BUG: Tool Server With UVX Failing To Discover Tools

by RICHARD 52 views

Hey everyone,

We've got a critical bug report regarding the kagent tool server when using uvx. It seems that after adding a new tool server, specifically the PagerDuty MCP server, things aren't working as expected. Let's dive into the details and see what's going on.

Prerequisites

Before we get started, it's worth noting that the reporter has already taken some important steps:

  • Searched existing issues to avoid duplicates.
  • Agreed to follow the Code of Conduct.
  • Confirmed they are using the latest version of the software.
  • Tried clearing cache/cookies or used incognito mode (if UI-related).
  • Verified they can consistently reproduce the issue.

These are all great practices when reporting a bug, so kudos to the reporter!

Affected Services

The affected service isn't explicitly identified, but it's related to the kagent tool server and the uvx command.

Impact/Severity

This is marked as a blocker, which means it's a pretty serious issue that's preventing the tool server from functioning correctly. This needs our attention ASAP.

Bug Description

Here's the core of the problem: After adding a new tool server using uvx, in this case, the PagerDuty MCP server (which, by the way, was tested locally and confirmed to be working), the tools are never discovered. The pod logs are showing some nasty error messages. Let's break down those errors:

| mcp-server 2025-08-22T11:05:52.800212Z    info    agent_core::readiness    Task 'state manager' complete (90.262125ms), marking |
| mcp-server error: failed to create directory `/.cache/uv`: Permission denied (os error 13)                                      |
| mcp-server 2025-08-22T11:06:34.656209Z    error    mcp::relay::pool    Failed to connect target pagerduty: connection closed: i |
| mcp-server 2025-08-22T11:06:34.661360Z    error    rmcp::transport::streamable_http_server::tower    Failed to create service:

The key errors here are:

  1. failed to create directory ".cache/uv": Permission denied (os error 13): This suggests a permission issue when the server tries to create a cache directory. This is a big red flag, as it indicates the process doesn't have the necessary rights to write to the file system.
  2. Failed to connect target pagerduty: connection closed: initialize response: This error indicates that the mcp server is having trouble connecting to the PagerDuty target. This could be due to a network issue, an incorrect configuration, or the permission problem mentioned above preventing proper initialization.
  3. Failed to create service: initialize failed: -32603: Failed to list connections: connection closed: initialize response: This error seems related to the rmcp transport layer and suggests that the service initialization is failing, likely due to the connection issues with PagerDuty.

It seems the permission denied error is the primary suspect here, potentially causing a cascade of other failures. This permission denied error is a common issue when running applications in containers, especially if the container's user doesn't have the correct permissions on the mounted volumes or directories.

In-Depth Look at Permission Issues

To really nail this down, let's zoom in on why permission denied errors are so crucial in containerized environments. When we're dealing with containers, especially in Kubernetes, we're often using volumes to persist data or share configurations. If the user inside the container (which the mcp-server runs as) doesn't have the right permissions to read from or write to these volumes, you'll hit the permission denied error. Think of it like trying to enter a room without the right key – you simply won't get in.

In this case, the mcp-server is trying to create a directory in /.cache/uv, suggesting it needs to cache something. Without the necessary permissions, this cache creation fails, and this failure seems to trigger a chain reaction. The server can't initialize properly because it can't cache data, and this, in turn, leads to connection failures with the PagerDuty target.

To fix this, we need to ensure the container has the permissions to create and write to the /.cache/uv directory. This might involve changing the user the container runs as, adjusting the permissions on the volume, or using Kubernetes security contexts to grant the necessary privileges. It's like giving the container the right key to unlock its full potential.

Analyzing Connection Failures and Their Impact

Now, let's shift gears slightly and dissect those connection failure messages. The error Failed to connect target pagerduty: connection closed: initialize response is a serious red flag. It means that the mcp-server is struggling to establish a stable link with the PagerDuty service. This could stem from several factors, including network glitches, incorrect endpoint configurations, or even the permission issues we just discussed.

The subsequent error, Failed to create service: initialize failed: -32603: Failed to list connections: connection closed: initialize response, provides even more clues. The -32603 error code hints at a more specific problem within the JSON-RPC communication protocol, which is often used for remote procedure calls. This suggests that the mcp-server isn't just failing to connect; it's failing during the initialization phase, specifically when trying to list connections.

This initialization failure could be a domino effect triggered by the initial permission denied error. If the server can't create its cache, it might not be able to properly store or retrieve connection details, leading to initialization hiccups. Think of it as trying to start a car with a dead battery – you can crank the engine all you want, but it won't fire up without the initial spark.

To resolve these connection issues, we need to investigate the root cause – which, in this case, seems to circle back to those permission problems. Once we've ensured the mcp-server has the necessary permissions to create its cache, we can then re-evaluate the connection to PagerDuty. If the problem persists, we might need to dive deeper into network configurations or the PagerDuty service itself. However, fixing the permission issue is the crucial first step in untangling this web of errors.

The Broader Implications of Session Termination Errors

Finally, let's not overlook those recurring session termination errors: Failed to close session <session_id>: Session error: Session service terminated. While these errors might seem secondary, they could be a symptom of a larger issue – the instability of the mcp-server due to the permission denied error and connection failures.

When a session service terminates unexpectedly, it often means something has gone wrong during the communication or processing of a request. In this context, if the mcp-server is struggling to maintain stable connections with the PagerDuty service, it's likely that sessions are being terminated prematurely. This can lead to incomplete operations, data inconsistencies, and a generally unreliable system.

Think of each session as a conversation between the mcp-server and the PagerDuty service. If the mcp-server keeps getting disconnected mid-conversation (due to the underlying issues), those sessions will be terminated abruptly. This not only disrupts the current operation but also leaves the system in a potentially inconsistent state.

To address these session termination errors, we need to tackle the root causes – the permission denied error and the connection failures. By ensuring the mcp-server can properly initialize, create its cache, and maintain stable connections, we'll create a more robust environment where sessions can be completed successfully. It's like fixing a leaky pipe to prevent water damage – by addressing the source of the problem, we can prevent further issues down the line.

Steps to Reproduce

The reporter provided a clear way to reproduce the bug:

  1. Add the new tool server.
  2. Use the uvx command with the rest of the module configurations.

The attached image gives us a visual of the uvx configuration, which is super helpful for debugging.

Image

Expected Behavior

Ideally, the new tools should be discovered and available in the tools list. This is the whole point of adding the tool server, after all!

Actual Behavior

Unfortunately, the tools are never discovered, and the pod outputs those error messages we discussed earlier. This is a blocker because it prevents users from utilizing the new tools.

Environment

Here's the environment information:

  • Kubernetes version: 1.33.2-gke.1240000
  • Kubernetes provider: GCP
  • kagent: v0.6.3

Knowing the Kubernetes version and provider is crucial for understanding the context of the issue. The kagent version is also important for identifying potential regressions or version-specific bugs.

CLI Bug Report

No CLI bug report was provided, but the logs give us plenty to work with.

Additional Context

There's no additional context provided, but the information we have is already quite comprehensive.

Logs

The provided logs are a goldmine! They confirm the permission denied error and the connection issues. Let's highlight the key parts again:

mcp-server error: failed to create directory `/.cache/uv`: Permission denied (os error 13)
mcp-server 2025-08-22T11:06:34.656209Z    error    mcp::relay::pool    Failed to connect target pagerduty: connection closed: initialize response    
mcp-server 2025-08-22T11:06:34.661360Z    error    rmcp::transport::streamable_http_server::tower    Failed to create service: initialize failed: -32603: Failed to list connections: connection closed: initialize response

The logs clearly show the repeated attempts to connect to PagerDuty and the subsequent failures. The session termination errors are also present, reinforcing the idea of an unstable connection.

mcp-server 2025-08-22T11:09:34.726636Z    error    rmcp::transport::streamable_http_server::tower    Failed to close session da7e4e8d-c0ce-45f6-a153-7c2943488250: Session error: Session service terminated

Screenshots

No screenshots were provided, but the logs and configuration image are sufficient for understanding the issue.

Are You Willing to Contribute?

The reporter is willing to submit a PR to fix this issue, which is fantastic! This kind of community involvement is what makes open source projects thrive.

Next Steps and Potential Solutions

Okay, guys, so where do we go from here? Given the information we've gathered, here's a breakdown of the next steps and potential solutions:

  1. Investigate the Permission Issue: This is the top priority. We need to figure out why the mcp-server doesn't have permissions to create the /.cache/uv directory. This might involve:
    • Checking the container's user context: What user is the mcp-server running as?
    • Examining the volume permissions: If a volume is mounted to /.cache/uv, what are the permissions on that volume?
    • Looking at Kubernetes Security Contexts: Are there any security contexts applied to the pod that might be restricting permissions?
  2. Address the Connection Failures: Once the permission issue is resolved, we need to re-evaluate the connection to the PagerDuty service. If the problem persists, we should:
    • Verify the PagerDuty endpoint configuration: Is the URL correct? Are there any network policies blocking the connection?
    • Check PagerDuty service health: Is PagerDuty itself experiencing any issues?
  3. Consider Session Termination Errors: If sessions are still being terminated after addressing the above issues, we might need to:
    • Implement retry mechanisms: Can we automatically retry failed session operations?
    • Improve error handling: Can we provide more informative error messages when sessions fail?
  4. Reproduce Locally: It's always a good idea to try and reproduce the issue locally. This allows us to debug in a controlled environment without affecting the production system.

Diving Deeper into Kubernetes Security Contexts

Let's take a more granular look at Kubernetes Security Contexts, as they often play a pivotal role in permission-related issues within pods. Security Contexts are a powerful feature in Kubernetes that allow you to define the security settings for your pods and containers. They control things like the user and group IDs the container runs as, capabilities, permissions, and more.

In the context of this bug report, a misconfigured Security Context could very well be the culprit behind the Permission denied error. For instance, if a Security Context specifies that the container should run as a non-root user but doesn't provide the necessary permissions to write to a particular directory, you'll run into this issue. It's like assigning someone a job but not giving them the tools they need to do it.

To diagnose this, we need to inspect the pod's Security Context configuration. This involves looking at the securityContext section in the pod's YAML definition. We should check for settings like runAsUser, runAsGroup, and fsGroup. If these settings are present, we need to ensure that the specified user and group have the permissions required to create the /.cache/uv directory. It's like checking the employee's job description to make sure they have the authority to access certain resources.

Furthermore, we should also consider the capabilities setting within the Security Context. Capabilities are a way to grant specific Linux kernel capabilities to a container, allowing it to perform certain privileged operations without running as root. If the container needs a particular capability to create the cache directory (which is unlikely in this case, but worth considering), we need to make sure it's included in the capabilities list. It's like giving someone a special tool that allows them to perform a specific task.

By thoroughly examining the Kubernetes Security Contexts, we can gain a better understanding of the security policies in place and identify any potential conflicts that might be causing the permission denied error. This is a crucial step in ensuring our containers have the right permissions to function correctly, without compromising the overall security of the cluster.

Examining Volume Mounts and Permissions in Kubernetes

Expanding on our investigation, let's now focus on volume mounts and their associated permissions within Kubernetes. Volume mounts are how we make storage available to containers within a pod. If the /.cache/uv directory is supposed to be backed by a persistent volume, then the permissions of that volume are absolutely critical.

In Kubernetes, volumes can be mounted with different access modes, such as ReadWriteOnce, ReadOnlyMany, or ReadWriteMany. These access modes dictate how the volume can be accessed by pods. However, even with the correct access mode, the file permissions on the underlying storage must also be aligned with the user context of the container.

If the volume is mounted with restrictive file permissions, even if the container has the right user ID, it might still encounter permission denied errors. This is akin to having the right key to a building but finding that the door to your specific office is locked. To troubleshoot this, we need to:

  1. Identify the Volume Mount: Check the pod's YAML definition to see if a volume is mounted to /.cache/uv. Look for the volumeMounts section within the container specification.
  2. Inspect the Volume: Once you've identified the volume, examine its definition in the Kubernetes cluster. This will tell you the type of volume (e.g., PersistentVolumeClaim, hostPath) and its configuration.
  3. Check File Permissions: If the volume is backed by a persistent volume claim (PVC), you'll need to investigate the underlying persistent volume (PV) and the storage it's using. Depending on the storage provider (e.g., GCE Persistent Disk, AWS EBS), you'll need to use the provider's tools to check the file permissions on the storage. If it's a hostPath volume, you'll need to check the permissions on the host filesystem.

Ensuring that the file permissions on the volume align with the user context of the container is a key step in resolving permission denied errors. It's about making sure that the container not only has access to the volume but also has the right to read and write files within it. This might involve adjusting the permissions on the volume itself, using Kubernetes features like fsGroup in the Security Context, or even provisioning volumes with the correct permissions from the start.

The Importance of Reproducing Locally for Effective Debugging

Before we wrap up our troubleshooting strategy, let's emphasize the sheer importance of reproducing the bug locally. While logs and error messages are invaluable, nothing beats the ability to step through the code, inspect variables, and truly understand what's going on under the hood. Reproducing locally allows us to create a controlled environment where we can experiment with different solutions without risking the stability of a production system. It's like practicing surgery in a simulation before operating on a patient.

To reproduce this bug locally, we need to set up an environment that closely mirrors the production environment. This includes:

  1. Kubernetes Cluster: Ideally, we'd want to use a local Kubernetes cluster, such as Minikube or kind, to replicate the Kubernetes environment.
  2. kagent Version: We should use the same kagent version (v0.6.3) as the production environment to ensure we're dealing with the same codebase.
  3. uvx Configuration: We need to replicate the uvx configuration that's causing the issue. This might involve copying the YAML files or using the same command-line arguments.
  4. PagerDuty MCP Server: We need to set up a local instance of the PagerDuty MCP server or mock its behavior to simulate the interaction.

Once we have a local environment set up, we can then follow the steps to reproduce the bug and observe the same errors. This gives us the opportunity to use debugging tools, such as debuggers or loggers, to pinpoint the exact line of code where the error occurs. We can also experiment with different fixes, such as changing file permissions or adjusting the uvx configuration, to see if they resolve the issue.

Reproducing locally is not just about finding the bug; it's also about understanding it. By stepping through the code and observing the system's behavior, we can gain a deeper understanding of the root cause of the problem. This not only helps us fix the current bug but also prevents similar bugs from occurring in the future. It's like learning how a car engine works – once you understand the principles, you can troubleshoot a wide range of problems.

Let's get this fixed, guys! We've got a clear path forward, and with some focused effort, we can get the kagent tool server working smoothly with uvx and PagerDuty.

Conclusion

In summary, the bug reported highlights a permission denied error preventing the mcp-server from creating a cache directory, leading to connection failures with the PagerDuty service and session termination errors. The next steps involve a thorough investigation of container permissions, volume mounts, and Kubernetes Security Contexts, with a strong emphasis on local reproduction for effective debugging. By addressing these issues, we can ensure the reliable operation of the kagent tool server and its integration with external services like PagerDuty.