Compare CodeQL and Jev on matched public methods

CODEQL.md

@@ -0,0 +1,65 @@
+# CodeQL comparison
+
+This track compares CodeQL with the saved Jev run on the same public method
+pairs. CodeQL analyzes each repository snapshot. Jev's saved decision for each
+method is read from `predictions/current/`.
+
+The cohort is listed in [`codeql-cohort.json`](codeql-cohort.json). A pair is
+counted only if both source states can be recreated, CodeQL extracts both
+target files, and the method text matches the recorded lines. Failed or
+unavailable snapshots are excluded from both models' counts. This is a subset
+of the public bug and security benchmarks, so its results are separate from
+the full-set model tables.
+
+Input revisions for this run: `bug-pairs-public@80cc6cbcf4b44e140706bcef3d40336ae81e7a05`,
+`security-pairs-public@0b3312a609892f4383e8252841ea94fdf74b2935`, and
+the SWE-rebench V2 Parquet file with SHA-256
+`0e0bf9355f892ad74ae98d4e1c404f39fd6654a8e351ee3e6ab162e4a64cd3ad`.
+
+CodeQL CLI 2.27.1 runs the published `security-extended` suite for security
+and `security-and-quality` for bugs. The query packs are pinned to
+`codeql/python-queries@1.8.11`, `codeql/javascript-queries@2.4.6`, and
+`codeql/cpp-queries@1.9.0`. For the bug track, only results tagged
+`correctness`, `reliability`, or `security` count; pure maintainability advice
+does not represent a bug. A finding counts for a method only when its primary
+SARIF location overlaps that method's recorded source lines. A finding
+elsewhere in the file is not assigned to the method.
+
+Python, JavaScript, TypeScript, C, and C++ snapshots use CodeQL's no-build
+extraction. For [SWE-rebench V2](https://huggingface.co/datasets/nebius/SWE-rebench-V2)
+bug pairs, the runner applies the dataset's gold patch to its pinned
+`base_commit` to reconstruct the repaired repository. It does not run project
+code or tests.
+
+To reproduce, download the public `benchmark.jsonl` files from
+[`bug-pairs-public`](https://huggingface.co/datasets/perchscan/bug-pairs-public)
+and [`security-pairs-public`](https://huggingface.co/datasets/perchscan/security-pairs-public)
+into `public/bug/` and `public/security/`. Download SWE-rebench V2's `train`
+Parquet file separately. Install Docker, the CodeQL CLI for your Docker
+architecture, its three query packs at the versions above, and DuckDB. Then
+run:
+
+```sh
+python3 codeql_compare.py scan \
+  --root /path/to/codeql-work \
+  --data /path/to/public \
+  --predictions predictions/current \
+  --codeql /path/to/codeql \
+  --rebench-parquet /path/to/swe-rebench-train.parquet
+
+python3 codeql_compare.py score \
+  --root /path/to/codeql-work \
+  --data /path/to/public \
+  --predictions predictions/current
+```
+
+The runner writes per-pair decisions and aggregate counts under the work
+directory. It resumes completed databases and SARIF analyses. CodeQL reports
+binary findings here, so it has no average-precision score or threshold curve
+to compare with Jev's probabilities. The semantic lint track is not included:
+stock CodeQL queries do not take the pair's written behavior rule as input.
+
+[GitHub's CodeQL documentation](https://docs.github.com/en/code-security/concepts/code-scanning/codeql/codeql-query-suites)
+describes the built-in suites and their intended coverage. The
+[CLI terms](https://docs.github.com/en/code-security/concepts/code-scanning/codeql/codeql-cli)
+cover its use on public repositories.

README.md

@@ -132,6 +132,28 @@ Inference costs cover scoring the method sides in each table. Jev costs are esti
 
 JevLike (192-byte input), Laya (512-token input), and Kev (packed-branch limit) could not score every full-context method. NanoJev was unavailable on Beam. They are excluded rather than ranked on partial results.
 
+## CodeQL comparison
+
+[CodeQL](https://codeql.github.com/) and Jev were evaluated on the same public method sides in a separate cohort. CodeQL analyzed full repository snapshots; Jev used its saved Perch inputs and recorded alert settings. A CodeQL finding counts when its primary location falls inside the labelled method. The matched set contains 52 bug pairs and 70 security pairs.
+
+### Bugs: 52 pairs
+
+| Tool | TP | FP | FN | Precision | Recall | F1 | False-positive rate |
+| --- | ---: | ---: | ---: | ---: | ---: | ---: | ---: |
+| CodeQL | 0 | 0 | 21 | — (0 alerts) | 0.0% | 0.0% | 0.0% |
+| Jev | 6 | 8 | 15 | 42.9% | 28.6% | 34.3% | 9.6% |
+
+### Security: 70 pairs
+
+| Tool | TP | FP | FN | Precision | Recall | F1 | False-positive rate |
+| --- | ---: | ---: | ---: | ---: | ---: | ---: | ---: |
+| CodeQL | 1 | 0 | 26 | 100.0% (1 alert) | 3.7% | 7.1% | 0.0% |
+| Jev | 8 | 12 | 19 | 40.0% | 29.6% | 34.0% | 10.6% |
+
+TP is a finding on a labelled issue, FP is a finding on a labelled clean method, and FN is a missed issue. False-positive rate is FP divided by clean methods: 83 for bugs and 113 for security. CodeQL found an [OpenJPEG integer-overflow cast](https://github.com/uclouvain/openjpeg/commit/ef01f18dfc6780b776d0674ed3e7415c6ef54d24) in `opj_pi_create_decode` before the repair; Jev did not alert on that pair.
+
+The [CodeQL protocol](CODEQL.md), [runner](codeql_compare.py), [matched method decisions](codeql-comparison/), and [cohort list](codeql-cohort.json) are published here. Four selected bug pairs and three security pairs were excluded because a source snapshot could not be analyzed. CodeQL returns findings rather than probabilities, so these rows have no average-precision score or threshold curve.
+
 ## Files and reproduction
 
 - [`results-current.jsonl`](https://huggingface.co/datasets/perchscan/benchmark-results/blob/main/results-current.jsonl): current-pack aggregate results for public and private splits; no private pair data.

codeql-cohort.json

@@ -0,0 +1,38 @@
+{
+  "description": "Public CodeQL comparison cohort with pinned Python, JavaScript, TypeScript, C, and C++ method pairs.",
+  "bug": [
+    "Kludex/starlette",
+    "pallets/flask",
+    "pytest-dev/pluggy",
+    "tox-dev/tox",
+    "mcollina/autocannon",
+    "mswjs/msw",
+    "canjs/can-zone",
+    "codemanki/cloudscraper",
+    "gtalarico/pyairtable",
+    "illinois/queue",
+    "jamesramsay/hercule",
+    "rstudio/vetiver-python",
+    "nodejs/llhttp",
+    "transmission/transmission",
+    "nginx/nginx",
+    "qpdf/qpdf"
+  ],
+  "security": [
+    "akshudev/pheonixappapi",
+    "authlib/joserfc",
+    "aio-libs/aiohttp-session",
+    "authlib/authlib",
+    "cole/aiosmtplib",
+    "jasmine/jasmine",
+    "agronholm/anyio",
+    "apragacz/django-rest-registration",
+    "executablebooks/markdown-it-py",
+    "axios/axios",
+    "nlnetlabs/unbound",
+    "catchorg/Catch2",
+    "nginx/nginx",
+    "rdesktop/rdesktop",
+    "uclouvain/openjpeg"
+  ]
+}

codeql-comparison/bug.jsonl

@@ -0,0 +1,52 @@
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.14, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.15, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "benign-bug:16543a356f058fbf47da2140", "repository": "illinois/queue"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.5, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.49, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-bug:2b17cee97206f6f87767489d", "repository": "gtalarico/pyairtable"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.21, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.22, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-bug:9f9b5320a1291eb425836819", "repository": "rstudio/vetiver-python"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.1, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.11, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "benign-bug:bcad204ebb52f5138d3ea837", "repository": "illinois/queue"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.35, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.36, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "benign-bug:cd3617eee6b31e2e36c369e6", "repository": "canjs/can-zone"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.25, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.26, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-bug:dc53b49f8bf0f2baa2deb1c2", "repository": "rstudio/vetiver-python"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.16, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.17, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:0494646d1c4bb487c1d41c15", "repository": "pallets/flask"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.51, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.55, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:0982969f8885f6c0bc652747", "repository": "Kludex/starlette"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.23, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.25, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:1d73e59da6afa698740048b2", "repository": "pallets/flask"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.1, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.1, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:27ffc0a2776b318a006f8a0a", "repository": "pytest-dev/pluggy"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.21, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.2, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:2fb877739a64dafa2f0e6dfe", "repository": "tox-dev/tox"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.23, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.22, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:34d6f55233db4cc5c9b8b617", "repository": "tox-dev/tox"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.27, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.27, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:439cc87c0c861e6970eb806e", "repository": "pytest-dev/pluggy"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.36, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.36, "label": 0, "role": "after"}], "language": "c", "pair_id": "benign-multilang:543f0598f6d59ba19b6e7047", "repository": "nginx/nginx"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.35, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.33, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:5f82850995d49c7beb717913", "repository": "tox-dev/tox"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.32, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.33, "label": 0, "role": "after"}], "language": "c", "pair_id": "benign-multilang:68c6079b04da087f6a515aed", "repository": "nginx/nginx"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.19, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.18, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:6d32d7eb744684348a67b665", "repository": "pytest-dev/pluggy"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.14, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.14, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:7f191b012f6552ec4e3de345", "repository": "pallets/flask"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.21, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.2, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:7f4862e69a0e367e72a649ee", "repository": "Kludex/starlette"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.19, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.19, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:87a694061fe6dc3509fd2510", "repository": "pytest-dev/pluggy"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.21, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.24, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:88cb7066d52682f3a04d6226", "repository": "pallets/flask"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.17, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.17, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:88e37d34d2ef27dc6516f26a", "repository": "pytest-dev/pluggy"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.22, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.23, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:8bd3f31f443ae77d438d5357", "repository": "tox-dev/tox"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.2, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.19, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:8ed2368192761fa8563b5d48", "repository": "tox-dev/tox"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.43, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.42, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:95b39ce7cab786378bb0c5ca", "repository": "Kludex/starlette"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.22, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.22, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:a80f355e10a01e4ea4cd8582", "repository": "pallets/flask"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.43, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.45, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:c7f1dd08f8b77a113657db85", "repository": "Kludex/starlette"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.29, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.3, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-multilang:ffaa63f5ce8b55206631aa8f", "repository": "Kludex/starlette"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.05, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.05, "label": 0, "role": "after"}], "language": "cpp", "pair_id": "heldout-benign:calibration:96ddf0294b047542802791b5", "repository": "qpdf/qpdf"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.19, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.2, "label": 0, "role": "after"}], "language": "c", "pair_id": "heldout-benign:validation:1d27793bcd82f2fb67bfa100", "repository": "nodejs/llhttp"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.16, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.17, "label": 0, "role": "after"}], "language": "c", "pair_id": "heldout-benign:validation:8a2a5828d8161892adfe148c", "repository": "nodejs/llhttp"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.35, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.35, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:canjs__can-zone-103:100fc77182c7", "repository": "canjs/can-zone"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.38, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.48, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:canjs__can-zone-119:2c6fd03ec8a3", "repository": "canjs/can-zone"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.53, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.53, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:codemanki__cloudscraper-127:29fbfea99352", "repository": "codemanki/cloudscraper"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.4, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.36, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:codemanki__cloudscraper-127:9d8a3e6fa2d6", "repository": "codemanki/cloudscraper"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.56, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.53, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:codemanki__cloudscraper-137:234a450877ad", "repository": "codemanki/cloudscraper"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.49, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.47, "label": 0, "role": "after"}], "language": "python", "pair_id": "swe-rebench:gtalarico__pyairtable-250:02e24170afd9", "repository": "gtalarico/pyairtable"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.38, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.39, "label": 0, "role": "after"}], "language": "python", "pair_id": "swe-rebench:gtalarico__pyairtable-250:7f8fddbaab28", "repository": "gtalarico/pyairtable"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.33, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.31, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:illinois__queue-214:c5e119e89b30", "repository": "illinois/queue"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.74, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.74, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:jamesramsay__hercule-220:085707b5e55c", "repository": "jamesramsay/hercule"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.72, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.67, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:jamesramsay__hercule-220:65fb9e5f38cf", "repository": "jamesramsay/hercule"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.61, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.64, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:jamesramsay__hercule-220:fcebf8deb381", "repository": "jamesramsay/hercule"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.61, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.59, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:mcollina__autocannon-267:ef8fc9a6aac1", "repository": "mcollina/autocannon"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.28, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.37, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:mcollina__autocannon-332:0e34114137ab", "repository": "mcollina/autocannon"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.25, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.37, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "swe-rebench:mcollina__autocannon-332:4fd12d70dd0f", "repository": "mcollina/autocannon"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.18, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.19, "label": 0, "role": "after"}], "language": "typescript", "pair_id": "swe-rebench:mswjs__msw-2509:0a28baf66879", "repository": "mswjs/msw"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.14, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.14, "label": 0, "role": "after"}], "language": "typescript", "pair_id": "swe-rebench:mswjs__msw-2509:611d9f264dc3", "repository": "mswjs/msw"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.19, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.17, "label": 0, "role": "after"}], "language": "typescript", "pair_id": "swe-rebench:mswjs__msw-2509:9734aa3b2d18", "repository": "mswjs/msw"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.24, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.21, "label": 0, "role": "after"}], "language": "typescript", "pair_id": "swe-rebench:mswjs__msw-2509:c91aba5e55d5", "repository": "mswjs/msw"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.23, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.29, "label": 0, "role": "after"}], "language": "c", "pair_id": "swe-rebench:nodejs__llhttp-245:013562950290", "repository": "nodejs/llhttp"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.13, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.22, "label": 0, "role": "after"}], "language": "cpp", "pair_id": "swe-rebench:qpdf__qpdf-289:1286d5497696", "repository": "qpdf/qpdf"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.14, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.45, "label": 0, "role": "after"}], "language": "python", "pair_id": "swe-rebench:rstudio__vetiver-python-201:97ccdd87e120", "repository": "rstudio/vetiver-python"}

codeql-comparison/results.json

@@ -0,0 +1,97 @@
+{
+  "bug": {
+    "missing_sides": [
+      {
+        "pair_id": "benign-bug:654f92c07b7e09c9a4bc00b9",
+        "reason": "CodeQL analysis unavailable",
+        "role": "before"
+      },
+      {
+        "pair_id": "swe-rebench:mcollina__autocannon-332:549c7e4f7eaa",
+        "reason": "source snapshot unavailable",
+        "role": "after"
+      },
+      {
+        "pair_id": "swe-rebench:transmission__transmission-5889:e7ed2acdc784",
+        "reason": "CodeQL analysis unavailable",
+        "role": "before"
+      },
+      {
+        "pair_id": "swe-rebench:transmission__transmission-6177:10de829bf14c",
+        "reason": "CodeQL analysis unavailable",
+        "role": "before"
+      }
+    ],
+    "models": {
+      "codeql": {
+        "f1": 0.0,
+        "fn": 21,
+        "fp": 0,
+        "fpr": 0.0,
+        "precision": null,
+        "recall": 0.0,
+        "recall_minus_fpr": 0.0,
+        "tn": 83,
+        "tp": 0
+      },
+      "jev": {
+        "f1": 0.34285714285714286,
+        "fn": 15,
+        "fp": 8,
+        "fpr": 0.0963855421686747,
+        "precision": 0.42857142857142855,
+        "recall": 0.2857142857142857,
+        "recall_minus_fpr": 0.189328743545611,
+        "tn": 75,
+        "tp": 6
+      }
+    },
+    "pairs": 52,
+    "requested_pairs": 56
+  },
+  "security": {
+    "missing_sides": [
+      {
+        "pair_id": "benign-multilang:92f8c1dd3d04cf1d36a9399f",
+        "reason": "CodeQL analysis unavailable",
+        "role": "after"
+      },
+      {
+        "pair_id": "benign-multilang:c6e0c1d6f8cead4e776f37c9",
+        "reason": "CodeQL analysis unavailable",
+        "role": "after"
+      },
+      {
+        "pair_id": "benign-multilang:fcdedd456a15c760f122a8a3",
+        "reason": "CodeQL analysis unavailable",
+        "role": "after"
+      }
+    ],
+    "models": {
+      "codeql": {
+        "f1": 0.07142857142857142,
+        "fn": 26,
+        "fp": 0,
+        "fpr": 0.0,
+        "precision": 1.0,
+        "recall": 0.037037037037037035,
+        "recall_minus_fpr": 0.037037037037037035,
+        "tn": 113,
+        "tp": 1
+      },
+      "jev": {
+        "f1": 0.3404255319148936,
+        "fn": 19,
+        "fp": 12,
+        "fpr": 0.10619469026548672,
+        "precision": 0.4,
+        "recall": 0.2962962962962963,
+        "recall_minus_fpr": 0.19010160603080956,
+        "tn": 101,
+        "tp": 8
+      }
+    },
+    "pairs": 70,
+    "requested_pairs": 73
+  }
+}

codeql-comparison/security.jsonl

@@ -0,0 +1,70 @@
+{"decisions": [{"codeql_alert": true, "codeql_rules": ["cpp/integer-multiplication-cast-to-long"], "jev_alert": false, "jev_score": 0.67, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.67, "label": 0, "role": "after"}], "language": "c", "pair_id": "1ec1e10d8ecc3aeec647c7f5", "repository": "uclouvain/openjpeg"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.9, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.94, "label": 0, "role": "after"}], "language": "c", "pair_id": "247ca4e518f9cfccd1235591", "repository": "nlnetlabs/unbound"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.75, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.75, "label": 0, "role": "after"}], "language": "c", "pair_id": "2738b17989a2f974474f276b", "repository": "uclouvain/openjpeg"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.76, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.77, "label": 0, "role": "after"}], "language": "c", "pair_id": "357c8e2348fbf98e5acbced4", "repository": "rdesktop/rdesktop"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.74, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.75, "label": 0, "role": "after"}], "language": "c", "pair_id": "47b7780c89aa5812110eed03", "repository": "uclouvain/openjpeg"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.74, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.75, "label": 0, "role": "after"}], "language": "c", "pair_id": "698e1aa9f5800ee5c7575233", "repository": "uclouvain/openjpeg"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.74, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.72, "label": 0, "role": "after"}], "language": "c", "pair_id": "a11da60389905c67b9a81b8d", "repository": "uclouvain/openjpeg"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.7, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.73, "label": 0, "role": "after"}], "language": "c", "pair_id": "benign-multilang:0de2751599cf46ca2047fba5", "repository": "nginx/nginx"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.15, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.16, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "benign-multilang:309f41718d6ffba903bbd7ba", "repository": "jasmine/jasmine"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.11, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.12, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "benign-multilang:369b29e7f6a8e1e696909108", "repository": "jasmine/jasmine"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.19, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.17, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "benign-multilang:65508d79a39df59871da37f9", "repository": "jasmine/jasmine"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.69, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.7, "label": 0, "role": "after"}], "language": "c", "pair_id": "benign-multilang:87cd5e290433a879b5aa7d56", "repository": "nginx/nginx"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.48, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.48, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "benign-multilang:9c09d122c4f97810401ec64a", "repository": "axios/axios"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.73, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.69, "label": 0, "role": "after"}], "language": "javascript", "pair_id": "benign-multilang:d8ccae467ff3c1bd79f50cd3", "repository": "axios/axios"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.36, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.39, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-security:06e47656484b0970265fb32a", "repository": "executablebooks/markdown-it-py"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.37, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.36, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-security:14ce8ac6a09dc33e62af5c0e", "repository": "aio-libs/aiohttp-session"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.18, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.18, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-security:37cc8f7b09a927a94981a054", "repository": "authlib/joserfc"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.3, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.28, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-security:39142125534d024277d80000", "repository": "aio-libs/aiohttp-session"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.49, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.48, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-security:87217e7c9bd73eeb33cbd25a", "repository": "agronholm/anyio"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.32, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.3, "label": 0, "role": "after"}], "language": "python", "pair_id": "benign-security:e5ef550f528b16a9f0b6a30f", "repository": "apragacz/django-rest-registration"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.68, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.69, "label": 0, "role": "after"}], "language": "c", "pair_id": "cdd762600e55fe2c3e0f5284", "repository": "rdesktop/rdesktop"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.66, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.67, "label": 0, "role": "after"}], "language": "c", "pair_id": "e53808b6fb6ba5f610474c8a", "repository": "uclouvain/openjpeg"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.69, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.69, "label": 0, "role": "after"}], "language": "c", "pair_id": "f72694bd37925e411875669a", "repository": "uclouvain/openjpeg"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.84, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.82, "label": 0, "role": "after"}], "language": "c", "pair_id": "fd45265c79745554ce66fbf1", "repository": "nlnetlabs/unbound"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.42, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.37, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:agronholm/anyio:68f58915f82d9be8109ebbbd8f5d70577d43f2ce:f290c0cdb2b2", "repository": "agronholm/anyio"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.5, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.51, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:aio-libs/aiohttp-session:1b356f01bbab57d041c9a75bacd72fbbf8524728:74e6e1a8c51f", "repository": "aio-libs/aiohttp-session"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.64, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.62, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:055a0d458fe1", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.64, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.66, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:09d18ade59a6", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.5, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.52, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:0d8ed684d4dd", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.54, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.46, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:1396217c8af5", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.58, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.6, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:1c7c39b59495", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.56, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.52, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:2d24444c6784", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.57, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.59, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:2ffd627cd903", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.52, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.54, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:39b366cfa8c5", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.45, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.45, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:42cf86d28da6", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.61, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.53, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:5fd9c3245e18", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.54, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.5, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:5ff4cecfb824", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.47, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.44, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:76cb9c02c4e7", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.5, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.53, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:831a6048c2af", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.59, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.52, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:878303403610", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.43, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.44, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:896052e3f6be", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.51, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.49, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:95dda39b9dbf", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.62, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.58, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:9660db178725", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.45, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.5, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:9df33b5f284e", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.55, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.56, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:a347d85efa83", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.6, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.59, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:a5df615c9b12", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.47, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.47, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:adfbfc5f755f", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.5, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.46, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:b5e63fd65164", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.44, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.43, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:be0ca64a9f71", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.5, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.52, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:c9a5bb254488", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.62, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.58, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:d53eca708124", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.51, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.55, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:dbfcb2475459", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.51, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.49, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:akshudev/pheonixappapi:0937419e323f5ea9013d43dc1b82fef9d7e05044:f6aea4de609e", "repository": "akshudev/pheonixappapi"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.37, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.37, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:apragacz/django-rest-registration:26d094fab65ea8c2694fdfb6a3ab95a7808b62d5:27e3aba12209", "repository": "apragacz/django-rest-registration"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.58, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.55, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:authlib/authlib:2808378611dd6fb2532b189a9087877d8f0c0489:03b7ed0be2d4", "repository": "authlib/authlib"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.36, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.45, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:authlib/authlib:2808378611dd6fb2532b189a9087877d8f0c0489:46632269336d", "repository": "authlib/authlib"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.32, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.31, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:authlib/authlib:2808378611dd6fb2532b189a9087877d8f0c0489:82226a00b11c", "repository": "authlib/authlib"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.11, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.1, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:authlib/joserfc:63932f169d924caffafa761af2122b82059017f7:1e1bfec393da", "repository": "authlib/joserfc"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.08, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.09, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:authlib/joserfc:63932f169d924caffafa761af2122b82059017f7:377c2fd05cf4", "repository": "authlib/joserfc"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.13, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.08, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:authlib/joserfc:63932f169d924caffafa761af2122b82059017f7:55c89b57471e", "repository": "authlib/joserfc"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.14, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.12, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:authlib/joserfc:63932f169d924caffafa761af2122b82059017f7:6724c80eb3cc", "repository": "authlib/joserfc"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.1, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.09, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:authlib/joserfc:63932f169d924caffafa761af2122b82059017f7:68555687586b", "repository": "authlib/joserfc"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.09, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.08, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:authlib/joserfc:63932f169d924caffafa761af2122b82059017f7:6ba9e7498b7e", "repository": "authlib/joserfc"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.12, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.1, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:authlib/joserfc:63932f169d924caffafa761af2122b82059017f7:cd19f9b43b92", "repository": "authlib/joserfc"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.1, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.09, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:authlib/joserfc:63932f169d924caffafa761af2122b82059017f7:fc5f55ff25ff", "repository": "authlib/joserfc"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.14, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.13, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:cole/aiosmtplib:9fab7ba1361dbf7622ede1315a24be805cff09c9:bc493834cf12", "repository": "cole/aiosmtplib"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.8, "label": 1, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.8, "label": 0, "role": "after"}], "language": "python", "pair_id": "github-advisory:executablebooks/markdown-it-py:53ca3e9c2b9e9b295f6abf7f4ad2730a9b70f68c:4d2bdf2323b5", "repository": "executablebooks/markdown-it-py"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.08, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.08, "label": 0, "role": "after"}], "language": "python", "pair_id": "heldout-benign:calibration:43d8471d0d0a0d650cce0a67", "repository": "cole/aiosmtplib"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.51, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": false, "jev_score": 0.48, "label": 0, "role": "after"}], "language": "python", "pair_id": "heldout-benign:calibration:d87930c84e8761971804001f", "repository": "cole/aiosmtplib"}
+{"decisions": [{"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.75, "label": 0, "role": "before"}, {"codeql_alert": false, "codeql_rules": [], "jev_alert": true, "jev_score": 0.76, "label": 0, "role": "after"}], "language": "c", "pair_id": "heldout-benign:validation:5d634a64b1bacdaf30615c64", "repository": "nlnetlabs/unbound"}

codeql_compare.py

@@ -0,0 +1,409 @@
+#!/usr/bin/env python3
+"""Run CodeQL on the pinned public cohort and compare method-level alerts.
+
+The caller supplies the downloaded public benchmark.jsonl files. GitHub's
+CodeQL CLI and query packs are installed separately; this script does not
+download or redistribute them.
+"""
+
+import argparse
+import concurrent.futures
+import json
+import re
+import shutil
+import subprocess
+import time
+from collections import defaultdict
+from functools import lru_cache
+from pathlib import Path
+from zipfile import ZipFile
+
+
+LANGUAGES = {"python": "python", "javascript": "javascript", "typescript": "javascript",
+             "c": "cpp", "c++": "cpp", "cpp": "cpp"}
+PACKS = {"python": "1.8.11", "javascript": "2.4.6", "cpp": "1.9.0"}
+
+
+def rows(path):
+    with open(path, encoding="utf-8") as stream:
+        for line in stream:
+            if line.strip():
+                yield json.loads(line)
+
+
+def selected_pairs(args):
+    cohort = json.loads(Path(args.cohort).read_text())
+    selected = {}
+    for domain in ("bug", "security"):
+        repos = set(cohort[domain])
+        selected[domain] = [
+            pair for pair in rows(Path(args.data) / domain / "benchmark.jsonl")
+            if pair["repository"] in repos
+            and pair["language"].lower() in LANGUAGES
+            and all(pair[role].get("revision") for role in ("before", "after"))
+        ]
+    return selected
+
+
+def run(command, log_path, timeout=None, container_name=None):
+    log_path.parent.mkdir(parents=True, exist_ok=True)
+    start = time.monotonic()
+    with log_path.open("w", encoding="utf-8") as log:
+        try:
+            result = subprocess.run(command, stdout=log, stderr=subprocess.STDOUT,
+                                    timeout=timeout)
+            code = result.returncode
+        except subprocess.TimeoutExpired:
+            if container_name:
+                subprocess.run(["docker", "stop", "--time", "2", container_name],
+                               stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+            log.write(f"CodeQL stage exceeded {timeout} seconds.\n")
+            code = 124
+    return code, round(time.monotonic() - start, 2)
+
+
+def prepare_rebench_patches(pairs, root, source_parquet):
+    """Recreate SWE-rebench repaired snapshots from its published gold patches."""
+    if not source_parquet:
+        return
+    instances = {}
+    for pair in pairs["bug"]:
+        if not pair["pair_id"].startswith("swe-rebench:"):
+            continue
+        if "+" in pair["after"]["revision"]:
+            continue
+        instance = pair["pair_id"].split(":", 2)[1]
+        if not re.fullmatch(r"[A-Za-z0-9_.-]+", instance):
+            raise ValueError(f"Invalid instance ID: {instance}")
+        instances[instance] = pair
+    if not instances:
+        return
+    quoted = ",".join("'" + instance + "'" for instance in sorted(instances))
+    parquet = Path(source_parquet).resolve().as_posix().replace("'", "''")
+    query = ("SELECT instance_id,base_commit,patch FROM read_parquet('"
+             + parquet + "') WHERE instance_id IN (" + quoted + ")")
+    response = subprocess.run(["duckdb", "-json", "-c", query], check=True,
+                              capture_output=True, text=True)
+    source_rows = {row["instance_id"]: row for row in json.loads(response.stdout)}
+    errors = []
+    for instance, pair in instances.items():
+        source = source_rows.get(instance)
+        if not source:
+            errors.append({"instance_id": instance, "reason": "missing source patch"})
+            continue
+        if pair["before"]["revision"] != source["base_commit"]:
+            errors.append({"instance_id": instance, "reason": "base commit mismatch"})
+            continue
+        repo = pair["repository"]
+        slug = repo.replace("/", "__")
+        git_dir = root / "git" / slug
+        checkout = root / "checkouts" / slug / pair["after"]["revision"]
+        patch_file = root / "patches" / f"{instance}.patch"
+        patch_file.parent.mkdir(parents=True, exist_ok=True)
+        patch_file.write_text(source["patch"], encoding="utf-8")
+        try:
+            if not git_dir.exists():
+                git_dir.parent.mkdir(parents=True, exist_ok=True)
+                subprocess.run(["git", "clone", "--filter=blob:none", "--no-checkout",
+                                f"https://github.com/{repo}.git", str(git_dir)], check=True,
+                               stdout=subprocess.DEVNULL, stderr=subprocess.PIPE)
+            have = subprocess.run(
+                ["git", "-C", str(git_dir), "cat-file", "-e",
+                 f"{source['base_commit']}^{{commit}}"],
+                stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL,
+            ).returncode == 0
+            if not have:
+                subprocess.run(["git", "-C", str(git_dir), "fetch", "origin",
+                                source["base_commit"]], check=True,
+                               stdout=subprocess.DEVNULL, stderr=subprocess.PIPE)
+            if not checkout.exists():
+                checkout.parent.mkdir(parents=True, exist_ok=True)
+                subprocess.run(["git", "-C", str(git_dir), "worktree", "add", "--detach",
+                                str(checkout), source["base_commit"]], check=True,
+                               stdout=subprocess.DEVNULL, stderr=subprocess.PIPE)
+                subprocess.run(["git", "-C", str(checkout), "apply", "--whitespace=nowarn",
+                                str(patch_file)], check=True,
+                               stdout=subprocess.DEVNULL, stderr=subprocess.PIPE)
+        except subprocess.CalledProcessError as error:
+            errors.append({"instance_id": instance,
+                           "reason": f"{error.cmd[0]} exited {error.returncode}"})
+    (root / "patch-errors.json").write_text(json.dumps(errors, indent=2) + "\n")
+
+
+def prepare_sources(pairs, root):
+    tasks = defaultdict(set)
+    for domain, group in pairs.items():
+        for pair in group:
+            repo = pair["repository"]
+            language = LANGUAGES[pair["language"].lower()]
+            for role in ("before", "after"):
+                tasks[(repo, pair[role]["revision"], language)].add(domain)
+
+    sources = {}
+    errors = []
+    for repo, revision, language in sorted(tasks):
+        if not re.fullmatch(r"[0-9a-f]{40}", revision):
+            errors.append({"repository": repo, "revision": revision,
+                           "reason": "not a Git commit"})
+            continue
+        slug = repo.replace("/", "__")
+        git_dir = root / "git" / slug
+        checkout = root / "checkouts" / slug / revision
+        try:
+            if not git_dir.exists():
+                git_dir.parent.mkdir(parents=True, exist_ok=True)
+                subprocess.run(
+                    ["git", "clone", "--filter=blob:none", "--no-checkout",
+                     f"https://github.com/{repo}.git", str(git_dir)],
+                    check=True, stdout=subprocess.DEVNULL, stderr=subprocess.PIPE,
+                )
+            if not checkout.exists():
+                checkout.parent.mkdir(parents=True, exist_ok=True)
+                have = subprocess.run(
+                    ["git", "-C", str(git_dir), "cat-file", "-e", f"{revision}^{{commit}}"],
+                    stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL,
+                ).returncode == 0
+                if not have:
+                    subprocess.run(["git", "-C", str(git_dir), "fetch", "origin", revision],
+                                   check=True, stdout=subprocess.DEVNULL, stderr=subprocess.PIPE)
+                subprocess.run(["git", "-C", str(git_dir), "worktree", "add", "--detach",
+                                str(checkout), revision], check=True,
+                               stdout=subprocess.DEVNULL, stderr=subprocess.PIPE)
+            sources[(repo, revision, language)] = (checkout, tasks[(repo, revision, language)])
+        except subprocess.CalledProcessError as error:
+            errors.append({"repository": repo, "revision": revision,
+                           "reason": f"{error.cmd[0]} exited {error.returncode}"})
+    (root / "source-errors.json").write_text(json.dumps(errors, indent=2) + "\n")
+    return sources
+
+
+def docker(args, name, *command):
+    return ["docker", "run", "--rm", "--name", name,
+            "-v", f"{Path(args.codeql).resolve()}:/opt/codeql:ro",
+            "-v", f"{Path(args.root).resolve()}:/work", args.image,
+            "/opt/codeql/codeql", *command]
+
+
+def scan_one(args, task):
+    (repo, revision, language), (checkout, domains) = task
+    root = Path(args.root).resolve()
+    slug = repo.replace("/", "__")
+    stem = f"{slug}-{revision[:12]}-{language}"
+    db = root / "dbs" / stem
+    log_dir = root / "logs"
+    result = {"repository": repo, "revision": revision, "language": language,
+              "domains": sorted(domains)}
+    if not (db / f"db-{language}").exists():
+        if db.exists():
+            shutil.rmtree(db)
+        container = f"codeql-create-{stem}".lower()
+        code, seconds = run(docker(args, container, "database", "create", f"/work/dbs/{stem}",
+                                  f"--language={language}", "--build-mode=none",
+                                  f"--source-root=/work/checkouts/{slug}/{revision}",
+                                  "--threads=4", "--ram=4096"),
+                            log_dir / f"{stem}-create.log", args.scan_timeout, container)
+        result["create_seconds"] = seconds
+        if code:
+            result["error"] = f"database create exit {code}"
+            return result
+    for domain in sorted(domains):
+        sarif = root / "sarif" / domain / f"{stem}.sarif"
+        if sarif.exists():
+            continue
+        sarif.parent.mkdir(parents=True, exist_ok=True)
+        suite = "security-extended" if domain == "security" else "security-and-quality"
+        query = (f"/work/packs/codeql/{language}-queries/{PACKS[language]}/"
+                 f"codeql-suites/{language}-{suite}.qls")
+        container = f"codeql-{domain}-{stem}".lower()
+        code, seconds = run(docker(args, container, "database", "analyze", f"/work/dbs/{stem}",
+                                  query, "--format=sarif-latest",
+                                  f"--output=/work/sarif/{domain}/{stem}.sarif",
+                                  "--threads=4", "--ram=4096"),
+                            log_dir / f"{stem}-{domain}-analyze.log", args.scan_timeout,
+                            container)
+        result[f"{domain}_analyze_seconds"] = seconds
+        if code:
+            result["error"] = f"{domain} analyze exit {code}"
+            return result
+    result["ok"] = True
+    return result
+
+
+def scan(args):
+    root = Path(args.root).resolve()
+    (root / "dbs").mkdir(parents=True, exist_ok=True)
+    pairs = selected_pairs(args)
+    prepare_rebench_patches(pairs, root, args.rebench_parquet)
+    sources = prepare_sources(pairs, root)
+    print(f"Fixed cohort: {len(pairs['bug'])} bug pairs, "
+          f"{len(pairs['security'])} security pairs, {len(sources)} databases", flush=True)
+    manifest = {domain: [p["pair_id"] for p in group] for domain, group in pairs.items()}
+    (root / "cohort-pair-ids.json").write_text(json.dumps(manifest, indent=2) + "\n")
+    with concurrent.futures.ThreadPoolExecutor(max_workers=args.jobs) as executor:
+        for result in concurrent.futures.as_completed(
+            [executor.submit(scan_one, args, task) for task in sources.items()]
+        ):
+            item = result.result()
+            with (root / "scan-status.jsonl").open("a", encoding="utf-8") as stream:
+                stream.write(json.dumps(item, sort_keys=True) + "\n")
+            print(f"{'OK' if item.get('ok') else 'FAILED'} "
+                  f"{item['repository']} {item['revision'][:12]} "
+                  f"{','.join(item['domains'])}", flush=True)
+
+
+def method_span(side):
+    lines = [int(match) for match in re.findall(r"(?m)^L(\d+)\|",
+                                                 side["state"]["method"]["source"])]
+    return (min(lines), max(lines)) if lines else None
+
+
+def source_matches(side, source_path):
+    content = source_path.read_text(errors="replace").replace("\r\n", "\n")
+    needle = side["source"].replace("\r\n", "\n").strip()
+    start = content.find(needle)
+    return start >= 0 and content.count("\n", 0, start) + 1 == method_span(side)[0]
+
+
+@lru_cache(maxsize=128)
+def archived_sources(archive):
+    with ZipFile(archive) as zipped:
+        return set(zipped.namelist())
+
+
+def codeql_alert(sarif, side, domain):
+    path = side["path"].lstrip("/")
+    span = method_span(side)
+    if not span:
+        raise ValueError(f"Missing line-numbered method: {path}")
+    data = json.loads(sarif.read_text())
+    alerts = []
+    for run_data in data["runs"]:
+        rule_tags = {
+            rule["id"]: set(rule.get("properties", {}).get("tags", []))
+            for rule in run_data["tool"]["driver"].get("rules", [])
+        }
+        for finding in run_data.get("results", []):
+            tags = rule_tags.get(finding["ruleId"], set())
+            if domain == "security" and "security" not in tags:
+                continue
+            if domain == "bug" and not tags.intersection(
+                ("correctness", "reliability", "security")
+            ):
+                continue
+            for location in finding.get("locations", [])[:1]:
+                physical = location.get("physicalLocation", {})
+                uri = physical.get("artifactLocation", {}).get("uri", "")
+                region = physical.get("region", {})
+                if uri.lstrip("/") != path or "startLine" not in region:
+                    continue
+                start = region["startLine"]
+                end = region.get("endLine", start)
+                if start <= span[1] and end >= span[0]:
+                    alerts.append(finding["ruleId"])
+    return sorted(set(alerts))
+
+
+def metrics(items):
+    items = list(items)
+    tp = sum(label and alert for label, alert in items)
+    fp = sum(not label and alert for label, alert in items)
+    fn = sum(label and not alert for label, alert in items)
+    tn = sum(not label and not alert for label, alert in items)
+    precision = tp / (tp + fp) if tp + fp else None
+    recall = tp / (tp + fn) if tp + fn else 0.0
+    fpr = fp / (fp + tn) if fp + tn else 0.0
+    f1 = (2 * precision * recall / (precision + recall)
+          if precision is not None and precision + recall else 0.0)
+    return {"tp": tp, "fp": fp, "fn": fn, "tn": tn, "precision": precision,
+            "recall": recall, "fpr": fpr, "f1": f1, "recall_minus_fpr": recall - fpr}
+
+
+def score(args):
+    root = Path(args.root).resolve()
+    selected = selected_pairs(args)
+    all_results = {}
+    for domain, group in selected.items():
+        jev = {(r["pair_id"], r["role"]): r for r in
+               rows(Path(args.predictions) / domain / "jev.jsonl")}
+        output = []
+        unavailable = []
+        for pair in group:
+            decisions = []
+            for role in ("before", "after"):
+                side = pair[role]
+                lang = LANGUAGES[pair["language"].lower()]
+                stem = f"{pair['repository'].replace('/', '__')}-{side['revision'][:12]}-{lang}"
+                sarif = root / "sarif" / domain / f"{stem}.sarif"
+                source_path = (root / "checkouts" / pair["repository"].replace("/", "__")
+                               / side["revision"] / side["path"])
+                if not sarif.exists() or (pair["pair_id"], role) not in jev:
+                    reason = ("source snapshot unavailable" if not source_path.exists()
+                              else "CodeQL analysis unavailable" if not sarif.exists()
+                              else "Jev prediction unavailable")
+                    unavailable.append({"pair_id": pair["pair_id"], "role": role,
+                                        "reason": reason})
+                    decisions = []
+                    break
+                archive = root / "dbs" / stem / "src.zip"
+                archived_name = (f"work/checkouts/{pair['repository'].replace('/', '__')}/"
+                                 f"{side['revision']}/{side['path']}")
+                if not source_path.exists():
+                    unavailable.append({"pair_id": pair["pair_id"], "role": role,
+                                        "reason": "source snapshot unavailable"})
+                    decisions = []
+                    break
+                if (not archive.exists()
+                        or archived_name not in archived_sources(archive)
+                        or not source_matches(side, source_path)):
+                    unavailable.append({"pair_id": pair["pair_id"], "role": role,
+                                        "reason": "target source not verified in CodeQL database"})
+                    decisions = []
+                    break
+                rules = codeql_alert(sarif, side, domain)
+                label = int(side["labels"][domain])
+                decisions.append({"role": role, "label": label, "codeql_alert": bool(rules),
+                                  "codeql_rules": rules,
+                                  "jev_alert": bool(jev[(pair["pair_id"], role)]["alert"]),
+                                  "jev_score": jev[(pair["pair_id"], role)]["score"]})
+            if decisions:
+                output.append({"pair_id": pair["pair_id"], "repository": pair["repository"],
+                               "language": pair["language"], "decisions": decisions})
+        model_scores = {}
+        for model in ("codeql", "jev"):
+            model_scores[model] = metrics(
+                (d["label"], d[f"{model}_alert"]) for row in output for d in row["decisions"]
+            )
+        all_results[domain] = {"pairs": len(output), "requested_pairs": len(group),
+                               "missing_sides": unavailable, "models": model_scores}
+        out = root / f"{domain}-codeql-comparison.jsonl"
+        out.write_text("".join(json.dumps(r, sort_keys=True) + "\n" for r in output))
+    (root / "codeql-comparison-results.json").write_text(
+        json.dumps(all_results, indent=2, sort_keys=True) + "\n"
+    )
+    print(json.dumps(all_results, indent=2))
+
+
+def main():
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("operation", choices=("scan", "score"))
+    parser.add_argument("--root", required=True)
+    parser.add_argument("--data", required=True, help="directory with bug/security/benchmark.jsonl")
+    parser.add_argument("--predictions", required=True, help="directory with bug/security/jev.jsonl")
+    parser.add_argument("--cohort", default=str(Path(__file__).with_name("codeql-cohort.json")))
+    parser.add_argument("--codeql", help="unpacked CodeQL CLI directory")
+    parser.add_argument("--rebench-parquet", help="SWE-rebench-V2 source Parquet with gold patches")
+    parser.add_argument("--image", default="node:22-bookworm")
+    parser.add_argument("--jobs", type=int, default=4)
+    parser.add_argument("--scan-timeout", type=int, default=600,
+                        help="seconds allowed per CodeQL database or analysis stage")
+    args = parser.parse_args()
+    if args.operation == "scan":
+        if not args.codeql:
+            parser.error("--codeql is required for scanning")
+        scan(args)
+    else:
+        score(args)
+
+
+if __name__ == "__main__":
+    main()

test_codeql_compare.py

@@ -0,0 +1,57 @@
+import json
+import sys
+import tempfile
+import unittest
+from pathlib import Path
+
+from codeql_compare import codeql_alert, method_span, metrics, run
+
+
+class CodeQLComparisonTests(unittest.TestCase):
+    def test_alert_requires_primary_location_inside_method_and_relevant_tag(self):
+        side = {
+            "path": "src/example.py",
+            "state": {"method": {"source": "L0010| def check():\nL0011|     return 1"}},
+        }
+        sarif = {
+            "runs": [{
+                "tool": {"driver": {"rules": [
+                    {"id": "py/security", "properties": {"tags": ["security"]}},
+                    {"id": "py/style", "properties": {"tags": ["maintainability"]}},
+                ]}},
+                "results": [
+                    {"ruleId": "py/security", "locations": [{"physicalLocation": {
+                        "artifactLocation": {"uri": "src/example.py"},
+                        "region": {"startLine": 11}}}]},
+                    {"ruleId": "py/security", "locations": [{"physicalLocation": {
+                        "artifactLocation": {"uri": "src/example.py"},
+                        "region": {"startLine": 30}}}]},
+                    {"ruleId": "py/style", "locations": [{"physicalLocation": {
+                        "artifactLocation": {"uri": "src/example.py"},
+                        "region": {"startLine": 10}}}]},
+                ],
+            }],
+        }
+        with tempfile.TemporaryDirectory() as directory:
+            file = Path(directory) / "result.sarif"
+            file.write_text(json.dumps(sarif))
+            self.assertEqual(method_span(side), (10, 11))
+            self.assertEqual(codeql_alert(file, side, "security"), ["py/security"])
+            self.assertEqual(codeql_alert(file, side, "bug"), ["py/security"])
+
+    def test_counts_include_false_negatives_and_clean_methods(self):
+        result = metrics(iter([(1, True), (1, False), (0, True), (0, False)]))
+        self.assertEqual([result[key] for key in ("tp", "fp", "fn", "tn")],
+                         [1, 1, 1, 1])
+        self.assertEqual(result["f1"], 0.5)
+        self.assertIsNone(metrics([(1, False), (0, False)])["precision"])
+
+    def test_scan_stage_has_bounded_runtime(self):
+        with tempfile.TemporaryDirectory() as directory:
+            code, _ = run([sys.executable, "-c", "import time; time.sleep(2)"],
+                          Path(directory) / "stage.log", timeout=0.1)
+            self.assertEqual(code, 124)
+
+
+if __name__ == "__main__":
+    unittest.main()