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Semgrep

Trail of BitsOfficialPublished by Trail of Bits

  • Skill
  • Workflow
  • Security
  • CC-BY-SA-4.0
  • Low risk
  • Has scripts

From the author

Runs a Semgrep security scan over a codebase: detects languages, selects rulesets, presents the plan for explicit approval, then runs every approved ruleset through scripts/run-scans.sh, which batches the semgrep processes and writes scans.json, and merges the output to SARIF. Supports two scan modes, "run all" for full ruleset coverage and "important only" for security findings at medium-to-high confidence and impact. Uses Semgrep Pro for cross-file taint analysis when it is available. Use when asked to scan code for vulnerabilities, run a security audit with Semgrep, find bugs, or perform static analysis. For the same scan without the approval gate, use the /static-analysis:semgrep-scan workflow.
— the description by Trail of Bits

AutoGineer summary

Written by AutoGineer from the skill’s own files, not by the author

This skill automates the execution of Semgrep security scans across a codebase. It manages the entire lifecycle of a scan: detecting languages, selecting appropriate rulesets, requiring explicit user approval for the scan plan, executing scans in parallel batches, and merging results into a unified SARIF file. It supports two modes: a full scan of all rulesets and an important-only mode that filters findings based on security category, confidence, and impact metadata.

What it does

  • Detects programming languages and checks for Semgrep Pro availability.
  • Selects relevant official and third-party rulesets based on detected languages.
  • Presents a detailed scan plan for explicit user approval before execution.
  • Executes scans using batched processes to generate raw JSON and SARIF outputs.
  • Applies optional post-filtering to focus on high-confidence security vulnerabilities.
  • Merges all scan results into a single, consolidated SARIF report.

When to use it

  • Performing a security audit of a codebase.
  • Identifying potential vulnerabilities prior to code review.
  • Scanning for known bug patterns.
  • Conducting first-pass static analysis.

Advantages

  • Enforces security best practices like disabling telemetry during scans.
  • Ensures consistent scan configuration through automated script execution.
  • Provides a clear approval gate to confirm scan scope and rulesets.
  • Supports cross-file taint analysis when Semgrep Pro is available.
  • Consolidates findings from multiple rulesets into a single report.

Usage examples

“Run a security scan on the current directory.”
The agent detects the languages, proposes a ruleset plan, and waits for your approval before running the scan.
“Perform an important-only security audit on /path/to/code.”
The agent configures the scan to filter for medium-to-high confidence security findings and generates a merged SARIF report.

Install

  1. Download the skill as a ZIP:

    https://mp-staging.autogineer.com/agent-skills/trailofbits/semgrep/download
  2. Unzip it into the cross-client skills folder of your project:

    mkdir -p .agents/skills && unzip semgrep.zip -d .agents/skills

Documentation by Trail of Bits

Semgrep Security Scan

Run a Semgrep scan with automatic language detection, parallel execution, and merged SARIF output.

Essential Principles

  1. Always use --metrics=off — Semgrep sends telemetry by default; --config auto also phones home. Every semgrep command must include --metrics=off to prevent data leakage during security audits.

  2. User must approve the scan plan (Step 3 is a hard gate) — The original "scan this codebase" request is NOT approval. Present exact rulesets, target, engine, and mode; wait for explicit "yes"/"proceed" before spawning scanners.

  3. Third-party rulesets are required, not optional — Trail of Bits, 0xdea, and Decurity rules catch vulnerabilities absent from the official registry. Include them whenever the detected language matches.

  4. scripts/run-scans.sh generates the commands; do not write them yourself — it builds every semgrep line from the approved list. That is what makes --metrics=off, the --include scoping rule, and the parallel dispatch properties of the code rather than instructions. Give it the approved rulesets and let it run.

  5. Always check for Semgrep Pro before scanning — Pro enables cross-file taint tracking and catches ~250% more true positives. Skipping the check means silently missing critical inter-file vulnerabilities.

  6. Report what did not run — scans.json carries failed and skipped alongside scans. A ruleset whose repo would not clone, or whose scan exited non-zero, must appear in the report. A partial scan presented as a complete one is worse than no scan.

When to Use

  • Security audit of a codebase

  • Finding vulnerabilities before code review

  • Scanning for known bug patterns

  • First-pass static analysis

When NOT to Use

  • Binary analysis → Use binary analysis tools

  • Already have Semgrep CI configured → Use existing pipeline

  • Need cross-file analysis but no Pro license → Consider CodeQL as alternative

  • Creating custom Semgrep rules → Use semgrep-rule-creator skill

  • Porting existing rules to other languages → Use semgrep-rule-variant-creator skill

Output Directory

All scan results, SARIF files, and temporary data are stored in a single output directory.

  • If the user specifies an output directory in their prompt, use it as OUTPUT_DIR.

  • If not specified, default to ./static_analysis_semgrep_1. If that already exists, increment to _2, _3, etc.

In both cases, always create the directory with mkdir -p before writing any files.

# Resolve output directory
if [ -n "$USER_SPECIFIED_DIR" ]; then
  OUTPUT_DIR="$USER_SPECIFIED_DIR"
else
  BASE="static_analysis_semgrep"
  N=1
  while [ -e "${BASE}_${N}" ]; do
    N=$((N + 1))
  done
  OUTPUT_DIR="${BASE}_${N}"
fi
mkdir -p "$OUTPUT_DIR/raw" "$OUTPUT_DIR/results"

The output directory is resolved once at the start of Step 1 and used throughout all subsequent steps.

$OUTPUT_DIR/
├── rulesets.json                # The approved plan (Step 3), read by run-scans.sh (Step 4)
├── scans.json                   # What ran, failed, skipped, and covered nothing (Step 4)
├── raw/                         # Per-scan raw output (unfiltered)
│   ├── python-python.json        # <language>-<ruleset> for language-scoped rules
│   ├── python-python.sarif
│   ├── python-django.json
│   ├── python-django.sarif
│   ├── all-security-audit.json   # all-<ruleset> for cross-language rules, run once
│   ├── all-security-audit.sarif
│   └── ...
└── results/                     # Final merged output
    └── results.sarif

Prerequisites

Required: Semgrep CLI (semgrep --version). If not installed, see Semgrep installation docs.

Optional: Semgrep Pro — enables cross-file taint tracking, inter-procedural analysis, and additional languages (Apex, C#, Elixir). Check with:

# --metrics=off because Principle 1 has no exceptions, and this is the first semgrep command
# of a run. stderr is kept because "OSS only" has several causes (logged out, no subscription,
# registry blocked) and the run downgrades silently for all of them.
if PRO_ERR=$(semgrep --pro --validate --metrics=off --config p/default 2>&1); then
  echo "Pro available"
else
  echo "OSS only"
  echo "  reason: $(printf '%s' "$PRO_ERR" | tail -n 3)"
fi

Limitations: OSS mode cannot track data flow across files. Pro mode uses -j 1 for cross-file analysis (slower per ruleset, but parallel rulesets compensate).

Scan Modes

Select mode in Step 2. Mode affects both the scan flags and post-processing.

ModeCoverageFindings Reported
Run allAll rulesets, all severity levelsEverything
Important onlyAll rulesets, pre- and post-filteredSecurity vulns only, medium-high confidence/impact

Important only applies two filter layers:

  1. Pre-filter: --severity WARNING --severity ERROR (CLI flag)

  2. Post-filter: JSON metadata — keeps only category=security, confidence∈{MEDIUM,HIGH}, impact∈{MEDIUM,HIGH}

See scan-modes.md for metadata criteria and jq filter commands.

Orchestration Architecture

┌──────────────────────────────────────────────────────────────────┐
│ MAIN SESSION (this skill)                                        │
│ Step 1: Detect languages + check Pro availability                │
│ Step 2: Select scan mode + rulesets (ref: rulesets.md)           │
│ Step 3: Present plan + rulesets, get approval [⛔ HARD GATE]     │
│ Step 4: Run scripts/run-scans.sh with the approved rulesets      │
│ Step 5: Post-filter, merge, report, delete repos/                │
└──────────────────────────────────────────────────────────────────┘
         │ Step 4: Bash
         ▼
┌──────────────────────────────────────────────────────────────────┐
│ scripts/run-scans.sh                                             │
│   clone       each third-party repo once, into repos/            │
│   generate    one semgrep command per ruleset                    │
│                ├── python     p/python, p/django   --include=*.py│
│                ├── javascript p/javascript         --include=*.js│
│                ├── docker     p/dockerfile                       │
│                └── cross-language  p/security-audit, p/secrets,  │
│                                    the cloned repos  (no filter) │
│   run         in batches of --jobs, exit code read per process   │
│   write       scans.json — scans, failed, skipped                │
└──────────────────────────────────────────────────────────────────┘

The approval gate stays in the session; the script is execution only and asks nothing. The approved list reaches it as a JSON file, so the scan cannot reach a ruleset the user declined.

Cross-language rulesets go in one shared unit rather than being repeated per language. p/security-audit, p/secrets, and the third-party repos scan the whole target unscoped, so running them once per language ran the identical command N times and left the SARIF merge to dedup the copies.

Running it as a Workflow

This plugin ships /static-analysis:semgrep-scan, which runs the whole scan end to end: detect languages and Pro, select rulesets from rulesets.md, run scripts/run-scans.sh, merge and report. Pass it a JSON object, not prose:

/static-analysis:semgrep-scan {"target": "/abs/path", "mode": "run-all"}

It does not stop for ruleset approval. Invoking it with a target is the opt-in, the same way /variant-analysis:variants works. That is safe to do because the scan is read-only over the target — no --autofix, every write inside the output directory — so the approval gate below is a scope confirmation rather than a safety one. What ran is recorded in rulesets.json and scans.json either way.

Use the workflow when you want the scan run; work the five steps below when the ruleset selection itself matters and you want to see and edit the list first.

Workflow

Follow the detailed workflow in scan-workflow.md. Summary:

StepActionGateKey Reference
1Resolve output dir, detect languages + Pro availability—Use Glob, not Bash
2Select scan mode + rulesets—rulesets.md
3Present plan, get explicit approval⛔ HARDAskUserQuestion
4Run the scans—scripts/run-scans.sh
5Post-filter, merge, report, clean up—Merge script (below)

Task enforcement: On invocation, create 5 tasks with blockedBy dependencies (each step blocks the previous). Step 3 is a HARD GATE — mark complete ONLY after user explicitly approves.

Merge command (Step 5):

# run-all
uv run --no-project {baseDir}/scripts/merge_sarif.py "$OUTPUT_DIR/raw" "$OUTPUT_DIR/results/results.sarif" \
  --scans "$OUTPUT_DIR/scans.json"

# important-only, once the JSON post-filter has run over every file in raw/
uv run --no-project {baseDir}/scripts/merge_sarif.py "$OUTPUT_DIR/raw" "$OUTPUT_DIR/results/results.sarif" \
  --important --scans "$OUTPUT_DIR/scans.json"

--scans drops the output of scans listed under .failed. A scan that died part-way may still have written a .sarif, and under --important that file has no post-filter beside it, which is an error rather than an empty filter. Without the flag one dead scan denies every healthy scan a merged result. The excluded files are named on stdout, so they can go in the report.

The post-filter reads metadata SARIF does not carry, so it cannot be re-run against the merged file; --important instead keeps the findings the JSON filter kept, matched on (rule, file, line). Without it results.sarif is unfiltered while the JSON side is not.

Workflow and agents

ComponentPurpose
scripts/run-scans.shBuilds every scan command from the approved rulesets, runs them in batches, and writes scans.json

Step 4 is a Bash call. No subagent runs any part of the scan: exit codes and finding counts are read from the processes and the JSON they wrote.

Rationalizations to Reject

ShortcutWhy It's Wrong
"User asked for scan, that's approval"Original request ≠ plan approval. Present plan, use AskUserQuestion, await explicit "yes"
"Step 3 task is blocking, just mark complete"Lying about task status defeats enforcement. Only mark complete after real approval
"I already know what they want"Assumptions cause scanning wrong directories/rulesets. Present plan for verification
"Just use default rulesets"User must see and approve exact rulesets before scan
"Add extra rulesets without asking"Modifying approved list without consent breaks trust
"Third-party rulesets are optional"Trail of Bits, 0xdea, Decurity catch vulnerabilities not in official registry — REQUIRED
"Use --config auto"Sends metrics; less control over rulesets
"I'll just run the semgrep commands myself"run-scans.sh is what enforces --metrics=off, the --include rule and the output-directory --exclude. Hand-written commands drop them silently
"The script failed, I'll run semgrep directly to get something"A non-zero exit means no scan succeeded. Report that and stop; a hand-run subset reads as a full scan
"Some scans failed, the run still finished"failed and skipped are part of scans.json. Report them or the user reads a partial scan as a clean one
"Pro is too slow, skip --pro"Cross-file analysis catches 250% more true positives; worth the time
"Semgrep handles GitHub URLs natively"URL handling fails on repos with non-standard YAML; always clone first
"Cleanup is optional"Cloned repos pollute the user's workspace and accumulate across runs
"Use . or relative path as target"Subagents need absolute paths to avoid ambiguity
"Let the user pick an output dir later"Output directory must be resolved at Step 1, before any files are created

Reference Index

FileContent
rulesets.mdComplete ruleset catalog and selection algorithm
scan-modes.mdPre/post-filter criteria and jq commands
WorkflowPurpose
scan-workflow.mdComplete 5-step scan execution process
scripts/run-scans.shThe scan runner Step 4 calls

Success Criteria

  • [ ] Output directory resolved (user-specified or auto-incremented default)

  • [ ] All generated files stored inside $OUTPUT_DIR

  • [ ] Languages detected with file counts; Pro status checked

  • [ ] Scan mode selected by user (run all / important only)

  • [ ] Rulesets include third-party rules for all detected languages

  • [ ] User explicitly approved the scan plan (Step 3 gate passed)

  • [ ] run-scans.sh exited 0 and wrote $OUTPUT_DIR/scans.json

  • [ ] failed and skipped from scans.json are empty, or listed in the report

  • [ ] Scans marked partial in scans.json are none, or listed in the report — they ran with some of their rules failing to compile

  • [ ] Every semgrep command used --metrics=off

  • [ ] Approved plan written to $OUTPUT_DIR/rulesets.json at the Step 3 gate, and passed to the scanner unchanged

  • [ ] coveredNothing from scans.json is empty, or listed in the report

  • [ ] oversized from scans.json is empty, or listed in the report — those files exceed --max-target-bytes and no ruleset opened them

  • [ ] Raw per-scan outputs stored in $OUTPUT_DIR/raw/

  • [ ] results.sarif exists in $OUTPUT_DIR/results/ and is valid JSON

  • [ ] Important-only mode: post-filter applied before merge, merge run with --important, unfiltered results preserved in raw/

  • [ ] Results summary reported with severity and category breakdown

  • [ ] Cloned repos (if any) cleaned up from $OUTPUT_DIR/repos/

Files

scripts/test_merge_sarif.py

# /// script
# requires-python = ">=3.11"
# dependencies = ["pytest>=8"]
# ///
"""Tests for merge_sarif.py, with the weight on --important.

The important-only merge rests on one claim: a finding's identity in semgrep's JSON output
(check_id, path, start.line) is the same triple SARIF carries as (ruleId, uri,
region.startLine). test_key_contract pins the field names this script reads, but builds both
halves itself, so only test_key_contract_against_real_semgrep can notice semgrep changing
either shape. That one runs semgrep and compares the two records of one real finding.

The negatives matter as much: a post-filter that ran over only some scans, or wrote a file
that will not parse, must fail the merge. Filtering against a partial key set drops real
findings from the primary deliverable and nothing downstream could notice. The exception is a
scan recorded under .failed in scans.json, whose output is whatever a dying process wrote:
--scans drops those, so one crashed scan cannot deny every healthy scan a deliverable.
"""

from __future__ import annotations

import json
import shutil
import subprocess
import sys
from pathlib import Path

import pytest
from merge_sarif import (
    filter_to_keys,
    json_key,
    merge_sarif_pure_python,
    sarif_key,
    surviving_keys,
)

SCRIPT = Path(__file__).with_name("merge_sarif.py")

RULE = "python.lang.security.insecure-hash-algorithms-md5.insecure-hash-algorithm-md5"
OTHER = "python.lang.security.audit.subprocess-shell-true.subprocess-shell-true"


def sarif_result(rule: str, uri: str, line: int) -> dict:
    return {
        "ruleId": rule,
        "message": {"text": "finding"},
        "locations": [
            {
                "physicalLocation": {
                    "artifactLocation": {"uri": uri},
                    "region": {"startLine": line, "startColumn": 1},
                }
            }
        ],
    }


def sarif_doc(*results: dict) -> dict:
    return {
        "version": "2.1.0",
        "runs": [{"tool": {"driver": {"name": "semgrep", "rules": []}}, "results": list(results)}],
    }


def json_result(rule: str, path: str, line: int) -> dict:
    return {"check_id": rule, "path": path, "start": {"line": line, "col": 1}, "extra": {}}


def write_scan(raw: Path, stem: str, sarif: list[dict], filtered: list[dict] | None) -> None:
    """One scan's output: the SARIF the merge reads, and optionally its post-filtered JSON."""
    (raw / f"{stem}.sarif").write_text(json.dumps(sarif_doc(*sarif)))
    if filtered is not None:
        (raw / f"{stem}-important.json").write_text(
            json.dumps({"results": filtered, "errors": [], "paths": {}})
        )


def run_merge(raw: Path, out: Path, *flags: str) -> subprocess.CompletedProcess:
    return subprocess.run(
        [sys.executable, str(SCRIPT), str(raw), str(out), *flags],
        capture_output=True,
        text=True,
    )


def count(sarif_file: Path) -> int:
    data = json.loads(sarif_file.read_text())
    return sum(len(run.get("results", [])) for run in data.get("runs", []))


# --------------------------------------------------------------- the cross-format contract


def test_key_contract():
    """The shapes this script expects, pinned.

    Both halves are built by this file from one literal path, so this fixes the field names
    `sarif_key` and `json_key` read and nothing more. It cannot notice semgrep changing either
    output — test_key_contract_against_real_semgrep below is the one that can.
    """
    from_json = json_result(RULE, "src/app.py", 5)
    from_sarif = sarif_result(RULE, "src/app.py", 5)
    assert json_key(from_json) == sarif_key(from_sarif) == (RULE, "src/app.py", 5)


MD5_RULE = """\
rules:
  - id: insecure-md5
    pattern: hashlib.md5(...)
    message: md5 is insecure
    languages: [python]
    severity: WARNING
"""


def semgrep_bin() -> str:
    """Fail rather than skip, the same reason run_workflow_tests.sh fails without node.

    A skip here reads as a clean run while the only check that could catch cross-format drift
    silently did not execute. semgrep is this plugin's own dependency and CI installs it.
    """
    found = shutil.which("semgrep")
    if not found:
        raise AssertionError(
            "semgrep is not installed, so the JSON/SARIF contract went unverified. "
            "Install it (uv tool install semgrep) — this suite must not pass without it."
        )
    return found


@pytest.mark.parametrize("absolute", [True, False])
def test_key_contract_against_real_semgrep(tmp_path, absolute):
    """The contract read out of semgrep itself, over one real finding.

    --important rests entirely on the claim that (check_id, path, start.line) in the JSON is
    (ruleId, uri, region.startLine) in the SARIF. Only this test can see that claim break: if
    semgrep changes either shape, the keys stop matching, every finding is dropped and the
    deliverable goes empty. run-scans.sh always passes an absolute target; the relative case is
    parametrized because a path shape is exactly where the two formats would diverge first.
    """
    src = tmp_path / "src"
    src.mkdir()
    (src / "app.py").write_text(
        "import hashlib\ndef f(x):\n    return hashlib.md5(x).hexdigest()\n"
    )
    rule = tmp_path / "md5.yaml"
    rule.write_text(MD5_RULE)
    json_out = tmp_path / "out.json"
    sarif_out = tmp_path / "out.sarif"

    proc = subprocess.run(
        [
            semgrep_bin(),
            "--metrics=off",
            "--config",
            str(rule),
            "--json",
            "-o",
            str(json_out),
            f"--sarif-output={sarif_out}",
            str(src) if absolute else "src",
        ],
        cwd=tmp_path,
        capture_output=True,
        text=True,
    )
    assert json_out.is_file(), f"semgrep wrote no JSON: {proc.stderr}"
    assert sarif_out.is_file(), f"semgrep wrote no SARIF: {proc.stderr}"

    json_results = json.loads(json_out.read_text())["results"]
    sarif_results = json.loads(sarif_out.read_text())["runs"][0]["results"]
    assert len(json_results) == 1, f"expected one JSON finding, got {len(json_results)}"
    assert len(sarif_results) == 1, f"expected one SARIF finding, got {len(sarif_results)}"

    # The whole contract in one line. A mismatch here is the empty-deliverable bug, found at
    # its source rather than as a zero-finding results.sarif nobody can explain.
    assert json_key(json_results[0]) == sarif_key(sarif_results[0])


def test_keys_differ_on_line():
    assert json_key(json_result(RULE, "src/app.py", 5)) != sarif_key(
        sarif_result(RULE, "src/app.py", 6)
    )


def test_sarif_key_tolerates_a_result_with_no_location():
    assert sarif_key({"ruleId": RULE}) == (RULE, "", 0)


# ------------------------------------------------------------------------- surviving_keys


def test_surviving_keys_reads_every_scan(tmp_path):
    raw = tmp_path
    write_scan(raw, "py", [sarif_result(RULE, "a.py", 5)], [json_result(RULE, "a.py", 5)])
    write_scan(raw, "secrets", [sarif_result(OTHER, "b.py", 9)], [json_result(OTHER, "b.py", 9)])
    keys = surviving_keys(sorted(raw.glob("*.sarif")))
    assert keys == {(RULE, "a.py", 5), (OTHER, "b.py", 9)}


def test_surviving_keys_is_empty_when_the_filter_kept_nothing(tmp_path):
    """A real outcome, distinct from a filter that never ran: the files exist and are empty."""
    write_scan(tmp_path, "python-python", [sarif_result(RULE, "a.py", 5)], [])
    assert surviving_keys(sorted(tmp_path.glob("*.sarif"))) == set()


def test_a_scan_with_no_filtered_json_fails_the_merge(tmp_path):
    """The silent-omission case: without this, that scan's findings vanish from results.sarif."""
    raw = tmp_path
    write_scan(raw, "py", [sarif_result(RULE, "a.py", 5)], [json_result(RULE, "a.py", 5)])
    write_scan(raw, "all-secrets", [sarif_result(OTHER, "b.py", 9)], None)
    with pytest.raises(ValueError, match="all-secrets-important.json"):
        surviving_keys(sorted(raw.glob("*.sarif")))


def test_an_unparseable_filter_file_fails_the_merge(tmp_path):
    write_scan(tmp_path, "python-python", [sarif_result(RULE, "a.py", 5)], [])
    (tmp_path / "python-python-important.json").write_text("not json")
    with pytest.raises(ValueError, match="not valid JSON"):
        surviving_keys(sorted(tmp_path.glob("*.sarif")))


def test_a_filter_file_with_no_results_array_fails_the_merge(tmp_path):
    """Catches a SARIF file handed in where a filtered JSON belongs; it would filter to nothing."""
    write_scan(tmp_path, "python-python", [sarif_result(RULE, "a.py", 5)], [])
    (tmp_path / "python-python-important.json").write_text(json.dumps(sarif_doc()))
    with pytest.raises(ValueError, match="no .results array"):
        surviving_keys(sorted(tmp_path.glob("*.sarif")))


# -------------------------------------------------------------------------- filter_to_keys


def test_filter_keeps_only_surviving_findings():
    merged = sarif_doc(sarif_result(RULE, "a.py", 5), sarif_result(OTHER, "a.py", 3))
    kept, dropped = filter_to_keys(merged, {(RULE, "a.py", 5)})
    assert (kept, dropped) == (1, 1)
    assert [r["ruleId"] for r in merged["runs"][0]["results"]] == [RULE]


def test_filter_against_an_empty_key_set_empties_the_results():
    merged = sarif_doc(sarif_result(RULE, "a.py", 5))
    assert filter_to_keys(merged, set()) == (0, 1)
    assert merged["runs"][0]["results"] == []


# ------------------------------------------------------------------------------ end to end


def test_important_merge_filters_the_deliverable(tmp_path):
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(
        raw,
        "python-python",
        [sarif_result(RULE, "a.py", 5), sarif_result(OTHER, "a.py", 3)],
        [json_result(RULE, "a.py", 5)],
    )
    out = tmp_path / "results" / "results.sarif"
    proc = run_merge(raw, out, "--important")
    assert proc.returncode == 0, proc.stderr
    assert count(out) == 1
    assert json.loads(out.read_text())["runs"][0]["results"][0]["ruleId"] == RULE


def test_run_all_merge_keeps_everything(tmp_path):
    """The default path must be unchanged by the flag's existence."""
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(
        raw,
        "python-python",
        [sarif_result(RULE, "a.py", 5), sarif_result(OTHER, "a.py", 3)],
        [json_result(RULE, "a.py", 5)],
    )
    out = tmp_path / "results" / "results.sarif"
    assert run_merge(raw, out).returncode == 0
    assert count(out) == 2


def test_important_without_a_post_filter_fails_and_writes_nothing(tmp_path):
    """The whole point of resolving keys before the merge: no half-right file on disk."""
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(raw, "python-python", [sarif_result(RULE, "a.py", 5)], None)
    out = tmp_path / "results" / "results.sarif"
    proc = run_merge(raw, out, "--important")
    assert proc.returncode == 1
    assert "post-filtered JSON" in proc.stderr
    assert not out.exists()


def test_a_total_key_mismatch_fails_the_merge(tmp_path):
    """Cross-format drift, forced: the filter kept a finding no merged result matches.

    Without the guard this writes a zero-finding results.sarif and exits 0, so important-only
    reports a clean run that found nothing while the JSON side has findings.
    """
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(
        raw,
        "python-python",
        [sarif_result(RULE, "src/app.py", 5)],
        [json_result(RULE, "/abs/proj/src/app.py", 5)],
    )
    out = tmp_path / "results" / "results.sarif"
    proc = run_merge(raw, out, "--important")
    assert proc.returncode == 1, proc.stdout
    assert "none of them matched" in proc.stderr
    assert not out.exists()


def test_a_filter_that_kept_nothing_is_not_a_mismatch(tmp_path):
    """The guard is conditioned on the key set, not on the kept count.

    A post-filter that legitimately excluded every finding is a real zero. If this goes red,
    important-only can no longer report an honest empty result.
    """
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(raw, "python-python", [sarif_result(RULE, "a.py", 5)], [])
    out = tmp_path / "results" / "results.sarif"
    proc = run_merge(raw, out, "--important")
    assert proc.returncode == 0, proc.stderr
    assert count(out) == 0


def test_a_partial_key_mismatch_still_merges(tmp_path):
    """One matching key is enough to prove the formats still agree; the rest is the filter."""
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(
        raw,
        "python-python",
        [sarif_result(RULE, "a.py", 5), sarif_result(OTHER, "a.py", 3)],
        [json_result(RULE, "a.py", 5), json_result(OTHER, "/elsewhere/a.py", 3)],
    )
    out = tmp_path / "results" / "results.sarif"
    proc = run_merge(raw, out, "--important")
    assert proc.returncode == 0, proc.stderr
    assert count(out) == 1


def test_important_leaves_an_existing_deliverable_alone_when_it_fails(tmp_path):
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(raw, "python-python", [sarif_result(RULE, "a.py", 5)], None)
    out = tmp_path / "results.sarif"
    out.write_text(json.dumps(sarif_doc(sarif_result(RULE, "a.py", 5))))
    before = out.read_text()
    assert run_merge(raw, out, "--important").returncode == 1
    assert out.read_text() == before


# --------------------------------------------------------------------- unparseable SARIF


def test_an_unparseable_sarif_is_named_on_stdout(tmp_path):
    """The silent-omission case this whole flag set exists to prevent.

    A scan can exit 0, write a valid .json — so it lands in .scans with a finding count — and
    still leave a truncated .sarif. The merge drops it and the total is short by exactly those
    findings. On stderr that was invisible to the report; it has to be in the same stream the
    Report phase reads, and named, or the run presents as clean.
    """
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(raw, "python-python", [sarif_result(RULE, "a.py", 5)], None)
    (raw / "python-broken.sarif").write_text('{"runs":[{"results":[')
    out = tmp_path / "results.sarif"
    proc = run_merge(raw, out)
    assert proc.returncode == 0, proc.stderr
    assert count(out) == 1, "the healthy scan must still merge"
    assert "unparseable" in proc.stdout
    assert "python-broken.sarif" in proc.stdout, "the file must be named, not just counted"


def test_every_sarif_unparseable_is_an_error(tmp_path):
    """Zero findings from zero readable files is a broken run, not a clean one."""
    raw = tmp_path / "raw"
    raw.mkdir()
    (raw / "python-broken.sarif").write_text('{"runs":[{"results":[')
    out = tmp_path / "results.sarif"
    proc = run_merge(raw, out)
    assert proc.returncode == 1
    assert "nothing to merge" in proc.stderr
    assert not out.exists()


def test_the_merge_returns_what_it_could_not_read(tmp_path):
    """The list is a return value, so a caller cannot forget to look at it."""
    write_scan(tmp_path, "ok", [sarif_result(RULE, "a.py", 5)], None)
    (tmp_path / "bad.sarif").write_text("{{{")
    merged, unparseable = merge_sarif_pure_python(sorted(tmp_path.glob("*.sarif")))
    assert [Path(p).name for p in unparseable] == ["bad.sarif"]
    assert sum(len(r["results"]) for r in merged["runs"]) == 1


# ------------------------------------------------------------------------- one merge backend


def test_the_merge_shells_out_to_nothing(tmp_path):
    """Run with an empty PATH, so any external merge tool is unreachable.

    The merge used to try `npx @microsoft/sarif-multitool` first and fall back to Python, which
    made the result depend on whether that package sat in the npx cache. Only the Python merge
    dedups on sarif_key, and multitool rewrites artifactLocation.uri, so on a machine that had
    it cached --important would match nothing and blame a semgrep format change. One backend,
    same answer everywhere.
    """
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(
        raw, "python-python", [sarif_result(RULE, "a.py", 5)], [json_result(RULE, "a.py", 5)]
    )
    out = tmp_path / "results.sarif"
    proc = subprocess.run(
        [sys.executable, str(SCRIPT), str(raw), str(out), "--important"],
        capture_output=True,
        text=True,
        env={"PATH": "", "HOME": str(tmp_path)},
    )
    assert proc.returncode == 0, proc.stderr
    assert count(out) == 1
    assert "multitool" not in proc.stdout.lower(), "no external merge tool may be consulted"

    # The empty PATH above proves the merge survives without a backend, not that it stopped
    # looking for one: a reintroduced optional branch would just fall back and pass. This is
    # the assertion that fails if one comes back.
    assert "import subprocess" not in SCRIPT.read_text(), (
        "merge_sarif.py must not shell out; a second merge backend disagrees with this one "
        "on dedup and on artifactLocation.uri, and which one runs would depend on the machine"
    )


# ------------------------------------------------------------------------------------ --scans


def write_scans_json(path: Path, succeeded: list[Path], failed: list[Path]) -> Path:
    """A scans.json in run-scans.sh's shape. Both lists carry the same `sarif` key."""
    path.write_text(
        json.dumps(
            {
                "scans": [
                    {"lang": "python", "ruleset": "p/python", "sarif": str(p)} for p in succeeded
                ],
                "failed": [
                    {"lang": "python", "ruleset": "p/x", "sarif": str(p), "error": "exited 7"}
                    for p in failed
                ],
                "skipped": [],
            }
        )
    )
    return path


def dead_scan(raw: Path, stem: str) -> Path:
    """A scan recorded under .failed: its SARIF is on disk with no post-filter beside it."""
    sarif = raw / f"{stem}.sarif"
    sarif.write_text(json.dumps(sarif_doc(sarif_result(OTHER, "b.py", 9))))
    return sarif


def test_a_failed_scan_no_longer_denies_every_other_scan_a_deliverable(tmp_path):
    """The point of the flag: one dead scan must not take the whole important-only merge."""
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(
        raw, "python-python", [sarif_result(RULE, "a.py", 5)], [json_result(RULE, "a.py", 5)]
    )
    dead = dead_scan(raw, "python-broken")
    scans = write_scans_json(tmp_path / "scans.json", [raw / "python-python.sarif"], [dead])
    out = tmp_path / "results.sarif"
    proc = run_merge(raw, out, "--important", "--scans", str(scans))
    assert proc.returncode == 0, proc.stderr
    assert count(out) == 1
    assert "python-broken.sarif" in proc.stdout, "the excluded file must be named for the report"


def test_the_same_run_without_scans_json_still_fails(tmp_path):
    """Pins that the flag is what makes it survivable, not a change in the merge's strictness."""
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(
        raw, "python-python", [sarif_result(RULE, "a.py", 5)], [json_result(RULE, "a.py", 5)]
    )
    dead_scan(raw, "python-broken")
    out = tmp_path / "results.sarif"
    assert run_merge(raw, out, "--important").returncode == 1
    assert not out.exists()


def test_a_succeeded_scan_missing_its_filter_still_fails(tmp_path):
    """Only failed scans are exempt.

    A healthy scan with no post-filter beside it still aborts the merge: its findings are real,
    and filtering against a key set that never saw them drops them from the deliverable with
    nothing downstream able to notice.
    """
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(
        raw, "python-python", [sarif_result(RULE, "a.py", 5)], [json_result(RULE, "a.py", 5)]
    )
    healthy = dead_scan(raw, "python-other")  # same shape, but recorded as a success below
    scans = write_scans_json(tmp_path / "scans.json", [raw / "python-python.sarif", healthy], [])
    out = tmp_path / "results.sarif"
    proc = run_merge(raw, out, "--important", "--scans", str(scans))
    assert proc.returncode == 1
    assert "python-other-important.json" in proc.stderr
    assert not out.exists()


def test_run_all_also_drops_a_failed_scan_output(tmp_path):
    """A dead process's file is not a scan result in either mode."""
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(raw, "python-python", [sarif_result(RULE, "a.py", 5)], None)
    dead = dead_scan(raw, "python-broken")
    scans = write_scans_json(tmp_path / "scans.json", [raw / "python-python.sarif"], [dead])
    out = tmp_path / "results.sarif"
    proc = run_merge(raw, out, "--scans", str(scans))
    assert proc.returncode == 0, proc.stderr
    assert count(out) == 1, "the failed scan's finding must not reach the merge"


def test_every_scan_failed_is_an_error_not_an_empty_merge(tmp_path):
    """Excluding everything would otherwise write an empty SARIF and report a clean run."""
    raw = tmp_path / "raw"
    raw.mkdir()
    dead = dead_scan(raw, "python-broken")
    scans = write_scans_json(tmp_path / "scans.json", [], [dead])
    out = tmp_path / "results.sarif"
    proc = run_merge(raw, out, "--scans", str(scans))
    assert proc.returncode == 1
    assert "nothing to merge" in proc.stderr
    assert not out.exists()


def test_a_scans_json_with_no_failed_array_is_rejected(tmp_path):
    """Catches the wrong file being passed; treating it as 'nothing failed' would be silent."""
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(
        raw, "python-python", [sarif_result(RULE, "a.py", 5)], [json_result(RULE, "a.py", 5)]
    )
    bad = tmp_path / "scans.json"
    bad.write_text(json.dumps({"scans": []}))
    out = tmp_path / "results.sarif"
    proc = run_merge(raw, out, "--important", "--scans", str(bad))
    assert proc.returncode == 1
    assert "not a scans.json" in proc.stderr
    assert not out.exists()


def test_scans_flag_without_a_path_is_rejected(tmp_path):
    raw = tmp_path / "raw"
    raw.mkdir()
    write_scan(raw, "python-python", [sarif_result(RULE, "a.py", 5)], None)
    proc = run_merge(raw, tmp_path / "results.sarif", "--scans")
    assert proc.returncode == 1
    assert "--scans needs" in proc.stderr


def test_an_empty_raw_directory_is_an_error(tmp_path):
    raw = tmp_path / "raw"
    raw.mkdir()
    assert run_merge(raw, tmp_path / "o.sarif").returncode == 1


# ------------------------------------------------------------------------------ merge dedup


def test_merge_dedups_one_finding_flagged_by_two_rulesets(tmp_path):
    """The reason the report counts from the merge and never sums per-scan counts."""
    write_scan(tmp_path, "python-python", [sarif_result(RULE, "a.py", 5)], None)
    write_scan(tmp_path, "all-audit", [sarif_result(RULE, "a.py", 5)], None)
    merged, _ = merge_sarif_pure_python(sorted(tmp_path.glob("*.sarif")))
    assert sum(len(run["results"]) for run in merged["runs"]) == 1

Requirements and compatibility

Written for: Claude Code

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.

Needs: Declares allowed tools, Names Claude Code tools, Needs Python

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Published by
Trail of Bits
Publisher
Trail of Bits (Official)
Source
trailofbits/skills · plugins/static-analysis/skills/semgrep · commit e4dd0bb
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Creative Commons Attribution-ShareAlike 4.0 International (redistribution allowed)
  • LICENSE (added by AutoGineer from LICENSE)
  • ATTRIBUTION.md (written by AutoGineer)
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