diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f82312a..b5c86ea 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -20,10 +20,28 @@ jobs:
- name: Enforce env contract parity
run: python3 scripts/check_env_contract.py
+ lint:
+ runs-on: ubuntu-latest
+ needs: [repo-hygiene]
+ steps:
+ - uses: actions/checkout@v4
+ - uses: actions/setup-python@v5
+ with:
+ python-version: "3.12"
+ - uses: astral-sh/setup-uv@v4
+ - run: uv sync --extra dev
+ - name: Ruff check
+ run: uv run ruff check .
+ - name: Ruff format check
+ run: uv run ruff format --check .
+ - name: Mypy
+ run: uv run mypy app/ --ignore-missing-imports
+
test:
runs-on: ubuntu-latest
needs:
- repo-hygiene
+ - lint
services:
postgres:
image: postgres:15
diff --git a/MODERNIZATION_PLAN.md b/MODERNIZATION_PLAN.md
new file mode 100644
index 0000000..6460767
--- /dev/null
+++ b/MODERNIZATION_PLAN.md
@@ -0,0 +1,628 @@
+# Scholarr Modernization Plan — Slices 2-10
+
+> **Slice 1 is complete** (commit `7736cab`): removed 114 stale `build/` files, fixed `.gitignore`, committed pending deletions, replaced `npm install` with `npm ci` in CI.
+>
+> Each slice below is a self-contained prompt designed for an LLM executor. Execute in order — each slice depends on the prior ones being complete.
+
+---
+
+## Slice 2: Create `structured_log()` Utility
+
+**Why:** The codebase has 19 `_log_*` helper functions (422 lines) and 138 instances of duplicated `"event"` keys in logging calls. A single utility eliminates all of it.
+
+**Files to create:**
+- `app/logging_utils.py`
+
+**Files to modify:**
+- `tests/unit/test_logging.py`
+
+**Context files (read but don't modify):**
+- `app/logging_config.py` — line 88 has `"event": getattr(record, "event", record.getMessage())` which means when no `event` key is in `extra`, it falls back to `getMessage()`. This is the mechanism that makes `structured_log()` work without duplicating the event name.
+- `app/logging_context.py`
+
+**Prompt:**
+```
+You are working on the scholarr repository. The current logging pattern has a DRY problem:
+
+1. Every log call duplicates the event name as both the message and in extra["event"]:
+ `logger.info("event.name", extra={"event": "event.name", "key": value})`
+
+2. There are 19 `_log_*` helper functions (422 lines total) that just wrap logger calls with typed signatures to build extra dicts.
+
+3. Metrics data (metric_name/metric_value) is mixed into log extra dicts but has no consumer.
+
+Create `app/logging_utils.py`:
+
+```python
+"""Structured logging utility — eliminates boilerplate across domain services."""
+
+from __future__ import annotations
+
+import logging
+from typing import Any
+
+
+def structured_log(
+ logger: logging.Logger,
+ level: str,
+ event: str,
+ /,
+ **fields: Any,
+) -> None:
+ """Emit a structured log entry.
+
+ The event name is passed as the log message. The JsonLogFormatter in
+ logging_config.py extracts it via record.getMessage() when no explicit
+ 'event' key exists in extra — so we do NOT duplicate it.
+
+ Usage:
+ structured_log(logger, "info", "ingestion.run_started", user_id=1, scholar_count=5)
+ """
+ fields.pop("metric_name", None)
+ fields.pop("metric_value", None)
+
+ log_method = getattr(logger, level.lower())
+ log_method(event, extra=fields)
+```
+
+Verify that `app/logging_config.py` line 88 already handles this correctly — when no `event` key is in extra, it falls back to getMessage() which returns the event string passed as the first argument. No changes to logging_config.py should be needed.
+
+Add tests in `tests/unit/test_logging.py` (append to existing file):
+- Test that `structured_log()` produces a log record where the JsonLogFormatter outputs the event name correctly
+- Test that `structured_log()` works with ConsoleLogFormatter
+- Test that metric_name/metric_value fields are stripped from output
+- Test that extra fields (user_id, scholar_id, etc.) appear in the formatted output
+
+Commit message: "refactor: add structured_log utility to eliminate logging boilerplate"
+```
+
+---
+
+## Slice 3: Migrate Ingestion Logging to `structured_log()`
+
+**Why:** `app/services/domains/ingestion/application.py` is 3,089 lines. 8 `_log_*` helpers consume ~239 lines. 34 inline logger calls duplicate event names and include dead metric fields. This slice removes ~300 lines.
+
+**Files to modify:**
+- `app/services/domains/ingestion/application.py`
+
+**Context files:**
+- `app/logging_utils.py` (created in Slice 2)
+
+**Prompt:**
+```
+You are working on the scholarr repository. The file `app/services/domains/ingestion/application.py` (3,089 lines) has 8 `_log_*` helper functions consuming ~239 lines, plus 34 inline logger calls with duplicated `"event":` keys and mixed `metric_name`/`metric_value` fields.
+
+Migrate ALL logging in this file to use `structured_log()` from `app.logging_utils`.
+
+1. Add `from app.logging_utils import structured_log` at the top.
+
+2. Delete these 8 helper methods entirely:
+ - `_log_request_delay_coercion` (line ~123, 21 lines)
+ - `_log_run_started` (line ~310, 36 lines)
+ - `_log_scholar_parsed` (line ~383, 28 lines)
+ - `_log_alert_thresholds` (line ~1013, 47 lines)
+ - `_log_safety_transition` (line ~1093, 42 lines)
+ - `_log_run_completed` (line ~1178, 28 lines)
+ - `_attempt_log_entry` (line ~1837, 16 lines)
+ - `_page_log_entry` (line ~1999, 21 lines)
+
+3. Replace every call to these deleted helpers with an inline `structured_log()` call. Example:
+
+ Before:
+ ```python
+ self._log_run_started(
+ user_id=user_id,
+ trigger_type=trigger_type,
+ scholar_count=scholar_count,
+ ...
+ )
+ ```
+
+ After:
+ ```python
+ structured_log(
+ logger, "info", "ingestion.run_started",
+ user_id=user_id,
+ trigger_type=trigger_type.value,
+ scholar_count=scholar_count,
+ ...
+ )
+ ```
+
+4. For ALL remaining inline `logger.info/warning/debug/exception()` calls:
+ - Replace with `structured_log()` where the call uses `extra={"event": ..., ...}` pattern
+ - Do NOT convert `logger.exception()` calls — keep them but remove the duplicated `"event"` key from their extra dict
+ - Remove `metric_name` and `metric_value` from all calls
+
+5. Do NOT change any business logic. Only logging call sites.
+
+Expected outcome: ~300 lines removed. All existing tests must pass unchanged.
+
+Commit message: "refactor: migrate ingestion service logging to structured_log"
+```
+
+---
+
+## Slice 4: Migrate All Remaining Services to `structured_log()`
+
+**Why:** 11 more `_log_*` helpers remain across 8 files (183 lines total), plus inline logger calls with the same duplication pattern in ~20 files.
+
+**Files to modify (all have `_log_*` helpers to delete):**
+- `app/services/domains/ingestion/scheduler.py` — `_log_queue_item_resolved` (line ~518, 21 lines)
+- `app/services/domains/arxiv/rate_limit.py` — `_log_request_scheduled` (199), `_log_request_completed` (216), `_log_cooldown_activated` (235)
+- `app/services/domains/arxiv/client.py` — `_log_cache_event` (283), `_log_request_skipped_for_cooldown` (299)
+- `app/services/domains/publications/pdf_resolution_pipeline.py` — `_log_arxiv_skip` (148)
+- `app/services/domains/unpaywall/application.py` — `_log_resolution_summary` (194)
+- `app/api/routers/publications.py` — `_log_retry_pdf_result` (343)
+- `app/api/routers/settings.py` — `_log_settings_update` (103)
+- `app/main.py` — `_log_startup_build_marker` (53)
+
+**Files to modify (inline `extra={"event":...}` pattern only — no helpers to delete):**
+- `app/http/middleware.py`
+- `app/db/session.py`
+- `app/auth/runtime.py`
+- `app/security/csrf.py`
+- `app/api/routers/scholars.py`
+- `app/api/routers/runs.py`
+- `app/api/routers/admin_dbops.py`
+- `app/api/routers/admin.py`
+- `app/api/routers/auth.py`
+- `app/api/routers/publications.py`
+- `app/services/domains/scholars/application.py`
+- `app/services/domains/runs/events.py`
+- `app/services/domains/openalex/client.py`
+- `app/services/domains/openalex/matching.py`
+- `app/services/domains/crossref/application.py`
+- `app/services/domains/publications/dedup.py`
+- `app/services/domains/publications/enrichment.py`
+- `app/services/domains/publications/pdf_queue.py`
+- `app/services/domains/scholar/source.py`
+- `app/services/domains/arxiv/gateway.py`
+
+**Prompt:**
+```
+You are working on the scholarr repository. Slice 3 migrated `ingestion/application.py` to `structured_log()`. Now do the same for ALL remaining files.
+
+1. Delete these `_log_*` helper functions and replace their call sites with inline `structured_log()`:
+
+ - `app/services/domains/ingestion/scheduler.py:~518` — `_log_queue_item_resolved` (21 lines)
+ - `app/services/domains/arxiv/rate_limit.py:~199` — `_log_request_scheduled` (17 lines)
+ - `app/services/domains/arxiv/rate_limit.py:~216` — `_log_request_completed` (19 lines)
+ - `app/services/domains/arxiv/rate_limit.py:~235` — `_log_cooldown_activated` (13 lines)
+ - `app/services/domains/arxiv/client.py:~283` — `_log_cache_event` (16 lines)
+ - `app/services/domains/arxiv/client.py:~299` — `_log_request_skipped_for_cooldown` (13 lines)
+ - `app/services/domains/publications/pdf_resolution_pipeline.py:~148` — `_log_arxiv_skip` (11 lines)
+ - `app/services/domains/unpaywall/application.py:~194` — `_log_resolution_summary` (21 lines)
+ - `app/api/routers/publications.py:~343` — `_log_retry_pdf_result` (24 lines)
+ - `app/api/routers/settings.py:~103` — `_log_settings_update` (15 lines)
+ - `app/main.py:~53` — `_log_startup_build_marker` (13 lines)
+
+2. In ALL files under `app/` that have inline `logger.info/warning/debug("event.name", extra={"event": "event.name", ...})` calls:
+ - Replace with `structured_log(logger, "level", "event.name", key=value, ...)`
+ - Add `from app.logging_utils import structured_log` import
+ - Remove `metric_name`/`metric_value` from all calls
+ - Keep `logger.exception()` calls but remove the duplicated `"event"` key from their extra dicts
+
+3. In `app/services/domains/openalex/client.py`, the lines that log `response.text` (lines ~87, ~137):
+ - Truncate: `response.text[:500]`
+
+4. Do NOT change any business logic. Only logging call sites.
+
+Verify: `grep -rn '"event":' app/ --include="*.py" | grep -v __pycache__` should return 0 matches.
+Verify: `grep -rn 'def _log_' app/ --include="*.py"` should return 0 matches.
+
+Commit message: "refactor: migrate all remaining logging to structured_log, remove boilerplate helpers"
+```
+
+---
+
+## Slice 5: Logging Relevance Audit — Reduce Noise, Improve Readability
+
+**Why:** Self-hosted users need clear, actionable logs. Current logging has verbose debug noise (per-HTTP-request, per-publication), overly long event names, and no console display optimization.
+
+**Files to modify:**
+- `app/services/domains/scholar/source.py`
+- `app/services/domains/ingestion/application.py`
+- `app/logging_config.py`
+- Any files with event names longer than ~40 chars
+
+**Prompt:**
+```
+You are working on the scholarr repository. The logging has been migrated to `structured_log()` (slices 2-4). Now audit log RELEVANCE and READABILITY for self-hosted users running this in Docker.
+
+1. **Remove redundant debug logs:**
+ - `app/services/domains/scholar/source.py`: Remove the 3 debug-level HTTP fetch events (fetch_started, search_fetch_started, publication_fetch_started). Keep only `fetch_succeeded` at DEBUG. The HTTP middleware already logs request.started/completed.
+ - `app/services/domains/ingestion/application.py`: Remove per-publication `publication.discovered` and `publication.created` DEBUG logs. The run_completed summary already reports totals.
+
+2. **Shorten overly long event names** (search all structured_log calls in app/):
+ - `ingestion.request_delay_coerced_to_policy_floor` → `ingestion.delay_coerced`
+ - `ingestion.safety_cooldown_cleared` → `ingestion.cooldown_cleared`
+ - Any other names longer than ~40 chars — shorten while preserving meaning
+
+3. **Improve console readability** in `app/logging_config.py` `ConsoleLogFormatter.format()`:
+ - Add a short-name mapping for common context fields in console output ONLY (JSON keeps full names):
+ ```python
+ _CONSOLE_SHORT_KEYS = {
+ "user_id": "user",
+ "scholar_id": "scholar",
+ "crawl_run_id": "run",
+ "run_id": "run",
+ }
+ ```
+ - Apply in the `for key in sorted(payload.keys())` loop
+
+4. Do NOT remove any WARNING or ERROR level logs. Only remove/demote DEBUG/INFO that are redundant.
+5. Do NOT change business logic.
+
+Commit message: "refactor: reduce log noise, improve event naming and console readability"
+```
+
+---
+
+## Slice 6: Add Ruff + Mypy to CI
+
+**Why:** No Python linting or type checking in CI. Code quality regressions go undetected.
+
+**Files to modify:**
+- `pyproject.toml`
+- `.github/workflows/ci.yml`
+
+**Prompt:**
+```
+You are working on the scholarr repository. Add Python linting and type checking to CI.
+
+1. In `pyproject.toml`, add ruff configuration:
+ ```toml
+ [tool.ruff]
+ target-version = "py312"
+ line-length = 120
+
+ [tool.ruff.lint]
+ select = ["E", "F", "W", "I", "UP", "B", "SIM", "RUF"]
+ ignore = ["E501"]
+
+ [tool.ruff.lint.isort]
+ known-first-party = ["app"]
+ ```
+
+2. In `pyproject.toml`, add mypy configuration:
+ ```toml
+ [tool.mypy]
+ python_version = "3.12"
+ ignore_missing_imports = true
+ check_untyped_defs = false
+ warn_unused_ignores = true
+ ```
+
+3. In `.github/workflows/ci.yml`, add a `lint` job after `repo-hygiene` and before `test`:
+ ```yaml
+ lint:
+ runs-on: ubuntu-latest
+ needs: [repo-hygiene]
+ steps:
+ - uses: actions/checkout@v4
+ - uses: actions/setup-python@v5
+ with:
+ python-version: "3.12"
+ - uses: astral-sh/setup-uv@v4
+ - run: uv sync --extra dev
+ - name: Ruff check
+ run: uv run ruff check .
+ - name: Ruff format check
+ run: uv run ruff format --check .
+ - name: Mypy
+ run: uv run mypy app/ --ignore-missing-imports
+ ```
+
+4. Update the `test` job's `needs` to include `lint`.
+
+5. Add `ruff` and `mypy` to dev dependencies in `pyproject.toml` under `[project.optional-dependencies]`.
+
+6. Run `ruff check .` locally and fix auto-fixable issues with `ruff check --fix .`. For unfixable issues, add targeted `noqa` comments only if fixing would change behavior.
+
+Commit message: "ci: add ruff linting and mypy type checking"
+```
+
+---
+
+## Slice 7: Add CodeQL + Dependabot
+
+**Why:** No security scanning. Missed vulnerabilities, no automated dependency updates.
+
+**Files to create:**
+- `.github/workflows/codeql.yml`
+- `.github/dependabot.yml`
+
+**Prompt:**
+```
+You are working on the scholarr repository. Add security scanning.
+
+1. Create `.github/workflows/codeql.yml`:
+ ```yaml
+ name: CodeQL
+
+ on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+ schedule:
+ - cron: "30 5 * * 1"
+
+ jobs:
+ analyze:
+ runs-on: ubuntu-latest
+ permissions:
+ security-events: write
+ contents: read
+ strategy:
+ matrix:
+ language: [python, javascript]
+ steps:
+ - uses: actions/checkout@v4
+ - uses: github/codeql-action/init@v3
+ with:
+ languages: ${{ matrix.language }}
+ - uses: github/codeql-action/autobuild@v3
+ - uses: github/codeql-action/analyze@v3
+ ```
+
+2. Create `.github/dependabot.yml`:
+ ```yaml
+ version: 2
+ updates:
+ - package-ecosystem: pip
+ directory: /
+ schedule:
+ interval: weekly
+ - package-ecosystem: npm
+ directory: /frontend
+ schedule:
+ interval: weekly
+ - package-ecosystem: github-actions
+ directory: /
+ schedule:
+ interval: weekly
+ ```
+
+Commit message: "ci: add CodeQL security scanning and Dependabot"
+```
+
+---
+
+## Slice 8: Fix Version Remnants + Adopt Semantic Release
+
+**Why:** Version `0.1.0` is hardcoded in 5 places (including `crossref/application.py:294`). `0.0.1` exists in `docs/website/package.json`. No CHANGELOG, no GitHub Releases.
+
+**Files to modify:**
+- `pyproject.toml`
+- `app/services/domains/crossref/application.py`
+
+**Files to create:**
+- `.github/workflows/release.yml`
+
+**Prompt:**
+```
+You are working on the scholarr repository. Set up automated versioning with python-semantic-release.
+
+1. Fix hardcoded version in `app/services/domains/crossref/application.py` (line ~294):
+ ```python
+ # Before:
+ etiquette = Etiquette(settings.app_name, "0.1.0", "https://scholarr.local", email)
+
+ # After:
+ from importlib.metadata import version as pkg_version
+ _APP_VERSION = pkg_version("scholarr")
+ # then in function:
+ etiquette = Etiquette(settings.app_name, _APP_VERSION, "https://scholarr.local", email)
+ ```
+
+2. In `pyproject.toml`, add semantic-release config:
+ ```toml
+ [tool.semantic_release]
+ version_toml = ["pyproject.toml:project.version"]
+ version_variables = ["frontend/package.json:version"]
+ branch = "main"
+ build_command = ""
+ commit_message = "chore(release): v{version}"
+ ```
+
+3. Create `.github/workflows/release.yml`:
+ ```yaml
+ name: Release
+
+ on:
+ push:
+ branches: [main]
+
+ jobs:
+ release:
+ runs-on: ubuntu-latest
+ if: github.repository == 'JustinZeus/scholarr'
+ permissions:
+ contents: write
+ id-token: write
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ fetch-depth: 0
+ token: ${{ secrets.GITHUB_TOKEN }}
+ - uses: actions/setup-python@v5
+ with:
+ python-version: "3.12"
+ - run: pip install python-semantic-release
+ - name: Semantic Release
+ id: release
+ run: semantic-release publish
+ env:
+ GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ ```
+
+4. Add `python-semantic-release` to dev dependencies in `pyproject.toml`.
+
+Note: `docs/website/package.json` version (`0.0.1`) is addressed in Slice 9 (docs rebuild). `frontend/package-lock.json` and `uv.lock` versions auto-update on next `npm install`/`uv sync`.
+
+Commit message: "ci: adopt python-semantic-release, fix hardcoded version strings"
+```
+
+---
+
+## Slice 9: Docs — Delete and Rebuild from Scratch
+
+**Why:** Current docs have split authority (two api-contract.md files), orphaned pages, stale version (`0.0.1`), and missing critical docs (testing, deployment, configuration reference). Clean slate is faster than migration.
+
+**Files to delete:**
+- `docs/` (entire directory)
+
+**Files to create:**
+- Complete new `docs/` tree
+
+**Prompt:**
+```
+You are working on the scholarr repository. Delete the entire `docs/` directory and rebuild from scratch.
+
+Target IA:
+
+docs/
+├── index.md # Landing page: what is scholarr, quick links
+├── user/
+│ ├── overview.md # What scholarr does, key concepts
+│ ├── getting-started.md # Install (docker compose), first run, add first scholar
+│ └── configuration.md # ALL env vars from .env.example, organized by category
+├── developer/
+│ ├── overview.md # Dev quickstart
+│ ├── architecture.md # FastAPI + SQLAlchemy + Vue 3, domain service boundaries
+│ ├── local-development.md # docker-compose.dev.yml, hot reload, running tests
+│ ├── contributing.md # PR process, conventional commits, code standards from agents.md
+│ ├── ingestion.md # Ingestion pipeline: parsing, rate limiting, safety gates
+│ ├── frontend-theme-inventory.md # Theme tokens, Tailwind integration
+│ └── testing.md # Test tiers (unit/integration/smoke), markers, fixtures, how to run
+├── operations/
+│ ├── overview.md # Ops quickstart
+│ ├── deployment.md # Production Docker, scaling, health checks
+│ ├── database-runbook.md # Backup, restore, integrity checks, migration procedures
+│ ├── scrape-safety-runbook.md # Rate limiting, cooldowns, CAPTCHA handling
+│ └── arxiv-runbook.md # ArXiv rate limits, cache, query patterns
+├── reference/
+│ ├── overview.md # Reference index
+│ ├── api.md # CANONICAL: envelope spec + endpoints + DTO contract
+│ ├── environment.md # Env var quick-reference (links to user/configuration.md)
+│ └── changelog.md # Placeholder: "auto-generated by semantic-release"
+└── website/
+ ├── docusaurus.config.js
+ ├── sidebars.js # ALL pages listed, no orphans
+ ├── package.json # version: "0.1.0"
+ └── src/css/custom.css
+
+Content guidelines:
+- Self-contained, scannable docs (headers, bullets, tables)
+- Frontmatter: `title`, `sidebar_position`
+- `configuration.md`: read `.env.example`, organize every variable with description, type, default, example
+- `testing.md`: pytest markers from pyproject.toml (`integration`, `db`, `migrations`, `schema`, `smoke`), container-based runner from agents.md, fixture org under tests/fixtures/
+- `api.md`: merge old `developer/api-contract.md` (DTO structure) and `reference/api-contract.md` (envelope spec). Include exact envelope shapes:
+ - Success: `{"data": ..., "meta": {"request_id": "..."}}`
+ - Error: `{"error": {"code": "...", "message": "...", "details": ...}, "meta": {"request_id": "..."}}`
+ - Publication semantics (modes, pagination, identifiers)
+ - Scholar portability endpoints
+- `deployment.md`: practical Docker commands from docker-compose.yml
+- `database-runbook.md`: reference scripts/db/ (backup_full.sh, restore_dump.sh, check_integrity.py, repair_publication_links.py)
+
+Docusaurus config:
+- url: "https://justinzeus.github.io"
+- baseUrl: "/scholarr/"
+- organizationName: "JustinZeus"
+- projectName: "scholarr"
+- onBrokenLinks: "throw"
+- docs path: ".." (reads from docs/ parent)
+- Exclude: "website/**", "README.md"
+
+Commit message: "docs: rebuild documentation from scratch with clean IA"
+```
+
+---
+
+## Slice 10: Begin `ingestion/application.py` Decomposition
+
+**Why:** After logging cleanup (slices 3+5), the file is ~2,700-2,800 lines. Still the largest source file by 3x. This begins decomposition with the safest extract: safety gate logic.
+
+**Files to modify:**
+- `app/services/domains/ingestion/application.py`
+
+**Files to create:**
+- `app/services/domains/ingestion/safety.py`
+
+**Prompt:**
+```
+You are working on the scholarr repository. `app/services/domains/ingestion/application.py` is ~2,700-2,800 lines (after logging cleanup). It contains the entire ingestion orchestration in a single class.
+
+Extract the FIRST logical chunk: safety gate logic.
+
+1. Read `app/services/domains/ingestion/application.py` fully.
+
+2. Identify safety/cooldown methods:
+ - `_enforce_safety_gate`
+ - `_raise_safety_blocked_start`
+ - Cooldown activation/clearing methods
+ - Alert threshold evaluation methods
+
+3. Create `app/services/domains/ingestion/safety.py`:
+ - Move identified methods to standalone functions or a small class
+ - Accept explicit parameters (no implicit self.xxx state)
+ - Keep same function signatures where possible
+
+4. Update `application.py` to import from `safety.py`.
+
+5. Run full test suite: `docker compose -f docker-compose.yml -f docker-compose.dev.yml run --rm app pytest tests/`
+ All tests must pass unchanged.
+
+Constraints from `agents.md`:
+- Max 50 lines per function
+- No flat files in `app/services/` root — all within `app/services/domains/ingestion/`
+- Fail fast, early returns, guard clauses
+
+Commit message: "refactor: extract ingestion safety gate logic to dedicated module"
+```
+
+---
+
+## Verification (after all slices)
+
+Run these checks to confirm everything is clean:
+
+```bash
+# 1. No tracked build artifacts
+git ls-files build/ | wc -l # expect: 0
+
+# 2. No duplicated event keys in logging
+grep -rn '"event":' app/ --include="*.py" | grep -v __pycache__ | wc -l # expect: 0
+
+# 3. No _log_ helper functions remain
+grep -rn 'def _log_' app/ --include="*.py" | wc -l # expect: 0
+
+# 4. No stale version strings
+grep -rn '0\.0\.1' . --include="*.py" --include="*.json" --include="*.toml" \
+ | grep -v node_modules | grep -v .venv | grep -v uv.lock | wc -l # expect: 0
+
+# 5. Docs build
+npm --prefix docs/website run build # expect: success, no broken links
+
+# 6. All tests pass
+docker compose -f docker-compose.yml -f docker-compose.dev.yml run --rm app pytest tests/
+```
+
+---
+
+## Slice Summary
+
+| # | Slice | Files Changed | Estimated Impact |
+|---|-------|---------------|------------------|
+| ~~1~~ | ~~Repo hygiene~~ | ~~120 files~~ | ~~-18,380 lines~~ **DONE** |
+| 2 | `structured_log()` utility | 2 files | +50 lines |
+| 3 | Migrate ingestion logging | 1 file | -300 lines |
+| 4 | Migrate remaining logging | ~20 files | -180 lines |
+| 5 | Logging noise/readability | ~5 files | -30 lines, better output |
+| 6 | Ruff + mypy in CI | 2 files | +50 lines config |
+| 7 | CodeQL + Dependabot | 2 files | +40 lines config |
+| 8 | Version fix + semantic-release | 3 files | +40 lines config |
+| 9 | Docs rebuild | full replacement | ~20 new files |
+| 10 | Ingestion decomposition | 2 files | net zero (move) |
diff --git a/alembic/env.py b/alembic/env.py
index 17575e4..127078d 100644
--- a/alembic/env.py
+++ b/alembic/env.py
@@ -1,13 +1,13 @@
-from logging.config import fileConfig
import os
+from logging.config import fileConfig
-from alembic import context
from sqlalchemy import pool
from sqlalchemy.engine import Connection
from sqlalchemy.ext.asyncio import async_engine_from_config
-from app.db.base import metadata
+from alembic import context
from app.db import models # noqa: F401
+from app.db.base import metadata
config = context.config
diff --git a/alembic/versions/20260216_0001_multi_user_schema.py b/alembic/versions/20260216_0001_multi_user_schema.py
index 221bbf7..6c9375e 100644
--- a/alembic/versions/20260216_0001_multi_user_schema.py
+++ b/alembic/versions/20260216_0001_multi_user_schema.py
@@ -8,10 +8,11 @@ Create Date: 2026-02-16 17:10:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
+from alembic import op
+
# revision identifiers, used by Alembic.
revision: str = "20260216_0001"
down_revision: str | Sequence[str] | None = None
diff --git a/alembic/versions/20260216_0002_add_user_admin_flag.py b/alembic/versions/20260216_0002_add_user_admin_flag.py
index e60de0f..5ea932d 100644
--- a/alembic/versions/20260216_0002_add_user_admin_flag.py
+++ b/alembic/versions/20260216_0002_add_user_admin_flag.py
@@ -7,9 +7,10 @@ Create Date: 2026-02-16 17:40:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
+
# revision identifiers, used by Alembic.
revision: str = "20260216_0002"
down_revision: str | Sequence[str] | None = "20260216_0001"
@@ -31,4 +32,3 @@ def upgrade() -> None:
def downgrade() -> None:
op.drop_column("users", "is_admin")
-
diff --git a/alembic/versions/20260216_0003_add_ingestion_queue.py b/alembic/versions/20260216_0003_add_ingestion_queue.py
index cc03867..4c81fa0 100644
--- a/alembic/versions/20260216_0003_add_ingestion_queue.py
+++ b/alembic/versions/20260216_0003_add_ingestion_queue.py
@@ -7,9 +7,10 @@ Create Date: 2026-02-16 23:45:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
+
# revision identifiers, used by Alembic.
revision: str = "20260216_0003"
down_revision: str | Sequence[str] | None = "20260216_0002"
diff --git a/alembic/versions/20260217_0004_queue_status_fields.py b/alembic/versions/20260217_0004_queue_status_fields.py
index 68da9dd..f6c29e6 100644
--- a/alembic/versions/20260217_0004_queue_status_fields.py
+++ b/alembic/versions/20260217_0004_queue_status_fields.py
@@ -7,9 +7,10 @@ Create Date: 2026-02-17 10:15:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
+
# revision identifiers, used by Alembic.
revision: str = "20260217_0004"
down_revision: str | Sequence[str] | None = "20260216_0003"
@@ -22,9 +23,7 @@ def upgrade() -> None:
inspector = sa.inspect(bind)
columns = {column["name"] for column in inspector.get_columns("ingestion_queue_items")}
indexes = {index["name"] for index in inspector.get_indexes("ingestion_queue_items")}
- checks = {
- constraint["name"] for constraint in inspector.get_check_constraints("ingestion_queue_items")
- }
+ checks = {constraint["name"] for constraint in inspector.get_check_constraints("ingestion_queue_items")}
if "status" not in columns:
op.add_column(
@@ -80,9 +79,7 @@ def downgrade() -> None:
inspector = sa.inspect(bind)
columns = {column["name"] for column in inspector.get_columns("ingestion_queue_items")}
indexes = {index["name"] for index in inspector.get_indexes("ingestion_queue_items")}
- checks = {
- constraint["name"] for constraint in inspector.get_check_constraints("ingestion_queue_items")
- }
+ checks = {constraint["name"] for constraint in inspector.get_check_constraints("ingestion_queue_items")}
if "ix_ingestion_queue_status_next_attempt" in indexes:
op.drop_index("ix_ingestion_queue_status_next_attempt", table_name="ingestion_queue_items")
diff --git a/alembic/versions/20260217_0005_manual_run_idempotency.py b/alembic/versions/20260217_0005_manual_run_idempotency.py
index 0375569..ad0269b 100644
--- a/alembic/versions/20260217_0005_manual_run_idempotency.py
+++ b/alembic/versions/20260217_0005_manual_run_idempotency.py
@@ -7,9 +7,10 @@ Create Date: 2026-02-17 16:20:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
+
# revision identifiers, used by Alembic.
revision: str = "20260217_0005"
down_revision: str | Sequence[str] | None = "20260217_0004"
@@ -70,9 +71,7 @@ def upgrade() -> None:
"crawl_runs",
["user_id", "idempotency_key"],
unique=True,
- postgresql_where=sa.text(
- "idempotency_key IS NOT NULL AND trigger_type = 'manual'::run_trigger_type"
- ),
+ postgresql_where=sa.text("idempotency_key IS NOT NULL AND trigger_type = 'manual'::run_trigger_type"),
)
diff --git a/alembic/versions/20260217_0006_scholar_profile_images.py b/alembic/versions/20260217_0006_scholar_profile_images.py
index 08035c8..f736737 100644
--- a/alembic/versions/20260217_0006_scholar_profile_images.py
+++ b/alembic/versions/20260217_0006_scholar_profile_images.py
@@ -7,9 +7,10 @@ Create Date: 2026-02-17 18:30:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
+
# revision identifiers, used by Alembic.
revision: str = "20260217_0006"
down_revision: str | Sequence[str] | None = "20260217_0005"
diff --git a/alembic/versions/20260217_0007_scholar_initial_page_fingerprint.py b/alembic/versions/20260217_0007_scholar_initial_page_fingerprint.py
index dcfd0f7..6022c4c 100644
--- a/alembic/versions/20260217_0007_scholar_initial_page_fingerprint.py
+++ b/alembic/versions/20260217_0007_scholar_initial_page_fingerprint.py
@@ -7,9 +7,10 @@ Create Date: 2026-02-17 18:55:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
+
# revision identifiers, used by Alembic.
revision: str = "20260217_0007"
down_revision: str | Sequence[str] | None = "20260217_0006"
diff --git a/alembic/versions/20260219_0008_user_settings_nav_visible_pages.py b/alembic/versions/20260219_0008_user_settings_nav_visible_pages.py
index df481fd..ef38677 100644
--- a/alembic/versions/20260219_0008_user_settings_nav_visible_pages.py
+++ b/alembic/versions/20260219_0008_user_settings_nav_visible_pages.py
@@ -7,10 +7,10 @@ Create Date: 2026-02-19 14:58:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
+from alembic import op
# revision identifiers, used by Alembic.
revision: str = "20260219_0008"
@@ -21,7 +21,7 @@ depends_on: str | Sequence[str] | None = None
TABLE_NAME = "user_settings"
DEFAULT_NAV_VISIBLE_PAGES_SQL = (
- "'[\"dashboard\",\"scholars\",\"publications\",\"settings\",\"style-guide\",\"runs\",\"users\"]'::jsonb"
+ '\'["dashboard","scholars","publications","settings","style-guide","runs","users"]\'::jsonb'
)
diff --git a/alembic/versions/20260219_0009_user_settings_scrape_safety_state.py b/alembic/versions/20260219_0009_user_settings_scrape_safety_state.py
index 9ea658b..175b6b7 100644
--- a/alembic/versions/20260219_0009_user_settings_scrape_safety_state.py
+++ b/alembic/versions/20260219_0009_user_settings_scrape_safety_state.py
@@ -7,10 +7,10 @@ Create Date: 2026-02-19 21:20:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
+from alembic import op
# revision identifiers, used by Alembic.
revision: str = "20260219_0009"
diff --git a/alembic/versions/20260219_0010_author_search_shared_state.py b/alembic/versions/20260219_0010_author_search_shared_state.py
index bc2b97d..0a07a42 100644
--- a/alembic/versions/20260219_0010_author_search_shared_state.py
+++ b/alembic/versions/20260219_0010_author_search_shared_state.py
@@ -7,10 +7,10 @@ Create Date: 2026-02-19 22:20:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
+from alembic import op
# revision identifiers, used by Alembic.
revision: str = "20260219_0010"
diff --git a/alembic/versions/20260220_0011_add_publication_doi.py b/alembic/versions/20260220_0011_add_publication_doi.py
index bb9a813..c286a00 100644
--- a/alembic/versions/20260220_0011_add_publication_doi.py
+++ b/alembic/versions/20260220_0011_add_publication_doi.py
@@ -7,9 +7,9 @@ Create Date: 2026-02-20 13:35:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
revision: str = "20260220_0011"
down_revision: str | Sequence[str] | None = "20260219_0010"
diff --git a/alembic/versions/20260220_0012_add_data_repair_jobs.py b/alembic/versions/20260220_0012_add_data_repair_jobs.py
index 242876d..6e7b53f 100644
--- a/alembic/versions/20260220_0012_add_data_repair_jobs.py
+++ b/alembic/versions/20260220_0012_add_data_repair_jobs.py
@@ -7,10 +7,10 @@ Create Date: 2026-02-20 23:35:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
+from alembic import op
revision: str = "20260220_0012"
down_revision: str | Sequence[str] | None = "20260220_0011"
diff --git a/alembic/versions/20260221_0013_add_publication_pdf_jobs.py b/alembic/versions/20260221_0013_add_publication_pdf_jobs.py
index 63db6b2..d7046d9 100644
--- a/alembic/versions/20260221_0013_add_publication_pdf_jobs.py
+++ b/alembic/versions/20260221_0013_add_publication_pdf_jobs.py
@@ -7,9 +7,9 @@ Create Date: 2026-02-21 12:25:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
revision: str = "20260221_0013"
down_revision: str | Sequence[str] | None = "20260220_0012"
diff --git a/alembic/versions/20260221_0014_add_scholar_publication_favorite_state.py b/alembic/versions/20260221_0014_add_scholar_publication_favorite_state.py
index 1fa8f29..7c06d52 100644
--- a/alembic/versions/20260221_0014_add_scholar_publication_favorite_state.py
+++ b/alembic/versions/20260221_0014_add_scholar_publication_favorite_state.py
@@ -7,9 +7,9 @@ Create Date: 2026-02-21 14:35:00
from __future__ import annotations
-from alembic import op
import sqlalchemy as sa
+from alembic import op
# revision identifiers, used by Alembic.
revision = "20260221_0014"
diff --git a/alembic/versions/20260221_0015_enforce_request_delay_floor.py b/alembic/versions/20260221_0015_enforce_request_delay_floor.py
index 688ce0a..122f055 100644
--- a/alembic/versions/20260221_0015_enforce_request_delay_floor.py
+++ b/alembic/versions/20260221_0015_enforce_request_delay_floor.py
@@ -9,9 +9,9 @@ from __future__ import annotations
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
# revision identifiers, used by Alembic.
revision: str = "20260221_0015"
@@ -30,11 +30,7 @@ LEGACY_CHECK_NAME_MIN_2 = "ck_user_settings_request_delay_seconds_min_2"
def _check_constraints() -> set[str]:
bind = op.get_bind()
inspector = sa.inspect(bind)
- return {
- str(item.get("name"))
- for item in inspector.get_check_constraints(TABLE_NAME)
- if item.get("name")
- }
+ return {str(item.get("name")) for item in inspector.get_check_constraints(TABLE_NAME) if item.get("name")}
def _drop_check_if_exists(name: str) -> None:
@@ -48,12 +44,7 @@ def _drop_check_if_exists(name: str) -> None:
def upgrade() -> None:
- op.execute(
- sa.text(
- "UPDATE user_settings SET request_delay_seconds = 2 "
- "WHERE request_delay_seconds < 2"
- )
- )
+ op.execute(sa.text("UPDATE user_settings SET request_delay_seconds = 2 WHERE request_delay_seconds < 2"))
_drop_check_if_exists(CHECK_NAME_MIN_1)
_drop_check_if_exists(LEGACY_CHECK_NAME_MIN_1)
diff --git a/alembic/versions/20260222_0016_add_publication_identifiers.py b/alembic/versions/20260222_0016_add_publication_identifiers.py
index cd824a2..9730a2d 100644
--- a/alembic/versions/20260222_0016_add_publication_identifiers.py
+++ b/alembic/versions/20260222_0016_add_publication_identifiers.py
@@ -7,9 +7,9 @@ Create Date: 2026-02-22 12:45:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
revision: str = "20260222_0016"
down_revision: str | Sequence[str] | None = "20260221_0015"
diff --git a/alembic/versions/20260224_0018_add_openalex_enriched_to_publications.py b/alembic/versions/20260224_0018_add_openalex_enriched_to_publications.py
index 1d7ecad..ee669fe 100644
--- a/alembic/versions/20260224_0018_add_openalex_enriched_to_publications.py
+++ b/alembic/versions/20260224_0018_add_openalex_enriched_to_publications.py
@@ -5,26 +5,29 @@ Revises: fa0c5e3262d5
Create Date: 2026-02-24 19:10:00.000000
"""
+
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
# revision identifiers, used by Alembic.
-revision: str = '20260224_0018'
-down_revision: str | Sequence[str] | None = 'fa0c5e3262d5'
+revision: str = "20260224_0018"
+down_revision: str | Sequence[str] | None = "fa0c5e3262d5"
branch_labels: str | Sequence[str] | None = None
depends_on: str | Sequence[str] | None = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
- op.add_column('publications', sa.Column('openalex_enriched', sa.Boolean(), server_default=sa.text('false'), nullable=False))
+ op.add_column(
+ "publications", sa.Column("openalex_enriched", sa.Boolean(), server_default=sa.text("false"), nullable=False)
+ )
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
- op.drop_column('publications', 'openalex_enriched')
+ op.drop_column("publications", "openalex_enriched")
# ### end Alembic commands ###
diff --git a/alembic/versions/20260224_0019_add_resolving_to_runstatus.py b/alembic/versions/20260224_0019_add_resolving_to_runstatus.py
index 645a32b..163747c 100644
--- a/alembic/versions/20260224_0019_add_resolving_to_runstatus.py
+++ b/alembic/versions/20260224_0019_add_resolving_to_runstatus.py
@@ -5,14 +5,14 @@ Revises: 20260224_0018
Create Date: 2026-02-24 22:20:00.000000
"""
+
from collections.abc import Sequence
from alembic import op
-
# revision identifiers, used by Alembic.
-revision: str = '20260224_0019'
-down_revision: str | Sequence[str] | None = '20260224_0018'
+revision: str = "20260224_0019"
+down_revision: str | Sequence[str] | None = "20260224_0018"
branch_labels: str | Sequence[str] | None = None
depends_on: str | Sequence[str] | None = None
diff --git a/alembic/versions/20260224_0020_add_openalex_last_attempt_at.py b/alembic/versions/20260224_0020_add_openalex_last_attempt_at.py
index 024f547..1b239f6 100644
--- a/alembic/versions/20260224_0020_add_openalex_last_attempt_at.py
+++ b/alembic/versions/20260224_0020_add_openalex_last_attempt_at.py
@@ -5,22 +5,23 @@ Revises: 20260224_0019
Create Date: 2026-02-24 22:50:00.000000
"""
+
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
# revision identifiers, used by Alembic.
-revision: str = '20260224_0020'
-down_revision: str | Sequence[str] | None = '20260224_0019'
+revision: str = "20260224_0020"
+down_revision: str | Sequence[str] | None = "20260224_0019"
branch_labels: str | Sequence[str] | None = None
depends_on: str | Sequence[str] | None = None
def upgrade() -> None:
- op.add_column('publications', sa.Column('openalex_last_attempt_at', sa.DateTime(timezone=True), nullable=True))
+ op.add_column("publications", sa.Column("openalex_last_attempt_at", sa.DateTime(timezone=True), nullable=True))
def downgrade() -> None:
- op.drop_column('publications', 'openalex_last_attempt_at')
+ op.drop_column("publications", "openalex_last_attempt_at")
diff --git a/alembic/versions/20260225_0021_enforce_single_active_run_per_user.py b/alembic/versions/20260225_0021_enforce_single_active_run_per_user.py
index daaa2a6..f5b20f2 100644
--- a/alembic/versions/20260225_0021_enforce_single_active_run_per_user.py
+++ b/alembic/versions/20260225_0021_enforce_single_active_run_per_user.py
@@ -7,9 +7,9 @@ Create Date: 2026-02-25 09:10:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
# revision identifiers, used by Alembic.
revision: str = "20260225_0021"
@@ -56,9 +56,7 @@ def upgrade() -> None:
"crawl_runs",
["user_id"],
unique=True,
- postgresql_where=sa.text(
- "status IN ('running'::run_status, 'resolving'::run_status)"
- ),
+ postgresql_where=sa.text("status IN ('running'::run_status, 'resolving'::run_status)"),
)
diff --git a/alembic/versions/20260225_0022_add_canonical_title_hash_to_publications.py b/alembic/versions/20260225_0022_add_canonical_title_hash_to_publications.py
index f73d280..97ba39d 100644
--- a/alembic/versions/20260225_0022_add_canonical_title_hash_to_publications.py
+++ b/alembic/versions/20260225_0022_add_canonical_title_hash_to_publications.py
@@ -7,9 +7,9 @@ Create Date: 2026-02-25 10:00:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
# revision identifiers, used by Alembic.
revision: str = "20260225_0022"
diff --git a/alembic/versions/20260226_0023_add_arxiv_runtime_state.py b/alembic/versions/20260226_0023_add_arxiv_runtime_state.py
index b75cd0e..b9efd0d 100644
--- a/alembic/versions/20260226_0023_add_arxiv_runtime_state.py
+++ b/alembic/versions/20260226_0023_add_arxiv_runtime_state.py
@@ -7,9 +7,9 @@ Create Date: 2026-02-26 12:40:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
+from alembic import op
# revision identifiers, used by Alembic.
revision: str = "20260226_0023"
diff --git a/alembic/versions/20260226_0024_add_arxiv_query_cache_entries.py b/alembic/versions/20260226_0024_add_arxiv_query_cache_entries.py
index fe2c0bc..8fddda4 100644
--- a/alembic/versions/20260226_0024_add_arxiv_query_cache_entries.py
+++ b/alembic/versions/20260226_0024_add_arxiv_query_cache_entries.py
@@ -7,10 +7,10 @@ Create Date: 2026-02-26 14:20:00.000000
from collections.abc import Sequence
-from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
+from alembic import op
# revision identifiers, used by Alembic.
revision: str = "20260226_0024"
diff --git a/app/api/__init__.py b/app/api/__init__.py
index 3ce55a6..9d48db4 100644
--- a/app/api/__init__.py
+++ b/app/api/__init__.py
@@ -1,2 +1 @@
from __future__ import annotations
-
diff --git a/app/api/errors.py b/app/api/errors.py
index 976ccb8..d926690 100644
--- a/app/api/errors.py
+++ b/app/api/errors.py
@@ -82,4 +82,3 @@ def register_api_exception_handlers(app: FastAPI) -> None:
message="Request validation failed.",
details=exc.errors(),
)
-
diff --git a/app/api/routers/__init__.py b/app/api/routers/__init__.py
index 3ce55a6..9d48db4 100644
--- a/app/api/routers/__init__.py
+++ b/app/api/routers/__init__.py
@@ -1,2 +1 @@
from __future__ import annotations
-
diff --git a/app/api/routers/admin.py b/app/api/routers/admin.py
index b1f99b8..416b084 100644
--- a/app/api/routers/admin.py
+++ b/app/api/routers/admin.py
@@ -86,7 +86,14 @@ async def create_user(
message=str(exc),
) from exc
- structured_log(logger, "info", "api.admin.user_created", admin_user_id=int(admin_user.id), target_user_id=int(created_user.id), target_is_admin=bool(created_user.is_admin))
+ structured_log(
+ logger,
+ "info",
+ "api.admin.user_created",
+ admin_user_id=int(admin_user.id),
+ target_user_id=int(created_user.id),
+ target_is_admin=bool(created_user.is_admin),
+ )
return success_payload(
request,
data=_serialize_user(created_user),
@@ -111,11 +118,7 @@ async def set_user_active(
code="user_not_found",
message="User not found.",
)
- if (
- int(target_user.id) == int(admin_user.id)
- and bool(target_user.is_active)
- and not bool(payload.is_active)
- ):
+ if int(target_user.id) == int(admin_user.id) and bool(target_user.is_active) and not bool(payload.is_active):
raise ApiException(
status_code=400,
code="cannot_deactivate_self",
@@ -126,7 +129,14 @@ async def set_user_active(
user=target_user,
is_active=bool(payload.is_active),
)
- structured_log(logger, "info", "api.admin.user_active_updated", admin_user_id=int(admin_user.id), target_user_id=int(updated_user.id), is_active=bool(updated_user.is_active))
+ structured_log(
+ logger,
+ "info",
+ "api.admin.user_active_updated",
+ admin_user_id=int(admin_user.id),
+ target_user_id=int(updated_user.id),
+ is_active=bool(updated_user.is_active),
+ )
return success_payload(
request,
data=_serialize_user(updated_user),
@@ -166,7 +176,13 @@ async def reset_user_password(
user=target_user,
password_hash=auth_service.hash_password(validated_password),
)
- structured_log(logger, "info", "api.admin.user_password_reset", admin_user_id=int(admin_user.id), target_user_id=int(target_user.id))
+ structured_log(
+ logger,
+ "info",
+ "api.admin.user_password_reset",
+ admin_user_id=int(admin_user.id),
+ target_user_id=int(target_user.id),
+ )
return success_payload(
request,
data={"message": f"Password reset: {target_user.email}"},
diff --git a/app/api/routers/admin_dbops.py b/app/api/routers/admin_dbops.py
index 57498c1..f465268 100644
--- a/app/api/routers/admin_dbops.py
+++ b/app/api/routers/admin_dbops.py
@@ -10,14 +10,14 @@ from app.api.errors import ApiException
from app.api.responses import success_payload
from app.api.schemas import (
AdminDbIntegrityEnvelope,
- AdminPdfQueueBulkEnqueueEnvelope,
- AdminPdfQueueRequeueEnvelope,
- AdminPdfQueueEnvelope,
AdminDbRepairJobsEnvelope,
- AdminRepairPublicationNearDuplicatesEnvelope,
- AdminRepairPublicationNearDuplicatesRequest,
+ AdminPdfQueueBulkEnqueueEnvelope,
+ AdminPdfQueueEnvelope,
+ AdminPdfQueueRequeueEnvelope,
AdminRepairPublicationLinksEnvelope,
AdminRepairPublicationLinksRequest,
+ AdminRepairPublicationNearDuplicatesEnvelope,
+ AdminRepairPublicationNearDuplicatesRequest,
)
from app.db.models import DataRepairJob, User
from app.db.session import get_db_session
@@ -25,8 +25,8 @@ from app.logging_utils import structured_log
from app.services.domains.dbops import (
collect_integrity_report,
list_repair_jobs,
- run_publication_near_duplicate_repair,
run_publication_link_repair,
+ run_publication_near_duplicate_repair,
)
from app.services.domains.publications import application as publication_service
@@ -136,7 +136,15 @@ async def get_integrity_report(
admin_user: User = Depends(get_api_admin_user),
):
report = await collect_integrity_report(db_session)
- structured_log(logger, "info", "api.admin.db.integrity_checked", admin_user_id=int(admin_user.id), status=report.get("status"), failure_count=len(report.get("failures", [])), warning_count=len(report.get("warnings", [])))
+ structured_log(
+ logger,
+ "info",
+ "api.admin.db.integrity_checked",
+ admin_user_id=int(admin_user.id),
+ status=report.get("status"),
+ failure_count=len(report.get("failures", [])),
+ warning_count=len(report.get("warnings", [])),
+ )
return success_payload(request, data=report)
@@ -151,7 +159,14 @@ async def get_repair_jobs(
admin_user: User = Depends(get_api_admin_user),
):
jobs = await list_repair_jobs(db_session, limit=limit)
- structured_log(logger, "info", "api.admin.db.repair_jobs_listed", admin_user_id=int(admin_user.id), limit=int(limit), job_count=len(jobs))
+ structured_log(
+ logger,
+ "info",
+ "api.admin.db.repair_jobs_listed",
+ admin_user_id=int(admin_user.id),
+ limit=int(limit),
+ job_count=len(jobs),
+ )
return success_payload(
request,
data={"jobs": [_serialize_repair_job(job) for job in jobs]},
@@ -186,7 +201,9 @@ async def get_pdf_queue(
status=normalized_status,
)
structured_log(
- logger, "info", "api.admin.db.pdf_queue_listed",
+ logger,
+ "info",
+ "api.admin.db.pdf_queue_listed",
admin_user_id=int(admin_user.id),
page=int(resolved_page),
page_size=int(resolved_limit),
@@ -232,7 +249,14 @@ async def requeue_pdf_lookup(
message="Publication not found.",
)
status, message = _requeue_response_state(queued=result.queued)
- structured_log(logger, "info", "api.admin.db.pdf_requeued", admin_user_id=int(admin_user.id), publication_id=int(publication_id), queued=bool(result.queued))
+ structured_log(
+ logger,
+ "info",
+ "api.admin.db.pdf_requeued",
+ admin_user_id=int(admin_user.id),
+ publication_id=int(publication_id),
+ queued=bool(result.queued),
+ )
return success_payload(
request,
data={
@@ -260,7 +284,15 @@ async def requeue_all_missing_pdfs(
request_email=admin_user.email,
limit=limit,
)
- structured_log(logger, "info", "api.admin.db.pdf_queue_requeue_all", admin_user_id=int(admin_user.id), limit=int(limit), requested_count=int(result.requested_count), queued_count=int(result.queued_count))
+ structured_log(
+ logger,
+ "info",
+ "api.admin.db.pdf_queue_requeue_all",
+ admin_user_id=int(admin_user.id),
+ limit=int(limit),
+ requested_count=int(result.requested_count),
+ queued_count=int(result.queued_count),
+ )
return success_payload(
request,
data={
@@ -301,7 +333,9 @@ async def trigger_publication_link_repair(
message=str(exc),
) from exc
structured_log(
- logger, "info", "api.admin.db.publication_link_repair_triggered",
+ logger,
+ "info",
+ "api.admin.db.publication_link_repair_triggered",
admin_user_id=int(admin_user.id),
scope_mode=payload.scope_mode,
target_user_id=int(payload.user_id) if payload.user_id is not None else None,
@@ -340,7 +374,16 @@ async def trigger_publication_near_duplicate_repair(
code="invalid_near_duplicate_repair_request",
message=str(exc),
) from exc
- structured_log(logger, "info", "api.admin.db.dedup_repair_triggered", admin_user_id=int(admin_user.id), dry_run=bool(payload.dry_run), selected_cluster_count=len(payload.selected_cluster_keys), job_id=int(result["job_id"]), status=result["status"])
+ structured_log(
+ logger,
+ "info",
+ "api.admin.db.dedup_repair_triggered",
+ admin_user_id=int(admin_user.id),
+ dry_run=bool(payload.dry_run),
+ selected_cluster_count=len(payload.selected_cluster_keys),
+ job_id=int(result["job_id"]),
+ status=result["status"],
+ )
return success_payload(request, data=result)
@@ -381,12 +424,17 @@ async def drop_all_publications(
await db_session.execute(delete(PublicationPdfJobEvent))
await db_session.execute(delete(PublicationPdfJob))
await db_session.execute(delete(Publication))
- await db_session.execute(
- update(ScholarProfile).values(baseline_completed=False)
- )
+ await db_session.execute(update(ScholarProfile).values(baseline_completed=False))
await db_session.commit()
- structured_log(logger, "warning", "api.admin.db.all_publications_dropped", admin_user_id=int(admin_user.id), admin_email=admin_user.email, deleted_count=int(total_publications))
+ structured_log(
+ logger,
+ "warning",
+ "api.admin.db.all_publications_dropped",
+ admin_user_id=int(admin_user.id),
+ admin_email=admin_user.email,
+ deleted_count=int(total_publications),
+ )
return success_payload(
request,
data={
diff --git a/app/api/routers/auth.py b/app/api/routers/auth.py
index 3faffa6..9b9f053 100644
--- a/app/api/routers/auth.py
+++ b/app/api/routers/auth.py
@@ -5,8 +5,8 @@ import logging
from fastapi import APIRouter, Depends, Request
from sqlalchemy.ext.asyncio import AsyncSession
-from app.api.errors import ApiException
from app.api.deps import get_api_current_user
+from app.api.errors import ApiException
from app.api.responses import success_payload
from app.api.schemas import (
AuthMeEnvelope,
@@ -16,14 +16,14 @@ from app.api.schemas import (
LoginRequest,
MessageEnvelope,
)
-from app.auth.deps import get_auth_service, get_login_rate_limiter
-from app.logging_utils import structured_log
-from app.auth.rate_limit import SlidingWindowRateLimiter
from app.auth import runtime as auth_runtime
+from app.auth.deps import get_auth_service, get_login_rate_limiter
+from app.auth.rate_limit import SlidingWindowRateLimiter
from app.auth.service import AuthService
from app.auth.session import set_session_user
from app.db.models import User
from app.db.session import get_db_session
+from app.logging_utils import structured_log
from app.security.csrf import ensure_csrf_token
from app.services.domains.users import application as user_service
@@ -37,7 +37,13 @@ def _login_limiter_key_and_email(request: Request, payload: LoginRequest) -> tup
def _raise_rate_limited(normalized_email: str, retry_after_seconds: int) -> None:
- structured_log(logger, "warning", "api.auth.login_rate_limited", email=normalized_email, retry_after_seconds=retry_after_seconds)
+ structured_log(
+ logger,
+ "warning",
+ "api.auth.login_rate_limited",
+ email=normalized_email,
+ retry_after_seconds=retry_after_seconds,
+ )
raise ApiException(
status_code=429,
code="rate_limited",
@@ -200,7 +206,9 @@ async def logout(
):
current_user = await auth_runtime.get_authenticated_user(request, db_session)
auth_runtime.invalidate_session(request)
- structured_log(logger, "info", "api.auth.logout", user_id=int(current_user.id) if current_user is not None else None)
+ structured_log(
+ logger, "info", "api.auth.logout", user_id=int(current_user.id) if current_user is not None else None
+ )
return success_payload(
request,
data={
diff --git a/app/api/routers/publications.py b/app/api/routers/publications.py
index 7048d6b..107f531 100644
--- a/app/api/routers/publications.py
+++ b/app/api/routers/publications.py
@@ -1,7 +1,7 @@
from __future__ import annotations
-from datetime import datetime, timezone
import logging
+from datetime import UTC, datetime
from typing import Literal
from fastapi import APIRouter, Depends, Path, Query, Request
@@ -183,7 +183,7 @@ def _resolve_publications_snapshot(
snapshot: str | None,
) -> tuple[datetime, str]:
if snapshot is None:
- now_utc = datetime.now(timezone.utc)
+ now_utc = datetime.now(UTC)
return now_utc, now_utc.isoformat()
try:
parsed = datetime.fromisoformat(snapshot)
@@ -194,8 +194,8 @@ def _resolve_publications_snapshot(
message="Invalid publications snapshot cursor.",
) from exc
if parsed.tzinfo is None:
- parsed = parsed.replace(tzinfo=timezone.utc)
- normalized = parsed.astimezone(timezone.utc)
+ parsed = parsed.replace(tzinfo=UTC)
+ normalized = parsed.astimezone(UTC)
return normalized, normalized.isoformat()
@@ -420,7 +420,9 @@ async def mark_all_publications_read(
db_session,
user_id=current_user.id,
)
- structured_log(logger, "info", "api.publications.mark_all_read", user_id=current_user.id, updated_count=updated_count)
+ structured_log(
+ logger, "info", "api.publications.mark_all_read", user_id=current_user.id, updated_count=updated_count
+ )
return success_payload(
request,
data={
@@ -440,18 +442,20 @@ async def mark_selected_publications_read(
db_session: AsyncSession = Depends(get_db_session),
current_user: User = Depends(get_api_current_user),
):
- selection_pairs = sorted(
- {
- (int(item.scholar_profile_id), int(item.publication_id))
- for item in payload.selections
- }
- )
+ selection_pairs = sorted({(int(item.scholar_profile_id), int(item.publication_id)) for item in payload.selections})
updated_count = await publication_service.mark_selected_as_read_for_user(
db_session,
user_id=current_user.id,
selections=selection_pairs,
)
- structured_log(logger, "info", "api.publications.mark_selected_read", user_id=current_user.id, requested_count=len(selection_pairs), updated_count=updated_count)
+ structured_log(
+ logger,
+ "info",
+ "api.publications.mark_selected_read",
+ user_id=current_user.id,
+ requested_count=len(selection_pairs),
+ updated_count=updated_count,
+ )
return success_payload(
request,
data={
@@ -486,7 +490,9 @@ async def retry_publication_pdf(
pdf_status=current.pdf_status,
)
structured_log(
- logger, "info", "api.publications.retry_pdf",
+ logger,
+ "info",
+ "api.publications.retry_pdf",
user_id=current_user.id,
scholar_profile_id=payload.scholar_profile_id,
publication_id=publication_id,
@@ -523,7 +529,15 @@ async def toggle_publication_favorite(
publication_id=publication_id,
is_favorite=payload.is_favorite,
)
- structured_log(logger, "info", "api.publications.favorite", user_id=current_user.id, scholar_profile_id=payload.scholar_profile_id, publication_id=publication_id, is_favorite=bool(payload.is_favorite))
+ structured_log(
+ logger,
+ "info",
+ "api.publications.favorite",
+ user_id=current_user.id,
+ scholar_profile_id=payload.scholar_profile_id,
+ publication_id=publication_id,
+ is_favorite=bool(payload.is_favorite),
+ )
return success_payload(
request,
data={
diff --git a/app/api/routers/runs.py b/app/api/routers/runs.py
index f6e6644..c25a127 100644
--- a/app/api/routers/runs.py
+++ b/app/api/routers/runs.py
@@ -5,13 +5,14 @@ import re
from typing import Any
from fastapi import APIRouter, Depends, Query, Request
+from fastapi.responses import StreamingResponse
from sqlalchemy.exc import IntegrityError
from sqlalchemy.ext.asyncio import AsyncSession
from app.api.deps import get_api_current_user
from app.api.errors import ApiException
from app.api.responses import success_payload
-from fastapi.responses import StreamingResponse
+from app.api.runtime_deps import get_ingestion_service
from app.api.schemas import (
ManualRunEnvelope,
QueueClearEnvelope,
@@ -29,7 +30,6 @@ from app.services.domains.runs import application as run_service
from app.services.domains.runs.events import event_generator
from app.services.domains.settings import application as user_settings_service
from app.settings import settings
-from app.api.runtime_deps import get_ingestion_service
logger = logging.getLogger(__name__)
@@ -77,10 +77,7 @@ def _normalize_idempotency_key(raw_value: str | None) -> str | None:
raise ApiException(
status_code=400,
code="invalid_idempotency_key",
- message=(
- "Invalid Idempotency-Key. Use 8-128 characters from: "
- "A-Z a-z 0-9 . _ : -"
- ),
+ message=("Invalid Idempotency-Key. Use 8-128 characters from: A-Z a-z 0-9 . _ : -"),
)
return candidate
@@ -130,11 +127,7 @@ def _normalize_attempt_log(value: Any) -> list[dict[str, Any]]:
"cstart": _int_value(item.get("cstart"), 0),
"state": _str_value(item.get("state")),
"state_reason": _str_value(item.get("state_reason")),
- "status_code": (
- _int_value(item.get("status_code"))
- if item.get("status_code") is not None
- else None
- ),
+ "status_code": (_int_value(item.get("status_code")) if item.get("status_code") is not None else None),
"fetch_error": _str_value(item.get("fetch_error")),
}
)
@@ -155,19 +148,12 @@ def _normalize_page_logs(value: Any) -> list[dict[str, Any]]:
"cstart": _int_value(item.get("cstart"), 0),
"state": _str_value(item.get("state")) or "unknown",
"state_reason": _str_value(item.get("state_reason")),
- "status_code": (
- _int_value(item.get("status_code"))
- if item.get("status_code") is not None
- else None
- ),
+ "status_code": (_int_value(item.get("status_code")) if item.get("status_code") is not None else None),
"publication_count": _int_value(item.get("publication_count"), 0),
"attempt_count": _int_value(item.get("attempt_count"), 0),
"has_show_more_button": _bool_value(item.get("has_show_more_button"), False),
"articles_range": _str_value(item.get("articles_range")),
- "warning_codes": [
- str(code)
- for code in (warning_codes if isinstance(warning_codes, list) else [])
- ],
+ "warning_codes": [str(code) for code in (warning_codes if isinstance(warning_codes, list) else [])],
}
)
return normalized
@@ -179,19 +165,11 @@ def _normalize_debug(value: Any) -> dict[str, Any] | None:
marker_counts = value.get("marker_counts_nonzero")
warning_codes = value.get("warning_codes")
return {
- "status_code": (
- _int_value(value.get("status_code"))
- if value.get("status_code") is not None
- else None
- ),
+ "status_code": (_int_value(value.get("status_code")) if value.get("status_code") is not None else None),
"final_url": _str_value(value.get("final_url")),
"fetch_error": _str_value(value.get("fetch_error")),
"body_sha256": _str_value(value.get("body_sha256")),
- "body_length": (
- _int_value(value.get("body_length"))
- if value.get("body_length") is not None
- else None
- ),
+ "body_length": (_int_value(value.get("body_length")) if value.get("body_length") is not None else None),
"has_show_more_button": (
_bool_value(value.get("has_show_more_button"), False)
if value.get("has_show_more_button") is not None
@@ -199,10 +177,7 @@ def _normalize_debug(value: Any) -> dict[str, Any] | None:
),
"articles_range": _str_value(value.get("articles_range")),
"state_reason": _str_value(value.get("state_reason")),
- "warning_codes": [
- str(code)
- for code in (warning_codes if isinstance(warning_codes, list) else [])
- ],
+ "warning_codes": [str(code) for code in (warning_codes if isinstance(warning_codes, list) else [])],
"marker_counts_nonzero": {
str(key): _int_value(count, 0)
for key, count in (marker_counts.items() if isinstance(marker_counts, dict) else [])
@@ -241,9 +216,7 @@ def _normalize_scholar_result(value: Any) -> dict[str, Any]:
"publication_count": _int_value(value.get("publication_count"), 0),
"start_cstart": _int_value(value.get("start_cstart"), 0),
"continuation_cstart": (
- _int_value(value.get("continuation_cstart"))
- if value.get("continuation_cstart") is not None
- else None
+ _int_value(value.get("continuation_cstart")) if value.get("continuation_cstart") is not None else None
),
"continuation_enqueued": _bool_value(value.get("continuation_enqueued"), False),
"continuation_cleared": _bool_value(value.get("continuation_cleared"), False),
@@ -289,7 +262,9 @@ async def _load_safety_state(
await db_session.commit()
await db_session.refresh(user_settings)
structured_log(
- logger, "info", "api.runs.safety_cooldown_cleared",
+ logger,
+ "info",
+ "api.runs.safety_cooldown_cleared",
user_id=user_id,
reason=previous_safety_state.get("cooldown_reason"),
cooldown_until=previous_safety_state.get("cooldown_until"),
@@ -299,7 +274,9 @@ async def _load_safety_state(
def _raise_manual_runs_disabled(*, user_id: int, safety_state: dict[str, Any]) -> None:
structured_log(
- logger, "warning", "api.runs.manual_blocked_policy",
+ logger,
+ "warning",
+ "api.runs.manual_blocked_policy",
user_id=user_id,
policy={"manual_run_allowed": False},
safety_state=safety_state,
@@ -463,7 +440,9 @@ async def _execute_manual_run(
def _raise_manual_blocked_safety(*, exc, user_id: int) -> None:
structured_log(
- logger, "info", "api.runs.manual_blocked_safety",
+ logger,
+ "info",
+ "api.runs.manual_blocked_safety",
user_id=user_id,
reason=exc.safety_state.get("cooldown_reason"),
cooldown_until=exc.safety_state.get("cooldown_until"),
@@ -613,12 +592,12 @@ async def cancel_run(
scholar_results = error_log.get("scholar_results")
if not isinstance(scholar_results, list):
scholar_results = []
-
+
safety_state = await _load_safety_state(
db_session,
user_id=current_user.id,
)
-
+
return success_payload(
request,
data={
@@ -657,7 +636,7 @@ async def run_manual(
try:
user_settings = await user_settings_service.get_or_create_settings(db_session, user_id=current_user.id)
-
+
# Initialize run (creates the record and performs safety checks)
run, scholars, start_cstart_map = await ingest_service.initialize_run(
db_session,
@@ -673,13 +652,14 @@ async def run_manual(
alert_network_failure_threshold=settings.ingestion_alert_network_failure_threshold,
alert_retry_scheduled_threshold=settings.ingestion_alert_retry_scheduled_threshold,
)
-
+
await db_session.commit()
-
+
# Kick off background execution
- from app.db.session import get_session_factory
import asyncio
-
+
+ from app.db.session import get_session_factory
+
asyncio.create_task(
ingest_service.execute_run(
session_factory=get_session_factory(),
@@ -700,7 +680,7 @@ async def run_manual(
idempotency_key=idempotency_key,
)
)
-
+
return success_payload(
request,
data={
@@ -714,7 +694,7 @@ async def run_manual(
"reused_existing_run": False,
"idempotency_key": idempotency_key,
"safety_state": await _load_safety_state(db_session, user_id=current_user.id),
- }
+ },
)
except ingestion_service.RunBlockedBySafetyPolicyError as exc:
await db_session.rollback()
@@ -740,7 +720,6 @@ async def run_manual(
_raise_manual_failed(exc=exc, user_id=current_user.id)
-
@router.get(
"/queue/items",
response_model=QueueListEnvelope,
@@ -891,7 +870,4 @@ async def stream_run_events(
code="run_not_found",
message="Run not found.",
)
- return StreamingResponse(
- event_generator(run_id),
- media_type="text/event-stream"
- )
+ return StreamingResponse(event_generator(run_id), media_type="text/event-stream")
diff --git a/app/api/routers/scholars.py b/app/api/routers/scholars.py
index c0a281b..fcdd1c4 100644
--- a/app/api/routers/scholars.py
+++ b/app/api/routers/scholars.py
@@ -27,8 +27,8 @@ from app.logging_utils import structured_log
from app.services.domains.ingestion import queue as ingestion_queue_service
from app.services.domains.portability import application as import_export_service
from app.services.domains.scholar import rate_limit as scholar_rate_limit
-from app.services.domains.scholars import application as scholar_service
from app.services.domains.scholar.source import ScholarSource
+from app.services.domains.scholars import application as scholar_service
from app.settings import settings
logger = logging.getLogger(__name__)
@@ -82,14 +82,18 @@ async def _enqueue_initial_scrape_job_for_scholar(
except Exception:
await db_session.rollback()
structured_log(
- logger, "warning", "api.scholars.initial_scrape_enqueue_failed",
+ logger,
+ "warning",
+ "api.scholars.initial_scrape_enqueue_failed",
user_id=user_id,
scholar_profile_id=profile.id,
)
return False
structured_log(
- logger, "info", "api.scholars.initial_scrape_enqueued",
+ logger,
+ "info",
+ "api.scholars.initial_scrape_enqueued",
user_id=user_id,
scholar_profile_id=profile.id,
reason=INITIAL_SCHOLAR_SCRAPE_QUEUE_REASON,
@@ -120,9 +124,7 @@ def _serialize_scholar(profile) -> dict[str, object]:
"is_enabled": bool(profile.is_enabled),
"baseline_completed": bool(profile.baseline_completed),
"last_run_dt": profile.last_run_dt,
- "last_run_status": (
- profile.last_run_status.value if profile.last_run_status is not None else None
- ),
+ "last_run_status": (profile.last_run_status.value if profile.last_run_status is not None else None),
}
@@ -139,7 +141,9 @@ async def _hydrate_scholar_metadata_if_needed(
should_skip, remaining_seconds = _is_create_hydration_rate_limited()
if should_skip:
structured_log(
- logger, "info", "api.scholars.create_metadata_hydration_skipped",
+ logger,
+ "info",
+ "api.scholars.create_metadata_hydration_skipped",
reason="scholar_request_throttle_active",
user_id=user_id,
scholar_profile_id=profile.id,
@@ -158,14 +162,18 @@ async def _hydrate_scholar_metadata_if_needed(
)
except TimeoutError:
structured_log(
- logger, "info", "api.scholars.create_metadata_hydration_skipped",
+ logger,
+ "info",
+ "api.scholars.create_metadata_hydration_skipped",
reason="create_timeout",
user_id=user_id,
scholar_profile_id=profile.id,
)
except Exception:
structured_log(
- logger, "warning", "api.scholars.create_metadata_hydration_failed",
+ logger,
+ "warning",
+ "api.scholars.create_metadata_hydration_failed",
user_id=user_id,
scholar_profile_id=profile.id,
)
@@ -185,9 +193,7 @@ def _search_kwargs() -> dict[str, object]:
"cooldown_block_threshold": settings.scholar_name_search_cooldown_block_threshold,
"cooldown_seconds": settings.scholar_name_search_cooldown_seconds,
"retry_alert_threshold": settings.scholar_name_search_alert_retry_count_threshold,
- "cooldown_rejection_alert_threshold": (
- settings.scholar_name_search_alert_cooldown_rejections_threshold
- ),
+ "cooldown_rejection_alert_threshold": (settings.scholar_name_search_alert_cooldown_rejections_threshold),
}
@@ -299,8 +305,7 @@ async def import_scholars_and_publications(
status_code=400,
code="invalid_import_schema_version",
message=(
- "Import schema version is not supported. "
- f"Expected {import_export_service.EXPORT_SCHEMA_VERSION}."
+ f"Import schema version is not supported. Expected {import_export_service.EXPORT_SCHEMA_VERSION}."
),
)
try:
@@ -393,7 +398,15 @@ async def search_scholars(
message=str(exc),
) from exc
- structured_log(logger, "info", "api.scholars.search.completed", user_id=current_user.id, query=query.strip(), candidate_count=len(parsed.candidates), state=parsed.state.value)
+ structured_log(
+ logger,
+ "info",
+ "api.scholars.search.completed",
+ user_id=current_user.id,
+ query=query.strip(),
+ candidate_count=len(parsed.candidates),
+ state=parsed.state.value,
+ )
return success_payload(
request,
data=_search_response_data(query, parsed),
@@ -422,7 +435,14 @@ async def toggle_scholar(
message="Scholar not found.",
)
updated = await scholar_service.toggle_scholar_enabled(db_session, profile=profile)
- structured_log(logger, "info", "api.scholars.toggled", user_id=current_user.id, scholar_profile_id=updated.id, is_enabled=updated.is_enabled)
+ structured_log(
+ logger,
+ "info",
+ "api.scholars.toggled",
+ user_id=current_user.id,
+ scholar_profile_id=updated.id,
+ is_enabled=updated.is_enabled,
+ )
return success_payload(
request,
data=_serialize_scholar(updated),
@@ -455,7 +475,9 @@ async def delete_scholar(
profile=profile,
upload_dir=settings.scholar_image_upload_dir,
)
- structured_log(logger, "info", "api.scholars.deleted", user_id=current_user.id, scholar_profile_id=scholar_profile_id)
+ structured_log(
+ logger, "info", "api.scholars.deleted", user_id=current_user.id, scholar_profile_id=scholar_profile_id
+ )
return success_payload(
request,
data={"message": "Scholar deleted."},
@@ -499,7 +521,9 @@ async def update_scholar_image_url(
message=str(exc),
) from exc
- structured_log(logger, "info", "api.scholars.image_url_updated", user_id=current_user.id, scholar_profile_id=updated.id)
+ structured_log(
+ logger, "info", "api.scholars.image_url_updated", user_id=current_user.id, scholar_profile_id=updated.id
+ )
return success_payload(
request,
data=_serialize_scholar(updated),
@@ -541,7 +565,15 @@ async def upload_scholar_image(
) from exc
image_size = len(image_bytes)
- structured_log(logger, "info", "api.scholars.image_uploaded", user_id=current_user.id, scholar_profile_id=updated.id, content_type=image.content_type, size_bytes=image_size)
+ structured_log(
+ logger,
+ "info",
+ "api.scholars.image_uploaded",
+ user_id=current_user.id,
+ scholar_profile_id=updated.id,
+ content_type=image.content_type,
+ size_bytes=image_size,
+ )
return success_payload(
request,
data=_serialize_scholar(updated),
diff --git a/app/api/routers/settings.py b/app/api/routers/settings.py
index e0c3f26..55e6a51 100644
--- a/app/api/routers/settings.py
+++ b/app/api/routers/settings.py
@@ -85,7 +85,9 @@ async def _clear_expired_cooldown_with_log(
await db_session.commit()
await db_session.refresh(user_settings)
structured_log(
- logger, "info", "api.settings.safety_cooldown_cleared",
+ logger,
+ "info",
+ "api.settings.safety_cooldown_cleared",
user_id=user_id,
reason=previous_safety_state.get("cooldown_reason"),
cooldown_until=previous_safety_state.get("cooldown_until"),
@@ -164,7 +166,9 @@ async def update_settings(
user_settings=updated,
)
structured_log(
- logger, "info", "api.settings.updated",
+ logger,
+ "info",
+ "api.settings.updated",
user_id=current_user.id,
auto_run_enabled=updated.auto_run_enabled,
run_interval_minutes=updated.run_interval_minutes,
diff --git a/app/api/schemas.py b/app/api/schemas.py
index e3b9ac7..0b7db35 100644
--- a/app/api/schemas.py
+++ b/app/api/schemas.py
@@ -671,7 +671,7 @@ class AdminRepairPublicationLinksRequest(BaseModel):
model_config = ConfigDict(extra="forbid")
@model_validator(mode="after")
- def validate_scope(self) -> "AdminRepairPublicationLinksRequest":
+ def validate_scope(self) -> AdminRepairPublicationLinksRequest:
if self.scope_mode == "single_user" and self.user_id is None:
raise ValueError("user_id is required when scope_mode=single_user.")
if self.scope_mode == "all_users" and self.user_id is not None:
@@ -680,10 +680,7 @@ class AdminRepairPublicationLinksRequest(BaseModel):
expected = "REPAIR ALL USERS"
provided = (self.confirmation_text or "").strip()
if provided != expected:
- raise ValueError(
- "confirmation_text must equal 'REPAIR ALL USERS' "
- "when applying a repair to all users."
- )
+ raise ValueError("confirmation_text must equal 'REPAIR ALL USERS' when applying a repair to all users.")
return self
@@ -735,7 +732,7 @@ class AdminRepairPublicationNearDuplicatesRequest(BaseModel):
model_config = ConfigDict(extra="forbid")
@model_validator(mode="after")
- def validate_apply_mode(self) -> "AdminRepairPublicationNearDuplicatesRequest":
+ def validate_apply_mode(self) -> AdminRepairPublicationNearDuplicatesRequest:
if self.dry_run:
return self
if not self.selected_cluster_keys:
@@ -744,8 +741,7 @@ class AdminRepairPublicationNearDuplicatesRequest(BaseModel):
provided = (self.confirmation_text or "").strip()
if provided != expected:
raise ValueError(
- "confirmation_text must equal 'MERGE SELECTED DUPLICATES' "
- "when applying near-duplicate merges."
+ "confirmation_text must equal 'MERGE SELECTED DUPLICATES' when applying near-duplicate merges."
)
return self
@@ -787,7 +783,7 @@ class SettingsData(BaseModel):
nav_visible_pages: list[str]
policy: SettingsPolicyData
safety_state: ScrapeSafetyStateData
-
+
openalex_api_key: str | None = None
crossref_api_token: str | None = None
crossref_api_mailto: str | None = None
diff --git a/app/auth/__init__.py b/app/auth/__init__.py
index 79644a4..b2c2619 100644
--- a/app/auth/__init__.py
+++ b/app/auth/__init__.py
@@ -1,2 +1 @@
"""Authentication package for scholarr."""
-
diff --git a/app/auth/deps.py b/app/auth/deps.py
index 50424ae..ec7613c 100644
--- a/app/auth/deps.py
+++ b/app/auth/deps.py
@@ -24,4 +24,3 @@ def get_login_rate_limiter() -> SlidingWindowRateLimiter:
max_attempts=settings.login_rate_limit_attempts,
window_seconds=settings.login_rate_limit_window_seconds,
)
-
diff --git a/app/auth/runtime.py b/app/auth/runtime.py
index c379cd3..077b7a1 100644
--- a/app/auth/runtime.py
+++ b/app/auth/runtime.py
@@ -6,8 +6,8 @@ from fastapi import Request
from sqlalchemy.ext.asyncio import AsyncSession
from app.auth.session import clear_session_user, get_session_user, set_session_user
-from app.logging_utils import structured_log
from app.db.models import User
+from app.logging_utils import structured_log
from app.security.csrf import CSRF_SESSION_KEY
from app.services.domains.users import application as user_service
diff --git a/app/auth/security.py b/app/auth/security.py
index f89b122..befcd7c 100644
--- a/app/auth/security.py
+++ b/app/auth/security.py
@@ -16,4 +16,3 @@ class PasswordService:
return bool(self._hasher.verify(password_hash, password))
except (InvalidHashError, VerificationError):
return False
-
diff --git a/app/auth/service.py b/app/auth/service.py
index 9772358..e13e3fe 100644
--- a/app/auth/service.py
+++ b/app/auth/service.py
@@ -21,9 +21,7 @@ class AuthService:
normalized_email = email.strip().lower()
if not normalized_email or not password:
return None
- result = await db_session.execute(
- select(User).where(User.email == normalized_email)
- )
+ result = await db_session.execute(select(User).where(User.email == normalized_email))
user = result.scalar_one_or_none()
if user is None or not user.is_active:
return None
diff --git a/app/auth/session.py b/app/auth/session.py
index 8c83197..cf52836 100644
--- a/app/auth/session.py
+++ b/app/auth/session.py
@@ -4,7 +4,6 @@ from dataclasses import dataclass
from starlette.requests import Request
-
SESSION_USER_ID_KEY = "auth_user_id"
SESSION_USER_EMAIL_KEY = "auth_user_email"
SESSION_USER_IS_ADMIN_KEY = "auth_user_is_admin"
diff --git a/app/db/base.py b/app/db/base.py
index 6fa2049..78cb78d 100644
--- a/app/db/base.py
+++ b/app/db/base.py
@@ -1,9 +1,8 @@
-from datetime import datetime, timezone
+from datetime import UTC, datetime
from sqlalchemy import MetaData, event
from sqlalchemy.orm import DeclarativeBase
-
NAMING_CONVENTION = {
"ix": "ix_%(column_0_label)s",
"uq": "uq_%(table_name)s_%(column_0_name)s",
@@ -21,7 +20,7 @@ class Base(DeclarativeBase):
def _set_updated_at_before_update(_mapper, _connection, target) -> None:
# Keep audit timestamps current for ORM-managed updates.
if hasattr(target, "updated_at"):
- target.updated_at = datetime.now(timezone.utc)
+ target.updated_at = datetime.now(UTC)
metadata = Base.metadata
diff --git a/app/db/models.py b/app/db/models.py
index 6a51811..66c6ff8 100644
--- a/app/db/models.py
+++ b/app/db/models.py
@@ -62,18 +62,10 @@ class User(Base):
id: Mapped[int] = mapped_column(primary_key=True)
email: Mapped[str] = mapped_column(String(255), nullable=False, unique=True)
password_hash: Mapped[str] = mapped_column(String(255), nullable=False)
- is_active: Mapped[bool] = mapped_column(
- Boolean, nullable=False, server_default=text("true")
- )
- is_admin: Mapped[bool] = mapped_column(
- Boolean, nullable=False, server_default=text("false")
- )
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ is_active: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("true"))
+ is_admin: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class UserSetting(Base):
@@ -89,18 +81,10 @@ class UserSetting(Base):
),
)
- user_id: Mapped[int] = mapped_column(
- ForeignKey("users.id", ondelete="CASCADE"), primary_key=True
- )
- auto_run_enabled: Mapped[bool] = mapped_column(
- Boolean, nullable=False, server_default=text("false")
- )
- run_interval_minutes: Mapped[int] = mapped_column(
- Integer, nullable=False, server_default=text("1440")
- )
- request_delay_seconds: Mapped[int] = mapped_column(
- Integer, nullable=False, server_default=text("10")
- )
+ user_id: Mapped[int] = mapped_column(ForeignKey("users.id", ondelete="CASCADE"), primary_key=True)
+ auto_run_enabled: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
+ run_interval_minutes: Mapped[int] = mapped_column(Integer, nullable=False, server_default=text("1440"))
+ request_delay_seconds: Mapped[int] = mapped_column(Integer, nullable=False, server_default=text("10"))
nav_visible_pages: Mapped[list[str]] = mapped_column(
JSONB,
nullable=False,
@@ -115,17 +99,13 @@ class UserSetting(Base):
)
scrape_cooldown_until: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
scrape_cooldown_reason: Mapped[str | None] = mapped_column(String(64))
-
+
openalex_api_key: Mapped[str | None] = mapped_column(String(255))
crossref_api_token: Mapped[str | None] = mapped_column(String(255))
crossref_api_mailto: Mapped[str | None] = mapped_column(String(255))
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class ScholarProfile(Base):
@@ -136,9 +116,7 @@ class ScholarProfile(Base):
)
id: Mapped[int] = mapped_column(primary_key=True)
- user_id: Mapped[int] = mapped_column(
- ForeignKey("users.id", ondelete="CASCADE"), nullable=False
- )
+ user_id: Mapped[int] = mapped_column(ForeignKey("users.id", ondelete="CASCADE"), nullable=False)
scholar_id: Mapped[str] = mapped_column(String(64), nullable=False)
display_name: Mapped[str | None] = mapped_column(String(255))
profile_image_url: Mapped[str | None] = mapped_column(Text)
@@ -146,22 +124,14 @@ class ScholarProfile(Base):
profile_image_upload_path: Mapped[str | None] = mapped_column(Text)
last_initial_page_fingerprint_sha256: Mapped[str | None] = mapped_column(String(64))
last_initial_page_checked_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
- is_enabled: Mapped[bool] = mapped_column(
- Boolean, nullable=False, server_default=text("true")
- )
- baseline_completed: Mapped[bool] = mapped_column(
- Boolean, nullable=False, server_default=text("false")
- )
+ is_enabled: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("true"))
+ baseline_completed: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
last_run_dt: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
last_run_status: Mapped[RunStatus | None] = mapped_column(
RUN_STATUS_DB_ENUM,
)
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class CrawlRun(Base):
@@ -172,51 +142,29 @@ class CrawlRun(Base):
"uq_crawl_runs_user_active",
"user_id",
unique=True,
- postgresql_where=text(
- "status IN ('running'::run_status, 'resolving'::run_status)"
- ),
+ postgresql_where=text("status IN ('running'::run_status, 'resolving'::run_status)"),
),
Index(
"uq_crawl_runs_user_manual_idempotency_key",
"user_id",
"idempotency_key",
unique=True,
- postgresql_where=text(
- "idempotency_key IS NOT NULL AND trigger_type = 'manual'::run_trigger_type"
- ),
+ postgresql_where=text("idempotency_key IS NOT NULL AND trigger_type = 'manual'::run_trigger_type"),
),
)
id: Mapped[int] = mapped_column(primary_key=True)
- user_id: Mapped[int] = mapped_column(
- ForeignKey("users.id", ondelete="CASCADE"), nullable=False
- )
- trigger_type: Mapped[RunTriggerType] = mapped_column(
- RUN_TRIGGER_TYPE_DB_ENUM, nullable=False
- )
- status: Mapped[RunStatus] = mapped_column(
- RUN_STATUS_DB_ENUM, nullable=False
- )
- start_dt: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ user_id: Mapped[int] = mapped_column(ForeignKey("users.id", ondelete="CASCADE"), nullable=False)
+ trigger_type: Mapped[RunTriggerType] = mapped_column(RUN_TRIGGER_TYPE_DB_ENUM, nullable=False)
+ status: Mapped[RunStatus] = mapped_column(RUN_STATUS_DB_ENUM, nullable=False)
+ start_dt: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
end_dt: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
- scholar_count: Mapped[int] = mapped_column(
- Integer, nullable=False, server_default=text("0")
- )
- new_pub_count: Mapped[int] = mapped_column(
- Integer, nullable=False, server_default=text("0")
- )
+ scholar_count: Mapped[int] = mapped_column(Integer, nullable=False, server_default=text("0"))
+ new_pub_count: Mapped[int] = mapped_column(Integer, nullable=False, server_default=text("0"))
idempotency_key: Mapped[str | None] = mapped_column(String(128))
- error_log: Mapped[dict] = mapped_column(
- JSONB, nullable=False, server_default=text("'{}'::jsonb")
- )
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ error_log: Mapped[dict] = mapped_column(JSONB, nullable=False, server_default=text("'{}'::jsonb"))
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class Publication(Base):
@@ -237,28 +185,16 @@ class Publication(Base):
title_raw: Mapped[str] = mapped_column(Text, nullable=False)
title_normalized: Mapped[str] = mapped_column(Text, nullable=False)
year: Mapped[int | None] = mapped_column(Integer)
- citation_count: Mapped[int] = mapped_column(
- Integer, nullable=False, server_default=text("0")
- )
+ citation_count: Mapped[int] = mapped_column(Integer, nullable=False, server_default=text("0"))
author_text: Mapped[str | None] = mapped_column(Text)
venue_text: Mapped[str | None] = mapped_column(Text)
pub_url: Mapped[str | None] = mapped_column(Text)
pdf_url: Mapped[str | None] = mapped_column(Text)
- canonical_title_hash: Mapped[str | None] = mapped_column(
- String(64), nullable=True, index=True
- )
- openalex_enriched: Mapped[bool] = mapped_column(
- Boolean, nullable=False, server_default=text("false")
- )
- openalex_last_attempt_at: Mapped[datetime | None] = mapped_column(
- DateTime(timezone=True), nullable=True
- )
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ canonical_title_hash: Mapped[str | None] = mapped_column(String(64), nullable=True, index=True)
+ openalex_enriched: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
+ openalex_last_attempt_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True), nullable=True)
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class PublicationIdentifier(Base):
@@ -300,12 +236,8 @@ class PublicationIdentifier(Base):
server_default=text("0"),
)
evidence_url: Mapped[str | None] = mapped_column(Text)
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class PublicationPdfJob(Base):
@@ -343,12 +275,8 @@ class PublicationPdfJob(Base):
last_requested_by_user_id: Mapped[int | None] = mapped_column(
ForeignKey("users.id", ondelete="SET NULL"),
)
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class PublicationPdfJobEvent(Base):
@@ -372,9 +300,7 @@ class PublicationPdfJobEvent(Base):
source: Mapped[str | None] = mapped_column(String(32))
failure_reason: Mapped[str | None] = mapped_column(String(64))
message: Mapped[str | None] = mapped_column(Text)
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class ScholarPublication(Base):
@@ -392,18 +318,10 @@ class ScholarPublication(Base):
ForeignKey("publications.id", ondelete="CASCADE"),
primary_key=True,
)
- is_read: Mapped[bool] = mapped_column(
- Boolean, nullable=False, server_default=text("false")
- )
- is_favorite: Mapped[bool] = mapped_column(
- Boolean, nullable=False, server_default=text("false")
- )
- first_seen_run_id: Mapped[int | None] = mapped_column(
- ForeignKey("crawl_runs.id", ondelete="SET NULL")
- )
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ is_read: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
+ is_favorite: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
+ first_seen_run_id: Mapped[int | None] = mapped_column(ForeignKey("crawl_runs.id", ondelete="SET NULL"))
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class IngestionQueueItem(Base):
@@ -458,12 +376,8 @@ class IngestionQueueItem(Base):
last_error: Mapped[str | None] = mapped_column(Text)
dropped_reason: Mapped[str | None] = mapped_column(String(128))
dropped_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class DataRepairJob(Base):
@@ -503,12 +417,8 @@ class DataRepairJob(Base):
error_text: Mapped[str | None] = mapped_column(Text)
started_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
finished_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class AuthorSearchRuntimeState(Base):
@@ -532,12 +442,8 @@ class AuthorSearchRuntimeState(Base):
nullable=False,
server_default=text("false"),
)
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class ArxivRuntimeState(Base):
@@ -546,12 +452,8 @@ class ArxivRuntimeState(Base):
state_key: Mapped[str] = mapped_column(String(64), primary_key=True)
next_allowed_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
cooldown_until: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
- created_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class ArxivQueryCacheEntry(Base):
@@ -570,12 +472,8 @@ class ArxivQueryCacheEntry(Base):
DateTime(timezone=True),
nullable=False,
)
- cached_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ cached_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class AuthorSearchCacheEntry(Base):
@@ -594,9 +492,5 @@ class AuthorSearchCacheEntry(Base):
DateTime(timezone=True),
nullable=False,
)
- cached_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
- updated_at: Mapped[datetime] = mapped_column(
- DateTime(timezone=True), nullable=False, server_default=func.now()
- )
+ cached_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
+ updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
diff --git a/app/db/session.py b/app/db/session.py
index 2223216..6d286ca 100644
--- a/app/db/session.py
+++ b/app/db/session.py
@@ -1,6 +1,6 @@
-from collections.abc import AsyncIterator
import logging
import os
+from collections.abc import AsyncIterator
from sqlalchemy import text
from sqlalchemy.ext.asyncio import (
@@ -32,7 +32,9 @@ def _normalized_pool_mode(raw_mode: str) -> str:
if mode in {"null", "queue"}:
return mode
structured_log(
- logger, "warning", "db.invalid_pool_mode_fallback",
+ logger,
+ "warning",
+ "db.invalid_pool_mode_fallback",
database_pool_mode=raw_mode,
fallback_mode="queue",
)
@@ -55,7 +57,9 @@ def get_engine() -> AsyncEngine:
_engine = create_async_engine(settings.database_url, **engine_kwargs)
structured_log(
- logger, "info", "db.engine_initialized",
+ logger,
+ "info",
+ "db.engine_initialized",
pool_mode=pool_mode,
)
return _engine
diff --git a/app/http/middleware.py b/app/http/middleware.py
index 1cbea46..00223e0 100644
--- a/app/http/middleware.py
+++ b/app/http/middleware.py
@@ -1,8 +1,8 @@
from __future__ import annotations
-from secrets import token_urlsafe
import logging
import time
+from secrets import token_urlsafe
from starlette.middleware.base import BaseHTTPMiddleware
from starlette.requests import Request
@@ -63,7 +63,9 @@ class RequestLoggingMiddleware(BaseHTTPMiddleware):
should_log = self._log_requests and not self._is_skipped_path(request.url.path)
if should_log:
structured_log(
- logger, "debug", "request.started",
+ logger,
+ "debug",
+ "request.started",
method=request.method,
path=request.url.path,
)
@@ -86,7 +88,9 @@ class RequestLoggingMiddleware(BaseHTTPMiddleware):
response.headers[REQUEST_ID_HEADER] = request_id
if should_log:
structured_log(
- logger, "debug", "request.completed",
+ logger,
+ "debug",
+ "request.completed",
method=request.method,
path=request.url.path,
status_code=response.status_code,
@@ -164,11 +168,7 @@ class SecurityHeadersMiddleware(BaseHTTPMiddleware):
csp_policy = self._csp_policy_for_path(request.url.path)
if self._csp_enabled and csp_policy:
- csp_header = (
- "Content-Security-Policy-Report-Only"
- if self._csp_report_only
- else "Content-Security-Policy"
- )
+ csp_header = "Content-Security-Policy-Report-Only" if self._csp_report_only else "Content-Security-Policy"
response.headers.setdefault(csp_header, csp_policy)
hsts = self._strict_transport_security_value()
diff --git a/app/logging_config.py b/app/logging_config.py
index 559a400..805fcbf 100644
--- a/app/logging_config.py
+++ b/app/logging_config.py
@@ -1,9 +1,9 @@
from __future__ import annotations
-from datetime import datetime, timezone
import json
import logging
import sys
+from datetime import UTC, datetime
from typing import Any
from app.logging_context import get_request_id
@@ -102,7 +102,9 @@ class JsonLogFormatter(logging.Formatter):
if key.lower() in self._redact_fields:
return "[REDACTED]"
if isinstance(value, dict):
- return {nested_key: self._redact_value(nested_key, nested_value) for nested_key, nested_value in value.items()}
+ return {
+ nested_key: self._redact_value(nested_key, nested_value) for nested_key, nested_value in value.items()
+ }
if isinstance(value, (list, tuple)):
return [self._redact_value(key, item) for item in value]
return value
@@ -177,7 +179,7 @@ def _normalize_level(level: str) -> int:
def _format_timestamp(created_ts: float) -> str:
- dt = datetime.fromtimestamp(created_ts, tz=timezone.utc)
+ dt = datetime.fromtimestamp(created_ts, tz=UTC)
return dt.strftime("%Y-%m-%d %H:%M:%SZ")
diff --git a/app/logging_context.py b/app/logging_context.py
index ee578fb..a45136b 100644
--- a/app/logging_context.py
+++ b/app/logging_context.py
@@ -2,7 +2,6 @@ from __future__ import annotations
from contextvars import ContextVar
-
_request_id_ctx: ContextVar[str | None] = ContextVar("request_id", default=None)
@@ -12,4 +11,3 @@ def get_request_id() -> str | None:
def set_request_id(value: str | None) -> None:
_request_id_ctx.set(value)
-
diff --git a/app/main.py b/app/main.py
index 522a552..e83cc16 100644
--- a/app/main.py
+++ b/app/main.py
@@ -1,7 +1,7 @@
from __future__ import annotations
-from contextlib import asynccontextmanager
import logging
+from contextlib import asynccontextmanager
from pathlib import Path
from fastapi import FastAPI, HTTPException
@@ -12,9 +12,7 @@ from starlette.middleware.sessions import SessionMiddleware
from app.api.errors import register_api_exception_handlers
from app.api.media import router as media_router
from app.api.router import router as api_router
-from app.api.runtime_deps import get_ingestion_service, get_scholar_source
-from app.db.session import check_database
-from app.db.session import close_engine
+from app.db.session import check_database, close_engine
from app.http.middleware import (
RequestLoggingMiddleware,
SecurityHeadersMiddleware,
@@ -54,19 +52,25 @@ scheduler_service = SchedulerService(
@asynccontextmanager
async def lifespan(_: FastAPI):
structured_log(
- logger, "info", "app.startup_build_marker",
+ logger,
+ "info",
+ "app.startup_build_marker",
build_marker=BUILD_MARKER,
frontend_enabled=settings.frontend_enabled,
scheduler_enabled=settings.scheduler_enabled,
log_format=settings.log_format,
)
-
- from app.db.session import get_session_factory
+
from sqlalchemy import text
+
+ from app.db.session import get_session_factory
+
try:
session_factory = get_session_factory()
async with session_factory() as session:
- await session.execute(text("UPDATE crawl_runs SET status = 'failed' WHERE status::text IN ('running', 'resolving')"))
+ await session.execute(
+ text("UPDATE crawl_runs SET status = 'failed' WHERE status::text IN ('running', 'resolving')")
+ )
await session.commit()
structured_log(logger, "info", "app.startup_orphaned_runs_cleaned")
except Exception as e:
@@ -107,9 +111,7 @@ app.add_middleware(
content_security_policy_report_only=settings.security_csp_report_only,
strict_transport_security_enabled=settings.security_strict_transport_security_enabled,
strict_transport_security_max_age=settings.security_strict_transport_security_max_age,
- strict_transport_security_include_subdomains=(
- settings.security_strict_transport_security_include_subdomains
- ),
+ strict_transport_security_include_subdomains=(settings.security_strict_transport_security_include_subdomains),
strict_transport_security_preload=settings.security_strict_transport_security_preload,
)
app.include_router(api_router)
diff --git a/app/security/__init__.py b/app/security/__init__.py
index 4033692..3cf1e91 100644
--- a/app/security/__init__.py
+++ b/app/security/__init__.py
@@ -1,2 +1 @@
"""Security middleware and helpers for scholarr."""
-
diff --git a/app/security/csrf.py b/app/security/csrf.py
index d2ed1c5..00119a9 100644
--- a/app/security/csrf.py
+++ b/app/security/csrf.py
@@ -38,7 +38,9 @@ class CSRFMiddleware(BaseHTTPMiddleware):
session_token = request.session.get(CSRF_SESSION_KEY)
if not session_token:
structured_log(
- logger, "warning", "csrf.missing_session_token",
+ logger,
+ "warning",
+ "csrf.missing_session_token",
method=request.method,
path=request.url.path,
)
@@ -56,7 +58,9 @@ class CSRFMiddleware(BaseHTTPMiddleware):
if not request_token or not compare_digest(str(session_token), str(request_token)):
structured_log(
- logger, "warning", "csrf.invalid_token",
+ logger,
+ "warning",
+ "csrf.invalid_token",
method=request.method,
path=request.url.path,
)
diff --git a/app/services/__init__.py b/app/services/__init__.py
index 167f869..6093d3d 100644
--- a/app/services/__init__.py
+++ b/app/services/__init__.py
@@ -1,2 +1 @@
"""Service layer for scholarr application workflows."""
-
diff --git a/app/services/domains/arxiv/application.py b/app/services/domains/arxiv/application.py
index 8b99096..255795f 100644
--- a/app/services/domains/arxiv/application.py
+++ b/app/services/domains/arxiv/application.py
@@ -1,11 +1,11 @@
from __future__ import annotations
from typing import TYPE_CHECKING
+
from app.services.domains.arxiv.gateway import (
build_arxiv_query,
get_arxiv_gateway,
)
-from app.services.domains.arxiv.errors import ArxivRateLimitError
if TYPE_CHECKING:
from app.services.domains.publications.types import PublicationListItem, UnreadPublicationItem
diff --git a/app/services/domains/arxiv/cache.py b/app/services/domains/arxiv/cache.py
index de16416..c0aa143 100644
--- a/app/services/domains/arxiv/cache.py
+++ b/app/services/domains/arxiv/cache.py
@@ -1,11 +1,11 @@
from __future__ import annotations
import asyncio
-from collections.abc import Awaitable, Callable, Mapping
-from dataclasses import asdict
-from datetime import datetime, timedelta, timezone
import hashlib
import json
+from collections.abc import Awaitable, Callable, Mapping
+from dataclasses import asdict
+from datetime import UTC, datetime, timedelta
from typing import Any
from sqlalchemy import delete, func, select
@@ -33,15 +33,12 @@ async def get_cached_feed(
) -> ArxivFeed | None:
timestamp = _as_utc(now_utc)
session_factory = get_session_factory()
- async with session_factory() as db_session:
- async with db_session.begin():
- result = await db_session.execute(
- select(ArxivQueryCacheEntry).where(
- ArxivQueryCacheEntry.query_fingerprint == query_fingerprint
- )
- )
- entry = result.scalar_one_or_none()
- return await _validate_cached_entry(db_session, entry=entry, now_utc=timestamp)
+ async with session_factory() as db_session, db_session.begin():
+ result = await db_session.execute(
+ select(ArxivQueryCacheEntry).where(ArxivQueryCacheEntry.query_fingerprint == query_fingerprint)
+ )
+ entry = result.scalar_one_or_none()
+ return await _validate_cached_entry(db_session, entry=entry, now_utc=timestamp)
async def set_cached_feed(
@@ -54,16 +51,15 @@ async def set_cached_feed(
) -> None:
timestamp = _as_utc(now_utc)
session_factory = get_session_factory()
- async with session_factory() as db_session:
- async with db_session.begin():
- await _write_cached_entry(
- db_session,
- query_fingerprint=query_fingerprint,
- feed=feed,
- ttl_seconds=ttl_seconds,
- max_entries=max_entries,
- now_utc=timestamp,
- )
+ async with session_factory() as db_session, db_session.begin():
+ await _write_cached_entry(
+ db_session,
+ query_fingerprint=query_fingerprint,
+ feed=feed,
+ ttl_seconds=ttl_seconds,
+ max_entries=max_entries,
+ now_utc=timestamp,
+ )
async def run_with_inflight_dedupe(
@@ -142,9 +138,7 @@ async def _write_cached_entry(
) -> None:
ttl = max(float(ttl_seconds), 0.0)
result = await db_session.execute(
- select(ArxivQueryCacheEntry).where(
- ArxivQueryCacheEntry.query_fingerprint == query_fingerprint
- )
+ select(ArxivQueryCacheEntry).where(ArxivQueryCacheEntry.query_fingerprint == query_fingerprint)
)
existing = result.scalar_one_or_none()
if ttl <= 0.0:
@@ -177,30 +171,22 @@ async def _prune_cache_entries(
now_utc: datetime,
max_entries: int,
) -> None:
- await db_session.execute(
- delete(ArxivQueryCacheEntry).where(ArxivQueryCacheEntry.expires_at <= now_utc)
- )
+ await db_session.execute(delete(ArxivQueryCacheEntry).where(ArxivQueryCacheEntry.expires_at <= now_utc))
bounded_max_entries = int(max_entries)
if bounded_max_entries <= 0:
return
- count_result = await db_session.execute(
- select(func.count()).select_from(ArxivQueryCacheEntry)
- )
+ count_result = await db_session.execute(select(func.count()).select_from(ArxivQueryCacheEntry))
entry_count = int(count_result.scalar_one() or 0)
overflow = max(0, entry_count - bounded_max_entries)
if overflow <= 0:
return
stale_result = await db_session.execute(
- select(ArxivQueryCacheEntry.query_fingerprint)
- .order_by(ArxivQueryCacheEntry.cached_at.asc())
- .limit(overflow)
+ select(ArxivQueryCacheEntry.query_fingerprint).order_by(ArxivQueryCacheEntry.cached_at.asc()).limit(overflow)
)
stale_keys = [str(row[0]) for row in stale_result.all()]
if stale_keys:
await db_session.execute(
- delete(ArxivQueryCacheEntry).where(
- ArxivQueryCacheEntry.query_fingerprint.in_(stale_keys)
- )
+ delete(ArxivQueryCacheEntry).where(ArxivQueryCacheEntry.query_fingerprint.in_(stale_keys))
)
@@ -275,9 +261,9 @@ def _as_string_list(value: object) -> list[str]:
def _as_utc(value: datetime | None) -> datetime:
if value is None:
- return datetime.now(timezone.utc)
+ return datetime.now(UTC)
if value.tzinfo is None:
- return value.replace(tzinfo=timezone.utc)
+ return value.replace(tzinfo=UTC)
return value
diff --git a/app/services/domains/arxiv/client.py b/app/services/domains/arxiv/client.py
index 7bbf87c..7318271 100644
--- a/app/services/domains/arxiv/client.py
+++ b/app/services/domains/arxiv/client.py
@@ -1,7 +1,7 @@
from __future__ import annotations
-from collections.abc import Awaitable, Callable
import logging
+from collections.abc import Awaitable, Callable
import httpx
@@ -103,9 +103,13 @@ class ArxivClient:
if self._cache_enabled:
cached = await get_cached_feed(query_fingerprint=query_fingerprint)
if cached is not None:
- structured_log(logger, "info", "arxiv.cache_hit", query_fingerprint=query_fingerprint, source_path=source_path)
+ structured_log(
+ logger, "info", "arxiv.cache_hit", query_fingerprint=query_fingerprint, source_path=source_path
+ )
return cached
- structured_log(logger, "info", "arxiv.cache_miss", query_fingerprint=query_fingerprint, source_path=source_path)
+ structured_log(
+ logger, "info", "arxiv.cache_miss", query_fingerprint=query_fingerprint, source_path=source_path
+ )
return await run_with_inflight_dedupe(
query_fingerprint=query_fingerprint,
fetch_feed=lambda: self._fetch_live_feed(
@@ -216,13 +220,13 @@ async def _request_arxiv_feed(
cooldown_status = await get_arxiv_cooldown_status()
if cooldown_status.is_active:
structured_log(
- logger, "warning", "arxiv.request_skipped_cooldown",
+ logger,
+ "warning",
+ "arxiv.request_skipped_cooldown",
source_path=source_path,
cooldown_remaining_seconds=float(cooldown_status.remaining_seconds),
)
- raise ArxivRateLimitError(
- f"arXiv global cooldown active ({cooldown_status.remaining_seconds:.0f}s remaining)"
- )
+ raise ArxivRateLimitError(f"arXiv global cooldown active ({cooldown_status.remaining_seconds:.0f}s remaining)")
async def _fetch() -> httpx.Response:
timeout_value = _timeout_seconds(timeout_seconds)
@@ -272,5 +276,3 @@ def _source_path_from_params(params: dict[str, object]) -> str:
if "id_list" in params:
return ARXIV_SOURCE_PATH_LOOKUP_IDS
return ARXIV_SOURCE_PATH_UNKNOWN
-
-
diff --git a/app/services/domains/arxiv/gateway.py b/app/services/domains/arxiv/gateway.py
index 67d9543..5c13b35 100644
--- a/app/services/domains/arxiv/gateway.py
+++ b/app/services/domains/arxiv/gateway.py
@@ -2,8 +2,8 @@ from __future__ import annotations
import logging
import re
-from typing import TYPE_CHECKING, Protocol
import unicodedata
+from typing import TYPE_CHECKING, Protocol
from app.logging_utils import structured_log
from app.services.domains.arxiv.client import ArxivClient
diff --git a/app/services/domains/arxiv/rate_limit.py b/app/services/domains/arxiv/rate_limit.py
index 52e2c3f..ddc5cab 100644
--- a/app/services/domains/arxiv/rate_limit.py
+++ b/app/services/domains/arxiv/rate_limit.py
@@ -1,10 +1,10 @@
from __future__ import annotations
import asyncio
+import logging
from collections.abc import Awaitable, Callable
from dataclasses import dataclass
-from datetime import datetime, timedelta, timezone
-import logging
+from datetime import UTC, datetime, timedelta
import httpx
from sqlalchemy import select, text
@@ -47,13 +47,11 @@ async def run_with_global_arxiv_limit(
async def get_arxiv_cooldown_status(*, now_utc: datetime | None = None) -> ArxivCooldownStatus:
- timestamp = _normalize_datetime(now_utc) or datetime.now(timezone.utc)
+ timestamp = _normalize_datetime(now_utc) or datetime.now(UTC)
session_factory = get_session_factory()
async with session_factory() as db_session:
result = await db_session.execute(
- select(ArxivRuntimeState.cooldown_until).where(
- ArxivRuntimeState.state_key == ARXIV_RUNTIME_STATE_KEY
- )
+ select(ArxivRuntimeState.cooldown_until).where(ArxivRuntimeState.state_key == ARXIV_RUNTIME_STATE_KEY)
)
cooldown_until = _normalize_datetime(result.scalar_one_or_none())
remaining_seconds = _cooldown_remaining_seconds(cooldown_until, now_utc=timestamp)
@@ -85,10 +83,14 @@ async def _run_serialized_fetch(
source_path=source_path,
)
structured_log(
- logger, "info", "arxiv.request_completed",
+ logger,
+ "info",
+ "arxiv.request_completed",
status_code=int(response.status_code),
wait_seconds=wait_seconds,
- cooldown_remaining_seconds=_cooldown_remaining_seconds(runtime_state.cooldown_until, now_utc=datetime.now(timezone.utc)),
+ cooldown_remaining_seconds=_cooldown_remaining_seconds(
+ runtime_state.cooldown_until, now_utc=datetime.now(UTC)
+ ),
source_path=source_path,
)
return response, hit_rate_limit
@@ -106,9 +108,7 @@ async def _acquire_arxiv_lock(db_session: AsyncSession) -> None:
async def _load_runtime_state_for_update(db_session: AsyncSession) -> ArxivRuntimeState:
result = await db_session.execute(
- select(ArxivRuntimeState)
- .where(ArxivRuntimeState.state_key == ARXIV_RUNTIME_STATE_KEY)
- .with_for_update()
+ select(ArxivRuntimeState).where(ArxivRuntimeState.state_key == ARXIV_RUNTIME_STATE_KEY).with_for_update()
)
state = result.scalar_one_or_none()
if state is not None:
@@ -124,13 +124,27 @@ async def _wait_for_allowed_slot_or_raise(
*,
source_path: str,
) -> float:
- now_utc = datetime.now(timezone.utc)
+ now_utc = datetime.now(UTC)
cooldown_seconds = _cooldown_remaining_seconds(runtime_state.cooldown_until, now_utc=now_utc)
if cooldown_seconds > 0:
- structured_log(logger, "info", "arxiv.request_scheduled", wait_seconds=0.0, source_path=source_path, cooldown_remaining_seconds=cooldown_seconds)
+ structured_log(
+ logger,
+ "info",
+ "arxiv.request_scheduled",
+ wait_seconds=0.0,
+ source_path=source_path,
+ cooldown_remaining_seconds=cooldown_seconds,
+ )
raise ArxivRateLimitError(f"arXiv global cooldown active ({cooldown_seconds:.0f}s remaining)")
wait_seconds = _next_allowed_wait_seconds(runtime_state.next_allowed_at, now_utc=now_utc)
- structured_log(logger, "info", "arxiv.request_scheduled", wait_seconds=wait_seconds, source_path=source_path, cooldown_remaining_seconds=0.0)
+ structured_log(
+ logger,
+ "info",
+ "arxiv.request_scheduled",
+ wait_seconds=wait_seconds,
+ source_path=source_path,
+ cooldown_remaining_seconds=0.0,
+ )
if wait_seconds > 0:
await asyncio.sleep(wait_seconds)
return wait_seconds
@@ -142,13 +156,15 @@ def _record_post_response_state(
response_status: int,
source_path: str,
) -> bool:
- now_utc = datetime.now(timezone.utc)
+ now_utc = datetime.now(UTC)
runtime_state.next_allowed_at = now_utc + timedelta(seconds=_min_interval_seconds())
if response_status == 429:
cooldown_seconds = _cooldown_seconds()
runtime_state.cooldown_until = now_utc + timedelta(seconds=cooldown_seconds)
structured_log(
- logger, "warning", "arxiv.cooldown_activated",
+ logger,
+ "warning",
+ "arxiv.cooldown_activated",
cooldown_remaining_seconds=cooldown_seconds,
source_path=source_path,
)
@@ -176,7 +192,7 @@ def _normalize_datetime(value: datetime | None) -> datetime | None:
if value is None:
return None
if value.tzinfo is None:
- return value.replace(tzinfo=timezone.utc)
+ return value.replace(tzinfo=UTC)
return value
@@ -186,5 +202,3 @@ def _min_interval_seconds() -> float:
def _cooldown_seconds() -> float:
return max(float(settings.arxiv_rate_limit_cooldown_seconds), 0.0)
-
-
diff --git a/app/services/domains/crossref/application.py b/app/services/domains/crossref/application.py
index 7212101..9b7076c 100644
--- a/app/services/domains/crossref/application.py
+++ b/app/services/domains/crossref/application.py
@@ -9,8 +9,8 @@ from typing import TYPE_CHECKING
from crossref.restful import Etiquette, Works
-from app.services.domains.doi.normalize import normalize_doi
from app.logging_utils import structured_log
+from app.services.domains.doi.normalize import normalize_doi
from app.settings import settings
if TYPE_CHECKING:
@@ -38,7 +38,7 @@ def _rate_limit_wait(min_interval_seconds: float) -> None:
def _normalized_tokens(value: str) -> list[str]:
- lowered = value.lower().replace("’", "'").replace("“", "\"").replace("”", "\"")
+ lowered = value.lower().replace("’", "'").replace("“", '"').replace("”", '"')
lowered = NON_ALNUM_RE.sub(" ", lowered)
return [token for token in TOKEN_RE.findall(lowered) if len(token) >= 3]
diff --git a/app/services/domains/dbops/__init__.py b/app/services/domains/dbops/__init__.py
index cdc5177..0439955 100644
--- a/app/services/domains/dbops/__init__.py
+++ b/app/services/domains/dbops/__init__.py
@@ -1,8 +1,8 @@
from app.services.domains.dbops.application import run_publication_link_repair
+from app.services.domains.dbops.integrity import collect_integrity_report
from app.services.domains.dbops.near_duplicate_repair import (
run_publication_near_duplicate_repair,
)
-from app.services.domains.dbops.integrity import collect_integrity_report
from app.services.domains.dbops.query import list_repair_jobs
__all__ = [
diff --git a/app/services/domains/dbops/application.py b/app/services/domains/dbops/application.py
index e7ace77..7c59033 100644
--- a/app/services/domains/dbops/application.py
+++ b/app/services/domains/dbops/application.py
@@ -1,6 +1,6 @@
from __future__ import annotations
-from datetime import datetime, timezone
+from datetime import UTC, datetime
from typing import Any
from sqlalchemy import delete, exists, func, select, update
@@ -8,7 +8,6 @@ from sqlalchemy.ext.asyncio import AsyncSession
from app.db.models import DataRepairJob, IngestionQueueItem, Publication, ScholarProfile, ScholarPublication
-
REPAIR_STATUS_PLANNED = "planned"
REPAIR_STATUS_RUNNING = "running"
REPAIR_STATUS_COMPLETED = "completed"
@@ -18,7 +17,7 @@ SCOPE_MODE_ALL_USERS = "all_users"
def _utcnow() -> datetime:
- return datetime.now(timezone.utc)
+ return datetime.now(UTC)
def _normalize_scope_mode(scope_mode: str) -> str:
@@ -105,11 +104,7 @@ async def _count_orphan_publications(db_session: AsyncSession) -> int:
stmt = (
select(func.count())
.select_from(Publication)
- .where(
- ~exists(
- select(1).where(ScholarPublication.publication_id == Publication.id)
- )
- )
+ .where(~exists(select(1).where(ScholarPublication.publication_id == Publication.id)))
)
result = await db_session.execute(stmt)
return int(result.scalar_one() or 0)
@@ -158,9 +153,7 @@ def _job_summary(
async def _delete_links_for_targets(db_session: AsyncSession, *, target_scholar_profile_ids: list[int]) -> int:
result = await db_session.execute(
- delete(ScholarPublication).where(
- ScholarPublication.scholar_profile_id.in_(target_scholar_profile_ids)
- )
+ delete(ScholarPublication).where(ScholarPublication.scholar_profile_id.in_(target_scholar_profile_ids))
)
return int(result.rowcount or 0)
@@ -171,9 +164,7 @@ async def _delete_queue_for_targets(
user_id: int | None,
target_scholar_profile_ids: list[int],
) -> int:
- stmt = delete(IngestionQueueItem).where(
- IngestionQueueItem.scholar_profile_id.in_(target_scholar_profile_ids)
- )
+ stmt = delete(IngestionQueueItem).where(IngestionQueueItem.scholar_profile_id.in_(target_scholar_profile_ids))
if user_id is not None:
stmt = stmt.where(IngestionQueueItem.user_id == user_id)
result = await db_session.execute(stmt)
@@ -203,9 +194,7 @@ async def _reset_scholar_tracking_state(
async def _delete_orphan_publications(db_session: AsyncSession) -> int:
result = await db_session.execute(
- delete(Publication).where(
- ~exists(select(1).where(ScholarPublication.publication_id == Publication.id))
- )
+ delete(Publication).where(~exists(select(1).where(ScholarPublication.publication_id == Publication.id)))
)
return int(result.rowcount or 0)
diff --git a/app/services/domains/dbops/integrity.py b/app/services/domains/dbops/integrity.py
index 4d9c43c..f05d9a3 100644
--- a/app/services/domains/dbops/integrity.py
+++ b/app/services/domains/dbops/integrity.py
@@ -1,6 +1,6 @@
from __future__ import annotations
-from datetime import datetime, timezone
+from datetime import UTC, datetime
from typing import Any
from sqlalchemy import func, select, text
@@ -168,7 +168,7 @@ async def collect_integrity_report(db_session: AsyncSession) -> dict[str, Any]:
return {
"status": _status_from_issues(failures=failures, warnings=warnings),
- "checked_at": datetime.now(timezone.utc).isoformat(),
+ "checked_at": datetime.now(UTC).isoformat(),
"failures": failures,
"warnings": warnings,
"checks": checks,
diff --git a/app/services/domains/dbops/near_duplicate_repair.py b/app/services/domains/dbops/near_duplicate_repair.py
index ab86c70..f7ebac8 100644
--- a/app/services/domains/dbops/near_duplicate_repair.py
+++ b/app/services/domains/dbops/near_duplicate_repair.py
@@ -1,6 +1,6 @@
from __future__ import annotations
-from datetime import datetime, timezone
+from datetime import UTC, datetime
from typing import Any
from sqlalchemy.ext.asyncio import AsyncSession
@@ -17,7 +17,7 @@ NEAR_DUP_DEFAULT_MAX_CLUSTERS = 25
def _utcnow() -> datetime:
- return datetime.now(timezone.utc)
+ return datetime.now(UTC)
def _normalized_cluster_keys(values: list[str] | None) -> list[str]:
diff --git a/app/services/domains/dbops/query.py b/app/services/domains/dbops/query.py
index 2e95e31..f65c582 100644
--- a/app/services/domains/dbops/query.py
+++ b/app/services/domains/dbops/query.py
@@ -16,7 +16,5 @@ async def list_repair_jobs(
limit: int = 50,
) -> list[DataRepairJob]:
bounded = _bounded_limit(limit)
- result = await db_session.execute(
- select(DataRepairJob).order_by(DataRepairJob.created_at.desc()).limit(bounded)
- )
+ result = await db_session.execute(select(DataRepairJob).order_by(DataRepairJob.created_at.desc()).limit(bounded))
return list(result.scalars())
diff --git a/app/services/domains/ingestion/application.py b/app/services/domains/ingestion/application.py
index 4b619d7..1098c1b 100644
--- a/app/services/domains/ingestion/application.py
+++ b/app/services/domains/ingestion/application.py
@@ -1,10 +1,10 @@
from __future__ import annotations
import asyncio
-from datetime import datetime, timedelta, timezone
import hashlib
import logging
import re
+from datetime import UTC, datetime, timedelta
from typing import Any
from sqlalchemy import or_, select, text
@@ -19,6 +19,11 @@ from app.db.models import (
ScholarProfile,
ScholarPublication,
)
+from app.logging_utils import structured_log
+from app.services.domains.arxiv.errors import ArxivRateLimitError
+from app.services.domains.doi.normalize import first_doi_from_texts
+from app.services.domains.ingestion import queue as queue_service
+from app.services.domains.ingestion import safety as run_safety_service
from app.services.domains.ingestion.constants import (
FAILED_STATES,
FAILURE_BUCKET_BLOCKED,
@@ -30,9 +35,6 @@ from app.services.domains.ingestion.constants import (
RESUMABLE_PARTIAL_REASONS,
RUN_LOCK_NAMESPACE,
)
-from app.services.domains.arxiv.errors import ArxivRateLimitError
-from app.services.domains.doi.normalize import first_doi_from_texts
-from app.services.domains.publication_identifiers import application as identifier_service
from app.services.domains.ingestion.fingerprints import (
_build_body_excerpt,
_dedupe_publication_candidates,
@@ -43,8 +45,6 @@ from app.services.domains.ingestion.fingerprints import (
canonical_title_for_dedup,
normalize_title,
)
-from app.services.domains.ingestion import queue as queue_service
-from app.services.domains.ingestion import safety as run_safety_service
from app.services.domains.ingestion.types import (
PagedLoopState,
PagedParseResult,
@@ -56,17 +56,17 @@ from app.services.domains.ingestion.types import (
RunProgress,
ScholarProcessingOutcome,
)
-from app.services.domains.settings import application as user_settings_service
+from app.services.domains.publication_identifiers import application as identifier_service
from app.services.domains.runs.events import run_events
from app.services.domains.scholar.parser import (
- ParseState,
ParsedProfilePage,
+ ParseState,
PublicationCandidate,
ScholarParserError,
parse_profile_page,
)
from app.services.domains.scholar.source import FetchResult, ScholarSource
-from app.logging_utils import structured_log
+from app.services.domains.settings import application as user_settings_service
from app.settings import settings
logger = logging.getLogger(__name__)
@@ -147,18 +147,20 @@ class ScholarIngestionService:
user_id: int,
trigger_type: RunTriggerType,
) -> None:
- now_utc = datetime.now(timezone.utc)
+ now_utc = datetime.now(UTC)
previous = run_safety_service.get_safety_event_context(user_settings, now_utc=now_utc)
if run_safety_service.clear_expired_cooldown(user_settings, now_utc=now_utc):
await db_session.commit()
await db_session.refresh(user_settings)
structured_log(
- logger, "info", "ingestion.cooldown_cleared",
+ logger,
+ "info",
+ "ingestion.cooldown_cleared",
user_id=user_id,
reason=previous.get("cooldown_reason"),
cooldown_until=previous.get("cooldown_until"),
)
- now_utc = datetime.now(timezone.utc)
+ now_utc = datetime.now(UTC)
if run_safety_service.is_cooldown_active(user_settings, now_utc=now_utc):
await self._raise_safety_blocked_start(
db_session,
@@ -183,7 +185,9 @@ class ScholarIngestionService:
)
await db_session.commit()
structured_log(
- logger, "warning", "ingestion.safety_policy_blocked_run_start",
+ logger,
+ "warning",
+ "ingestion.safety_policy_blocked_run_start",
user_id=user_id,
trigger_type=trigger_type.value,
reason=safety_state.get("cooldown_reason"),
@@ -204,14 +208,9 @@ class ScholarIngestionService:
start_cstart_by_scholar_id: dict[int, int] | None,
) -> tuple[set[int] | None, dict[int, int]]:
filtered_scholar_ids = (
- {int(value) for value in scholar_profile_ids}
- if scholar_profile_ids is not None
- else None
+ {int(value) for value in scholar_profile_ids} if scholar_profile_ids is not None else None
)
- start_cstart_map = {
- int(key): max(0, int(value))
- for key, value in (start_cstart_by_scholar_id or {}).items()
- }
+ start_cstart_map = {int(key): max(0, int(value)) for key, value in (start_cstart_by_scholar_id or {}).items()}
return filtered_scholar_ids, start_cstart_map
async def _load_target_scholars(
@@ -521,7 +520,9 @@ class ScholarIngestionService:
page_logs=paged_parse_result.page_logs,
)
structured_log(
- logger, "warning", "ingestion.scholar_parse_failed",
+ logger,
+ "warning",
+ "ingestion.scholar_parse_failed",
scholar_profile_id=scholar.id,
scholar_id=scholar.scholar_id,
state=paged_parse_result.parsed_page.state.value,
@@ -679,7 +680,7 @@ class ScholarIngestionService:
max_pages_per_scholar: int,
page_size: int,
) -> tuple[datetime, PagedParseResult, dict[str, Any]]:
- run_dt = datetime.now(timezone.utc)
+ run_dt = datetime.now(UTC)
paged_parse_result = await self._fetch_and_parse_all_pages_with_retry(
scholar=scholar,
run=run,
@@ -698,7 +699,9 @@ class ScholarIngestionService:
self._apply_first_page_profile_metadata(scholar=scholar, paged_parse_result=paged_parse_result, run_dt=run_dt)
parsed_page = paged_parse_result.parsed_page
structured_log(
- logger, "info", "ingestion.scholar_parsed",
+ logger,
+ "info",
+ "ingestion.scholar_parsed",
user_id=user_id,
crawl_run_id=run.id,
scholar_profile_id=scholar.id,
@@ -796,9 +799,7 @@ class ScholarIngestionService:
scholar_results=progress.scholar_results,
scholar_profile_id=scholar_profile_id,
)
- next_succeeded, next_failed, next_partial = ScholarIngestionService._result_counters(
- outcome.result_entry
- )
+ next_succeeded, next_failed, next_partial = ScholarIngestionService._result_counters(outcome.result_entry)
if prior_index is None:
progress.scholar_results.append(outcome.result_entry)
ScholarIngestionService._adjust_progress_counts(
@@ -809,9 +810,7 @@ class ScholarIngestionService:
)
return
previous_entry = progress.scholar_results[prior_index]
- prev_succeeded, prev_failed, prev_partial = ScholarIngestionService._result_counters(
- previous_entry
- )
+ prev_succeeded, prev_failed, prev_partial = ScholarIngestionService._result_counters(previous_entry)
progress.scholar_results[prior_index] = outcome.result_entry
ScholarIngestionService._adjust_progress_counts(
progress=progress,
@@ -829,7 +828,7 @@ class ScholarIngestionService:
exc: Exception,
) -> ScholarProcessingOutcome:
scholar.last_run_status = RunStatus.FAILED
- scholar.last_run_dt = datetime.now(timezone.utc)
+ scholar.last_run_dt = datetime.now(UTC)
logger.exception(
"ingestion.scholar_unexpected_failure",
extra={
@@ -933,7 +932,7 @@ class ScholarIngestionService:
) -> None:
pre_apply_state = run_safety_service.get_safety_event_context(
user_settings,
- now_utc=datetime.now(timezone.utc),
+ now_utc=datetime.now(UTC),
)
safety_state, cooldown_trigger_reason = run_safety_service.apply_run_safety_outcome(
user_settings,
@@ -944,11 +943,13 @@ class ScholarIngestionService:
network_failure_threshold=alert_summary.network_failure_threshold,
blocked_cooldown_seconds=settings.ingestion_safety_cooldown_blocked_seconds,
network_cooldown_seconds=settings.ingestion_safety_cooldown_network_seconds,
- now_utc=datetime.now(timezone.utc),
+ now_utc=datetime.now(UTC),
)
if cooldown_trigger_reason is not None:
structured_log(
- logger, "warning", "ingestion.safety_cooldown_entered",
+ logger,
+ "warning",
+ "ingestion.safety_cooldown_entered",
user_id=user_id,
crawl_run_id=int(run.id),
reason=cooldown_trigger_reason,
@@ -962,7 +963,9 @@ class ScholarIngestionService:
)
elif pre_apply_state.get("cooldown_active") and not safety_state.get("cooldown_active"):
structured_log(
- logger, "info", "ingestion.cooldown_cleared",
+ logger,
+ "info",
+ "ingestion.cooldown_cleared",
user_id=user_id,
crawl_run_id=int(run.id),
reason=pre_apply_state.get("cooldown_reason"),
@@ -979,7 +982,7 @@ class ScholarIngestionService:
alert_summary: RunAlertSummary,
idempotency_key: str | None,
) -> None:
- run.end_dt = datetime.now(timezone.utc)
+ run.end_dt = datetime.now(UTC)
if run.status != RunStatus.CANCELED:
run.status = self._resolve_run_status(
scholar_count=len(scholars),
@@ -1062,7 +1065,26 @@ class ScholarIngestionService:
new_publication_count=run.new_pub_count,
)
- async def _initialize_run_for_user(self, db_session: AsyncSession, *, user_id: int, trigger_type: RunTriggerType, scholar_profile_ids: set[int] | None, start_cstart_by_scholar_id: dict[int, int] | None, request_delay_seconds: int, network_error_retries: int, retry_backoff_seconds: float, rate_limit_retries: int, rate_limit_backoff_seconds: float, max_pages_per_scholar: int, page_size: int, idempotency_key: str | None, alert_blocked_failure_threshold: int, alert_network_failure_threshold: int, alert_retry_scheduled_threshold: int) -> tuple[Any, CrawlRun, list[ScholarProfile], dict[int, int]]:
+ async def _initialize_run_for_user(
+ self,
+ db_session: AsyncSession,
+ *,
+ user_id: int,
+ trigger_type: RunTriggerType,
+ scholar_profile_ids: set[int] | None,
+ start_cstart_by_scholar_id: dict[int, int] | None,
+ request_delay_seconds: int,
+ network_error_retries: int,
+ retry_backoff_seconds: float,
+ rate_limit_retries: int,
+ rate_limit_backoff_seconds: float,
+ max_pages_per_scholar: int,
+ page_size: int,
+ idempotency_key: str | None,
+ alert_blocked_failure_threshold: int,
+ alert_network_failure_threshold: int,
+ alert_retry_scheduled_threshold: int,
+ ) -> tuple[Any, CrawlRun, list[ScholarProfile], dict[int, int]]:
user_settings = await self._load_user_settings_for_run(
db_session,
user_id=user_id,
@@ -1116,7 +1138,9 @@ class ScholarIngestionService:
alert_retry_scheduled_threshold: int,
) -> CrawlRun:
structured_log(
- logger, "info", "ingestion.run_started",
+ logger,
+ "info",
+ "ingestion.run_started",
user_id=user_id,
trigger_type=trigger_type.value,
scholar_count=len(scholars),
@@ -1143,9 +1167,7 @@ class ScholarIngestionService:
except IntegrityError as exc:
if _is_active_run_integrity_error(exc):
await db_session.rollback()
- raise RunAlreadyInProgressError(
- f"Run already in progress for user_id={user_id}."
- ) from exc
+ raise RunAlreadyInProgressError(f"Run already in progress for user_id={user_id}.") from exc
raise
return run
@@ -1177,8 +1199,11 @@ class ScholarIngestionService:
await db_session.refresh(run)
if run.status == RunStatus.CANCELED:
structured_log(
- logger, "info", "ingestion.run_canceled",
- run_id=run.id, user_id=user_id,
+ logger,
+ "info",
+ "ingestion.run_canceled",
+ run_id=run.id,
+ user_id=user_id,
)
return progress
await self._wait_between_scholars(index=index, request_delay_seconds=request_delay_seconds)
@@ -1217,8 +1242,11 @@ class ScholarIngestionService:
await db_session.refresh(run)
if run.status == RunStatus.CANCELED:
structured_log(
- logger, "info", "ingestion.run_canceled",
- run_id=run.id, user_id=user_id,
+ logger,
+ "info",
+ "ingestion.run_canceled",
+ run_id=run.id,
+ user_id=user_id,
)
break
await self._wait_between_scholars(index=index, request_delay_seconds=request_delay_seconds)
@@ -1263,7 +1291,9 @@ class ScholarIngestionService:
)
if alert_summary.alert_flags["blocked_failure_threshold_exceeded"]:
structured_log(
- logger, "warning", "ingestion.alert_blocked_failure_threshold_exceeded",
+ logger,
+ "warning",
+ "ingestion.alert_blocked_failure_threshold_exceeded",
user_id=user_id,
crawl_run_id=int(run.id),
blocked_failure_count=alert_summary.blocked_failure_count,
@@ -1271,7 +1301,9 @@ class ScholarIngestionService:
)
if alert_summary.alert_flags["network_failure_threshold_exceeded"]:
structured_log(
- logger, "warning", "ingestion.alert_network_failure_threshold_exceeded",
+ logger,
+ "warning",
+ "ingestion.alert_network_failure_threshold_exceeded",
user_id=user_id,
crawl_run_id=int(run.id),
network_failure_count=alert_summary.network_failure_count,
@@ -1279,7 +1311,9 @@ class ScholarIngestionService:
)
if alert_summary.alert_flags["retry_scheduled_threshold_exceeded"]:
structured_log(
- logger, "warning", "ingestion.alert_retry_scheduled_threshold_exceeded",
+ logger,
+ "warning",
+ "ingestion.alert_retry_scheduled_threshold_exceeded",
user_id=user_id,
crawl_run_id=int(run.id),
retries_scheduled_count=failure_summary.retries_scheduled_count,
@@ -1319,7 +1353,9 @@ class ScholarIngestionService:
effective_delay = self._effective_request_delay_seconds(request_delay_seconds)
if effective_delay != _int_or_default(request_delay_seconds, effective_delay):
structured_log(
- logger, "warning", "ingestion.delay_coerced",
+ logger,
+ "warning",
+ "ingestion.delay_coerced",
user_id=user_id,
requested_request_delay_seconds=_int_or_default(request_delay_seconds, 0),
effective_request_delay_seconds=effective_delay,
@@ -1332,8 +1368,12 @@ class ScholarIngestionService:
request_delay_seconds=effective_delay,
network_error_retries=network_error_retries,
retry_backoff_seconds=retry_backoff_seconds,
- rate_limit_retries=rate_limit_retries if rate_limit_retries is not None else settings.ingestion_rate_limit_retries,
- rate_limit_backoff_seconds=rate_limit_backoff_seconds if rate_limit_backoff_seconds is not None else settings.ingestion_rate_limit_backoff_seconds,
+ rate_limit_retries=rate_limit_retries
+ if rate_limit_retries is not None
+ else settings.ingestion_rate_limit_retries,
+ rate_limit_backoff_seconds=rate_limit_backoff_seconds
+ if rate_limit_backoff_seconds is not None
+ else settings.ingestion_rate_limit_backoff_seconds,
max_pages_per_scholar=max_pages_per_scholar,
page_size=page_size,
)
@@ -1383,13 +1423,17 @@ class ScholarIngestionService:
run, user_settings, attached_scholars = await self._prepare_execute_run(
db_session, run_id=run_id, user_id=user_id, scholars=scholars
)
-
+
paging_kwargs = self._paging_kwargs(
request_delay_seconds=request_delay_seconds,
network_error_retries=network_error_retries,
retry_backoff_seconds=retry_backoff_seconds,
- rate_limit_retries=rate_limit_retries if rate_limit_retries is not None else settings.ingestion_rate_limit_retries,
- rate_limit_backoff_seconds=rate_limit_backoff_seconds if rate_limit_backoff_seconds is not None else settings.ingestion_rate_limit_backoff_seconds,
+ rate_limit_retries=rate_limit_retries
+ if rate_limit_retries is not None
+ else settings.ingestion_rate_limit_retries,
+ rate_limit_backoff_seconds=rate_limit_backoff_seconds
+ if rate_limit_backoff_seconds is not None
+ else settings.ingestion_rate_limit_backoff_seconds,
max_pages_per_scholar=max_pages_per_scholar,
page_size=page_size,
)
@@ -1427,7 +1471,9 @@ class ScholarIngestionService:
run.status = RunStatus.RESOLVING
await db_session.commit()
structured_log(
- logger, "info", "ingestion.run_completed",
+ logger,
+ "info",
+ "ingestion.run_completed",
user_id=user_id,
crawl_run_id=run.id,
status=run.status.value,
@@ -1471,7 +1517,8 @@ class ScholarIngestionService:
scholar_ids = [s.id for s in scholars]
scholars_result = await db_session.execute(
- select(ScholarProfile).where(ScholarProfile.id.in_(scholar_ids))
+ select(ScholarProfile)
+ .where(ScholarProfile.id.in_(scholar_ids))
.order_by(ScholarProfile.created_at.asc(), ScholarProfile.id.asc())
)
return run, user_settings, list(scholars_result.scalars().all())
@@ -1481,7 +1528,7 @@ class ScholarIngestionService:
run_to_fail = await cleanup_session.get(CrawlRun, run_id)
if run_to_fail:
run_to_fail.status = RunStatus.FAILED
- run_to_fail.end_dt = datetime.now(timezone.utc)
+ run_to_fail.end_dt = datetime.now(UTC)
run_to_fail.error_log["terminal_exception"] = str(exc)
await cleanup_session.commit()
@@ -1568,17 +1615,21 @@ class ScholarIngestionService:
alert_network_failure_threshold=alert_network_failure_threshold,
alert_retry_scheduled_threshold=alert_retry_scheduled_threshold,
)
-
+
paging_kwargs = self._paging_kwargs(
request_delay_seconds=self._effective_request_delay_seconds(request_delay_seconds),
network_error_retries=network_error_retries,
retry_backoff_seconds=retry_backoff_seconds,
- rate_limit_retries=rate_limit_retries if rate_limit_retries is not None else settings.ingestion_rate_limit_retries,
- rate_limit_backoff_seconds=rate_limit_backoff_seconds if rate_limit_backoff_seconds is not None else settings.ingestion_rate_limit_backoff_seconds,
+ rate_limit_retries=rate_limit_retries
+ if rate_limit_retries is not None
+ else settings.ingestion_rate_limit_retries,
+ rate_limit_backoff_seconds=rate_limit_backoff_seconds
+ if rate_limit_backoff_seconds is not None
+ else settings.ingestion_rate_limit_backoff_seconds,
max_pages_per_scholar=max_pages_per_scholar,
page_size=page_size,
)
-
+
threshold_kwargs = self._threshold_kwargs(
alert_blocked_failure_threshold=alert_blocked_failure_threshold,
alert_network_failure_threshold=alert_network_failure_threshold,
@@ -1628,7 +1679,9 @@ class ScholarIngestionService:
await db_session.commit()
structured_log(
- logger, "info", "ingestion.run_completed",
+ logger,
+ "info",
+ "ingestion.run_completed",
user_id=user_id,
crawl_run_id=run.id,
status=run.status.value,
@@ -1663,8 +1716,7 @@ class ScholarIngestionService:
return await self._source.fetch_profile_html(scholar_id)
return FetchResult(
requested_url=(
- "https://scholar.google.com/citations"
- f"?hl=en&user={scholar_id}&cstart={cstart}&pagesize={page_size}"
+ f"https://scholar.google.com/citations?hl=en&user={scholar_id}&cstart={cstart}&pagesize={page_size}"
),
status_code=None,
final_url=None,
@@ -1682,8 +1734,7 @@ class ScholarIngestionService:
)
return FetchResult(
requested_url=(
- "https://scholar.google.com/citations"
- f"?hl=en&user={scholar_id}&cstart={cstart}&pagesize={page_size}"
+ f"https://scholar.google.com/citations?hl=en&user={scholar_id}&cstart={cstart}&pagesize={page_size}"
),
status_code=None,
final_url=None,
@@ -1702,7 +1753,10 @@ class ScholarIngestionService:
) -> bool:
if parsed_page.state == ParseState.NETWORK_ERROR:
return network_attempt_count <= network_error_retries
- if parsed_page.state == ParseState.BLOCKED_OR_CAPTCHA and parsed_page.state_reason == "blocked_http_429_rate_limited":
+ if (
+ parsed_page.state == ParseState.BLOCKED_OR_CAPTCHA
+ and parsed_page.state_reason == "blocked_http_429_rate_limited"
+ ):
return rate_limit_attempt_count <= rate_limit_retries
return False
@@ -1725,7 +1779,9 @@ class ScholarIngestionService:
attempt_label = network_attempt_count
structured_log(
- logger, "warning", "ingestion.scholar_retry_scheduled",
+ logger,
+ "warning",
+ "ingestion.scholar_retry_scheduled",
scholar_id=scholar_id,
cstart=cstart,
attempt_count=attempt_label,
@@ -1759,24 +1815,29 @@ class ScholarIngestionService:
page_size=page_size,
)
parsed_page = self._parse_profile_page_or_layout_error(fetch_result=fetch_result)
-
+
if parsed_page.state == ParseState.NETWORK_ERROR:
network_attempts += 1
total_attempts = network_attempts
- elif parsed_page.state == ParseState.BLOCKED_OR_CAPTCHA and parsed_page.state_reason == "blocked_http_429_rate_limited":
+ elif (
+ parsed_page.state == ParseState.BLOCKED_OR_CAPTCHA
+ and parsed_page.state_reason == "blocked_http_429_rate_limited"
+ ):
rate_limit_attempts += 1
total_attempts = rate_limit_attempts
else:
total_attempts = network_attempts + rate_limit_attempts + 1
- attempt_log.append({
- "attempt": total_attempts,
- "cstart": cstart,
- "state": parsed_page.state.value,
- "state_reason": parsed_page.state_reason,
- "status_code": fetch_result.status_code,
- "fetch_error": fetch_result.error,
- })
+ attempt_log.append(
+ {
+ "attempt": total_attempts,
+ "cstart": cstart,
+ "state": parsed_page.state.value,
+ "state_reason": parsed_page.state_reason,
+ "status_code": fetch_result.status_code,
+ "fetch_error": fetch_result.error,
+ }
+ )
if not self._should_retry_page_fetch(
parsed_page=parsed_page,
@@ -1995,18 +2056,20 @@ class ScholarIngestionService:
) -> None:
state.pages_attempted += 1
state.attempt_log.extend(page_attempt_log)
- state.page_logs.append({
- "page": state.pages_attempted,
- "cstart": state.current_cstart,
- "state": parsed_page.state.value,
- "state_reason": parsed_page.state_reason,
- "status_code": fetch_result.status_code,
- "publication_count": len(parsed_page.publications),
- "articles_range": parsed_page.articles_range,
- "has_show_more_button": parsed_page.has_show_more_button,
- "warning_codes": parsed_page.warnings,
- "attempt_count": len(page_attempt_log),
- })
+ state.page_logs.append(
+ {
+ "page": state.pages_attempted,
+ "cstart": state.current_cstart,
+ "state": parsed_page.state.value,
+ "state_reason": parsed_page.state_reason,
+ "status_code": fetch_result.status_code,
+ "publication_count": len(parsed_page.publications),
+ "articles_range": parsed_page.articles_range,
+ "has_show_more_button": parsed_page.has_show_more_button,
+ "warning_codes": parsed_page.warnings,
+ "attempt_count": len(page_attempt_log),
+ }
+ )
state.fetch_result = fetch_result
state.parsed_page = parsed_page
@@ -2052,18 +2115,20 @@ class ScholarIngestionService:
)
first_page_fingerprint_sha256 = build_initial_page_fingerprint(parsed_page)
attempt_log = list(first_attempt_log)
- page_logs = [{
- "page": 1,
- "cstart": start_cstart,
- "state": parsed_page.state.value,
- "state_reason": parsed_page.state_reason,
- "status_code": fetch_result.status_code,
- "publication_count": len(parsed_page.publications),
- "articles_range": parsed_page.articles_range,
- "has_show_more_button": parsed_page.has_show_more_button,
- "warning_codes": parsed_page.warnings,
- "attempt_count": len(first_attempt_log),
- }]
+ page_logs = [
+ {
+ "page": 1,
+ "cstart": start_cstart,
+ "state": parsed_page.state.value,
+ "state_reason": parsed_page.state_reason,
+ "status_code": fetch_result.status_code,
+ "publication_count": len(parsed_page.publications),
+ "articles_range": parsed_page.articles_range,
+ "has_show_more_button": parsed_page.has_show_more_button,
+ "warning_codes": parsed_page.warnings,
+ "attempt_count": len(first_attempt_log),
+ }
+ ]
return fetch_result, parsed_page, first_page_fingerprint_sha256, attempt_log, page_logs
async def _paginate_loop(
@@ -2098,7 +2163,9 @@ class ScholarIngestionService:
await db_session.refresh(run)
if run.status == RunStatus.CANCELED:
structured_log(
- logger, "info", "ingestion.pagination_canceled",
+ logger,
+ "info",
+ "ingestion.pagination_canceled",
run_id=run.id,
)
self._set_truncated_state(
@@ -2217,12 +2284,17 @@ class ScholarIngestionService:
rate_limit_backoff_seconds: float,
max_pages: int,
page_size: int,
- previous_initial_page_fingerprint_sha256: str | None = None
+ previous_initial_page_fingerprint_sha256: str | None = None,
) -> PagedParseResult:
bounded_max_pages = max(1, int(max_pages))
bounded_page_size = max(1, int(page_size))
- fetch_result, parsed_page, first_page_fingerprint_sha256, attempt_log, page_logs = (
- await self._fetch_initial_page_context(
+ (
+ fetch_result,
+ parsed_page,
+ first_page_fingerprint_sha256,
+ attempt_log,
+ page_logs,
+ ) = await self._fetch_initial_page_context(
scholar_id=scholar.scholar_id,
start_cstart=start_cstart,
bounded_page_size=bounded_page_size,
@@ -2230,7 +2302,7 @@ class ScholarIngestionService:
retry_backoff_seconds=retry_backoff_seconds,
rate_limit_retries=rate_limit_retries,
rate_limit_backoff_seconds=rate_limit_backoff_seconds,
- ))
+ )
shortcut_result = self._short_circuit_initial_page(
start_cstart=start_cstart,
previous_initial_page_fingerprint_sha256=previous_initial_page_fingerprint_sha256,
@@ -2275,9 +2347,7 @@ class ScholarIngestionService:
*,
run_id: int,
) -> bool:
- check_result = await db_session.execute(
- select(CrawlRun.status).where(CrawlRun.id == run_id)
- )
+ check_result = await db_session.execute(select(CrawlRun.status).where(CrawlRun.id == run_id))
status = check_result.scalar_one_or_none()
if status is None:
raise RuntimeError(f"Missing crawl_run for run_id={run_id}.")
@@ -2302,12 +2372,10 @@ class ScholarIngestionService:
)
from app.services.domains.openalex.matching import find_best_match
- run_result = await db_session.execute(
- select(CrawlRun.user_id).where(CrawlRun.id == run_id)
- )
+ run_result = await db_session.execute(select(CrawlRun.user_id).where(CrawlRun.id == run_id))
user_id = run_result.scalar_one()
- now = datetime.now(timezone.utc)
+ now = datetime.now(UTC)
cooldown_threshold = now - timedelta(days=7)
stmt = (
@@ -2355,21 +2423,28 @@ class ScholarIngestionService:
)
except OpenAlexBudgetExhaustedError:
structured_log(
- logger, "warning", "ingestion.openalex_budget_exhausted",
+ logger,
+ "warning",
+ "ingestion.openalex_budget_exhausted",
run_id=run_id,
)
break # Stop all enrichment — budget won't reset until midnight UTC
except OpenAlexRateLimitError:
structured_log(
- logger, "warning", "ingestion.openalex_rate_limited",
+ logger,
+ "warning",
+ "ingestion.openalex_rate_limited",
run_id=run_id,
)
await asyncio.sleep(60)
continue
except Exception as e:
structured_log(
- logger, "warning", "ingestion.openalex_enrichment_failed",
- error=str(e), run_id=run_id,
+ logger,
+ "warning",
+ "ingestion.openalex_enrichment_failed",
+ error=str(e),
+ run_id=run_id,
)
continue
@@ -2406,7 +2481,9 @@ class ScholarIngestionService:
merge_count = await sweep_identifier_duplicates(db_session)
if merge_count:
structured_log(
- logger, "info", "ingestion.identifier_dedup_sweep",
+ logger,
+ "info",
+ "ingestion.identifier_dedup_sweep",
merged_count=merge_count,
run_id=run_id,
)
@@ -2444,7 +2521,9 @@ class ScholarIngestionService:
return True
except ArxivRateLimitError:
structured_log(
- logger, "warning", "ingestion.arxiv_rate_limited",
+ logger,
+ "warning",
+ "ingestion.arxiv_rate_limited",
run_id=run_id,
publication_id=int(publication.id),
detail="arXiv temporarily disabled for remaining enrichment pass",
@@ -2498,17 +2577,18 @@ class ScholarIngestionService:
from app.services.domains.openalex.client import OpenAlexClient
from app.services.domains.openalex.matching import find_best_match
-
+
client = OpenAlexClient(api_key=settings.openalex_api_key, mailto=settings.crossref_api_mailto)
-
+
# Batch requests by 25 to stay within URL length limits
batch_size = 25
enriched: list[PublicationCandidate] = []
-
+
import re
+
for i in range(0, len(publications), batch_size):
- batch = publications[i:i + batch_size]
-
+ batch = publications[i : i + batch_size]
+
titles = []
for p in batch:
if not p.title:
@@ -2519,29 +2599,27 @@ class ScholarIngestionService:
safe_title = " ".join(safe_title.split())
if safe_title:
titles.append(safe_title)
-
+
if not titles:
enriched.extend(batch)
continue
-
+
query = "|".join(t for t in titles)
try:
- openalex_works = await client.get_works_by_filter(
- {"title.search": query}, limit=batch_size * 3
- )
+ openalex_works = await client.get_works_by_filter({"title.search": query}, limit=batch_size * 3)
except Exception as e:
logger.warning(
"ingestion.openalex_enrichment_failed",
- extra={"error": str(e), "batch_size": len(batch), "scholar_id": scholar.id}
+ extra={"error": str(e), "batch_size": len(batch), "scholar_id": scholar.id},
)
openalex_works = []
-
+
for p in batch:
match = find_best_match(
target_title=p.title,
target_year=p.year,
target_authors=p.authors_text or (scholar.display_name or scholar.scholar_id),
- candidates=openalex_works
+ candidates=openalex_works,
)
if match:
new_p = PublicationCandidate(
@@ -2627,7 +2705,7 @@ class ScholarIngestionService:
"pub_url": publication.pub_url,
"scholar_profile_id": scholar.id,
"scholar_label": scholar.display_name or scholar.scholar_id,
- "first_seen_at": datetime.now(timezone.utc).isoformat(),
+ "first_seen_at": datetime.now(UTC).isoformat(),
"new_publication_count": int(run.new_pub_count or 0),
},
)
@@ -2647,9 +2725,7 @@ class ScholarIngestionService:
) -> Publication | None:
if not cluster_id:
return None
- result = await db_session.execute(
- select(Publication).where(Publication.cluster_id == cluster_id)
- )
+ result = await db_session.execute(select(Publication).where(Publication.cluster_id == cluster_id))
return result.scalar_one_or_none()
async def _find_publication_by_fingerprint(
@@ -2658,9 +2734,7 @@ class ScholarIngestionService:
*,
fingerprint: str,
) -> Publication | None:
- result = await db_session.execute(
- select(Publication).where(Publication.fingerprint_sha256 == fingerprint)
- )
+ result = await db_session.execute(select(Publication).where(Publication.fingerprint_sha256 == fingerprint))
return result.scalar_one_or_none()
@staticmethod
@@ -2685,9 +2759,7 @@ class ScholarIngestionService:
canonical_title_hash: str,
) -> Publication | None:
result = await db_session.execute(
- select(Publication).where(
- Publication.canonical_title_hash == canonical_title_hash
- )
+ select(Publication).where(Publication.canonical_title_hash == canonical_title_hash)
)
return result.scalar_one_or_none()
@@ -2816,9 +2888,7 @@ class ScholarIngestionService:
) -> tuple[str | None, int]:
if outcome == "partial":
reason = (pagination_truncated_reason or "").strip()
- if reason in RESUMABLE_PARTIAL_REASONS or reason.startswith(
- RESUMABLE_PARTIAL_REASON_PREFIXES
- ):
+ if reason in RESUMABLE_PARTIAL_REASONS or reason.startswith(RESUMABLE_PARTIAL_REASON_PREFIXES):
return reason, queue_service.normalize_cstart(
continuation_cstart if continuation_cstart is not None else fallback_cstart
)
@@ -2852,13 +2922,9 @@ class ScholarIngestionService:
"has_show_more_button": parsed_page.has_show_more_button,
"has_operation_error_banner": parsed_page.has_operation_error_banner,
"warning_codes": parsed_page.warnings,
- "marker_counts_nonzero": {
- key: value for key, value in parsed_page.marker_counts.items() if value > 0
- },
+ "marker_counts_nonzero": {key: value for key, value in parsed_page.marker_counts.items() if value > 0},
"body_length": len(fetch_result.body),
- "body_sha256": hashlib.sha256(fetch_result.body.encode("utf-8")).hexdigest()
- if fetch_result.body
- else None,
+ "body_sha256": hashlib.sha256(fetch_result.body.encode("utf-8")).hexdigest() if fetch_result.body else None,
"body_excerpt": _build_body_excerpt(fetch_result.body),
"attempt_log": attempt_log,
}
@@ -2876,9 +2942,7 @@ class ScholarIngestionService:
user_id: int,
) -> bool:
result = await db_session.execute(
- text(
- "SELECT pg_try_advisory_xact_lock(:namespace, :user_key)"
- ),
+ text("SELECT pg_try_advisory_xact_lock(:namespace, :user_key)"),
{
"namespace": RUN_LOCK_NAMESPACE,
"user_key": int(user_id),
diff --git a/app/services/domains/ingestion/fingerprints.py b/app/services/domains/ingestion/fingerprints.py
index 9f67f0f..7c3156d 100644
--- a/app/services/domains/ingestion/fingerprints.py
+++ b/app/services/domains/ingestion/fingerprints.py
@@ -3,8 +3,8 @@ from __future__ import annotations
import hashlib
import json
import re
-from typing import Any
import unicodedata
+from typing import Any
from urllib.parse import urljoin
from app.services.domains.ingestion.constants import (
@@ -14,7 +14,7 @@ from app.services.domains.ingestion.constants import (
TITLE_ALNUM_RE,
WORD_RE,
)
-from app.services.domains.scholar.parser import ParseState, ParsedProfilePage, PublicationCandidate
+from app.services.domains.scholar.parser import ParsedProfilePage, ParseState, PublicationCandidate
# Scholar-specific noise patterns stripped before canonical comparison.
# Applied in order; each targets a different Scholar metadata injection style.
@@ -381,4 +381,4 @@ def _build_body_excerpt(body: str, *, max_chars: int = 220) -> str | None:
return None
if len(flattened) <= max_chars:
return flattened
- return f"{flattened[:max_chars - 1]}..."
+ return f"{flattened[: max_chars - 1]}..."
diff --git a/app/services/domains/ingestion/queue.py b/app/services/domains/ingestion/queue.py
index 7494420..2016f63 100644
--- a/app/services/domains/ingestion/queue.py
+++ b/app/services/domains/ingestion/queue.py
@@ -1,7 +1,7 @@
from __future__ import annotations
from dataclasses import dataclass
-from datetime import datetime, timedelta, timezone
+from datetime import UTC, datetime, timedelta
from sqlalchemy import select
from sqlalchemy.ext.asyncio import AsyncSession
@@ -115,7 +115,7 @@ async def upsert_job(
run_id: int | None,
delay_seconds: int,
) -> IngestionQueueItem:
- now = datetime.now(timezone.utc)
+ now = datetime.now(UTC)
next_attempt_dt = now + timedelta(seconds=max(0, int(delay_seconds)))
item = await _get_item_for_user_scholar(
db_session,
@@ -171,9 +171,7 @@ async def delete_job_by_id(
*,
job_id: int,
) -> bool:
- result = await db_session.execute(
- select(IngestionQueueItem).where(IngestionQueueItem.id == job_id)
- )
+ result = await db_session.execute(select(IngestionQueueItem).where(IngestionQueueItem.id == job_id))
item = result.scalar_one_or_none()
if item is None:
return False
@@ -222,10 +220,8 @@ async def increment_attempt_count(
*,
job_id: int,
) -> IngestionQueueItem | None:
- now = datetime.now(timezone.utc)
- result = await db_session.execute(
- select(IngestionQueueItem).where(IngestionQueueItem.id == job_id)
- )
+ now = datetime.now(UTC)
+ result = await db_session.execute(select(IngestionQueueItem).where(IngestionQueueItem.id == job_id))
item = result.scalar_one_or_none()
if item is None:
return None
@@ -239,10 +235,8 @@ async def reset_attempt_count(
*,
job_id: int,
) -> IngestionQueueItem | None:
- now = datetime.now(timezone.utc)
- result = await db_session.execute(
- select(IngestionQueueItem).where(IngestionQueueItem.id == job_id)
- )
+ now = datetime.now(UTC)
+ result = await db_session.execute(select(IngestionQueueItem).where(IngestionQueueItem.id == job_id))
item = result.scalar_one_or_none()
if item is None:
return None
@@ -259,10 +253,8 @@ async def reschedule_job(
reason: str,
error: str | None = None,
) -> IngestionQueueItem | None:
- now = datetime.now(timezone.utc)
- result = await db_session.execute(
- select(IngestionQueueItem).where(IngestionQueueItem.id == job_id)
- )
+ now = datetime.now(UTC)
+ result = await db_session.execute(select(IngestionQueueItem).where(IngestionQueueItem.id == job_id))
item = result.scalar_one_or_none()
if item is None:
return None
@@ -282,10 +274,8 @@ async def mark_retrying(
job_id: int,
reason: str | None = None,
) -> IngestionQueueItem | None:
- now = datetime.now(timezone.utc)
- result = await db_session.execute(
- select(IngestionQueueItem).where(IngestionQueueItem.id == job_id)
- )
+ now = datetime.now(UTC)
+ result = await db_session.execute(select(IngestionQueueItem).where(IngestionQueueItem.id == job_id))
item = result.scalar_one_or_none()
if item is None:
return None
@@ -305,10 +295,8 @@ async def mark_dropped(
reason: str,
error: str | None = None,
) -> IngestionQueueItem | None:
- now = datetime.now(timezone.utc)
- result = await db_session.execute(
- select(IngestionQueueItem).where(IngestionQueueItem.id == job_id)
- )
+ now = datetime.now(UTC)
+ result = await db_session.execute(select(IngestionQueueItem).where(IngestionQueueItem.id == job_id))
item = result.scalar_one_or_none()
if item is None:
return None
@@ -329,10 +317,8 @@ async def mark_queued_now(
reason: str,
reset_attempt_count: bool = False,
) -> IngestionQueueItem | None:
- now = datetime.now(timezone.utc)
- result = await db_session.execute(
- select(IngestionQueueItem).where(IngestionQueueItem.id == job_id)
- )
+ now = datetime.now(UTC)
+ result = await db_session.execute(select(IngestionQueueItem).where(IngestionQueueItem.id == job_id))
item = result.scalar_one_or_none()
if item is None:
return None
diff --git a/app/services/domains/ingestion/safety.py b/app/services/domains/ingestion/safety.py
index debb8c5..a8385a9 100644
--- a/app/services/domains/ingestion/safety.py
+++ b/app/services/domains/ingestion/safety.py
@@ -1,6 +1,6 @@
from __future__ import annotations
-from datetime import datetime, timedelta, timezone
+from datetime import UTC, datetime, timedelta
from typing import Any
from app.db.models import UserSetting
@@ -18,7 +18,7 @@ _COUNTER_LAST_EVALUATED_RUN_ID = "last_evaluated_run_id"
def _utcnow() -> datetime:
- return datetime.now(timezone.utc)
+ return datetime.now(UTC)
def _safe_int(value: Any, default: int = 0) -> int:
@@ -41,8 +41,8 @@ def _normalize_datetime(value: datetime | None) -> datetime | None:
if value is None:
return None
if value.tzinfo is None:
- return value.replace(tzinfo=timezone.utc)
- return value.astimezone(timezone.utc)
+ return value.replace(tzinfo=UTC)
+ return value.astimezone(UTC)
def _state_dict(settings: UserSetting) -> dict[str, Any]:
@@ -100,9 +100,7 @@ def _recommended_action(reason: str | None) -> str | None:
"increase request delay, and avoid repeated manual retries."
)
if reason == COOLDOWN_REASON_NETWORK_FAILURE_THRESHOLD:
- return (
- "Network failures crossed the threshold. Verify connectivity and retry after cooldown."
- )
+ return "Network failures crossed the threshold. Verify connectivity and retry after cooldown."
return None
@@ -159,14 +157,10 @@ def _update_run_counters(
counters[_COUNTER_LAST_NETWORK_FAILURE_COUNT] = bounded_network_failures
counters[_COUNTER_LAST_EVALUATED_RUN_ID] = int(run_id)
counters[_COUNTER_CONSECUTIVE_BLOCKED_RUNS] = (
- int(counters[_COUNTER_CONSECUTIVE_BLOCKED_RUNS]) + 1
- if bounded_blocked_failures > 0
- else 0
+ int(counters[_COUNTER_CONSECUTIVE_BLOCKED_RUNS]) + 1 if bounded_blocked_failures > 0 else 0
)
counters[_COUNTER_CONSECUTIVE_NETWORK_RUNS] = (
- int(counters[_COUNTER_CONSECUTIVE_NETWORK_RUNS]) + 1
- if bounded_network_failures > 0
- else 0
+ int(counters[_COUNTER_CONSECUTIVE_NETWORK_RUNS]) + 1 if bounded_network_failures > 0 else 0
)
return bounded_blocked_failures, bounded_network_failures
diff --git a/app/services/domains/ingestion/scheduler.py b/app/services/domains/ingestion/scheduler.py
index 1f2267a..4aa8bc0 100644
--- a/app/services/domains/ingestion/scheduler.py
+++ b/app/services/domains/ingestion/scheduler.py
@@ -1,9 +1,9 @@
from __future__ import annotations
import asyncio
-from dataclasses import dataclass
-from datetime import datetime, timedelta, timezone
import logging
+from dataclasses import dataclass
+from datetime import UTC, datetime, timedelta
from sqlalchemy import select
from sqlalchemy.ext.asyncio import AsyncSession
@@ -17,24 +17,22 @@ from app.db.models import (
UserSetting,
)
from app.db.session import get_session_factory
+from app.logging_utils import structured_log
from app.services.domains.ingestion import queue as queue_service
from app.services.domains.ingestion.application import (
RunAlreadyInProgressError,
RunBlockedBySafetyPolicyError,
ScholarIngestionService,
)
-from app.logging_utils import structured_log
-from app.services.domains.settings import application as user_settings_service
from app.services.domains.scholar.source import LiveScholarSource
+from app.services.domains.settings import application as user_settings_service
from app.settings import settings
logger = logging.getLogger(__name__)
def _request_delay_floor_seconds() -> int:
- return user_settings_service.resolve_request_delay_minimum(
- settings.ingestion_min_request_delay_seconds
- )
+ return user_settings_service.resolve_request_delay_minimum(settings.ingestion_min_request_delay_seconds)
def _effective_request_delay_seconds(value: int | None) -> int:
@@ -96,7 +94,9 @@ class SchedulerService:
return
self._task = asyncio.create_task(self._run_loop(), name="scholarr-scheduler")
structured_log(
- logger, "info", "scheduler.started",
+ logger,
+ "info",
+ "scheduler.started",
tick_seconds=self._tick_seconds,
network_error_retries=self._network_error_retries,
retry_backoff_seconds=self._retry_backoff_seconds,
@@ -137,13 +137,13 @@ class SchedulerService:
async def _tick_once(self) -> None:
if self._continuation_queue_enabled:
await self._drain_continuation_queue()
-
+
await self._drain_pdf_queue()
candidates = await self._load_candidates()
if not candidates:
return
- now = datetime.now(timezone.utc)
+ now = datetime.now(UTC)
for candidate in candidates:
if not await self._is_due(candidate, now=now):
continue
@@ -170,10 +170,12 @@ class SchedulerService:
def _candidate_from_row(row: tuple, *, now_utc: datetime) -> _AutoRunCandidate | None:
user_id, run_interval_minutes, request_delay_seconds, cooldown_until, cooldown_reason = row
if cooldown_until is not None and cooldown_until.tzinfo is None:
- cooldown_until = cooldown_until.replace(tzinfo=timezone.utc)
+ cooldown_until = cooldown_until.replace(tzinfo=UTC)
if cooldown_until is not None and cooldown_until > now_utc:
structured_log(
- logger, "info", "scheduler.run_skipped_safety_cooldown_precheck",
+ logger,
+ "info",
+ "scheduler.run_skipped_safety_cooldown_precheck",
user_id=int(user_id),
reason=cooldown_reason,
cooldown_until=cooldown_until,
@@ -192,7 +194,7 @@ class SchedulerService:
if not settings.ingestion_automation_allowed:
return []
rows = await self._load_candidate_rows()
- now_utc = datetime.now(timezone.utc)
+ now_utc = datetime.now(UTC)
candidates: list[_AutoRunCandidate] = []
for row in rows:
candidate = self._candidate_from_row(row, now_utc=now_utc)
@@ -216,9 +218,7 @@ class SchedulerService:
if last_run is None:
return True
- next_due_dt = last_run + timedelta(
- minutes=candidate.run_interval_minutes
- )
+ next_due_dt = last_run + timedelta(minutes=candidate.run_interval_minutes)
return now >= next_due_dt
async def _run_candidate_ingestion(
@@ -252,7 +252,9 @@ class SchedulerService:
except RunBlockedBySafetyPolicyError as exc:
await session.rollback()
structured_log(
- logger, "info", "scheduler.run_skipped_safety_cooldown",
+ logger,
+ "info",
+ "scheduler.run_skipped_safety_cooldown",
user_id=candidate.user_id,
reason=exc.safety_state.get("cooldown_reason"),
cooldown_until=exc.safety_state.get("cooldown_until"),
@@ -269,7 +271,9 @@ class SchedulerService:
if run_summary is None:
return
structured_log(
- logger, "info", "scheduler.run_completed",
+ logger,
+ "info",
+ "scheduler.run_completed",
user_id=candidate.user_id,
run_id=run_summary.crawl_run_id,
status=run_summary.status.value,
@@ -278,7 +282,7 @@ class SchedulerService:
)
async def _drain_continuation_queue(self) -> None:
- now = datetime.now(timezone.utc)
+ now = datetime.now(UTC)
session_factory = get_session_factory()
async with session_factory() as session:
jobs = await queue_service.list_due_jobs(
@@ -305,7 +309,9 @@ class SchedulerService:
await session.commit()
if dropped is not None:
structured_log(
- logger, "warning", "scheduler.queue_item_dropped_max_attempts",
+ logger,
+ "warning",
+ "scheduler.queue_item_dropped_max_attempts",
queue_item_id=job.id,
user_id=job.user_id,
scholar_profile_id=job.scholar_profile_id,
@@ -352,7 +358,9 @@ class SchedulerService:
await session.commit()
if dropped is not None:
structured_log(
- logger, "info", "scheduler.queue_item_dropped_scholar_unavailable",
+ logger,
+ "info",
+ "scheduler.queue_item_dropped_scholar_unavailable",
queue_item_id=job.id,
user_id=job.user_id,
scholar_profile_id=job.scholar_profile_id,
@@ -371,8 +379,11 @@ class SchedulerService:
)
await recovery_session.commit()
structured_log(
- logger, "info", "scheduler.queue_item_deferred_lock",
- queue_item_id=job.id, user_id=job.user_id,
+ logger,
+ "info",
+ "scheduler.queue_item_deferred_lock",
+ queue_item_id=job.id,
+ user_id=job.user_id,
)
async def _reschedule_queue_job_safety_cooldown(
@@ -395,7 +406,9 @@ class SchedulerService:
)
await recovery_session.commit()
structured_log(
- logger, "info", "scheduler.queue_item_deferred_safety_cooldown",
+ logger,
+ "info",
+ "scheduler.queue_item_deferred_safety_cooldown",
queue_item_id=job.id,
user_id=job.user_id,
reason=exc.safety_state.get("cooldown_reason"),
@@ -423,8 +436,12 @@ class SchedulerService:
)
await recovery_session.commit()
structured_log(
- logger, "warning", "scheduler.queue_item_dropped_after_exception",
- queue_item_id=job.id, user_id=job.user_id, attempt_count=queue_item.attempt_count,
+ logger,
+ "warning",
+ "scheduler.queue_item_dropped_after_exception",
+ queue_item_id=job.id,
+ user_id=job.user_id,
+ attempt_count=queue_item.attempt_count,
)
return
delay_seconds = queue_service.compute_backoff_seconds(
@@ -489,15 +506,23 @@ class SchedulerService:
await session.commit()
if queue_item is None:
structured_log(
- logger, "info", "scheduler.queue_item_resolved",
- queue_item_id=job.id, user_id=job.user_id,
- run_id=run_summary.crawl_run_id, status=run_summary.status.value,
+ logger,
+ "info",
+ "scheduler.queue_item_resolved",
+ queue_item_id=job.id,
+ user_id=job.user_id,
+ run_id=run_summary.crawl_run_id,
+ status=run_summary.status.value,
)
return
structured_log(
- logger, "info", "scheduler.queue_item_progressed",
- queue_item_id=job.id, user_id=job.user_id,
- run_id=run_summary.crawl_run_id, status=run_summary.status.value,
+ logger,
+ "info",
+ "scheduler.queue_item_progressed",
+ queue_item_id=job.id,
+ user_id=job.user_id,
+ run_id=run_summary.crawl_run_id,
+ status=run_summary.status.value,
attempt_count=int(queue_item.attempt_count),
)
return
@@ -505,28 +530,50 @@ class SchedulerService:
if queue_item is None:
await session.commit()
structured_log(
- logger, "info", "scheduler.queue_item_resolved",
- queue_item_id=job.id, user_id=job.user_id,
- run_id=run_summary.crawl_run_id, status=run_summary.status.value,
+ logger,
+ "info",
+ "scheduler.queue_item_resolved",
+ queue_item_id=job.id,
+ user_id=job.user_id,
+ run_id=run_summary.crawl_run_id,
+ status=run_summary.status.value,
)
return
if int(queue_item.attempt_count) >= self._continuation_max_attempts:
await queue_service.mark_dropped(session, job_id=job.id, reason="max_attempts_after_run")
await session.commit()
structured_log(
- logger, "warning", "scheduler.queue_item_dropped_max_attempts_after_run",
- queue_item_id=job.id, user_id=job.user_id,
+ logger,
+ "warning",
+ "scheduler.queue_item_dropped_max_attempts_after_run",
+ queue_item_id=job.id,
+ user_id=job.user_id,
attempt_count=queue_item.attempt_count,
- run_id=run_summary.crawl_run_id, status=run_summary.status.value,
+ run_id=run_summary.crawl_run_id,
+ status=run_summary.status.value,
)
return
- delay_seconds = queue_service.compute_backoff_seconds(base_seconds=self._continuation_base_delay_seconds, attempt_count=int(queue_item.attempt_count), max_seconds=self._continuation_max_delay_seconds)
- await queue_service.reschedule_job(session, job_id=job.id, delay_seconds=delay_seconds, reason=queue_item.reason, error=queue_item.last_error)
+ delay_seconds = queue_service.compute_backoff_seconds(
+ base_seconds=self._continuation_base_delay_seconds,
+ attempt_count=int(queue_item.attempt_count),
+ max_seconds=self._continuation_max_delay_seconds,
+ )
+ await queue_service.reschedule_job(
+ session,
+ job_id=job.id,
+ delay_seconds=delay_seconds,
+ reason=queue_item.reason,
+ error=queue_item.last_error,
+ )
await session.commit()
structured_log(
- logger, "info", "scheduler.queue_item_rescheduled_failed",
- queue_item_id=job.id, user_id=job.user_id,
- run_id=run_summary.crawl_run_id, status=run_summary.status.value,
+ logger,
+ "info",
+ "scheduler.queue_item_rescheduled_failed",
+ queue_item_id=job.id,
+ user_id=job.user_id,
+ run_id=run_summary.crawl_run_id,
+ status=run_summary.status.value,
attempt_count=int(queue_item.attempt_count),
delay_seconds=delay_seconds,
)
@@ -545,7 +592,7 @@ class SchedulerService:
async def _drain_pdf_queue(self) -> None:
from app.services.domains.publications.pdf_queue import drain_ready_jobs
-
+
session_factory = get_session_factory()
async with session_factory() as session:
try:
@@ -556,7 +603,9 @@ class SchedulerService:
)
if processed > 0:
structured_log(
- logger, "info", "scheduler.pdf_queue_drain_completed",
+ logger,
+ "info",
+ "scheduler.pdf_queue_drain_completed",
processed_count=processed,
)
except Exception:
diff --git a/app/services/domains/openalex/client.py b/app/services/domains/openalex/client.py
index f6db5fd..83edc20 100644
--- a/app/services/domains/openalex/client.py
+++ b/app/services/domains/openalex/client.py
@@ -1,6 +1,4 @@
-import asyncio
import logging
-from typing import Any, Mapping
import httpx
from tenacity import (
@@ -23,11 +21,13 @@ class OpenAlexClientError(Exception):
class OpenAlexRateLimitError(OpenAlexClientError):
"""Transient rate limit (too many requests per second)."""
+
pass
class OpenAlexBudgetExhaustedError(OpenAlexClientError):
"""Daily API budget exhausted — retrying is futile until midnight UTC."""
+
pass
@@ -64,7 +64,7 @@ class OpenAlexClient:
return None
url = f"{OPENALEX_BASE_URL}/works/{clean_doi}"
-
+
headers = {}
if self.mailto:
headers["User-Agent"] = f"scholar-scraper/1.0 (mailto:{self.mailto})"
@@ -79,9 +79,7 @@ class OpenAlexClient:
if response.status_code == 429:
remaining = response.headers.get("X-RateLimit-Remaining-USD", "")
if remaining == "0" or remaining.startswith("-"):
- raise OpenAlexBudgetExhaustedError(
- "Daily API budget exhausted; retrying won't help until midnight UTC"
- )
+ raise OpenAlexBudgetExhaustedError("Daily API budget exhausted; retrying won't help until midnight UTC")
raise OpenAlexRateLimitError("Rate limit exceeded fetching OpenAlex work by DOI")
if response.status_code >= 400:
logger.warning("OpenAlex API error: %s %s", response.status_code, response.text[:500])
@@ -110,13 +108,13 @@ class OpenAlexClient:
# Example: {"doi": "10.foo|10.bar", "title.search": "query"}
filter_str = ",".join(f"{k}:{v}" for k, v in filters.items())
-
+
params = self._base_params.copy()
params["filter"] = filter_str
params["per-page"] = str(limit)
url = f"{OPENALEX_BASE_URL}/works"
-
+
headers = {}
if self.mailto:
headers["User-Agent"] = f"scholar-scraper/1.0 (mailto:{self.mailto})"
@@ -129,9 +127,7 @@ class OpenAlexClient:
if response.status_code == 429:
remaining = response.headers.get("X-RateLimit-Remaining-USD", "")
if remaining == "0" or remaining.startswith("-"):
- raise OpenAlexBudgetExhaustedError(
- "Daily API budget exhausted; retrying won't help until midnight UTC"
- )
+ raise OpenAlexBudgetExhaustedError("Daily API budget exhausted; retrying won't help until midnight UTC")
raise OpenAlexRateLimitError("Rate limit exceeded fetching OpenAlex works list")
if response.status_code >= 400:
logger.warning("OpenAlex API error (filters=%s): %s %s", filters, response.status_code, response.text[:500])
@@ -139,7 +135,7 @@ class OpenAlexClient:
data = response.json()
results = data.get("results") or []
-
+
parsed_works = []
for raw_work in results:
try:
diff --git a/app/services/domains/openalex/matching.py b/app/services/domains/openalex/matching.py
index cfa511c..40c25ba 100644
--- a/app/services/domains/openalex/matching.py
+++ b/app/services/domains/openalex/matching.py
@@ -24,11 +24,11 @@ def _clean_string(s: str | None) -> str:
def _author_overlap_score(target_authors: str | None, candidate_authors: list[str]) -> bool:
if not target_authors or not candidate_authors:
return False
-
+
target_clean = _clean_string(target_authors)
if not target_clean:
return False
-
+
for candidate in candidate_authors:
cand_clean = _clean_string(candidate)
if cand_clean and (cand_clean in target_clean or target_clean in cand_clean):
@@ -36,7 +36,7 @@ def _author_overlap_score(target_authors: str | None, candidate_authors: list[st
# Alternatively check rapidfuzz token_set_ratio
if cand_clean and fuzz.token_set_ratio(target_clean, cand_clean) > 80:
return True
-
+
return False
@@ -62,12 +62,12 @@ def find_best_match(
for cand in candidates:
if not cand.title:
continue
-
+
clean_cand = _clean_string(cand.title)
-
+
# Primary sort: string similarity ratio
score = fuzz.ratio(clean_target, clean_cand)
-
+
if score >= TITLE_MATCH_THRESHOLD:
scored_candidates.append((score, cand))
@@ -76,13 +76,12 @@ def find_best_match(
# Sort descending by score
scored_candidates.sort(key=lambda x: x[0], reverse=True)
-
+
best_score = scored_candidates[0][0]
-
+
# Extract all candidates within the tiebreaker margin
top_scored_candidates = [
- (score, cand) for score, cand in scored_candidates
- if best_score - score <= TIEBREAKER_MARGIN
+ (score, cand) for score, cand in scored_candidates if best_score - score <= TIEBREAKER_MARGIN
]
if len(top_scored_candidates) == 1:
@@ -91,18 +90,18 @@ def find_best_match(
# We have a tie or near-tie. Use year and author overlap to break the tie.
# Score candidates: +1 for year match (within 1 year), +1 for author overlap
tiebreaker_scores: list[tuple[int, float, OpenAlexWork]] = []
-
+
for original_score, cand in top_scored_candidates:
tb_score = 0
if target_year is not None and cand.publication_year is not None:
if abs(target_year - cand.publication_year) <= 1:
tb_score += 1
-
+
candidate_author_names = [a.display_name for a in cand.authors if a.display_name]
if _author_overlap_score(target_authors, candidate_author_names):
tb_score += 1
-
+
tiebreaker_scores.append((tb_score, original_score, cand))
-
+
tiebreaker_scores.sort(key=lambda x: (x[0], x[1]), reverse=True)
return tiebreaker_scores[0][2]
diff --git a/app/services/domains/openalex/types.py b/app/services/domains/openalex/types.py
index 0d86754..8abf375 100644
--- a/app/services/domains/openalex/types.py
+++ b/app/services/domains/openalex/types.py
@@ -1,8 +1,8 @@
from __future__ import annotations
+from collections.abc import Mapping
from dataclasses import dataclass, field
-from datetime import datetime
-from typing import Any, Mapping
+from typing import Any
@dataclass(frozen=True)
@@ -28,24 +28,24 @@ class OpenAlexWork:
@classmethod
def from_api_dict(cls, data: Mapping[str, Any]) -> OpenAlexWork:
ids = data.get("ids") or {}
-
+
# Extract DOI without the https://doi.org/ prefix
doi = ids.get("doi")
if doi and doi.startswith("https://doi.org/"):
doi = doi[16:]
-
+
# Extract PMID without the url prefix
pmid = ids.get("pmid")
if pmid and pmid.startswith("https://pubmed.ncbi.nlm.nih.gov/"):
pmid = pmid[32:]
-
+
# Extract PMCID without the url prefix
pmcid = ids.get("pmcid")
if pmcid and pmcid.startswith("https://www.ncbi.nlm.nih.gov/pmc/articles/"):
pmcid = pmcid[42:]
open_access = data.get("open_access") or {}
-
+
authors = []
for authorship in data.get("authorships") or []:
author_data = authorship.get("author") or {}
diff --git a/app/services/domains/portability/application.py b/app/services/domains/portability/application.py
index 7e0b56e..6285c5d 100644
--- a/app/services/domains/portability/application.py
+++ b/app/services/domains/portability/application.py
@@ -18,7 +18,7 @@ from app.services.domains.portability.publication_import import (
_upsert_imported_publication,
)
from app.services.domains.portability.scholar_import import _upsert_imported_scholars
-from app.services.domains.portability.types import ImportExportError, ImportedPublicationInput
+from app.services.domains.portability.types import ImportedPublicationInput, ImportExportError
async def import_user_data(
@@ -58,8 +58,8 @@ async def import_user_data(
__all__ = [
"EXPORT_SCHEMA_VERSION",
- "MAX_IMPORT_SCHOLARS",
"MAX_IMPORT_PUBLICATIONS",
+ "MAX_IMPORT_SCHOLARS",
"ImportExportError",
"ImportedPublicationInput",
"export_user_data",
diff --git a/app/services/domains/portability/exporting.py b/app/services/domains/portability/exporting.py
index 5c89006..2f50247 100644
--- a/app/services/domains/portability/exporting.py
+++ b/app/services/domains/portability/exporting.py
@@ -1,6 +1,6 @@
from __future__ import annotations
-from datetime import datetime, timezone
+from datetime import UTC, datetime
from typing import Any
from sqlalchemy import select
@@ -11,7 +11,7 @@ from app.services.domains.portability.constants import EXPORT_SCHEMA_VERSION
def _exported_at_iso() -> str:
- return datetime.now(timezone.utc).replace(microsecond=0).isoformat()
+ return datetime.now(UTC).replace(microsecond=0).isoformat()
def _serialize_export_scholar(profile: ScholarProfile) -> dict[str, Any]:
@@ -58,9 +58,7 @@ async def export_user_data(
user_id: int,
) -> dict[str, Any]:
scholars_result = await db_session.execute(
- select(ScholarProfile)
- .where(ScholarProfile.user_id == user_id)
- .order_by(ScholarProfile.id.asc())
+ select(ScholarProfile).where(ScholarProfile.user_id == user_id).order_by(ScholarProfile.id.asc())
)
publication_result = await db_session.execute(
select(
diff --git a/app/services/domains/portability/normalize.py b/app/services/domains/portability/normalize.py
index 60dd619..176bfc5 100644
--- a/app/services/domains/portability/normalize.py
+++ b/app/services/domains/portability/normalize.py
@@ -104,6 +104,4 @@ def _validate_import_sizes(
if len(scholars) > MAX_IMPORT_SCHOLARS:
raise ImportExportError(f"Import exceeds max scholars ({MAX_IMPORT_SCHOLARS}).")
if len(publications) > MAX_IMPORT_PUBLICATIONS:
- raise ImportExportError(
- f"Import exceeds max publications ({MAX_IMPORT_PUBLICATIONS})."
- )
+ raise ImportExportError(f"Import exceeds max publications ({MAX_IMPORT_PUBLICATIONS}).")
diff --git a/app/services/domains/portability/publication_import.py b/app/services/domains/portability/publication_import.py
index 7654586..afcb580 100644
--- a/app/services/domains/portability/publication_import.py
+++ b/app/services/domains/portability/publication_import.py
@@ -6,8 +6,8 @@ from sqlalchemy import select
from sqlalchemy.ext.asyncio import AsyncSession
from app.db.models import Publication, ScholarProfile, ScholarPublication
-from app.services.domains.ingestion.application import build_publication_url, normalize_title
from app.services.domains.doi.normalize import normalize_doi
+from app.services.domains.ingestion.application import build_publication_url, normalize_title
from app.services.domains.portability.normalize import (
_normalize_citation_count,
_normalize_optional_text,
@@ -22,9 +22,7 @@ async def _find_publication_by_cluster(
*,
cluster_id: str,
) -> Publication | None:
- result = await db_session.execute(
- select(Publication).where(Publication.cluster_id == cluster_id)
- )
+ result = await db_session.execute(select(Publication).where(Publication.cluster_id == cluster_id))
return result.scalar_one_or_none()
@@ -33,9 +31,7 @@ async def _find_publication_by_fingerprint(
*,
fingerprint_sha256: str,
) -> Publication | None:
- result = await db_session.execute(
- select(Publication).where(Publication.fingerprint_sha256 == fingerprint_sha256)
- )
+ result = await db_session.execute(select(Publication).where(Publication.fingerprint_sha256 == fingerprint_sha256))
return result.scalar_one_or_none()
diff --git a/app/services/domains/portability/scholar_import.py b/app/services/domains/portability/scholar_import.py
index 74e6ec1..c0a4c48 100644
--- a/app/services/domains/portability/scholar_import.py
+++ b/app/services/domains/portability/scholar_import.py
@@ -15,9 +15,7 @@ async def _load_user_scholar_map(
*,
user_id: int,
) -> dict[str, ScholarProfile]:
- result = await db_session.execute(
- select(ScholarProfile).where(ScholarProfile.user_id == user_id)
- )
+ result = await db_session.execute(select(ScholarProfile).where(ScholarProfile.user_id == user_id))
profiles = list(result.scalars().all())
return {profile.scholar_id: profile for profile in profiles}
@@ -70,9 +68,7 @@ async def _upsert_imported_scholars(
for item in scholars:
try:
scholar_id = scholar_service.validate_scholar_id(str(item["scholar_id"]))
- display_name = scholar_service.normalize_display_name(
- str(item.get("display_name") or "")
- )
+ display_name = scholar_service.normalize_display_name(str(item.get("display_name") or ""))
override_url = scholar_service.normalize_profile_image_url(
_normalize_optional_text(item.get("profile_image_override_url"))
)
diff --git a/app/services/domains/publication_identifiers/__init__.py b/app/services/domains/publication_identifiers/__init__.py
index 9331dc0..d6a4263 100644
--- a/app/services/domains/publication_identifiers/__init__.py
+++ b/app/services/domains/publication_identifiers/__init__.py
@@ -1,7 +1,7 @@
from app.services.domains.publication_identifiers.application import (
DisplayIdentifier,
- display_identifier_for_publication_id,
derive_display_identifier_from_values,
+ display_identifier_for_publication_id,
overlay_pdf_queue_items_with_display_identifiers,
overlay_publication_items_with_display_identifiers,
sync_identifiers_for_publication_fields,
@@ -10,8 +10,8 @@ from app.services.domains.publication_identifiers.application import (
__all__ = [
"DisplayIdentifier",
- "display_identifier_for_publication_id",
"derive_display_identifier_from_values",
+ "display_identifier_for_publication_id",
"overlay_pdf_queue_items_with_display_identifiers",
"overlay_publication_items_with_display_identifiers",
"sync_identifiers_for_publication_fields",
diff --git a/app/services/domains/publication_identifiers/application.py b/app/services/domains/publication_identifiers/application.py
index 31f506c..47fe940 100644
--- a/app/services/domains/publication_identifiers/application.py
+++ b/app/services/domains/publication_identifiers/application.py
@@ -55,7 +55,9 @@ def _fallback_candidates_from_values(
if doi:
normalized_doi = normalize_doi(doi)
if normalized_doi:
- candidates.append(_candidate(IdentifierKind.DOI, doi, normalized_doi, "legacy_doi", CONFIDENCE_HIGH, pub_url))
+ candidates.append(
+ _candidate(IdentifierKind.DOI, doi, normalized_doi, "legacy_doi", CONFIDENCE_HIGH, pub_url)
+ )
candidates.extend(_url_identifier_candidates(values=values, source="legacy_urls"))
return _dedup_candidates(candidates)
@@ -332,10 +334,13 @@ async def _existing_identifier_by_kind(
kind: str,
) -> PublicationIdentifier | None:
result = await db_session.execute(
- select(PublicationIdentifier).where(
+ select(PublicationIdentifier)
+ .where(
PublicationIdentifier.publication_id == publication_id,
PublicationIdentifier.kind == kind,
- ).order_by(PublicationIdentifier.confidence_score.desc()).limit(1)
+ )
+ .order_by(PublicationIdentifier.confidence_score.desc())
+ .limit(1)
)
return result.scalar_one_or_none()
@@ -380,7 +385,9 @@ def _overlay_publication_item(
item: PublicationListItem,
display_identifier: DisplayIdentifier | None,
) -> PublicationListItem:
- fallback = display_identifier or derive_display_identifier_from_values(doi=None, pub_url=item.pub_url, pdf_url=item.pdf_url)
+ fallback = display_identifier or derive_display_identifier_from_values(
+ doi=None, pub_url=item.pub_url, pdf_url=item.pdf_url
+ )
return replace(item, display_identifier=fallback)
@@ -447,8 +454,7 @@ def _best_display_identifier_map(rows: list[PublicationIdentifier]) -> dict[int,
return {
publication_id: display
for publication_id, display in (
- (publication_id, _best_display_identifier(candidates))
- for publication_id, candidates in grouped.items()
+ (publication_id, _best_display_identifier(candidates)) for publication_id, candidates in grouped.items()
)
if display is not None
}
diff --git a/app/services/domains/publications/application.py b/app/services/domains/publications/application.py
index f51c79a..b36f2ec 100644
--- a/app/services/domains/publications/application.py
+++ b/app/services/domains/publications/application.py
@@ -1,21 +1,21 @@
from __future__ import annotations
from app.services.domains.publications.counts import (
- count_for_user,
count_favorite_for_user,
+ count_for_user,
count_latest_for_user,
count_unread_for_user,
)
-from app.services.domains.publications.listing import (
- list_for_user,
- retry_pdf_for_user,
- list_unread_for_user,
-)
from app.services.domains.publications.enrichment import (
hydrate_pdf_enrichment_state,
schedule_missing_pdf_enrichment_for_user,
schedule_retry_pdf_enrichment_for_row,
)
+from app.services.domains.publications.listing import (
+ list_for_user,
+ list_unread_for_user,
+ retry_pdf_for_user,
+)
from app.services.domains.publications.modes import (
MODE_ALL,
MODE_LATEST,
@@ -23,6 +23,13 @@ from app.services.domains.publications.modes import (
MODE_UNREAD,
resolve_publication_view_mode,
)
+from app.services.domains.publications.pdf_queue import (
+ count_pdf_queue_items,
+ enqueue_all_missing_pdf_jobs,
+ enqueue_retry_pdf_job_for_publication_id,
+ list_pdf_queue_items,
+ list_pdf_queue_page,
+)
from app.services.domains.publications.queries import (
get_latest_run_id_for_user,
get_publication_item_for_user,
@@ -33,42 +40,35 @@ from app.services.domains.publications.read_state import (
mark_selected_as_read_for_user,
set_publication_favorite_for_user,
)
-from app.services.domains.publications.pdf_queue import (
- count_pdf_queue_items,
- enqueue_all_missing_pdf_jobs,
- enqueue_retry_pdf_job_for_publication_id,
- list_pdf_queue_page,
- list_pdf_queue_items,
-)
from app.services.domains.publications.types import PublicationListItem, UnreadPublicationItem
__all__ = [
"MODE_ALL",
- "MODE_UNREAD",
"MODE_LATEST",
"MODE_NEW",
+ "MODE_UNREAD",
"PublicationListItem",
"UnreadPublicationItem",
- "resolve_publication_view_mode",
- "get_latest_run_id_for_user",
- "publications_query",
- "get_publication_item_for_user",
- "list_for_user",
- "list_unread_for_user",
- "retry_pdf_for_user",
- "hydrate_pdf_enrichment_state",
- "schedule_retry_pdf_enrichment_for_row",
- "list_pdf_queue_items",
- "list_pdf_queue_page",
+ "count_favorite_for_user",
+ "count_for_user",
+ "count_latest_for_user",
"count_pdf_queue_items",
+ "count_unread_for_user",
"enqueue_all_missing_pdf_jobs",
"enqueue_retry_pdf_job_for_publication_id",
- "schedule_missing_pdf_enrichment_for_user",
- "count_for_user",
- "count_favorite_for_user",
- "count_unread_for_user",
- "count_latest_for_user",
+ "get_latest_run_id_for_user",
+ "get_publication_item_for_user",
+ "hydrate_pdf_enrichment_state",
+ "list_for_user",
+ "list_pdf_queue_items",
+ "list_pdf_queue_page",
+ "list_unread_for_user",
"mark_all_unread_as_read_for_user",
"mark_selected_as_read_for_user",
+ "publications_query",
+ "resolve_publication_view_mode",
+ "retry_pdf_for_user",
+ "schedule_missing_pdf_enrichment_for_user",
+ "schedule_retry_pdf_enrichment_for_row",
"set_publication_favorite_for_user",
]
diff --git a/app/services/domains/publications/dedup.py b/app/services/domains/publications/dedup.py
index 5bf1d43..d2e17a6 100644
--- a/app/services/domains/publications/dedup.py
+++ b/app/services/domains/publications/dedup.py
@@ -1,9 +1,9 @@
from __future__ import annotations
-from dataclasses import dataclass
import hashlib
import logging
-from typing import Iterable
+from collections.abc import Iterable
+from dataclasses import dataclass
from sqlalchemy import delete, select
from sqlalchemy.ext.asyncio import AsyncSession
@@ -113,9 +113,7 @@ async def _load_publication(
*,
publication_id: int,
) -> Publication | None:
- result = await db_session.execute(
- select(Publication).where(Publication.id == publication_id)
- )
+ result = await db_session.execute(select(Publication).where(Publication.id == publication_id))
return result.scalar_one_or_none()
@@ -160,9 +158,7 @@ async def _migrate_scholar_links(
dup_links = dup_links_result.scalars().all()
winner_profiles_result = await db_session.execute(
- select(ScholarPublication.scholar_profile_id).where(
- ScholarPublication.publication_id == winner_id
- )
+ select(ScholarPublication.scholar_profile_id).where(ScholarPublication.publication_id == winner_id)
)
winner_profiles: set[int] = {row for (row,) in winner_profiles_result}
@@ -346,11 +342,7 @@ def _candidate_from_row(
def _normalized_tokens(tokens: Iterable[str]) -> set[str]:
- return {
- token
- for token in tokens
- if len(token) >= NEAR_DUP_MIN_TOKEN_LENGTH and token not in NEAR_DUP_STOPWORDS
- }
+ return {token for token in tokens if len(token) >= NEAR_DUP_MIN_TOKEN_LENGTH and token not in NEAR_DUP_STOPWORDS}
def _cluster_candidate_groups(
diff --git a/app/services/domains/publications/enrichment.py b/app/services/domains/publications/enrichment.py
index 8a6b04f..49cf9c6 100644
--- a/app/services/domains/publications/enrichment.py
+++ b/app/services/domains/publications/enrichment.py
@@ -4,12 +4,12 @@ import logging
from sqlalchemy.ext.asyncio import AsyncSession
+from app.logging_utils import structured_log
from app.services.domains.publications.pdf_queue import (
enqueue_missing_pdf_jobs,
enqueue_retry_pdf_job,
overlay_pdf_job_state,
)
-from app.logging_utils import structured_log
from app.services.domains.publications.types import PublicationListItem
logger = logging.getLogger(__name__)
@@ -30,7 +30,9 @@ async def schedule_missing_pdf_enrichment_for_user(
rows=items,
max_items=max_items,
)
- structured_log(logger, "info", "publications.enrichment.scheduled", user_id=user_id, publication_count=len(queued_ids))
+ structured_log(
+ logger, "info", "publications.enrichment.scheduled", user_id=user_id, publication_count=len(queued_ids)
+ )
return len(queued_ids)
@@ -47,7 +49,14 @@ async def schedule_retry_pdf_enrichment_for_row(
request_email=request_email,
row=item,
)
- structured_log(logger, "info", "publications.enrichment.retry_scheduled", user_id=user_id, publication_id=item.publication_id, queued=queued)
+ structured_log(
+ logger,
+ "info",
+ "publications.enrichment.retry_scheduled",
+ user_id=user_id,
+ publication_id=item.publication_id,
+ queued=queued,
+ )
return queued
diff --git a/app/services/domains/publications/listing.py b/app/services/domains/publications/listing.py
index 5290f6f..92e7462 100644
--- a/app/services/domains/publications/listing.py
+++ b/app/services/domains/publications/listing.py
@@ -51,10 +51,7 @@ async def list_for_user(
snapshot_before=snapshot_before,
)
)
- rows = [
- publication_list_item_from_row(row, latest_run_id=latest_run_id)
- for row in result.all()
- ]
+ rows = [publication_list_item_from_row(row, latest_run_id=latest_run_id) for row in result.all()]
return await identifier_service.overlay_publication_items_with_display_identifiers(
db_session,
items=rows,
diff --git a/app/services/domains/publications/pdf_queue.py b/app/services/domains/publications/pdf_queue.py
index 0313f11..880b1a2 100644
--- a/app/services/domains/publications/pdf_queue.py
+++ b/app/services/domains/publications/pdf_queue.py
@@ -1,9 +1,9 @@
from __future__ import annotations
import asyncio
-from dataclasses import dataclass
-from datetime import datetime, timedelta, timezone
import logging
+from dataclasses import dataclass
+from datetime import UTC, datetime, timedelta
from sqlalchemy import Select, and_, func, literal, or_, select, union_all
from sqlalchemy.ext.asyncio import AsyncSession
@@ -17,6 +17,7 @@ from app.db.models import (
User,
)
from app.db.session import get_session_factory
+from app.logging_utils import structured_log
from app.services.domains.publication_identifiers import application as identifier_service
from app.services.domains.publication_identifiers.types import DisplayIdentifier
from app.services.domains.publications.pdf_resolution_pipeline import (
@@ -27,7 +28,6 @@ from app.services.domains.unpaywall.application import (
FAILURE_RESOLUTION_EXCEPTION,
OaResolutionOutcome,
)
-from app.logging_utils import structured_log
from app.settings import settings
PDF_STATUS_UNTRACKED = "untracked"
@@ -85,7 +85,7 @@ class PdfQueuePage:
def _utcnow() -> datetime:
- return datetime.now(timezone.utc)
+ return datetime.now(UTC)
def _publication_ids(rows: list[PublicationListItem]) -> list[int]:
@@ -472,7 +472,13 @@ async def _resolve_publication_row(
# Propagate upward so the batch loop can stop immediately.
raise
except Exception as exc: # pragma: no cover - defensive network boundary
- structured_log(logger, "warning", "publications.pdf_queue.resolve_failed", publication_id=row.publication_id, error=str(exc))
+ structured_log(
+ logger,
+ "warning",
+ "publications.pdf_queue.resolve_failed",
+ publication_id=row.publication_id,
+ error=str(exc),
+ )
outcome = _failed_outcome(row=row)
arxiv_rate_limited = False
await _persist_outcome(
@@ -514,9 +520,19 @@ async def _run_resolution_task(
)
if arxiv_rate_limited and arxiv_lookup_allowed:
arxiv_lookup_allowed = False
- structured_log(logger, "warning", "pdf_queue.arxiv_batch_disabled", detail="arXiv temporarily disabled for remaining batch after rate limit")
+ structured_log(
+ logger,
+ "warning",
+ "pdf_queue.arxiv_batch_disabled",
+ detail="arXiv temporarily disabled for remaining batch after rate limit",
+ )
except OpenAlexBudgetExhaustedError:
- structured_log(logger, "warning", "pdf_queue.budget_exhausted", detail="Stopping PDF resolution batch — OpenAlex daily budget exhausted")
+ structured_log(
+ logger,
+ "warning",
+ "pdf_queue.budget_exhausted",
+ detail="Stopping PDF resolution batch — OpenAlex daily budget exhausted",
+ )
break
@@ -679,7 +695,7 @@ async def _missing_pdf_candidates(
limit: int,
) -> list[PublicationListItem]:
bounded_limit = max(1, min(int(limit), 5000))
- now = datetime.now(timezone.utc)
+ now = datetime.now(UTC)
cooldown_threshold = now - timedelta(days=7)
result = await db_session.execute(
@@ -701,10 +717,7 @@ async def _missing_pdf_candidates(
.order_by(Publication.updated_at.desc(), Publication.id.desc())
.limit(bounded_limit)
)
- return [
- _queue_candidate_from_publication(publication)
- for publication in result.scalars()
- ]
+ return [_queue_candidate_from_publication(publication) for publication in result.scalars()]
async def enqueue_all_missing_pdf_jobs(
@@ -902,9 +915,7 @@ async def count_pdf_queue_items(
if normalized_status == PDF_STATUS_UNTRACKED:
result = await db_session.execute(_untracked_queue_count_select())
return int(result.scalar_one() or 0)
- tracked_result = await db_session.execute(
- _tracked_queue_count_select(status=normalized_status)
- )
+ tracked_result = await db_session.execute(_tracked_queue_count_select(status=normalized_status))
tracked_count = int(tracked_result.scalar_one() or 0)
if normalized_status is not None:
return tracked_count
@@ -946,9 +957,7 @@ async def drain_ready_jobs(
limit: int,
max_attempts: int,
) -> int:
- result = await db_session.execute(
- select(User.id).where(User.is_active.is_(True)).order_by(User.id.asc()).limit(1)
- )
+ result = await db_session.execute(select(User.id).where(User.is_active.is_(True)).order_by(User.id.asc()).limit(1))
system_user_id = result.scalar_one_or_none()
if system_user_id is None:
return 0
diff --git a/app/services/domains/publications/pdf_resolution_pipeline.py b/app/services/domains/publications/pdf_resolution_pipeline.py
index 37efa6b..88a07ca 100644
--- a/app/services/domains/publications/pdf_resolution_pipeline.py
+++ b/app/services/domains/publications/pdf_resolution_pipeline.py
@@ -1,15 +1,15 @@
from __future__ import annotations
-from dataclasses import dataclass
import logging
+from dataclasses import dataclass
from typing import Any
+from app.logging_utils import structured_log
from app.services.domains.arxiv.application import ArxivRateLimitError
from app.services.domains.arxiv.guards import arxiv_skip_reason_for_item
from app.services.domains.openalex.client import OpenAlexBudgetExhaustedError
from app.services.domains.publications.types import PublicationListItem
from app.services.domains.unpaywall.application import OaResolutionOutcome, resolve_publication_oa_outcomes
-from app.logging_utils import structured_log
from app.settings import settings
logger = logging.getLogger(__name__)
@@ -66,6 +66,7 @@ async def _openalex_outcome(
return None
import re
+
safe_title = re.sub(r"[^\w\s]", " ", row.title)
safe_title = " ".join(safe_title.split())
if not safe_title:
@@ -107,12 +108,24 @@ async def _arxiv_outcome(
from app.services.domains.arxiv.application import discover_arxiv_id_for_publication
if not allow_lookup:
- structured_log(logger, "info", "pdf_resolution.arxiv_skipped", publication_id=int(row.publication_id), skip_reason="batch_arxiv_cooldown_active")
+ structured_log(
+ logger,
+ "info",
+ "pdf_resolution.arxiv_skipped",
+ publication_id=int(row.publication_id),
+ skip_reason="batch_arxiv_cooldown_active",
+ )
return None
skip_reason = arxiv_skip_reason_for_item(item=row)
if skip_reason is not None:
- structured_log(logger, "info", "pdf_resolution.arxiv_skipped", publication_id=int(row.publication_id), skip_reason=skip_reason)
+ structured_log(
+ logger,
+ "info",
+ "pdf_resolution.arxiv_skipped",
+ publication_id=int(row.publication_id),
+ skip_reason=skip_reason,
+ )
return None
try:
@@ -134,7 +147,6 @@ async def _arxiv_outcome(
return None
-
async def _oa_outcome(
*,
row: PublicationListItem,
diff --git a/app/services/domains/publications/queries.py b/app/services/domains/publications/queries.py
index d642a73..89dd1d1 100644
--- a/app/services/domains/publications/queries.py
+++ b/app/services/domains/publications/queries.py
@@ -228,9 +228,7 @@ def publication_list_item_from_row(
is_read=bool(is_read),
is_favorite=bool(is_favorite),
first_seen_at=created_at,
- is_new_in_latest_run=(
- latest_run_id is not None and int(first_seen_run_id or 0) == latest_run_id
- ),
+ is_new_in_latest_run=(latest_run_id is not None and int(first_seen_run_id or 0) == latest_run_id),
)
diff --git a/app/services/domains/publications/read_state.py b/app/services/domains/publications/read_state.py
index 41fc31a..b816d59 100644
--- a/app/services/domains/publications/read_state.py
+++ b/app/services/domains/publications/read_state.py
@@ -17,11 +17,7 @@ def _normalized_selection_pairs(selections: list[tuple[int, int]]) -> set[tuple[
def _scoped_scholar_ids_query(*, user_id: int):
- return (
- select(ScholarProfile.id)
- .where(ScholarProfile.user_id == user_id)
- .scalar_subquery()
- )
+ return select(ScholarProfile.id).where(ScholarProfile.user_id == user_id).scalar_subquery()
async def mark_all_unread_as_read_for_user(
diff --git a/app/services/domains/runs/application.py b/app/services/domains/runs/application.py
index 0019446..4f6e27f 100644
--- a/app/services/domains/runs/application.py
+++ b/app/services/domains/runs/application.py
@@ -25,21 +25,21 @@ from app.services.domains.runs.types import (
)
__all__ = [
+ "QUEUE_STATUS_DROPPED",
"QUEUE_STATUS_QUEUED",
"QUEUE_STATUS_RETRYING",
- "QUEUE_STATUS_DROPPED",
- "QueueListItem",
"QueueClearResult",
+ "QueueListItem",
"QueueTransitionError",
+ "clear_queue_item_for_user",
+ "drop_queue_item_for_user",
"extract_run_summary",
+ "get_manual_run_by_idempotency_key",
+ "get_queue_item_for_user",
+ "get_run_for_user",
+ "list_queue_items_for_user",
"list_recent_runs_for_user",
"list_runs_for_user",
- "get_run_for_user",
- "get_manual_run_by_idempotency_key",
- "list_queue_items_for_user",
- "get_queue_item_for_user",
- "retry_queue_item_for_user",
- "drop_queue_item_for_user",
- "clear_queue_item_for_user",
"queue_status_counts_for_user",
+ "retry_queue_item_for_user",
]
diff --git a/app/services/domains/runs/events.py b/app/services/domains/runs/events.py
index ef28069..7f4a71e 100644
--- a/app/services/domains/runs/events.py
+++ b/app/services/domains/runs/events.py
@@ -1,14 +1,16 @@
import asyncio
import json
import logging
-from typing import Any, AsyncGenerator, Dict, Set
+from collections.abc import AsyncGenerator
+from typing import Any
logger = logging.getLogger(__name__)
+
class RunEventPublisher:
def __init__(self) -> None:
# Maps run_id to a set of subscriber queues
- self._subscribers: Dict[int, Set[asyncio.Queue]] = {}
+ self._subscribers: dict[int, set[asyncio.Queue]] = {}
def subscribe(self, run_id: int) -> asyncio.Queue:
if run_id not in self._subscribers:
@@ -27,12 +29,9 @@ class RunEventPublisher:
async def publish(self, run_id: int, event_type: str, data: dict[str, Any]) -> None:
if run_id not in self._subscribers:
return
-
- message = {
- "type": event_type,
- "data": data
- }
-
+
+ message = {"type": event_type, "data": data}
+
# Fan-out to all active subscribers for this run
for queue in list(self._subscribers[run_id]):
try:
@@ -40,8 +39,10 @@ class RunEventPublisher:
except asyncio.QueueFull:
logger.warning(f"Subscriber queue full for run {run_id}, dropping message")
+
run_events = RunEventPublisher()
+
async def event_generator(run_id: int) -> AsyncGenerator[str, None]:
queue = run_events.subscribe(run_id)
try:
diff --git a/app/services/domains/runs/queue_service.py b/app/services/domains/runs/queue_service.py
index d69ce21..530e5b5 100644
--- a/app/services/domains/runs/queue_service.py
+++ b/app/services/domains/runs/queue_service.py
@@ -41,9 +41,7 @@ async def get_queue_item_for_user(
queue_item_id: int,
) -> QueueListItem | None:
result = await db_session.execute(
- queue_item_select(user_id=user_id)
- .where(IngestionQueueItem.id == queue_item_id)
- .limit(1)
+ queue_item_select(user_id=user_id).where(IngestionQueueItem.id == queue_item_id).limit(1)
)
row = result.one_or_none()
if row is None:
diff --git a/app/services/domains/runs/runs_service.py b/app/services/domains/runs/runs_service.py
index 1cb9aa2..72901ec 100644
--- a/app/services/domains/runs/runs_service.py
+++ b/app/services/domains/runs/runs_service.py
@@ -35,9 +35,7 @@ async def list_runs_for_user(
.limit(limit)
)
if failed_only:
- stmt = stmt.where(
- CrawlRun.status.in_([RunStatus.FAILED, RunStatus.PARTIAL_FAILURE])
- )
+ stmt = stmt.where(CrawlRun.status.in_([RunStatus.FAILED, RunStatus.PARTIAL_FAILURE]))
result = await db_session.execute(stmt)
return list(result.scalars().all())
diff --git a/app/services/domains/runs/summary.py b/app/services/domains/runs/summary.py
index 9555558..b18ceb8 100644
--- a/app/services/domains/runs/summary.py
+++ b/app/services/domains/runs/summary.py
@@ -24,9 +24,7 @@ def _summary_int_dict(summary: dict[str, Any], key: str) -> dict[str, int]:
if not isinstance(value, dict):
return {}
return {
- str(item_key): _safe_int(item_value, 0)
- for item_key, item_value in value.items()
- if isinstance(item_key, str)
+ str(item_key): _safe_int(item_value, 0) for item_key, item_value in value.items() if isinstance(item_key, str)
}
@@ -34,11 +32,7 @@ def _summary_bool_dict(summary: dict[str, Any], key: str) -> dict[str, bool]:
value = summary.get(key)
if not isinstance(value, dict):
return {}
- return {
- str(item_key): bool(item_value)
- for item_key, item_value in value.items()
- if isinstance(item_key, str)
- }
+ return {str(item_key): bool(item_value) for item_key, item_value in value.items() if isinstance(item_key, str)}
def _retry_counts(summary: dict[str, Any]) -> dict[str, int]:
diff --git a/app/services/domains/scholar/author_rows.py b/app/services/domains/scholar/author_rows.py
index 8acd783..42a8b2b 100644
--- a/app/services/domains/scholar/author_rows.py
+++ b/app/services/domains/scholar/author_rows.py
@@ -79,9 +79,7 @@ class ScholarAuthorSearchParser(HTMLParser):
return
affiliation = normalize_space("".join(self._candidate["aff_parts"])) or None
- email_domain = _extract_verified_email_domain(
- normalize_space("".join(self._candidate["eml_parts"])) or None
- )
+ email_domain = _extract_verified_email_domain(normalize_space("".join(self._candidate["eml_parts"])) or None)
cited_by_text = normalize_space("".join(self._candidate["cby_parts"]))
cited_by_match = re.search(r"\d+", cited_by_text)
cited_by_count = int(cited_by_match.group(0)) if cited_by_match else None
@@ -97,10 +95,7 @@ class ScholarAuthorSearchParser(HTMLParser):
profile_url = build_absolute_scholar_url(self._candidate["name_href"])
if not profile_url:
- profile_url = (
- "https://scholar.google.com/citations"
- f"?hl=en&user={scholar_id}"
- )
+ profile_url = f"https://scholar.google.com/citations?hl=en&user={scholar_id}"
self.candidates.append(
ScholarSearchCandidate(
diff --git a/app/services/domains/scholar/parser.py b/app/services/domains/scholar/parser.py
index 060e825..26b2faf 100644
--- a/app/services/domains/scholar/parser.py
+++ b/app/services/domains/scholar/parser.py
@@ -3,40 +3,29 @@ from __future__ import annotations
from app.services.domains.scholar.author_rows import (
ScholarAuthorSearchParser,
count_author_search_markers,
- parse_scholar_id_from_href,
)
from app.services.domains.scholar.parser_constants import SCRIPT_STYLE_RE
from app.services.domains.scholar.parser_types import (
- ParseState,
ParsedAuthorSearchPage,
ParsedProfilePage,
PublicationCandidate,
ScholarDomInvariantError,
ScholarMalformedDataError,
- ScholarParserError,
- ScholarSearchCandidate,
)
from app.services.domains.scholar.parser_utils import (
strip_tags,
)
from app.services.domains.scholar.profile_rows import (
- ScholarRowParser,
count_markers,
extract_articles_range,
extract_profile_image_url,
extract_profile_name,
- extract_rows,
has_operation_error_banner,
has_show_more_button,
- parse_citation_count,
- parse_cluster_id_from_href,
parse_publications,
- parse_year,
)
from app.services.domains.scholar.source import FetchResult
from app.services.domains.scholar.state_detection import (
- classify_block_or_captcha_reason,
- classify_network_error_reason,
detect_author_search_state,
detect_state,
)
diff --git a/app/services/domains/scholar/profile_rows.py b/app/services/domains/scholar/profile_rows.py
index 6a63274..38faf0a 100644
--- a/app/services/domains/scholar/profile_rows.py
+++ b/app/services/domains/scholar/profile_rows.py
@@ -12,7 +12,6 @@ from app.services.domains.scholar.parser_types import PublicationCandidate
from app.services.domains.scholar.parser_utils import (
attr_class,
attr_href,
- attr_src,
build_absolute_scholar_url,
normalize_space,
strip_tags,
@@ -260,7 +259,7 @@ def has_show_more_button(html: str) -> bool:
def has_operation_error_banner(html: str) -> bool:
lowered = html.lower()
- if "id=\"gsc_a_err\"" not in lowered and "id='gsc_a_err'" not in lowered:
+ if 'id="gsc_a_err"' not in lowered and "id='gsc_a_err'" not in lowered:
return False
return "can't perform the operation now" in lowered or "cannot perform the operation now" in lowered
diff --git a/app/services/domains/scholar/source.py b/app/services/domains/scholar/source.py
index 7e34f01..3930f2e 100644
--- a/app/services/domains/scholar/source.py
+++ b/app/services/domains/scholar/source.py
@@ -17,18 +17,12 @@ SCHOLAR_PROFILE_URL = "https://scholar.google.com/citations"
DEFAULT_PAGE_SIZE = 100
DEFAULT_USER_AGENTS = [
- (
- "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 "
- "(KHTML, like Gecko) Chrome/131.0.0.0 Safari/537.36"
- ),
+ ("Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/131.0.0.0 Safari/537.36"),
(
"Mozilla/5.0 (Macintosh; Intel Mac OS X 14_7) AppleWebKit/605.1.15 "
"(KHTML, like Gecko) Version/18.1 Safari/605.1.15"
),
- (
- "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:131.0) "
- "Gecko/20100101 Firefox/131.0"
- ),
+ ("Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:131.0) Gecko/20100101 Firefox/131.0"),
]
logger = logging.getLogger(__name__)
@@ -44,8 +38,7 @@ class FetchResult:
class ScholarSource(Protocol):
- async def fetch_profile_html(self, scholar_id: str) -> FetchResult:
- ...
+ async def fetch_profile_html(self, scholar_id: str) -> FetchResult: ...
async def fetch_profile_page_html(
self,
@@ -53,16 +46,14 @@ class ScholarSource(Protocol):
*,
cstart: int,
pagesize: int,
- ) -> FetchResult:
- ...
+ ) -> FetchResult: ...
async def fetch_author_search_html(
self,
query: str,
*,
start: int,
- ) -> FetchResult:
- ...
+ ) -> FetchResult: ...
class LiveScholarSource:
@@ -145,7 +136,9 @@ class LiveScholarSource:
@staticmethod
def _network_error_result(requested_url: str, exc: URLError) -> FetchResult:
structured_log(
- logger, "warning", "scholar_source.fetch_network_error",
+ logger,
+ "warning",
+ "scholar_source.fetch_network_error",
requested_url=requested_url,
)
return FetchResult(
@@ -159,7 +152,9 @@ class LiveScholarSource:
@staticmethod
def _http_error_result(requested_url: str, exc: HTTPError) -> FetchResult:
structured_log(
- logger, "warning", "scholar_source.fetch_http_error",
+ logger,
+ "warning",
+ "scholar_source.fetch_http_error",
requested_url=requested_url,
status_code=exc.code,
)
@@ -176,7 +171,9 @@ class LiveScholarSource:
body = response.read().decode("utf-8", errors="replace")
status_code = getattr(response, "status", 200)
structured_log(
- logger, "debug", "scholar_source.fetch_succeeded",
+ logger,
+ "debug",
+ "scholar_source.fetch_succeeded",
requested_url=requested_url,
status_code=status_code,
)
diff --git a/app/services/domains/scholars/application.py b/app/services/domains/scholars/application.py
index 18ffdae..3b66643 100644
--- a/app/services/domains/scholars/application.py
+++ b/app/services/domains/scholars/application.py
@@ -1,13 +1,11 @@
from __future__ import annotations
import asyncio
-from dataclasses import replace
-from datetime import datetime
-from datetime import timedelta
-from datetime import timezone
import logging
import os
import random
+from dataclasses import replace
+from datetime import UTC, datetime, timedelta
from uuid import uuid4
from sqlalchemy import delete, func, select, text
@@ -15,9 +13,10 @@ from sqlalchemy.exc import IntegrityError
from sqlalchemy.ext.asyncio import AsyncSession
from app.db.models import AuthorSearchCacheEntry, AuthorSearchRuntimeState, ScholarProfile
+from app.logging_utils import structured_log
from app.services.domains.scholar.parser import (
- ParseState,
ParsedAuthorSearchPage,
+ ParseState,
ScholarParserError,
parse_author_search_page,
parse_profile_page,
@@ -34,33 +33,30 @@ from app.services.domains.scholars.constants import (
DEFAULT_AUTHOR_SEARCH_COOLDOWN_REJECTION_ALERT_THRESHOLD,
DEFAULT_AUTHOR_SEARCH_COOLDOWN_SECONDS,
DEFAULT_AUTHOR_SEARCH_INTERVAL_JITTER_SECONDS,
- MAX_AUTHOR_SEARCH_LIMIT,
DEFAULT_AUTHOR_SEARCH_MIN_INTERVAL_SECONDS,
DEFAULT_AUTHOR_SEARCH_RETRY_ALERT_THRESHOLD,
+ MAX_AUTHOR_SEARCH_LIMIT,
SEARCH_CACHED_BLOCK_REASON,
SEARCH_COOLDOWN_REASON,
SEARCH_DISABLED_REASON,
)
-from app.logging_utils import structured_log
from app.services.domains.scholars.exceptions import ScholarServiceError
from app.services.domains.scholars.search_hints import (
_merge_warnings,
_policy_blocked_author_search_result,
_trim_author_search_result,
- resolve_profile_image,
- scrape_state_hint,
)
from app.services.domains.scholars.uploads import (
_ensure_upload_root,
_resolve_upload_path,
_safe_remove_upload,
- resolve_upload_file_path,
)
from app.services.domains.scholars.validators import (
normalize_display_name,
normalize_profile_image_url,
validate_scholar_id,
)
+
logger = logging.getLogger(__name__)
@@ -247,7 +243,7 @@ async def _cache_get_author_search_result(
return None
expires_at = entry.expires_at
if expires_at.tzinfo is None:
- expires_at = expires_at.replace(tzinfo=timezone.utc)
+ expires_at = expires_at.replace(tzinfo=UTC)
if expires_at <= now_utc:
await db_session.delete(entry)
return None
@@ -305,27 +301,19 @@ async def _prune_author_search_cache(
now_utc: datetime,
max_entries: int,
) -> None:
- await db_session.execute(
- delete(AuthorSearchCacheEntry).where(AuthorSearchCacheEntry.expires_at <= now_utc)
- )
+ await db_session.execute(delete(AuthorSearchCacheEntry).where(AuthorSearchCacheEntry.expires_at <= now_utc))
bounded_max_entries = max(1, int(max_entries))
- count_result = await db_session.execute(
- select(func.count()).select_from(AuthorSearchCacheEntry)
- )
+ count_result = await db_session.execute(select(func.count()).select_from(AuthorSearchCacheEntry))
entry_count = int(count_result.scalar_one() or 0)
overflow = max(0, entry_count - bounded_max_entries)
if overflow <= 0:
return
stale_keys_result = await db_session.execute(
- select(AuthorSearchCacheEntry.query_key)
- .order_by(AuthorSearchCacheEntry.cached_at.asc())
- .limit(overflow)
+ select(AuthorSearchCacheEntry.query_key).order_by(AuthorSearchCacheEntry.cached_at.asc()).limit(overflow)
)
stale_keys = [str(row[0]) for row in stale_keys_result.all()]
if stale_keys:
- await db_session.execute(
- delete(AuthorSearchCacheEntry).where(AuthorSearchCacheEntry.query_key.in_(stale_keys))
- )
+ await db_session.execute(delete(AuthorSearchCacheEntry).where(AuthorSearchCacheEntry.query_key.in_(stale_keys)))
def _is_author_search_block_state(parsed: ParsedAuthorSearchPage) -> bool:
@@ -340,7 +328,7 @@ def _author_search_cooldown_remaining_seconds(
if cooldown_until is None:
return 0
if cooldown_until.tzinfo is None:
- cooldown_until = cooldown_until.replace(tzinfo=timezone.utc)
+ cooldown_until = cooldown_until.replace(tzinfo=UTC)
remaining_seconds = int((cooldown_until - now_utc).total_seconds())
return max(0, remaining_seconds)
@@ -432,7 +420,9 @@ def _normalize_author_search_inputs(query: str, limit: int) -> tuple[str, int, s
def _disabled_search_result(*, normalized_query: str, bounded_limit: int) -> ParsedAuthorSearchPage:
structured_log(
- logger, "warning", "scholar_search.disabled_by_configuration",
+ logger,
+ "warning",
+ "scholar_search.disabled_by_configuration",
query=normalized_query,
)
return _policy_blocked_author_search_result(
@@ -452,13 +442,15 @@ def _normalize_runtime_cooldown_state(
cooldown_until = runtime_state.cooldown_until
updated = False
if cooldown_until.tzinfo is None:
- cooldown_until = cooldown_until.replace(tzinfo=timezone.utc)
+ cooldown_until = cooldown_until.replace(tzinfo=UTC)
runtime_state.cooldown_until = cooldown_until
updated = True
if now_utc < cooldown_until:
return updated
structured_log(
- logger, "info", "scholar_search.cooldown_expired",
+ logger,
+ "info",
+ "scholar_search.cooldown_expired",
cooldown_until_utc=cooldown_until.isoformat(),
)
runtime_state.cooldown_until = None
@@ -494,7 +486,9 @@ def _emit_cooldown_threshold_alert(
if bool(runtime_state.cooldown_alert_emitted):
return True
structured_log(
- logger, "error", "scholar_search.cooldown_rejection_threshold_exceeded",
+ logger,
+ "error",
+ "scholar_search.cooldown_rejection_threshold_exceeded",
query=normalized_query,
cooldown_rejection_count=int(runtime_state.cooldown_rejection_count),
threshold=threshold,
@@ -518,7 +512,9 @@ def _cooldown_block_result(
cooldown_rejection_alert_threshold=cooldown_rejection_alert_threshold,
)
structured_log(
- logger, "warning", "scholar_search.cooldown_active",
+ logger,
+ "warning",
+ "scholar_search.cooldown_active",
query=normalized_query,
cooldown_remaining_seconds=cooldown_remaining_seconds,
cooldown_until_utc=runtime_state.cooldown_until.isoformat() if runtime_state.cooldown_until else None,
@@ -549,7 +545,9 @@ async def _cache_hit_result(
if cached is None:
return None
structured_log(
- logger, "info", "scholar_search.cache_hit",
+ logger,
+ "info",
+ "scholar_search.cache_hit",
query=normalized_query,
state=cached.state.value,
state_reason=cached.state_reason,
@@ -576,7 +574,7 @@ def _throttle_sleep_seconds(
else:
last_live_request_at = runtime_state.last_live_request_at
if last_live_request_at.tzinfo is None:
- last_live_request_at = last_live_request_at.replace(tzinfo=timezone.utc)
+ last_live_request_at = last_live_request_at.replace(tzinfo=UTC)
runtime_state.last_live_request_at = last_live_request_at
updated = True
enforced_wait_seconds = (
@@ -603,7 +601,9 @@ async def _wait_for_author_search_throttle(
if sleep_seconds <= 0.0:
return updated
structured_log(
- logger, "info", "scholar_search.throttle_wait",
+ logger,
+ "info",
+ "scholar_search.throttle_wait",
query=normalized_query,
sleep_seconds=round(sleep_seconds, 3),
)
@@ -659,7 +659,9 @@ def _with_retry_warnings(
if retry_scheduled_count < threshold:
return merged
structured_log(
- logger, "warning", "scholar_search.retry_threshold_exceeded",
+ logger,
+ "warning",
+ "scholar_search.retry_threshold_exceeded",
query=normalized_query,
retry_scheduled_count=retry_scheduled_count,
threshold=threshold,
@@ -688,19 +690,23 @@ def _apply_block_circuit_breaker(
return merged_parsed
runtime_state.consecutive_blocked_count = int(runtime_state.consecutive_blocked_count) + 1
structured_log(
- logger, "warning", "scholar_search.block_detected",
+ logger,
+ "warning",
+ "scholar_search.block_detected",
query=normalized_query,
state_reason=merged_parsed.state_reason,
consecutive_blocked_count=int(runtime_state.consecutive_blocked_count),
)
if int(runtime_state.consecutive_blocked_count) < max(1, int(cooldown_block_threshold)):
return merged_parsed
- runtime_state.cooldown_until = datetime.now(timezone.utc) + timedelta(seconds=max(60, int(cooldown_seconds)))
+ runtime_state.cooldown_until = datetime.now(UTC) + timedelta(seconds=max(60, int(cooldown_seconds)))
runtime_state.consecutive_blocked_count = 0
runtime_state.cooldown_rejection_count = 0
runtime_state.cooldown_alert_emitted = False
structured_log(
- logger, "error", "scholar_search.cooldown_activated",
+ logger,
+ "error",
+ "scholar_search.cooldown_activated",
query=normalized_query,
cooldown_until_utc=runtime_state.cooldown_until.isoformat() if runtime_state.cooldown_until else None,
)
@@ -739,11 +745,11 @@ async def _cooldown_or_cache_result(
) -> tuple[ParsedAuthorSearchPage | None, bool]:
runtime_state_updated = _normalize_runtime_cooldown_state(
runtime_state,
- now_utc=datetime.now(timezone.utc),
+ now_utc=datetime.now(UTC),
)
cooldown_remaining_seconds = _author_search_cooldown_remaining_seconds(
runtime_state,
- datetime.now(timezone.utc),
+ datetime.now(UTC),
)
if cooldown_remaining_seconds > 0:
return (
@@ -759,18 +765,35 @@ async def _cooldown_or_cache_result(
cached_result = await _cache_hit_result(
db_session,
query_key=query_key,
- now_utc=datetime.now(timezone.utc),
+ now_utc=datetime.now(UTC),
normalized_query=normalized_query,
bounded_limit=bounded_limit,
)
return cached_result, runtime_state_updated
-async def _perform_live_author_search(db_session: AsyncSession, *, source: ScholarSource, runtime_state: AuthorSearchRuntimeState, normalized_query: str, query_key: str, network_error_retries: int, retry_backoff_seconds: float, min_interval_seconds: float, interval_jitter_seconds: float, retry_alert_threshold: int, cooldown_block_threshold: int, cooldown_seconds: int, blocked_cache_ttl_seconds: int, cache_ttl_seconds: int, cache_max_entries: int) -> tuple[ParsedAuthorSearchPage, bool]:
+async def _perform_live_author_search(
+ db_session: AsyncSession,
+ *,
+ source: ScholarSource,
+ runtime_state: AuthorSearchRuntimeState,
+ normalized_query: str,
+ query_key: str,
+ network_error_retries: int,
+ retry_backoff_seconds: float,
+ min_interval_seconds: float,
+ interval_jitter_seconds: float,
+ retry_alert_threshold: int,
+ cooldown_block_threshold: int,
+ cooldown_seconds: int,
+ blocked_cache_ttl_seconds: int,
+ cache_ttl_seconds: int,
+ cache_max_entries: int,
+) -> tuple[ParsedAuthorSearchPage, bool]:
runtime_state_updated = await _wait_for_author_search_throttle(
runtime_state=runtime_state,
normalized_query=normalized_query,
- now_utc=datetime.now(timezone.utc),
+ now_utc=datetime.now(UTC),
min_interval_seconds=min_interval_seconds,
interval_jitter_seconds=interval_jitter_seconds,
)
@@ -780,7 +803,7 @@ async def _perform_live_author_search(db_session: AsyncSession, *, source: Schol
network_error_retries=network_error_retries,
retry_backoff_seconds=retry_backoff_seconds,
)
- runtime_state.last_live_request_at = datetime.now(timezone.utc)
+ runtime_state.last_live_request_at = datetime.now(UTC)
merged = _with_retry_warnings(
parsed,
retry_warnings=retry_warnings,
@@ -806,12 +829,30 @@ async def _perform_live_author_search(db_session: AsyncSession, *, source: Schol
parsed=merged,
ttl_seconds=float(ttl_seconds),
max_entries=cache_max_entries,
- now_utc=datetime.now(timezone.utc),
+ now_utc=datetime.now(UTC),
)
return merged, True
-async def search_author_candidates(*, source: ScholarSource, db_session: AsyncSession, query: str, limit: int, network_error_retries: int = 1, retry_backoff_seconds: float = 1.0, search_enabled: bool = True, cache_ttl_seconds: int = 21_600, blocked_cache_ttl_seconds: int = DEFAULT_AUTHOR_SEARCH_BLOCKED_CACHE_TTL_SECONDS, cache_max_entries: int = DEFAULT_AUTHOR_SEARCH_CACHE_MAX_ENTRIES, min_interval_seconds: float = DEFAULT_AUTHOR_SEARCH_MIN_INTERVAL_SECONDS, interval_jitter_seconds: float = DEFAULT_AUTHOR_SEARCH_INTERVAL_JITTER_SECONDS, cooldown_block_threshold: int = DEFAULT_AUTHOR_SEARCH_COOLDOWN_BLOCK_THRESHOLD, cooldown_seconds: int = DEFAULT_AUTHOR_SEARCH_COOLDOWN_SECONDS, retry_alert_threshold: int = DEFAULT_AUTHOR_SEARCH_RETRY_ALERT_THRESHOLD, cooldown_rejection_alert_threshold: int = DEFAULT_AUTHOR_SEARCH_COOLDOWN_REJECTION_ALERT_THRESHOLD) -> ParsedAuthorSearchPage:
+async def search_author_candidates(
+ *,
+ source: ScholarSource,
+ db_session: AsyncSession,
+ query: str,
+ limit: int,
+ network_error_retries: int = 1,
+ retry_backoff_seconds: float = 1.0,
+ search_enabled: bool = True,
+ cache_ttl_seconds: int = 21_600,
+ blocked_cache_ttl_seconds: int = DEFAULT_AUTHOR_SEARCH_BLOCKED_CACHE_TTL_SECONDS,
+ cache_max_entries: int = DEFAULT_AUTHOR_SEARCH_CACHE_MAX_ENTRIES,
+ min_interval_seconds: float = DEFAULT_AUTHOR_SEARCH_MIN_INTERVAL_SECONDS,
+ interval_jitter_seconds: float = DEFAULT_AUTHOR_SEARCH_INTERVAL_JITTER_SECONDS,
+ cooldown_block_threshold: int = DEFAULT_AUTHOR_SEARCH_COOLDOWN_BLOCK_THRESHOLD,
+ cooldown_seconds: int = DEFAULT_AUTHOR_SEARCH_COOLDOWN_SECONDS,
+ retry_alert_threshold: int = DEFAULT_AUTHOR_SEARCH_RETRY_ALERT_THRESHOLD,
+ cooldown_rejection_alert_threshold: int = DEFAULT_AUTHOR_SEARCH_COOLDOWN_REJECTION_ALERT_THRESHOLD,
+) -> ParsedAuthorSearchPage:
normalized_query, bounded_limit, query_key = _normalize_author_search_inputs(query, limit)
if not search_enabled:
return _disabled_search_result(
@@ -924,17 +965,13 @@ async def set_profile_image_upload(
normalized_content_type = (content_type or "").strip().lower()
extension = ALLOWED_IMAGE_UPLOAD_CONTENT_TYPES.get(normalized_content_type)
if extension is None:
- raise ScholarServiceError(
- "Unsupported image type. Use JPEG, PNG, WEBP, or GIF."
- )
+ raise ScholarServiceError("Unsupported image type. Use JPEG, PNG, WEBP, or GIF.")
if not image_bytes:
raise ScholarServiceError("Uploaded image file is empty.")
if len(image_bytes) > max_upload_bytes:
- raise ScholarServiceError(
- f"Uploaded image exceeds {max_upload_bytes} bytes."
- )
+ raise ScholarServiceError(f"Uploaded image exceeds {max_upload_bytes} bytes.")
upload_root = _ensure_upload_root(upload_dir, create=True)
user_dir = upload_root / str(profile.user_id)
diff --git a/app/services/domains/scholars/constants.py b/app/services/domains/scholars/constants.py
index 7ee18ad..0602acd 100644
--- a/app/services/domains/scholars/constants.py
+++ b/app/services/domains/scholars/constants.py
@@ -32,39 +32,25 @@ SEARCH_CACHED_BLOCK_REASON = "search_temporarily_disabled_from_cached_blocked_re
STATE_REASON_HINTS: dict[str, str] = {
SEARCH_DISABLED_REASON: (
- "Scholar name search is currently disabled by service policy. "
- "Add scholars by profile URL or Scholar ID."
+ "Scholar name search is currently disabled by service policy. Add scholars by profile URL or Scholar ID."
),
SEARCH_COOLDOWN_REASON: (
"Scholar name search is temporarily paused after repeated block responses. "
"Use Scholar URL/ID adds until cooldown expires."
),
SEARCH_CACHED_BLOCK_REASON: (
- "A recent blocked response was cached to reduce traffic. "
- "Retry later or add by Scholar URL/ID."
+ "A recent blocked response was cached to reduce traffic. Retry later or add by Scholar URL/ID."
),
"network_dns_resolution_failed": (
- "DNS resolution failed while reaching scholar.google.com. "
- "Verify container DNS/network and retry."
- ),
- "network_timeout": (
- "Request timed out before Google Scholar responded. "
- "Increase delay/backoff and retry."
- ),
- "network_tls_error": (
- "TLS handshake/certificate validation failed. "
- "Verify outbound TLS/network configuration."
- ),
- "blocked_http_429_rate_limited": (
- "Google Scholar rate-limited the request. "
- "Slow request cadence and retry later."
+ "DNS resolution failed while reaching scholar.google.com. Verify container DNS/network and retry."
),
+ "network_timeout": ("Request timed out before Google Scholar responded. Increase delay/backoff and retry."),
+ "network_tls_error": ("TLS handshake/certificate validation failed. Verify outbound TLS/network configuration."),
+ "blocked_http_429_rate_limited": ("Google Scholar rate-limited the request. Slow request cadence and retry later."),
"blocked_unusual_traffic_detected": (
- "Google Scholar flagged traffic as unusual. "
- "Increase delay/jitter and reduce concurrent scraping."
+ "Google Scholar flagged traffic as unusual. Increase delay/jitter and reduce concurrent scraping."
),
"blocked_accounts_redirect": (
- "Request was redirected to Google Account sign-in. "
- "Treat as access block and retry later."
+ "Request was redirected to Google Account sign-in. Treat as access block and retry later."
),
}
diff --git a/app/services/domains/scholars/search_hints.py b/app/services/domains/scholars/search_hints.py
index f905c14..b33cb1b 100644
--- a/app/services/domains/scholars/search_hints.py
+++ b/app/services/domains/scholars/search_hints.py
@@ -1,7 +1,7 @@
from __future__ import annotations
from app.db.models import ScholarProfile
-from app.services.domains.scholar.parser import ParseState, ParsedAuthorSearchPage
+from app.services.domains.scholar.parser import ParsedAuthorSearchPage, ParseState
from app.services.domains.scholars.constants import (
MAX_AUTHOR_SEARCH_LIMIT,
STATE_REASON_HINTS,
diff --git a/app/services/domains/scholars/validators.py b/app/services/domains/scholars/validators.py
index 1c79baa..e102eb1 100644
--- a/app/services/domains/scholars/validators.py
+++ b/app/services/domains/scholars/validators.py
@@ -27,9 +27,7 @@ def normalize_profile_image_url(value: str | None) -> str | None:
return None
if len(candidate) > MAX_IMAGE_URL_LENGTH:
- raise ScholarServiceError(
- f"Image URL must be {MAX_IMAGE_URL_LENGTH} characters or fewer."
- )
+ raise ScholarServiceError(f"Image URL must be {MAX_IMAGE_URL_LENGTH} characters or fewer.")
parsed = urlparse(candidate)
if parsed.scheme.lower() not in {"http", "https"} or not parsed.netloc:
diff --git a/app/services/domains/settings/application.py b/app/services/domains/settings/application.py
index 7f435e8..3636bf6 100644
--- a/app/services/domains/settings/application.py
+++ b/app/services/domains/settings/application.py
@@ -60,9 +60,7 @@ def parse_run_interval_minutes(value: str, *, minimum: int = HARD_MIN_RUN_INTERV
raise UserSettingsServiceError("Check interval must be a whole number.") from exc
effective_minimum = resolve_run_interval_minimum(minimum)
if parsed < effective_minimum:
- raise UserSettingsServiceError(
- f"Check interval must be at least {effective_minimum} minutes."
- )
+ raise UserSettingsServiceError(f"Check interval must be at least {effective_minimum} minutes.")
return parsed
@@ -73,9 +71,7 @@ def parse_request_delay_seconds(value: str, *, minimum: int = HARD_MIN_REQUEST_D
raise UserSettingsServiceError("Request delay must be a whole number.") from exc
effective_minimum = resolve_request_delay_minimum(minimum)
if parsed < effective_minimum:
- raise UserSettingsServiceError(
- f"Request delay must be at least {effective_minimum} seconds."
- )
+ raise UserSettingsServiceError(f"Request delay must be at least {effective_minimum} seconds.")
return parsed
@@ -102,23 +98,20 @@ def parse_nav_visible_pages(value: object) -> list[str]:
missing_required = [page for page in REQUIRED_NAV_PAGES if page not in seen]
if missing_required:
- raise UserSettingsServiceError(
- "Dashboard, Scholars, and Settings must remain visible."
- )
+ raise UserSettingsServiceError("Dashboard, Scholars, and Settings must remain visible.")
return deduped
from app.settings import settings as app_settings
+
async def get_or_create_settings(
db_session: AsyncSession,
*,
user_id: int,
) -> UserSetting:
- result = await db_session.execute(
- select(UserSetting).where(UserSetting.user_id == user_id)
- )
+ result = await db_session.execute(select(UserSetting).where(UserSetting.user_id == user_id))
settings = result.scalar_one_or_none()
if settings is not None:
return settings
diff --git a/app/services/domains/unpaywall/application.py b/app/services/domains/unpaywall/application.py
index 8b4d528..0febe51 100644
--- a/app/services/domains/unpaywall/application.py
+++ b/app/services/domains/unpaywall/application.py
@@ -1,11 +1,12 @@
from __future__ import annotations
-from dataclasses import dataclass
import logging
import re
+from dataclasses import dataclass
from typing import TYPE_CHECKING
from urllib.parse import unquote
+from app.logging_utils import structured_log
from app.services.domains.crossref.application import discover_doi_for_publication
from app.services.domains.doi.normalize import normalize_doi
from app.services.domains.unpaywall.pdf_discovery import (
@@ -13,7 +14,6 @@ from app.services.domains.unpaywall.pdf_discovery import (
resolve_pdf_from_landing_page,
)
from app.services.domains.unpaywall.rate_limit import wait_for_unpaywall_slot
-from app.logging_utils import structured_log
from app.settings import settings
if TYPE_CHECKING:
@@ -67,11 +67,8 @@ def _publication_doi(item: PublicationListItem | UnreadPublicationItem) -> str |
stored = None
if getattr(item, "display_identifier", None) and item.display_identifier.kind == "doi":
stored = normalize_doi(item.display_identifier.value)
-
- explicit_doi = (
- _extract_explicit_doi(item.pub_url)
- or _extract_explicit_doi(item.venue_text)
- )
+
+ explicit_doi = _extract_explicit_doi(item.pub_url) or _extract_explicit_doi(item.venue_text)
if explicit_doi:
return explicit_doi
pub_url_doi = _extract_doi_candidate(item.pub_url)
@@ -289,10 +286,7 @@ def _resolved_pdf_count(outcomes: dict[int, OaResolutionOutcome]) -> int:
def _outcome_metadata(outcomes: dict[int, OaResolutionOutcome]) -> dict[int, tuple[str | None, str | None]]:
- return {
- publication_id: (outcome.doi, outcome.pdf_url)
- for publication_id, outcome in outcomes.items()
- }
+ return {publication_id: (outcome.doi, outcome.pdf_url) for publication_id, outcome in outcomes.items()}
async def _resolve_outcome_for_item(
@@ -347,7 +341,9 @@ async def _safe_outcome_for_item(
allow_crossref=allow_crossref,
)
except Exception as exc: # pragma: no cover - defensive network boundary
- structured_log(logger, "warning", "unpaywall.resolve_item_failed", publication_id=item.publication_id, error=str(exc))
+ structured_log(
+ logger, "warning", "unpaywall.resolve_item_failed", publication_id=item.publication_id, error=str(exc)
+ )
return _outcome_with_failure(
item=item,
failure_reason=FAILURE_RESOLUTION_EXCEPTION,
@@ -410,7 +406,9 @@ async def resolve_publication_oa_outcomes(
email=email,
)
structured_log(
- logger, "info", "unpaywall.resolve_completed",
+ logger,
+ "info",
+ "unpaywall.resolve_completed",
publication_count=len(items),
doi_input_count=_doi_input_count(items),
search_attempt_count=_search_attempt_count(targets=targets),
diff --git a/app/services/domains/unpaywall/pdf_discovery.py b/app/services/domains/unpaywall/pdf_discovery.py
index 5f82a58..312bf04 100644
--- a/app/services/domains/unpaywall/pdf_discovery.py
+++ b/app/services/domains/unpaywall/pdf_discovery.py
@@ -1,7 +1,7 @@
from __future__ import annotations
-from html.parser import HTMLParser
import re
+from html.parser import HTMLParser
from urllib.parse import urljoin, urlparse
from app.services.domains.unpaywall.rate_limit import wait_for_unpaywall_slot
diff --git a/app/services/domains/users/application.py b/app/services/domains/users/application.py
index 7f019c4..e07f514 100644
--- a/app/services/domains/users/application.py
+++ b/app/services/domains/users/application.py
@@ -39,9 +39,7 @@ async def get_user_by_id(db_session: AsyncSession, user_id: int) -> User | None:
async def get_user_by_email(db_session: AsyncSession, email: str) -> User | None:
- result = await db_session.execute(
- select(User).where(User.email == normalize_email(email))
- )
+ result = await db_session.execute(select(User).where(User.email == normalize_email(email)))
return result.scalar_one_or_none()
@@ -95,4 +93,3 @@ async def set_user_password_hash(
await db_session.commit()
await db_session.refresh(user)
return user
-
diff --git a/app/settings.py b/app/settings.py
index 51ebcf4..175480e 100644
--- a/app/settings.py
+++ b/app/settings.py
@@ -1,5 +1,5 @@
-from dataclasses import dataclass
import os
+from dataclasses import dataclass
DEFAULT_SECURITY_PERMISSIONS_POLICY = (
"accelerometer=(), autoplay=(), camera=(), display-capture=(), "
@@ -266,7 +266,7 @@ class Settings:
crossref_timeout_seconds: float = _env_float("CROSSREF_TIMEOUT_SECONDS", 8.0)
crossref_min_interval_seconds: float = _env_float("CROSSREF_MIN_INTERVAL_SECONDS", 0.6)
crossref_max_lookups_per_request: int = _env_int("CROSSREF_MAX_LOOKUPS_PER_REQUEST", 8)
-
+
openalex_api_key: str | None = os.getenv("OPENALEX_API_KEY")
crossref_api_token: str | None = os.getenv("CROSSREF_API_TOKEN")
crossref_api_mailto: str | None = os.getenv("CROSSREF_API_MAILTO")
diff --git a/frontend/src/theme/presets/deutan-blue.js b/frontend/src/theme/presets/deutan-blue.js
new file mode 100644
index 0000000..d8ecba2
--- /dev/null
+++ b/frontend/src/theme/presets/deutan-blue.js
@@ -0,0 +1,313 @@
+export default {
+ "id": "deutan-blue-75",
+ "label": "Deutan Colorblind - Blue",
+ "description": "Colorblind-oriented theme with blue-led emphasis and deutan-safer state separation.",
+ "modes": {
+ "light": {
+ "scale": {
+ "brand": {
+ "50": "#f3f7ff",
+ "100": "#e6efff",
+ "200": "#c9dbff",
+ "300": "#a6c1ff",
+ "400": "#7ea2f5",
+ "500": "#5f84dc",
+ "600": "#4a6bc0",
+ "700": "#3e589b",
+ "800": "#35497d",
+ "900": "#2e3f68",
+ "950": "#1d2742"
+ },
+ "info": {
+ "50": "#f0f7fa",
+ "100": "#dcedf4",
+ "200": "#bcd9e8",
+ "300": "#93bfd8",
+ "400": "#669fc4",
+ "500": "#4b82a8",
+ "600": "#3b6887",
+ "700": "#31546d",
+ "800": "#2b465a",
+ "900": "#253b4c",
+ "950": "#16242f"
+ },
+ "success": {
+ "50": "#f2f8ff",
+ "100": "#deefff",
+ "200": "#bddfff",
+ "300": "#93c9ff",
+ "400": "#62acef",
+ "500": "#3e8fd1",
+ "600": "#2f72ad",
+ "700": "#285c8c",
+ "800": "#244d73",
+ "900": "#213f5d",
+ "950": "#15273a"
+ },
+ "warning": {
+ "50": "#fff8ef",
+ "100": "#ffedd2",
+ "200": "#ffd7a3",
+ "300": "#ffbb6b",
+ "400": "#f49c38",
+ "500": "#db7f1d",
+ "600": "#b86516",
+ "700": "#945013",
+ "800": "#784214",
+ "900": "#633814",
+ "950": "#381d0a"
+ },
+ "danger": {
+ "50": "#fcf4fb",
+ "100": "#f7e6f5",
+ "200": "#efcdea",
+ "300": "#e2a7d8",
+ "400": "#ce79bf",
+ "500": "#b856a4",
+ "600": "#9b3f89",
+ "700": "#7f3470",
+ "800": "#692e5d",
+ "900": "#57294d",
+ "950": "#311428"
+ }
+ },
+ "surface": {
+ "app": "#f4f7fb",
+ "nav": "#ffffff",
+ "nav_active": "#dce9ff",
+ "card": "#ffffff",
+ "card_muted": "#edf3fb",
+ "table": "#ffffff",
+ "table_header": "#f4f7fb",
+ "input": "#ffffff",
+ "overlay": "#1c2430"
+ },
+ "text": {
+ "primary": "#1f2937",
+ "secondary": "#41536b",
+ "muted": "#6a7a8f",
+ "inverse": "#ffffff",
+ "link": "#3e589b"
+ },
+ "border": {
+ "default": "#d8e2ee",
+ "strong": "#bccbdb",
+ "subtle": "#edf3fb",
+ "interactive": "#7ea2f5"
+ },
+ "focus": {
+ "ring": "#5f84dc",
+ "ring_offset": "#f4f7fb"
+ },
+ "action": {
+ "primary": {
+ "bg": "#5f84dc",
+ "border": "#5f84dc",
+ "text": "#ffffff",
+ "hover_bg": "#4a6bc0",
+ "hover_border": "#4a6bc0",
+ "hover_text": "#ffffff"
+ },
+ "secondary": {
+ "bg": "#edf3fb",
+ "border": "#d8e2ee",
+ "text": "#1f2937",
+ "hover_bg": "#dce9ff",
+ "hover_border": "#bccbdb",
+ "hover_text": "#111827"
+ },
+ "ghost": {
+ "bg": "#f4f7fb",
+ "border": "#d8e2ee",
+ "text": "#3e589b",
+ "hover_bg": "#edf3fb",
+ "hover_border": "#bccbdb",
+ "hover_text": "#2e3f68"
+ },
+ "danger": {
+ "bg": "#f7e6f5",
+ "border": "#efcdea",
+ "text": "#7f3470",
+ "hover_bg": "#efcdea",
+ "hover_border": "#e2a7d8",
+ "hover_text": "#692e5d"
+ }
+ },
+ "state": {
+ "info": {
+ "bg": "#dcedf4",
+ "border": "#bcd9e8",
+ "text": "#31546d"
+ },
+ "success": {
+ "bg": "#deefff",
+ "border": "#bddfff",
+ "text": "#285c8c"
+ },
+ "warning": {
+ "bg": "#ffedd2",
+ "border": "#ffd7a3",
+ "text": "#945013"
+ },
+ "danger": {
+ "bg": "#f7e6f5",
+ "border": "#efcdea",
+ "text": "#7f3470"
+ }
+ }
+ },
+ "dark": {
+ "scale": {
+ "brand": {
+ "50": "#f3f7ff",
+ "100": "#e6efff",
+ "200": "#c9dbff",
+ "300": "#a6c1ff",
+ "400": "#7ea2f5",
+ "500": "#5f84dc",
+ "600": "#4a6bc0",
+ "700": "#3e589b",
+ "800": "#35497d",
+ "900": "#2e3f68",
+ "950": "#1d2742"
+ },
+ "info": {
+ "50": "#f0f7fa",
+ "100": "#dcedf4",
+ "200": "#bcd9e8",
+ "300": "#93bfd8",
+ "400": "#669fc4",
+ "500": "#4b82a8",
+ "600": "#3b6887",
+ "700": "#31546d",
+ "800": "#2b465a",
+ "900": "#253b4c",
+ "950": "#16242f"
+ },
+ "success": {
+ "50": "#f2f8ff",
+ "100": "#deefff",
+ "200": "#bddfff",
+ "300": "#93c9ff",
+ "400": "#62acef",
+ "500": "#3e8fd1",
+ "600": "#2f72ad",
+ "700": "#285c8c",
+ "800": "#244d73",
+ "900": "#213f5d",
+ "950": "#15273a"
+ },
+ "warning": {
+ "50": "#fff8ef",
+ "100": "#ffedd2",
+ "200": "#ffd7a3",
+ "300": "#ffbb6b",
+ "400": "#f49c38",
+ "500": "#db7f1d",
+ "600": "#b86516",
+ "700": "#945013",
+ "800": "#784214",
+ "900": "#633814",
+ "950": "#381d0a"
+ },
+ "danger": {
+ "50": "#fcf4fb",
+ "100": "#f7e6f5",
+ "200": "#efcdea",
+ "300": "#e2a7d8",
+ "400": "#ce79bf",
+ "500": "#b856a4",
+ "600": "#9b3f89",
+ "700": "#7f3470",
+ "800": "#692e5d",
+ "900": "#57294d",
+ "950": "#311428"
+ }
+ },
+ "surface": {
+ "app": "#111827",
+ "nav": "#172131",
+ "nav_active": "#3e589b",
+ "card": "#172131",
+ "card_muted": "#1d2a3d",
+ "table": "#172131",
+ "table_header": "#1d2a3d",
+ "input": "#0d1522",
+ "overlay": "#05070b"
+ },
+ "text": {
+ "primary": "#e8eef7",
+ "secondary": "#bfd0e6",
+ "muted": "#8ea1ba",
+ "inverse": "#111827",
+ "link": "#a6c1ff"
+ },
+ "border": {
+ "default": "#27364b",
+ "strong": "#334760",
+ "subtle": "#1d2a3d",
+ "interactive": "#5f84dc"
+ },
+ "focus": {
+ "ring": "#7ea2f5",
+ "ring_offset": "#111827"
+ },
+ "action": {
+ "primary": {
+ "bg": "#5f84dc",
+ "border": "#5f84dc",
+ "text": "#0b1020",
+ "hover_bg": "#7ea2f5",
+ "hover_border": "#7ea2f5",
+ "hover_text": "#0b1020"
+ },
+ "secondary": {
+ "bg": "#1d2a3d",
+ "border": "#334760",
+ "text": "#e8eef7",
+ "hover_bg": "#27364b",
+ "hover_border": "#41536b",
+ "hover_text": "#ffffff"
+ },
+ "ghost": {
+ "bg": "#111827",
+ "border": "#27364b",
+ "text": "#bfd0e6",
+ "hover_bg": "#1d2a3d",
+ "hover_border": "#334760",
+ "hover_text": "#ffffff"
+ },
+ "danger": {
+ "bg": "#311428",
+ "border": "#7f3470",
+ "text": "#efcdea",
+ "hover_bg": "#421b35",
+ "hover_border": "#9b3f89",
+ "hover_text": "#f7e6f5"
+ }
+ },
+ "state": {
+ "info": {
+ "bg": "#253b4c",
+ "border": "#31546d",
+ "text": "#dcedf4"
+ },
+ "success": {
+ "bg": "#213f5d",
+ "border": "#285c8c",
+ "text": "#deefff"
+ },
+ "warning": {
+ "bg": "#633814",
+ "border": "#945013",
+ "text": "#ffd7a3"
+ },
+ "danger": {
+ "bg": "#311428",
+ "border": "#7f3470",
+ "text": "#efcdea"
+ }
+ }
+ }
+ }
+};
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 4990b4b..79c61b1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,6 +27,8 @@ dependencies = [
dev = [
"pytest>=8.3,<9.0",
"pytest-asyncio>=0.25,<0.26",
+ "ruff>=0.9",
+ "mypy>=1.14",
]
[tool.pytest.ini_options]
@@ -41,6 +43,24 @@ markers = [
"smoke: smoke tests for containerized runtime",
]
+[tool.ruff]
+target-version = "py312"
+line-length = 120
+extend-exclude = ["alembic/versions"]
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I", "UP", "B", "SIM", "RUF"]
+ignore = ["E501", "B008", "RUF001"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["app"]
+
+[tool.mypy]
+python_version = "3.12"
+ignore_missing_imports = true
+check_untyped_defs = false
+warn_unused_ignores = true
+
[tool.setuptools]
include-package-data = true
diff --git a/scripts/check_frontend_api_contract.py b/scripts/check_frontend_api_contract.py
index 07ba856..52e6e97 100755
--- a/scripts/check_frontend_api_contract.py
+++ b/scripts/check_frontend_api_contract.py
@@ -103,9 +103,7 @@ def main() -> int:
print(f"- {method} {route}")
return 1
- print(
- f"Frontend API contract check passed: {len(frontend_routes)} frontend routes match backend definitions."
- )
+ print(f"Frontend API contract check passed: {len(frontend_routes)} frontend routes match backend definitions.")
return 0
diff --git a/tests/conftest.py b/tests/conftest.py
index 0fb19ed..323a396 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -6,12 +6,12 @@ import re
from collections.abc import AsyncIterator, Iterator
import pytest
-from alembic import command
from alembic.config import Config
-from sqlalchemy.engine import make_url
from sqlalchemy import text
+from sqlalchemy.engine import make_url
from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
+from alembic import command
from app.auth.deps import get_login_rate_limiter
from app.db.session import close_engine
from app.settings import settings
@@ -52,9 +52,7 @@ def _resolve_test_database_url() -> str | None:
parsed = make_url(base)
if not parsed.database:
return None
- derived_database = (
- parsed.database if parsed.database.endswith("_test") else f"{parsed.database}_test"
- )
+ derived_database = parsed.database if parsed.database.endswith("_test") else f"{parsed.database}_test"
return parsed.set(database=derived_database).render_as_string(hide_password=False)
@@ -85,9 +83,7 @@ def ensure_test_database_exists(database_url: str) -> Iterator[None]:
if not database_name:
raise RuntimeError("TEST_DATABASE_URL must include a database name.")
if not DB_NAME_SAFE_RE.fullmatch(database_name):
- raise RuntimeError(
- "TEST_DATABASE_URL database name must match [A-Za-z0-9_]+ for safe auto-provisioning."
- )
+ raise RuntimeError("TEST_DATABASE_URL database name must match [A-Za-z0-9_]+ for safe auto-provisioning.")
admin_name = "postgres" if database_name != "postgres" else "template1"
admin_url = parsed.set(database=admin_name)
diff --git a/tests/integration/helpers.py b/tests/integration/helpers.py
index d1f5c68..135f271 100644
--- a/tests/integration/helpers.py
+++ b/tests/integration/helpers.py
@@ -6,6 +6,7 @@ from sqlalchemy.ext.asyncio import AsyncSession
from app.auth.security import PasswordService
+
def login_user(client: TestClient, *, email: str, password: str) -> None:
bootstrap_response = client.get("/api/v1/auth/csrf")
assert bootstrap_response.status_code == 200
diff --git a/tests/integration/test_api_v1.py b/tests/integration/test_api_v1.py
index 7da04a6..c3e67e3 100644
--- a/tests/integration/test_api_v1.py
+++ b/tests/integration/test_api_v1.py
@@ -1,7 +1,7 @@
from __future__ import annotations
import asyncio
-from datetime import datetime, timedelta, timezone
+from datetime import UTC, datetime, timedelta
from pathlib import Path
import pytest
@@ -12,8 +12,8 @@ from sqlalchemy.ext.asyncio import AsyncSession
from app.api.runtime_deps import get_scholar_source
from app.main import app
from app.services.domains.publications.types import PublicationListItem
-from app.services.domains.settings import application as user_settings_service
from app.services.domains.scholar.source import FetchResult
+from app.services.domains.settings import application as user_settings_service
from app.settings import settings
from tests.integration.helpers import insert_user, login_user
@@ -412,10 +412,7 @@ async def test_api_admin_dbops_integrity_and_repair_flow(db_session: AsyncSessio
assert integrity_response.status_code == 200
integrity_payload = integrity_response.json()["data"]
assert integrity_payload["status"] in {"ok", "warning", "failed"}
- assert any(
- check["name"] == "missing_pdf_url"
- for check in integrity_payload["checks"]
- )
+ assert any(check["name"] == "missing_pdf_url" for check in integrity_payload["checks"])
repair_response = client.post(
"/api/v1/admin/db/repairs/publication-links",
@@ -450,10 +447,7 @@ async def test_api_admin_dbops_integrity_and_repair_flow(db_session: AsyncSessio
assert page_two_payload["has_prev"] is True
untracked_response = client.get("/api/v1/admin/db/pdf-queue?limit=20&status=untracked")
assert untracked_response.status_code == 200
- assert any(
- item["status"] == "untracked"
- for item in untracked_response.json()["data"]["items"]
- )
+ assert any(item["status"] == "untracked" for item in untracked_response.json()["data"]["items"])
link_count_result = await db_session.execute(
text("SELECT count(*) FROM scholar_publications WHERE publication_id = :publication_id"),
@@ -1272,9 +1266,9 @@ async def test_api_settings_get_and_update(db_session: AsyncSession) -> None:
assert settings_payload["policy"]["min_run_interval_minutes"] == user_settings_service.resolve_run_interval_minimum(
settings.ingestion_min_run_interval_minutes
)
- assert settings_payload["policy"]["min_request_delay_seconds"] == user_settings_service.resolve_request_delay_minimum(
- settings.ingestion_min_request_delay_seconds
- )
+ assert settings_payload["policy"][
+ "min_request_delay_seconds"
+ ] == user_settings_service.resolve_request_delay_minimum(settings.ingestion_min_request_delay_seconds)
assert settings_payload["policy"]["automation_allowed"] is settings.ingestion_automation_allowed
assert settings_payload["policy"]["manual_run_allowed"] is settings.ingestion_manual_run_allowed
assert settings_payload["policy"]["blocked_failure_threshold"] == max(
@@ -1482,10 +1476,7 @@ async def test_api_runs_manual_and_queue_actions(db_session: AsyncSession) -> No
queue_list_response = client.get("/api/v1/runs/queue/items")
assert queue_list_response.status_code == 200
- assert any(
- int(item["id"]) == queue_item_id
- for item in queue_list_response.json()["data"]["queue_items"]
- )
+ assert any(int(item["id"]) == queue_item_id for item in queue_list_response.json()["data"]["queue_items"])
retry_response = client.post(f"/api/v1/runs/queue/{queue_item_id}/retry", headers=headers)
assert retry_response.status_code == 200
@@ -1766,7 +1757,7 @@ async def test_api_settings_clears_expired_scrape_safety_cooldown(
)
user_settings.scrape_safety_state = {"blocked_start_count": 2}
user_settings.scrape_cooldown_reason = "blocked_failure_threshold_exceeded"
- user_settings.scrape_cooldown_until = datetime.now(timezone.utc) - timedelta(seconds=15)
+ user_settings.scrape_cooldown_until = datetime.now(UTC) - timedelta(seconds=15)
await db_session.commit()
client = TestClient(app)
diff --git a/tests/integration/test_data_repair_jobs.py b/tests/integration/test_data_repair_jobs.py
index f291866..dc02904 100644
--- a/tests/integration/test_data_repair_jobs.py
+++ b/tests/integration/test_data_repair_jobs.py
@@ -160,10 +160,7 @@ async def _assert_apply_effects(
)
baseline_completed = await _count_rows(
db_session,
- sql=(
- "SELECT count(*) FROM scholar_profiles "
- "WHERE id = :scholar_profile_id AND baseline_completed = false"
- ),
+ sql=("SELECT count(*) FROM scholar_profiles WHERE id = :scholar_profile_id AND baseline_completed = false"),
params={"scholar_profile_id": scholar_profile_id},
)
publication_count = await _count_rows(
diff --git a/tests/integration/test_deferred_enrichment.py b/tests/integration/test_deferred_enrichment.py
index c51861e..ff15345 100644
--- a/tests/integration/test_deferred_enrichment.py
+++ b/tests/integration/test_deferred_enrichment.py
@@ -1,22 +1,24 @@
from __future__ import annotations
+from datetime import UTC, datetime
+from unittest.mock import AsyncMock, MagicMock, patch
+
import pytest
-from unittest.mock import patch, AsyncMock, MagicMock
from sqlalchemy import select
from sqlalchemy.ext.asyncio import AsyncSession
-from datetime import datetime, timezone
-from app.db.models import CrawlRun, Publication, ScholarProfile, ScholarPublication, RunStatus, RunTriggerType
+from app.db.models import CrawlRun, Publication, RunStatus, RunTriggerType, ScholarProfile, ScholarPublication
from app.services.domains.ingestion.application import ScholarIngestionService
from app.services.domains.openalex.types import OpenAlexWork
from tests.integration.helpers import insert_user
+
@pytest.mark.integration
@pytest.mark.asyncio
async def test_deferred_enrichment_sweeps_previous_runs(db_session: AsyncSession) -> None:
# 1. Setup: Create user and scholar
user_id = await insert_user(db_session, email="test@example.com", password="password123")
-
+
scholar = ScholarProfile(
user_id=user_id,
scholar_id="SaiiI5MAAAAJ",
@@ -25,17 +27,17 @@ async def test_deferred_enrichment_sweeps_previous_runs(db_session: AsyncSession
)
db_session.add(scholar)
await db_session.flush()
-
+
# 2. Simulate a previous FAILED run that left an un-enriched publication
failed_run = CrawlRun(
user_id=user_id,
status=RunStatus.FAILED,
trigger_type=RunTriggerType.MANUAL,
- start_dt=datetime.now(timezone.utc),
+ start_dt=datetime.now(UTC),
)
db_session.add(failed_run)
await db_session.flush()
-
+
pub = Publication(
title_raw="A fast quantum mechanical algorithm for database search",
title_normalized="a fast quantum mechanical algorithm for database search",
@@ -45,7 +47,7 @@ async def test_deferred_enrichment_sweeps_previous_runs(db_session: AsyncSession
)
db_session.add(pub)
await db_session.flush()
-
+
link = ScholarPublication(
scholar_profile_id=scholar.id,
publication_id=pub.id,
@@ -53,17 +55,17 @@ async def test_deferred_enrichment_sweeps_previous_runs(db_session: AsyncSession
)
db_session.add(link)
await db_session.commit()
-
+
# 3. Create a NEW run
new_run = CrawlRun(
user_id=user_id,
status=RunStatus.RUNNING,
trigger_type=RunTriggerType.MANUAL,
- start_dt=datetime.now(timezone.utc),
+ start_dt=datetime.now(UTC),
)
db_session.add(new_run)
await db_session.commit()
-
+
# 4. Mock OpenAlex client to return enrichment data
mock_work = OpenAlexWork(
openalex_id="W1234567",
@@ -76,26 +78,30 @@ async def test_deferred_enrichment_sweeps_previous_runs(db_session: AsyncSession
is_oa=True,
oa_url="http://example.com/grover.pdf",
)
-
+
mock_source = MagicMock()
service = ScholarIngestionService(source=mock_source)
-
+
# We patch the client at its source, and also mock arXiv to avoid real HTTP calls
- with patch("app.services.domains.openalex.client.OpenAlexClient") as MockClient, \
- patch("app.services.domains.arxiv.application.discover_arxiv_id_for_publication", new=AsyncMock(return_value=None)):
+ with (
+ patch("app.services.domains.openalex.client.OpenAlexClient") as MockClient,
+ patch(
+ "app.services.domains.arxiv.application.discover_arxiv_id_for_publication", new=AsyncMock(return_value=None)
+ ),
+ ):
mock_instance = MockClient.return_value
mock_instance.get_works_by_filter = AsyncMock(return_value=[mock_work])
# 5. Execute the enrichment pass for the NEW run
await service._enrich_pending_publications(db_session, run_id=new_run.id)
await db_session.commit()
-
+
# 6. Verification: The publication from the FAILED run should now be enriched
await db_session.refresh(pub)
assert pub.openalex_enriched is True
assert pub.citation_count == 1000
assert pub.pdf_url == "http://example.com/grover.pdf"
-
+
# Double check it was indeed processed
stmt = select(Publication).where(Publication.id == pub.id)
result = await db_session.execute(stmt)
diff --git a/tests/integration/test_fixture_probe_runs.py b/tests/integration/test_fixture_probe_runs.py
index 65361f2..0e721e5 100644
--- a/tests/integration/test_fixture_probe_runs.py
+++ b/tests/integration/test_fixture_probe_runs.py
@@ -34,8 +34,7 @@ def _blocked_fetch(*, scholar_id: str, body: str) -> FetchResult:
requested_url=f"https://scholar.google.com/citations?hl=en&user={scholar_id}",
status_code=200,
final_url=(
- "https://accounts.google.com/v3/signin/identifier"
- "?continue=https%3A%2F%2Fscholar.google.com%2Fcitations"
+ "https://accounts.google.com/v3/signin/identifier?continue=https%3A%2F%2Fscholar.google.com%2Fcitations"
),
body=body,
error=None,
diff --git a/tests/integration/test_migrations.py b/tests/integration/test_migrations.py
index 0155cbc..0bb3440 100644
--- a/tests/integration/test_migrations.py
+++ b/tests/integration/test_migrations.py
@@ -29,9 +29,7 @@ EXPECTED_REVISION = "20260226_0024"
@pytest.mark.migrations
@pytest.mark.asyncio
async def test_migration_creates_expected_tables(db_session: AsyncSession) -> None:
- result = await db_session.execute(
- text("SELECT tablename FROM pg_tables WHERE schemaname = 'public'")
- )
+ result = await db_session.execute(text("SELECT tablename FROM pg_tables WHERE schemaname = 'public'"))
table_names = {row[0] for row in result}
assert EXPECTED_TABLES.issubset(table_names)
diff --git a/tests/integration/test_run_lifecycle_consistency.py b/tests/integration/test_run_lifecycle_consistency.py
index 28020e6..b74ec1f 100644
--- a/tests/integration/test_run_lifecycle_consistency.py
+++ b/tests/integration/test_run_lifecycle_consistency.py
@@ -338,8 +338,8 @@ async def test_partial_discovery_exception_keeps_new_pub_count_consistent(
monkeypatch.setattr(service, "_resolve_publication", _resolve_publication_stub)
- from app.services.domains.scholar.parser_types import PublicationCandidate
from app.db.models import ScholarProfile
+ from app.services.domains.scholar.parser_types import PublicationCandidate
scholar = await db_session.get(ScholarProfile, scholar_profile_id)
assert scholar is not None
@@ -505,9 +505,7 @@ async def test_publications_pagination_snapshot_stays_stable_across_inserts(
)
assert first_page_again_response.status_code == 200
first_page_again = first_page_again_response.json()["data"]
- first_page_again_ids = [
- int(item["publication_id"]) for item in first_page_again["publications"]
- ]
+ first_page_again_ids = [int(item["publication_id"]) for item in first_page_again["publications"]]
assert first_page_again_ids == first_page_ids
assert not (set(first_page_ids) & set(second_page_ids))
diff --git a/tests/smoke/test_db_connectivity.py b/tests/smoke/test_db_connectivity.py
index 848a034..ba9ce76 100644
--- a/tests/smoke/test_db_connectivity.py
+++ b/tests/smoke/test_db_connectivity.py
@@ -20,4 +20,3 @@ async def test_database_connectivity_from_database_url() -> None:
assert result.scalar_one() == 1
finally:
await engine.dispose()
-
diff --git a/tests/smoke/test_migration_schema.py b/tests/smoke/test_migration_schema.py
index c12be25..d107388 100644
--- a/tests/smoke/test_migration_schema.py
+++ b/tests/smoke/test_migration_schema.py
@@ -1,6 +1,6 @@
+import pytest
from alembic.config import Config
from alembic.script import ScriptDirectory
-import pytest
from sqlalchemy import text
from sqlalchemy.ext.asyncio import AsyncSession
diff --git a/tests/unit/services/domains/arxiv/test_cache.py b/tests/unit/services/domains/arxiv/test_cache.py
index 2f15891..1586a1b 100644
--- a/tests/unit/services/domains/arxiv/test_cache.py
+++ b/tests/unit/services/domains/arxiv/test_cache.py
@@ -2,7 +2,7 @@ from __future__ import annotations
import asyncio
import gc
-from datetime import datetime, timedelta, timezone
+from datetime import UTC, datetime, timedelta
import pytest
from sqlalchemy import select
@@ -59,7 +59,7 @@ def test_build_query_fingerprint_normalizes_search_and_id_params() -> None:
@pytest.mark.asyncio
async def test_cache_entry_expires_and_is_deleted(db_session: AsyncSession) -> None:
query_fingerprint = build_query_fingerprint(params={"search_query": "ti:test", "start": 0})
- now_utc = datetime(2026, 2, 26, 12, 0, tzinfo=timezone.utc)
+ now_utc = datetime(2026, 2, 26, 12, 0, tzinfo=UTC)
await set_cached_feed(
query_fingerprint=query_fingerprint,
@@ -79,9 +79,7 @@ async def test_cache_entry_expires_and_is_deleted(db_session: AsyncSession) -> N
)
result = await db_session.execute(
- select(ArxivQueryCacheEntry).where(
- ArxivQueryCacheEntry.query_fingerprint == query_fingerprint
- )
+ select(ArxivQueryCacheEntry).where(ArxivQueryCacheEntry.query_fingerprint == query_fingerprint)
)
assert hit is not None
assert miss is None
@@ -118,6 +116,7 @@ async def test_inflight_owner_failure_without_joiner_has_no_unretrieved_exceptio
loop.set_exception_handler(_capture_exception)
try:
+
async def _failing_fetch() -> ArxivFeed:
raise RuntimeError("owner_failed")
diff --git a/tests/unit/services/domains/arxiv/test_client.py b/tests/unit/services/domains/arxiv/test_client.py
index 445d3cd..b51273d 100644
--- a/tests/unit/services/domains/arxiv/test_client.py
+++ b/tests/unit/services/domains/arxiv/test_client.py
@@ -1,7 +1,8 @@
from __future__ import annotations
import asyncio
-from datetime import datetime, timezone
+from datetime import UTC, datetime
+
import httpx
import pytest
from sqlalchemy.ext.asyncio import AsyncSession
@@ -35,7 +36,9 @@ async def test_client_search_builds_query_and_sort_params() -> None:
captured["params"] = params
captured["request_email"] = request_email
captured["timeout_seconds"] = timeout_seconds
- return httpx.Response(200, text=_CLIENT_FEED_XML, request=httpx.Request("GET", "https://export.arxiv.org/api/query"))
+ return httpx.Response(
+ 200, text=_CLIENT_FEED_XML, request=httpx.Request("GET", "https://export.arxiv.org/api/query")
+ )
client = ArxivClient(request_fn=_request_fn)
feed = await client.search(
@@ -66,7 +69,9 @@ async def test_client_lookup_ids_builds_id_list_param() -> None:
async def _request_fn(*, params, request_email, timeout_seconds):
captured["params"] = params
- return httpx.Response(200, text=_CLIENT_FEED_XML, request=httpx.Request("GET", "https://export.arxiv.org/api/query"))
+ return httpx.Response(
+ 200, text=_CLIENT_FEED_XML, request=httpx.Request("GET", "https://export.arxiv.org/api/query")
+ )
client = ArxivClient(request_fn=_request_fn)
await client.lookup_ids(id_list=["1234.5678", " 9999.0001 "], start=0, max_results=2)
@@ -76,7 +81,9 @@ async def test_client_lookup_ids_builds_id_list_param() -> None:
@pytest.mark.asyncio
async def test_client_search_rejects_invalid_sort_by() -> None:
async def _unused_request_fn(*, params, request_email, timeout_seconds):
- return httpx.Response(200, text=_CLIENT_FEED_XML, request=httpx.Request("GET", "https://export.arxiv.org/api/query"))
+ return httpx.Response(
+ 200, text=_CLIENT_FEED_XML, request=httpx.Request("GET", "https://export.arxiv.org/api/query")
+ )
client = ArxivClient(request_fn=_unused_request_fn)
with pytest.raises(ArxivClientValidationError):
@@ -86,7 +93,9 @@ async def test_client_search_rejects_invalid_sort_by() -> None:
@pytest.mark.asyncio
async def test_client_lookup_ids_rejects_empty_list() -> None:
async def _unused_request_fn(*, params, request_email, timeout_seconds):
- return httpx.Response(200, text=_CLIENT_FEED_XML, request=httpx.Request("GET", "https://export.arxiv.org/api/query"))
+ return httpx.Response(
+ 200, text=_CLIENT_FEED_XML, request=httpx.Request("GET", "https://export.arxiv.org/api/query")
+ )
client = ArxivClient(request_fn=_unused_request_fn)
with pytest.raises(ArxivClientValidationError):
@@ -96,7 +105,9 @@ async def test_client_lookup_ids_rejects_empty_list() -> None:
@pytest.mark.asyncio
async def test_client_search_rejects_negative_start() -> None:
async def _unused_request_fn(*, params, request_email, timeout_seconds):
- return httpx.Response(200, text=_CLIENT_FEED_XML, request=httpx.Request("GET", "https://export.arxiv.org/api/query"))
+ return httpx.Response(
+ 200, text=_CLIENT_FEED_XML, request=httpx.Request("GET", "https://export.arxiv.org/api/query")
+ )
client = ArxivClient(request_fn=_unused_request_fn)
with pytest.raises(ArxivClientValidationError):
@@ -172,7 +183,7 @@ async def test_request_feed_skips_live_call_when_global_cooldown_is_active(
return ArxivCooldownStatus(
is_active=True,
remaining_seconds=61.0,
- cooldown_until=datetime(2026, 2, 26, 12, 1, tzinfo=timezone.utc),
+ cooldown_until=datetime(2026, 2, 26, 12, 1, tzinfo=UTC),
)
async def _unexpected_limit_call(*, fetch, source_path): # pragma: no cover - defensive
diff --git a/tests/unit/services/domains/arxiv/test_guards.py b/tests/unit/services/domains/arxiv/test_guards.py
index 6acc042..0ebe422 100644
--- a/tests/unit/services/domains/arxiv/test_guards.py
+++ b/tests/unit/services/domains/arxiv/test_guards.py
@@ -1,6 +1,6 @@
from __future__ import annotations
-from datetime import datetime, timezone
+from datetime import UTC, datetime
from app.services.domains.arxiv.guards import arxiv_skip_reason_for_item
from app.services.domains.publication_identifiers.types import DisplayIdentifier
@@ -25,7 +25,7 @@ def _item(
pub_url=pub_url,
pdf_url=pdf_url,
is_read=False,
- first_seen_at=datetime.now(timezone.utc),
+ first_seen_at=datetime.now(UTC),
is_new_in_latest_run=True,
display_identifier=display_identifier,
)
diff --git a/tests/unit/services/domains/arxiv/test_parser.py b/tests/unit/services/domains/arxiv/test_parser.py
index 5ff78a8..f93d719 100644
--- a/tests/unit/services/domains/arxiv/test_parser.py
+++ b/tests/unit/services/domains/arxiv/test_parser.py
@@ -50,6 +50,8 @@ def test_parse_arxiv_feed_raises_on_invalid_xml() -> None:
def test_parse_arxiv_feed_raises_on_invalid_opensearch_integer() -> None:
- payload = _VALID_FEED_XML.replace("2", "x")
+ payload = _VALID_FEED_XML.replace(
+ "2", "x"
+ )
with pytest.raises(ArxivParseError):
parse_arxiv_feed(payload)
diff --git a/tests/unit/services/domains/arxiv/test_rate_limit.py b/tests/unit/services/domains/arxiv/test_rate_limit.py
index 86ad949..69b4947 100644
--- a/tests/unit/services/domains/arxiv/test_rate_limit.py
+++ b/tests/unit/services/domains/arxiv/test_rate_limit.py
@@ -1,7 +1,7 @@
from __future__ import annotations
import asyncio
-from datetime import datetime, timedelta, timezone
+from datetime import UTC, datetime, timedelta
import httpx
import pytest
@@ -20,7 +20,7 @@ async def test_arxiv_rate_limit_respects_cooldown(db_session: AsyncSession) -> N
db_session.add(
ArxivRuntimeState(
state_key=ARXIV_RUNTIME_STATE_KEY,
- cooldown_until=datetime.now(timezone.utc) + timedelta(seconds=30),
+ cooldown_until=datetime.now(UTC) + timedelta(seconds=30),
)
)
await db_session.commit()
@@ -43,6 +43,7 @@ async def test_arxiv_rate_limit_persists_cooldown_after_429(db_session: AsyncSes
object.__setattr__(settings, "arxiv_min_interval_seconds", 0.0)
object.__setattr__(settings, "arxiv_rate_limit_cooldown_seconds", 5.0)
try:
+
async def _fetch() -> httpx.Response:
return httpx.Response(429, text="rate limited")
@@ -57,7 +58,7 @@ async def test_arxiv_rate_limit_persists_cooldown_after_429(db_session: AsyncSes
)
state = result.scalar_one()
assert state.cooldown_until is not None
- assert state.cooldown_until > datetime.now(timezone.utc)
+ assert state.cooldown_until > datetime.now(UTC)
@pytest.mark.asyncio
@@ -120,6 +121,7 @@ async def test_arxiv_rate_limit_logs_cooldown_activation(
object.__setattr__(settings, "arxiv_min_interval_seconds", 0.0)
object.__setattr__(settings, "arxiv_rate_limit_cooldown_seconds", 5.0)
try:
+
async def _fetch() -> httpx.Response:
return httpx.Response(429, text="rate limited")
@@ -133,9 +135,7 @@ async def test_arxiv_rate_limit_logs_cooldown_activation(
object.__setattr__(settings, "arxiv_min_interval_seconds", previous_interval)
object.__setattr__(settings, "arxiv_rate_limit_cooldown_seconds", previous_cooldown)
- cooldown_events = [
- entry for entry in logged_warning if entry.get("event") == "arxiv.cooldown_activated"
- ]
+ cooldown_events = [entry for entry in logged_warning if entry.get("event") == "arxiv.cooldown_activated"]
assert cooldown_events
assert cooldown_events[0]["source_path"] == "lookup_ids"
assert float(cooldown_events[0]["cooldown_remaining_seconds"]) > 0.0
@@ -143,7 +143,7 @@ async def test_arxiv_rate_limit_logs_cooldown_activation(
@pytest.mark.asyncio
async def test_get_arxiv_cooldown_status_reads_active_cooldown(db_session: AsyncSession) -> None:
- now_utc = datetime(2026, 2, 26, 13, 0, tzinfo=timezone.utc)
+ now_utc = datetime(2026, 2, 26, 13, 0, tzinfo=UTC)
existing = await db_session.get(ArxivRuntimeState, ARXIV_RUNTIME_STATE_KEY)
if existing is None:
db_session.add(
diff --git a/tests/unit/services/domains/openalex/test_client.py b/tests/unit/services/domains/openalex/test_client.py
index 4b31cb3..5aab58f 100644
--- a/tests/unit/services/domains/openalex/test_client.py
+++ b/tests/unit/services/domains/openalex/test_client.py
@@ -1,6 +1,6 @@
-import pytest
from app.services.domains.openalex.types import OpenAlexWork
+
def test_parse_openalex_work_from_api_dict() -> None:
raw_api_response = {
"id": "https://openalex.org/W2741809807",
@@ -13,28 +13,19 @@ def test_parse_openalex_work_from_api_dict() -> None:
"doi": "https://doi.org/10.1038/s41586-020-0315-z",
"mag": "2741809807",
"pmid": "https://pubmed.ncbi.nlm.nih.gov/32040050",
- "pmcid": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325852"
- },
- "open_access": {
- "is_oa": True,
- "oa_url": "https://example.com/pdf"
+ "pmcid": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325852",
},
+ "open_access": {"is_oa": True, "oa_url": "https://example.com/pdf"},
"authorships": [
{
"author_position": "first",
- "author": {
- "id": "https://openalex.org/A1969205032",
- "display_name": "Giuseppe Carleo"
- }
+ "author": {"id": "https://openalex.org/A1969205032", "display_name": "Giuseppe Carleo"},
},
{
"author_position": "middle",
- "author": {
- "id": "https://openalex.org/A4356881717",
- "display_name": "Ignacio Cirac"
- }
- }
- ]
+ "author": {"id": "https://openalex.org/A4356881717", "display_name": "Ignacio Cirac"},
+ },
+ ],
}
work = OpenAlexWork.from_api_dict(raw_api_response)
@@ -52,6 +43,7 @@ def test_parse_openalex_work_from_api_dict() -> None:
assert work.authors[0].display_name == "Giuseppe Carleo"
assert work.authors[1].display_name == "Ignacio Cirac"
+
def test_parse_openalex_work_empty() -> None:
work = OpenAlexWork.from_api_dict({"id": "W123"})
assert work.openalex_id == "W123"
diff --git a/tests/unit/services/domains/openalex/test_matching.py b/tests/unit/services/domains/openalex/test_matching.py
index b8583a0..7d01d0b 100644
--- a/tests/unit/services/domains/openalex/test_matching.py
+++ b/tests/unit/services/domains/openalex/test_matching.py
@@ -1,54 +1,62 @@
-import pytest
-from app.services.domains.openalex.types import OpenAlexWork
from app.services.domains.openalex.matching import find_best_match
+from app.services.domains.openalex.types import OpenAlexWork
+
def test_find_best_match_exact_title():
cand1 = OpenAlexWork.from_api_dict({"id": "W1", "title": "Exact Title of the Paper"})
cand2 = OpenAlexWork.from_api_dict({"id": "W2", "title": "Totally Different Paper"})
-
+
match = find_best_match("Exact Title of the Paper", 2020, "Author A", [cand1, cand2])
assert match is not None
assert match.openalex_id == "W1"
+
def test_find_best_match_fuzzy_title():
# Only differences are punctuation or minor phrasing (e.g., matching a preprint title vs published)
cand1 = OpenAlexWork.from_api_dict({"id": "W1", "title": "Fuzzier Title: A Study on OpenAlex"})
cand2 = OpenAlexWork.from_api_dict({"id": "W2", "title": "Some completely unrelated work"})
-
+
match = find_best_match("Fuzzier Title A Study on OpenAlex", 2021, "Author B", [cand1, cand2])
assert match is not None
assert match.openalex_id == "W1"
+
def test_find_best_match_rejects_low_score():
cand1 = OpenAlexWork.from_api_dict({"id": "W1", "title": "Cats in hats"})
-
+
match = find_best_match("Dogs with logs", 2020, "Author A", [cand1])
assert match is None
+
def test_find_best_match_year_tiebreaker():
# Both titles are very similar, one has exact year.
cand1 = OpenAlexWork.from_api_dict({"id": "W1", "title": "The exact same title", "publication_year": 2018})
cand2 = OpenAlexWork.from_api_dict({"id": "W2", "title": "The exact same title", "publication_year": 2020})
-
+
match = find_best_match("The exact same title", 2020, "Author A", [cand1, cand2])
assert match is not None
assert match.openalex_id == "W2"
+
def test_find_best_match_author_tiebreaker():
# Titles and years match exactly. Author overlap decides it.
- cand1 = OpenAlexWork.from_api_dict({
- "id": "W1",
- "title": "A popular title",
- "publication_year": 2020,
- "authorships": [{"author": {"display_name": "Smith, J"}}]
- })
- cand2 = OpenAlexWork.from_api_dict({
- "id": "W2",
- "title": "A popular title",
- "publication_year": 2020,
- "authorships": [{"author": {"display_name": "Doe, J"}}]
- })
-
+ cand1 = OpenAlexWork.from_api_dict(
+ {
+ "id": "W1",
+ "title": "A popular title",
+ "publication_year": 2020,
+ "authorships": [{"author": {"display_name": "Smith, J"}}],
+ }
+ )
+ cand2 = OpenAlexWork.from_api_dict(
+ {
+ "id": "W2",
+ "title": "A popular title",
+ "publication_year": 2020,
+ "authorships": [{"author": {"display_name": "Doe, J"}}],
+ }
+ )
+
# Target authors contains "Doe"
match = find_best_match("A popular title", 2020, "A Einstein, J Doe", [cand1, cand2])
assert match is not None
diff --git a/tests/unit/services/domains/publications/test_dedup.py b/tests/unit/services/domains/publications/test_dedup.py
index 1f0f4dd..d2875c3 100644
--- a/tests/unit/services/domains/publications/test_dedup.py
+++ b/tests/unit/services/domains/publications/test_dedup.py
@@ -110,12 +110,14 @@ async def test_merge_duplicate_publication_migrates_links_and_identifiers() -> N
async def test_merge_duplicate_publication_rejects_missing_publications() -> None:
session = AsyncMock()
- with patch(
- "app.services.domains.publications.dedup._load_publication",
- new=AsyncMock(side_effect=[None, None]),
+ with (
+ patch(
+ "app.services.domains.publications.dedup._load_publication",
+ new=AsyncMock(side_effect=[None, None]),
+ ),
+ pytest.raises(ValueError),
):
- with pytest.raises(ValueError):
- await merge_duplicate_publication(session, winner_id=1, dup_id=2)
+ await merge_duplicate_publication(session, winner_id=1, dup_id=2)
@pytest.mark.asyncio
diff --git a/tests/unit/test_fingerprints.py b/tests/unit/test_fingerprints.py
index f05b69d..3965c8e 100644
--- a/tests/unit/test_fingerprints.py
+++ b/tests/unit/test_fingerprints.py
@@ -1,7 +1,5 @@
from __future__ import annotations
-import pytest
-
from app.services.domains.ingestion.fingerprints import (
_dedupe_publication_candidates,
canonical_title_for_dedup,
@@ -36,28 +34,40 @@ class TestFuzzyTitlesMatch:
assert fuzzy_titles_match("Deep Learning for NLP", "deep learning for nlp") is True
def test_minor_word_difference(self) -> None:
- assert fuzzy_titles_match(
- "A Survey on Deep Learning Methods for NLP",
- "Survey on Deep Learning Methods for NLP",
- ) is True
+ assert (
+ fuzzy_titles_match(
+ "A Survey on Deep Learning Methods for NLP",
+ "Survey on Deep Learning Methods for NLP",
+ )
+ is True
+ )
def test_punctuation_difference(self) -> None:
- assert fuzzy_titles_match(
- "Attention Is All You Need",
- "Attention Is All You Need.",
- ) is True
+ assert (
+ fuzzy_titles_match(
+ "Attention Is All You Need",
+ "Attention Is All You Need.",
+ )
+ is True
+ )
def test_colon_vs_dash_subtitle(self) -> None:
- assert fuzzy_titles_match(
- "Deep Learning: A Comprehensive Survey",
- "Deep Learning - A Comprehensive Survey",
- ) is True
+ assert (
+ fuzzy_titles_match(
+ "Deep Learning: A Comprehensive Survey",
+ "Deep Learning - A Comprehensive Survey",
+ )
+ is True
+ )
def test_completely_different_titles(self) -> None:
- assert fuzzy_titles_match(
- "Deep Learning for NLP",
- "Climate Change Impact on Agriculture",
- ) is False
+ assert (
+ fuzzy_titles_match(
+ "Deep Learning for NLP",
+ "Climate Change Impact on Agriculture",
+ )
+ is False
+ )
def test_short_title_no_false_positive(self) -> None:
assert fuzzy_titles_match("On Trees", "On Forests") is False
@@ -67,16 +77,22 @@ class TestFuzzyTitlesMatch:
def test_custom_threshold(self) -> None:
# Lower threshold catches more distant matches
- assert fuzzy_titles_match(
- "A Survey on Deep Learning",
- "Survey on Machine Learning Approaches",
- threshold=0.3,
- ) is True
+ assert (
+ fuzzy_titles_match(
+ "A Survey on Deep Learning",
+ "Survey on Machine Learning Approaches",
+ threshold=0.3,
+ )
+ is True
+ )
# Default threshold rejects them
- assert fuzzy_titles_match(
- "A Survey on Deep Learning",
- "Survey on Machine Learning Approaches",
- ) is False
+ assert (
+ fuzzy_titles_match(
+ "A Survey on Deep Learning",
+ "Survey on Machine Learning Approaches",
+ )
+ is False
+ )
class TestDedupePublicationCandidates:
@@ -203,27 +219,19 @@ class TestDedupePublicationCandidates:
class TestCanonicalTitleForDedup:
def test_strips_doi_suffix(self) -> None:
title = "Adam: A Method for Stochastic Optimization. doi: 10.48550/arxiv.1412.6980"
- assert canonical_title_for_dedup(title) == normalize_title(
- "Adam: A Method for Stochastic Optimization"
- )
+ assert canonical_title_for_dedup(title) == normalize_title("Adam: A Method for Stochastic Optimization")
def test_strips_arxiv_metadata_suffix(self) -> None:
title = "Adam: A Method for Stochastic Optimization. arXiv, Jan 29, 2017"
- assert canonical_title_for_dedup(title) == normalize_title(
- "Adam: A Method for Stochastic Optimization"
- )
+ assert canonical_title_for_dedup(title) == normalize_title("Adam: A Method for Stochastic Optimization")
def test_strips_preprint_parenthetical(self) -> None:
title = "Adam: A method for stochastic optimization, preprint (2014)"
- assert canonical_title_for_dedup(title) == normalize_title(
- "Adam: A method for stochastic optimization"
- )
+ assert canonical_title_for_dedup(title) == normalize_title("Adam: A method for stochastic optimization")
def test_strips_venue_sentence_suffix(self) -> None:
title = "Adam a method for stochastic optimization. Comput. Sci"
- assert canonical_title_for_dedup(title) == normalize_title(
- "Adam a method for stochastic optimization"
- )
+ assert canonical_title_for_dedup(title) == normalize_title("Adam a method for stochastic optimization")
def test_strips_trailing_year_in_parens(self) -> None:
assert canonical_title_for_dedup("Deep Learning (2018)") == normalize_title("Deep Learning")
@@ -242,10 +250,7 @@ class TestCanonicalTitleForDedup:
assert len(set(canonicals)) == 1, f"Expected one canonical, got: {canonicals}"
def test_strips_mojibake_conference_suffix(self) -> None:
- noisy = (
- "†œAdam: A method for stochastic optimization, "
- "†3rd Int. Conf. Learn. Represent. ICLR 2015-Conf"
- )
+ noisy = "†œAdam: A method for stochastic optimization, †3rd Int. Conf. Learn. Represent. ICLR 2015-Conf"
clean = "Adam: A method for stochastic optimization"
assert canonical_title_for_dedup(noisy) == normalize_title(clean)
diff --git a/tests/unit/test_ingestion_arxiv_rate_limit.py b/tests/unit/test_ingestion_arxiv_rate_limit.py
index 470a59f..6f25796 100644
--- a/tests/unit/test_ingestion_arxiv_rate_limit.py
+++ b/tests/unit/test_ingestion_arxiv_rate_limit.py
@@ -31,6 +31,7 @@ async def test_discover_identifiers_for_enrichment_disables_arxiv_on_rate_limit(
_raise_rate_limit,
)
monkeypatch.setattr(identifier_service, "sync_identifiers_for_publication_fields", _sync_fields)
+
async def _publish_noop(*args, **kwargs) -> None:
_ = (args, kwargs)
diff --git a/tests/unit/test_logging.py b/tests/unit/test_logging.py
index 696cb2a..a4d8d99 100644
--- a/tests/unit/test_logging.py
+++ b/tests/unit/test_logging.py
@@ -7,10 +7,10 @@ from unittest.mock import AsyncMock
from fastapi.testclient import TestClient
+from app.http.middleware import REQUEST_ID_HEADER, parse_skip_paths
from app.logging_config import ConsoleLogFormatter, JsonLogFormatter, parse_redact_fields
from app.logging_utils import structured_log
from app.main import app
-from app.http.middleware import REQUEST_ID_HEADER, parse_skip_paths
def test_json_log_formatter_redacts_sensitive_fields() -> None:
diff --git a/tests/unit/test_publication_pdf_queue_policy.py b/tests/unit/test_publication_pdf_queue_policy.py
index 5f8cbeb..e8e1a94 100644
--- a/tests/unit/test_publication_pdf_queue_policy.py
+++ b/tests/unit/test_publication_pdf_queue_policy.py
@@ -1,6 +1,6 @@
from __future__ import annotations
-from datetime import datetime, timedelta, timezone
+from datetime import UTC, datetime, timedelta
from types import SimpleNamespace
import pytest
@@ -25,7 +25,9 @@ def _job(
)
-def _row(*, pub_url: str | None = "https://scholar.google.com/citations?view_op=view_citation&citation_for_view=abc:xyz") -> SimpleNamespace:
+def _row(
+ *, pub_url: str | None = "https://scholar.google.com/citations?view_op=view_citation&citation_for_view=abc:xyz"
+) -> SimpleNamespace:
return SimpleNamespace(
publication_id=1,
scholar_profile_id=1,
@@ -39,13 +41,13 @@ def _row(*, pub_url: str | None = "https://scholar.google.com/citations?view_op=
pdf_url=None,
is_read=False,
is_favorite=False,
- first_seen_at=datetime(2026, 2, 22, 12, 0, tzinfo=timezone.utc),
+ first_seen_at=datetime(2026, 2, 22, 12, 0, tzinfo=UTC),
is_new_in_latest_run=True,
)
def test_pdf_queue_auto_enqueue_blocks_recent_attempt(monkeypatch: pytest.MonkeyPatch) -> None:
- now = datetime(2026, 2, 21, 12, 0, tzinfo=timezone.utc)
+ now = datetime(2026, 2, 21, 12, 0, tzinfo=UTC)
monkeypatch.setattr(pdf_queue, "_utcnow", lambda: now)
monkeypatch.setattr(pdf_queue, "_auto_retry_first_interval_seconds", lambda: 3_600)
monkeypatch.setattr(pdf_queue, "_auto_retry_interval_seconds", lambda: 86_400)
@@ -59,7 +61,7 @@ def test_pdf_queue_auto_enqueue_blocks_recent_attempt(monkeypatch: pytest.Monkey
def test_pdf_queue_auto_enqueue_blocks_recent_first_retry(monkeypatch: pytest.MonkeyPatch) -> None:
- now = datetime(2026, 2, 21, 12, 0, tzinfo=timezone.utc)
+ now = datetime(2026, 2, 21, 12, 0, tzinfo=UTC)
monkeypatch.setattr(pdf_queue, "_utcnow", lambda: now)
monkeypatch.setattr(pdf_queue, "_auto_retry_first_interval_seconds", lambda: 3_600)
monkeypatch.setattr(pdf_queue, "_auto_retry_interval_seconds", lambda: 86_400)
@@ -73,7 +75,7 @@ def test_pdf_queue_auto_enqueue_blocks_recent_first_retry(monkeypatch: pytest.Mo
def test_pdf_queue_auto_enqueue_blocks_after_max_attempts(monkeypatch: pytest.MonkeyPatch) -> None:
- now = datetime(2026, 2, 21, 12, 0, tzinfo=timezone.utc)
+ now = datetime(2026, 2, 21, 12, 0, tzinfo=UTC)
monkeypatch.setattr(pdf_queue, "_utcnow", lambda: now)
monkeypatch.setattr(pdf_queue, "_auto_retry_first_interval_seconds", lambda: 3_600)
monkeypatch.setattr(pdf_queue, "_auto_retry_interval_seconds", lambda: 86_400)
@@ -87,7 +89,7 @@ def test_pdf_queue_auto_enqueue_blocks_after_max_attempts(monkeypatch: pytest.Mo
def test_pdf_queue_auto_enqueue_blocks_second_retry_within_day(monkeypatch: pytest.MonkeyPatch) -> None:
- now = datetime(2026, 2, 21, 12, 0, tzinfo=timezone.utc)
+ now = datetime(2026, 2, 21, 12, 0, tzinfo=UTC)
monkeypatch.setattr(pdf_queue, "_utcnow", lambda: now)
monkeypatch.setattr(pdf_queue, "_auto_retry_first_interval_seconds", lambda: 3_600)
monkeypatch.setattr(pdf_queue, "_auto_retry_interval_seconds", lambda: 86_400)
@@ -103,7 +105,7 @@ def test_pdf_queue_auto_enqueue_blocks_second_retry_within_day(monkeypatch: pyte
def test_pdf_queue_manual_requeue_bypasses_cooldown_and_max_attempts(
monkeypatch: pytest.MonkeyPatch,
) -> None:
- now = datetime(2026, 2, 21, 12, 0, tzinfo=timezone.utc)
+ now = datetime(2026, 2, 21, 12, 0, tzinfo=UTC)
monkeypatch.setattr(pdf_queue, "_utcnow", lambda: now)
monkeypatch.setattr(pdf_queue, "_auto_retry_first_interval_seconds", lambda: 3_600)
monkeypatch.setattr(pdf_queue, "_auto_retry_interval_seconds", lambda: 86_400)
diff --git a/tests/unit/test_publication_pdf_resolution_pipeline.py b/tests/unit/test_publication_pdf_resolution_pipeline.py
index 9016dad..8574a5e 100644
--- a/tests/unit/test_publication_pdf_resolution_pipeline.py
+++ b/tests/unit/test_publication_pdf_resolution_pipeline.py
@@ -1,13 +1,13 @@
from __future__ import annotations
-from datetime import datetime, timezone
+from datetime import UTC, datetime
from types import SimpleNamespace
import pytest
from app.services.domains.arxiv.errors import ArxivRateLimitError
-from app.services.domains.publications import pdf_resolution_pipeline as pipeline
from app.services.domains.publication_identifiers.types import DisplayIdentifier
+from app.services.domains.publications import pdf_resolution_pipeline as pipeline
from app.services.domains.unpaywall.application import OaResolutionOutcome
@@ -25,7 +25,7 @@ def _row(*, display_identifier: DisplayIdentifier | None = None) -> SimpleNamesp
pdf_url=None,
is_read=False,
is_favorite=False,
- first_seen_at=datetime(2026, 2, 22, 12, 0, tzinfo=timezone.utc),
+ first_seen_at=datetime(2026, 2, 22, 12, 0, tzinfo=UTC),
is_new_in_latest_run=True,
)
@@ -61,7 +61,7 @@ async def test_pipeline_prefers_openalex_before_arxiv(monkeypatch: pytest.Monkey
async def _fail_arxiv(row, *, request_email: str | None = None, allow_lookup: bool = True):
_ = (row, request_email, allow_lookup)
- raise AssertionError(f"arXiv should not run when OpenAlex candidate exists.")
+ raise AssertionError("arXiv should not run when OpenAlex candidate exists.")
monkeypatch.setattr(pipeline, "_openalex_outcome", _fake_openalex)
monkeypatch.setattr(pipeline, "_arxiv_outcome", _fail_arxiv)
diff --git a/tests/unit/test_request_delay_policy.py b/tests/unit/test_request_delay_policy.py
index f8eb767..f45039e 100644
--- a/tests/unit/test_request_delay_policy.py
+++ b/tests/unit/test_request_delay_policy.py
@@ -1,9 +1,9 @@
from __future__ import annotations
-from datetime import datetime, timezone
+from datetime import UTC, datetime
-from app.services.domains.ingestion.application import ScholarIngestionService
from app.services.domains.ingestion import scheduler as scheduler_module
+from app.services.domains.ingestion.application import ScholarIngestionService
from app.settings import settings
@@ -37,7 +37,7 @@ def test_scheduler_candidate_row_clamps_request_delay() -> None:
try:
candidate = scheduler_module.SchedulerService._candidate_from_row(
(1, 15, 1, None, None),
- now_utc=datetime(2026, 2, 21, tzinfo=timezone.utc),
+ now_utc=datetime(2026, 2, 21, tzinfo=UTC),
)
assert candidate is not None
assert candidate.request_delay_seconds == 6
diff --git a/tests/unit/test_run_safety.py b/tests/unit/test_run_safety.py
index 60cd87c..81671d9 100644
--- a/tests/unit/test_run_safety.py
+++ b/tests/unit/test_run_safety.py
@@ -1,6 +1,6 @@
from __future__ import annotations
-from datetime import datetime, timedelta, timezone
+from datetime import UTC, datetime, timedelta
from app.db.models import UserSetting
from app.services.domains.ingestion import safety as run_safety
@@ -8,7 +8,7 @@ from app.services.domains.ingestion import safety as run_safety
def test_apply_run_safety_outcome_triggers_blocked_cooldown() -> None:
settings = UserSetting(user_id=1, scrape_safety_state={})
- now = datetime(2026, 2, 19, 20, 0, tzinfo=timezone.utc)
+ now = datetime(2026, 2, 19, 20, 0, tzinfo=UTC)
safety_state, reason = run_safety.apply_run_safety_outcome(
settings,
@@ -32,7 +32,7 @@ def test_apply_run_safety_outcome_triggers_blocked_cooldown() -> None:
def test_clear_expired_cooldown() -> None:
- now = datetime(2026, 2, 19, 20, 0, tzinfo=timezone.utc)
+ now = datetime(2026, 2, 19, 20, 0, tzinfo=UTC)
settings = UserSetting(
user_id=1,
scrape_safety_state={"blocked_start_count": 3},
@@ -51,7 +51,7 @@ def test_clear_expired_cooldown() -> None:
def test_apply_run_safety_outcome_triggers_network_cooldown() -> None:
settings = UserSetting(user_id=1, scrape_safety_state={})
- now = datetime(2026, 2, 19, 20, 0, tzinfo=timezone.utc)
+ now = datetime(2026, 2, 19, 20, 0, tzinfo=UTC)
safety_state, reason = run_safety.apply_run_safety_outcome(
settings,
@@ -75,7 +75,7 @@ def test_apply_run_safety_outcome_triggers_network_cooldown() -> None:
def test_register_cooldown_blocked_start_increments_counter() -> None:
- now = datetime(2026, 2, 19, 20, 0, tzinfo=timezone.utc)
+ now = datetime(2026, 2, 19, 20, 0, tzinfo=UTC)
settings = UserSetting(
user_id=1,
scrape_safety_state={"blocked_start_count": 1},
@@ -91,7 +91,7 @@ def test_register_cooldown_blocked_start_increments_counter() -> None:
def test_get_safety_event_context_contains_structured_fields() -> None:
- now = datetime(2026, 2, 19, 20, 0, tzinfo=timezone.utc)
+ now = datetime(2026, 2, 19, 20, 0, tzinfo=UTC)
settings = UserSetting(
user_id=1,
scrape_safety_state={"cooldown_entry_count": 4},
diff --git a/tests/unit/test_scholar_search_safety.py b/tests/unit/test_scholar_search_safety.py
index b3c35da..ff21c1e 100644
--- a/tests/unit/test_scholar_search_safety.py
+++ b/tests/unit/test_scholar_search_safety.py
@@ -3,9 +3,9 @@ from __future__ import annotations
import pytest
from sqlalchemy.ext.asyncio import AsyncSession
-from app.services.domains.scholars import application as scholar_service
from app.services.domains.scholar.parser import ParseState
from app.services.domains.scholar.source import FetchResult
+from app.services.domains.scholars import application as scholar_service
pytestmark = [pytest.mark.integration, pytest.mark.db]
@@ -51,8 +51,7 @@ def _blocked_author_search_fetch() -> FetchResult:
requested_url="https://scholar.google.com/citations?hl=en&view_op=search_authors&mauthors=ada",
status_code=200,
final_url=(
- "https://accounts.google.com/v3/signin/identifier"
- "?continue=https%3A%2F%2Fscholar.google.com%2Fcitations"
+ "https://accounts.google.com/v3/signin/identifier?continue=https%3A%2F%2Fscholar.google.com%2Fcitations"
),
body="Sign in",
error=None,
diff --git a/tests/unit/test_unpaywall_pdf_discovery.py b/tests/unit/test_unpaywall_pdf_discovery.py
index 16e1c27..48270e0 100644
--- a/tests/unit/test_unpaywall_pdf_discovery.py
+++ b/tests/unit/test_unpaywall_pdf_discovery.py
@@ -61,7 +61,7 @@ class _FakeClient:
def __init__(self, pages: dict[str, _FakeResponse]) -> None:
self._pages = pages
- async def get(self, url: str, follow_redirects: bool = True): # noqa: ARG002
+ async def get(self, url: str, follow_redirects: bool = True):
return self._pages[url]
@@ -69,7 +69,7 @@ class _FakeClient:
async def test_resolve_pdf_from_landing_page_follows_one_hop_html_candidate(
monkeypatch: pytest.MonkeyPatch,
) -> None:
- async def _skip_wait(*args, **kwargs): # noqa: ARG001, ANN002
+ async def _skip_wait(*args, **kwargs):
return None
monkeypatch.setattr(pdf_discovery, "wait_for_unpaywall_slot", _skip_wait)
@@ -81,7 +81,7 @@ async def test_resolve_pdf_from_landing_page_follows_one_hop_html_candidate(
landing_url: _FakeResponse(
status_code=200,
content_type="text/html",
- text=f"View article",
+ text=f'View article',
),
hop_url: _FakeResponse(
status_code=200,
diff --git a/tests/unit/test_unpaywall_resolution.py b/tests/unit/test_unpaywall_resolution.py
index b29cc2c..6dc7481 100644
--- a/tests/unit/test_unpaywall_resolution.py
+++ b/tests/unit/test_unpaywall_resolution.py
@@ -1,12 +1,12 @@
from __future__ import annotations
from dataclasses import replace
-from datetime import datetime, timezone
+from datetime import UTC, datetime
import pytest
-from app.services.domains.publications.types import PublicationListItem
from app.services.domains.publication_identifiers.types import DisplayIdentifier
+from app.services.domains.publications.types import PublicationListItem
from app.services.domains.unpaywall import application as unpaywall_app
@@ -35,7 +35,7 @@ def _item(publication_id: int) -> PublicationListItem:
display_identifier=None,
pdf_url=None,
is_read=False,
- first_seen_at=datetime.now(timezone.utc),
+ first_seen_at=datetime.now(UTC),
is_new_in_latest_run=True,
)
diff --git a/uv.lock b/uv.lock
index f4f139b..c151172 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,5 +1,5 @@
version = 1
-revision = 1
+revision = 3
requires-python = ">=3.12"
resolution-markers = [
"python_full_version >= '3.14'",
@@ -15,18 +15,18 @@ dependencies = [
{ name = "sqlalchemy" },
{ name = "typing-extensions" },
]
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version = "0.7.0"
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[[package]]
@@ -37,9 +37,9 @@ dependencies = [
{ name = "idna" },
{ name = "typing-extensions", marker = "python_full_version < '3.13'" },
]
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@@ -49,9 +49,9 @@ source = { registry = "https://pypi.org/simple" }
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@@ -923,8 +1059,10 @@ dependencies = [
[package.optional-dependencies]
dev = [
+ { name = "mypy" },
{ name = "pytest" },
{ name = "pytest-asyncio" },
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{ name = "python-multipart", specifier = ">=0.0.9,<0.1" },
{ name = "rapidfuzz", specifier = ">=3.14.3" },
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{ name = "uvicorn", extras = ["standard"], specifier = ">=0.34,<0.35" },
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