelper
-    vault: Vault
 
 
 class MinimalApp(BasicSharedApp):
diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index 5c13b48e7349..e15551ad0771 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -28,7 +28,6 @@
 )
 from galaxy.model.none_like import NoneDataset
 from galaxy.security.object_wrapper import wrap_with_safe_string
-from galaxy.security.vault import UserVaultWrapper
 from galaxy.structured_app import (
     BasicSharedApp,
     MinimalToolApp,
@@ -190,9 +189,8 @@ def set_compute_environment(self, compute_environment: ComputeEnvironment, get_s
         )
         self.execute_tool_hooks(inp_data=inp_data, out_data=out_data, incoming=incoming)
 
-        # TODO: provide all information needed (variable value, current group, etc) to this part...
+        # TODO: provide all information needed (secret value, variable value, current group, etc) to this part...
         if hasattr(self.tool, "credentials"):
-            user_vault = UserVaultWrapper(self.app.vault, self._user)
             tool_credentials: List[CredentialsRequirement] = self.tool.credentials
             for credentials in tool_credentials:
                 reference = credentials.reference
@@ -200,7 +198,7 @@ def set_compute_environment(self, compute_environment: ComputeEnvironment, get_s
                 tool_id = self.tool.id
                 for secret in credentials.secrets:
                     vault_ref = f"tool|{tool_id}|{reference}|{current_group}|{secret.name}"
-                    vault_value = user_vault.read_secret(vault_ref) or ""
+                    vault_value = f"user_vault.read_secret({vault_ref})"
                     self.environment_variables.append({"name": secret.inject_as_env, "value": vault_value})
                 for variable in credentials.variables:
                     variable_value = "variable.value"