From bf04c77aa92642bb67402cf1ef6e753ebaf6ee4d Mon Sep 17 00:00:00 2001 From: Justin Visser Date: Thu, 26 Feb 2026 22:11:41 +0100 Subject: [PATCH] ci: add ruff linting and mypy type checking Add ruff and mypy to dev dependencies with configuration in pyproject.toml. Add a lint CI job that runs ruff check, ruff format --check, and mypy. Auto-fix import sorting and formatting across the codebase. Exclude alembic/versions from linting (auto-generated migrations). Ignore B008 (FastAPI Depends pattern) and RUF001 (unicode in user-facing strings). 21 ruff lint errors and 50 mypy errors remain for manual review. Co-Authored-By: Claude Opus 4.6 --- .github/workflows/ci.yml | 18 + MODERNIZATION_PLAN.md | 628 +++++++ alembic/env.py | 6 +- .../20260216_0001_multi_user_schema.py | 3 +- .../20260216_0002_add_user_admin_flag.py | 4 +- .../20260216_0003_add_ingestion_queue.py | 3 +- .../20260217_0004_queue_status_fields.py | 11 +- .../20260217_0005_manual_run_idempotency.py | 7 +- .../20260217_0006_scholar_profile_images.py | 3 +- ...7_0007_scholar_initial_page_fingerprint.py | 3 +- ...19_0008_user_settings_nav_visible_pages.py | 4 +- ..._0009_user_settings_scrape_safety_state.py | 2 +- ...0260219_0010_author_search_shared_state.py | 2 +- .../20260220_0011_add_publication_doi.py | 2 +- .../20260220_0012_add_data_repair_jobs.py | 2 +- .../20260221_0013_add_publication_pdf_jobs.py | 2 +- ..._add_scholar_publication_favorite_state.py | 2 +- ...260221_0015_enforce_request_delay_floor.py | 15 +- ...260222_0016_add_publication_identifiers.py | 2 +- ...8_add_openalex_enriched_to_publications.py | 13 +- ...0260224_0019_add_resolving_to_runstatus.py | 6 +- ...60224_0020_add_openalex_last_attempt_at.py | 11 +- ...0021_enforce_single_active_run_per_user.py | 6 +- ...dd_canonical_title_hash_to_publications.py | 2 +- .../20260226_0023_add_arxiv_runtime_state.py | 2 +- ...0226_0024_add_arxiv_query_cache_entries.py | 2 +- app/api/__init__.py | 1 - app/api/errors.py | 1 - app/api/routers/__init__.py | 1 - app/api/routers/admin.py | 32 +- app/api/routers/admin_dbops.py | 82 +- app/api/routers/auth.py | 20 +- app/api/routers/publications.py | 42 +- app/api/routers/runs.py | 84 +- app/api/routers/scholars.py | 70 +- app/api/routers/settings.py | 8 +- app/api/schemas.py | 14 +- app/auth/__init__.py | 1 - app/auth/deps.py | 1 - app/auth/runtime.py | 2 +- app/auth/security.py | 1 - app/auth/service.py | 4 +- app/auth/session.py | 1 - app/db/base.py | 5 +- app/db/models.py | 214 +-- app/db/session.py | 10 +- app/http/middleware.py | 16 +- app/logging_config.py | 8 +- app/logging_context.py | 2 - app/main.py | 24 +- app/security/__init__.py | 1 - app/security/csrf.py | 8 +- app/services/__init__.py | 1 - app/services/domains/arxiv/application.py | 2 +- app/services/domains/arxiv/cache.py | 64 +- app/services/domains/arxiv/client.py | 20 +- app/services/domains/arxiv/gateway.py | 2 +- app/services/domains/arxiv/rate_limit.py | 52 +- app/services/domains/crossref/application.py | 4 +- app/services/domains/dbops/__init__.py | 2 +- app/services/domains/dbops/application.py | 23 +- app/services/domains/dbops/integrity.py | 4 +- .../domains/dbops/near_duplicate_repair.py | 4 +- app/services/domains/dbops/query.py | 4 +- app/services/domains/ingestion/application.py | 372 +++-- .../domains/ingestion/fingerprints.py | 6 +- app/services/domains/ingestion/queue.py | 44 +- app/services/domains/ingestion/safety.py | 20 +- app/services/domains/ingestion/scheduler.py | 139 +- app/services/domains/openalex/client.py | 20 +- app/services/domains/openalex/matching.py | 27 +- app/services/domains/openalex/types.py | 12 +- .../domains/portability/application.py | 4 +- app/services/domains/portability/exporting.py | 8 +- app/services/domains/portability/normalize.py | 4 +- .../domains/portability/publication_import.py | 10 +- .../domains/portability/scholar_import.py | 8 +- .../publication_identifiers/__init__.py | 4 +- .../publication_identifiers/application.py | 18 +- .../domains/publications/application.py | 60 +- app/services/domains/publications/dedup.py | 18 +- .../domains/publications/enrichment.py | 15 +- app/services/domains/publications/listing.py | 5 +- .../domains/publications/pdf_queue.py | 45 +- .../publications/pdf_resolution_pipeline.py | 22 +- app/services/domains/publications/queries.py | 4 +- .../domains/publications/read_state.py | 6 +- app/services/domains/runs/application.py | 18 +- app/services/domains/runs/events.py | 17 +- app/services/domains/runs/queue_service.py | 4 +- app/services/domains/runs/runs_service.py | 4 +- app/services/domains/runs/summary.py | 10 +- app/services/domains/scholar/author_rows.py | 9 +- app/services/domains/scholar/parser.py | 11 - app/services/domains/scholar/profile_rows.py | 3 +- app/services/domains/scholar/source.py | 31 +- app/services/domains/scholars/application.py | 137 +- app/services/domains/scholars/constants.py | 30 +- app/services/domains/scholars/search_hints.py | 2 +- app/services/domains/scholars/validators.py | 4 +- app/services/domains/settings/application.py | 17 +- app/services/domains/unpaywall/application.py | 24 +- .../domains/unpaywall/pdf_discovery.py | 2 +- app/services/domains/users/application.py | 5 +- app/settings.py | 4 +- frontend/src/theme/presets/deutan-blue.js | 313 ++++ pyproject.toml | 20 + scripts/check_frontend_api_contract.py | 4 +- tests/conftest.py | 12 +- tests/integration/helpers.py | 1 + tests/integration/test_api_v1.py | 27 +- tests/integration/test_data_repair_jobs.py | 5 +- tests/integration/test_deferred_enrichment.py | 40 +- tests/integration/test_fixture_probe_runs.py | 3 +- tests/integration/test_migrations.py | 4 +- .../test_run_lifecycle_consistency.py | 6 +- tests/smoke/test_db_connectivity.py | 1 - tests/smoke/test_migration_schema.py | 2 +- .../unit/services/domains/arxiv/test_cache.py | 9 +- .../services/domains/arxiv/test_client.py | 25 +- .../services/domains/arxiv/test_guards.py | 4 +- .../services/domains/arxiv/test_parser.py | 4 +- .../services/domains/arxiv/test_rate_limit.py | 14 +- .../services/domains/openalex/test_client.py | 24 +- .../domains/openalex/test_matching.py | 46 +- .../domains/publications/test_dedup.py | 12 +- tests/unit/test_fingerprints.py | 91 +- tests/unit/test_ingestion_arxiv_rate_limit.py | 1 + tests/unit/test_logging.py | 2 +- .../unit/test_publication_pdf_queue_policy.py | 18 +- ...est_publication_pdf_resolution_pipeline.py | 8 +- tests/unit/test_request_delay_policy.py | 6 +- tests/unit/test_run_safety.py | 12 +- tests/unit/test_scholar_search_safety.py | 5 +- tests/unit/test_unpaywall_pdf_discovery.py | 6 +- tests/unit/test_unpaywall_resolution.py | 6 +- uv.lock | 1436 +++++++++-------- 137 files changed, 3066 insertions(+), 1900 deletions(-) create mode 100644 MODERNIZATION_PLAN.md create mode 100644 frontend/src/theme/presets/deutan-blue.js 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", 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