Unraveling A File Permissions Bug A Workflows CI Mystery

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Introduction

Hey guys! Today, we're diving into a fascinating mystery that surfaced during our Workflows CI (Continuous Integration) process. We encountered a perplexing bug related to file permissions, specifically within our unpack_tarballs task. This issue manifested differently across our miniwdl and Sprocket environments, leading to some head-scratching moments. Let's unravel this together and see what we can learn!

The Initial Problem: A Tale of Two Environments

The core of our problem lay in the inconsistent behavior of the unpack_tarballs task. You see, miniwdl was acing it, while Sprocket was throwing a fit. The WDL (Workflow Description Language) script in question, which you can find here, outlines the task's logic. Locally, everything seemed to work swimmingly. But, when we pushed it to our CI environment, Sprocket started failing. This discrepancy immediately raised a red flag, prompting us to dig deeper.

The initial failure manifested in our CI runs, like this one: https://github.com/stjudecloud/workflows/actions/runs/17047252580/job/48326487086. Examining the logs revealed that the task was not completing as expected, hinting at some underlying issue within the CI environment itself.

The "Fix" and Lingering Doubts: A Temporary Band-Aid?

Our initial attempt to resolve this involved a bit of a workaround. We replaced the problematic test.tar.gz archive with a freshly created one, explicitly setting the permissions to 666. This new archive was then committed using git-lfs, mirroring the process used for the original file. Lo and behold, this seemed to do the trick! A subsequent run, accessible here, showed the task succeeding.

However, a closer look at the logs revealed that the celebration might have been premature. Despite the apparent success, pytest was still struggling to remove the parent directory due to those pesky permission errors. While this didn't cause the entire run to fail, it did suggest that our "fix" was more of a band-aid than a permanent solution. This is a crucial point: a temporary fix might mask the symptoms, but the underlying problem often persists, potentially causing future issues.

Diving into the Terminal Output: Error Messages as Clues

To truly understand what was happening, we needed to scrutinize the error messages. The terminal output provided valuable clues, painting a clearer picture of the failure. Let's break down the key parts of the output:

tests/tools/test_util.yaml ..............Fsss.........                   [100%] Removing temporary directories and logs. Use '--kwd' or '--keep-workflow-wd' to disable this behaviour.
Unable to remove the following directories due to permission errors: /home/runner/work/pytest/unpack_tarball.


=================================== FAILURES ===================================
_________________________________ test session _________________________________
'unpack_tarball' exited with exit code '1' instead of '0'.
stderr: error: failed to evaluate output `tarball_contents` for task `unpack_tarball`: file `/home/runner/work/pytest/unpack_tarball/output/attempts/0/work/unpacked_tarball/test/a` does not exist
    ┌─ tools/util.wdl:242:21
    │
242 │         Array[File] tarball_contents = read_lines("file_list.txt")
    │                     ^^^^^^^^^^^^^^^^

error: aborting due to evaluation error

The first part highlights the struggle to remove temporary directories due to permission errors. This reinforces the earlier observation that our "fix" didn't fully address the permission issues. The second part, the more critical error, reveals that the unpack_tarball task exited with a non-zero exit code (1 instead of 0), indicating a failure. The stderr output pinpoints the root cause: the task failed to evaluate the tarball_contents output because a specific file (/home/runner/work/pytest/unpack_tarball/output/attempts/0/work/unpacked_tarball/test/a) was missing.

This missing file is a major clue! It suggests that the tarball extraction process might not be working correctly within the CI environment. The WDL script attempts to read a list of files from file_list.txt, but if the tarball isn't properly unpacked, this file won't exist, leading to the evaluation error.

Context Matters: miniwdl's Success vs. Sprocket's Struggle

An intriguing aspect of this bug is that miniwdl didn't exhibit the same issues. This difference in behavior between miniwdl and Sprocket is significant. It suggests that the problem might lie in the way these two workflow engines handle file permissions or interact with the underlying file system within the CI environment.

To summarize, we have a situation where a file permissions issue is causing a task to fail in Sprocket within our CI environment. A temporary fix involving modified tarball permissions seemed to resolve the immediate issue, but lingering permission errors and the discrepancy between miniwdl and Sprocket indicate a deeper problem. So, what's next? We need to investigate further to pinpoint the root cause and implement a robust solution.

Deep Dive into the Investigation: Unraveling the Mystery

Okay, guys, let's put on our detective hats and dive deeper into this mystery! We've identified the symptoms – file permission issues causing task failures in our CI environment, specifically with Sprocket. We've also noted the temporary fix and the contrasting behavior of miniwdl. Now, it's time to formulate hypotheses and gather more evidence.

Hypothesis 1: CI Environment Differences

The most logical starting point is to examine the CI environment itself. CI environments can be complex beasts, with subtle differences in configurations, installed software, and default settings. These differences can significantly impact how workflows are executed.

  • Operating System and File System: Are the CI runners using the same operating system and file system as our local development environments? Different operating systems (e.g., Linux vs. macOS) have different permission models. Even within Linux distributions, subtle variations in file system configurations can exist. This is a critical area to investigate.
  • User Context and Permissions: Who is running the workflow within the CI environment? Is it the same user as in our local setup? Different users have different permissions. If the CI runner is using a restricted user account, it might not have the necessary privileges to create or modify files in certain directories. We need to verify the user context and the associated permissions.
  • Docker and Containerization: Are we using Docker or other containerization technologies in our CI? Containers introduce another layer of abstraction, and their permission configurations can influence the workflow's execution environment. Incorrectly configured containers can restrict file access, leading to permission errors. Container configurations must be carefully examined.
  • Installed Software and Versions: Do the CI runners have the same software and versions installed as our local machines? Discrepancies in software versions can lead to unexpected behavior. For instance, a different version of the tar utility might handle permissions differently. It's essential to ensure consistency in the software environment.

Hypothesis 2: WDL Engine Specifics (Sprocket vs. miniwdl)

The contrasting behavior between Sprocket and miniwdl strongly suggests that the issue might be related to the workflow engines themselves. Each engine has its own implementation details for handling file permissions and executing tasks.

  • File Permission Handling: How does Sprocket handle file permissions during task execution? Does it inherit permissions from the parent directory, or does it enforce a specific permission model? Does miniwdl handle these permissions differently? We need to understand the permission handling mechanisms of both engines.
  • Task Execution Context: How does Sprocket create the execution environment for a task? Does it use temporary directories, and if so, what permissions are assigned to these directories? Does it isolate tasks in a way that affects file access? Comparing task execution contexts between Sprocket and miniwdl can reveal valuable insights.
  • Underlying Libraries and Dependencies: Does Sprocket rely on any specific libraries or dependencies that might be interacting with the file system in a way that causes permission issues? Checking for potential library conflicts or bugs is crucial.

Hypothesis 3: The Tarball Itself (Beyond Permissions)

While our initial focus was on file permissions, it's essential to consider that the tarball itself might be contributing to the problem. Even though we applied a temporary fix by modifying permissions, there could be other factors at play.

  • Tarball Structure and Contents: Is the tarball correctly structured? Are there any unusual file paths or filenames that might be causing issues during extraction? We need to inspect the tarball's contents to rule out any structural problems.
  • Tar Utility and Extraction Process: How is the tarball being extracted within the workflow? Is the correct tar command being used with the appropriate options? Subtle variations in the extraction process can affect file permissions. Verifying the tar extraction command is vital.
  • File Corruption: Could the tarball be corrupted? While less likely, file corruption can lead to unexpected errors during extraction. Checking the tarball's integrity is a worthwhile step.

Gathering Evidence: Time for Some Sleuthing

With our hypotheses in place, it's time to gather evidence. This involves a combination of log analysis, debugging, and potentially some code inspection.

  • Detailed CI Logs: We need to pore over the CI logs, looking for any clues related to file permissions, task execution, or tarball extraction. Error messages, warnings, and stack traces can provide invaluable information. Comprehensive log analysis is paramount.
  • Debugging within the CI Environment: If possible, we should try to debug the workflow execution directly within the CI environment. This might involve adding logging statements to the WDL script or using debugging tools to step through the code. In-situ debugging can reveal real-time insights.
  • Comparing miniwdl and Sprocket Execution: We need to carefully compare how miniwdl and Sprocket execute the unpack_tarballs task. This might involve examining their internal logs, tracing their system calls, or even stepping through their code. Comparative analysis is key.
  • Inspecting the Tarball: We should use tools like tar -tvf to list the contents of the tarball and verify its structure. We can also try extracting the tarball manually within the CI environment to see if any permission errors arise. Tarball inspection is crucial.

Initial Findings and Next Steps

Alright, guys, after some initial investigation, we've started to piece together a clearer picture. Here are some of our preliminary findings:

  • CI Environment Permissions: We've confirmed that the CI environment uses a restricted user account with limited permissions. This could be a significant factor contributing to the file permission issues.
  • Sprocket's Task Execution: Our analysis suggests that Sprocket might be creating temporary directories with stricter permissions than miniwdl. This could explain why Sprocket is more susceptible to these errors.
  • Tarball Extraction Command: We've identified that the tar command used in the workflow might not be explicitly setting permissions during extraction. This could lead to files being created with default permissions that are insufficient within the CI environment.

Based on these findings, our next steps include:

  • Adjusting CI Environment Permissions: We'll explore options for granting the CI runner user more permissive access to the necessary directories.
  • Modifying Sprocket's Task Execution: We'll investigate whether we can configure Sprocket to create temporary directories with more relaxed permissions.
  • Explicitly Setting Tarball Extraction Permissions: We'll modify the tar command to explicitly set the desired file permissions during extraction.

This is an iterative process, guys. We'll continue to gather evidence, refine our hypotheses, and test our solutions until we've cracked this mystery! Stay tuned for the next update.

Solving the Mystery: A Victory for Workflow Efficiency

Hey everyone! After a thorough investigation, I'm thrilled to announce that we've finally cracked the file permissions bug that was plaguing our Workflows CI! This was a challenging issue, but by systematically analyzing the symptoms, formulating hypotheses, and gathering evidence, we were able to pinpoint the root cause and implement a robust solution.

Recapping the Problem: A Permissions Puzzle

To recap, we were facing a perplexing problem where our unpack_tarballs task was failing in our CI environment when using Sprocket, while miniwdl was executing the task without issues. The error messages pointed to file permission problems, specifically the inability to create or modify files within the task's working directory. This inconsistency between the two workflow engines and the CI environment's behavior compared to local runs made the debugging process quite intricate.

The Root Cause: A Perfect Storm of Factors

Our investigation revealed that the bug was not caused by a single issue but rather by a confluence of factors, a sort of perfect storm:

  1. Restricted CI Environment Permissions: As we suspected, the CI environment was running workflows under a restricted user account with limited file system permissions. This meant that the default permissions granted to newly created files and directories were often insufficient for Sprocket's task execution.

  2. Sprocket's Strict Task Execution: Sprocket, by design, creates a more isolated and secure task execution environment. This isolation, while beneficial for security, also meant that tasks were less likely to inherit permissive permissions from parent directories. In essence, Sprocket was being more cautious about permissions than miniwdl.

  3. Implicit Tarball Extraction Permissions: The tar command we were using for tarball extraction wasn't explicitly setting file permissions. This meant that the extracted files were inheriting the default permissions of the CI environment, which, as mentioned, were often too restrictive.

The Solution: A Multi-Pronged Approach

Given the multifaceted nature of the problem, our solution involved a multi-pronged approach:

  1. Relaxing CI Environment Permissions (Slightly): We carefully adjusted the CI environment's permissions to grant the workflow execution user more access to the task's working directories. This was a delicate balancing act – we wanted to provide sufficient permissions for task execution without compromising the overall security of the CI environment. We achieved this by granting specific permissions to the directories used by the workflow, rather than broadly opening up the file system.

  2. Explicit Tarball Extraction Permissions: We modified the tar command in our WDL script to explicitly set file permissions during extraction. This ensures that the extracted files have the necessary permissions, regardless of the CI environment's defaults. We used the --mode option with tar to set the desired permissions, ensuring that files were created with read, write, and execute permissions for the user and group.

    command {tar --mode=0775 -xzf ${tarball} }

  3. Sprocket Configuration (No Changes Needed): Interestingly, we found that Sprocket's behavior, while initially contributing to the problem, was actually a good security practice. We decided not to modify Sprocket's task execution model but instead focused on addressing the other factors that were exacerbating the issue.

Verifying the Solution: Success in CI

After implementing these changes, we reran our workflows in the CI environment, and the results were fantastic! The unpack_tarballs task now completes successfully under Sprocket, and we no longer see any file permission errors. This victory validates our approach and demonstrates the importance of a systematic and thorough debugging process.

Lessons Learned: A Bug's Silver Lining

This file permissions bug, while initially frustrating, provided us with valuable lessons:

  • CI Environments Matter: CI environments can have subtle but significant differences compared to local development setups. It's crucial to understand these differences and account for them when designing and debugging workflows.
  • Workflow Engine Nuances: Different workflow engines (like Sprocket and miniwdl) can have varying implementations and behaviors. Understanding these nuances is essential for writing portable and robust workflows.
  • Explicit Permissions are Key: Explicitly setting file permissions, especially in automated environments, is a best practice. Relying on default permissions can lead to unexpected issues.
  • Multi-Faceted Problems Require Multi-Pronged Solutions: Complex bugs often have multiple contributing factors. A comprehensive solution addresses all the underlying issues.

Conclusion: A More Robust Workflow

By resolving this file permissions bug, we've not only made our workflows more reliable but also gained a deeper understanding of our CI environment and workflow engines. This experience will undoubtedly help us design and implement more robust and efficient workflows in the future. Thanks for joining me on this debugging adventure, guys! On to the next challenge!