\\n

📝 Walkthrough

\\n\\n\\n\\n## Walkthrough\\n\\nAdds a `classify-store` second pipeline stage to leakmine: `mine.classify_from_store` reads PR candidates from an existing SQLite store, fetches patch diffs, runs `signals.classify`, and writes `classifier='patch'` labels. A matching CLI subcommand is wired, the bare `\\\"oom\\\"` keyword is removed from signals, and docs/tests/gitignore are updated.\\n\\n## Changes\\n\\n**leakmine classify-store pipeline stage**\\n\\n| Layer / File(s) | Summary |\\n|---|---|\\n| **Remove bare `oom` keyword from signals**
`leakmine/signals.py`, `leakmine/tests/test_leakmine.py` | Removes `\\\"oom\\\"` substring from `Ecosystem.keywords` default, retaining `\\\"out of memory\\\"`, and adds `test_signals_no_oom_substring_noise` asserting substring noise no longer triggers leak-keyword evidence. |\\n| **`classify_from_store` core orchestration**
`leakmine/mine.py`, `leakmine/tests/test_leakmine.py` | Introduces `classify_from_store`: reads PR candidates from SQLite by ecosystem, fetches each patch diff, runs `signals.classify`, filters by `min_score`, updates `MineResult` counters/rows, and persists patch-tier labels via `schema.insert_label`. `test_classify_from_store` seeds two candidates, supplies a fake fetcher, and asserts `seen/fetched/kept` counts and one stored label. |\\n| **CLI `classify-store` subcommand**
`leakmine/cli.py` | Adds `cmd_classify_store` and registers `classify-store` in `main()` with `--store`, `--ecosystem`, `--min-score`, `--sleep`, `--limit`, `--out-dir`, `--token`; writes `classified.json` and `summary.md` to `out_dir`. |\\n| **Docs and gitignore**
`docs/leakfix-mine.md`, `.gitignore` | Updates pipeline docs to describe the two-stage flow and adds `classify-store` CLI example; adds gitignore patterns for `leakmine-out/`, `bq-out/`, `ch-out/`, `*-leakmine-out/`. |\\n\\n## Estimated code review effort\\n\\n🎯 3 (Moderate) | ⏱️ ~20 minutes\\n\\n## Possibly related PRs\\n\\n- [PhysShell/OwnAudit#24](https://github.com/PhysShell/OwnAudit/pull/24): Overlaps at `leakmine/signals.py` and the CLI/test modules that this PR extends with the classify-store stage.\\n- [PhysShell/OwnAudit#25](https://github.com/PhysShell/OwnAudit/pull/25): Adds `mine.run()` and the `mine` CLI stage that produces the SQLite store consumed by the new `classify_from_store`.\\n\\n## Poem\\n\\n> 🐇 Hop, hop — no more \\\"oom\\\" ghost in the night,\\n> The patch queue now closes with classify right.\\n> We fetch every diff, score each fix with care,\\n> Insert the patch label — a label most fair.\\n> The store is now whole, from ingest to end,\\n> A two-stage pipeline this rabbit will tend! 🌿\\n\\n

\\n\\n\\n\\n\\n

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🚥 Pre-merge checks | ✅ 4 | ❌ 1

\\n\\n### ❌ Failed checks (1 warning)\\n\\n| Check name | Status | Explanation | Resolution |\\n| :----------------: | :--------- | :------------------------------------------------------------------------------------ | :--------------------------------------------------------------------------------- |\\n| Docstring Coverage | ⚠️ Warning | Docstring coverage is 18.18% which is insufficient. The required threshold is 80.00%. | Write docstrings for the functions missing them to satisfy the coverage threshold. |\\n\\n

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✅ Passed checks (4 passed)

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\\n\\n\\n\\n\\n

\\n

✨ Finishing Touches

\\n\\n

\\n

📝 Generate docstrings

\\n\\n- [ ] Create stacked PR\\n- [ ] Commit on current branch\\n\\n

\\n

🧪 Generate unit tests (beta)

\\n\\n- [ ] Create PR with unit tests\\n- [ ] Commit unit tests in branch `claude/own-language-market-research-jgrrgm`\\n\\n

\\n\\n

\\n\\n\\n\\n\\n---\\n\\n\\n\\n\\n_{Comment `@coderabbitai help` to get the list of available commands.}\\n\\n\",\"path\":null,\"side\":null,\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"**_{_{![P2 Badge](https://img.shields.io/badge/P2-yellow?style=flat)}} Skip processed PRs before applying classify-store limits**\\n\\nWhen `classify-store` is rerun, for example after an interruption or to process a large BigQuery queue in `--limit`-sized batches, this query selects every PR in the ecosystem again. The loop then inserts another `classifier='patch'` label for kept rows and records nothing for below-threshold rows, so repeated limited runs keep burning the GitHub diff quota on the same first candidates instead of advancing through the queue. Filter or mark processed candidates, including misses, before applying the limit.\\n\\nUseful? React with 👍 / 👎.\",\"path\":\"leakmine/mine.py\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"\\n### 💡 Codex Review\\n\\nHere are some automated review suggestions for this pull request.\\n\\n**Reviewed commit:** `68c97760e8`\\n \\n\\n

ℹ️ About Codex in GitHub

\\n
\\n\\n[Your team has set up Codex to review pull requests in this repo](https://chatgpt.com/codex/cloud/settings/general). Reviews are triggered when you\\n- Open a pull request for review\\n- Mark a draft as ready\\n- Comment \\\"@codex review\\\".\\n\\nIf Codex has suggestions, it will comment; otherwise it will react with 👍.\\n\\n\\n\\n\\nCodex can also answer questions or update the PR. Try commenting \\\"@codex address that feedback\\\".\\n \\n

\",\"path\":null,\"side\":null,\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"_🗄️ Data Integrity & Integration_ | _🟠 Major_ | _⚡ Quick win_\\n\\n**Only queue candidates that still need a patch verdict.**\\n\\n`run()` already writes `classifier='patch'` labels, but this query reselects every PR in the store. Re-running `classify-store` against a `mine` or previously classified DB will refetch the same diffs and either append duplicate patch labels or fail on a uniqueness constraint. Because it also calls `fetchall()`, `--limit` cannot stop the initial full-table load. Filter out rows that already have a patch label and stream/limit the SQL result instead.\\n\\n

\\n

Suggested query shape

\\n\\n```diff\\n- cur = conn.execute(\\n- \\\"SELECT repo, number, title, body FROM candidates WHERE ecosystem=? AND kind='pr'\\\",\\n- (eco_key,),\\n- )\\n- for repo, number, title, body in cur.fetchall():\\n- if limit is not None and res.seen >= limit:\\n- break\\n+ sql = \\\"\\\"\\\"\\n+ SELECT c.repo, c.number, c.title, c.body\\n+ FROM candidates AS c\\n+ LEFT JOIN labels AS l\\n+ ON l.candidate_id = c.id AND l.classifier = 'patch'\\n+ WHERE c.ecosystem=? AND c.kind='pr' AND l.candidate_id IS NULL\\n+ ORDER BY c.id\\n+ \\\"\\\"\\\"\\n+ params = [eco_key]\\n+ if limit is not None:\\n+ sql += \\\" LIMIT ?\\\"\\n+ params.append(limit)\\n+ for repo, number, title, body in conn.execute(sql, params):\\n```\\n

\\n\\n\\n\\n

\\n

📝 Committable suggestion

\\n\\n> ‼️ **IMPORTANT**\\n> Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.\\n\\n```suggestion\\n sql = \\\"\\\"\\\"\\n SELECT c.repo, c.number, c.title, c.body\\n FROM candidates AS c\\n LEFT JOIN labels AS l\\n ON l.candidate_id = c.id AND l.classifier = 'patch'\\n WHERE c.ecosystem=? AND c.kind='pr' AND l.candidate_id IS NULL\\n ORDER BY c.id\\n \\\"\\\"\\\"\\n params = [eco_key]\\n if limit is not None:\\n sql += \\\" LIMIT ?\\\"\\n params.append(limit)\\n for repo, number, title, body in conn.execute(sql, params):\\n res.seen += 1\\n patch = fetch_patch(repo, number, token=token)\\n if sleep:\\n time.sleep(sleep)\\n if not patch:\\n continue\\n res.fetched += 1\\n cls = signals.classify(eco_key, title=title or \\\"\\\", body=body or \\\"\\\", patch=patch)\\n if cls.score < min_score:\\n continue\\n res.kept += 1\\n res.rows.append({\\n \\\"ecosystem\\\": eco_key, \\\"repo\\\": repo, \\\"number\\\": number,\\n \\\"title\\\": title, \\\"category\\\": cls.category, \\\"score\\\": cls.score,\\n \\\"is_likely_fix\\\": cls.is_likely_fix, \\\"evidence\\\": cls.evidence,\\n })\\n schema.insert_label(conn, f\\\"{repo}#{number}\\\", cls.category, cls.score,\\n cls.evidence, \\\"patch\\\")\\n```\\n\\n

\\n\\n\\n\\n

\\n

🤖 Prompt for AI Agents

\\n\\n```\\nVerify each finding against current code. Fix only still-valid issues, skip the\\nrest with a brief reason, keep changes minimal, and validate.\\n\\nIn `@leakmine/mine.py` around lines 149 - 173, The PR selection in run() is\\nreprocessing every candidate, including ones that already have a patch verdict,\\nwhich can create duplicate patch labels or hit uniqueness errors. Update the SQL\\nin the candidates query to exclude rows that already have a patch label (for\\nexample by checking the labels store for classifier='patch' / verdict='patch'),\\nand stop using fetchall() so the loop can stream rows and respect --limit\\nwithout loading the full table first. Keep the rest of the classification flow\\nin run() and schema.insert_label unchanged.\\n```\\n\\n

\\n\\n\\n\\n\\n\\n\\n\\n\",\"path\":\"leakmine/mine.py\",\"side\":\"RIGHT\",\"line\":null}{\"type\":\"pull_request_comment\",\"body\":\"**Actionable comments posted: 1**\\n\\n

\\n

🤖 Prompt for all review comments with AI agents

\\n\\n```\\nVerify each finding against current code. Fix only still-valid issues, skip the\\nrest with a brief reason, keep changes minimal, and validate.\\n\\nInline comments:\\nIn `@leakmine/mine.py`:\\n- Around line 149-173: The PR selection in run() is reprocessing every\\ncandidate, including ones that already have a patch verdict, which can create\\nduplicate patch labels or hit uniqueness errors. Update the SQL in the\\ncandidates query to exclude rows that already have a patch label (for example by\\nchecking the labels store for classifier='patch' / verdict='patch'), and stop\\nusing fetchall() so the loop can stream rows and respect --limit without loading\\nthe full table first. Keep the rest of the classification flow in run() and\\nschema.insert_label unchanged.\\n```\\n\\n

\\n\\n

\\n

🪄 Autofix (Beta)

\\n\\nFix all unresolved CodeRabbit comments on this PR:\\n\\n- [ ] Push a commit to this branch (recommended)\\n- [ ] Create a new PR with the fixes\\n\\n

\\n\\n---\\n\\n

\\n

ℹ️ Review info

\\n\\n

\\n

⚙️ Run configuration

\\n\\n**Configuration used**: defaults\\n\\n**Review profile**: CHILL\\n\\n**Plan**: Pro Plus\\n\\n**Run ID**: `68abfcb6-be2a-4bfe-baf0-b0f2011ba56b`\\n\\n

\\n\\n

\\n

📥 Commits

\\n\\nReviewing files that changed from the base of the PR and between a400c0da7450952c0e6db4fbb21537faec7cd4d3 and 68c97760e87aa7f1099108b8b64bdcd2b292ac23.\\n\\n

\\n\\n

\\n

📒 Files selected for processing (6)

\\n\\n* `.gitignore`\\n* `docs/leakfix-mine.md`\\n* `leakmine/cli.py`\\n* `leakmine/mine.py`\\n* `leakmine/signals.py`\\n* `leakmine/tests/test_leakmine.py`\\n\\n

\\n\\n

\\n\\n\",\"path\":null,\"side\":null,\"line\":null}","text_elements",[],{"_398":585,"_379":380,"_400":386},{"_401":586,"_403":-5,"_42":-5,"_404":-5,"_405":-5,"_96":326,"_92":407},[587],{"_46":581,"_92":588},"input_text",{"_398":590,"_379":380,"_400":386},{"_401":591,"_403":-5,"_42":-5,"_404":-5,"_405":-5,"_96":326,"_92":407},[592],{"_46":593,"_92":588},"\n /workspace/OwnAudit\n bash\n 2026-06-28\n Etc/UTC\n",{"_398":595,"_379":380,"_400":386},{"_401":596,"_403":-5,"_42":-5,"_404":-5,"_405":-5,"_96":597,"_92":407},[598,599],"developer",{"_46":601,"_92":588},{"_46":600,"_92":588},"\n## Skills\nA skill is a set of local instructions to follow that is stored in a `SKILL.md` file. Below is the list of skills that can be used. Each entry includes a name, description, and file path so you can open the source for full instructions when using a specific skill.\n### Available skills\n- imagegen: Generate or edit raster images when the task benefits from AI-created bitmap visuals such as photos, illustrations, textures, sprites, mockups, or transparent-background cutouts. Use when Codex should create a brand-new image, transform an existing image, or derive visual variants from references, and the output should be a bitmap asset rather than repo-native code or vector. Do not use when the task is better handled by editing existing SVG/vector/code-native assets, extending an established icon or logo system, or building the visual directly in HTML/CSS/canvas. (file: /opt/codex/skills/.system/imagegen/SKILL.md)\n- openai-docs: Use when the user asks how to build with OpenAI products or APIs and needs up-to-date official documentation with citations, help choosing the latest model for a use case, or model upgrade and prompt-upgrade guidance; prioritize OpenAI docs MCP tools, use bundled references only as helper context, and restrict any fallback browsing to official OpenAI domains. (file: /opt/codex/skills/.system/openai-docs/SKILL.md)\n- plugin-creator: Create and scaffold plugin directories for Codex with a required `.codex-plugin/plugin.json`, optional plugin folders/files, and baseline placeholders you can edit before publishing or testing. Use when Codex needs to create a new local plugin, add optional plugin structure, or generate or update repo-root `.agents/plugins/marketplace.json` entries for plugin ordering and availability metadata. (file: /opt/codex/skills/.system/plugin-creator/SKILL.md)\n- skill-creator: Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Codex's capabilities with specialized knowledge, workflows, or tool integrations. (file: /opt/codex/skills/.system/skill-creator/SKILL.md)\n- skill-installer: Install Codex skills into $CODEX_HOME/skills from a curated list or a GitHub repo path. Use when a user asks to list installable skills, install a curated skill, or install a skill from another repo (including private repos). (file: /opt/codex/skills/.system/skill-installer/SKILL.md)\n### How to use skills\n- Discovery: The list above is the skills available in this session (name + description + file path). Skill bodies live on disk at the listed paths.\n- Trigger rules: If the user names a skill (with `$SkillName` or plain text) OR the task clearly matches a skill's description shown above, you must use that skill for that turn. Multiple mentions mean use them all. Do not carry skills across turns unless re-mentioned.\n- Missing/blocked: If a named skill isn't in the list or the path can't be read, say so briefly and continue with the best fallback.\n- How to use a skill (progressive disclosure):\n 1) After deciding to use a skill, open its `SKILL.md`. Read only enough to follow the workflow.\n 2) When `SKILL.md` references relative paths (e.g., `scripts/foo.py`), resolve them relative to the skill directory listed above first, and only consider other paths if needed.\n 3) If `SKILL.md` points to extra folders such as `references/`, load only the specific files needed for the request; don't bulk-load everything.\n 4) If `scripts/` exist, prefer running or patching them instead of retyping large code blocks.\n 5) If `assets/` or templates exist, reuse them instead of recreating from scratch.\n- Coordination and sequencing:\n - If multiple skills apply, choose the minimal set that covers the request and state the order you'll use them.\n - Announce which skill(s) you're using and why (one short line). If you skip an obvious skill, say why.\n- Context hygiene:\n - Keep context small: summarize long sections instead of pasting them; only load extra files when needed.\n - Avoid deep reference-chasing: prefer opening only files directly linked from `SKILL.md` unless you're blocked.\n - When variants exist (frameworks, providers, domains), pick only the relevant reference file(s) and note that choice.\n- Safety and fallback: If a skill can't be applied cleanly (missing files, unclear instructions), state the issue, pick the next-best approach, and continue.\n","\nFilesystem sandboxing defines which files can be read or written. `sandbox_mode` is `danger-full-access`: No filesystem sandboxing - all commands are permitted. Network access is enabled.\nApproval policy is currently never. Do not provide the `sandbox_permissions` for any reason, commands will be rejected.\n","turn/started",{"_379":380,"_87":604},{"_103":-5,"_42":386,"_387":605,"_389":390,"_391":606},[],"inProgress",{"_391":608,"_379":380},{"_609":610,"_92":611},"activeFlags",[],"active","thread/started",{"_614":615},"thread",{"_616":-5,"_617":-5,"_618":619,"_620":621,"_446":447,"_622":15,"_623":-5,"_624":-5,"_625":-5,"_626":627,"_42":380,"_628":629,"_181":-5,"_630":-5,"_161":631,"_632":199,"_633":-5,"_451":634,"_391":635,"_636":-5,"_77":637,"_638":621},"agentNickname","agentRole","cliVersion","0.128.0","createdAt",1782624976,"ephemeral","extra","forkedFromId","gitInfo","historyMode","legacy","modelProvider","openai","parentThreadId","/opt/codex/sessions/2026/06/28/rollout-2026-06-28T05-36-16-019f0cba-7fff-7ef0-a10d-a4d467e14ecf.jsonl","preview","recencyAt","vscode",{"_92":395},"threadSource",[],"updatedAt",[],"messages",[642],{"_42":643,"_644":645,"_646":647,"_648":647,"_401":649,"_391":650,"_403":-5,"_651":32,"_652":653,"_654":655,"_656":-5},"e402954f-66a6-45c4-8472-ae236154ce7e","author",{"_96":326,"_181":-5,"_652":665},"create_time",1782624976.061932,"update_time",{"_661":46,"_662":663},"finished_successfully","weight","metadata",{"_657":658},"recipient","all","channel","l1239dk1",{"_659":660},"inline_comments",[],"content_type","parts",[664],"Good catch (both @coderabbitai and @chatgpt-codex-connector flagged it) — fixed in a568293. `classify_from_store` is now **resumable**:\n\n- The candidate query is an **anti-join** — `LEFT JOIN labels ... AND l.classifier='patch' WHERE l.candidate_id IS NULL` — so already-attempted PRs are excluded in SQL, and `--limit` is pushed into the query (`ORDER BY c.id` for stable batch order). Reruns/batches stream only the unprocessed head; no full-table `fetchall()`, no re-burned diff quota, no duplicate labels.\n- Every attempt is labelled at the patch tier so all states are skipped next run: the real category when kept, **`below-threshold`** for a fetched low-score miss, **`fetch-failed`** when no diff came back (delete those to retry).\n\nAdded a resume assertion: a second run processes nothing and re-fetches no diffs. 33 tests pass under `python3` and `-O`.\n\n---\n_Generated by [Claude Code](https://claude.ai/code)_\nleakmine: drop noisy \"oom\" keyword + classify-store (queue → patch-tier verdict)\n\n## What\n\nTwo changes, both driven by the live ClickHouse run we just did (1065 real 2024 PRs mined with zero GCP/auth):\n\n### (a) Drop the noisy `\"oom\"` keyword\nThe live run exposed a real defect in our own keyword list. Leak keywords are matched as **substrings** — in `signals.classify`/`metadata_score` (Python `in`) *and* in the BigQuery/ClickHouse discovery SQL — so bare `\"oom\"` (for \"out of memory\") matched **zoom / room / doom / bloom**. It accounted for **646 of 947** kept rows in the real run (~68% junk). Removed it (`\"out of memory\"` carries the meaning safely) and documented the keyword list as substring-unsafe.\n\n### (b) `classify-store` — close the loop from queue to verdict\n`bq-ingest` gives a **metadata-tier queue** (title/body keyword + PR size, no diff → no category). The new `mine.classify_from_store` + `classify-store` CLI takes those stored candidates, **fetches each diff** (`collect.fetch_patch`), and runs the **real** `signals.classify` (title+body+patch) → category + patch-signal score, writing a `classifier='patch'` label. The metadata tier was the queue; this is the verdict.\n\n```\nbq-ingest -> store (metadata queue) -> classify-store -> patch-tier verdict\n```\n\nNetwork is isolated behind the injected `fetch_patch`, so it unit-tests offline (CI never reaches out); run it with `$GITHUB_TOKEN` for the 5000/hr REST limit.\n\n## Also\n- `.gitignore` the generated mining out-dirs (`leakmine-out/`, `bq-out/`, `ch-out/`).\n- docs/leakfix-mine.md §14 updated with the `classify-store` step.\n\n## Tests / CI\n33 tests pass under `python3` and `python3 -O` (+2: `\"oom\"` no longer matches zoom/room; `classify_from_store` fetches → classifies → labels with dedup/score-filter). Existing suite green.\n\n🤖 Generated with [Claude Code](https://claude.com/claude-code)\n\n---\n_Generated by [Claude Code](https://claude.ai/code/session_01W6Lbeeoqy7v3wjzV43iLun)_\n\n\n\n## Summary by CodeRabbit\n\n* **New Features**\n * Added a new command to classify stored PR candidates after patch diffs are fetched, with output summaries saved for review.\n * Expanded the pipeline docs with a clearer step-by-step example and a new CLI invocation.\n\n* **Bug Fixes**\n * Improved keyword matching so unrelated text no longer triggers leak-related results from a loose “oom” match.\n * Updated ignored files to avoid checking in local leak-mining run outputs.\n\n\n\n\n\n[![Review Change Stack](https://storage.googleapis.com/coderabbit_public_assets/review-stack-in-coderabbit-ui.svg)](https://app.coderabbit.ai/change-stack/PhysShell/OwnAudit/pull/27?utm_source=github_walkthrough&utm_medium=github&utm_campaign=change_stack)\n\n\n\n\n

📝 Walkthrough

\n\n\n\n## Walkthrough\n\nAdds a `classify-store` second pipeline stage to leakmine: `mine.classify_from_store` reads PR candidates from an existing SQLite store, fetches patch diffs, runs `signals.classify`, and writes `classifier='patch'` labels. A matching CLI subcommand is wired, the bare `\"oom\"` keyword is removed from signals, and docs/tests/gitignore are updated.\n\n## Changes\n\n**leakmine classify-store pipeline stage**\n\n| Layer / File(s) | Summary |\n|---|---|\n| **Remove bare `oom` keyword from signals**
`leakmine/signals.py`, `leakmine/tests/test_leakmine.py` | Removes `\"oom\"` substring from `Ecosystem.keywords` default, retaining `\"out of memory\"`, and adds `test_signals_no_oom_substring_noise` asserting substring noise no longer triggers leak-keyword evidence. |\n| **`classify_from_store` core orchestration**
`leakmine/mine.py`, `leakmine/tests/test_leakmine.py` | Introduces `classify_from_store`: reads PR candidates from SQLite by ecosystem, fetches each patch diff, runs `signals.classify`, filters by `min_score`, updates `MineResult` counters/rows, and persists patch-tier labels via `schema.insert_label`. `test_classify_from_store` seeds two candidates, supplies a fake fetcher, and asserts `seen/fetched/kept` counts and one stored label. |\n| **CLI `classify-store` subcommand**
`leakmine/cli.py` | Adds `cmd_classify_store` and registers `classify-store` in `main()` with `--store`, `--ecosystem`, `--min-score`, `--sleep`, `--limit`, `--out-dir`, `--token`; writes `classified.json` and `summary.md` to `out_dir`. |\n| **Docs and gitignore**
`docs/leakfix-mine.md`, `.gitignore` | Updates pipeline docs to describe the two-stage flow and adds `classify-store` CLI example; adds gitignore patterns for `leakmine-out/`, `bq-out/`, `ch-out/`, `*-leakmine-out/`. |\n\n## Estimated code review effort\n\n🎯 3 (Moderate) | ⏱️ ~20 minutes\n\n## Possibly related PRs\n\n- [PhysShell/OwnAudit#24](https://github.com/PhysShell/OwnAudit/pull/24): Overlaps at `leakmine/signals.py` and the CLI/test modules that this PR extends with the classify-store stage.\n- [PhysShell/OwnAudit#25](https://github.com/PhysShell/OwnAudit/pull/25): Adds `mine.run()` and the `mine` CLI stage that produces the SQLite store consumed by the new `classify_from_store`.\n\n## Poem\n\n> 🐇 Hop, hop — no more \"oom\" ghost in the night,\n> The patch queue now closes with classify right.\n> We fetch every diff, score each fix with care,\n> Insert the patch label — a label most fair.\n> The store is now whole, from ingest to end,\n> A two-stage pipeline this rabbit will tend! 🌿\n\n

\n\n\n\n\n

🚥 Pre-merge checks | ✅ 4 | ❌ 1

\n\n### ❌ Failed checks (1 warning)\n\n| Check name | Status | Explanation | Resolution |\n| :----------------: | :--------- | :------------------------------------------------------------------------------------ | :--------------------------------------------------------------------------------- |\n| Docstring Coverage | ⚠️ Warning | Docstring coverage is 18.18% which is insufficient. The required threshold is 80.00%. | Write docstrings for the functions missing them to satisfy the coverage threshold. |\n\n

✅ Passed checks (4 passed)

\n\n

\n\n\n\n\n

✨ Finishing Touches

\n\n

📝 Generate docstrings

\n\n- [ ] Create stacked PR\n- [ ] Commit on current branch\n\n

🧪 Generate unit tests (beta)

\n\n- [ ] Create PR with unit tests\n- [ ] Commit unit tests in branch `claude/own-language-market-research-jgrrgm`\n\n

\n\n

\n\n\n\n\n---\n\n\n\n\n_{Comment `@coderabbitai help` to get the list of available commands.}\n\n\n**_{_{![P2 Badge](https://img.shields.io/badge/P2-yellow?style=flat)}} Skip processed PRs before applying classify-store limits**\n\nWhen `classify-store` is rerun, for example after an interruption or to process a large BigQuery queue in `--limit`-sized batches, this query selects every PR in the ecosystem again. The loop then inserts another `classifier='patch'` label for kept rows and records nothing for below-threshold rows, so repeated limited runs keep burning the GitHub diff quota on the same first candidates instead of advancing through the queue. Filter or mark processed candidates, including misses, before applying the limit.\n\nUseful? React with 👍 / 👎.\n\n### 💡 Codex Review\n\nHere are some automated review suggestions for this pull request.\n\n**Reviewed commit:** `68c97760e8`\n \n\n

ℹ️ About Codex in GitHub

\n
\n\n[Your team has set up Codex to review pull requests in this repo](https://chatgpt.com/codex/cloud/settings/general). Reviews are triggered when you\n- Open a pull request for review\n- Mark a draft as ready\n- Comment \"@codex review\".\n\nIf Codex has suggestions, it will comment; otherwise it will react with 👍.\n\n\n\n\nCodex can also answer questions or update the PR. Try commenting \"@codex address that feedback\".\n \n

\n_🗄️ Data Integrity & Integration_ | _🟠 Major_ | _⚡ Quick win_\n\n**Only queue candidates that still need a patch verdict.**\n\n`run()` already writes `classifier='patch'` labels, but this query reselects every PR in the store. Re-running `classify-store` against a `mine` or previously classified DB will refetch the same diffs and either append duplicate patch labels or fail on a uniqueness constraint. Because it also calls `fetchall()`, `--limit` cannot stop the initial full-table load. Filter out rows that already have a patch label and stream/limit the SQL result instead.\n\n

Suggested query shape

\n\n```diff\n- cur = conn.execute(\n- \"SELECT repo, number, title, body FROM candidates WHERE ecosystem=? AND kind='pr'\",\n- (eco_key,),\n- )\n- for repo, number, title, body in cur.fetchall():\n- if limit is not None and res.seen >= limit:\n- break\n+ sql = \"\"\"\n+ SELECT c.repo, c.number, c.title, c.body\n+ FROM candidates AS c\n+ LEFT JOIN labels AS l\n+ ON l.candidate_id = c.id AND l.classifier = 'patch'\n+ WHERE c.ecosystem=? AND c.kind='pr' AND l.candidate_id IS NULL\n+ ORDER BY c.id\n+ \"\"\"\n+ params = [eco_key]\n+ if limit is not None:\n+ sql += \" LIMIT ?\"\n+ params.append(limit)\n+ for repo, number, title, body in conn.execute(sql, params):\n```\n

\n\n\n\n

📝 Committable suggestion

\n\n> ‼️ **IMPORTANT**\n> Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.\n\n```suggestion\n sql = \"\"\"\n SELECT c.repo, c.number, c.title, c.body\n FROM candidates AS c\n LEFT JOIN labels AS l\n ON l.candidate_id = c.id AND l.classifier = 'patch'\n WHERE c.ecosystem=? AND c.kind='pr' AND l.candidate_id IS NULL\n ORDER BY c.id\n \"\"\"\n params = [eco_key]\n if limit is not None:\n sql += \" LIMIT ?\"\n params.append(limit)\n for repo, number, title, body in conn.execute(sql, params):\n res.seen += 1\n patch = fetch_patch(repo, number, token=token)\n if sleep:\n time.sleep(sleep)\n if not patch:\n continue\n res.fetched += 1\n cls = signals.classify(eco_key, title=title or \"\", body=body or \"\", patch=patch)\n if cls.score < min_score:\n continue\n res.kept += 1\n res.rows.append({\n \"ecosystem\": eco_key, \"repo\": repo, \"number\": number,\n \"title\": title, \"category\": cls.category, \"score\": cls.score,\n \"is_likely_fix\": cls.is_likely_fix, \"evidence\": cls.evidence,\n })\n schema.insert_label(conn, f\"{repo}#{number}\", cls.category, cls.score,\n cls.evidence, \"patch\")\n```\n\n

\n\n\n\n

🤖 Prompt for AI Agents

\n\n```\nVerify each finding against current code. Fix only still-valid issues, skip the\nrest with a brief reason, keep changes minimal, and validate.\n\nIn `@leakmine/mine.py` around lines 149 - 173, The PR selection in run() is\nreprocessing every candidate, including ones that already have a patch verdict,\nwhich can create duplicate patch labels or hit uniqueness errors. Update the SQL\nin the candidates query to exclude rows that already have a patch label (for\nexample by checking the labels store for classifier='patch' / verdict='patch'),\nand stop using fetchall() so the loop can stream rows and respect --limit\nwithout loading the full table first. Keep the rest of the classification flow\nin run() and schema.insert_label unchanged.\n```\n\n

\n\n\n\n\n\n\n\n\n**Actionable comments posted: 1**\n\n

🤖 Prompt for all review comments with AI agents

\n\n```\nVerify each finding against current code. Fix only still-valid issues, skip the\nrest with a brief reason, keep changes minimal, and validate.\n\nInline comments:\nIn `@leakmine/mine.py`:\n- Around line 149-173: The PR selection in run() is reprocessing every\ncandidate, including ones that already have a patch verdict, which can create\nduplicate patch labels or hit uniqueness errors. Update the SQL in the\ncandidates query to exclude rows that already have a patch label (for example by\nchecking the labels store for classifier='patch' / verdict='patch'), and stop\nusing fetchall() so the loop can stream rows and respect --limit without loading\nthe full table first. Keep the rest of the classification flow in run() and\nschema.insert_label unchanged.\n```\n\n

\n\n

🪄 Autofix (Beta)

\n\nFix all unresolved CodeRabbit comments on this PR:\n\n- [ ] Push a commit to this branch (recommended)\n- [ ] Create a new PR with the fixes\n\n

\n\n---\n\n

ℹ️ Review info

\n\n

⚙️ Run configuration

\n\n**Configuration used**: defaults\n\n**Review profile**: CHILL\n\n**Plan**: Pro Plus\n\n**Run ID**: `68abfcb6-be2a-4bfe-baf0-b0f2011ba56b`\n\n

\n\n

📥 Commits

\n\nReviewing files that changed from the base of the PR and between a400c0da7450952c0e6db4fbb21537faec7cd4d3 and 68c97760e87aa7f1099108b8b64bdcd2b292ac23.\n\n

\n\n

📒 Files selected for processing (6)

\n\n* `.gitignore`\n* `docs/leakfix-mine.md`\n* `leakmine/cli.py`\n* `leakmine/mine.py`\n* `leakmine/signals.py`\n* `leakmine/tests/test_leakmine.py`\n\n

\n\n

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Bare python3 or pytest:"," PYTHONPATH=. python3 leakmine/tests/test_leakmine.py","Covers the honest core: diff parsing, patch-signal classification (incl. penalties), SZZ","attribution + before/after correspondence + lead-time over a REAL temp git repo, the","verdict combiner (unique catch / unique miss), metrics aggregation, the over-vetted sweep","selection, and deterministic query/SQL generation. -O-safe (explicit raises, no bare assert).","\"\"\"","import json","import os","import sqlite3","import subprocess","import sys","import tempfile","HERE = os.path.dirname(os.path.abspath(__file__))","ROOT = os.path.dirname(os.path.dirname(HERE))","sys.path.insert(0, ROOT)","from leakmine import ( # noqa: E402"," bigquery, collect, confirm, diffparse, metrics, mine, schema, signals, sweep, szz,",")","def _expect(cond, msg):"," if not cond:"," raise AssertionError(msg)","# ---- diffparse -------------------------------------------------------------------","REACT_PATCH = \"\"\"diff --git a/src/Widget.tsx b/src/Widget.tsx","--- a/src/Widget.tsx","+++ b/src/Widget.tsx","@@ -10,5 +10,9 @@ export function Widget() {"," useEffect(() => {"," const onResize = () => setW(window.innerWidth);"," window.addEventListener('resize', onResize);","- }, []);","+ return () => {","+ window.removeEventListener('resize', onResize);","+ };","+ }, []);","+ // cleanup added"," }","def test_diffparse():"," fds = diffparse.parse_patch(REACT_PATCH)"," _expect(len(fds) == 1, \"one file diff\")"," fd = fds[0]"," _expect(fd.path == \"src/Widget.tsx\", f\"path {fd.path}\")"," added = \"\\n\".join(fd.added_text())"," _expect(\"removeEventListener\" in added, \"added removeEventListener\")"," # the fix removed old line 13 (`}, []);`) — it must register as touched."," _expect(fd.touches_old_line(13, window=0), \"old line 13 removed/replaced\")"," _expect(not fd.touches_old_line(10, window=0), \"context line 10 untouched\")"," _expect(fd.touches_old_line(11, window=2), \"window admits near line\")","def test_diffparse_body_lines_with_header_prefixes():"," # a removed SQL comment renders as \"--- ...\" at column 0; inside the hunk budget it"," # must be body content, not misread as a file header."," patch = (\"diff --git a/q.sql b/q.sql\\n--- a/q.sql\\n+++ b/q.sql\\n\""," \"@@ -1,2 +1,2 @@\\n--- old comment\\n+-- new comment\\n SELECT 1;\\n\")"," fds = diffparse.parse_patch(patch)"," _expect(len(fds) == 1, f\"one file, got {len(fds)}\")"," _expect(\"-- old comment\" in fds[0].removed_text(), \"removed comment captured as body\")"," _expect(\"-- new comment\" in fds[0].added_text(), \"added comment captured as body\")","def test_diffparse_bare_multifile():"," # bare patch (no `diff --git`): the second file's \"--- \" must start a NEW FileDiff,"," # not overwrite the first."," patch = (\"--- a/one.py\\n+++ b/one.py\\n@@ -1,1 +1,1 @@\\n-a\\n+b\\n\""," \"--- a/two.py\\n+++ b/two.py\\n@@ -1,1 +1,1 @@\\n-c\\n+d\\n\")"," _expect(len(fds) == 2, f\"two files, got {len(fds)}\")"," _expect({f.path for f in fds} == {\"one.py\", \"two.py\"}, f\"paths {[f.path for f in fds]}\")","# ---- signals ---------------------------------------------------------------------","def test_signals_react():"," cls = signals.classify(\"react_ts\", title=\"Fix memory leak in Widget\","," body=\"useEffect never removed the resize listener\", patch=REACT_PATCH)"," _expect(cls.category == signals.SUBSCRIPTION, f\"category {cls.category}\")"," _expect(cls.is_likely_fix, f\"likely fix, score={cls.score}\")"," _expect(\"title:leak-keyword\" in cls.evidence, \"title keyword scored\")","def test_signals_docs_penalty():"," docs = (\"diff --git a/README.md b/README.md\\n--- a/README.md\\n+++ b/README.md\\n\""," \"@@ -1,1 +1,2 @@\\n context\\n+a note about leaks\\n\")"," cls = signals.classify(\"react_ts\", title=\"docs: mention memory leak\", body=\"\", patch=docs)"," _expect(\"penalty:docs-only\" in cls.evidence, \"docs-only penalised\")"," _expect(not cls.is_candidate, f\"docs-only not a candidate, score={cls.score}\")","def test_signals_dotnet_event():"," patch = (\"diff --git a/A.xaml.cs b/A.xaml.cs\\n--- a/A.xaml.cs\\n+++ b/A.xaml.cs\\n\""," \"@@ -5,3 +5,4 @@\\n void Wire() {\\n- svc.Tick += OnTick;\\n\""," \"+ svc.Tick += OnTick;\\n+ Unloaded += (s,e) => svc.Tick -= OnTick;\\n }\\n\")"," cls = signals.classify(\"dotnet_wpf\", title=\"Fix event handler leak\", body=\"\", patch=patch)"," _expect(cls.is_candidate, f\"candidate, score={cls.score}\")","def test_signals_java_executor_single_form():"," # a fix that adds ONLY .shutdown() (not both forms) must still clear the threshold."," patch = (\"diff --git a/Svc.java b/Svc.java\\n--- a/Svc.java\\n+++ b/Svc.java\\n\""," \"@@ -5,2 +5,3 @@\\n void stop() {\\n+ pool.shutdown();\\n }\\n\")"," cls = signals.classify(\"java_spring\", title=\"fix ExecutorService memory leak\", body=\"\", patch=patch)"," _expect(cls.category == signals.TASK, f\"category {cls.category}\")"," _expect(cls.is_candidate, f\"single-form shutdown is a candidate, score={cls.score}\")","# ---- szz attribution + correspondence --------------------------------------------","def _finding(tool, rule, file, line, **kw):"," return szz.Finding(tool=tool, rule=rule, file=file, line=line, **kw)","def test_attribution_causal_vs_coincidental():"," f_on_fix = _finding(\"ownaudit\", \"OWN-EFFECT\", \"src/Widget.tsx\", 13)"," att = szz.attribute(REACT_PATCH, f_on_fix, window=0)"," _expect(att.fix_touches, \"finding on removed line is causal\")"," f_elsewhere = _finding(\"eslint\", \"no-leak\", \"src/Widget.tsx\", 200)"," att2 = szz.attribute(REACT_PATCH, f_elsewhere, window=2)"," _expect(not att2.fix_touches, \"far-away finding not causal\")"," _expect(att2.in_changed_file, \"but still in the changed file\")","def test_correspondence_confirmed_vs_lucky():"," target = _finding(\"ownaudit\", \"OWN-EFFECT\", \"src/Widget.tsx\", 13, resolution=\"semantic\")"," before = [target]"," after = [] # gone after"," corr = szz.correspond(before, after, REACT_PATCH, target, window=0)"," _expect(corr.confirmed_catch, \"flagged before, gone after, causal -> confirmed\")"," # coincidental: finding far from the fix also 'disappears' (e.g. file reshuffled)."," lucky = _finding(\"eslint\", \"x\", \"src/Widget.tsx\", 999)"," corr2 = szz.correspond([lucky], [], REACT_PATCH, lucky, window=2)"," _expect(corr2.detected_before and corr2.gone_after, \"before/after set\")"," _expect(not corr2.causal, \"not on fixed lines\")"," _expect(not corr2.confirmed_catch, \"gone-but-not-causal is NOT a confirmed catch\")","RENAME_PATCH = \"\"\"diff --git a/src/Old.tsx b/src/New.tsx","rename from src/Old.tsx","rename to src/New.tsx","--- a/src/Old.tsx","+++ b/src/New.tsx","@@ -10,3 +10,4 @@ export function Widget() {","+ }, []); // touched, but the leak is NOT actually fixed","+ // (rule still fires on the new path below)","def test_correspondence_rename_not_confirmed():"," # fix renames Old.tsx -> New.tsx and edits the line, but the SAME rule still fires on"," # the renamed file. That is a file-move, not a fix: it must NOT count as confirmed."," before = [_finding(\"ownaudit\", \"OWN-EFFECT\", \"src/Old.tsx\", 11)]"," after = [_finding(\"ownaudit\", \"OWN-EFFECT\", \"src/New.tsx\", 11)] # persists under new path"," corr = szz.correspond(before, after, RENAME_PATCH, before[0], window=2)"," _expect(corr.detected_before, \"flagged before\")"," _expect(not corr.gone_after, \"rule still fires on the renamed path -> not gone\")"," _expect(not corr.confirmed_catch, \"rename+persisting finding is NOT a confirmed catch\")","# ---- lead-time over a real temp git repo -----------------------------------------","def _git(repo, *args, date=\"2024-01-01T00:00:00\"):"," env = {**os.environ,"," \"GIT_AUTHOR_NAME\": \"t\", \"GIT_AUTHOR_EMAIL\": \"t@t\","," \"GIT_COMMITTER_NAME\": \"t\", \"GIT_COMMITTER_EMAIL\": \"t@t\","," \"GIT_AUTHOR_DATE\": date, \"GIT_COMMITTER_DATE\": date}"," return subprocess.run([\"git\", \"-C\", repo, *args], env=env,"," capture_output=True, text=True, check=True)","def test_lead_time():"," with tempfile.TemporaryDirectory() as repo:"," _git(repo, \"init\", \"-q\", \"-b\", \"main\")"," path = os.path.join(repo, \"svc.cs\")"," # commit 1: introduce a leaking line."," with open(path, \"w\") as fh:"," fh.write(\"class S {\\n void M() { Tick += OnTick; }\\n}\\n\")"," _git(repo, \"add\", \".\")"," _git(repo, \"commit\", \"-qm\", \"intro\", date=\"2024-01-01T00:00:00\")"," leak_sha = _git(repo, \"rev-parse\", \"HEAD\").stdout.strip()"," # a couple of unrelated commits."," for i, d in enumerate((\"2024-02-01T00:00:00\", \"2024-03-01T00:00:00\")):"," with open(os.path.join(repo, f\"f{i}.txt\"), \"w\") as fh:"," fh.write(\"x\\n\")"," _git(repo, \"add\", \".\"); _git(repo, \"commit\", \"-qm\", f\"noise{i}\", date=d)"," # the human fix: change line 2."," fh.write(\"class S {\\n void M() { Tick += OnTick; Unloaded += () => Tick -= OnTick; }\\n}\\n\")"," _git(repo, \"add\", \".\"); _git(repo, \"commit\", \"-qm\", \"fix leak\", date=\"2024-04-01T00:00:00\")"," lt = szz.lead_time(repo, leak_sha, \"svc.cs\", 2)"," _expect(lt.found, \"fix located in history\")"," # 2 intervening commits (noise0, noise1); the fix commit itself is excluded."," _expect(lt.commits_between == 2, f\"2 intervening commits, got {lt.commits_between}\")"," _expect(lt.fix_date.startswith(\"2024-04-01\"), f\"fix date {lt.fix_date}\")","# ---- confirm (verdict combiner) --------------------------------------------------","def test_judge_unique_catch_and_miss():"," own_before = [_finding(\"ownaudit\", \"OWN-EFFECT\", \"src/Widget.tsx\", 13, resolution=\"interproc\")]"," cand = confirm.Candidate("," id=\"c1\", ecosystem=\"react_ts\", title=\"fix memory leak\", body=\"listener leak\","," patch=REACT_PATCH,"," before={\"ownaudit\": own_before, \"eslint\": []},"," after={\"ownaudit\": [], \"eslint\": []},"," )"," v = confirm.judge(cand, ownaudit_tool=\"ownaudit\", baseline_tools=(\"eslint\",))"," _expect(v.is_real_fix, \"real fix\")"," _expect(\"ownaudit\" in v.caught_by, \"ownaudit caught\")"," _expect(v.unique_to_ownaudit, \"unique to ownaudit (eslint missed)\")"," _expect(\"eslint\" in v.missed_by, \"eslint in missed_by\")"," _expect(v.own_resolution == \"interproc\", f\"resolution {v.own_resolution}\")","def test_judge_tool_catch_does_not_define_real_fix():"," # a borderline patch (candidate but score < 10) that a tool confirm-catches must NOT be"," # promoted to a \"real fix\" — ground truth is the patch signal, not the tool's catch."," patch = (\"diff --git a/a.tsx b/a.tsx\\n--- a/a.tsx\\n+++ b/a.tsx\\n\""," \"@@ -1,3 +1,3 @@\\n function setup() {\\n- window.addEventListener('x', f);\\n\""," \"+ window.removeEventListener('x', f);\\n }\\n\")"," id=\"b1\", ecosystem=\"react_ts\", title=\"improve effect cleanup\", body=\"\", patch=patch,"," before={\"ownaudit\": [_finding(\"ownaudit\", \"OWN-X\", \"a.tsx\", 2)]},"," after={\"ownaudit\": []},"," v = confirm.judge(cand, ownaudit_tool=\"ownaudit\")"," _expect(\"ownaudit\" in v.caught_by, \"catch still recorded\")"," _expect(not v.is_real_fix, \"tool catch must not define a real fix\")"," _expect(\"borderline-send-to-review\" in v.notes, \"routed to review instead\")","def test_fp_after_matches_rule_and_file():"," patch = (\"diff --git a/a.cs b/a.cs\\n--- a/a.cs\\n+++ b/a.cs\\n\""," \"@@ -5,2 +5,3 @@\\n void M() {\\n+ DoThing();\\n }\\n\")"," # same (rule, file) survives on a touched file -> precision smell."," same = confirm.Candidate("," id=\"f1\", ecosystem=\"dotnet_wpf\", title=\"t\", body=\"\", patch=patch,"," before={\"ownaudit\": [_finding(\"ownaudit\", \"R1\", \"a.cs\", 5)]},"," after={\"ownaudit\": [_finding(\"ownaudit\", \"R1\", \"a.cs\", 5)]},"," _expect(confirm._fp_after(same, \"ownaudit\"), \"surviving same rule+file is a smell\")"," # a DIFFERENT rule on the same file must not count."," diff = confirm.Candidate("," id=\"f2\", ecosystem=\"dotnet_wpf\", title=\"t\", body=\"\", patch=patch,"," after={\"ownaudit\": [_finding(\"ownaudit\", \"R2\", \"a.cs\", 9)]},"," _expect(not confirm._fp_after(diff, \"ownaudit\"), \"unrelated rule must not inflate fp_after\")","def test_judge_unique_miss():"," # a real fix (strong patch signal) that NO tool caught -> the precious blind-spot bucket."," id=\"c2\", ecosystem=\"react_ts\", title=\"fix memory leak\", body=\"listener leak\","," patch=REACT_PATCH, before={\"ownaudit\": [], \"eslint\": []}, after={\"ownaudit\": [], \"eslint\": []},"," _expect(v.is_real_fix, \"still a real fix by patch signal\")"," _expect(not v.caught_by, \"no tool caught it\")"," _expect(\"real-fix-no-tool-caught\" in v.notes, \"flagged as shared blind spot\")","# ---- metrics ---------------------------------------------------------------------","def test_metrics_aggregate():"," vs = ["," confirm.Verdict(\"a\", \"react_ts\", \"subscription-leak\", 12, True,"," caught_by=[\"ownaudit\"], missed_by=[\"eslint\"], unique_to_ownaudit=True,"," own_resolution=\"interproc\"),"," confirm.Verdict(\"b\", \"react_ts\", \"timer-leak\", 11, True,"," caught_by=[\"ownaudit\", \"eslint\"], unique_to_ownaudit=False,"," own_resolution=\"syntactic\"),"," confirm.Verdict(\"c\", \"react_ts\", \"subscription-leak\", 9, True, caught_by=[],"," missed_by=[\"ownaudit\", \"eslint\"], notes=[\"real-fix-no-tool-caught\"]),"," ]"," rep = metrics.aggregate(vs, ownaudit_tool=\"ownaudit\", baseline_tools=(\"eslint\",))"," _expect(rep.n_real_fixes == 3, \"3 real fixes\")"," _expect(rep.catches[\"ownaudit\"] == 2, \"ownaudit caught 2\")"," _expect(rep.unique_to_ownaudit == 1, \"1 unique to ownaudit\")"," _expect(rep.unique_miss == 1, \"1 shared blind spot\")"," _expect(abs(rep.recall_on_corpus[\"ownaudit\"] - 2 / 3) < 1e-3, \"ownaudit recall 2/3\")"," _expect(rep.by_tier.get(\"interproc\") == 1 and rep.by_tier.get(\"syntactic\") == 1, \"tier split\")"," md = metrics.render_markdown(rep)"," _expect(\"LeakFixMine\" in md and \"by analysis tier\" in md, \"markdown renders\")","# ---- sweep (over-vetted selection) -----------------------------------------------","def test_sweep_over_vetted():"," polished = sweep.Package(\"Serilog\", \"nuget\", downloads=10**8, stars=6000, maintainers=8,"," open_issues=10, age_days=3000, has_ci=True, shape=\"library\")"," appish = sweep.Package(\"acme-dashboard\", \"npm\", downloads=10**6, stars=400, maintainers=2,"," open_issues=120, age_days=400, has_ci=False, shape=\"application\")"," sp = sweep.over_vetted_score(polished)"," sa = sweep.over_vetted_score(appish)"," _expect(sp.vetted > sa.vetted, \"polished lib scores more vetted\")"," _expect(\"high-stars-per-issue\" in sp.reason, \"stars/issue signal fires\")"," # many polished libs + a few apps; cap must let apps through despite higher downloads."," pkgs = [sweep.Package(f\"lib{i}\", \"nuget\", downloads=10**8, stars=8000, maintainers=9,"," open_issues=5, age_days=3000, has_ci=True, shape=\"library\")"," for i in range(8)]"," pkgs += [appish, sweep.Package(\"ctrl-plane\", \"npm\", downloads=5 * 10**5, stars=200,"," open_issues=90, age_days=300, shape=\"application\")]"," chosen = sweep.select_targets(pkgs, n=5, max_vetted_fraction=0.4)"," names = {c.pkg.name for c in chosen}"," n_vetted = sum(1 for c in chosen if c.vetted >= 0.6)"," _expect(n_vetted <= 2, f\"vetted cap (<=40% of 5) respected, got {n_vetted}\")"," _expect(names & {\"acme-dashboard\", \"ctrl-plane\"}, \"an app-shaped repo got in\")","def test_sweep_underfill_is_intentional():"," # an all-vetted pool can't fill n without breaching the cap: underfill is intentional,"," # NOT a backfill with the very libs the cap excludes."," for i in range(10)]"," _expect(len(chosen) == 2, f\"hard cap -> 2 of 5 (intentional underfill), got {len(chosen)}\")"," _expect(all(c.vetted >= 0.6 for c in chosen), \"the two admitted are the vetted libs\")","# ---- collect (deterministic query/SQL gen) ---------------------------------------","def test_queries_and_sql():"," qs = collect.github_search_queries(\"react_ts\", merged_after=\"2023-01-01\")"," _expect(all(\"merged:>=2023-01-01\" in q for q in qs), \"date qualifier appended\")"," _expect(any(\"useEffect\" in q for q in qs), \"useEffect query present\")"," sql = collect.gharchive_sql(\"dotnet_wpf\", date_from=\"20240101\", date_to=\"20241231\")"," _expect(\"_TABLE_SUFFIX BETWEEN '20240101' AND '20241231'\" in sql, \"partition-scoped\")"," _expect(\"PullRequestEvent\" in sql and \"memory leak\" in sql, \"PR + keyword filter\")"," _expect(\"pull_request.title\" in sql and \"pull_request.body\" in sql, \"title AND body matched\")","def test_fetch_search_with_fake_http():"," fake = json.dumps({\"items\": ["," {\"number\": 7, \"title\": \"fix leak\", \"html_url\": \"https://x/pr/7\","," \"repository_url\": \"https://api.github.com/repos/acme/widget\", \"pull_request\": {}},"," ]}).encode()"," got = collect.fetch_search(\"q\", http=lambda url, token: fake)"," _expect(len(got) == 1 and got[0].kind == \"pr\", \"parsed one PR\")"," _expect(got[0].repo == \"acme/widget\", f\"repo parsed: {got[0].repo}\")","def test_fetch_patch_with_fake_http():"," calls = {}"," def fake_http(url, token):"," calls[\"url\"] = url"," calls[\"token\"] = token"," return \"diff --git a/a b/a\\n@@ -1 +1 @@\\n-x\\n+y\\n\""," out = collect.fetch_patch(\"acme/w\", 7, token=\"T\", http=fake_http)"," _expect(out.startswith(\"diff --git\"), \"returns diff text\")"," _expect(calls[\"url\"].endswith(\"/repos/acme/w/pulls/7\"), f\"url {calls['url']}\")"," _expect(calls[\"token\"] == \"T\", \"token threaded through\")"," # a fetch error must degrade to \"\" (one bad PR can't abort a mining run), not raise."," def boom(url, token):"," raise RuntimeError(\"network\")"," _expect(collect.fetch_patch(\"a/b\", 1, http=boom) == \"\", \"fetch error -> empty string\")","def test_mine_run_orchestration():"," cands = ["," collect.Candidate(\"\", \"acme/w\", 1, \"pr\", \"fix memory leak\", \"u1\", \"listener leak\"),"," collect.Candidate(\"\", \"acme/w\", 1, \"pr\", \"dup of #1\", \"u1\", \"\"), # dedup by (repo,#)"," collect.Candidate(\"\", \"acme/x\", 2, \"pr\", \"chore: tidy\", \"u2\", \"\"), # weak -> dropped"," collect.Candidate(\"\", \"acme/y\", 3, \"issue\", \"an issue\", \"u3\", \"\"), # not a PR -> skip"," weak = (\"diff --git a/x.tsx b/x.tsx\\n--- a/x.tsx\\n+++ b/x.tsx\\n\""," \"@@ -1,1 +1,1 @@\\n-const a = 1;\\n+const a = 2;\\n\")"," patches = {(\"acme/w\", 1): REACT_PATCH, (\"acme/x\", 2): weak}"," def fake_search(query, *, token=\"\", per_page=50):"," return cands # query pack repeats the same hits; dedup must collapse them"," def fake_patch(repo, number, *, token=\"\"):"," return patches.get((repo, number), \"\")"," conn = schema.connect(\":memory:\")"," res = mine.run(\"react_ts\", search=fake_search, fetch_patch=fake_patch, conn=conn, min_score=7)"," _expect(res.seen == 2, f\"PR-only + deduped examined, got {res.seen}\")"," _expect(res.kept == 1, f\"only the real leak fix kept, got {res.kept}\")"," _expect(res.rows and res.rows[0][\"repo\"] == \"acme/w\", \"kept the leak fix\")"," _expect(res.rows[0][\"category\"] == signals.SUBSCRIPTION, \"classified as subscription\")"," _expect(schema.count(conn, \"candidates\") == 1, \"kept candidate stored\")"," _expect(schema.count(conn, \"labels\") == 1, \"kept label stored\")"," _expect(\"mining run\" in res.summary_md(), \"summary renders\")","# ---- schema (store round-trip) ---------------------------------------------------","def test_schema_store():"," schema.insert_candidate(conn, {\"id\": \"c1\", \"ecosystem\": \"react_ts\", \"repo\": \"a/b\","," \"number\": 1, \"kind\": \"pr\", \"title\": \"fix leak\", \"merged\": 1})"," schema.insert_label(conn, \"c1\", \"subscription-leak\", 12, [\"patch:subscription-leak\"], \"patch\")"," v = confirm.Verdict(\"c1\", \"react_ts\", \"subscription-leak\", 12, True,"," caught_by=[\"ownaudit\"], unique_to_ownaudit=True)"," schema.insert_verdict(conn, v)"," _expect(schema.count(conn, \"candidates\") == 1, \"candidate stored\")"," _expect(schema.count(conn, \"labels\") == 1, \"label stored\")"," _expect(schema.count(conn, \"verdicts\") == 1, \"verdict stored\")","def test_candidate_upsert_preserves_children():"," # re-inserting a candidate must UPDATE in place, not DELETE+reinsert — otherwise (with"," # FK on) it would orphan/cascade the child label below."," schema.insert_candidate(conn, {\"id\": \"c1\", \"ecosystem\": \"react_ts\", \"title\": \"old\", \"merged\": 1})"," schema.insert_label(conn, \"c1\", \"subscription-leak\", 12, [\"e\"], \"patch\")"," schema.insert_candidate(conn, {\"id\": \"c1\", \"ecosystem\": \"react_ts\", \"title\": \"new\", \"merged\": 1})"," _expect(schema.count(conn, \"candidates\") == 1, \"still one candidate\")"," _expect(schema.count(conn, \"labels\") == 1, \"child label survived the re-insert\")"," title = conn.execute(\"SELECT title FROM candidates WHERE id='c1'\").fetchone()[0]"," _expect(title == \"new\", f\"row updated in place, title={title}\")","def test_schema_verdict_idempotent():"," # re-confirming the same candidate upserts, so resume never double-counts verdicts."," schema.insert_candidate(conn, {\"id\": \"c1\", \"ecosystem\": \"react_ts\", \"title\": \"t\", \"merged\": 1})"," v = confirm.Verdict(\"c1\", \"react_ts\", \"subscription-leak\", 12, True, caught_by=[\"ownaudit\"])"," schema.insert_verdict(conn, v) # second confirm of the same candidate"," _expect(schema.count(conn, \"verdicts\") == 1, \"verdict upserts, not duplicated\")","def test_schema_foreign_keys_enforced():"," # FK enforcement is ON: a verdict for an unknown candidate must be rejected."," v = confirm.Verdict(\"ghost\", \"react_ts\", \"subscription-leak\", 12, True)"," try:"," schema.insert_verdict(conn, v)"," raised = False"," except sqlite3.IntegrityError: # specifically the FK rejection, not any error"," raised = True"," _expect(raised, \"orphan verdict rejected by foreign-key constraint\")","def test_bq_gharchive_sql():"," sql = bigquery.gharchive_discovery_sql(\"dotnet_wpf\", date_from=\"20240101\", date_to=\"20241231\","," max_changed_files=80)"," # assert the actual OR boolean, not mere field presence (an AND regression must fail)."," _expect((\"title')) LIKE '%memory leak%' OR \""," \"LOWER(COALESCE(JSON_EXTRACT_SCALAR(payload,'$.pull_request.body'),'')) \""," \"LIKE '%memory leak%'\") in sql, \"title OR body, not AND\")"," _expect(\"base.repo.language')) = 'c#'\" in sql, \"language filter\")"," _expect(\"changed_files') AS INT64) <= 80\" in sql, \"size cap applied\")"," _expect(\"QUALIFY ROW_NUMBER()\" in sql, \"deduped to one row per PR\")"," # size cap can be disabled."," nocap = bigquery.gharchive_discovery_sql(\"react_ts\", date_from=\"20240101\", date_to=\"20240131\","," max_changed_files=0)"," _expect(\"changed_files') AS INT64) <=\" not in nocap, \"cap omitted when 0\")","def test_bq_contents_sweep_sql():"," s = bigquery.contents_sweep_sql(\"react_ts\", sample=True)"," _expect(\"sample_files\" in s and \"sample_contents\" in s, \"uses cheap sample tables by default\")"," _expect(\"REGEXP_CONTAINS(c.content, r'addEventListener\\\\(')\" in s, \"acquire regex present\")"," _expect(\"NOT REGEXP_CONTAINS(c.content, r'removeEventListener')\" in s, \"cleanup-absence test\")"," full = bigquery.contents_sweep_sql(\"react_ts\", sample=False)"," _expect(\"github_repos.files`\" in full and \"github_repos.contents`\" in full, \"full tables\")"," _expect(\"2.7TB\" in full, \"full scan is cost-warned\")"," # an ecosystem without sweep pairs raises rather than emit garbage."," raised = False"," bigquery.contents_sweep_sql(\"nim\")"," except ValueError:"," _expect(raised, \"missing sweep pairs -> explicit error\")","def test_bq_metadata_score():"," hi, ev = bigquery.metadata_score(\"dotnet_wpf\", title=\"Fix memory leak in view\","," body=\"event handler retained\", changed_files=4)"," _expect(hi >= 4 and \"small-pr\" in ev, f\"focused leak fix ranks high, {hi}\")"," lo, ev2 = bigquery.metadata_score(\"dotnet_wpf\", title=\"Fix memory leak\", body=\"\","," changed_files=500)"," # +3 title keyword, -3 mega penalty -> 0; assert the score, not just the evidence."," _expect(lo == 0 and \"penalty:mega-pr\" in ev2, f\"mega-PR penalty zeroes the score, {lo}\")"," none, _ = bigquery.metadata_score(\"dotnet_wpf\", title=\"add feature\", body=\"\", changed_files=3)"," _expect(none < 4, \"no-keyword PR below threshold\")","def test_bq_ingest_ndjson():"," ndjson = \"\\n\".join(["," json.dumps({\"repo\": \"a/b\", \"number\": 1, \"title\": \"Fix memory leak\", \"body\": \"x\","," \"changed_files\": 3, \"html_url\": \"u1\"}),"," json.dumps({\"repo\": \"a/b\", \"number\": 1, \"title\": \"dup\", \"body\": \"\", \"changed_files\": 3}),"," json.dumps({\"repo\": \"c/d\", \"number\": 9, \"title\": \"add feature\", \"body\": \"\","," \"changed_files\": 2}), # no keyword -> dropped"," ])"," rows = bigquery.read_ndjson(ndjson)"," res = bigquery.ingest_rows(rows, \"dotnet_wpf\", min_meta_score=4, conn=conn)"," _expect(res.seen == 2, f\"deduped by (repo,number), got {res.seen}\")"," _expect(res.kept == 1, f\"only the keyword'd small PR kept, got {res.kept}\")"," _expect(res.rows[0][\"repo\"] == \"a/b\", \"kept the leak PR\")"," _expect(schema.count(conn, \"candidates\") == 1 and schema.count(conn, \"labels\") == 1, \"stored\")"," _expect(\"metadata tier\" in res.summary_md(), \"summary flags the tier\")","def test_signals_no_oom_substring_noise():"," # bare \"oom\" was removed (it matched zoom/room/doom under substring) — junk titles must"," # not register a leak keyword, but a real leak title still must."," for junk in (\"Refactor Room screen\", \"bump react-zoom-pan-pinch\", \"New Gloomier Bangs\"):"," cls = signals.classify(\"react_ts\", title=junk, body=\"\", patch=\"\")"," _expect(\"title:leak-keyword\" not in cls.evidence, f\"{junk!r} must not match a keyword\")"," cls = signals.classify(\"react_ts\", title=\"fix memory leak\", body=\"\", patch=\"\")"," _expect(\"title:leak-keyword\" in cls.evidence, \"real leak title still matches\")","def test_classify_from_store():"," schema.insert_candidate(conn, {\"id\": \"a/b#1\", \"ecosystem\": \"react_ts\", \"repo\": \"a/b\","," \"number\": 1, \"kind\": \"pr\", \"title\": \"fix memory leak\","," \"body\": \"listener leak\", \"merged\": 1})"," schema.insert_candidate(conn, {\"id\": \"c/d#2\", \"ecosystem\": \"react_ts\", \"repo\": \"c/d\","," \"number\": 2, \"kind\": \"pr\", \"title\": \"chore: tidy\","," \"body\": \"\", \"merged\": 1})"," patches = {(\"a/b\", 1): REACT_PATCH,"," (\"c/d\", 2): \"diff --git a/x.tsx b/x.tsx\\n--- a/x.tsx\\n+++ b/x.tsx\\n\""," \"@@ -1,1 +1,1 @@\\n-const a = 1;\\n+const a = 2;\\n\"}"," fetched = []"," fetched.append((repo, number))"," res = mine.classify_from_store(conn, \"react_ts\", fetch_patch=fake_patch, min_score=7)"," _expect(res.seen == 2, f\"both stored PRs examined, {res.seen}\")"," _expect(res.fetched == 2, f\"both diffs fetched, {res.fetched}\")"," _expect(res.kept == 1, f\"only the real leak fix kept at patch tier, {res.kept}\")"," _expect(res.rows[0][\"repo\"] == \"a/b\" and res.rows[0][\"category\"] == signals.SUBSCRIPTION,"," \"patch-tier category assigned\")"," # every attempt is labelled at the patch tier: the real category + a below-threshold miss."," total = conn.execute(\"SELECT COUNT(*) FROM labels WHERE classifier='patch'\").fetchone()[0]"," real = conn.execute(\"SELECT COUNT(*) FROM labels WHERE classifier='patch' \""," \"AND label NOT IN ('below-threshold','fetch-failed')\").fetchone()[0]"," _expect(total == 2 and real == 1, f\"2 patch labels, 1 real verdict; got {total}/{real}\")"," # resume: a second run must skip everything already attempted — no re-fetch, no dupes."," res2 = mine.classify_from_store(conn, \"react_ts\", fetch_patch=fake_patch, min_score=7)"," _expect(res2.seen == 0, f\"resume processes nothing, got {res2.seen}\")"," _expect(len(fetched) == 2, f\"no diffs re-fetched on resume, got {len(fetched)}\")","def test_bq_ingest_rejects_contents_rows():"," # contents-sweep rows (repo/path/signal, no PR number) must fail fast, not silently drop."," rows = [{\"repo\": \"a/b\", \"path\": \"src/x.tsx\", \"signal\": \"listener\"}]"," bigquery.ingest_rows(rows, \"react_ts\")"," _expect(raised, \"contents-sweep rows rejected by bq-ingest\")","def main():"," tests = [v for k, v in sorted(globals().items()) if k.startswith(\"test_\") and callable(v)]"," for t in tests:"," t()"," print(f\"ok - {len(tests)} leakmine tests passed\")","if __name__ == \"__main__\":"," main()","leakmine/mine.py",[1138],{"_684":685,"_686":1139,"_401":1140,"_689":59},190,[1141,199,1142,1143,1144,1145,1146,199,1147,1148,1149,1150,199,1151,1152,696,1153,199,1154,1155,199,1156,199,199,1157,1158,1159,1160,1161,1162,1163,199,1164,1165,1166,1167,1168,1169,1170,1171,1172,1173,1170,1174,1170,1175,1176,1177,1178,1179,1180,1181,1182,1183,1184,1185,199,199,1186,1187,1188,1189,1190,1191,1192,1193,1194,1195,1196,1197,1198,1199,1200,1201,1202,1203,199,1204,1205,199,1206,1207,1208,1209,1210,1211,1212,1213,1214,1215,199,1216,1217,1218,1219,1213,1220,199,1221,1222,1213,1223,1224,1225,1226,1227,1228,1229,1230,1231,1232,1233,1234,1235,1236,1237,1238,1239,1240,1241,1242,1243,1244,1245,1246,199,199,1247,1248,1249,1188,1189,1192,1193,1250,1196,1197,1251,1252,1253,1254,199,1255,1256,199,1257,1258,1259,1260,1261,1262,1263,1203,1264,1265,1266,1267,1268,1269,1270,1271,1272,1273,859,1274,1275,1276,1277,1278,1279,1280,1281,1208,1209,1282,1283,1284,1285,1286,1287,1288,1284,1289,1290,1291,1292,1293,1294,1295,1246],"\"\"\"Mining orchestrator — discover → fetch patch → classify → store, one ecosystem at a time.","This is the CI-runnable arm of the pipeline (docs/leakfix-mine.md §4/§10). It chains the","GitHub-Search query pack (`collect.github_search_queries`) → per-PR patch fetch","(`collect.fetch_patch`) → patch-signal classification (`signals.classify`), dedups by","(repo, number), keeps everything scoring at/above the candidate threshold, and writes the","result to the SQLite store plus a JSON dataset and a markdown summary.","Deliberately scoped to **discovery + classification** — the part that runs cleanly on a","hosted runner with only `GITHUB_TOKEN`. The before/after tool comparison (`confirm` /","`metrics`) needs per-repo checkout + analyzer builds, so it stays a local / self-hosted","step; see docs/leakfix-mine.md §7.","Network access is isolated behind the injected `search` / `fetch_patch` callables, so the","orchestration unit-tests offline with fakes (CI never reaches out).","from __future__ import annotations","import time","from dataclasses import dataclass, field","from . import collect, schema, signals","@dataclass","class MineResult:"," ecosystem: str"," rows: list[dict] = field(default_factory=list) # one per kept candidate"," seen: int = 0 # candidates examined (post-dedup)"," fetched: int = 0 # patches successfully fetched"," kept: int = 0 # candidates >= min_score"," def summary_md(self) -> str:"," by_cat: dict[str, int] = {}"," for r in self.rows:"," by_cat[r[\"category\"]] = by_cat.get(r[\"category\"], 0) + 1"," lines = ["," f\"# LeakFixMine — `{self.ecosystem}` mining run\","," \"\","," f\"- candidates examined: **{self.seen}**\","," f\"- patches fetched: **{self.fetched}**\","," f\"- kept (>= threshold): **{self.kept}**\","," \"## kept by category\","," \"| category | kept |\","," \"|---|---:|\","," ]"," for cat, c in sorted(by_cat.items(), key=lambda kv: -kv[1]):"," lines.append(f\"| {cat} | {c} |\")"," lines += [\"\", \"## kept candidates\", \"\", \"| score | category | repo#PR | title |\","," \"|---:|---|---|---|\"]"," for r in sorted(self.rows, key=lambda r: -r[\"score\"])[:100]:"," title = (r[\"title\"] or \"\").replace(\"|\", \"\\\\|\")[:80]"," lines.append(f\"| {r['score']} | {r['category']} | {r['repo']}#{r['number']} | {title} |\")"," return \"\\n\".join(lines) + \"\\n\"","def run("," ecosystem: str,"," *,"," token: str = \"\","," merged_after: str = \"\","," per_query: int = 50,"," min_score: int = 7,"," sleep: float = 0.0,"," conn=None,"," search=None,"," fetch_patch=None,",") -> MineResult:"," \"\"\"Mine one ecosystem. `search(query, *, token, per_page) -> list[Candidate]` and"," `fetch_patch(repo, number, *, token) -> str` default to the live `collect` helpers but"," are injected as fakes in tests. `sleep` throttles between API calls to stay under the"," Search API's ~30 req/min; pass 0 in tests.\"\"\""," search = search or collect.fetch_search"," fetch_patch = fetch_patch or collect.fetch_patch"," res = MineResult(ecosystem=ecosystem)"," seen: set[tuple[str, int]] = set()"," for query in collect.github_search_queries(ecosystem, merged_after=merged_after):"," candidates = search(query, token=token, per_page=per_query)"," if sleep:"," time.sleep(sleep)"," for cand in candidates:"," key = (cand.repo, cand.number)"," if cand.kind != \"pr\" or key in seen:"," continue"," seen.add(key)"," res.seen += 1"," patch = fetch_patch(cand.repo, cand.number, token=token)"," if sleep:"," time.sleep(sleep)"," if not patch:"," res.fetched += 1"," cls = signals.classify(ecosystem, title=cand.title, body=cand.body, patch=patch)"," if cls.score < min_score:"," res.kept += 1"," row = {"," \"ecosystem\": ecosystem,"," \"repo\": cand.repo,"," \"number\": cand.number,"," \"url\": cand.url,"," \"title\": cand.title,"," \"category\": cls.category,"," \"score\": cls.score,"," \"is_candidate\": cls.is_candidate,"," \"is_likely_fix\": cls.is_likely_fix,"," \"evidence\": cls.evidence,"," }"," res.rows.append(row)"," if conn is not None:"," schema.insert_candidate(conn, {"," \"id\": f\"{cand.repo}#{cand.number}\", \"ecosystem\": ecosystem,"," \"query\": query, \"repo\": cand.repo, \"number\": cand.number,"," \"kind\": \"pr\", \"title\": cand.title, \"body\": cand.body,"," \"state\": \"merged\", \"merged\": 1, \"url\": cand.url,"," })"," schema.insert_label(conn, f\"{cand.repo}#{cand.number}\", cls.category,"," cls.score, cls.evidence, \"patch\")"," return res","def classify_from_store("," conn,"," eco_key: str,"," limit=None,"," \"\"\"Close the loop: take the candidate PRs already in the store (from a BigQuery /"," GH-Archive ingest, which only had title/body metadata), fetch each diff, and run the"," REAL patch-tier `signals.classify`. The metadata tier was a fetch *queue*; this is the"," verdict — category + patch-signal score, kept at `min_score`."," `fetch_patch(repo, number, *, token) -> str` defaults to the live `collect` helper and"," is injected as a fake in tests."," RESUMABLE: every attempted PR gets a `classifier='patch'` label — the real category when"," kept, `below-threshold` for a fetched-but-low-score miss, `fetch-failed` when no diff came"," back — and any PR that already has such a label is skipped BEFORE `--limit` is counted. So"," `--limit`-sized batches (and reruns after an interruption) advance through the queue"," instead of re-burning diff quota on the same head. To retry failures, delete their"," `fetch-failed` labels."," \"\"\""," res = MineResult(ecosystem=eco_key)"," # Exclude already-attempted candidates IN SQL (anti-join on a patch-tier label) and push"," # --limit into the query, so reruns/batches stream only the unprocessed head instead of"," # loading the whole table and re-burning diff quota. ORDER BY c.id makes the batch order"," # stable (and materialises the result, so the in-loop label inserts can't disturb it)."," sql = ("," \"SELECT c.repo, c.number, c.title, c.body FROM candidates AS c \""," \"LEFT JOIN labels AS l ON l.candidate_id = c.id AND l.classifier = 'patch' \""," \"WHERE c.ecosystem = ? AND c.kind = 'pr' AND l.candidate_id IS NULL \""," \"ORDER BY c.id\""," params = [eco_key]"," if limit is not None:"," sql += \" LIMIT ?\""," params.append(limit)"," for repo, number, title, body in conn.execute(sql, params):"," cid = f\"{repo}#{number}\""," res.seen += 1"," patch = fetch_patch(repo, number, token=token)"," if not patch:"," schema.insert_label(conn, cid, \"fetch-failed\", 0, [], \"patch\")"," continue"," res.fetched += 1"," cls = signals.classify(eco_key, title=title or \"\", body=body or \"\", patch=patch)"," if cls.score < min_score:"," schema.insert_label(conn, cid, \"below-threshold\", cls.score, cls.evidence, \"patch\")"," res.kept += 1"," res.rows.append({"," \"ecosystem\": eco_key, \"repo\": repo, \"number\": number,"," \"title\": title, \"category\": cls.category, \"score\": cls.score,"," \"is_likely_fix\": cls.is_likely_fix, \"evidence\": cls.evidence,"," })"," schema.insert_label(conn, cid, cls.category, cls.score, cls.evidence, \"patch\")",[1297,1298,1299,1300,1301,1302,1303],{"_661":46,"_46":1314},{"_661":1305,"_161":1136,"_684":1312,"_686":1313},{"_661":46,"_46":1311},{"_661":1305,"_161":1136,"_684":1309,"_686":1310},{"_661":46,"_46":1308},{"_661":1305,"_161":678,"_684":1306,"_686":1307},{"_661":46,"_46":1304},"\n\nNo additional code changes were needed, so I did not create a new commit or PR.\n\n**Testing**\n* ✅ `python3 -m pytest leakmine/tests/test_leakmine.py`\n* ✅ `python3 -O -m pytest leakmine/tests/test_leakmine.py`","repo_file_citation",532,564,"\n* Confirmed test coverage asserts patch-tier labelling for both kept and below-threshold attempts, then verifies a second run processes nothing and re-fetches no diffs. ",175,189,"\n* Confirmed every attempted PR is marked at patch tier: kept classifications use the real category, low-score fetched diffs get `below-threshold`, and missing diffs get `fetch-failed`, preventing re-fetching on reruns. ",146,169,"### Summary\n* Verified the review feedback is already addressed in the current branch at `a568293`: `classify_from_store` now documents resumable behavior, skips candidates that already have a `classifier='patch'` label before applying `--limit`, streams the SQL result without `fetchall()`, and uses stable `ORDER BY c.id` batching. ",{"_92":326,"_42":84,"_96":326,"_1317":1318,"_1319":1320,"_1321":1322,"_132":-5,"_119":1323},[83],"input_items",[1342,1343,1344,1345,1346,1347,1348],"external_post_config",{"_1324":1325,"_263":196,"_1326":305,"_274":-5,"_1327":257,"_1328":-5,"_1329":-5,"_1330":1331,"_1332":1333,"_1334":-5,"_1335":-5,"_1336":1337,"_1338":15,"_1339":59,"_1340":54,"_1341":15},"user_model_slug","slug",1782624968.382171,"installation_id",131220309,"pr_number","repo_id","gitlab_service_account_project_id","review_trigger","comment_id",4824996199,"comment_type","issue","pr_write_guard_token","pending_pr_reaction_id","pending_comment_reaction_id",375634853,"comment_if_no_findings","comment_on_error","share_url","is_parallel_review",{"_92":407,"_96":326,"_401":1362},{"_312":313,"_314":1358,"_1359":319,"_1360":129,"_322":-5,"_92":1361},{"_92":1349,"_314":1357,"_161":-5,"_1351":-5,"_1352":-5},{"_92":1349,"_314":1356,"_161":1136,"_1351":1354,"_1352":-5},{"_92":1349,"_314":1355,"_161":-5,"_1351":-5,"_1352":-5},{"_92":1349,"_314":1353,"_161":1136,"_1351":1354,"_1352":-5},{"_92":1349,"_314":1350,"_161":-5,"_1351":-5,"_1352":-5},"pull_request_comment","**Actionable comments posted: 1**\n\n

🤖 Prompt for all review comments with AI agents

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🪄 Autofix (Beta)

\n\nFix all unresolved CodeRabbit comments on this PR:\n\n- [ ] Push a commit to this branch (recommended)\n- [ ] Create a new PR with the fixes\n\n

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⚙️ Run configuration

\n\n**Configuration used**: defaults\n\n**Review profile**: CHILL\n\n**Plan**: Pro Plus\n\n**Run ID**: `68abfcb6-be2a-4bfe-baf0-b0f2011ba56b`\n\n

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\n\nReviewing files that changed from the base of the PR and between a400c0da7450952c0e6db4fbb21537faec7cd4d3 and 68c97760e87aa7f1099108b8b64bdcd2b292ac23.\n\n

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📒 Files selected for processing (6)

\n\n* `.gitignore`\n* `docs/leakfix-mine.md`\n* `leakmine/cli.py`\n* `leakmine/mine.py`\n* `leakmine/signals.py`\n* `leakmine/tests/test_leakmine.py`\n\n

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\n\n","side","line","_🗄️ Data Integrity & Integration_ | _🟠 Major_ | _⚡ Quick win_\n\n**Only queue candidates that still need a patch verdict.**\n\n`run()` already writes `classifier='patch'` labels, but this query reselects every PR in the store. Re-running `classify-store` against a `mine` or previously classified DB will refetch the same diffs and either append duplicate patch labels or fail on a uniqueness constraint. Because it also calls `fetchall()`, `--limit` cannot stop the initial full-table load. Filter out rows that already have a patch label and stream/limit the SQL result instead.\n\n

Suggested query shape

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🤖 Prompt for AI Agents

\n\n\n\n\n\n\n\n","RIGHT","\n### 💡 Codex Review\n\nHere are some automated review suggestions for this pull request.\n\n**Reviewed commit:** `68c97760e8`\n \n\n

ℹ️ About Codex in GitHub

","**_{_{![P2 Badge](https://img.shields.io/badge/P2-yellow?style=flat)}} Skip processed PRs before applying classify-store limits**\n\nWhen `classify-store` is rerun, for example after an interruption or to process a large BigQuery queue in `--limit`-sized batches, this query selects every PR in the ecosystem again. The loop then inserts another `classifier='patch'` label for kept rows and records nothing for below-threshold rows, so repeated limited runs keep burning the GitHub diff quota on the same first candidates instead of advancing through the queue. Filter or mark processed candidates, including misses, before applying the limit.\n\nUseful? React with 👍 / 👎.","\n\n\n[![Review Change Stack](https://storage.googleapis.com/coderabbit_public_assets/review-stack-in-coderabbit-ui.svg)](https://app.coderabbit.ai/change-stack/PhysShell/OwnAudit/pull/27?utm_source=github_walkthrough&utm_medium=github&utm_campaign=change_stack)\n\n\n\n\n

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\n\n\n\n\n---\n\n\n\n\n_{Comment `@coderabbitai help` to get the list of available commands.}\n\n","## What\n\nTwo changes, both driven by the live ClickHouse run we just did (1065 real 2024 PRs mined with zero GCP/auth):\n\n### (a) Drop the noisy `\"oom\"` keyword\nThe live run exposed a real defect in our own keyword list. Leak keywords are matched as **substrings** — in `signals.classify`/`metadata_score` (Python `in`) *and* in the BigQuery/ClickHouse discovery SQL — so bare `\"oom\"` (for \"out of memory\") matched **zoom / room / doom / bloom**. It accounted for **646 of 947** kept rows in the real run (~68% junk). Removed it (`\"out of memory\"` carries the meaning safely) and documented the keyword list as substring-unsafe.\n\n### (b) `classify-store` — close the loop from queue to verdict\n`bq-ingest` gives a **metadata-tier queue** (title/body keyword + PR size, no diff → no category). The new `mine.classify_from_store` + `classify-store` CLI takes those stored candidates, **fetches each diff** (`collect.fetch_patch`), and runs the **real** `signals.classify` (title+body+patch) → category + patch-signal score, writing a `classifier='patch'` label. The metadata tier was the queue; this is the verdict.\n\n```\nbq-ingest -> store (metadata queue) -> classify-store -> patch-tier verdict\n```\n\nNetwork is isolated behind the injected `fetch_patch`, so it unit-tests offline (CI never reaches out); run it with `$GITHUB_TOKEN` for the 5000/hr REST limit.\n\n## Also\n- `.gitignore` the generated mining out-dirs (`leakmine-out/`, `bq-out/`, `ch-out/`).\n- docs/leakfix-mine.md §14 updated with the `classify-store` step.\n\n## Tests / CI\n33 tests pass under `python3` and `python3 -O` (+2: `\"oom\"` no longer matches zoom/room; `classify_from_store` fetches → classifies → labels with dedup/score-filter). Existing suite green.\n\n🤖 Generated with [Claude Code](https://claude.com/claude-code)\n\n---\n_Generated by [Claude Code](https://claude.ai/code/session_01W6Lbeeoqy7v3wjzV43iLun)_\n\n\n\n## Summary by CodeRabbit\n\n* **New Features**\n * Added a new command to classify stored PR candidates after patch diffs are fetched, with output summaries saved for review.\n * Expanded the pipeline docs with a clearer step-by-step example and a new CLI invocation.\n\n* **Bug Fixes**\n * Improved keyword matching so unrelated text no longer triggers leak-related results from a loose “oom” match.\n * Updated ignored files to avoid checking in local leak-mining run outputs.\n\n","base_ref","head_ref","pull_request_info",[1363],{"_661":46,"_46":1364},"Good catch (both @coderabbitai and @chatgpt-codex-connector flagged it) — fixed in a568293. `classify_from_store` is now **resumable**:\n\n- The candidate query is an **anti-join** — `LEFT JOIN labels ... AND l.classifier='patch' WHERE l.candidate_id IS NULL` — so already-attempted PRs are excluded in SQL, and `--limit` is pushed into the query (`ORDER BY c.id` for stable batch order). Reruns/batches stream only the unprocessed head; no full-table `fetchall()`, no re-burned diff quota, no duplicate labels.\n- Every attempt is labelled at the patch tier so all states are skipped next run: the real category when kept, **`below-threshold`** for a fetched low-score miss, **`fetch-failed`** when no diff came back (delete those to retry).\n\nAdded a resume assertion: a second run processes nothing and re-fetches no diffs. 33 tests pass under `python3` and `-O`.\n\n---\n_Generated by [Claude 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