---
phase: 04-add-jq-and-yq-for-querying-large-json-and-yaml-files
verified: 2026-01-27T12:00:00Z
status: passed
score: 17/17 must-haves verified
human_verification:
  - test: "Query a large (>100MB) JSON file"
    expected: "The query_json tool should return a result within the 30-second timeout, or a graceful timeout error, without crashing the server."
    why_human: "Verifies real-world performance and resource handling that static analysis cannot."
  - test: "Run fs-mcp on Windows, macOS, and Linux (Ubuntu/Fedora) without jq/yq installed"
    expected: "The server should start, print the correct, platform-specific installation instructions for the missing tools, and the query tools should return a helpful error message when called."
    why_human: "Verifies the platform-detection logic and installation instructions are correct for each OS."
  - test: "Instruct an agent to analyze a large (>1MB) JSON file"
    expected: "The agent should first attempt to `read_files`, receive the error message suggesting `query_json`, and then use `query_json` to explore the file's structure and content without trying to read the whole file again."
    why_human: "Verifies the agent's ability to follow the new 'guidance' provided by the enhanced `read_files` tool, which is the core of the 'grep -> read -> query' pattern."
---

# Phase 4: Add jq and yq for querying large json and yaml files Verification Report

**Phase Goal:** Agents can efficiently query large JSON and YAML files without context overflow, completing the grep → read → query pattern.
**Verified:** 2026-01-27T12:00:00Z
**Status:** ✓ PASSED
**Re-verification:** No — initial verification

## Goal Achievement

All `must_haves` derived from the phase plan have been programmatically verified. The implementation successfully provides tools for querying large JSON and YAML files and guides the agent to use them, achieving the phase goal.

### Observable Truths

| #   | Truth                                                        | Status     | Evidence                                                                                                                              |
| --- | ------------------------------------------------------------ | ---------- | ------------------------------------------------------------------------------------------------------------------------------------- |
| 1   | Server detects jq availability at startup                    | ✓ VERIFIED | `server.py` calls `utils.check_jq()` in `initialize()`.                                                                               |
| 2   | Server detects yq availability at startup                    | ✓ VERIFIED | `server.py` calls `utils.check_yq()` in `initialize()`.                                                                               |
| 3   | Server continues running if jq or yq are missing             | ✓ VERIFIED | The checks in `initialize()` only print warnings. The tools return error strings if the dependency is missing, they do not raise exceptions. |
| 4   | Platform-specific install instructions shown for missing tools | ✓ VERIFIED | `utils.py` contains `check_jq` and `check_yq` functions that generate platform-specific installation command strings.                |
| 5   | Agent can query JSON files using jq expressions              | ✓ VERIFIED | `query_json` tool exists in `server.py` and calls `jq` via a subprocess.                                                              |
| 6   | Agent can query YAML files using yq expressions              | ✓ VERIFIED | `query_yaml` tool exists in `server.py` and calls `yq` via a subprocess.                                                              |
| 7   | Query results are bounded to 100 items max                   | ✓ VERIFIED | Both `query_json` and `query_yaml` implement logic to truncate output to 100 lines and append a truncation message.                   |
| 8   | Queries timeout after 30 seconds to prevent hangs            | ✓ VERIFIED | Both tools pass a `timeout=30` parameter to `subprocess.run` and handle the `TimeoutExpired` exception.                             |
| 9   | `read_files` suggests query tools for large JSON/YAML files  | ✓ VERIFIED | `read_files` in `server.py` checks file size and extension, returning a detailed error message guiding the agent to use query tools.    |

**Score:** 9/9 truths verified

### Required Artifacts

| Artifact                | Expected                                                 | Status     | Details                                                                                                                                 |
| ----------------------- | -------------------------------------------------------- | ---------- | --------------------------------------------------------------------------------------------------------------------------------------- |
| `src/fs_mcp/utils.py`   | jq/yq availability checks and install guidance           | ✓ VERIFIED | `check_jq` and `check_yq` functions are present, substantive, and follow the established `check_ripgrep` pattern.                       |
| `src/fs_mcp/server.py`  | Global availability flags (`IS_JQ_AVAILABLE`, etc.)      | ✓ VERIFIED | Global flags are defined at the module level and set within the `initialize()` function.                                                |
| `src/fs_mcp/server.py`  | `query_json` and `query_yaml` tools                      | ✓ VERIFIED | Both tools are implemented with `@mcp.tool()` decorator, have correct signatures, and contain logic for subprocess execution and error handling. |
| `src/fs_mcp/server.py`  | Enhanced `read_files` with large file detection          | ✓ VERIFIED | `read_files` signature includes `large_file_passthrough`, and the implementation contains the logic to block and guide agents.       |

### Key Link Verification

| From               | To                 | Via                           | Status     | Details                                                                    |
| ------------------ | ------------------ | ----------------------------- | ---------- | -------------------------------------------------------------------------- |
| `server.initialize`  | `utils.check_jq`   | Function call                 | ✓ WIRED    | `server.py:52` calls `check_jq`.                                           |
| `server.initialize`  | `utils.check_yq`   | Function call                 | ✓ WIRED    | `server.py:56` calls `check_yq`.                                           |
| `query_json`       | `jq` subprocess    | `subprocess.run`              | ✓ WIRED    | `server.py:774` executes the `jq` command.                                 |
| `query_yaml`       | `yq` subprocess    | `subprocess.run`              | ✓ WIRED    | `server.py:841` executes the `yq` command.                                 |
| `read_files`       | token size check   | `os.path.getsize` / 4         | ✓ WIRED    | `server.py:215-217` performs the file size check and token estimation.       |

### Requirements Coverage

No specific requirements from `REQUIREMENTS.md` were mapped to this phase.

### Anti-Patterns Found

| File                  | Line | Pattern                       | Severity | Impact                                                                          |
| --------------------- | ---- | ----------------------------- | -------- | ------------------------------------------------------------------------------- |
| `src/fs_mcp/server.py`  | 649  | Placeholder implementation    | ⚠️ Warning | The `grounding_search` tool is a placeholder. This is a pre-existing issue. |

No new blocking anti-patterns were introduced.

### Human Verification Required

The core implementation is verified, but real-world agent behavior and cross-platform compatibility require human testing.

1.  **Query a large (>100MB) JSON file**
    *   **Test:** Use `query_json` on a very large file with a simple query (e.g., `keys`).
    *   **Expected:** The tool should return a result within the 30-second timeout, or a graceful timeout error, without crashing the server.
    *   **Why human:** Verifies real-world performance and resource handling that static analysis cannot.

2.  **Verify platform-specific dependency checks**
    *   **Test:** Run `uvx fs-mcp` on Windows, macOS, and Linux (Ubuntu/Fedora) without `jq` or `yq` installed.
    *   **Expected:** The server should start, print the correct, platform-specific installation instructions for the missing tools. When the query tools are called, they should return a helpful error message.
    *   **Why human:** Verifies the platform-detection logic and installation instructions are correct for each OS.

3.  **Verify agent guidance workflow**
    *   **Test:** Instruct an agent to analyze a large JSON file (e.g., >1MB `package-lock.json`).
    *   **Expected:** The agent should first try `read_files`, get the error suggesting `query_json`, and then correctly use `query_json` to explore the file's structure (e.g., with `keys` or `.packages | keys`) instead of trying to read the file again with the passthrough flag.
    *   **Why human:** This is the ultimate test of the phase goal. It verifies that the "guidance" implemented in the tool is effective at changing agent behavior to follow the intended `grep -> read -> query` pattern.

---

_Verified: 2026-01-27T12:00:00Z_
_Verifier: Claude (gsd-verifier)_
