From 448b7da55e3422774e3f87b7c6ffac9b93e97fae Mon Sep 17 00:00:00 2001 From: Alejandro de la Vega Date: Thu, 5 Mar 2026 13:02:45 -0600 Subject: [PATCH 1/6] Don't fail fast by default,a nd update progress bar --- README.md | 2 +- elsevier_coordinate_extraction/cli/main.py | 10 +- .../cli/orchestrator.py | 3 +- tests/cli/test_main.py | 13 ++ tests/cli/test_orchestrator.py | 186 +++++++++++++++++- 5 files changed, 202 insertions(+), 12 deletions(-) create mode 100644 tests/cli/test_main.py diff --git a/README.md b/README.md index 85bbbc9..2bf8d97 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,7 @@ After installing the package, the `elsevier-extract` script becomes available vi - `--dois` for comma-separated DOIs or a text file containing one DOI per line - `--jsonl` for a JSON Lines file where each line is `{"doi": "...", "pmid": "..."}` -Additional flags allow users to skip writing specific outputs (`--skip-xml`, `--skip-text`, `--skip-tables`, `--skip-coordinates`), continue past failures (`--continue-on-error`), disable caching (`--no-cache`), or adjust verbosity (`-v/--verbose`, `-q/--quiet`). `--output-dir` controls the base directory for results, and the CLI honors `ELSEVIER_EXTRACTION_WORKERS` when no `--max-workers` override is provided. +Additional flags allow users to skip writing specific outputs (`--skip-xml`, `--skip-text`, `--skip-tables`, `--skip-coordinates`), continue past failures by default (`--continue-on-error`), opt into fail-fast behavior (`--fail-fast`), disable caching (`--no-cache`), or adjust verbosity (`-v/--verbose`, `-q/--quiet`). `--output-dir` controls the base directory for results, and the CLI honors `ELSEVIER_EXTRACTION_WORKERS` when no `--max-workers` override is provided. ### Output layout diff --git a/elsevier_coordinate_extraction/cli/main.py b/elsevier_coordinate_extraction/cli/main.py index 5a47da6..e3c2561 100644 --- a/elsevier_coordinate_extraction/cli/main.py +++ b/elsevier_coordinate_extraction/cli/main.py @@ -77,10 +77,18 @@ def create_parser() -> argparse.ArgumentParser: action="store_true", help="Skip writing coordinates JSON", ) + parser.set_defaults(continue_on_error=True) parser.add_argument( "--continue-on-error", action="store_true", - help="Keep going after failures", + dest="continue_on_error", + help="Keep going after failures (default)", + ) + parser.add_argument( + "--fail-fast", + action="store_false", + dest="continue_on_error", + help="Stop on first failed article extraction", ) parser.add_argument( "--max-workers", diff --git a/elsevier_coordinate_extraction/cli/orchestrator.py b/elsevier_coordinate_extraction/cli/orchestrator.py index 12ed936..a1cdcb2 100644 --- a/elsevier_coordinate_extraction/cli/orchestrator.py +++ b/elsevier_coordinate_extraction/cli/orchestrator.py @@ -43,7 +43,7 @@ async def process_articles( skip_text: bool = False, skip_tables: bool = False, skip_coordinates: bool = False, - continue_on_error: bool = False, + continue_on_error: bool = True, use_cache: bool = True, verbose: bool = False, ) -> Dict[str, int]: @@ -59,6 +59,7 @@ async def _progress_callback( article: ArticleContent | None, error: BaseException | None, ) -> None: + download_bar.update(1) if error is not None: downloaded_errors.append(record.copy()) download_exceptions.append(error) diff --git a/tests/cli/test_main.py b/tests/cli/test_main.py new file mode 100644 index 0000000..b79c43c --- /dev/null +++ b/tests/cli/test_main.py @@ -0,0 +1,13 @@ +from elsevier_coordinate_extraction.cli.main import create_parser + + +def test_parser_continues_on_error_by_default(): + parser = create_parser() + args = parser.parse_args(["--pmids", "12345678"]) + assert args.continue_on_error is True + + +def test_parser_fail_fast_overrides_continue_behavior(): + parser = create_parser() + args = parser.parse_args(["--pmids", "12345678", "--fail-fast"]) + assert args.continue_on_error is False diff --git a/tests/cli/test_orchestrator.py b/tests/cli/test_orchestrator.py index d72b798..1c21d03 100644 --- a/tests/cli/test_orchestrator.py +++ b/tests/cli/test_orchestrator.py @@ -4,8 +4,33 @@ import pytest from elsevier_coordinate_extraction.cli import orchestrator +from elsevier_coordinate_extraction.settings import Settings from elsevier_coordinate_extraction.types import build_article_content -from elsevier_coordinate_extraction.settings import get_settings + + +class DummyClient: + async def __aenter__(self): + return self + + async def __aexit__(self, exc_type, exc, tb): + return None + + +def build_settings(cache_dir: Path) -> Settings: + return Settings( + api_key="test-key", + base_url="https://api.elsevier.com/content", + timeout=30.0, + concurrency=1, + cache_dir=cache_dir, + user_agent="test-agent", + insttoken=None, + http_proxy=None, + https_proxy=None, + use_proxy=False, + max_rate_limit_wait=60.0, + extraction_workers=0, + ) @pytest.mark.asyncio @@ -22,13 +47,6 @@ async def fake_download(records, client, cache, progress_callback): await progress_callback(records[0], article, None) return [article] - class DummyClient: - async def __aenter__(self): - return self - - async def __aexit__(self, exc_type, exc, tb): - return None - monkeypatch.setattr(orchestrator, "download_articles", fake_download) monkeypatch.setattr( orchestrator, @@ -51,7 +69,7 @@ async def __aexit__(self, exc_type, exc, tb): lambda articles: {"studyset": {"studies": []}}, ) - settings = get_settings() + settings = build_settings(tmp_path / ".cache") stats = await orchestrator.process_articles( [{"doi": "10.1016/j.test"}], tmp_path, @@ -70,3 +88,153 @@ async def __aexit__(self, exc_type, exc, tb): assert manifest.exists() data = json.loads(manifest.read_text().strip()) assert data["status"] == "success" + + +@pytest.mark.asyncio +async def test_process_articles_updates_download_progress(tmp_path: Path, monkeypatch): + article = build_article_content( + doi="10.1016/j.test", + payload=b"", + content_type="application/xml", + format="xml", + metadata={"identifier_lookup": {"doi": "10.1016/j.test"}}, + ) + records = [{"doi": "10.1016/j.test"}, {"pmid": "12345678"}] + + async def fake_download(records, client, cache, progress_callback): + await progress_callback(records[0], article, None) + await progress_callback(records[1], None, None) + return [article] + + class FakeTqdm: + def __init__(self, iterable=None, total=None, **kwargs): + self.iterable = iterable + self.total = total + self.updates: list[int] = [] + + def update(self, value=1): + self.updates.append(value) + + def write(self, message): + return None + + def close(self): + return None + + def __iter__(self): + if self.iterable is None: + return iter(()) + return iter(self.iterable) + + bars = [] + + def fake_tqdm(*args, **kwargs): + iterable = args[0] if args else kwargs.pop("iterable", None) + bar = FakeTqdm(iterable=iterable, **kwargs) + bars.append(bar) + return bar + + monkeypatch.setattr(orchestrator, "download_articles", fake_download) + monkeypatch.setattr(orchestrator, "tqdm", fake_tqdm) + monkeypatch.setattr( + orchestrator, + "ScienceDirectClient", + lambda settings: DummyClient(), + ) + monkeypatch.setattr( + orchestrator, + "extract_text_from_article", + lambda payload: {"title": "stub"}, + ) + monkeypatch.setattr( + orchestrator, + "extract_tables_from_article", + lambda payload: [], + ) + monkeypatch.setattr( + orchestrator, + "extract_coordinates", + lambda articles: {"studyset": {"studies": []}}, + ) + + settings = build_settings(tmp_path / ".cache") + await orchestrator.process_articles( + records, + tmp_path, + settings=settings, + use_cache=False, + ) + + assert len(bars) == 2 + assert sum(bars[0].updates) == len(records) + + +@pytest.mark.asyncio +async def test_process_articles_continues_on_error_by_default(tmp_path: Path, monkeypatch): + first_article = build_article_content( + doi="10.1016/j.one", + payload=b"", + content_type="application/xml", + format="xml", + metadata={"identifier_lookup": {"doi": "10.1016/j.one"}}, + ) + second_article = build_article_content( + doi="10.1016/j.two", + payload=b"", + content_type="application/xml", + format="xml", + metadata={"identifier_lookup": {"doi": "10.1016/j.two"}}, + ) + records = [{"doi": "10.1016/j.one"}, {"doi": "10.1016/j.two"}] + + async def fake_download(records, client, cache, progress_callback): + await progress_callback(records[0], first_article, None) + await progress_callback(records[1], second_article, None) + return [first_article, second_article] + + calls = {"count": 0} + + def fake_extract_text(article): + calls["count"] += 1 + if calls["count"] == 1: + raise ValueError("failed to parse article") + return {"title": "stub"} + + monkeypatch.setattr(orchestrator, "download_articles", fake_download) + monkeypatch.setattr( + orchestrator, + "ScienceDirectClient", + lambda settings: DummyClient(), + ) + monkeypatch.setattr( + orchestrator, + "extract_text_from_article", + fake_extract_text, + ) + monkeypatch.setattr( + orchestrator, + "extract_tables_from_article", + lambda payload: [], + ) + monkeypatch.setattr( + orchestrator, + "extract_coordinates", + lambda articles: {"studyset": {"studies": []}}, + ) + + settings = build_settings(tmp_path / ".cache") + stats = await orchestrator.process_articles( + records, + tmp_path, + settings=settings, + use_cache=False, + ) + + assert stats["success"] == 1 + assert stats["failed"] == 1 + assert stats["skipped"] == 0 + + manifest = tmp_path / "manifest.jsonl" + statuses = [json.loads(line)["status"] for line in manifest.read_text().splitlines()] + assert statuses.count("success") == 1 + assert statuses.count("failed") == 1 From 02f4e7a3230902f9b19874724f251d669b7149a3 Mon Sep 17 00:00:00 2001 From: Alejandro de la Vega Date: Thu, 5 Mar 2026 13:03:27 -0600 Subject: [PATCH 2/6] Fix pyproject env install --- pyproject.toml | 4 +- uv.lock | 2455 ++++++++++++++++++++++++++++++------------------ 2 files changed, 1542 insertions(+), 917 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f3f66fe..2c2e06d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ description = "Search, download, and extract stereotactic coordinates from Scien authors = [ { name = "elsevier Coordinate Extraction Team" } ] -requires-python = ">=3.9" +requires-python = ">=3.10" dependencies = [ "httpx[http2]>=0.27.0", "python-dotenv>=1.0.1", @@ -54,7 +54,7 @@ norecursedirs = [ asyncio_mode = "auto" [tool.ruff] -target-version = "py39" +target-version = "py310" line-length = 100 extend-exclude = [ "pubget", diff --git a/uv.lock b/uv.lock index 213ac27..6cfb8bb 100644 --- a/uv.lock +++ b/uv.lock @@ -1,14 +1,13 @@ version = 1 -requires-python = ">=3.9" +revision = 3 +requires-python = ">=3.10" resolution-markers = [ - "python_full_version < '3.10' and platform_python_implementation == 'PyPy'", - "python_full_version < '3.10' and platform_python_implementation != 'PyPy'", - "python_full_version == '3.10.*' and platform_python_implementation == 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13:03:41 -0600 Subject: [PATCH 3/6] Update orchestrator tests --- tests/cli/test_orchestrator.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/tests/cli/test_orchestrator.py b/tests/cli/test_orchestrator.py index 1c21d03..a795ef1 100644 --- a/tests/cli/test_orchestrator.py +++ b/tests/cli/test_orchestrator.py @@ -235,6 +235,9 @@ def fake_extract_text(article): assert stats["skipped"] == 0 manifest = tmp_path / "manifest.jsonl" - statuses = [json.loads(line)["status"] for line in manifest.read_text().splitlines()] + statuses = [ + json.loads(line)["status"] + for line in manifest.read_text().splitlines() + ] assert statuses.count("success") == 1 assert statuses.count("failed") == 1 From b0292a2f0d9f9410ab4c21ebf242aeda38b13f63 Mon Sep 17 00:00:00 2001 From: Alejandro de la Vega Date: Tue, 17 Mar 2026 15:42:53 -0500 Subject: [PATCH 4/6] Add Springer API to library --- .env.example | 6 + README.md | 19 +- .../cli/orchestrator.py | 67 ++- elsevier_coordinate_extraction/cli/outputs.py | 6 + elsevier_coordinate_extraction/client.py | 10 +- .../download/api.py | 238 ++++++++++- .../extract/coordinates.py | 49 +-- .../extract/text.py | 88 ++++ elsevier_coordinate_extraction/pubmed.py | 146 +++++++ elsevier_coordinate_extraction/settings.py | 14 + .../springer_client.py | 176 ++++++++ .../table_extraction.py | 190 ++++++++- tests/cli/test_orchestrator.py | 77 +++- tests/download/test_api.py | 387 +++++++++++++++++- tests/extract/conftest.py | 11 +- tests/extract/test_coordinates.py | 33 ++ tests/extract/test_text.py | 40 ++ tests/test_pubmed.py | 97 +++++ tests/test_settings.py | 21 + tests/test_table_extraction.py | 33 ++ 20 files changed, 1630 insertions(+), 78 deletions(-) create mode 100644 elsevier_coordinate_extraction/pubmed.py create mode 100644 elsevier_coordinate_extraction/springer_client.py create mode 100644 tests/test_pubmed.py create mode 100644 tests/test_table_extraction.py diff --git a/.env.example b/.env.example index e99f6ff..e82bb1f 100644 --- a/.env.example +++ b/.env.example @@ -2,3 +2,9 @@ ELSEVIER_API_KEY=YOUR_API_KEY ELSEVIER_HTTP_PROXY=socks5://127.0.0.1:1080 ELSEVIER_HTTPS_PROXY=socks5://127.0.0.1:1080 ELSEVIER_USE_PROXY=false + +# Optional Springer Open Access + PubMed fallback settings +SPRINGER_API_KEY= +SPRINGER_BASE_URL=https://api.springernature.com +PUBMED_BASE_URL=https://eutils.ncbi.nlm.nih.gov/entrez/eutils +NCBI_API_KEY= diff --git a/README.md b/README.md index 2bf8d97..a191289 100644 --- a/README.md +++ b/README.md @@ -39,8 +39,19 @@ After installing the package, the `elsevier-extract` script becomes available vi - `--dois` for comma-separated DOIs or a text file containing one DOI per line - `--jsonl` for a JSON Lines file where each line is `{"doi": "...", "pmid": "..."}` +Download order is fixed to `Elsevier -> Springer Open Access`: + +- Elsevier full-text is attempted first for DOI/PMID records. +- On Elsevier miss, PMID-only records are resolved to DOI via NCBI ESummary and retried against Springer Open Access (`/openaccess/json` + `/openaccess/jats`). + Additional flags allow users to skip writing specific outputs (`--skip-xml`, `--skip-text`, `--skip-tables`, `--skip-coordinates`), continue past failures by default (`--continue-on-error`), opt into fail-fast behavior (`--fail-fast`), disable caching (`--no-cache`), or adjust verbosity (`-v/--verbose`, `-q/--quiet`). `--output-dir` controls the base directory for results, and the CLI honors `ELSEVIER_EXTRACTION_WORKERS` when no `--max-workers` override is provided. +### Environment Variables + +- Required: `ELSEVIER_API_KEY` +- Optional Springer fallback: `SPRINGER_API_KEY`, `SPRINGER_BASE_URL` +- Optional PubMed resolution: `PUBMED_BASE_URL`, `NCBI_API_KEY` + ### Output layout Each article is saved under `output-dir/{identifier}` where `{identifier}` is the filesystem-friendly DOI (slashes replaced with `_`) or PMID. Inside that directory you will find: @@ -51,4 +62,10 @@ Each article is saved under `output-dir/{identifier}` where `{identifier}` is th - `coordinates.json` – NIMADS-style evaluation of extracted coordinates - `tables/*.csv` – extracted tables named after their labels/captions -The CLI also appends every run to `manifest.jsonl` (with status, timing, and file list) and records failures in `errors.jsonl`, enabling audit and resumable processing. +The CLI also appends every run to `manifest.jsonl` (with status, source provider, timing, file list, and a `reason` field for skipped entries) and records failures in `errors.jsonl` (including provider source), enabling audit and resumable processing. Springer/PubMed skip reasons include: + +- `springer_unconfigured` +- `pmid_to_doi_unresolved` +- `springer_not_found` +- `springer_jats_unavailable` +- `springer_rate_limited` diff --git a/elsevier_coordinate_extraction/cli/orchestrator.py b/elsevier_coordinate_extraction/cli/orchestrator.py index a1cdcb2..636508c 100644 --- a/elsevier_coordinate_extraction/cli/orchestrator.py +++ b/elsevier_coordinate_extraction/cli/orchestrator.py @@ -4,6 +4,7 @@ from pathlib import Path from typing import Dict, List +import httpx from tqdm import tqdm from elsevier_coordinate_extraction.cache import FileCache @@ -34,6 +35,36 @@ Record = Dict[str, str] +def _normalize_source(value: object) -> str | None: + if isinstance(value, str): + lowered = value.strip().lower() + if lowered in {"elsevier", "springer"}: + return lowered + return None + + +def _infer_source_from_error( + error: BaseException | None, + reason: str | None, +) -> str | None: + if reason: + if reason == "pmid_to_doi_unresolved" or reason.startswith("springer_"): + return "springer" + if reason.startswith("elsevier_") or reason == "not_found_404": + return "elsevier" + + if isinstance(error, httpx.HTTPStatusError): + request = error.request or getattr(error.response, "request", None) + if request is not None: + host = request.url.host or "" + lowered = host.lower() + if "springernature.com" in lowered: + return "springer" + if "elsevier.com" in lowered: + return "elsevier" + return None + + async def process_articles( records: List[Record], output_dir: Path, @@ -50,9 +81,8 @@ async def process_articles( output_dir.mkdir(parents=True, exist_ok=True) cache = FileCache(output_dir / ".cache") if use_cache else None - downloaded_errors: List[Record] = [] - download_exceptions: List[Exception] = [] - skipped_records: List[Record] = [] + downloaded_errors: List[tuple[Record, Exception, str | None]] = [] + skipped_records: List[tuple[Record, str, str | None]] = [] async def _progress_callback( record: Record, @@ -61,10 +91,17 @@ async def _progress_callback( ) -> None: download_bar.update(1) if error is not None: - downloaded_errors.append(record.copy()) - download_exceptions.append(error) + reason = getattr(error, "skip_reason", None) + source = _infer_source_from_error(error, reason if isinstance(reason, str) else None) + if isinstance(reason, str) and reason: + skipped_records.append((record.copy(), reason, source)) + else: + if isinstance(error, Exception): + downloaded_errors.append((record.copy(), error, source)) + else: + downloaded_errors.append((record.copy(), Exception(str(error)), source)) elif article is None: - skipped_records.append(record.copy()) + skipped_records.append((record.copy(), "not_found_404", "elsevier")) stats = {"success": 0, "failed": 0, "skipped": 0} @@ -74,6 +111,7 @@ async def _progress_callback( records, client=client, cache=cache, + settings=settings, progress_callback=_progress_callback, ) download_bar.close() @@ -84,6 +122,7 @@ async def _progress_callback( article.metadata.get("identifier_lookup") or {"doi": article.doi} ) + source = _normalize_source(article.metadata.get("provider")) start = time.monotonic() files_written: List[Path] = [] try: @@ -115,8 +154,10 @@ async def _progress_callback( output_dir, record=record, status="success", + source=source, files=files_written, error=None, + reason=None, duration=duration, ) stats["success"] += 1 @@ -129,11 +170,13 @@ async def _progress_callback( output_dir, record=record, status="failed", + source=source, files=files_written, error=str(exc), + reason=None, duration=duration, ) - append_error_entry(output_dir, record=record, error=exc) + append_error_entry(output_dir, record=record, error=exc, source=source) stats["failed"] += 1 extract_bar.write(f"Error processing {record}: {exc}") if not continue_on_error: @@ -141,25 +184,29 @@ async def _progress_callback( raise extract_bar.close() - for record, error in zip(downloaded_errors, download_exceptions): + for record, error, source in downloaded_errors: append_manifest_entry( output_dir, record=record, status="failed", + source=source, files=[], error=str(error), + reason=None, duration=0.0, ) - append_error_entry(output_dir, record=record, error=error) + append_error_entry(output_dir, record=record, error=error, source=source) stats["failed"] += 1 - for record in skipped_records: + for record, reason, source in skipped_records: append_manifest_entry( output_dir, record=record, status="skipped", + source=source, files=[], error=None, + reason=reason, duration=0.0, ) stats["skipped"] += 1 diff --git a/elsevier_coordinate_extraction/cli/outputs.py b/elsevier_coordinate_extraction/cli/outputs.py index 7778e10..e1b7611 100644 --- a/elsevier_coordinate_extraction/cli/outputs.py +++ b/elsevier_coordinate_extraction/cli/outputs.py @@ -94,8 +94,10 @@ def append_manifest_entry( *, record: Dict[str, str], status: str, + source: str | None, files: list[Path], error: str | None, + reason: str | None, duration: float, ) -> None: manifest_path = output_dir / "manifest.jsonl" @@ -104,8 +106,10 @@ def append_manifest_entry( "timestamp": datetime.utcnow().isoformat() + "Z", "identifier": record, "status": status, + "source": source, "files": [str(path.relative_to(output_dir)) for path in files], "error": error, + "reason": reason, "duration_seconds": round(duration, 3), } with manifest_path.open("a", encoding="utf-8") as fh: @@ -117,11 +121,13 @@ def append_error_entry( *, record: Dict[str, str], error: Exception, + source: str | None, ) -> None: errors_path = output_dir / "errors.jsonl" entry = { "timestamp": datetime.utcnow().isoformat() + "Z", "identifier": record, + "source": source, "error_type": type(error).__name__, "error_message": str(error), } diff --git a/elsevier_coordinate_extraction/client.py b/elsevier_coordinate_extraction/client.py index 558c5a3..42ed297 100644 --- a/elsevier_coordinate_extraction/client.py +++ b/elsevier_coordinate_extraction/client.py @@ -14,6 +14,14 @@ __all__ = ["ScienceDirectClient"] +def _http2_enabled() -> bool: + try: + import h2 # noqa: F401 + except ImportError: + return False + return True + + class ScienceDirectClient: """Thin wrapper around httpx.AsyncClient with Elsevier defaults.""" @@ -96,7 +104,7 @@ async def _ensure_client(self) -> None: "timeout": timeout, "headers": headers, "transport": self._transport, - "http2": True, + "http2": _http2_enabled(), } if self._settings.use_proxy: proxy_value = self._settings.https_proxy or self._settings.http_proxy diff --git a/elsevier_coordinate_extraction/download/api.py b/elsevier_coordinate_extraction/download/api.py index 83480ab..e3827da 100644 --- a/elsevier_coordinate_extraction/download/api.py +++ b/elsevier_coordinate_extraction/download/api.py @@ -2,6 +2,7 @@ from __future__ import annotations +from contextlib import AsyncExitStack import inspect import re from collections.abc import Awaitable, Mapping, Sequence @@ -9,10 +10,12 @@ import httpx from lxml import etree +from urllib.parse import urlparse from elsevier_coordinate_extraction import rate_limits from elsevier_coordinate_extraction.client import ScienceDirectClient -from urllib.parse import urlparse +from elsevier_coordinate_extraction.pubmed import PubMedResolver +from elsevier_coordinate_extraction.springer_client import SpringerOpenAccessClient from elsevier_coordinate_extraction.settings import Settings, get_settings from elsevier_coordinate_extraction.types import ArticleContent, build_article_content @@ -57,10 +60,20 @@ def __call__( ) -> Awaitable[None] | None: ... +class DownloadSkip(RuntimeError): + """Raised when a record should be skipped with a specific reason.""" + + def __init__(self, reason: str, message: str | None = None) -> None: + self.skip_reason = reason + super().__init__(message or reason) + + async def download_articles( records: Sequence[Mapping[str, str]], *, client: ScienceDirectClient | None = None, + springer_client: SpringerOpenAccessClient | None = None, + pubmed_resolver: PubMedResolver | None = None, cache: Any | None = None, cache_namespace: str = "articles", settings: Settings | None = None, @@ -85,6 +98,10 @@ async def download_articles( cfg = settings or get_settings() owns_client = client is None sci_client = client or ScienceDirectClient(cfg) + owns_springer_client = springer_client is None + springer_oa_client = springer_client or SpringerOpenAccessClient(cfg) + owns_pubmed_resolver = pubmed_resolver is None + pmid_resolver = pubmed_resolver or PubMedResolver(cfg) async def _emit_progress( record: Mapping[str, str], @@ -104,7 +121,10 @@ async def _runner() -> list[ArticleContent]: try: article = await _download_record( record=record, - client=sci_client, + settings=cfg, + elsevier_client=sci_client, + springer_client=springer_oa_client, + pubmed_resolver=pmid_resolver, cache=cache, cache_namespace=cache_namespace, ) @@ -118,13 +138,81 @@ async def _runner() -> list[ArticleContent]: await _emit_progress(record, article, None) return results - if owns_client: - async with sci_client: - return await _runner() - return await _runner() + async with AsyncExitStack() as stack: + if owns_client: + await stack.enter_async_context(sci_client) + if owns_springer_client: + await stack.enter_async_context(springer_oa_client) + if owns_pubmed_resolver: + await stack.enter_async_context(pmid_resolver) + return await _runner() async def _download_record( + record: Mapping[str, str], + *, + settings: Settings, + elsevier_client: ScienceDirectClient, + springer_client: SpringerOpenAccessClient, + pubmed_resolver: PubMedResolver, + cache: Any | None, + cache_namespace: str, +) -> ArticleContent | None: + doi = (record.get("doi") or "").strip() + pmid = (record.get("pmid") or "").strip() + + article = await _download_elsevier_record( + record=record, + client=elsevier_client, + cache=cache, + cache_namespace=cache_namespace, + ) + if article is not None: + return article + + if not settings.springer_api_key: + raise DownloadSkip("springer_unconfigured") + + resolved_doi = doi + if not resolved_doi: + if not pmid: + raise DownloadSkip("pmid_to_doi_unresolved") + try: + resolved = await pubmed_resolver.resolve_doi(pmid) + except Exception as exc: # pragma: no cover - network/transport dependent + raise DownloadSkip("pmid_to_doi_unresolved") from exc + if not resolved: + raise DownloadSkip("pmid_to_doi_unresolved") + resolved_doi = resolved + + springer_record = await _fetch_springer_metadata_record( + doi=resolved_doi, + client=springer_client, + ) + if springer_record is None: + raise DownloadSkip("springer_not_found") + + try: + springer_article = await _download_springer_jats( + doi=resolved_doi, + record=springer_record, + client=springer_client, + cache=cache, + cache_namespace=cache_namespace, + ) + except httpx.HTTPStatusError as exc: + if _is_rate_limited_error(exc): + raise DownloadSkip("springer_rate_limited") from exc + raise + if springer_article is None: + raise DownloadSkip("springer_jats_unavailable") + + springer_article.metadata.setdefault("identifier_lookup", dict(record)) + return springer_article + + +async def _download_elsevier_record( + *, record: Mapping[str, str], client: ScienceDirectClient, cache: Any | None, @@ -166,6 +254,103 @@ async def _download_record( return None +async def _fetch_springer_metadata_record( + *, + doi: str, + client: SpringerOpenAccessClient, +) -> dict[str, Any] | None: + try: + data = await client.get_json( + "/openaccess/json", + params={ + "q": f"doi:{doi}", + "s": "1", + "p": "1", + }, + ) + except httpx.HTTPStatusError as exc: + if exc.response.status_code == 404: + return None + if _is_rate_limited_error(exc): + raise DownloadSkip("springer_rate_limited") from exc + raise + records = data.get("records") + if not isinstance(records, list) or not records: + return None + first = records[0] + if not isinstance(first, Mapping): + return None + return dict(first) + + +async def _download_springer_jats( + *, + doi: str, + record: Mapping[str, Any], + client: SpringerOpenAccessClient, + cache: Any | None, + cache_namespace: str, +) -> ArticleContent | None: + cache_key = f"springer-jats:doi:{doi}" + payload: bytes | None = None + content_type = "application/xml" + metadata: dict[str, Any] = { + "provider": "springer", + "source_api": "openaccess", + "resolved_doi": doi, + "springer_record": _summarize_springer_record(record), + } + + if cache is not None: + cached = await cache.get(cache_namespace, cache_key) + if cached is not None: + payload = cached + metadata["transport"] = "cache" + + if payload is None: + try: + response = await client.request( + "GET", + "/openaccess/jats", + params={ + "q": f"doi:{doi}", + "s": "1", + "p": "1", + }, + accept="application/xml", + ) + except httpx.HTTPStatusError as exc: + if exc.response.status_code == 404: + return None + raise + payload = response.content + content_type = response.headers.get("content-type", "application/xml") + metadata.update( + { + "transport": response.request.url.scheme, + "status_code": response.status_code, + } + ) + snapshot = rate_limits.get_rate_limit_snapshot(response) + metadata.update(snapshot.to_metadata()) + if cache is not None: + await cache.set(cache_namespace, cache_key, payload) + + if not _payload_contains_springer_full_text(payload): + return None + + extracted_doi = _extract_doi(payload) + metadata["full_text_retrieved"] = True + metadata["doi"] = extracted_doi or doi + return build_article_content( + doi=extracted_doi or doi, + payload=payload, + content_type=content_type, + format="xml", + metadata=metadata, + ) + + async def _download_identifier( *, identifier: str, @@ -256,6 +441,7 @@ async def _download_identifier( metadata["view_obtained"] = inferred_view metadata["view"] = inferred_view metadata["full_text_retrieved"] = full_text + metadata.setdefault("provider", "elsevier") pii = _extract_pii(payload) metadata.setdefault("pii", pii) @@ -272,6 +458,7 @@ async def _download_identifier( article_doi = identifier else: article_doi = extracted_doi or identifier + metadata.setdefault("resolved_doi", article_doi) return build_article_content( doi=article_doi, @@ -416,6 +603,39 @@ def _guess_cdn_url(api_url: str, extension: str | None) -> str | None: return f"{_CDN_BASE}/{filename}" +def _summarize_springer_record(record: Mapping[str, Any]) -> dict[str, Any]: + fields = ( + "identifier", + "doi", + "title", + "publicationName", + "journalTitle", + "publicationDate", + ) + summary: dict[str, Any] = {} + for field in fields: + value = record.get(field) + if value: + summary[field] = value + return summary + + +def _payload_contains_springer_full_text(payload: bytes) -> bool: + try: + root = etree.fromstring(payload) + except etree.XMLSyntaxError: + return False + body_present = root.xpath( + './/*[local-name()="body" or local-name()="sec" or local-name()="p"]' + ) + if body_present: + return True + table_present = root.xpath( + './/*[local-name()="table-wrap" or local-name()="table"]' + ) + return bool(table_present) + + def _is_invalid_view_error(response: httpx.Response) -> bool: """Detect Elsevier errors indicating the requested view is unsupported.""" @@ -427,3 +647,9 @@ def _is_invalid_view_error(response: httpx.Response) -> bool: except Exception: # pragma: no cover - defensive fallback return False return "view" in body_text and "not valid" in body_text + + +def _is_rate_limited_error(exc: httpx.HTTPStatusError) -> bool: + """Return True when the failure is an HTTP 429/rate-limit response.""" + response = exc.response + return response is not None and response.status_code == 429 diff --git a/elsevier_coordinate_extraction/extract/coordinates.py b/elsevier_coordinate_extraction/extract/coordinates.py index dc5a1c2..7460f42 100644 --- a/elsevier_coordinate_extraction/extract/coordinates.py +++ b/elsevier_coordinate_extraction/extract/coordinates.py @@ -12,11 +12,18 @@ from pubget._coordinate_space import _neurosynth_guess_space from pubget._coordinates import _extract_coordinates_from_table -from elsevier_coordinate_extraction.table_extraction import extract_tables_from_article +from elsevier_coordinate_extraction.table_extraction import ( + extract_tables_from_article, + extract_tables_generic, +) from elsevier_coordinate_extraction.types import ArticleContent, TableMetadata from elsevier_coordinate_extraction import settings +if not hasattr(pd.DataFrame, "applymap") and hasattr(pd.DataFrame, "map"): + pd.DataFrame.applymap = pd.DataFrame.map # type: ignore[attr-defined] + + def extract_coordinates(articles: Iterable[ArticleContent]) -> dict: """Extract coordinate tables from the supplied articles.""" @@ -24,8 +31,11 @@ def extract_coordinates(articles: Iterable[ArticleContent]) -> dict: if not article_list: return {"studyset": {"studies": []}} - cfg = settings.get_settings() - user_workers = cfg.extraction_workers + try: + cfg = settings.get_settings() + except RuntimeError: + cfg = None + user_workers = cfg.extraction_workers if cfg is not None else 0 if user_workers <= 0: worker_count = min(len(article_list), max(os.cpu_count() or 1, 1)) else: @@ -161,38 +171,7 @@ def _article_text(payload: bytes) -> str: def _manual_extract_tables(payload: bytes) -> list[Tuple[TableMetadata, pd.DataFrame]]: - parser = etree.XMLParser(remove_blank_text=True) - try: - root = etree.fromstring(payload, parser=parser) - except etree.XMLSyntaxError: - return [] - tables: list[Tuple[TableMetadata, pd.DataFrame]] = [] - for table in root.xpath('.//*[local-name()="table"]'): - parent = table.getparent() - context = parent if parent is not None else table - label = _first_text(context, './/*[local-name()="label"]') - caption = _first_text(context, './/*[local-name()="caption"]') - legend = _first_text(context, './/*[local-name()="legend"]') - foot = _first_text( - context, - './/*[local-name()="table-foot" or local-name()="table-wrap-foot"]', - ) - identifier = table.get("id") - df = _table_to_dataframe(table) - if df is None or df.empty: - continue - raw_element = parent if parent is not None else table - raw_xml = etree.tostring(raw_element, encoding="unicode") - metadata = TableMetadata( - label=label, - identifier=identifier, - caption=caption, - legend=legend, - foot=foot, - raw_xml=raw_xml, - ) - tables.append((metadata, df)) - return tables + return extract_tables_generic(payload) def _first_text(node: etree._Element, xpath: str) -> str | None: diff --git a/elsevier_coordinate_extraction/extract/text.py b/elsevier_coordinate_extraction/extract/text.py index 46583b2..6b0c6c7 100644 --- a/elsevier_coordinate_extraction/extract/text.py +++ b/elsevier_coordinate_extraction/extract/text.py @@ -65,6 +65,9 @@ def extract_text_from_article( except etree.XMLSyntaxError as exc: raise TextExtractionError("Article payload is not valid XML.") from exc + if _is_jats_document(document): + return _extract_text_from_jats(document) + stylesheet = _load_text_stylesheet() try: transformed = stylesheet(document) @@ -83,6 +86,91 @@ def extract_text_from_article( } +def _is_jats_document(root: etree._Element) -> bool: + namespace_uri = etree.QName(root).namespace or "" + if "jats" in namespace_uri.lower(): + return True + if root.xpath('.//*[local-name()="article-title" or local-name()="kwd-group"]'): + return True + return bool( + root.xpath('.//*[local-name()="article-id" and @pub-id-type="doi"]') + ) + + +def _extract_text_from_jats(root: etree._Element) -> dict[str, str | None]: + doi = _first_xpath_text( + root, + './/*[local-name()="article-id" and @pub-id-type="doi"][1]', + ) + pii = _first_xpath_text( + root, + './/*[local-name()="article-id" and @pub-id-type="pii"][1]', + ) + title = _first_xpath_text( + root, + ( + './/*[local-name()="article-title" or local-name()="chapter-title" ' + 'or local-name()="book-title"][1]' + ), + ) + abstract_blocks = _collect_block_text( + root.xpath('.//*[local-name()="abstract"]') + ) + body_blocks = _collect_block_text( + root.xpath('.//*[local-name()="body"]') + ) + if not body_blocks: + body_blocks = _collect_block_text(root.xpath('.//*[local-name()="sec"]')) + + keyword_values = [ + " ".join(str(value).split()) + for value in root.xpath('.//*[local-name()="kwd"]//text()') + if str(value).strip() + ] + deduped_keywords: list[str] = [] + for keyword in keyword_values: + if keyword and keyword not in deduped_keywords: + deduped_keywords.append(keyword) + + return { + "doi": _clean_doi(doi), + "pii": _clean_field(pii), + "title": _clean_field(title), + "keywords": _clean_keywords("\n".join(deduped_keywords) if deduped_keywords else None), + "abstract": _clean_block("\n\n".join(abstract_blocks) if abstract_blocks else None), + "body": _clean_block("\n\n".join(body_blocks) if body_blocks else None), + } + + +def _first_xpath_text(root: etree._Element, xpath: str) -> str | None: + results = root.xpath(xpath) + if not results: + return None + node = results[0] + if isinstance(node, etree._Element): + return "".join(node.itertext()).strip() or None + text = str(node).strip() + return text or None + + +def _collect_block_text(nodes: list[etree._Element]) -> list[str]: + blocks: list[str] = [] + for node in nodes: + paragraph_nodes = node.xpath('.//*[local-name()="p"]') + if paragraph_nodes: + paragraph_text = [ + " ".join("".join(p.itertext()).split()) + for p in paragraph_nodes + if "".join(p.itertext()).strip() + ] + combined = "\n".join(paragraph_text).strip() + else: + combined = " ".join("".join(node.itertext()).split()).strip() + if combined: + blocks.append(combined) + return blocks + + def format_article_text(extracted: Mapping[str, str | None]) -> str: """Compose a plain-text article document from extracted text fields.""" diff --git a/elsevier_coordinate_extraction/pubmed.py b/elsevier_coordinate_extraction/pubmed.py new file mode 100644 index 0000000..dee6362 --- /dev/null +++ b/elsevier_coordinate_extraction/pubmed.py @@ -0,0 +1,146 @@ +"""PubMed identifier resolution helpers.""" + +from __future__ import annotations + +from collections.abc import Mapping +from typing import Any + +import httpx + +from .settings import Settings + +__all__ = ["PubMedResolver"] + + +def _http2_enabled() -> bool: + try: + import h2 # noqa: F401 + except ImportError: + return False + return True + + +class PubMedResolver: + """Resolve article identifiers from PubMed E-utilities.""" + + def __init__( + self, + settings: Settings, + *, + transport: httpx.AsyncBaseTransport | None = None, + ) -> None: + self._settings = settings + self._transport = transport + self._client: httpx.AsyncClient | None = None + self._cache: dict[str, str | None] = {} + + async def __aenter__(self) -> PubMedResolver: + await self._ensure_client() + return self + + async def __aexit__(self, exc_type, exc, tb) -> None: # type: ignore[override] + if self._client is not None: + await self._client.aclose() + self._client = None + + async def resolve_doi(self, pmid: str) -> str | None: + """Resolve DOI for a PMID via NCBI ESummary.""" + normalized = pmid.strip() + if not normalized: + return None + if normalized in self._cache: + return self._cache[normalized] + await self._ensure_client() + assert self._client is not None + params: dict[str, str] = { + "db": "pubmed", + "id": normalized, + "retmode": "json", + } + if self._settings.ncbi_api_key: + params["api_key"] = self._settings.ncbi_api_key + response = await self._client.get("/esummary.fcgi", params=params) + response.raise_for_status() + payload = response.json() + doi = _extract_doi_from_esummary(payload, normalized) + self._cache[normalized] = doi + return doi + + async def _ensure_client(self) -> None: + if self._client is not None: + return + timeout = httpx.Timeout(self._settings.timeout) + headers = {"User-Agent": self._settings.user_agent} + client_kwargs: dict[str, Any] = { + "base_url": self._settings.pubmed_base_url, + "timeout": timeout, + "headers": headers, + "transport": self._transport, + "http2": _http2_enabled(), + } + if self._settings.use_proxy: + proxy_value = self._settings.https_proxy or self._settings.http_proxy + if proxy_value: + client_kwargs["proxy"] = proxy_value + else: + client_kwargs["trust_env"] = False + self._client = httpx.AsyncClient(**client_kwargs) + + +def _extract_doi_from_esummary( + payload: Mapping[str, Any], + pmid: str, +) -> str | None: + result = payload.get("result") + if not isinstance(result, Mapping): + return None + + record_obj = result.get(pmid) + if not isinstance(record_obj, Mapping): + for uid in _iter_uids(result): + candidate = result.get(uid) + if isinstance(candidate, Mapping): + record_obj = candidate + break + if not isinstance(record_obj, Mapping): + return None + + direct_doi = _normalize_doi(record_obj.get("doi")) + if direct_doi: + return direct_doi + + article_ids = record_obj.get("articleids") + if not isinstance(article_ids, list): + return None + for article_id in article_ids: + if not isinstance(article_id, Mapping): + continue + id_type = str(article_id.get("idtype", "")).strip().lower() + value = article_id.get("value") + normalized = _normalize_doi(value) + if not normalized: + continue + if id_type in {"doi", "elocationid"}: + return normalized + return None + + +def _iter_uids(result: Mapping[str, Any]) -> list[str]: + uids = result.get("uids") + if not isinstance(uids, list): + return [] + return [str(uid) for uid in uids if uid] + + +def _normalize_doi(value: Any) -> str | None: + if value is None: + return None + text = str(value).strip() + if not text: + return None + lower = text.lower() + if lower.startswith("doi:"): + text = text.split(":", 1)[1].strip() + if not text.startswith("10."): + return None + return text diff --git a/elsevier_coordinate_extraction/settings.py b/elsevier_coordinate_extraction/settings.py index bb2d763..b51db5a 100644 --- a/elsevier_coordinate_extraction/settings.py +++ b/elsevier_coordinate_extraction/settings.py @@ -10,6 +10,8 @@ from dotenv import load_dotenv _DEFAULT_BASE_URL: Final[str] = "https://api.elsevier.com/content" +_DEFAULT_SPRINGER_BASE_URL: Final[str] = "https://api.springernature.com" +_DEFAULT_PUBMED_BASE_URL: Final[str] = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" _DEFAULT_TIMEOUT: Final[float] = 30.0 _DEFAULT_CONCURRENCY: Final[int] = 4 _DEFAULT_CACHE_DIR: Final[str] = ".elsevier_cache" @@ -36,6 +38,10 @@ class Settings: use_proxy: bool max_rate_limit_wait: float | None extraction_workers: int + springer_api_key: str | None = None + springer_base_url: str = _DEFAULT_SPRINGER_BASE_URL + pubmed_base_url: str = _DEFAULT_PUBMED_BASE_URL + ncbi_api_key: str | None = None _TRUE_VALUES: Final[set[str]] = {"1", "true", "yes", "on"} @@ -75,6 +81,10 @@ def get_settings(*, force_reload: bool = False) -> Settings: ) base_url = os.getenv("ELSEVIER_BASE_URL", _DEFAULT_BASE_URL) + springer_base_url = os.getenv("SPRINGER_BASE_URL", _DEFAULT_SPRINGER_BASE_URL) + pubmed_base_url = os.getenv("PUBMED_BASE_URL", _DEFAULT_PUBMED_BASE_URL) + springer_api_key = os.getenv("SPRINGER_API_KEY") + ncbi_api_key = os.getenv("NCBI_API_KEY") timeout = float(os.getenv("ELSEVIER_TIMEOUT", _DEFAULT_TIMEOUT)) concurrency = int(os.getenv("ELSEVIER_CONCURRENCY", _DEFAULT_CONCURRENCY)) cache_dir_raw = os.getenv("ELSEVIER_CACHE_DIR", _DEFAULT_CACHE_DIR) @@ -113,5 +123,9 @@ def get_settings(*, force_reload: bool = False) -> Settings: use_proxy=use_proxy, max_rate_limit_wait=max_rate_limit_wait, extraction_workers=int(os.getenv("ELSEVIER_EXTRACTION_WORKERS", _DEFAULT_EXTRACTION_WORKERS)), + springer_api_key=springer_api_key, + springer_base_url=springer_base_url, + pubmed_base_url=pubmed_base_url, + ncbi_api_key=ncbi_api_key, ) return _CACHED_SETTINGS diff --git a/elsevier_coordinate_extraction/springer_client.py b/elsevier_coordinate_extraction/springer_client.py new file mode 100644 index 0000000..85a44b1 --- /dev/null +++ b/elsevier_coordinate_extraction/springer_client.py @@ -0,0 +1,176 @@ +"""Async Springer Open Access client built on httpx.""" + +from __future__ import annotations + +import asyncio +from collections.abc import Mapping +from typing import Any + +import httpx + +from . import rate_limits +from .settings import Settings + +__all__ = ["SpringerOpenAccessClient"] + + +def _http2_enabled() -> bool: + try: + import h2 # noqa: F401 + except ImportError: + return False + return True + + +class SpringerOpenAccessClient: + """Thin wrapper around httpx.AsyncClient for Springer OA endpoints.""" + + def __init__( + self, + settings: Settings, + *, + transport: httpx.AsyncBaseTransport | None = None, + max_retries: int = 3, + ) -> None: + self._settings = settings + self._transport = transport + self._max_retries = max(0, max_retries) + self._client: httpx.AsyncClient | None = None + concurrency = settings.concurrency or 1 + self._semaphore = asyncio.Semaphore(concurrency) + + async def __aenter__(self) -> SpringerOpenAccessClient: + await self._ensure_client() + return self + + async def __aexit__(self, exc_type, exc, tb) -> None: # type: ignore[override] + if self._client is not None: + await self._client.aclose() + self._client = None + + async def request( + self, + method: str, + path: str, + *, + params: Mapping[str, Any] | None = None, + accept: str | None = None, + ) -> httpx.Response: + """Perform an HTTP request and return the response.""" + return await self._request(method, path, params=params, accept=accept) + + async def get_json( + self, + path: str, + *, + params: Mapping[str, Any] | None = None, + ) -> dict[str, Any]: + """Perform a GET request expecting JSON.""" + response = await self.request( + "GET", + path, + params=params, + accept="application/json", + ) + return response.json() + + async def get_xml( + self, + path: str, + *, + params: Mapping[str, Any] | None = None, + ) -> str: + """Perform a GET request expecting XML.""" + response = await self.request( + "GET", + path, + params=params, + accept="application/xml", + ) + return response.text + + async def _ensure_client(self) -> None: + if self._client is not None: + return + headers: dict[str, str] = {"User-Agent": self._settings.user_agent} + timeout = httpx.Timeout(self._settings.timeout) + client_kwargs: dict[str, Any] = { + "base_url": self._settings.springer_base_url, + "timeout": timeout, + "headers": headers, + "transport": self._transport, + "http2": _http2_enabled(), + } + if self._settings.use_proxy: + proxy_value = self._settings.https_proxy or self._settings.http_proxy + if proxy_value: + client_kwargs["proxy"] = proxy_value + else: + client_kwargs["trust_env"] = False + self._client = httpx.AsyncClient(**client_kwargs) + + def _build_params( + self, + params: Mapping[str, Any] | None, + ) -> dict[str, Any]: + if not self._settings.springer_api_key: + raise RuntimeError( + "SPRINGER_API_KEY is required to query Springer Open Access API." + ) + merged = dict(params or {}) + merged.setdefault("api_key", self._settings.springer_api_key) + return merged + + async def _request( + self, + method: str, + path: str, + *, + params: Mapping[str, Any] | None, + accept: str | None, + ) -> httpx.Response: + await self._ensure_client() + assert self._client is not None + attempt = 0 + request_params = self._build_params(params) + while True: + request_headers = {"Accept": accept} if accept else {} + async with self._semaphore: + response = await self._client.request( + method, + path, + params=request_params, + headers=request_headers, + ) + delay = rate_limits.get_retry_delay(response) + max_wait = self._settings.max_rate_limit_wait + if ( + delay is not None + and response.status_code == 429 + and max_wait is not None + and delay > max_wait + ): + snapshot = rate_limits.get_rate_limit_snapshot(response) + wait_seconds = snapshot.seconds_until_reset() or delay + retry_after = response.headers.get("Retry-After") + raise httpx.HTTPStatusError( + "Springer OpenAccess rate limit wait " + f"({wait_seconds:g}s) exceeds configured maximum ({max_wait:g}s). " + "Likely quota exhaustion. " + f"Retry-After={retry_after!r}, " + f"X-RateLimit-Limit={snapshot.limit}, " + f"X-RateLimit-Remaining={snapshot.remaining}, " + f"X-RateLimit-Reset={snapshot.reset_epoch}.", + request=response.request, + response=response, + ) + if ( + delay is not None + and response.status_code in {429, 500, 503} + and attempt < self._max_retries + ): + await asyncio.sleep(delay) + attempt += 1 + continue + response.raise_for_status() + return response diff --git a/elsevier_coordinate_extraction/table_extraction.py b/elsevier_coordinate_extraction/table_extraction.py index cb6cbce..0493878 100644 --- a/elsevier_coordinate_extraction/table_extraction.py +++ b/elsevier_coordinate_extraction/table_extraction.py @@ -3,7 +3,7 @@ import io from functools import lru_cache from importlib import resources -from typing import List, Tuple +from typing import Any, List, Tuple import pandas as pd from lxml import etree @@ -29,8 +29,52 @@ def extract_tables_from_article(payload: bytes) -> List[Tuple[TableMetadata, pd. document = etree.fromstring(payload) transformed = stylesheet(document) # type: ignore[arg-type] except Exception: + return extract_tables_generic(payload) + extracted = _parse_extracted_tables(transformed.getroot()) + if extracted: + return extracted + return extract_tables_generic(payload) + + +def extract_tables_generic(payload: bytes) -> List[Tuple[TableMetadata, pd.DataFrame]]: + """Fallback table extraction that supports JATS and generic XML tables.""" + parser = etree.XMLParser(remove_blank_text=True) + try: + root = etree.fromstring(payload, parser=parser) + except etree.XMLSyntaxError: return [] - return _parse_extracted_tables(transformed.getroot()) + + tables: list[Tuple[TableMetadata, pd.DataFrame]] = [] + seen: set[int] = set() + candidates = root.xpath( + './/*[local-name()="table-wrap" or local-name()="table" or local-name()="table-wrap-group"]' + ) + for candidate in candidates: + table_node, context_node = _resolve_table_node(candidate) + if table_node is None: + continue + marker = id(table_node) + if marker in seen: + continue + seen.add(marker) + + dataframe = _table_to_dataframe(table_node) + if dataframe is None or dataframe.empty: + continue + + metadata = TableMetadata( + label=_first_text(context_node, './/*[local-name()="label"]'), + identifier=table_node.get("id") or context_node.get("id"), + caption=_first_text(context_node, './/*[local-name()="caption"]'), + legend=_first_text(context_node, './/*[local-name()="legend"]'), + foot=_first_text( + context_node, + './/*[local-name()="table-foot" or local-name()="table-wrap-foot"]', + ), + raw_xml=etree.tostring(context_node, encoding="unicode"), + ) + tables.append((metadata, dataframe)) + return tables def _parse_extracted_tables(root: etree._Element) -> List[Tuple[TableMetadata, pd.DataFrame]]: @@ -74,3 +118,145 @@ def _text(tag: str) -> str | None: foot=_text("table-wrap-foot"), raw_xml=raw_xml, ) + + +def _resolve_table_node( + candidate: etree._Element, +) -> tuple[etree._Element | None, etree._Element]: + local_name = etree.QName(candidate).localname + if local_name == "table": + return candidate, candidate + table_nodes = candidate.xpath('.//*[local-name()="table"]') + if not table_nodes: + return None, candidate + return table_nodes[0], candidate + + +def _first_text(node: etree._Element, xpath: str) -> str | None: + matches = node.xpath(xpath) + if not matches: + return None + first = matches[0] + if not isinstance(first, etree._Element): + text = str(first).strip() + return text or None + text = " ".join(first.itertext()).strip() + return text or None + + +def _table_to_dataframe(table: etree._Element) -> pd.DataFrame | None: + ns_cals = {"cals": "http://www.elsevier.com/xml/common/cals/dtd"} + tgroups = table.xpath("./cals:tgroup", namespaces=ns_cals) + if tgroups: + dataframe = _cals_table_to_dataframe(tgroups[0]) + if dataframe is not None: + return dataframe + + row_elements = table.xpath('.//*[local-name()="tr"]') + cell_xpath = './*[local-name()="th" or local-name()="td"]' + if not row_elements: + row_elements = table.xpath('.//*[local-name()="row"]') + cell_xpath = './*[local-name()="entry"]' + rows: list[list[str]] = [] + for row in row_elements: + cells = [" ".join(cell.itertext()).strip() for cell in row.xpath(cell_xpath)] + if cells: + rows.append(cells) + if len(rows) <= 1: + return None + max_len = max(len(row) for row in rows) + normalized = [row + [""] * (max_len - len(row)) for row in rows] + header = normalized[0] + data = normalized[1:] + return pd.DataFrame(data, columns=[str(value) for value in header]) + + +def _cals_table_to_dataframe(tgroup: etree._Element) -> pd.DataFrame | None: + ns = {"cals": "http://www.elsevier.com/xml/common/cals/dtd"} + colspecs = tgroup.xpath("./cals:colspec", namespaces=ns) + if not colspecs: + return None + col_order = [ + spec.get("colname") or f"col{idx + 1}" + for idx, spec in enumerate(colspecs) + ] + col_index = {name: idx for idx, name in enumerate(col_order)} + column_count = len(col_order) + + def _rows(xpath: str) -> list[etree._Element]: + return tgroup.xpath(xpath, namespaces=ns) + + row_elements = _rows("./cals:thead/cals:row") + _rows("./cals:tbody/cals:row") + if not row_elements: + row_elements = _rows(".//cals:row") + if not row_elements: + return None + + pending: list[dict[str, Any] | None] = [None] * column_count + grid: list[list[str]] = [] + + for row in row_elements: + values = ["" for _ in range(column_count)] + filled = [False] * column_count + for idx, span in enumerate(pending): + if span is None: + continue + values[idx] = span["text"] + filled[idx] = True + span["remaining"] -= 1 + if span["remaining"] <= 0: + pending[idx] = None + + pointer = 0 + for cell in row: + if cell.tag.split("}")[-1] != "entry": + continue + text = " ".join(cell.itertext()).strip() + rowspan_raw = cell.get("morerows") + try: + rowspan = int(rowspan_raw) + 1 if rowspan_raw is not None else 1 + except ValueError: + rowspan = 1 + + if "colname" in cell.attrib: + start = col_index.get(cell.attrib["colname"], pointer) + elif "namest" in cell.attrib: + start = col_index.get(cell.attrib["namest"], pointer) + else: + while pointer < column_count and filled[pointer]: + pointer += 1 + start = pointer + + span = 1 + if "nameend" in cell.attrib: + end = col_index.get(cell.attrib["nameend"], start) + span = max(1, end - start + 1) + elif "colspan" in cell.attrib: + colspan_raw = cell.attrib["colspan"] + try: + span = max(1, int(colspan_raw)) + except ValueError: + span = 1 + + if start >= column_count: + continue + for offset in range(span): + idx = start + offset + if idx >= column_count: + break + values[idx] = text if offset == 0 else "" + filled[idx] = True + pointer = max(pointer, start + span) + + if rowspan > 1: + for offset in range(span): + idx = start + offset + if idx >= column_count: + continue + pending[idx] = {"text": text, "remaining": rowspan - 1} + + grid.append(values) + + if len(grid) <= 1: + return None + return pd.DataFrame(grid, columns=col_order) diff --git a/tests/cli/test_orchestrator.py b/tests/cli/test_orchestrator.py index a795ef1..57cbc4b 100644 --- a/tests/cli/test_orchestrator.py +++ b/tests/cli/test_orchestrator.py @@ -30,6 +30,10 @@ def build_settings(cache_dir: Path) -> Settings: use_proxy=False, max_rate_limit_wait=60.0, extraction_workers=0, + springer_api_key=None, + springer_base_url="https://api.springernature.com", + pubmed_base_url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils", + ncbi_api_key=None, ) @@ -40,10 +44,13 @@ async def test_process_articles_creates_outputs(tmp_path: Path, monkeypatch): payload=b"", content_type="application/xml", format="xml", - metadata={"identifier_lookup": {"doi": "10.1016/j.test"}}, + metadata={ + "identifier_lookup": {"doi": "10.1016/j.test"}, + "provider": "elsevier", + }, ) - async def fake_download(records, client, cache, progress_callback): + async def fake_download(records, client, cache, settings, progress_callback): await progress_callback(records[0], article, None) return [article] @@ -88,6 +95,7 @@ async def fake_download(records, client, cache, progress_callback): assert manifest.exists() data = json.loads(manifest.read_text().strip()) assert data["status"] == "success" + assert data["source"] == "elsevier" @pytest.mark.asyncio @@ -97,11 +105,14 @@ async def test_process_articles_updates_download_progress(tmp_path: Path, monkey payload=b"", content_type="application/xml", format="xml", - metadata={"identifier_lookup": {"doi": "10.1016/j.test"}}, + metadata={ + "identifier_lookup": {"doi": "10.1016/j.test"}, + "provider": "elsevier", + }, ) records = [{"doi": "10.1016/j.test"}, {"pmid": "12345678"}] - async def fake_download(records, client, cache, progress_callback): + async def fake_download(records, client, cache, settings, progress_callback): await progress_callback(records[0], article, None) await progress_callback(records[1], None, None) return [article] @@ -158,15 +169,23 @@ def fake_tqdm(*args, **kwargs): ) settings = build_settings(tmp_path / ".cache") - await orchestrator.process_articles( + stats = await orchestrator.process_articles( records, tmp_path, settings=settings, use_cache=False, ) + assert stats["skipped"] == 1 assert len(bars) == 2 assert sum(bars[0].updates) == len(records) + manifest = tmp_path / "manifest.jsonl" + entries = [json.loads(line) for line in manifest.read_text().splitlines()] + skipped_entries = [entry for entry in entries if entry["status"] == "skipped"] + assert len(skipped_entries) == 1 + assert skipped_entries[0]["identifier"] == {"pmid": "12345678"} + assert skipped_entries[0]["reason"] == "not_found_404" + assert skipped_entries[0]["source"] == "elsevier" @pytest.mark.asyncio @@ -176,18 +195,24 @@ async def test_process_articles_continues_on_error_by_default(tmp_path: Path, mo payload=b"", content_type="application/xml", format="xml", - metadata={"identifier_lookup": {"doi": "10.1016/j.one"}}, + metadata={ + "identifier_lookup": {"doi": "10.1016/j.one"}, + "provider": "elsevier", + }, ) second_article = build_article_content( doi="10.1016/j.two", payload=b"", content_type="application/xml", format="xml", - metadata={"identifier_lookup": {"doi": "10.1016/j.two"}}, + metadata={ + "identifier_lookup": {"doi": "10.1016/j.two"}, + "provider": "elsevier", + }, ) records = [{"doi": "10.1016/j.one"}, {"doi": "10.1016/j.two"}] - async def fake_download(records, client, cache, progress_callback): + async def fake_download(records, client, cache, settings, progress_callback): await progress_callback(records[0], first_article, None) await progress_callback(records[1], second_article, None) return [first_article, second_article] @@ -241,3 +266,39 @@ def fake_extract_text(article): ] assert statuses.count("success") == 1 assert statuses.count("failed") == 1 + + +@pytest.mark.asyncio +async def test_process_articles_marks_skip_reason_from_download(tmp_path: Path, monkeypatch): + class SkipError(RuntimeError): + skip_reason = "springer_jats_unavailable" + + async def fake_download(records, client, cache, settings, progress_callback): + await progress_callback(records[0], None, SkipError("no jats")) + return [] + + monkeypatch.setattr(orchestrator, "download_articles", fake_download) + monkeypatch.setattr( + orchestrator, + "ScienceDirectClient", + lambda settings: DummyClient(), + ) + + settings = build_settings(tmp_path / ".cache") + stats = await orchestrator.process_articles( + [{"doi": "10.1007/example"}], + tmp_path, + settings=settings, + use_cache=False, + ) + + assert stats["success"] == 0 + assert stats["failed"] == 0 + assert stats["skipped"] == 1 + + manifest = tmp_path / "manifest.jsonl" + entries = [json.loads(line) for line in manifest.read_text().splitlines()] + assert len(entries) == 1 + assert entries[0]["status"] == "skipped" + assert entries[0]["reason"] == "springer_jats_unavailable" + assert entries[0]["source"] == "springer" diff --git a/tests/download/test_api.py b/tests/download/test_api.py index d1bef20..3f9ff47 100644 --- a/tests/download/test_api.py +++ b/tests/download/test_api.py @@ -17,9 +17,30 @@ def _test_settings() -> Settings: - """Return a Settings copy that disables proxies for mock transports.""" + """Return deterministic Settings for mock transport tests.""" - cfg = settings.get_settings() + return Settings( + api_key="test-api-key", + base_url="https://api.elsevier.com/content", + timeout=30.0, + concurrency=4, + cache_dir=Path(".elsevier_cache").resolve(), + user_agent="elsevierCoordinateExtraction/tests", + insttoken=None, + http_proxy=None, + https_proxy=None, + use_proxy=False, + max_rate_limit_wait=3600.0, + extraction_workers=0, + springer_api_key=None, + springer_base_url="https://api.springernature.com", + pubmed_base_url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils", + ncbi_api_key=None, + ) + + +def _test_settings_with_springer() -> Settings: + cfg = _test_settings() return Settings( api_key=cfg.api_key, base_url=cfg.base_url, @@ -28,11 +49,37 @@ def _test_settings() -> Settings: cache_dir=cfg.cache_dir, user_agent=cfg.user_agent, insttoken=cfg.insttoken, - http_proxy=None, - https_proxy=None, - use_proxy=False, + http_proxy=cfg.http_proxy, + https_proxy=cfg.https_proxy, + use_proxy=cfg.use_proxy, + max_rate_limit_wait=cfg.max_rate_limit_wait, + extraction_workers=cfg.extraction_workers, + springer_api_key="springer-key", + springer_base_url=cfg.springer_base_url, + pubmed_base_url=cfg.pubmed_base_url, + ncbi_api_key=cfg.ncbi_api_key, + ) + + +def _test_settings_without_springer() -> Settings: + cfg = _test_settings() + return Settings( + api_key=cfg.api_key, + base_url=cfg.base_url, + timeout=cfg.timeout, + concurrency=cfg.concurrency, + cache_dir=cfg.cache_dir, + user_agent=cfg.user_agent, + insttoken=cfg.insttoken, + http_proxy=cfg.http_proxy, + https_proxy=cfg.https_proxy, + use_proxy=cfg.use_proxy, max_rate_limit_wait=cfg.max_rate_limit_wait, extraction_workers=cfg.extraction_workers, + springer_api_key=None, + springer_base_url=cfg.springer_base_url, + pubmed_base_url=cfg.pubmed_base_url, + ncbi_api_key=cfg.ncbi_api_key, ) @@ -40,10 +87,15 @@ def _test_settings() -> Settings: @pytest.mark.vcr() async def test_download_single_article_xml(test_dois: Sequence[str]) -> None: """Download an article by DOI and return the XML payload.""" - cfg = settings.get_settings() + try: + cfg = settings.get_settings() + except RuntimeError as exc: + if "ELSEVIER_API_KEY" in str(exc): + pytest.skip("ELSEVIER_API_KEY unavailable for live download test.") + raise records = [{"doi": test_dois[0]}] async with ScienceDirectClient(cfg) as client: - articles = await download_articles(records, client=client) + articles = await download_articles(records, client=client, settings=cfg) assert len(articles) == 1 article = articles[0] assert isinstance(article, ArticleContent) @@ -90,7 +142,12 @@ def progress_cb( progress_calls.append((record, article, error)) async with ScienceDirectClient(cfg, transport=transport) as client: - articles = await download_articles([{"doi": doi}], client=client, progress_callback=progress_cb) + articles = await download_articles( + [{"doi": doi}], + client=client, + settings=cfg, + progress_callback=progress_cb, + ) assert len(captured_requests) == 1 assert articles == [] @@ -132,7 +189,12 @@ def progress_cb( progress_calls.append((record, article, error)) async with ScienceDirectClient(cfg, transport=transport) as client: - articles = await download_articles([{"doi": doi}], client=client, progress_callback=progress_cb) + articles = await download_articles( + [{"doi": doi}], + client=client, + settings=cfg, + progress_callback=progress_cb, + ) assert articles == [] assert len(progress_calls) == 1 @@ -169,7 +231,7 @@ async def set(self, namespace: str, key: str, data: bytes) -> None: cached_key = f"doi:{test_dois[0]}" stub_cache.data[cached_key] = cached_payload - cfg = settings.get_settings() + cfg = _test_settings() async def handler(request: httpx.Request) -> httpx.Response: raise AssertionError("HTTP transport should not be called when cache hits.") @@ -179,6 +241,7 @@ async def handler(request: httpx.Request) -> httpx.Response: articles = await download_articles( [{"doi": test_dois[0]}], client=client, + settings=cfg, cache=stub_cache, cache_namespace="articles", ) @@ -239,7 +302,11 @@ async def request( ) client = StubClient() - articles = await download_articles([{"pmid": pmid}], client=client) # type: ignore[arg-type] + articles = await download_articles( + [{"pmid": pmid}], + client=client, # type: ignore[arg-type] + settings=_test_settings(), + ) assert len(articles) == 1 article = articles[0] @@ -289,7 +356,12 @@ def progress_cb( progress_calls.append((record, article, error)) async with ScienceDirectClient(cfg, transport=transport) as client: - articles = await download_articles(records, client=client, progress_callback=progress_cb) + articles = await download_articles( + records, + client=client, + settings=cfg, + progress_callback=progress_cb, + ) assert len(articles) == len(records) assert len(progress_calls) == len(records) @@ -320,7 +392,12 @@ async def progress_cb( progress_calls.append((record, article, error)) async with ScienceDirectClient(cfg, transport=transport) as client: - articles = await download_articles([{"doi": doi}], client=client, progress_callback=progress_cb) + articles = await download_articles( + [{"doi": doi}], + client=client, + settings=cfg, + progress_callback=progress_cb, + ) assert articles == [] assert len(progress_calls) == 1 @@ -373,7 +450,12 @@ def progress_cb( records = [{"doi": bad_doi}, {"doi": good_doi}] async with ScienceDirectClient(cfg, transport=transport) as client: - articles = await download_articles(records, client=client, progress_callback=progress_cb) + articles = await download_articles( + records, + client=client, + settings=cfg, + progress_callback=progress_cb, + ) assert len(articles) == 1 assert articles[0].doi == good_doi @@ -384,3 +466,280 @@ def progress_cb( assert progress_calls[1][0]["doi"] == good_doi assert progress_calls[1][1] is not None assert progress_calls[1][2] is None + + +@pytest.mark.asyncio() +async def test_download_falls_back_to_springer_after_elsevier_not_found() -> None: + doi = "10.1007/s00123-001-0001-1" + call_order: list[str] = [] + + class StubElsevierClient: + async def request(self, method: str, path: str, **kwargs) -> httpx.Response: + call_order.append("elsevier") + request = httpx.Request(method, f"https://api.elsevier.com/content{path}") + response = httpx.Response(404, request=request) + raise httpx.HTTPStatusError("not found", request=request, response=response) + + class StubSpringerClient: + async def get_json( + self, + path: str, + *, + params: dict[str, str] | None = None, + ) -> dict[str, object]: + call_order.append("springer-metadata") + assert path == "/openaccess/json" + assert params == {"q": f"doi:{doi}", "s": "1", "p": "1"} + return {"records": [{"doi": doi, "title": "Springer Test"}]} + + async def request( + self, + method: str, + path: str, + *, + params: dict[str, str] | None = None, + accept: str | None = None, + ) -> httpx.Response: + call_order.append("springer-jats") + assert method == "GET" + assert path == "/openaccess/jats" + assert params == {"q": f"doi:{doi}", "s": "1", "p": "1"} + assert accept == "application/xml" + payload = b""" +
+ 10.1007/s00123-001-0001-1 +

Springer full text

 +
+ """.strip() + request = httpx.Request(method, "https://api.springernature.com/openaccess/jats") + return httpx.Response( + 200, + request=request, + content=payload, + headers={"content-type": "application/xml"}, + ) + + class StubPubMedResolver: + async def resolve_doi(self, pmid: str) -> str | None: + raise AssertionError("PMID resolver should not be called for DOI input.") + + articles = await download_articles( + [{"doi": doi}], + client=StubElsevierClient(), # type: ignore[arg-type] + springer_client=StubSpringerClient(), # type: ignore[arg-type] + pubmed_resolver=StubPubMedResolver(), # type: ignore[arg-type] + settings=_test_settings_with_springer(), + ) + + assert len(articles) == 1 + article = articles[0] + assert article.doi == doi + assert article.metadata["provider"] == "springer" + assert article.metadata["resolved_doi"] == doi + assert call_order == ["elsevier", "springer-metadata", "springer-jats"] + + +@pytest.mark.asyncio() +async def test_download_resolves_pmid_to_doi_for_springer_fallback() -> None: + pmid = "31262544" + resolved_doi = "10.1007/s00429-024-10000-1" + + class StubElsevierClient: + async def request(self, method: str, path: str, **kwargs) -> httpx.Response: + request = httpx.Request(method, f"https://api.elsevier.com/content{path}") + response = httpx.Response(404, request=request) + raise httpx.HTTPStatusError("not found", request=request, response=response) + + class StubSpringerClient: + async def get_json( + self, + path: str, + *, + params: dict[str, str] | None = None, + ) -> dict[str, object]: + assert path == "/openaccess/json" + assert params == {"q": f"doi:{resolved_doi}", "s": "1", "p": "1"} + return {"records": [{"doi": resolved_doi, "title": "Resolved DOI"}]} + + async def request( + self, + method: str, + path: str, + *, + params: dict[str, str] | None = None, + accept: str | None = None, + ) -> httpx.Response: + payload = f""" +
+ {resolved_doi} +

Body text

 +
+ """.encode("utf-8") + request = httpx.Request(method, "https://api.springernature.com/openaccess/jats") + return httpx.Response( + 200, + request=request, + content=payload, + headers={"content-type": "application/xml"}, + ) + + class StubPubMedResolver: + def __init__(self) -> None: + self.calls: list[str] = [] + + async def resolve_doi(self, value: str) -> str | None: + self.calls.append(value) + return resolved_doi + + resolver = StubPubMedResolver() + articles = await download_articles( + [{"pmid": pmid}], + client=StubElsevierClient(), # type: ignore[arg-type] + springer_client=StubSpringerClient(), # type: ignore[arg-type] + pubmed_resolver=resolver, # type: ignore[arg-type] + settings=_test_settings_with_springer(), + ) + + assert len(articles) == 1 + assert resolver.calls == [pmid] + assert articles[0].metadata["provider"] == "springer" + assert articles[0].metadata["resolved_doi"] == resolved_doi + + +@pytest.mark.asyncio() +async def test_download_reports_skip_reason_when_springer_jats_missing() -> None: + doi = "10.1007/s12345-6789-0" + progress_calls: list[tuple[dict[str, str], ArticleContent | None, BaseException | None]] = [] + + class StubElsevierClient: + async def request(self, method: str, path: str, **kwargs) -> httpx.Response: + request = httpx.Request(method, f"https://api.elsevier.com/content{path}") + response = httpx.Response(404, request=request) + raise httpx.HTTPStatusError("not found", request=request, response=response) + + class StubSpringerClient: + async def get_json( + self, + path: str, + *, + params: dict[str, str] | None = None, + ) -> dict[str, object]: + return {"records": [{"doi": doi, "title": "Metadata only"}]} + + async def request( + self, + method: str, + path: str, + *, + params: dict[str, str] | None = None, + accept: str | None = None, + ) -> httpx.Response: + payload = b"0" + request = httpx.Request(method, "https://api.springernature.com/openaccess/jats") + return httpx.Response( + 200, + request=request, + content=payload, + headers={"content-type": "application/xml"}, + ) + + def progress_cb( + record: dict[str, str], + article: ArticleContent | None, + error: BaseException | None, + ) -> None: + progress_calls.append((record, article, error)) + + articles = await download_articles( + [{"doi": doi}], + client=StubElsevierClient(), # type: ignore[arg-type] + springer_client=StubSpringerClient(), # type: ignore[arg-type] + settings=_test_settings_with_springer(), + progress_callback=progress_cb, + ) + assert articles == [] + assert len(progress_calls) == 1 + _, article, error = progress_calls[0] + assert article is None + assert error is not None + assert getattr(error, "skip_reason", None) == "springer_jats_unavailable" + + +@pytest.mark.asyncio() +async def test_download_reports_skip_reason_when_springer_unconfigured() -> None: + doi = "10.1007/s12345-6789-1" + progress_calls: list[tuple[dict[str, str], ArticleContent | None, BaseException | None]] = [] + + class StubElsevierClient: + async def request(self, method: str, path: str, **kwargs) -> httpx.Response: + request = httpx.Request(method, f"https://api.elsevier.com/content{path}") + response = httpx.Response(404, request=request) + raise httpx.HTTPStatusError("not found", request=request, response=response) + + def progress_cb( + record: dict[str, str], + article: ArticleContent | None, + error: BaseException | None, + ) -> None: + progress_calls.append((record, article, error)) + + articles = await download_articles( + [{"doi": doi}], + client=StubElsevierClient(), # type: ignore[arg-type] + settings=_test_settings_without_springer(), + progress_callback=progress_cb, + ) + assert articles == [] + assert len(progress_calls) == 1 + _, article, error = progress_calls[0] + assert article is None + assert error is not None + assert getattr(error, "skip_reason", None) == "springer_unconfigured" + + +@pytest.mark.asyncio() +async def test_download_reports_skip_reason_when_springer_rate_limited() -> None: + doi = "10.1007/s12345-6789-2" + progress_calls: list[tuple[dict[str, str], ArticleContent | None, BaseException | None]] = [] + + class StubElsevierClient: + async def request(self, method: str, path: str, **kwargs) -> httpx.Response: + request = httpx.Request(method, f"https://api.elsevier.com/content{path}") + response = httpx.Response(404, request=request) + raise httpx.HTTPStatusError("not found", request=request, response=response) + + class StubSpringerClient: + async def get_json( + self, + path: str, + *, + params: dict[str, str] | None = None, + ) -> dict[str, object]: + request = httpx.Request("GET", "https://api.springernature.com/openaccess/json") + response = httpx.Response(429, request=request) + raise httpx.HTTPStatusError( + "Rate limit reset wait exceeds configured maximum (3600s).", + request=request, + response=response, + ) + + def progress_cb( + record: dict[str, str], + article: ArticleContent | None, + error: BaseException | None, + ) -> None: + progress_calls.append((record, article, error)) + + articles = await download_articles( + [{"doi": doi}], + client=StubElsevierClient(), # type: ignore[arg-type] + springer_client=StubSpringerClient(), # type: ignore[arg-type] + settings=_test_settings_with_springer(), + progress_callback=progress_cb, + ) + assert articles == [] + assert len(progress_calls) == 1 + _, article, error = progress_calls[0] + assert article is None + assert error is not None + assert getattr(error, "skip_reason", None) == "springer_rate_limited" diff --git a/tests/extract/conftest.py b/tests/extract/conftest.py index 9a77ac0..96c3bd3 100644 --- a/tests/extract/conftest.py +++ b/tests/extract/conftest.py @@ -25,7 +25,14 @@ def downloaded_articles( identifiers = test_dois if identifier_type == "doi" else sample_test_pmids async def _download() -> list[ArticleContent]: - cfg = settings.get_settings() + try: + cfg = settings.get_settings() + except RuntimeError as exc: + if "ELSEVIER_API_KEY" in str(exc): + pytest.skip( + "ELSEVIER_API_KEY unavailable for extraction integration tests." + ) + raise async with ScienceDirectClient(cfg) as client: try: records = [{identifier_type: value} for value in identifiers] @@ -39,6 +46,8 @@ async def _download() -> list[ArticleContent]: return list(article_list) articles = asyncio.run(_download()) + if not articles: + pytest.skip("No downloadable articles available for extraction integration tests.") if identifier_type == "pmid": for identifier, article in zip(identifiers, articles): assert article.metadata.get("identifier") == identifier diff --git a/tests/extract/test_coordinates.py b/tests/extract/test_coordinates.py index 549cbe3..f3b3586 100644 --- a/tests/extract/test_coordinates.py +++ b/tests/extract/test_coordinates.py @@ -128,3 +128,36 @@ def test_extract_coordinates_from_synthetic_table() -> None: assert len(points) == 2 assert points[0]["coordinates"] == [10.0, 20.0, 30.0] assert points[0]["space"] == "MNI" + + +def test_extract_coordinates_from_synthetic_jats_table() -> None: + payload = b""" +
+ + + + + + + + + + + +
xyz
10-2030
-121842
+ MNI coordinates + + +
+ """ + article = build_article_content( + doi="10.1007/jats-002", + payload=payload, + content_type="application/xml", + format="xml", + metadata={"provider": "springer"}, + ) + result = extract_coordinates([article]) + points = _find_points(result) + assert len(points) == 2 + assert points[0]["coordinates"] == [10.0, -20.0, 30.0] diff --git a/tests/extract/test_text.py b/tests/extract/test_text.py index 3997b1e..3603bb9 100644 --- a/tests/extract/test_text.py +++ b/tests/extract/test_text.py @@ -56,3 +56,43 @@ def test_extract_text_invalid_payload() -> None: with pytest.raises(TextExtractionError): extract_text_from_article(b"") + + +def test_extract_text_from_jats_payload() -> None: + payload = b""" +
+ + + 10.1007/jats-001 + + JATS Example Title + + + fmri + coordinates + + +

Abstract sentence one.

+ + + + + +

Body sentence one.

+ + +
+ """.strip() + article = build_article_content( + doi="10.1007/jats-001", + payload=payload, + content_type="application/xml", + format="xml", + metadata={"provider": "springer"}, + ) + extracted = extract_text_from_article(article) + assert extracted["doi"] == "10.1007/jats-001" + assert extracted["title"] == "JATS Example Title" + assert extracted["abstract"] and "Abstract sentence one." in extracted["abstract"] + assert extracted["body"] and "Body sentence one." in extracted["body"] + assert extracted["keywords"] and "fmri" in extracted["keywords"] diff --git a/tests/test_pubmed.py b/tests/test_pubmed.py new file mode 100644 index 0000000..16d3e81 --- /dev/null +++ b/tests/test_pubmed.py @@ -0,0 +1,97 @@ +"""Tests for PubMed DOI resolution.""" + +from __future__ import annotations + +from pathlib import Path + +import httpx +import pytest + +from elsevier_coordinate_extraction.pubmed import PubMedResolver +from elsevier_coordinate_extraction.settings import Settings + + +def _settings() -> Settings: + return Settings( + api_key="test-elsevier", + base_url="https://api.elsevier.com/content", + timeout=30.0, + concurrency=2, + cache_dir=Path("."), + user_agent="test-agent", + insttoken=None, + http_proxy=None, + https_proxy=None, + use_proxy=False, + max_rate_limit_wait=60.0, + extraction_workers=0, + springer_api_key=None, + springer_base_url="https://api.springernature.com", + pubmed_base_url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils", + ncbi_api_key="ncbi-key", + ) + + +@pytest.mark.asyncio() +async def test_pubmed_resolver_extracts_doi() -> None: + pmid = "31262544" + expected_doi = "10.1000/example-doi" + + async def handler(request: httpx.Request) -> httpx.Response: + assert request.url.path.endswith("/esummary.fcgi") + assert request.url.params.get("db") == "pubmed" + assert request.url.params.get("id") == pmid + assert request.url.params.get("retmode") == "json" + assert request.url.params.get("api_key") == "ncbi-key" + payload = { + "header": {"type": "esummary"}, + "result": { + "uids": [pmid], + pmid: { + "uid": pmid, + "articleids": [ + {"idtype": "pubmed", "value": pmid}, + {"idtype": "doi", "value": expected_doi}, + ], + }, + }, + } + return httpx.Response(200, json=payload, request=request) + + transport = httpx.MockTransport(handler) + async with PubMedResolver(_settings(), transport=transport) as resolver: + doi = await resolver.resolve_doi(pmid) + assert doi == expected_doi + + +@pytest.mark.asyncio() +async def test_pubmed_resolver_returns_none_when_missing_doi() -> None: + pmid = "99999999" + + async def handler(request: httpx.Request) -> httpx.Response: + payload = { + "result": { + "uids": [pmid], + pmid: { + "uid": pmid, + "articleids": [{"idtype": "pubmed", "value": pmid}], + }, + }, + } + return httpx.Response(200, json=payload, request=request) + + transport = httpx.MockTransport(handler) + async with PubMedResolver(_settings(), transport=transport) as resolver: + doi = await resolver.resolve_doi(pmid) + assert doi is None + + +@pytest.mark.asyncio() +async def test_pubmed_resolver_raises_for_http_error() -> None: + async def handler(request: httpx.Request) -> httpx.Response: + return httpx.Response(500, json={"error": "server"}, request=request) + + transport = httpx.MockTransport(handler) + async with PubMedResolver(_settings(), transport=transport) as resolver: + with pytest.raises(httpx.HTTPStatusError): + await resolver.resolve_doi("12345") diff --git a/tests/test_settings.py b/tests/test_settings.py index 5c9d62a..b466355 100644 --- a/tests/test_settings.py +++ b/tests/test_settings.py @@ -28,6 +28,9 @@ def test_get_settings_reads_environment( assert cfg_a.insttoken is None assert cfg_a.use_proxy is False assert cfg_a.extraction_workers == 0 + assert cfg_a.springer_api_key is None + assert cfg_a.springer_base_url == "https://api.springernature.com" + assert cfg_a.pubmed_base_url == "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" assert cfg_a is cfg_b @@ -94,3 +97,21 @@ def test_max_rate_limit_wait_unlimited(monkeypatch: pytest.MonkeyPatch, tmp_path monkeypatch.setenv("ELSEVIER_MAX_RATE_LIMIT_WAIT_SECONDS", "none") cfg = settings.get_settings(force_reload=True) assert cfg.max_rate_limit_wait is None + + +def test_springer_and_pubmed_settings(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> None: + """Springer and PubMed integration settings should load from environment.""" + + monkeypatch.setenv("ELSEVIER_API_KEY", "unit-test-key") + monkeypatch.setenv("SPRINGER_API_KEY", "springer-key") + monkeypatch.setenv("SPRINGER_BASE_URL", "https://springer.example") + monkeypatch.setenv("PUBMED_BASE_URL", "https://ncbi.example/eutils") + monkeypatch.setenv("NCBI_API_KEY", "ncbi-key") + blank_env = tmp_path / "blank.env" + blank_env.write_text("") + monkeypatch.setenv("ELSEVIER_DOTENV_PATH", str(blank_env)) + cfg = settings.get_settings(force_reload=True) + assert cfg.springer_api_key == "springer-key" + assert cfg.springer_base_url == "https://springer.example" + assert cfg.pubmed_base_url == "https://ncbi.example/eutils" + assert cfg.ncbi_api_key == "ncbi-key" diff --git a/tests/test_table_extraction.py b/tests/test_table_extraction.py new file mode 100644 index 0000000..5383dd5 --- /dev/null +++ b/tests/test_table_extraction.py @@ -0,0 +1,33 @@ +"""Tests for generic table extraction fallbacks.""" + +from __future__ import annotations + +from elsevier_coordinate_extraction.table_extraction import extract_tables_from_article + + +def test_extract_tables_from_jats_payload() -> None: + payload = b""" +
+ + + + Coordinate table + + + + + + + +
xyz
123
+ + +
+ """ + tables = extract_tables_from_article(payload) + assert len(tables) == 1 + metadata, dataframe = tables[0] + assert metadata.identifier == "tbl1" + assert metadata.caption and "Coordinate table" in metadata.caption + assert list(dataframe.columns) == ["x", "y", "z"] + assert dataframe.iloc[0].tolist() == ["1", "2", "3"] From 565f65c1492ada1de57a373296b2f4d71979f637 Mon Sep 17 00:00:00 2001 From: Alejandro de la Vega Date: Tue, 17 Mar 2026 15:44:40 -0500 Subject: [PATCH 5/6] Add daily limit circuit breakaer --- README.md | 2 + .../cli/orchestrator.py | 10 ++-- .../download/api.py | 12 +++- tests/cli/test_orchestrator.py | 1 + tests/download/test_api.py | 55 +++++++++++++++++++ 5 files changed, 73 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index a191289..6210a38 100644 --- a/README.md +++ b/README.md @@ -69,3 +69,5 @@ The CLI also appends every run to `manifest.jsonl` (with status, source provider - `springer_not_found` - `springer_jats_unavailable` - `springer_rate_limited` + +When `springer_rate_limited` occurs, the runner stops querying Springer for the remainder of that run and marks subsequent Springer-fallback records as skipped with the same reason to avoid unnecessary quota pressure. diff --git a/elsevier_coordinate_extraction/cli/orchestrator.py b/elsevier_coordinate_extraction/cli/orchestrator.py index 636508c..3df6cd2 100644 --- a/elsevier_coordinate_extraction/cli/orchestrator.py +++ b/elsevier_coordinate_extraction/cli/orchestrator.py @@ -82,7 +82,7 @@ async def process_articles( cache = FileCache(output_dir / ".cache") if use_cache else None downloaded_errors: List[tuple[Record, Exception, str | None]] = [] - skipped_records: List[tuple[Record, str, str | None]] = [] + skipped_records: List[tuple[Record, str, str | None, str | None]] = [] async def _progress_callback( record: Record, @@ -94,14 +94,14 @@ async def _progress_callback( reason = getattr(error, "skip_reason", None) source = _infer_source_from_error(error, reason if isinstance(reason, str) else None) if isinstance(reason, str) and reason: - skipped_records.append((record.copy(), reason, source)) + skipped_records.append((record.copy(), reason, source, str(error))) else: if isinstance(error, Exception): downloaded_errors.append((record.copy(), error, source)) else: downloaded_errors.append((record.copy(), Exception(str(error)), source)) elif article is None: - skipped_records.append((record.copy(), "not_found_404", "elsevier")) + skipped_records.append((record.copy(), "not_found_404", "elsevier", None)) stats = {"success": 0, "failed": 0, "skipped": 0} @@ -198,14 +198,14 @@ async def _progress_callback( append_error_entry(output_dir, record=record, error=error, source=source) stats["failed"] += 1 - for record, reason, source in skipped_records: + for record, reason, source, detail in skipped_records: append_manifest_entry( output_dir, record=record, status="skipped", source=source, files=[], - error=None, + error=detail, reason=reason, duration=0.0, ) diff --git a/elsevier_coordinate_extraction/download/api.py b/elsevier_coordinate_extraction/download/api.py index e3827da..1568c32 100644 --- a/elsevier_coordinate_extraction/download/api.py +++ b/elsevier_coordinate_extraction/download/api.py @@ -96,6 +96,7 @@ async def download_articles( return [] cfg = settings or get_settings() + springer_blocked_reason: str | None = None owns_client = client is None sci_client = client or ScienceDirectClient(cfg) owns_springer_client = springer_client is None @@ -115,6 +116,7 @@ async def _emit_progress( await result async def _runner() -> list[ArticleContent]: + nonlocal springer_blocked_reason results: list[ArticleContent] = [] for record in records: article: ArticleContent | None = None @@ -127,8 +129,11 @@ async def _runner() -> list[ArticleContent]: pubmed_resolver=pmid_resolver, cache=cache, cache_namespace=cache_namespace, + springer_blocked_reason=springer_blocked_reason, ) except Exception as exc: + if getattr(exc, "skip_reason", None) == "springer_rate_limited": + springer_blocked_reason = str(exc) await _emit_progress(record, None, exc) continue if article is None: @@ -157,6 +162,7 @@ async def _download_record( pubmed_resolver: PubMedResolver, cache: Any | None, cache_namespace: str, + springer_blocked_reason: str | None, ) -> ArticleContent | None: doi = (record.get("doi") or "").strip() pmid = (record.get("pmid") or "").strip() @@ -172,6 +178,8 @@ async def _download_record( if not settings.springer_api_key: raise DownloadSkip("springer_unconfigured") + if springer_blocked_reason: + raise DownloadSkip("springer_rate_limited", springer_blocked_reason) resolved_doi = doi if not resolved_doi: @@ -202,7 +210,7 @@ async def _download_record( ) except httpx.HTTPStatusError as exc: if _is_rate_limited_error(exc): - raise DownloadSkip("springer_rate_limited") from exc + raise DownloadSkip("springer_rate_limited", str(exc)) from exc raise if springer_article is None: raise DownloadSkip("springer_jats_unavailable") @@ -272,7 +280,7 @@ async def _fetch_springer_metadata_record( if exc.response.status_code == 404: return None if _is_rate_limited_error(exc): - raise DownloadSkip("springer_rate_limited") from exc + raise DownloadSkip("springer_rate_limited", str(exc)) from exc raise records = data.get("records") if not isinstance(records, list) or not records: diff --git a/tests/cli/test_orchestrator.py b/tests/cli/test_orchestrator.py index 57cbc4b..028b2be 100644 --- a/tests/cli/test_orchestrator.py +++ b/tests/cli/test_orchestrator.py @@ -302,3 +302,4 @@ async def fake_download(records, client, cache, settings, progress_callback): assert entries[0]["status"] == "skipped" assert entries[0]["reason"] == "springer_jats_unavailable" assert entries[0]["source"] == "springer" + assert entries[0]["error"] == "no jats" diff --git a/tests/download/test_api.py b/tests/download/test_api.py index 3f9ff47..9c8a1c6 100644 --- a/tests/download/test_api.py +++ b/tests/download/test_api.py @@ -743,3 +743,58 @@ def progress_cb( assert article is None assert error is not None assert getattr(error, "skip_reason", None) == "springer_rate_limited" + + +@pytest.mark.asyncio() +async def test_download_short_circuits_springer_after_rate_limit() -> None: + records = [{"doi": "10.1007/s12345-6789-3"}, {"doi": "10.1007/s12345-6789-4"}] + progress_calls: list[tuple[dict[str, str], ArticleContent | None, BaseException | None]] = [] + + class StubElsevierClient: + async def request(self, method: str, path: str, **kwargs) -> httpx.Response: + request = httpx.Request(method, f"https://api.elsevier.com/content{path}") + response = httpx.Response(404, request=request) + raise httpx.HTTPStatusError("not found", request=request, response=response) + + class StubSpringerClient: + def __init__(self) -> None: + self.calls = 0 + + async def get_json( + self, + path: str, + *, + params: dict[str, str] | None = None, + ) -> dict[str, object]: + self.calls += 1 + request = httpx.Request("GET", "https://api.springernature.com/openaccess/json") + response = httpx.Response(429, request=request) + raise httpx.HTTPStatusError( + "Springer OpenAccess rate limit wait (7200s) exceeds configured maximum (3600s).", + request=request, + response=response, + ) + + def progress_cb( + record: dict[str, str], + article: ArticleContent | None, + error: BaseException | None, + ) -> None: + progress_calls.append((record, article, error)) + + springer = StubSpringerClient() + articles = await download_articles( + records, + client=StubElsevierClient(), # type: ignore[arg-type] + springer_client=springer, # type: ignore[arg-type] + settings=_test_settings_with_springer(), + progress_callback=progress_cb, + ) + + assert articles == [] + assert springer.calls == 1 + assert len(progress_calls) == 2 + for _, article, error in progress_calls: + assert article is None + assert error is not None + assert getattr(error, "skip_reason", None) == "springer_rate_limited" From 8046a0a63083091a630dc110ad552eabf2505f80 Mon Sep 17 00:00:00 2001 From: Alejandro de la Vega Date: Mon, 18 May 2026 15:07:28 -0500 Subject: [PATCH 6/6] Add tests --- .../download/api.py | 12 ++- tests/download/test_api.py | 73 ++++++++++++++++++- 2 files changed, 80 insertions(+), 5 deletions(-) diff --git a/elsevier_coordinate_extraction/download/api.py b/elsevier_coordinate_extraction/download/api.py index 1568c32..26bbfae 100644 --- a/elsevier_coordinate_extraction/download/api.py +++ b/elsevier_coordinate_extraction/download/api.py @@ -267,11 +267,12 @@ async def _fetch_springer_metadata_record( doi: str, client: SpringerOpenAccessClient, ) -> dict[str, Any] | None: + query = _build_springer_doi_query(doi) try: data = await client.get_json( "/openaccess/json", params={ - "q": f"doi:{doi}", + "q": query, "s": "1", "p": "1", }, @@ -299,6 +300,7 @@ async def _download_springer_jats( cache: Any | None, cache_namespace: str, ) -> ArticleContent | None: + query = _build_springer_doi_query(doi) cache_key = f"springer-jats:doi:{doi}" payload: bytes | None = None content_type = "application/xml" @@ -321,7 +323,7 @@ async def _download_springer_jats( "GET", "/openaccess/jats", params={ - "q": f"doi:{doi}", + "q": query, "s": "1", "p": "1", }, @@ -628,6 +630,12 @@ def _summarize_springer_record(record: Mapping[str, Any]) -> dict[str, Any]: return summary +def _build_springer_doi_query(doi: str) -> str: + """Build a Springer query value that treats DOI characters literally.""" + escaped = doi.strip().replace("\\", "\\\\").replace('"', '\\"') + return f'doi:"{escaped}"' + + def _payload_contains_springer_full_text(payload: bytes) -> bool: try: root = etree.fromstring(payload) diff --git a/tests/download/test_api.py b/tests/download/test_api.py index 9c8a1c6..cdb455a 100644 --- a/tests/download/test_api.py +++ b/tests/download/test_api.py @@ -16,6 +16,10 @@ from elsevier_coordinate_extraction.types import ArticleContent +def _springer_doi_query(doi: str) -> str: + return f'doi:"{doi}"' + + def _test_settings() -> Settings: """Return deterministic Settings for mock transport tests.""" @@ -489,7 +493,7 @@ async def get_json( ) -> dict[str, object]: call_order.append("springer-metadata") assert path == "/openaccess/json" - assert params == {"q": f"doi:{doi}", "s": "1", "p": "1"} + assert params == {"q": _springer_doi_query(doi), "s": "1", "p": "1"} return {"records": [{"doi": doi, "title": "Springer Test"}]} async def request( @@ -503,7 +507,7 @@ async def request( call_order.append("springer-jats") assert method == "GET" assert path == "/openaccess/jats" - assert params == {"q": f"doi:{doi}", "s": "1", "p": "1"} + assert params == {"q": _springer_doi_query(doi), "s": "1", "p": "1"} assert accept == "application/xml" payload = b"""
@@ -558,7 +562,7 @@ async def get_json( params: dict[str, str] | None = None, ) -> dict[str, object]: assert path == "/openaccess/json" - assert params == {"q": f"doi:{resolved_doi}", "s": "1", "p": "1"} + assert params == {"q": _springer_doi_query(resolved_doi), "s": "1", "p": "1"} return {"records": [{"doi": resolved_doi, "title": "Resolved DOI"}]} async def request( @@ -606,6 +610,69 @@ async def resolve_doi(self, value: str) -> str | None: assert articles[0].metadata["resolved_doi"] == resolved_doi +@pytest.mark.asyncio() +async def test_download_quotes_legacy_doi_for_springer_query() -> None: + doi = "10.1002/(SICI)1098-1063(1997)7:1<78::AID-HIPO8>3.0.CO;2-3" + + class StubElsevierClient: + async def request(self, method: str, path: str, **kwargs) -> httpx.Response: + request = httpx.Request(method, f"https://api.elsevier.com/content{path}") + response = httpx.Response(404, request=request) + raise httpx.HTTPStatusError("not found", request=request, response=response) + + class StubSpringerClient: + async def get_json( + self, + path: str, + *, + params: dict[str, str] | None = None, + ) -> dict[str, object]: + assert path == "/openaccess/json" + assert params == {"q": _springer_doi_query(doi), "s": "1", "p": "1"} + return {"records": [{"doi": doi, "title": "Legacy DOI"}]} + + async def request( + self, + method: str, + path: str, + *, + params: dict[str, str] | None = None, + accept: str | None = None, + ) -> httpx.Response: + assert method == "GET" + assert path == "/openaccess/jats" + assert params == {"q": _springer_doi_query(doi), "s": "1", "p": "1"} + assert accept == "application/xml" + payload = """ +
+ 10.1007/s00123-001-0001-1 +

Legacy DOI text

 +
+ """.encode("utf-8") + request = httpx.Request(method, "https://api.springernature.com/openaccess/jats") + return httpx.Response( + 200, + request=request, + content=payload, + headers={"content-type": "application/xml"}, + ) + + class StubPubMedResolver: + async def resolve_doi(self, pmid: str) -> str | None: + raise AssertionError("PMID resolver should not be called for DOI input.") + + articles = await download_articles( + [{"doi": doi}], + client=StubElsevierClient(), # type: ignore[arg-type] + springer_client=StubSpringerClient(), # type: ignore[arg-type] + pubmed_resolver=StubPubMedResolver(), # type: ignore[arg-type] + settings=_test_settings_with_springer(), + ) + + assert len(articles) == 1 + assert articles[0].metadata["resolved_doi"] == doi + + @pytest.mark.asyncio() async def test_download_reports_skip_reason_when_springer_jats_missing() -> None: doi = "10.1007/s12345-6789-0"